Claims
- 1. A method for monitoring differential expression of a plurality of genes in a first Bacillus cell relative to expression of the same genes in one or more second Bacillus cells, comprising:
(a) adding a mixture of labeled nucleic acid probes isolated from the Bacillus cells to a substrate containing an array of Bacillus GSTs under conditions where the nucleic acids hybridize to complementary sequences of the Bacillus GSTs in the array, wherein the nucleic acids from the first Bacillus cell and the one or more second Bacillus cells are labeled with a first reporter and one or more different second reporters, respectively; and (b) examining the array under conditions wherein the relative expression of the genes in the Bacillus cells is determined by the observed hybridization reporter signal of each spot in the array in which (i) the Bacillus GSTs in the array that hybridize to the nucleic acids obtained from either the first or the one or more second Bacillus cells produce a distinct first hybridization reporter signal or one or more second hybridization reporter signals, respectively, and (ii) the Bacillus GSTs in the array that hybridize to the nucleic acids obtained from both the first and one or more second Bacillus cells produce a distinct combined hybridization reporter signal.
- 2. The method of claim 1, wherein the Bacillus GSTs are selected from the group consisting of Bacillus alkalophilus, Bacillus amyloliquefaciens, Bacillus brevis, Bacillus circulans, Bacillus clausii, Bacillus coagulans, Bacillus firmus, Bacillus lautus, Bacillus lentus, Bacillus licheniformis, Bacillus megaterium, Bacillus pumilus, Bacillus stearothermophilus, Bacillus subtilis, and Bacillus thuringiensis GSTs.
- 3. The method of claim 1, wherein the Bacillus GSTs are Bacillus licheniformis GSTs.
- 4. The method of claim 3, wherein the Bacillus licheniformis GSTs are selected from the group consisting of SEQ ID NOs. 1-4448, nucleic acid fragments of SEQ ID NOs. 1-4448, and nucleic acid sequences having at least 85% homology to SEQ ID NOs. 1-4448.
- 5. The method of claim 3, wherein the Bacillus licheniformis GSTs are SEQ ID NOs. 1-4448.
- 6. The method of claim 3, wherein the Bacillus licheniformis GSTs are nucleic acid fragments of SEQ ID NOs. 1-4448.
- 7. The method of claim 3, wherein the Bacillus licheniformis GSTs are nucleic acid sequences having at least 85% homology to SEQ ID NOs. 1-4448.
- 8. The method of claim 7, wherein the Bacillus licheniformis GSTs are nucleic acid sequences having at least 90% homology to SEQ ID NOs. 1-4448.
- 9. The method of claim 8, wherein the Bacillus licheniformis GSTs are nucleic acid sequences having at least 95% homology to SEQ ID NOs. 1-4448.
- 10. The method of claim 1, wherein the Bacillus GSTs are Bacillus clausii GSTs.
- 11. The method of claim 10, wherein the Bacillus clausii GSTs are selected from the group consisting of SEQ ID NOs. 4449-8481, nucleic acid fragments of SEQ ID NOs. 4449-8481, and nucleic acid sequences having at least 85% homology to SEQ ID NOs. 4449-8481.
- 12. The method of claim 10, wherein the Bacillus clausii GSTs are SEQ ID NOs. 4449-8481.
- 13. The method of claim 10, wherein the Bacillus clausii GSTs are nucleic acid fragments of SEQ ID NOs. 4449-8481.
- 14. The method of claim 10, wherein the Bacillus clausii GSTs are nucleic acid sequences having at least 85% homology to SEQ ID NOs. 4449-8481.
- 15. The method of claim 14, wherein the Bacillus clausii GSTs are nucleic acid sequences having at least 90% homology to SEQ ID NOs. 4449-8481.
- 16. The method of claim 15, wherein the Bacillus clausii GSTs are nucleic acid sequences having at least 95% homology to SEQ ID NOs. 4449-8481.
- 17. The method of any of claims 1-16, wherein the Bacillus cells are selected from the group consisting of a Bacillus alkalophilus, Bacillus amyloliquefaciens, Bacillus brevis, Bacillus circulars, Bacillus clausii, Bacillus coagulans, Bacillus firmus, Bacillus lautus, Bacillus lentus, Bacillus licheniformis, Bacillus megaterium, Bacillus pumilus, Bacillus stearothermophilus, Bacillus subtilis, and Bacillus thuringiensis cell.
