Molecules for diagnostics and therapeutics

TECHNICAL FIELD

[0001] The present invention relates to human molecules and to the use of these sequences in the diagnosis, study, prevention, and treatment of diseases associated with, as well as effects of exogenous compounds on, the expression of human molecules.

BACKGROUND OF THE INVENTION

[0002] The human genome is comprised of thousands of genes, many encoding gene products that function in the maintenance and growth of the various cells and tissues in the body. Aberrant expression or mutations in these genes and their products is the cause of, or is associated with, a variety of human diseases such as cancer and other cell proliferative disorders, autoimmune/inflammatory disorders, infections, developmental disorders, endocrine disorders, metabolic disorders, neurological disorders, gastrointestinal disorders, transport disorders, and connective tissue disorders. The identification of these genes and their products is the basis of an ever-expanding effort to find markers for early detection of diseases, and targets for their prevention and treatment. Therefore, these genes and their products are useful as diagnostics and therapeutics. These genes may encode, for example, enzyme molecules, molecules associated with growth and development, biochemical pathway molecules, extracellular information transmission molecules, receptor molecules, intracellular signaling molecules, membrane transport molecules, protein modification and maintenance molecules, nucleic acid synthesis and modification molecules, adhesion molecules, antigen recognition molecules, secreted and extracellular matrix molecules, cytoskeletal molecules, ribosomal molecules, electron transfer associated molecules, transcription factor molecules, chromatin molecules, cell membrane molecules, and organelle associated molecules.

[0003] For example, cancer represents a type of cell proliferative disorder that affects nearly every tissue in the body. A wide variety of molecules, either aberrantly expressed or mutated, can be the cause of, or involved with, various cancers because tissue growth involves complex and ordered patterns of cell proliferation, cell differentiation, and apoptosis. Cell proliferation must be regulated to maintain both the number of cells and their spatial organization. This regulation depends upon the appropriate expression of proteins which control cell cycle progression in response to extracellular signals such as growth factors and other mitogens, and intracellular cues such as DNA damage or nutrient starvation. Molecules which directly or indirectly modulate cell cycle progression fall into several categories, including growth factors and their receptors, second messenger and signal transduction proteins, oncogene products, tumor-suppressor proteins, and mitosis-promoting factors. Aberrant expression or mutations in any of these gene products can result in cell proliferative disorders such as cancer. Oncogenes are genes generally derived from normal genes that, through abnormal expression or mutation, can effect the transformation of a normal cell to a malignant one (oncogenesis). Oncoproteins, encoded by oncogenes, can affect cell proliferation in a variety of ways and include growth factors, growth factor receptors, intracellular signal transducers, nuclear transcription factors, and cell-cycle control proteins. In contrast, tumor-suppressor genes are involved in inhibiting cell proliferation. Mutations which cause reduced function or loss of function in tumor-suppressor genes result in aberrant cell proliferation and cancer. Although many different genes and their products have been found to be associated with cell proliferative disorders such as cancer, many more may exist that are yet to be discovered.

[0004] DNA-based arrays can provide a simple way to explore the expression of a single polymorphic gene or a large number of genes. When the expression of a single gene is explored, DNA-based arrays are employed to detect the expression of specific gene variants. For example, a p53 tumor suppressor gene array is used to determine whether individuals are carrying mutations that predispose them to cancer. A cytochrome p450 gene array is useful to determine whether individuals have one of a number of specific mutations that could result in increased drug metabolism, drug resistance or drug toxicity.

[0005] DNA-based array technology is especially relevant for the rapid screening of expression of a large number of genes. There is a growing awareness that gene expression is affected in a global fashion. A genetic predisposition, disease or therapeutic treatment may affect, directly or indirectly, the expression of a large number of genes. In some cases the interactions may be expected, such as when the genes are part of the same signaling pathway. In other cases, such as when the genes participate in separate signaling pathways, the interactions may be totally unexpected. Therefore, DNA-based arrays can be used to investigate how genetic predisposition, disease, or therapeutic treatment affects the expression of a large number of genes.

[0006] Enzyme Molecules

[0007] The cellular processes of biogenesis and biodegradation involve a number of key enzyme classes including oxidoreductases, transferases, hydrolases, lyases, isomerases, and ligases. These enzyme classes are each comprised of numerous substrate-specific enzymes having precise and well regulated functions. These enzymes function by facilitating metabolic processes such as glycolysis, the tricarboxylic cycle, and fatty acid metabolism; synthesis or degradation of amino acids, steroids, phospholipids, alcohols, etc.; regulation of cell signalling, proliferation, inflamation, apoptosis, etc., and through catalyzing critical steps in DNA replication and repair, and the process of translation.

[0008] Oxidoreductases

[0009] Many pathways of biogenesis and biodegradation require oxidoreductase (dehydrogenase or reductase) activity, coupled to the reduction or oxidation of a donor or acceptor cofactor. Potential cofactors include cytochromes, oxygen, disulfide, iron-sulfur proteins, flavin adenine dinucleotide (FAD), and the nicotinamide adenine dinucleotides NAD and NADP (Newsholme, E. A. and A. R. Leech (1983) Biochemistry for the Medical Sciences, John Wiley and Sons, Chichester, U. K., pp. 779-793). Reductase activity catalyzes the transfer of electrons between substrate(s) and cofactor(s) with concurrent oxidation of the cofactor. The reverse dehydrogenase reaction catalyzes the reduction of a cofactor and consequent oxidation of the substrate. Oxidoreductase enzymes are a broad superfamily of proteins that catalyze numerous reactions in all cells of organisms ranging from bacteria to plants to humans. These reactions include metabolism of sugar, certain detoxification reactions in the liver, and the synthesis or degradation of fatty acids, amino acids, glucocorticoids, estrogens, androgens, and prostaglandins. Different family members are named according to the direction in which their reactions are typically catalyzed; thus they may be referred to as oxidoreductases, oxidases, reductases, or dehydrogenases. In addition, family members often have distinct cellular localizations, including the cytosol, the plasma membrane, mitochondrial inner or outer membrane, and peroxisomes.

[0010] Short-chain alcohol dehydrogenases (SCADs) are a family of dehydrogenases that only share 15% to 30% sequence identity, with similarity predominantly in the coenzyme binding domain and the substrate binding domain. In addition to the well-known role in detoxification of ethanol, SCADs are also involved in synthesis and degradation of fatty acids, steroids, and some prostaglandins, and are therefore implicated in a variety of disorders such as lipid storage disease, myopathy, SCAD deficiency, and certain genetic disorders. For example, retinol dehydrogenase is a SCAD-family member (Simon, A. et al. (1995) J. Biol. Chem. 270:1107-1112) that converts retinol to retinal, the precursor of retinoic acid. Retinoic acid, a regulator of differentiation and apoptosis, has been shown to down-regulate genes involved in cell proliferation and inflammation (Chai, X. et al., (1995) J. Biol. Chem. 270:3900-3904). In addition, retinol dehydrogenase has been lined to hereditary eye diseases such as autosomal recessive childhood-onset severe retinal dystrophy (Simon, A. et al. (1996) Genomics 36:424-430).

[0011] Propagation of nerve impulses, modulation of cell proliferation and differentiation, induction of the immune response, and tissue homeostasis involve neurotransmitter metabolism (Weiss, B. (1991) Neurotoxicology 12:379-386; Collins, S. M. et al. (1992) Ann. N.Y. Acad. Sci. 664:415-424; Brown, J. K and H. Imam (1991) J. Inherit. Metab. Dis. 14:436-458). Many pathways of neurotransmitter metabolism require oxidoreductase activity, coupled to reduction or oxidation of a cofactor, such as NAD+/NADH (Newsholme, E. A. and A. R. Leech (1983) Biochemistry for the Medical Sciences, John Wiley and Sons, Chichester, U.K. pp. 779-793). Degradation of catecholamines (epinephrine or norepinephrine) requires alcohol dehydrogenase (in the brain) or aldehyde dehydrogenase (in peripheral tissue). NAD+-dependent aldehyde dehydrogenase oxidizes 5-hydroxyindole-3-acetate (the product of 5-hydroxytryptamine (serotonin) metabolism) in the brain, blood platelets, liver and pulmonary endothelium (Newsholme, supra, p. 786). Other neurotransmitter degradation pathways that utilize NAD+/NADH-dependent oxidoreductase activity include those of L-DOPA (precursor of dopamine, a neuronal excitatory compound), glycine (an inhibitory neurotransmitter in the brain and spinal cord), histamine (liberated from mast cells during the inflammatory response), and taurine (an inhibitory neurotransmitter of the brain stem, spinal cord and retina) (Newsholme, supra, pp. 790, 792). Epigenetic or genetic defects in neurotransmitter metabolic pathways can result in a spectrum of disease states in different tissues including Parkinson disease and inherited myoclonus (McCance, K. L. and S. E. Huether (1994) Pathophysiology, Mosby-Year Book, Inc., St. Louis Mo., pp. 402-404; Gundlach, A. L. (1990) FASEB J. 4:2761-2766).

[0012] Tetrahydrofolate is a derivatized glutamate molecule that acts as a carrier, providing activated one-carbon units to a wide variety of biosynthetic reactions, including synthesis of purines, pyrimidines, and the amino acid methionine. Tetrahydrofolate is generated by the activity of a holoenzyme complex called tetrahydrofolate synthase, which includes three enzyme activities: tetrahydrofolate dehydrogenase, tetrahydrofolate cyclohydrolase, and tetrahydrofolate synthetase. Thus, tetrahydrofolate dehydrogenase plays an important role in generating building blocks for nucleic and amino acids, crucial to proliferating cells.

[0013] 3-Hydroxyacyl-CoA dehydrogenase (3HACD) is involved in fatty acid metabolism. It catalyzes the reduction of 3-hydroxyacyl-CoA to 3-oxoacyl-CoA, with concomitant oxidation of NAD to NADH, in the mitochondria and peroxisomes of eukaryotic cells. In peroxisomes, 3HACD and enoyl-CoA hydratase form an enzyme complex called bifunctional enzyme, defects in which are associated with peroxisomal bifunctional enzyme deficiency. This interruption in fatty acid metabolism produces accumulation of very-long chain fatty acids, disrupting development of the brain, bone, and adrenal glands. Infants born with this deficiency typically die within 6 months (Watkins, P. et al. (1989) J. Clin. Invest. 83:771-777; Online Mendelian Inheritance in Man (OMIM), #261515). The neurodegeneration that is characteristic of Alzheimer's disease involves development of extracellular plaques in certain brain regions. A major protein component of these plaques is the peptide amyloid-β (Aβ), which is one of several cleavage products of amyloid precursor protein (APP). 3HACD has been shown to bind the Aβ peptide, and is overexpressed in neurons affected in Alzheimer's disease. In addition, an antibody against 3HACD can block the toxic effects of Aβ in a cell culture model of Alzheimer's disease (Yan, S. et al. (1997) Nature 389:689-695; OMIM, #602057).

[0014] Steroids, such as estrogen, testosterone, corticosterone, and others, are generated from a common precursor, cholesterol, and are interconverted into one another. A wide variety of enzymes act upon cholesterol, including a number of dehydrogenases. Steroid dehydrogenases, such as the hydroxysteroid dehydrogenases, are involved in hypertension, fertility, and cancer (Duax, W. L. and D. Ghosh (1997) Steroids 62:95-100). One such dehydrogenase is 3-oxo-5-α-steroid dehydrogenase (OASD), a microsomal membrane protein highly expressed in prostate and other androgen-responsive tissues. OASD catalyzes the conversion of testosterone into dihydrotestosterone, which is the most potent androgen. Dihydrotestosterone is essential for the formation of the male phenotype during embryogenesis, as well as for proper androgen-mediated growth of tissues such as the prostate and male genitalia. A defect in OASD that prevents the conversion of testosterone into dihydrotestosterone leads to a rare form of male pseudohermaphroditis, characterized by defective formation of the external genitalia (Andersson, S. et al. (1991) Nature 354:159-161; Labrie, F. et al. (1992) Endocrinology 131:1571-1573; OMIM #264600). Thus, OASD plays a central role in sexual differentiation and androgen physiology.

[0015] 17β-hydroxysteroid dehydrogenase (17βHSD6) plays an important role in the regulation of the male reproductive hormone, dihydrotestosterone (DHTT). 17βHSD6 acts to reduce levels of DHTT by oxidizing a precursor of DHTT, 3α-diol, to androsterone which is readily glucuronidated and removed from tissues. 17βHSD6 is active with both androgen and estrogen substrates when expressed in embryonic kidney 293 cells. At least five other isozymes of 17βHSD have been identified that catalyze oxidation and/or reduction reactions in various tissues with preferences for different steroid substrates (Biswas, M. G. and D. W. Russell (1997) J. Biol. Chem. 272:15959-15966). For example, 17βHSD1 preferentially reduces estradiol and is abundant in the ovary and placenta. 17βHSD2 catalyzes oxidation of androgens and is present in the endometrium and placenta. 17βHSD3 is exclusively a reductive enzyme in the testis (Geissler, W. M. et al. (1994) Nat. Genet. 7:34-39). An excess of androgens such as DHTT can contribute to certain disease states such as benign prostatic hyperplasia and prostate cancer.

[0016] Oxidoreductases are components of the fatty acid metabolism pathways in mitochondria and peroxisomes. The main beta-oxidation pathway degrades both saturated and unsaturated fatty acids, while the auxiliary pathway performs additional steps required for the degradation of unsaturated fatty acids. The auxiliary beta-oxidation enzyme 2,4-dienoyl-CoA reductase catalyzes the removal of even-numbered double bonds from unsaturated fatty acids prior to their entry into the main beta-oxidation pathway. The enzyme may also remove odd-numbered double bonds from unsaturated fatty acids (Koivuranta, K. T. et al. (1994) Biochem. J. 304:787-792; Smeland, T. E. et al. (1992) Proc. Natl. Acad. Sci. USA 89:6673-6677). 2,4-dienoyl-CoA reductase is located in both mitochondria and peroxisomes. Inherited deficiencies in mitochondrial and peroxisomal beta-oxidation enzymes are associated with severe diseases, some of which manifest themselves soon after birth and lead to death within a few years. Defects in beta-oxidation are associated with Reye's syndrome, Zellweger syndrome, neonatal adrenoleukodystrophy, infantile Refsum's disease, acyl-CoA oxidase deficiency, and bifunctional protein deficiency (Suzuki, Y. et al. (1994) Am. J. Hum. Genet. 54:36-43; Hoefler, supra; Cotran, R. S. et al. (1994) Robbins Pathologic Basis of Disease, W. B. Saunders Co., Philadelphia Pa., p.866). Peroxisomal beta-oxidation is impaired in cancerous tissue. Although neoplastic human breast epithelial cells have the same number of peroxisomes as do normal cells, fatty acyl-CoA oxidase activity is lower than in control tissue (el Bouhtoury, F. et al. (1992) J. Pathol. 166:27-35). Human colon carcinomas have fewer peroxisomes than normal colon tissue and have lower fatty-acyl-CoA oxidase and bifunctional enzyme (including enoyl-CoA hydratase) activities than normal tissue (Cable, S. et al. (1992) Virchows Arch. B Cell Pathol. Incl. Mol. Pathol. 62:221-226). Another important oxidoreductase is isocitrate dehydrogenase, which catalyzes the conversion of isocitrate to a-ketoglutarate, a substrate of the citric acid cycle. Isocitrate dehydrogenase can be either NAD or NADP dependent, and is found in the cytosol, mitochondria, and peroxisomes. Activity of isocitrate dehydrogenase is regulated developmentally, and by hormones, neurotransmitters, and growth factors.

[0017] Hydroxypyruvate reductase (HPR), a peroxisomal 2-hydroxyacid dehydrogenase in the glycolate pathway, catalyzes the conversion of hydroxypyruvate to glycerate with the oxidation of both NADH and NADPH. The reverse dehydrogenase reaction reduces NAD+ and NADP+. HPR recycles nucleotides and bases back into pathways leading to the synthesis of ATP and GTP. ATP and GTP are used to produce DNA and RNA and to control various aspects of signal transduction and energy metabolism. Inhibitors of purine nucleotide biosynthesis have long been employed as antiproliferative agents to treat cancer and viral diseases. HPR also regulates biochemical synthesis of serine and cellular serine levels available for protein synthesis.

[0018] The mitochondrial electron transport (or respiratory) chain is a series of oxidoreductase-type enzyme complexes in the mitochondrial membrane that is responsible for the transport of electrons from NADH through a series of redox centers within these complexes to oxygen, and the coupling of this oxidation to the synthesis of ATP (oxidative phosphorylation). ATP then provides the primary source of energy for driving a cell's many energy-requiring reactions. The key complexes in the respiratory chain are NADH:ubiquinone oxidoreductase (complex I), succinate:ubiquinone oxidoreductase (complex II), cytochrome c1-b oxidoreductase (complex III), cytochrome c oxidase (complex IV), and ATP synthase (complex V) (Alberts, B. et al. (1994) Molecular Biology of the Cell, Garland Publishing, Inc., New York N.Y., pp. 677-678). All of these complexes are located on the inner matrix side of the mitochondrial membrane except complex II, which is on the cytosolic side. Complex II transports electrons generated in the citric acid cycle to the respiratory chain. The electrons generated by oxidation of succinate to fumarate in the citric acid cycle are transferred through electron carriers in complex II to membrane bound ubiquinone (Q). Transcriptional regulation of these nuclear-encoded genes appears to be the predominant means for controlling the biogenesis of respiratory enzymes. Defects and altered expression of enzymes in the respiratory chain are associated with a variety of disease conditions.

[0019] Other dehydrogenase activities using NAD as a cofactor are also important in mitochondrial function. 3-hydroxyisobutyrate dehydrogenase (3HBD), important in valine catabolism, catalyzes the NAD-dependent oxidation of 3-hydroxyisobutyrate to methylmalonate semialdehyde within mitochondria. Elevated levels of 3-hydroxyisobutyrate have been reported in a number of disease states, including ketoacidosis, methylmalonic acidemia, and other disorders associated with deficiencies in methylmalonate semialdehyde dehydrogenase (Rougraff, P. M. et al. (1989) J. Biol. Chem. 264:5899-5903).

[0020] Another mitochondrial dehydrogenase important in amino acid metabolism is the enzyme isovaleryl-CoA-dehydrogenase (IVD). IVD is involved in leucine metabolism and catalyzes the oxidation of isovaleryl-CoA to 3-methylcrotonyl-CoA. Human IVD is a tetrameric flavoprotein that is encoded in the nucleus and synthesized in the cytosol as a 45 kDa precursor with a mitochondrial import signal sequence. A genetic deficiency, caused by a mutation in the gene encoding IVD, results in the condition known as isovaleric acidemia. This mutation results in inefficient mitochondrial import and processing of the IVD precursor (Vockley, J. et al. (1992) J. Biol. Chem. 267:2494-2501).

[0021] Transferases

[0022] Transferases are enzymes that catalyze the transfer of molecular groups. The reaction may involve an oxidation, reduction, or cleavage of covalent bonds, and is often specific to a substrate or to particular sites on a type of substrate. Transferases participate in reactions essential to such functions as synthesis and degradation of cell components, regulation of cell functions including cell signaling, cell proliferation, inflamation, apoptosis, secretion and excretion. Transferases are involved in key steps in disease processes involving these functions. Transferases are frequently classified according to the type of group transferred. For example, methyl transferases transfer one-carbon methyl groups, amino transferases transfer nitrogenous amino groups, and similarly denominated enzymes transfer aldehyde or ketone, acyl, glycosyl, alkyl or aryl, isoprenyl, saccharyl, phosphorous-containing, sulfur-containing, or selenium-containing groups, as well as small enzymatic groups such as Coenzyme A.

[0023] Acyl transferases include peroxisomal carnitine octanoyl transferase, which is involved in the fatty acid beta-oxidation pathway, and mitochondrial carnitine palmitoyl transferases, involved in fatty acid metabolism and transport. Choline O-acetyl transferase catalyzes the biosynthesis of the neurotransmitter acetylcholine.

[0024] Amino transferases play key roles in protein synthesis and degradation, and they contribute to other processes as well. For example, the amino transferase 5-aminolevulinic acid synthase catalyzes the addition of succinyl-CoA to glycine, the first step in heme biosynthesis. Other amino transferases participate in pathways important for neurological function and metabolism. For example, glutamine-phenylpyruvate amino transferase, also known as glutamine transaminase K (GTK), catalyzes several reactions with a pyridoxal phosphate cofactor. GTK catalyzes the reversible conversion of L-glutamine and phenylpyruvate to 2-oxoglutaramate and L-phenylalanine. Other amino acid substrates for GTK include L-methionine, L-histidine, and L-tyrosine. GTK also catalyzes the conversion of kynurenine to kynurenic acid, a tryptophan metabolite that is an antagonist of the N-methyl-D-aspartate (NA) receptor in the brain and may exert a neuromodulatory function. Alteration of the kynurenine metabolic pathway may be associated with several neurological disorders. GTK also plays a role in the metabolism of halogenated xenobiotics conjugated to glutathione, leading to nephrotoxicity in rats and neurotoxicity in humans. GTK is expressed in kidney, liver, and brain. Both human and rat GTKs contain a putative pyridoxal phosphate binding site (ExPASy ENZYME: EC 2.6.1.64; Perry, S. J. et al. (1993) Mol. Pharmacol. 43:660-665; Perry, S. et al. (1995) FEBS Lett. 360:277-280; and Alberati-Giani, D. et al. (1995) J. Neurochem. 64:1448-1455). A second amino transferase associated with this pathway is kynurenine/α-aminoadipate amino transferase (AadAT). AadAT catalyzes the reversible conversion of α-aminoadipate and α-ketoglutarate to α-ketoadipate and L-glutamate during lysine metabolism. AadAT also catalyzes the transamination of kynurenine to kynurenic acid. A cytosolic AadAT is expressed in rat kidney, liver, and brain (Nakatani, Y. et al. (1970) Biochim. Biophys. Acta 198:219-228; Buchli, R. et al. (1995) J. Biol. Chem. 270:29330-29335).

[0025] Glycosyl transferases include the mammalian UDP-glucouronosyl transferases, a family of membrane-bound microsomal enzymes catalyzing the transfer of glucouronic acid to lipophilic substrates in reactions that play important roles in detoxification and excretion of drugs, carcinogens, and other foreign substances. Another mammalian glycosyl transferase, mammalian UDP-galactose-ceramide galactosyl transferase, catalyzes the transfer of galactose to ceramide in the synthesis of galactocerebrosides in myelin membranes of the nervous system. The UDP-glycosyl transferases share a conserved signature domain of about 50 amino acid residues (PROSITE: PDOC00359, http://expasy.hcuge.ch/sprot/prosite.html).

[0026] Methyl transferases are involved in a variety of pharmacologically important processes. Nicotinamide N-methyl transferase catalyzes the N-methylation of nicotinamides and other pyridines, an important step in the cellular handling of drugs and other foreign compounds. Phenylethanolamine N-methyl transferase catalyzes the conversion of noradrenalin to adrenalin. 6-O-methylguanine-DNA methyl transferase reverses DNA methylation, an important step in carcinogenesis. Uroporphyrin-III C-methyl transferase, which catalyzes the transfer of two methyl groups from S-adenosyl-L-methionine to uroporphyrinogen III, is the first specific enzyme in the biosynthesis of cobalamin, a dietary enzyme whose uptake is deficient in pernicious anemia. Protein-arginine methyl transferases catalyze the posttranslational methylation of arginine residues in proteins, resulting in the mono- and dimethylation of arginine on the guanidino group. Substrates include histones, myelin basic protein, and heterogeneous nuclear ribonucleoproteins involved in mRNA processing, splicing, and transport. Protein-arginine methyl transferase interacts with proteins upregulated by mitogens, with proteins involved in chronic lymphocytic leukemia, and with interferon, suggesting an important role for methylation in cytokine receptor signaling (Lin, W.-J. et al. (1996) J. Biol. Chem. 271:15034-15044; Abramovich, C. et al. (1997) EMBO J. 16:260-266; and Scott, H. S. et al. (1998) Genomics 48:330-340).

[0027] Phosphotransferases catalyze the transfer of high-energy phosphate groups and are important in energy-requiring and -releasing reactions. The metabolic enzyme creatine kinase catalyzes the reversible phosphate transfer between creatine/creatine phosphate and ATP/ADP. Glycocyamine linase catalyzes phosphate transfer from ATP to guanidoacetate, and arginine kinase catalyzes phosphate transfer from ATP to arginine. A cysteine-containing active site is conserved in this family (PROSITE: PDOC00103).

[0028] Prenyl transferases are heterodimers, consisting of an alpha and a beta subunit, that catalyze the transfer of an isoprenyl group. An example of a prenyl transferase is the mammalian protein farnesyl transferase. The alpha subunit of farnesyl transferase consists of 5 repeats of 34 amino acids each, with each repeat containing an invariant tryptophan (PROSITE: PDOC00703).

[0029] Saccharyl transferases are glycating enzymes involved in a variety of metabolic processes. Oligosacchryl transferase-48, for example, is a receptor for advanced glycation endproducts. Accumulation of these endproducts is observed in vascular complications of diabetes, macrovascular disease, renal insufficiency, and Alzheimer's disease (Thornalley, P. J. (1998) Cell Mol. Biol. (Noisy-Le-Grand) 44:1013-1023).

[0030] Coenzyme A (CoA) transferase catalyzes the transfer of CoA between two carboxylic acids. Succinyl CoA:3-oxoacid CoA transferase, for example, transfers CoA from succinyl-CoA to a recipient such as acetoacetate. Acetoacetate is essential to the metabolism of ketone bodies, which accumulate in tissues affected by metabolic disorders such as diabetes (PROSITE: PDOC00980).

[0031] Hydrolases

[0032] Hydrolysis is the breaking of a covalent bond in a substrate by introduction of a molecule of water. The reaction involves a nucleophilic attack by the water molecule's oxygen atom on a target bond in the substrate. The water molecule is split across the target bond, breaking the bond and generating two product molecules. Hydrolases participate in reactions essential to such functions as synthesis and degradation of cell components, and for regulation of cell functions including cell signaling, cell proliferation, inflamation, apoptosis, secretion and excretion. Hydrolases are involved in key steps in disease processes involving these functions. Hydrolytic enzymes, or hydrolases, may be grouped by substrate specificity into classes including phosphatases, peptidases, lysophospholipases, phosphodiesterases, glycosidases, and glyoxalases.

[0033] Phosphatases hydrolytically remove phosphate groups from proteins, an energy-providing step that regulates many cellular processes, including intracellular signaling pathways that in turn control cell growth and differentiation, cell-cell contact, the cell cycle, and oncogenesis.

[0034] Lysophospholipases (LPLs) regulate intracellular lipids by catalyzing the hydrolysis of ester bonds to remove an acyl group, a key step in lipid degradation. Small LPL isoforms, approximately 15-30 kD, function as hydrolases; larger isoforms function both as hydrolases and transacylases. A particular substrate for LPLs, lysophosphatidylcholine, causes lysis of cell membranes. LPL activity is regulated by signaling molecules important in numerous pathways, including the inflammatory response.

[0035] Peptidases, also called proteases, cleave peptide bonds that form the backbone of peptide or protein chains. Proteolytic processing is essential to cell growth, differentiation, remodeling, and homeostasis as well as inflammation and immune response. Since typical protein half-lives range from hours to a few days, peptidases are continually cleaving precursor proteins to their active form, removing signal sequences from targeted proteins, and degrading aged or defective proteins. Peptidases function in bacterial, parasitic, and viral invasion and replication within a host. Examples of peptidases include trypsin and chymotrypsin (components of the complement cascade and the blood-clotting cascade) lysosomal cathepsins, calpains, pepsin, renin, and chymosin (Beynon, R. J. and J. S. Bond (1994) Proteolytic Enzymes: A Practical Approach, Oxford University Press, New York N.Y., pp. 1-5).

[0036] The phosphodiesterases catalyze the hydrolysis of one of the two ester bonds in a phosphodiester compound. Phosphodiesterases are therefore crucial to a variety of cellular processes. Phosphodiesterases include DNA and RNA endo- and exo-nucleases, which are essential to cell growth and replication as well as protein synthesis. Another phosphodiesterase is acid sphingomyelinase, which hydrolyzes the membrane phospholipid sphingomyelin to ceramide and phosphorylcholine. Phosphorylcholine is used in the synthesis of phosphatidylcholine, which is involved in numerous intracellular signaling pathways. Ceramide is an essential precursor for the generation of gangliosides, membrane lipids found in high concentration in neural tissue. Defective acid sphingomyelinase phosphodiesterase leads to a build-up of sphingomyelin molecules in lysosomes, resulting in Niemann-Pick disease.

[0037] Glycosidases catalyze the cleavage of hemiacetyl bonds of glycosides, which are compounds that contain one or more sugar. Mammalian lactase-phlorizin hydrolase, for example, is an intestinal enzyme that splits lactose. Mammalian beta-galactosidase removes the terminal galactose from gangliosides, glycoproteins, and glycosaminoglycans, and deficiency of this enzyme is associated with a gangliosidosis known as Morquio disease type B. Vertebrate lysosomal alpha-glucosidase, which hydrolyzes glycogen, maltose, and isomaltose, and vertebrate intestinal sucrase-isomaltase, which hydrolyzes sucrose, maltose, and isomaltose, are widely distributed members of this family with highly conserved sequences at their active sites.

[0038] The glyoxylase system is involved in gluconeogenesis, the production of glucose from storage compounds in the body. It consists of glyoxylase I, which catalyzes the formation of S-D-lactoylglutathione from methyglyoxal, a side product of triose-phosphate energy metabolism, and glyoxylase II, which hydrolyzes S-D-lactoylglutathione to D-lactic acid and reduced glutathione. Glyoxylases are involved in hyperglycemia, non-insulin-dependent diabetes mellitus, the detoxification of bacterial toxins, and in the control of cell proliferation and microtubule assembly.

[0039] Lyases

[0040] Lyases are a class of enzymes that catalyze the cleavage of C—C, C—O, C—N, C—S, C-(halide), P—O or other bonds without hydrolysis or oxidation to form two molecules, at least one of which contains a double bond (Stryer, L. (1995) Biochemistry W.H. Freeman and Co. New York, N.Y. p.620). Lyases are critical components of cellular biochemistry with roles in metabolic energy production including fatty acid metabolism, as well as other diverse enzymatic processes. Further classification of lyases reflects the type of bond cleaved as well as the nature of the cleaved group.

[0041] The group of C—C lyases include carboxyl-lyases (decarboxylases), aldehyde-lyases (aldolases), oxo-acid-lyases and others. The C—O lyase group includes hydro-lyases, lyases acting on polysaccharides and other lyases. The C—N lyase group includes ammonia-lyases, amidine-lyases, amine-lyases (deaminases) and other lyases.

[0042] Proper regulation of lyases is critical to normal physiology. For example, mutation induced deficiencies in the uroporphyrinogen decarboxylase can lead to photosensitive cutaneous lesions in the genetically-lied disorder familial porphyria cutanea tarda (Mendez, M. et al. (1998) Am. J. Genet. 63:1363-1375). It has also been shown that adenosine deaminase (ADA) deficiency stems from genetic mutations in the ADA gene, resulting in the disorder severe combined immunodeficiency disease (SCID) (Hershfield, M. S. (1998) Semin. Hematol. 35:291-298).

[0043] Isomerases

[0044] Isomerases are a class of enzymes that catalyze geometric or structural changes within a molecule to form a single product. This class includes racemases and epimerases, cis-trans-isomerases, intramolecular oxidoreductases, intramolecular transferases (mutases) and intramolecular lyases. Isomerases are critical components of cellular biochemistry with roles in metabolic energy production including glycolysis, as well as other diverse enzymatic processes (Stryer, L. (1995) Biochemistry, W.H. Freeman and Co., New York N.Y., pp.483-507).

[0045] Racemases are a subset of isomerases that catalyze inversion of a molecules configuration around the asymmetric carbon atom in a substrate having a single center of asymmetry, thereby interconvering two racemers. Epimerases are another subset of isomerases that catalyze inversion of configuration around an asymmetric carbon atom in a substrate with more than one center of symmetry, thereby interconverting two epimers. Racemases and epimerases can act on amino acids and derivatives, hydroxy acids and derivatives, as well as carbohydrates and derivatives. The interconversion of UDP-galactose and UDP-glucose is catalyzed by UDP-galactose-4′-epimerase. Proper regulation and function of this epimerase is essential to the synthesis of glycoproteins and glycolipids. Elevated blood galactose levels have been correlated with UDP-galactose-4′-epimerase deficiency in screening programs of infants (Gitzelmann, R. (1972) Helv. Paediat. Acta 27:125-130).

[0046] Oxidoreductases can be isomerases as well. Oxidoreductases catalyze the reversible transfer of electrons from a substrate that becomes oxidized to a substrate that becomes reduced. This class of enzymes includes dehydrogenases, hydroxylases, oxidases, oxygenases, peroxidases, and reductases. Proper maintenance of oxidoreductase levels is physiologically important. For example, genetically-liked deficiencies in lipoamide dehydrogenase can result in lactic acidosis (Robinson, B. H. et al. (1977) Pediat. Res. 11:1198-1202).

[0047] Another subgroup of isomerases are the transferases (or mutases). Transferases transfer a chemical group from one compound (the donor) to another compound (the acceptor). The types of groups transferred by these enzymes include acyl groups, amino groups, phosphate groups (phosphotransferases or phosphomutases), and others. The transferase carnitine palmitoyltransferase is an important component of fatty acid metabolism. Genetically-linked deficiencies in this transferase can lead to myopathy (Scriver, C. R. et al. (1995) The Metabolic and Molecular Basis of Inherited Disease, McGraw-Hill, New York N.Y., pp.1501-1533).

[0048] Yet another subgroup of isomerases are the topoisomersases. Topoisomerases are enzymes that affect the topological state of DNA. For example, defects in topoisomerases or their regulation can affect normal physiology. Reduced levels of topoisomerase II have been correlated with some of the DNA processing defects associated with the disorder ataxia-telangiectasia (Singh, S. P. et al. (1988) Nucleic Acids Res. 16:3919-3929).

[0049] Ligases

[0050] Ligases catalyze the formation of a bond between two substrate molecules. The process involves the hydrolysis of a pyrophosphate bond in ATP or a similar energy donor. Ligases are classified based on the nature of the type of bond they form, which can include carbon-oxygen, carbon-sulfur, carbon-nitrogen, carbon-carbon and phosphoric ester bonds.

[0051] Ligases forming carbon-oxygen bonds include the aminoacyl-transfer RNA (tRNA) synthetases which are important RNA-associated enzymes with roles in translation. Protein biosynthesis depends on each amino acid forming a linkage with the appropriate tRNA. The aminoacyl-tRNA synthetases are responsible for the activation and correct attachment of an amino acid with its cognate tRNA. The 20 aminoacyl-tRNA synthetase enzymes can be divided into two structural classes, and each class is characterized by a distinctive topology of the catalytic domain. Class I enzymes contain a catalytic domain based on the nucleotide-binding Rossman fold. Class II enzymes contain a central catalytic domain, which consists of a seven-stranded antiparallel β-sheet motif, as well as N- and C-terminal regulatory domains. Class II enzymes are separated into two groups based on the heterodimeric or homodimeric structure of the enzyme; the latter group is further subdivided by the structure of the N- and C-terminal regulatory domains (Hartlein, M. and S. Cusack (1995) J. Mol. Evol. 40:519-530). Autoantibodies against aminoacyl-tRNAs are generated by patients with dermatomyositis and polymyositis, and correlate strongly with complicating interstitial lung disease (ILD). These antibodies appear to be generated in response to viral infection, and coxsackie virus has been used to induce experimental viral myositis in animals.

[0052] Ligases forming carbon-sulfur bonds (Acid-thiol ligases) mediate a large number of cellular biosynthetic intermediary metabolism processes involve intermolecular transfer of carbon atom-containing substrates (carbon substrates). Examples of such reactions include the tricarboxylic acid cycle, synthesis of fatty acids and long-chain phospholipids, synthesis of alcohols and aldehydes, synthesis of intermediary metabolites, and reactions involved in the amino acid degradation pathways. Some of these reactions require input of energy, usually in the form of conversion of ATP to either ADP or AMP and pyrophosphate.

[0053] In many cases, a carbon substrate is derived from a small molecule containing at least two carbon atoms. The carbon substrate is often covalently bound to a larger molecule which acts as a carbon substrate carrier molecule within the cell. In the biosynthetic mechanisms described above, the carrier molecule is coenzyme A. Coenzyme A (CoA) is structurally related to derivatives of the nucleotide ADP and consists of 4′-phosphopantetheine linked via a phosphodiester bond to the alpha phosphate group of adenosine 3′,5′-bisphosphate. The terminal thiol group of 4′-phosphopantetheine acts as the site for carbon substrate bond formation. The predominant carbon substrates which utilize CoA as a carrier molecule during biosynthesis and intermediary metabolism in the cell are acetyl, succinyl, and propionyl moieties, collectively referred to as acyl groups. Other carbon substrates include enoyl lipid, which acts as a fatty acid oxidation intermediate, and carnitine, which acts as an acetyl-CoA flux regulator/mitochondrial acyl group transfer protein. Acyl-CoA and acetyl-CoA are synthesized in the cell by acyl-CoA synthetase and acetyl-CoA synthetase, respectively.

[0054] Activation of fatty acids is mediated by at least three forms of acyl-CoA synthetase activity: i) acetyl-CoA synthetase, which activates acetate and several other low molecular weight-carboxylic acids and is found in muscle mitochondria and the cytosol of other tissues; ii) medium-chain acyl-CoA synthetase, which activates fatty acids containing between four and eleven carbon atoms (predominantly from dietary sources), and is present only in liver mitochondria; and iii) acyl CoA synthetase, which is specific for long chain fatty acids with between six and twenty carbon atoms, and is found in microsomes and the mitochondria. Proteins associated with acyl-CoA synthetase activity have been identified from many sources including bacteria, yeast, plants, mouse, and man. The activity of acyl-CoA synthetase may be modulated by phosphorylation of the enzyme by cAMP-dependent protein kinase.

[0055] Ligases forming carbon-nitrogen bonds include amide synthases such as glutamine synthetase (glutamate-ammonia ligase) that catalyzes the amination of glutamic acid to glutamine by ammonia using the energy of ATP hydrolysis. Glutamine is the primary source for the amino group in various amide transfer reactions involved in de novo pyrimidine nucleotide synthesis and in purine and pyrimidine ribonucleotide interconversions. Overexpression of glutamine synthetase has been observed in primary liver cancer (Christa, L. et al. (1994) Gastroent. 106:1312-1320).

[0056] Acid-amino-acid ligases (peptide synthases) are represented by the ubiquitin proteases which are associated with the ubiquitin conjugation system (UCS), a major pathway for the degradation of cellular proteins in eukaryotic cells and some bacteria. The UCS mediates the elimination of abnormal proteins and regulates the half-lives of important regulatory proteins that control cellular processes such as gene transcription and cell cycle progression. In the UCS pathway, proteins targeted for degradation are conjugated to a ubiquitin (Ub), a small heat stable protein. Ub is first activated by a ubiquitin-activating enzyme (E1), and then transferred to one of several Ub-conjugating enzymes (E2). E2 then links the Ub molecule through its C-terminal glycine to an internal lysine (acceptor lysine) of a target protein. The ubiquitinated protein is then recognized and degraded by proteasome, a large, multisubunit proteolytic enzyme complex, and ubiquitin is released for reutilization by ubiquitin protease. The UCS is implicated in the degradation of mitotic cyclic kinases, oncoproteins, tumor suppressor genes such as p53, viral proteins, cell surface receptors associated with signal transduction, transcriptional regulators, and mutated or damaged proteins (Ciechanover, A. (1994) Cell 79:13-21). A murine proto-oncogene, Unp, encodes a nuclear ubiquitin protease whose overexpression leads to oncogenic transformation of NIH3T3 cells, and the human homolog of this gene is consistently elevated in small cell tumors and adenocarcinomas of the lung (Gray, D. A. (1995) Oncogene 10:2179-2183).

[0057] Cyclo-ligases and other carbon-nitrogen ligases comprise various enzymes and enzyme complexes that participate in the de novo pathways to purine and pyrimidine biosynthesis. Because these pathways are critical to the synthesis of nucleotides for replication of both RNA and DNA, many of these enzymes have been the targets of clinical agents for the treatment of cell proliferative disorders such as cancer and infectious diseases.

[0058] Purine biosynthesis occurs de novo from the amino acids glycine and glutamine, and other small molecules. Three of the key reactions in this process are catalyzed by a trifunctional enzyme composed of glycinamide-ribonucleotide synthetase (GARS), aminoimidazole ribonucleotide synthetase (AIRS), and glycinamide ribonucleotide transformylase (GART). Together these three enzymes combine ribosylamine phosphate with glycine to yield phosphoribosyl aminoimidazole, a precursor to both adenylate and guanylate nucleotides. This trifunctional protein has been implicated in the pathology of Downs syndrome (Aimi, J. et al. (1990) Nucleic Acid Res. 18:6665-6672). Adenylosuccinate synthetase catalyzes a later step in purine biosynthesis that converts inosinic acid to adenylosuccinate, a key step on the path to ATP synthesis. This enzyme is also similar to another carbon-nitrogen ligase, argininosuccinate synthetase, that catalyzes a similar reaction in the urea cycle (Powell, S. M. et al. (1992) FEBS Lett. 303:4-10).

[0059] Like the de novo biosynthesis of purines, de novo synthesis of the pyrimidine nucleotides uridylate and cytidylate also arises from a common precursor, in this instance the nucleotide orotidylate derived from orotate and phosphoribosyl pyrophosphate (PPRP). Again a trifunctional enzyme comprising three carbon-nitrogen ligases plays a key role in the process. In this case the enzymes aspartate transcarbamylase (ATCase), carbamyl phosphate synthetase II, and dihydroorotase (DHOase) are encoded by a single gene called CAD. Together these three enzymes combine the initial reactants in pyrimidine biosynthesis, glutamine, CO2, and ATP to form dihydroorotate, the precursor to orotate and orotidylate (Iwahana, H. et al. (1996) Biochem. Biophys. Res. Commun. 219:249-255). Further steps then lead to the synthesis of uridine nucleotides from orotidylate. Cytidine nucleotides are derived from uridine-5′-triphosphate (UTP) by the amidation of UTP using glutamine as the amino donor and the enzyme CTP synthetase. Regulatory mutations in the human CTP synthetase are believed to confer multi-drug resistance to agents widely used in cancer therapy (Yamauchi, M. et al. (1990) EMBO J. 9:2095-2099).

[0060] Ligases forming carbon-carbon bonds include the carboxylases acetyl-CoA carboxylase and pyruvate carboxylase. Acetyl-CoA carboxylase catalyzes the carboxylation of acetyl-CoA from CO2 and H2O using the energy of ATP hydrolysis. Acetyl-CoA carboxylase is the rate-limiting step in the biogenesis of long-chain fatty acids. Two isoforms of acetyl-CoA carboxylase, types I and types II, are expressed inhuman in a tissue-specific manner (Ha, J. et al. (1994) Eur. J. Biochem. 219:297-306). Pyruvate carboxylase is a nuclear-encoded mitochondrial enzyme that catalyzes the conversion of pyruvate to oxaloacetate, a key intermediate in the citric acid cycle.

[0061] Ligases forming phosphoric ester bonds include the DNA ligases involved in both DNA replication and repair. DNA ligases seal phosphodiester bonds between two adjacent nucleotides in a DNA chain using the energy from ATP hydrolysis to first activate the free 5′-phosphate of one nucleotide and then react it with the 3′-OH group of the adjacent nucleotide. This resealing reaction is used in both DNA replication to join small DNA fragments called Okazaki fragments that are transiently formed in the process of replicating new DNA, and in DNA repair. DNA repair is the process by which accidental base changes, such as those produced by oxidative damage, hydrolytic attack, or uncontrolled methylation of DNA, are corrected before replication or transcription of the DNA can occur. Bloom's syndrome is an inherited human disease in which individuals are partially deficient in DNA ligation and consequently have an increased incidence of cancer (Alberts, B. et al. (1994) The Molecular Biology of the Cell, Garland Publishing Inc., New York N.Y., p. 247).

[0062] Molecules Associated with Growth and Development

[0063] Human growth and development requires the spatial and temporal regulation of cell differentiation, cell proliferation, and apoptosis. These processes coordinately control reproduction, aging, embryogenesis, morphogenesis, organogenesis, and tissue repair and maintenance. At the cellular level, growth and development is governed by the cell's decision to enter into or exit from the cell division cycle and by the cell's commitment to a terminally differentiated state. These decisions are made by the cell in response to extracellular signals and other environmental cues it receives. The following discussion focuses on the molecular mechanisms of cell division, reproduction, cell differentiation and proliferation, apoptosis, and aging.

[0064] Cell Division

[0065] Cell division is the fundamental process by which all living things grow and reproduce. In unicellular organisms such as yeast and bacteria, each cell division doubles the number of organisms, while in multicellular species many rounds of cell division are required to replace cells lost by wear or by programmed cell death, and for cell differentiation to produce a new tissue or organ. Details of the cell division cycle may vary, but the basic process consists of three principle events. The first event, interphase, involves preparations for cell division, replication of the DNA, and production of essential proteins. In the second event, mitosis, the nuclear material is divided and separates to opposite sides of the cell. The final event, cytokinesis, is division and fission of the cell cytoplasm. The sequence and timing of cell cycle transitions is under the control of the cell cycle regulation system which controls the process by positive or negative regulatory circuits at various check points.

[0066] Regulated progression of the cell cycle depends on the integration of growth control pathways with the basic cell cycle machinery. Cell cycle regulators have been identified by selecting for human and yeast cDNAs that block or activate cell cycle arrest signals in the yeast mating pheromone pathway when they are overexpressed. Known regulators include human CPR (cell cycle progression restoration) genes, such as CPR8 and CPR2, and yeast CDC (cell division control) genes, including CDC91, that block the arrest signals. The CPR genes express a variety of proteins including cyclins, tumor suppressor binding proteins, chaperones, transcription factors, translation factors, and RNA-binding proteins (Edwards, M. C. et al.(1997) Genetics 147:1063-1076).

[0067] Several cell cycle transitions, including the entry and exit of a cell from mitosis, are dependent upon the activation and inhibition of cyclin-dependent kinases (Cdks). The Cdks are composed of a kinase subunit, Cdk, and an activating subunit, cyclin, in a complex that is subject to many levels of regulation. There appears to be a single Cdk in Saccharomyces cerevisiae and Saccharomyces pombe whereas mammals have a variety of specialized Cdks. Cyclins act by binding to and activating cyclin-dependent protein kinases which then phosphorylate and activate selected proteins involved in the mitotic process. The Cdk-cyclin complex is both positively and negatively regulated by phosphorylation, and by targeted degradation involving molecules such as CDC4 and CDC53. In addition, Cdks are further regulated by binding to inhibitors and other proteins such as Suc1 that modify their specificity or accessibility to regulators (Patra, D. and W. G. Dunphy (1996) Genes Dev. 10:1503-1515; and Mathias, N. et al. (1996) Mol. Cell Biol. 16:6634-6643).

[0068] Reproduction

[0069] The male and female reproductive systems are complex and involve many aspects of growth and development. The anatomy and physiology of the male and female reproductive systems are reviewed in (Guyton, A. C. (1991) Textbook of Medical Physiology, W.B. Saunders Co., Philadelphia Pa., pp. 899-928).

[0070] The male reproductive system includes the process of spermatogenesis, in which the sperm are formed, and male reproductive functions are regulated by various hormones and their effects on accessory sexual organs, cellular metabolism, growth, and other bodily functions.

[0071] Spermatogenesis begins at puberty as a result of stimulation by gonadotropic hormones released from the anterior pituitary. Immature sperm (spermatogonia) undergo several mitotic cell divisions before undergoing meiosis and full maturation. The testes secrete several male sex hormones, the most abundant being testosterone, that is essential for growth and division of the immature sperm, and for the masculine characteristics of the male body. Three other male sex hormones, gonadotropin-releasing hormone (GnRH), luteinizing hormone (LH), and follicle-stimulating hormone (FSH) control sexual function.

[0072] The uterus, ovaries, fallopian tubes, vagina, and breasts comprise the female reproductive system. The ovaries and uterus are the source of ova and the location of fetal development, respectively. The fallopian tubes and vagina are accessory organs attached to the top and bottom of the uterus, respectively. Both the uterus and ovaries have additional roles in the development and loss of reproductive capability during a female's lifetime. The primary role of the breasts is lactation. Multiple endocrine signals from the ovaries, uterus, pituitary, hypothalamus, adrenal glands, and other tissues coordinate reproduction and lactation. These signals vary during the monthly menstruation cycle and during the female's lifetime. Similarly, the sensitivity of reproductive organs to these endocrine signals varies during the female's lifetime.

[0073] A combination of positive and negative feedback to the ovaries, pituitary and hypothalamus glands controls physiologic changes during the monthly ovulation and endometrial cycles. The anterior pituitary secretes two major gonadotropin hormones, follicle-stimulating hormone (FSH) and luteinizing hormone (LH), regulated by negative feedback of steroids, most notably by ovarian estradiol. If fertilization does not occur, estrogen and progesterone levels decrease. This sudden reduction of the ovarian hormones leads to menstruation, the desquamation of the endometrium.

[0074] Hormones further govern all the steps of pregnancy, parturition, lactation, and menopause. During pregnancy large quantities of human chorionic gonadotropin (hCG), estrogens, progesterone, and human chorionic somatomammotropin (hCS) are formed by the placenta. hCG, a glycoprotein similar to luteinizing hormone, stimulates the corpus luteum to continue producing more progesterone and estrogens, rather than to involute as occurs if the ovum is not fertilized. hCS is similar to growth hormone and is crucial for fetal nutrition.

[0075] The female breast also matures during pregnancy. Large amounts of estrogen secreted by the placenta trigger growth and branching of the breast milk ductal system while lactation is initiated by the secretion of prolactin by the pituitary gland.

[0076] Parturition involves several hormonal changes that increase uterine contractility toward the end of pregnancy, as follows. The levels of estrogens increase more than those of progesterone. Oxytocin is secreted by the neurohypophysis. Concomitantly, uterine sensitivity to oxytocin increases. The fetus itself secretes oxytocin, cortisol (from adrenal glands), and prostaglandins.

[0077] Menopause occurs when most of the ovarian follicles have degenerated. The ovary then produces less estradiol, reducing the negative feedback on the pituitary and hypothalamus glands. Mean levels of circulating FSH and LH increase, even as ovulatory cycles continue. Therefore, the ovary is less responsive to gonadotropins, and there is an increase in the time between menstrual cycles. Consequently, menstrual bleeding ceases and reproductive capability ends.

[0078] Cell Differentiation and Proliferation

[0079] Tissue growth involves complex and ordered patterns of cell proliferation, cell differentiation, and apoptosis. Cell proliferation must be regulated to maintain both the number of cells and their spatial organization. This regulation depends upon the appropriate expression of proteins which control cell cycle progression in response to extracellular signals, such as growth factors and other mitogens, and intracellular cues, such as DNA damage or nutrient starvation. Molecules which directly or indirectly modulate cell cycle progression fall into several categories, including growth factors and their receptors, second messenger and signal transduction proteins, oncogene products, tumor-suppressor proteins, and mitosis-promoting factors.

[0080] Growth factors were originally described as serum factors required to promote cell proliferation. Most growth factors are large, secreted polypeptides that act on cells in their local environment. Growth factors bind to and activate specific cell surface receptors and initiate intracellular signal transduction cascades. Many growth factor receptors are classified as receptor tyrosine kinases which undergo autophosphorylation upon ligand binding. Autophosphorylation enables the receptor to interact with signal transduction proteins characterized by the presence of SH2 or SH3 domains (Src homology regions 2 or 3). These proteins then modulate the activity state of small G-proteins, such as Ras, Rab, and Rho, along with GTPase activating proteins (GAPs), guanine nucleotide releasing proteins (GNRPs), and other guanine nucleotide exchange factors. Small G proteins act as molecular switches that activate other downstream events, such as mitogen-activated protein kinase (MAP kinase) cascades. MAP kinases ultimately activate transcription of mitosis-promoting genes.

[0081] In addition to growth factors, small signaling peptides and hormones also influence cell proliferation. These molecules bind primarily to another class of receptor, the trimeric G-protein coupled receptor (GPCR), found predominantly on the surface of immune, neuronal and neuroendocrine cells. Upon ligand binding, the GPCR activates a trimeric G protein which in turn triggers increased levels of intracellular second messengers such as phospholipase C, Ca2+, and cyclic AMP. Most GPCR-mediated signaling pathways indirectly promote cell proliferation by causing the secretion or breakdown of other signaling molecules that have direct mitogenic effects. These signaling cascades often involve activation of kinases and phosphatases. Some growth factors, such as some members of the transforming growth factor beta (TGF-β) family, act on some cells to stimulate cell proliferation and on other cells to inhibit it. Growth factors may also stimulate a cell at one concentration and inhibit the same cell at another concentration. Most growth factors also have a multitude of other actions besides the regulation of cell growth and division: they can control the proliferation, survival, differentiation, migration, or function of cells depending on the circumstance. For example, the tumor necrosis factor/nerve growth factor (TNF/NGF) family can activate or inhibit cell death, as well as regulate proliferation and differentiation. The cell response depends on the type of cell, its stage of differentiation and transformation status, which surface receptors are stimulated, and the types of stimuli acting on the cell (Smith, A. et al. (1994) Cell 76:959-962; and Nocentini, G. et al. (1997) Proc. Natl. Acad. Sci. USA 94:6216-6221).

[0082] Neighboring cells in a tissue compete for growth factors, and when provided with “unlimited” quantities in a perfused system will grow to even higher cell densities before reaching density-dependent inhibition of cell division. Cells often demonstrate an anchorage dependence of cell division as well. This anchorage dependence may be associated with the formation of focal contacts linking the cytoskeleton with the extracellular matrix (ECM). The expression of ECM components can be stimulated by growth factors. For example, TGF-β stimulates fibroblasts to produce a variety of ECM proteins, including fibronectin, collagen, and tenascin (Pearson, C. A. et al. (1988) EMBO J. 7:2677-2981). In fact, for some cell types specific ECM molecules, such as laminin or fibronectin, may act as growth factors. Tenascin-C and -R, expressed in developing and lesioned neural tissue, provide stimulatory/anti-adhesive or inhibitory properties, respectively, for axonal growth (Faissner, A. (1997) Cell Tissue Res. 290:331-341).

[0083] Cancers are associated with the activation of oncogenes which are derived from normal cellular genes. These oncogenes encode oncoproteins which convert normal cells into malignant cells. Some oncoproteins are mutant isoforms of the normal protein, and other oncoproteins are abnormally expressed with respect to location or amount of expression. The latter category of oncoprotein causes cancer by altering transcriptional control of cell proliferation. Five classes of oncoproteins are known to affect cell cycle controls. These classes include growth factors, growth factor receptors, intracellular signal transducers, nuclear transcription factors, and cell-cycle control proteins. Viral oncogenes are integrated into the human genome after infection of human cells by certain viruses. Examples of viral oncogenes include v-src, v-abl, and v-fps.

[0084] Many oncogenes have been identified and characterized. These include sis, erbA, erbB, her-2, mutated Gs, src, abl, ras, crk, jun, fos, myc, and mutated tumor-suppressor genes such as RB, p53, mdm2, Cip1, p16, and cyclin D. Transformation of normal genes to oncogenes may also occur by chromosomal translocation. The Philadelphia chromosome, characteristic of chronic myeloid leukemia and a subset of acute lymphoblastic leukemias, results from a reciprocal translocation between chromosomes 9 and 22 that moves a truncated portion of the proto-oncogene c-abl to the breakpoint cluster region (bcr) on chromosome 22.

[0085] Tumor-suppressor genes are involved in regulating cell proliferation. Mutations which cause reduced or loss of function in tumor-suppressor genes result in uncontrolled cell proliferation. For example, the retinoblastoma gene product (RB), in a non-phosphorylated state, binds several early-response genes and suppresses their transcription, thus blocking cell division. Phosphorylation of RB causes it to dissociate from the genes, releasing the suppression, and allowing cell division to proceed.

[0086] Anoptosis

[0087] Apoptosis is the genetically controlled process by which unneeded or defective cells undergo programmed cell death. Selective elimination of cells is as important for morphogenesis and tissue remodeling as is cell proliferation and differentiation. Lack of apoptosis may result in hyperplasia and other disorders associated with increased cell proliferation. Apoptosis is also a critical component of the immune response. Immune cells such as cytotoxic T-ells and natural killer cells prevent the spread of disease by inducing apoptosis in tumor cells and virus-infected cells. In addition, immune cells that fail to distinguish self molecules from foreign molecules must be eliminated by apoptosis to avoid an autoimmune response.

[0088] Apoptotic cells undergo distinct morphological changes. Hallmarks of apoptosis include cell shrinkage, nuclear and cytoplasmic condensation, and alterations in plasma membrane topology. Biochemically, apoptotic cells are characterized by increased intracellular calcium concentration, fragmentation of chromosomal DNA, and expression of novel cell surface components.

[0089] The molecular mechanisms of apoptosis are highly conserved, and many of the key protein regulators and effectors of apoptosis have been identified. Apoptosis generally proceeds in response to a signal which is transduced intracellularly and results in altered patterns of gene expression and protein activity. Signaling molecules such as hormones and cytokines are known both to stimulate and to inhibit apoptosis through interactions with cell surface receptors. Transcription factors also play an important role in the onset of apoptosis. A number of downstream effector molecules, particularly proteases such as the cysteine proteases called caspases, have been implicated in the degradation of cellular components and the proteolytic activation of other apoptotic effectors.

[0090] Aging and Senescence

[0091] Studies of the aging process or senescence have shown a number of characteristic cellular and molecular changes (Fauci et al. (1998) Harrison's Principles of Eternal Medicine, McGraw-Hill, New York N.Y., p.37). These characteristics include increases in chromosome structural abnormalities, DNA cross-linking, incidence of single-stranded breaks in DNA, losses in DNA methylation, and degradation of telomere regions. In addition to these DNA changes, post-translational alterations of proteins increase including, deamidation, oxidation, cross-linking, and nonenzymatic glycation. Still further molecular changes occur in the mitochondria of aging cells through deterioration of structure. These changes eventually contribute to decreased function in every organ of the body.

[0092] Biochemical Pathway Molecules

[0093] Biochemical pathways are responsible for regulating metabolism, growth and development, protein secretion and trafficking, environmental responses, and ecological interactions including immune response and response to parasites.

[0094] DNA Replication

[0095] Deoxyribonucleic acid (DNA), the genetic material, is found in both the nucleus and mitochondria of human cells. The bulk of human DNA is nuclear, in the form of linear chromosomes, while mitochondrial DNA is circular. DNA replication begins at specific sites called origins of replication. Bidirectional synthesis occurs from the origin via two growing forks that move in opposite directions. Replication is semi-conservative, with each daughter duplex containing one old strand and its newly synthesized complementary partner. Proteins involved in DNA replication include DNA polymerases, DNA primase, telomerase, DNA helicase, topoisomerases, DNA ligases, replication factors, and DNA-binding proteins.

[0096] DNA Recombination and Repair

[0097] Cells are constantly faced with replication errors and environmental assault (such as ultraviolet irradiation) that can produce DNA damage. Damage to DNA consists of any change that modifies the structure of the molecule. Changes to DNA can be divided into two general classes, single base changes and structural distortions. Any damage to DNA can produce a mutation, and the mutation may produce a disorder, such as cancer.

[0098] Changes in DNA are recognized by repair systems within the cell. These repair systems act to correct the damage and thus prevent any deleterious affects of a mutational event. Repair systems can be divided into three general types, direct repair, excision repair, and retrieval systems. Proteins involved in DNA repair include DNA polymerase, excision repair proteins, excision and cross link repair proteins, recombination and repair proteins, RAD51 proteins, and BLN and WRN proteins that are homologs of RecQ helicase. When the repair systems are eliminated, cells become exceedingly sensitive to environmental mutagens, such as ultraviolet irradiation. Patients with disorders associated with a loss in DNA repair systems often exhibit a high sensitivity to environmental mutagens. Examples of such disorders include xeroderma pigmentosum (XP), Bloom's syndrome (BS), and Werner's syndrome CWS) (Yamagata, K. et al. (1998) Proc. Natl. Acad. Sci. USA 95:8733-8738), ataxia telangiectasia, Cockayne's syndrome, and Fanconi's anemia.

[0099] Recombination is the process whereby new DNA sequences are generated by the movements of large pieces of DNA. In homologous recombination, which occurs during meiosis and DNA repair, parent DNA duplexes align at regions of sequence similarity, and new DNA molecules form by the breakage and joining of homologous segments. Proteins involved include RAD51 recombinase. In site-specific recombination, two specific but not necessarily homologous DNA sequences are exchanged. In the immune system this process generates a diverse collection of antibody and T cell receptor genes. Proteins involved in site-specific recombination in the immune system include recombination activating genes 1 and 2 (RAG1 and RAG2). A defect in immune system site-specific recombination causes severe combined immunodeficiency disease in mice.

[0100] RNA Metabolism

[0101] Ribonucleic acid (RNA) is a linear single-stranded polymer of four nucleotides, ATP, CTP, UTP, and GTP. In most organisms, RNA is transcribed as a copy of DNA, the genetic material of the organism. In retroviruses RNA rather than DNA serves as the genetic material. RNA copies of the genetic material encode proteins or serve various structural, catalytic, or regulatory roles in organisms. RNA is classified according to its cellular localization and function. Messenger RNAs (mRNAs) encode polypeptides. Ribosomal RNAs (rRNAs) are assembled, along with ribosomal proteins, into ribosomes, which are cytoplasmic particles that translate mRNA into polypeptides. Transfer RNAs (tRNAs) are cytosolic adaptor molecules that function in mRNA translation by recognizing both an mRNA codon and the amino acid that matches that codon. Heterogeneous nuclear RNAs (hnRNAs) include mRNA precursors and other nuclear RNAs of various sizes. Small nuclear RNAs (snRNAs) are a part of the nuclear spliceosome complex that removes intervening, non-coding sequences (introns) and rejoins exons in pre-mRNAs.

[0102] RNA Transcription

[0103] The transcription process synthesizes an RNA copy of DNA. Proteins involved include multi-subunit RNA polymerases, transcription factors IIA, IIB, IID, IIE, IIF, IIH, and IIJ. Many transcription factors incorporate DNA-binding structural motifs which comprise either α-helices or β-sheets that bind to the major groove of DNA. Four well-characterized structural motifs are helix-turn-helix, zinc finger, leucine zipper, and helix-loop-helix.

[0104] RNA Processing

[0105] Various proteins are necessary for processing of transcribed RNAs in the nucleus. Pre-mRNA processing steps include capping at the 5′ end with methylguanosine, polyadenylating the 3′ end, and splicing to remove introns. The spliceosomal complex is comprised of five small nuclear ribonucleoprotein particles (snRNPs) designated U1, U2, U4, U5, and U6. Each snRNP contains a single species of snRNA and about ten proteins. The RNA components of some snRNPs recognize and base-pair with intron consensus sequences. The protein components mediate spliceosome assembly and the splicing reaction. Autoantibodies to snRNP proteins are found in the blood of patients with systemic lupus erythematosus (Stryer, L. (1995) Biochemistry W.H. Freeman and Company, New York N.Y., p. 863).

[0106] Heterogeneous nuclear ribonucleoproteins (hnRNPs) have been identified that have roles in splicing, exporting of the mature RNAs to the cytoplasm, and mRNA translation (Biamonti, G. et al. (1998) Clin. Exp. Rheumatol. 16:317-326). Some examples of hnRNPs include the yeast proteins Hrp1p, involved in cleavage and polyadenylation at the 3 end of the RNA; Cbp80p, involved in capping the 5′ end of the RNA; and Npl3p, a homolog of mammalian hnRNP A1, involved in export of mRNA from the nucleus (Shen, E. C. et al. (1998) Genes Dev. 12:679-691). HnRNPs have been shown to be important targets of the autoimmune response in rheumatic diseases (Biamonti, supra).

[0107] Many snRNP proteins, hnRNP proteins, and alternative splicing factors are characterized by an RNA recognition motif (RRM). (Reviewed in Birney, E. et al. (1993) Nucleic Acids Res. 21:5803-5816.) The RRM is about 80 amino acids in length and forms four β-strands and two α-helices arranged in an α/β sandwich. The RRM contains a core RNP-1 octapeptide motif along with surrounding conserved sequences.

[0108] RNA Stability and Degradation

[0109] RNA helicases alter and regulate RNA conformation and secondary structure by using energy derived from ATP hydrolysis to destabilize and unwind RNA duplexes. The most well-characterized and ubiquitous family of RNA helicases is the DEAD-box family, so named for the conserved B-type ATP-binding motif which is diagnostic of proteins in this family. Over 40 DEAD-box helicases have been identified in organisms as diverse as bacteria, insects, yeast, amphibians, mammals, and plants. DEAD-box helicases function in diverse processes such as translation initiation, splicing, ribosome assembly, and RNA editing, transport, and stability. Some DEAD-box helicases play tissue- and stage-specific roles in spermatogenesis and embryogenesis. (Reviewed in Linder, P. et al. (1989) Nature 337:121-122.)

[0110] Overexpression of the DEAD-box 1 protein (DDX1) may play a role in the progression of neuroblastoma (Nb) and retinoblastoma (Rb) tumors. Other DEAD-box helicases have been implicated either directly or indirectly in ultraviolet light-induced tumors, B cell lymphoma, and myeloid malignancies. (Reviewed in Godbout, R. et al. (1998) J. Biol. Chem. 273:21161-21168.)

[0111] Ribonucleases (RNases) catalyze the hydrolysis of phosphodiester bonds in RNA chains, thus cleaving the RNA. For example, RNase P is a ribonucleoprotein enzyme which cleaves the 5′ end of pre-tRNAs as part of their maturation process. RNase H digests the RNA strand of an RNA/DNA hybrid. Such hybrids occur in cells invaded by retroviruses, and RNase H is an important enzyme in the retroviral replication cycle. RNase H domains are often found as a domain associated with reverse transcriptases. RNase activity in serum and cell extracts is elevated in a variety of cancers and infectious diseases. (Schein, C. H. (1997) Nat. Biotechnol. 15:529-536). Regulation of RNase activity is being investigated as a means to control tumor angiogenesis, allergic reactions, viral infection and replication, and fungal infections.

[0112] Protein Translation

[0113] The eukaryotic ribosome is composed of a 60S (large) subunit and a 40S (small) subunit, which together form the 80S ribosome. In addition to the 18S, 28S, 5S, and 5.8S rRNAs, the ribosome also contains more than fifty proteins. The ribosomal proteins have a prefix which denotes the subunit to which they belong, either L (large) or S (small). Three important sites are identified on the ribosome. The aminoacyl-tRNA site (A site) is where charged tRNAs (with the exception of the initiator-tRNA) bind on arrival at the ribosome. The peptidyl-tRNA site (P site) is where new peptide bonds are formed, as well as where the initiator tRNA binds. The exit site (E site) is where deacylated tRNAs bind prior to their release from the ribosome. (Translation is reviewed in Stryer, L. (1995) Biochemistry, W.H. Freeman and Company, New York N.Y., pp. 875-908; and Lodish, E et al. (1995) Molecular Cell Biology, Scientific American Books, New York N.Y., pp. 119-138.)

[0114] tRNA Charging

[0115] Protein biosynthesis depends on each amino acid forming a linkage with the appropriate tRNA. The aminoacyl-tRNA synthetases are responsible for the activation and correct attachment of an amino acid with its cognate tRNA. The 20 aminoacyl-tRNA synthetase enzymes can be divided into two structural classes, Class I and Class II. Autoantibodies against aminoacyl-tRNAs are generated by patients with dermatomyositis and polymyositis, and correlate strongly with complicating interstitial lung disease (MD). These antibodies appear to be generated in response to viral infection, and coxsackie virus has been used to induce experimental viral myositis in animals.

[0116] Translation Initiation

[0117] Initiation of translation can be divided into three stages. The first stage brings an initiator transfer RNA (Met-tRNAf) together with the 40S ribosomal subunit to form the 43S preinitiation complex. The second stage binds the 43S preinitiation complex to the mRNA, followed by migration of the complex to the correct AUG initiation codon. The third stage brings the 60S ribosomal subunit to the 40S subunit to generate an 80S ribosome at the initiation codon. Regulation of translation primarily involves the first and second stage in the initiation process (Pain, V. M. (1996) Eur. J. Biochem. 236:747-771).

[0118] Several initiation factors, many of which contain multiple subunits, are involved in bringing an initiator tRNA and 40S ribosomal subunit together. eIF2, a guanine nucleotide binding protein, recruits the initiator tRNA to the 40S ribosomal subunit. Only when eIF2 is bound to GTP does it associate with the initiator tRNA. eIF2B, a guanine nucleotide exchange protein, is responsible for converting eIF2 from the GDP-bound inactive form to the GTP-bound active form. Two other factors, eIF1A and eIF3 bind and stabilize the 40S subunit by interacting with 18S ribosomal RNA and specific ribosomal structural proteins. eIF3 is also involved in association of the 40S ribosomal subunit with mRNA. The Met-tRNAf, eIF1A, eIF3, and 40S ribosomal subunit together make up the 43S preinitiation complex (Pain, supra).

[0119] Additional factors are required for binding of the 43S preinitiation complex to an mRNA molecule, and the process is regulated at several levels. eIF4F is a complex consisting of three proteins: eIF4E, eIF4A, and eIF4G. eIF4E recognizes and binds to the mRNA 5′-terminal m7GTP cap, eIF4A is a bidirectional RNA-dependent helicase, and eIF4G is a scaffolding polypeptide. eIF4G has three binding domains. The N-terminal third of eIF4G interacts with eIF4E, the central third interacts with eIF4A, and the C-terminal third interacts with eIF3 bound to the 43S preinitiation complex. Thus, eIF4G acts as a bridge between the 40S ribosomal subunit and the mRNA (Hentze, M. W. (1997) Science 275:500-501).

[0120] The ability of eIF4F to initiate binding of the 43S preinitiation complex is regulated by structural features of the mRNA. The mRNA molecule has an untranslated region (UTR) between the 5′ cap and the AUG start codon. In some mRNAs this region forms secondary structures that impede binding of the 43S preinitiation complex. The helicase activity of eIF4A is thought to function in removing this secondary structure to facilitate binding of the 43S preinitiation complex (Pain, supra).

[0121] Translation Elongation

[0122] Elongation is the process whereby additional amino acids are joined to the initiator methionine to form the complete polypeptide chain. The elongation factors EF1α, EF1βγ, and EF2 are involved in elongating the polypeptide chain following initiation. EF1α is a GTP-binding protein. In EF1α's GTP-bound form, it brings an aminoacyl-tRNA to the ribosome's A site. The amino acid attached to the newly arrived aminoacyl-tRNA forms a peptide bond with the initiator methionine. The GTP on EF1α is hydrolyzed to GDP, and EF1α-GDP dissociates from the ribosome. EF1βγ binds EF1α-GDP and induces the dissociation of GDP from EF1α, allowing EF1α to bind GTP and a new cycle to begin.

[0123] As subsequent aminoacyl-tRNAs are brought to the ribosome, EF-G, another GTP-binding protein, catalyzes the translocation of tRNAs from the A site to the P site and finally to the E site of the ribosome. This allows the processivity of translation.

[0124] Translation Termination

[0125] The release factor eRF carries out termination of translation. eRF recognizes stop codons in the mRNA, leading to the release of the polypeptide chain from the ribosome.

[0126] Post-Translational Pathways

[0127] Proteins maybe modified after translation by the addition of phosphate, sugar, prenyl, fatty acid, and other chemical groups. These modifications are often required for proper protein activity. Enzymes involved in post-translational modification include kinases, phosphatases, glycosyltransferases, and prenyltransferases. The conformation of proteins may also be modified after translation by the introduction and rearrangement of disulfide bonds (rearrangement catalyzed by protein disulfide isomerase), the isomerization of proline sidechains by prolyl isomerase, and by interactions with molecular chaperone proteins.

[0128] Proteins may also be cleaved by proteases. Such cleavage may result in activation, inactivation, or complete degradation of the protein. Proteases include serine proteases, cysteine proteases, aspartic proteases, and metalloproteases. Signal peptidase in the endoplasmic reticulum (ER) lumen cleaves the signal peptide from membrane or secretory proteins that are imported into the ER. Ubiquitin proteases are associated with the ubiquitin conjugation system (UCS), a major pathway for the degradation of cellular proteins in eukaryotic cells and some bacteria. The UCS mediates the elimination of abnormal proteins and regulates the half-lives of important regulatory proteins that control cellular processes such as gene transcription and cell cycle progression. In the UCS pathway, proteins targeted for degradation are conjugated to a ubiquitin, a small heat stable protein. Proteins involved in the UCS include ubiquitin-activating enzyme, ubiquitin-conjugating enzymes, ubiquitin-ligases, and ubiquitin C-terminal hydrolases. The ubiquitinated protein is then recognized and degraded by the proteasome, a large, multisubunit proteolytic enzyme complex, and ubiquitin is released for reutilization by ubiquitin protease.

[0129] Lipid Metabolism

[0130] Lipids are water-insoluble, oily or greasy substances that are soluble in nonpolar solvents such as chloroform or ether. Neutral fats (triacylglycerols) serve as major fuels and energy stores. Polar lipids, such as phospholipids, sphingolipids, glycolipids, and cholesterol, are key structural components of cell membranes.

[0131] Lipid metabolism is involved in human diseases and disorders. In the arterial disease atherosclerosis, fatty lesions form on the inside of the arterial wall. These lesions promote the loss of arterial flexibility and the formation of blood clots (Guyton, A. C. Textbook of Medical Physiology (1991) W. B. Saunders Company, Philadelphia Pa., pp.760-763). In Tay-Sachs disease, the GM2 ganglioside (a sphingolipid) accumulates in lysosomes of the central nervous system due to a lack of the enzyme N-acetylhexosaminidase. Patients suffer nervous system degeneration leading to early death (Fauci, A. S. et al. (1998) Harrison's Principles of internal Medicine McGraw-Hill, New York N.Y., p. 2171). The Niemann-Pick diseases are caused by defects in lipid metabolism. Niemann-Pick diseases types A and B are caused by accumulation of sphingomyelin (a sphingolipid) and other lipids in the central nervous system due to a defect in the enzyme sphingomyelinase, leading to neurodegeneration and lung disease. Niemann-Pick disease type C results from a defect in cholesterol transport, leading to the accumulation of sphingomyelin and cholesterol in lysosomes and a secondary reduction in sphingomyelinase activity. Neurological symptoms such as grand mal seizures, ataxia, and loss of previously learned speech, manifest 1-2 years after birth. A mutation in the NPC protein, which contains a putative cholesterol-sensing domain, was found in a mouse model of Niemann-Pick disease type C (Fauci, supra, p. 2175; Loftus, S. K. et al. (1997) Science 277:232-235). Lipid metabolism is reviewed in Stryer, L. (1995) Biochemistry, W.H. Freeman and Company, New York N.Y.; Lehninger, A. (1982) Principles of Biochemistry Worth Publishers, Inc., New York N.Y.; and ExPASy “Biochemical Pathways” index of Boehringer Mannheim World Wide Web site.)

[0132] Fatty Acid Synthesis

[0133] Fatty acids are long-chain organic acids with a single carboxyl group and a long non-polar hydrocarbon tail. Long-chain fatty acids are essential components of glycolipids, phospholipids, and cholesterol, which are building blocks for biological membranes, and of triglycerides, which are biological fuel molecules. Long-chain fatty acids are also substrates for eicosanoid production, and are important in the functional modification of certain complex carbohydrates and proteins. 16-carbon and 18-carbon fatty acids are the most common.

[0134] Fatty acid synthesis occurs in the cytoplasm. In the first step, acetyl-Coenzyme A (CoA) carboxylase (ACC) synthesizes malonyl-CoA from acetyl-CoA and bicarbonate. The enzymes which catalyze the remaining reactions are covalently linked into a single polypeptide chain, referred to as the multifunctional enzyme fatty acid synthase (FAS). FAS catalyzes the synthesis of palmitate from acetyl-CoA and malonyl-CoA. FAS contains acetyl transferase, malonyl transferase, β-ketoacetyl synthase, acyl carrier protein, β-ketoacyl reductase, dehydratase, enoyl reductase, and thioesterase activities. The final product of the FAS reaction is the 16-carbon fatty acid palmitate. Further elongation, as well as unsaturation, of palmitate by accessory enzymes of the ER produces the variety of long chain fatty acids required by the individual cell. These enzymes include a NADH-cytochrome b5 reductase, cytochrome b5, and a desaturase.

[0135] Phospholipid and Triacylglycerol Synthesis

[0136] Triacylglycerols, also known as triglycerides and neutral fats, are major energy stores in animals. Triacylglycerols are esters of glycerol with three fatty acid chains. Glycerol-3-phosphate is produced from dihydroxyacetone phosphate by the enzyme glycerol phosphate dehydrogenase or from glycerol by glycerol kinase. Fatty acid-CoA's are produced from fatty acids by fatty acyl-CoA synthetases. Glyercol-3-phosphate is acylated with two fatty acyl-CoA's by the enzyme glycerol phosphate acyltransferase to give phosphatidate. Phosphatidate phosphatase converts phosphatidate to diacylglycerol, which is subsequently acylated to a triacylglyercol by the enzyme diglyceride acyltransferase. Phosphatidate phosphatase and diglyceride acyltransferase form a triacylglyerol synthetase complex bound to the ER membrane.

[0137] A major class of phospholipids are the phosphoglycerides, which are composed of a glycerol backbone, two fatty acid chains, and a phosphorylated alcohol. Phosphoglycerides are components of cell membranes. Principal phosphoglycerides are phosphatidyl choline, phosphatidyl ethanolamine, phosphatidyl serine, phosphatidyl inositol, and diphosphatidyl glycerol. Many enzymes involved in phosphoglyceride synthesis are associated with membranes (Meyers, R. A. (1995) Molecular Biology and Biotechnoloy, VCH Publishers Inc., New York N.Y., pp. 494-501). Phosphatidate is converted to CDP-diacylglycerol by the enzyme phosphatidate cytidylyltransferase (ExPASy ENZYME EC 2.7.7.41). Transfer of the diacylglycerol group from CDP-diacylglycerol to serine to yield phosphatidyl serine, or to inositol to yield phosphatidyl inositol, is catalyzed by the enzymes CDP-diacylglycerol-serine O-phosphatidyltransferase and CDP-diacylglycerol-inositol 3-phosphatidyltransferase, respectively (ExPASy ENZYME EC 2.7.8.8; ExPASy ENZYME EC 2.7.8.11). The enzyme phosphatidyl serine decarboxylase catalyzes the conversion of phosphatidyl serine to phosphatidyl ethanolamine, using a pyruvate cofactor (Voelker, D. R. (1997) Biochim. Biophys. Acta 1348:236-244). Phosphatidyl choline is formed using diet-derived choline by the reaction of CDP-choline with 1,2-diacylglycerol, catalyzed by diacylglycerol cholinephosphotransferase (ExPASy ENZYME 2.7.8.2).

[0138] Sterol, Steroid, and Isoprenoid Metabolism

[0139] Cholesterol, composed of four fused hydrocarbon rings with an alcohol at one end, moderates the fluidity of membranes in which it is incorporated. In addition, cholesterol is used in the synthesis of steroid hormones such as cortisol progesterone, estrogen, and testosterone. Bile salts derived from cholesterol facilitate the digestion of lipids. Cholesterol in the skin forms a barrier that prevents excess water evaporation from the body. Farnesyl and geranylgeranyl groups, which are derived from cholesterol biosynthesis intermediates, are post-translationally added to signal transduction proteins such as ras and protein-targeting proteins such as rab. These modifications are important for the activities of these proteins (Guyton, supra; Stryer, supra, pp. 279-280, 691-702, 934).

[0140] Mammals obtain cholesterol derived from both de novo biosynthesis and the diet. The liver is the major site of cholesterol biosynthesis in mammals. Two acetyl-CoA molecules initially condense to form acetoacetyl-CoA, catalyzed by a thiolase. Acetoacetyl-CoA condenses with a third acetyl-CoA to form hydroxymethylglutaryl-CoA (HMG-CoA), catalyzed by HMG-CoA synthase. Conversion of HMG-CoA to cholesterol is accomplished via a series of enzymatic steps known as the mevalonate pathway. The rate-limiting step is the conversion of HMG-CoA to mevalonate by HMG-CoA reductase. The drug lovastatin, a potent inhibitor of HMG-CoA reductase, is given to patients to reduce their serum cholesterol levels. Other mevalonate pathway enzymes include mevalonate kinase, phosphomevalonate kinase, diphosphomevalonate decarboxylase, isopentenyldiphosphate isomerase, dimethylallyl transferase, geranyl transferase, farnesyl-diphosphate farnesyltransferase, squalene monooxygenase, lanosterol synthase, lathosterol oxidase, and 7-dehydrocholesterol reductase.

[0141] Cholesterol is used in the synthesis of steroid hormones such as cortisol, progesterone, aldosterone, estrogen, and testosterone. First, cholesterol is converted to pregnenolone by cholesterol monooxygenases. The other steroid hormones are synthesized from pregnenolone by a series of enzyme-catalyzed reactions including oxidations, isomerizations, hydroxylations, reductions, and demethylations. Examples of these enzymes include steroid Δ-isomerase, 3β-hydroxy-Δ5-steroid dehydrogenase, steroid 21-monooxygenase, steroid 19-hydroxylase, and 3β-hydroxysteroid dehydrogenase. Cholesterol is also the precursor to vitamin D.

[0142] Numerous compounds contain 5-carbon isoprene units derived from the mevalonate pathway intermediate isopentenyl pyrophosphate. Isoprenoid groups are found in vitamin K, ubiquinone, retinal, dolichol phosphate (a carrier of oligosaccharides needed for N-linked glycosylation), and farnesyl and geranylgeranyl groups that modify proteins. Enzymes involved include farnesyl transferase, polyprenyl transferases, dolichyl phosphatase, and dolichyl kinase.

[0143] Sphingobipid Metabolism

[0144] Sphingolipids are an important class of membrane lipids that contain sphingosine, a long chain amino alcohol. They are composed of one long-chain fatty acid, one polar head alcohol, and sphingosine or sphingosine derivative. The three classes of sphingolipids are sphingomyelins, cerebrosides, and gangliosides. Sphingomyelins, which contain phosphocholine or phosphoethanolamine as their head group, are abundant in the myelin sheath surrounding nerve cells. Galactocerebrosides, which contain a glucose or galactose head group, are characteristic of the brain. Other cerebrosides are found in nonneural tissues. Gangliosides, whose head groups contain multiple sugar units, are abundant in the brain, but are also found in nonneural tissues.

[0145] Sphingolipids are built on a sphingosine backbone. Sphingosine is acylated to ceramide by the enzyme sphingosine acetyltransferase. Ceramide and phosphatidyl choline are converted to sphingomyelin by the enzyme ceramide choline phosphotransferase. Cerebrosides are synthesized by the linkage of glucose or galactose to ceramide by a transferase. Sequential addition of sugar residues to ceramide by transferase enzymes yields gangliosides.

[0146] Eicosanoid Metabolism

[0147] Eicosanoids, including prostaglandins, prostacyclin, thromboxanes, and leukotrienes, are 20-carbon molecules derived from fatty acids. Eicosanoids are signaling molecules which have roles in pain, fever, and inflammation. The precursor of all eicosanoids is arachidonate, which is generated from phospholipids by phospholipase A2 and from diacylglycerols by diacylglycerol lipase. Leukotrienes are produced from arachidonate by the action of lipoxygenases. Prostaglandin synthase, reductases, and isomerases are responsible for the synthesis of the prostaglandins. Prostaglandins have roles in inflammation, blood flow, ion transport, synaptic transmission, and sleep. Prostacyclin and the thromboxanes are derived from a precursor prostaglandin by the action of prostacyclin synthase and thromboxane synthases, respectively.

[0148] Ketone Body Metabolism

[0149] Pairs of acetyl-CoA molecules derived from fatty acid oxidation in the liver can condense to form acetoacetyl-CoA, which subsequently forms acetoacetate, D-3-hydroxybutyrate, and acetone. These three products are known as ketone bodies. Enzymes involved in ketone body metabolism include HMG-CoA synthetase, HMG-CoA cleavage enzyme, D-3-hydroxybutyrate dehydrogenase, acetoacetate decarboxylase, and 3-ketoacyl-CoA transferase. Ketone bodies are a normal fuel supply of the heart and renal cortex. Acetoacetate produced by the liver is transported to cells where the acetoacetate is converted back to acetyl-CoA and enters the citric acid cycle. In times of starvation, ketone bodies produced from stored triacylglyerols become an important fuel source, especially for the brain. Abnormally high levels of ketone bodies are observed in diabetics. Diabetic coma can result if ketone body levels become too great

[0150] Lipid Mobilization

[0151] Within cells, fatty acids are transported by cytoplasmic fatty acid binding proteins (Online Mendelian Inheritance in Man (OMIM)*134650 Fatty Acid-Binding Protein 1, Liver; FABP1). Diazepam binding inhibitor (DBI), also known as endozepine and acyl CoA-binding protein, is an endogenous γ-aminobutyric acid (GABA) receptor ligand which is thought to down-regulate the effects of GABA. DBI binds medium- and longchain acyl-CoA esters with very high affinity and may function as an intracellular carrier of acyl-CoA esters (OMIM*125950 Diazepam Binding Inhibitor; DBI; PROSITE PDOC00686 Acyl-CoA-binding protein signature).

[0152] Fat stored in liver and adipose triglycerides may be released by hydrolysis and transported in the blood. Free fatty acids are transported in the blood by albumin. Triacyiglycerols and cholesterol esters in the blood are transported in lipoprotein particles. The particles consist of a core of hydrophobic lipids surrounded by a shell of polar lipids and apolipoproteins. The protein components serve in the solubilization of hydrophobic lipids and also contain cell-targeting signals. Lipoproteins include chylomicrons, chylomicron remnmants, very-low-density lipoproteins (VLDL), intermediate-density lipoproteins (IDL), low-density lipoproteins (LDL), and high-density lipoproteins (HDL). There is a strong inverse correlation between the levels of plasma HDL and risk of premature coronary heart disease.

[0153] Triacylglycerols in chylomicrons and VLDL are hydrolyzed by lipoprotein lipases that line blood vessels in muscle and other tissues that use fatty acids. Cell surface LDL receptors bind LDL particles which are then internalized by endocytosis. Absence of the LDL receptor, the cause of the disease familial hypercholesterolemia, leads to increased plasma cholesterol levels and ultimately to atherosclerosis. Plasma cholesteryl ester transfer protein mediates the transfer of cholesteryl esters from HDL to apolipoprotein B-containing lipoproteins. Cholesteryl ester transfer protein is important in the reverse cholesterol transport system and may play a role in atherosclerosis (Yamashita, S. et al. (1997) Curr. Opin. Lipidol. 8:101-110). Macrophage scavenger receptors, which bind and internalize modified lipoproteins, play a role in lipid transport and may contribute to atherosclerosis (Greaves, D. R. et al. (1998) Curr. Opin. Lipidol. 9:425-432).

