Claim 1

A method of identifying a stress condition to which a plant cell has been exposed, the method comprising:
a) contacting nucleic acid molecules representative of expressed polynucleotides in the plant cell with an array of probes representative of the plant cell genome; and
b) detecting a profile of expressed polynucleotides in the plant cell characteristic of a stress response, thereby identifying the stress condition to which the plant cell was exposed.

Claim 18

A method for determining whether a test plant has been exposed to an abiotic stress, the method comprising

• contacting nucleic acid molecules representative of expressed polynucleotides in cells of the test plant with at least one nucleic acid probe under conditions suitable for selective hybridization to a complementary nucleotide sequence, wherein

the probe comprises at least 15 nucleotides of a plant stress-regulated gene, provided said gene does not comprise a nucleotide sequence of a polynucleotide as set forth in any of SEQ ID NOS:156, 229, 233, 558, 573, 606, 635, 787, 813, 1263, 1386, 1391, 1405, 1445, 1484, 1589, 1609, 1634, 1726, 1866, 1918 or 1928, or a nucleotide sequence complementary thereto, whereby

detecting selective hybridization of at least one nucleic acid probe, or detecting a change in a level of selective hybridization as compared to a level of selective hybridization obtained using nucleic acid molecules representative of expressed polynucleotides in cells of a plant known not have been exposed to an abiotic stress, indicates that the test plant has been exposed to an abiotic stress, and whereby

an absence of selective hybridization of at least one nucleic acid probe indicates that the test plant has not been exposed to an abiotic stress.

Claim 22

A method for determining whether a test plant has been exposed to a cold stress, the method comprising

• contacting nucleic acid molecules representative of expressed polynucleotides in cells of the test plant with at least one nucleic acid probe under conditions suitable for selective hybridization to a complementary nucleotide sequence, wherein

the probe comprises at least 15 nucleotides of a nucleotide sequence as set forth in any of SEQ ID NOS:1-155, 157-228, 230-232, 234-557, 559-572, 574-605, 607-634, 636-786, 788-812, 814-1261, or a nucleotide sequence complementary thereto, whereby

detecting selective hybridization of at least one nucleic acid probe, or detecting a change in a level of selective hybridization as compared to a level of selective hybridization obtained using nucleic acid molecules representative of expressed polynucleotides in cells of a plant known not have been exposed to a cold stress, indicates that the test plant has been exposed to a cold stress, and whereby

an absence of selective hybridization of at least one nucleic acid probe indicates that the test plant has not been exposed to a cold stress.

Claim 23

A method for determining whether a test plant has been exposed to a saline stress, the method comprising

• contacting nucleic acid molecules representative of expressed polynucleotides in cells of the test plant with at least one nucleic acid probe under conditions suitable for selective hybridization to a complementary nucleotide sequence, wherein

the probe comprises at least 15 nucleotides of a nucleotide sequence as set forth in any of SEQ ID NOS:2226-2427, or a nucleotide sequence complementary thereto, whereby

detecting selective hybridization of at least one nucleic acid probe, or detecting a change in a level of selective hybridization as compared to a level of selective hybridization obtained using nucleic acid molecules representative of expressed polynucleotides in cells of a plant known not have been exposed to a saline stress, indicates that the test plant has been exposed to a saline stress, and whereby

an absence of selective hybridization of at least one nucleic acid probe indicates that the test plant has not been exposed to a saline stress.

Claim 24

A method for determining whether a test plant has been exposed to an osmotic stress, the method comprising

• contacting nucleic acid molecules representative of expressed polynucleotides in cells of the test plant with at least one nucleic acid probe under conditions suitable for selective hybridization to a complementary nucleotide sequence, wherein

the probe comprises at least 15 nucleotides of a nucleotide sequence as set forth in two or more of SEQ ID NOS:2428-2585, or a nucleotide sequence complementary thereto, whereby

detecting selective hybridization of at least one nucleic acid probe, or detecting a change in a level of selective hybridization as compared to a level of selective hybridization obtained using nucleic acid molecules representative of expressed polynucleotides in cells of a plant known not have been exposed to an osmotic stress, indicates that the test plant has been exposed to an osmotic stress, and whereby

an absence of selective hybridization of at least one nucleic acid probe indicates that the test plant has not been exposed to an osmotic stress.

Claim 25

A method for determining whether a test plant has been exposed to a combination of abiotic stress conditions, the method comprising

• contacting nucleic acid molecules representative of expressed polynucleotides in cells of the test plant with at least one nucleic acid probe under conditions suitable for selective hybridization to a complementary nucleotide sequence, whereby

detecting selective hybridization of at least one nucleic acid probe, or detecting a change in a level of selective hybridization as compared to a level of selective hybridization obtained using nucleic acid molecules representative of expressed polynucleotides in cells of a plant known not have been exposed to a combination of stress conditions, indicates that the test plant has been exposed to a combination of abiotic stress conditions, and whereby

an absence of selective hybridization of at least one nucleic acid probe indicates that the test plant has not been exposed to a combination of abiotic stress conditions.

Claim 30

A method for determining whether a test plant has been exposed to a cold stress and an osmotic stress, the method comprising

• contacting nucleic acid molecules representative of expressed polynucleotides in cells of the test plant with at least one nucleic acid probe under conditions suitable for selective hybridization to a complementary nucleotide sequence, wherein

the probe comprises at least 15 nucleotides of a nucleotide sequence as set forth in any of SEQ ID NOS:1699-1969, or a nucleotide sequence complementary thereto, whereby

detecting selective hybridization of at least one nucleic acid probe, or detecting a change in a level of selective hybridization as compared to a level of selective hybridization obtained using nucleic acid molecules representative of expressed polynucleotides in cells of a plant known not have been exposed to a cold stress and an osmotic stress, indicates that the test plant has been exposed to a cold stress and an osmotic stress, and whereby

an absence of selective hybridization of at least one nucleic acid probe indicates that the test plant has not been exposed to a cold stress and an osmotic stress.