- 18. The method of any of claims 1-17, wherein the Bacillus cells are the same cell.
- 19. The method of any of claims 1-17, wherein the first Bacillus cell is a Bacillus licheniformis or Bacillus clausii cell.
- 20. The method of claim 19, wherein the Bacillus licheniformis cells are Bacillus licheniformis ATCC 14580 cells.
- 21. The method of claim 19, wherein the Bacillus clausii cells are Bacillus clausii NCIB 10309 cells.
- 22. The method of any of claims 1-17, wherein the one or more second Bacillus cells are Bacillus licheniformis or Bacillus clausii cells.
- 23. The method of claim 22, wherein the Bacillus licheniformis cells are Bacillus licheniformis ATCC 14580 cells.
- 24. The method of claim 22, wherein the Bacillus clausii cells are Bacillus clausii NCIB 10309 cells.
- 25. The method of any of claims 1-17, wherein the Bacillus cells are one or more different cells.
- 26. The method of any of claims 1-25, wherein the hybridization conditions are selected from the group consisting of very low, low, low-medium, medium, medium-high, high, and very high stringency conditions.
- 27. The method of any of claims 1-26, wherein the reporters are calorimetric, radioactive, or fluorescent reporters.
- 28. A computer readable medium having recorded thereon an array of Bacillus GSTs.
- 29. The computer readable medium of claim 28, wherein the Bacillus GSTs are selected from the group consisting of Bacillus alkalophilus, Bacillus amyloliquefaciens, Bacillus brevis, Bacillus circulans, Bacillus clausii, Bacillus coagulans, Bacillus firmus, Bacillus lautus, Bacillus lentus, Bacillus licheniformis, Bacillus megaterium, Bacillus pumilus, Bacillus stearothermophilus, Bacillus subtilis, and Bacillus thuringiensis GSTs.
- 30. The computer readable medium of claim 28, wherein the Bacillus GSTs are Bacillus licheniformis GSTs.
- 31. The computer readable medium of claim 30, wherein the Bacillus licheniformis GSTs are selected from the group consisting of SEQ ID NOs. 1-4448, nucleic acid fragments of SEQ ID NOs. 1-4448, and nucleic acid sequences having at least 85% homology to SEQ ID NOs. 1-4448.
- 32. The computer readable medium of claim 30, wherein the Bacillus licheniformis GSTs are SEQ ID NOs. 1-4448.
- 33. The computer readable medium of claim 30, wherein the Bacillus licheniformis GSTs are nucleic acid fragments of SEQ ID NOs. 1-4448.
- 34. The computer readable medium of claim 30, wherein the Bacillus licheniformis GSTs are nucleic acid sequences having at least 85% homology to SEQ ID NOs. 1-4448.
- 35. The computer readable medium of claim 34, wherein the Bacillus licheniformis GSTs are nucleic acid sequences having at least 90% homology to SEQ ID NOs. 1-4448.
- 36. The computer readable medium of claim 35, wherein the Bacillus licheniformis GSTs are nucleic acid sequences having at least 95% homology to SEQ ID NOs. 1-4448.
- 37. The computer readable medium of claim 28, wherein the Bacillus GSTs are Bacillus clausii GSTs.
- 38. The computer readable medium of claim 37, wherein the Bacillus clausii GSTs are selected from the group consisting of SEQ ID NOs. 4449-8481, nucleic acid fragments of SEQ ID NOs. 4449-8481, and nucleic acid sequences having at least 85% homology to SEQ ID NOs. 4449-8481.
- 39. The computer readable medium of claim 37, wherein the Bacillus clausii GSTs are SEQ ID NOs. 4449-8481.
- 40. The computer readable medium of claim 37, wherein the Bacillus clausii GSTs are nucleic acid fragments of SEQ ID NOs. 4449-8481.
- 41. The computer readable medium of claim 37, wherein the Bacillus clausii GSTs are nucleic acid sequences having at least 85% homology to SEQ ID NOs. 4449-8481.
- 42. The computer readable medium of claim 41, wherein the Bacillus clausii GSTs are nucleic acid sequences having at least 90% homology to SEQ ID NOs. 4449-8481.
- 43. The computer readable medium of claim 42, wherein the Bacillus clausii GSTs are nucleic acid sequences having at least 95% homology to SEQ ID NOs. 4449-8481.