[0154] Proteins involved in cholesterol uptake and biosynthesis are tightly regulated in response to cellular cholesterol levels. The sterol regulatory element binding protein (SREBP) is a sterol-responsive transcription factor. Under normal cholesterol conditions, SREBP resides in the ER membrane. When cholesterol levels are low, a regulated cleavage of SREBP occurs which releases the extracellular domain of the protein. This cleaved domain is then transported to the nucleus where it activates the transcription of the LDL receptor gene, and genes encoding enzymes of cholesterol synthesis, by binding the sterol regulatory element (SRE) upstream of the genes (Yang, J. et al. (1995) J. Biol. Chem. 270:12152-12161). Regulation of cholesterol uptake and biosynthesis also occurs via the oxysterol-binding protein (OSBP). OSBP is a high-affinity intracellular receptor for a variety of oxysterols that down-regulate cholesterol synthesis and stimulate cholesterol esterification (Lagace, T. A. et al. (1997) Biochem. J. 326:205-213).

[0155] Beta-Oxidation

[0156] Mitochondrial and peroxisomal beta-oxidation enzymes degrade saturated and unsaturated fatty acids by sequential removal of two-carbon units from CoA-activated fatty acids. The main beta-oxidation pathway degrades both saturated and unsaturated fatty acids while the auxiliary pathway performs additional steps required for the degradation of unsaturated fatty acids.

[0157] The pathways of mitochondrial and peroxisomal beta-oxidation use similar enzymes, but have different substrate specificities and functions. Mitochondria oxidize short-, medium-, and long-chain fatty acids to produce energy for cells. Mitochondrial beta-oxidation is a major energy source for cardiac and skeletal muscle. In liver, it provides ketone bodies to the peripheral circulation when glucose levels are low as in starvation, endurance exercise, and diabetes (Eaton, S. et al. (1996) Biochem. J. 320:345-357). Peroxisomes oxidize medium-, long-, and very-long-chain fatty acids, dicarboxylic fatty acids, branched fatty acids, prostaglandins, xenobiotics, and bile acid intermediates. The chief roles of peroxisomal beta-oxidation are to shorten toxic lipophilic carboxylic acids to facilitate their excretion and to shorten very-long-chain fatty acids prior to mitochondrial beta-oxidation (Mannaerts, G. P. and P. P. van Veldhoven (1993) Biochimie 75:147-158).

[0158] Enzymes involved in beta-oxidation include acyl CoA synthetase, carnitine acyltransferase, acyl CoA dehydrogenases, enoyl CoA hydratases, L-3-hydroxyacyl CoA dehydrogenase, β-ketothiolase, 2,4-dienoyl CoA reductase, and isomerase.

[0159] Lipid Cleavage and Degradation

[0160] Triglycerides are hydrolyzed to fatty acids and glycerol by lipases. Lysophospholipases (LPLs) are widely distributed enzymes that metabolize intracellular lipids, and occur in numerous isoforms. Small isoforms, approximately 15-30 kD, function as hydrolases; large isoforms, those exceeding 60 kD, function both as hydrolases and transacylases. A particular substrate for LPLs, lysophosphatidylcholine, causes lysis of cell membranes when it is formed or imported into a cell LPLs are regulated by lipid factors including acylcarnitine, arachidonic acid, and phosphatidic acid. These lipid factors are signaling molecules important in numerous pathways, including the inflammatory response. (Anderson, R. et al. (1994) Toxicol. Appl. Pharmacol. 125:176-183; Selle, H et al. (1993); Eur. J. Biochem. 212:411-416.)

[0161] The secretory phospholipase A2 (PLA2) superfamily comprises a number of heterogeneous enzymes whose common feature is to hydrolyze the sn-2 fatty acid acyl ester bond of phosphoglycerides. Hydrolysis of the glycerophospholipids releases free fatty acids and lysophospholipids. PLA2 activity generates precursors for the biosynthesis of biologically active lipids, hydroxy fatty acids, and platelet-activating factor. PLA2 hydrolysis of the sn-2 ester bond in phospholipids generates free fatty acids, such as arachidonic acid and lysophospholipids.

[0162] Carbon and Carbohydrate Metabolism

[0163] Carbohydrates, including sugars or saccharides, starch, and cellulose, are aldehyde or ketone compounds with multiple hydroxyl groups. The importance of carbohydrate metabolism is demonstrated by the sensitive regulatory system in place for maintenance of blood glucose levels. Two pancreatic hormones, insulin and glucagon, promote increased glucose uptake and storage by cells, and increased glucose release from cells, respectively. Carbohydrates have three important roles in mammalian cells. First, carbohydrates are used as energy stores, fuels, and metabolic intermediates. Carbohydrates are broken down to form energy in glycolysis and are stored as glycogen for later use. Second, the sugars deoxyribose and ribose form part of the structural support of DNA and RNA, respectively. Third, carbohydrate modifications are added to secreted and membrane proteins and lipids as they traverse the secretory pathway. Cell surface carbohydrate-containing macromolecules, including glycoproteins, glycolipids, and transmembrane proteoglycans, mediate adhesion with other cells and with components of the extracellular matrix. The extracellular matrix is comprised of diverse glycoproteins, glycosaminoglycans (GAGs), and carbohydrate-binding proteins which are secreted from the cell and assembled into an organized meshwork in close association with the cell surface. The interaction of the cell with the surrounding matrix profoundly influences cell shape, strength, flexibility, motility, and adhesion. These dynamic properties are intimately associated with signal transduction pathways controlling cell proliferation and differentiation, tissue construction, and embryonic development.

[0164] Carbohydrate metabolism is altered in several disorders including diabetes mellitus, hyperglycemia, hypoglycemia, galactosemia, galactokinase deficiency, and UDP-galactose-4-epimerase deficiency (Fauci, A. S. et al. (1998) Harrison's Principles of Internal Medicine, McGraw-Hill, New York N.Y., pp. 2208-2209). Altered carbohydrate metabolism is associated with cancer. Reduced GAG and proteoglycan expression is associated with human lung carcinomas (Nackaerts, K. et al. (1997) Int. J. Cancer 74:335-345). The carbohydrate determinants sialyl Lewis A and sialyl Lewis X are frequently expressed on human cancer cells (Kannagi, R. (1997) Glycoconj. J. 14:577-584). Alterations of the N-linked carbohydrate core structure of cell surface glycoproteins are linked to colon and pancreatic cancers (Schwarz, R. E. et al. (1996) Cancer Lett. 107:285-291). Reduced expression of the Sda blood group carbohydrate structure in cell surface glycolipids and glycoproteins is observed in gastrointestinal cancer (Dohi, T. et al. (1996) Int. J. Cancer 67:626-663). (Carbon and carbohydrate metabolism is reviewed in Stryer, L. (1995) Biochemistry W.H. Freeman and Company, New York N.Y.; Lehninger, A. L. (1982) Principles of Biochemistry Worth Publishers Inc., New York N.Y.; and Lodish, H et al. (1995) Molecular Cell Biology Scientific American Books, New York N.Y.)

[0165] Glycolysis

[0166] Enzymes of the glycolytic pathway convert the sugar glucose to pyruvate while simultaneously producing ATP. The pathway also provides building blocks for the synthesis of cellular components such as long-chain fatty acids. After glycolysis, pyrvuate is converted to acetyl-Coenzyme A, which, in aerobic organisms, enters the citric acid cycle. Glycolytic enzymes include hexokinase, phosphoglucose isomerase, phosphofructokinase, aldolase, triose phosphate isomerase, glyceraldehyde 3-phosphate dehydrogenase, phosphoglycerate kinase, phosphoglyceromutase, enolase, and pyruvate kinase. Of these, phosphofructokinase, hexokinase, and pyruvate kinase are important in regulating the rate of glycolysis.

[0167] Gluconeogenesis

[0168] Gluconeogenesis is the synthesis of glucose from noncarbohydrate precursors such as lactate and amino acids. The pathway, which functions mainly in times of starvation and intense exercise, occurs mostly in the liver and kidney. Responsible enzymes include pyruvate carboxylase, phosphoenolpyruvate carboxykinase, fructose 1,6-bisphosphatase, and glucose-6-phosphatase.

[0169] Pentose Phosphate Pathway

[0170] Pentose phosphate pathway enzymes are responsible for generating the reducing agent NADPH, while at the same time oxidizing glucose-6-phosphate to ribose-5-phosphate. Ribose-5-phosphate and its derivatives become part of important biological molecules such as ATP, Coenzyme A, NAD+, FAD, RNA, and DNA. The pentose phosphate pathway has both oxidative and non-oxidative branches. The oxidative branch steps, which are catalyzed by the enzymes glucose-6-phosphate dehydrogenase, lactonase, and 6-phosphogluconate dehydrogenase, convert glucose-6-phosphate and NADP+ to ribulose-6-phosphate and NADPH. The non-oxidative branch steps, which are catalyzed by the enzymes phosphopentose isomerase, phosphopentose epimerase, transketolase, and transaldolase, allow the interconversion of three-, four-, five-, six-, and seven-carbon sugars.

[0171] Glucouronate Metabolism

[0172] Glucuronate is a monosaccharide which, in the form of D-glucuronic acid, is found in the GAGs chondroitin and dermatan. D-glucuronic acid is also important in the detoxification and excretion of foreign organic compounds such as phenol. Enzymes involved in glucuronate metabolism include UDP-glucose dehydrogenase and glucuronate reductase.

[0173] Disaccharide Metabolism

[0174] Disaccharides must be hydrolyzed to monosaccharides to be digested. Lactose, a disaccharide found in milk, is hydrolyzed to galactose and glucose by the enzyme lactase. Maltose is derived from plant starch and is hydrolyzed to glucose by the enzyme maltase. Sucrose is derived from plants and is hydrolyzed to glucose and fructose by the enzyme sucrase. Trehalose, a disaccharide found mainly in insects and mushrooms, is hydrolyzed to glucose by the enzyme trehalase (OMIM*275360 Trehalase; Ruf, J. et al. (1990) J. Biol. Chem. 265:15034-15039). Lactase, maltase, sucrase, and trehalase are bound to mucosal cells lining the small intestine, where they participate in the digestion of dietary disaccharides. The enzyme lactose synthetase, composed of the catalytic subunit galactosyltransferase and the modifier subunit α-lactalbumin, converts UDP-galactose and glucose to lactose in the mammary glands.

[0175] Glycogen, Starch, and Chitin Metabolism

[0176] Glycogen is the storage form of carbohydrates in mammals. Mobilization of glycogen maintains glucose levels between meals and during muscular activity. Glycogen is stored mainly in the liver and in skeletal muscle in the form of cytoplasmic granules. These granules contain enzymes that catalyze the synthesis and degradation of glycogen, as well as enzymes that regulate these processes. Enzymes that catalyze the degradation of glycogen include glycogen phosphorylase, a transferase, x-1,6-glucosidase, and phosphoglucomutase. Enzymes that catalyze the synthesis of glycogen include UDP-glucose pyrophosphorylase, glycogen synthetase, a branching enzyme, and nucleoside diphosphokinase. The enzymes of glycogen synthesis and degradation are tightly regulated by the hormones insulin, glucagon, and epinephrine. Starch, a plant-derived polysaccharide, is hydrolyzed to maltose, maltotriose, and α-dextrin by α-amylase, an enzyme secreted by the salivary glands and pancreas. Chitin is a polysaccharide found in insects and crustacea. A chitotriosidase is secreted by macrophages and may play a role in the degradation of chitin-containing pathogens (Boot, R. G. et al. (1995) J. Biol. Chem. 270:26252-26256).

[0177] Peptidoglycans and Glycosaminoglycans

[0178] Glycosaminoglycans (GAGs) are anionic linear unbranched polysaccharides composed of repetitive disaccharide units. These repetitive units contain a derivative of an amino sugar, either glucosamine or galactosamine. GAGs exist free or as part of proteoglycans, large molecules composed of a core protein attached to one or more GAGs. GAGs are found on the cell surface, inside cells, and in the extracellular matrix. Changes in GAG levels are associated with several autoimmune diseases including autoimmune thyroid disease, autoimmune diabetes mellitus, and systemic lupus erythematosus (Hansen, C. et al. (1996) Clin. Exp. Rheum. 14 (Suppl. 15):S59-S67). GAGs include chondroitin sulfate, keratan sulfate, heparin, heparan sulfate, dermatan sulfate, and hyaluronan.

[0179] The GAG hyaluronan (HA) is found in the extracellular matrix of many cells, especially in soft connective tissues, and is abundant in synovial fluid (Pitsillides, A. A. et al. (1993) Int. J. Exp. Pathol. 74:27-34). HA seems to play important roles in cell regulation, development, and differentiation (Laurent, T. C. and J. R. Fraser (1992) FASEB J. 6:2397-2404). Hyaluronidase is an enzyme that degrades HA to oligosaccharides. Hyaluronidases may function in cell adhesion, infection, angiogenesis, signal transduction, reproduction, cancer, and inflammation.

[0180] Proteoglycans, also known as peptidoglycans, are found in the extracellular matrix of connective tissues such as cartilage and are essential for distributing the load in weight-bearing joints. Cell-surface-attached proteoglycans anchor cells to the extracellular matrix. Both extracellular and cell-surface proteoglycans bind growth factors, facilitating their binding to cell-surface receptors and subsequent triggering of signal transduction pathways.

[0181] Amino Acid and Nitrogen Metabolism

[0182] NH4+ is assimilated into amino acids by the actions of two enzymes, glutamate dehydrogenase and glutamine synthetase. The carbon skeletons of amino acids come from the intermediates of glycolysis, the pentose phosphate pathway, or the citric acid cycle. Of the twenty amino acids used in proteins, humans can synthesize only thirteen (nonessential amino acids). The remaining nine must come from the diet (essential amino acids). Enzymes involved in nonessential amino acid biosynthesis include glutamate kinase dehydrogenase, pyrroline carboxylate reductase, asparagine synthetase, phenylalanine oxygenase, methionine adenosyltransferase, adenosylhomocysteinase, cystathionine, β-synthase, cystathionine γ-lyase, phosphoglycerate dehydrogenase, phosphoserine transaminase, phosphoserine phosphatase, serine hydroxylmethyltransferase, and glycine synthase.

[0183] Metabolism of amino acids takes place almost entirely in the liver, where the amino group is removed by aminotransferases (transaminases), for example, alanine aminotransferase. The amino group is transferred to α-ketoglutarate to form glutamate. Glutamate dehydrogenase converts glutamate to NH4+ and α-ketoglutarate. NH4+ is converted to urea by the urea cycle which is catalyzed by the enzymes arginase, ornithine transcarbamoylase, arginosuccinate synthetase, and arginosuccinase. Carbamoyl phosphate synthetase is also involved in urea formation. Enzymes involved in the metabolism of the carbon skeleton of amino acids include serine dehydratase, asparaginase, glutaminase, propionyl CoA carboxylase, methylmalonyl CoA mutase, branched-chain α-keto dehydrogenase complex, isovaleryl CoA dehydrogenase, β-methylcrotonyl CoA carboxylase, phenylalanine hydroxylase, p-hydroxylphenylpyruvate hydroxylase, and homogentisate oxidase.

[0184] Polyamines, which include spermidine, putrescine, and spermine, bind tightly to nucleic acids and are abundant in rapidly proliferating cells. Enzymes involved in polyamine synthesis include ornithine decarboxylase.

[0185] Diseases involved in amino acid and nitrogen metabolism include hyperammonemia, carbamoyl phosphate synthetase deficiency, urea cycle enzyme deficiencies, methylmalonic aciduria, maple syrup disease, alcaptonuria, and phenylketonuria

[0186] Energy Metabolism

[0187] Cells derive energy from metabolism of ingested compounds that may be roughly categorized as carbohydrates, fats, or proteins. Energy is also stored in polymers such as triglycerides (fats) and glycogen (carbohydrates). Metabolism proceeds along separate reaction pathways connected by key intermediates such as acetyl coenzyme A (acetyl-CoA). Metabolic pathways feature anaerobic and aerobic degradation, coupled with the energy-requiring reactions such as phosphorylation of adenosine diphosphate (ADP) to the triphosphate (ATP) or analogous phosphorylations of guanosine (GDP/GTP), uridine (UDP/UTP), or cytidine (CDP/CTP). Subsequent dephosphorylation of the triphosphate drives reactions needed for cell maintenance, growth, and proliferation.

[0188] Digestive enzymes convert carbohydrates and sugars to glucose; fructose and galactose are converted in the liver to glucose. Enzymes involved in these conversions include galactose-1-phosphate uridyl transferase and UDP-galactose-4 epimerase. In the cytoplasm, glycolysis converts glucose to pyruvate in a series of reactions coupled to ATP synthesis.

[0189] Pyruvate is transported into the mitochondria and converted to acetyl-CoA for oxidation via the citric acid cycle, involving pyruvate dehydrogenase components, dihydrolipoyl transacetylase, and dihydrolipoyl dehydrogenase. Enzymes involved in the citric acid cycle include: citrate synthetase, aconitases, isocitrate dehydrogenase, alpha-ketoglutarate dehydrogenase complex including transsuccinylases, succinyl CoA synthetase, succinate dehydrogenase, fumarases, and malate dehydrogenase. Acetyl CoA is oxidized to CO2 with concomitant formation of NADH, FADH2, and GTP. In oxidative phosphorylation, the transport of electrons from NADH and FADH2 to oxygen by dehydrogenases is coupled to the synthesis of ATP from ADP and Pi by the F0F1 ATPase complex in the mitochondrial inner membrane. Enzyme complexes responsible for electron transport and ATP synthesis include the F0F1 ATPase complex, ubiquinone(CoQ)-cytochrome c reductase, ubiquinone reductase, cytochrome b, cytochrome c1, FeS protein, and cytochrome c oxidase.

[0190] Triglycerides are hydrolyzed to fatty acids and glycerol by lipases. Glycerol is then phosphorylated to glycerol-3-phosphate by glycerol kinase and glycerol phosphate dehydrogenase, and degraded by the glycolysis. Patty acids are transported into the mitochondria as fatty acyl-carnitine esters and undergo oxidative degradation.

[0191] In addition to metabolic disorders such as diabetes and obesity, disorders of energy metabolism are associated with cancers (Dorward, A. et al. (1997) J. Bioenerg. Biomembr. 29:385-392), autism (Lombard, J. (1998) Med. Hypotheses 50:497-500), neurodegenerative disorders (Alexi, T. et al. (1998) Neuroreport 9:R57-64), and neuromuscular disorders (DiMauro, S. et al. (1998) Biochim. Biophys. Acta 1366:199-210). The myocardium is heavily dependent on oxidative metabolism, so metabolic dysfunction often leads to heart disease (DiMauro, S. and M. Hirano (1998) Curr. Opin. Cardiol. 13:190-197).

[0192] For a review of energy metabolism enzymes and intermediates, see Stryer, L. et al. (1995) Biochemistry, W.H. Freeman and Co., San Francisco Calif., pp. 443-652. For a review of energy metabolism regulation, see Lodish, H. et al. (1995) Molecular Cell Biology, Scientific American Books, New York N.Y., pp. 744-770.

[0193] Cofactor Metabolism

[0194] Cofactors, including coenzymes and prosthetic groups, are small molecular weight inorganic or organic compounds that are required for the action of an enzyme. Many cofactors contain vitamins as a component. Cofactors include thiamine pyrophosphate, flavin adenine dinucleotide, flavin mononucleotide, nicotinamide adenine dinucleotide, pyridoxal phosphate, coenzyme A, tetrahydrofolate, lipoamide, and heme. The vitamins biotin and cobalamin are associated with enzymes as well. Heme, a prosthetic group found in myoglobin and hemoglobin, consists of protoporphyrin group bound to iron. Porphyrin groups contain four substituted pyrroles covalently joined in a ring, often with a bound metal atom. Enzymes involved in porphyrin synthesis include δ-aminolevulinate synthase, δ-aminolevulinate dehydrase, porphobilinogen deaminase, and cosynthase. Deficiencies in heme formation cause porphyrias. Heme is broken down as a part of erythrocyte turnover. Enzymes involved in heme degradation include heme oxygenase and biliverdin reductase.

[0195] Iron is a required cofactor for many enzymes. Besides the heme-containing enzymes, iron is found in iron-sulfur clusters in proteins including aconitase, succinate dehydrogenase, and NADH-Q reductase. Iron is transported in the blood by the protein transferrin. Binding of transferrin to the transferrin receptor on cell surfaces allows uptake by receptor mediated endocytosis. Cytosolic iron is bound to ferritin protein.

[0196] A molybdenum-containing cofactor (molybdopterin) is found in enzymes including sulfite oxidase, xanthine dehydrogenase, and aldehyde oxidase. Molybdopterin biosynthesis is performed by two molybdenum cofactor synthesizing enzymes. Deficiencies in these enzymes cause mental retardation and lens dislocation. Other diseases caused by defects in cofactor metabolism include pernicious anemia and methylmalonic aciduria.

[0197] Secretion and Trafficking

[0198] Eukaryotic cells are bound by a lipid bilayer membrane and subdivided into functionally distinct, membrane bound compartments. The membranes maintain the essential differences between the cytosol, the extracellular environment, and the lumenal space of each intracellular organelle. As lipid membranes are highly impermeable to most polar molecules, transport of essential nutrients, metabolic waste products, cell signaling molecules, macromolecules and proteins across lipid membranes and between organelles must be mediated by a variety of transport-associated molecules.

[0199] Protein Trafficking

[0200] In eukaryotes, some proteins are synthesized on ER-bound ribosomes, co-translationally imported into the ER, delivered from the ER to the Golgi complex for post-translational processing and sorting, and transported from the Golgi to specific intracellular and extracellular destinations. All cells possess a constitutive transport process which maintains homeostasis between the cell and its environment. In many differentiated cell types, the basic machinery is modified to carry out specific transport functions. For example, in endocrine glands, hormones and other secreted proteins are packaged into secretory granules for regulated exocytosis to the cell exterior. In macrophage, foreign extracellular material is engulfed (phagocytosis) and delivered to lysosomes for degradation. In fat and muscle cells, glucose transporters are stored in vesicles which fuse with the plasma membrane only in response to insulin stimulation

[0201] The Secretory Pathway

[0202] Synthesis of most integral membrane proteins, secreted proteins, and proteins destined for the lumen of a particular organelle occurs on ER-bound ribosomes. These proteins are co-translationally imported into the ER. The proteins leave the ER via membrane-bound vesicles which bud off the ER at specific sites and fuse with each other (homotypic fusion) to form the ER-Golgi Intermediate Compartment (ERGIC). The ERGIC matures progressively through the cis, medial, and trans cisternal stacks of the Golgi, modifying the enzyme composition by retrograde transport of specific Golgi enzymes. In this way, proteins moving through the Golgi undergo post-translational modification, such as glycosylation. The final Golgi compartment is the Trans-Golgi Network (TGN), where both membrane and lumenal proteins are sorted for their final destination. Transport vesicles destined for intracellular compartments, such as the lysosome, bud off the TGN. What remains is a secretory vesicle which contains proteins destined for the plasma membrane, such as receptors, adhesion molecules, and ion channels, and secretory proteins, such as hormones, neurotransmitters, and digestive enzymes. Secretory vesicles eventually fuse with the plasma membrane (Glick, B. S. and V. Malhotra (1998) Cell 95:883-889).

[0203] The secretory process can be constitutive or regulated. Most cells have a constitutive pathway for secretion, whereby vesicles derived from maturation of the TGN require no specific signal to fuse with the plasma membrane. In many cells, such as endocrine cells, digestive cells, and neurons, vesicle pools derived from the TGN collect in the cytoplasm and do not fuse with the plasma membrane until they are directed to by a specific signal.

[0204] Endocytosis

[0205] Endocytosis, wherein cells internalize material from the extracellular environment, is essential for transmission of neuronal, metabolic, and proliferative signals; uptake of many essential nutrients; and defense against invading organisms. Most cells exhibit two forms of endocytosis. The first, phagocytosis, is an actin-driven process exemplified in macrophage and neutrophils. Material to be endocytosed contacts numerous cell surface receptors which stimulate the plasma membrane to extend and surround the particle, enclosing it in a membrane-bound phagosome. In the mammalian immune system, IgG-coated particles bind Fc receptors on the surface of phagocytic leukocytes. Activation of the Fc receptors initiates a signal cascade involving src-family cytosolic kinases and the monomeric GTP-binding (G) protein Rho. The resulting actin reorganization leads to phagocytosis of the particle. This process is an important component of the humoral immune response, allowing the processing and presentation of bacterial-derived peptides to antigen-specific T-lymphocytes.

[0206] The second form of endocytosis, pinocytosis, is a more generalized uptake of material from the external milieu. Like phagocytosis, pinocytosis is activated by ligand binding to cell surface receptors. Activation of individual receptors stimulates an internal response that includes coalescence of the receptor-ligand complexes and formation of clathrin-coated pits. Invagination of the plasma membrane at clathrin-coated pits produces an endocytic vesicle within the cell cytoplasm. These vesicles undergo homotypic fusion to form an early endosomal (EE) compartment. The tubulovesicular EE serves as a sorting site for incoming material. ATP-driven proton pumps in the EE membrane lowers the pH of the BE lumen (pH 6.3-6.8). The acidic environment causes many ligands to dissociate from their receptors. The receptors, along with membrane and other integral membrane proteins, are recycled back to the plasma membrane by budding off the tubular extensions of the EE in recycling vesicles (RV). This selective removal of recycled components produces a carrier vesicle containing ligand and other material from the external environment. The carrier vesicle fuses with TGN-derived vesicles which contain hydrolytic enzymes. The acidic environment of the resulting late endosome (LE) activates the hydrolytic enzymes which degrade the ligands and other material. As digestion takes place, the LE fuses with the lysosome where digestion is completed (MeIlman, I. (1996) Annu. Rev. Cell Dev. Biol. 12:575-625).

[0207] Recycling vesicles may return directly to the plasma membrane. Receptors internalized and returned directly to the plasma membrane have a turnover rate of 2-3 minutes. Some RVs undergo microtubule-directed relocation to a perinuclear site, from which they then return to the plasma membrane. Receptors following this route have a turnover rate of 5-10 minutes. Still other RVs are retained within the cell until an appropriate signal is received (MeIlman, supra; and James, D. E. et al. (1994) Trends Cell Biol. 4:120-126).

[0208] Vesicle Formation

[0209] Several steps in the transit of material along the secretory and endocytic pathways require the formation of transport vesicles. Specifically, vesicles form at the transitional endoplasmic reticulum (tER), the rim of Golgi cisternae, the face of the Trans-Golgi Network (TGN), the plasma membrane (PM), and tubular extensions of the endosomes. The process begins with the budding of a vesicle out of the donor membrane. The membrane-bound vesicle contains proteins to be transported and is surrounded by a protective coat made up of protein subunits recruited from the cytosol. The initial budding and coating processes are controlled by a cytosolic ras-like GTP-binding protein, ADP-ribosylating factor (Arf), and adapter proteins (AP). Different isoforms of both Arf and AP are involved at different sites of budding. Another small G-protein, dynamin, forms a ring complex around the neck of the forming vesicle and may provide the mechanochemical force to accomplish the final step of the budding process. The coated vesicle complex is then transported through the cytosol. During the transport process, Arf-bound GTP is hydrolyzed to GDP and the coat dissociates from the transport vesicle (West, M. A. et al. (1997) J. Cell Biol. 138:1239-1254). Two different classes of coat protein have also been identified. Clathrin coats form on the TGN and PM surfaces, whereas coatomer or COP coats form on the ER and Golgi. COP coats can further be distinguished as COPI, involved in retrograde traffic through the Golgi and from the Golgi to the ER, and COPII, involved in anterograde traffic from the BR to the Golgi (MeIlman, supra). The COP coat consists of two major components, a G-protein (Arf or Sar) and coat protomer (coatomer). Coatomer is an equimolar complex of seven proteins, termed alpha-, beta-, beta′-, gamma-, delta-, epsilon- and zeta-COP. (Harter, C. and F. T. Wieland (1998) Proc. Natl. Acad. Sci. USA 95:11649-11654.)

[0210] Membrane Fusion

[0211] Transport vesicles undergo homotypic or heterotypic fusion in the secretory and endocytotic pathways. Molecules required for appropriate targeting and fusion of vesicles with their target membrane include proteins incorporated in the vesicle membrane, the target membrane, and proteins recruited from the cytosol. During budding of the vesicle from the donor compartment, an integral membrane protein, VAMP (vesicle-associated membrane protein) is incorporated into the vesicle. Soon after the vesicle uncoats, a cytosolic prenylated GTP-binding protein, Rab (a member of the Ras superfamily), is inserted into the vesicle membrane. GTP-bound Rab proteins are directed into nascent transport vesicles where they interact with VAMP. Following vesicle transport, GTPase activating proteins (GAPs) in the target membrane convert Rab proteins to the GDP-bound form. A cytosolic protein, guanine-nucleotide dissociation inhibitor (GDI) helps return GDP-bound Rab proteins to their membrane of origin. Several Rab isoforms have been identified and appear to associate with specific compartments within the cell. Rab proteins appear to play a role in mediating the function of a viral gene, Rev, which is essential for replication of HIV-1, the virus responsible for AIDS (Flavell, R. A. et al. (1996) Proc. Natl. Acad. Sci., USA 93:4421-4424).

[0212] Docking of the transport vesicle with the target membrane involves the formation of a complex between the vesicle SNAP receptor (v-SNARE), target membrane (t-) SNAREs, and certain other membrane and cytosolic proteins. Many of these other proteins have been identified although their exact functions in the docking complex remain uncertain (Tellam, J. T. et al. (1995) J. Biol. Chem. 270:5857-5863; and Hata, Y. and T. C. Sudhof (1995) J. Biol. Chem. 270:13022-13028). N-ethylmaleimide sensitive factor (NSF) and soluble NSF-attachment protein (α-SNAP and β-SNAP) are two such proteins that are conserved from yeast to man and function in most intracellular membrane fusion reactions. Sec1 represents a family of yeast proteins that function at many different stages in the secretory pathway including membrane fusion. Recently, mammalian homologs of Sec1, called Munc-18 proteins, have been identified (Katagiri, H. et al. (1995) J. Biol. Chem. 270:4963-4966; Hata et al. supra).

[0213] The SNARE complex involves three SNARE molecules, one in the vesicular membrane and two in the target membrane. Synaptotagmin is an integral membrane protein in the synaptic vesicle which associates with the t-SNARE syntaxin in the docking complex. Synaptotagmin binds calcium in a complex with negatively charged phospholipids, which allows the cytosolic SNAP protein to displace synaptotagmin from syntaxin and fusion to occur. Thus, synaptotagmin is a negative regulator of fusion in the neuron (Littleton, J. T. et al. (1993) Cell 74:1125-1134). The most abundant membrane protein of synaptic vesicles appears to be the glycoprotein synaptophysin, a 38 kDa protein with four transmembrane domains.

[0214] Specificity between a vesicle and its target is derived from the v-SNARE, t-SNAREs, and associated proteins involved. Different isoforms of SNAREs and Rabs show distinct cellular and subcellular distributions. VAMP-1/synaptobrevin, membrane-anchored synaptosome-associated protein of 25 kDa (SNAP-25), syntaxin-1, Rab3A, Rab15, and Rab23 are predominantly expressed in the brain and nervous system. Different syntaxin, VAMP, and Rab proteins are associated with distinct subcellular compartments and their vesicular carriers.

[0215] Nuclear Transport

[0216] Transport of proteins and RNA between the nucleus and the cytoplasm occurs through nuclear pore complexes (NPCs). NPC-mediated transport occurs in both directions through the nuclear envelope. All nuclear proteins are imported from the cytoplasm, their site of synthesis. tRNA and mRNA are exported from the nucleus, their site of synthesis, to the cytoplasm, their site of function. Processing of small nuclear RNAs involves export into the cytoplasm, assembly with proteins and modifications such as hypermethylation to produce small nuclear ribonuclear proteins (snRNPs), and subsequent import of the snRNPs back into the nucleus. The assembly of ribosomes requires the initial import of ribosomal proteins from the cytoplasm, their incorporation with RNA into ribosomal subunits, and export back to the cytoplasm. (Görlich, D. and I. W. Mattaj (1996) Science 271:1513-1518.)

[0217] The transport of proteins and mRNAs across the NPC is selective, dependent on nuclear localization signals, and generally requires association with nuclear transport factors. Nuclear localization signals (NLS) consist of short stretches of amino acids enriched in basic residues. NLS are found on proteins that are targeted to the nucleus, such as the glucocorticoid receptor. The NLS is recognized by the NLS receptor, importin, which then interacts with the monomeric GTP-binding protein Ran. This NLS protein/receptor/Ran complex navigates the nuclear pore with the help of the homodimeric protein nuclear transport factor 2 (NTF2). NTF2 binds the GDP-bound form of Ran and to multiple proteins of the nuclear pore complex containing FXFG repeat motifs, such as p62. (Paschal, B. et al. (1997) J. Biol. Chem. 272:21534-21539; and Wong, D. H. et al. (1997) Mol. Cell Biol. 17:3755-3767). Some proteins are dissociated before nuclear mRNAs are transported across the NPC while others are dissociated shortly after nuclear mRNA transport across the NPC and are reimported into the nucleus.

[0218] Disease Correlation

[0219] The etiology of numerous human diseases and disorders can be attributed to defects in the transport or secretion of proteins. For example, abnormal hormonal secretion is linked to disorders such as diabetes insipidus (vasopressin), hyper- and hypoglycemia (insulin, glucagon), Grave's disease and goiter (thyroid hormone), and Cushing's and Addison's diseases (adrenocorticotropic hormone, ACTH). Moreover, cancer cells secrete excessive amounts of hormones or other biologically active peptides. Disorders related to excessive secretion of biologically active peptides by tumor cells include fasting hypoglycemia due to increased insulin secretion from insulinoma-islet cell tumors; hypertension due to increased epinephrine and norepinephrine secreted from pheochromocytomas of the adrenal medulla and sympathetic paraganglia; and carcinoid syndrome, which is characterized by abdominal cramps, diarrhea, and valvular heart disease caused by excessive amounts of vasoactive substances such as serotonin, bradykinin, histamine, prostaglandins, and polypeptide hormones, secreted from intestinal tumors. Biologically active peptides that are ectopically synthesized in and secreted from tumor cells include ACTH and vasopressin (lung and pancreatic cancers); parathyroid hormone (lung and bladder cancers); calcitonin (lung and breast cancers); and thyroid-stimulating hormone (medullary thyroid carcinoma). Such peptides may be useful as diagnostic markers for tumorigenesis (Schwartz, M. Z. (1997) Semin. Pediatr. Surg. 3:141-146; and Said, S. I. and G. R. Faloona (1975) N. Engl. J. Med. 293:155-160).

[0220] Defective nuclear transport may play a role in cancer. The BRCA1 protein contains three potential NLSs which interact with importin alpha, and is transported into the nucleus by the importin/NPC pathway. In breast cancer cells the BRCA1 protein is aberrantly localized in the cytoplasm. The mislocation of the BRCA1 protein in breast cancer cells may be due to a defect in the NPC nuclear import pathway (Chen, C. F. et al. (1996) J. Biol. Chem. 271:32863-32868).

[0221] It has been suggested that in some breast cancers, the tumor-suppressing activity of p53 is inactivated by the sequestration of the protein in the cytoplasm, away from its site of action in the cell nucleus. Cytoplasmic wild-type p53 was also found in human cervical carcinoma cell lines. (Moll, U. M. et al. (1992) Proc. Natl. Acad. Sci. USA 89:7262-7266; and Liang, X. H. et al. (1993) Oncogene 8:2645-2652.)

[0222] Environmental Responses

[0223] Organisms respond to the environment by a number of pathways. Heat shock proteins, including hsp 70, hsp60, hsp90, and hsp 40, assist organisms in coping with heat damage to cellular proteins.

[0224] Aquaporins (AQP) are channels that transport water and, in some cases, nonionic small solutes such as urea and glycerol. Water movement is important for a number of physiological processes including renal fluid filtration, aqueous humor generation in the eye, cerebrospinal fluid production in the brain, and appropriate hydration of the lung. Aquaporins are members of the major intrinsic protein (MWP) family of membrane transporters (King, L. S. and P. Agre (1996) Annu. Rev. Physiol. 58:619-648; Ishlbashi, K. et al. (1997) J. Biol. Chew 272:20782-20786). The study of aquaporins may have relevance to understanding edema formation and fluid balance in both normal physiology and disease states (King, supra). Mutations in AQP2 cause autosomal recessive nephrogenic diabetes insipidus (OMIM*107777 Aquaporin 2; AQP2). Reduced AQP4 expression in skeletal muscle may be associated with Duchenne muscular dystrophy (Frigeri, A. et al. (1998) J. Clin. Invest. 102:695-703). Mutations in AQP0 cause autosomal dominant cataracts in the mouse (OMIM*154050 Major Intrinsic Protein of Lens Fiber; MIP).

[0225] The metallothioneins (MTs) are a group of small (61 amino acids), cysteine-rich proteins that bind heavy metals such as cadmium, zinc, mercury, lead, and copper and are thought to play a role in metal detoxification or the metabolism and homeostasis of metals. Arsenite-resistance proteins have been identified in hamsters that are resistant to toxic levels of arsenite (Rossman, T. G. et al. (1997) Mutat. Res. 386:307-314).

[0226] Humans respond to light and odors by specific protein pathways. Proteins involved in light perception include rhodopsin, transducin, and cGMP phosphodiesterase. Proteins involved in odor perception include multiple olfactory receptors. Other proteins are important in human Circadian rhythms and responses to wounds.

[0227] Immunity and Host Defense

[0228] All vertebrates have developed sophisticated and complex immune systems that provide protection from viral, bacterial, fungal and parasitic infections. Included in these systems are the processes of humoral immunity, the complement cascade and the inflammatory response (Paul, W. E. (1993) Fundamental Immunology, Raven Press, Ltd., New York N.Y., pp.1-20).

[0229] The cellular components of the humoral immune system include six different types of leukocytes: monocytes, lymphocytes, polymorphonuclear granulocytes (consisting of neutrophils, eosinophils, and basophils) and plasma cells. Additionally, fragments of megakaryocytes, a seventh type of white blood cell in the bone marrow, occur in large numbers in the blood as platelets.

[0230] Leukocytes are formed from two stem cell lineages in bone marrow. The mycloid stem cell line produces granulocytes and monocytes and, the lymphoid stem cell produces lymphocytes. Lymphoid cells travel to the thymus, spleen and lymph nodes, where they mature and differentiate into lymphocytes. Leukocytes are responsible for defending the body against invading pathogens. Neutrophils and monocytes attack invading bacteria, viuses, and other pathogens and destroy them by phagocytosis. Monocytes enter tissues and differentiate into macrophages which are extremely phagocytic. Lymphocytes and plasma cells are a part of the immune system which recognizes specific foreign molecules and organisms and inactivates them, as well as signals other cells to attack the invaders.

[0231] Granulocytes and monocytes are formed and stored in the bone marrow until needed. Megakaryocytes are produced in bone marrow, where they fragment into platelets and are released into the bloodstream. The main function of platelets is to activate the blood clotting mechanism. Lymphocytes and plasma cells are produced in various lymphogenous organs, including the lymph nodes, spleen, thymus, and tonsils.

[0232] Both neutrophils and macrophages exhibit chemotaxis towards sites of inflammation. Tissue inflammation in response to pathogen invasion results in production of chemo-attractants for leukocytes, such as endotoxins or other bacterial products, prostaglandins, and products of leukocytes or platelets.

[0233] Basophils participate in the release of the chemicals involved in the inflammatory process. The main function of basophils is secretion of these chemicals to such a degree that they have been referred to as “unicellular endocrine glands.” A distinct aspect of basophilic secretion is that the contents of granules go directly into the extracellular environment, not into vacuoles as occurs with neutrophils, eosinophils and monocytes. Basophils have receptors for the Fc fragment of immunoglobulin 1 (IgE) that are not present on other leukocytes. Crossliking of membrane IgE with anti-IgE or other ligands triggers degranulation.

[0234] Eosinophils are bi- or multi-nucleated white blood cells which contain eosinophilic granules. Their plasma membrane is characterized by Ig receptors, particularly IgG and IgE. Generally, eosinophils are stored in the bone marrow until recruited for use at a site of inflammation or invasion. They have specific functions in parasitic infections and allergic reactions, and are thought to detoxify some of the substances released by mast cells and basophils which cause inflammation. Additionally, they phagocytize antigen-antibody complexes and further help prevent spread of the inflammation.

[0235] Macrophages are monocytes that have left the blood stream to settle in tissue. Once monocytes have migrated into tissues, they do not re-enter the bloodstream. The mononuclear phagocyte system is comprised of precursor cells in the bone marrow, monocytes in circulation, and macrophages in tissues. The system is capable of very fast and extensive phagocytosis. A macrophage may phagocytize over 100 bacteria, digest them and extrude residues, and then survive for many more months. Macrophages are also capable of ingesting large particles, including red blood cells and malarial parasites. They increase several-fold in size and transform into macrophages that are characteristic of the tissue they have entered, surviving in tissues for several months.

[0236] Mononuclear phagocytes are essential in defending the body against invasion by foreign pathogens, particularly intracellular microorganisms such as M. tuberculosis, listeria, leishmania and toxoplasma. Macrophages can also control the growth of tumorous cells, via both phagocytosis and secretion of hydrolytic enzymes. Another important function of macrophages is that of processing antigen and presenting them in a biochemically modified form to lymphocytes.

[0237] The immune system responds to invading microorganisms in two major ways: antibody production and cell mediated responses. Antibodies are immunoglobulin proteins produced by B-lymphocytes which bind to specific antigens and cause inactivation or promote destruction of the antigen by other cells. Cell-mediated immune responses involve T-lymphocytes (T cells) that react with foreign antigen on the surface of infected host cells. Depending on the type of T cell, the infected cell is either killed or signals are secreted which activate macrophages and other cells to destroy the infected cell (Paul, supra).

[0238] T-lymphocytes originate in the bone marrow or liver in fetuses. Precursor cells migrate via the blood to the thymus, where they are processed to mature into T-lymphocytes. This processing is crucial because of positive and negative selection of T cells that will react with foreign antigen and not with self molecules. After processing, T cells continuously circulate in the blood and secondary lymphoid tissues, such as lymph nodes, spleen, certain epithelium-associated tissues in the gastrointestinal tract, respiratory tract and skin. When T-lymphocytes are presented with the complementary antigen, they are stimulated to proliferate and release large numbers of activated T cells into the lymph system and the blood system. These activated T cells can survive and circulate for several days. At the same time, T memory cells are created, which remain in the lymphoid tissue for months or years. Upon subsequent exposure to that specific antigen, these memory cells will respond more rapidly and with a stronger response than induced by the original antigen. This creates an “immunological memory” that can provide immunity for years.

[0239] There are two major types of T cells: cytotoxic T cells destroy infected host cells, and helper T cells activate other white blood cells via chemical signals. One class of helper cell, TH1, activates macrophages to destroy ingested microorganisms, while another, TH2, stimulates the production of antibodies by B cells.

[0240] Cytotoxic T cells directly attack the infected target cell. In virus-infected cells, peptides derived from viral proteins are generated by the proteasome. These peptides are transported into the ER by the transporter associated with antigen processing (TAP) (Pamer, E. and P. Cresswell (1998) Annu. Rev. Immunol. 16:323-358). Once inside the ER, the peptides bind MHC I chains, and the peptide/MHC I complex is transported to the cell surface. Receptors on the surface of T cells bind to antigen presented on cell surface MHC molecules. Once activated by binding to antigen, T cells secrete γ-interferon, a signal molecule that induces the expression of genes necessary for presenting viral (or other) antigens to cytotoxic T cells. Cytotoxic T cells kill the infected cell by stimulating programmed cell death

[0241] Helper T cells constitute up to 75% of the total T cell population. They regulate the immune functions by producing a variety of lymphokines that act on other cells in the immune system and on bone marrow. Among these lymphokines are: interleukins-2,3,4,5,6; granulocyte-monocyte colony stimulating factor, and γ-interferon.

[0242] Helper T cells are required for most B cells to respond to antigen. When an activated helper cell contacts a B cell, its centrosome and Golgi apparatus become oriented toward the B cell aiding the directing of signal molecules, such as transmembrane-bound protein called CD40 ligand, onto the B cell surface to interact with the CD40 transmembrane protein. Secreted signals also help B cells to proliferate and mature and, in some cases, to switch the class of antibody being produced.

[0243] B-lymphocytes (B cells) produce antibodies which react with specific antigenic proteins presented by pathogens. Once activated, B cells become filled with extensive rough endoplasmic reticulum and are known as plasma cells. As with T cells, interaction of B cells with antigen stimulates proliferation of only those B cells which produce antibody specific to that antigen. There are five classes of antibodies, known as immunoglobulins, which together comprise about 20% of total plasma protein. Each class mediates a characteristic biological response after antigen binding. Upon activation by specific antigen B cells switch from making membrane-bound antibody to secretion of that antibody.

[0244] Antibodies, or immunoglobulins (Ig), are the founding members of the Ig superfamily and the central components of the humoral immune response. Antibodies are either expressed on the surface of B cells or secreted by B cells into the circulation. Antibodies bind and neutralize blood-borne foreign antigens. The prototypical antibody is a tetramer consisting of two identical heavy polypeptide chains (H-chains) and two identical light polypeptide chains (L-chains) interlinked by disulfide bonds. This arrangement confers the characteristic Y-shape to antibody molecules. Antibodies are classified based on their H-chain composition. The five antibody classes, IgA, IgD, IgE, IgG and IgM, are defined by the α, δ, ε, γ, and μ H-chain types. There are two types of L-chains, κ and λ, either of which may associate as a pair with any H-chain pair. IgG, the most common class of antibody found in the circulation, is tetrameric, while the other classes of antibodies are generally variants or multimers of this basic structure.

[0245] H-chains and L-chains each contain an N-terminal variable region and a C-terminal constant region. Both H-chains and L-chains contain repeated Ig domains. For example, a typical H-chain contains four Ig domains, three of which occur within the constant region and one of which occurs within the variable region and contributes to the formation of the antigen recognition site. Likewise, a typical L-chain contains two Ig domains, one of which occurs within the constant region and one of which occurs within the variable region. In addition, H chains such as μhave been shown to associate with other polypeptides during differentiation of the B cell.

[0246] Antibodies can be described in terms of their two main functional domains. Antigen recognition is mediated by the Fab (antigen binding fragment) region of the antibody, while effector functions are mediated by the Fc (crystallizable fragment) region. Binding of antibody to an antigen, such as a bacterium, triggers the destruction of the antigen by phagocytic white blood cells such as macrophages and neutrophils. These cells express surface receptors that specifically bind to the antibody Fc region and allow the phagocytic cells to engulf, ingest, and degrade the antibody-bound antigen. The Fc receptors expressed by phagocytic cells are single-pass transmembrane glycoproteins of about 300 to 400 amino acids (Sears, D. W. et al. (1990) J. Immunol. 144:371-378). The extracellular portion of the Fc receptor typically contains two or three Ig domains.

[0247] Diseases which cause over- or under-abundance of any one type of leukocyte usually result in the entire immune defense system becoming involved. A well-known autoimmune disease is AIDS (Acquired Immunodeficiency Syndrome) where the number of helper T cells is depleted, leaving the patient susceptible to infection by microorganisms and parasites. Another widespread medical condition attributable to the immune system is that of allergic reactions to certain antigens. Allergic reactions include: hay fever, asthma, anaphylaxis, and urticaria (hives). Leukemias are an excess production of white blood cells, to the point where a major portion of the body's metabolic resources are directed solely at proliferation of white blood cells, leaving other tissues to starve. Leukopenia or agranulocytosis occurs when the bone marrow stops producing white blood cells. This leaves the body unprotected against foreign microorganisms, including those which normally inhabit skin, mucous membranes, and gastrointestinal tract. If all white blood cell production stops completely, infection win occur within two days and death may follow only 1 to 4 days later.

[0248] Impaired phagocytosis occurs in several diseases, including monocytic leukemia, systemic lupus, and granulomatous disease. In such a situation, macrophages can phagocytize normally, but the enveloped organism is not killed. A defect in the plasma membrane enzyme which converts oxygen to lethally reactive forms results in abscess formation in liver, lungs, spleen, lymph nodes, and beneath the skin. Eosinophilia is an excess of eosinophils commonly observed in patients with allergies (hay fever, asthma), allergic reactions to drugs, rheumatoid arthritis, and cancers (Hodgkin's disease, lung, and liver cancer) (Isselbacher, K. J. et al. (1994) Harrison's Principles of Internal Medicine, McGraw-Hill, Inc., New York N.Y.).

[0249] Host defense is further augmented by the complement system. The complement system serves as an effector system and is involved in infectious agent recognition. It can function as an independent immune network or in conjunction with other humoral immune responses. The complement system is comprised of numerous plasma and membrane proteins that act in a cascade of reaction sequences whereby one component activates the next. The result is a rapid and amplified response to infection through either an inflammatory response or increased phagocytosis.

[0250] The complement system has more than 30 protein components which can be divided into functional groupings including modified serine proteases, membrane-binding proteins and regulators of complement activation. Activation occurs through two different pathways the classical and the alternative. Both pathways serve to destroy infectious agents through distinct triggering mechanisms that eventually merge with the involvement of the component C3.

[0251] The classical pathway requires antibody binding to infectious agent antigens. The antibodies serve to define the target and initiate the complement system cascade, culminating in the destruction of the infectious agent. In this pathway, since the antibody guides initiation of the process, the complement can be seen as an effector arm of the humoral immune system.

[0252] The alternative pathway of the complement system does not require the presence of pre-existing antibodies for targeting infectious agent destruction. Rather, this pathway, through low levels of an activated component, remains constantly primed and provides surveillance in the non-immune host to enable targeting and destruction of infectious agents. In this case foreign material triggers the cascade, thereby facilitating phagocytosis or lysis (Paul, supra, pp.918-919).

[0253] Another important component of host defense is the process of inflammation. Inflammatory responses are divided into four categories on the basis of pathology and include allergic inflammation, cytotoxic antibody mediated inflammation, immune complex mediated inflammation and monocyte mediated inflammation. Inflammation manifests as a combination of each of these forms with one predominating.

[0254] Allergic acute inflammation is observed in individuals wherein specific antigens stimulate IgE antibody production. Mast cells and basophils are subsequently activated by the attachment of antigen-IgE complexes, resulting in the release of cytoplasmic granule contents such as histamine. The products of activated mast cells can increase vascular permeability and constrict the smooth muscle of breathing passages, resulting in anaphylaxis or asthma. Acute inflammation is also mediated by cytotoxic antibodies and can result in the destruction of tissue through the binding of complement-fixing antibodies to cells. The responsible antibodies are of the IgG or IgM types. Resultant clinical disorders include autoimmune hemolytic anemia and thrombocytopenia as associated with systemic lupus erythematosis.

[0255] Immune complex mediated acute inflammation involves the IgG or IgM antibody types which combine with antigen to activate the complement cascade. When such immune complexes bind to neutrophils and macrophages they activate the respiratory burst to form protein- and vessel-damaging agents such as hydrogen peroxide, hydroxyl radical, hypochlorous acid, and chloramines. Clinical manifestations include rheumatoid arthritis and systemic lupus erythematosus.

[0256] In chronic inflammation or delayed-type hypersensitivity, macrophages are activated and process antigen for presentation to T cells that subsequently produce lymphokines and monokines. This type of inflammatory response is likely important for defense against intracellular parasites and certain viruses. Clinical associations include, granulomatous disease, tuberculosis, leprosy, and sarcoidosis (Paul, W. E., supra, pp.1017-1018).

[0257] Extracellular Information Transmission Molecules

[0258] Intercellular communication is essential for the growth and survival of multicellular organisms, and in particular, for the function of the endocrine, nervous, and immune systems. In addition, intercellular communication is critical for developmental processes such as tissue construction and organogenesis, in which cell proliferation, cell differentiation, and morphogenesis must be spatially and temporally regulated in a precise and coordinated manner. Cells communicate with one another through the secretion and uptake of diverse types of signaling molecules such as hormones, growth factors, neuropeptides, and cytokines.

[0259] Hormones

[0260] Hormones are signaling molecules that coordinately regulate basic physiological processes from embryogenesis throughout adulthood. These processes include metabolism, respiration, reproduction, excretion, fetal tissue differentiation and organogenesis, growth and development, homeostasis, and the stress response. Hormonal secretions and the nervous system are tightly integrated and interdependent. Hormones are secreted by endocrine glands, primarily the hypothalamus and pituitary, the thyroid and parathyroid, the pancreas, the adrenal glands, and the ovaries and testes.

[0261] The secretion of hormones into the circulation is tightly controlled. Hormones are often secreted in diurnal, pulsatile, and cyclic patterns. Hormone secretion is regulated by perturbations in blood biochemistry, by other upstream-acting hormones, by neural impulses, and by negative feedback loops. Blood hormone concentrations are constantly monitored and adjusted to maintain optimal, steady-state levels. Once secreted, hormones act only on those target cells that express specific receptors.

[0262] Most disorders of the endocrine system are caused by either hyposecretion or hypersecretion of hormones. Hyposecretion often occurs when a hormone's gland of origin is damaged or otherwise impaired. Hypersecretion often results from the proliferation of tumors derived from hormone-secreting cells. Inappropriate hormone levels may also be caused by defects in regulatory feedback loops or in the processing of hormone precursors. Endocrine malfunction may also occur when the target cell fails to respond to the hormone.

[0263] Hormones can be classified biochemically as polypeptides, steroids, eicosanoids, or amines. Polypeptides, which include diverse hormones such as insulin and growth hormone, vary in size and function and are often synthesized as inactive precursors that are processed intracellularly into mature, active forms. Amines, which include epinephrine and dopamine, are amino acid derivatives that function in neuroendocrine signaling. Steroids, which include the cholesterol-derived hormones estrogen and testosterone, function in sexual development and reproduction. Eicosanoids, which include prostaglandins and prostacyclins, are fatty acid derivatives that function in a variety of processes. Most polypeptides and some amines are soluble in the circulation where they are highly susceptible to proteolytic degradation within seconds after their secretion. Steroids and lipids are insoluble and must be transported in the circulation by carrier proteins. The following discussion will focus primarily on polypeptide hormones.

[0264] Hormones secreted by the hypothalamus and pituitary gland play a critical role in endocrine function by coordinately regulating hormonal secretions from other endocrine glands in response to neural signals. Hypothalamic hormones include thyrotropin-releasing hormone, gonadotropin-releasing hormone, somatostatin, growth-hormone releasing factor, corticotropin-releasing hormone, substance P, dopamine, and prolactin-releasing hormone. These hormones directly regulate the secretion of hormones from the anterior lobe of the pituitary. Hormones secreted by the anterior pituitary include adrenocorticotropic hormone (ACTH), melanocyte-stimulating hormone, somatotropic hormones such as growth hormone and prolactin, glycoprotein hormones such as thyroid-stimulating hormone, luteinizing hormone (LH), and follicle-stimulating hormone (FSH), β-lipotropin, and β-endorphins. These hormones regulate hormonal secretions from the thyroid, pancreas, and adrenal glands, and act directly on the reproductive organs to stimulate ovulation and spermatogenesis. The posterior pituitary synthesizes and secretes antidiuretic hormone (ADH, vasopressin) and oxytocin.

[0265] Disorders of the hypothalamus and pituitary often result from lesions such as primary brain tumors, adenomas, infarction associated with pregnancy, hypophysectomy, aneurysms, vascular malformations, thrombosis, infections, immunological disorders, and complications due to head trauma. Such disorders have profound effects on the function of other endocrine glands. Disorders associated with hypopituitarism include hypogonadism, Sheehan syndrome, diabetes insipidus, Kallman's disease, Hand-Schuller-Christian disease, letterer-Siwe disease, sarcoidosis, empty sella syndrome, and dwarfism. Disorders associated with hyperpituitarism include acromegaly, giantism, and syndrome of inappropriate ADH secretion (SIADH), often caused by benign adenomas.

[0266] Hormones secreted by the thyroid and parathyroid primarily control metabolic rates and the regulation of serum calcium levels, respectively. Thyroid hormones include calcitonin, somatostatin, and thyroid hormone. The parathyroid secretes parathyroid hormone. Disorders associated with hypothyroidism include goiter, myxedema, acute thyroiditis associated with bacterial infection, subacute thyroiditis associated with viral infection, autoimmune thyroiditis (Hashimoto's disease), and cretinism. Disorders associated with hyperthyroidism include thyrotoxicosis and its various forms, Grave's disease, pretibial myxedema, toxic multinodular goiter, thyroid carcinoma, and Plummer's disease. Disorders associated with hyperparathyroidism include Conn disease (chronic hypercalemia) leading to bone resorption and parathyroid hyperplasia.

[0267] Hormones secreted by the pancreas regulate blood glucose levels by modulating the rates of carbohydrate, fat, and protein metabolism. Pancreatic hormones include insulin, glucagon, amylin, γ-aminobutyric acid, gastrin, somatostatin, and pancreatic polypeptide. The principal disorder associated with pancreatic dysfunction is diabetes mellitus caused by insufficient insulin activity. Diabetes mellitus is generally classified as either Type I (insulin-dependent, juvenile diabetes) or Type II (non-insulin-dependent, adult diabetes). The treatment of both forms by insulin replacement therapy is well known. Diabetes mellitus often leads to acute complications such as hypoglycemia (insulin shock), coma, diabetic ketoacidosis, lactic acidosis, and chronic complications leading to disorders of the eye, kidney, skin, bone, joint, cardiovascular system, nervous system, and to decreased resistance to infection.

[0268] The anatomy, physiology, and diseases related to hormonal function are reviewed in McCance, K. L. and S. E. Huether (1994) Pathohsiology: The Biological Basis for Disease in Adults and Children, Mosby-Year Book, Inc., St. Louis Mo.; Greenspan, F. S. and J. D. Baxter (1994) Basic and Clinical Endocrinology, Appleton and Lange, East Norwalk Conn.

[0269] Growth Factors

[0270] Growth factors are secreted proteins that mediate intercellular communication. Unlike hormones, which travel great distances via the circulatory system, most growth factors are primarily local mediators that act on neighboring cells. Most growth factors contain a hydrophobic N-terminal signal peptide sequence which directs the growth factor into the secretory pathway. Most growth factors also undergo post-translational modifications within the secretory pathway. These modifications can include proteolysis, glycosylation, phosphorylation, and intramolecular disulfide bond formation. Once secreted, growth factors bind to specific receptors on the surfaces of neighboring target cells, and the bound receptors trigger intracellular signal transduction pathways. These signal transduction pathways elicit specific cellular responses in the target cells. These responses can include the modulation of gene expression and the stimulation or inhibition of cell division, cell differentiation, and cell motility.

[0271] Growth factors fall into at least two broad and overlapping classes. The broadest class includes the large polypeptide growth factors, which are wide-ranging in their effects. These factors include epidermal growth factor (EGF), fibroblast growth factor (FGF), transforming growth factor-β(TGF-β), insulin-like growth factor (IGF), nerve growth factor (NGF), and platelet-derived growth factor (PDGF), each defining a family of numerous related factors. The large polypeptide growth factors, with the exception of NGF, act as mitogens on diverse cell types to stimulate wound healing, bone synthesis and remodeling, extracellular matrix synthesis, and proliferation of epithelial, epidermal, and connective tissues. Members of the TGF-β, EGF, and FGF families also function as inductive signals in the differentiation of embryonic tissue. NGF functions specifically as a neurotrophic factor, promoting neuronal growth and differentiation.

[0272] Another class of growth factors includes the hematopoietic growth factors, which are narrow in their target specificity. These factors stimulate the proliferation and differentiation of blood cells such as B-lymphocytes, T-lymphocytes, erythrocytes, platelets, eosinophils, basophils, neutrophils, macrophages, and their stem cell precursors. These factors include the colony-stimulating factors G-CSF, M-CSF, GM-CSF, and CSF1-3), erythopoietin, and the cytokines. The cytolines are specialized hematopoietic factors secreted by cells of the immune system and are discussed in detail below.

[0273] Growth factors play critical roles in neoplastic transformation of cells in vitro and in tumor progression in vivo. Overexpression of the large polypeptide growth factors promotes the proliferation and transformation of cells in culture. Inappropriate expression of these growth factors by tumor cells in vivo may contribute to tumor vascularization and metastasis. Inappropriate activity of hematopoietic growth factors can result in anemias, leukemias, and lymphomas. Moreover, growth factors are both structurally and functionally related to oncoproteins, the potentially cancer-causing products of proto-oncogenes. Certain FGF and PDGF family members are themselves homologous to oncoproteins, whereas receptors for some members of the EGF, NGF, and FGF families are encoded by proto-oncogenes. Growth factors also affect the transcriptional regulation of both proto-oncogenes and oncosuppressor genes (Pimentel, E. (1994) Handbook of Growth Factors, CRC Press, Ann Arbor Mich.; McKay, I. and I. Leigh, eds. (1993) Growth Factors: A Practical Approach, Oxford University Press, New York N.Y.; Habenicht, A., ed. (1990) Growth Factors. Differentiation Factors, and Cytokines, Springer-Verlag, New York N.Y.).

[0274] In addition, some of the large polypeptide growth factors play crucial roles in the induction of the primordial germ layers in the developing embryo. This induction ultimately results in the formation of the embryonic mesoderm, ectoderm, and endoderm which in turn provide the framework for the entire adult body plan. Disruption of this inductive process would be catastrophic to embryonic development.

[0275] Small Peptide Factors—Neuropeptides and Vasomediators

[0276] Neuropeptides and vasomediators (NP/VM) comprise a family of small peptide factors, typically of 20 amino acids or less. These factors generally function in neuronal excitation and inhibition of vasoconstriction/vasodilation, muscle contraction, and hormonal secretions from the brain and other endocrine tissues. Included in this family are neuropeptides and neuropeptide hormones such as bombesin, neuropeptide Y, neurotensin, neuromedin N, melanocortins, opioids, galanin, somatostatin, tachykinins, urotensin II and related peptides involved in smooth muscle stimulation, vasopressin, vasoactive intestinal peptide, and circulatory system-borne signaling molecules such as angiotensin, complement, calcitonin, endothelins, formyl-methionyl peptides, glucagon, cholecystokinin, gastrin, and many of the peptide hormones discussed above. NP/VMs can transduce signals directly, modulate the activity or release of other neurotransmitters and hormones, and act as catalytic enzymes in signaling cascades. The effects of NP/VMs range from extremely brief to long-lasting. (Reviewed in Martin, C. P. et al. (1985) Endocrine Physiology, Oxford University Press, New York N.Y., pp. 57-62.)

[0277] Cytokines

[0278] Cytokines comprise a family of signaling molecules that modulate the immune system and the inflammatory response. Cytokines are usually secreted by leukocytes, or white blood cells, in response to injury or infection. Cytokines function as growth and differentiation factors that act primarily on cells of the immune system such as B- and T-lymphocytes, monocytes, macrophages, and granulocytes. Like other signaling molecules, cytokines bind to specific plasma membrane receptors and trigger intracellular signal transduction pathways which alter gene expression patterns. There is considerable potential for the use of cytokines in the treatment of inflammation and immune system disorders.

[0279] Cytokine structure and function have been extensively characterized in vitro. Most cytokines are small polypeptides of about 30 kilodaltons or less. Over 50 cytokines have been identified from human and rodent sources. Examples of cytokine subfamilies include the interferons (IFN-α, -β, and -γ), the interleukins (IL1-IL13), the tumor necrosis factors (ITN-α and -β), and the chemokines. Many cytokines have been produced using recombinant DNA techniques, and the activities of individual cytokines have been determined in vitro. These activities include regulation of leukocyte proliferation, differentiation, and motility.

[0280] The activity of an individual cytokine in vitro may not reflect the full scope of that cytokine's activity in vivo. Cytokines are not expressed individually in vivo but are instead expressed in combination with a multitude of other cytokines when the organism is challenged with a stimulus. Together, these cytokines collectively modulate the immune response in a manner appropriate for that particular stimulus. Therefore, the physiological activity of a cytokine is determined by the stimulus itself and by complex interactive networks among co-expressed cytokines which may demonstrate both synergistic and antagonistic relationships.

[0281] Chemokines comprise a cytokine subfamily with over 30 members. (Reviewed in Wells, T. N. C. and M. C. Peitsch (1997) J. Leukoc. Biol. 61:545-550.) Chemokines were initially identified as chemotactic proteins that recruit monocytes and macrophages to sites of inflammation. Recent evidence indicates that chemokines may also play key roles in hematopoiesis and HIV-1 infection. Chemokines are small proteins which range from about 6-15 kilodaltons in molecular weight Chemokines are further classified as C, CC, CXC, or CX3C based on the number and position of critical cysteine residues. The CC chemokines, for example, each contain a conserved motif consisting of two consecutive cysteines followed by two additional cysteines which occur downstream at 24- and 16-residue intervals, respectively (ExPASy PROSITE database, documents PS00472 and PDOC00434). The presence and spacing of these four cysteine residues are highly conserved, whereas the intervening residues diverge significantly. However, a conserved tyrosine located about 15 residues downstream of the cysteine doublet seems to be important for chemotactic activity. Most of the human genes encoding CC chemokines are clustered on chromosome 17, although there are a few examples of CC chemokine genes that map elsewhere. Other chemokines include lymphotactin (C chemokine); macrophage chemotactic and activating factor (MCAF/MCP-1; CC chemokine); platelet factor 4 and IL-8 (CXC chemokines); and fractalkine and neurotractin (CX3C chemokines). (Reviewed in Luster, A. D. (1998) N. Engl. J. Med. 338:436-445.)

[0282] Receptor Molecules

[0283] The term receptor describes proteins that specifically recognize other molecules. The category is broad and includes proteins with a variety of functions. The bulk of receptors are cell surface proteins which bind extracellular ligands and produce cellular responses in the areas of growth, differentiation, endocytosis, and immune response. Other receptors facilitate the selective transport of proteins out of the endoplasmic reticulum and localize enzymes to particular locations in the cell. The term may also be applied to proteins which act as receptors for ligands with known or unknown chemical composition and which interact with other cellular components. For example, the steroid hormone receptors bind to and regulate transcription of DNA.

[0284] Regulation of cell proliferation, differentiation, and migration is important for the formation and function of tissues. Regulatory proteins such as growth factors coordinately control these cellular processes and act as mediators in cell-cell signaling pathways. Growth factors are secreted proteins that bind to specific cell-surface receptors on target cells. The bound receptors trigger intracellular signal transduction pathways which activate various downstream effectors that regulate gene expression, cell division, cell differentiation, cell motility, and other cellular processes.

[0285] Cell surface receptors are typically integral plasma membrane proteins. These receptors recognize hormones such as catecholamines; peptide hormones; growth and differentiation factors; small peptide factors such as thyrotropin-releasing hormone; galanin, somatostatin, and tachykinins; and circulatory system-borne signaling molecules. Cell surface receptors on immune system cells recognize antigens, antibodies, and major histocompatibility complex (MHC)-bound peptides. Other cell surface receptors bind ligands to be internalized by the cell. This receptor-mediated endocytosis functions in the uptake of low density lipoproteins (LDL), transferrin, glucose- or mannose-terminal glycoproteins, galactose-terminal glycoproteins, immunoglobulins, phosphovitellogenins, fibrin, proteinase-inhibitor complexes, plasminogen activators, and thrombospondin (Lodish, H. et al. (1995) Molecular Cell Biology, Scientific American Books, New York N.Y., p. 723; Mikhailenko, L et al. (1997) J. Biol. Chem 272:6784-6791).

[0286] Receptor Protein Kinases

[0287] Many growth factor receptors, including receptors for epidermal growth factor, platelet-derived growth factor, fibroblast growth factor, as well as the growth modulator α-thrombin, contain intrinsic protein kinase activities. When growth factor binds to the receptor, it triggers the autophosphorylation of a serine, threonine, or tyrosine residue on the receptor. These phosphorylated sites are recognition sites for the binding of other cytoplasmic signaling proteins. These proteins participate in signaling pathways that eventually link the initial receptor activation at the cell surface to the activation of a specific intracellular target molecule. In the case of tyrosine residue autophosphorylation, these signaling proteins contain a common domain referred to as a Src homology (SH) domain. SH2 domains and SH3 domains are found in phospholipase C-γ, PI-3-K p85 regulatory subunit, Ras-GTPase activating protein, and pp60c-Src (Lowenstein, E. J. et al. (1992) Cell 70:431-442). The cytokine family of receptors share a different common binding domain and include transmembrane receptors for growth hormone (GH), interleukins, erythropoietin, and prolactin.

[0288] Other receptors and second messenger-binding proteins have intrinsic serine/threonine protein kinase activity. These include activin/TGF-β/BMP-superfamily receptors, calcium- and diacylglycerol-activated/phospholipid-dependant protein kinase (PK-C), and RNA-dependant protein kinase (PK-R). In addition, other serine/threonine protein kinases, including nematode Twitchin, have fibronectin-like, immunoglobulin C2-lie domains.

[0289] G-Protein Coupled Receptors

[0290] G-protein coupled receptors (GPCRs) are integral membrane proteins characterized by the presence of seven hydrophobic transmembrane domains which span the plasma membrane and form a bundle of antiparallel alpha (α) helices. These proteins range in size from under 400 to over 1000 amino acids (Strosberg, A. D. (1991) Eur. J. Biochem. 196:1-10; Coughlin, S. R. (1994) Curr. Opin. Cell Biol. 6:191-197). The amino-terminus of the GPCR is extracellular, of variable length and often glycosylated; the carboxy-terminus is cytoplasmic and generally phosphorylated. Extracellular loops of the GPCR alternate with intracellular loops and link the transmembrane domains. The most conserved domains of GPCRs are the transmembrane domains and the first two cytoplasmic loops. The transmembrane domains account for structural and functional features of the receptor. In most cases, the bundle of CL helices forms a binding pocket. In addition, the extracellular N-terminal segment or one or more of the three extracellular loops may also participate in ligand binding. Ligand binding activates the receptor by inducing a conformational change in intracellular portions of the receptor. The activated receptor, in turn, interacts with an intracellular heterotrimeric guanine nucleotide binding (G) protein complex which mediates further intracellular signaling activities, generally the production of second messengers such as cyclic AMP (cAMP), phospholipase C, inositol triphosphate, or interactions with ion channel proteins (Baldwin, J. M. (1994) Curr. Opin. Cell Biol. 6:180-190).

[0291] GPCRs include those for acetylcholine, adenosine, epinephrine and norepinephlrine, bombesin, bradykinin, chemokines, dopamine, endothelin, γ-aminobutyric acid (GABA), follicle-stimulating hormone (FSH), glutamate, gonadotropin-releasing hormone (GnRH), hepatocyte growth factor, histamine, leukotrienes, melanocortins, neuropeptide Y, opioid peptides, opsins, prostanoids, serotonin, somatostatin, tachykinins, thrombin, thyrotropin-releasing hormone (TRH), vasoactive intestinal polypeptide family, vasopressin and oxytocin, and orphan receptors.

[0292] GPCR mutations, which may cause loss of function or constitutive activation, have been associated with numerous human diseases (Coughlin, supra). For instance, retinitis pigmentosa may arise from mutations in the rhodopsin gene. Rhodopsin is the retinal photoreceptor which is located within the discs of the eye rod cell. Parma, J. et al. (1993, Nature 365:649-651) report that somatic activating mutations in the thyrotropin receptor cause hyperfunctioning thyroid adenomas and suggest that certain GPCRs susceptible to constitutive activation may behave as protooncogenes.

[0293] Nuclear Receptors

[0294] Nuclear receptors bind small molecules such as hormones or second messengers, leading to increased receptor-binding affinity to specific chromosomal DNA elements. In addition the affinity for other nuclear proteins may also be altered. Such binding and protein-protein interactions may regulate and modulate gene expression. Examples of such receptors include the steroid hormone receptors family, the retinoic acid receptors family, and the thyroid hormone receptors family.

[0295] Ligand-Gated Receptor Ion Channels

[0296] Ligand-gated receptor ion channels fall into two categories. The first category, extracellular ligand-gated receptor ion channels (ELGs), rapidly transduce neurotransmitter-binding events into electrical signals, such as fast synaptic neurotransmission. BLG function is regulated by post-translational modification. The second category, intracellular ligand-gated receptor ion channels (ILGs), are activated by many intracellular second messengers and do not require post-translational modification(s) to effect a channel-opening response.

[0297] ELGs depolarize excitable cells to the threshold of action potential generation. In non-excitable cells, ELGs permit a limited calcium ion-influx during the presence of agonist. ELGs include channels directly gated by neurotransmitters such as acetylcholine, L-glutamate, glycine, ATP, serotonin, GABA, and histamine. ELG genes encode proteins having strong structural and functional similarities. ILGs are encoded by distinct and unrelated gene families and include receptors for cAMP, cGMP, calcium ions, ATP, and metabolites of arachidonic acid.

[0298] Macrophage Scavenger Receptors

[0299] Macrophage scavenger receptors with broad ligand specificity may participate in the binding of low density lipoproteins (LDL) and foreign antigens. Scavenger receptors types I and H are trimeric membrane proteins with each subunit containing a small N-terminal intracellular domain, a transmembrane domain, a large extracellular domain, and a C-terminal cysteine-rich domain. The extracellular domain contains a short spacer domain, an α-helical coiled-coil domain, and a triple helical collagenous domain. These receptors have been shown to bind a spectrum of ligands, including chemically modified lipoproteins and albumin, polyribonucleotides, polysaccharides, phospholipids, and asbestos (Matsumoto, A. et al. (1990) Proc. Natl. Acad. Sci. USA 87:9133-9137; Elomaa, O. et al. (1995) Cell 80:603-609). The scavenger receptors are thought to play a key role in atherogenesis by mediating uptake of modified LDL in arterial walls, and in host defense by binding bacterial endotoxins, bacteria, and protozoa.

[0300] T-Cell Receptors

[0301] T cells play a dual role in the immune system as effectors and regulators, coupling antigen recognition with the transmission of signals that induce cell death in infected cells and stimulate proliferation of other immune cells. Although a population of T cells can recognize a wide range of different antigens, an individual T cell can only recognize a single antigen and only when it is presented to the T cell receptor (TCR) as a peptide complexed with a major histocompatibility molecule (MHC) on the surface of an antigen presenting cell. The TCR on most T cells consists of immunoglobulin-like integral membrane glycoproteins containing two polypeptide subunits, α and β, of similar molecular weight. Both TCR subunits have an extracellular domain containing both variable and constant regions, a transmembrane domain that traverses the membrane once, and a short intracellular domain (Saito, H. et al. (1984) Nature 309:757-762). The genes for the TCR subunits are constructed through somatic rearrangement of different gene segments. Interaction of antigen in the proper MHC context with the TCR initiates signaling cascades that induce the proliferation, maturation, and function of cellular components of the immune system (Weiss, A. (1991) Annu. Rev. Genet. 25:487-510). Rearrangements in TCR genes and alterations in TCR expression have been noted in lymphomas, leukemias, autoimmune disorders, and immunodeficiency disorders (Aisenberg, A. C. et al. (1985) N. Engl. J. Med. 313:529-533; Weiss, supra).

[0302] Intracellular Signaling Molecules

[0303] Intracellular signaling is the general process by which cells respond to extracellular signals (hormones, neurotransmitters, growth and differentiation factors, etc.) through a cascade of biochemical reactions that begins with the binding of a signaling molecule to a cell membrane receptor and ends with the activation of an intracellular target molecule. Intermediate steps in the process involve the activation of various cytoplasmic proteins by phosphorylation via protein kinases, and their deactivation by protein phosphatases, and the eventual translocation of some of these activated proteins to the cell nucleus where the transcription of specific genes is triggered. The intracellular signaling process regulates all types of cell functions including cell proliferation, cell differentiation, and gene transcription, and involves a diversity of molecules including protein kinases and phosphatases, and second messenger molecules, such as cyclic nucleotides, calcium-calmodulin, inositol, and various immogens, that regulate protein phosphorylation.

[0304] Protein Phosphorlation

[0305] Protein kinases and phosphatases play a key role in the intracellular signaling process by controlling the phosphorylation and activation of various signaling proteins. The high energy phosphate for this reaction is generally transferred from the adenosine triphosphate molecule (ATP) to a particular protein by a protein kinase and removed from that protein by a protein phosphatase. Protein kinases are roughly divided into two groups: those that phosphorylate tyrosine residues (protein tyrosine kinases, PTK) and those that phosphorylate serine or threonine residues (serine/threonine kinases, STK). A few protein kinases have dual specificity for serine/threonine and tyrosine residues. Almost all kinases contain a conserved 250-300 amino acid catalytic domain containing specific residues and sequence motifs characteristic of the kinase family (Hardie, G. and S. Hanks (1995) The Protein Kinase Facts Books, Vol I:7-20, Academic Press, San Diego Calif.).

[0306] STKs include the second messenger dependent protein kinases such as the cyclic-AMP dependent protein kinases (PKA), involved in mediating hormone-induced cellular responses; calcium-calmodulin (CaM) dependent protein kinases, involved in regulation of smooth muscle contraction, glycogen breakdown, and neurotransmission; and the mitogen-activated protein kinases (MAP) which mediate signal transduction from the cell surface to the nucleus via phosphorylation cascades. Altered PKA expression is implicated in a variety of disorders and diseases including cancer, thyroid disorders, diabetes, atherosclerosis, and cardiovascular disease (Isselbacher, K. J. et al. (1994) Harrison's Principles of Internal Medicine, McGraw-Hill, New York N.Y., pp. 416-431, 1887).

[0307] PTKs are divided into transmembrane, receptor PTKs and nontransmembrane, non-receptor PTKs. Transmembrane PTKs are receptors for most growth factors. Non-receptor PTKs lack transmembrane regions and, instead, form complexes with the intracellular regions of cell surface receptors. Receptors that function through non-receptor PTKs include those for cytokines and hormones (growth hormone and prolactin) and antigen-specific receptors on T and B lymphocytes. Many of these PTKs were first identified as the products of mutant oncogenes in cancer cells in which their activation was no longer subject to normal cellular controls. In fact, about one third of the known oncogenes encode PTKs, and it is well known that cellular transformation (oncogenesis) is often accompanied by increased tyrosine phosphorylation activity (Charbonneau, H. and N. K. Tonks (1992) Annu. Rev. Cell Biol. 8:463-493).

[0308] An additional family of protein kinases previously thought to exist only in procaryotes is the histidine protein kinase family (BPK). HPKs bear little homology with mammalian STKs or PTKs but have distinctive sequence motifs of their own (Davie, J. R. et al. (1995) J. Biol. Chem. 270:19861-19867). A histidine residue in the N-terminal half of the molecule (region 1) is an autophosphorylation site. Three additional motifs located in the C-terminal half of the molecule include an invariant asparagine residue in region II and two glycine-rich loops characteristic of nucleotide binding domains in regions III and IV. Recently a branched chain alpha-ketoacid dehydrogenase kinase has been found with characteristics of HPK in rat (Davie, supra).

[0309] Protein phosphatases regulate the effects of protein kinases by removing phosphate groups from molecules previously activated by kinases. The two principal categories of protein phosphatases are the protein (serine/threonine) phosphatases (PPs) and the protein tyrosine phosphatases (PTPs). PPs dephosphorylate phosphoserine/threonine residues and are important regulators of many cAMP-mediated hormone responses (Cohen, P. (1989) Annu. Rev. Biochem. 58:453-508). PTPs reverse the effects of protein tyrosine kinases and play a significant role in cell cycle and cell signaling processes (Charbonneau, supra). As previously noted, many PTKs are encoded by oncogenes, and oncogenesis is often accompanied by increased tyrosine phosphorylation activity. It is therefore possible that PTPs may prevent or reverse cell transformation and the growth of various cancers by controlling the levels of tyrosine phosphorylation in cells. This hypothesis is supported by studies showing that overexpression of PTPs can suppress transformation in cells, and that specific inhibition of PTPs can enhance cell transformation (Charbonneau, supra).

[0310] Phospholipid and Inositol-Phosphate Signaling

[0311] Inositol phospholipids (phosphoinositides) are involved in an intracellular signaling pathway that begins with binding of a signaling molecule to a G-protein linked receptor in the plasma membrane. This leads to the phosphorylation of phosphatidylinositol (PI) residues on the inner side of the plasma membrane to the biphosphate state (PIP2) by inositol kinases. Simultaneously, the G-protein linked receptor binding stimulates a trimeric G-protein which in turn activates a phosphoinositide-specific phospholipase C-β. Phospholipase C-β then cleaves PIP2 into two products, inositol triphosphate (IP3) and diacylglycerol. These two products act as mediators for separate signaling events. IP3 diffuses through the plasma membrane to induce calcium release from the endoplasmic reticulum (ER), while diacylglycerol remains in the membrane and helps activate protein kinase C, an STK that phosphorylates selected proteins in the target cell. The calcium response initiated by IP3 is terminated by the dephosphorylation of IP3 by specific inositol phosphatases. Cellular responses that are mediated by this pathway are glycogen breakdown in the liver in response to vasopressin, smooth muscle contraction in response to acetylcholine, and thrombin-induced platelet aggregation

[0312] Cyclic Nucleotide Signaling

[0313] Cyclic nucleotides (cAMP and cGMP) function as intracellular second messengers to transduce a variety of extracellular signals including hormones, light, and neurotransmitters. In particular, cyclic-AMP dependent protein kinases (PKA) are thought to account for all of the effects of cAMP in most mammalian cells, including various hormone-induced cellular responses. Visual excitation and the phototransmission of light signals in the eye is controlled by cyclic-GMP regulated, Ca2+-specific channels. Because of the importance of cellular levels of cyclic nucleotides in mediating these various responses, regulating the synthesis and breakdown of cyclic nucleotides is an important matter. Thus adenylyl cyclase, which synthesizes cAMP from AMP, is activated to increase cAMP levels in muscle by binding of adrenaline to β-andrenergic receptors, while activation of guanylate cyclase and increased cGMP levels in photoreceptors leads to reopening of the Ca2+-specific channels and recovery of the dark state in the eye. In contrast, hydrolysis of cyclic nucleotides by cAMP and cGMP-specific phosphodiesterases (PDEs) produces the opposite of these and other effects mediated by increased cyclic nucleotide levels. PDEs appear to be particularly important in the regulation of cyclic nucleotides, considering the diversity found in this family of proteins. At least seven families of mammalian PDEs (PDE1-7) have been identified based on substrate specificity and affinity, sensitivity to cofactors, and sensitivity to inhibitory drugs (Beavo, J. A. (1995) Physiological Reviews 75:725-748). PDB inhibitors have been found to be particularly useful in treating various clinical disorders. Rolipram, a specific inhibitor of PDE4, has been used in the treatment of depression, and similar inhibitors are undergoing evaluation as anti-inflammatory agents. Theophylline is a nonspecific PDE inhibitor used in the treatment of bronchial asthma and other respiratory diseases (Banner, K. H. and C. P. Page (1995) Eur. Respir. J. 8:996-1000).

[0314] G-Protein Signaling

[0315] Guanine nucleotide binding proteins (G-proteins) are critical mediators of signal transduction between a particular class of extracellular receptors, the G-protein coupled receptors (GPCR), and intracellular second messengers such as cAMP and Ca2+. G-proteins are linked to the cytosolic side of a GPCR such that activation of the GPCR by ligand binding stimulates binding of the G-protein to GTP, inducing an “active” state in the G-protein. In the active state, the G-protein acts as a signal to trigger other events in the cell such as the increase of cAMP levels or the release of Ca+ into the cytosol from the ER, which, in turn, regulate phosphorylation and activation of other intracellular proteins. Recycling of the G-protein to the inactive state involves hydrolysis of the bound GTP to GDP by a GTPase activity in the G-protein. (See Alberts, B. et al. (1994) Molecular Biology of the Cell, Garland Publishing, Inc., New York N.Y., pp.734-759.) Two structurally distinct classes of G-proteins are recognized: heterotrimeric G-proteins, consisting of three different subunits, and monomeric, low molecular weight (LMW), G-proteins consisting of a single polypeptide chain.

[0316] The three polypeptide subunits of heterotrimeric G-proteins are the α, β, and γ subunits. The α subunit binds and hydrolyzes GTP. The β and γ subunits form a tight complex that anchors the protein to the inner side of the plasma membrane. The β subunits, also known as G-β proteins or β transducins, contain seven tandem repeats of the WD-repeat sequence motif, a motif found in many proteins with regulatory functions. Mutations and variant expression of β transducin proteins are linked with various disorders (Neer, E. J. et al. (1994) Nature 371:297-300; Margottin, F. et al. (1998) Mol. Cell 1:565-574).

[0317] LMW GTP-proteins are GTPases which regulate cell growth, cell cycle control, protein secretion, and intracellular vesicle interaction. They consist of single polypeptides which, like the α subunit of the heterotrimeric G-proteins, are able to bind and hydrolyze GTP, thus cycling between an inactive and an active state. At least sixty members of the LMW G-protein superfamily have been identified and are currently grouped into the six subfamilies of ras, rho, arf, sar1, ran, and rab. Activated ras genes were initially found in human cancers, and subsequent studies confirmed that ras function is critical in determining whether cells continue to grow or become differentiated. Other members of the LMW G-protein superfamily have roles in signal transduction that vary with the function of the activated genes and the locations of the G-proteins.

[0318] Guanine nucleotide exchange factors regulate the activities of LMW G-proteins by determining whether GTP or GDP is bound. GTPase-activating protein (GAP) binds to GTP-ras and induces it to hydrolyze GTP to GDP. In contrast, guanine nucleotide releasing protein (GNRP) binds to GDP-ras and induces the release of GDP and the binding of GTP.

[0319] Other regulators of G-protein signaling (RGS) also exist that act primarily by negatively regulating the G-protein pathway by an unknown mechanism (Druey, K. M. et al. (1996) Nature 379:742-746). Some 15 members of the RGS family have been identified. RGS family members are related structurally through similarities in an approximately 120 amino acid region termed the RGS domain and functionally by their ability to inhibit the interleukin (cytokine) induction of MAP kinase in cultured mammalian 293T cells (Druey, supra).