Claim 31

A method for determining whether a test plant has been exposed to a cold stress and a saline stress, the method comprising

• contacting nucleic acid molecules representative of expressed polynucleotides in cells of the test plant with at least one nucleic acid probe under conditions suitable for selective hybridization to a complementary nucleotide sequence, wherein

the probe comprises at least 15 nucleotides of a nucleotide sequence as set forth in any of SEQ ID NOS:1970-2226, or a nucleotide sequence complementary thereto, whereby

detecting selective hybridization of at least one nucleic acid probe, or detecting a change in a level of selective hybridization as compared to a level of selective hybridization obtained using nucleic acid molecules representative of expressed polynucleotides in cells of a plant known not have been exposed to a cold stress and a saline stress, indicates that the test plant has been exposed to a cold stress and a saline stress, and whereby

an absence of selective hybridization of at least one nucleic acid probe indicates that the test plant has not been exposed to a cold stress and a saline stress.

Claim 32

A method for determining whether a test plant has been exposed to an osmotic stress and a saline stress, the method comprising

• contacting nucleic acid molecules representative of expressed polynucleotides in the test plant with at least one nucleic acid probe under conditions suitable for selective hybridization to a complementary nucleotide sequence, wherein

the probe comprises at least 15 nucleotides of a nucleotide sequence as set forth in any of SEQ ID NOS:2586-2703, or a nucleotide sequence complementary thereto, whereby

detecting selective hybridization of at least one nucleic acid probe, or detecting a change in a level of selective hybridization as compared to a level of selective hybridization obtained using nucleic acid molecules representative of expressed polynucleotides in cells of a plant known not have been exposed to an osmotic stress and a saline stress, indicates that the test plant has been exposed to an osmotic stress and a saline stress, and whereby

an absence of selective hybridization of at least one nucleic acid probe indicates that the test plant has not been exposed to an osmotic stress and a saline stress.

Claim 33

A method for determining whether a test plant has been exposed to a cold stress, a saline stress and an osmotic stress, the method comprising

• contacting nucleic acid molecules representative of expressed polynucleotides in cells of the test plant with a plurality of nucleic acid probes under conditions suitable for selective hybridization to a complementary nucleotide sequence, wherein

the probe comprises at least 15 nucleotides of a nucleotide sequence as set forth in any of SEQ ID NOS:1262-1698, or a nucleotide sequence complementary thereto, whereby

detecting selective hybridization of at least one nucleic acid probe, or detecting a change in a level of selective hybridization as compared to a level of selective hybridization obtained using nucleic acid molecules representative of expressed polynucleotides in cells of a plant known not have been exposed to a cold stress, a saline stress, and an osmotic stress, indicates that the test plant has been exposed to a cold stress, a saline stress and an osmotic stress, and whereby

an absence of selective hybridization of at least one nucleic acid probe indicates that the test plant has not been exposed to a cold stress, a saline stress and an osmotic stress.

Claim 34

A method for determining whether a test plant has been exposed to a cold stress, the method comprising

• detecting a level of expression of at least one polynucleotide comprising a nucleotide sequence as set forth in SEQ ID NOS:1-155, 157-229, 230-232, 234-557, 559-572, 574-605, 607-634, 636-634, 636-786, 788812, and 814-1261 in cells of the test plant, wherein

detecting a level of expression that is at least about two-fold different from a level of expression of the at least one polynucleotide in cells of a plant not exposed to a cold stress, or detecting a level of expression that is less than about two-fold different from a level of expression of the at least one polynucleotide in cells of a plant known to be exposed to a cold stress, indicates the test plant has been exposed to a cold stress, or wherein

detecting a level of expression that is less than at least about two-fold different from a level of expression of the at least one polynucleotide in cells of a plant not exposed to a cold stress, or detecting a level of expression that is at least two-fold different from a level of expression of the at least one polynucleotide in cells of a plant known to be exposed to a cold stress, indicates the test plant has not been exposed to a cold stress.

Claim 35

A method for determining whether a test plant has been exposed to a saline stress, the method comprising

• detecting a level of expression of at least one polynucleotide comprising a nucleotide sequence as set forth in SEQ ID NOS:2226-2427 in cells of the test plant, wherein

detecting a level of expression that is at least about two-fold different from a level of expression of the at least one polynucleotide in cells of a plant not exposed to a saline stress, or detecting a level of expression that is less than about two-fold different from a level of expression of the at least one polynucleotide in cells of a plant known to be exposed to a saline stress, indicates the test plant has been exposed to a saline stress, or wherein

detecting a level of expression that is less than about two-fold different from a level of expression of the at least one polynucleotide in cells of a plant not exposed to a saline stress, or detecting a level of expression that is at least about two-fold different from a level of expression of the at least one polynucleotide in cells of a plant known to be exposed to a saline stress, indicates the test plant has not been exposed to a saline stress.

Claim 36

A method for determining whether a test plant has been exposed to an osmotic stress, the method comprising

• detecting a level of expression of at least one polynucleotide comprising a nucleotide sequence as set forth in SEQ ID NOS:2428-2585 in cells of the test plant, wherein

detecting a level of expression that is at least about two-fold different from a level of expression of the at least one polynucleotide in cells of a plant not exposed to an osmotic stress, or detecting a level of expression that is less than about two-fold different from a level of expression of the at least one polynucleotide in cells of a plant known to be exposed to an osmotic stress, indicates the test plant has been exposed to a osmotic stress, or wherein

detecting a level of expression that is less than about two-fold different from level of expression of the at least one polynucleotide in cells of a plant not exposed to an osmotic stress, or detecting a level of expression that is at least about two-fold different from a level of expression of the at least one polynucleotide in cells of a plant known to be exposed to an osmotic stress, indicates the test plant has not been exposed to a osmotic stress.