- 44. The computer readable medium of any of claims 28-43, wherein the medium is selected from the group consisting of a floppy dick, a hard disk, random access memory (RAM), read only memory (ROM), and CD-ROM.
- 45. A computer-based system for monitoring differential expression of a plurality of genes in a first Bacillus cell relative to expression of the same genes in one or more second Bacillus cells comprising the following elements:
(a) a data storage means comprising Bacillus GSTs; (b) a search means for comparing a target sequence to a Bacillus GST sequence of the data storage means of step (a) to identify homologous sequences; and (c) a retrieval means for obtaining the homologous sequence(s) of step (b).
- 46. The computer-based system of claim 45, wherein the Bacillus GSTs are selected from the group consisting of Bacillus alkalophilus, Bacillus amyloliquefaciens, Bacillus brevis, Bacillus circulars, Bacillus clausii, Bacillus coagulans, Bacillus firmus, Bacillus lautus, Bacillus lentus, Bacillus licheniformis, Bacillus megaterium, Bacillus pumilus, Bacillus stearothermophilus, Bacillus subtilis, and Bacillus thuringiensis GSTs.
- 47. The computer-based system of claim 45, wherein the Bacillus GSTs are Bacillus licheniformis GSTs.
- 48. The computer-based system of claim 47, wherein the Bacillus licheniformis GSTs are selected from the group consisting of SEQ ID NOs. 1-4448, nucleic acid fragments of SEQ ID NOs. 1-4448, and nucleic acid sequences having at least 85% homology to SEQ ID NOs. 1-4448.
- 49. The computer-based system of claim 47, wherein the Bacillus licheniformis GSTs are SEQ ID NOs. 1-4448.
- 50. The computer-based system of claim 47, wherein the Bacillus licheniformis GSTs are nucleic acid fragments of SEQ ID NOs. 1-4448.
- 51. The computer-based system of claim 47, wherein the Bacillus licheniformis GSTs are nucleic acid sequences having at least 85% homology to SEQ ID NOs. 1-4448.
- 52. The computer-based system of claim 51, wherein the Bacillus licheniformis GSTs are nucleic acid sequences having at least 90% homology to SEQ ID NOs. 1-4448.
- 53. The computer-based system of claim 52, wherein the Bacillus licheniformis GSTs are nucleic acid sequences having at least 95% homology to SEQ ID NOs. 1-4448.
- 54. The computer-based system of claim 45, wherein the Bacillus GSTs are Bacillus clausii GSTs.
- 55. The computer-based system of claim 54, wherein the Bacillus clausii GSTs are selected from the group consisting of SEQ ID NOs. 4449-8481, nucleic acid fragments of SEQ ID NOs. 4449-8481, and nucleic acid sequences having at least 85% homology to the sequences of SEQ ID NOs. 4449-8481.
- 56. The computer-based system of claim 54, wherein the Bacillus clausii GSTs are SEQ ID NOs. 4449-8481.
- 57. The computer-based system of claim 54, wherein the Bacillus clausii GSTs are nucleic acid fragments of SEQ ID NOs. 4449-8481.
- 58. The computer-based system of claim 54, wherein the Bacillus clausii GSTs are nucleic acid sequences having at least 85% homology to SEQ ID NOs. 4449-8481.
- 59. The computer-based system of claim 58, wherein the Bacillus clausii GSTs are nucleic acid sequences having at least 90% homology to SEQ ID NOs. 4449-8481.
- 60. The computer-based system of claim 59, wherein the Bacillus clausii GSTs are nucleic acid sequences having at least 95% homology to SEQ ID NOs. 4449-8481.
- 61. The computer-based system of any of claims 45-60, wherein the Bacillus cells are selected from the group consisting of a Bacillus alkalophilus, Bacillus amyloliquefaciens, Bacillus brevis, Bacillus circulars, Bacillus clausii, Bacillus coagulans, Bacillus firmus, Bacillus lautus, Bacillus lentus, Bacillus licheniformis, Bacillus megaterium, Bacillus pumilus, Bacillus stearothermophilus, and Bacillus thuringiensis cell.
- 62. The computer-based system of any of claims 45-60, wherein the Bacillus cells are the same cell.
- 63. The computer-based system of any of claims 45-60, wherein the first Bacillus cell is a Bacillus licheniformis or Bacillus clausii cell.