[0320] Calcium Signaling Molecules

[0321] Ca+2 is another second messenger molecule that is even more widely used as an intracellular mediator than cAMP. Two pathways exist by which Ca+2 can enter the cytosol in response to extracellular signals: One pathway acts primarily in nerve signal transduction where Ca+2 enters a nerve terminal through a voltage-gated Ca+2 channel. The second is a more ubiquitous pathway in which Ca+2 is released from the ER into the cytosol in response to binding of an extracellular signaling molecule to a receptor. Ca2+ directly activates regulatory enzymes, such as protein kinase C, which trigger signal transduction pathways. Ca2+ also binds to specific Ca2+-binding proteins (CBPs) such as calmodulin (CaM) which then activate multiple target proteins in the cell including enzymes, membrane transport pumps, and ion channels. CaM interactions are involved in a multitude of cellular processes including, but not limited to, gene regulation, DNA synthesis, cell cycle progression, mitosis, cytokinesis, cytoskeletal organization, muscle contraction, signal transduction, ion homeostasis, exocytosis, and metabolic regulation (Celio, M. R. et al. (1996) Guidebook to Calcium-binding Proteins, Oxford University Press, Oxford, UK, pp. 15-20). Some CBPs can serve as a storage depot for Ca2+ in an inactive state. Calsequestrin is one such CBP that is expressed in isoforms specific to cardiac muscle and skeletal muscle. It is suggested that calsequestrin binds Ca2+ in a rapidly exchangeable state that is released during Ca2+-signaling conditions (Celio, M. R. et al. (1996) Guidebook to Calcium-binding Proteins, Oxford University Press, New York N.Y., pp. 222-224).

[0322] Cyclins

[0323] Cell division is the fundamental process by which all living things grow and reproduce. In most organisms, the cell cycle consists of three principle steps; interphase, mitosis, and cytokinesis. Interphase, involves preparations for cell division, replication of the DNA and production of essential proteins. In mitosis, the nuclear material is divided and separates to opposite sides of the cell. Cytokinesis is the final division and fission of the cell cytoplasm to produce the daughter cells.

[0324] The entry and exit of a cell from mitosis is regulated by the synthesis and destruction of a family of activating proteins called cyclins. Cyclins act by binding to and activating a group of cyclin-dependent protein kinases (Cdks) which then phosphorylate and activate selected proteins involved in the mitotic process. Several types of cyclins exist. (Ciechanover, A. (1994) Cell 79:13-21.) Two principle types are mitotic cyclin, or cyclin B, which controls entry of the cell into mitosis, and G1 cyclin, which controls events that drive the cell out of mitosis.

[0325] Signal Complex Scaffolding Proteins

[0326] Certain proteins in intracellular signaling pathways serve to link or cluster other proteins involved in the signaling cascade. A conserved protein domain called the PDZ domain has been identified in various membrane-associated signaling proteins. This domain has been implicated in receptor and ion channel clustering and in the targeting of multiprotein signaling complexes to specialized functional regions of the cytosolic face of the plasma membrane. (For a review of PDZ domain-containing proteins, see Ponting, C. P. et al. (1997) Bioessays 19:469-479.) A large proportion of PDZ domains are found in the eukaryotic MAGUK (membrane-associated guanylate kinase) protein family, members of which bind to the intracellular domains of receptors and channels. However, PDZ domains are also found in diverse membrane-localized proteins such as protein tyrosine phosphatases, serine/threonine kinases, G-protein cofactors, and synapse-associated proteins such as syntrophins and neuronal nitric oxide synthase (nNOS). Generally, about one to three PDZ domains are found in a given protein, although up to nine PDZ domains have been identified in a single protein.

[0327] Membrane Transport Molecules

[0328] The plasma membrane acts as a barrier to most molecules. Transport between the cytoplasm and the extracellular environment, and between the cytoplasm and lumenal spaces of cellular organelles requires specific transport proteins. Each transport protein carries a particular class of molecule, such as ions, sugars, or amino acids, and often is specific to a certain molecular species of the class. A variety of human inherited diseases are caused by a mutation in a transport protein. For example, cystinuria is an inherited disease that results from the inability to transport cystine, the disulfide-linked dimer of cysteine, from the urine into the blood. Accumulation of cystine in the urine leads to the formation of cystine stones in the kidneys.

[0329] Transport proteins are multi-pass transmembrane proteins, which either actively transport molecules across the membrane or passively allow them to cross. Active transport involves directional pumping of a solute across the membrane, usually against an electrochemical gradient. Active transport is tightly coupled to a source of metabolic energy, such as ATP hydrolysis or an electrochemically favorable ion gradient. Passive transport involves the movement of a solute down its electrochemical gradient. Transport proteins can be further classified as either carrier proteins or channel proteins. Carrier proteins, which can function in active or passive transport, bind to a specific solute to be transported and undergo a conformational change which transfers the bound solute across the membrane. Channel proteins, which only function in passive transport, form hydrophilic pores across the membrane. When the pores open, specific solutes, such as inorganic ions, pass through the membrane and down the electrochemical gradient of the solute.

[0330] Carrier proteins which transport a single solute from one side of the membrane to the other are called uniporters. In contrast, coupled transporters link the transfer of one solute with simultaneous or sequential transfer of a second solute, either in the same direction (symport) or in the opposite direction (antiport). For example, intestinal and kidney epithelium contains a variety of symporter systems driven by the sodium gradient that exists across the plasma membrane. Sodium moves into the cell down its electrochemical gradient and brings the solute into the cell with it. The sodium gradient that provides the driving force for solute uptake is maintained by the ubiquitous Na+/K+ ATPase. Sodium-coupled transporters include the mammalian glucose transporter (SGLT1), iodide transporter (NIS), and multivitamin transporter (SMVT). All three transporters have twelve putative transmembrane segments, extracellular glycosylation sites, and cytoplasmically-oriented N- and C-termini. NIS plays a crucial role in the evaluation, diagnosis, and treatment of various thyroid pathologies because it is the molecular basis for radioiodide thyroid-imaging techniques and for specific targeting of radioisotopes to the thyroid gland (Levy, O. et al. (1997) Proc. Natl. Acad. Sci. USA 94:5568-5573). SMVT is expressed in the intestinal mucosa, kidney, and placenta, and is implicated in the transport of the water-soluble vitamins, e.g., biotin and pantothenate (Prasad, P. D. et al. (1998) J. Biol. Chem. 273:7501-7506).

[0331] Transporters play a major role in the regulation of pH, excretion of drugs, and the cellular K+/Na+ balance. Monocarboxylate anion transporters are proton-coupled symporters with a broad substrate specificity that includes L-lactate, pyruvate, and the ketone bodies acetate, acetoacetate, and beta-hydroxybutyrate. At least seven isoforms have been identified to date. The isoforms are predicted to have twelve transmembrane (TM) helical domains with a large intracellular loop between TM6 and TM7, and play a critical role in maintaining intracellular pH by removing the protons that are produced stoichiometrically with lactate during glycolysis. The best characterized H(+)-monocarboxylate transporter is that of the erythrocyte membrane, which transports L-lactate and a wide range of other aliphatic monocarboxylates. Other cells possess H(+)-linked monocarboxylate transporters with differing substrate and inhibitor selectivities. In particular, cardiac muscle and tumor cells have transporters that differ in their Km values for certain substrates, including stereoselectivity for L- over D-lactate, and in their sensitivity to inhibitors. There are Na(+)-monocarboxylate cotransporters on the luminal surface of intestinal and kidney epithelia, which allow the uptake of lactate, pyruvate, and ketone bodies in these tissues. In addition, there are specific and selective transporters for organic cations and organic anions in organs including the kidney, intestine and liver. Organic anion transporters are selective for hydrophobic, charged molecules with electron-attracting side groups. Organic cation transporters, such as the ammonium transporter, mediate the secretion of a variety of drugs and endogenous metabolites, and contribute to the maintenance of intercellular pH. (Poole, R. C. and A. P. Halestrap (1993) Am J. Physiol. 264:C761-C782; Price, N. T. et al. (1998) Biochem. J. 329:321-328; and Martinelle, K. and I. Haggstrom (1993) J. Biotechnol. 30: 339-350.)

[0332] The largest and most diverse family of transport proteins known is the ATP-binding cassette (ABC) transporters. As a family, ABC transporters can transport substances that differ markedly in chemical structure and size, ranging from small molecules such as ions, sugars, amino acids, peptides, and phospholipids, to lipopeptides, large proteins, and complex hydrophobic drugs. ABC proteins consist of four modules: two nucleotide-binding domains (NBD), which hydrolyze ATP to supply the energy required for transport, and two membrane-spanning domains (MSD), each containing six putative transmembrane segments. These four modules may be encoded by a single gene, as is the case for the cystic fibrosis transmembrane regulator (CFTR), or by separate genes. When encoded by separate genes, each gene product contains a single NBD and MSD. These “half-molecules” form homo- and heterodimers, such as Tap1 and Tap2, the endoplasmic reticulum-based major histocompatibility (MHC) peptide transport system. Several genetic diseases are attributed to defects in ABC transporters, such as the following diseases and their corresponding proteins: cystic fibrosis (CFTR, an ion channel), adrenoleukodystrophy (adrenoleukodystrophy protein, ALDP), Zellweger syndrome (peroxisomal membrane protein-70, PMP70), and hyperinsulinemic hypoglycemia (sulfonylurea receptor, SUR). Overexpression of the multidrug resistance (MDR) protein, another ABC transporter, in human cancer cells makes the cells resistant to a variety of cytotoxic drugs used in chemotherapy (Taglight, D. and S. Michaelis (1998) Meth. Enzymol. 292:131-163).

[0333] Transport of fatty acids across the plasma membrane can occur by diffusion, a high capacity, low affinity process. However, under normal physiological conditions a significant fraction of fatty acid transport appears to occur via a high affinity, low capacity protein-mediated transport process. Fatty acid transport protein (FATP), an integral membrane protein with four transmembrane segments, is expressed in tissues exhibiting high levels of plasma membrane fatty acid flux, such as muscle, heart, and adipose. Expression of FATP is upregulated in 3T3-L1 cells during adipose conversion, and expression in COS7 fibroblasts elevates uptake of long-chain fatty acids (Hui, T. Y. et al. (1998) J. Biol. Chem. 273:27420-27429).

[0334] Ion Channels

[0335] The electrical potential of a cell is generated and maintained by controlling the movement of ions across the plasma membrane. The movement of ions requires ion channels, which form an ion-selective pore within the membrane. There are two basic types of ion channels, ion transporters and gated ion channels. Ion transporters utilize the energy obtained from ATP hydrolysis to actively transport an ion against the ion's concentration gradient. Gated ion channels allow passive flow of an ion down the ion's electrochemical gradient under restricted conditions. Together, these types of ion channels generate, maintain, and utilize an electrochemical gradient that is used in 1) electrical impulse conduction down the axon of a nerve cell, 2) transport of molecules into cells against concentration gradients, 3) initiation of muscle contraction, and 4) endocrine cell secretion.

[0336] Ion transporters generate and maintain the resting electrical potential of a cell. Utilizing the energy derived from ATP hydrolysis, they transport ions against the ion's concentration gradient. These transmembrane ATPases are divided into three families. The phosphorylated (P) class ion transporters, including Na+-K+ ATPase, Ca2+-ATPase, and H+-ATPase, are activated by a phosphorylation event. P-class ion transporters are responsible for maintaining resting potential distributions such that cytosolic concentrations of Na+ and Ca2+ are low and cytosolic concentration of K+ is high. The vacuolar (V) class of ion transporters includes H+ pumps on intracellular organelles, such as lysosomes and Golgi. V-class ion transporters are responsible for generating the low pH within the lumen of these organelles that is required for function. The coupling factor (F) class consists of H+ pumps in the mitochondria. F-class ion transporters utilize a proton gradient to generate ATP from ADP and inorganic phosphate (P).

[0337] The resting potential of the cell is utilized in many processes involving carrier proteins and gated ion channels. Carrier proteins utilize the resting potential to transport molecules into and out of the cell. Amino acid and glucose transport into many cells is linked to sodium ion co-transport (symport) so that the movement of Na+ down an electrochemical gradient drives transport of the other molecule up a concentration gradient. Similarly, cardiac muscle links transfer of Ca2+ out of the cell with transport of Na+ into the cell (antiport).

[0338] Ion channels share common structural and mechanistic themes. The channel consists of four or five subunits or protein monomers that are arranged like a barrel in the plasma membrane. Each subunit typically consists of six potential transmembrane segments (S1, S2, S3, S4, S5, and S6). The center of the barrel forms a pore lined by α-helices or β-strands. The side chains of the amino acid residues comprising the α-helices or β-strands establish the charge (cation or anion) selectivity of the channel. The degree of selectivity, or what specific ions are allowed to pass through the channel, depends on the diameter of the narrowest part of the pore.

[0339] Gated ion channels control ion flow by regulating the opening and closing of pores. These channels are categorized according to the manner of regulating the gating function. Mechanically-gated channels open pores in response to mechanical stress, voltage-gated channels open pores in response to changes in membrane potential, and ligand-gated channels open pores in the presence of a specific ion, nucleotide, or neurotransmitter.

[0340] Voltage-gated Na+ and K+ channels are necessary for the function of electrically excitable cells, such as nerve and muscle cells. Action potentials, which lead to neurotransmitter release and muscle contraction, arise from large, transient changes in the permeability of the membrane to Na+ and K+ ions. Depolarization of the membrane beyond the threshold level opens voltage-gated Na+ channels. Sodium ions flow into the cell, further depolarizing the membrane and opening more voltage-gated Na+ channels, which propagates the depolarization down the length of the cell. Depolarization also opens voltage-gated potassium channels. Consequently, potassium ions flow outward, which leads to repolarization of the membrane. Voltage-gated channels utilize charged residues in the fourth transmembrane segment (S4) to sense voltage change. The open state lasts only about 1 millisecond, at which time the channel spontaneously converts into an inactive state that cannot be opened irrespective of the membrane potential. Inactivation is mediated by the channel's N-terminus, which acts as a plug that closes the pore. The transition from an inactive to a closed state requires a return to resting potential.

[0341] Voltage-gated Na+ channels are heterotrimeric complexes composed of a 260 kDa pore forming α subunit that associates with two smaller auxiliary subunits, β1 and β2. The β2 subunit is an integral membrane glycoprotein that contains an extracellular Ig domain, and its association with a and β1 subunits correlates with increased functional expression of the channel, a change in its gating properties, and an increase in whole cell capacitance due to an increase in membrane surface area. (Isom, L. L. et al. (1995) Cell 83:433-442.)

[0342] Voltage-gated Ca2+ channels are involved in presynaptic neurotransmitter release, and heart and skeletal muscle contraction. The voltage-gated Ca2+ channels from skeletal muscle (L-type) and brain (N-type) have been purified, and though their functions differ dramatically, they have similar subunit compositions. The channels are composed of three subunits. The α1 subunit forms the membrane pore and voltage sensor, while the α2δ and β subunits modulate the voltage-dependence, gating properties, and the current amplitude of the channel. These subunits are encoded by at least six α1, one α2δ, and four β genes. A fourth subunit, γ, has been identified in skeletal muscle. (Walker, D. et al. (1998) J. Biol. Chem. 273:2361-2367; and Jay, S. D. et al. (1990) Science 248:490-492.)

[0343] Chloride channels are necessary in endocrine secretion and in regulation of cytosolic and organelle pH. In secretory epithelial cells, Cl− enters the cell across a basolateral membrane through an Na+, K+/Cl− cotransporter, accumulating in the cell above its electrochemical equilibrium concentration. Secretion of Cl− from the apical surface, in response to hormonal stimulation, leads to flow of Na+ and water into the secretory lumen. The cystic fibrosis transmembrane conductance regulator (CFTR) is a chloride channel encoded by the gene for cystic fibrosis, a common fatal genetic disorder in humans. Loss of CFTR function decreases transepithelial water secretion and, as a result, the layers of mucus that coat the respiratory tree, pancreatic ducts, and intestine are dehydrated and difficult to clear. The resulting blockage of these sites leads to pancreatic insufficiency, “meconium ileus”, and devastating “chronic obstructive pulmonary disease” (A1-Awqati, Q. et al. (1992) J. Exp. Biol. 172:245-266).

[0344] Many intracellular organelles contain H+-ATPase pumps that generate transmembrane pH and electrochemical differences by moving protons from the cytosol to the organelle lumen. If the membrane of the organelle is permeable to other ions, then the electrochemical gradient can be abrogated without affecting the pH differential. In fact, removal of the electrochemical barrier allows more H+ to be pumped across the membrane, increasing the pH differential. Cl− is the sole counterion of H+ translocation in a number of organelles, including chromaffin granules, Golgi vesicles, lysosomes, and endosomes. Functions that require a low vacuolar pH include uptake of small molecules such as biogenic amines in chromaffin granules, processing of vacuolar constituents such as pro-hormones by proteolytic enzymes, and protein degradation in lysosomes (A1-Awqati, supra).

[0345] Ligand-gated channels open their pores when an extracellular or intracellular mediator binds to the channel. Neurotransmitter-gated channels are channels that open when a neurotransmitter binds to their extracellular domain. These channels exist in the postsynaptic membrane of nerve or muscle cells. There are two types of neurotransmitter-gated channels. Sodium channels open in response to excitatory neurotransmitters, such as acetylcholine, glutamate, and serotonin. This opening causes an influx of Na+ and produces the initial localized depolarization that activates the voltage-gated channels and starts the action potential. Chloride channels open in response to inhibitory neurotransmitters, such as γ-aminobutyiic acid (GABA) and glycine, leading to hyperpolarization of the membrane and the subsequent generation of an action potential.

[0346] Ligand-gated channels can be regulated by intracellular second messengers. Calcium-activated K+ channels are gated by internal calcium ions. In nerve cells, an influx of calcium during depolarization opens K+ channels to modulate the magnitude of the action potential (Ishi, T. M. et al. (1997) Proc. Natl. Acad. Sci. USA 94:11651-11656). Cyclic nucleotide-gated (CNG) channels are gated by cytosolic cyclic nucleotides. The best examples of these are the cAMP-gated Na+ channels involved in olfaction and the cGMP-gated cation channels involved in vision. Both systems involve ligand-mediated activation of a G-protein coupled receptor which then alters the level of cyclic nucleotide within the cell.

[0347] Ion channels are expressed in a number of tissues where they are implicated in a variety of processes. CNG channels, while abundantly expressed in photoreceptor and olfactory sensory cells, are also found in kidney, lung, pineal, retinal ganglion cells, testis, aorta, and brain. Calcium-activated K+ channels maybe responsible for the vasodilatory effects of bradykinin in the kidney and for shunting excess K+ from brain capillary endothelial cells into the blood. They are also implicated in repolarzing granulocytes after agonist-stimulated depolarization (Ishi, supra). Ion channels have been the target for many drug therapies. Neurotransmitter-gated channels have been targeted in therapies for treatment of insomnia, anxiety, depression, and schizophrenia. Voltage-gated channels have been targeted in therapies for arrhythmia, ischemic stroke, head trauma, and neurodegenerative disease (Taylor, C. P. and L. S. Narasimhan (1997) Adv. Pharmacol. 39:47-98).

[0348] Disease Correlation

[0349] The etiology of numerous human diseases and disorders can be attributed to defects in the transport of molecules across membranes. Defects in the trafficking of membrane-bound transporters and ion channels are associated with several disorders, e.g. cystic fibrosis, glucose-galactose malabsorption syndrome, hypercholesterolemia, von Gierke disease, and certain forms of diabetes mellitus. Single-gene defect diseases resulting in an inability to transport small molecules across membranes include, e.g., cystinuria, iminoglycinuria, Hartup disease, and Fanconi disease (van't Hoff, W. G. (1996) Exp. Nephrol. 4:253-262; Talente, G. M. et al. (1994) Ann. Intern. Med. 120:218-226; and Chillon, M. et al. (1995) New Engl. J. Med. 332:1475-1480).

[0350] Protein Modification and Maintenance Molecules

[0351] The cellular processes regulating modification and maintenance of protein molecules coordinate their conformation, stabilization, and degradation. Each of these processes is mediated by key enzymes or proteins such as proteases, protease inhibitors, transferases, isomerases, and molecular chaperones.

[0352] Proteases

[0353] Proteases cleave proteins and peptides at the peptide bond that forms the backbone of the peptide and protein chain. Proteolytic processing is essential to cell growth, differentiation, remodeling, and homeostasis as well as inflammation and immune response. Typical protein half-lives range from hours to a few days, so that within all living cells, precursor proteins are being cleaved to their active form, signal sequences proteolytically removed from targeted proteins, and aged or defective proteins degraded by proteolysis. Proteases function in bacterial, parasitic, and viral invasion and replication within a host. Four principal categories of mammalian proteases have been identified based on active site structure, mechanism of action, and overall three-dimensional structure. (Beynon, R. J. and J. S. Bond (1994) Proteolytic Enzymes: A Practical Approach, Oxford University Press, New York N.Y., pp. 1-5).

[0354] The serine proteases (SPs) have a serine residue, usually within a conserved sequence, in an active site composed of the serine, an aspartate, and a histidine residue. SPs include the digestive enzymes trypsin and chymotrypsin, components of the complement cascade and the blood-clotting cascade, and enzymes that control extracellular protein degradation. The main SP sub-families are trypases, which cleave after arginine or lysine; aspartases, which cleave after aspartate; chymases, which cleave after phenylalanine or leucine; metases, which cleavage after methionine; and serases which cleave after serine. Enterokinase, the initiator of intestinal digestion, is a serine protease found in the intestinal brush border, where it cleaves the acidic propeptide from trypsinogen to yield active trypsin (Kitamoto, Y. et al. (1994) Proc. Natl. Acad. Sci. USA 91:7588-7592). Prolylcarboxypeptidase, a lysosomal serine peptidase that cleaves peptides such as angiotensin II and III and [des-Arg9] bradykinin, shares sequence homology with members of both the serine carboxypeptidase and prolylendopeptidase families (Tan, F. et al. (1993) J. Biol. Chem. 268:16631-16638).

[0355] Cysteine proteases (CPs) have a cysteine as the major catalytic residue at an active site where catalysis proceeds via an intermediate thiol ester and is facilitated by adjacent histidine and aspartic acid residues. CPs are involved in diverse cellular processes ranging from the processing of precursor proteins to intracellular degradation. Mammalian CPs include lysosomal cathepsins and cytosolic calcium activated proteases, calpains. CPs are produced by monocytes, macrophages and other cells of the immune system which migrate to sites of inflammation and secrete molecules involved in tissue repair. Overabundance of these repair molecules plays a role in certain disorders. In autoimmune diseases such as rheumatoid arthritis, secretion of the cysteine peptidase cathepsin C degrades collagen, laminin, elastin and other structural proteins found in the extracellular matrix of bones.

[0356] Aspartic proteases are members of the cathepsin family of lysosomal proteases and include pepsin A, gastricsin, chymosin, renin, and cathepsins D and E. Aspartic proteases have a pair of aspartic acid residues in the active site, and are most active in the pH 2-3 range, in which one of the aspartate residues is ionized, the other un-ionized. Aspartic proteases include bacterial penicillopepsin, mammalian pepsin, renin, chymosin, and certain fungal proteases. Abnormal regulation and expression of cathepsins is evident in various inflammatory disease states. In cells isolated from inflamed synovia, the mRNA for stromelysin, cytokines, TIMP-1, cathepsin, gelatinase, and other molecules is preferentially expressed. Expression of cathepsins L and D is elevated in synovial tissues from patients with rheumatoid arthritis and osteoarthritis. Cathepsin L expression may also contribute to the influx of mononuclear cells which exacerbates the destruction of the rheumatoid synovium. (Keyszer, G. M. (1995) Arthritis Rheum. 38:976-984.) The increased expression and differential regulation of the cathepsins are linked to the metastatic potential of a variety of cancers and as such are of therapeutic and prognostic interest (Chambers, A. F. et al. (1993) Crit. Rev. Oncog. 4:95-114).

[0357] Metalloproteases have active sites that include two glutamic acid residues and one histidine residue that serve as binding sites for zinc. Carboxypeptidases A and B are the principal mammalian metalloproteases. Both are exoproteases of similar structure and active sites. Carboxypeptidase A, like chymotrypsin, prefers C-terminal aromatic and aliphatic side chains of hydrophobic nature, whereas carboxypeptidase B is directed toward basic arginine and lysine residues. Glycoprotease (GCP), or O-sialoglycoprotein endopeptidase, is a metallopeptidase which specifically cleaves O-sialoglycoproteins such as glycophorin A. Another metallopeptidase, placental leucine aminopeptidase (P-LAP) degrades several peptide hormones such as oxytocin and vasopressin, suggesting a role in maintaining homeostasis during pregnancy, and is expressed in several tissues (Rogi, T. et al. (1996) J. Biol. Chem. 271:56-61).

[0358] Ubiquitin proteases are associated with the ubiquitin conjugation system (UCS), a major pathway for the degradation of cellular proteins in eukaryotic cells and some bacteria. The UCS mediates the elimination of abnormal proteins and regulates the half-lives of important regulatory proteins that control cellular processes such as gene transcription and cell cycle progression. In the UCS pathway, proteins targeted for degradation are conjugated to a ubiquitin, a small heat stable protein. The ubiquitinated protein is then recognized and degraded by proteasome, a large, multisubunit proteolytic enzyme complex, and ubiquitin is released for reutilization by ubiquitin protease. The UCS is implicated in the degradation of mitotic cyclic kinases, oncoproteins, tumor suppressor genes such as p53, viral proteins, cell surface receptors associated with signal transduction, transcriptional regulators, and mutated or damaged proteins (Ciechanover, A. (1994) Cell 79:13-21). A murine proto-oncogene, Unp, encodes a nuclear ubiquitin protease whose overexpression leads to oncogenic transformation of NIH3T3 cells, and the human homolog of this gene is consistently elevated in small cell tumors and adenocarcinomas of the lung (Gray, D. A. (1995) Oncogene 10:2179-2183).

[0359] Signal Peptidases

[0360] The mechanism for the translocation process into the endoplasmic reticulum (ER) involves the recognition of an N-terminal signal peptide on the elongating protein. The signal peptide directs the protein and attached ribosome to a receptor on the ER membrane. The polypeptide chain passes through a pore in the ER membrane into the lumen while the N-terminal signal peptide remains attached at the membrane surface. The process is completed when signal peptidase located inside the ER cleaves the signal peptide from the protein and releases the protein into the lumen.

[0361] Protease Inhibitors

[0362] Protease inhibitors and other regulators of protease activity control the activity and effects of proteases. Protease inhibitors have been shown to control pathogenesis in animal models of proteolytic disorders (Murphy, G. (1991) Agents Actions Suppl. 35:69-76). Low levels of the cystatins, low molecular weight inhibitors of the cysteine proteases, correlate with malignant progression of tumors. (Calkins, C. et al. (1995) Biol. Biochem. Hoppe Seyler 376:71-80). Serpins are inhibitors of mammalian plasma serine proteases. Many serpins serve to regulate the blood clotting cascade and/or the complement cascade in mammals. Sp32 is a positive regulator of the mammalian acrosomal protease, acrosin, that binds the proenzyme, proacrosin, and thereby aides in packaging the enzyme into the acrosomal matrix (Baba, T. et al. (1994) J. Biol. Chem. 269:10133-10140). The Kunitz family of serine protease inhibitors are characterized by one or more “Kunitz domains” containing a series of cysteine residues that are regularly spaced over approximately 50 amino acid residues and form three intrachain disulfide bonds. Members of this family include aprotinin, tissue factor pathway inhibitor (TFPI-1 and TFPI-2), inter-α-trypsin inhibitor, and bikunin. (Marlor, C. W. et al (1997) J. Biol. Chem. 272:12202-12208.) Members of this family are potent inhibitors (in the nanomolar range) against serine proteases such as kallikrein and plasmin. Aprotnin has clinical utility in reduction of perioperative blood loss.

[0363] A major portion of all proteins synthesized in eukaryotic cells are synthesized on &e cytosolic surface of the endoplasmic reticulum (ER). Before these immature proteins are distributed to other organelles in the cell or are secreted, they must be transported into the interior lumen of the ER where post-translational modifications are performed. These modifications include protein folding and the formation of disulfide bonds, and N-linked glycosylations.

[0364] Protein Isomerases

[0365] Protein folding in the ER is aided by two principal types of protein isomerases, protein disulfide isomerase (PDI), and peptidyl-prolyl isomerase (PPI). PDI catalyzes the oxidation of free sulfhydryl groups in cysteine residues to form intramolecular disulfide bonds in proteins. PPI, an enzyme that catalyzes the isomerization of certain proline imidic bonds in oligopeptides and proteins, is considered to govern one of the rate limiting steps in the folding of many proteins to their final functional conformation. The cyclophilins represent a major class of PPI that was originally identified as the major receptor for the immunosuppressive drug cyclosporin A (Handschumacher, R. E. et al. (1984) Science 226: 544-547).

[0366] Protein Glycosylation

[0367] The glycosylation of most soluble secreted and membrane-bound proteins by oligosaccharides linked to asparagine residues in proteins is also performed in the ER. This reaction is catalyzed by a membrane-bound enzyme, oligosaccharyl transferase. Although the exact purpose of this “N-linked” glycosylation is unknown, the presence of oligosaccharides tends to make a glycoprotein resistant to protease digestion. In addition, oligosaccharides attached to cell-surface proteins called selectins are known to function in cell-cell adhesion processes (Alberts, B. et al. (1994) Molecular Biology of the Cell, Garland Publishing Co., New York N.Y., p.608). “O-linked” glycosylation of proteins also occurs in the ER by the addition of N-acetylgalactosamine to the hydroxyl group of a serine or threonine residue followed by the sequential addition of other sugar residues to the first. This process is catalysed by a series of glycosyltransferases each specific for a particular donor sugar nucleotide and acceptor molecule (Lodish, H. et al. (1995) Molecular Cell Biology, W.H. Freeman and Co., New York N.Y., pp.700-708). In many cases, both N- and O-linked oligosaccharides appear to be required for the secretion of proteins or the movement of plasma membrane glycoproteins to the cell surface.

[0368] An additional glycosylation mechanism operates in the ER specifically to target lysosomal enzymes to lysosomes and prevent their secretion. Lysosomal enzymes in the ER receive an N-linked oligosaccharide, like plasma membrane and secreted proteins, but are then phosphorylated on one or two mannose residues. The phosphorylation of mannose residues occurs in two steps, the first step being the addition of an N-acetylglucosamine phosphate residue by N-acetylglucosamine phosphotransferase, and the second the removal of the N-acetylglucosamine group by phosphodiesterase. The phosphorylated mannose residue then targets the lysosomal enzyme to a mannose 6-phosphate receptor which transports it to a lysosome vesicle (Lodish, supra, pp. 708-711).

[0369] Chaperones

[0370] Molecular chaperones are proteins that aid in the proper folding of immature proteins and refolding of improperly folded ones, the assembly of protein subunits, and in the transport of unfolded proteins across membranes. Chaperones are also called heat-shock proteins (hsp) because of their tendency to be expressed in dramatically increased amounts following brief exposure of cells to elevated temperatures. This latter property most likely reflects their need in the refolding of proteins that have become denatured by the high temperatures. Chaperones may be divided into several classes according to their location, function, and molecular weight, and include hsp60, TCP1, hsp70, hsp40 (also called DnaJ), and hsp90. For example, hsp90 binds to steroid hormone receptors, represses transcription in the absence of the ligand, and provides proper folding of the ligand-binding domain of the receptor in the presence of the hormone (Burston, S. G. and A. R. Clarke (1995) Essays Biochem. 29:125-136). Hsp60 and hsp70 chaperones aid in the transport and folding of newly synthesized proteins. Hsp70 acts early in protein folding, binding a newly synthesized protein before it leaves the ribosome and transporting the protein to the mitochondria or ER before releasing the folded protein. Hsp60, along with hsp10, binds misfolded proteins and gives them the opportunity to refold correctly. All chaperones share an affinity for hydrophobic patches on incompletely folded proteins and the ability to hydrolyze ATP. The energy of ATP hydrolysis is used to release the hsp-bound protein in its properly folded state (Alberts, supra, pp 214, 571-572).

[0371] Nucleic Acid Synthesis and Modification Molecules

[0372] Polymerases

[0373] DNA and RNA replication are critical processes for cell replication and function. DNA and RNA replication are mediated by the enzymes DNA and RNA polymerase, respectively, by a “templating” process in which the nucleotide sequence of a DNA or RNA strand is copied by complementary base-pairing into a complementary nucleic acid sequence of either DNA or RNA. However, there are fundamental differences between the two processes.

[0374] DNA polymerase catalyzes the stepwise addition of a deoxyribonucleotide to the 3′-OH end of a polynucleotide strand (the primer strand) that is paired to a second (template) strand. The new DNA strand therefore grows in the 5′ to 3′ direction (Alberts, B. et al. (1994) The Molecular Biology of the Cell, Garland Publishing Inc., New York N.Y., pp. 251-254). The substrates for the polymerization reaction are the corresponding deoxynucleotide triphosphates which must base-pair with the correct nucleotide on the template strand in order to be recognized by the polymerase. Because DNA exists as a double-stranded helix, each of the two strands may serve as a template for the formation of a new complementary strand. Each of the two daughter cells of the dividing cell therefore inherits a new DNA double helix containing one old and one new strand. Thus, DNA is said to be replicated “semiconservatively” by DNA polymerase. In addition to the synthesis of new DNA, DNA polymerase is also involved in the repair of damaged DNA as discussed below under “Ligases.”

[0375] In contrast to DNA polymerase, RNA polymerase uses a DNA template strand to “transcribe” DNA into RNA using ribonucleotide triphosphates as substrates. Like DNA polymerization, RNA polymerization proceeds in a 5′ to 3′ direction by addition of a ribonucleoside monophosphate to the 3′-OH end of a growing RNA chain. DNA transcription generates messenger RNAs (mRNA) that carry information for protein synthesis, as well as the transfer, ribosomal, and other RNAs that have structural or catalytic functions. In eukaryotes, three discrete RNA polymerases synthesize the three different types of RNA (Alberts, supra, pp. 367-368). RNA polymerase I makes the large ribosomal RNAs, RNA polymerase II makes the mRNAs that will be translated into proteins, and RNA polymerase III makes a variety of small, stable RNAs, including 5S ribosomal RNA and the transfer RNAs (tRNA). In all cases, RNA synthesis is initiated by binding of the RNA polymerase to a promoter region on the DNA and synthesis begins at a start site within the promoter. Synthesis is completed at a broad, general stop or termination region in the DNA where both the polymerase and the completed RNA chain are released.

[0376] Ligases

[0377] DNA repair is the process by which accidental base changes, such as those produced by oxidative damage, hydrolytic attack, or uncontrolled methylation of DNA are corrected before replication or transcription of the DNA can occur. Because of the efficiency of the DNA repair process, fewer than one in one thousand accidental base changes causes a mutation (Alberts, supra, pp. 245-249). The three steps common to most types of DNA repair are (1) excision of the damaged or altered base or nucleotide by DNA nucleases, leaving a gap; (2) insertion of the correct nucleotide in this gap by DNA polymerase using the complementary strand as the template; and (3) sealing the break left between the inserted nucleotide(s) and the existing DNA strand by DNA ligase. In the last reaction, DNA ligase uses the energy from ATP hydrolysis to activate the 5′ end of the broken phosphodiester bond before forming the new bond with the 3′-OH of the DNA strand. In Bloom's syndrome, an inherited human disease, individuals are partially deficient in DNA ligation and consequently have an increased incidence of cancer (Alberts, supra, p. 247).

[0378] Nucleases

[0379] Nucleases comprise both enzymes that hydrolyze DNA (DNase) and RNA (RNase). They serve different purposes in nucleic acid metabolism. Nucleases hydrolyze the phosphodiester bonds between adjacent nucleotides either at internal positions (endonucleases) or at the terminal 3′ or 5′ nucleotide positions (exonucleases). A DNA exonuclease activity in DNA polymerase, for example, serves to remove improperly paired nucleotides attached to the 3′-OH end of the growing DNA strand by the polymerase and thereby serves a “proofreading” function. As mentioned above, DNA endonuclease activity is involved in the excision step of the DNA repair process.

[0380] RNases also serve a variety of functions. For example, RNase P is a ribonucleoprotein enzyme which cleaves the 5′ end of pre-tRNAs as part of their maturation process. RNase H digests the RNA strand of an RNA/DNA hybrid. Such hybrids occur in cells invaded by retroviruses, and RNase H is an important enzyme in the retroviral replication cycle. Pancreatic RNase secreted by the pancreas into the intestine hydrolyzes RNA present in ingested foods. RNase activity in serum and cell extracts is elevated in a variety of cancers and infectious diseases (Schein, C. H. (1997) Nat Biotechnol. 15:529-536). Regulation of RNase activity is being investigated as a means to control tumor angiogenesis, allergic reactions, viral infection and replication, and fungal infections.

[0381] Methylases

[0382] Methylation of specific nucleotides occurs in both DNA and RNA, and serves different functions in the two macromolecules. Methylation of cytosine residues to form 5-methyl cytosine in DNA occurs specifically at CG sequences which are base-paired with one another in the DNA double-helix. This pattern of methylation is passed from generation to generation during DNA replication by an enzyme called “maintenance methylase” that acts preferentially on those CG sequences that are base-paired with a CG sequence that is already methylated. Such methylation appears to distinguish active from inactive genes by preventing the binding of regulatory proteins that “turn on” the gene, but permit the binding of proteins that inactivate the gene (Alberts, supra, pp. 448-451). In RNA metabolism, “tRNA methylase” produces one of several nucleotide modifications in tRNA that affect the conformation and base-pairing of the molecule and facilitate the recognition of the appropriate mRNA codons by specific tRNAs. The primary methylation pattern is the dimethylation of guanine residues to form N,N-dimethyl guanine.

[0383] Helicases and Single-Stranded Binding Proteins

[0384] Helicases are enzymes that destabilize and unwind double helix structures in both DNA and RNA. Since DNA replication occurs more or less simultaneously on both strands, the two strands must first separate to generate a replication “fork” for DNA polymerase to act on. Two types of replication proteins contribute to this process, DNA helicases and single-stranded binding proteins. DNA helicases hydrolyze ATP and use the energy of hydrolysis to separate the DNA strands. Single-stranded binding proteins (SSBs) then bind to the exposed DNA strands without covering the bases, thereby temporarily stabilizing them for templating by the DNA polymerase (Alberts, supra, pp. 255-256).

[0385] RNA helicases also alter and regulate RNA conformation and secondary structure. Lie the DNA helicases, RNA helicases utilize energy derived from ATP hydrolysis to destabilize and unwind RNA duplexes. The most well-characterized and ubiquitous family of RNA helicases is the DEAD-box family, so named for the conserved B-type ATP-binding motif which is diagnostic of proteins in this family. Over 40 DEAD-box helicases have been identified in organisms as diverse as bacteria, insects, yeast, amphibians, mammals, and plants. DEAD-box helicases function in diverse processes such as translation initiation, splicing, ribosome assembly, and RNA editing, transport, and stability. Some DEAD-box helicases play tissue- and stage-specific roles in spermatogenesis and embryogenesis. Overexpression of the DEAD-box 1 protein (DDX1) may play a role in the progression of neuroblastoma (Nb) and retinoblastoma (Rb) tumors (Godbout, R. et al. (1998) J. Biol. Chem. 273:21161-21168). These observations suggest that DDX1 may promote or enhance tumor progression by altering the normal secondary structure and expression levels of RNA in cancer cells. Other DEAD-box helicases have been implicated either directly or indirectly in tumorigenesis (Discussed in Godbout, supra). For example, murine p68 is mutated in ultraviolet light-induced tumors, and human DDX6 is located at a chromosomal breakpoint associated with B-cell lymphoma. Similarly, a chimeric protein comprised of DDX10 and NUP98, a nucleoporin protein, maybe involved in the pathogenesis of certain myeloid malignancies.

[0386] Topoisomerases

[0387] Besides the need to separate DNA strands prior to replication, the two strands must be “unwound” from one another prior to their separation by DNA helicases. This function is performed by proteins known as DNA topoisomerases. DNA topoisomerase effectively acts as a reversible nuclease that hydrolyzes a phosphodiesterase bond in a DNA strand, permitting the two strands to rotate freely about one another to remove the strain of the helix, and then rejoins the original phosphodiester bond between the two strands. Two types of DNA topoisomerase exist, types I and II. DNA Topoisomerase I causes a single-strand break in a DNA helix to allow the rotation of the two strands of the helix about the remaining phosphodiester bond in the opposite strand. DNA topoisomerase II causes a transient break in both strands of a DNA helix where two double helices cross over one another. This type of topoisomerase can efficiently separate two interlocked DNA circles (Alberts, supra, pp.260-262). Type II topoisomerases are largely confined to proliferating cells in eukaryotes, such as cancer cells. For this reason they are targets for anticancer drugs. Topoisomerase II has been implicated in multi-drug resistance (MDR) as it appears to aid in the repair of DNA damage inflicted by DNA binding agents such as doxorubicin and vincristine.

[0388] Recombinases

[0389] Genetic recombination is the process of rearranging DNA sequences within an organism's genome to provide genetic variation for the organism in response to changes in the environment. DNA recombination allows variation in the particular combination of genes present in an individual's genome, as well as the timing and level of expression of these genes (see Alberts, supra, pp. 263-273). Two broad classes of genetic recombination are commonly recognized, general recombination and site-specific recombination. General recombination involves genetic exchange between any homologous pair of DNA sequences usually located on two copies of the same chromosome. The process is aided by enzymes called recombinases that “nick” one strand of a DNA duplex more or less randomly and permit exchange with the complementary strand of another duplex. The process does not normally change the arrangement of genes on a chromosome. In site-specific recombination, the recombinase recognizes specific nucleotide sequences present in one or both of the recombining molecules. Base-pairing is not involved in this form of recombination and therefore does not require DNA homology between the recombining molecules. Unlike general recombination, this form of recombination can alter the relative positions of nucleotide sequences in chromosomes.

[0390] Splicing Factors

[0391] Various proteins are necessary for processing of transcribed RNAs in the nucleus. Pre-mRNA processing steps include capping at the 5′ end with methylguanosine, polyadenylating the 3′ end, and splicing to remove introns. The primary RNA transcript from DNA is a faithful copy of the gene containing both exon and intron sequences, and the latter sequences must be cut out of the RNA transcript to produce an mRNA that codes for a protein. This “splicing” of the mRNA sequence takes place in the nucleus with the aid of a large, multicomponent ribonucleoprotein complex known as a spliceosome. The spliceosomal complex is composed of five small nuclear ribonucleoprotein particles (snRNPs) designated U1, U2, U4, U5, and U6, and a number of additional proteins. Each snRNP contains a single species of snRNA and about ten proteins. The RNA components of some snRNPs recognize and base pair with intron consensus sequences. The protein components mediate spliceosome assembly and the splicing reaction. Autoantibodies to snRNP proteins are found in the blood of patients with systemic lupus erythematosus (Stryer, L. (1995) Biochemistry, W.H. Freeman and Company, New York N.Y., p. 863).

[0392] Adhesion Molecules

[0393] The surface of a cell is rich in transmembrane proteoglycans, glycoproteins, glycolipids, and receptors. These macromolecules mediate adhesion with other cells and with components of the extracellular matrix (ECM). The interaction of the cell with its surroundings profoundly influences cell shape, strength, flexibility, motility, and adhesion. These dynamic properties are intimately associated with signal transduction pathways controlling cell proliferation and differentiation, tissue construction, and embryonic development.

[0394] Cadherins

[0395] Cadherins comprise a family of calcium-dependent glycoproteins that function in mediating cell-cell adhesion in virtually all solid tissues of multicellular organisms. These proteins share multiple repeats of a cadherin-specific motif, and the repeats form the folding units of the cadherin extracellular domain. Cadherin molecules cooperate to form focal contacts, or adhesion plaques, between adjacent epithelial cells. The cadherin family includes the classical cadherins and protocadherins. Classical cadherins include the E-cadherin, N-cadherin, and P-cadherin subfamilies. E-cadherin is present on many types of epithelial cells and is especially important for embryonic development. N-cadherin is present on nerve, muscle, and lens cells and is also critical for embryonic development. P-cadherin is present on cells of the placenta and epidermis. Recent studies report that protocadherins are involved in a variety of cell-cell interactions (Suzuki, S. T. (1996) J. Cell Sci. 109:2609-2611). The intracellular anchorage of cadherins is regulated by their dynamic association with catenins, a family of cytoplasmic signal transduction proteins associated with the actin cytoskeleton. The anchorage of cadherins to the actin cytoskeleton appears to be regulated by protein tyrosine phosphorylation, and the cadherins are the target of phosphorylation-induced junctional disassembly (Aberle, R et al. (1996) J. Cell. Biochem 61:514-523).

[0396] Integrins

[0397] Integrins are ubiquitous transmembrane adhesion molecules that link the ECM to the internal cytoskeleton. Integrins are composed of two noncovalently associated transmembrane glycoprotein subunits called α and β. Integrins function as receptors that play a role in signal transduction. For example, binding of integrin to its extracellular ligand may stimulate changes in intracellular calcium levels or protein kinase activity (Sjaastad, M. D. and W. J. Nelson (1997) BioEssays 19:47-55). At least ten cell surface receptors of the integrin family recognize the ECM component fibronectin, which is involved in many different biological processes including cell migration and embryogenesis (Johansson, S. et al. (1997) Front. Biosci. 2:D126-D146).

[0398] Lectins

[0399] Lectins comprise a ubiquitous family of extracellular glycoproteins which bind cell surface carbohydrates specifically and reversibly, resulting in the agglutination of cells (reviewed in Drickamer, K. and M. E. Taylor (1993) Annu. Rev. Cell Biol. 9:237-264). This function is particularly important for activation of the immune response. Lectins mediate the agglutination and mitogenic stimulation of lymphocytes at sites of inflammation (Lasky, L. A. (1991) J. Cell. Biochem. 45:139-146; Paietta, E. et al. (1989) J. Immunol. 143:2850-2857).

[0400] Lectins are further classified into subfamilies based on carbohydrate-binding specificity and other criteria. The galectin subfamily, in particular, includes lectins that bind β-galactoside carbohydrate moieties in a thiol-dependent manner (reviewed in Hadari, Y. R. et al. (1998) J. Biol. Chem. 270:3447-3453). Galectins are widely expressed and developmentally regulated. Because all galectins lack an N-terminal signal peptide, it is suggested that galectins are externalized through an a typical secretory mechanism. Two classes of galectins have been defined based on molecular weight and oligomerization properties. Small galectins form homodimers and are about 14 to 16 kilodaltons in mass, while large galectins are monomeric and about 29-37 kilodaltons.

[0401] Galectins contain a characteristic carbohydrate recognition domain (CRD). The CRD is about 140 amino acids and contains several stretches of about 1-10 amino acids which are highly conserved among all galectins. A particular 6-amino acid motif within the CRD contains conserved tryptophan and arginine residues which are critical for carbohydrate binding. The CRD of some galectins also contains cysteine residues which maybe important for disulfide bond formation. Secondary structure predictions indicate that the CRD forms several β-sheets.

[0402] Galectins play a number of roles in diseases and conditions associated with cell-cell and cell-matrix interactions. For example, certain galectins associate with sites of inflammation and bind to cell surface immunoglobulin E molecules. In addition, galectins may play an important role in cancer metastasis. Galectin overexpression is correlated with the metastatic potential of cancers in humans and mice. Moreover, anti-galectin antibodies inhibit processes associated with cell transformation, such as cell aggregation and anchorage-independent growth (See, for example, Su, Z.-Z. et al. (1996) Proc. Natl. Acad. Sci. USA 93:7252-7257).

[0403] Selectins

[0404] Selectins, or LEC-CAMs, comprise a specialized lectin subfamily involved primarily in inflammation and leukocyte adhesion (Reviewed in Lasky, supra). Selectins mediate the recruitment of leukocytes from the circulation to sites of acute inflammation and are expressed on the surface of vascular endothelial cells in response to cytokine signaling. Selectins bind to specific ligands on the leukocyte cell membrane and enable the leukocyte to adhere to and migrate along the endothelial surface. Binding of selectin to its ligand leads to polarized rearrangement of the actin cytoskeleton and stimulates signal transduction within the leukocyte (Brenner, B. et al. (1997) Biochem. Biophys. Res. Commun. 231:802-807; Hidari, K. I. et al. (1997) J. Biol. Chem. 272:28750-28756). Members of the selectin family possess three characteristic motifs: a lectin or carbohydrate recognition domain; an epidermal growth factor-like domain; and a variable number of short consensus repeats (scr or “sushi” repeats) which are also present in complement regulatory proteins. The selectins include lymphocyte adhesion molecule-1 (Lam-1 or L-selectin), endothelial leukocyte adhesion molecule-1 (ELAM-1 or E-selectin), and granule membrane protein-140 (GMP-140 or P-selectin) (Johnston, G. I. et al. (1989) Cell 56:1033-1044).

[0405] Antigen Recognition Molecules

[0406] All vertebrates have developed sophisticated and complex immune systems that provide protection from viral, bacterial, fungal, and parasitic infections. A key feature of the immune system is its ability to distinguish foreign molecules, or antigens, from “self” molecules. This ability is mediated primarily by secreted and transmembrane proteins expressed by leukocytes (white blood cells) such as lymphocytes, granulocytes, and monocytes. Most of these proteins belong to the immunoglobulin (Ig) superfamily, members of which contain one or more repeats of a conserved structural domain. This Ig domain is comprised of antiparallel β sheets joined by a disulfide bond in an arrangement called the Ig fold. Members of the Ig superfamily include T-cell receptors, major histocompatibility (MHC) proteins, antibodies, and immune cell-specific surface markers such as CD4, CD8, and CD28.

[0407] MHC proteins are cell surface markers that bind to and present foreign antigens to T cells. MHC molecules are classified as either class I or class II. Class I MHC molecules (MHC I) are expressed on the surface of almost all cells and are involved in the presentation of antigen to cytotoxic T cells. For example, a cell infected with virus will degrade intracellular viral proteins and express the protein fragments bound to MHC I molecules on the cell surface. The MHC I/antigen complex is recognized by cytotoxic T-cells which destroy the infected cell and the virus with Class II MHC molecules are expressed primarily on specialized antigen-presenting cells of the immune system, such as B-cells and macrophages. These cells ingest foreign proteins from the extracellular fluid and express MHC II/antigen complex on the cell surface. This complex activates helper T-cells, which then secrete cytokines and other factors that stimulate the immune response. MHC molecules also play an important role in organ rejection following transplantation. Rejection occurs when the recipient's T-cells respond to foreign MHC molecules on the transplanted organ in the same way as to self MHC molecules bound to foreign antigen. (Reviewed in Alberts, B. et al. (1994) Molecular Biology of the Cell, Garland Publishing, New York N.Y., pp. 1229-1246.)

[0408] Antibodies, or immunoglobulins, are either expressed on the surface of B-cells or secreted by B-cells into the circulation. Antibodies bind and neutralize foreign antigens in the blood and other extracellular fluids. The prototypical antibody is a tetramer consisting of two identical heavy polypeptide chains (H-chains) and two identical light polypeptide chains (L-chains) interlinked by disulfide bonds. This arrangement confers the characteristic Y-shape to antibody molecules. Antibodies are classified based on their H-chain composition. The five antibody classes, IgA, IgD, IgE, IgG and IgM, are defined by the α, δ, ε, δ, and μ H-chain types. There are two types of L-chains, κ and λ, either of which may associate as a pair with any H-chain pair. IgG, the most common class of antibody found in the circulation, is tetrameric, while the other classes of antibodies are generally variants or multimers of this basic structure.

[0409] H-chains and L-chains each contain an N-terminal variable region and a C-terminal constant region. The constant region consists of about 110 amino acids in L-chains and about 330 or 440 amino acids in H-chains. The amino acid sequence of the constant region is nearly identical among H- or L-chains of a particular class. The variable region consists of about 110 amino acids in both H- and L-chains. However, the amino acid sequence of the variable region differs among H- or L-chains of a particular class. Within each H- or L-chain variable region are three hypervariable regions of extensive sequence diversity, each consisting of about 5 to 10 amino acids. In the antibody molecule, the H- and L-chain hypervariable regions come together to form the antigen recognition site. (Reviewed in Alberts, supra, pp. 1206-1213 and 1216-1217.)

[0410] Both H-chains and L-chains contain repeated Ig domains. For example, a typical H-chain contains four Ig domains, three of which occur within the constant region and one of which occurs within the variable region and contributes to the formation of the antigen recognition site. Likewise, a typical L-chain contains two Ig domains, one of which occurs within the constant region and one of which occurs within the variable region.

[0411] The immune system is capable of recognizing and responding to any foreign molecule that enters the body. Therefore, the immune system must be armed with a full repertoire of antibodies against all potential antigens. Such antibody diversity is generated by somatic rearrangement of gene segments encoding variable and constant regions. These gene segments are joined together by site-specific recombination which occurs between highly conserved DNA sequences that flank each gene segment. Because there are hundreds of different gene segments, millions of unique genes can be generated combinatorially. In addition, imprecise joining of these segments and an unusually high rate of somatic mutation within these segments further contribute to the generation of a diverse antibody population.

[0412] T-cell receptors are both structurally and functionally related to antibodies. (Reviewed in Alberts, supra, pp. 1228-1229.) T-cell receptors are cell surface proteins that bind foreign antigens and mediate diverse aspects of the immune response. A typical T-cell receptor is a heterodimer comprised of two disulfide-linked polypeptide chains called α and β. Each chain is about 280 amino acids in length and contains one variable region and one constant region. Each variable or constant region folds into an Ig domain. The variable regions from the α and β chains come together in the heterodimer to form the antigen recognition site. T-cell receptor diversity is generated by somatic rearrangement of gene segments encoding the α and β chains. T-ell receptors recognize small peptide antigens that are expressed on the surface of antigen-presenting cells and pathogen-infected cells. These peptide antigens are presented on the cell surface in association with major histocompatibility proteins which provide the proper context for antigen recognition.

[0413] Secreted and Extracellular Matrix Molecules

[0414] Protein secretion is essential for cellular function. Protein secretion is mediated by a signal peptide located at the amino terminus of the protein to be secreted. The signal peptide is comprised of about ten to twenty hydrophobic amino acids which target the nascent protein from the ribosome to the endoplasmic reticulum (ER). Proteins targeted to the ER may either proceed through the secretory pathway or remain in any of the secretory organelles such as the ER, Golgi apparatus, or lysosomes. Proteins that transit through the secretory pathway are either secreted into the extracellular space or retained in the plasma membrane. Secreted proteins are often synthesized as inactive precursors that are activated by post-translational processing events during transit through the secretory pathway. Such events include glycosylation, proteolysis, and removal of the signal peptide by a signal peptidase. Other events that may occur during protein transport include chaperone-dependent unfolding and folding of the nascent protein and interaction of the protein with a receptor or pore complex. Examples of secreted proteins with amino terminal signal peptides include receptors, extracellular matrix molecules, cytokines, hormones, growth and differentiation factors, neuropeptides, vasomediators, ion channels, transporters/pumps, and proteases. (Reviewed in Alberts, B. et al. (1994) Molecular Biology of The Cell, Garland Publishing, New York N.Y., pp. 557-560, 582-592.)

[0415] The extracellular matrix (ECM) is a complex network of glycoproteins, polysaccharides, proteoglycans, and other macromolecules that are secreted from the cell into the extracellular space. The ECM remains in close association with the cell surface and provides a supportive meshwork that profoundly influences cell shape, motility, strength, flexibility, and adhesion. In fact, adhesion of a cell to its surrounding matrix is required for cell survival except in the case of metastatic tumor cells, which have overcome the need for cell-ECM anchorage. This phenomenon suggests that the ECM plays a critical role in the molecular mechanisms of growth control and metastasis. (Reviewed in Ruoslahti, E. (1996) Sci. Am. 275:72-77.) Furthermore, the ECM determines the structure and physical properties of connective tissue and is particularly important for morphogenesis and other processes associated with embryonic development and pattern formation.

[0416] The collagens comprise a family of ECM proteins that provide structure to bone, teeth, skin, ligaments, tendons, cartilage, blood vessels, and basement membranes. Multiple collagen proteins have been identified. Three collagen molecules fold together in a triple helix stabilized by interchain disulfide bonds. Bundles of these triple helices then associate to form fibrils. Collagen primary structure consists of hundreds of (Gly-X-Y) repeats where about a third of the X and Y residues are Pro. Glycines are crucial to helix formation as the bulkier amino acid sidechains cannot fold into the triple helical conformation. Because of these strict sequence requirements, mutations in collagen genes have severe consequences. Osteogenesis imperfecta patients have brittle bones that fracture easily; in severe cases patients die in utero or at birth. Ehlers-Danlos syndrome patients have hyperelastic skin, hypermobile joints, and susceptibility to aortic and intestinal rupture. Chondrodysplasia patients have short stature and ocular disorders. Alport syndrome patients have hematuria, sensorineural deafness, and eye lens deformation. (Isselbacher, K. J. et al. (1994) Harrison's Principles of Internal Medicine, McGraw-Hill, Inc., New York N.Y., pp. 2105-2117; and Creighton, T. E. (1984) Proteins, Structures and Molecular Principles, W.H. Freeman and Company, New York N.Y., pp. 191-197.)

[0417] Elastin and related proteins confer elasticity to tissues such as skin, blood vessels, and lungs. Elastin is a highly hydrophobic protein of about 750 amino acids that is rich in proline and glycine residues. Elastin molecules are highly cross-liked, forming an extensive extracellular network of fibers and sheets. Elastin fibers are surrounded by a sheath of microfibrils which are composed of a number of glycoproteins, including fibrillin Mutations in the gene encoding fibrillin are responsible for Marfan's syndrome, a genetic disorder characterized by defects in connective tissue. In severe cases, the aortas of afflicted individuals are prone to rupture. (Reviewed in Alberts, supra, pp. 984-986.)

[0418] Fibronectin is a large ECM glycoprotein found in all vertebrates. Fibronectin exists as a dimer of two subunits, each containing about 2,500 amino acids. Each subunit folds into a rod-like structure containing multiple domains. The domains each contain multiple repeated modules, the most common of which is the type III fibronectin repeat. The type III fibronectin repeat is about 90 amino acids in length and is also found in other ECM proteins and in some plasma membrane and cytoplasmic proteins. Furthermore, some type III fibronectin repeats contain a characteristic tripeptide consisting of Arginine-Glycine-Aspartic acid (RGD). The RGD sequence is recognized by the integrin family of cell surface receptors and is also found in other ECM proteins. Disruption of both copies of the gene encoding fibronectin causes early embryonic lethality in mice. The mutant embryos display extensive morphological defects, including defects in the formation of the notochord, somites, heart, blood vessels, neural tube, and extraembryonic structures. (Reviewed in Alberts, supra, pp. 986-987.)

[0419] Laminin is a major glycoprotein component of the basal lamina which underlies and supports epithelial cell sheets. Laminin is one of the first ECM proteins synthesized in the developing embryo. Laminin is an 850 kilodalton protein composed of three polypeptide chains joined in the shape of a cross by disulfide bonds. Laminin is especially important for angiogenesis and in particular, for guiding the formation of capillaries. (Reviewed in Alberts, supra, pp. 990-991.)

[0420] There are many other types of proteinaceous ECM components, most of which can be classified as proteoglycans. Proteoglycans are composed of unbranched polysaccharide chains (glycosaminoglycans) attached to protein cores. Common proteoglycans include aggrecan, betaglycan, decorin, perlecan, serglycin, and syndecan-1. Some of these molecules not only provide mechanical support, but also bind to extracellular signaling molecules, such as fibroblast growth factor and transforming growth factor A, suggesting a role for proteoglycans in cell-cell communication and cell growth. (Reviewed in Alberts, supra, pp. 973-978.) Likewise, the glycoproteins tenascin-C and tenascin-R are expressed in developing and lesioned neural tissue and provide stimulatory and anti-adhesive (inhibitory) properties, respectively, for axonal growth. (Faissner, A. (1997) Cell Tissue Res. 290:331-341.)

[0421] Cytoskeletal Molecules

[0422] The cytoskeleton is a cytoplasmic network of protein fibers that mediate cell shape, structure, and movement. The cytoskeleton supports the cell membrane and forms tracks along which organelles and other elements move in the cytosol. The cytoskeleton is a dynamic structure that allows cells to adopt various shapes and to carry out directed movements. Major cytoskeletal fibers include the microtubules, the microfilaments, and the intermediate filaments. Motor proteins, including myosin, dynein, and kinesin, drive movement of or along the fibers. The motor protein dynamin drives the formation of membrane vesicles. Accessory or associated proteins modify the structure or activity of the fibers while cytoskeletal membrane anchors connect the fibers to the cell membrane.

[0423] Tubulins

[0424] Microtubules, cytoskeletal fibers with a diameter of about 24 nm, have multiple roles in the cell Bundles of microtubules form cilia and flagella, which are whip-like extensions of the cell membrane that are necessary for sweeping materials across an epithelium and for swimming of sperm, respectively. Marginal bands of microtubules in red blood cells and platelets are important for these cells' pliability. Organelles, membrane vesicles, and proteins are transported in the cell along tracks of microtubules. For example, microtubules run through nerve cell axons, allowing bi-directional transport of materials and membrane vesicles between the cell body and the nerve terminal. Failure to supply the nerve terminal with these vesicles blocks the transmission of neural signals. Microtubules are also critical to chromosomal movement during cell division. Both stable and short-lived populations of microtubules exist in the cell.

[0425] Microtubules are polymers of GTP-binding tubulin protein subunits. Each subunit is a heterodimer of α- and β-tubulin, multiple isoforms of which exist. The hydrolysis of GTP is linked to the addition of tubulin subunits at the end of a microtubule. The subunits interact head to tail to form protofilaments; the protofilaments interact side to side to form a microtubule. A microtubule is polarized, one end ringed with α-tubulin and the other with β-tubulin, and the two ends differ in their rates of assembly. Generally, each microtubule is composed of 13 protofilaments although 11 or 15 protofilament-microtubules are sometimes found. Cilia and flagella contain doublet microtubules. Microtubules grow from specialized structures known as centrosomes or microtubule-organizing centers (MTOCs). MTOCs may contain one or two centrioles, which are pinwheel arrays of triplet microtubules. The basal body, the organizing center located at the base of a cilium or flagellum, contains one centriole. Gamma tubulin present in the MTOC is important for nucleating the polymerization of α- and β-tubulin heterodimers but does not polymerize into microtubules.

[0426] Microtubule-Associated Proteins

[0427] Microtubule-associated proteins (MAPs) have roles in the assembly and stabilization of microtubules. One major family of MAPs, assembly MAPs, can be identified in neurons as well as non-neuronal cells. Assembly MAPs are responsible for cross-linking microtubules in the cytosol. These MAPs are organized into two domains: a basic microtubule-binding domain and an acidic projection domain. The projection domain is the binding site for membranes, intermediate filaments, or other microtubules. Based on sequence analysis, assembly MAPs can be further grouped into two types: Type I and Type II. Type I MAPs, which include MAP1A and MAP1B, are large, filamentous molecules that co-purify with microtubules and are abundantly expressed in brain and testes. Type I MAPs contain several repeats of a positively-charged amino acid sequence motif that binds and neutralizes negatively charged tubulin, leading to stabilization of microtubules. MAP1A and MAP1B are each derived from a single precursor polypeptide that is subsequently proteolytically processed to generate one heavy chain and one light chain.

[0428] Another light chain, LC3, is a 16.4 kDa molecule that binds MAP1A, MAP1B, and microtubules. It is suggested that LC3 is synthesized from a source other than the MAP1A or MAP1B transcripts, and that the expression of LC3 may be important in regulating the microtubule binding activity of MAP1A and MAP1B during cell proliferation (Mann, S. S. et al. (1994) J. Biol. Chem. 269:11492-11497).

[0429] Type II MAPs, which include MAP2a, MAP2b, MAP2c, MAP4, and Tau, are characterized by three to four copies of an 18-residue sequence in the microtubule-binding domain. MAP2a, MAP2b, and MAP2c are found only in dendrites, MAP4 is found in non-neuronal cells, and Tau is found in axons and dendrites of nerve cells. Alternative splicing of the Tau mRNA leads to the existence of multiple forms of Tau protein. Tau phosphorylation is altered in neurodegenerative disorders such as Alzheimer's disease, Pick's disease, progressive supranuclear palsy, corticobasal degeneration, and familial frontotemporal dementia and Parkinsonism linked to chromosome 17. The altered Tau phosphorylation leads to a collapse of the microtubule network and the formation of intraneuronal Tau aggregates (Spillantini, M. G. and M. Goedert (1998) Trends Neurosci. 21:428-433).

[0430] The protein pericentrin is found in the MTOC and has a role in microtubule assembly.

[0431] Actins

[0432] Microfilaments, cytoskeletal filaments with a diameter of about 7-9 nm, are vital to cell locomotion, cell shape, cell adhesion, cell division, and muscle contraction. Assembly and disassembly of the microfilaments allow cells to change their morphology. Microfilaments are the polymerized form of actin, the most abundant intracellular protein in the eukaryotic cell. Human cells contain six isoforms of actin. The three α-actins are found in different kinds of muscle, nonmuscle β-actin and nonmuscle γ-actin are found in nonmuscle cells, and another γ-actin is found in intestinal smooth muscle cells. G-actin, the monomeric form of actin, polymerizes into polarized, helical F-actin filaments, accompanied by the hydrolysis of ATP to ADP. Actin filaments associate to form bundles and networks, providing a framework to support the plasma membrane and determine cell shape. These bundles and networks are connected to the cell membrane. In muscle cells, thin filaments containing actin slide past thick filaments containing the motor protein myosin during contraction. A family of actin-related proteins exist that are not part of the actin cytoskeleton, but rather associate with microtubules and dynein.

[0433] Actin-Associated Proteins

[0434] Actin-associated proteins have roles in cross-lining, severing, and stabilization of actin filaments and in sequestering actin monomers. Several of the actin-associated proteins have multiple functions. Bundles and networks of actin filaments are held together by actin cross-linking proteins. These proteins have two actin-binding sites, one for each filament. Short cross-lining proteins promote bundle formation while longer, more flexible cross-linking proteins promote network formation. Calmodulin-like calcium-binding domains in actin cross-lining proteins allow calcium regulation of cross-linking. Group I cross-liking proteins have unique actin-binding domains and include the 30 kD protein, EF-1a, fascin, and scruin. Group II cross-linking proteins have a 7,000-MW actin-binding domain and include villin and dematin. Group III cross-linking proteins have pairs of a 26,000-MW actin-binding domain and include fimbrin, spectrin, dystrophin, ABP 120, and filamin.

[0435] Severing proteins regulate the length of actin filaments by breaking them into short pieces or by blocking their ends. Severing proteins include gCAP39, severin (fragmin), gelsolin, and villin. Capping proteins can cap the ends of actin filaments, but cannot break filaments. Capping proteins include CapZ and tropomodulin. The proteins thymosin and profilin sequester actin monomers in the cytosol, allowing a pool of unpolymerized actin to exist. The actin-associated proteins tropomyosin, troponin, and caldesmon regulate muscle contraction in response to calcium.

[0436] Intermediate Filaments and Associated Proteins

[0437] Intermediate filaments (IFs) are cytoskeletal fibers with a diameter of about 10 nm, intermediate between that of microfilaments and microtubules. IFs serve structural roles in the cell, reinforcing cells and organizing cells into tissues. IFs are particularly abundant in epidermal cells and in neurons. IFs are extremely stable, and, in contrast to microfilaments and microtubules, do not function in cell motility.

[0438] Five types of IF proteins are known in mammals. Type I and Type II proteins are the acidic and basic keratins, respectively. Heterodimers of the acidic and basic keratins are the building blocks of keratin IFs. Keratins are abundant in soft epithelia such as skin and cornea, hard epithelia such as nails and hair, and in epithelia that line internal body cavities. Mutations in keratin genes lead to epithelial diseases including epidermolysis bullosa simplex, bullous congenital ichthyosiform erythroderma (epidermolytic hyperkeratosis), non-epidermolytic and epidermolytic palmoplantar keratoderma, ichthyosis bullosa of Si{dot over (e)}mens, pachyonychia congenita, and white sponge nevus. Some of these diseases result in severe skin blistering. (See, e.g., Wawersik, M. et al. (1997) J. Biol. Chem. 272:32557-32565; and Corden L. D. and W. H. McLean (1996) Exp. Dermatol. 5:297-307.)

[0439] Type III IF proteins include desmin, glial fibrillary acidic protein, vimentin, and peripherin. Desmin filaments in muscle cells link myofibrils into bundles and stabilize sarcomeres in contracting muscle. Glial fibrillary acidic protein filaments are found in the glial cells that surround neurons and astrocytes. Vimentin filaments are found in blood vessel endothelial cells, some epithelial cells, and mesenchymal cells such as fibroblasts, and are commonly associated with microtubules. Vimentin filaments may have roles in keeping the nucleus and other organelles in place in the cell. Type IV IFs include the neurofilaments and nestin. Neurofilaments, composed of three polypeptides NF-L, NF-M, and NF-H, are frequently associated with microtubules in axons. Neurofilaments are responsible for the radial growth and diameter of an axon, and ultimately for the speed of nerve impulse transmission. Changes in phosphorylation and metabolism of neurofilaments are observed in neurodegenerative diseases including amyotrophic lateral sclerosis, Parknson's disease, and Alzheimer's disease (Julien, J. P. and W. E. Mushynski (1998) Prog. Nucleic Acid Res. Mol. Biol. 61:1-23). Type V IFs, the lamins, are found in the nucleus where they support the nuclear membrane.

[0440] IFs have a central α-helical rod region interrupted by short nonhelical linker segments. The rod region is bracketed, in most cases, by non-helical head and tail domains. The rod regions of intermediate filament proteins associate to form a coiled-coil dimer. A highly ordered assembly process leads from the dimers to the IFs. Neither ATP nor GTP is needed for IF assembly, unlike that of microfilaments and microtubules.

[0441] IF-associated proteins (IFAPs) mediate the interactions of IFs with one another and with other cell structures. IFAPs cross-link IFs into a bundle, into a network, or to the plasma membrane, and may cross-link IFs to the microfilament and microtubule cytoskeleton. Microtubules and IFs are in particular closely associated. IFAPs include BPAG1, plakoglobin, desmoplakin I, desmoplakin II, plectin, ankyrin, filaggrin, and lamin B receptor.

[0442] Cytoskeletal-Membrane Anchors

[0443] Cytoskeletal fibers are attached to the plasma membrane by specific proteins. These attachments are important for maintaining cell shape and for muscle contraction. In erythrocytes, the spectrin-actin cytoskeleton is attached to cell membrane by three proteins, band 4.1, ankyrn, and adducin. Defects in this attachment result in abnormally shaped cells which are more rapidly degraded by the spleen, leading to anemia. In platelets, the spectrin-actin cytoskeleton is also linked to the membrane by ankyrin; a second actin network is anchored to the membrane by filamin. In muscle cells the protein dystrophin links actin filaments to the plasma membrane; mutations in the dystrophin gene lead to Duchenne muscular dystrophy. In adherens junctions and adhesion plaques the peripheral membrane proteins α-actinin and vinculin attach actin filaments to the cell membrane.

[0444] IFs are also attached to membranes by cytoskeletal-membrane anchors. The nuclear lamina is attached to the inner surface of the nuclear membrane by the lamin B receptor. Vimentin IFs are attached to the plasma membrane by ankyrin and plectin. Desmosome and hemidesmosome membrane junctions hold together epithelial cells of organs and skin. These membrane junctions allow shear forces to be distributed across the entire epithelial cell layer, thus providing strength and rigidity to the epithelium. IFs in epithelial cells are attached to the desmosome by plakoglobin and desmoplakins. The proteins that link IFs to hemidesmosomes are not known. Desmin IFs surround the sarcomere in muscle and are linked to the plasma membrane by paranemin, synemin, and ankyrin.

[0445] Myosin-Related Motor Proteins

[0446] Myosins are actin-activated ATPases, found in eukaryotic cells, that couple hydrolysis of ATP with motion. Myosin provides the motor function for muscle contraction and intracellular movements such as phagocytosis and rearrangement of cell contents during mitotic cell division (cytokinesis). The contractile unit of skeletal muscle, termed the sarcomere, consists of highly ordered arrays of thin actin-containing filaments and thick myosin-containing filaments. Crossbridges form between the thick and thin filaments, and the ATP-dependent movement of myosin heads within the thick filaments pulls the thin filaments, shortening the sarcomere and thus the muscle fiber.

[0447] Myosins are composed of one or two heavy chains and associated light chains. Myosin heavy chains contain an amino-terminal motor or head domain, a neck that is the site of light-chain binding, and a carboxy-terminal tail domain. The tail domains may associate to form an α-helical coiled coil. Conventional myosins, such as those found in muscle tissue, are composed of two myosin heavy-chain subunits, each associated with two light-chain subunits that bind at the neck region and play a regulatory role. Unconventional myosins, believed to function in intracellular motion, may contain either one or two heavy chains and associated light chains. There is evidence for about 25 myosin heavy chain genes in vertebrates, more than half of them unconventional.

[0448] Dynein-Related Motor Proteins

[0449] Dyneins are (−) end-directed motor proteins which act on microtubules. Two classes of dyneins, cytosolic and axonemal, have been identified. Cytosolic dyneins are responsible for translocation of materials along cytoplasmic microtubules, for example, transport from the nerve terminal to the cell body and transport of endocytic vesicles to lysosomes. Cytoplasmic dyneins are also reported to play a role in mitosis. Axonemal dyneins are responsible for the beating of flagella and cilia. Dynein on one microtubule doublet walks along the adjacent microtubule doublet. This sliding force produces bending forces that cause the flagellum or cilium to beat Dyneins have a native mass between 1000 and 2000 kDa and contain either two or three force-producing heads driven by the hydrolysis of ATP. The heads are linked via stalks to a basal domain which is composed of a highly variable number of accessory intermediate and light chains.

[0450] Kinesin-Related Motor Proteins

[0451] Kinesins are (+) end-directed motor proteins which act on microtubules. The prototypical kinesin molecule is involved in the transport of membrane-bound vesicles and organelles. This function is particularly important for axonal transport in neurons. Kinesin is also important in all cell types for the transport of vesicles from the Golgi complex to the endoplasmic reticulum. This role is critical for maintaining the identity and functionality of these secretory organelles.

[0452] Kinesins define a ubiquitous, conserved family of over 50 proteins that can be classified into at least 8 subfamilies based on primary amino acid sequence, domain structure, velocity of movement, and cellular function. Reviewed in Moore, J. D. and S. A. Endow (1996) Bioessays 18:207-219; and Hoyt, A. M. (1994) Curr. Opin. Cell Biol. 6:63-68.) The prototypical kinesin molecule is a heterotetramer comprised of two heavy polypeptide chains (KHCs) and two light polypeptide chains (KLCs). The KHC subunits are typically referred to as “kinesin.” KHC is about 1000 amino acids in length, and KLC is about 550 amino acids in length. Two KHCs dimerize to form a rod-shaped molecule with three distinct regions of secondary structure. At one end of the molecule is a globular motor domain that functions in ATP hydrolysis and microtubule binding. Kinesin motor domains are highly conserved and share over 70% identity. Beyond the motor domain is an α-helical coiled-coil region which mediates dimerization. At the other end of the molecule is a fan-shaped tail that associates with molecular cargo. The tail is formed by the interaction of the KHC C-termini with the two KLCs.

[0453] Members of the more divergent subfamilies of kinesins are called kinesin-related proteins (KRPs), many of which function during mitosis in eukaryotes (Hoyt, supra). Some KRPs are required for assembly of the mitotic spindle. In vivo and in vitro analyses suggest that these KRPs exert force on microtubules that comprise the mitotic spindle, resulting in the separation of spindle poles. Phosphorylation of KRP is required for this activity. Failure to assemble the mitotic spindle results in abortive mitosis and chromosomal aneuploidy, the latter condition being characteristic of cancer cells. In addition, a unique KRP, centromere protein E, localizes to the kinetochore of human mitotic chromosomes and may play a role in their segregation to opposite spindle poles.

[0454] Dynamin-Related Motor Proteins

[0455] Dynamin is a large GTPase motor protein that functions as a “molecular pinchase,” generating a mechanochemical force used to sever membranes. This activity is important in forming clathrin-coated vesicles from coated pits in endocytosis and in the biogenesis of synaptic vesicles in neurons. Binding of dynamin to a membrane leads to dynamin's self-assembly into spirals that may act to constrict a flat membrane surface into a tubule. GTP hydrolysis induces a change in conformation of the dynamin polymer that pinches the membrane tubule, leading to severing of the membrane tubule and formation of a membrane vesicle. Release of GDP and inorganic phosphate leads to dynamin disassembly. Following disassembly the dynamin may either dissociate from the membrane or remain associated to the vesicle and be transported to another region of the cell. Three homologous dynamin genes have been discovered, in addition to several dynamin-related proteins. Conserved dynamin regions are the N-terminal GTP-binding domain, a central pleckstrin homology domain that binds membranes, a central coiled-coil region that may activate dynamin's GTPase activity, and a C-terminal proline-rich domain that contains several motifs that bind SH3 domains on other proteins. Some dynamin-related proteins do not contain the pleckstrin homology domain or the proline-rich domain (See McNiven, M. A. (1998) Cell 94:151-154; Scaife, R. M. and R. L. Margolis (1997) Cell. Signal. 9:395-401.)

[0456] The cytoskeleton is reviewed in Lodish, H. et al. (1995) Molecular Cell Biology, Scientific American Books, New York N.Y.

[0457] Ribosomal Molecules

[0458] Ribosomal RNAs (rRNAs) are assembled, along with ribosomal proteins, into ribosomes, which are cytoplasmic particles that translate messenger RNA into polypeptides. The eukaryotic ribosome is composed of a 60S (large) subunit and a 40S (small) subunit, which together form the 80S ribosome. In addition to the 18S, 28S, 5S, and 5.8S rRNAs, the ribosome also contains more than fifty proteins. The ribosomal proteins have a prefix which denotes the subunit to which they belong, either L (large) or S (small). Ribosomal protein activities include binding rRNA and organizing the conformation of the junctions between rRNA helices (Woodson, S. A. and N. B. Leontis (1998) Curr. Opin. Struct. Biol. 8:294-300; Ramakrishnan, V. and S. W. White (1998) Trends Biochem. Sci. 23:208-212.) Three important sites are identified on the ribosome. The aminoacyl-tRNA site (A site) is where charged tRNAs, (with the exception of the initiator-tRNA) bind on arrival at the ribosome. The peptidyl-tRNA site (P site) is where new peptide bonds are formed, as well as where the initiator tRNA binds. The exit site (E site) is where deacylated tRNAs bind prior to their release from the ribosome. (The ribosome is reviewed in Stryer, L. (1995) Biochemistry W.H. Freeman and Company, New York N.Y., pp. 888-908; and Lodish, H. et al. (1995) Molecular Cell Biology Scientific American Books, New York N.Y. pp. 119-138.)

[0459] Chromatin Molecules

[0460] The nuclear DNA of eukaryotes is organized into chromatin. Two types of chromatin are observed: euchromatin, some of which may be transcribed, and heterochromatin so densely packed that much of it is inaccessible to transcription. Chromatin packing thus serves to regulate protein expression in eukaryotes. Bacteria lack chromatin and the chromatin-packing level of gene regulation.

[0461] The fundamental unit of chromatin is the nucleosome of 200 DNA base pairs associated with two copies each of histones H2A, H2B, H3, and H4. Adjascent nucleosomes are linked by another class of histones, H1. Low molecular weight non-histone proteins called the high mobility group (HMG), associated with chromatin, may function in the unwinding of DNA and stabilization of single-stranded DNA. Chromodomain proteins function in compaction of chromatin into its transcriptionally silent heterochromatin form.

[0462] During mitosis, all DNA is compacted into heterochromatin and transcription ceases. Transcription in interphase begins with the activation of a region of chromatin. Active chromatin is decondensed. Decondensation appears to be accompanied by changes in binding coefficient, phosphorylation and acetylation states of chromatin histones. HMG proteins HMG13 and HMG17 selectively bind activated chromatin. Topoisomerases remove superhelical tension on DNA. The activated region decondenses, allowing gene regulatory proteins and transcription factors to assemble on the DNA.

[0463] Patterns of chromatin structure can be stably inherited, producing heritable patterns of gene expression. In mammals, one of the two X chromosomes in each female cell is inactivated by condensation to heterochromatin during zygote development. The inactive state of this chromosome is inherited, so that adult females are mosaics of clusters of paternal-X and maternal-X clonal cell groups. The condensed X chromosome is reactivated in meiosis.

[0464] Chromatin is associated with disorders of protein expression such as thalassemia, a genetic anemia resulting from the removal of the locus control region (LCR) required for decondensation of the globin gene locus.

[0465] For a review of chromatin structure and function see Alberts, B. et al. (1994) Molecular Cell Biology, third edition, Garland Publishing, Inc., New York N.Y., pp. 351-354, 433-439.

[0466] Electron Transfer Associated Molecules

[0467] Electron carriers such as cytochromes accept electrons from NADH or FADH2 and donate them to other electron carriers. Most electron-transferring proteins, except ubiquinone, are prosthetic groups such as flavins, heme, FeS clusters, and copper, bound to inner membrane proteins. Adrenodoxin, for example, is an FeS protein that forms a complex with NADPH:adrenodoxin reductase and cytochrome p450. Cytochromes contain a heme prosthetic group, a porphyrin ring containing a tightly bound iron atom. Electron transfer reactions play a crucial role in cellular energy production.

[0468] Energy is produced by the oxidation of glucose and fatty acids. Glucose is initially converted to pyruvate in the cytoplasm. Fatty acids and pyruvate are transported to the mitochondria for complete oxidation to CO2 coupled by enzymes to the transport of electrons from NADH and FADH2 to oxygen and to the synthesis of ATP (oxidative phosphorylation) from ADP and Pi.

[0469] Pyruvate is transported into the mitochondria and converted to acetyl-CoA for oxidation via the citric acid cycle, involving pyruvate dehydrogenase components, dihydrolipoyl transacetylase, and dihydrolipoyl dehydrogenase. Enzymes involved in the citric acid cycle include: citrate synthetase, aconitases, isocitrate dehydrogenase, alpha-ketoglutarate dehydrogenase complex including transsuccinylases, succinyl CoA synthetase, succinate dehydrogenase, fumarases, and malate dehydrogenase. Acetyl CoA is oxidized to CO2 with concomitant formation of NADH, FADH2, and GTP. In oxidative phosphorylation, the transfer of electrons from NADH and FADH2 to oxygen by dehydrogenases is coupled to the synthesis of ATP from ADP and Pi by the F0F1 ATPase complex in the mitochondrial inner membrane. Enzyme complexes responsible for electron transport and ATP synthesis include the F0F1, ATPase complex, ubiquinone(CoQ)-cytochrome c reductase, ubiquinone reductase, cytochrome b, cytochrome c1, FeS protein, and cytochrome c oxidase.

[0470] ATP synthesis requires membrane transport enzymes including the phosphate transporter and the ATP-ADP antiport protein. The ATP-binding casette (ABC) superfamily has also been suggested as belonging to the mitochondrial transport group (Hogue, D. L. et al. (1999) J. Mol. Biol. 285:379-399). Brown fat uncoupling protein dissipates oxidative energy as heat, and may be involved the fever response to infection and trauma (Cannon, B. et al. (1998) Ann. NY Acad. Sci. 856:171-187).

[0471] Mitochondria are oval-shaped organelles comprising an outer membrane, a tightly folded inner membrane, an intermembrane space between the outer and inner membranes, and a matrix inside the inner membrane. The outer membrane contains many porin molecules that allow ions and charged molecules to enter the intermembrane space, while the inner membrane contains a variety of transport proteins that transfer only selected molecules. Mitochondria are the primary sites of energy production in cells.

[0472] Mitochondria contain a small amount of DNA. Human mitochondrial DNA encodes 13 proteins, 22 tRNAs, and 2 rRNAs. Mitochondrial-DNA encoded proteins include NADH-Q reductase, a cytochrome reductase subunit, cytochrome oxidase subunits, and ATP synthase subunits.

[0473] Electron-transfer reactions also occur outside the mitochondria in locations such as the endoplasmic reticulum, which plays a crucial role in lipid and protein biosynthesis. Cytochrome b5 is a central electron donor for various reductive reactions occurring on the cytoplasmic surface of liver endoplasmic reticulum. Cytochrome b5 has been found in Golgi, plasma, endoplasmic reticulum (ER), and microbody membranes.

[0474] For a review of mitochondrial metabolism and regulation, see Lodish, H. et al. (1995) Molecular Cell Biology, Scientific American Books, New York N.Y., pp. 745-797 and Stryer (1995) Biochemistry, W.H. Freeman and Co., San Francisco Calif., pp 529-558, 988-989.

[0475] The majority of mitochondrial proteins are encoded by nuclear genes, are synthesized on cytosolic ribosomes, and are imported into the mitochondria Nuclear-encoded proteins which are destined for the mitochondrial matrix typically contain positively-charged amino terminal signal sequences. Import of these preproteins from the cytoplasm requires a multisubunit protein complex in the outer membrane known as the translocase of outer mitochondrial membrane (TOM; previously designated MOM; Pfanner, N. et al. (1996) Trends Biochem. Sci. 21:51-52) and at least three inner membrane proteins which comprise the translocase of inner mitochondrial membrane TIM; previously designated MIM; Pfanner, supra). An inside-negative membrane potential across the inner mitochondrial membrane is also required for preprotein import. Preproteins are recognized by surface receptor components of the TOM complex and are translocated through a proteinaceous pore formed by other TOM components. Proteins targeted to the matrix are then recognized by the import machinery of the TIM complex. The import systems of the outer and inner membranes can function independently (Segui-Real, B. et al. (1993) EMBO J. 12:2211-2218).

[0476] Once precursor proteins are in the mitochondria, the leader peptide is cleaved by a signal peptidase to generate the mature protein. Most leader peptides are removed in a one step process by a protease termed mitochondrial processing peptidase (MPP) (Paces, V. et al. (1993) Proc. Natl. Acad. Sci. USA 90:5355-5358). In some cases a two-step process occurs in which MPP generates an intermediate precursor form which is cleaved by a second enzyme, mitochondrial intermediate peptidase, to generate the mature protein.

[0477] Mitochondrial dysfunction leads to impaired calcium buffering, generation of free radicals that may participate in deleterious intracellular and extracellular processes, changes in mitochondrial permeability and oxidative damage which is observed in several neurodegenerative diseases. Neurodegenerative diseases linked to mitochondrial dysfunction include some forms of Alzheimer's disease, Friedreich's ataxia, familial amyotrophic lateral sclerosis, and Huntington's disease (Beal, M. F. (1998) Biochim. Biophys. Acta 1366:211-213). The myocardium is heavily dependent on oxidative metabolism, so mitochondrial dysfunction often leads to heart disease (DiMauro, S. and M. Hirano (1998) Curr. Opin. Cardiol 13:190-197). Mitochondria are implicated in disorders of cell proliferation, since they play an important role in a cell's decision to proliferate or self-destruct through apoptosis. The oncoprotein Bcl-2, for example, promotes cell proliferation by stabilizing mitochondrial membranes so that apoptosis signals are not released (Susin, S. A. (1998) Biochim. Biophys. Acta 1366:151-165).

[0478] Transcription Factor Molecules

[0479] Multicellular organisms are comprised of diverse cell types that differ dramatically both in structure and function. The identity of a cell is determined by its characteristic pattern of gene expression, and different cell types express overlapping but distinctive sets of genes throughout development. Spatial and temporal regulation of gene expression is critical for the control of cell proliferation, cell differentiation, apoptosis, and other processes that contribute to organismal development. Furthermore, gene expression is regulated in response to extracellular signals that mediate cell-cell communication and coordinate the activities of different cell types. Appropriate gene regulation also ensures that cells function efficiently by expressing only those genes whose functions are required at a given time.