Claim 37

A method for determining whether a test plant has been exposed to a cold stress and an osmotic stress, the method comprising

• detecting a level of expression of at least one polynucleotide comprising a nucleotide sequence as set forth in SEQ ID NOS:1699-1969 in cells of the test plant, wherein

detecting a level of expression that is at least about two-fold different from a level of expression of the at least one polynucleotide in cells of a plant not exposed to a cold stress and an osmotic stress, or detecting a level of expression that is less than about two-fold different from a level of expression of the at least one polynucleotide in cells of a plant known to be exposed to a cold stress and an osmotic stress, indicates the test plant has been exposed to a cold stress and an osmotic stress, or wherein

detecting a level of expression that is less than about two-fold different from as a level of expression of the at least one polynucleotide in cells of a plant not exposed to a cold stress and an osmotic stress, or detecting a level of expression that is at least about two-fold different from a level of expression of the at least one polynucleotide in cells of a plant known to be exposed to a cold stress and an osmotic stress, indicates the test plant has not been exposed to a cold stress and an osmotic stress.

Claim 38

A method for determining whether a test plant has been exposed to a cold stress and a saline stress, the method comprising

• detecting a level of expression of at least one polynucleotide comprising a nucleotide sequence as set forth in SEQ ID NOS:1970-2226 in cells of the test plant, wherein

detecting a level of expression that is at least about two-fold different from a level of expression of the at least one polynucleotide in cells of a plant not exposed to a cold stress and a saline stress, or detecting a level of expression that is less than about two-fold different from as a level of expression of the at least one polynucleotide in cells of a plant known to be exposed to a cold stress and a saline stress, indicates the test plant has been exposed to a cold stress and a saline stress, or wherein

detecting a level of expression that is less than about two-fold different from as a level of expression of the at least one polynucleotide in cells of a plant not exposed to a cold stress and a saline stress, or detecting a level of expression that is at least about two-fold different from a level of expression of the at least one polynucleotide in cells of a plant known to be exposed to a cold stress and a saline stress, indicates the test plant has not been exposed to a cold stress and a saline stress.

Claim 39

A method for determining whether a test plant has been exposed to a saline stress and an osmotic stress, the method comprising

• detecting a level of expression of at least one polynucleotide comprising a nucleotide sequence as set forth in SEQ ID NOS:2586-2703 in cells of the test plant, wherein

detecting a level of expression that is at least about two-fold different from a level of expression of the at least one polynucleotide in cells of a plant not exposed to a saline stress and an osmotic stress, or detecting a level of expression that is less than about two-fold different from a level of expression of the at least one polynucleotide in cells of a plant known to be exposed to a saline stress and an osmotic stress, indicates the test plant has been exposed to a saline stress and an osmotic stress, or wherein

detecting a level of expression that is less than about two-fold different from a level of expression of the at least one polynucleotide in cells of a plant not exposed to a saline stress and an osmotic stress, or detecting a level of expression that is at least about two-fold different from a level of expression of the at least one polynucleotide in cells of a plant known to be exposed to saline stress and an osmotic stress, indicates the test plant has not been exposed to a saline stress and an osmotic stress.

Claim 40

A method for determining whether a test plant has been exposed to a cold stress, the method comprising

• detecting a level of expression of at least one polynucleotide comprising a nucleotide sequence as set forth SEQ ID NOS:1-155, 157-229, 230-232, 234-557, 559-572, 574-605, 607-634, 636-634, 636-786, 788812, and 814-1261 in cells of the test plant, wherein

detecting a level of expression that is at least about two-fold different from a level of expression of the at least one polynucleotide in cells of a plant not exposed to a cold stress, or detecting a level of expression that is less than about two-fold different from a level of expression of the at least one polynucleotide in cells of a plant known to be exposed to a cold stress, indicates the test plant has been exposed to a cold stress, or wherein

detecting a level of expression that is less than about two-fold different from a level of expression of the at least one polynucleotide in cells of a plant not exposed to a cold stress, or detecting a level of expression that is at least about two-fold different from a level of expression of the at least one polynucleotide in cells of a plant known to be exposed to a cold stress, indicates the test plant has not been exposed to a cold stress.

Claim 41

A method for determining whether a test plant has been exposed to a cold stress, a saline stress and an osmotic stress, the method comprising

• detecting a level of expression of at least one polynucleotide comprising a nucleotide sequence as set forth in SEQ ID NOS:1262-1698 in cells of the test plant, wherein

detecting a level of expression that is at least about two-fold different from a level of expression of the at least one polynucleotide in cells of a plant not exposed to a cold stress, a saline stress and an osmotic stress, or detecting a level of expression that is less than about two-fold different from a level of expression of the at least one polynucleotide in cells of a plant known to be exposed to a cold stress, a saline stress and an osmotic stress, indicates the test plant has been exposed to a cold stress, a saline stress and an osmotic stress, or wherein

detecting a level of expression that is less than about two-fold different from a level of expression of the at least one polynucleotide in cells of a plant not exposed to a cold stress, a saline stress and an osmotic stress, or detecting a level of expression that is at least about two-fold different from a level of expression of the at least one polynucleotide in cells of a plant known to be exposed to a cold stress, a saline stress and an osmotic stress, indicates the test plant has not been exposed to a cold stress, a saline stress and an osmotic stress.