- 64. The computer-based system of claim 63, wherein the Bacillus licheniformis cells are Bacillus licheniformis ATCC 14580 cells.
- 65. The computer-based system of claim 63, wherein the Bacillus clausii cells are Bacillus clausii NCIB 10309 cells.
- 66. The computer-based system of any of claims 45-60, wherein the one or more second Bacillus cells are Bacillus licheniformis or Bacillus clausii cells.
- 67. The computer-based system of claim 66, wherein the Bacillus licheniformis cells are Bacillus licheniformis ATCC 14580 cells.
- 68. The computer-based system of claim 66, wherein the Bacillus clausii cells are Bacillus clausii NCIB 10309 cells.
- 69. The computer-based system of any of claims 45-60, wherein the Bacillus cells are one or more different cells.
- 70. A substrate comprising an array of Bacillus GSTs.
- 71. The substrate of claim 70, wherein the Bacillus GSTs are selected from the group consisting of Bacillus alkalophilus, Bacillus amyloliquefaciens, Bacillus brevis, Bacillus circulans, Bacillus clausii, Bacillus coagulans, Bacillus firmus, Bacillus lautus, Bacillus lentus, Bacillus licheniformis, Bacillus megaterium, Bacillus pumilus, Bacillus stearothermophilus, Bacillus subtilis, and Bacillus thuringiensis GSTs.
- 72. The substrate of claim 70, wherein the Bacillus GSTs are Bacillus licheniformis GSTs.
- 73. The substrate of claim 72, wherein the Bacillus licheniformis GSTs are selected from the group consisting of SEQ ID NOs. 1-4448, nucleic acid fragments of SEQ ID NOs. 1-4448, and nucleic acid sequences having at least 85% homology to SEQ ID NOs. 1-4448.
- 74. The substrate of claim 72, wherein the Bacillus licheniformis GSTs are SEQ ID NOs. 1-4448.
- 75. The substrate of claim 72, wherein the Bacillus licheniformis GSTs are nucleic acid fragments of SEQ ID NOs. 1-4448.
- 76. The substrate of claim 72, wherein the Bacillus licheniformis GSTs are nucleic acid sequences having at least 85% homology to SEQ ID NOs. 1-4448.
- 77. The substrate of claim 76, wherein the Bacillus licheniformis GSTs are nucleic acid sequences having at least 90% homology to SEQ ID NOs. 1-4448.
- 78. The substrate of claim 77, wherein the Bacillus licheniformis GSTs are nucleic acid sequences having at least 95% homology to SEQ ID NOs. 1-4448.
- 79. The substrate of claim 70, wherein the Bacillus GSTs are Bacillus clausii GSTs.
- 80. The substrate of claim 79, wherein the Bacillus clausii GSTs are selected from the group consisting of SEQ ID NOs. 4449-8481, nucleic acid fragments of SEQ ID NOs. 4449-8481, and nucleic acid sequences having at least 85% homology to SEQ ID NOs. 4449-8481.
- 81. The substrate of claim 79, wherein the Bacillus clausii GSTs are SEQ ID NOs. 4449-8481.
- 82. The substrate of claim 79, wherein the Bacillus clausii GSTs are nucleic acid fragments of SEQ ID NOs. 4449-8481.
- 83. The substrate of claim 79, wherein the Bacillus clausii GSTs are nucleic acid sequences having at least 85% homology to SEQ ID NOs. 4449-8481.
- 84. The substrate of claim 83, wherein the Bacillus clausii GSTs are nucleic acid sequences having at least 90% homology to SEQ ID NOs. 4449-8481.
- 85. The substrate of claim 84, wherein the Bacillus clausii GSTs are nucleic acid sequences having at least 95% homology to SEQ ID NOs. 4449-8481.
CROSS-REFERENCE TO RELATED APPLICATIONS
[0001] This application is a continuation-in-part of pending U.S. application Ser. No. 09/680,598 filed on Oct. 6, 2000, and claims priority from U.S. provisional application Serial No. 60/082,217 filed on Mar. 27, 2001, which applications are fully incorporated herein by reference.
Provisional Applications (1)
|
Number |
Date |
Country |
|
60279526 |
Mar 2001 |
US |
Continuation in Parts (1)
|
Number |
Date |
Country |
Parent |
09680598 |
Oct 2000 |
US |
Child |
09974300 |
Oct 2001 |
US |