[0480] Transcriptional regulatory proteins are essential for the control of gene expression. Some of these proteins function as transcription factors that initiate, activate, repress, or terminate gene transcription. Transcription factors generally bind to the promoter, enhancer, and upstream regulatory regions of a gene in a sequence-specific manner, although some factors bind regulatory elements within or downstream of a gene's coding region. Transcription factors may bind to a specific region of DNA singly or as a complex with other accessory factors. (Reviewed in Lewin, B. (1990) Genes IV, Oxford University Press, New York N.Y., and Cell Press, Cambridge Mass., pp. 554-570.)

[0481] The double helix structure and repeated sequences of DNA create topological and chemical features which can be recognized by transcription factors these features are hydrogen bond donor and acceptor groups, hydrophobic patches, major and minor grooves, and regular, repeated stretches of sequence which induce distinct bends in the helix. Typically, transcription factors recognize specific DNA sequence motifs of about 20 nucleotides in length. Multiple, adjacent transcription factor-binding motifs may be required for gene regulation.

[0482] Many transcription factors incorporate DNA-binding structural motifs which comprise either α helices or β sheets that bind to the major groove of DNA. Four well-characterized structural motifs are helix-turn-helix, zinc finger, leucine zipper, and helix-loop-helix. Proteins containing these motifs may act alone as monomers, or they may form homo- or heterodimers that interact with DNA.

[0483] The helix-turn-helix motif consists of two αhelices connected at a fixed angle by a short chain of amino acids. One of the helices binds to the major groove. Helix-turn-helix motifs are exemplified by the homeobox motif which is present in homeodomain proteins. These proteins are critical for specifying the anterior-posterior body axis during development and are conserved throughout the animal kingdom. The Antennapedia and Ultrabithorax proteins of Drosophila melanogaster are prototypical homeodomain proteins (Pabo, C. O. and R. T. Sauer (1992) Annu. Rev. Biochem. 61:1053-1095).

[0484] The zinc finger motif, which binds zinc ions, generally contains tandem repeats of about 30 amino acids consisting of periodically spaced cysteine and histidine residues. Examples of this sequence pattern, designated C2H2 and C3HC4 (“RING” finger), have been described (Lewin, supra. Zinc finger proteins each contain an α helix and an antiparallel β sheet whose proximity and conformation are maintained by the zinc ion. Contact with DNA is made by the arginine preceeding the α helix and by the second, third, and sixth residues of the α helix. Variants of the zinc finger motif include poorly defined cysteine-rich motifs which bind zinc or other metal ions. These motifs may not contain histidine residues and are generally nonrepetitive.

[0485] The leucine zipper motif comprises a stretch of amino acids rich in leucine which can form an amphipathic α helix. This structure provides the basis for dimerization of two leucine zipper proteins. The region adjacent to the leucine zipper is usually basic, and upon protein dimerization, is optimally positioned for binding to the major groove. Proteins containing such motifs are generally referred to as bZIP transcription factors.

[0486] The helix-loop-helix motif (HLH) consists of a short CL helix connected by a loop to a longer a helix. The loop is flexible and allows the two helices to fold back against each other and to bind to DNA. The transcription factor Myc contains a prototypical HLH motif.

[0487] Most transcription factors contain characteristic DNA binding motifs, and variations on the above motifs and new motifs have been and are currently being characterized (Faisst, S. and S. Meyer (1992) Nucleic Acids Res. 20:3-26).

[0488] Many neoplastic disorders in humans can be attributed to inappropriate gene expression. Malignant cell growth may result from either excessive expression of tumor promoting genes or insufficient expression of tumor suppressor genes (Cleary, M. L. (1992) Cancer Surv. 15:89-104). Chromosomal translocations may also produce chimeric loci which fuse the coding sequence of one gene with the regulatory regions of a second unrelated gene. Such an arrangement likely results in inappropriate gene transcription, potentially contributing to malignancy.

[0489] In addition, the immune system responds to infection or trauma by activating a cascade of events that coordinate the progressive selection, amplification, and mobilization of cellular defense mechanisms. A complex and balanced program of gene activation and repression is involved in this process. However, hyperactivity of the immune system as a result of improper or insufficient regulation of gene expression may result in considerable tissue or organ damage. This damage is well documented in immunological responses associated with arthritis, allergens, heart attack, stroke, and infections (Isselbacher, K. J. et al. (1996) Harrison's Principles of Internal Medicine, 13/e, McGraw Hill, Inc. and Teton Data Systems Software).

[0490] Furthermore, the generation of multicellular organisms is based upon the induction and coordination of cell differentiation at the appropriate stages of development. Central to this process is differential gene expression, which confers the distinct identities of cells and tissues throughout the body. Failure to regulate gene expression during development can result in developmental disorders. Human developmental disorders caused by mutations in zinc finger-type transcriptional regulators include: urogenenital developmental abnormalities associated with WT1; Greig cephalopolysyndactyly, Pallister-Hall syndrome, and postaxial polydactyly type A (GLI3); and Townes-Brocks syndrome, characterized by anal, renal, limb, and ear abnormalities (SALL1) (Engelkamp, D. and V. van Heyningen (1996) Curr. Opin. Genet. Dev. 6:334-342; Kohlhase, J. et al. (1999) Am. J. Hutn. Genet. 64:435-445).

[0491] Cell Membrane Molecules

[0492] Eukaryotic cells are surrounded by plasma membranes which enclose the cell and maintain an environment inside the cell that is distinct from its surroundings. In addition, eukaryotic organisms are distinct from prokaryotes in possessing many intracellular organelle and vesicle structures. Many of the metabolic reactions which distinguish eukaryotic biochemistry from prokaryotic biochemistry take place within these structures. The plasma membrane and the membranes surrounding organelles and vesicles are composed of phosphoglycerides, fatty acids, cholesterol, phospholipids, glycolipids, proteoglycans, and proteins. These components confer identity and functionality to the membranes with which they associate.

[0493] Integral Membrane Proteins

[0494] The majority of known integral membrane proteins are transmembrane proteins (TM) which are characterized by an extracellular, a transmembrane, and an intracellular domain. TM domains are typically comprised of 15 to 25 hydrophobic amino acids which are predicted to adopt an α-helical conformation. TM proteins are classified as bitopic (Types I and II) and polytopic (Types III and IV) (Singer, S. J. (1990) Annu. Rev. Cell Biol. 6:247-296). Bitopic proteins span the membrane once while polytopic proteins contain multiple membrane-spanning segments. TM proteins function as cell-surface receptors, receptor-interacting proteins, transporters of ions or metabolites, ion channels, cell anchoring proteins, and cell type-specific surface antigens.

[0495] Many membrane proteins (MPs) contain amino acid sequence motifs that target these proteins to specific subcellular sites. Examples of these motifs include PDZ domains, KDEL, RGD, NGR, and GSL sequence motifs, von Willebrand factor A (vWFA) domains, and EGP-like domains. RGD, NGR, and GSL motif-containing peptides have been used as drug delivery agents in targeted cancer treatment of tumor vasculature (Arap, W. et al. (1998) Science 279:377-380). Furthermore, MPS may also contain amino acid sequence motifs, such as the carbohydrate recognition domain (CRD), that mediate interactions with extracellular or intracellular molecules.

[0496] G-Protein Coupled Receptors

[0497] G-protein coupled receptors (GPCR) are a superfamily of integral membrane proteins which transduce extracelular signals. GPCRs include receptors for biogenic amines, lipid mediators of inflammation, peptide hormones, and sensory signal mediators. The structure of these highly-conserved receptors consists of seven hydrophobic transmembrane regions, an extracellular N-terminus, and a cytoplasmic C-terminus. Three extracellular loops alternate with three intracellular loops to link the seven transmembrane regions. Cysteine disulfide bridges connect die second and third extracellular loops. The most conserved regions of GPCRs are the transmembrane regions and the first two cytoplasmic loops. A conserved, acidic-Arg-aromatic residue triplet present in the second cytoplasmic loop may interact with G proteins. A GPCR consensus pattern is characteristic of most proteins belonging to this superfamily (ExPASy PROSITE document PS00237; and Watson, S. and S. Arkinstall (1994) The G-protein linked Receptor Facts Book, Academic Press, San Diego Calif., pp. 2-6). Mutations and changes in transcriptional activation of GPCR-encoding genes have been associated with neurological disorders such as schizophrenia, Parkinson's disease, Alzheimer's disease, drug addiction, and feeding disorders.

[0498] Scavenger Receptors

[0499] Macrophage scavenger receptors with broad ligand specificity may participate in the binding of low density lipoproteins (LDL) and foreign antigens. Scavenger receptors types I and II are trimeric membrane proteins with each subunit containing a small N-terminal intracellular domain, a transmembrane domain, a large extracellular domain, and a C-terminal cysteine-rich domain. The extracellular domain contains a short spacer region, an α-helical coiled-coil region, and a triple helical collagen-like region. These receptors have been shown to bind a spectrum of ligands, including chemically modified lipoproteins and albumin, polyribonucleotides, polysaccharides, phospholipids, and asbestos (Matsumoto, A. et al. (1990) Proc. Natl. Acad. Sci. USA 87:9133-9137; and Elomaa, O. et al (1995) Cell 80:603-609). The scavenger receptors are thought to play a key role in atherogenesis by mediating uptake of modified LDL in arterial walls, and in host defense by binding bacterial endotoxins, bacteria, and protozoa.

[0500] Tetraspan Family Proteins

[0501] The transmembrane 4 superfamily (TM4SF) or tetraspan family is a multigene family encoding type 1 ml integral membrane proteins (Wright, M. D. and M. G. Tomlinson (1994) Immunol. Today 15:588-594). The TM4SF is comprised of membrane proteins which traverse the cell membrane four times. Members of the TM4SF include platelet and endothelial cell membrane proteins, melanoma-associated antigens, leukocyte surface glycoproteins, colonal carcinoma antigens, tumor-associated antigens, and surface proteins of the schistosome parasites (Jankowski, S. A. (1994) Oncogene 9:1205-1211). Members of the TM4SF share about 25-30% amino acid sequence identity with one another.

[0502] A number of TM4SP members have been implicated in signal transduction, control of cell adhesion, regulation of cell growth and proliferation, including development and oncogenesis, and cell motility, including tumor cell metastasis. Expression of TM4SF proteins is associated with a variety of tumors and the level of expression maybe altered when cells are growing or activated.

[0503] Tumor Antigens

[0504] Tumor antigens are cell surface molecules that are differentially expressed in tumor cells relative to normal cells. Tumor antigens distinguish tumor cells immunologically from normal cells and provide diagnostic and therapeutic targets for human cancers (Takagi, S. et al. (1995) Int. J. Cancer 61:706-715; Liu, E. et al. (1992) Oncogene 7:1027-1032).

[0505] Leukocyte Antigens

[0506] Other types of cell surface antigens include those identified on leukocytic cells of the immune system. These antigens have been identified using systematic, monoclonal antibody (mAb)-based “shot gun, techniques. These techniques have resulted in the production of hundreds of mAbs directed against unknown cell surface leukocytic antigens. These antigens have been grouped into “clusters of differentiation” based on common immunocytochemical localization patterns in various differentiated and undifferentiated leukocytic cell types. Antigens in a given cluster are presumed to identify a single cell surface protein and are assigned a “cluster of differentiation” or “CD” designation. Some of the genes encoding proteins identified by CD antigens have been cloned and verified by standard molecular biology techniques. CD antigens have been characterized as both transmembrane proteins and cell surface proteins anchored to the plasma membrane via covalent attachment to fatty acid-containing glycolipids such as glycosylphosphatidylinositol (GPI). (Reviewed in Barclay, A. N. et al. (1995) The Leucocyte Antigen Facts Book, Academic Press, San Diego Calif., pp. 17-20.)

[0507] Ion Channels

[0508] Ion channels are found in the plasma membranes of virtually every cell in the body. For example, chloride channels mediate a variety of cellular functions including regulation of membrane potentials and absorption and secretion of ions across epithelial membranes. Chloride channels also regulate the pH of organelles such as the Golgi apparatus and endosomes (see, e.g., Greger, R. (1988) Annu. Rev. Physiol. 50:111-122). Electrophysiological and pharmacological properties of chloride channels, including ion conductance, current-voltage relationships, and sensitivity to modulators, suggest that different chloride channels exist in muscles, neurons, fibroblasts, epithelial cells, and lymphocytes.

[0509] Many ion channels have sites for phosphorylation by one or more protein kinases including protein kinase A, protein kinase C, tyrosine kinase, and casein kinase II, all of which regulate ion channel activity in cells. Inappropriate phosphorylation of proteins in cells has been linked to changes in cell cycle progression and cell differentiation. Changes in the cell cycle have been linked to induction of apoptosis or cancer. Changes in cell differentiation have been linked to diseases and disorders of the reproductive system, immune system, skeletal muscle, and other organ systems.

[0510] Proton Pumps

[0511] Proton ATPases comprise a large class of membrane proteins that use the energy of ATP hydrolysis to generate an electrochemical proton gradient across a membrane. The resultant gradient may be used to transport other ions across the membrane (Na+, K+, or Cl−) or to maintain organelle pH. Proton ATPases are further subdivided into the mitochondrial F-ATPases, the plasma membrane ATPases, and the vacuolar ATPases. The vacuolar ATPases establish and maintain an acidic pH within various organelles involved in the processes of endocytosis and exocytosis (Mellman, I. et al. (1986) Annu. Rev. Biochem. 55:663-700).

[0512] Proton-coupled, 12 membrane-spanning domain transporters such as PEPT 1 and PEPT 2 are responsible for gastrointestinal absorption and for renal reabsorption of peptides using an electrochemical H+ gradient as the driving force. Another type of peptide transporter, the TAP transporter, is a heterodimer consisting of TAP 1 and TAP 2 and is associated with antigen processing. Peptide antigens are transported across the membrane of the endoplasmic reticulum by TAP so they can be expressed on the cell surface in association with MHC molecules. Each TAP protein consists of multiple hydrophobic membrane spanning segments and a highly conserved ATP-binding cassette (Boll, M. et al. (1996) Proc. Natl. Acad. Sci. USA 93:284-289). Pathogenic microorganisms, such as herpes simplex virus, may encode inhibitors of TAP-mediated peptide transport in order to evade immune surveillance (Marusina, K. and J. J Manaco (1996) Curr. Opin. Hematol. 3:19-26).

[0513] ABC Transporters

[0514] The ATP-binding cassette (ABC) transporters, also called the “traffic ATPases”, comprise a superfamily of membrane proteins that mediate transport and channel functions in prokaryotes and eukaryotes (Higgins, C. F. (1992) Annu. Rev. Cell Biol. 8:67-113). ABC proteins share a similar overall structure and significant sequence homology. All ABC proteins contain a conserved domain of approximately two hundred amino acid residues which includes one or more nucleotide binding domains. Mutations in ABC transporter genes are associated with various disorders, such as hyperbilirubinemia II/Dubin-Johnson syndrome, recessive Stargardt's disease, X-linked adrenoleukodystrophy, multidrug resistance, celiac disease, and cystic fibrosis.

[0515] Peripheral and Anchored Membrane Proteins

[0516] Some membrane proteins are not membrane-spanning but are attached to the plasma membrane via membrane anchors or interactions with integral membrane proteins. Membrane anchors are covalently joined to a protein post-translationally and include such moieties as prenyl, myristyl, and glycosylphosphatidyl inositol groups. Membrane localization of peripheral and anchored proteins is important for their function in processes such as receptor-mediated signal transduction. For example, prenylation of Ras is required for its localization to the plasma membrane and for its normal and oncogenic functions in signal transduction.

[0517] Vesicle Coat Proteins

[0518] Intercellular communication is essential for the development and survival of multicellular organisms. Cells communicate with one another through the secretion and uptake of protein signaling molecules. The uptake of proteins into the cell is achieved by the endocytic pathway, in which the interaction of extracellular signaling molecules with plasma membrane receptors results in the formation of plasma membrane-derived vesicles that enclose and transport the molecules into the cytosol. These transport vesicles fuse with and mature into endosomal and lysosomal (digestive) compartments. The secretion of proteins from the cell is achieved by exocytosis, in which molecules inside of the cell proceed through the secretory pathway. In this pathway, molecules transit from the ER to the Golgi apparatus and finally to the plasma membrane, where they are secreted from the cell.

[0519] Several steps in the transit of material along the secretory and endocytic pathways require the formation of transport vesicles. Specifically, vesicles form at the transitional endoplasmic reticulum (tER), the rim of Golgi cisternae, the face of the Trans-Golgi Network (TGN), the plasma membrane (PM), and tubular extensions of the endosomes. Vesicle formation occurs when a region of membrane buds off from the donor organelle. The membrane-bound vesicle contains proteins to be transported and is surrounded by a proteinaceous coat, the components of which are recruited from the cytosol. Two different classes of coat protein have been identified. Clathrin coats form on vesicles derived from the TGN and PM, whereas coatomer (COP) coats form on vesicles derived from the ER and Golgi. COP coats can be further classified as COPI, involved in retrograde traffic through the Golgi and from the Golgi to the ER, and COPII, involved in anterograde traffic from the ER to the Golgi (Mellman, supra).

[0520] In clathrin-based vesicle formation, adapter proteins bring vesicle cargo and coat proteins together at the surface of the budding membrane. Adapter protein-1 and -2 select cargo from the TGN and plasma membrane, respectively, based on molecular information encoded on the cytoplasmic tail of integral membrane cargo proteins. Adapter proteins also recruit clathrin to the bud site. Clathrin is a protein complex consisting of three large and three small polypeptide chains arranged in a three-legged structure called a triskelion. Multiple triskelions and other coat proteins appear to self-assemble on the membrane to form a coated pit. This assembly process may serve to deform the membrane into a budding vesicle. GTP-bound ADP-ribosylation factor (Arf) is also incorporated into the coated assembly. Another small G-protein, dynamin, forms a ring complex around the neck of the forming vesicle and may provide the mechanochemical force to seal the bud, thereby releasing the vesicle. The coated vesicle complex is then transported through the cytosol. During the transport process, Arf-bound GTP is hydrolyzed to GDP, and the coat dissociates from the transport vesicle (West, M. A. et al. (1997) J. Cell Biol. 138:1239-1254).

[0521] Vesicles which bud from the ER and the Golgi are covered with a protein coat similar to the clathrin coat of endocytic and TGN vesicles. The coat protein (COP) is assembled from cytosolic precursor molecules at specific budding regions on the organelle. The COP coat consists of two major components, a G-protein (Arf or Sar) and coat protomer (coatomer). Coatomer is an equimolar complex of seven proteins, termed alpha-, beta-, beta′-, gamma-, delta-, epsilon- and zeta-COP. The coatomer complex binds to dilysine motifs contained on the cytoplasmic tails of integral membrane proteins. These include the KKXX retrieval motif of membrane proteins of the ER and dicbasic/diphenylamine motifs of members of the p24 family. The p24 family of type I membrane proteins represent the major membrane proteins of COPI vesicles (Harter, C. and F. T. Wieland (1998) Proc. Natl. Acad. Sci. USA 95:11649-11654).

[0522] Organelle Associated Molecules

[0523] Eukaryotic cells are organized into various cellular organelles which has the effect of separating specific molecules and their functions from one another and from the cytosol. Within the cell, various membrane structures surround and define these organelles while allowing them to interact with one another and the cell environment through both active and passive transport processes. Important cell organelles include the nucleus, the Golgi apparatus, the endoplasmic reticulum, mitochondria, peroxisomes, lysosomes, endosomes, and secretory vesicles.

[0524] Nucleus

[0525] The cell nucleus contains all of the genetic information of the cell in the form of DNA, and the components and machinery necessary for replication of DNA and for transcription of DNA into RNA. (See Alberts, B. et al. (1994) Molecular Biology of the Cell, Garland Publishing Inc., New York N.Y., pp. 335-399.) DNA is organized into compact structures in the nucleus by interactions with various DNA-binding proteins such as histones and non-histone chromosomal proteins. DNA-specific nucleases, DNAses, partially degrade these compacted structures prior to DNA replication or transcription. DNA replication takes place with the aid of DNA helicases which unwind the double-stranded DNA helix, and DNA polymerases that duplicate the separated DNA strands.

[0526] Transcriptional regulatory proteins are essential for the control of gene expression. Some of these proteins function as transcription factors that initiate, activate, repress, or terminate gene transcription. Transcription factors generally bind to the promoter, enhancer, and upstream regulatory regions of a gene in a sequence-specific manner, although some factors bind regulatory elements within or downstream of a gene's coding region. Transcription factors may bind to a specific region of DNA singly or as a complex with other accessory factors. (Reviewed in Lewin, B. (1990) Genes IV, Oxford University Press, New York N.Y., and Cell Press, Cambridge Mass., pp. 554-570.) Many transcription factors incorporate DNA-binding structural motifs which comprise either α helices or β sheets that bind to the major groove of DNA. Four well-characterized structural motifs are helix-turn-helix, zinc finger, leucine zipper, and helix-loop-helix. Proteins containing these motifs may act alone as monomers, or they may form homo- or heterodimers that interact with DNA.

[0527] Many neoplastic disorders in humans can be attributed to inappropriate gene expression. Malignant cell growth may result from either excessive expression of tumor promoting genes or insufficient expression of tumor suppressor genes (Cleary, M. L. (1992) Cancer Surv. 15:89-104). Chromosomal translocations may also produce chimeric loci which fuse the coding sequence of one gene with the regulatory regions of a second unrelated gene. Such an arrangement likely results in inappropriate gene transcription, potentially contributing to malignancy.

[0528] In addition, the immune system responds to infection or trauma by activating a cascade of events that coordinate the progressive selection, amplification, and mobilization of cellular defense mechanisms. A complex and balanced program of gene activation and repression is involved in this process. However, hyperactivity of the immune system as a result of improper or insufficient regulation of gene expression may result in considerable tissue or organ damage. This damage is well documented in immunological responses associated with arthritis, allergens, heart attack, stroke, and infections Isselbacher, K. J. et al. (1996) Harrison's Principles of Internal Medicine, 13/e, McGraw Hill, Inc. and Teton Data Systems Software).

[0529] Transcription of DNA into RNA also takes place in the nucleus catalyzed by RNA polymerases. Three types of RNA polymerase exist. RNA polymerase I makes large ribosomal RNAs, while RNA polymerase I makes a variety of small, stable RNAs including 5S ribosomal RNA and the transfer RNAs (tRNA). RNA polymerase. It transcribes genes that will be translated into proteins. The primary transcript of RNA polymerase II is called heterogenous nuclear. RNA (hnRNA), and must be further processed by splicing to remove non-coding sequences called introns. RNA splicing is mediated by small nuclear ribonucleoprotein complexes, or snRNPs, producing mature messenger RNA (mRNA) which is then transported out of the nucleus for translation into proteins.

[0530] Nucleolus

[0531] The nucleolus is a highly organized subcompartment in the nucleus that contains high concentrations of RNA and proteins and functions mainly in ribosomal RNA synthesis and assembly (Alberts, et al. supra, pp. 379-382). Ribosomal RNA (rRNA) is a structural RNA that is complexed with proteins to form ribonucleoprotein structures called ribosomes. Ribosomes provide the platform on which protein synthesis takes place.

[0532] Ribosomes are assembled in the nucleolus initially from a large, 45S rRNA combined with a variety of proteins imported from the cytoplasm, as well as smaller, 5S rRNAs. Later processing of the immature ribosome results in formation of smaller ribosomal subunits which are transported from the nucleolus to the cytoplasm where they are assembled into functional ribosomes.

[0533] Endoplasmic Reticulum

[0534] In eukaryotes, proteins are synthesized within the endoplasmic reticulum (ER), delivered from the BR to the Golgi apparatus for post-translational processing and sorting, and transported from the Golgi to specific intracellular and extracellular destinations. Synthesis of integral membrane proteins, secreted proteins, and proteins destined for the lumen of a particular organelle occurs on the rough endoplasmic reticulum (ER). The rough ER is so named because of the rough appearance in electron micrographs imparted by the attached ribosomes on which protein synthesis proceeds. Synthesis of proteins destined for the ER actually begins in the cytosol with the synthesis of a specific signal peptide which directs the growing polypeptide and its attached ribosome to the ER membrane where the signal peptide is removed and protein synthesis is completed. Soluble proteins destined for the ER lumen, for secretion, or for transport to the lumen of other organelles pass completely into the ER lumen. Transmembrane proteins destined for the BR or for other cell membranes are translocated across the ER membrane but remain anchored in the lipid bilayer of the membrane by one or more membrane-spanning α-helical regions.

[0535] Translocated polypeptide chains destined for other organelles or for secretion also fold and assemble in the ER lumen with the aid of certain “resident” ER proteins. Protein folding in the ER is aided by two principal types of protein isomerases, protein disulfide isomerase (PDI), and peptidyl-prolyl isomerase (PPI). PDI catalyzes the oxidation of free sulfhydryl groups in cysteine residues to form intramolecular disulfide bonds in proteins. PPI, an enzyme that catalyzes the isomerization of certain proline imide bonds in oligopeptides and proteins, is considered to govern one of the rate limiting steps in the folding of many proteins to their final functional conformation. The cyclophilins represent a major class of PPI that was originally identified as the major receptor for the immunosuppressive drug cyclosporin A (Handschumacher, R. E. et al. (1984) Science 226:544-547). Molecular “chaperones” such as BiP (binding protein) in the ER recognize incorrectly folded proteins as well as proteins not yet folded into their final form and bind to them, both to prevent improper aggregation between them, and to promote proper folding.

[0536] The “N-linked” glycosylation of most soluble secreted and membrane-bound proteins by oligosacchrides linked to asparagine residues in proteins is also performed in the ER. This reaction is is catalyzed by a membrane-bound enzyme, oligosaccharyl transferase.

[0537] Golgi Apparatus

[0538] The Golgi apparatus is a complex structure that lies adjacent to the ER in eukaryotic cells and serves primarily as a sorting and dispatching station for products of the ER (Alberts, et al. supra, pp. 600-610). Additional posttranslational processing, principally additional glycosylation, also occurs in, the Golgi. Indeed, the Golgi is a major site of carbohydrate synthesis, including most of the glycosaminoglycans of the extracellular matrix. N-linked oligosaccharides, added to proteins in the ER, are also further modified in the Golgi by the addition of more sugar residues to form complex N-linked oligosaccharides. “O-linked” glycosylation of proteins also occurs in the Golgi by the addition of N-acetylgalactosamine to the hydroxyl group of a serine or threonine residue followed by the sequential addition of other sugar residues to the first. This process is catalyzed by a series of glycosyltransferases each specific for a particular donor sugar nucleotide and acceptor molecule (Lodish, H. et al. (1995) Molecular Cell Biology, W.H. Freeman and Co., New York N.Y., pp.700-708). In many cases, both N- and O-linked oligosaccharides appear to be required for the secretion of proteins or the movement of plasma membrane glycoproteins to the cell surface.

[0539] The terminal compartment of the Golgi is the Trans-Golgi Network (TGN), where both membrane and lumenal proteins are sorted for their final destination. Transport (or secretory) vesicles destined for intracellular compartments, such as lysosomes, bud off of the TGN. Other transport vesicles bud off containing proteins destined for the plasma membrane, such as receptors, adhesion molecules, and ion channels, and secretory proteins, such as hormones, neurotransmitters, and digestive enzymes.

[0540] Vacuoles

[0541] The vacuole system is a collection of membrane bound compartments in eukaryotic cells that functions in the processes of endocytosis and exocytosis. They include phagosomes, lysosomes, endosomes, and secretory vesicles. Endocytosis is the process in cells of internalizing nutrients, solutes or small particles (pinocytosis) or large particles such as internalized receptors, viruses, bacteria, or bacterial toxins (phagocytosis). Exocytosis is the process of transporting molecules to the cell surface. It facilitates placement or localization of membrane-bound receptors or other membrane proteins and secretion of hormones, neurotransmitters, digestive enzymes, wastes, etc.

[0542] A common property of all of these vacuoles is an acidic pH environment ranging from approximately pH 4.5-5.0. This acidity is maintained by the presence of a proton ATPase that uses the energy of ATP hydrolysis to generate an electrochemical proton gradient across a membrane (Mellman, I. et al. (1986) Annu. Rev. Biochem. 55:663-700). Eukaryotic vacuolar proton ATPase (vp-ATPase) is a multimeric enzyme composed of 3-10 different subunits. One of these subunits is a highly hydrophobic polypeptide of approximately 16 kDa that is similar to the proteolipid component of vp-ATPases from eubacteria, fungi, and plant vacuoles (Mandel, M. et al. (1988) Proc. Natl. Acad. Sci. USA 85:5521-5524). The 16 kDa proteolipid component is the major subunit of the membrane portion of vp-ATPase and functions in the transport of protons across the membrane.

[0543] Lysosomes

[0544] Lysosomes are membranous vesicles containing various hydrolytic enzymes used for the controlled intracellular digestion of macromolecules. Lysosomes contain some 40 types of enzymes including proteases, nucleases, glycosidases, lipases, phospholipases, phosphatases, and sulfatases, all of which are acid hydrolases that function at a pH of about 5. Lysosomes are surrounded by a unique membrane containing transport proteins that allow the final products of macromolecule degradation, such as sugars, amino acids, and nucleotides, to be transported to the cytosol where they may be either excreted or reutilized by the cell. A vp-ATPase, such as that described above, maintains the acidic environment necessary for hydrolytic activity (Alberts, supra. pp. 610-611).

[0545] Endosomes

[0546] Endosomes are another type of acidic vacuole that is used to transport substances from the cell surface to the interior of the cell in the process of endocytosis. Like lysosomes, endosomes have an acidic environment provided by a vp-ATPase (Alberts et al. supra, pp. 610-618). Two types of endosomes are apparent based on tracer uptake studies that distinguish their time of formation in the cell and their cellular location. Early endosomes are found near the plasma membrane and appear to function primarily in the recycling of internalized receptors back to the cell surface. Late endosomes appear later in the endocytic process close to the Golgi apparatus and the nucleus, and appear to be associated with delivery of endocytosed material to lysosomes or to the TGN where they may be recycled. Specific proteins are associated with particular transport vesicles and their target compartments that may provide selectivity in targeting vesicles to their proper compartments. A cytosolic prenylated GTP-binding protein, Rab, is one such protein. Rabs 4, 5, and 11 are associated with the early endosome, whereas Rabs 7 and 9 associate with the late endosome.

[0547] Mitochondria

[0548] Mitochondria are oval-shaped organelles comprising an outer membrane, a tightly folded inner membrane, an intermembrane space between the outer and inner membranes, and a matrix inside the inner membrane. The outer membrane contains many porin molecules that allow ions and charged molecules to enter the intermembrane space, while the inner membrane contains a variety of transport proteins that transfer only selected molecules. Mitochondria are the primary sites of energy production in cells.

[0549] Energy is produced by the oxidation of glucose and fatty acids. Glucose is initially converted to pyruvate in the cytoplasm. Fatty acids and pyruvate are transported to the mitochondria for complete oxidation to CO2 coupled by enzymes to the transport of electrons from NADH and FADH2 to oxygen and to the synthesis of ATP (oxidative phosphorylation) from ADP and Pi.

[0550] Pyruvate is transported into the mitochondria and converted to acetyl-CoA for oxidation via the citric acid cycle, involving pyruvate dehydrogenase components, dihydrolipoyl transacetylase, and dihydrolipoyl dehydrogenase. Enzymes involved in the citric acid cycle include: citrate synthetase, aconitases, isocitrate dehydrogenase, alpha-ketoglutarate dehydrogenase complex including transsuccinylases, succinyl CoA synthetase, succinate dehydrogenase, fumarases, and malate dehydrogenase. Acetyl CoA is oxidized to CO2 with concomitant formation of NADH, FADH2, and GTP. In oxidative phosphorylation, the transfer of electrons from NADH and FADH2 to oxygen by dehydrogenases is coupled to the synthesis of ATP from ADP and Pi by the F0F1 ATPase complex in the mitochondrial inner membrane. Enzyme complexes responsible for electron transport and ATP synthesis include the F0F1 ATPase complex, ubiquinone(CoQ)-cytochrome c reductase, ubiquinone reductase, cytochrome b, cytochrome c1, FeS protein, and cytochrome c oxidase.

[0551] Peroxisomes

[0552] Peroxisomes, like mitochondria, are a major site of oxygen utilization. They contain one or more enzymes, such as catalase and urate oxidase, that use molecular oxygen to remove hydrogen atoms from specific organic substrates in an oxidative reaction that produces hydrogen peroxide (Alberts, supra, pp. 574-577). Catalase oxidizes a variety of substrates including phenols, formic acid, formaldehyde, and alcohol and is important in peroxisomes of liver and kidney cells for detoxifying various toxic molecules that enter the bloodstream. Another major function of oxidative reactions in peroxisomes is the breakdown of fatty acids in a process called β oxidation. β oxidation results in shortening of the alkyl chain of fatty acids by blocks of two carbon atoms that are converted to acetyl CoA and exported to the cytosol for reuse in biosynthetic reactions.

[0553] Also like mitochondria, peroxisomes import their proteins from the cytosol using a specific signal sequence located near the C-terminus of the protein. The importance of this import process is evident in the inherited human disease Zellweger syndrome, in which a defect in importing proteins into perixosomes leads to a perixosomal deficiency resulting in severe abnormalities in the brain, liver, and kidneys, and death soon after birth. One form of this disease has been shown to be due to a mutation in the gene encoding a perixosomal integral membrane protein called peroxisome assembly factor-1.

[0554] The discovery of new human molecules satisfies a need in the art by providing new compositions which are useful in the diagnosis, study, prevention, and treatment of diseases associated with, as well as effects of exogenous compounds on, the expression of human molecules.

SUMMARY OF THE INVENTION

[0555] The present invention relates to nucleic acid sequences comprising human diagnostic and therapeutic polynucleotides (dithp) as presented in the Sequence Listing. The dithp uniquely identify genes encoding human structural, functional, and regulatory molecules.

[0556] The invention provides an isolated polynucleotide selected from the group consisting of a) a polynucleotide comprising a polynucleotide sequence selected from the group consisting of SEQ ID NO:1-56; b) a polynucleotide comprising a naturally occurring polynucleotide sequence at least 90% identical to a polynucleotide sequence selected from the group consisting of SEQ ID NO:1-56; c) a polynucleotide complementary to the polynucleotide of a); d) a polynucleotide complementary to the polynucleotide of b); and e) an RNA equivalent of a) through d). In one alternative, the polynucleotide comprises a polynucleotide sequence selected from the group consisting of SEQ ID NO: 1-56. In another alternative, the polynucleotide comprises at least 30 contiguous nucleotides of a polynucleotide selected from the group consisting of a) a polynucleotide comprising a polynucleotide sequence selected from the group consisting of SEQ ID NO:1-56; b) a polynucleotide comprising a naturally occurring polynucleotide comprising a polynucleotide sequence at least 90% identical to a polynucleotide sequence selected from the group consisting of SEQ ID NO:1-56; c) a polynucleotide complementary to the polynucleotide of a); d) a polynucleotide complementary to the polynucleotide of b); and e) an RNA equivalent of a) through d). In another alternative, the polynucleotide comprises at least 60 contiguous nucleotides of a polynucleotide selected from the group consisting of a) a polynucleotide comprising a polynucleotide sequence selected from the group consisting of SEQ ID NO:1-56; b) a polynucleotide comprising a naturally occurring polynucleotide comprising a polynucleotide sequence at least 90% identical to a polynucleotide sequence selected from the group consisting of SEQ ID NO:1-56; c) a polynucleotide complementary to the polynucleotide of a); d) a polynucleotide complementary to the polynucleotide of b); and e) an RNA equivalent of a) through d). The invention further provides a composition for the detection of expression of human diagnostic and therapeutic polynucleotides comprising at least one isolated polynucleotide comprising a polynucleotide selected from the group consisting of a) a polynucleotide comprising a polynucleotide sequence selected from the group consisting of SEQ ID NO:1-56; b) a polynucleotide comprising a naturally occurring polynucleotide sequence at least 90% identical to a polynucleotide sequence selected from the group consisting of SEQ ID NO:1-56; c) a polynucleotide complementary to the polynucleotide of a); d) a polynucleotide complementary to the polynucleotide of b); and e) an RNA equivalent of a) through d); and a detectable label.

[0557] The invention also provides a method for detecting a target polynucleotide in a sample, said target polynucleotide having a polynucleotide sequence of a polyneucleotide selected from the group consisting of a) a polynucleotide comprising a polynucleotide sequence of a polynucleotide selected from the group consisting of SEQ ID NO:1-56; b) a polynucleotide comprising a naturally occurring polynucleotide sequence at least 90% identical to a polynucleotide sequence selected from the group consisting of SEQ ID NO:1-56; c) a polynucleotide complementary to the polynucleotide of a); d) a polynucleotide complementary to the polynucleotide of b); and e) an RNA equivalent of a) through d). The method comprises a) amplifying said target polynucleotide or fragment thereof using polymerase chain reaction amplification, and b) detecting the presence or absence of said amplified target polynucleotide or fragment thereof, and, optionally, if present, the amount thereof.

[0558] The invention also provides a method for detecting a target polynucleotide in a sample, said target polynucleotide having a polynucleotide sequence of a polynucleotide selected from the group consisting of a) a polynucleotide comprising a polynucleotide sequence selected from the group consisting of SEQ ID NO:1-56; b) a polynucleotide comprising a naturally occurring polynucleotide sequence at least 90% identical to a polynucleotide sequence selected from the group consisting of SEQ ID NO:1-56; c) a polynucleotide complementary to the polynucleotide of a); d) a polynucleotide complementary to the polynucleotide of b); and e) an RNA equivalent of a) through d). The method comprises a) hybridizing the sample with a probe comprising at least 20 contiguous nucleotides comprising a sequence complementary to said target polynucleotide in the sample, and which probe specifically hybridizes to said target polynucleotide, under conditions whereby a hybridization complex is formed between said probe and said target polynucleotide, and b) detecting the presence or absence of said hybridization complex, and, optionally, if present, the amount thereof. In one alternative, the invention provides a composition comprising a target polynucleotide of the method, wherein said probe comprises at least 30 contiguous nucleotides. In one alternative, the invention provides a composition comprising a target polynucleotide of the method, wherein said probe comprises at least 60 contiguous nucleotides.

[0559] The invention further provides a recombinant polynucleotide comprising a promoter sequence operably linked to an isolated polynucleotide selected from the group consisting of a) a polynucleotide comprising a polynucleotide sequence selected from the group consisting of SEQ ID NO:1-56; b) a polynucleotide comprising a naturally occurring polynucleotide sequence at least 90% identical to a polynucleotide sequence selected from the group consisting of SEQ ID NO:1-56; c) a polynucleotide complementary to the polynucleotide of a); d) a polynucleotide complementary to the polynucleotide of b); and e) an RNA equivalent of a) through d). In one alternative, the invention provides a cell transformed with the recombinant polynucleotide. In another alternative, the invention provides a transgenic organism comprising the recombinant polynucleotide.

[0560] The invention also provides a method for producing a human diagnostic and therapeutic polypeptide, the method comprising a) culturing a cell under conditions suitable for expression of the human diagnostic and therapeutic polypeptide, wherein said cell is transformed with a recombinant polynucleotide, said recombinant polynucleotide comprising an isolated polynucleotide selected from the group consisting of i) a polynucleotide comprising a polynucleotide sequence selected from the group consisting of SEQ ID NO:1-56; ii) a polynucleotide comprising a naturally occurring polynucleotide sequence at least 90% identical to a polynucleotide sequence selected from the group consisting of SEQ ID NO:1-56; iii) a polynucleotide complementary to the polynucleotide of i); iv) a polynucleotide complementary to the polynucleotide of ii); and v) an RNA equivalent of i) through iv), and b) recovering the human diagnostic and therapeutic polypeptide so expressed. The invention additionally provides a method wherein the polypeptide has an amino acid sequence selected from the group consisting of SEQ ID NO:57-113.

[0561] The invention also provides an isolated human diagnostic and therapeutic polypeptide (DITHP) encoded by at least one polynucleotide comprising a polynucleotide sequence selected from the group consisting of SEQ ID NO:1-56. The invention further provides a method of screening for a test compound that specifically binds to the polypeptide having an amino acid sequence selected from the group consisting of SEQ ID NO:57-113. The method comprises a) combining the polypeptide having an amino acid sequence selected from the group consisting of SEQ ID NO:57-113 with at least one test compound under suitable conditions, and b) detecting binding of the polypeptide having an amino acid sequence selected from the group consisting of SEQ ID NO:57-113 to the test compound, thereby identifying a compound that specifically binds to the polypeptide having an amino acid sequence selected from the group consisting of SEQ ID NO:57-113.

[0562] The invention further provides a microarray wherein at least one element of the microarray is an isolated polynucleotide comprising at least 30 contiguous nucleotides of a polynucleotide selected from the group consisting of a) a polynucleotide comprising a polynucleotide sequence selected from the group consisting of SEQ ID NO:1-56; b) a polynucleotide comprising a naturally occurring polynucleotide sequence at least 90% identical to a polynucleotide sequence selected from the group consisting of SEQ ID NO:1-56; c) a polynucleotide complementary to the polynucleotide of a); d) a polynucleotide complementary to the polynucleotide of b); and e) an RNA equivalent of a) through d). The invention also provides a method for generating a transcript image of a sample which contains polynucleotides. The method comprises a) labeling the polynucleotides of the sample, b) contacting the elements of the microarray with the labeled polynucleotides of the sample under conditions suitable for the formation of a hybridization complex, and c) quantifying the expression of the polynucleotides in the sample.

[0563] Additionally, the invention provides a method for screening a compound for effectiveness in altering expression of a target polynucleotide, wherein said target polynucleotide comprises a polynucleotide selected from the group consisting of a) a polynucleotide comprising a polynucleotide sequence selected from the group consisting of SEQ ID NO:1-56; b) a polynucleotide comprising a naturally occurring polynucleotide sequence at least 90% identical to a polynucleotide sequence selected from the group consisting of SEQ ID NO:1-56; c) a polynucleotide complementary to the polynucleotide of a); d) a polynucleotide complementary to the polynucleotide of b); and e) an RNA equivalent of a) through d). The method comprises a) exposing a sample comprising the target polynucleotide to a compound, b) detecting altered expression of the target polynucleotide, and c) comparing the expression of the target polynucleotide in the presence of varying amounts of the compound and in the absence of the compound.

[0564] The invention further provides a method for assessing toxicity of a test compound, said method comprising a) treating a biological sample containing nucleic acids with the test compound; b) hybridizing the nucleic acids of the treated biological sample with a probe comprising at least 20 contiguous nucleotides of a polynucleotide selected from the group consisting of i) a polynucleotide comprising a polynucleotide sequence selected from the group consisting of SEQ ID NO:1-56; ii) a polynucleotide comprising a naturally occurring polynucleotide sequence at least 90% identical to a polynucleotide sequence selected from the group consisting of SEQ ID NO:1-56; iii) a polynucleotide complementary to the polynucleotide of i); iv) a polynucleotide complementary to the polynucleotide of ii); and v) an RNA equivalent of i) through iv). Hybridization occurs under conditions whereby a specific hybridization complex is formed between said probe and a target polynucleotide in the biological sample, said target polynucleotide comprising a polynucleotide sequence of a polynucleotide selected from the group consisting of i) a polynucleotide comprising a polynucleotide sequence selected from the group consisting of SEQ ID NO:1-56; ii) a polynucleotide comprising a naturally occurring polynucleotide sequence at least 90% identical to a polynucleotide sequence selected from the group consisting of SEQ ID NO:1-56; iii) a polynucleotide complementary to the polynucleotide of i); iv) a polynucleotide complementary to the polynucleotide of ii); and v) an RNA equivalent of i) through iv), and alternatively, the target polynucleotide comprises a polynucleotide sequence of a fragment of a polynucleotide selected from the group consisting of i-v above; c) quantifying the amount of hybridization complex; and d) comparing the amount of hybridization complex in the treated biological sample with the amount of hybridization complex in an untreated biological sample, wherein a difference in the amount of hybridization complex in the treated biological sample is indicative of toxicity of the test compound.

[0565] The invention further provides an isolated polypeptide selected from the group consisting of a) a polypeptide comprising an amino acid sequence selected from the group consisting of SEQ ID NO:57-113, b) a polypeptide comprising a naturally occurring amino acid sequence at least 90% identical to an amino acid sequence selected from the group consisting of SEQ ID NO:57-113, c) a biologically active fragment of a polypeptide having an amino acid sequence selected from the group consisting of SEQ ID NO:57-113, and d) an immunogenic fragment of a polypeptide having an amino acid sequence selected from the group consisting of SEQ ID NO:57-113. In one alternative, the invention provides an isolated polypeptide comprising an amino acid sequence selected from the group consisting of SEQ ID NO:57-113.

[0566] The invention further provides an isolated polynucleotide encoding a polypeptide selected from the group consisting of a) a polypeptide comprising an amino acid sequence selected from the group consisting of SEQ ID NO:57-113, b) a polypeptide comprising a naturally occurring amino acid sequence at least 90% identical to an amino acid sequence selected from the group consisting of SEQ ID NO:57-113, c) a biologically active fragment of a polypeptide having an amino acid sequence selected from the group consisting of SEQ ID NO:57-113, and d) an immunogenic fragment of a polypeptide having an amino acid sequence selected from the group consisting of SEQ ID NO:57-113. In one alternative, the polynucleotide encodes a polypeptide comprising an amino acid sequence selected from the group consisting of SEQ ID NO:57-113. In another alternative, the polynucleotide comprises a polynucleotide sequence selected from the group consisting of SEQ ID NO:1-56.

[0567] Additionally, the invention provides an isolated antibody which specifically binds to a polypeptide selected from the group consisting of a) a polypeptide comprising an amino acid sequence selected from the group consisting of SEQ ID NO:57-113, b) a polypeptide comprising a naturally occurring amino acid sequence at least 90% identical to an amino acid sequence selected from the group consisting of SEQ ID NO:57-113, c) a biologically active fragment of a polypeptide having an amino acid sequence selected from the group consisting of SEQ ID NO:57-113, and d) an immunogenic fragment of a polypeptide having an amino acid sequence selected from the group consisting of SEQ ID NO:57-113.

[0568] The invention further provides a composition comprising a polypeptide selected from the group consisting of a) a polypeptide comprising an amino acid sequence selected from the group consisting of SEQ ID NO:57-113, b) a polypeptide comprising a naturally occurring amino acid sequence at least 90% identical to an amino acid sequence selected from the group consisting of SEQ ID NO:57-113, c) a biologically active fragment of a polypeptide having an amino acid sequence selected from the group consisting of SEQ ID NO:57-113, and d) an immunogenic fragment of a polypeptide having an amino acid sequence selected from the group consisting of SEQ ID NO:57-113, and a pharmaceutically acceptable excipient. In one embodiment, the composition comprises a polypeptide having an amino acid sequence selected from the group consisting of SEQ ID NO:57-113. The invention additionally provides a method of treating a disease or condition associated with decreased expression of functional DITHP, comprising administering to a patient in need of such treatment the composition.

[0569] The invention also provides a method for screening a compound for effectiveness as an agonist of a polypeptide selected from the group consisting of a) a polypeptide comprising an amino acid sequence selected from the group consisting of SEQ ID NO:57-113, b) a polypeptide comprising a naturally occurring amino acid sequence at least 90% identical to an amino acid sequence selected from the group consisting of SEQ ID NO:57-113, c) a biologically active fragment of a polypeptide having an amino acid sequence selected from the group consisting of SEQ ID NO:57-113, and d) an immunogenic fragment of a polypeptide having an amino acid sequence selected from the group consisting of SEQ ID NO:57-113. The method comprises a) exposing a sample comprising the polypeptide to a compound, and b) detecting agonist activity in the sample. In one alternative, the invention provides a composition comprising an agonist compound identified by the method and a pharmaceutically acceptable excipient. In another alternative, the invention provides a method of treating a disease or condition associated with decreased expression of functional DITHP, comprising administering to a patient in need of such treatment the composition.

[0570] Additionally, the invention provides a method for screening a compound for effectiveness as an antagonist of a polypeptide selected from the group consisting of a) a polypeptide comprising an amino acid sequence selected from the group consisting of SEQ ID NO:57-113, b) a polypeptide comprising a naturally occurring amino acid sequence at least 90% identical to an amino acid sequence selected from the group consisting of SEQ ID NO:57-113, c) a biologically active fragment of a polypeptide having an amino acid sequence selected from the group consisting of SEQ ID NO:57-113, and d) an immunogenic fragment of a polypeptide having an amino acid sequence selected from the group consisting of SEQ ID NO:57-113. The method comprises a) exposing a sample comprising the polypeptide to a compound, and b) detecting antagonist activity in the sample. In one alternative, the invention provides a composition comprising an antagonist compound identified by the method and a pharmaceutically acceptable excipient. In another alternative, the invention provides a method of treating a disease or condition associated with overexpression of functional DITHP, comprising administering to a patient in need of such treatment the composition.

[0571] The invention further provides a method of screening for a compound that modulates the activity of a polypeptide selected from the group consisting of a) a polypeptide comprising an amino acid sequence selected from the group consisting of SEQ ID NO:57-113, b) a polypeptide comprising a naturally occurring amino acid sequence at least 90% identical to an amino acid sequence selected from the group consisting of SEQ ID NO:57-113, c) a biologically active fragment of a polypeptide having an amino acid sequence selected from the group consisting of SEQ ID NO:57-113, and d) an immunogenic fragment of a polypeptide having an amino acid sequence selected from the group consisting of SEQ ID NO:57-113. The method comprises a) combining the polypeptide with at least one test compound under conditions permissive for the activity of the polypeptide, b) assessing the activity of the polypeptide in the presence of the test compound, and c) comparing the activity of the polypeptide in the presence of the test compound with the activity of the polypeptide in the absence of the test compound, wherein a change in the activity of the polypeptide in the presence of the test compound is indicative of a compound that modulates the activity of the polypeptide.

DESCRIPTION OF THE TABLES

[0572] Table 1 shows the sequence identification numbers (SEQ ID NO:s) and template identification numbers (template IDs) corresponding to the polynucleotides of the present invention, along with the sequence identification numbers (SEQ ID NO:s) and open reading frame identification numbers (ORF IDs) corresponding to polypeptides encoded by the template ID.

[0573] Table 2 shows the sequence identification numbers (SEQ ID NO:s) and template identification numbers (template IDs) corresponding to the polynucleotides of the present invention, along with their GenBank hits (GI Numbers), probability scores, and functional annotations corresponding to the GenBank hits.

[0574] Table 3 shows the sequence identification numbers (SEQ ID NO:s) and template identification numbers (template IDs) corresponding to the polynucleotides of the present invention, along with polynucleotide segments of each template sequence as defined by the indicated “start” and “stop” nucleotide positions. The reading frames of the polynucleotide segments and the Pfam hits, Pfam descriptions, and E-values corresponding to the polypeptide domains encoded by the polynucleotide segments are indicated.

[0575] Table 4 shows the sequence identification numbers (SEQ ID NO:s) and template identification numbers (template IDs) corresponding to the polynucleotides of the present invention, along with polynucleotide segments of each template sequence as defined by the indicated “start” and “stop” nucleotide positions. The reading frames of the polynucleotide segments are shown, and the polypeptides encoded by the polynucleotide segments constitute either signal peptide (SP) or transmembrane (TM) domains, as indicated. For TM domains, the membrane topology of the encoded polypeptide sequence is indicated as being transmembrane or on the cytosolic or non-cytosolic side of the cell membrane or organelle.

[0576] Table 5 shows the sequence identification numbers (SEQ ID NO:s) and template identification numbers (template IDs) corresponding to the polynucleotides of the present invention, along with component sequence identification numbers (component IDs) corresponding to each template. The component sequences, which were used to assemble the template sequences, are defined by the indicated “start” and “stop” nucleotide positions along each template.

[0577] Table 6 shows the tissue distribution profiles for the templates of the invention.

[0578] Table 7 shows the sequence identification numbers (SEQ ID NO:s) corresponding to the polypeptides of the present invention, along with the reading frames used to obtain the polypeptide segments, the lengths of the polypeptide segments, the “start” and “stop” nucleotide positions of the polynucleotide sequences used to define the encoded polypeptide segments, the GenBank hits (GI Numbers), probability scores, and functional annotations corresponding to the GenBank hits.

[0579] Table 8 summarizes the bioinformatics tools which are useful for analysis of the polynucleotides of the present invention. The first column of Table 8 lists analytical tools, programs, and algorithms, the second column provides brief descriptions thereof, the third column presents appropriate references, all of which are incorporated by reference herein in their entirety, and the fourth column presents, where applicable, the scores, probability values, and other parameters used to evaluate the strength of a match between two sequences (the higher the score, the greater the homology between two sequences).

DETAILED DESCRIPTION OF THE INVENTION

[0580] Before the nucleic acid sequences and methods are presented, it is to be understood that this invention is not limited to the particular machines, methods, and materials described. Although particular embodiments are described, machines, methods, and materials similar or equivalent to these embodiments may be used to practice the invention. The preferred machines, methods, and materials set forth are not intended to limit the scope of the invention which is limited only by the appended claims.

[0581] The singular forms “a”, “an”, and “the” include plural reference unless the context clearly dictates otherwise. All technical and scientific terms have the meanings commonly understood by one of ordinary skill in the art. All publications are incorporated by reference for the purpose of describing and disclosing the cell lines, vectors, and methodologies which are presented and which might be used in connection with the invention. Noting in the specification is to be construed as an admission that the invention is not entitled to antedate such disclosure by virtue of prior invention.

[0582] Definitions

[0583] As used herein, the lower case “dithp” refers to a nucleic acid sequence, while the upper case “DITHP” refers to an amino acid sequence encoded by dithp. A “full-length” dithp refers to a nucleic acid sequence containing the entire coding region of a gene endogenously expressed in human tissue.

[0584] “Adjuvants” are materials such as Freund's adjuvant, mineral gels (aluminum hydroxide), and surface active substances (lysolecithin, pluronic polyols, polyanions, peptides, oil emulsions, keyhole limpet hemocyanin, and dinitrophenol) which maybe administered to increase a host's immunological response.

[0585] “Allele” refers to an alternative form of a nucleic acid sequence. Alleles result from a “mutation,” a change or an alternative reading of the genetic code. Any given gene may have none, one, or many allelic forms. Mutations which give rise to alleles include deletions, additions, or substitutions of nucleotides. Each of these changes may occur alone, or in combination with the others, one or more times in a given nucleic acid sequence. The present invention encompasses allelic dithp.

[0586] An “allelic variant” is an alternative form of the gene encoding DITHP. Allelic variants may result from at least one mutation in the nucleic acid sequence and may result in altered mRNAs or in polypeptides whose structure or function may or may not be altered. A gene may have none, one, or many allelic variants of its naturally occurring form. Common mutational changes which give rise to allelic variants are generally ascribed to natural deletions, additions, or substitutions of nucleotides. Each of these types of changes may occur alone, or in combination with the others, one or more times in a given sequence.

[0587] “Altered” nucleic acid sequences encoding DITHP include those sequences with deletions, insertions, or substitutions of different nucleotides, resulting in a polypeptide the same as DITHP or a polypeptide with at least one functional characteristic of Dee. Included within this definition are polymorphisms which may or may not be readily detectable using a particular oligonucleotide probe of the polynucleotide encoding DITHP, and improper or unexpected hybridization to allelic variants, with a locus other than the normal chromosomal locus for the polynucleotide sequence encoding DITHP. The encoded protein may also be “altered,” and may contain deletions, insertions, or substitutions of amino acid residues which produce a silent change and result in a functionally equivalent DITHP. Deliberate amino acid substitutions may be made on the basis of similarity in polarity, charge, solubility, hydrophobicity, hydrophilicity, and/or the amphipathic nature of the residues, as long as the biological or immunological activity of DITHP is retained. For example, negatively charged amino acids may include aspartic acid and glutamic acid, and positively charged amino acids may include lysine and arginine. Amino acids with uncharged polar side chains having similar hydrophilicity values may include: asparagine and glutamine; and serine and threonine. Amino acids with uncharged side chains having similar hydrophilicity values may include: leucine, isoleucine, and valine; glycine and alanine; and phenylalanine and tyrosine.

[0588] “Amino acid sequence” refers to a peptide, a polypeptide, or a protein of either natural or synthetic origin. The amino acid sequence is not limited to the complete, endogenous amino acid sequence and may be a fragment, epitope, variant, or derivative of a protein expressed by a nucleic acid sequence.

[0589] “Amplification” refers to the production of additional copies of a sequence and is carried out using polymerase chain reaction (PCR) technologies well known in the art.

[0590] “Antibody” refers to intact molecules as well as to fragments thereof, such as Fab, F(ab′)2, and Fv fragments, which are capable of binding the epitopic determinant. Antibodies that bind DITHP polypeptides can be prepared using intact polypeptides or using fragments containing small peptides of interest as the immunizing antigen. The polypeptide or peptide used to immunize an animal (e.g., a mouse, a rat, or a rabbit) can be derived from the translation of RNA, or synthesized chemically, and can be conjugated to a carrier protein if desired. Commonly used carriers that are chemically coupled to peptides include bovine serum albumin, thyroglobulin, and keyhole limpet hemocyanin (KLH). The coupled peptide is then used to immunize the animal.

[0591] The term “aptamer” refers to a nucleic acid or oligonucleotide molecule that binds to a specific molecular target. Aptamers are derived from an in vitro evolutionary process (e.g., SELEX (Systematic Evolution of Ligands by EXponential Enrichment), described in U.S. Pat. No. 5,270,163), which selects for target-specific aptamer sequences from large combinatorial libraries. Aptamer compositions may be double-stranded or single-stranded, and may include deoxyribonucleotides, ribonucleotides, nucleotide derivatives, or other nucleotide-like molecules. The nucleotide components of an aptamer may have modified sugar groups (e.g., the 2′-OH group of a ribonucleotide may be replaced by 2′-F or 2′-NH2), which may improve a desired property, e.g., resistance to nucleases or longer lifetime in blood. Aptamers may be conjugated to other molecules, e.g., a high molecular weight carrier to slow clearance of the aptamer from the circulatory system. Aptamers may be specifically cross-linked to their cognate ligands, e.g., by photo-activation of a cross-linker. (See, e.g., Brody, E. N. and L. Gold (2000) J. Biotechnol. 74:5-13.) The term “intramer” refers to an aptamer which is expressed in vivo. For example, a vaccinia virus-based RNA expression system has been used to express specific RNA aptamers at high levels in the cytoplasm of leukocytes (Blind, M. et al. (1999) Proc. Natl. Acad. Sci. USA 96:3606-3610).

[0592] The term “spiegelmer” refers to an aptamer which includes L-DNA, L-RNA, or other left-handed nucleotide derivatives or nucleotide-like molecules. Aptamers containing left-handed nucleotides are resistant to degradation by naturally occurring enzymes, which normally act on substrates containing right-handed nucleotides.

[0593] “Antisense sequence” refers to a sequence capable of specifically hybridizing to a target sequence. The antisense sequence may include DNA, RNA, or any nucleic acid mimic or analog such as peptide nucleic acid (PNA); oligonucleotides having modified backbone linkages such as phosphorothioates, methylphosphonates, or benzylphosphonates; oligonucleotides having modified sugar groups such as 2′-methoxyethyl sugars or 2′-methoxyethoxy sugars; or oligonucleotides having modified bases such as 5-methyl cytosine, 2′-deoxyuracil, or 7-deaza-2′-deoxyguanosine.

[0594] “Antisense technology” refers to any technology which relies on the specific hybridization of an antisense sequence to a target sequence.

[0595] A “bin” is a portion of computer memory space used by a computer program for storage of data, and bounded in such a manner that data stored in a bin may be retrieved by the program.

[0596] “Biologically active” refers to an amino acid sequence having a structural, regulatory, or biochemical function of a naturally occurring amino acid sequence.

[0597] “Clone joining” is a process for combining gene bins based upon the bins' containing sequence information from the same clone. The sequences may assemble into a primary gene transcript as well as one or more splice variants.

[0598] “Complementary” describes the relationship between two single-stranded nucleic acid sequences that anneal by base-pairing (5′-A-G-T-3′ pairs with its complement 3′-T-C-A-5′).

[0599] A “component sequence” is a nucleic acid sequence selected by a computer program such as PHRED and used to assemble a consensus or template sequence from one or more component sequences.

[0600] A “consensus sequence” or “template sequence” is a nucleic acid sequence which has been assembled from overlapping sequences, using a computer program for fragment assembly such as the GELVIEW fragment assembly system (Genetics Computer Group (GCG), Madison Wis.) or using a relational database management system (RDMS).

[0601] “Conservative amino acid substitutions” are those substitutions that, when made, least interfere with the properties of the original protein, i.e., the structure and especially the function of the protein is conserved and not significantly changed by such substitutions. The table below shows amino acids which may be substituted for an original amino acid in a protein and which are regarded as conservative substitutions.

1Original ResidueConservative SubstitutionAlaGly, SerArgHis, LysAsnAsp, Gln, HisAspAsn, GluCysAla, SerGlnAsn, Glu, HisGluAsp, Gln, HisGlyAlaHisAsn, Arg, Gln, GluIleLeu, ValLeuIle, ValLysArg, Gln, GluMetLeu, IlePheHis, Met, Leu, Trp, TyrSerCys,ThrThrSer, ValTrpPhe, TyrTyrHis, Phe, TrpValIle, Leu, Thr

[0602] Conservative substitutions generally maintain (a) the structure of the polypeptide backbone in the area of the substitution, for example, as a beta sheet or alpha helical conformation, (b) the charge or hydrophobicity of the molecule at the target site, or (c) the bulk of the side chain.

[0603] “Deletion” refers to a change in either a nucleic or amino acid sequence in which at least one nucleotide or amino acid residue, respectively, is absent.

[0604] “Derivative” refers to the chemical modification of a nucleic acid sequence, such as by replacement of hydrogen by an alkyl, acyl, amino, hydroxyl, or other group.

[0605] “Differential expression” refers to increased or upregulated; or decreased, downregulated, or absent gene or protein expression, determined by comparing at least two different samples. Such comparisons maybe carried out between, for example, a treated and an untreated sample, or a diseased and a normal sample.

[0606] The terms “element” and “array element” refer to a polynucleotide, polypeptide, or other chemical compound having a unique and defined position on a microarray.

[0607] The term “modulate” refers to a change in the activity of DITHP. For example, modulation may cause an increase or a decrease in protein activity, binding characteristics, or any other biological, functional or immunological properties of DITHP.

[0608] “E-value” refers to the statistical probability that a match between two sequences occurred by chance.

[0609] “Exon shuffling” refers to the recombination of different coding regions (exons). Since an exon may represent a structural or functional domain of the encoded protein, new proteins may be assembled through the novel reassortment of stable substructures, thus allowing acceleration of the evolution of new protein functions.

[0610] A “fragment” is a unique portion of dithp or DITHP which is identical in sequence to but shorter in length than the parent sequence. A fragment may comprise up to the entire length of the defined sequence, minus one nucleotide/amino acid residue. For example, a fragment may comprise from 10 to 1000 contiguous amino acid residues or nucleotides. A fragment used as a probe, primer, antigen, therapeutic molecule, or for other purposes, maybe at least 5, 10, 15, 16, 20, 25, 30, 40, 50, 60, 75, 100, 150, 250 or at least 500 contiguous amino acid residues or nucleotides in length. Fragments may be preferentially selected from certain regions of a molecule. For example, a polypeptide fragment may comprise a certain length of contiguous amino acids selected from the first 250 or 500 amino acids (or first 25% or 50%) of a polypeptide as shown in a certain defined sequence. Clearly these lengths are exemplary, and any length that is supported by the specification, including the Sequence Listing and the figures, may be encompassed by the present embodiments.

[0611] A fragment of dithp comprises a region of unique polynucleotide sequence that specifically identifies dithp, for example, as distinct from any other sequence in the same genome. A fragment of dithp is useful, for example, in hybridization and amplification technologies and in analogous methods that distinguish dithp from related polynucleotide sequences. The precise length of a fragment of dithp and the region of dithp to which the fragment corresponds are routinely determinable by one of ordinary skill in the art based on the intended purpose for the fragment.

[0612] A fragment of DITHP is encoded by a fragment of dithp. A fragment of DITHP comprises a region of unique amino acid sequence that specifically identifies DITHP. For example, a fragment of DITHP is useful as an immunogenic peptide for the development of antibodies that specifically recognize DITHP. The precise length of a fragment of DITHP and the region of DITHP to which the fragment corresponds are routinely determinable by one of ordinary skill in the art based on the intended purpose for the fragment.

[0613] A “full length” nucleotide sequence is one containing at least a start site for translation to a protein sequence, followed by an open reading frame and a stop site, and encoding a “full length” polypeptide.

[0614] “Hit” refers to a sequence whose annotation will be used to describe a given template. Criteria for selecting the top hit are as follows: if the template has one or more exact nucleic acid matches, the top hit is the exact match with highest percent identity. If the template has no exact matches but has significant protein hits, the top hit is the protein hit with the lowest E-value. If the template has no significant protein hits, but does have significant non-exact nucleotide hits, the top hit is the nucleotide hit with the lowest E-value.

[0615] “Homology” refers to sequence similarity either between a reference nucleic acid sequence and at least a fragment of a dithp or between a reference amino acid sequence and a fragment of a DITHP.

[0616] “Hybridization” refers to the process by which a strand of nucleotides anneals with a complementary strand through base pairing. Specific hybridization is an indication that two nucleic acid sequences share a high degree of identity. Specific hybridization complexes form under defined annealing conditions, and remain hybridized after the “washing” step. The defined hybridization conditions include the annealing conditions and the washing step(s), the latter of which is particularly important in determining the stringency of the hybridization process, with more stringent conditions allowing less non-specific binding, i.e., binding between pairs of nucleic acid probes that are not perfectly matched. Permissive conditions for annealing of nucleic acid sequences are routinely determinable and may be consistent among hybridization experiments, whereas wash conditions may be varied among experiments to achieve the desired stringency.

[0617] Generally, stringency of hybridization is expressed with reference to the temperature under which the wash step is carried out. Generally, such wash temperatures are selected to be about 5° C. to 20° C. lower than the thermal melting point (Tm) for the specific sequence at a defined ionic strength and pH. The Tm is the temperature (under defined ionic strength and pH) at which 50% of the target sequence hybridizes to a perfectly matched probe. An equation for calculating Tm and conditions for nucleic acid hybridization is well known and can be found in Sambrook et al., 1989, Molecular Cloning: A Laboratory Manual, 2nd ed., vol. 1-3, Cold Spring Harbor Press, Plainview N.Y.; specifically see volume 2, chapter 9.

[0618] High stringency conditions for hybridization between polynucleotides of the present invention include wash conditions of 68° C. in the presence of about 0.2×SSC and about 0.1% SDS, for 1 hour. Alternatively, temperatures of about 65° C., 60° C., or 55° C. may be used. SSC concentration may be varied from about 0.2 to 2×SSC, with SDS being present at about 0.1%. Typically, blocking reagents are used to block non-specific hybridization. Such blocking reagents include, for instance, denatured salmon sperm DNA at about 100-200 μg/ml. Useful variations on these conditions will be readily apparent to those skilled in the art. Hybridization, particularly under high stringency conditions, may be suggestive of evolutionary similarity between the nucleotides. Such similarity is strongly indicative of a similar role for the nucleotides and their resultant proteins.

[0619] Other parameters, such as temperature, salt concentration, and detergent concentration may be varied to achieve the desired stringency. Denaturants, such as formamide at a concentration of about 35-50% v/v, may also be used under particular circumstances, such as RNA:DNA hybridizations. Appropriate hybridization conditions are routinely determinable by one of ordinary skill in the art.

[0620] “Immunologically active” or “immunogenic” describes the potential for a natural, recombinant, or synthetic peptide, epitope, polypeptide, or protein to induce antibody production in appropriate animals, cells, or cell lines.

[0621] “Immune response” can refer to conditions associated with inflammation, trauma, immune disorders, or infectious or genetic disease, etc. These conditions can be characterized by expression of various factors, e.g., cytokines, chemokines, and other signaling molecules, which may affect cellular and systemic defense systems.

[0622] An “immunogenic fragment” is a polypeptide or oligopeptide fragment of Dithp which is capable of eliciting an immune response when introduced into a living organism, for example, a mammal. The term “immunogenic fragment” also includes any polypeptide or oligopeptide fragment of DITHP which is useful in any of the antibody production methods disclosed herein or known in the art.

[0623] “Insertion” or “addition” refers to a change in either a nucleic or amino acid sequence in which at least one nucleotide or residue, respectively, is added to the sequence.

[0624] “Labeling” refers to the covalent or noncovalent joining of a polynucleotide, polypeptide, or antibody with a reporter molecule capable of producing a detectable or measurable signal.

[0625] “Microarray” is any arrangement of nucleic acids, amino acids, antibodies, etc., on a to substrate. The substrate may be a solid support such as beads, glass, paper, nitrocellulose, nylon, or an appropriate membrane.

[0626] “Linkers” are short stretches of nucleotide sequence which may be added to a vector or a dithp to create restriction endonuclease sites to facilitate cloning. “Polylmkers” are engineered to incorporate multiple restriction enzyme sites and to provide for the use of enzymes which leave 5′ or 3′ overhangs (e.g., BamHI, EcoRI, and HindIII) and those which provide blunt ends (e.g., EcoRV, SnaBI, and StuI).

[0627] “Naturally occurning” refers to an endogenous polynucleotide or polypeptide that may be isolated from viruses or prokaryotic or eukaryotic cells.

[0628] “Nucleic acid sequence” refers to the specific order of nucleotides joined by phosphodiester bonds in a linear, polymeric arrangement. Depending on the number of nucleotides, the nucleic acid sequence can be considered an oligomer, oligonucleotide, or polynucleotide. The nucleic acid can be DNA, RNA, or any nucleic acid analog, such as PNA, may be of genomic or synthetic origin, may be either double-stranded or single-stranded, and can represent either the sense or antisense (complementary) strand.

[0629] “Oligomer” refers to a nucleic acid sequence of at least about 60 nucleotides and as many as about 60 nucleotides, preferably about 15 to 40 nucleotides, and most preferably between about 20 and nucleotides, that may be used in hybridization or amplification technologies. Oligomers may be used as, e.g., primers for PCR, and are usually chemically synthesized.

[0630] “Operably linked” refers to the situation in which a first nucleic acid sequence is placed in a functional relationship with the second nucleic acid sequence. For instance, a promoter is operably linked to a coding sequence if the promoter affects the transcription or expression of the coding sequence. Generally, operably linked DNA sequences may be in close proximity or contiguous and, where necessary to join two protein coding regions, in the same reading frame.

[0631] “Peptide nucleic acid” (PNA) refers to a DNA mimic in which nucleotide bases are attached to a pseudopeptide backbone to increase stability. PNAs, also designated antigene agents, can prevent gene expression by targeting complementary messenger RNA.

[0632] The phrases “percent identity” and “% identity”, as applied to polynucleotide sequences, refer to the percentage of residue matches between at least two polynucleotide sequences aligned using a standardized algorithm. Such an algorithm may insert, in a standardized and reproducible way, gaps in the sequences being compared in order to optimize alignment between two sequences, and therefore achieve a more meaningful comparison of the two sequences.

[0633] Percent identity between polynucleotide sequences may be determined using the default parameters of the CLUSTAL V algorithm as incorporated into the MEGALIGN version 3.12e sequence alignment program. This program is part of the LASERGENE software package, a suite of molecular biological analysis programs (DNASTAR, Madison Wis.). CLUSTAL V is described in Higgins, D. G. and Sharp, P. M. (1989) CABIOS 5:151-153 and in Higgins, D. G. et al. (1992) CABIOS 8:189-191. For pairwise alignments of polynucleotide sequences, the default parameters are set as follows: Ktuple=2, gap penalty-5, window=4, and “diagonals saved”=4. The “weighted” residue weight table is selected as the default. Percent identity is reported by CLUSTAL V as the “percent similarity” between aligned polynucleotide sequence pairs.

[0634] Alternatively, a suite of commonly used and freely available sequence comparison algorithms is provided by the National Center for Biotechnology Information (NCBI) Basic Local Alignment Search Tool (BLAST) (Altschul, S. F. et al. (1990) J. Mol. Biol. 215:403-410), which is available from several sources, including the NCBI, Bethesda, Md., and on the Internet at http://www.ncbi.nlm.nih.gov/BLAST/. The BLAST software suite includes various sequence analysis programs including “blastn,” that is used to determine alignment between a known polynucleotide sequence and other sequences on a variety of databases. Also available is a tool called “BLAST 2 Sequences” that is used for direct pairwise comparison of two nucleotide sequences. “BLAST 2 Sequences” can be accessed and used interactively at http://www.ncbi.nlm.nih.gov/gorf/bl2/. The “BLAST 2 Sequences” tool can be used for both blastn and blastp (discussed below). BLAST programs are commonly used with gap and other parameters set to default settings. For example, to compare two nucleotide sequences, one may use blastn with the “BLAST 2 Sequences” tool Version 2.0.9 (May 7, 1999) set at default parameters. Such default parameters may be, for example:

[0635] Matrix: BLOSUM62

[0636] Reward for match: 1

[0637] Penalty for mismatch: −2

[0638] Open Gap: 5 and Extension Gap: 2 penalties

[0639] Gap×drop-off: 50

[0640] Expect: 10

[0641] Word Size: 11

[0642] Filter: on

[0643] Percent identity may be measured over the length of an entire defined sequence, for example, as defined by a particular SEQ ID number, or may be measured over a shorter length, for example, over the length of a fragment taken from a larger, defined sequence, for instance, a fragment of at least 20, at least 30, at least 40, at least 50, at least 70, at least 100, or at least 200 contiguous nucleotides. Such lengths are exemplary only, and it is understood that any fragment length supported by the sequences shown herein, in figures or Sequence Listings, may be used to describe a length over which percentage identity may be measured.

[0644] Nucleic acid sequences that do not show a high degree of identity may nevertheless encode similar amino acid sequences due to the degeneracy of the genetic code. It is understood that changes in nucleic acid sequence can be made using this degeneracy to produce multiple nucleic acid sequences that all encode substantially the same protein.

[0645] The phrases “percent identity” and “% identity”, as applied to polypeptide sequences, refer to the percentage of residue matches between at least two polypeptide sequences aligned using a standardized algorithm. Methods of polypeptide sequence alignment are well-known. Some alignment methods take into account conservative amino acid substitutions. Such conservative substitutions, explained in more detail above, generally preserve the hydrophobicity and acidity of the substituted residue, thus preserving the structure (and therefore function) of the folded polypeptide.

[0646] Percent identity between polypeptide sequences may be determined using the default parameters of the CLUSTAL V algorithm as incorporated into the MEGALIGN version 3.12e sequence alignment program (described and referenced above). For pairwise alignments of polypeptide sequences using CLUSTAL V, the default parameters are set as follows: Ktuple=1, gap penalty=3, window=5, and “diagonals saved”=5. The PAM250 matrix is selected as the default residue weight table. As with polynucleotide alignments, the percent identity is reported by CLUSTAL V as the “percent similarity” between aligned polypeptide sequence pairs.

[0647] Alternatively the NCBI BLAST software suite may be used. For example, for a pairwise comparison of two polypeptide sequences, one may use the “BLAST 2 Sequences” tool Version 2.0.9 (May 7, 1999) with blastp set at default parameters. Such default parameters maybe, for example:

[0648] Matrix: BLOSUM62

[0649] Open Gap: 11 and Extension Gap: 1 penalty

[0650] Gap×drop-off 50

[0651] Expect: 10

[0652] Word Size: 3

[0653] Filter: on

[0654] Percent identity may be measured over the length of an entire defined polypeptide sequence, for example, as defined by a particular SEQ ID number, or may be measured over a shorter length, for example, over the length of a fragment taken from a larger, defined polypeptide sequence, for instance, a fragment of at least 15, at least 20, at least 30, at least 40, at least 50, at least 70 or at least 150 contiguous residues. Such lengths are exemplary only, and it is understood that any fragment length supported by the sequences shown herein, in figures or Sequence Listings, may be used to describe a length over which percentage identity may be measured.

[0655] “Post-translational modification” of a DITHP may involve lipidation, glycosylation, phosphorylation, acetylation, racemization, proteolytic cleavage, and other modifications known in the art. These processes may occur synthetically or biochemically. Biochemical modifications will vary by cell type depending on the enzymatic milieu and the DITHP.

[0656] “Probe” refers to dithp or fragments thereof, which are used to detect identical, allelic or related nucleic acid sequences. Probes are isolated oligonucleotides or polynucleotides attached to a detectable label or reporter molecule. Typical labels include radioactive isotopes, ligands, chemiluminescent agents, and enzymes. ‘Primers’ are short nucleic acids, usually DNA oligonucleotides, which may be annealed to a target polynucleotide by complementary base-pairing. The primer may then be extended along the target DNA strand by a DNA polymerase enzyme. Primer pairs can be used for amplification (and identification) of a nucleic acid sequence, e.g., by the polymerase chain reaction (PCR).

[0657] Probes and primers as used in the present invention typically comprise at least 15 contiguous nucleotides of a known sequence. In order to enhance specificity, longer probes and primers may also be employed, such as probes and primers that comprise at least 20, 30, 40, 50, 60, 70, 80, 90, 100, or at least 150 consecutive nucleotides of the disclosed nucleic acid sequences. Probes and primers may be considerably longer than these examples, and it is understood that any length supported by the specification, including the figures and Sequence Listing, may be used.

[0658] Methods for preparing and using probes and primers are described in the references, for example Sambrook et al., 1989, Molecular Cloning: A Laboratory Manual, 21′ ed., vol. 1-3, Cold Spring Harbor Press, Plainview N.Y.; Ausubel et al., 1987, Current Protocols in Molecular Biology, Greene Publ. Assoc. & Wiley-Intersciences, New York N.Y.; Innis et al., 1990, PCR Protocols. A Guide to Methods and Applications, Academic Press, San Diego Calif. PCR primer pairs can be derived from a known sequence, for example, by using computer programs intended for that purpose such as Primer (Version 0.5, 1991, Whitehead Institute for Biomedical Research, Cambridge Mass.).

[0659] Oligonucleotides for use as primers are selected using software known in the art for such purpose. For example, OLIGO 4.06 software is useful for the selection of PCR primer pairs of up to 100 nucleotides each, and for the analysis of oligonucleotides and larger polynucleotides of up to 5,000 nucleotides from an input polynucleotide sequence of up to 32 kilobases. Similar primer selection programs have incorporated additional features for expanded capabilities. For example, the PrimOU primer selection program (available to the public from the Genome Center at University of Texas South West Medical Center, Dallas Tex.) is capable of choosing specific primers from megabase sequences and is thus useful for designing primers on a genome-wide scope. The Primer3 primer selection program (available to the public from the Whitehead Institute/MIT Center for Genome Research, Cambridge Mass.) allows the user to input a “mispriming library,” in which sequences to avoid as primer binding sites are user-specified. Primer3 is useful, in particular, for the selection of oligonucleotides for microarrays. (The source code for the latter two primer selection programs may also be obtained from their respective sources and modified to meet the user's specific needs.) The PrimeGen program (available to the public from the UK Human Genome Mapping Project Resource Centre, Cambridge UK) designs primers based on multiple sequence alignments, thereby allowing selection of primers that hybridize to either the most conserved or least conserved regions of aligned nucleic acid sequences. Hence, this program is useful for identification of both unique and conserved oligonucleotides and polynucleotide fragments. The oligonucleotides and polynucleotide fragments identified by any of the above selection methods are useful in hybridization technologies, for example, as PCR or sequencing primers, microarray elements, or specific probes to identify fully or partially complementary polynucleotides in a sample of nucleic acids. Methods of oligonucleotide selection are not limited to those described above.

[0660] “Purified” refers to molecules, either polynucleotides or polypeptides that are isolated or separated from their natural environment and are at least 60% free, preferably at least 75% free, and most preferably at least 90% free from other compounds with which they are naturally associated.

[0661] A “recombinant nucleic acid” is a sequence that is not naturally occurring or has a sequence that is made by an artificial combination of two or more otherwise separated segments of sequence. This artificial combination is of the accomplished by chemical synthesis or, more commonly, by the artificial manipulation of isolated segments of nucleic acids, e.g., by genetic engineering techniques such as those described in Sambrook, supra. The term recombinant includes nucleic acids that have been altered solely by addition, substitution, or deletion of a portion of the nucleic acid. Frequently, a recombinant nucleic acid may include a nucleic acid sequence operably linked to a promoter sequence. Such a recombinant nucleic acid may be part of a vector that is used, for example, to transform a cell.

[0662] Alternatively, such recombinant nucleic acids maybe part of a viral vector, e.g., based on a vaccinia virus, that could be use to vaccinate a mammal wherein the recombinant nucleic acid is expressed, inducing a protective immunological response in the mammal.

[0663] “Regulatory element” refers to a nucleic acid sequence from nontranslated regions of a gene, and includes enhancers, promoters, introns, and 3′ untranslated regions, which interact with host proteins to carry out or regulate transcription or translation.

[0664] “Reporter” molecules are chemical or biochemical moieties used for labeling a nucleic acid, an amino acid, or an antibody. They include radionuclides; enzymes; fluorescent, chemiluminescent, or chromogenic agents; substrates; cofactors; inhibitors; magnetic particles; and other moieties known in the art.

[0665] An “RNA equivalent,” in reference to a DNA sequence, is composed of the same linear sequence of nucleotides as the reference DNA sequence with the exception that all occurrences of the nitrogenous base thymine are replaced with uracil, and the sugar backbone is composed of ribose instead of deoxyribose.

[0666] “Sample” is used in its broadest sense. Samples may contain nucleic or amino acids, antibodies, or other materials, and maybe derived from any source (e.g., bodily fluids including, but not limited to, saliva, blood, and urine; chromosome(s), organelles, or membranes isolated from a cell; genomic DNA, RNA, or cDNA in solution or bound to a substrate; and cleared cells or tissues or blots or imprints from such cells or tissues).

[0667] “Specific binding” or “specifically binding” refers to the interaction between a protein or peptide and its agonist, antibody, antagonist, or other binding partner. The interaction is dependent upon the presence of a particular structure of the protein, e.g., the antigenic determinant or epitope, recognized by the binding molecule. For example, if an antibody is specific for epitope “A,” the presence of a polypeptide containing epitope A, or the presence of free unlabeled A, in a reaction containing free labeled A and the antibody will reduce the amount of labeled A that binds to the antibody.

[0668] “Substitution” refers to the replacement of at least one nucleotide or amino acid by a different nucleotide or amino acid.

[0669] “Substrate” refers to any suitable rigid or semi-rigid support including, e.g., membranes, filters, chips, slides, wafers, fibers, magnetic or nonmagnetic beads, gels, tubing, plates, polymers, microparticles or capillaries. The substrate can have a variety of surface forms, such as wells, trenches, pins, channels and pores, to which polynucleotides or polypeptides are bound.

[0670] A “transcript image” or “expression profile” refers to the collective pattern of gene expression by a particular cell type or tissue under given conditions at a given time.

[0671] “Transformation” refers to a process by which exogenous DNA enters a recipient cell.

[0672] Transformation may occur under natural or artificial conditions using various methods well known in the art. Transformation may rely on any known method for the insertion of foreign nucleic acid sequences into a prokaryotic or eukaryotic host cell. The method is selected based on the host cell being transformed.

[0673] “Transformants” include stably transformed cells in which the inserted DNA is capable of replication either as an autonomously replicating plasmid or as part of the host chromosome, as well as cells which transiently express inserted DNA or RNA.

[0674] A “transgenic organism,” as used herein, is any organism, including but not limited to animals and plants, in which one or more of the cells of the organism contains heterologous nucleic acid introduced by way of human intervention, such as by transgenic techniques well known in the art. The nucleic acid is introduced into the cell, directly or indirectly by introduction into a precursor of the cell, by way of deliberate genetic manipulation, such as by microinjection or by infection with a recombinant virus. The term genetic manipulation does not include classical cross-breeding, or in vitro fertilization, but rather is directed to the introduction of a recombinant DNA molecule. The transgenic organisms contemplated in accordance with the present invention include bacteria, cyanobacteria, fungi, and plants and animals. The isolated DNA of the present invention can be introduced into the host by methods known in the art, for example infection, transfection, transformation or transconjugation. Techniques for transferring the DNA of the present invention into such organisms are widely known and provided in references such as Sambrook et al. (1989), supra.

[0675] A “variant” of a particular nucleic acid sequence is defined as a nucleic acid sequence having at least 25% sequence identity to the particular nucleic acid sequence over a certain length of one of the nucleic acid sequences using blastn with the “BLAST 2 Sequences” tool Version 2.0.9 (May 7, 1999) set at default parameters. Such a pair of nucleic acids may show, for example, at least 30%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% or greater sequence identity over a certain defined length. The variant may result in “conservative” amino acid changes which do not affect structural and/or chemical properties. A variant may be described as, for example, an “allelic” (as defined above), “splice,” “species,” or “polymorphic” variant. A splice variant may have significant identity to a reference molecule, but will generally have a greater or lesser number of polynucleotides due to alternate splicing of exons during mRNA processing. The corresponding polypeptide may possess additional functional domains or lack domains that are present in the reference molecule. Species variants are polynucleotide sequences that vary from one species to another. The resulting polypeptides generally will have significant amino acid identity relative to each other. A polymorphic variant is a variation in the polynucleotide sequence of a particular gene between individuals of a given species. Polymorphic variants also may encompass “single nucleotide polymorphisms” (SNPs) in which the polynucleotide sequence varies by one base. The presence of SNPs may be indicative of, for example, a certain population, a disease state, or a propensity for a disease state.

[0676] In an alternative, variants of the polynucleotides of the present invention may be generated through recombinant methods. One possible method is a DNA shuffling technique such as MOLECULARBREEDING (Maxygen Inc., Santa Clara Calif.; described in U.S. Pat. No. 5,837,458; Chang, C.-C. et al. (1999) Nat. Biotechnol. 17:793-797; Christians, F. C. et al. (1999) Nat. Biotechnol. 17:259-264; and Crameri, A. et al. (1996) Nat. Biotechnol. 14:315-319) to alter or improve the biological properties of DITHP, such as its biological or enzymatic activity or its ability to bind to other molecules or compounds. DNA shuffling is a process by which a library of gene variants is produced using PCR-mediated recombination of gene fragments. The library is then subjected to selection or screening procedures that identify those gene variants with the desired properties. These preferred variants may then be pooled and further subjected to recursive rounds of DNA shuffling and selection/screening. Thus, genetic diversity is created through “artificial” breeding and rapid molecular evolution. For example, fragments of a single gene containing random point mutations may be recombined, screened, and then reshuffled until the desired properties are optimized. Alternatively, fragments of a given gene may be recombined with fragments of homologous genes in the same gene family, either from the same or different species, thereby maximizing the genetic diversity of multiple naturally occurring genes in a directed and controllable manner.