Claim 42

A method of producing a transgenic plant comprising plant cells that exhibit altered responsiveness to at least one stress condition, the method comprising

• introducing a polynucleotide portion of a plant stress-regulated gene into a plant cell genome, wherein the polynucleotide portion of the stress-regulated gene does not comprise a nucleotide sequence as set forth in any of SEQ ID NOS:156, 229, 233, 558, 573, 606, 635, 787, 813, 1263, 1386, 1391, 1405, 1445, 1484, 1589, 1609, 1634, 1726, 1866, 1918 or 1928, whereby the polynucleotide portion of the plant stress-regulated gene modulates a response of the plant cells to at least one stress condition, thereby producing a transgenic plant comprising plant cells that exhibit altered responsiveness to the stress condition.

Claim 46

A method of producing a transgenic plant comprising plant cells that exhibit altered responsiveness to a combination of at least two stress conditions, the method comprising

• introducing a polynucleotide portion of a plant stress-regulated gene into a plant cell genome, whereby the polynucleotide portion of the plant stress-regulated gene modulates a response of the plant cells to a combination of at least two stress conditions, thereby producing a transgenic plant comprising plant cells that exhibit altered responsiveness to the stress conditions.

Claim 85

A method of selecting a plant having an altered resistance to an abiotic stress condition or a combination of abiotic stress conditions, the method comprising:

a) contacting nucleic acid molecules representative of expressed polynucleotides in a plant cell of a plant to be examined for having an altered resistance to an abiotic stress with a nucleic acid probes that selectively hybridizes under stringent conditions to a plant stress-regulated gene comprising a nucleotide sequence as set forth in any of SEQ ID NO:1-5379;

b) detecting a level of selective hybridization of the nucleic acid probes to a nucleic acid molecule representative of an expressed polynucleotide in the plant cell, wherein the level of selective hybridization corresponds to the level of the expressed polynucleotide in the plant cell, which is indicative of resistance of the plant to an abiotic stress; and

c) selecting a plant having a level of expression of a polynucleotide indicative of altered resistance to an abiotic stress condition.

A method of modulating the responsiveness of a plant cell to a stress condition, the method comprising

• introducing a polynucleotide portion of a plant stress-regulated gene into the plant cell, wherein said gene comprises a nucleotide sequence of a polynucleotide as set forth in any of SEQ ID NOS:1-155, 157-228, 230-232, 234-557, 559-572, 574-605, 607-634, 636-786, 788-812, 814-1262, 1264-1386, 1387-1390, 1392-1404, 1406-1444, 1446-1483, 1485-1588, 1590-1608, 1610-1633, 1634-1725, 1727-1865, 1867-1917, 1919-1927, 1929-2855, 2857-2928, 2930-2932, 2934-3256, 3258-3271, 3273-3304, 3306-3323, 3325-3333, 3335-3485, 3487-3511, 3313-3956, 3958-4078, 4080-4097, 4099-4136, 4138-4175, 4177-4279, 4281-4299, 4301-4324, 4326-4414, 4416-4552, 4554-4602, and 4604-5379, thereby modulating the responsiveness of the plant cell to a stress condition.

A method of expressing a heterologous nucleotide sequence in a plant cell, the method comprising

• introducing into the plant cell a plant stress-regulated regulatory element operatively linked to the heterologous nucleotide sequence, wherein said regulatory element comprises a nucleotide sequence as set forth in any of SEQ ID NOS:2704-2855, 2857-2928, 2930-2932, 2934-3256, 3258-3271, 3273-3304, 3306-3323, 3325-3333, 3335-3485, 3487-3511, 3313-3956, 3958-4078, 4080-4097, 4099-4136, 4138-4175, 4177-4279, 4281-4299, 4301-4324, 4326-4414, 4416-4552, 4554-4602, and 4604-5379, whereby, upon exposure of the plant cell to stress condition, the heterologous nucleotide sequence is expressed in the plant cell.

A method of modulating the activity of a biological pathway in a plant cell involving a plant stress-regulated polypeptide, the method comprising

• introducing a polynucleotide portion of a plant stress-regulated gene into the plant cell, wherein the plant stress-regulated gene comprises a nucleotide sequence as set forth in any of SEQ ID NOS:1-155, 157-228, 230-232, 234-557, 559-572, 574-605, 607-634, 636-786, 788-812, 814-1262, 1264-1386, 1387-1390, 1392-1404, 1406-1444, 1446-1483, 1485-1588, 1590-1608, 1610-1633, 1634-1725, 1727-1865,1867-1917, 1919-1927, 1929-2855, 2857-2928, 2930-2932, 2934-3256, 3258-3271, 3273-3304, 3306-3323, 3325-3333, 3335-3485, 3487-3511, 3313-3956, 3958-4078, 4080-4097, 4099-4136, 4138-4175, 4177-4279, 4281-4299, 4301-4324, 4326-4414, 4416-4552, 4554-4602, and 4604-5379, thereby modulating the activity of the biological pathway.

A method of identifying a polynucleotide that modulates a stress response in a plant cell, the methods comprising:

a) contacting an array of probes representative of a plant cell genome and nucleic acid molecules expressed in plant cell exposed to the stress;

b) detecting a nucleic acid molecule that is expressed at a level different from a level of expression in the absence of the stress;

c) introducing the nucleic acid molecule of step b) into a plant cell; and

d) detecting a modulated response of the plant cell of step c) to a stress, thereby identifying a polynucleotide that modulates a stress response in a plant cell.

A transgenic plant, which contains a transgene comprising a polynucleotide portion of plant stress-regulated gene, wherein the gene comprises

• a nucleotide sequence as set forth in any of SEQ ID NOS:1-155, 157-228, 230-232, 234-SS7, 559-572, 574-605, 607-634, 636-786, 788-812, 814-1262, 1264-1386, 1387-1390, 1392-1404, 1406-1444, 1446-1483, 1485-1588, 1590-1608, 1610-1633, 1634-1725, 1727-1865, 1867-1917, 1919-1927, 1929-2855, 2857-2928, 2930-2932, 2934-3256, 3258-3271, 3273-3304, 3306-3323, 3325-3333, 3335-3485, 3487-3511, 3313-3956, 3958-4078, 4080-4097, 4099-4136, 4138-4175, 4177-4279, 4281-4299, 4301-4324, 4326-4414, 4416-4552, 4554-4602, and 4604-5379.

A plant stress-regulated gene regulatory element, wherein the gene comprises

• a nucleotide sequence as set forth in any of SEQ ID NOS:1-155, 157228, 230-232, 234-557, 559-572, 574-605, 607-634, 636-786, 788-812, 814-1262, 1264-1386, 1387-1390, 1392-1404, 1406-1444, 1446-1483, 1485-1588, 1590-1608, 1610-1633, 1634-1725, 1727-1865, 1867-1917, 1919-1927, 1929-2855, 2857-2928, 2930-2932, 2934-3256, 3258-3271, 3273-3304, 3306-3323, 3325-3333, 3335-3485, 3487-3511, 3313-3956, 3958-4078, 4080-4097, 4099-4136, 4138-4175, 4177-4279, 4281-4299, 4301-4324, 4326-4414, 4416-4552, 4554-4602, and 4604-5379.

A method for identifying a polynucleotide involved in a stress response of a plant, the method comprising:

a) contacting nucleic acid molecules representative of expressed polynucleotides in plant cells of a plant exposed to a stress condition or combination of stress conditions with an array of probes representative of the plant cell genome; and

b) detecting a nucleic acid molecule that exhibits at least a two-fold change in the level of expression as compared to the level of the nucleic acid molecule in a corresponding plant cell of a plant that was not exposed to the stress condition, thereby identifying a polynucleotide involved in a stress response of the plant.

A computer readable medium having stored thereon computer executable instructions for performing a method comprising:

a) receiving data on expression in a cell of a plant of a nucleic acid molecule having at least 70% sequence identity to a nucleotide sequence comprising any of SEQ ID NO. 1-5379; and

b) comparing the data on expression of the nucleic acid molecule with data on expression of the nucleic acid in a cell of a plant that has not been exposed to an abiotic stress, of a plant that has been exposed to an abiotic stress condition or combination of abiotic stress conditions, or of a combination of such plants.

A computer-readable medium having stored thereon a data structure comprising:

• sequence data for at least one nucleic acid molecule having at least 70% nucleic acid sequence identity to a polynucleotide having a nucleotide sequence as set forth in any of SEQ ID NO. 1-5379 or a nucleotide sequence complementary thereto; and

• a module receiving the nucleic acid molecule sequence data, which compares the nucleic acid molecule sequence data to a least one other nucleic acid sequence.

A method for determining whether a test plant has been exposed to an abiotic stress condition, the method comprising

• contacting nucleic acid molecules representative of expressed polynucleotides in cells of the test plant with at least one nucleic acid probe under conditions suitable for selective hybridization to a complementary nucleotide sequence, wherein

the probe comprises at least 15 nucleotides of a nucleotide sequence as set forth in any of SEQ ID NOS:1-155, 157-228, 230-232, 234-557, 559-572, 574-605, 607-634, 636-786, 788-812, 814-1261, 2227-2585, 2704-2857-2928, 2930-2932, 2934-3256, 3258-3271, 3273-3304, 3306-3323, 3325-3333, 3335-3485, 3487-3511, 3313-3955, and 4910-5263, or a nucleotide sequence complementary thereto, whereby

detecting selective hybridization of at least one nucleic acid probe, or detecting a change in a level of selective hybridization as compared to a level of selective hybridization obtained using nucleic acid molecules representative of expressed polynucleotides in cells of a plant known not have been exposed to an abiotic stress, indicates that the test plant has been exposed to an abiotic stress condition, and whereby

an absence of selective hybridization of at least one nucleic acid probe indicates that the test plant has not been exposed to an abiotic stress condition.

A method for determining whether a test plant has been exposed to a combination of abiotic stress conditions, the method comprising

• contacting nucleic acid molecules representative of expressed polynucleotides in cells of the test plant with at least one nucleic acid probe under conditions suitable for selective hybridization to a complementary nucleotide sequence, wherein

the probe comprises at least 15 nucleotides of a nucleotide sequence as set forth in any of SEQ ID NOS:1262-2226, 2586-2703, 3956-4909, and 5264-5379, or a nucleotide sequence complementary thereto, whereby

detecting selective hybridization of at least one nucleic acid probe, or detecting a change in a level of selective hybridization as compared to a level of selective hybridization obtained using nucleic acid molecules representative of expressed polynucleotides in cells of a plant known not have been exposed to a combination of stress conditions, indicates that the test plant has been exposed to a combination of abiotic stress conditions, and whereby

an absence of selective hybridization of at least one nucleic acid probe indicates that the test plant has not been exposed to a combination of abiotic stress conditions.