[0677] A “variant” of a particular polypeptide sequence is defined as a polypeptide sequence having at least 40% sequence identity to the particular polypeptide sequence over a certain length of one of the polypeptide sequences using blastp with the “BLAST 2 Sequences” tool Version 2.0.9 (May 7, 1999) set at default parameters. Such a pair of polypeptides may show, for example, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% or greater identity over a certain defined length of one of the polypeptides.

THE INVENTION

[0678] In a particular embodiment, cDNA sequences derived from human tissues and cell lines were aligned based on nucleotide sequence identity and assembled into “consensus” or “template” sequences which are designated by the template identification numbers (template IDs) in column 2 of Table 2. The sequence identification numbers (SEQ ID NO:s) corresponding to the template IDs are shown in column 1. The template sequences have similarity to GenBank sequences, or “hits,” as designated by the GI Numbers in column 3. The statistical probability of each GenBank hit is indicated by a probability score in column 4, and the functional annotation corresponding to each GenBank hit is listed in column 5.

[0679] The invention incorporates the nucleic acid sequences of these templates as disclosed in the Sequence Listing and the use of these sequences in the diagnosis and treatment of disease states characterized by defects in human molecules. The invention further utilizes these sequences in hybridization and amplification technologies, and in particular, in technologies which assess gene expression patterns correlated with specific cells or tissues and their responses in vivo or in vitro to pharmaceutical agents, toxins, and other treatments. In this manner, the sequences of the present invention are used to develop a transcript image for a particular cell or tissue.

[0680] Derivation of Nucleic Acid Sequences

[0681] cDNA was isolated from libraries constructed using RNA derived from normal and diseased human tissues and cell lines. The human tissues and cell lines used for cDNA library construction were selected from a broad range of sources to provide a diverse population of cDNAs representative of gene transcription throughout the human body. Descriptions of the human tissues and cell lines used for cDNA library construction are provided in the LIFESEQ database (Incyte Genomics, Inc. (Incyte), Palo Alto Calif.). Human tissues were broadly selected from, for example, cardiovascular, dermatologic, endocrine, gastrointestinal, hematopoietic/immune system, musculoskeletal, neural, reproductive, and urologic sources.

[0682] Cell lines used for cDNA library construction were derived from, for example, leukemic cells, teratocarcinomas, neuroepitheliomas, cervical carcinoma, lung fibroblasts, and endothelial cells. Such cell lines include, for example, THP-1, Jurkat, HUVEC, hN12, WI38, HeLa, and other cell lines commonly used and available from public depositories (American Type Culture Collection, Manassas Va.). Prior to mRNA isolation, cell lines were untreated, treated with a pharmaceutical agent such as 5′-aza-2′-deoxycytidine, treated with an activating agent such as lipopolysaccharide in the case of leukocytic cell lines, or, in the case of endothelial cell lines, subjected to shear stress.

[0683] Sequencing of the cDNAs

[0684] Methods for DNA sequencing are well known in the art. Conventional enzymatic methods employ the Klenow fragment of DNA polymerase I, SEQUENASE DNA polymerase (U.S. Biochemical Corporation, Cleveland Ohio), Taq polymerase (Applied Biosystems, Foster City Calif.), thermostable T7 polymerase (Amersham Pharmacia Biotech, Inc. (Amersham Pharmacia Biotech), Piscataway N.J.), or combinations of polymerases and proofreading exonucleases such as those found in the ELONGASE amplification system (Life Technologies Inc. (Life Technologies), Gaithersburg Md.), to extend the nucleic acid sequence from an oligonucleotide primer annealed to the DNA template of interest. Methods have been developed for the use of both single-stranded and double-stranded templates. Chain termination reaction products may be electrophoresed on urea-polyacrylamide gels and detected either by autoradiography (for radioisotope-labeled nucleotides) or by fluorescence (for fluorophore-labeled nucleotides). Automated methods for mechanized reaction preparation, sequencing, and analysis using fluorescence detection methods have been developed. Machines used to prepare cDNAs for sequencing can include the MICROLAB 2200 liquid transfer system (Hamilton Company (Hamilton), Reno Nev.), Peltier thermal cycler (PTC200; MJ Research, Inc. (MJ Research), Watertown Mass.), and ABI CATALYST 800 thermal cycler (Applied Biosystems). Sequencing can be carried out using, for example, the ABI 373 or 377 (Applied Biosystems) or MEGABACE 1000 (Molecular Dynamics, Inc. (Molecular Dynamics), Sunnyvale Calif.) DNA sequencing systems, or other automated and manual sequencing systems well known in the art.

[0685] The nucleotide sequences of the Sequence Listing have been prepared by current, state-of-the art, automated methods and, as such, may contain occasional sequencing errors or unidentified nucleotides. Such unidentified nucleotides are designated by an N. These infrequent unidentified bases do not represent a hindrance to practicing the invention for those skilled in the art. Several methods employing standard recombinant techniques maybe used to correct errors and complete the missing sequence information. (See, e.g., those described in Ausubel, F. M. et al. (1997) Short Protocols in Molecular Biology, John Wiley & Sons, New York N.Y.; and Sambrook, J. et al. (1989) Molecular Cloning. A Laboratory Manual, Cold Spring Harbor Press, Plainview N.Y.)

[0686] Assembly of cDNA Sequences

[0687] Human polynucleotide sequences may be assembled using programs or algorithms well known in the art. Sequences to be assembled are related, wholly or in part, and may be derived from a single or many different transcripts. Assembly of the sequences can be performed using such programs as PHRAP (Phils Revised Assembly Program) and the GELVIEW fragment assembly system (GCG), or other methods known in the art.

[0688] Alternatively, cDNA sequences are used as “component” sequences that are assembled into “template” or “consensus” sequences as follows. Sequence chromatograms are processed, verified, and quality scores are obtained using PHRED. Raw sequences are edited using an editing pathway known as Block 1 (See, e.g., the LIFESEQ Assembled User Guide, Incyte Genoimics, Palo Alto, Calif.). A series of BLAST comparisons is performed and low-information segments and repetitive elements (e.g., dinucleotide repeats, Alu repeats, etc.) are replaced by “n's”, or masked, to prevent spurious matches. Mitochondrial and ribosomal RNA sequences are also removed. The processed sequences are then loaded into a relational database management system (RDMS) which assigns edited sequences to existing templates, if available. When additional sequences are added into the RDMS, a process is initiated which modifies existing templates or creates new templates from works in progress (i.e., nonfinal assembled sequences) containing queued sequences or the sequences themselves. After the new sequences have been assigned to templates, the templates can be merged into bins. If multiple templates exist in one bin, the bin can be split and the templates reannotated.

[0689] Once gene bins have been generated based upon sequence alignments, bins are “clone joined” based upon clone information. Clone joining occurs when the 5′ sequence of one clone is present in one bin and the 3′ sequence from the same clone is present in a different bin, indicating that the two bins should be merged into a single bin. Only bins which share at least two different clones are merged.

[0690] A resultant template sequence may contain either a partial or a full length open reading frame, or all or part of a genetic regulatory element. This variation is due in part to the fact that the full length cDNAs of many genes are several hundred, and sometimes several thousand, bases in length. With current technology, cDNAs comprising the coding regions of large genes cannot be cloned because of vector limitations, incomplete reverse transcription of the mRNA, or incomplete “second strand” synthesis. Template sequences maybe extended to include additional contiguous sequences derived from the parent RNA transcript using a variety of methods known to those of skill in the art. Extension may thus be used to achieve the full length coding sequence of a gene.

[0691] Analysis of the cDNA Sequences

[0692] The cDNA sequences are analyzed using a variety of programs and algorithms which are well known in the art. (See, e.g., Ausubel, 1997, supra, Chapter 7.7; Meyers, R. A. (Ed.) (1995) Molecular Biology and Biotechnology, Wiley V C H, New York N.Y., pp. 856-853; and Table 8.) These analyses comprise both reading frame determinations, e.g., based on triplet codon periodicity for particular organisms (Fickett, J. W. (1982) Nucleic Acids Res. 10:5303-5318); analyses of potential start and stop codons; and homology searches.

[0693] Computer programs known to those of skill in the art for performing computer-assisted searches for amino acid and nucleic acid sequence similarity, include, for example, Basic Local Alignment Search Tool (BLAST; Altschul, S. F. (1993) J. Mol. Evol. 36:290-300; Altschul, S. F. et al. (1990) J. Mol. Biol. 215:403-410). BLAST is especially useful in determining exact matches and comparing two sequence fragments of arbitrary but equal lengths, whose alignment is locally maximal and for which the alignment score meets or exceeds a threshold or cutoff score set by the user (Karlin, S. et al. (1988) Proc. Natl. Acad. Sci. USA 85:841-845). Using an appropriate search tool (e.g., BLAST or HMM), GenBank, SwissProt, BLOCKS, PFAM and other databases maybe searched for sequences containing regions of homology to a query dithp or DITHP of the present invention.

[0694] Other approaches to the identification, assembly, storage, and display of nucleotide and polypeptide sequences are provided in “Relational Database for Storing Biomolecule Information,” U.S. Ser. No. 08/947,845, filed Oct. 9, 1997; “Project-Based Full-Length Biomolecular Sequence Database,” U.S. Ser. No. 08/811,758, filed Mar. 6, 1997; and “Relational Database and System for Storing Information Relating to Biomolecular Sequences,” U.S. Ser. No. 09/034,807, filed Mar. 4, 1998, all of which are incorporated by reference herein in their entirety.

[0695] Protein hierarchies can be assigned to the putative encoded polypeptide based on, e.g., motif, BLAST, or biological analysis. Methods for assigning these hierarchies are described, for example, in “Database System Employing Protein Function Hierarchies for Viewing Biomolecular Sequence Data,” U.S. Ser. No. 08/812,290, filed Mar. 6, 1997, incorporated herein by reference.

[0696] Identification of Human Diagnostic and Therapeutic Molecules Encoded by Dithp

[0697] The identities of the DITHP encoded by the dithp of the present invention were obtained by analysis of the assembled cDNA sequences.

[0698] SEQ ID NO:57 and SEQ ID NO:58, encoded by SEQ ID NO:1 and SEQ ID NO:2, respectively, are, for example, human enzyme molecules.

[0699] SEQ ID NO:59, SEQ ID NO:60, and SEQ ID NO:61, encoded by SEQ ID NO:3, SEQ ID NO:4, and SEQ ID NO:5, respectively, are, for example, receptor molecules.

[0700] SEQ ID NO:62 and SEQ ID NO:63, encoded by SEQ ID NO:6 and SEQ ID NO:7, respectively, are, for example, intracellular signaling molecules.

[0701] SEQ ID NO:64, SEQ ID NO:65, SEQ ID NO:66, SEQ ID NO:67, SEQ ID NO:68, SEQ ID NO:69, and SEQ ID NO:70, encoded by SEQ ID NO:8, SEQ ID NO:9, SEQ ID NO:10, SEQ ID NO:11, SEQ ID NO:12, SEQ ID NO:13, and SEQ ID NO:14, respectively, are, for example, transcription factor molecules.

[0702] SEQ ID NO:71, SEQ ID NO:72, SEQ ID NO:73, SEQ ID NO:74, SEQ ID NO:75, SEQ ID NO:76, SEQ ID NO:77, SEQ ID NO:78, SEQ ID NO:79, SEQ ID NO:80, SEQ ID NO:81, SEQ ID NO:82, SEQ ID NO:83, SEQ ID NO:84, SEQ ID NO:85, SEQ ID NO:86, SEQ ID NO:87, and SEQ ID NO:88, encoded by SEQ ID NO:15, SEQ ID NO:16, SEQ ID NO:17, SEQ ID NO:18, SEQ ID NO:19, SEQ ID NO:20, SEQ ID NO:21, SEQ ID NO:22, SEQ ID NO:23, SEQ ID NO:24, SEQ ID NO:25, SEQ ID NO:26, SEQ ID NO:27, SEQ ID NO:28, SEQ ID NO:29, SEQ ID NO:30, SEQ ID NO:31, and SEQ ID NO:32, respectively, are, for example, Zn finger-type transcriptional regulators.

[0703] SEQ ID NO:89 and SEQ ID NO:90, encoded by SEQ ID NO:33 and SEQ ED NO:34, respectively, are, for example, membrane transport molecules.

[0704] SEQ ID NO:91, SEQ ID NO:92, SEQ ID NO:93, and SEQ ID NO:94, encoded by SEQ ID NO:35, SEQ ID NO:36, SEQ ID NO:37, and SEQ ID NO:38, respectively, are, for example, protein modification and maintenance molecules.

[0705] SEQ ID NO:95, encoded by SEQ ID NO:39 is, for example, an adhesion molecule.

[0706] SEQ ID NO:96 and SEQ ID NO:97, encoded by SEQ ID NO:40 and SEQ ID NO:41, respectively, are, for example, antigen recognition molecules.

[0707] SEQ ID NO:98, encoded by SEQ ID NO:42 is, for example, an electron transfer associated molecule.

[0708] SEQ ID NO:99 and SEQ ID NO:100, encoded by SEQ ID NO:43 and SEQ ID NO:44, respectively, are, for example, cytoskeletal molecules.

[0709] SEQ ID NO:101 and SEQ ID NO:102, encoded by SEQ ID NO:45 and SEQ ID NO:46, respectively, are, for example, human cell membrane molecules.

[0710] SEQ ID NO:103, SEQ ID NO:104, SEQ ID NO:105, SEQ ID NO:106, and SEQ ID NO:107, encoded by SEQ ID NO:47, SEQ ID NO:48, SEQ ID NO:49, SEQ ID NO:50, and SEQ ID NO:50, respectively, are, for example, organelle associated molecules.

[0711] SEQ ID NO:108 and SEQ ID NO:109, encoded by SEQ ID NO:51 and SEQ ID NO:52, respectively, are, for example, biochemical pathway molecules.

[0712] SEQ ID NO:110, SEQ ID NO:111, SEQ ID NO:112, and SEQ ID NO:113, encoded by SEQ ID NO:53, SEQ ID NO:54, SEQ ID NO:55, and SEQ ID NO:56, respectively, are, for example, molecules associated with growth and development.

[0713] Sequences of Human Diagnostic and Therapeutic Molecules

[0714] The dithp of the present invention may be used for a variety of diagnostic and therapeutic purposes. For example, a dithp may be used to diagnose a particular condition, disease, or disorder associated with human molecules. Such conditions, diseases, and disorders include, but are not limited to, a cell proliferative disorder, such as actinic keratosis, arteriosclerosis, atherosclerosis, bursitis, cirrhosis, hepatitis, mixed connective tissue disease (MCD), myelofibrosis, paroxysmal nocturnal hemoglobinuria, polycythemia vera, psoriasis, primary thrombocythemia, and cancers including adenocarcinoma, leukemia, lymphoma, melanoma, myeloma, sarcoma, teratocarcinoma, and, in particular, a cancer of the adrenal gland, bladder, bone, bone marrow, brain, breast, cervix, gall bladder, ganglia, gastrointestinal tract, heart, kidney, liver, lung, muscle, ovary, pancreas, parathyroid, penis, prostate, salivary glands, skin, spleen, testis, thymus, thyroid, and uterus; an autoimmune/inflammatory disorder, such as inflammation, actinic keratosis, acquired immunodeficiency syndrome (AIDS), Addison's disease, adult respiratory distress syndrome, allergies, ankylosing spondylitis, amyloidosis, anemia, arteriosclerosis, asthma, atherosclerosis, autoimmune hemolytic anemia, autoimmune thyroiditis, bronchitis, bursitis, cholecystitis, cirrhosis, contact dermatitis, Crohn's disease, atropic dermatitis, dermatomyositis, diabetes mellitus, emphysema, erythroblastosis fetalis, erythema nodosum, atrophic gastritis, glomerulonephritis, Goodpasture's syndrome, gout, Graves' disease, Hashimoto's thyroiditis, paroxysmal nocturnal hemoglobinuria, hepatitis, hypereosinophilia, irritable bowel syndrome, episodic lymphopenia with lymphocytotoxins, mixed connective tissue disease (MCTD), multiple sclerosis, myasthenia gravis, myocardial or pericardial inflammation, myelofibrosis, osteoarthritis, osteoporosis, pancreatitis, polycythemia vera, polymyositis, psoriasis, Reiter's syndrome, rheumatoid arthritis, scleroderma, Sjögren's syndrome, systemic anaphylaxis, systemic lupus erythematosus, systemic sclerosis, primary thrombocythemia, thrombocytopenic purpura, ulcerative colitis, uveitis, Werner syndrome, complications of cancer, hemodialysis, and extracorporeal circulation, trauma, and hematopoietic cancer including lymphoma, leukemia, and myeloma; an infection caused by a viral agent classified as adenovirus, arenavirus, bunyavirus, calicivirus, coronavirus, filovirns, hepadnavinis, herpesvirus, flavivirus, ortlhomyxovirus, parvovirus, papovavirus, paramyxovirus, picornavirus, poxvirus, reovirus, retrovirus, rhabdovirus, or togavirus; an infection caused by a bacterial agent classified as pneumococcus, staphylococcus, streptococcus, bacillus, corynebacterium, clostridium, meningococcus, gonococcus, listeria, moraxella, kingella, haemophilus, legionella, bordetella, gram-negative enterobacterium including shigella, salmonella, or campylobacter, pseudomonas, vibrio, brucella, francisella, yersinia, bartonella, norcardium, actinomyces, mycobacterium, spirochaetale, rickettsia, chlamydia, or mycoplasma; an infection caused by a fungal agent classified as aspergiltus, blastomyces, dermatophytes, cryptococcus, coccidioides, malasezzia, histoplasma, or other mycosis-causing fungal agent; and an infection caused by a parasite classified as plasmodium or malaria-causing, parasitic entamoeba, leishmania, trypanosoma, toxoplasma, pneumocystis carinii, intestinal protozoa such as giardia, trichomonas, tissue nematode such as trichinella, intestinal nematode such as ascaris, lymphatic filial nematode, trematode such as schistosoma, and cestrode such as tapeworm; a developmental disorder such as renal tubular acidosis, anemia, Cushing's syndrome, achondroplastic dwarfism Ducnenne and Becker muscular dystrophy, epilepsy, gonadal dysgenesis, WAGR syndrome (Wilms' tumor, aniridia, genitourinary abnormalities, and mental retardation), Smith-Magenis syndrome, myelodysplastic syndrome, hereditary mucoepithelial dysplasia, hereditary keratodermas, hereditary neuropathies such as Charcot-Marie-Tooth disease and neurofibromatosis, hypothyroidism, hydrocephalus, seizure disorders such as Syndenham's chorea and cerebral palsy, spina bifida, anencephaly, craniorachischisis, congenital glaucoma, cataract, and sensorineural hearing loss; an endocrine disorder such as a disorder of the hypothalamus and/or pituitary resulting from lesions such as a primary brain tumor, adenoma, infarction associated with pregnancy, hypophysectomy, aneurysm, vascular malformation, thrombosis, infection, immunological disorder, and complication due to head trauma; a disorder associated with hypopituitarism including hypogonadism, Sheehan syndrome, diabetes insipidus, Kallman's disease, Hand-Schuller-Christian disease, Letterer-Siwe disease, sarcoidosis, empty sella syndrome, and dwarfism; a disorder associated with hyperpituitarism including acromegaly, giantism, and syndrome of inappropriate antidiuretic hormone (ADH) secretion (SIADH) often caused by benign adenoma; a disorder associated with hypothyroidism including goiter, myxedema, acute thyroiditis associated with bacterial infection, subacute thyroiditis associated with viral infection, autoimmune thyroiditis (Hashimoto's disease), and cretinism; a disorder associated with hyperthyroidism including thyrotoxicosis and its various forms, Grave's disease, pretibial myxedema, toxic multinodular goiter, thyroid carcinoma, and Plummer's disease; a disorder associated with hyperparathyroidism including Conn disease (chronic hypercalemia); a pancreatic disorder such as Type I or Type II diabetes mellitus and associated complications; a disorder associated with the adrenals such as hyperplasia, carcinoma, or adenoma of the adrenal cortex, hypertension associated with alkalosis, amyloidosis, hypokalemia, Cushing's disease, Liddle's syndrome, and Arnold-Healy-Gordon syndrome, pheochromocytoma tumors, and Addison's disease; a disorder associated with gonadal steroid hormones such as: in women, abnormal prolactin production, infertility, endometriosis, perturbation of the menstrual cycle, polycystic ovarian disease, hyperprolactinemia, isolated gonadotropin deficiency, amenorrhea, galactorrhea, hermaphroditism, hirsutism and virilization, breast cancer, and, in post-menopausal women, osteoporosis; and, in men, Leydig cell deficiency, male climacteric phase, and germinal cell aplasia, a hypergonadal disorder associated with Leydig cell tumors, androgen resistance associated with absence of androgen receptors, syndrome of 5 α-reductase, and gynecomastia; a metabolic disorder such as Addison's disease, cerebrotendinous xanthomatosis, congenital adrenal hyperplasia, coumarin resistance, cystic fibrosis, diabetes, fatty hepatocirrhosis, fructose-1,6-diphosphatase deficiency, galactosemia, goiter, glucagonoma, glycogen storage diseases, hereditary fructose intolerance, hyperadrenalism, hypoadrenalism, hyperparathyroidism, hypoparathyroidism, hypercholesterolemia, hyperthyroidism, hypoglycemia, hypothyroidism, hyperlipidemia, hyperlipemia, lipid myopathies, lipodystrophies, lysosomal storage diseases, mannosidosis, neuraminidase deficiency, obesity, pentosuria phenylketonuria, pseudovitamin D-deficiency rickets; disorders of carbohydrate metabolism such as congenital type II dyserythropoietic anemia, diabetes, insulin-dependent diabetes mellitus, non-insulin-dependent diabetes mellitus, fructose-1,6-diphosphatase deficiency, galactosemia, glucagonoma, hereditary fructose intolerance, hypoglycemia, mannosidosis, neuramindase deficiency, obesity, galactose epimerase deficiency, glycogen storage diseases, lysosomal storage diseases, fructosuria, pentosuria, and inherited abnormalities of pyruvate metabolism; disorders of lipid metabolism such as fatty liver, cholestasis, primary biliary cirrhosis, carnitine deficiency, carnitine palmitoyltransferase deficiency, myoadenylate deaminase deficiency, hypertriglyceridemia, lipid storage disorders such Fabry's disease, Gaucher's disease, Niemann-Pick's disease, metachromatic leukodystrophy, adrenoleukodystrophy, GM2 gangliosidosis, and ceroid lipofuscinosis, abetalipoproteinemia, Tangier disease, hyperlipoproteinemia, diabetes mellitus, lipodystrophy, lipomatoses, acute paniculitis, disseminated fat necrosis, adiposis dolorosa, lipoid adrenal hyperplasia, minimal change disease, lipomas, atherosclerosis, hypercholesterolemia, hypercholesteroleia with hypertriglyceridemia, primary hypoalphalipoproteinemia, hypothyroidism, renal disease, liver disease, lecithin:cholesterol acyltransferase deficiency, cerebrotendinous xanthomatosis, sitosterolemia, hypocholesterolemia, Tay-Sachs disease, Sandlhoff's disease, hyperlipidemia, hyperlipemia, lipid myopathies, and obesity; and disorders of copper metabolism such as Menke's disease, Wilson's disease, and Ehlers-Danlos syndrome type I; a neurological disorder such as epilepsy, ischemic cerebrovascular disease, stroke, cerebral neoplasms, Alzheimer's disease, Pick's disease, Huntington's disease, dementia, Parkinson's disease and other extrapyramidal disorders, amyotrophic lateral sclerosis and other motor neuron disorders, progressive neural muscular atrophy, retinitis pigmentosa, hereditary ataxias, multiple sclerosis and other demyelinating diseases, bacterial and viral meningitis, brain abscess, subdural empyema, epidural abscess, suppurative intracranial thrombophlebitis, myelitis and radiculitis, viral central nervous system disease, prion diseases including kuru, Creutzfeldt-Jakob disease, and Gerstmann-Straussler-Scheinker syndrome, fatal familial insomnia, nutritional and metabolic diseases of the nervous system, neurofibromatosis, tuberous sclerosis, cerebelloretinal hemangioblastomatosis, encephalotrigeminal syndrome, mental retardation and other developmental disorder of the central nervous system, cerebral palsy, a neuroskeletal disorder, an autonomic nervous system disorder, a cranial nerve disorder, a spinal cord disease, muscular dystrophy and other neuromuscular disorder, a peripheral nervous system disorder, dermatomyositis and polymyositis, inherited, metabolic, endocrine, and toxic myopathy, myasthenia gravis, periodic paralysis, a mental disorder including mood, anxiety, and schizophrenic disorders, seasonal affective disorder (SAD), akathesia, amnesia, catatonia, diabetic neuropathy, tardive dyskinesia, dystonias, paranoid psychoses, postherpetic neuralgia, and Tourette's disorder; a gastrointestinal disorder including ulcerative colitis, gastric and duodenal ulcers, cystinuria, dibasicaminoaciduria, hypercystinuria, lysinuria, hartnup disease, tryptophan malabsorption, methionine malabsorption, histidinuria, iminoglycinuria, dicarboxylicaminoaciduria, cystinosis, renal glycosuria, hypouricemia, familial hypophophatemic rickets, congenital chloridorrhea, distal renal tubular acidosis, Menkes' disease, Wilson's disease, lethal diarrhea, juvenile pernicious anemia, folate malabsorption, adrenoleukodystrophy, hereditary myoglobinuria, and Zellweger syndrome; a transport disorder such as akinesia, amyotrophic lateral sclerosis, ataxia telangiectasia, cystic fibrosis, Becker's muscular dystrophy, Bell's palsy, Charcot-Marie Tooth disease, diabetes mellitus, diabetes insipidus, diabetic neuropathy, Duchenne muscular dystrophy, hyperkalemic periodic paralysis, normokalemic periodic paralysis, Parkinson's disease, malignant hyperthermia, multidrug resistance, myasthenia gravis, myotonic dystrophy, catatonia, tardive dyskinesia, dystonias, peripheral neuropathy, cerebral neoplasms, prostate cancer, cardiac disorders associated with transport, e.g., angina, bradyarrythmia, tachyarrthmia, hypertension, Long QT syndrome, myocarditis, cardiomyopathy, nemaline myopathy, centronuclear myopathy, lipid myopathy, mitochondrial myopathy, thyrotoxic myopathy, ethanol myopathy, dermatomyositis, inclusion body myositis, infectious myositis, and polymyositis, neurological disorders associated with transport, e.g., Alzheimer's disease, amnesia, bipolar disorder, dementia, depression, epilepsy, Tourette's disorder, paranoid psychoses, and schizophrenia, and other disorders associated with transport, e.g., neurofibromatosis, postherpetic neuralgia, trigeminal neuropathy, sarcoidosis, sickle cell anemia, cataracts, infertility, pulmonary artery stenosis, sensorineural autosomal deafness, hyperglycemia, hypoglycemia, Grave's disease, goiter, glucose-galactose malabsorption syndrome, hypercholesterolemia, Cushing's disease, and Addison's disease; and a connective tissue disorder such as osteogenesis imperfecta, Ehlers-Danlos syndrome, chondrodysplasias, Marfan syndrome, Alport syndrome, familial aortic aneurysm, achondroplasia, mucopolysaccharidoses, osteoporosis, osteopetrosis, Paget's disease, rickets, osteomalacia, hyperparathyroidism, renal osteodystrophy, osteonecrosis, osteomyelitis, osteoma, osteoid osteoma, osteoblastoma, osteosarcoma, osteochondroma, chondroma, chondroblastoma, chondromyxoid fibroma, chondrosarcoma, fibrous cortical defect, nonossifying fibroma, fibrous dysplasia, fibrosarcoma, malignant fibrous histiocytoma, Ewing's sarcoma, primitive neuroectodermal tumor, giant cell tumor, osteoarthritis, rheumatoid arthritis, ankylosing spondyloarthritis, Reiter's syndrome, psoriatic arthritis, enteropathic arthritis, infectious arthritis, gout, gouty arthritis, calcium pyrophosphate crystal deposition disease, ganglion, synovial cyst, villonodular synovitis, systemic sclerosis, Dupuytren's contracture, hepatic fibrosis, lupus erytematosus, mixed connective tissue disease, epidermolysis bullosa simplex, bullous congenital ichthyosiform erythroderma (epidermolytic hyperkeratosis), non-epidermolytic and epidermolytic palmoplantar keratoderma, ichthyosis bullosa of Siemens, pachyonychia congenita, and white sponge nevus. The dithp can be used to detect the presence of, or to quantify the amount of, a dithp-related polynucleotide in a sample. This information is then compared to information obtained from appropriate reference samples, and a diagnosis is established. Alternatively, a polynucleotide complementary to a given dithp can inhibit or inactivate a therapeutically relevant gene related to the dithp.

[0715] Analysis of Dithp Expression Patterns

[0716] The expression of dithp may be routinely assessed by hybridization-based methods to determine, for example, the tissue-specificity, disease-specificity, or developmental stage-specificity of dithp expression. For example, the level of expression of dithp may be compared among different cell types or tissues, among diseased and normal cell types or tissues, among cell types or tissues at different developmental stages, or among cell types or tissues undergoing various treatments. This type of analysis is useful, for example, to assess the relative levels of dithp expression in fully or partially differentiated cells or tissues, to determine if changes in dithp expression levels are correlated with the development or progression of specific disease states, and to assess the response of a cell or tissue to a specific therapy, for example, in pharmacological or toxicological studies. Methods for the analysis of dithp expression are based on hybridization and amplification technologies and include membrane-based procedures such as northern blot analysis, high-throughput procedures that utilize, for example, microarrays, and PCR-based procedures.

[0717] Hybridization and Genetic Analysis

[0718] The dithp, their fragments, or complementary sequences, may be used to identify the presence of and/or to determine the degree of similarity between two (or more) nucleic acid sequences. The dithp may be hybridized to naturally occurring or recombinant nucleic acid sequences under appropriately selected temperatures and salt concentrations. Hybridization with a probe based on the nucleic acid sequence of at least one of the dithp allows for the detection of nucleic acid sequences, including genomic sequences, which are identical or related to the dithp of the Sequence Listing. Probes may be selected from non-conserved or unique regions of at least one of the polynucleotides of SEQ ID NO:1-56 and tested for their ability to identify or amplify the target nucleic acid sequence using standard protocols.

[0719] Polynucleotide sequences that are capable of hybridizing, in particular, to those shown in SEQ ID NO:1-56 and fragments thereof, can be identified using various conditions of stringency. (See, e.g., Wahl, G. M. and S. L. Berger (1987) Methods Enzymol. 152:399-407; Kimmel, A. R. (1987) Methods Enzymol. 152:507-511.) Hybridization conditions are discussed in “definitions.”

[0720] A probe for use in Southern or northern hybridization may be derived from a fragment of a dithp sequence, or its complement, that is up to several hundred nucleotides in length and is either single-stranded or double-stranded. Such probes may be hybridized in solution to biological materials such as plasmids, bacterial, yeast, or human artificial chromosomes, cleared or sectioned tissues, or to artificial substrates containing dithp. Microarrays are particularly suitable for identifying the presence of and detecting the level of expression for multiple genes of interest by examining gene expression correlated with, e.g., various stages of development, treatment with a drug or compound, or disease progression. An array analogous to a dot or slot blot may be used to arrange and link polynucleotides to the surface of a substrate using one or more of the following: mechanical (vacuum), chemical, thermal, or UV bonding procedures. Such an array may contain any number of dithp and may be produced by hand or by using available devices, materials, and machines.

[0721] Microarrays may be prepared, used, and analyzed using methods known in the art. (See, e.g., Brennan, T. M. et al. (1995) U.S. Pat. No. 5,474,796; Schena, M. et al. (1996) Proc. Natl. Acad. Sci. USA 93:10614-10619; Baldeschweiler et al. (1995) PCT application WO95/251116; Shalon, D. et al. (1995) PCT application WO95/35505; Heller, R. A. et al. (1997) Proc. Natl. Acad. Sci. USA 94:2150-2155; and Heller, M. J. et al. (1997) U.S. Pat. No. 5,605,662.)

[0722] Probes may be labeled by either PCR or enzymatic techniques using a variety of commercially available reporter molecules. For example, commercial kits are available for radioactive and chemiluminescent labeling (Amersham Pharmacia Biotech) and for alkaline phosphatase labeling (Life Technologies). Alternatively, dithp maybe cloned into commercially available vectors for the production of RNA probes. Such probes may be transcribed in the presence of at least one labeled nucleotide (e.g., 32P-ATP, Amersham Pharmacia Biotech).

[0723] Additionally the polynucleotides of SEQ ID NO:1-56 or suitable fragments thereof can be used to isolate fall length cDNA sequences utilizing hybridization and/or amplification procedures well known in the art, e.g., cDNA library screening, PCR amplification, etc. The molecular cloning of such fall length cDNA sequences may employ the method of cDNA library screening with probes using the hybridization, stringency, washing, and probing strategies described above and in Ausubel, supra, Chapters 3, 5, and 6. These procedures may also be employed with genomic libraries to isolate genomic sequences of dithp in order to analyze, e.g., regulatory elements. Genetic Mapping

[0724] Gene identification and mapping are important in the investigation and treatment of almost all conditions, diseases, and disorders. Cancer, cardiovascular disease, Alzheimer's disease, arthritis, diabetes, and mental illnesses are of particular interest. Each of these conditions is more complex than the single gene defects of sickle cell anemia or cystic fibrosis, with select groups of genes being predictive of predisposition for a particular condition, disease, or disorder. For example, cardiovascular disease may result from malfunctioning receptor molecules that fail to clear cholesterol from the bloodstream, and diabetes may result when a particular individual's immune system is activated by an infection and attacks the insulin-producing cells of the pancreas. In some studies; Alzheimer's disease has been linked to a gene on chromosome 21; other studies predict a different gene and location. Mapping of disease genes is a complex and reiterative process and generally proceeds from genetic linkage analysis to physical mapping.

[0725] As a condition is noted among members of a family, a genetic linkage map traces parts of chromosomes that are inherited in the same pattern as the condition. Statistics link the inheritance of particular conditions to particular regions of chromosomes, as defined by RFLP or other markers. (See, for example, Lander, E. S. and Botstein, D. (1986) Proc. Natl. Acad. Sci. USA 83:7353-7357.) Occasionally, genetic markers and their locations are known from previous studies. More often, however, the markers are simply stretches of DNA that differ among individuals. Examples of genetic linkage maps can be found in various scientific journals or at the Online Mendelian Inheritance in Man (OMIM) World Wide Web site.

[0726] In another embodiment of the invention, dithp sequences may be used to generate hybridization probes useful in chromosomal mapping of naturally occurring genomic sequences. Either coding or noncoding sequences of dithp may be used, and in some instances, noncoding sequences maybe preferable over coding sequences. For example, conservation of a dithp coding sequence among members of a multi-gene family may potentially cause undesired cross hybridization during chromosomal mapping. The sequences may be mapped to a particular chromosome, to a specific region of a chromosome, or to artificial chromosome constructions, e.g., human artificial chromosomes (HACs), yeast artificial chromosomes (YACs), bacterial artificial chromosomes (BACs), bacterial P1 constructions, or single chromosome cDNA libraries. (See, e.g., Harrington, J. J. et al. (1997) Nat. Genet 15:345-355; Price, C. M. (1993) Blood Rev. 7:127-134; and Trask, B. J. (1991) Trends Genet. 7:149-154.)

[0727] Fluorescent in situ hybridization (FISH) may be correlated with other physical chromosome mapping techniques and genetic map data. (See, e.g., Meyers, supra, pp. 965-968.) Correlation between the location of dithp on a physical chromosomal map and a specific disorder, or a predisposition to a specific disorder, may help define the region of DNA associated with that disorder. The dithp sequences may also be used to detect polymorphisms that are genetically linked to the inheritance of a particular condition, disease, or disorder.

[0728] In situ hybridization of chromosomal preparations and genetic mapping techniques, such as linkage analysis using established chromosomal markers, may be used for extending existing genetic maps. Often the placement of a gene on the chromosome of another mammalian species, such as mouse, may reveal associated markers even if the number or arm of the corresponding human chromosome is not known. These new marker sequences can be mapped to human chromosomes and may provide valuable information to investigators searching for disease genes using positional cloning or other gene discovery techniques. Once a disease or syndrome has been crudely correlated by genetic linkage with a particular genomic region, e.g., ataxia-telangiectasia to 11q22-23, any sequences mapping to that area may represent associated or regulatory genes for further investigation. (See, e.g., Gatti, R. A. et al. (1988) Nature 336:577-580.) The nucleotide sequences of the subject invention may also be used to detect differences in chromosomal architecture due to translocation, inversion, etc., among normal, carrier, or affected individuals.

[0729] Once a disease-associated gene is mapped to a chromosomal region, the gene must be cloned in order to identify mutations or other alterations (e.g., translocations or inversions) that may be correlated with disease. This process requires a physical map of the chromosomal region containing the disease-gene of interest along with associated markers. A physical map is necessary for determining the nucleotide sequence of and order of marker genes on a particular chromosomal region. Physical mapping techniques are well known in the art and require the generation of overlapping sets of cloned DNA fragments from a particular organelle, chromosome, or genome. These clones are analyzed to reconstruct and catalog their order. Once the position of a marker is determined, the DNA from that region is obtained by consulting the catalog and selecting clones from that region. The gene of interest is located through positional cloning techniques using hybridization or similar methods.

[0730] Diagnostic Uses

[0731] The dithp of the present invention may be used to design probes useful in diagnostic assays. Such assays, well known to those skilled in the art, may be used to detect or confirm conditions, disorders, or diseases associated with abnormal levels of dithp expression. Labeled probes developed from dithp sequences are added to a sample under hybridizing conditions of desired stringency. In some instances, dithp, or fragments or oligonucleotides derived from dithp, may be used as primers in amplification steps prior to hybridization. The amount of hybridization complex formed is quantified and compared with standards for that cell or tissue. If dithp expression varies significantly from the standard, the assay indicates the presence of the condition, disorder, or disease. Qualitative or quantitative diagnostic methods may include northern, dot blot, or other membrane or dip-stick based technologies or multiple-sample format technologies such as PCR, enzyme-linked immunosorbent assay (ELISA)-like, pin, or chip-based assays.

[0732] The probes described above may also be used to monitor the progress of conditions, disorders, or diseases associated with abnormal levels of dithp expression, or to evaluate the efficacy of a particular therapeutic treatment. The candidate probe may be identified from the dithp that are specific to a given human tissue and have not been observed in GenBank or other genome databases. Such a probe may be used in animal studies, preclinical tests, clinical trials, or in monitoring the treatment of an individual patient. In a typical process, standard expression is established by methods well known in the art for use as a basis of comparison, samples from patients affected by the disorder or disease are combined with the probe to evaluate any deviation from the standard profile, and a therapeutic agent is administered and effects are monitored to generate a treatment profile. Efficacy is evaluated by determining whether the expression progresses toward or returns to the standard normal pattern. Treatment profiles may be generated over a period of several days or several months. Statistical methods well known to those skilled in the art maybe use to determine the significance of such therapeutic agents.

[0733] The polynucleotides are also useful for identifying individuals from minute biological samples, for example, by matching the RFLP pattern of a sample's DNA to that of an individual's DNA. The polynucleotides of the present invention can also be used to determine the actual base-by-base DNA sequence of selected portions of an individual's genome. These sequences can be used to prepare PCR primers for amplifying and isolating such selected DNA, which can then be sequenced. Using this technique, an individual can be identified through a unique set of DNA sequences. Once a unique ID database is established for an individual, positive identification of that individual can be made from extremely small tissue samples.

[0734] In a particular aspect, oligonucleotide primers derived from the dithp of the invention may be used to detect single nucleotide polymorphisms (SNPs). SNPs are substitutions, insertions and deletions that are a frequent cause of inherited or acquired genetic disease in humans. Methods of SNP detection include, but are not limited to, single-stranded conformation polymorphism (SSCP) and fluorescent SSCP (fSSCP) methods. In SSCP, oligonucleotide primers derived from dithp are used to amplify DNA using the polymerase chain reaction (PCR). The DNA may be derived, for example, from diseased or normal tissue, biopsy samples, bodily fluids, and the like. SNPs in the DNA cause differences in the secondary and tertiary structures of PCR products in single-stranded form, and these differences are detectable using gel electrophoresis in non-denaturing gels. In fSCCP, the oligonucleotide primers are fluorescently labeled, which allows detection of the amplimers in high-throughput equipment such as DNA sequencing machines. Additionally, sequence database analysis methods, termed in silico SNP (is SNP), are capable of identifying polymorphisms by comparing the sequences of individual overlapping DNA fragments which assemble into a common consensus sequence. These computer-based methods filter out sequence variations due to laboratory preparation of DNA and sequencing errors using statistical models and automated analyses of DNA sequence chromatograms. In the alternative, SNPs may be detected and characterized by mass spectrometry using, for example, the high throughput MASSARRAY system (Sequenom, Inc., San Diego Calif.).

[0735] DNA-based identification techniques are critical in forensic technology. DNA sequences taken from very small biological samples such as tissues, e.g., hair or skin, or body fluids, e.g., blood, saliva, semen, etc., can be amplified using, e.g., PCR, to identify individuals. (See, e.g., Erlich, H. (1992) PCR Technology, Freeman and Co., New York, N.Y.). Similarly, polynucleotides of the present invention can be used as polymorphic markers.

[0736] There is also a need for reagents capable of identifying the source of a particular tissue. Appropriate reagents can comprise, for example, DNA probes or primers prepared from the sequences of the present invention that are specific for particular tissues. Panels of such reagents can identify tissue by species and/or by organ type. In a similar fashion, these reagents can be used to screen tissue cultures for contamination.

[0737] The polynucleotides of the present invention can also be used as molecular weight markers on nucleic acid gels or Southern blots, as diagnostic probes for the presence of a specific mRNA in a particular cell type, in the creation of subtracted cDNA libraries which aid in the discovery of novel polynucleotides, in selection and synthesis of oligomers for attachment to an array or other support, and as an antigen to elicit an immune response.

[0738] Disease Model Systems Using Dithp,

[0739] The dithp of the invention or their mammalian homologs may be “knocked out” in an animal model system using homologous recombination in embryonic stem (ES) cells. Such techniques are well known in the art and are useful for the generation of animal models of human disease. (See, e.g., U.S. Pat. No. 5,175,383 and U.S. Pat. No. 5,767,337.) For example, mouse ES cells, such as the mouse 129/SvJ cell line, are derived from the early mouse embryo and grown in culture. The ES cells are transformed with a vector containing the gene of interest disrupted by a marker gene, e.g., the neomycin phosphotransferase gene (neo; Capecchi, M. R. (1989) Science 244:1288-1292). The vector integrates into the corresponding region of the host genome by homologous recombination. Alternatively, homologous recombination takes place using the Cre-loxP system to knockout a gene of interest in a tissue- or developmental stage-specific manner (Marth, J. D. (1996) Clin. Invest. 97:1999-2002; Wagner, K. U. et al. (1997) Nucleic Acids Res. 25:4323-4330). Transformed ES cells are identified and microinjected into mouse cell blastocysts such as those from the C57BL/6 mouse strain. The blastocysts are surgically transferred to pseudopregnant dams, and the resulting chimeric progeny are genotyped and bred to produce heterozygous or homozygous strains. Transgenic animals thus generated may be tested with potential therapeutic or toxic agents.

[0740] The dithp of the invention may also be manipulated in vitro in ES cells derived from human blastocysts. Human ES cells have the potential to differentiate into at least eight separate cell lineages including endoderm, mesoderm, and ectodermal cell types. These cell lineages differentiate into, for example, neural cells, hematopoietic lineages, and cardiomyocytes (Thomson, J. A. et al. (1998) Science 282:1145-1147).

[0741] The dithp of the invention can also be used to create knockin” humanized animals (pigs) or transgenic animals (mice or rats) to model human disease. With knocking technology, a region of dithp is injected into animal ES cells, and the injected sequence integrates into the animal cell genome. Transformed cells are injected into blastulae, and the blastulae are implanted as described above. Transgenic progeny or inbred lines are studied and treated with potential pharmaceutical agents to obtain information on treatment of a human disease. Alternatively, a mammal inbred to overexpress dithp, resulting, e.g., in the secretion of DITHP in its milk, may also serve as a convenient source of that protein (Janne, J. et al. (1998) Biotechnol. Annu. Rev. 4:55-74).

[0742] Screening Assays

[0743] DITHP encoded by polynucleotides of the present invention may be used to screen for molecules that bind to or are bound by the encoded polypeptides. The binding of the polypeptide and the molecule may activate (agonist), increase, inhibit (antagonist), or decrease activity of the polypeptide or the bound molecule. Examples of such molecules include antibodies, oligonucleotides, proteins (e.g., receptors), or small molecules.

[0744] Preferably, the molecule is closely related to the natural ligand of the polypeptide, e.g., a ligand or fragment thereof, a natural substrate, or a structural or functional mimetic. (See, Coligan et al., (1991) Current Protocols in Immunology 1(2): Chapter 5.) Similarly, the molecule can be closely related to the natural receptor to which the polypeptide binds, or to at least a fragment of the receptor, e.g., the active site. In either case, the molecule can be rationally designed using known techniques. Preferably, the screening for these molecules involves producing appropriate cells which express the polypeptide, either as a secreted protein or on the cell membrane. Preferred cells include cells from mammals, yeast, Drosophiila, or E. coli. Cells expressing the polypeptide or cell membrane fractions which contain the expressed polypeptide are then contacted with a test compound and binding, stimulation, or inhibition of activity of either the polypeptide or the molecule is analyzed.

[0745] An assay may simply test binding of a candidate compound to the polypeptide, wherein binding is detected by a fluorophore, radioisotope, enzyme conjugate, or other detectable label. Alternatively, the assay may assess binding in the presence of a labeled competitor.

[0746] Additionally, the assay can be carried out using cell-free preparations, polypeptide/molecule affixed to a solid support, chemical libraries, or natural product mixtures. The assay may also simply comprise the steps of mixing a candidate compound with a solution containing a polypeptide, measuring polypeptide/molecule activity or binding, and comparing the polypeptide/molecule activity or binding to a standard.

[0747] Preferably, an ELISA assay using, e.g., a monoclonal or polyclonal antibody, can measure polypeptide level in a sample. The antibody can measure polypeptide level by either binding, directly or indirectly, to the polypeptide or by competing with the polypeptide for a substrate.

[0748] All of the above assays can be used in a diagnostic or prognostic context. The molecules discovered using these assays can be used to treat disease or to bring about a particular result in a patient (e.g., blood vessel growth) by activating or inhibiting the polypeptide/molecule. Moreover, the assays can discover agents which may inhibit or enhance the production of the polypeptide from suitably manipulated cells or tissues.

[0749] Transcript Imaging and Toxicological Testing

[0750] Another embodiment relates to the use of dithp to develop a transcript image of a tissue or cell type. A transcript image represents the global pattern of gene expression by a particular tissue or cell type. Global gene expression patterns are analyzed by quantifying the number of expressed genes and their relative abundance under given conditions and at a given time. (See Seilhamer et al., “Comparative Gene Transcript Analysis,” U.S. Pat. No. 5,840,484, expressly incorporated by reference herein.) Thus a transcript image may be generated by hybridizing the polynucleotides of the present invention or their complements to the totality of transcripts or reverse transcripts of a particular tissue or cell type. In one embodiment, the hybridization takes place in high-throughput format, wherein the polynucleotides of the present invention or their complements comprise a subset of a plurality of elements on a microarray. The resultant transcript image would provide a profile of gene activity pertaining to human molecules for diagnostics and therapeutics.

[0751] Transcript images which profile dithp expression may be generated using transcripts isolated from tissues, cell lines, biopsies, or other biological samples. The transcript image may thus reflect dithp expression in vivo, as in the case of a tissue or biopsy sample, or in vitro, as in the case of a cell line.

[0752] Transcript images which profile dithp expression may also be used in conjunction with in vitro model systems and preclinical evaluation of pharmaceuticals, as well as toxicological testing of industrial and naturally-occurring environmental compounds. All compounds induce characteristic gene expression patterns, frequently termed molecular fingerprints or toxicant signatures, which are indicative of mechanisms of action and toxicity (Nuwaysir, E. F. et al. (1999) Mol. Carcinog. 24:153-159; Steiner, S. and Anderson, N. L. (2000) Toxicol. Lett. 112-113:467-71, expressly incorporated by reference herein). If a test compound has a signature similar to that of a compound with known toxicity, it is likely to share those toxic properties. These fingerprints or signatures are most useful and refined when they contain expression information from a large number of genes and gene families. Ideally, a genome-wide measurement of expression provides the highest quality signature. Even genes whose expression is not altered by any tested compounds are important as well, as the levels of expression of these genes are used to normalize the rest of the expression data. The normalization procedure is useful for comparison of expression data after treatment with different compounds. While the assignment of gene function to elements of a toxicant signature aids in interpretation of toxicity mechanisms, knowledge of gene function is not necessary for the statistical matching of signatures which leads to prediction of toxicity. (See, for example, Press Release 00-02 from the National Institute of Environmental Health Sciences, released Feb. 29, 2000, available at http://www.niehs.nih.gov/oc/news/toxchip.htm.) Therefore, it is important and desirable in toxicological screening using toxicant signatures to include all expressed gene sequences.

[0753] In one embodiment, the toxicity of a test compound is assessed by treating a biological sample containing nucleic acids with the test compound. Nucleic acids that are expressed in the treated biological sample are hybridized with one or more probes specific to the polynucleotides of the present invention, so that transcript levels corresponding to the polynucleotides of the present invention may be quantified. The transcript levels in the treated biological sample are compared with levels in an untreated biological sample. Differences in the transcript levels between the two samples are indicative of a toxic response caused by the test compound in the treated sample.

[0754] Another particular embodiment relates to the use of DRIP encoded by polynucleotides of the present invention to analyze the proteome of a tissue or cell type. The term proteome refers to the global pattern of protein expression in a particular tissue or cell type. Each protein component of a proteome can be subjected individually to further analysis. Proteome expression patterns, or profiles, are analyzed by quantifying the number of expressed proteins and their relative abundance under given conditions and at a given time. A profile of a cell's proteome may thus be generated by separating and analyzing the polypeptides of a particular tissue or cell type. In one embodiment, the separation is achieved using two-dimensional gel electrophoresis, in which proteins from a sample are separated by isoelectric focusing in the first dimension, and then according to molecular weight by sodium dodecyl sulfate slab gel electrophoresis in the second dimension (Steiner and Anderson, supra). The proteins are visualized in the gel as discrete and uniquely positioned spots, typically by staining the gel with an agent such as Coomassie Blue or silver or fluorescent stains. The optical density of each protein spot is generally proportional to the level of the protein in the sample. The optical densities of equivalently positioned protein spots from different samples, for example, from biological samples either treated or untreated with a test compound or therapeutic agent, are compared to identify any changes in protein spot density related to the treatment. The proteins in the spots are partially sequenced using, for example, standard methods employing chemical or enzymatic cleavage followed by mass spectrometry. The identity of the protein in a spot may be determined by comparing its partial sequence, preferably of at least 5 contiguous amino acid residues, to the polypeptide sequences of the present invention. In some cases, further sequence data may be obtained for definitive protein identification

[0755] A proteomic profile may also be generated using antibodies specific for DITHP to quantify the levels of DITHP expression. In one embodiment, the antibodies are used as elements on a microarray, and protein expression levels are quantified by exposing the microarray to the sample and detecting the levels of protein bound to each array element (Lueking, A. et al. (1999) Anal. Biochem. 270:103-11; Mendoze, L. G. et al. (1999) Biotechniques 27:778-88). Detection maybe performed by a variety of methods known in the art, for example, by reacting the proteins in the sample with a thiol- or amino-reactive fluorescent compound and detecting the amount of fluorescence bound at each array element.

[0756] Toxicant signatures at the proteome level are also useful for toxicological screening, and should be analyzed in parallel with toxicant signatures at the transcript level. There is a poor correlation between transcript and protein abundances for some proteins in some tissues (Anderson, N. L. and Seilhamer, J. (1997) Electrophoresis 18:533-537), so proteome toxicant signatures may be useful in the analysis of compounds which do not significantly affect the transcript image, but which alter the proteomic profile. In addition, the analysis of transcripts in body fluids is difficult, due to rapid degradation of mRNA, so proteomic profiling may be more reliable and informative in such cases.

[0757] In another embodiment, the toxicity of a test compound is assessed by treating a biological sample containing proteins with the test compound. Proteins that are expressed in the treated biological sample are separated so that the amount of each protein can be quantified. The amount of each protein is compared to the amount of the corresponding protein in an untreated biological sample. A difference in the amount of protein between the two samples is indicative of a toxic response to the test compound in the treated sample. Individual proteins are identified by sequencing the amino acid residues of the individual proteins and comparing these partial sequences to the DITHP encoded by polynucleotides of the present invention.

[0758] In another embodiment, the toxicity of a test compound is assessed by treating a biological sample containing proteins with the test compound. Proteins from the biological sample are incubated with antibodies specific to the DITHP encoded by polynucleotides of the present invention. The amount of protein recognize by the antibodies is quantified. The amount of protein in the treated biological sample is compared with the amount in an untreated biological sample. A difference in the amount of protein between the two samples is indicative of a toxic response to the test compound in the treated sample.

[0759] Transcript images may be used to profile dithp expression in distinct tissue types. This process can be used to determine human molecule activity in a particular tissue type relative to this activity in a different tissue type. Transcript images may be used to generate a profile of dithp expression characteristic of diseased tissue. Transcript images of tissues before and after treatment may be used for diagnostic purposes, to monitor the progression of disease, and to monitor the efficacy of drug treatments for diseases which affect the activity of human molecules.

[0760] Transcript images of cell lines can be used to assess human molecule activity and/or to identify cell lines that lack or misregulate this activity. Such cell lines may then be treated with pharmaceutical agents, and a transcript image following treatment may indicate the efficacy of these agents in restoring desired levels of this activity. A similar approach may be used to assess the toxicity of pharmaceutical agents as reflected by undesirable changes in human molecule activity. Candidate pharmaceutical agents may be evaluated by comparing their associated transcript images with those of pharmaceutical agents of known effectiveness.

[0761] Antisense Molecules

[0762] The polynucleotides of the present invention are useful in antisense technology. Antisense technology or therapy relies on the modulation of expression of a target protein through the specific binding of an antisense sequence to a target sequence encoding the target protein or directing its expression. (See, e.g., Agrawal, S., ed. (1996) Antisense Therapeutics, Humana Press Inc., Totawa N.J.; Alama, A. et al. (1997) Pharmacol. Res. 36(3):171-178; Crooke, S. T. (1997) Adv. Pharmacol. 40:1-49; Sharma, H. W. and R. Narayanan (1995) Bioessays 17(12):1055-1063; and Lavrosky, Y. et al. (1997) Biochem. Mol. Med. 62(1):11-22.) An antisense sequence is a polynucleotide sequence capable of specifically hybridizing to at least a portion of the target sequence. Antisense sequences bind to cellular mRNA and/or genomic DNA, affecting translation and/or transcription. Antisense sequences can be DNA, RNA, or nucleic acid mimics and analogs. (See, e.g., Rossi, J. J. et al. (1991) Antisense Res. Dev. 1(3):285-288; Lee, R. et al. (1998) Biochemistry 37(3):900-1010; Pardridge, W. M. et al. (1995) Proc. Natl. Acad. Sci. USA 92(12):5592-5596; and Nielsen, P. E. and Haaima, G. (1997) Chem. Soc. Rev. 96:73-78.) Typically, the binding which results in modulation of expression occurs through hybridization or binding of complementary base pairs. Antisense sequences can also bind to DNA duplexes through specific interactions in the major groove of the double helix.

[0763] The polynucleotides of the present invention and fragments thereof can be used as antisense sequences to modify the expression of the polypeptide encoded by dithp. The antisense sequences can be produced ex vivo, such as by using any of the ABI nucleic acid synthesizer series (Applied Biosystems) or other automated systems known in the art. Antisense sequences can also be produced biologically, such as by transforming an appropriate host cell with an expression vector containing the sequence of interest (See, e.g., Agrawal, supra.)

[0764] In therapeutic use, any gene delivery system suitable for introduction of the antisense sequences into appropriate target cells can be used. Antisense sequences can be delivered intracellularly in the form of an expression plasmid which, upon transcription, produces a sequence complementary to at least a portion of the cellular sequence encoding the target protein. (See, e.g., Slater, J. E., et al. (1998) J. Allergy Clin Immunol. 102(3):469475; and Scanlon, K. J., et al. (1995) 9(13):1288-1296.) Antisense sequences can also be introduced intracellularly through the use of viral vectors, such as retrovirus and adeno-associated virus vectors. (See, e.g., Miller, A. D. (1990) Blood 76:271; Ausubel, F. M. et al. (1995) Current Protocols in Molecular Biology, John Wiley & Sons, New York N.Y.; Uckert, W. and W. Walther (1994) Pharmacol. Ther. 63(3):323-347.) Other gene delivery mechanisms include liposome-derived systems, artificial viral envelopes, and other systems known in the art. (See, e.g., Rossi, J. J. (1995) Br. Med. Bull. 51(1):217-225; Boado, R. J. et al. (1998) J. Pharm. Sci. 87(11):1308-1315; and Morris, M. C. et al. (1997) Nucleic Acids Res. 25(14):2730-2736.)

[0765] Expression

[0766] In order to express a biologically active DITHP, the nucleotide sequences encoding DITHP or fragments thereof maybe inserted into an appropriate expression vector, i.e., a vector which contains the necessary elements for transcriptional and translational control of the inserted coding sequence in a suitable host. Methods which are well known to those skilled in the art may be used to construct expression vectors containing sequences encoding DITHP and appropriate transcriptional and translational control elements. These methods include in vitro recombinant DNA techniques, synthetic techniques, and in vivo genetic recombination. (See, e.g., Sambrook, supra, Chapters 4, 8, 16, and 17; and Ausubel, supra, Chapters 9, 10, 13, and 16.)

[0767] A variety of expression vector/host systems may be utilized to contain and express sequences encoding DITHP. These include, but are not limited to, microorganisms such as bacteria transformed with recombinant bacteriophage, plasmid, or cosmid DNA expression vectors; yeast transformed with yeast expression vectors; insect cell systems infected with viral expression vectors (e.g., baculovirus); plant cell systems transformed with viral expression vectors (e.g., cauliflower mosaic virus, CaMV, or tobacco mosaic virus, TMV) or with bacterial expression vectors (e.g., Ti or pBR322 plasmids); or animal (mammalian) cell systems. (See, e.g., Sambrook, supra; Ausubel, 1995, supra, Van Heeke, G. and S. M. Schuster (1989) J. Biol. Chem. 264:5503-5509; Bitter, G. A. et al. (1987) Methods Enzymol. 153:516-544; Scorer, C. A. et al. (1994) Bio/Technology 12:181-184; Engelhard, E. K. et al. (1994) Proc. Natl. Acad. Sci. USA 91:3224-3227; Sandig, V. et al. (1996) Hum. Gene Ther. 7:1937-1945; Takamatsu, N. (1987) EMBO J. 6:307-311; Coruzzi, G. et al. (1984) EMBO J. 3:1671-1680; Broglie, R. et al. (1984) Science 224:838-843; Winter, J. et al. (1991) Results Probl. Cell Differ. 17:85-105; The McGraw Hill Yearbook of Science and Technology (1992) McGraw Hill, New York N.Y., pp. 191-196; Logan, J. and T. Shenk (1984) Proc. Natl. Acad. Sci. USA 81:3655-3659; and Harrington, J. J. et al. (1997) Nat Genet. 15:345-355.) Expression vectors derived from retroviruses, adenoviruses, or herpes or vaccinia viruses, or from various bacterial plasmids, maybe used for delivery of nucleotide sequences to the targeted organ, tissue, or cell population (See, e.g., Di Nicola, M. et al. (1998) Cancer Gen. Ther. 5(6):350-356; Yu, M. et al., (1993) Proc. Natl. Acad. Sci. USA 90(13):6340-6344; Buller, R. M. et al. (1985) Nature 317(6040):813-815; McGregor, D. P. et al. (1994) Mol. Immunol. 31(3):219-226; and Verma, I. M. and N. Somia (1997) Nature 389:239-242.) The invention is not limited by the host cell employed.

[0768] For long term production of recombinant proteins in mammalian systems, stable expression of DITHP in cell lines is preferred. For example, sequences encoding DITHP can be transformed into cell lines using expression vectors which may contain viral origins of replication and/or endogenous expression elements and a selectable marker gene on the same or on a separate vector. Any number of selection systems maybe used to recover transformed cell lines. (See, e.g., Wigler, M. et al. (1977) Cell 11:223-232; Lowy, I. et al. (1980) Cell 22:817-823.; Wigler, M. et al. (1980) Proc. Natl. Acad. Sci. USA 77:3567-3570; Colbere-Garapin, F. et al. (1981) J. Mol. Biol. 150:1-14; Hartman, S. C. and R. C. Mulligan (1988) Proc. Natl. Acad. Sci. USA 85:8047-8051; Rhodes, C. A. (1995) Methods Mol. Biol. 55:121-131.)

[0769] Therapeutic Uses of Dithp

[0770] The dithp of the invention may be used for somatic or germline gene therapy. Gene therapy may be performed to (i) correct a genetic deficiency (e.g., in the cases of severe combined immunodeficiency (SCID)-X1 disease characterized by X-linked inheritance (Cavazzana-Calvo, M. et al. (2000) Science 288:669-672), severe combined immunodeficiency syndrome associated with an inherited adenosine deaminase (ADA) deficiency (Blaese, R. M. et al. (1995) Science 270:475-480; Bordignon, C. et al. (1995) Science 270:470-475), cystic fibrosis (Zabner, J. et al. (1993) Cell 75:207-216; Crystal, R. G. et al. (1995) Hum. Gene Therapy 6:643-666; Crystal, R. G. et al. (1995) Hum. Gene Therapy 6:667-703), thalassemias, familial hypercholesterolemia, and hemophilia resulting from Factor VIII or Factor IX deficiencies (Crystal, R. G. (1995) Science 270:404-410; Verma, I. M. and Somia, N. (1997) Nature 389:239-242)), (ii) express a conditionally lethal gene product (e.g., in the case of cancers which result from unregulated cell proliferation), or (iii) express a protein which affords protection against intracellular parasites (e.g., against human retroviruses, such as human immunodeficiency virus (HIV) (Baltimore, D. (1988) Nature 335:395-396; Poeschla, E. et al. (1996) Proc. Natl. Acad. Sci. USA. 93:11395-11399), hepatitis B or C virus (HBV, HCV); fungal parasites, such as Candida albicans and Paracoccidioides brasiliensis; and protozoan parasites such as Plasmodium falciparum and Trypanosoma cruzi). In the case where a genetic deficiency in dithp expression or regulation causes disease, the expression of dithp from an appropriate population of transduced cells may alleviate the clinical manifestations caused by the genetic deficiency.

[0771] In a further embodiment of the invention, diseases or disorders caused by deficiencies in dithp are treated by constructing mammalian expression vectors comprising dithp and introducing these vectors by mechanical means into dithp-deficient cells. Mechanical transfer technologies for use with cells in vivo or ex vitro include (i) direct DNA microinjection into individual cells, (ii) ballistic gold particle delivery, (iii) liposome-mediated transfection, (iv) receptor-mediated gene transfer, and (v) the use of DNA transposons (Morgan, R. A. and Anderson, W. F. (1993) Annu. Rev. Biochem. 62:191-217; Ivics, Z. (1997) Cell 91:501-510; Boulay, J-L. and Récipon, H. (1998) Curr. Opin. Biotechnol. 9:445-450).

[0772] Expression vectors that may be effective for the expression of dithp include, but are not limited to, the PCDNA 3.1, EPITAG, PRCCMV2, PREP, PVAX vectors (Invitrogen, Carlsbad Calif.), PCMV-SCRIPT, PCMV-TAG, PEGSH/PERV (Stratagene, La Jolla Calif.), and PTET-OFF, PTET-ON, PTRE2, PTRE2-LUC, PTK-HYG (Clontech, Palo Alto Calif.). The dithp of the invention may be expressed using (i) a constitutively active promoter, (e.g., from cytomegalovirus (CMV), Rous sarcoma virus (RSV), SV40 virus, thymidine kinase (TK), or β-actin genes), (ii) an inducible promoter (e.g., the tetracycline-regulated promoter (Gossen, M. and Bujard, H. (1992) Proc. Natl. Acad. Sci. U.S.A. 89:5547-5551; Gossen, M. et al., (1995) Science 268:1766-1769; Rossi, F. M. V. and Blau, H. M. (1998) Curr. Opin. Biotechnol. 9:451-456), commercially available in the T-REX plasmnid (Invitrogen); the ecdysone-inducible promoter (available in the plasmids PVGRXR and PIND; Invitrogen); the FK506/rapamycin inducible promoter; or the RU486/mifepristone inducible promoter (Rossi, F. M. V. and Blau, H. M. supra), or (iii) a tissue-specific promoter or the native promoter of the endogenous gene encoding DITHP from a normal individual.

[0773] Commercially available liposome transformation kits (e.g., the PERFECT LIPID TANSFECTION KIT, available from Invitrogen) allow one with ordinary skill in the art to deliver polynucleotides to target cells in culture and require minimal effort to optimize experimental parameters. In the alternative, transformation is performed using the calcium phosphate method (Graham, F. L. and Eb, A. J. (1973) Virology 52:456-467), or by electroporation (Neumann, E. et al. (1982) EMBO J. 1:841-845). The introduction of DNA to primary cells requires modification of these standardized mammalian transfection protocols.

[0774] In another embodiment of the invention, diseases or disorders caused by genetic defects with respect to dithp expression are treated by constructing a retrovirus vector consisting of (i) dithp under the control of an independent promoter or the retrovirus long terminal repeat (LTR) promoter, (ii) appropriate RNA packaging signals, and (iii) a Rev-responsive element (RRE) along with additional retrovirus cis-acting RNA sequences and coding sequences required for efficient vector propagation. Retrovirus vectors (e.g., PFB and PFBNEO) are commercially available (Stratagene) and are based on published data (Riviere, I. et al. (1995) Proc. Natl. Acad. Sci. U.S.A. 92:6733-6737), incorporated by reference herein. The vector is propagated in an appropriate vector producing cell line (VPCL) that expresses an envelope gene with a tropism for receptors on the target cells or a promiscuous envelope protein such as VSVg (Armentano, D. et al. (1987) J. Virol. 61:1647-1650; Bender, M. A. et al. (1987) J. Virol. 61:1639-1646; Adam, M. A. and Miller, A. D. (1988) J. Virol. 62:3802-3806; Dull, T. et al. (1998) J. Virol. 72:8463-8471; Zufferey, R. et al. (1998) J. Virol. 72:9873-9880). U.S. Pat. No. 5,910,434 to Rigg (“Method for obtaining retrovirus packaging cell lines producing high transducing efficiency retroviral supernatant”) discloses a method for obtaining retrovirus packaging cell lines and is hereby incorporated by reference. Propagation of retrovirus vectors, transduction of a population of cells (e.g., CD4+ T-cells), and the return of transduced cells to a patient are procedures well known to persons skilled in the art of gene therapy and have been well documented (Ranga, U. et al. (1997) J. Virol. 71:7020-7029; Bauer, G. et al. (1997) Blood 89:2259-2267; Bonyhadi, M. L. (1997) J. Virol. 71:4707-4716; Ranga, U. et al. (1998) Proc. Natl. Acad. Sci. U.S.A. 95:1201-1206; Su, L. (1997) Blood 89:2283-2290).

[0775] In the alternative, an adenovirus-based gene therapy delivery system is used to deliver dithp to cells which have one or more genetic abnormalities with respect to the expression of dithp. The construction and packaging of adenovirus-based vectors are well known to those with ordinary skill in the art. Replication defective adenovirus vectors have proven to be versatile for importing genes encoding immunoregulatory proteins into intact islets in the pancreas (Csete, M. E. et al. (1995) Transplantation 27:263-268). Potentially useful adenoviral vectors are described in U.S. Pat. No. 5,707,618 to Armentano (“Adenovirus vectors for gene therapy”), hereby incorporated by reference. For adenoviral vectors, see also Antinozzi, P. A. et al. (1999) Annu. Rev. Nutr. 19:511-544 and Verma, I. M. and Somia, N. (1997) Nature 18:389:239-242, both incorporated by reference herein.

[0776] In another alternative, a herpes-based, gene therapy delivery system is used to deliver dithp to target cells which have one or more genetic abnormalities with respect to the expression of dithp. The use of herpes simplex virus (HSV)-based vectors may be especially valuable for introducing dithp to cells of the central nervous system, for which HSV has a tropism. The construction and packaging of herpes-based vectors are well known to those with ordinary skill in the art. A replication-competent herpes simplex virus (HSV) type 1-based vector has been used to deliver a reporter gene to the eyes of primates (Liu, X. et al. (1999) Exp. Eye Res.169:385-395). The construction of a HSV-1 virus vector has also been disclosed in detail in U.S. Pat. No. 5,804,413 to DeLuca (“Herpes simplex virus strains for gene transfer”), which is hereby incorporated by reference. U.S. Pat. No. 5,804,413 teaches the use of recombinant HSV d92 which consists of a genome containing at least one exogenous gene to be transferred to a cell under the control of the appropriate promoter for purposes including human gene therapy. Also taught by this patent are the construction and use of recombinant HSV strains deleted for ICP4, ICP27 and ICP22: For HSV vectors, see also Goins, W. F. et al. 1999 J. Biol. 73:519-532 and Xu, R et al., (1994) Dev. Biol 163:152-161, hereby incorporated by reference. The manipulation of cloned herpesvirus sequences, the generation of recombinant virus following the transfection of multiple plasmids containing different segments of the large herpesvirus genomes, the growth and propagation of herpesvirus, and the infection of cells with herpesvirus are techniques well known to those of ordinary skill in the art.

[0777] In another alternative, an alphavirus (positive, single-stranded RNA virus) vector is used to deliver dithp to target cells. The biology of the prototypic alphavirus, Semliki Forest Virus (SFV), has been studied extensively and gene transfer vectors have been based on the SFV genome (Garoff, H. and Li, K-J. (1998) Curr. Opin. Biotech. 9:464-469). During alphavirus RNA replication, a subgenomic RNA is generated that normally encodes the viral capsid proteins. This subgenomic RNA replicates to higher levels than the full-length genomic RNA, resulting in the overproduction of capsid proteins relative to the viral proteins with enzymatic activity (e.g., protease and polymerase). Similarly, inserting dithp into the alphavirus genome in place of the capsid-coding region results in the production of a large number of dithp RNAs and the synthesis of high levels of DITHP in vector transduced cells. While alphavirus infection is typically associated with cell lysis within a few days, the ability to establish a persistent infection in hamster normal kidney cells (BHK-21) with a variant of Sindbis virus (SIN) indicates that the lytic replication of alphaviruses can be altered to suit the needs of the gene therapy application (Dryga, S. A. et al. (1997) Virology 228:74-83). The wide host range of alphaviruses will allow the introduction of dithp into a variety of cell types. The specific transduction of a subset of cells in a population may require the sorting of cells prior to transduction. The methods of manipulating infectious cDNA clones of alphaviruses, performing alphavirus cDNA and RNA transfections, and performing alphavirus infections, are well known to those with ordinary skill in the art.

[0778] Antibodies

[0779] Anti-DITHP antibodies may be used to analyze protein expression levels. Such antibodies include, but are not limited to, polyclonal, monoclonal, chimeric, single chain, and Fab fragments. For descriptions of and protocols of antibody technologies, see, e.g., Pound J. D. (1998) Immunochemical Protocols, Humana Press, Totowa, N.J.

[0780] The amino acid sequence encoded by the dithp of the Sequence Listing may be analyzed by appropriate software (e.g., LASERGENE NAVIGATOR software, DNASTAR) to determine regions of high immunogenicity. The optimal sequences for immunization are selected from the C-terminus, the N-terminus, and those intervening, hydrophilic regions of the polypeptide which are likely to be exposed to the external environment when the polypeptide is in its natural conformation. Analysis used to select appropriate epitopes is also described by Ausubel (1997, supra, Chapter 11.7). Peptides used for antibody induction do not need to have biological activity; however, they must be antigenic. Peptides used to induce specific antibodies may have an amino acid sequence consisting of at least five amino acids, preferably at least 10 amino acids, and most preferably at least 15 amino acids. A peptide which mimics an antigenic fragment of the natural polypeptide may be fused with another protein such as keyhole limpet hemocyanin (KLH; Sigma, St Louis Mo.) for antibody production. A peptide encompassing an antigenic region may be expressed from a dithp, synthesized as described above, or purified from human cells.

[0781] Procedures well known in the art may be used for the production of antibodies. Various hosts including mice, goats, and rabbits, maybe immunized by injection with a peptide. Depending on the host species, various adjuvants may be used to increase immunological response.

[0782] In one procedure, peptides about 15 residues in length may be synthesized using an ABI 431A peptide synthesizer (Applied Biosystems) using fmoc-chemistry and coupled to KLH (Sigma) by reaction with M-maleimidobenzoyl-N-hydroxysuccinimide ester (Ausubel, 1995, supra). Rabbits are immunized with the peptide-KLH complex in complete Freund's adjuvant. The resulting antisera are tested for antipeptide activity by binding the peptide to plastic, blocking with 1% bovine serum albumin (BSA), reacting with rabbit antisera, washing, and reacting with radioiodinated goat anti-rabbit IgG. Antisera with antipeptide activity are tested for anti-DRIP activity using protocols well known in the art, including ELISA, radioimmunoassay (RIA), and immunoblotting.

[0783] In another procedure, isolated and purified peptide may be used to immunize mice (about 100 μg of peptide) or rabbits (about 1 mg of peptide). Subsequently, the peptide is radioiodinated and used to screen the immunized animals' B-lymphocytes for production of antipeptide antibodies. Positive cells are then used to produce hybridomas using standard techniques. About 20 mg of peptide is sufficient for labeling and screening several thousand clones. Hybridomas of interest are detected by screening with radioiodinated peptide to identify those fusions producing peptide-specific monoclonal antibody. In a typical protocol, wells of a multi-well plate (FAST, Becton-Dickinson, Palo Alto, Calif.) are coated with affinity-purified, specific rabbit-anti-mouse (or suitable anti-species IgG) antibodies at 10 mg/mL The coated wells are blocked with 1% BSA and washed and exposed to supernatants from hybridomas. After incubation, the wells are exposed to radiolabeled peptide at 1 mg/ml.

[0784] Clones producing antibodies bind a quantity of labeled peptide that is detectable above background. Such clones are expanded and subjected to 2 cycles of cloning. Cloned hybridomas are injected into pristane-treated mice to produce ascites, and monoclonal antibody is purified from the ascitic fluid by affinity chromatography on protein A (Amersham Pharmacia Biotech). Several procedures for the production of monoclonal antibodies, including in vitro production, are described in Pound (supra). Monoclonal antibodies with antipeptide activity are tested for anti-DITHP activity using protocols well known in the art, including ELISA, RIA, and immunoblotting.

[0785] Antibody fragments containing specific binding sites for an epitope may also be generated. For example, such fragments include, but are not limited to, the F(ab′)2 fragments produced by pepsin digestion of the antibody molecule, and the Fab fragments generated by reducing the disulfide bridges of the F(ab)2 fragments. Alternatively, construction of Fab expression libraries in filamentous bacteriophage allows rapid and easy identification of monoclonal fragments with desired specificity (Pound, supra, Chaps. 45-47). Antibodies generated against polypeptide encoded by dithp can be used to purify and characterize full-length DITHP protein and its activity, binding partners, etc.

[0786] Assays Using Antibodies

[0787] Anti-DITHP antibodies may be used in assays to quantify the amount of DITHP found in a particular human cell. Such assays include methods utilizing the antibody and a label to detect expression level under normal or disease conditions. The peptides and antibodies of the invention may be used with or without modification or labeled by joining them, either covalently or noncovalently, with a reporter molecule.

[0788] Protocols for detecting and measuring protein expression using either polyclonal or monoclonal antibodies are well known in the art. Examples include ELISA, RIA, and fluorescent activated cell sorting (FACS). Such immunoassays typically involve the formation of complexes between the DITHP and its specific antibody and the measurement of such complexes. These and other assays are described in Pound (supra).

[0789] Without further elaboration, it is believed that one skilled in the art can, using the preceding description, utilize the present invention to its fullest extent. The following preferred specific embodiments are, therefore, to be construed as merely illustrative, and not limitative of the remainder of the disclosure in any way whatsoever.

[0790] The disclosures of all patents, applications, and publications mentioned above and below, including U.S. Ser. No. 60/261,865, U.S. Ser. No. 60/262,599, U.S. Ser. No. 60/263,102, U.S. Ser. No. 60/262,662, U.S. Ser. No. 60/263,064, U.S. Ser. No. 60/263,330, U.S. Ser. No. 60/263,065, U.S. Ser. No. 60/263,329, U.S. Ser. No. 60/262,207, U.S. Ser. No. 60/262,209, U.S. Ser. No. 60/262,208, U.S. Ser. No. 60/262,164, U.S. Ser. No. 60/262,215, U.S. Ser. No. 60/263,063, U.S. Ser. No. 60/261,864, U.S. Ser. No. 60/262,760, U.S. Ser. No. 60/261,622, U.S. Ser. No. 60/263,077, and U.S. Ser. No. 60/263,069 are hereby expressly incorporated by reference.

EXAMPLES

[0791] I. Construction of cDNA Libraries

[0792] RNA was purchased from CLONTECH Laboratories, Inc. (Palo Alto Calif.) or isolated from various tissues. Some tissues were homogenized and lysed in guanidinium isothiocyanate, while others were homogenized and lysed in phenol or in a suitable mixture of denaturants, such as TRIZOL (Life Technologies), a monophasic solution of phenol and guanidine is thiocyanate. The resulting lysates were centrifuged over CsCl cushions or extracted with chloroform RNA was precipitated with either isopropanol or sodium acetate and ethanol, or by other routine methods.

[0793] Phenol extraction and precipitation of RNA were repeated as necessary to increase RNA purity. In most cases, RNA was treated with DNase. For most libraries, poly(A+) RNA was isolated using oligo d(T)-coupled paramagnetic particles (Promega Corporation (Promega), Madison Wis.), OLIGOTEX latex particles (QIAGEN, Inc. (QIAGEN), Valencia Calif.), or an OLIGOTEX mRNA purification kit (QIAGEN). Alternatively, RNA was isolated directly from tissue lysates using other RNA isolation kits, e.g., the POLY(A)PURR mRNA purification kit (Ambion, Inc., Austin Tex.).

[0794] In some cases, Stratagene was provided with RNA and constructed the corresponding cDNA libraries. Otherwise, cDNA was synthesized and cDNA libraries were constructed with the UNIZAP vector system (Stratagene Cloning Systems, Inc. (Stratagene), La Jolla Calif.) or SUPERSCRIPT plasmid system Me Technologies), using the recommended procedures or similar methods known in the art. (See, e.g., Ausubel, 1997, supra, Chapters 5.1 through 6.6.) Reverse transcription was initiated using oligo d(T) or random primers. Synthetic oligonucleotide adapters were ligated to double stranded cDNA, and the cDNA was digested with the appropriate restriction enzyme or enzymes. For most libraries, the cDNA was size-selected (300-1000 bp) using SEPHACRYL S1000, SEPHAROSE CL2B, or SEPHAROSE CL4B column chromatography (Amersham Pharmacia Biotech) or preparative agarose gel electrophoresis. cDNAs were ligated into compatible restriction enzyme sites of the polylinker of a suitable plasmid, e.g., PBLUESCRIPT plasmid (Stratagene), PSPORT1 plasmid (Life Technologies), PCDNA2.1 plasmid (Invitrogen, Carlsbad Calif.), PBK-CMV plasmid (Stratagene), PCR2-TOPOTA plasmid (Invitrogen), PCMV-ICIS plasmid (Stratagene), pIGEN (Incyte Genomics, Palo Alto Calif.), pRARE (Incyte Genomics), or pINCY (Incyte Genomics), or derivatives thereof. Recombinant plasmids were transformed into competent E. coli cells including XL1-Blue, XL1-BlueMRP, or SOLR from Stratagene or DH5α, DH10B, or ElectroMAX DH10B from Life Technologies.

[0795] II. Isolation of cDNA Clones

[0796] Plasmids were recovered from host cells by in vivo excision using the UNIZAP vector system (Stratagene) or by cell lysis. Plasmids were purified using at least one of the following: the Magic or WIZARD Minipreps DNA purification system (Promega); the AGTC Miniprep purification kit (Edge BioSystems, Gaithersburg Md.); and the QIAWELL 8, QIAWELL 8 Plus, and QIAWELL 8 Ultra plasmid purification systems or the R.E.A.L. PREP 96 plasmid purification kit (QIAGEN). Following precipitation, plasmids were resuspended in 0.1 ml of distilled water and stored, with or without lyophilization, at 4° C.

[0797] Alternatively, plasmid DNA was amplified from host cell lysates using direct link PCR in a high-throughput format. (Rao, V. B. (1994) Anal. Biochem. 216:1-14.) Host cell lysis and thermal cycling steps were carried out in a single reaction mixture. Samples were processed and stored in 384-well plates, and the concentration of amplified plasmid DNA was quantified fluorometrically using PICOGREEN dye (Molecular Probes, Inc. (Molecular Probes), Eugene Oreg.) and a FLUOROSKAN II fluorescence scanner (Labsystems Oy, Helsinki, Finland).

[0798] III. Sequencing and Analysis

[0799] cDNA sequencing reactions were processed using standard methods or high-throughput instrumentation such as the ABI CATALYST 800 thermal cycler (Applied Biosystems) or the PTC-200 thermal cycler (MJ Research) in conjunction with the HYDRA microdispenser (Robbins Scientific Corp., Sunnyvale Calif.) or the MICROLAB 2200 liquid transfer system (Hamilton). cDNA sequencing reactions were prepared using reagents provided by Amersham Pharmacia Biotech or supplied in ABI sequencing kits such as the ABI PRISM BIGDYE Terminator cycle sequencing ready reaction kit (Applied Biosystems). Electrophoretic separation of cDNA sequencing reactions and detection of labeled polynucleotides were carried out using the MEGABACE 1000 DNA sequencing system (Molecular Dynamics); the ABI PRISM 373 or 377 sequencing system (Applied Biosystems) in conjunction with standard ABI protocols and base calling software; or other sequence analysis systems known in the art. Reading frames within the cDNA sequences were identified using standard methods (reviewed in Ausubel, 1997, supra, Chapter 7.7). Some of the cDNA sequences were selected for extension using the techniques disclosed in Example VIII.

[0800] IV. Assembly and Analysis of Sequences

[0801] Component sequences from chromatograms were subject to PHRED analysis and assigned a quality score. The sequences having at least a required quality score were subject to various pre-processing editing pathways to eliminate, e.g., low quality 3′ ends, vector and linker sequences, polyA tails, Alu repeats, mitochondrial and ribosomal sequences, bacterial contamination sequences, and sequences smaller than 50 base pairs. In particular, low-information sequences and repetitive elements (e.g., dinucleotide repeats, Alu repeats, etc.) were replaced by “n's”, or masked, to prevent spurious matches.

[0802] Processed sequences were then subject to assembly procedures in which the sequences were assigned to gene bins (bins). Each sequence could only belong to one bin. Sequences in each gene bin were assembled to produce consensus sequences (templates). Subsequent new sequences were added to existing bins using BLASTn (v.1.4 WashU) and CROSSMATCH. Candidate pairs were identified as all BLAST hits having a quality score greater than or equal to 150. Alignments of at least 82% local identity were accepted into the bin. The component sequences from each bin were assembled using a version of PHRAP. Bins with several overlapping component sequences were assembled using DEEP PHRAP. The orientation (sense or antisense) of each assembled template was determined based on the number and orientation of its component sequences. Template sequences as disclosed in the sequence listing correspond to sense strand sequences (the “forward” reading frames), to the best determination. The complementary (antisense) strands are inherently disclosed herein. The component sequences which were used to assemble each template consensus sequence are listed in Table 5, along with their positions along the template nucleotide sequences.

[0803] Bins were compared against each other and those having local similarity of at least 82% were combined and reassembled. Reassembled bins having templates of insufficient overlap (less than 95% local identity) were re-split. Assembled templates were also subject to analysis by STITCHER/EXON MAPPER algorithms which analyze the probabilities of the presence of splice variants, alternatively spliced exons, splice junctions, differential expression of alternative spliced genes across tissue types or disease states, etc. These resulting bins were subject to several rounds of the above assembly procedures.

[0804] Once gene bins were generated based upon sequence alignments, bins were clone joined based upon clone information. If the 5′ sequence of one clone was present in one bin and the 3′ sequence from the same clone was present in a different bin, it was likely that the two bins actually belonged together in a single bin. The resulting combined bins underwent assembly procedures to regenerate the consensus sequences.

[0805] The final assembled templates were subsequently annotated using the following procedure. Template sequences were analyzed using BLASTn (v2.0, NCBI) versus gbpri (GenBank version 126). “Hits” were defined as an exact match having from 95% local identity over 200 base pairs through 100% local identity over 100 base pairs, or a homolog match having an E-value, i.e. a probability score, of <1×10-8. The hits were subject to frameshift FASTx versus GENPEPT (GenBank version 126). (See Table 8). In this analysis, a homolog match was defined as having an E-value of ≦1×10−8. The assembly method used above was described in “System and Methods for Analyzing Biomolecular Sequences,” U.S. Ser. No. 09/276,534, filed Mar. 25, 1999, and the LIFESEQ Gold user manual (Incyte) both incorporated by reference herein.

[0806] Following assembly, template sequences were subjected to motif, BLAST, and functional analyses, and categorized in protein hierarchies using methods described in, e.g., “Database System Employing Protein Function Hierarchies for Viewing Biomolecular Sequence Data,” U.S. Ser. No. 08/812,290, filed Mar. 6, 1997; “Relational Database for Storing Biomolecule Information,” U.S. Ser. No. 08/947,845, filed Oct. 9, 1997; “Project-Based Full-Length Biomolecular Sequence Database,” U.S. Ser. No. 08/811,758, fled Mar. 6, 1997; and “Relational Database and System for Storing Information Relating to Biomolecular Sequences,” U.S. Ser. No. 09/034,807, filed Mar. 4, 1998, all of which are incorporated by reference herein.

[0807] The template sequences were further analyzed by translating each template in all three forward reading frames and searching each translation against the Pfam database of hidden Markov model-based protein families and domains using the R software package (available to the public from Washington University School of Medicine, St. Louis Mo.). Regions of templates which, when translated, contain similarity to Pfam consensus sequences are reported in Table 3, along with descriptions of Pfam protein domains and families. Only those Pfam hits with an E-value of ≦1×10−3 are reported. (See also World Wide Web site http://pfam.wustl.edu/for detailed descriptions of Pfam protein domains and families.)