A method for determining whether a test plant has been exposed to an abiotic stress condition or combination of abiotic stress conditions, the method comprising

detecting a level of expression of at least one polynucleotide comprising a nucleotide sequence as set forth in any of SEQ ID NOS:1-155, 157-228, 230-232, 234-557, 559-572, 574-605, 607-634, 636-786, 788-812, 814-1262, 1264-1386, 1387-1390, 1392-1404, 1406-1444, 1446-1483, 1485-1588, 1590-1608, 1610-1633, 1634-1725, 1727-1865, 1867-1917, 1919-1927, 1929-2855, 2857-2928, 2930-2932, 2934-3256, 3258-3271, 3273-3304, 3306-3323, 3325-3333, 3335-3485, 3487-3511, 3313-3956, 3958-4078, 4080-4097, 4099-4136, 4138-4175, 4177-4279, 4281-4299, 4301-4324, 4326-4414, 4416-4552, 4554-4602, and 4604-5379, in cells of the test plant, wherein

detecting a level of expression that is at least about two-fold different from a level of expression of the at least one polynucleotide in cells of a plant not exposed to an abiotic stress or combination of abiotic stresses, or detecting a level of expression that is less than about two-fold different from a level of expression of the at least one polynucleotide in cells of a plant known to be exposed to an abiotic stress or combination of abiotic stresses, indicates the test plant has been exposed to an abiotic stress or combination of abiotic stresses, or wherein

detecting a level of expression that is less than at least about two-fold different from a level of expression of the at least one polynucleotide in cells of a plant not exposed to an abiotic stress or combination of abiotic stresses, or detecting a level of expression that is at least two-fold different from a level of expression of the at least one polynucleotide in cells of a plant known to be exposed to an abiotic stress or combination of abiotic stresses, indicates the test plant has not been exposed to an abiotic stress or combination of abiotic stresses.

A method of identifying a stress condition to which a plant cell has been exposed, the method comprising:

a) contacting nucleic acid molecules representative of expressed polynucleotides in the plant cell with an array of probes representative of the plant cell genome; and

b) detecting a profile of expressed polynucleotides in the plant cell characteristic of a stress response, thereby identifying the stress condition to which the plant cell was exposed.

A method of producing a transgenic plant comprising plant cells that exhibit altered responsiveness to at least one stress condition, the method comprising

• introducing a polynucleotide portion of a plant stress-regulated gene into a plant cell genome, wherein

the polynucleotide portion of the stress-regulated gene comprises a nucleotide sequence as set forth in any of 1-155, 157-228, 230-232, 234-557, 559-572, 574-605, 607-634, 636-786, 788-812, 814-1262, 1264-1386, 1387-1390, 1392-1404, 1406-1444, 1446-1483, 1485-1588, 1590-1608, 1610-1633, 1634-1725, 1727-1865, 1867-1917, 1919-1927, 1929-2855, 2857-2928, 2930-2932, 2934-3256, 3258-3271, 3273-3304, 3306-3323, 3325-3333, 3335-3485, 3487-3511, 3313-3956, 3958-4078, 4080-4097, 4099-4136, 4138-4175, 4177-4279, 4281-4299, 4301-4324, 4326-4414, 4416-4552, 4554-4602, and 4604-5379, whereby the polynucleotide portion of the plant stress-regulated gene modulates a response of the plant cells to at least one stress condition, thereby producing a transgenic plant comprising plant cells that exhibit altered responsiveness to the stress condition.

A transgenic plant, which contains a transgene comprising a polynucleotide portion of plant stress-regulated gene, wherein the gene comprises

• a nucleotide sequence as set forth in any of SEQ ID NOS:1-155, 157-228, 230-232, 234-557, 559-572, 574-605, 607-634, 636-786, 788-812, 814-1262, 1264-1386, 1387-1390, 1392-1404, 1406-1444, 1446-1483, 1485-1588, 1590-1608, 1610-1633, 1634-1725, 1727-1865, 1867-1917, 1919-1927, 1929-2855, 2857-2928, 2930-2932, 2934-3256, 3258-3271, 3273-3304, 3306-3323, 3325-3333, 3335-3485, 3487-3511, 3313-3956, 3958-4078, 4080-4097, 4099-4136, 4138-4175, 4177-4279, 4281-4299, 4301-4324, 4326-4414, 4416-4552, 4554-4602, and 4604-5379.

A plant stress-regulated gene regulatory element, wherein the gene comprises

• a nucleotide sequence as set forth in any of SEQ ID NOS:1-155, 157-228, 230-232, 234-557, 559-572, 574-605, 607-634, 636-786, 788-812, 814-1262, 1264-1386, 1387-1390, 1392-1404, 1406-1444, 1446-1483, 1485-1588, 1590-1608, 1610-1633, 1634-1725, 1727-1865, 1867-1917, 1919-1927, 1929-2855, 2857-2928, 2930-2932, 2934-3256, 3258-3271, 3273-3304, 3306-3323, 3325-3333, 3335-3485, 3487-3511, 3313-3956, 3958-4078, 4080-4097, 4099-4136, 4138-4175, 4177-4279, 4281-4299, 4301-4324, 4326-4414, 4416-4552, 4554-4602, and 4604-5379.

A method of selecting a plant having an altered resistance to an abiotic stress condition or a combination of abiotic stress conditions, the method comprising:

a) contacting nucleic acid molecules representative of expressed polynucleotides in a plant cell of a plant to be examined for having an altered resistance to an abiotic stress with a nucleic acid probe that selectively hybridizes under stringent conditions to a plant stress-regulated gene comprising a nucleotide sequence as set forth in any of SEQ ID NO:1-155, 157-228, 230-232, 234-557, 559-572, 574-605, 607-634, 636-786, 788-812, 814-1262, 1264-1386, 1387-1390, 1392-1404, 1406-1444, 1446-1483, 1485-1588, 1590-1608, 1610-1633, 1634-1725, 1727-1865, 1867-1917, 1919-1927, 1929-2855, 2857-2928, 2930-2932, 2934-3256, 3258-3271, 3273-3304, 3306-3323, 3325-3333, 3335-3485, 3487-3511, 3313-3956, 3958-4078, 4080-4097, 4099-4136, 4138-4175, 4177-4279, 4281-4299, 4301-4324, 4326-4414, 4416-4552, 4554-4602, and 4604-5379;

b) detecting a level of selective hybridization of the nucleic acid probes to a nucleic acid molecule representative of an expressed polynucleotide in the plant cell, wherein the level of selective hybridization corresponds to the level of the expressed polynucleotide in the plant cell, which is indicative of resistance of the plant to an abiotic stress; and

c) selecting a plant having a level of expression of a polynucleotide indicative of altered resistance to an abiotic stress condition.

A method for identifying a polynucleotide involved in a stress response of a plant, the method comprising:

a) contacting nucleic acid molecules representative of expressed polynucleotides in plant cells of a plant exposed to a stress condition or combination of stress conditions with an array of probes representative of the plant cell genome; and

b) detecting a nucleic acid molecule that exhibits at least a two-fold change in the level of expression as compared to the level of the nucleic acid molecule in a corresponding plant cell of a plant that was not exposed to the stress condition, thereby identifying a polynucleotide involved in a stress response of the plant.

A computer readable medium having stored thereon computer executable instructions for performing a method comprising:

a) receiving data on expression in a cell of a plant of a nucleic acid molecule having at least 70% sequence identity to a nucleotide sequence comprising any of SEQ ID NO. 1-5379; and

b) comparing the data on expression of the nucleic acid molecule with data on expression of the nucleic acid in a cell of a plant that has not been exposed to an abiotic stress, of a plant that has been exposed to an abiotic stress condition or combination of abiotic stress conditions, or of a combination of such plants.

A computer-readable medium having stored thereon a data structure comprising:

• sequence data for at least one nucleic acid molecule having at least 70% nucleic acid sequence identity to a polynucleotide having a nucleotide sequence as set forth in any of SEQ ID NO. 1-5379 or a nucleotide sequence complementary thereto; and

• a module receiving the nucleic acid molecule sequence data, which compares the nucleic acid molecule sequence data to a least one other nucleic acid sequence.

Claim 1

A method of identifying a stress condition to which a plant cell has been exposed, the method comprising:
a) contacting nucleic acid molecules representative of expressed polynucleotides in the plant cell with an array of probes representative of the plant cell genome; and
b) detecting a profile of expressed polynucleotides in the plant cell characteristic of a stress response, thereby identifying the stress condition to which the plant cell was exposed.

Claim 18

A method for determining whether a test plant has been exposed to an abiotic stress, the method comprising

• contacting nucleic acid molecules representative of expressed polynucleotides in cells of the test plant with at least one nucleic acid probe under conditions suitable for selective hybridization to a complementary nucleotide sequence, wherein

the probe comprises at least 15 nucleotides of a plant stress-regulated gene, provided said gene does not comprise a nucleotide sequence of a polynucleotide as set forth in any of SEQ ID NOS:156, 229, 233, 558, 573, 606, 635, 787, 813, 1263, 1386, 1391, 1405, 1445, 1484, 1589, 1609, 1634, 1726, 1866, 1918 or 1928,or a nucleotide sequence complementary thereto, whereby

detecting selective hybridization of at least one nucleic acid probe, or detecting a change in a level of selective hybridization as compared to a level of selective hybridization obtained using nucleic acid molecules representative of expressed polynucleotides in cells of a plant known not have been exposed to an abiotic stress, indicates that the test plant has been exposed to an abiotic stress, and whereby

an absence of selective hybridization of at least one nucleic acid probe indicates that the test plant has not been exposed to an abiotic stress.

Claim 22

A method for determining whether a test plant has been exposed to a cold stress, the method comprising

• contacting nucleic acid molecules representative of expressed polynucleotides in cells of the test plant with at least one nucleic acid probe under conditions suitable for selective hybridization to a complementary nucleotide sequence, wherein

the probe comprises at least 15 nucleotides of a nucleotide sequence as set forth in any of SEQ ID NOS:1-155, 157-228, 230-232, 234-557, 559-572, 574-605, 607-634, 636-786, 788-812, 814-1261, or a nucleotide sequence complementary thereto, whereby

detecting selective hybridization of at least one nucleic acid probe, or detecting a change in a level of selective hybridization as compared to a level of selective hybridization obtained using nucleic acid molecules representative of expressed polynucleotides in cells of a plant known not have been exposed to a cold stress, indicates that the test plant has been exposed to a cold stress, and whereby

an absence of selective hybridization of at least one nucleic acid probe indicates that the test plant has not been exposed to a cold stress.

Claim 23

A method for determining whether a test plant has been exposed to a saline stress, the method comprising

• contacting nucleic acid molecules representative of expressed polynucleotides in cells of the test plant with at least one nucleic acid probe under conditions suitable for selective hybridization to a complementary nucleotide sequence, wherein

the probe comprises at least 15 nucleotides of a nucleotide sequence as set forth in any of SEQ ID NOS:2226-2427, or a nucleotide sequence complementary thereto, whereby

detecting selective hybridization of at least one nucleic acid probe, or detecting a change in a level of selective hybridization as compared to a level of selective hybridization obtained using nucleic acid molecules representative of expressed polynucleotides in cells of a plant known not have been exposed to a saline stress, indicates that the test plant has been exposed to a saline stress, and whereby

an absence of selective hybridization of at least one nucleic acid probe indicates that the test plant has not been exposed to a saline stress.