[0808] Additionally, the template sequences were translated in all three forward reading frames, and each translation was searched against hidden Markov models for signal peptides using the HMMER software package. Construction of hidden Markov models and their usage in sequence analysis has been described. (See, for example, Eddy, S. R. (1996) Curr. Opin. Str. Biol. 6:361-365.) Only those signal peptide hits with a cutoff score of 11 bits or greater are reported. A cutoff score of 11 bits or greater corresponds to at least about 91-94% true-positives in signal peptide prediction. Template sequences were also translated in all three forward reading frames, and each translation was searched against TMHMMER, a program that uses a hidden Markov model (HMM) to delineate transmembrane segments on protein sequences and determine orientation (Sonnhammer, E. L. et al. (1998) Proc. Sixth Intl. Conf. On Intelligent Systems for Mol. Biol., Glasgow et al., eds., The Am. Assoc. for Artificial Intelligence (AAAI) Press, Menlo Park, Calif., and MIT Press, Cambridge, Mass., pp. 175-182.) Regions of templates which, when translated, contain similarity to signal peptide or transmembrane consensus sequences are reported in Table 4.

[0809] The results of HMMER analysis as reported in Tables 3 and 4 may support the results of BLAST analysis as reported in Table 2 or may suggest alternative or additional properties of template-encoded polypeptides not previously uncovered by BLAST or other analyses. Template sequences are further analyzed using the bioinformatics tools listed in Table 8, or using sequence analysis software known in the art such as MACDNASIS PRO software (Hitachi Software Engineering, South San Francisco Calif.) and LASERGENE software (DNASTAR).

[0810] Template sequences may be further queried against public databases such as the GenBank rodent, mammalian, vertebrate, prokaryote, and eukaryote databases.

[0811] The template sequences were translated to derive the corresponding longest open reading frame as presented by the polypeptide sequences as reported in Table 7. Alternatively, a polypeptide of the invention may begin at any of the methionine residues within the full length translated polypeptide. Polypeptide sequences were subsequently analyzed by querying against the GenBank protein database (GENPEPT, (GenBank version 126)). Full length polynucleotide sequences are also analyzed using MACDNASIS PRO software (Hitachi Software Engineering, South San Francisco Calif.) and LASERGBNE software (DNASTAR). Polynucleotide and polypeptide sequence alignments are generated using default parameters specified by the CLUSTAL algorithm as incorporated into the MEGALIGN multisequence alignment program (DNASTAR), which also calculates the percent identity between aligned sequences.

[0812] Table 7 shows sequences with homology to the polypeptides of the invention as identified by BLAST analysis against the GenBank protein (GENPEPT) database. Column 1 shows the polypeptide sequence identification number (SEQ ID NO:) for the polypeptide segments of the invention. Column 2 shows the reading frame used in the translation of the polynucleotide sequences encoding the polypeptide segments. Column 3 shows the length of the translated polypeptide segments. Columns 4 and 5 show the start and stop nucleotide positions of the polynucleotide sequences encoding the polypeptide segments. Column 6 shows the GenBank identification number (GI Number) of the nearest GenBank homolog. Column 7 shows the probability score for the match between each polypeptide and its GenBank homolog. Column 8 shows the annotation of the GenBank homolog.

[0813] V. Analysis of Polynucleotide Expression

[0814] Northern analysis is a laboratory technique used to detect the presence of a transcript of a gene and involves the hybridization of a labeled nucleotide sequence to a membrane on which RNAs from a particular cell type or tissue have been bound. (See, e.g., Sambrook, supra, ch. 7; Ausubel, 1995, supra, ch. 4 and 16.)

[0815] Analogous computer techniques applying BLAST were used to search for identical or related molecules in cDNA databases such as GenBank or LIFESEQ (Incyte Genomics). This analysis is much faster than multiple membrane-based hybridizations. In addition, the sensitivity of the computer search can be modified to determine whether any particular match is categorized as exact or similar. The basis of the search is the product score, which is defined as:

\frac{BLAST Score \times Percent Identity}{5 \times minimum {length (Seq . 1), length (Seq . 2)}}

[0816] The product score takes into account both the degree of similarity between two sequences and the length of the sequence match. The product score is a normalized value between 0 and 100, and is calculated as follows: the BLAST score is multiplied by the percent nucleotide identity and the product is divided by (5 times the length of the shorter of the two sequences). The BLAST score is calculated by assigning a score of +5 for every base that matches in a high-scoring segment pair (HSP), and −4 for every mismatch. Two sequences may share more than one HSP (separated by gaps). If there is more than one HSP, then the pair with the highest BLAST score is used to calculate the product score. The product score represents a balance between fractional overlap and quality in a BLAST alignment. For example, a product score of 100 is produced only for 100% identity over the entire length of the shorter of the two sequences being compared. A product score of 70 is produced either by 100% identity and 70% overlap at one end, or by 88% identity and 100% overlap at the other. A product score of 50 is produced either by 100% identity and 50% overlap at one end, or 79% identity and 100% overlap.

[0817] VI. Tissue Distribution Profiling

[0818] A tissue distribution profile is determined for each template by compiling the cDNA library tissue classifications of its component cDNA sequences. Each component sequence, is derived from a cDNA library constructed from a human tissue. Each human tissue is classified into one of the following categories: cardiovascular system; connective tissue; digestive system; embryonic structures; endocrine system; exocrine glands; genitalia, female; genitalia, male; germ cells; hemic and immune system; liver; musculoskeletal system; nervous system; pancreas; respiratory system; sense organs; skin; stomatognathic system; unclassified/mixed; or urinary tract. Template sequences, component sequences, and cDNA library/tissue information are found in the LIFESEQ GOLD database (Incyte Genomics, Palo Alto Calif.).

[0819] Table 6 shows the tissue distribution profile for the templates of the invention. For each template, the three most frequently observed tissue categories are shown in column 3, along with the percentage of component sequences belonging to each category. Only tissue categories with percentage values of ≧10% are shown. A tissue distribution of “widely distributed” in column 3 indicates percentage values of <10% in all tissue categories.

[0820] VII. Transcript Image Analysis

[0821] Transcript images are generated as described in Seilhamer et al., “Comparative Gene Transcript Analysis,” U.S. Pat. No. 5,840,484, incorporated herein by reference.

[0822] VIII. Extension of Polynucleotide Sequences and Isolation of a Full-Length cDNA

[0823] Oligonucleotide primers designed using a dithp of the Sequence Listing are used to extend the nucleic acid sequence. One primer is synthesized to initiate 5′ extension of the template, and the other primer, to initiate 3′ extension of the template. The initial primers may be designed using OLIGO 4.06 software (National Biosciences, Inc. (National Biosciences), Plymouth Minn.), or another appropriate program, to be about 22 to 30 nucleotides in length, to have a GC content of about 50% or more, and to anneal to the target sequence at temperatures of about 68° C. to about 72° C. Any stretch of nucleotides which would result in hairpin structures and prier-primer dimerizations are avoided. Selected human cDNA libraries are used to extend the sequence. If more than one extension is necessary or desired, additional or nested sets of primers are designed.

[0824] High fidelity amplification is obtained by PCR using methods well known in the art. PCR is performed in 96-well plates using the PTC-200 thermal cycler (MJ Research). The reaction mix contains DNA template, 200 nmol of each primer, reaction buffer containing Mg2+, (NH4)2SO4, and β-mercaptoethanol, Taq DNA polymerase (Amersham Pharmacia Biotech), ELONGASE enzyme (Life Technologies), and Pfu DNA polymerase (Stratagene), with the following parameters for primer pair PCI A and PCI B: Step 1: 94° C., 3 min; Step 2: 94° C., 15 sec; Step 3: 60° C., 1 min; Step 4: 68° C., 2 min; Step 5: Steps 2, 3, and 4 repeated 20 times; Step 6: 68° C., 5 min; Step 7: storage at 4° C. In the alternative, the parameters for primer pair T7 and SK+ are as follows: Step 1: 94° C., 3 min; Step 2: 94° C., 15 sec; Step 3: 57° C., 1 min; Step 4: 68° C., 2 min; Step 5: Steps 2, 3, and 4 repeated 20 times; Step 6: 68° C., 5 ml; Step 7: storage at 4° C.

[0825] The concentration of DNA in each well is determined by dispensing 100 μl PICOGREEN quantitation reagent (0.25% (v/v); Molecular Probes) dissolved in 1×Tris-EDTA (TE) and 0.5 μl of undiluted PCR product into each well of an opaque fluorimeter plate (Corning Incorporated (Corning), Corning N.Y.), allowing the DNA to bind to the reagent. The plate is scanned in a FLUOROSKAN II (Labsystems Oy) to measure the fluorescence of the sample and to quantify the concentration of DNA. A 5 μl to 10 μl aliquot of the reaction mixture is analyzed by electrophoresis on a 1% agarose mini-gel to determine which reactions are successful in extending the sequence.

[0826] The extended nucleotides are desalted and concentrated, transferred to 384-well plates, digested with CviJI cholera virus endonuclease (Molecular Biology Research, Madison Wis.), and sonicated or sheared prior to religation into pUC 18 vector (Amersham Pharmacia Biotech). For shotgun sequencing, the digested nucleotides are separated on low concentration (0.6 to 0.8%) agarose gels, fragments are excised, and agar digested with AGAR ACE (Promega). Extended clones are religated using T4 ligase (New England Biolabs, Inc., Beverly Mass.) into pUC 18 vector (Amersham Pharmacia Biotech), treated with Pfu DNA polymerase (Stratagene) to fill-in restriction site overhangs, and transfected into competent E. coli cells. Transformed cells are selected on antibiotic-containing media, individual colonies are picked and cultured overnight at 37° C. in 384-well plates in LB/2×carbenicillin liquid media.

[0827] The cells are lysed, and DNA is amplified by PCR using Taq DNA polymerase (Amersham Pharmacia Biotech) and Pfu DNA polymerase (Stratagene) with the following parameters: Step 1: 94° C., 3 min; Step 2: 94° C., 15 sec; Step 3: 60° C., 1 min; Step 4: 72° C., 2 min; Step 5: steps 2, 3, and 4 repeated 29 times; Step 6: 72° C., 5 min; Step 7: storage at 4° C. DNA is quantified by PICOGREEN reagent (Molecular Probes) as described above. Samples with low DNA recoveries are reamplified using the same conditions as described above. Samples are diluted with 20% dimethysulfoxide (1:2, v/v), and sequenced using DYENAMIC energy transfer sequencing primers and the DYENAMIC DIRECT kit (Amersham Pharmacia Biotech) or the ABI PRISM BIGDYE Terminator cycle sequencing ready reaction kit (Applied Biosystems).

[0828] In like manner, the dithp is used to obtain regulatory sequences (promoters, introns, and enhancers) using the procedure above, oligonucleotides designed for such extension, and an appropriate genomic library.

[0829] IX. Labeling of Probes and Southern Hybridization Analyses

[0830] Hybridization probes derived from the dithp of the Sequence Listing are employed for screening cDNAs, mRNAs, or genomic DNA. The labeling of probe nucleotides between 100 and 1000 nucleotides in length is specifically described, but essentially the same procedure may be used with larger cDNA fragments. Probe sequences are labeled at room temperature for 30 minutes using a T4 polynucleotide kinase, γ32P-ATP, and 0.5×One-Phor-All Plus (Amersham Pharmacia Biotech) buffer and purified using a ProbeQuant G-50 Microcolumn (Amersham Pharmacia Biotech). The probe mixture is diluted to 107 dpm/μg/ml hybridization buffer and used in a typical membrane-based hybridization analysis.

[0831] The DNA is digested with a restriction endonuclease such as Eco RV and is electrophoresed through a 0.7% agarose gel. The DNA fragments are transferred from the agarose to nylon membrane (NYTRAN Plus, Schleicher & Schuell, Inc., Keene N. H.) using procedures specified by the manufacturer of the membrane. Prehybridization is carried out for three or more hours at 68° C., and hybridization is carried out overnight at 68° C. To remove non-specific signals, blots are sequentially washed at room temperature under increasingly stringent conditions, up to 0.1×saline sodium citrate (SSC) and 0.5% sodium dodecyl sulfate. After the blots are placed in a PHOSPHORIMAGER cassette (Molecular Dynamics) or are exposed to autoradiography film, hybridization patterns of standard and experimental lanes are compared. Essentially the same procedure is employed when screening RNA.

[0832] X. Chromosome Mapping of Dithp

[0833] The cDNA sequences which were used to assemble SEQ ID NO:1-56 are compared with sequences from the Incyte LIFESEQ database and public domain databases using BLAST and other implementations of the Smith-Waterman algorithm. Sequences from these databases that match SEQ ID NO:1-56 are assembled into clusters of contiguous and overlapping sequences using assembly algorithms such as PHRAP (Table 8). Radiation hybrid and genetic mapping data available from public resources such as the Stanford Human Genome Center (SHGC), Whitehead institute for Genome Research (WIGR), and Généthon are used to determine if any of the clustered sequences have been previously mapped. Inclusion of a mapped sequence in a cluster will result in the assignment of all sequences of that cluster, including its particular SEQ ID NO:, to that map location. The genetic map locations of SEQ ID NO:1-56 are described as ranges, or intervals, of human chromosomes. The map position of an interval, in centiMorgans, is measured relative to the terminus of the chromosome's p-arm. (The centiMorgan (cM) is a unit of measurement based on recombination frequencies between chromosomal markers. On average, 1 cM is roughly equivalent to 1 megabase (Mb) of DNA in humans, although this can vary widely due to hot and cold spots of recombination.) The cM distances are based on genetic markers mapped by Généthon which provide boundaries for radiation hybrid markers whose sequences were included in each of the clusters.

[0834] XI. Microarray Analysis

[0835] Probe Preparation from Tissue or Cell Samples

[0836] Total RNA is isolated from tissue samples using the guanidinium thiocyanate method and polyA+ RNA is purified using the oligo (dT) cellulose method. Each polyA+ RNA sample is reverse transcribed using MMLV reverse-transcriptase, 0.05 pg/μl oligo-dT primer (21mer), 1× first strand buffer, 0.03 units/μl RNase inhibitor, 500 μM dATP, 500 μM dGTP, 500 μM dTTP, 40 μM dCTP, 40 μM dCTP-Cy3 (BDS) or dCTP-Cy5 (Amersham Pharmacia Biotech). The reverse transcription reaction is performed in a 25 ml volume containing 200 ng polyA+ RNA with GEMBRIGHT kits (Incyte). Specific control polyA+ RNAs are synthesized by in vitro transcription from non-coding yeast genomic DNA (W. Lei, unpublished). As quantitative controls, the control mRNAs at 0.002 ng, 0.02 ng, 0.2 ng, and 2 ng are diluted into reverse transcription reaction at ratios of 1:100,000, 1:10,000, 1:1000, 1:100 (w/w) to sample mRNA respectively. The control mRNAs are diluted into reverse transcription reaction at ratios of 1:3, 3:1, 1:10, 10:1, 1:25, 25:1 (w/w) to sample mRNA differential expression patterns. After incubation at 37° C. for 2 hr, each reaction sample (one with Cy3 and another with Cy5 labeling) is treated with 2.5 ml of 0.5M sodium hydroxide and incubated for 20 minutes at 85° C. to the stop the reaction and degrade the RNA. Probes are purified using two successive CHROMA SPIN 30 gel filtration spin columns (CLONTECH Laboratories, Inc. (CLONTECH), Palo Alto Calif.) and after combining, both reaction samples are ethanol precipitated using 1 ml of glycogen (1 mg/ml), 60 ml sodium acetate, and 300 ml of 100% ethanol. The probe is then dried to completion using a SpeedVAC (Savant Instruments Inc., Holbrook N.Y.) and resuspended in 14 μl 5×SSC/0.2% SDS.

[0837] Microarray Preparation

[0838] Sequences of the present invention are used to generate array elements. Each array element is amplified from bacterial cells containing vectors with cloned cDNA inserts. PCR amplification uses primers complementary to the vector sequences flanking the cDNA insert. Array elements are amplified in thirty cycles of PCR from an initial quantity of 1-2 ng to a final quantity greater than 5 μg. Amplified array elements are then purified using SEPHACRYL-400 (Amersham Pharmacia Biotech).

[0839] Purified array elements are immobilized on polymer-coated glass slides. Glass microscope slides (Corning) are cleaned by ultrasound in 0.1% SDS and acetone, with extensive distilled water washes between and after treatments. Glass slides are etched in 4% hydrofluoric acid (VWR Scientific Products Corporation (VWR), West Chester, Pa.), washed extensively in distilled water, and coated with 0.05% aminopropyl silane (Sigma) in 95% ethanol. Coated slides are cured in a 110° C. oven.

[0840] Array elements are applied to the coated glass substrate using a procedure described in U.S. Pat. No. 5,807,522, incorporated herein by reference. 1 μl of the array element DNA, at an average concentration of 100 ng/μl, is loaded into the open capillary printing element by a high-speed robotic apparatus. The apparatus then deposits about 5 nl of array element sample per slide.

[0841] Microarrays are UV-crosslinked using a STRATALINKER UV-crosslinker (Stratagene). Microarrays are washed at room temperature once in 0.2% SDS and three times in distilled water. Non-specific binding sites are blocked by incubation of microarrays in 0.2% casein in phosphate buffered saline (PBS) (Tropix, Inc., Bedford, Mass.) for 30 minutes at 60° C. followed by washes in 0.2% SDS and distilled water as before.

[0842] Hybridization

[0843] Hybridization reactions contain 9 μl of probe mixture consisting of 0.2 μg each of Cy3 and Cy5 labeled cDNA synthesis products in 5×SSC, 0.2% SDS hybridization buffer. The probe mixture is heated to 65° C. for 5 minutes and is aliquoted onto the microarray surface and covered with an 1.8 cm2 coverslip. The arrays are transferred to a waterproof chamber having a cavity just slightly larger than a microscope slide. The chamber is kept at 100% humidity internally by the addition of 140 μl of 5×SSC in a corner of the chamber. The chamber containing the arrays is incubated for about 6.5 hours at 60° C. The arrays are washed for 10 min at 45° C. in a first wash buffer (1×SSC, 0.1% SDS), three times for 10 minutes each at 45° C. in a second wash buffer (0.1×SSC), and dried.

[0844] Detection

[0845] Reporter-labeled hybridization complexes are detected with a microscope equipped with an Innova 70 mixed gas 10 W laser (Coherent, Inc., Santa Clara Calif.) capable of generating spectral lines at 488 nm for excitation of Cy3 and at 632 nm for excitation of Cy5. The excitation laser light is focused on the array using a 20× microscope objective (Nikon, Inc., Melville N.Y.). The slide containing the array is placed on a computer-controlled X-Y stage on the microscope and raster-scanned past the objective. The 1.8 cm×1.8 cm array used in the present example is scanned with a resolution of 20 micrometers.

[0846] In two separate scans, a mixed gas multiline laser excites the two fluorophores sequentially. Emitted light is split, based on wavelength, into two photomultiplier tube detectors (PMT R1477, Hamamatsu Photonics Systems, Bridgewater N.J.) corresponding to the two fluorophores. Appropriate filters positioned between the array and the photomultiplier tubes are used to filter the signals. The emission maxima of the fluorophores used are 565 nm for Cy3 and 650 nm for Cy5. Each array is typically scanned twice, one scan per fluorophore using the appropriate filters at the laser source, although the apparatus is capable of recording the spectra from both fluorophores simultaneously.

[0847] The sensitivity of the scans is typically calibrated using the signal intensity generated by a cDNA control species added to the probe mix at a known concentration. A specific location on the array contains a complementary DNA sequence, allowing the intensity of the signal at that location to be correlated with a weight ratio of hybridizing species of 1:100,000. When two probes from different sources (e.g., representing test and control cells), each labeled with a different fluorophore, are hybridized to a single array for the purpose of identifying genes that are differentially expressed, the calibration is done by labeling samples of the calibrating cDNA with the two fluorophores and adding identical amounts of each to the hybridization mixture.

[0848] The output of the photomultiplier tube is digitized using a 12-bit RTI-835H analog-to-digital (A/D) conversion board (Analog Devices, Inc., Norwood, Mass.) installed in an IBM-compatible PC computer. The digitized data are displayed as an image where the signal intensity is mapped using a linear 20-color transformation to a pseudocolor scale ranging from blue (low signal) to red (high signal). The data is also analyzed quantitatively. Where two different fluorophores are excited and measured simultaneously, the data are first corrected for optical crosstalk (due to overlapping emission spectra) between the fluorophores using each fluorophore's emission spectrum.

[0849] A grid is superimposed over the fluorescence signal image such that the signal from each spot is centered in each element of the grid. The fluorescence signal within each element is then integrated to obtain a numerical value corresponding to the average intensity of the signal. The software used for signal analysis is the GEMTOOLS gene expression analysis program (Incyte).

[0850] XII. Complementary Nucleic Acids

[0851] Sequences complementary to the dithp are used to detect, decrease, or inhibit expression of the naturally occurring nucleotide. The use of oligonucleotides comprising from about 15 to 30 base pairs is typical in the art. However, smaller or larger sequence fragments can also be used. Appropriate oligonucleotides are designed from the dithp using OLIGO 4.06 software (National Biosciences) or other appropriate programs and are synthesized using methods standard in the art or ordered from a commercial supplier. To inhibit transcription, a complementary oligonucleotide is designed from the most unique 5′ sequence and used to prevent transcription factor binding to the promoter sequence. To inhibit translation, a complementary oligonucleotide is designed to prevent ribosomal binding and processing of the transcript.

[0852] XIII. Expression of DITHP

[0853] Expression and purification of DITHP is accomplished using bacterial or virus-based expression systems. For expression of DITHP in bacteria, cDNA is subcloned into an appropriate vector containing an antibiotic resistance gene and an inducible promoter that directs high levels of cDNA transcription. Examples of such promoters include, but are not limited to, the trp-lac (tac) hybrid promoter and the T5 or T7 bacteriophage promoter in conjunction with the lac operator regulatory element. Recombinant vectors are transformed into suitable bacterial hosts, e.g., BL21(DE3). Antibiotic resistant bacteria express DITHP upon induction with isopropyl beta-D-thiogalactopyranoside (IPTG). Expression of DITHP in eukaryotic cells is achieved by infecting insect or mammalian cell lines with recombinant Autoraphica californica nuclear polyhedrosis virus (AcMNPV), commonly known as baculovirus. The nonessential polyhedrin gene of baculovirus is replaced with cDNA encoding DITHP by either homologous recombination or bacterial-mediated transposition involving transfer plasmid intermediates. Viral infectivity is maintained and the strong polyhedrin promoter drives high levels of cDNA transcription. Recombinant baculovirus is used to infect Spodoptera frugiperda (Sf9) insect cells in most cases, or human hepatocytes, in some cases. Infection of the latter requires additional genetic modifications to baculovirus. (See e.g., Engelhard, supra; and Sandig, supra.)

[0854] In most expression systems, DITHP is synthesized as a fusion protein with, e.g., glutathione S-transferase (GST) or a peptide epitope tag, such as FLAG or 6-His, permitting rapid, single-step, affinity-based purification of recombinant fusion protein from crude cell lysates. GST, a 26-kilodalton enzyme from Schistosoma japonicum, enables the purification of fusion proteins on immobilized glutathione under conditions that maintain protein activity and antigenicity (Amersham Pharmacia Biotech). Following purification, the GST moiety can be proteolytically cleaved from DITHP at specifically engineered sites. FLAG, an 8-amino acid peptide, enables immunoaffinity purification using commercially available monoclonal and polyclonal anti-FLAG antibodies (Eastman Kodak Company, Rochester N.Y.). 6-His, a stretch of six consecutive histidine residues, enables purification on metal-chelate resins (QIAGEN). Methods for protein expression and purification are discussed in Ausubel (1995, supra, Chapters 10 and 16). Purified DITHP obtained by these methods can be used directly in the following activity assay.

[0855] XIV. Demonstration of DITHP Activity

[0856] DITHP activity is demonstrated through a variety of specific assays, some of which are outlined below.

[0857] Oxidoreductase activity of DITHP is measured by the increase in extinction coefficient of NAD(P)H coenzyme at 340 nm for the measurement of oxidation activity, or the decrease in extinction coefficient of NAD(P)H coenzyme at 340 nm for the measurement of reduction activity (Daziel, K. (1963) J. Biol. Chem. 238:2850-2858). One of three substrates maybe used: Asn-βGal, biocytidine, or ubiquinone-10. The respective subunits of the enzyme reaction, for example, cytochtome c1-b oxidoreductase and cytochrome c, are reconstituted. The reaction mixture contains a)1-2 mg/ml DITHP; and b) 15 mM substrate, 2.4 mM NAD(P)+ in 0.1 M phosphate buffer, pH 7.1 (oxidation reaction), or 2.0 mM NAD(P)H, in 0.1 M Na2HPO4 buffer, pH 7.4 (reduction reaction); in a total volume of 0.1 ml. Changes in absorbance at 340 nm (A340) are measured at 23.5° C. using a recording spectrophotometer (Shimadzu Scientific Instruments, Inc., Pleasanton Calif.). The amount of NAD(P)H is stoichiometrically equivalent to the amount of substrate initially present, and the change in A340 is a direct measure of the amount of NAD(P)H produced; ΔA340=6620[NADH]. Oxidoreductase activity of DITHP activity is proportional to the amount of NAD(P)H present in the assay.

[0858] Transferase activity of DITHP is measured through assays such as a methyl transferase assay in which the transfer of radiolabeled methyl groups between a donor substrate and an acceptor substrate is measured (Bokar, J. A. et al. (1994) J. Biol. Chem. 269:17697-17704). Reaction mixtures (50 μl final volume) contain 15 mM HEPES, pH 7.9, 1.5 mM MgCl2, 10 mM dithiothreitol, 3% polyvinylalcohol, 1.5 μCi [methyl-3H]AdoMet (0.375 μM AdoMet) (DuPont-NEN), 0.6 μg DITHP, and acceptor substrate (0.4 μg [35S]RNA or 6-mercaptopurine (6-MP) to 1 mM final concentration). Reaction mixtures are incubated at 30° C. for 30 minutes, then 65° C. for 5 minutes. The products are separated by chromatography or electrophoresis and the level of methyl transferase activity is determined by quantification of methyl-3H recovery.

[0859] DITHP hydrolase activity is measured by the hydrolysis of appropriate synthetic peptide substrates conjugated with various chromogenic molecules in which the degree of hydrolysis is quantified by spectrophotometric (or fluorometric) absorption of the released chromophore. (Beynon, R. J. and J. S. Bond (1994) Proteolytic Enzymes: A Practical Approach, Oxford University Press, New York N.Y., pp. 25-55) Peptide substrates are designed according to the category of protease activity as endopeptidase (serine, cysteine, aspartic proteases), animopeptidase (leucine aminopeptidase), or carboxypeptidase (Carboxypeptidase A and B, procollagen C-protemase).

[0860] DITHP isomerase activity such as peptidyl prolyl cis/trans isomerase activity can be assayed by an enzyme assay described by Rahfeld, J. U., et al. (1994) (FEBS Lett. 352: 180-184). The assay is performed at 10° C. in 35 mM HEPES buffer, pH 7.8, containing chymotrypsin (0.5 mg/ml) and DITHP at a variety of concentrations. Under these assay conditions, the substrate, Suc-Ala-Xaa-Pro-Phe-4-NA, is in equilibrium with respect to the prolyl bond, with 80-95% in trans and 5-20% in cis conformation. An aliquot (2 ul) of the substrate dissolved in dimethyl sulfoxide (10 mg/ml) is added to the reaction mixture described above. Only the cis isomer of the substrate is a substrate for cleavage by chymotrypsin. Thus, as the substrate is isomerized by DITHP, the product is cleaved by chymotrypsin to produce 4-nitroanilide, which is detected by it's absorbance at 390 nm. 4-Nitroanilide appears in a time-dependent and a DITHP concentration-dependent manner.

[0861] An assay for DITHP activity associated with growth and development measures cell proliferation as the amount of newly initiated DNA synthesis in Swiss mouse 3T3 cells. A plasmid containing polynucleotides encoding DITHP is transfected into quiescent 3T3 cultured cells using methods well known in the art. The transiently transfected cells are then incubated in the presence of [3H]thymidine, a radioactive DNA precursor. Where applicable, varying amounts of DITHP ligand are added to the transfected cells. Incorporation of [3H]thymidine into acid-precipitable DNA is measured over an appropriate time interval, and the amount incorporated is directly proportional to the amount of newly synthesized DNA.

[0862] Growth factor activity of DITHP is measured by the stimulation of DNA synthesis in Swiss mouse 3T3 cells (McKay, I. and I. Leigh, eds. (1993) Growth Factors: A Practical Approach, Oxford University Press, New York N.Y.). Initiation of DNA synthesis indicates the cells' entry into the mitotic cycle and their commitment to undergo later division. 3T3 cells are competent to respond to most growth factors, not only those that are mitogenic, but also those that are involved in embryonic induction. This competence is possible because the in vivo specificity demonstrated by some growth factors is not necessarily inherent but is determined by the responding tissue. In this assay, varying amounts of DITHP are added to quiescent 3T3 cultured cells in the presence of [3H]thymidine, a radioactive DNA precursor. DITHP for this assay can be obtained by recombinant means or from biochemical preparations. Incorporation of [3H]thymidine into acid-precipitable DNA is measured over an appropriate time interval, and the amount incorporated is directly proportional to the amount of newly synthesized DNA. A linear dose-response curve over at least a hundred-fold DITHP concentration range is indicative of growth factor activity. One unit of activity per milliliter is defined as the concentration of DITHP producing a 50% response level, where 100% represents maximal incorporation of [3H]thymidine into acid-precipitable DNA.

[0863] Alternatively, an assay for cytokine activity of DITHP measures the proliferation of leukocytes. In this assay, the amount of tritrated thymidine incorporated into newly synthesized DNA is used to estimate proliferative activity. Varying amounts of DITHP are added to cultured leukocytes, such as granulocytes, monocytes, or lymphocytes, in the presence of [3H]thymidine, a radioactive DNA precursor. DITHP for this assay can be obtained by recombinant means or from biochemical preparations. Incorporation of [3H]thymidine into acid-precipitable DNA is measured over an appropriate time interval, and the amount incorporated is directly proportional to the amount of newly synthesized DNA. A linear dose-response curve over at least a hundred-fold DITHP concentration range is indicative of DITHP activity. One unit of activity per milliliter is conventionally defined as the concentration of DITHP producing a 50% response level, where 100% represents maximal incorporation of [3H]thymidine into acid-precipitable DNA.

[0864] An alternative assay for DITHP cytokine activity utilizes a Boyden micro chamber (Neuroprobe, Cabin John MD) to measure leukocyte chemotaxis (Vicari, supra). In this assay, about 105 migratory cells such as macrophages or monocytes are placed in cell culture media in the upper compartment of the chamber. Varying dilutions of DITHP are placed in the lower compartment. The two compartments are separated by a 5 or 8 micron pore polycarbonate filter (Nucleopore, Pleasanton Calif.). After incubation at 37° C. for 80 to 120 minutes, the filters are fixed in methanol and stained with appropriate labeling agents. Cells which migrate to the other side of the filter are counted using standard microscopy. The chemotactic index is calculated by dividing the number of migratory cells counted when DITHP is present in the lower compartment by the number of migratory cells counted when only media is present in the lower compartment. The chemotactic index is proportional to the activity of DITHP.

[0865] Alternatively, cell lines or tissues transformed with a vector containing dithp can be assayed for DITHP activity by immunoblotting. Cells are denatured in SDS in the presence of β-mercaptoethanol, nucleic acids removed by ethanol precipitation, and proteins purified by acetone precipitation. Pellets are resuspended in 20 mM tris buffer at pH 7.5 and incubated with Protein G-Sepharose pre-coated with an antibody specific for DITHP. After washing, the Sepharose beads are boiled in electrophoresis sample buffer, and the eluted proteins subjected to SDS-PAGE. The SDS-PAGE is transferred to a nitrocellulose membrane for immunoblotting, and the DITHP activity is assessed by visualizing and quantifying bands on the blot using the antibody specific for DITHP as the primary antibody and 125I-labeled IgG specific for the primary antibody as the secondary antibody.

[0866] DITHP kinase activity is measured by phosphorylation of a protein substrate using γ-labeled [32P]-ATP and quantitation of the incorporated radioactivity using a radioisotope counter. DITHP is incubated with the protein substrate, [32P]-ATP, and an appropriate kinase buffer. The [32P] incorporated into the product is separated from free [32P]-ATP by electrophoresis and the incorporated [32P] is counted. The amount of [32P] recovered is proportional to the kinase activity of DITHP in the assay. A determination of the specific amino acid residue phosphorylated is made by phosphoamino acid analysis of the hydrolyzed protein.

[0867] In the alternative, DITHP activity is measured by the increase in cell proliferation resulting from transformation of a mammalian cell line such as COS7, HeLa or CHO with an eukaryotic expression vector encoding DITHP. Eukaryotic expression vectors are commercially available, and the techniques to introduce them into cells are well known to those skilled in the art. The cells are incubated for 48-72 hours after transformation under conditions appropriate for the cell line to allow expression of Dye. Phase microscopy is then used to compare the mitotic index of transformed versus control cells. An increase in the mitotic index indicates DITHP activity.

[0868] In a further alternative, an assay for DITHP signaling activity is based upon the ability of GPCR family proteins to modulate G protein-activated second messenger signal transduction pathways (e.g., cAMP; Gaudin, P. et al. (1998) J. Biol. Chem. 273:4990-4996). A plasmid encoding full length DITHP is transfected into a mammalian cell line (e.g., Chinese hamster ovary (CHO) or human embryonic kidney (HEK-293) cell lines) using methods well-known in the art. Transfected cells are grown in 12-well trays in culture medium for 48 hours, then the culture medium is discarded, and the attached cells are gently washed with PBS. The cells are then incubated in culture medium with or without ligand for 30 minutes, then the medium is removed and cells lysed by treatment with 1 M perchloric acid. The cAMP levels in the lysate are measured by radioimmunoassay using methods well-known in the art. Changes in the levels of cAMP in the lysate from cells exposed to ligand compared to those without ligand are proportional to the amount of DITHP present in the transfected cells.

[0869] Alternatively, an assay for DITHP protein phosphatase activity measures the hydrolysis of P-nitrophenyl phosphate (PNPP). DITHP is incubated together with PNPP in HEPES buffer pH 7.5, in the presence of 0.1% β-mercaptoethanol at 37° C. for 60 min. The reaction is stopped by the addition of 6 ml of 10 N NaOH, and the increase in light absorbance of the reaction mixture at 410 nm resulting from the hydrolysis of PNPP is measured using a spectrophotometer. The increase in light absorbance is proportional to the phosphatase activity of DITHP in the assay (Diamond, R. H. et al. (1994) Mol Cell Biol 14:3752-3762).

[0870] An alternative assay measures DITHP-mediated G-protein signaling activity by monitoring the mobilization of Ca++ as an indicator of the signal transduction pathway stimulation. (See, e.g., Gryokievicz, G. et al. (1985) J. Biol. Chem. 260:3440; McColl, S. et al. (1993) J. Immunol. 150:4550-4555; and Aussel, C. et al. (1988) J. Immunol. 140:215-220). The assay requires preloading neutrophils or T cells with a fluorescent dye such as FURA-2 or BCECF (Universal Imaging Corp, Westchester Pa.) whose emission characteristics are altered by Ca++ binding. When the cells are exposed to one or more activating stimuli artificially (e.g., anti-CD3 antibody ligation of the T cell receptor) or physiologically (e.g., by allogeneic stimulation), Ca++ flux takes place. This flux can be observed and quantified by assaying the cells in a fluorometer or fluorescent activated cell sorter. Measurements of Ca++ flux are compared between cells in their normal state and those transfected with DITHP. Increased Ca++ mobilization attributable to increased DITHP concentration is proportional to DITHP activity.

[0871] DITHP transport activity is assayed by measuring uptake of labeled substrates into Xenopus laevis oocytes. Oocytes at stages V and VI are injected with DITHP mRNA (10 ng per oocyte) and incubated for 3 days at 18° C. in OR2 medium (82.5 mM NaCl, 2.5 mM KCl, 1 mM CaCl2, 1 mM MgCl2, 1 mM Na2HPO4, 5 mM Hepes, 3.8 mM NaOH, 50 μg/ml gentamycin, pH 7.8) to allow expression of DITHP protein. Oocytes are then transferred to standard uptake medium (100 mM NaCl, 2 mM KCl, 1 mM CaCl2, 1 mM MgCl2, 10 mM Hepes/Tris pH 7.5). Uptake of various substrates (e.g., amino acids, sugars, drugs, ions, and neurotransmitters) is initiated by adding labeled substrate (e.g. radiolabeled with 3H, fluorescently labeled with rhodamine, etc.) to the oocytes. After incubating for 30 minutes, uptake is terminated by washing the oocytes three times in Na+-free medium, measuring the incorporated label, and comparing with controls. DITHP transport activity is proportional to the level of internalized labeled substrate.

[0872] DITHP transferase activity is demonstrated by a test for galactosyltransferase activity. This can be determined by measuring the transfer of radiolabeled galactose from UDP-galactose to a GlcNAc-terminated oligosaccharide chain (Kolbinger, F. et al. (1998) J. Biol. Chem. 273:58-65). The sample is incubated with 14 μl of assay stock solution (180 mM sodium cacodylate, pH 6.5, 1 mg/ml bovine serum albumin, 0.26 mM UDP-galactose, 2 μl of UDP-[3H]galactose), 1 μl of MnCl2 (500 mM), and 2.5 μl of GlcNAcβO—(CH2)—CO2Me (37 mg/ml in dimethyl sulfoxide) for 60 minutes at 37° C. The reaction is quenched by the addition of 1 ml of water and loaded on a C18 Sep-Pak cartridge (Waters), and the column is washed twice with 5 ml of water to remove unreacted UDP-[3H]galactose. The [3H]galactosylated GlcNAcβO—(CH2)—CO2Me remains bound to the column during the water washes and is eluted with 5 ml of methanol. Radioactivity in the eluted material is measured by liquid scintillation counting and is proportional to galactosyltransferase activity in the starting sample.

[0873] In the alternative, DITHP induction by heat or toxins may be demonstrated using primary cultures of human fibroblasts or human cell lines such as CCL-13, HEK293, or HEP G2 (ATCC). To heat induce DITHP expression, aliquots of cells are incubated at 42° C. for 15, 30, or 60 minutes. Control aliquots are incubated at 37° C. for the same time periods. To induce DITHP expression by toxins, aliquots of cells are treated with 100 μM arsenite or 20 mM azetidine-2-carboxylic acid for 0, 3, 6, or 12 hours. After exposure to heat, arsenite, or the amino acid analogue, samples of the treated cells are harvested and cell lysates prepared for analysis by western blot. Cells are lysed in lysis buffer containing 1% Nonidet P-40, 0.15 M NaCl, 50 mM Tris-HCl, 5 mM EDTA, 2 mM N-ethylmaleimide, 2 mM phenylmethylsulfonyl fluoride, 1 mg/ml leupeptin, and 1 mg/ml pepstatin. Twenty micrograms of the cell lysate is separated on an 8% SDS-PAGE gel and transferred to a membrane. After blocking with 5% nonfat dry milk/phosphate-buffered saline for 1 h, the membrane is incubated overnight at 4° C. or at room temperature for 2-4 hours with a 1:1000 dilution of anti-DITHP serum in 2% nonfat dry milk/phosphate-buffered saline. The membrane is then washed and incubated with a 1:1000 dilution of horseradish peroxidase-conjugated goat anti-rabbit IgG in 2% dry milk/phosphate-buffered saline. After washing with 0.1% Tween 20 in phosphate-buffered saline, the DITHP protein is detected and compared to controls using chemiluminescence.

[0874] Alternatively, DITHP protease activity is measured by the hydrolysis of appropriate synthetic peptide substrates conjugated with various chromogenic molecules in which the degree of hydrolysis is quantified by spectrophotometric (or fluorometric) absorption of the released chromophore (Beynon, R. J. and J. S. Bond (1994) Proteolytic Enzymes: A Practical Approach, Oxford University Press, New York, N.Y., pp.25-55). Peptide substrates are designed according to the category of protease activity as endopeptidase (serine, cysteine, aspartic proteases, or metalloproteases), aminopeptidase (leucine aminopeptidase), or carboxypeptidase (carboxypeptidases A and B, procollagen C-proteinase). Commonly used chromogens are 2-naphthylamine, 4-nitroaniline, and furylacrylic acid. Assays are performed at ambient temperature and contain an aliquot of the enzyme and the appropriate substrate in a suitable buffer. Reactions are carried out in an optical cuvette, and the increase/decrease in absorbance of the chromogen released during hydrolysis of the peptide substrate is measured. The change in absorbance is proportional to the DITHP protease activity in the assay.

[0875] In the alternative, an assay for DITHP protease activity takes advantage of fluorescence resonance energy transfer (FRET) that occurs when one donor and one acceptor fluorophore with an appropriate spectral overlap are in close proximity. A flexible peptide linker containing a cleavage site specific for PRTS is fused between a red-shifted variant (RSGFP4) and a blue variant (BFP5) of Green Fluorescent Protein. This fusion protein has spectral properties that suggest energy transfer is occurring from BFP5 to RSGFP4. When the fusion protein is incubated with DITHP, the substrate is cleaved, and the two fluorescent proteins dissociate. This is accompanied by a marked decrease in energy transfer which is quantified by comparing the emission spectra before and after the addition of DITHP (Mitra, RD. et al. (1996) Gene 173:13-17). This assay can also be performed in living cells. In this case the fluorescent substrate protein is expressed constitutively in cells and DITHP is introduced on an inducible vector so that FRET can be monitored in the presence and absence of DITHP (Sagot, L et al. (1999) FEBS Lett 447:53-57).

[0876] A method to determine the nucleic acid binding activity of DITHP involves a polyacrylamide gel mobility-shift assay. In preparation for this assay, DITHP is expressed by transforming a mammalian cell line such as COS7, HeLa or CHO with a eukaryotic expression vector containing DITHP cDNA. The cells are incubated for 48-72 hours after transformation under conditions appropriate for the cell line to allow expression and accumulation of DITHP. Extracts containing solubilized proteins can be prepared from cells expressing DITHP by methods well known in the art. Portions of the extract containing DITHP are added to [32P]-labeled RNA or DNA. Radioactive nucleic acid can be synthesized in vitro by techniques well known in the art. The mixtures are incubated at 25° C. in the presence of RNase- and DNase-inhibitors under buffered conditions for 5-10 minutes. After incubation, the samples are analyzed by polyacrylamide gel electrophoresis followed by autoradiography. The presence of a band on the autoradiogram indicates the formation of a complex between DITHP and the radioactive transcript. A band of similar mobility will not be present in samples prepared using control extracts prepared from untransformed cells.

[0877] In the alternative, a method to determine the methylase activity of a DITHP measures transfer of radiolabeled methyl groups between a donor substrate and an acceptor substrate. Reaction mixtures (50 μl final volume) contain 15 mM HEPES, pH 7.9, 1.5 mM MgCl2, 10 mM dithiothreitol, 3% polyvinylalcohol, 1.5 μCi [methyl-3H]AdoMet (0.375 μM AdoMet) (DuPont-NEN), 0.6 μg DITHP, and acceptor substrate (e.g., 0.4 μg [35S]RNA, or 6-mercaptopurine (6-MP) to 1 mM final concentration). Reaction mixtures are incubated at 30° C. for 30 minutes, then 65° C. for 5 minutes. Analysis of [methyl-3H]RNA is as follows: 1) 50 μl of 2×loading buffer (20 mM Tris-HCl, pH 7.6, 1 M LiCl, 1 mM EDTA, 1% sodium dodecyl sulphate (SDS)) and 50 μl oligo d(T)-cellulose (10 mg/ml in 1×loading buffer) are added to the reaction mixture, and incubated at ambient temperature with shaking for 30 minutes. 2) Reaction mixtures are transferred to a 96-well filtration plate attached to a vacuum apparatus. 3) Each sample is washed sequentially with three 2.4 ml aliquots of 1×oligo d(T) loading buffer containing 0.5% SDS, 0.1% SDS, or no SDS. and 4) RNA is eluted with 300 μl of water into a 96-well collection plate, transferred to scintillation vials containing liquid scintillant, and radioactivity determined. Analysis of [methyl-3H]6-MP is as follows: 1) 500 μl 0.5 M borate buffer, pH 10.0, and then 2.5 ml of 20% (v/v) isoamyl alcohol in toluene are added to the reaction mixtures. 2) The samples mixed by vigorous vortexing for ten seconds. 3) After centrifugation at 700 g for 10 minutes, 1.5 ml of the organic phase is transferred to scintillation vials containing 0.5 ml absolute ethanol and liquid scintillant, and radioactivity determined, and 4) Results are corrected for the extraction of 6-MP into the organic phase (approximately 41%).

[0878] An assay for adhesion activity of DITHP measures the disruption of cytoskeletal filament networks upon overexpression of DITHP in cultured cell lines (Rezniczek, G. A. et al. (1998) J. Cell Biol. 141:209-225). cDNA encoding DITHP is subcloned into a mammalian expression vector that drives high levels of cDNA expression. This construct is transfected into cultured cells, such as rat kangaroo PtK2 or rat bladder carcinoma 804G cells. Actin filaments and intermediate filaments such as keratin and vimentin are visualized by immunofluorescence microscopy using antibodies and techniques well known in the art. The configuration and abundance of cytoskeletal filaments can be assessed and quantified using confocal imaging techniques. In particular, the bundling and collapse of cytoskeletal filament networks is indicative of DITHP adhesion activity.

[0879] Alternatively, an assay for DITHP activity measures the expression of DITHP on the cell surface. cDNA encoding DITHP is transfected into a non-leukocytic cell line. Cell surface proteins are labeled with biotin (de la Fuente, M. A. et al. (1997) Blood 90:2398-2405). Immunoprecipitations are performed using DITHP-specific antibodies, and immunoprecipitated samples are analyzed using SDS-PAGE and immunoblotting techniques. The ratio of labeled immunoprecipitant to unlabeled immunoprecipitant is proportional to the amount of DITHP expressed on the cell surface.

[0880] Alternatively, an assay for DITHP activity measures the amount of cell aggregation induced by overexpression of DITHP. In this assay, cultured cells such as NIH3T3 are transfected with cDNA encoding DITHP contained within a suitable mammalian expression vector under control of a strong promoter. Cotransfection with cDNA encoding a fluorescent marker protein, such as Green Fluorescent Protein (CLONTECH), is useful for identifying stable transfectants. The amount of cell agglutination, or clumping, associated with transfected cells is compared with that associated with untransfected cells. The amount of cell agglutination is a direct measure of DITHP activity.

[0881] DITHP may recognize and precipitate antigen from serum. This activity can be measured by the quantitative precipitin reaction (Golub, E. S. et al. (1987) Immunology: A Synthesis, Sinauer Associates, Sunderland Mass., pages 113-115). DITHP is isotopically labeled using methods known in the art. Various serum concentrations are added to constant amounts of labeled DITHP. DITHP-antigen complexes precipitate out of solution and are collected by centrifugation. The amount of precipitable DITHP-antigen complex is proportional to the amount of radioisotope detected in the precipitate. The amount of precipitable DITHP-antigen complex is plotted against the serum concentration. For various serum concentrations, a characteristic precipitation curve is obtained, in which the amount of precipitable DITHP-antigen complex initially increases proportionately with increasing serum concentration, peaks at the equivalence point, and then decreases proportionately with further increases in serum concentration. Thus, the amount of precipitable DITHP-antigen complex is a measure of DITHP activity which is characterized by sensitivity to both limiting and excess quantities of antigen.

[0882] A microtubule motility assay for DITHP measures motor protein activity. In this assay, recombinant DITHP is immobilized onto a glass slide or similar substrate. Taxol-stabilized bovine brain microtubules (commercially available) in a solution containing ATP and cytosolic extract are perfused onto the slide. Movement of microtubules as driven by DITHP motor activity can be visualized and quantified using video-enhanced light microscopy and image analysis techniques. DITHP motor protein activity is directly proportional to the frequency and velocity of microtubule movement.

[0883] Alternatively, an assay for DITHP measures the formation of protein filaments in vitro. A solution of DITHP at a concentration greater than the “critical concentration” for polymer assembly is applied to carbon-coated grids. Appropriate nucleation sites may be supplied in the solution. The grids are negative stained with 0.7% (w/v) aqueous uranyl acetate and examined by electron microscopy. The appearance of filaments of approximately 25 nm (microtubules), 8 nm (actin), or 10 nm (intermediate filaments) is a demonstration of protein activity.

[0884] DITHP electron transfer activity is demonstrated by oxidation or reduction of NADP. Substrates such as Asn-βGal, biocytidine, or ubiquinone-10 may be used. The reaction mixture contains 1-2 mg/ml HORP, 15 mM substrate, and 2.4 mM NAD(P)+in 0.1 M phosphate buffer, pH 7.1 (oxidation reaction), or 2.0 mM NAD(P)H, in 0.1 M Na2HPO4 buffer, pH 7.4 (reduction reaction); in a total volume of 0.1 ml. FAD may be included with NAD, according to methods well known in the art. Changes in absorbance are measured using a recording spectrophotometer. The amount of NAD(P)H is stoichiometrically equivalent to the amount of substrate initially present, and the change in A340 is a direct measure of the amount of NAD(P)H produced; ΔA340=6620[NADH]. DITHP activity is proportional to the amount of NAD(P)H present in the assay. The increase in extinction coefficient of NAD(P)H coenzyme at 340 nm is a measure of oxidation activity, or the decrease in extinction coefficient of NAD(P)H coenzyme at 340 nm is a measure of reduction activity (Dalziel, K. (1963) J. Biol. Chem. 238:2850-2858).

[0885] DITHP transcription factor activity is measured by its ability to stimulate transcription of a reporter gene (Liu, H. Y. et al. (1997) EMBO J. 16:5289-5298). The assay entails the use of a well characterized reporter gene construct, LexAop-LacZ, that consists of LexA DNA transcriptional control elements (LexAop) fused to sequences encoding the E. coli LacZ enzyme. The methods for constructing and expressing fusion genes, introducing them into cells, and measuring LacZ enzyme activity, are well known to those skilled in the art. Sequences encoding DITHP are cloned into a plasmid that directs the synthesis of a fusion protein, LexA-DITHP, consisting of DITHP and a DNA binding domain derived from the LexA transcription factor. The resulting plasmid, encoding a lexAop-DITHP fusion protein, is introduced into yeast cells along with a plasmid containing the LexAop-LacZ reporter gene. The amount of LacZ enzyme activity associated with LexA-DITHP transfected cells, relative to control cells, is proportional to the amount of transcription stimulated by the DITHP.

[0886] Chromatin activity of DITHP is demonstrated by measuring sensitivity to DNase I (Dawson, B. A. et al. (1989) J. Biol. Chem. 264:12830-12837). Samples are treated with DNase I, followed by insertion of a cleavable biotinylated nucleotide analog, 5-[(N-biotinamido)hexanoamidothyl-1,3-thiopropionyl-3-aminoallyl]-2′-deoxyuridine 5′-triphosphate using nick-repair techniques well known to those skilled in the art. Following purification and digestion with EcoRI restriction endonuclease, biotinylated sequences are affinity isolated by sequential binding to streptavidin and biotincellulose.

[0887] Another specific assay demonstrates the ion conductance capacity of DITHP using an electrophysiological assay. DITHP is expressed by transforming a mammalian cell line such as COS7, HeLa or CHO with a eukaryotic expression vector encoding DITHP. Eukaryotic expression vectors are commercially available, and the techniques to introduce them into cells are well known to those skilled in the art. A small amount of a second plasmid, which expresses any one of a number of marker genes such as β-galactosidase, is co-transformed into the cells in order to allow rapid identification of those cells which have taken up and expressed the foreign DNA. The cells are incubated for 48-72 hours after transformation under conditions appropriate for the cell line to allow expression and accumulation of DITHP and β-galactosidase. Transformed cells expressing β-galactosidase are stained blue when a suitable calorimetric substrate is added to the culture media under conditions that are well known in the art. Stained cells are tested for differences in membrane conductance due to various ions by electrophysiological techniques that are well known in the art. Untransformed cells, and/or cells transformed with either vector sequences alone or β-galactosidase sequences alone, are used as controls and tested in parallel. The contribution of DITHP to cation or anion conductance can be shown by incubating the cells using antibodies specific for either DITHP. The respective antibodies will bind to the extracellular side of DITHP, thereby blocking the pore in the ion channel, and the associated conductance.

[0888] XV. Functional Assays

[0889] DITHP function is assessed by expressing dithp at physiologically elevated levels in mammalian cell culture systems. cDNA is subcloned into a mammalian expression vector containing a strong promoter that drives high levels of cDNA expression. Vectors of choice include pCMV SPORT (Life Technologies) and pCR3.1 (Invitrogen Corporation, Carlsbad Calif.), both of which contain the cytomegalovirus promoter. 5-10 μg of recombinant vector are transiently transfected into a human cell line, preferably of endothelial or hematopoietic origin, using either liposome formulations or electroporation. 1-2 μg of an additional plasmid containing sequences encoding a marker protein are co-transfected.

[0890] Expression of a marker protein provides a means to distinguish transfected cells from nontransfected cells and is a reliable predictor of cDNA expression from the recombinant vector. Marker proteins of choice include, e.g., Green Fluorescent Protein (GFP; CLONTECH), CD64, or a CD64-GFP fusion protein. Flow cytometry (FCM), an automated laser optics-based technique, is used to identify transfected cells expressing GFP or CD64-GFP and to evaluate the apoptotic state of the cells and other cellular properties.

[0891] FCM detects and quantifies the uptake of fluorescent molecules that diagnose events preceding or coincident with cell death. These events include changes in nuclear DNA content as measured by staining of DNA with propidium iodide; changes in cell size and granularity as measured by forward light scatter and 90 degree side light scatter; down-regulation of DNA synthesis as measured by decrease in bromodeoxyuridine uptake; alterations in expression of cell surface and intracellular proteins as measured by reactivity with specific antibodies; and alterations in plasma membrane composition as measured by the binding of fluorescein-conjugated Annexin V protein to the cell surface. Methods in flow cytometry are discussed in Ormerod, M. G. (1994) Flow Cytometry, Oxford, New York N.Y.

[0892] The influence of DITHP on gene expression can be assessed using highly purified populations of cells transfected with sequences encoding DITHP and either CD64 or CD64-GFP. CD64 and CD64-GFP are expressed on the surface of transfected cells and bind to conserved regions of human immunoglobulin G (IgG). Transfected cells are efficiently separated from nontransfected cells using magnetic beads coated with either human IgG or antibody against CD64 (DYNAL, Inc., Lake Success N.Y.). mRNA can be purified from the cells using methods well known by those of skill in the art. Expression of mRNA encoding DITHP and other genes of interest can be analyzed by northern analysis or microarray techniques.

[0893] XVI. Production of Antibodies

[0894] DITHP substantially purified using polyacrylamide gel electrophoresis (PAGE; see, e.g., Harrington, M. G. (1990) Methods Enzymol. 182:488-495), or other purification techniques, is used to immunize rabbits and to produce antibodies using standard protocols.

[0895] Alternatively, the DITHP amino acid sequence is analyzed using LASERGENE software (DNASTAR) to determine regions of high immunogenicity, and a corresponding peptide is synthesized and used to raise antibodies by means known to those of skill in the art. Methods for selection of appropriate epitopes, such as those near the C-terminus or in hydrophilic regions are well described in the art. (See, e.g., Ausubel, 1995, supra, Chapter 11.)

[0896] Typically, peptides 15 residues in length are synthesized using an ABI 431A peptide synthesizer (Applied Biosystems) using fmoc-chemistry and coupled to KLH (Sigma) by reaction with N-maleimidobenzoyl-N-hydroxysuccinimide ester (MBS) to increase immunogenicity. (See, e.g., Ausubel, supra.) Rabbits are immunized with the peptide-KLH complex in complete Freund's adjuvant. Resulting antisera are tested for antipeptide activity by, for example, binding the peptide to plastic, blocking with 1% BSA, reacting with rabbit antisera, washing, and reacting with radio-iodinated goat anti-rabbit IgG. Antisera with antipeptide activity are tested for anti-DITHP activity using protocols well known in the art, including ELISA, RIA, and immunoblotting.

[0897] XVII. Purification of Naturally Occurring DITHP Using Specific Antibodies

[0898] Naturally occurring or recombinant DITHP is substantially purified by immunoaffinity chromatography using antibodies specific for DITHP. An immunoaffinity column is constructed by covalently coupling anti-DITHP antibody to an activated chromatographic resin, such as CNBr-activated SEPHAROSE (Amersham Pharmacia Biotech). After the coupling, the resin is blocked and washed according to the manufacturer's instructions.

[0899] Media containing DITHP are passed over the immunoaffinity column, and the column is washed under conditions that allow the preferential absorbance of DITHP (e.g., high ionic strength buffers in the presence of detergent). The column is eluted under conditions that disrupt antibody/DITHP binding (e.g., a buffer of pH 2 to pH 3, or a high concentration of a chaotrope, such as urea or thiocyanate ion), and DITHP is collected.

[0900] XVIII. Identification of Molecules Which Interact With DITHP

[0901] DITHP, or biologically active fragments thereof, are labeled with 125I Bolton-Hunter reagent. (See, e.g., Bolton, A. E. and W. M. Hunter (1973) Biochem. J. 133:529-539.) Candidate molecules previously arrayed in the wells of a multi-well plate are incubated with the labeled DITHP, washed, and any wells with labeled DITHP complex are assayed. Data obtained using different concentrations of DITHP are used to calculate values for the number, affinity, and association of DITHP with the candidate molecules.

[0902] Alternatively, molecules interacting with DITHP are analyzed using the yeast two-hybrid system as described in Fields, S. and O. Song (1989) Nature 340:245-246, or using commercially available kits based on the two-hybrid system, such as the MATCHMAKER system (CLONTECH).

[0903] DITHP may also be used in the PATHCALLING process (CuraGen Corp., New Haven Conn.) which employs the yeast two-hybrid system in a high-throughput manner to determine all interactions between the proteins encoded by two large libraries of genes (Nandabalan, K et al. (2000) U.S. Pat. No. 6,057,101).

[0904] All publications and patents mentioned in the above specification are herein incorporated by reference. Various modifications and variations of the described method and system of the invention will be apparent to those skilled in the art without departing from the scope and spirit of the invention. Although the invention has been described in connection with specific preferred embodiments, it should be understood that the invention as claimed should not be unduly limited to such specific embodiments. Indeed, various modifications of the above-described modes for carrying out the invention which are obvious to those skilled in the field of molecular biology or related fields are intended to be within the scope of the following claims.

2TABLE 1SEQ ID NO:Template IDSEQ ID NO:ORF ID1LI:1983416.1:2001JAN1257LI:1983416.1.orf1:2001JAN122LI:332263.1:2001JAN1258LI:332263.1.orf1:2001JAN123LI:333886.4:2001JAN1259LI:333886.4.orf2:2001JAN124LI:478508.1:2001JAN1260LI:478508.1.orf3:2001JAN125LI:307470.1:2001JAN1261LI:307470.1.orf1:2001JAN126LI:058298.1:2001JAN1262LI:058298.1.orf1:2001JAN127LI:205527.5:2001JAN1263LI:205527.5.orf1:2001JAN128LI:231587.1:2001JAN1264LI:231587.1.orf2:2001JAN129LI:402919.1:2001JAN1265LI:402919.1.orf2:2001JAN1210LI:463283.1:2001JAN1266LI:463283.1.orf2:2001JAN1211LI:072560.1:2001JAN1267LI:072560.1.orf3:2001JAN1212LI:1953096.1:2001JAN1268LI:1953096.1.orf3:2001JAN1213LI:1076016.1:2001JAN1269LI:1076016.1.orf1:2001JAN1214LI:2082796.1:2001JAN1270LI:2082796.1.orf1:2001JAN1215LI:335681.3:2001JAN1271LI:335681.3.orf3:2001JAN1216LI:214150.1:2001JAN1272LI:214150.1.orf1:2001JAN1217LI:322783.15:2001JAN1273LI:322783.15.orf1:2001JAN1218LI:422993.1:2001JAN1274LI:422993.1.orf1:2001JAN1219LI:1172885.1:2001JAN1275LI:1172885.1.orf3:2001JAN1220LI:1088359.1:2001JAN1276LI:1088359.1.orf1:2001JAN1221LI:813422.1:2001JAN1277LI:813422.1.orf2:2001JAN1222LI:1186426.1:2001JAN1278LI:1186426.1.orf1:2001JAN1223LI:1182817.1:2001JAN1279LI:1182817.1.orf3:2001JAN1224LI:1170153.9:2001JAN1280LI:1170153.9.orf1:2001JAN1225LI:1171553.1:2001JAN1281LI:1171553.1.orf3:2001JAN1226LI:2121978.1:2001JAN1282LI:2121978.1.orf1:2001JAN1227LI:1174292.5:2001JAN1283LI:1174292.5.orf2:2001JAN1228LI:1179173.1:2001JAN1284LI:1179173.1.orf2:2001JAN1229LI:2122025.1:2001JAN1285LI:2122025.1.orf3:2001JAN1230LI:2049224.1:2001JAN1286LI:2049224.1.orf1:2001JAN1231LI:758541.1:2001JAN1287LI:758541.1.orf3:2001JAN1232LI:137815.1:2001JAN1288LI:137815.1.orf3:2001JAN1233LI:335097.1:2001JAN1289LI:335097.1.orf3:2001JAN1234LI:232059.2:2001JAN1290LI:232059.2.orf3:2001JAN1235LI:400109.2:2001JAN1291LI:400109.2.orf1:2001JAN1236LI:329770.1:2001JAN1292LI:329770.1.orf1:2001JAN1237LI:898841.9:2001JAN1293LI:898841.9.orf2:2001JAN1238LI:1183848.3:2001JAN1294LI:1183848.3.orf1:2001JAN1239LI:2037121.1:2001JAN1295LI:2037121.1.orf2:2001JAN1240LI:356090.1:2001JAN1296LI:356090.1.orf1:2001JAN1241LI:212142.1:2001JAN1297LI:212142.1.orf1:2001JAN1242LI:1096706.1:2001JAN1298LI:1096706.1.orf1:2001JAN1243LI:012622.1:2001JAN1299LI:012622.1.orf1:2001JAN1244LI:1171095.29:2001JAN12100LI:1171095.29.orf3:2001JAN1245LI:023813.1:2001JAN12101LI:023813.1.orf2:2001JAN1246LI:229030.1:2001JAN12102LI:229030.1.orf3:2001JAN1247LI:1072894.9:2001JAN12103LI:1072894.9.orf3:2001JAN1248LI:2031263.1:2001JAN12104LI:2031263.1.orf3:2001JAN1249LI:432285.3:2001JAN12105LI:432285.3.orf3:2001JAN1250LI:1177772.30:2001JAN12106LI:1177772.30.orf2a:2001JAN1250LI:1177772.30:2001JAN12107LI:1177772.30.orf2b:2001JAN1251LI:475420.2:2001JAN12108LI:475420.2.orf3:2001JAN1252LI:017599.3:2001JAN12109LI:017599.3.orf3:2001JAN1253LI:030502.2:2001JAN12110LI:030502.2.orf1:2001JAN1254LI:1181337.3:2001JAN12111LI:1181337.3.orf3:2001JAN1255LI:1164672.3:2001JAN12112LI:1164672.3.orf2:2001JAN1256LI:1167059.4:2001JAN12113LI:1167059.4.orf3:2001JAN12

[0905]

3

TABLE 2

Probability

SEQ ID NO:
Template ID
GI Number
Score
Annotation

1
LI:1983416.1:2001JAN12
g2909860
3.00E−20
NADH-ubiquinone oxidoreductase

subunit CI-KFYI (Homo sapiens)

2
LI:332263.1:2001JAN12
g5817244
5.00E−42
dJ20N2.1 (novel protein similar to

yeast and bacterial cytosine

deaminase) (Homo sapiens)

3
LI:333886.4:2001JAN12
g31207
3.00E−27
put.thyroid hormone receptor (Homo

sapiens
)

4
LI:478508.1:2001JAN12
g12840055
4.00E−49
putative (Mus musculus)

5
LI:307470.1:2001JAN12
g10437569
2.00E−23
unnamed protein product (Homo

sapiens
)

6
LI:058298.1:2001JAN12
g36615
1.00E−102
serine/threonine protein kinase

(Homo sapiens)

7
LI:205527.5:2001JAN12
g1561718
1.00E−49
Human 14-3-3 epsilon mRNA,

complete cds.

8
LI:231587.1:2001JAN12
g1872200
6.00E−13
alternatively spliced product using

exon 13A (Homo sapiens)

9
LI:402919.1:2001JAN12
g15277706
4.00E−73
homeobox protein GBX-2b (Xenopus

laevis
)

10
LI:463283.1:2001JAN12
g10437485
5.00E−31
unnamed protein product (Homo

sapiens
)

11
LI:072560.1:2001JAN12
g1872200
4.00E−23
alternatively spliced product using

exon 13A (Homo sapiens)

12
LI:1953096.1:2001JAN12
g10437569
2.00E−18
unnamed protein product (Homo

sapiens
)

13
LI:1076016.1:2001JAN12
g7341372
2.00E−33
retinoblastoma-binding protein 1-

related protein (Rattus norvegicus)

14
LI:2082796.1:2001JAN12
g4323152
3.00E−30
Ets-protein Spi-C (Mus musculus)

15
LI:335681.3:2001JAN12
g14456631
2.00E−44
dJ54B20.4 (novel KRAB box

containing C2H2 type zinc finger

protein) (Homo sapiens)

16
LI:214150.1:2001JAN12
g1020145
5.00E−20
DNA binding protein (Homo sapiens)

17
LI:322783.15:2001JAN12
g7159799
2.00E−13
dJ351K20.1.1 (novel C3HC4 type Zinc

finger (RING finger) protein (isoform

1)) (Homo sapiens)

18
LI:422993.1:2001JAN12
g10440136
4.00E−84
unnamed protein product (Homo

sapiens
)

19
LI:1172885.1:2001JAN12
g468708
1.00E−28
zinc finger protein (Homo sapiens)

20
LI:1088359.1:2001JAN12
g1336158
4.00E−46
pancreas only zinc finger protein

(Rattus norvegicus)

21
LI:813422.1:2001JAN12
g7023216
1.00E−16
unnamed protein product (Homo

sapiens
)

22
LI:1186426.1:2001JAN12
g506502
1.00E−141
NK10 (Mus musculus)

23
LI:1182817.1:2001JAN12
g1020145
0
DNA binding protein (Homo sapiens)

24
LI:1170153.9:2001JAN12
g7023216
7.00E−68
unnamed protein product (Homo

sapiens
)

25
LI:1171553.1:2001JAN12
g6088100
1.00E−29
zinc finger protein (ZFD25) (Homo

sapiens
)

26
LI:2121978.1:2001JAN12
g6118383
2.00E−14
zinc finger protein ZNF223 (Homo

sapiens
)

27
LI:1174292.5:2001JAN12
g7959207
0
KIAA1473 protein (Homo sapiens)

28
LI:1179173.1:2001JAN12
g10835284
0
Zinc finger protein ZNF223 (amino

acids 82-482) (Homo sapiens)

29
LI:2122025.1:2001JAN12
g2689444
1.00E−93
ZNF134 (Homo sapiens)

30
LI:2049224.1:2001JAN12
g7023216
3.00E−55
unnamed protein product (Homo

sapiens
)

31
LI:758541.1:2001JAN12
g340444
3.00E−61
zinc finger protein 41 (Homo sapiens)

32
LI:137815.1:2001JAN12
g6984172
0
zinc finger protein ZNF226 (Homo

sapiens
)

33
LI:335097.1:2001JAN12
g7020440
1.00E−24
unnamed protein product (Homo

sapiens
)

34
LI:232059.2:2001JAN12
g9280152
6.00E−23
unnamed protein product (Macaca

fascicularis
)

35
LI:400109.2:2001JAN12
g12698182
5.00E−29
hypothetical protein (Macaca

fascicularis
)

36
LI:329770.1:2001JAN12
g10437569
3.00E−26
unnamed protein product (Homo

sapiens
)

37
LI:898841.9:2001JAN12
g7542490
4.00E−07
FK506 binding protein precursor

(Homo sapiens)

38
LI:1183848.3:2001JAN12
g32063
0
Human hepatoma mRNA for serine

protease hepsin

39
LI:2037121.1:2001JAN12
g1042082
1.00E−27
laminin alpha 4 chain (Homo

40
LI:356090.1:2001JAN12
g10437485
2.00E−13
unnamed protein product (Homo

sapiens
)

41
LI:212142.1:2001JAN12
g8980667
3.00E−12
PADI-H protein (Homo sapiens)

42
LI:1096706.1:2001JAN12
g12698182
2.00E−20
hypothetical protein (Macaca

fascicularis
)

43
LI:012622.1:2001JAN12
g3724141
3.00E−62
myosin I (Rattus norvegicus)

44
LI:1171095.29:2001JAN12
g56054
2.00E−22
D100 (Rattus norvegicus)

45
LI:023813.1:2001JAN12
g6690248
3.00E−24
PRO0657 (Homo sapiens)

46
LI:229030.1:2001JAN12
g10437485
1.00E−20
unnamed protein product (Homo

sapiens
)

47
LI:1072894.9:2001JAN12
g6523797
4.00E−08
adrenal gland protein AD-002

(Homo sapiens)

48
LI:2031263.1:2001JAN12
g9588408
1.00E−82
dJ1184F4.4 (novel protein similar to

nucleolar protein 4 (NOL4) (NOLP))

(Homo sapiens)

49
LI:432285.3:2001JAN12
g386987
6.00E−47
ornithine aminotransferase (Homo

sapiens
)

50
LI:1177772.30:2001JAN12
g8101070
0

Homo sapiens
golgin-like protein

(GLP) gene, complete cds

51
LI:475420.2:2001JAN12
g4689280
0
retinoid-binding protein IRBP (Mus

musculus
)

52
LI:017599.3:2001JAN12
g13559179
6.00E−11
dJ1049G16.2.2 (continued from

bA456N23.2 in Em: AL353777 and

dJ237J2.1 in Em: AL021394) (Homo

sapiens
)

53
LI:030502.2:2001JAN12
g7020440
5.00E−24
unnamed protein product (Homo

sapiens
)

54
LI:1181337.3:2001JAN12
g1196425
1.00E−31
envelope protein (Homo sapiens)

55
LI:1164672.3:2001JAN12
g11078529
6.00E−38
putative gag-pro-pol polyprotein

(DG-75 Murine leukemia virus)

56
LI:1167059.4:2001JAN12
g7688657
0
septin 10 (Homo sapiens)

[0906]

4

TABLE 3

SEQ

ID

NO:
Template ID
Start
Stop
Frame
Pfam Hlt
Pfam Description
E-value

3
LI: 333886.4: JAN 12, 2001
779
820
forward 2
zf-C4
Zinc finger, C4 type (two domains)
0.00000073

6
LI: 058298.1: JAN 12, 2001
268
966
forward 1
pkinase
Protein kinase domain
8.1E−56

9
LI: 402919.1: JAN 12, 2001
1183
1353
forward 1
homeobox
Homeobox domain
4.4E−31

15
LI: 335681.3: JAN 12, 2001
384
572
forward 3
KRAB
KRAB box
7.6E−46

15
LI: 335681.3: JAN 12, 2001
1002
1070
forward 3
zf-C2H2
Zinc finger, C2H2 type
0.000089

19
LI: 1172885.1: JAN 12, 2001
390
458
forward 3
zf-C2H2
Zinc finger, C2H2 type
0.00000068

20
LI: 1088359.1: JAN 12, 2001
169
237
forward 1
zf-C2H2
Zinc finger, C2H2 type
0.00000037

20
LI: 1088359.1: JAN 12, 2001
590
658
forward 2
zf-C2H2
Zinc finger, C2H2 type
0.0000073

21
LI: 813422.1: JAN 12, 2001
204
416
forward 3
KRAB
KRAB box
2.7E−20

22
LI: 1186426.1: JAN 12, 2001
706
774
forward 1
zf-C2H2
Zinc finger, C2H2 type
0.00000014

23
LI: 1182817.1: JAN 12, 2001
255
443
forward 3
KRAB
KRAB box
2.1E−45

23
LI: 1182817.1: JAN 12, 2001
1458
1526
forward 3
zf-C2H2
Zinc finger, C2H2 type
0.00000054

27
LI: 1174292.5: JAN 12, 2001
164
352
forward 2
KRAB
KRAB box
3.2E−41

27
LI: 1174292.5: JAN 12, 2001
1334
1402
forward 2
zf-C2H2
Zinc finger, C2H2 type
0.000002

28
LI: 1179173.1: JAN 12, 2001
221
406
forward 2
KRAB
KRAB box
1.9E−33

28
LI: 1179173.1: JAN 12, 2001
1229
1297
forward 2
zf-C2H2
Zinc finger, C2H2 type
0.00000073

29
LI: 2122025.1: JAN 12, 2001
229
396
forward 1
KRAB
KRAB box
2.9E−17

29
LI: 2122025.1: JAN 12, 2001
801
869
forward 3
zf-C2H2
Zinc finger, C2H2 type
0.000000089

30
LI: 2049224.1: JAN 12, 2001
94
240
forward 1
KRAB
KRAB box
5.4E−24

31
LI: 758541.1: JAN 12, 2001
273
341
forward 3
zf-C2H2
Zinc finger, C2H2 type
0.00000071

32
LI: 137815.1: JAN 12, 2001
522
695
forward 3
KRAB
KRAB box
1.4E-14

32
LI: 137815.1: JAN 12, 2001
2136
2204
forward 3
zf-C2H2
Zinc finger, C2H2 type
0.00000051

43
LI: 012622.1: JAN 12, 2001
1083
1424
forward 3
myosin_head
Myosin head (motor domain)
3.6E−28

43
LI: 012622.1: JAN 12, 2001
487
687
forward 1
myosin_head
Myosin head (motor domain)
1.2E−23

43
LI: 012622.1: JAN 12, 2001
920
991
forward 2
myosin_head
Myosin head (motor domain)
7.6E−09

51
LI: 475420.2: JAN 12, 2001
561
1589
forward 3
IRBP
Interphotoreceptor retinoid-binding pro
1.4E−185

51
LI: 475420.2: JAN 12, 2001
2410
3453
forward 1
IRBP
Interphotoreceptor retinoid-binding pro
8E−38

51
LI: 475420.2: JAN 12, 2001
2519
3403
forward 2
IRBP
Interphotoreceptor retinoid-binding pro
0.0000063

55
LI: 1164672.3: JAN 12, 2001
945
1115
forward 3
gag_MA
Matrix protein (MA), p15
2.8E−15

56
LI: 1167059.4: JAN 12, 2001
267
1088
forward 3
GTP_CDC
Cell division protein
2E−114

[0907]

5

TABLE 4

SEQ ID NO:
Template ID
Start
Stop
Frame
Domain
Topology

1
LI: 1983416.1: JAN 12, 2001
1
94
forward 2
TM
Cytosolic

1
LI: 1983416.1: JAN 12, 2001
95
117
forward 2
TM
Transmembrane

1
LI: 1983416.1: JAN 12, 2001
118
120
forward 2
TM
Non-cytosolic

2
LI: 332263.1: JAN 12, 2001
1
622
forward 1
TM
Non-cytosolic

2
LI: 332263.1: JAN 12, 2001
623
645
forward 1
TM
Transmembrane

2
LI: 332263.1: JAN 12, 2001
646
656
forward 1
TM
Cytosolic

2
LI: 332263.1: JAN 12, 2001
657
679
forward 1
TM
Transmembrane

2
LI: 332263.1: JAN 12, 2001
680
693
forward 1
TM
Non-cytosolic

2
LI: 332263.1: JAN 12, 2001
694
716
forward 1
TM
Transmembrane

2
LI: 332263.1: JAN 12, 2001
717
755
forward 1
TM
Cytosolic

2
LI: 332263.1: JAN 12, 2001
756
778
forward 1
TM
Transmembrane

2
LI: 332263.1: JAN 12, 2001
779
1110
forward 1
TM
Non-cytosolic

2
LI: 332263.1: JAN 12, 2001
1
650
forward 2
TM
Non-cytosolic

2
LI: 332263.1: JAN 12, 2001
651
673
forward 2
TM
Transmembrane

2
LI: 332263.1: JAN 12, 2001
674
693
forward 2
TM
Cytosolic

2
LI: 332263.1: JAN 12, 2001
694
716
forward 2
TM
Transmembrane

2
LI: 332263.1: JAN 12, 2001
717
754
forward 2
TM
Non-cytosolic

2
LI: 332263.1: JAN 12, 2001
755
777
forward 2
TM
Transmembrane

2
LI: 332263.1: JAN 12, 2001
778
783
forward 2
TM
Cytosolic

2
LI: 332263.1: JAN 12, 2001
784
803
forward 2
TM
Transmembrane

2
LI: 332263.1: JAN 12, 2001
804
1109
forward 2
TM
Non-cytosolic

2
LI: 332263.1: JAN 12, 2001
1
748
forward 3
TM
Non-cytosolic

2
LI: 332263.1: JAN 12, 2001
749
766
forward 3
TM
Transmembrane

2
LI: 332263.1: JAN 12, 2001
767
772
forward 3
TM
Cytosolic

2
LI: 332263.1: JAN 12, 2001
773
795
forward 3
TM
Transmembrane

2
LI: 332263.1: JAN 12, 2001
796
1109
forward 3
TM
Non-cytosolic

5
LI: 307470.1: JAN 12, 2001
1
34
forward 3
TM
Cytosolic

5
LI: 307470.1: JAN 12, 2001
35
57
forward 3
TM
Transmembrane

5
LI: 307470.1: JAN 12, 2001
58
320
forward 3
TM
Non-cytosolic

6
LI: 058298.1: JAN 12, 2001
1
430
forward 3
TM
Non-cytosolic

6
LI: 058298.1: JAN 12, 2001
431
453
forward 3
TM
Transmembrane

6
LI: 058298.1: JAN 12, 2001
454
529
forward 3
TM
Cytosolic

6
LI: 058298.1: JAN 12, 2001
530
552
forward 3
TM
Transmembrane

6
LI: 058298.1: JAN 12, 2001
553
558
forward 3
TM
Non-cytosolic

7
LI: 205527.5: JAN 12, 2001
1
14
forward 1
TM
Non-cytosolic

7
LI: 205527.5: JAN 12, 2001
15
35
forward 1
TM
Transmembrane

7
LI: 205527.5: JAN 12, 2001
36
47
forward 1
TM
Cytosolic

7
LI: 205527.5: JAN 12, 2001
48
70
forward 1
TM
Transmembrane

7
LI: 205527.5: JAN 12, 2001
71
90
forward 1
TM
Non-cytosolic

7
LI: 205527.5: JAN 12, 2001
1
14
forward 2
TM
Non-cytosolic

7
LI: 205527.5: JAN 12, 2001
15
37
forward 2
TM
Transmembrane

7
LI: 205527.5: JAN 12, 2001
38
89
forward 2
TM
Cytosolic

7
LI: 205527.5: JAN 12, 2001
1
14
forward 3
TM
Non-cytosolic

7
LI: 205527.5: JAN 12, 2001
15
37
forward 3
TM
Transmembrane

7
LI: 205527.5: JAN 12, 2001
38
89
forward 3
TM
Cytosolic

9
LI: 402919.1: JAN 12, 2001
1
572
forward 1
TM
Non-cytosolic

9
LI: 402919.1: JAN 12, 2001
573
595
forward 1
TM
Transmembrane

9
LI: 402919.1: JAN 12, 2001
596
668
forward 1
TM
Cytosolic

9
LI: 402919.1: JAN 12, 2001
669
691
forward 1
TM
Transmembrane

9
LI: 402919.1: JAN 12, 2001
692
700
forward 1
TM
Non-cytosolic

9
LI: 402919.1: JAN 12, 2001
701
723
forward 1
TM
Transmembrane

9
LI: 402919.1: JAN 12, 2001
724
741
forward 1
TM
Cytosolic

9
LI: 402919.1: JAN 12, 2001
1
571
forward 3
TM
Non-cytosolic

9
LI: 402919.1: JAN 12, 2001
572
594
forward 3
TM
Transmembrane

9
LI: 402919.1: JAN 12, 2001
595
676
forward 3
TM
Cytosolic

9
LI: 402919.1: JAN 12, 2001
677
699
forward 3
TM
Transmembrane

9
LI: 402919.1: JAN 12, 2001
700
708
forward 3
TM
Non-cytosolic

9
LI: 402919.1: JAN 12, 2001
709
731
forward 3
TM
Transmembrane

9
LI: 402919.1: JAN 12, 2001
732
740
forward 3
TM
Cytosolic

11
LI: 072560.1: JAN 12, 2001
1
285
forward 1
TM
Cytosolic

11
LI: 072560.1: JAN 12, 2001
286
308
forward 1
TM
Transmembrane

11
LI: 072560.1: JAN 12, 2001
309
322
forward 1
TM
Non-cytosolic

11
LI: 072560.1: JAN 12, 2001
323
345
forward 1
TM
Transmembrane

11
LI: 072560.1: JAN 12, 2001
346
349
forward 1
TM
Cytosolic

11
LI: 072560.1: JAN 12, 2001
350
372
forward 1
TM
Transmembrane

11
LI: 072560.1: JAN 12, 2001
373
485
forward 1
TM
Non-cytosolic

11
LI: 072560.1: JAN 12, 2001
486
508
forward 1
TM
Transmembrane

11
LI: 072560.1: JAN 12, 2001
509
520
forward 1
TM
Cytosolic

11
LI: 072560.1: JAN 12, 2001
521
540
forward 1
TM
Transmembrane

11
LI: 072560.1: JAN 12, 2001
541
861
forward 1
TM
Non-cytosolic

11
LI: 072560.1: JAN 12, 2001
1
325
forward 2
TM
Non-cytosolic

11
LI: 072560.1: JAN 12, 2001
326
348
forward 2
TM
Transmembrane

11
LI: 072560.1: JAN 12, 2001
349
349
forward 2
TM
Cytosolic

11
LI: 072560.1: JAN 12, 2001
350
372
forward 2
TM
Transmembrane

11
LI: 072560.1: JAN 12, 2001
373
861
forward 2
TM
Non-cytosolic

14
LI: 2082796.1: JAN 12, 2001
1
6
forward 2
TM
Cytosolic

14
LI: 2082796.1: JAN 12, 2001
7
29
forward 2
TM
Transmembrane

14
LI: 2082796.1: JAN 12, 2001
30
196
forward 2
TM
Non-cytosolic

17
LI: 322783.15: JAN 12, 2001
1
128
forward 2
TM
Cytosolic

17
LI: 322783.15: JAN 12, 2001
129
151
forward 2
TM
Transmembrane

17
LI: 322783.15: JAN 12, 2001
152
254
forward 2
TM
Non-cytosolic

18
LI: 422993.1: JAN 12, 2001
1
14
forward 1
TM
Non-cytosolic

18
LI: 422993.1: JAN 12, 2001
15
37
forward 1
TM
Transmembrane

18
LI: 422993.1: JAN 12, 2001
38
110
forward 1
TM
Cytosolic

18
LI: 422993.1: JAN 12, 2001
111
133
forward 1
TM
Transmembrane

18
LI: 422993.1: JAN 12, 2001
134
152
forward 1
TM
Non-cytosolic

18
LI: 422993.1: JAN 12, 2001
153
172
forward 1
TM
Transmembrane

18
LI: 422993.1: JAN 12, 2001
173
476
forward 1
TM
Cytosolic

18
LI: 422993.1: JAN 12, 2001
1
14
forward 2
TM
Non-cytosolic

18
LI: 422993.1: JAN 12, 2001
15
37
forward 2
TM
Transmembrane

18
LI: 422993.1: JAN 12, 2001
38
48
forward 2
TM
Cytosolic

18
LI: 422993.1: JAN 12, 2001
49
71
forward 2
TM
Transmembrane

18
LI: 422993.1: JAN 12, 2001
72
476
forward 2
TM
Non-cytosolic

18
LI: 422993.1: JAN 12, 2001
1
14
forward 3
TM
Non-cytosolic

18
LI: 422993.1: JAN 12, 2001
15
37
forward 3
TM
Transmembrane

18
LI: 422993.1: JAN 12, 2001
38
108
forward 3
TM
Cytosolic

18
LI: 422993.1: JAN 12, 2001
109
126
forward 3
TM
Transmembrane

18
LI: 422993.1: JAN 12, 2001
127
475
forward 3
TM
Non-cytosolic

20
LI: 1088359.1: JAN 12, 2001
1
682
forward 1
TM
Non-cytosolic

20
LI: 1088359.1: JAN 12, 2001
683
705
forward 1
TM
Transmembrane

20
LI: 1088359.1: JAN 12, 2001
706
765
forward 1
TM
Cytosolic

20
LI: 1088359.1: JAN 12, 2001
766
788
forward 1
TM
Transmembrane

20
LI: 1088359.1: JAN 12, 2001
789
835
forward 1
TM
Non-cytosolic

20
LI: 1088359.1: JAN 12, 2001
836
858
forward 1
TM
Transmembrane

20
LI: 1088359.1: JAN 12, 2001
859
950
forward 1
TM
Cytosolic

20
LI: 1088359.1: JAN 12, 2001
1
595
forward 2
TM
Non-cytosolic

20
LI: 1088359.1: JAN 12, 2001
596
618
forward 2
TM
Transmembrane

20
LI: 1088359.1: JAN 12, 2001
619
630
forward 2
TM
Cytosolic

20
LI: 1088359.1: JAN 12, 2001
631
653
forward 2
TM
Transmembrane

20
LI: 1088359.1: JAN 12, 2001
654
949
forward 2
TM
Non-cytosolic

21
LI: 813422.1: JAN 12, 2001
1
275
forward 1
TM
Cytosolic

21
LI: 813422.1: JAN 12, 2001
276
298
forward 1
TM
Transmembrane

21
LI: 813422.1: JAN 12, 2001
299
630
forward 1
TM
Non-cytosolic

22
LI: 1186426.1: JAN 12, 2001
1
19
forward 2
TM
Non-cytosolic

22
LI: 1186426.1: JAN 12, 2001
20
42
forward 2
TM
Transmembrane

22
LI: 1186426.1: JAN 12, 2001
43
332
forward 2
TM
Cytosolic

22
LI: 1186426.1: JAN 12, 2001
333
355
forward 2
TM
Transmembrane

22
LI: 1186426.1: JAN 12, 2001
356
649
forward 2
TM
Non-cytosolic

23
LI: 1182817.1: JAN 12, 2001
1
1063
forward 3
TM
Non-cytosolic

23
LI: 1182817.1: JAN 12, 2001
1064
1086
forward 3
TM
Transmembrane

23
LI: 1182817.1: JAN 12, 2001
1087
1172
forward 3
TM
Cytosolic

23
LI: 1182817.1: JAN 12, 2001
1173
1195
forward 3
TM
Transmembrane

23
LI: 1182817.1: JAN 12, 2001
1196
1526
forward 3
TM
Non-cytosolic

24
LI: 1170153.9: JAN 12, 2001
1
56
forward 2
TM
Cytosolic

24
LI: 1170153.9: JAN 12, 2001
57
79
forward 2
TM
Transmembrane

24
LI: 1170153.9: JAN 12, 2001
80
83
forward 2
TM
Non-cytosolic

24
LI: 1170153.9: JAN 12, 2001
84
106
forward 2
TM
Transmembrane

24
LI: 1170153.9: JAN 12, 2001
107
470
forward 2
TM
Cytosolic

24
LI: 1170153.9: JAN 12, 2001
1
20
forward 3
TM
Cytosolic

24
LI: 1170153.9: JAN 12, 2001
21
43
forward 3
TM
Transmembrane

24
LI: 1170153.9: JAN 12, 2001
44
57
forward 3
TM
Non-cytosolic

24
LI: 1170153.9: JAN 12, 2001
58
80
forward 3
TM
Transmembrane

24
LI: 1170153.9: JAN 12, 2001
81
275
forward 3
TM
Cytosolic

24
LI: 1170153.9: JAN 12, 2001
276
298
forward 3
TM
Transmembrane

24
LI: 1170153.9: JAN 12, 2001
299
469
forward 3
TM
Non-cytosolic

28
LI: 1179173.1: JAN 12, 2001
1
731
forward 1
TM
Non-cytosolic

28
LI: 1179173.1: JAN 12, 2001
732
754
forward 1
TM
Transmembrane

28
LI: 1179173.1: JAN 12, 2001
755
778
forward 1
TM
Cytosolic

28
LI: 1179173.1: JAN 12, 2001
1
543
forward 2
TM
Non-cytosolic

28
LI: 1179173.1: JAN 12, 2001
544
566
forward 2
TM
Transmembrane

28
LI: 1179173.1: JAN 12, 2001
567
778
forward 2
TM
Cytosolic

31
LI: 758541.1: JAN 12, 2001
1
524
forward 1
TM
Non-cytosolic

31
LI: 758541.1: JAN 12, 2001
525
547
forward 1
TM
Transmembrane

31
LI: 758541.1: JAN 12, 2001
548
551
forward 1
TM
Cytosolic

31
LI: 758541.1: JAN 12, 2001
552
574
forward 1
TM
Transmembrane

31
LI: 758541.1: JAN 12, 2001
575
618
forward 1
TM
Non-cytosolic

31
LI: 758541.1: JAN 12, 2001
619
641
forward 1
TM
Transmembrane

31
LI: 758541.1: JAN 12, 2001
642
647
forward 1
TM
Cytosolic

31
LI: 758541.1: JAN 12, 2001
648
670
forward 1
TM
Transmembrane

31
LI: 758541.1: JAN 12, 2001
671
689
forward 1
TM
Non-cytosolic

31
LI: 758541.1: JAN 12, 2001
690
712
forward 1
TM
Transmembrane

31
LI: 758541.1: JAN 12, 2001
713
716
forward 1
TM
Cytosolic

31
LI: 758541.1: JAN 12, 2001
717
739
forward 1
TM
Transmembrane

31
LI: 758541.1: JAN 12, 2001
740
769
forward 1
TM
Non-cytosolic

31
LI: 758541.1: JAN 12, 2001
770
792
forward 1
TM
Transmembrane

31
LI: 758541.1: JAN 12, 2001
793
845
forward 1
TM
Cytosolic

31
LI: 758541.1: JAN 12, 2001
846
868
forward 1
TM
Transmembrane

31
LI: 758541.1: JAN 12, 2001
869
882
forward 1
TM
Non-cytosolic

31
LI: 758541.1: JAN 12, 2001
883
905
forward 1
TM
Transmembrane

31
LI: 758541.1: JAN 12, 2001
906
917
forward 1
TM
Cytosolic

31
LI: 758541.1: JAN 12, 2001
918
940
forward 1
TM
Transmembrane

31
LI: 758541.1: JAN 12, 2001
941
944
forward 1
TM
Non-cytosolic

31
LI: 758541.1: JAN 12, 2001
945
967
forward 1
TM
Transmembrane

31
LI: 758541.1: JAN 12, 2001
968
977
forward 1
TM
Cytosolic

31
LI: 758541.1: JAN 12, 2001
1
319
forward 2
TM
Non-cytosolic

31
LI: 758541.1: JAN 12, 2001
320
342
forward 2
TM
Transmembrane

31
LI: 758541.1: JAN 12, 2001
343
454
forward 2
TM
Cytosolic

31
LI: 758541.1: JAN 12, 2001
455
472
forward 2
TM
Transmembrane

31
LI: 758541.1: JAN 12, 2001
473
544
forward 2
TM
Non-cytosolic

31
LI: 758541.1: JAN 12, 2001
545
567
forward 2
TM
Transmembrane

31
LI: 758541.1: JAN 12, 2001
568
626
forward 2
TM
Cytosolic

31
LI: 758541.1: JAN 12, 2001
627
649
forward 2
TM
Transmembrane

31
LI: 758541.1: JAN 12, 2001
650
663
forward 2
TM
Non-cytosolic

31
LI: 758541.1: JAN 12, 2001
664
686
forward 2
TM
Transmembrane

31
LI: 758541.1: JAN 12, 2001
687
706
forward 2
TM
Cytosolic

31
LI: 758541.1: JAN 12, 2001
707
729
forward 2
TM
Transmembrane

31
LI: 758541.1: JAN 12, 2001
730
767
forward 2
TM
Non-cytosolic

31
LI: 758541.1: JAN 12, 2001
768
790
forward 2
TM
Transmembrane

31
LI: 758541.1: JAN 12, 2001
791
823
forward 2
TM
Cytosolic

31
LI: 758541.1: JAN 12, 2001
824
846
forward 2
TM
Transmembrane

31
LI: 758541.1: JAN 12, 2001
847
855
forward 2
TM
Non-cytosolic

31
LI: 758541.1: JAN 12, 2001
856
875
forward 2
TM
Transmembrane

31
LI: 758541.1: JAN 12, 2001
876
977
forward 2
TM
Cytosolic

31
LI: 758541.1: JAN 12, 2001
1
455
forward 3
TM
Cytosolic

31
LI: 758541.1: JAN 12, 2001
456
478
forward 3
TM
Transmembrane

31
LI: 758541.1: JAN 12, 2001
479
544
forward 3
TM
Non-cytosolic

31
LI: 758541.1: JAN 12, 2001
545
567
forward 3
TM
Transmembrane

31
LI: 758541.1: JAN 12, 2001
568
621
forward 3
TM
Cytosolic

31
LI: 758541.1: JAN 12, 2001
622
640
forward 3
TM
Transmembrane

31
LI: 758541.1: JAN 12, 2001
641
700
forward 3
TM
Non-cytosolic

31
LI: 758541.1: JAN 12, 2001
701
723
forward 3
TM
Transmembrane

31
LI: 758541.1: JAN 12, 2001
724
761
forward 3
TM
Cytosolic

31
LI: 758541.1: JAN 12, 2001
762
784
forward 3
TM
Transmembrane

31
LI: 758541.1: JAN 12, 2001
785
834
forward 3
TM
Non-cytosolic

31
LI: 758541.1: JAN 12, 2001
835
857
forward 3
TM
Transmembrane

31
LI: 758541.1: JAN 12, 2001
858
877
forward 3
TM
Cytosolic

31
LI: 758541.1: JAN 12, 2001
878
900
forward 3
TM
Transmembrane

31
LI: 758541.1: JAN 12, 2001
901
943
forward 3
TM
Non-cytosolic

31
LI: 758541.1: JAN 12, 2001
944
966
forward 3
TM
Transmembrane

31
LI: 758541.1: JAN 12, 2001
967
976
forward 3
TM
Cytosolic

32
LI: 137815.1: JAN 12, 2001
1
1561
forward 1
TM
Non-cytosolic

32
LI: 137815.1: JAN 12, 2001
1562
1584
forward 1
TM
Transmembrane

32
LI: 137815.1: JAN 12, 2001
1585
1596
forward 1
TM
Cytosolic

32
LI: 137815.1: JAN 12, 2001
1597
1619
forward 1
TM
Transmembrane

32
LI: 137815.1: JAN 12, 2001
1620
1657
forward 1
TM
Non-cytosolic

32
LI: 137815.1: JAN 12, 2001
1
1235
forward 2
TM
Non-cytosolic

32
LI: 137815.1: JAN 12, 2001
1236
1253
forward 2
TM
Transmembrane

32
LI: 137815.1: JAN 12, 2001
1254
1259
forward 2
TM
Cytosolic

32
LI: 137815.1: JAN 12, 2001
1260
1282
forward 2
TM
Transmembrane

32
LI: 137815.1: JAN 12, 2001
1283
1613
forward 2
TM
Non-cytosolic

32
LI: 137815.1: JAN 12, 2001
1614
1636
forward 2
TM
Transmembrane

32
LI: 137815.1: JAN 12, 2001
1637
1656
forward 2
TM
Cytosolic

32
LI: 137815.1: JAN 12, 2001
1
1050
forward 3
TM
Non-cytosolic

32
LI: 137815.1: JAN 12, 2001
1051
1073
forward 3
TM
Transmembrane

32
LI: 137815.1: JAN 12, 2001
1074
1144
forward 3
TM
Cytosolic

32
LI: 137815.1: JAN 12, 2001
1145
1167
forward 3
TM
Transmembrane

32
LI: 137815.1: JAN 12, 2001
1168
1192
forward 3
TM
Non-cytosolic

32
LI: 137815.1: JAN 12, 2001
1193
1215
forward 3
TM
Transmembrane

32
LI: 137815.1: JAN 12, 2001
1216
1235
forward 3
TM
Cytosolic

32
LI: 137815.1: JAN 12, 2001
1236
1256
forward 3
TM
Transmembrane

32
LI: 137815.1: JAN 12, 2001
1257
1265
forward 3
TM
Non-cytosolic

32
LI: 137815.1: JAN 12, 2001
1266
1288
forward 3
TM
Transmembrane

32
LI: 137815.1: JAN 12, 2001
1289
1593
forward 3
TM
Cytosolic

32
LI: 137815.1: JAN 12, 2001
1594
1616
forward 3
TM
Transmembrane

32
LI: 137815.1: JAN 12, 2001
1617
1656
forward 3
TM
Non-cytosolic

33
LI: 335097.1: JAN 12, 2001
1
92
forward 3
TM
Non-cytosolic

33
LI: 335097.1: JAN 12, 2001
93
115
forward 3
TM
Transmembrane

33
LI: 335097.1: JAN 12, 2001
116
252
forward 3
TM
Cytosolic

33
LI: 335097.1: JAN 12, 2001
253
275
forward 3
TM
Transmembrane

33
LI: 335097.1: JAN 12, 2001
276
405
forward 3
TM
Non-cytosolic

34
LI: 232059.2: JAN 12, 2001
1
18
forward 1
TM
Cytosolic

34
LI: 232059.2: JAN 12, 2001
19
41
forward 1
TM
Transmembrane

34
LI: 232059.2: JAN 12, 2001
42
60
forward 1
TM
Non-cytosolic

34
LI: 232059.2: JAN 12, 2001
61
83
forward 1
TM
Transmembrane

34
LI: 232059.2: JAN 12, 2001
84
89
forward 1
TM
Cytosolic

34
LI: 232059.2: JAN 12, 2001
90
112
forward 1
TM
Transmembrane

34
LI: 232059.2: JAN 12, 2001
113
115
forward 1
TM
Non-cytosolic

34
LI: 232059.2: JAN 12, 2001
116
138
forward 1
TM
Transmembrane

34
LI: 232059.2: JAN 12, 2001
139
231
forward 1
TM
Cytosolic

34
LI: 232059.2: JAN 12, 2001
232
254
forward 1
TM
Transmembrane

34
LI: 232059.2: JAN 12, 2001
255
277
forward 1
TM
Non-cytosolic

34
LI: 232059.2: JAN 12, 2001
278
300
forward 1
TM
Transmembrane

34
LI: 232059.2: JAN 12, 2001
301
319
forward 1
TM
Cytosolic

34
LI: 232059.2: JAN 12, 2001
320
342
forward 1
TM
Transmembrane

34
LI: 232059.2: JAN 12, 2001
343
436
forward 1
TM
Non-cytosolic

34
LI: 232059.2: JAN 12, 2001
1
12
forward 2
TM
Cytosolic

34
LI: 232059.2: JAN 12, 2001
13
35
forward 2
TM
Transmembrane

34
LI: 232059.2: JAN 12, 2001
36
221
forward 2
TM
Non-cytosolic

34
LI: 232059.2: JAN 12, 2001
222
244
forward 2
TM
Transmembrane

34
LI: 232059.2: JAN 12, 2001
245
250
forward 2
TM
Cytosolic

34
LI: 232059.2: JAN 12, 2001
251
273
forward 2
TM
Transmembrane

34
LI: 232059.2: JAN 12, 2001
274
287
forward 2
TM
Non-cytosolic

34
LI: 232059.2: JAN 12, 2001
288
310
forward 2
TM
Transmembrane

34
LI: 232059.2: JAN 12, 2001
311
436
forward 2
TM
Cytosolic

34
LI: 232059.2: JAN 12, 2001
1
14
forward 3
TM
Non-cytosolic

34
LI: 232059.2: JAN 12, 2001
15
32
forward 3
TM
Transmembrane

34
LI: 232059.2: JAN 12, 2001
33
59
forward 3
TM
Cytosolic

34
LI: 232059.2: JAN 12, 2001
60
82
forward 3
TM
Transmembrane

34
LI: 232059.2: JAN 12, 2001
83
91
forward 3
TM
Non-cytosolic

34
LI: 232059.2: JAN 12, 2001
92
113
forward 3
TM
Transmembrane

34
LI: 232059.2: JAN 12, 2001
114
261
forward 3
TM
Cytosolic

34
LI: 232059.2: JAN 12, 2001
262
284
forward 3
TM
Transmembrane

34
LI: 232059.2: JAN 12, 2001
285
435
forward 3
TM
Non-cytosolic

35
LI: 400109.2: JAN 12, 2001
1
418
forward 1
TM
Non-cytosolic

35
LI: 400109.2: JAN 12, 2001
419
438
forward 1
TM
Transmembrane

35
LI: 400109.2: JAN 12, 2001
439
449
forward 1
TM
Cytosolic

35
LI: 400109.2: JAN 12, 2001
450
472
forward 1
TM
Transmembrane

35
LI: 400109.2: JAN 12, 2001
473
527
forward 1
TM
Non-cytosolic

35
LI: 400109.2: JAN 12, 2001
1
19
forward 2
TM
Non-cytosolic

35
LI: 400109.2: JAN 12, 2001
20
39
forward 2
TM
Transmembrane

35
LI: 400109.2: JAN 12, 2001
40
62
forward 2
TM
Cytosolic

35
LI: 400109.2: JAN 12, 2001
63
85
forward 2
TM
Transmembrane

35
LI: 400109.2: JAN 12, 2001
86
144
forward 2
TM
Non-cytosolic

35
LI: 400109.2: JAN 12, 2001
145
167
forward 2
TM
Transmembrane

35
LI: 400109.2: JAN 12, 2001
168
238
forward 2
TM
Cytosolic

35
LI: 400109.2: JAN 12, 2001
239
261
forward 2
TM
Transmembrane

35
LI: 400109.2: JAN 12, 2001
262
527
forward 2
TM
Non-cytosolic

36
LI: 329770.1: JAN 12, 2001
1
414
forward 1
TM
Non-cytosolic

36
LI: 329770.1: JAN 12, 2001
415
437
forward 1
TM
Transmembrane

36
LI: 329770.1: JAN 12, 2001
438
580
forward 1
TM
Cytosolic

36
LI: 329770.1: JAN 12, 2001
581
603
forward 1
TM
Transmembrane

36
LI: 329770.1: JAN 12, 2001
604
617
forward 1
TM
Non-cytosolic

36
LI: 329770.1: JAN 12, 2001
618
637
forward 1
TM
Transmembrane

36
LI: 329770.1: JAN 12, 2001
638
679
forward 1
TM
Cytosolic

36
LI: 329770.1: JAN 12, 2001
1
298
forward 2
TM
Non-cytosolic

36
LI: 329770.1: JAN 12, 2001
299
318
forward 2
TM
Transmembrane

36
LI: 329770.1: JAN 12, 2001
319
367
forward 2
TM
Cytosolic

36
LI: 329770.1: JAN 12, 2001
368
390
forward 2
TM
Transmembrane

36
LI: 329770.1: JAN 12, 2001
391
404
forward 2
TM
Non-cytosolic

36
LI: 329770.1: JAN 12, 2001
405
427
forward 2
TM
Transmembrane

36
LI: 329770.1: JAN 12, 2001
428
521
forward 2
TM
Cytosolic

36
LI: 329770.1: JAN 12, 2001
522
544
forward 2
TM
Transmembrane

36
LI: 329770.1: JAN 12, 2001
545
553
forward 2
TM
Non-cytosolic

36
LI: 329770.1: JAN 12, 2001
554
568
forward 2
TM
Transmembrane

36
LI: 329770.1: JAN 12, 2001
569
580
forward 2
TM
Cytosolic

36
LI: 329770.1: JAN 12, 2001
581
603
forward 2
TM
Transmembrane

36
LI: 329770.1: JAN 12, 2001
604
678
forward 2
TM
Non-cytosolic

36
LI: 329770.1: JAN 12, 2001
1
22
forward 3
TM
Non-cytosolic

36
LI: 329770.1: JAN 12, 2001
23
45
forward 3
TM
Transmembrane

36
LI: 329770.1: JAN 12, 2001
46
159
forward 3
TM
Cytosolic

36
LI: 329770.1: JAN 12, 2001
160
182
forward 3
TM
Transmembrane

36
LI: 329770.1: JAN 12, 2001
183
212
forward 3
TM
Non-cytosolic

36
LI: 329770.1: JAN 12, 2001
213
230
forward 3
TM
Transmembrane

36
LI: 329770.1: JAN 12, 2001
231
350
forward 3
TM
Cytosolic

36
LI: 329770.1: JAN 12, 2001
351
373
forward 3
TM
Transmembrane

36
LI: 329770.1: JAN 12, 2001
374
412
forward 3
TM
Non-cytosolic

36
LI: 329770.1: JAN 12, 2001
413
435
forward 3
TM
Transmembrane

36
LI: 329770.1: JAN 12, 2001
436
553
forward 3
TM
Cytosolic

36
LI: 329770.1: JAN 12, 2001
554
576
forward 3
TM
Transmembrane

36
LI: 329770.1: JAN 12, 2001
577
579
forward 3
TM
Non-cytosolic

36
LI: 329770.1: JAN 12, 2001
580
602
forward 3
TM
Transmembrane

36
LI: 329770.1: JAN 12, 2001
603
678
forward 3
TM
Cytosolic

42
LI: 1096706.1: JAN 12, 2001
1
119
forward 2
TM
Cytosolic

42
LI: 1096706.1: JAN 12, 2001
120
142
forward 2
TM
Transmembrane

42
LI: 1096706.1: JAN 12, 2001
143
161
forward 2
TM
Non-cytosolic

42
LI: 1096706.1: JAN 12, 2001
162
184
forward 2
TM
Transmembrane

42
LI: 1096706.1: JAN 12, 2001
185
205
forward 2
TM
Cytosolic

46
LI: 229030.1: JAN 12, 2001
1
40
forward 3
TM
Cytosolic

46
LI: 229030.1: JAN 12, 2001
41
63
forward 3
TM
Transmembrane

46
LI: 229030.1: JAN 12, 2001
64
82
forward 3
TM
Non-cytosolic

46
LI: 229030.1: JAN 12, 2001
83
105
forward 3
TM
Transmembrane

46
LI: 229030.1: JAN 12, 2001
106
177
forward 3
TM
Cytosolic

47
LI: 1072894.9: JAN 12, 2001
1
55
forward 1
TM
Cytosolic

47
LI: 1072894.9: JAN 12, 2001
1
55
forward 2
TM
Cytosolic

49
LI: 432285.3: JAN 12, 2001
1
46
forward 1
TM
Cytosolic

49
LI: 432285.3: JAN 12, 2001
47
69
forward 1
TM
Transmembrane

49
LI: 432285.3: JAN 12, 2001
70
83
forward 1
TM
Non-cytosolic

49
LI: 432285.3: JAN 12, 2001
84
106
forward 1
TM
Transmembrane

49
LI: 432285.3: JAN 12, 2001
107
112
forward 1
TM
Cytosolic

49
LI: 432285.3: JAN 12, 2001
113
135
forward 1
TM
Transmembrane

49
LI: 432285.3: JAN 12, 2001
136
688
forward 1
TM
Non-cytosolic

49
LI: 432285.3: JAN 12, 2001
689
711
forward 1
TM
Transmembrane

49
LI: 432285.3: JAN 12, 2001
712
717
forward 1
TM
Cytosolic

49
LI: 432285.3: JAN 12, 2001
718
740
forward 1
TM
Transmembrane

49
LI: 432285.3: JAN 12, 2001
741
754
forward 1
TM
Non-cytosolic

49
LI: 432285.3: JAN 12, 2001
755
777
forward 1
TM
Transmembrane

49
LI: 432285.3: JAN 12, 2001
778
875
forward 1
TM
Cytosolic

49
LI: 432285.3: JAN 12, 2001
1
3
forward 2
TM
Non-cytosolic

49
LI: 432285.3: JAN 12, 2001
4
23
forward 2
TM
Transmembrane

49
LI: 432285.3: JAN 12, 2001
24
42
forward 2
TM
Cytosolic

49
LI: 432285.3: JAN 12, 2001
43
65
forward 2
TM
Transmembrane

49
LI: 432285.3: JAN 12, 2001
66
875
forward 2
TM
Non-cytosolic

49
LI: 432285.3: JAN 12, 2001
1
14
forward 3
TM
Non-cytosolic

49
LI: 432285.3: JAN 12, 2001
15
34
forward 3
TM
Transmembrane

49
LI: 432285.3: JAN 12, 2001
35
40
forward 3
TM
Cytosolic

49
LI: 432285.3: JAN 12, 2001
41
63
forward 3
TM
Transmembrane

49
LI: 432285.3: JAN 12, 2001
64
875
forward 3
TM
Non-cytosolic

51
LI: 475420.2: JAN 12, 2001
1
1482
forward 1
TM
Non-cytosolic

51
LI: 475420.2: JAN 12, 2001
1483
1505
forward 1
TM
Transmembrane

51
LI: 475420.2: JAN 12, 2001
1506
1517
forward 1
TM
Cytosolic

51
LI: 475420.2: JAN 12, 2001
1518
1540
forward 1
TM
Transmembrane

51
LI: 475420.2: JAN 12, 2001
1541
1572
forward 1
TM
Non-cytosolic

51
LI: 475420.2: JAN 12, 2001
1
1484
forward 2
TM
Non-cytosolic

51
LI: 475420.2: JAN 12, 2001
1485
1507
forward 2
TM
Transmembrane

51
LI: 475420.2: JAN 12, 2001
1508
1527
forward 2
TM
Cytosolic

51
LI: 475420.2: JAN 12, 2001
1528
1550
forward 2
TM
Transmembrane

51
LI: 475420.2: JAN 12, 2001
1551
1571
forward 2
TM
Non-cytosolic

51
LI: 475420.2: JAN 12, 2001
1
1491
forward 3
TM
Non-cytosolic

51
LI: 475420.2: JAN 12, 2001
1492
1514
forward 3
TM
Transmembrane

51
LI: 475420.2: JAN 12, 2001
1515
1520
forward 3
TM
Cytosolic

51
LI: 475420.2: JAN 12, 2001
1521
1543
forward 3
TM
Transmembrane

51
LI: 475420.2: JAN 12, 2001
1544
1571
forward 3
TM
Non-cytosolic

52
LI: 017599.3: JAN 12, 2001
1
12
forward 1
TM
Cytosolic

52
LI: 017599.3: JAN 12, 2001
13
31
forward 1
TM
Transmembrane

52
LI: 017599.3: JAN 12, 2001
32
280
forward 1
TM
Non-cytosolic

52
LI: 017599.3: JAN 12, 2001
281
303
forward 1
TM
Transmembrane

52
LI: 017599.3: JAN 12, 2001
304
306
forward 1
TM
Cytosolic

52
LI: 017599.3: JAN 12, 2001
1
6
forward 3
TM
Cytosolic

52
LI: 017599.3: JAN 12, 2001
7
29
forward 3
TM
Transmembrane

52
LI: 017599.3: JAN 12, 2001
30
268
forward 3
TM
Non-cytosolic

52
LI: 017599.3: JAN 12, 2001
269
291
forward 3
TM
Transmembrane

52
LI: 017599.3: JAN 12, 2001
292
306
forward 3
TM
Cytosolic

54
LI: 1181337.3: JAN 12, 2001
1
118
forward 3
TM
Non-cytosolic

54
LI: 1181337.3: JAN 12, 2001
119
141
forward 3
TM
Transmembrane

54
LI: 1181337.3: JAN 12, 2001
142
278
forward 3
TM
Cytosolic

54
LI: 1181337.3: JAN 12, 2001
279
301
forward 3
TM
Transmembrane

54
LI: 1181337.3: JAN 12, 2001
302
340
forward 3
TM
Non-cytosolic

56
LI: 1167059.4: JAN 12, 2001
1
462
forward 1
TM
Non-cytosolic

56
LI: 1167059.4: JAN 12, 2001
463
485
forward 1
TM
Transmembrane

56
LI: 1167059.4: JAN 12, 2001
486
693
forward 1
TM
Cytosolic

56
LI: 1167059.4: JAN 12, 2001
694
716
forward 1
TM
Transmembrane

56
LI: 1167059.4: JAN 12, 2001
717
725
forward 1
TM
Non-cytosolic

56
LI: 1167059.4: JAN 12, 2001
726
743
forward 1
TM
Transmembrane

56
LI: 1167059.4: JAN 12, 2001
744
755
forward 1
TM
Cytosolic

56
LI: 1167059.4: JAN 12, 2001
756
775
forward 1
TM
Transmembrane

56
LI: 1167059.4: JAN 12, 2001
776
838
forward 1
TM
Non-cytosolic

56
LI: 1167059.4: JAN 12, 2001
839
861
forward 1
TM
Transmembrane

56
LI: 1167059.4: JAN 12, 2001
862
881
forward 1
TM
Cytosolic

56
LI: 1167059.4: JAN 12, 2001
882
904
forward 1
TM
Transmembrane

56
LI: 1167059.4: JAN 12, 2001
905
932
forward 1
TM
Non-cytosolic

56
LI: 1167059.4: JAN 12, 2001
933
953
forward 1
TM
Transmembrane

56
LI: 1167059.4: JAN 12, 2001
954
956
forward 1
TM
Cytosolic

56
LI: 1167059.4: JAN 12, 2001
1
778
forward 3
TM
Non-cytosolic

56
LI: 1167059.4: JAN 12, 2001
779
801
forward 3
TM
Transmembrane

56
LI: 1167059.4: JAN 12, 2001
802
813
forward 3
TM
Cytosolic

56
LI: 1167059.4: JAN 12, 2001
814
836
forward 3
TM
Transmembrane

56
LI: 1167059.4: JAN 12, 2001
837
845
forward 3
TM
Non-cytosolic

56
LI: 1167059.4: JAN 12, 2001
846
865
forward 3
TM
Transmembrane

56
LI: 1167059.4: JAN 12, 2001
866
876
forward 3
TM
Cytosolic

56
LI: 1167059.4: JAN 12, 2001
877
899
forward 3
TM
Transmembrane

56
LI: 1167059.4: JAN 12, 2001
900
928
forward 3
TM
Non-cytosolic

56
LI: 1167059.4: JAN 12, 2001
929
951
forward 3
TM
Transmembrane

56
LI: 1167059.4: JAN 12, 2001
952
955
forward 3
TM
Cytosolic

[0908]

6

TABLE 5

SEQ ID NO:
Template ID
Component ID
Start
Stop

1
LI:1983416.1:2001JAN12
8140319T1
1
363

1
LI:1983416.1:2001JAN12
7976079H1
22
435

2
LI:332263.1:2001JAN12
458423T6
1542
2088

2
LI:332263.1:2001JAN12
71850401V1
1544
2090

2
LI:332263.1:2001JAN12
g3896002
1549
1997

2
LI:332263.1:2001JAN12
g7374740
1910
2260

2
LI:332263.1:2001JAN12
70312653D1
465
944

2
LI:332263.1:2001JAN12
70314846D1
465
874

2
LI:332263.1:2001JAN12
71852779V1
1707
2560

2
LI:332263.1:2001JAN12
71852887V1
1020
1925

2
LI:332263.1:2001JAN12
70313794D1
992
1621

2
LI:332263.1:2001JAN12
70311926D1
991
1426

2
LI:332263.1:2001JAN12
71851150V1
1024
1885

2
LI:332263.1:2001JAN12
5463866H1
1037
1234

2
LI:332263.1:2001JAN12
70313280D1
1098
1667

2
LI:332263.1:2001JAN12
70313919D1
1098
1533

2
LI:332263.1:2001JAN12
70312150D1
1098
1405

2
LI:332263.1:2001JAN12
70312922D1
1099
1614

2
LI:332263.1:2001JAN12
70313561D1
1098
1464

2
LI:332263.1:2001JAN12
6709051H1
1101
1689

2
LI:332263.1:2001JAN12
71852837V1
1125
2056

2
LI:332263.1:2001JAN12
70312621D1
1115
1727

2
LI:332263.1:2001JAN12
g7279826
1119
1580

2
LI:332263.1:2001JAN12
70314358D1
1126
1688

2
LI:332263.1:2001JAN12
3838795H1
1624
1927

2
LI:332263.1:2001JAN12
70312119D1
542
1078

2
LI:332263.1:2001JAN12
70314905D1
544
936

2
LI:332263.1:2001JAN12
4045920H1
545
843

2
LI:332263.1:2001JAN12
7206449H1
572
1142

2
LI:332263.1:2001JAN12
1379201H1
595
760

2
LI:332263.1:2001JAN12
71851568V1
636
1476

2
LI:332263.1:2001JAN12
6292760H1
1447
1667

2
LI:332263.1:2001JAN12
71854502V1
1444
2128

2
LI:332263.1:2001JAN12
71853944V1
1463
2097

2
LI:332263.1:2001JAN12
71852987V1
1548
2374

2
LI:332263.1:2001JAN12
5094039H1
1506
1774

2
LI:332263.1:2001JAN12
g3922068
1536
2000

2
LI:332263.1:2001JAN12
2792057H1
973
1290

2
LI:332263.1:2001JAN12
71853948V1
1619
2269

2
LI:332263.1:2001JAN12
71853977V1
1622
2375

2
LI:332263.1:2001JAN12
71791379V1
1614
1966

2
LI:332263.1:2001JAN12
71852744V1
1617
2535

2
LI:332263.1:2001JAN12
71852463V1
1606
2613

2
LI:332263.1:2001JAN12
71851278V1
1612
2325

2
LI:332263.1:2001JAN12
71852263V1
1552
2473

2
LI:332263.1:2001JAN12
70314220D1
1407
1859

2
LI:332263.1:2001JAN12
71853922V1
1494
2529

2
LI:332263.1:2001JAN12
70314489D1
1431
1835

2
LI:332263.1:2001JAN12
3435614T6
1433
1944

2
LI:332263.1:2001JAN12
71853327V1
1433
2106

2
LI:332263.1:2001JAN12
2699409H1
1434
1726

2
LI:332263.1:2001JAN12
6546955H1
1441
1992

2
LI:332263.1:2001JAN12
71853660V1
1441
1913

2
LI:332263.1:2001JAN12
g2716813
1441
1992

2
LI:332263.1:2001JAN12
6294741H1
1447
1786

2
LI:332263.1:2001JAN12
71854495V1
1488
2361

2
LI:332263.1:2001JAN12
71853577V1
1598
2510

2
LI:332263.1:2001JAN12
71850908V1
1607
2470

2
LI:332263.1:2001JAN12
g3147676
1584
1993

2
LI:332263.1:2001JAN12
71850788V1
1595
2362

2
LI:332263.1:2001JAN12
72333294V1
1589
2170

2
LI:332263.1:2001JAN12
70311711D1
465
989

2
LI:332263.1:2001JAN12
70312113D1
465
936

2
LI:332263.1:2001JAN12
70313820D1
465
936

2
LI:332263.1:2001JAN12
70313450D1
465
930

2
LI:332263.1:2001JAN12
70314581D1
465
913

2
LI:332263.1:2001JAN12
70313195D1
465
856

2
LI:332263.1:2001JAN12
71853150V1
1231
1647

2
LI:332263.1:2001JAN12
71854540V1
1264
2359

2
LI:332263.1:2001JAN12
4067866H1
1254
1555

2
LI:332263.1:2001JAN12
71854017V1
1259
2106

2
LI:332263.1:2001JAN12
71854180V1
1276
2074

2
LI:332263.1:2001JAN12
71852017V1
1271
2193

2
LI:332263.1:2001JAN12
71852613V1
1273
1952

2
LI:332263.1:2001JAN12
1783069H1
1299
1550

2
LI:332263.1:2001JAN12
71854868V1
1304
1854

2
LI:332263.1:2001JAN12
71854722V1
1310
2040

2
LI:332263.1:2001JAN12
71854441V1
1316
2052

2
LI:332263.1:2001JAN12
71852902V1
1318
2084

2
LI:332263.1:2001JAN12
g5591690
1332
1638

2
LI:332263.1:2001JAN12
689587H1
1335
1587

2
LI:332263.1:2001JAN12
71850440V1
1364
2213

2
LI:332263.1:2001JAN12
71852044V1
1390
2459

2
LI:332263.1:2001JAN12
g3988317
1882
1992

2
LI:332263.1:2001JAN12
5852582H1
1883
1992

2
LI:332263.1:2001JAN12
71852773V1
1976
2805

2
LI:332263.1:2001JAN12
g5544052
2019
2259

2
LI:332263.1:2001JAN12
71851901V1
2081
2539

2
LI:332263.1:2001JAN12
6882753H1
2112
2643

2
LI:332263.1:2001JAN12
2464771T6
2148
2207

2
LI:332263.1:2001JAN12
71855066V1
2148
2738

2
LI:332263.1:2001JAN12
956688H1
2203
2259

2
LI:332263.1:2001JAN12
2050914H1
2372
2632

2
LI:332263.1:2001JAN12
6275080H2
2429
2907

2
LI:332263.1:2001JAN12
4631208T6
2496
2611

2
LI:332263.1:2001JAN12
4631208F6
2503
2640

2
LI:332263.1:2001JAN12
4631208H1
2504
2668

2
LI:332263.1:2001JAN12
2675055T6
2801
3292

2
LI:332263.1:2001JAN12
6882753J1
2851
3454

2
LI:332263.1:2001JAN12
g3675996
2881
3330

2
LI:332263.1:2001JAN12
g4738663
2987
3330

2
LI:332263.1:2001JAN12
g5540864
3200
3330

2
LI:332263.1:2001JAN12
71851008V1
1140
1785

2
LI:332263.1:2001JAN12
g1933806
1159
1471

2
LI:332263.1:2001JAN12
g7456875
1179
1578

2
LI:332263.1:2001JAN12
71851136V1
1177
2042

2
LI:332263.1:2001JAN12
71851292V1
1183
2132

2
LI:332263.1:2001JAN12
71854201V1
1205
1881

2
LI:332263.1:2001JAN12
71516539V1
1195
1890

2
LI:332263.1:2001JAN12
2356586F6
1227
1487

2
LI:332263.1:2001JAN12
2356586H1
1227
1475

2
LI:332263.1:2001JAN12
g6713066
832
1290

2
LI:332263.1:2001JAN12
5990242H1
835
1128

2
LI:332263.1:2001JAN12
71514509V1
864
1666

2
LI:332263.1:2001JAN12
5803858H1
909
1231

2
LI:332263.1:2001JAN12
4669412H1
913
1126

2
LI:332263.1:2001JAN12
7445962T1
925
1465

2
LI:332263.1:2001JAN12
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939
1369

2
LI:332263.1:2001JAN12
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933
1798

2
LI:332263.1:2001JAN12
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1005
1905

2
LI:332263.1:2001JAN12
3435614F6
766
1303

2
LI:332263.1:2001JAN12
3435614H1
766
1015

2
LI:332263.1:2001JAN12
2541284H1
767
1020

2
LI:332263.1:2001JAN12
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782
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2
LI:332263.1:2001JAN12
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822
1195

2
LI:332263.1:2001JAN12
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86
258

2
LI:332263.1:2001JAN12
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128
628

2
LI:332263.1:2001JAN12
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213
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2
LI:332263.1:2001JAN12
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213
495

2
LI:332263.1:2001JAN12
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229
529

2
LI:332263.1:2001JAN12
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251
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2
LI:332263.1:2001JAN12
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286
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2
LI:332263.1:2001JAN12
2464771H1
286
540

2
LI:332263.1:2001JAN12
g746839
347
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2
LI:332263.1:2001JAN12
2495063F6
395
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2
LI:332263.1:2001JAN12
2495063H1
395
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2
LI:332263.1:2001JAN12
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435
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2
LI:332263.1:2001JAN12
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2
LI:332263.1:2001JAN12
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2
LI:332263.1:2001JAN12
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LI:332263.1:2001JAN12
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2
LI:332263.1:2001JAN12
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2
LI:332263.1:2001JAN12
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1644
2306

2
LI:332263.1:2001JAN12
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1875
2556

2
LI:332263.1:2001JAN12
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1837
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LI:332263.1:2001JAN12
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1534
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2
LI:332263.1:2001JAN12
71851502V1
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LI:332263.1:2001JAN12
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1126
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2
LI:332263.1:2001JAN12
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2
LI:332263.1:2001JAN12
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2
LI:332263.1:2001JAN12
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2
LI:332263.1:2001JAN12
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542
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2
LI:332263.1:2001JAN12
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715
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2
LI:332263.1:2001JAN12
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1000

2
LI:332263.1:2001JAN12
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745
936

2
LI:332263.1:2001JAN12
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2
LI:332263.1:2001JAN12
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LI:332263.1:2001JAN12
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LI:332263.1:2001JAN12
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2
LI:332263.1:2001JAN12
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LI:332263.1:2001JAN12
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2
LI:332263.1:2001JAN12
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2
LI:332263.1:2001JAN12
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1381
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2
LI:332263.1:2001JAN12
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1407
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2
LI:332263.1:2001JAN12
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1550
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2
LI:332263.1:2001JAN12
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1553
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LI:332263.1:2001JAN12
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LI:332263.1:2001JAN12
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LI:332263.1:2001JAN12
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2
LI:332263.1:2001JAN12
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2
LI:332263.1:2001JAN12
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LI:332263.1:2001JAN12
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2
LI:332263.1:2001JAN12
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2
LI:332263.1:2001JAN12
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2
LI:332263.1:2001JAN12
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276

2
LI:332263.1:2001JAN12
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11
251

2
LI:332263.1:2001JAN12
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30
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2
LI:332263.1:2001JAN12
1647392F6
75
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2
LI:332263.1:2001JAN12
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LI:332263.1:2001JAN12
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LI:332263.1:2001JAN12
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LI:332263.1:2001JAN12
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LI:332263.1:2001JAN12
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LI:332263.1:2001JAN12
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1126
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LI:332263.1:2001JAN12
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LI:332263.1:2001JAN12
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LI:332263.1:2001JAN12
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LI:332263.1:2001JAN12
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2
LI:332263.1:2001JAN12
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2
LI:332263.1:2001JAN12
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465
909

2
LI:332263.1:2001JAN12
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472
855

2
LI:332263.1:2001JAN12
5039112H2
488
732

2
LI:332263.1:2001JAN12
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536
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2
LI:332263.1:2001JAN12
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539
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2
LI:332263.1:2001JAN12
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1776
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LI:332263.1:2001JAN12
71853831V1
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2148

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LI:332263.1:2001JAN12
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2
LI:332263.1:2001JAN12
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2
LI:332263.1:2001JAN12
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2
LI:332263.1:2001JAN12
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2
LI:332263.1:2001JAN12
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LI:332263.1:2001JAN12
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LI:332263.1:2001JAN12
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2
LI:332263.1:2001JAN12
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1907
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LI:333886.4:2001JAN12
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475

3
LI:333886.4:2001JAN12
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850

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LI:333886.4:2001JAN12
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57
727

3
LI:333886.4:2001JAN12
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58
751

3
LI:333886.4:2001JAN12
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777

3
LI:333886.4:2001JAN12
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862

3
LI:333886.4:2001JAN12
55138886H1
92
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3
LI:333886.4:2001JAN12
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106
737

3
LI:333886.4:2001JAN12
2932976H1
116
386

3
LI:333886.4:2001JAN12
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3
LI:333886.4:2001JAN12
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232
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3
LI:333886.4:2001JAN12
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329
522

3
LI:333886.4:2001JAN12
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477
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3
LI:333886.4:2001JAN12
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505
717

4
LI:478508.1:2001JAN12
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175
420

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LI:478508.1:2001JAN12
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256

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LI:478508.1:2001JAN12
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LI:478508.1:2001JAN12
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195
275

4
LI:478508.1:2001JAN12
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1
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4
LI:478508.1:2001JAN12
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76
256

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LI:478508.1:2001JAN12
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112
709

4
LI:478508.1:2001JAN12
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286
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4
LI:478508.1:2001JAN12
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331
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LI:478508.1:2001JAN12
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LI:478508.1:2001JAN12
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609
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LI:478508.1:2001JAN12
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212
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LI:478508.1:2001JAN12
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264
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4
LI:478508.1:2001JAN12
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264
516

4
LI:478508.1:2001JAN12
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197
256

5
LI:307470.1:2001JAN12
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LI:307470.1:2001JAN12
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445
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LI:307470.1:2001JAN12
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5
LI:307470.1:2001JAN12
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431
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5
LI:307470.1:2001JAN12
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1
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6
LI:058298.1:2001JAN12
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1083
1678

6
LI:058298.1:2001JAN12
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1331

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LI:058298.1:2001JAN12
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670
1228

6
LI:058298.1:2001JAN12
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417
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LI:058298.1:2001JAN12
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558
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LI:058298.1:2001JAN12
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LI:058298.1:2001JAN12
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LI:058298.1:2001JAN12
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LI:058298.1:2001JAN12
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LI:058298.1:2001JAN12
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LI:058298.1:2001JAN12
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LI:058298.1:2001JAN12
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LI:058298.1:2001JAN12
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225

8
LI:231587.1:2001JAN12
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1
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8
LI:231587.1:2001JAN12
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145
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8
LI:231587.1:2001JAN12
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441
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384
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LI:402919.1:2001JAN12
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519
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LI:402919.1:2001JAN12
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LI:402919.1:2001JAN12
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12
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LI:1076016.1:2001JAN12
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LI:335681.3:2001JAN12
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15
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15
LI:335681.3:2001JAN12
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15
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15
LI:335681.3:2001JAN12
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LI:335681.3:2001JAN12
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15
LI:335681.3:2001JAN12
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15
LI:335681.3:2001JAN12
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LI:335681.3:2001JAN12
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16
LI:214150.1:2001JAN12
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602
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16
LI:214150.1:2001JAN12
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16
LI:214150.1:2001JAN12
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1
595

16
LI:214150.1:2001JAN12
71984038V1
159
703

16
LI:214150.1:2001JAN12
4646294F6
422
703

16
LI:214150.1:2001JAN12
4646294H1
422
689

16
LI:214150.1:2001JAN12
3703252F6
495
703

16
LI:214150.1:2001JAN12
3703252H1
495
717

17
LI:322783.15:2001JAN12
7208772H1
1
115

17
LI:322783.15:2001JAN12
7609888J1
131
685

17
LI:322783.15:2001JAN12
2650602H1
184
425

17
LI:322783.15:2001JAN12
2763906H1
195
433

17
LI:322783.15:2001JAN12
7207858T8
317
765

17
LI:322783.15:2001JAN12
7154586H1
1
527

17
LI:322783.15:2001JAN12
7206356H1
1
490

17
LI:322783.15:2001JAN12
7207535H1
3
379

17
LI:322783.15:2001JAN12
7209140H1
1
622

17
LI:322783.15:2001JAN12
7209489H1
1
618

17
LI:322783.15:2001JAN12
7210871H1
1
603

17
LI:322783.15:2001JAN12
7685079H1
1
550

17
LI:322783.15:2001JAN12
6964009H1
1
560

18
LI:422993.1:2001JAN12
6310043H1
1
415

18
LI:422993.1:2001JAN12
6310340F8
1
394

18
LI:422993.1:2001JAN12
4722590H1
52
213

18
LI:422993.1:2001JAN12
6310043T8
205
700

18
LI:422993.1:2001JAN12
8094246H1
542
1031

18
LI:422993.1:2001JAN12
7594841H1
808
1359

18
LI:422993.1:2001JAN12
g6639991
1013
1429

18
LI:422993.1:2001JAN12
g7457143
1021
1425

18
LI:422993.1:2001JAN12
g7320380
1064
1434

19
LI:1172885.1:2001JAN12
1923488T6
101
575

19
LI:1172885.1:2001JAN12
4768094T6
42
599

19
LI:1172885.1:2001JAN12
4874348H1
194
468

19
LI:1172885.1:2001JAN12
1923296T6
203
574

19
LI:1172885.1:2001JAN12
5085341F6
204
638

19
LI:1172885.1:2001JAN12
1923488R6
1
438

19
LI:1172885.1:2001JAN12
1923296R6
1
389

19
LI:1172885.1:2001JAN12
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1
299

19
LI:1172885.1:2001JAN12
1923488H1
1
280

19
LI:1172885.1:2001JAN12
5760908T8
24
486

19
LI:1172885.1:2001JAN12
5085341H1
182
384

19
LI:1172885.1:2001JAN12
1914106H1
242
502

20
LI:1088359.1:2001JAN12
3956181H1
1975
2272

20
LI:1088359.1:2001JAN12
6779755F6
1953
2564

20
LI:1088359.1:2001JAN12
3603043H1
1971
2277

20
LI:1088359.1:2001JAN12
5309011H1
1972
2212

20
LI:1088359.1:2001JAN12
2201396T6
1496
2090

20
LI:1088359.1:2001JAN12
71250004V1
1516
2177

20
LI:1088359.1:2001JAN12
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1205
1871

20
LI:1088359.1:2001JAN12
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1166
1771

20
LI:1088359.1:2001JAN12
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1146
1697

20
LI:1088359.1:2001JAN12
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1948
2220

20
LI:1088359.1:2001JAN12
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1198
2149

20
LI:1088359.1:2001JAN12
6532650H1
1247
1746

20
LI:1088359.1:2001JAN12
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1931
2620

20
LI:1088359.1:2001JAN12
71064441V1
1780
2297

20
LI:1088359.1:2001JAN12
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1822
2360

20
LI:1088359.1:2001JAN12
5203628H1
1841
2141

20
LI:1088359.1:2001JAN12
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1710
2238

20
LI:1088359.1:2001JAN12
2503778F6
1732
2264

20
LI:1088359.1:2001JAN12
2503778H1
1732
2000

20
LI:1088359.1:2001JAN12
861926H1
1484
1742

20
LI:1088359.1:2001JAN12
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20
LI:1088359.1:2001JAN12
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1705
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20
LI:1088359.1:2001JAN12
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1627
2541

20
LI:1088359.1:2001JAN12
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1135
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20
LI:1088359.1:2001JAN12
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1084
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20
LI:1088359.1:2001JAN12
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1453
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LI:1088359.1:2001JAN12
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1455
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20
LI:1088359.1:2001JAN12
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1410
2328

20
LI:1088359.1:2001JAN12
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1424
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20
LI:1088359.1:2001JAN12
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1424
1597

20
LI:1088359.1:2001JAN12
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1479
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20
LI:1088359.1:2001JAN12
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1600
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20
LI:1088359.1:2001JAN12
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1621
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20
LI:1088359.1:2001JAN12
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1632
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20
LI:1088359.1:2001JAN12
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1039
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20
LI:1088359.1:2001JAN12
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20
LI:1088359.1:2001JAN12
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934
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20
LI:1088359.1:2001JAN12
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917
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20
LI:1088359.1:2001JAN12
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1342
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20
LI:1088359.1:2001JAN12
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1390
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20
LI:1088359.1:2001JAN12
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1279
1781

20
LI:1088359.1:2001JAN12
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1303
1627

20
LI:1088359.1:2001JAN12
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1328
1970

20
LI:1088359.1:2001JAN12
71063338V1
1340
2064

20
LI:1088359.1:2001JAN12
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1326
1764

20
LI:1088359.1:2001JAN12
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2027
2636

20
LI:1088359.1:2001JAN12
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2042
2325

20
LI:1088359.1:2001JAN12
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1566
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20
LI:1088359.1:2001JAN12
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1573
2089

20
LI:1088359.1:2001JAN12
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1555
2067

20
LI:1088359.1:2001JAN12
3346980H1
1272
1572

20
LI:1088359.1:2001JAN12
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1260
1972

20
LI:1088359.1:2001JAN12
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889
1467

20
LI:1088359.1:2001JAN12
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849
1498

20
LI:1088359.1:2001JAN12
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1
602

20
LI:1088359.1:2001JAN12
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1
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20
LI:1088359.1:2001JAN12
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1
211

20
LI:1088359.1:2001JAN12
6490754R6
89
647

20
LI:1088359.1:2001JAN12
6490754R9
109
644

20
LI:1088359.1:2001JAN12
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158
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20
LI:1088359.1:2001JAN12
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165
1068

20
LI:1088359.1:2001JAN12
4791776F8
165
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20
LI:1088359.1:2001JAN12
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165
442

20
LI:1088359.1:2001JAN12
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165
324

20
LI:1088359.1:2001JAN12
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199
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20
LI:1088359.1:2001JAN12
5923409H1
259
577

20
LI:1088359.1:2001JAN12
71066229V1
279
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20
LI:1088359.1:2001JAN12
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338
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20
LI:1088359.1:2001JAN12
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341
972

20
LI:1088359.1:2001JAN12
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358
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20
LI:1088359.1:2001JAN12
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447
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20
LI:1088359.1:2001JAN12
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462
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20
LI:1088359.1:2001JAN12
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463
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20
LI:1088359.1:2001JAN12
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476
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20
LI:1088359.1:2001JAN12
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504
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20
LI:1088359.1:2001JAN12
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20
LI:1088359.1:2001JAN12
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531
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20
LI:1088359.1:2001JAN12
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520
1234

20
LI:1088359.1:2001JAN12
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551
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20
LI:1088359.1:2001JAN12
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577
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20
LI:1088359.1:2001JAN12
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599
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20
LI:1088359.1:2001JAN12
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625
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20
LI:1088359.1:2001JAN12
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633
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20
LI:1088359.1:2001JAN12
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638
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20
LI:1088359.1:2001JAN12
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20
LI:1088359.1:2001JAN12
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645
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20
LI:1088359.1:2001JAN12
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647
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20
LI:1088359.1:2001JAN12
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672
1340

20
LI:1088359.1:2001JAN12
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664
1305

20
LI:1088359.1:2001JAN12
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668
1328

20
LI:1088359.1:2001JAN12
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684
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20
LI:1088359.1:2001JAN12
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1508

20
LI:1088359.1:2001JAN12
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20
LI:1088359.1:2001JAN12
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694
1329

20
LI:1088359.1:2001JAN12
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698
1369

20
LI:1088359.1:2001JAN12
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699
1328

20
LI:1088359.1:2001JAN12
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703
968

20
LI:1088359.1:2001JAN12
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716
1449

20
LI:1088359.1:2001JAN12
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729
1417

20
LI:1088359.1:2001JAN12
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729
1554

20
LI:1088359.1:2001JAN12
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828
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20
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811
1250

20
LI:1088359.1:2001JAN12
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811
1104

20
LI:1088359.1:2001JAN12
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2024
2310

20
LI:1088359.1:2001JAN12
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2582

20
LI:1088359.1:2001JAN12
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20
LI:1088359.1:2001JAN12
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1
548

20
LI:1088359.1:2001JAN12
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2005
2242

20
LI:1088359.1:2001JAN12
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2005
2244

20
LI:1088359.1:2001JAN12
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971
1667

20
LI:1088359.1:2001JAN12
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1516
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20
LI:1088359.1:2001JAN12
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936
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930
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20
LI:1088359.1:2001JAN12
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936
1615

20
LI:1088359.1:2001JAN12
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1200
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20
LI:1088359.1:2001JAN12
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20
LI:1088359.1:2001JAN12
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LI:1088359.1:2001JAN12
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2113
2637

20
LI:1088359.1:2001JAN12
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2123
2672

20
LI:1088359.1:2001JAN12
2503778T6
2164
2661

20
LI:1088359.1:2001JAN12
4059690T6
2170
2633

20
LI:1088359.1:2001JAN12
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2170
2444

20
LI:1088359.1:2001JAN12
5897857H1
2170
2442

20
LI:1088359.1:2001JAN12
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2202
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LI:1088359.1:2001JAN12
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2222
2633

20
LI:1088359.1:2001JAN12
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LI:1088359.1:2001JAN12
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2259
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20
LI:1088359.1:2001JAN12
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2259
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LI:1088359.1:2001JAN12
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2262
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LI:1088359.1:2001JAN12
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2537

20
LI:1088359.1:2001JAN12
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2530

20
LI:1088359.1:2001JAN12
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2263
2709

20
LI:1088359.1:2001JAN12
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2267
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20
LI:1088359.1:2001JAN12
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2309
2811

20
LI:1088359.1:2001JAN12
7259781T6
2314
2519

20
LI:1088359.1:2001JAN12
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2327
2705

20
LI:1088359.1:2001JAN12
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2348
2595

20
LI:1088359.1:2001JAN12
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2348
2559

20
LI:1088359.1:2001JAN12
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2353
2633

20
LI:1088359.1:2001JAN12
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2370
2849

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LI:1088359.1:2001JAN12
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2371
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LI:1088359.1:2001JAN12
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2369
2628

20
LI:1088359.1:2001JAN12
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LI:1088359.1:2001JAN12
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LI:1088359.1:2001JAN12
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2434
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LI:1088359.1:2001JAN12
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LI:1088359.1:2001JAN12
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20
LI:1088359.1:2001JAN12
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2458
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20
LI:1088359.1:2001JAN12
g7278916
2461
2848

20
LI:1088359.1:2001JAN12
g3298627
2466
2625

20
LI:1088359.1:2001JAN12
3424273H1
2493
2633

20
LI:1088359.1:2001JAN12
g3191621
2514
2847

20
LI:1088359.1:2001JAN12
g2910683
2519
2770

20
LI:1088359.1:2001JAN12
241452H1
2543
2637

20
LI:1088359.1:2001JAN12
g3134539
2641
2850

20
LI:1088359.1:2001JAN12
g6035581
2726
2846

21
LI:813422.1:2001JAN12
894136H1
24
202

21
LI:813422.1:2001JAN12
3685359F6
46
515

21
LI:813422.1:2001JAN12
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93
592

21
LI:813422.1:2001JAN12
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93
413

21
LI:813422.1:2001JAN12
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98
520

21
LI:813422.1:2001JAN12
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104
554

21
LI:813422.1:2001JAN12
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131
651

21
LI:813422.1:2001JAN12
8124465H1
11
671

21
LI:813422.1:2001JAN12
70164598V1
1430
1890

21
LI:813422.1:2001JAN12
g1485371
1771
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21
LI:813422.1:2001JAN12
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1
169

21
LI:813422.1:2001JAN12
6593962H1
1
169

21
LI:813422.1:2001JAN12
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11
650

21
LI:813422.1:2001JAN12
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25
315

21
LI:813422.1:2001JAN12
8102680H1
45
624

21
LI:813422.1:2001JAN12
3685359H1
46
358

21
LI:813422.1:2001JAN12
g4689970
203
625

21
LI:813422.1:2001JAN12
3685359T6
278
556

21
LI:813422.1:2001JAN12
2497517T6
380
534

21
LI:813422.1:2001JAN12
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407
888

21
LI:813422.1:2001JAN12
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392
534

21
LI:813422.1:2001JAN12
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426
932

21
LI:813422.1:2001JAN12
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413
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21
LI:813422.1:2001JAN12
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491
1010

21
LI:813422.1:2001JAN12
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21
LI:813422.1:2001JAN12
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600
1080

21
LI:813422.1:2001JAN12
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731
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21
LI:813422.1:2001JAN12
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822
1303

21
LI:813422.1:2001JAN12
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869
1371

21
LI:813422.1:2001JAN12
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967
1150

21
LI:813422.1:2001JAN12
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998
1514

21
LI:813422.1:2001JAN12
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1059
1493

21
LI:813422.1:2001JAN12
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1116
1651

21
LI:813422.1:2001JAN12
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1118
1714

21
LI:813422.1:2001JAN12
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1137
1627

21
LI:813422.1:2001JAN12
5263856H2
1149
1244

21
LI:813422.1:2001JAN12
3338768H1
1244
1485

21
LI:813422.1:2001JAN12
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1277
1766

21
LI:813422.1:2001JAN12
466542H1
1322
1470

21
LI:813422.1:2001JAN12
6433091H1
1331
1735

21
LI:813422.1:2001JAN12
6433091T8
1413
1735

22
LI:1186426.1:2001JAN12
4030602T6
1584
1906

22
LI:1186426.1:2001JAN12
7068262H1
1789
1906

22
LI:1186426.1:2001JAN12
1749930H1
1799
1906

22
LI:1186426.1:2001JAN12
3929925T6
1513
1906

22
LI:1186426.1:2001JAN12
3765992T6
1529
1906

22
LI:1186426.1:2001JAN12
3973648H1
1445
1721

22
LI:1186426.1:2001JAN12
2639995T6
1563
1906

22
LI:1186426.1:2001JAN12
4140846T9
26
550

22
LI:1186426.1:2001JAN12
7254119H1
491
935

22
LI:1186426.1:2001JAN12
3280090F7
1697
1906

22
LI:1186426.1:2001JAN12
g389786
1040
1462

22
LI:1186426.1:2001JAN12
1269724F1
1117
1602

22
LI:1186426.1:2001JAN12
6934544H1
1361
1875

22
LI:1186426.1:2001JAN12
111294F1
1503
1906

22
LI:1186426.1:2001JAN12
3418022H2
1525
1769

22
LI:1186426.1:2001JAN12
1309523H1
961
1135

22
LI:1186426.1:2001JAN12
g3281713
1105
1463

22
LI:1186426.1:2001JAN12
111294T6
1556
1906

22
LI:1186426.1:2001JAN12
g6476089
1689
1906

22
LI:1186426.1:2001JAN12
1269724H1
1117
1324

22
LI:1186426.1:2001JAN12
3236461H1
424
641

22
LI:1186426.1:2001JAN12
2639995H1
830
1076

22
LI:1186426.1:2001JAN12
4326477F6
1
381

22
LI:1186426.1:2001JAN12
4123479H1
1222
1457

22
LI:1186426.1:2001JAN12
4729333H1
1304
1392

22
LI:1186426.1:2001JAN12
g2823562
1641
1906

22
LI:1186426.1:2001JAN12
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22
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22
LI:1186426.1:2001JAN12
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1005
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22
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204
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22
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491
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22
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22
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22
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22
LI:1186426.1:2001JAN12
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3
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22
LI:1186426.1:2001JAN12
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1737
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22
LI:1186426.1:2001JAN12
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52
314

22
LI:1186426.1:2001JAN12
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22
LI:1186426.1:2001JAN12
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830
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22
LI:1186426.1:2001JAN12
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1442
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LI:1186426.1:2001JAN12
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430
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22
LI:1186426.1:2001JAN12
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23
LI:1182817.1:2001JAN12
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LI:1182817.1:2001JAN12
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2480

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LI:1182817.1:2001JAN12
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23
LI:1182817.1:2001JAN12
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150
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LI:1182817.1:2001JAN12
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LI:1182817.1:2001JAN12
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LI:1182817.1:2001JAN12
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LI:1171553.1:2001JAN12
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25
LI:1171553.1:2001JAN12
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25
LI:1171553.1:2001JAN12
g505547
1561
1902

25
LI:1171553.1:2001JAN12
3962293T9
1585
2087

25
LI:1171553.1:2001JAN12
3602618H1
1594
1910

25
LI:1171553.1:2001JAN12
290776H1
1807
2108

25
LI:1171553.1:2001JAN12
184712T6
1814
2183

25
LI:1171553.1:2001JAN12
4858565T7
1822
2105

25
LI:1171553.1:2001JAN12
g4988603
1835
2223

25
LI:1171553.1:2001JAN12
g3960390
1835
2221

25
LI:1171553.1:2001JAN12
g1927397
1853
2221

25
LI:1171553.1:2001JAN12
8017138J1
1894
2548

25
LI:1171553.1:2001JAN12
3384759F6
1910
2209

25
LI:1171553.1:2001JAN12
3384759H1
1910
2169

25
LI:1171553.1:2001JAN12
g4302161
1919
2222

25
LI:1171553.1:2001JAN12
70749172V1
1960
2572

25
LI:1171553.1:2001JAN12
g2787880
1983
2141

25
LI:1171553.1:2001JAN12
70747353V1
2179
2724

25
LI:1171553.1:2001JAN12
70749489V1
2180
2650

25
LI:1171553.1:2001JAN12
5574155H1
2196
2448

25
LI:1171553.1:2001JAN12
70755004V1
2200
2348

25
LI:1171553.1:2001JAN12
6052963J1
2302
2656

25
LI:1171553.1:2001JAN12
7690493H1
2419
2507

25
LI:1171553.1:2001JAN12
5574155T9
2501
3038

25
LI:1171553.1:2001JAN12
2766073T6
2548
3111

25
LI:1171553.1:2001JAN12
70747745V1
1127
1742

25
LI:1171553.1:2001JAN12
70750202V1
1148
1612

25
LI:1171553.1:2001JAN12
184712R6
1194
1548

25
LI:1171553.1:2001JAN12
184712F1
1659
2241

25
LI:1171553.1:2001JAN12
6052963H1
1669
2170

25
LI:1171553.1:2001JAN12
70754414V1
1512
2077

25
LI:1171553.1:2001JAN12
2766073H1
32
324

25
LI:1171553.1:2001JAN12
3371190H1
1
209

25
LI:1171553.1:2001JAN12
70747296V1
25
598

25
LI:1171553.1:2001JAN12
70761984V1
32
354

25
LI:1171553.1:2001JAN12
70748552V1
550
1139

25
LI:1171553.1:2001JAN12
6169913H1
1538
1838

25
LI:1171553.1:2001JAN12
7042860H1
1597
2163

25
LI:1171553.1:2001JAN12
7042860R8
1598
2194

25
LI:1171553.1:2001JAN12
7042860F8
1598
2138

25
LI:1171553.1:2001JAN12
70749765V1
348
964

25
LI:1171553.1:2001JAN12
55068831J1
385
518

25
LI:1171553.1:2001JAN12
55068831H1
409
544

25
LI:1171553.1:2001JAN12
70746739V1
510
1038

25
LI:1171553.1:2001JAN12
184712H1
1194
1376

25
LI:1171553.1:2001JAN12
70747506V1
1250
1838

25
LI:1171553.1:2001JAN12
1505781H1
1400
1614

25
LI:1171553.1:2001JAN12
4858565F7
1410
1865

25
LI:1171553.1:2001JAN12
4858565H1
1410
1511

25
LI:1171553.1:2001JAN12
70746771V1
1445
1779

25
LI:1171553.1:2001JAN12
3962267T9
1640
2089

25
LI:1171553.1:2001JAN12
g6035502
1747
2212

25
LI:1171553.1:2001JAN12
g2558367
1752
2212

25
LI:1171553.1:2001JAN12
70754307V1
1787
2120

25
LI:1171553.1:2001JAN12
g727817
1802
2212

25
LI:1171553.1:2001JAN12
8138155T1
1801
2119

25
LI:1171553.1:2001JAN12
7941653H1
255
470

25
LI:1171553.1:2001JAN12
5543896H1
555
768

25
LI:1171553.1:2001JAN12
70755134V1
644
854

25
LI:1171553.1:2001JAN12
70750777V1
646
1254

25
LI:1171553.1:2001JAN12
70751065V1
639
1255

25
LI:1171553.1:2001JAN12
5543896F8
555
924

26
LI:2121978.1:2001JAN12
8324855J1
1
480

27
LI:1174292.5:2001JAN12
5044943H1
84
333

27
LI:1174292.5:2001JAN12
g2241254
2042
2437

27
LI:1174292.5:2001JAN12
g5636089
2156
2617

27
LI:1174292.5:2001JAN12
1301303H1
516
762

27
LI:1174292.5:2001JAN12
70814001V1
939
1593

27
LI:1174292.5:2001JAN12
g746862
3364
3540

27
LI:1174292.5:2001JAN12
6516637H1
68
608

27
LI:1174292.5:2001JAN12
4344244H1
1252
1532

27
LI:1174292.5:2001JAN12
4384858H1
7
184

27
LI:1174292.5:2001JAN12
1365434H1
2289
2535

27
LI:1174292.5:2001JAN12
5482659H1
1734
2004

27
LI:1174292.5:2001JAN12
g3899860
2211
2617

27
LI:1174292.5:2001JAN12
5102048T6
2204
2326

27
LI:1174292.5:2001JAN12
1752713H1
2457
2688

27
LI:1174292.5:2001JAN12
2865004H1
72
380

27
LI:1174292.5:2001JAN12
70649482V1
1205
1839

27
LI:1174292.5:2001JAN12
6191116H1
2712
3038

27
LI:1174292.5:2001JAN12
g5673730
2732
3079

27
LI:1174292.5:2001JAN12
388169H1
3680
3970

27
LI:1174292.5:2001JAN12
042436H1
2883
3106

27
LI:1174292.5:2001JAN12
4251908H1
2926
3179

27
LI:1174292.5:2001JAN12
71297258V1
3076
3182

27
LI:1174292.5:2001JAN12
3488035H1
3112
3390

27
LI:1174292.5:2001JAN12
71297162V1
3116
3390

27
LI:1174292.5:2001JAN12
70989354V1
3116
3390

27
LI:1174292.5:2001JAN12
70991039V1
3116
3390

27
LI:1174292.5:2001JAN12
g747217
3856
4045

27
LI:1174292.5:2001JAN12
g1445214
3885
4067

27
LI:1174292.5:2001JAN12
g714619
3321
3680

27
LI:1174292.5:2001JAN12
5608250H1
3909
3961

27
LI:1174292.5:2001JAN12
6020701H1
3322
3769

27
LI:1174292.5:2001JAN12
g2705436
3348
3852

27
LI:1174292.5:2001JAN12
g747112
3374
3685

27
LI:1174292.5:2001JAN12
8124277H1
3374
3973

27
LI:1174292.5:2001JAN12
5608250T8
3429
3967

27
LI:1174292.5:2001JAN12
5608250T9
3442
3767

27
LI:1174292.5:2001JAN12
g3837152
1560
1843

27
LI:1174292.5:2001JAN12
2550171H1
1740
1993

27
LI:1174292.5:2001JAN12
3840552H1
1997
2285

27
LI:1174292.5:2001JAN12
2350960H1
2399
2607

27
LI:1174292.5:2001JAN12
2557405H1
1914
2164

27
LI:1174292.5:2001JAN12
2456601H1
59
289

27
LI:1174292.5:2001JAN12
6128031H1
1999
2529

27
LI:1174292.5:2001JAN12
70815791V1
1165
1644

27
LI:1174292.5:2001JAN12
g4304113
2044
2440

27
LI:1174292.5:2001JAN12
7254181R8
884
1495

27
LI:1174292.5:2001JAN12
70814328V1
181
762

27
LI:1174292.5:2001JAN12
g4683259
3338
3790

27
LI:1174292.5:2001JAN12
8182827H1
662
1269

27
LI:1174292.5:2001JAN12
70826763V1
2359
2609

27
LI:1174292.5:2001JAN12
g4196728
2388
2846

27
LI:1174292.5:2001JAN12
4301604H1
2418
2612

27
LI:1174292.5:2001JAN12
4027709H1
2465
2731

27
LI:1174292.5:2001JAN12
6128479T8
2560
2943

27
LI:1174292.5:2001JAN12
70810235V1
2522
2617

27
LI:1174292.5:2001JAN12
6194322H1
2712
3013

27
LI:1174292.5:2001JAN12
6128031F8
1999
2620

27
LI:1174292.5:2001JAN12
6076876H1
2024
2311

27
LI:1174292.5:2001JAN12
6128031T6
2081
2448

27
LI:1174292.5:2001JAN12
7327090H1
2104
2697

27
LI:1174292.5:2001JAN12
6128480H1
2143
2729

27
LI:1174292.5:2001JAN12
6128479F8
2143
2763

27
LI:1174292.5:2001JAN12
6128891H1
2143
2562

27
LI:1174292.5:2001JAN12
7172292T8
2243
2517

27
LI:1174292.5:2001JAN12
1365434T6
2273
2578

27
LI:1174292.5:2001JAN12
7766871J2
2314
2914

27
LI:1174292.5:2001JAN12
3561406H1
1483
1778

27
LI:1174292.5:2001JAN12
4439362H1
1519
1719

27
LI:1174292.5:2001JAN12
70390707D1
1593
1933

27
LI:1174292.5:2001JAN12
g475796
1666
1965

27
LI:1174292.5:2001JAN12
6208291H1
1702
2311

27
LI:1174292.5:2001JAN12
5320810H1
1734
1980

27
LI:1174292.5:2001JAN12
5320570H1
1734
2000

27
LI:1174292.5:2001JAN12
5324762H1
1734
1987

27
LI:1174292.5:2001JAN12
3397356F7
1785
2399

27
LI:1174292.5:2001JAN12
1746188T6
1802
2287

27
LI:1174292.5:2001JAN12
1702474T6
1836
1892

27
LI:1174292.5:2001JAN12
5482373T6
1858
2283

27
LI:1174292.5:2001JAN12
8104182H1
1879
2319

27
LI:1174292.5:2001JAN12
8104182J1
1884
2330

27
LI:1174292.5:2001JAN12
319207H1
1881
2258

27
LI:1174292.5:2001JAN12
5899378H1
1892
2158

27
LI:1174292.5:2001JAN12
70815211V1
1965
2551

27
LI:1174292.5:2001JAN12
60208741U1
1978
2340

27
LI:1174292.5:2001JAN12
g6475480
2316
2617

27
LI:1174292.5:2001JAN12
g5673074
3338
3538

27
LI:1174292.5:2001JAN12
70812295V1
1120
1393

27
LI:1174292.5:2001JAN12
g2208504
1444
1861

27
LI:1174292.5:2001JAN12
1301303T6
1173
1784

27
LI:1174292.5:2001JAN12
70811699V1
1455
1954

27
LI:1174292.5:2001JAN12
5728849H1
1354
1717

27
LI:1174292.5:2001JAN12
1746188F6
1866
2381

27
LI:1174292.5:2001JAN12
6128031F6
2020
2593

27
LI:1174292.5:2001JAN12
5728849F6
1353
2069

27
LI:1174292.5:2001JAN12
60215486U1
97
564

27
LI:1174292.5:2001JAN12
g1445215
3338
3404

27
LI:1174292.5:2001JAN12
60215481U1
1050
1509

27
LI:1174292.5:2001JAN12
6396723F6
386
976

27
LI:1174292.5:2001JAN12
7928421H1
2214
2613

27
LI:1174292.5:2001JAN12
g560245
2903
3075

27
LI:1174292.5:2001JAN12
1365434R6
2289
2615

27
LI:1174292.5:2001JAN12
1702474F6
386
650

27
LI:1174292.5:2001JAN12
4109619H1
3832
3960

27
LI:1174292.5:2001JAN12
g6574959
1498
1847

27
LI:1174292.5:2001JAN12
768224H1
1611
1853

27
LI:1174292.5:2001JAN12
g3919927
1576
1862

27
LI:1174292.5:2001JAN12
1617118H1
1883
2084

27
LI:1174292.5:2001JAN12
g2595201
1686
1937

27
LI:1174292.5:2001JAN12
g3418456
1521
1855

27
LI:1174292.5:2001JAN12
2790135H2
1934
2165

27
LI:1174292.5:2001JAN12
2772125H1
1139
1391

27
LI:1174292.5:2001JAN12
2731430H1
1394
1629

27
LI:1174292.5:2001JAN12
3817084H1
1911
2178

27
LI:1174292.5:2001JAN12
g3298942
1530
1835

27
LI:1174292.5:2001JAN12
4125311H1
2066
2333

27
LI:1174292.5:2001JAN12
60215482U1
938
1468

27
LI:1174292.5:2001JAN12
70812078V1
991
1587

27
LI:1174292.5:2001JAN12
70816015V1
1001
1641

27
LI:1174292.5:2001JAN12
70812080V1
1018
1527

27
LI:1174292.5:2001JAN12
70813268V1
927
1553

27
LI:1174292.5:2001JAN12
70816143V1
1092
1570

27
LI:1174292.5:2001JAN12
6729472H1
616
1207

27
LI:1174292.5:2001JAN12
g5152323
3337
3574

27
LI:1174292.5:2001JAN12
2844156H1
966
1241

27
LI:1174292.5:2001JAN12
5559861H1
1900
2117

27
LI:1174292.5:2001JAN12
5102048F6
1738
2323

27
LI:1174292.5:2001JAN12
g2240918
1727
2076

27
LI:1174292.5:2001JAN12
70813591V1
1051
1615

27
LI:1174292.5:2001JAN12
6631603R8
998
1491

27
LI:1174292.5:2001JAN12
4765479H1
54
306

27
LI:1174292.5:2001JAN12
5482373F6
1743
2340

27
LI:1174292.5:2001JAN12
6128479H1
2143
2613

27
LI:1174292.5:2001JAN12
2861529H1
53
318

27
LI:1174292.5:2001JAN12
5102048H1
1738
1987

27
LI:1174292.5:2001JAN12
6747886H1
2212
2407

27
LI:1174292.5:2001JAN12
g5878968
2163
2615

27
LI:1174292.5:2001JAN12
7701481H1
1307
1889

27
LI:1174292.5:2001JAN12
g566560
3338
3654

27
LI:1174292.5:2001JAN12
3461329H1
277
389

27
LI:1174292.5:2001JAN12
70816833V1
315
898

27
LI:1174292.5:2001JAN12
433634R6
384
784

27
LI:1174292.5:2001JAN12
60208742U1
925
1401

27
LI:1174292.5:2001JAN12
60215479U1
651
1094

27
LI:1174292.5:2001JAN12
4315517H1
787
1068

27
LI:1174292.5:2001JAN12
70816149V1
794
1420

27
LI:1174292.5:2001JAN12
3782084H1
817
1132

27
LI:1174292.5:2001JAN12
70811782V1
916
1405

27
LI:1174292.5:2001JAN12
60203788U2
925
1401

27
LI:1174292.5:2001JAN12
6128891F8
2143
2643

27
LI:1174292.5:2001JAN12
4384858F6
7
196

27
LI:1174292.5:2001JAN12
6082132F8
10
562

27
LI:1174292.5:2001JAN12
7363981H1
13
574

27
LI:1174292.5:2001JAN12
60215484U1
78
548

27
LI:1174292.5:2001JAN12
70813546V1
123
762

27
LI:1174292.5:2001JAN12
70814644V1
218
864

27
LI:1174292.5:2001JAN12
2477153T6
247
577

27
LI:1174292.5:2001JAN12
g2818305
2081
2437

27
LI:1174292.5:2001JAN12
3592751H1
1315
1636

27
LI:1174292.5:2001JAN12
433634R1
384
898

27
LI:1174292.5:2001JAN12
g2599099
1684
1933

27
LI:1174292.5:2001JAN12
1550876T6
1862
2217

27
LI:1174292.5:2001JAN12
70814410V1
91
643

27
LI:1174292.5:2001JAN12
g2384652
1
2293

27
LI:1174292.5:2001JAN12
3275520H1
1
267

27
LI:1174292.5:2001JAN12
70811649V1
7
569

27
LI:1174292.5:2001JAN12
60208699U1
2017
2372

27
LI:1174292.5:2001JAN12
g1891978
1747
2137

27
LI:1174292.5:2001JAN12
1550876H1
1837
2043

27
LI:1174292.5:2001JAN12
1545224H1
1315
1498

27
LI:1174292.5:2001JAN12
2906831H1
1704
1836

27
LI:1174292.5:2001JAN12
3364048H1
1584
1765

27
LI:1174292.5:2001JAN12
2945872H2
1247
1544

27
LI:1174292.5:2001JAN12
7254181H1
884
1461

27
LI:1174292.5:2001JAN12
g5513770
2188
2617

27
LI:1174292.5:2001JAN12
779596H1
1056
1326

27
LI:1174292.5:2001JAN12
g664566
1506
1802

27
LI:1174292.5:2001JAN12
7943284J2
1497
1841

27
LI:1174292.5:2001JAN12
g1616477
1678
1860

27
LI:1174292.5:2001JAN12
6082132H1
20
407

27
LI:1174292.5:2001JAN12
3021414H1
2182
2377

27
LI:1174292.5:2001JAN12
3254104H1
1004
1277

27
LI:1174292.5:2001JAN12
g4329312
1394
1859

27
LI:1174292.5:2001JAN12
2348110H1
2399
2615

27
LI:1174292.5:2001JAN12
70814746V1
1226
1834

27
LI:1174292.5:2001JAN12
755739H1
1448
1674

27
LI:1174292.5:2001JAN12
5732209H1
1270
1535

27
LI:1174292.5:2001JAN12
7584421H1
1245
1737

27
LI:1174292.5:2001JAN12
g5548346
2246
2617

27
LI:1174292.5:2001JAN12
5689379H1
1614
1715

27
LI:1174292.5:2001JAN12
g1616476
785
1181

27
LI:1174292.5:2001JAN12
g664580
1416
1705

27
LI:1174292.5:2001JAN12
1360406T6
1290
1760

27
LI:1174292.5:2001JAN12
4514655H1
294
381

27
LI:1174292.5:2001JAN12
1702474H1
386
498

27
LI:1174292.5:2001JAN12
6074842H1
1520
1813

27
LI:1174292.5:2001JAN12
6041309H1
1714
2123

27
LI:1174292.5:2001JAN12
g1891852
2042
2437

27
LI:1174292.5:2001JAN12
5482373H1
1734
2021

27
LI:1174292.5:2001JAN12
70649463V1
1148
1652

27
LI:1174292.5:2001JAN12
334466H1
1881
2130

27
LI:1174292.5:2001JAN12
2764772H1
1399
1641

27
LI:1174292.5:2001JAN12
5899894H1
1916
2173

27
LI:1174292.5:2001JAN12
7244360H1
2089
2437

27
LI:1174292.5:2001JAN12
6128479F6
2143
2707

27
LI:1174292.5:2001JAN12
3716538H1
674
909

27
LI:1174292.5:2001JAN12
4774519H1
1609
1880

27
LI:1174292.5:2001JAN12
5589184H1
39
184

27
LI:1174292.5:2001JAN12
4913344H1
1669
1835

27
LI:1174292.5:2001JAN12
575477H1
1578
1835

27
LI:1174292.5:2001JAN12
4597333H1
1546
1800

27
LI:1174292.5:2001JAN12
70813490V1
669
1202

27
LI:1174292.5:2001JAN12
7701481J1
1978
2604

27
LI:1174292.5:2001JAN12
755739R6
1448
1831

27
LI:1174292.5:2001JAN12
g678136
3335
3663

27
LI:1174292.5:2001JAN12
g5151992
1602
1864

27
LI:1174292.5:2001JAN12
70814293V1
779
1402

27
LI:1174292.5:2001JAN12
g4664424
2195
2615

27
LI:1174292.5:2001JAN12
g3837532
2113
2437

27
LI:1174292.5:2001JAN12
g564175
1932
2171

27
LI:1174292.5:2001JAN12
5709938H1
1909
2174

27
LI:1174292.5:2001JAN12
6128891F6
2145
2707

27
LI:1174292.5:2001JAN12
g879187
1531
1840

27
LI:1174292.5:2001JAN12
70812860V1
2123
2615

27
LI:1174292.5:2001JAN12
3488035F6
3122
3390

27
LI:1174292.5:2001JAN12
3183652H1
6
324

27
LI:1174292.5:2001JAN12
2764773H1
1399
1642

27
LI:1174292.5:2001JAN12
2428891H1
1599
1835

27
LI:1174292.5:2001JAN12
3397356H1
1785
2025

27
LI:1174292.5:2001JAN12
70816599V1
1156
1685

27
LI:1174292.5:2001JAN12
1550876R6
1838
2261

27
LI:1174292.5:2001JAN12
2550171F6
1740
1989

27
LI:1174292.5:2001JAN12
433634F1
1976
2437

27
LI:1174292.5:2001JAN12
70813630V1
237
858

27
LI:1174292.5:2001JAN12
2861529F6
53
380

27
LI:1174292.5:2001JAN12
70812624V1
1037
1575

27
LI:1174292.5:2001JAN12
1746188H1
1866
2133

27
LI:1174292.5:2001JAN12
3779637H1
560
850

28
LI:1179173.1:2001JAN12
6164529H1
1072
1533

28
LI:1179173.1:2001JAN12
5283094H1
1138
1400

28
LI:1179173.1:2001JAN12
6600320H1
1072
1454

28
LI:1179173.1:2001JAN12
727252H1
1883
2111

28
LI:1179173.1:2001JAN12
6081360T8
1932
2279

28
LI:1179173.1:2001JAN12
2786323H1
2131
2249

28
LI:1179173.1:2001JAN12
6164529T6
1572
1686

28
LI:1179173.1:2001JAN12
6520424H1
1804
2335

28
LI:1179173.1:2001JAN12
g1971271
1319
1597

28
LI:1179173.1:2001JAN12
6164529T8
1169
1639

28
LI:1179173.1:2001JAN12
6081360F8
1351
1985

28
LI:1179173.1:2001JAN12
4889636T6
1382
1648

28
LI:1179173.1:2001JAN12
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1523
1811

28
LI:1179173.1:2001JAN12
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1007
1299

28
LI:1179173.1:2001JAN12
4889636F6
1007
1392

28
LI:1179173.1:2001JAN12
6081360H1
1351
1876

28
LI:1179173.1:2001JAN12
g6118382
1
2015

28
LI:1179173.1:2001JAN12
5725584H1
1
388

28
LI:1179173.1:2001JAN12
3745368H2
25
207

28
LI:1179173.1:2001JAN12
g5742181
34
302

28
LI:1179173.1:2001JAN12
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96
556

28
LI:1179173.1:2001JAN12
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1072
1484

28
LI:1179173.1:2001JAN12
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1072
1379

28
LI:1179173.1:2001JAN12
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1072
1720

28
LI:1179173.1:2001JAN12
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1232
1520

28
LI:1179173.1:2001JAN12
937525H1
1064
1351

28
LI:1179173.1:2001JAN12
5282850H1
1263
1516

28
LI:1179173.1:2001JAN12
g5658771
1411
1639

28
LI:1179173.1:2001JAN12
6558444H1
859
1370

28
LI:1179173.1:2001JAN12
3658534F7
1247
1639

28
LI:1179173.1:2001JAN12
3739433F6
1521
1634

28
LI:1179173.1:2001JAN12
60216052V1
11
529

28
LI:1179173.1:2001JAN12
6558444F8
859
1440

29
LI:2122025.1:2001JAN12
4370549F8
2
347

29
LI:2122025.1:2001JAN12
4370472H1
1
262

29
LI:2122025.1:2001JAN12
4370472F6
2
368

29
LI:2122025.1:2001JAN12
g3739050
260
586

29
LI:2122025.1:2001JAN12
6781939J1
281
891

29
LI:2122025.1:2001JAN12
8104872H1
358
992

29
LI:2122025.1:2001JAN12
8104872J1
630
1235

29
LI:2122025.1:2001JAN12
097477H1
794
982

29
LI:2122025.1:2001JAN12
4370549H1
3
258

30
LI:2049224.1:2001JAN12
g3250058
1
408

30
LI:2049224.1:2001JAN12
067219H1
160
348

30
LI:2049224.1:2001JAN12
g2368818
1
243

30
LI:2049224.1:2001JAN12
2782984H1
105
239

30
LI:2049224.1:2001JAN12
7385848H1
96
444

31
LI:758541.1:2001JAN12
1258696F1
2110
2489

31
LI:758541.1:2001JAN12
70156506V1
2129
2444

31
LI:758541.1:2001JAN12
71705990V1
2129
2473

31
LI:758541.1:2001JAN12
1271182F6
2132
2409

31
LI:758541.1:2001JAN12
3979272H1
1155
1447

31
LI:758541.1:2001JAN12
6395057H1
1160
1430

31
LI:758541.1:2001JAN12
5078504H1
1174
1321

31
LI:758541.1:2001JAN12
6834194H1
1198
1672

31
LI:758541.1:2001JAN12
3979272T8
1393
1960

31
LI:758541.1:2001JAN12
452374H1
1438
1669

31
LI:758541.1:2001JAN12
3979260T7
1488
1969

31
LI:758541.1:2001JAN12
2421844H1
1600
1705

31
LI:758541.1:2001JAN12
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1770
2218

31
LI:758541.1:2001JAN12
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1783
2218

31
LI:758541.1:2001JAN12
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1783
2429

31
LI:758541.1:2001JAN12
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1783
1960

31
LI:758541.1:2001JAN12
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1783
2085

31
LI:758541.1:2001JAN12
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1783
2433

31
LI:758541.1:2001JAN12
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1783
2462

31
LI:758541.1:2001JAN12
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1783
2163

31
LI:758541.1:2001JAN12
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1783
2205

31
LI:758541.1:2001JAN12
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1783
2434

31
LI:758541.1:2001JAN12
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1783
2425

31
LI:758541.1:2001JAN12
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1783
2042

31
LI:758541.1:2001JAN12
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1783
1960

31
LI:758541.1:2001JAN12
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1783
2453

31
LI:758541.1:2001JAN12
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1783
2218

31
LI:758541.1:2001JAN12
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1783
2221

31
LI:758541.1:2001JAN12
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1783
2219

31
LI:758541.1:2001JAN12
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1783
2218

31
LI:758541.1:2001JAN12
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1783
2218

31
LI:758541.1:2001JAN12
2326508R6
1784
2219

31
LI:758541.1:2001JAN12
g4326139
1797
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31
LI:758541.1:2001JAN12
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1812
2091

31
LI:758541.1:2001JAN12
3215974F6
1813
1986

31
LI:758541.1:2001JAN12
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1823
1961

31
LI:758541.1:2001JAN12
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1859
2218

31
LI:758541.1:2001JAN12
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1873
1927

31
LI:758541.1:2001JAN12
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1905
2207

31
LI:758541.1:2001JAN12
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1905
2218

31
LI:758541.1:2001JAN12
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1905
2218

31
LI:758541.1:2001JAN12
g2567347
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2218

31
LI:758541.1:2001JAN12
5283619H1
1925
2024

31
LI:758541.1:2001JAN12
1258696F6
2003
2460

31
LI:758541.1:2001JAN12
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2070
2153

31
LI:758541.1:2001JAN12
3452781H1
2107
2231

31
LI:758541.1:2001JAN12
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2107
2473

31
LI:758541.1:2001JAN12
1348613H1
2110
2219

31
LI:758541.1:2001JAN12
1346319H1
2110
2219

31
LI:758541.1:2001JAN12
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1097
1513

31
LI:758541.1:2001JAN12
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1103
1583

31
LI:758541.1:2001JAN12
2821583H1
1103
1394

31
LI:758541.1:2001JAN12
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1154
1446

31
LI:758541.1:2001JAN12
3979272F8
1155
1712

31
LI:758541.1:2001JAN12
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254
538

31
LI:758541.1:2001JAN12
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272
553

31
LI:758541.1:2001JAN12
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281
523

31
LI:758541.1:2001JAN12
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354
552

31
LI:758541.1:2001JAN12
5160182T9
455
1005

31
LI:758541.1:2001JAN12
2820133H1
457
735

31
LI:758541.1:2001JAN12
1547544T6
498
1084

31
LI:758541.1:2001JAN12
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554
990

31
LI:758541.1:2001JAN12
2406449T6
569
1069

31
LI:758541.1:2001JAN12
4181687H1
621
869

31
LI:758541.1:2001JAN12
4181608H1
621
870

31
LI:758541.1:2001JAN12
60111434B1
627
1093

31
LI:758541.1:2001JAN12
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667
1108

31
LI:758541.1:2001JAN12
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31
LI:758541.1:2001JAN12
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1183

31
LI:758541.1:2001JAN12
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31
LI:758541.1:2001JAN12
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899
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31
LI:758541.1:2001JAN12
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899
1386

31
LI:758541.1:2001JAN12
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980
1419

31
LI:758541.1:2001JAN12
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999
1647

31
LI:758541.1:2001JAN12
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1014
1380

31
LI:758541.1:2001JAN12
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1079
1223

31
LI:758541.1:2001JAN12
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1293

31
LI:758541.1:2001JAN12
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1382

31
LI:758541.1:2001JAN12
1258696H1
2135
2222

31
LI:758541.1:2001JAN12
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2174
2727

31
LI:758541.1:2001JAN12
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2193
2444

31
LI:758541.1:2001JAN12
781388T6
2289
2473

31
LI:758541.1:2001JAN12
781388R6
2289
2453

31
LI:758541.1:2001JAN12
781388H1
2289
2467

31
LI:758541.1:2001JAN12
60111441B1
2309
2467

31
LI:758541.1:2001JAN12
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2320
2869

31
LI:758541.1:2001JAN12
3812114F6
2324
2453

31
LI:758541.1:2001JAN12
7631964J1
2327
2468

31
LI:758541.1:2001JAN12
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2352
2444

31
LI:758541.1:2001JAN12
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2360
2453

31
LI:758541.1:2001JAN12
3563461H1
2371
2663

31
LI:758541.1:2001JAN12
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2636

31
LI:758541.1:2001JAN12
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2403
2761

31
LI:758541.1:2001JAN12
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2512
2760

31
LI:758541.1:2001JAN12
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2761

31
LI:758541.1:2001JAN12
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2699
2916

31
LI:758541.1:2001JAN12
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2723
2881

31
LI:758541.1:2001JAN12
3838635H1
2845
2927

31
LI:758541.1:2001JAN12
g2841729
2848
2932

31
LI:758541.1:2001JAN12
2719179F6
1
402

31
LI:758541.1:2001JAN12
6783407H2
86
659

31
LI:758541.1:2001JAN12
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123
433

31
LI:758541.1:2001JAN12
7119178F8
145
377

31
LI:758541.1:2001JAN12
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145
377

31
LI:758541.1:2001JAN12
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154
755

31
LI:758541.1:2001JAN12
5208572H1
154
391

31
LI:758541.1:2001JAN12
6513345H1
217
757

31
LI:758541.1:2001JAN12
6513345F7
217
819

32
LI:137815.1:2001JAN12
71261842V1
2415
2921

32
LI:137815.1:2001JAN12
6332261H1
3662
3993

32
LI:137815.1:2001JAN12
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3684
3990

32
LI:137815.1:2001JAN12
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3686
4200

32
LI:137815.1:2001JAN12
g1545726
3690
3991

32
LI:137815.1:2001JAN12
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3704
3990

32
LI:137815.1:2001JAN12
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4245

32
LI:137815.1:2001JAN12
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32
LI:137815.1:2001JAN12
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4164
4695

32
LI:137815.1:2001JAN12
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4173
4503

32
LI:137815.1:2001JAN12
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4328
4931

32
LI:137815.1:2001JAN12
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4336
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32
LI:137815.1:2001JAN12
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3506
3778

32
LI:137815.1:2001JAN12
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3546
3955

32
LI:137815.1:2001JAN12
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3660
3990

32
LI:137815.1:2001JAN12
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3065
3607

32
LI:137815.1:2001JAN12
6485489R9
3117
3664

32
LI:137815.1:2001JAN12
1432090R7
3125
3626

32
LI:137815.1:2001JAN12
1432090H1
3125
3357

32
LI:137815.1:2001JAN12
7258715T6
3158
3439

32
LI:137815.1:2001JAN12
g2433198
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3364

32
LI:137815.1:2001JAN12
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32
LI:137815.1:2001JAN12
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3193
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32
LI:137815.1:2001JAN12
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3561

32
LI:137815.1:2001JAN12
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3369
3880

32
LI:137815.1:2001JAN12
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3403
3925

32
LI:137815.1:2001JAN12
g1764406
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3732

32
LI:137815.1:2001JAN12
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3460
3579

32
LI:137815.1:2001JAN12
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3465
3996

32
LI:137815.1:2001JAN12
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3487
3990

32
LI:137815.1:2001JAN12
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2863
3421

32
LI:137815.1:2001JAN12
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2890
3413

32
LI:137815.1:2001JAN12
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2916
3360

32
LI:137815.1:2001JAN12
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2913
3461

32
LI:137815.1:2001JAN12
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2922
3432

32
LI:137815.1:2001JAN12
8269736U1
3033
3459

32
LI:137815.1:2001JAN12
g4891355
4388
4848

32
LI:137815.1:2001JAN12
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4544
4960

32
LI:137815.1:2001JAN12
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4544
4826

32
LI:137815.1:2001JAN12
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4544
4800

32
LI:137815.1:2001JAN12
1795115H1
4562
4811

32
LI:137815.1:2001JAN12
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32
LI:137815.1:2001JAN12
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32
LI:137815.1:2001JAN12
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4957

32
LI:137815.1:2001JAN12
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4857

32
LI:137815.1:2001JAN12
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32
LI:137815.1:2001JAN12
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32
LI:137815.1:2001JAN12
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2595

32
LI:137815.1:2001JAN12
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2887

32
LI:137815.1:2001JAN12
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2374
2797

32
LI:137815.1:2001JAN12
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1445
2079

32
LI:137815.1:2001JAN12
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1776
2058

32
LI:137815.1:2001JAN12
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1828
2395

32
LI:137815.1:2001JAN12
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1835
2432

32
LI:137815.1:2001JAN12
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1957
2487

32
LI:137815.1:2001JAN12
7258715H1
1957
2465

32
LI:137815.1:2001JAN12
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1973
2205

32
LI:137815.1:2001JAN12
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4342
4427

32
LI:137815.1:2001JAN12
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4360
4630

32
LI:137815.1:2001JAN12
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4336
4866

32
LI:137815.1:2001JAN12
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4336
4620

32
LI:137815.1:2001JAN12
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4336
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32
LI:137815.1:2001JAN12
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1838

32
LI:137815.1:2001JAN12
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1280
1834

32
LI:137815.1:2001JAN12
71261548V1
2422
2883

32
LI:137815.1:2001JAN12
652364H1
2470
2729

32
LI:137815.1:2001JAN12
71261266V1
2486
2879

32
LI:137815.1:2001JAN12
5513919H1
2502
2732

32
LI:137815.1:2001JAN12
5513919F6
2509
3011

32
LI:137815.1:2001JAN12
71261293V1
2518
3046

32
LI:137815.1:2001JAN12
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2545
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32
LI:137815.1:2001JAN12
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2671
3244

32
LI:137815.1:2001JAN12
71262028V1
2714
3239

32
LI:137815.1:2001JAN12
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2703
3337

32
LI:137815.1:2001JAN12
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2800
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32
LI:137815.1:2001JAN12
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2813
3460

32
LI:137815.1:2001JAN12
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32
LI:137815.1:2001JAN12
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829
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32
LI:137815.1:2001JAN12
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829
1325

32
LI:137815.1:2001JAN12
5684319F8
836
1279

32
LI:137815.1:2001JAN12
8113031H1
896
1497

32
LI:137815.1:2001JAN12
5684319H1
792
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32
LI:137815.1:2001JAN12
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1
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32
LI:137815.1:2001JAN12
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619

32
LI:137815.1:2001JAN12
3649382F6
30
375

32
LI:137815.1:2001JAN12
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30
242

32
LI:137815.1:2001JAN12
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34
311

32
LI:137815.1:2001JAN12
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34
482

32
LI:137815.1:2001JAN12
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335
631

32
LI:137815.1:2001JAN12
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396
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32
LI:137815.1:2001JAN12
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774
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32
LI:137815.1:2001JAN12
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774
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32
LI:137815.1:2001JAN12
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32
LI:137815.1:2001JAN12
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4711
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33
LI:335097.1:2001JAN12
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33
LI:335097.1:2001JAN12
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33
LI:335097.1:2001JAN12
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33
LI:335097.1:2001JAN12
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33
LI:335097.1:2001JAN12
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33
LI:335097.1:2001JAN12
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33
LI:335097.1:2001JAN12
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LI:335097.1:2001JAN12
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LI:335097.1:2001JAN12
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33
LI:335097.1:2001JAN12
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33
LI:335097.1:2001JAN12
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33
LI:335097.1:2001JAN12
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33
LI:335097.1:2001JAN12
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33
LI:335097.1:2001JAN12
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LI:335097.1:2001JAN12
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33
LI:335097.1:2001JAN12
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33
LI:335097.1:2001JAN12
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33
LI:335097.1:2001JAN12
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33
LI:335097.1:2001JAN12
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33
LI:335097.1:2001JAN12
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33
LI:335097.1:2001JAN12
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33
LI:335097.1:2001JAN12
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33
LI:335097.1:2001JAN12
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33
LI:335097.1:2001JAN12
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33
LI:335097.1:2001JAN12
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33
LI:335097.1:2001JAN12
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33
LI:335097.1:2001JAN12
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33
LI:335097.1:2001JAN12
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33
LI:335097.1:2001JAN12
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LI:335097.1:2001JAN12
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33
LI:335097.1:2001JAN12
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33
LI:335097.1:2001JAN12
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LI:335097.1:2001JAN12
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LI:335097.1:2001JAN12
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LI:335097.1:2001JAN12
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LI:335097.1:2001JAN12
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LI:335097.1:2001JAN12
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33
LI:335097.1:2001JAN12
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LI:335097.1:2001JAN12
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LI:335097.1:2001JAN12
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34
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LI:232059.2:2001JAN12
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LI:232059.2:2001JAN12
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34
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34
LI:232059.2:2001JAN12
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34
LI:232059.2:2001JAN12
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LI:232059.2:2001JAN12
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34
LI:232059.2:2001JAN12
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34
LI:232059.2:2001JAN12
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LI:232059.2:2001JAN12
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LI:232059.2:2001JAN12
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34
LI:232059.2:2001JAN12
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34
LI:232059.2:2001JAN12
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34
LI:232059.2:2001JAN12
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34
LI:232059.2:2001JAN12
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34
LI:232059.2:2001JAN12
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34
LI:232059.2:2001JAN12
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765
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34
LI:232059.2:2001JAN12
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806
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34
LI:232059.2:2001JAN12
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34
LI:232059.2:2001JAN12
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34
LI:232059.2:2001JAN12
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35
LI:400109.2:2001JAN12
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35
LI:400109.2:2001JAN12
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35
LI:400109.2:2001JAN12
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35
LI:400109.2:2001JAN12
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35
LI:400109.2:2001JAN12
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35
LI:400109.2:2001JAN12
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35
LI:400109.2:2001JAN12
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35
LI:400109.2:2001JAN12
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35
LI:400109.2:2001JAN12
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35
LI:400109.2:2001JAN12
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35
LI:400109.2:2001JAN12
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35
LI:400109.2:2001JAN12
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35
LI:400109.2:2001JAN12
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254
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35
LI:400109.2:2001JAN12
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35
LI:400109.2:2001JAN12
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35
LI:400109.2:2001JAN12
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35
LI:400109.2:2001JAN12
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LI:400109.2:2001JAN12
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35
LI:400109.2:2001JAN12
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35
LI:400109.2:2001JAN12
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677
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35
LI:400109.2:2001JAN12
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673
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35
LI:400109.2:2001JAN12
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LI:400109.2:2001JAN12
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35
LI:400109.2:2001JAN12
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35
LI:400109.2:2001JAN12
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LI:400109.2:2001JAN12
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35
LI:400109.2:2001JAN12
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35
LI:400109.2:2001JAN12
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35
LI:400109.2:2001JAN12
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LI:400109.2:2001JAN12
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LI:400109.2:2001JAN12
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LI:400109.2:2001JAN12
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LI:400109.2:2001JAN12
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LI:400109.2:2001JAN12
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LI:400109.2:2001JAN12
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LI:400109.2:2001JAN12
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709
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35
LI:400109.2:2001JAN12
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35
LI:400109.2:2001JAN12
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LI:400109.2:2001JAN12
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738
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LI:400109.2:2001JAN12
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744
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35
LI:400109.2:2001JAN12
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LI:400109.2:2001JAN12
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LI:400109.2:2001JAN12
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LI:400109.2:2001JAN12
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LI:400109.2:2001JAN12
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36
LI:329770.1:2001JAN12
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1145

36
LI:329770.1:2001JAN12
70605038V1
809
1103

36
LI:329770.1:2001JAN12
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868
1098

36
LI:329770.1:2001JAN12
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36
LI:329770.1:2001JAN12
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1335

36
LI:329770.1:2001JAN12
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36
LI:329770.1:2001JAN12
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36
LI:329770.1:2001JAN12
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1272

36
LI:329770.1:2001JAN12
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1246

36
LI:329770.1:2001JAN12
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36
LI:329770.1:2001JAN12
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36
LI:329770.1:2001JAN12
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1227

36
LI:329770.1:2001JAN12
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809
1219

36
LI:329770.1:2001JAN12
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809
1215

36
LI:329770.1:2001JAN12
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809
1166

36
LI:329770.1:2001JAN12
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846
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36
LI:329770.1:2001JAN12
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1364

36
LI:329770.1:2001JAN12
2428620H1
1101
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36
LI:329770.1:2001JAN12
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36
LI:329770.1:2001JAN12
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1085

36
LI:329770.1:2001JAN12
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1073

36
LI:329770.1:2001JAN12
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809
1063

36
LI:329770.1:2001JAN12
70692842V1
809
1068

37
LI:898841.9:2001JAN12
7192534H1
331
915

37
LI:898841.9:2001JAN12
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1
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37
LI:898841.9:2001JAN12
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269
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37
LI:898841.9:2001JAN12
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381
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37
LI:898841.9:2001JAN12
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165
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38
LI:1183848.3:2001JAN12
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1
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39
LI:2037121.1:2001JAN12
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78
644

39
LI:2037121.1:2001JAN12
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122
588

39
LI:2037121.1:2001JAN12
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119
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39
LI:2037121.1:2001JAN12
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138
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39
LI:2037121.1:2001JAN12
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153
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39
LI:2037121.1:2001JAN12
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162
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39
LI:2037121.1:2001JAN12
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39
LI:2037121.1:2001JAN12
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39
LI:2037121.1:2001JAN12
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39
LI:2037121.1:2001JAN12
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312
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39
LI:2037121.1:2001JAN12
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39
LI:2037121.1:2001JAN12
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39
LI:2037121.1:2001JAN12
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1
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39
LI:2037121.1:2001JAN12
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1
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39
LI:2037121.1:2001JAN12
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40
LI:356090.1:2001JAN12
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31
416

40
LI:356090.1:2001JAN12
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40
LI:356090.1:2001JAN12
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40
LI:356090.1:2001JAN12
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LI:356090.1:2001JAN12
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40
LI:356090.1:2001JAN12
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LI:356090.1:2001JAN12
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40
LI:356090.1:2001JAN12
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40
LI:356090.1:2001JAN12
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31
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40
LI:356090.1:2001JAN12
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40
LI:356090.1:2001JAN12
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40
LI:356090.1:2001JAN12
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84
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40
LI:356090.1:2001JAN12
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40
LI:356090.1:2001JAN12
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1
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40
LI:356090.1:2001JAN12
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40
LI:356090.1:2001JAN12
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40
LI:356090.1:2001JAN12
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40
LI:356090.1:2001JAN12
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31
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40
LI:356090.1:2001JAN12
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40
LI:356090.1:2001JAN12
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580
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40
LI:356090.1:2001JAN12
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162
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40
LI:356090.1:2001JAN12
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339
660

40
LI:356090.1:2001JAN12
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1
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40
LI:356090.1:2001JAN12
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160
656

40
LI:356090.1:2001JAN12
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168
655

40
LI:356090.1:2001JAN12
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271
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40
LI:356090.1:2001JAN12
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40
LI:356090.1:2001JAN12
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40
LI:356090.1:2001JAN12
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290
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40
LI:356090.1:2001JAN12
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40
LI:356090.1:2001JAN12
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233
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40
LI:356090.1:2001JAN12
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481
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40
LI:356090.1:2001JAN12
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144
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40
LI:356090.1:2001JAN12
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470
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40
LI:356090.1:2001JAN12
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148
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40
LI:356090.1:2001JAN12
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419
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40
LI:356090.1:2001JAN12
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385
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40
LI:356090.1:2001JAN12
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378
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40
LI:356090.1:2001JAN12
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361
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40
LI:356090.1:2001JAN12
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60
648

40
LI:356090.1:2001JAN12
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237
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40
LI:356090.1:2001JAN12
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187
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40
LI:356090.1:2001JAN12
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375
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40
LI:356090.1:2001JAN12
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40
LI:356090.1:2001JAN12
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204
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40
LI:356090.1:2001JAN12
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37
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40
LI:356090.1:2001JAN12
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32
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40
LI:356090.1:2001JAN12
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40
LI:356090.1:2001JAN12
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31
230

40
LI:356090.1:2001JAN12
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31
202

40
LI:356090.1:2001JAN12
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1
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40
LI:356090.1:2001JAN12
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31
87

41
LI:212142.1:2001JAN12
g4897764
1
216

41
LI:212142.1:2001JAN12
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15
216

41
LI:212142.1:2001JAN12
3125917H1
61
150

41
LI:212142.1:2001JAN12
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63
712

41
LI:212142.1:2001JAN12
7764545H1
254
692

41
LI:212142.1:2001JAN12
7764545J1
254
692

42
LI:1096706.1:2001JAN12
4295414T9
1
617

43
LI:012622.1:2001JAN12
g4312998
1
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43
LI:012622.1:2001JAN12
g6700341
153
590

43
LI:012622.1:2001JAN12
6931850H1
236
761

43
LI:012622.1:2001JAN12
7756516J1
387
1015

43
LI:012622.1:2001JAN12
3689349H1
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43
LI:012622.1:2001JAN12
3394763H1
691
781

43
LI:012622.1:2001JAN12
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690
1340

43
LI:012622.1:2001JAN12
6392108H1
693
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43
LI:012622.1:2001JAN12
1437717F6
753
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43
LI:012622.1:2001JAN12
1437229H1
753
1000

43
LI:012622.1:2001JAN12
1437717H1
753
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43
LI:012622.1:2001JAN12
7086440F8
874
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43
LI:012622.1:2001JAN12
7086440H1
874
1454

43
LI:012622.1:2001JAN12
7757759H1
1044
1589

44
LI:1171095.29:2001JAN12
70514692V1
1
564

44
LI:1171095.29:2001JAN12
70515574V1
1
559

44
LI:1171095.29:2001JAN12
70513802V1
24
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44
LI:1171095.29:2001JAN12
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24
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44
LI:1171095.29:2001JAN12
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24
543

44
LI:1171095.29:2001JAN12
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24
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44
LI:1171095.29:2001JAN12
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24
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44
LI:1171095.29:2001JAN12
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24
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44
LI:1171095.29:2001JAN12
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24
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44
LI:1171095.29:2001JAN12
70514171D1
26
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44
LI:1171095.29:2001JAN12
70515381V1
31
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44
LI:1171095.29:2001JAN12
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31
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44
LI:1171095.29:2001JAN12
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31
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44
LI:1171095.29:2001JAN12
70513785D1
31
564

44
LI:1171095.29:2001JAN12
70513772D1
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44
LI:1171095.29:2001JAN12
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45
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44
LI:1171095.29:2001JAN12
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44
LI:1171095.29:2001JAN12
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66
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44
LI:1171095.29:2001JAN12
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44
LI:1171095.29:2001JAN12
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44
LI:1171095.29:2001JAN12
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96
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44
LI:1171095.29:2001JAN12
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102
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44
LI:1171095.29:2001JAN12
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122
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44
LI:1171095.29:2001JAN12
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125
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44
LI:1171095.29:2001JAN12
g2103046
124
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44
LI:1171095.29:2001JAN12
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131
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44
LI:1171095.29:2001JAN12
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137
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44
LI:1171095.29:2001JAN12
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138
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44
LI:1171095.29:2001JAN12
70514692D1
152
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44
LI:1171095.29:2001JAN12
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159
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44
LI:1171095.29:2001JAN12
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200
389

44
LI:1171095.29:2001JAN12
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200
389

44
LI:1171095.29:2001JAN12
g2254275
204
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44
LI:1171095.29:2001JAN12
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44
LI:1171095.29:2001JAN12
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44
LI:1171095.29:2001JAN12
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234
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44
LI:1171095.29:2001JAN12
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234
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44
LI:1171095.29:2001JAN12
3449606H1
246
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44
LI:1171095.29:2001JAN12
g1784240
275
514

44
LI:1171095.29:2001JAN12
4377119H1
277
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44
LI:1171095.29:2001JAN12
g1954855
288
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44
LI:1171095.29:2001JAN12
3124873H1
498
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44
LI:1171095.29:2001JAN12
70512732D1
31
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44
LI:1171095.29:2001JAN12
70515917V1
31
559

44
LI:1171095.29:2001JAN12
70514610D1
31
422

45
LI:023813.1:2001JAN12
71246354V1
852
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45
LI:023813.1:2001JAN12
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850
1202

45
LI:023813.1:2001JAN12
71596641V1
2162
2520

45
LI:023813.1:2001JAN12
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2118
2514

45
LI:023813.1:2001JAN12
g5545806
2100
2469

45
LI:023813.1:2001JAN12
2755737H1
1325
1596

45
LI:023813.1:2001JAN12
71597229V1
1138
1902

45
LI:023813.1:2001JAN12
71054104V1
851
1401

45
LI:023813.1:2001JAN12
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851
1451

45
LI:023813.1:2001JAN12
2472188H1
1765
1977

45
LI:023813.1:2001JAN12
2463019T6
1771
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45
LI:023813.1:2001JAN12
1286176H1
850
1034

45
LI:023813.1:2001JAN12
7741963H1
850
1118

45
LI:023813.1:2001JAN12
6157360H1
2261
2468

45
LI:023813.1:2001JAN12
g1506001
2271
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45
LI:023813.1:2001JAN12
g4267102
2278
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45
LI:023813.1:2001JAN12
g3770756
2096
2473

45
LI:023813.1:2001JAN12
4914048H1
1409
1693

45
LI:023813.1:2001JAN12
71592042V1
850
1130

45
LI:023813.1:2001JAN12
g1315098
850
1095

45
LI:023813.1:2001JAN12
4156980H1
1391
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45
LI:023813.1:2001JAN12
3520639H1
1120
1422

45
LI:023813.1:2001JAN12
556535H1
2257
2461

45
LI:023813.1:2001JAN12
g3895296
2251
2469

45
LI:023813.1:2001JAN12
1419166H1
1325
1607

45
LI:023813.1:2001JAN12
2755745H1
1325
1600

45
LI:023813.1:2001JAN12
g7374134
2240
2469

45
LI:023813.1:2001JAN12
4844744H1
2244
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45
LI:023813.1:2001JAN12
4844776H1
2308
2501

45
LI:023813.1:2001JAN12
g4987618
2224
2469

45
LI:023813.1:2001JAN12
g2942442
2206
2475

45
LI:023813.1:2001JAN12
g4136671
2110
2472

45
LI:023813.1:2001JAN12
1286176T6
2063
2423

45
LI:023813.1:2001JAN12
950236R1
1718
2383

45
LI:023813.1:2001JAN12
5072230H1
1718
1994

45
LI:023813.1:2001JAN12
950236H1
1718
1968

45
LI:023813.1:2001JAN12
3516550H1
1725
1985

45
LI:023813.1:2001JAN12
7448845T1
1729
2366

45
LI:023813.1:2001JAN12
71593395V1
1816
2547

45
LI:023813.1:2001JAN12
5602569H1
1761
1993

45
LI:023813.1:2001JAN12
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1115
1864

45
LI:023813.1:2001JAN12
1488869H1
1103
1357

45
LI:023813.1:2001JAN12
1702260F6
1093
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45
LI:023813.1:2001JAN12
1702260H1
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1305

45
LI:023813.1:2001JAN12
71595470V1
1105
1757

45
LI:023813.1:2001JAN12
1487475H1
1103
1385

45
LI:023813.1:2001JAN12
71594429V1
1093
1743

45
LI:023813.1:2001JAN12
6958590H1
850
1282

45
LI:023813.1:2001JAN12
70140481V1
850
1173

45
LI:023813.1:2001JAN12
70142136V1
850
1164

45
LI:023813.1:2001JAN12
1286176F6
850
1334

45
LI:023813.1:2001JAN12
g3191322
2205
2468

45
LI:023813.1:2001JAN12
3218695T6
2052
2429

45
LI:023813.1:2001JAN12
g725047
2051
2401

45
LI:023813.1:2001JAN12
71594637V1
1327
2025

45
LI:023813.1:2001JAN12
1721227F6
1325
1761

45
LI:023813.1:2001JAN12
71591773V1
1091
1721

45
LI:023813.1:2001JAN12
70133279V1
1079
1559

45
LI:023813.1:2001JAN12
g6991686
1087
1721

45
LI:023813.1:2001JAN12
634943H1
1089
1382

45
LI:023813.1:2001JAN12
1498980H1
1074
1362

45
LI:023813.1:2001JAN12
7928488H1
1081
1698

45
LI:023813.1:2001JAN12
7931758H1
850
1378

45
LI:023813.1:2001JAN12
g1966143
850
1313

45
LI:023813.1:2001JAN12
71054101V1
847
1366

45
LI:023813.1:2001JAN12
g7378159
850
1101

45
LI:023813.1:2001JAN12
71591833V1
850
1498

45
LI:023813.1:2001JAN12
4335886H1
1278
1566

45
LI:023813.1:2001JAN12
71597001V1
1285
1918

45
LI:023813.1:2001JAN12
5595621H1
1315
1452

45
LI:023813.1:2001JAN12
3521153H1
1066
1385

45
LI:023813.1:2001JAN12
71051986V1
518
1089

45
LI:023813.1:2001JAN12
71594280V1
775
1482

45
LI:023813.1:2001JAN12
70140433V1
827
1145

45
LI:023813.1:2001JAN12
71597103V1
831
1380

45
LI:023813.1:2001JAN12
2124855H1
841
1157

45
LI:023813.1:2001JAN12
2124855F6
841
953

45
LI:023813.1:2001JAN12
71593716V1
847
1517

45
LI:023813.1:2001JAN12
70133724V1
2051
2455

45
LI:023813.1:2001JAN12
g5100629
2030
2468

45
LI:023813.1:2001JAN12
g3253783
2046
2469

45
LI:023813.1:2001JAN12
70170790V1
1276
1689

45
LI:023813.1:2001JAN12
71051344V1
1266
2006

45
LI:023813.1:2001JAN12
71051690V1
1265
1890

45
LI:023813.1:2001JAN12
7660427J1
404
574

45
LI:023813.1:2001JAN12
71597195V1
433
1082

45
LI:023813.1:2001JAN12
71627104V1
461
574

45
LI:023813.1:2001JAN12
70142671V1
464
936

45
LI:023813.1:2001JAN12
2425791H1
509
574

45
LI:023813.1:2001JAN12
6533432F8
511
1134

45
LI:023813.1:2001JAN12
616178H1
2013
2292

45
LI:023813.1:2001JAN12
g7044121
2017
2471

45
LI:023813.1:2001JAN12
71591588V1
1237
1953

45
LI:023813.1:2001JAN12
71051086V1
1229
1806

45
LI:023813.1:2001JAN12
3938096H1
1235
1354

45
LI:023813.1:2001JAN12
70136311V1
1050
1457

45
LI:023813.1:2001JAN12
71596758V1
1049
1740

45
LI:023813.1:2001JAN12
71593352V1
1783
2547

45
LI:023813.1:2001JAN12
2579582H1
391
574

45
LI:023813.1:2001JAN12
g650612
2193
2470

45
LI:023813.1:2001JAN12
2330443H1
2200
2467

45
LI:023813.1:2001JAN12
70139578V1
2170
2458

45
LI:023813.1:2001JAN12
g650611
2174
2447

45
LI:023813.1:2001JAN12
764838H1
2013
2311

45
LI:023813.1:2001JAN12
g2987604
2011
2301

45
LI:023813.1:2001JAN12
1242649H1
1604
1829

45
LI:023813.1:2001JAN12
71596934V1
1617
2367

45
LI:023813.1:2001JAN12
7760577H1
1636
2298

45
LI:023813.1:2001JAN12
70140562V1
1632
2127

45
LI:023813.1:2001JAN12
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1693
2345

45
LI:023813.1:2001JAN12
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2547

45
LI:023813.1:2001JAN12
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1583
2231

45
LI:023813.1:2001JAN12
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1586
2241

45
LI:023813.1:2001JAN12
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1227
1502

45
LI:023813.1:2001JAN12
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1227
1745

45
LI:023813.1:2001JAN12
5603955H1
1224
1448

45
LI:023813.1:2001JAN12
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1036
1482

45
LI:023813.1:2001JAN12
2917935H1
2164
2444

45
LI:023813.1:2001JAN12
2753762H1
2166
2441

45
LI:023813.1:2001JAN12
g4735992
2050
2468

45
LI:023813.1:2001JAN12
6575246H1
1211
1668

45
LI:023813.1:2001JAN12
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391
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45
LI:023813.1:2001JAN12
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45
LI:023813.1:2001JAN12
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391
943

45
LI:023813.1:2001JAN12
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2048
2346

45
LI:023813.1:2001JAN12
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2010
2334

45
LI:023813.1:2001JAN12
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1034
1433

45
LI:023813.1:2001JAN12
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391
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45
LI:023813.1:2001JAN12
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2010
2323

45
LI:023813.1:2001JAN12
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1027
1587

45
LI:023813.1:2001JAN12
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1028
1440

45
LI:023813.1:2001JAN12
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1021
1628

45
LI:023813.1:2001JAN12
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1021
1317

45
LI:023813.1:2001JAN12
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332
572

45
LI:023813.1:2001JAN12
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391
1002

45
LI:023813.1:2001JAN12
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2007
2326

45
LI:023813.1:2001JAN12
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1016
1745

45
LI:023813.1:2001JAN12
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974
1690

45
LI:023813.1:2001JAN12
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991
1696

45
LI:023813.1:2001JAN12
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1005
1305

45
LI:023813.1:2001JAN12
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1009
1603

45
LI:023813.1:2001JAN12
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319
632

45
LI:023813.1:2001JAN12
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2164
2422

45
LI:023813.1:2001JAN12
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1992
2461

45
LI:023813.1:2001JAN12
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1992
2432

45
LI:023813.1:2001JAN12
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2005
2477

45
LI:023813.1:2001JAN12
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2014
2487

45
LI:023813.1:2001JAN12
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1847

45
LI:023813.1:2001JAN12
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1565
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45
LI:023813.1:2001JAN12
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45
LI:023813.1:2001JAN12
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928
1185

45
LI:023813.1:2001JAN12
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937
1471

45
LI:023813.1:2001JAN12
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912
1199

45
LI:023813.1:2001JAN12
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907
1700

45
LI:023813.1:2001JAN12
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2161
2468

45
LI:023813.1:2001JAN12
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2152
2458

45
LI:023813.1:2001JAN12
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2163
2380

45
LI:023813.1:2001JAN12
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2165
2469

45
LI:023813.1:2001JAN12
1721227T6
2124
2431

45
LI:023813.1:2001JAN12
1339952H1
2136
2403

45
LI:023813.1:2001JAN12
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1975
2234

45
LI:023813.1:2001JAN12
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1992
2267

45
LI:023813.1:2001JAN12
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1556
1747

45
LI:023813.1:2001JAN12
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1203
1688

45
LI:023813.1:2001JAN12
3186948H1
1198
1517

45
LI:023813.1:2001JAN12
g6402027
1962
2469

45
LI:023813.1:2001JAN12
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1965
2470

45
LI:023813.1:2001JAN12
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1970
2467

45
LI:023813.1:2001JAN12
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1952
2097

45
LI:023813.1:2001JAN12
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1538
2325

45
LI:023813.1:2001JAN12
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1532
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45
LI:023813.1:2001JAN12
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1540
2136

45
LI:023813.1:2001JAN12
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1550
2241

45
LI:023813.1:2001JAN12
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1562
1841

45
LI:023813.1:2001JAN12
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1520
2295

45
LI:023813.1:2001JAN12
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1521
1816

45
LI:023813.1:2001JAN12
4516659H1
1510
1786

45
LI:023813.1:2001JAN12
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900
1197

45
LI:023813.1:2001JAN12
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293
588

45
LI:023813.1:2001JAN12
71596922V1
288
564

45
LI:023813.1:2001JAN12
3581039F6
293
574

45
LI:023813.1:2001JAN12
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1947
2256

45
LI:023813.1:2001JAN12
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1190
1820

45
LI:023813.1:2001JAN12
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1191
1567

45
LI:023813.1:2001JAN12
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1189
1471

45
LI:023813.1:2001JAN12
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1189
1484

45
LI:023813.1:2001JAN12
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1189
1486

45
LI:023813.1:2001JAN12
1389880T6
230
571

45
LI:023813.1:2001JAN12
7196709H1
201
574

45
LI:023813.1:2001JAN12
g791516
2129
2474

45
LI:023813.1:2001JAN12
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1939
2460

45
LI:023813.1:2001JAN12
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1505
1995

45
LI:023813.1:2001JAN12
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894
1747

45
LI:023813.1:2001JAN12
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894
1494

45
LI:023813.1:2001JAN12
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113
343

45
LI:023813.1:2001JAN12
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58
571

45
LI:023813.1:2001JAN12
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58
313

45
LI:023813.1:2001JAN12
1389880H1
1
201

45
LI:023813.1:2001JAN12
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2120
2337

45
LI:023813.1:2001JAN12
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2120
2350

45
LI:023813.1:2001JAN12
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2121
2433

45
LI:023813.1:2001JAN12
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1490
2344

45
LI:023813.1:2001JAN12
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1502
1781

45
LI:023813.1:2001JAN12
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1
234

45
LI:023813.1:2001JAN12
3218695F6
1
276

45
LI:023813.1:2001JAN12
7959362H1
1
333

45
LI:023813.1:2001JAN12
7404590H1
1
298

45
LI:023813.1:2001JAN12
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1
450

45
LI:023813.1:2001JAN12
7738695J1
1
571

45
LI:023813.1:2001JAN12
8131981H1
3
619

45
LI:023813.1:2001JAN12
g2261700
1936
2478

45
LI:023813.1:2001JAN12
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1895
2153

45
LI:023813.1:2001JAN12
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1491
2207

45
LI:023813.1:2001JAN12
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1139
1798

45
LI:023813.1:2001JAN12
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1149
1803

45
LI:023813.1:2001JAN12
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1155
1488

45
LI:023813.1:2001JAN12
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1162
1490

45
LI:023813.1:2001JAN12
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1174
1446

45
LI:023813.1:2001JAN12
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864
1126

45
LI:023813.1:2001JAN12
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878
1401

45
LI:023813.1:2001JAN12
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863
962

45
LI:023813.1:2001JAN12
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1886
2219

45
LI:023813.1:2001JAN12
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1890
2429

45
LI:023813.1:2001JAN12
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1825
2212

45
LI:023813.1:2001JAN12
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1830
2450

45
LI:023813.1:2001JAN12
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1840
2110

45
LI:023813.1:2001JAN12
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1852
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45
LI:023813.1:2001JAN12
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1881
2444

45
LI:023813.1:2001JAN12
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1908
2470

45
LI:023813.1:2001JAN12
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1463
2179

45
LI:023813.1:2001JAN12
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1484
1938

45
LI:023813.1:2001JAN12
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1458
2079

45
LI:023813.1:2001JAN12
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1331
1552

45
LI:023813.1:2001JAN12
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1331
1545

45
LI:023813.1:2001JAN12
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1334
1737

45
LI:023813.1:2001JAN12
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1337
1750

45
LI:023813.1:2001JAN12
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1363
2053

45
LI:023813.1:2001JAN12
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1365
1952

45
LI:023813.1:2001JAN12
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1376
2039

45
LI:023813.1:2001JAN12
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1392
2134

45
LI:023813.1:2001JAN12
3050780H1
1331
1650

45
LI:023813.1:2001JAN12
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848
1541

45
LI:023813.1:2001JAN12
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858
1466

45
LI:023813.1:2001JAN12
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858
1466

45
LI:023813.1:2001JAN12
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862
1380

45
LI:023813.1:2001JAN12
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1
226

45
LI:023813.1:2001JAN12
1609990H1
2120
2373

45
LI:023813.1:2001JAN12
g852616
2114
2475

45
LI:023813.1:2001JAN12
71592734V1
2155
2546

45
LI:023813.1:2001JAN12
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2107
2470

45
LI:023813.1:2001JAN12
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1823
2000

45
LI:023813.1:2001JAN12
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1829
2220

45
LI:023813.1:2001JAN12
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1801
1939

45
LI:023813.1:2001JAN12
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1809
2425

45
LI:023813.1:2001JAN12
1702260T6
1810
2430

45
LI:023813.1:2001JAN12
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1815
2016

45
LI:023813.1:2001JAN12
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1796
2413

45
LI:023813.1:2001JAN12
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1796
1900

45
LI:023813.1:2001JAN12
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1831
2484

45
LI:023813.1:2001JAN12
g1315027
1797
2315

45
LI:023813.1:2001JAN12
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1778
2022

45
LI:023813.1:2001JAN12
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1780
2099

45
LI:023813.1:2001JAN12
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1794
2116

45
LI:023813.1:2001JAN12
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1772
2068

45
LI:023813.1:2001JAN12
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1773
2221

45
LI:023813.1:2001JAN12
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1453
1762

45
LI:023813.1:2001JAN12
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1432
1729

45
LI:023813.1:2001JAN12
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1439
1753

45
LI:023813.1:2001JAN12
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1445
1942

45
LI:023813.1:2001JAN12
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1454
2042

45
LI:023813.1:2001JAN12
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1409
1615

45
LI:023813.1:2001JAN12
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1422
2132

45
LI:023813.1:2001JAN12
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1425
2038

45
LI:023813.1:2001JAN12
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1433
2206

45
LI:023813.1:2001JAN12
71597347V1
1430
2185

45
LI:023813.1:2001JAN12
g791515
1327
1564

45
LI:023813.1:2001JAN12
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1331
1556

45
LI:023813.1:2001JAN12
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1325
1527

45
LI:023813.1:2001JAN12
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1327
1835

45
LI:023813.1:2001JAN12
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1325
1551

46
LI:229030.1:2001JAN12
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1
185

46
LI:229030.1:2001JAN12
4781167H1
1
172

46
LI:229030.1:2001JAN12
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1
534

46
LI:229030.1:2001JAN12
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54
179

46
LI:229030.1:2001JAN12
1432196R7
54
404

46
LI:229030.1:2001JAN12
1437682H1
432
534

47
LI:1072894.9:2001JAN12
4201204H1
1
166

48
LI:2031263.1:2001JAN12
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470
957

48
LI:2031263.1:2001JAN12
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509
731

48
LI:2031263.1:2001JAN12
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516
731

48
LI:2031263.1:2001JAN12
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373
711

48
LI:2031263.1:2001JAN12
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496
711

48
LI:2031263.1:2001JAN12
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124
709

48
LI:2031263.1:2001JAN12
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124
653

48
LI:2031263.1:2001JAN12
g4524399
543
966

48
LI:2031263.1:2001JAN12
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504
966

48
LI:2031263.1:2001JAN12
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565
965

48
LI:2031263.1:2001JAN12
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1
236

49
LI:432285.3:2001JAN12
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2437

49
LI:432285.3:2001JAN12
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2435

49
LI:432285.3:2001JAN12
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49
LI:432285.3:2001JAN12
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2056
2627

49
LI:432285.3:2001JAN12
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2072
2591

49
LI:432285.3:2001JAN12
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2604

49
LI:432285.3:2001JAN12
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2098
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49
LI:432285.3:2001JAN12
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2578

49
LI:432285.3:2001JAN12
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2628

49
LI:432285.3:2001JAN12
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1592

49
LI:432285.3:2001JAN12
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1693

49
LI:432285.3:2001JAN12
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49
LI:432285.3:2001JAN12
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1633

49
LI:432285.3:2001JAN12
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49
LI:432285.3:2001JAN12
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1203
1635

49
LI:432285.3:2001JAN12
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1222
1861

49
LI:432285.3:2001JAN12
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1240
1772

49
LI:432285.3:2001JAN12
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1248
1549

49
LI:432285.3:2001JAN12
55013979H1
1253
1552

49
LI:432285.3:2001JAN12
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1284
2060

49
LI:432285.3:2001JAN12
71346959V1
1304
1902

49
LI:432285.3:2001JAN12
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1407
1897

49
LI:432285.3:2001JAN12
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1410
1875

49
LI:432285.3:2001JAN12
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1419
2050

49
LI:432285.3:2001JAN12
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1427
2053

49
LI:432285.3:2001JAN12
71342850V1
1429
2154

49
LI:432285.3:2001JAN12
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1440
2043

49
LI:432285.3:2001JAN12
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1461
2074

49
LI:432285.3:2001JAN12
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1490
2163

49
LI:432285.3:2001JAN12
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1527
2154

49
LI:432285.3:2001JAN12
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1527
2114

49
LI:432285.3:2001JAN12
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1556
2033

49
LI:432285.3:2001JAN12
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1564
1987

49
LI:432285.3:2001JAN12
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1564
1987

49
LI:432285.3:2001JAN12
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1621
2200

49
LI:432285.3:2001JAN12
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1635
2292

49
LI:432285.3:2001JAN12
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1
423

49
LI:432285.3:2001JAN12
7946452J1
308
903

49
LI:432285.3:2001JAN12
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473
1108

49
LI:432285.3:2001JAN12
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472
982

49
LI:432285.3:2001JAN12
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474
1071

49
LI:432285.3:2001JAN12
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487
1160

49
LI:432285.3:2001JAN12
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492
1108

49
LI:432285.3:2001JAN12
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492
1096

49
LI:432285.3:2001JAN12
7644549H1
492
1058

49
LI:432285.3:2001JAN12
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493
1059

49
LI:432285.3:2001JAN12
71343349V1
493
1060

49
LI:432285.3:2001JAN12
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493
1044

49
LI:432285.3:2001JAN12
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493
986

49
LI:432285.3:2001JAN12
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504
1142

49
LI:432285.3:2001JAN12
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508
1062

49
LI:432285.3:2001JAN12
8114451H1
523
1151

49
LI:432285.3:2001JAN12
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530
783

49
LI:432285.3:2001JAN12
7674896H2
535
1005

49
LI:432285.3:2001JAN12
7644549J1
568
1058

49
LI:432285.3:2001JAN12
7994832H1
608
1170

49
LI:432285.3:2001JAN12
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619
991

49
LI:432285.3:2001JAN12
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663
1244

49
LI:432285.3:2001JAN12
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668
1004

49
LI:432285.3:2001JAN12
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668
995

49
LI:432285.3:2001JAN12
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698
1465

49
LI:432285.3:2001JAN12
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766
1344

49
LI:432285.3:2001JAN12
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841
1398

49
LI:432285.3:2001JAN12
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880
1220

49
LI:432285.3:2001JAN12
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916
1611

49
LI:432285.3:2001JAN12
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978
1602

49
LI:432285.3:2001JAN12
7655122H1
985
1333

49
LI:432285.3:2001JAN12
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999
1652

49
LI:432285.3:2001JAN12
7372249H2
1027
1652

49
LI:432285.3:2001JAN12
8262293J1
1056
1704

49
LI:432285.3:2001JAN12
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1059
1720

49
LI:432285.3:2001JAN12
71342856V1
1063
1802

49
LI:432285.3:2001JAN12
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1073
1656

49
LI:432285.3:2001JAN12
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1097
1649

49
LI:432285.3:2001JAN12
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2180
2621

49
LI:432285.3:2001JAN12
g7043837
2204
2613

49
LI:432285.3:2001JAN12
g7236448
2240
2604

49
LI:432285.3:2001JAN12
g7150142
2255
2607

50
LI:1177772.30:2001JAN12
2071589H1
714
910

50
LI:1177772.30:2001JAN12
5436974H1
770
1056

50
LI:1177772.30:2001JAN12
2847830H1
777
1037

50
LI:1177772.30:2001JAN12
898674R1
817
1377

50
LI:1177772.30:2001JAN12
898674H1
818
1129

50
LI:1177772.30:2001JAN12
898674R6
818
1355

50
LI:1177772.30:2001JAN12
3020293H1
818
1041

50
LI:1177772.30:2001JAN12
040214H1
828
1006

50
LI:1177772.30:2001JAN12
898674T6
985
1437

50
LI:1177772.30:2001JAN12
1259464T6
1283
1376

50
LI:1177772.30:2001JAN12
702465H1
1332
1553

50
LI:1177772.30:2001JAN12
3902427R8
642
1080

50
LI:1177772.30:2001JAN12
3900374H1
642
917

50
LI:1177772.30:2001JAN12
629849H1
711
951

50
LI:1177772.30:2001JAN12
3859594F8
441
1043

50
LI:1177772.30:2001JAN12
1221785H1
475
714

50
LI:1177772.30:2001JAN12
g4901036
545
1003

50
LI:1177772.30:2001JAN12
g5367522
545
1005

50
LI:1177772.30:2001JAN12
2657123H1
597
838

50
LI:1177772.30:2001JAN12
g1550158
607
777

50
LI:1177772.30:2001JAN12
1259464F6
427
895

50
LI:1177772.30:2001JAN12
4993792H1
80
355

50
LI:1177772.30:2001JAN12
2770226H1
98
344

50
LI:1177772.30:2001JAN12
5918564H1
125
390

50
LI:1177772.30:2001JAN12
2264783H1
691
921

50
LI:1177772.30:2001JAN12
831367H1
696
965

50
LI:1177772.30:2001JAN12
4750163H1
624
782

50
LI:1177772.30:2001JAN12
1614463F6
39
505

50
LI:1177772.30:2001JAN12
1614459H1
39
234

50
LI:1177772.30:2001JAN12
8054823J1
68
607

50
LI:1177772.30:2001JAN12
5206754H1
1
236

50
LI:1177772.30:2001JAN12
5206754F6
1
598

50
LI:1177772.30:2001JAN12
1549994H1
33
224

51
LI:475420.2:2001JAN12
6330686F6
555
1150

51
LI:475420.2:2001JAN12
8185916H1
586
1194

51
LI:475420.2:2001JAN12
6330686H1
762
1150

51
LI:475420.2:2001JAN12
1483315H1
835
1120

51
LI:475420.2:2001JAN12
6145789H1
2015
2462

51
LI:475420.2:2001JAN12
6149407H1
2030
2592

51
LI:475420.2:2001JAN12
8188384H1
2111
2726

51
LI:475420.2:2001JAN12
g1472143
2086
2376

51
LI:475420.2:2001JAN12
8181166H1
2955
3574

51
LI:475420.2:2001JAN12
6146433H1
2956
3163

51
LI:475420.2:2001JAN12
8186187H1
3109
3666

51
LI:475420.2:2001JAN12
6150104H1
3201
3641

51
LI:475420.2:2001JAN12
8100783H1
3279
3933

51
LI:475420.2:2001JAN12
g2016435
3531
3837

51
LI:475420.2:2001JAN12
8097088H1
3549
3991

51
LI:475420.2:2001JAN12
8097549H1
3735
4022

51
LI:475420.2:2001JAN12
6340939H1
3803
4391

51
LI:475420.2:2001JAN12
g2017181
3842
4030

51
LI:475420.2:2001JAN12
8183327H1
4017
4567

51
LI:475420.2:2001JAN12
6867808H1
4147
4675

51
LI:475420.2:2001JAN12
g2016647
4168
4297

51
LI:475420.2:2001JAN12
g6038570
4298
4714

51
LI:475420.2:2001JAN12
g1472041
4346
4716

51
LI:475420.2:2001JAN12
g1068067
4520
4680

51
LI:475420.2:2001JAN12
g2806108
4524
4706

51
LI:475420.2:2001JAN12
g1099271
4524
4661

51
LI:475420.2:2001JAN12
6330686T6
1
488

51
LI:475420.2:2001JAN12
g186532
334
4722

51
LI:475420.2:2001JAN12
g1068090
344
609

51
LI:475420.2:2001JAN12
g186542
453
4689

52
LI:017599.3:2001JAN12
2885076H1
12
63

52
LI:017599.3:2001JAN12
2885076F6
1
178

52
LI:017599.3:2001JAN12
6598423T8
1
219

52
LI:017599.3:2001JAN12
6598762H1
1
301

52
LI:017599.3:2001JAN12
6598723H1
1
299

52
LI:017599.3:2001JAN12
6598762T8
1
252

52
LI:017599.3:2001JAN12
3896326F8
31
309

52
LI:017599.3:2001JAN12
3896326H1
31
286

52
LI:017599.3:2001JAN12
5742947R9
166
322

52
LI:017599.3:2001JAN12
5742947H1
166
322

52
LI:017599.3:2001JAN12
6707259H1
254
852

52
LI:017599.3:2001JAN12
5742947T9
413
757

52
LI:017599.3:2001JAN12
2885076T6
555
883

52
LI:017599.3:2001JAN12
2938069F6
572
871

52
LI:017599.3:2001JAN12
2938069H1
572
834

52
LI:017599.3:2001JAN12
2655191T6
588
878

52
LI:017599.3:2001JAN12
2655191H1
595
884

52
LI:017599.3:2001JAN12
2655191F6
595
920

52
LI:017599.3:2001JAN12
4660519H1
626
901

52
LI:017599.3:2001JAN12
g3254496
666
920

52
LI:017599.3:2001JAN12
g3847200
675
912

52
LI:017599.3:2001JAN12
4516785H1
731
914

52
LI:017599.3:2001JAN12
7157677U1
745
904

52
LI:017599.3:2001JAN12
6598723T8
1
251

52
LI:017599.3:2001JAN12
6598762F8
1
322

52
LI:017599.3:2001JAN12
6598723F8
1
355

53
LI:030502.2:2001JAN12
8032011J1
1
572

53
LI:030502.2:2001JAN12
70930471V1
1154
1569

53
LI:030502.2:2001JAN12
70931474V1
1154
1560

53
LI:030502.2:2001JAN12
71278069V1
1154
1433

53
LI:030502.2:2001JAN12
70923503V1
1154
1258

53
LI:030502.2:2001JAN12
71277322V1
1154
1598

53
LI:030502.2:2001JAN12
70930623V1
1154
1499

53
LI:030502.2:2001JAN12
71277956V1
1154
1411

53
LI:030502.2:2001JAN12
71277472V1
1154
1287

53
LI:030502.2:2001JAN12
70929129V1
1194
1571

53
LI:030502.2:2001JAN12
71278383V1
1214
1869

53
LI:030502.2:2001JAN12
70925686V1
1295
1997

53
LI:030502.2:2001JAN12
70932060V1
1307
1972

53
LI:030502.2:2001JAN12
70931561V1
1355
1969

53
LI:030502.2:2001JAN12
71278147V1
1372
2012

53
LI:030502.2:2001JAN12
70931763V1
1389
1974

53
LI:030502.2:2001JAN12
70929419V1
1416
1975

53
LI:030502.2:2001JAN12
71278304V1
1433
2020

53
LI:030502.2:2001JAN12
70932623V1
1428
1967

53
LI:030502.2:2001JAN12
71277655V1
1457
2020

53
LI:030502.2:2001JAN12
70932226V1
407
894

53
LI:030502.2:2001JAN12
4419243F6
407
824

53
LI:030502.2:2001JAN12
4419243H1
407
662

53
LI:030502.2:2001JAN12
70931122V1
578
871

53
LI:030502.2:2001JAN12
71278467V1
667
1322

53
LI:030502.2:2001JAN12
70931820V1
768
1322

53
LI:030502.2:2001JAN12
70929807V1
777
1300

53
LI:030502.2:2001JAN12
70931538V1
1152
1537

53
LI:030502.2:2001JAN12
71278648V1
1154
1506

53
LI:030502.2:2001JAN12
70924640V1
1154
1258

53
LI:030502.2:2001JAN12
70924914V1
1154
1209

53
LI:030502.2:2001JAN12
71278312V1
1154
1609

53
LI:030502.2:2001JAN12
71277968V1
1154
1344

53
LI:030502.2:2001JAN12
70932007V1
1154
1603

53
LI:030502.2:2001JAN12
71277644V1
1154
1601

53
LI:030502.2:2001JAN12
70929617V1
1154
1589

53
LI:030502.2:2001JAN12
70931179V1
1154
1595

53
LI:030502.2:2001JAN12
3859766H1
546
838

53
LI:030502.2:2001JAN12
70929235V1
407
871

53
LI:030502.2:2001JAN12
70930027V1
407
871

53
LI:030502.2:2001JAN12
71277273V1
407
871

53
LI:030502.2:2001JAN12
g4124898
493
704

53
LI:030502.2:2001JAN12
70931645V1
479
871

53
LI:030502.2:2001JAN12
71278044V1
467
871

53
LI:030502.2:2001JAN12
g820797
1707
1980

53
LI:030502.2:2001JAN12
71277723V1
1773
2013

53
LI:030502.2:2001JAN12
2011581H1
334
449

53
LI:030502.2:2001JAN12
g874529
403
764

53
LI:030502.2:2001JAN12
g766269
403
673

53
LI:030502.2:2001JAN12
g8099152
405
1666

53
LI:030502.2:2001JAN12
70929351V1
407
871

53
LI:030502.2:2001JAN12
71277386V1
407
871

53
LI:030502.2:2001JAN12
70932434V1
407
871

53
LI:030502.2:2001JAN12
70931404V1
407
871

53
LI:030502.2:2001JAN12
70929721V1
407
871

53
LI:030502.2:2001JAN12
70929619V1
407
871

53
LI:030502.2:2001JAN12
70977552V1
1608
1967

53
LI:030502.2:2001JAN12
70932714V1
439
871

53
LI:030502.2:2001JAN12
4419243T6
1578
1922

53
LI:030502.2:2001JAN12
g767063
433
657

53
LI:030502.2:2001JAN12
70931214V1
1566
1978

53
LI:030502.2:2001JAN12
71278359V1
408
903

53
LI:030502.2:2001JAN12
71276789V1
1543
1967

53
LI:030502.2:2001JAN12
g5836378
1510
1972

53
LI:030502.2:2001JAN12
70929884V1
1530
1963

54
LI:1181337.3:2001JAN12
6934884H1
1
588

54
LI:1181337.3:2001JAN12
815760T6
459
1013

54
LI:1181337.3:2001JAN12
2184261H1
463
755

54
LI:1181337.3:2001JAN12
2184260F6
463
898

54
LI:1181337.3:2001JAN12
2255550H1
501
753

54
LI:1181337.3:2001JAN12
70451917V1
543
1024

54
LI:1181337.3:2001JAN12
70449692V1
585
903

54
LI:1181337.3:2001JAN12
70451723V1
585
900

54
LI:1181337.3:2001JAN12
2043836H1
603
733

54
LI:1181337.3:2001JAN12
g3430411
615
854

54
LI:1181337.3:2001JAN12
2184260T6
629
997

54
LI:1181337.3:2001JAN12
1493761H1
667
889

54
LI:1181337.3:2001JAN12
1496146R6
775
854

55
LI:1164672.3:2001JAN12
g1157951
2392
2839

55
LI:1164672.3:2001JAN12
7755283J1
2394
2765

55
LI:1164672.3:2001JAN12
756033H1
3356
3604

55
LI:1164672.3:2001JAN12
866648T6
2119
2286

55
LI:1164672.3:2001JAN12
g5595551
2437
2845

55
LI:1164672.3:2001JAN12
7383094H1
1810
2395

55
LI:1164672.3:2001JAN12
2894951F6
1
429

55
LI:1164672.3:2001JAN12
2894951H1
1
117

55
LI:1164672.3:2001JAN12
1634912H1
92
320

55
LI:1164672.3:2001JAN12
1816787T6
97
451

55
LI:1164672.3:2001JAN12
1816787H1
98
360

55
LI:1164672.3:2001JAN12
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98
409

55
LI:1164672.3:2001JAN12
g2036703
132
279

55
LI:1164672.3:2001JAN12
3237162H1
133
195

55
LI:1164672.3:2001JAN12
1690115F7
133
368

55
LI:1164672.3:2001JAN12
1603661H1
133
212

55
LI:1164672.3:2001JAN12
1690115T6
133
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55
LI:1164672.3:2001JAN12
g6229204
160
409

55
LI:1164672.3:2001JAN12
1986232T6
187
409

55
LI:1164672.3:2001JAN12
1986232H1
188
446

55
LI:1164672.3:2001JAN12
8262634J1
227
388

55
LI:1164672.3:2001JAN12
3564974H1
260
423

55
LI:1164672.3:2001JAN12
1643573H1
308
423

55
LI:1164672.3:2001JAN12
1643573T6
308
467

55
LI:1164672.3:2001JAN12
4051181H1
371
429

55
LI:1164672.3:2001JAN12
4052417F8
371
898

55
LI:1164672.3:2001JAN12
4051181F8
371
898

55
LI:1164672.3:2001JAN12
2995077T6
529
937

55
LI:1164672.3:2001JAN12
2995077H1
611
796

55
LI:1164672.3:2001JAN12
2995077F6
611
771

55
LI:1164672.3:2001JAN12
3751116H1
611
833

55
LI:1164672.3:2001JAN12
g5235208
849
1280

55
LI:1164672.3:2001JAN12
g2820365
863
1322

55
LI:1164672.3:2001JAN12
g1741719
871
979

55
LI:1164672.3:2001JAN12
g2264625
954
1300

55
LI:1164672.3:2001JAN12
6407448H1
976
1258

55
LI:1164672.3:2001JAN12
6407432H1
976
1185

55
LI:1164672.3:2001JAN12
437434H1
980
1080

55
LI:1164672.3:2001JAN12
3072137H1
981
1226

55
LI:1164672.3:2001JAN12
4329238H1
997
1137

55
LI:1164672.3:2001JAN12
2578767H2
1043
1285

55
LI:1164672.3:2001JAN12
g6398050
1057
1454

55
LI:1164672.3:2001JAN12
g4686426
1081
1454

55
LI:1164672.3:2001JAN12
g5635461
1095
1462

55
LI:1164672.3:2001JAN12
115832F1
1181
1581

55
LI:1164672.3:2001JAN12
g704608
1822
2014

55
LI:1164672.3:2001JAN12
2728931H1
1905
2031

55
LI:1164672.3:2001JAN12
g759773
1908
1998

55
LI:1164672.3:2001JAN12
7389323H1
2519
3019

55
LI:1164672.3:2001JAN12
g6073511
2654
3077

55
LI:1164672.3:2001JAN12
g5178940
2662
3080

55
LI:1164672.3:2001JAN12
5328272H1
1980
2215

55
LI:1164672.3:2001JAN12
g2218566
2080
2399

55
LI:1164672.3:2001JAN12
6395302H1
2096
2393

55
LI:1164672.3:2001JAN12
7617935J1
2116
2542

55
LI:1164672.3:2001JAN12
2564401H1
2135
2414

55
LI:1164672.3:2001JAN12
2895936H1
2143
2422

55
LI:1164672.3:2001JAN12
g1926078
2148
2598

55
LI:1164672.3:2001JAN12
g724400
2292
2488

55
LI:1164672.3:2001JAN12
8052194J1
2359
2934

55
LI:1164672.3:2001JAN12
7755283H1
2394
2765

55
LI:1164672.3:2001JAN12
g5178355
2665
3076

55
LI:1164672.3:2001JAN12
g4737811
2668
3077

55
LI:1164672.3:2001JAN12
g6198225
2668
3077

55
LI:1164672.3:2001JAN12
g6439534
2673
3077

55
LI:1164672.3:2001JAN12
g1925910
2674
3077

55
LI:1164672.3:2001JAN12
g4900356
2674
3084

55
LI:1164672.3:2001JAN12
g3174348
2676
3080

55
LI:1164672.3:2001JAN12
g5109634
2678
3077

55
LI:1164672.3:2001JAN12
6574952H1
2693
3153

55
LI:1164672.3:2001JAN12
g5546242
2693
3077

55
LI:1164672.3:2001JAN12
g2218494
2708
3086

55
LI:1164672.3:2001JAN12
g4108015
2709
3078

55
LI:1164672.3:2001JAN12
g2568007
2723
3083

55
LI:1164672.3:2001JAN12
g4453777
2745
3077

55
LI:1164672.3:2001JAN12
g2945277
2862
3077

55
LI:1164672.3:2001JAN12
8052322J1
2925
3389

55
LI:1164672.3:2001JAN12
7730052J1
2939
3477

55
LI:1164672.3:2001JAN12
g5754243
3014
3406

55
LI:1164672.3:2001JAN12
7617935H1
3034
3446

55
LI:1164672.3:2001JAN12
6942180H1
3097
3480

55
LI:1164672.3:2001JAN12
3069338H1
3097
3388

55
LI:1164672.3:2001JAN12
60271408D1
3154
3734

55
LI:1164672.3:2001JAN12
g1401976
3243
3617

55
LI:1164672.3:2001JAN12
g714256
3243
3352

55
LI:1164672.3:2001JAN12
7698452H1
3310
3798

55
LI:1164672.3:2001JAN12
2728368F6
1614
1862

55
LI:1164672.3:2001JAN12
2728368H1
1614
1858

55
LI:1164672.3:2001JAN12
5542670H1
1750
1961

55
LI:1164672.3:2001JAN12
g2035434
1786
2010

55
LI:1164672.3:2001JAN12
2727222H1
1516
1735

55
LI:1164672.3:2001JAN12
2727222F6
1516
1974

55
LI:1164672.3:2001JAN12
7382402H1
1614
2129

55
LI:1164672.3:2001JAN12
109051H1
1242
1454

55
LI:1164672.3:2001JAN12
g1741665
1185
1454

55
LI:1164672.3:2001JAN12
4147817H1
1209
1441

55
LI:1164672.3:2001JAN12
g6463199
1236
1454

55
LI:1164672.3:2001JAN12
3069638H1
1403
1680

56
LI:1167059.4:2001JAN12
1274804H1
1781
2014

56
LI:1167059.4:2001JAN12
1274804F1
1781
2322

56
LI:1167059.4:2001JAN12
1274804F6
1783
2384

56
LI:1167059.4:2001JAN12
6956773R8
1907
2461

56
LI:1167059.4:2001JAN12
1598831H1
1939
2119

56
LI:1167059.4:2001JAN12
909852R6
2484
2869

56
LI:1167059.4:2001JAN12
4172054F8
2513
2638

56
LI:1167059.4:2001JAN12
4172054H1
2513
2632

56
LI:1167059.4:2001JAN12
5290168H1
2513
2637

56
LI:1167059.4:2001JAN12
g2254483
2568
2639

56
LI:1167059.4:2001JAN12
909852H1
2482
2651

56
LI:1167059.4:2001JAN12
909913H1
2483
2737

56
LI:1167059.4:2001JAN12
g2569187
2335
2611

56
LI:1167059.4:2001JAN12
5688131H1
2406
2685

56
LI:1167059.4:2001JAN12
779951H1
2428
2638

56
LI:1167059.4:2001JAN12
3480033H1
2443
2633

56
LI:1167059.4:2001JAN12
5688131F6
2445
2628

56
LI:1167059.4:2001JAN12
909852T6
2483
2715

56
LI:1167059.4:2001JAN12
2074623F6
1994
2598

56
LI:1167059.4:2001JAN12
4415757H1
2021
2272

56
LI:1167059.4:2001JAN12
3945872T8
2042
2490

56
LI:1167059.4:2001JAN12
1274804T6
1990
2460

56
LI:1167059.4:2001JAN12
3096033H1
2111
2356

56
LI:1167059.4:2001JAN12
2354687H1
2143
2365

56
LI:1167059.4:2001JAN12
5153807H1
2145
2395

56
LI:1167059.4:2001JAN12
6403753F8
2150
2638

56
LI:1167059.4:2001JAN12
4312207H1
2167
2455

56
LI:1167059.4:2001JAN12
g4079119
2193
2638

56
LI:1167059.4:2001JAN12
g6038165
2219
2638

56
LI:1167059.4:2001JAN12
g4001840
2220
2641

56
LI:1167059.4:2001JAN12
70286076V1
34
142

56
LI:1167059.4:2001JAN12
1271773H1
34
269

56
LI:1167059.4:2001JAN12
70281003V1
34
567

56
LI:1167059.4:2001JAN12
70280328V1
34
503

56
LI:1167059.4:2001JAN12
1271773T6
93
480

56
LI:1167059.4:2001JAN12
70522769V1
328
686

56
LI:1167059.4:2001JAN12
g7669975
610
2821

56
LI:1167059.4:2001JAN12
411210H1
1146
1261

56
LI:1167059.4:2001JAN12
412693H1
1146
1368

56
LI:1167059.4:2001JAN12
g1324449
1192
1595

56
LI:1167059.4:2001JAN12
6280938H1
1359
1627

56
LI:1167059.4:2001JAN12
6283790H1
1359
1592

56
LI:1167059.4:2001JAN12
3329321H1
1383
1673

56
LI:1167059.4:2001JAN12
70522794V1
1387
2001

56
LI:1167059.4:2001JAN12
2286345H1
1414
1651

56
LI:1167059.4:2001JAN12
3552749H1
1432
1582

56
LI:1167059.4:2001JAN12
2673881H1
1436
1651

56
LI:1167059.4:2001JAN12
4792347F6
1
527

56
LI:1167059.4:2001JAN12
70282235V1
34
518

56
LI:1167059.4:2001JAN12
70279436V1
34
512

56
LI:1167059.4:2001JAN12
2791254H1
33
153

56
LI:1167059.4:2001JAN12
70279978V1
34
612

56
LI:1167059.4:2001JAN12
70278067V1
34
524

56
LI:1167059.4:2001JAN12
g7152964
2242
2638

56
LI:1167059.4:2001JAN12
6059623F8
2255
2544

56
LI:1167059.4:2001JAN12
g4534234
2273
2640

56
LI:1167059.4:2001JAN12
5307220H1
2276
2507

56
LI:1167059.4:2001JAN12
g4686416
2276
2622

56
LI:1167059.4:2001JAN12
1923562T6
2333
2600

[0909]

7

TABLE 6

SEQ ID NO:
Template ID
Tissue Distribution

1
LI:1983416.1:2001JAN12
Digestive System - 83%, Female Genitalia - 17%

2
LI:332263.1:2001JAN12
Connective Tissue - 14%, Musculoskeletal System - 14%, Male Genitalia - 12%

3
LI:333886.4:2001JAN12
Unclassified/Mixed - 79%

4
LI:478508.1:2001JAN12
Germ Cells - 63%, Male Genitalia - 16%, Unclassified/Mixed - 10%, Nervous System - 10%

5
LI:307470.1:2001JAN12
Nervous System - 55%, Female Genitalia - 27%, Hemic and Immune System - 18%

6
LI:058298.1:2001JAN12
Urinary Tract- 75%, Male Genitalia - 25%

7
LI:205527.5:2001JAN12
Nervous System - 100%

8
LI:231587.1:2001JAN12
Nervous System - 57%, Female Genitalia - 43%

9
LI:402919.1:2001JAN12
Germ Cells - 45%, Nervous System - 33%

10
LI:463283.1:2001JAN12
Female Genitalia - 50%, Respiratory System - 50%

11
LI:072560.1:2001JAN12
Female Genitalia - 58%, Nervous System - 16%, Endocrine System - 15%

12
LI:1953096.1:2001JAN12
Respiratory System - 100%

13
LI:1076016.1:2001JAN12
Sense Organs - 69%, Liver - 11%, Pancreas - 10%

14
LI:2082796.1:2001JAN12
Hemic and Immune System - 100%

15
LI:335681.3:2001JAN12
Unclassified/Mixed 30%, Exocrine Glands - 28%, Male Genitalia - 15%

16
LI:214150.1:2001JAN12
Pancreas - 50%, Nervous System - 27%, Male Genitalia - 23%

17
LI:322783.15:2001JAN12
Connective Tissue - 87%

18
LI:422993.1:2001JAN12
Liver - 46%, Sense Organs - 40%

19
LI:1172885.1:2001JAN12
Exocrine Glands - 48%, Male Genitalia - 14%, Digestive System - 14%, Nervous System - 14%

20
LI:1088359.1:2001JAN12
Respiratory System - 16%, Embryonic Structures - 16%, Female Genitalia - 13%

21
LI:813422.1:2001JAN12
Stomatognathic System - 33%, Sense Organs - 22%, Cardiovascular System - 15%

22
LI:1186426.1:2001JAN12
Musculoskeletal System - 22%, Digestive System - 15%, Endocrine System - 13%

23
LI:1182817.1:2001JAN12
Stomatognathic System - 20%, Sense Organs - 13%

24
LI:1170153.9:2001JAN12
Female Genitalia - 88%, Male Genitalia - 13%

25
LI:1171553.1:2001JAN12
Urinary Tract- 27%, Sense Organs - 19%, Embryonic Structures - 13%

26
LI:2121978.1:2001JAN12
Hemic and Immune System - 100%

27
LI:1174292.5:2001JAN12
Urinary Tract- 10%

28
LI:1179173.1:2001JAN12
Respiratory System - 33%, Musculoskeletal System - 14%

29
LI:2122025.1:2001JAN12
Unclassified/Mixed - 55%, Female Genitalia - 34%

30
LI:2049224.1:2001JAN12
Endocrine System - 30%, Cardiovascular System - 25%, Exocrine Glands - 25%

31
LI:758541.1:2001JAN12
Exocrine Glands -51%, Unclassified/Mixed - 13%

32
LI:137815.1:2001JAN12
Skin - 31%, Cardiovascular System - 15%, Sense Organs - 13%

33
LI:335097.1:2001JAN12
Embryonic Structures - 24%, Nervous System - 24%, Musculoskeletal System - 16%

34
LI:232059.2:2001JAN12
Urinary Tract - 51%, Endocrine System - 12%

35
LI:400109.2:2001JAN12
Embryonic Structures - 17%, Germ Cells - 16%

36
LI:329770.1:2001JAN12
Liver - 90%

37
LI:898841.9:2001JAN12
Endocrine System - 89%, Nervous System - 11%

38
LI:1183848.3:2001JAN12
Pancreas - 100%

39
LI:2037121.1:2001JAN12
Female Genitalia - 51%, Unclassified/Mixed - 23%, Musculoskeletal System - 12%

40
LI:356090.1:2001JAN12
Respiratory System - 91%

41
LI:212142.1:2001JAN12
Urinary Tract - 64%, Digestive System - 19%, Musculoskeletal System - 10%

42
LI:1096706.1:2001JAN12
Nervous System - 100%

43
LI:012622.1:2001JAN12
Unclassified/Mixed - 41%, Endocrine System - 17%, Pancreas - 16%

44
LI:1171095.29:2001JAN12
Hemic and Immune System - 31%, Digestive System - 12%

45
LI:023813.1:2001JAN12
Hemic and Immune System - 23%, Urinary Tract - 16%, Digestive System - 10%

46
LI:229030.1:2001JAN12
Pancreas - 65%, Digestive System - 18%, Respiratory System - 18%

47
LI:1072894.9:2001JAN12
Nervous System - 100%

48
LI:2031263.1:2001JAN12
Unclassified/Mixed - 54%, Germ Cells - 21%, Digestive System - 12%

49
LI:432285.3:2001JAN12
Stomatognathic System - 34%, Connective Tissue - 25%, Cardiovascular System - 13%

50
LI:1177772.30:2001JAN12
Sense Organs - 39%, Respiratory System - 11%

51
LI:475420.2:2001JAN12
Sense Organs - 82%, Endocrine System - 15%

52
LI:017599.3:2001JAN12
Respiratory System - 50%, Cardiovascular System - 23%, Pancreas - 13%

53
LI:030502.2:2001JAN12
Germ Cells - 68%, Liver - 16%

54
LI:1181337.3:2001JAN12
Digestive System - 51%, Unclassified/Mixed - 21%, Female Genitalia - 13%, Male Genitalia - 13%

55
LI:1164672.3:2001JAN12
Female Genitalia - 36%, Urinary Tract - 16%, Skin - 11%

56
LI:1167059.4:2001JAN12
Urinary Tract - 28%, Skin - 16%

[0910]

8

TABLE 7

SEQ

ID NO:
Frame
Length
Start
Stop
GI Number
Probability Score
Annotation

57
1
83
1
249
g3335126
3.00E−11
CI-KFYI protein

57
1
83
1
249
g2909860
3.00E−11
NADH-ubiquinone oxidoreductase subunit CI-KFYI

57
1
83
1
249
g12858549
2.00E−05
putative

59
2
144
191
622
g31207
9.00E−16
put.thyroid hormone receptor

59
2
144
191
622
g180253
9.00E−16
c-erbA

59
2
144
191
622
g4426901
1.00E−13
thyroid hormone receptor betal

60
3
169
246
752
g12840055
1.00E−29
putative

60
3
169
246
752
g12838464
2.00E−22
putative

60
3
169
246
752
g12858779
6.00E−08
putative

61
1
66
556
753
g16551806
8.00E−18
(AK056408) unnamed protein product

61
1
66
556
753
g16041132
4.00E−17
hypothetical protein

61
1
66
556
753
g7020292
1.00E−16
unnamed protein product

62
1
154
277
738
g36615
2.00E−57
serine/threonine protein kinase

62
1
154
277
738
g6580288
4.00E−49
contains similarity to Pfam domain: PF00069 (Eukaryotic protein kinase

domain), Score = 307.5, E-value = 5.1e−89, N = 1

62
1
154
277
738
g7297009
2.00E−48
CG7236 gene product

64
2
77
179
409
g14043238
2.00E−09
Similar to hypothetical protein PRO1722

64
2
77
179
409
g403460
4.00E−09
transformation-related protein

64
2
77
179
409
g11493483
5.00E−09
PRO2550

65
2
258
281
1054
g5106978
1.00E−71
homeobox protein GBX2

65
2
258
281
1054
g755767
3.00E−70
Stra7

65
2
258
281
1054
g3676057
3.00E−70
gastrulation-brain-homeobox-2

68
3
61
39
221
g15341934
4.00E−05
Unknown (protein for MGC: 8826)

70
1
109
259
585
g4323152
1.00E−30
Ets-protein Spi-C

71
3
276
333
1160
g15986451
3.00E−49
Kruppel-type zinc-finger protein ZIM3

71
3
276
333
1160
g16551859
5.00E−49
(AK056452) unnamed protein product

71
3
276
333
1160
g14456631
2.00E−47
dJ54B20.4 (novel KRAB box containing C2H2 type zinc finger protein)

74
1
205
547
1161
g10440136
4.00E−96
unnamed protein product

74
1
205
547
1161
g12846755
1.00E−94
putative

74
1
205
547
1161
g12840994
1.00E−94
putative

75
3
66
393
590
g16552067
7.00E−22
(AK056615) unnamed protein product

75
3
66
393
590
g16549180
4.00E−19
(AK054606) unnamed protein product

75
3
66
393
590
g10437767
1.00E−18
unnamed protein product

76
1
144
1
432
g55483
2.00E−44
Zfp-1 protein (AA 1-424)

76
1
144
1
432
g387162
2.00E−44
finger protein (put.); putative

76
1
144
1
432
g5757626
5.00E−26
C2H2 zinc finger protein

78
1
263
1
789
g506502
1.00E−141
NK10

78
1
263
1
789
g16552044
1.00E−138
(AK056596) unnamed protein product

78
1
263
1
789
g488555
1.00E−92
zinc finger protein ZNF135

79
3
884
3
2654
g498152
0
ha0946 protein is Kruppel-related.

79
3
884
3
2654
g11181880
0
bA1021O19.1 (zinc finger protein 33a (KOX 31))

79
3
884
3
2654
g938238
0
ZNF11B

81
3
256
1101
1868
g16549180
6.00E−40
(AK054606) unnamed protein product

81
3
256
1101
1868
g14250716
2.00E−28
Unknown (protein for MGC: 13310)

81
3
256
1101
1868
g2224593
3.00E−26
KIAA0326

83
2
566
134
1831
g2384653
0
Krueppel family zinc finger protein

83
2
566
134
1831
g4559318
0
BC273239_1

83
2
566
134
1831
g16306806
0
(BC006528) zinc finger protein 43 (HTF6)

84
2
520
98
1657
g6118383
0
zinc finger protein ZNF223

84
2
520
98
1657
g10835284
0
Zinc finger protein ZNF223 (amino acids 82-482)

84
2
520
98
1657
g6598826
0
ZNF230-like

85
3
233
513
1211
g2689444
6.00E−76
ZNF134

85
3
233
513
1211
g16552811
2.00E−69
(AK057209) unnamed protein product

85
3
233
513
1211
g488553
8.00E−69
zinc finger protein ZNF134

86
1
141
22
444
g7023216
3.00E−55
unnamed protein product

86
1
141
22
444
g7023703
6.00E−30
unnamed protein product

86
1
141
22
444
g16878329
9.00E−22
(BC017357) Unknown (protein for MGC: 29628)

87
3
112
42
377
g5679576
2.00E−62
zinc finger 41

87
3
112
42
377
g340444
2.00E−62
zinc finger protein 41

87
3
112
42
377
g15787775
2.00E−62
bB479F17.3 (zinc finger protein 41)

88
3
839
393
2909
g6409379
0
zinc finger protein ZNF229

88
3
839
393
2909
g10864174
0
ZNF229 (amino acids 1-420)

88
3
839
393
2909
g6984172
0
zinc finger protein ZNF226

91
1
77
370
600
g1389766
3.00E−13
unknown

91
1
77
370
600
g6855613
5.00E−13
PRO0974

91
1
77
370
600
g9929935
1.00E−09
hypothetical protein

92
1
70
505
714
g12698182
1.00E−19
hypothetical protein

92
1
70
505
714
g10439739
9.00E−19
unnamed protein product

92
1
70
505
714
g14388331
6.00E−18
hypothetical protein

97
1
61
115
297
g1871540
8.00E−06
plakophilin 2b

97
1
61
115
297
g13623263
2.00E−05
Similar to inhibitor of kappa light polypeptide gene enhancer in B-cells,

kinase beta

99
1
197
400
990
g3724141
2.00E−61
myosin I

99
1
197
400
990
g7297714
6.00E−37
Myo31DF gene product

99
1
197
400
990
g466256
6.00E−37
myosin-IA

102
3
88
171
434
g10437485
4.00E−21
unnamed protein product

102
3
88
171
434
g10437569
1.00E−20
unnamed protein product

102
3
88
171
434
g10441877
6.00E−19
unknown

103
3
51
9
161
g8926741
4.00E−08
hypothetical protein

103
3
51
9
161
g8926693
4.00E−08
hypothetical protein

103
3
51
9
161
g6841518
4.00E−08
HSPC148

105
3
105
939
1253
g16877350
7.00E−09
(BC016928) ornithine aminotransferase (gyrate atrophy)

105
3
105
939
1253
g386987
7.00E−09
ornithine aminotransferase

105
3
105
939
1253
g34138
7.00E−09
precursor (AA −35 to 404)

108
3
401
954
2156
g386835
0
interstitial retinol-binding protein precursor

108
3
401
954
2156
g307075
0
retinol-binding protein

108
3
401
954
2156
g307074
0
IRBP precursor

111
3
183
6
554
g1196425
5.00E−32
envelope protein

111
3
183
6
554
g323899
2.00E−06
envelope protein precursor

111
3
183
6
554
g10946419
2.00E−06
envelope protein

112
2
106
3068
3385
g6688950
7.00E−29
viral polyprotein

112
2
106
3068
3385
g6688948
7.00E−29
viral polypeptide

112
2
106
3068
3385
g6688946
7.00E−29
viral polypeptide

113
3
370
51
1160
g7688657
0
septin 10

113
3
370
51
1160
g10432915
0
unnamed protein product

113
3
370
51
1160
g7023141
1.00E−146
unnamed protein product

[0911]

9

TABLE 8

Program
Description
Reference
Parameter Threshold

ABIFACTURA
A program that removes vector
Applied Biosystems,

sequences and masks ambiguous bases
Foster City, CA.

in nucleic acid sequences.

ABI/PARACEL
A Fast Data Finder useful in
Applied Biosystems,
Mismatch <50%

FDF
comparing and annotating
Foster City, CA; Paracel

amino acid or nucleic acid
Inc., Pasadena, CA.

sequences.

ABI
A program that assembles
Applied Biosystems,

AutoAssembler
nucleic acid sequences.
Foster City, CA.

BLAST
A Basic Local Alignment Search
Altschul, S. F. et al.
ESTs: Probability value = 1.0E−8 or less;

Tool useful in sequence
(1990) J. Mol. Biol. 215:
Full Length sequences: Probability value =

similarity search for amino
403-410; Altschul,
1.0E−10 or less

acid and nucleic acid
S. F. et al. (1997)

sequences. BLAST includes
Nucleic Acids

five functions: blastp,
Res. 25:3389-3402.

blastn, blastx, tblastn, and

tblastx.

FASTA
A Pearson and Lipman algorithm
Pearson, W. R. and D. J.
ESTs: fasta E value = 1.06E−6; Assembled

that searches for similarity
Lipman (1988) Proc.
ESTs: fasta Identity = 95% or greater and

between a query sequence and a
Natl. Acad Sci. USA
Match length = 200 bases or greater; fastx E

group of sequences of the same
85:2444-2448;
value = 1.0E−8 or less; Full Length

type. FASTA comprises as least
Pearson, W. R. (1990)
sequences: fastx score = 100 or greater

five functions: fasta, tfasta,
Methods Enzymol.

fastx, tfastx, and ssearch.
183:63-98; and

Smith, T. F. and M. S. Waterman

(1981) Adv. Appl. Math. 2:482-489.

BLIMPS
A BLocks IMProved Searcher that
Henikoff, S. and J. G.
Probability value = 1.0E−3 or less

matches a sequence against those
Henikoff (1991) Nucleic

in BLOCKS, PRINTS, DOMO, PRODOM,
Acids Res. 19:6565-6572;

and PFAM databases to search for
Henikoff, J. G. and S.

gene families, sequence homology,
Henikoff (1996) Methods

and structural fingerprint regions.
Enzymol. 266:88-105;

and Attwood, T. K. et al. (1997)

J. Chem. Inf. Comput. Sci.

37:417-424.

HMMER
An algorithm for searching a query
Krogh, A. et al. (1994) J.
PFAM hits: Probability value = 1.0E−3 or

sequence against hidden Markov model
Mol. Biol. 235:1501-
less;

(HMM)-based databases of protein
1531; Sonnhammer, E. L. L.
Signal peptide hits: Score = 0 or greater

family consensus sequences, such as
et al. (1988) Nucleic

PFAM.
Acids Res. 26:320-322;

Durbin, R. et al. (1998)

Our World View, in a Nutshell,

Cambridge Univ. Press,

pp. 1-350.

ProfileScan
An algorithm that searches for
Gribskov, M. et al. (1988)
Normalized quality score ≧ GCG-specified

structural and sequence motifs
CABIOS 4:61-66;
“HIGH” value for that particular Prosite

in protein sequences that match
Gribskov, M. et al. (1989)
motif. Generally, score = 1.4-2.1.

sequence patterns
Methods Enzymol.

defined in Prosite.
183:146-159; Bairoch, A.

et al. (1997) Nucleic

Acids Res. 25:217-221.

Phred
A base-calling algorithm that
Ewing, B. et al. (1998)

examines automated sequencer
Genome Res. 8:175-185;

traces with high sensitivity
Ewing, B. and P. Green (1998)

and probability.
Genome Res. 8:186-194.

Phrap
A Phils Revised Assembly Program
Smith, T. F. and M. S. Waterman
Score = 120 or greater;

including SWAT and CrossMatch,
(1981) Adv. Appl. Math. 2:482-489;
Match length = 56 or greater

programs based on efficient
Smith, T. F. and M. S. Waterman

implementation of the Smith-Waterman
(1981) J. Mol. Biol. 147:195-197;

algorithm, useful in searching
and Green, P., University of

sequence homology and
Washington, Seattle, WA.

assembling DNA sequences.

Consed
A graphical tool for viewing and
Gordon, D. et al. (1998) Genome

editing Phrap assemblies.
Res. 8:195-202.

SPScan
A weight matrix analysis program
Nielson, H. et al. (1997) Protein
Score = 3.5 or greater

that scans protein sequences for
Engineering 10:1-6; Claverie,

the presence of secretory signal peptides.
J. M. and S. Audic (1997)

CABIOS 12:431-439.

TMAP
A program that uses weight matrices
Persson, B. and P. Argos (1994)

to delineate transmembrane segments on
J. Mol. Biol. 237:182-192;

protein sequences and determine
Persson, B. and P. Argos (1996)

orientation.
Protein Sci. 5:363-371.

TMHMMER
A program that uses a hidden Markov
Sonnhammer, E. L. et al. (1998)

model (HMM) to delineate transmembrane
Proc. Sixth Intl. Conf. On

segments on protein sequences and
Intelligent Systems for Mol.

determine orientation.
Biol., Glasgow et al., eds.,

The Am. Assoc. for

Artificial Intelligence (AAAI)

Press, Menlo Park, CA,

and MIT Press, Cambridge, MA,

pp. 175-182.

Motifs
A program that searches amino acid
Bairoch, A. et al. (1997)

sequences for patterns that matched
Nucleic Acids Res. 25:217-221;

those defined in Prosite.
Wisconsin Package Program

Manual, version 9, page M51-59,

Genetics

Computer Group, Madison, WI.

[0912]

Molecules for diagnostics and therapeutics

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