Claim 24

A method for determining whether a test plant has been exposed to an osmotic stress, the method comprising

• contacting nucleic acid molecules representative of expressed polynucleotides in cells of the test plant with at least one nucleic acid probe under conditions suitable for selective hybridization to a complementary nucleotide sequence, wherein

the probe comprises at least 15 nucleotides of a nucleotide sequence as set forth in two or more of SEQ ID NOS:2428-2585, or a nucleotide sequence complementary thereto, whereby

detecting selective hybridization of at least one nucleic acid probe, or detecting a change in a level of selective hybridization as compared to a level of selective hybridization obtained using nucleic acid molecules representative of expressed polynucleotides in cells of a plant known not have been exposed to an osmotic stress, indicates that the test plant has been exposed to an osmotic stress, and whereby

an absence of selective hybridization of at least one nucleic acid probe indicates that the test plant has not been exposed to an osmotic stress.

Claim 25

A method for determining whether a test plant has been exposed to a combination of abiotic stress conditions, the method comprising

• contacting nucleic acid molecules representative of expressed polynucleotides in cells of the test plant with at least one nucleic acid probe under conditions suitable for selective hybridization to a complementary nucleotide sequence, whereby

detecting selective hybridization of at least one nucleic acid probe, or detecting a change in a level of selective hybridization as compared to a level of selective hybridization obtained using nucleic acid molecules representative of expressed polynucleotides in cells of a plant known not have been exposed to a combination of stress conditions, indicates that the test plant has been exposed to a combination of abiotic stress conditions, and whereby

an absence of selective hybridization of at least one nucleic acid probe indicates that the test plant has not been exposed to a combination of abiotic stress conditions.

Claim 30

A method for determining whether a test plant has been exposed to a cold stress and an osmotic stress, the method comprising

• contacting nucleic acid molecules representative of expressed polynucleotides in cells of the test plant with at least one nucleic acid probe under conditions suitable for selective hybridization to a complementary nucleotide sequence, wherein

the probe comprises at least 15 nucleotides of a nucleotide sequence as set forth in any of SEQ ID NOS:1699-1969, or a nucleotide sequence complementary thereto, whereby

detecting selective hybridization of at least one nucleic acid probe, or detecting a change in a level of selective hybridization as compared to a level of selective hybridization obtained using nucleic acid molecules representative of expressed polynucleotides in cells of a plant known not have been exposed to a cold stress and an osmotic stress, indicates that the test plant has been exposed to a cold stress and an osmotic stress, and whereby

an absence of selective hybridization of at least one nucleic acid probe indicates that the test plant has not been exposed to a cold stress and an osmotic stress.

Claim 31

A method for determining whether a test plant has been exposed to a cold stress and a saline stress, the method comprising

• contacting nucleic acid molecules representative of expressed polynucleotides in cells of the test plant with at least one nucleic acid probe under conditions suitable for selective hybridization to a complementary nucleotide sequence, wherein

the probe comprises at least 15 nucleotides of a nucleotide sequence as set forth in any of SEQ ID NOS:1970-2226, or a nucleotide sequence complementary thereto, whereby

detecting selective hybridization of at least one nucleic acid probe, or detecting a change in a level of selective hybridization as compared to a level of selective hybridization obtained using nucleic acid molecules representative of expressed polynucleotides in cells of a plant known not have been exposed to a cold stress and a saline stress, indicates that the test plant has been exposed to a cold stress and a saline stress, and whereby

an absence of selective hybridization of at least one nucleic acid probe indicates that the test plant has not been exposed to a cold stress and a saline stress.

Claim 32

A method for determining whether a test plant has been exposed to an osmotic stress and a saline stress, the method comprising

• contacting nucleic acid molecules representative of expressed polynucleotides in the test plant with at least one nucleic acid probe under conditions suitable for selective hybridization to a complementary nucleotide sequence, wherein

the probe comprises at least 15 nucleotides of a nucleotide sequence as set forth in any of SEQ ID NOS:2586-2703, or a nucleotide sequence complementary thereto, whereby

detecting selective hybridization of at least one nucleic acid probe, or detecting a change in a level of selective hybridization as compared to a level of selective hybridization obtained using nucleic acid molecules representative of expressed polynucleotides in cells of a plant known not have been exposed to an osmotic stress and a saline stress, indicates that the test plant has been exposed to an osmotic stress and a saline stress, and whereby

an absence of selective hybridization of at least one nucleic acid probe indicates that the test plant has not been exposed to an osmotic stress and a saline stress.

Claim 33

A method for determining whether a test plant has been exposed to a cold stress, a saline stress and an osmotic stress, the method comprising

• contacting nucleic acid molecules representative of expressed polynucleotides in cells of the test plant with a plurality of nucleic acid probes under conditions suitable for selective hybridization to a complementary nucleotide sequence, wherein

the probe comprises at least 15 nucleotides of a nucleotide sequence as set forth in any of SEQ ID NOS:1262-1698, or a nucleotide sequence complementary thereto, whereby

detecting selective hybridization of at least one nucleic acid probe, or detecting a change in a level of selective hybridization as compared to a level of selective hybridization obtained using nucleic acid molecules representative of expressed polynucleotides in cells of a plant known not have been exposed to a cold stress, a saline stress, and an osmotic stress, indicates that the test plant has been exposed to a cold stress, a saline stress and an osmotic stress, and whereby

an absence of selective hybridization of at least one nucleic acid probe indicates that the test plant has not been exposed to a cold stress, a saline stress and an osmotic stress.

Claim 34

A method for determining whether a test plant has been exposed to a cold stress, the method comprising

• detecting a level of expression of at least one polynucleotide comprising a nucleotide sequence as set forth in SEQ ID NOS:1-155, 157-229, 230-232, 234-557, 559-572, 574-605, 607-634, 636-634, 636-786, 788812, and 814-1261 in cells of the test plant, wherein

detecting a level of expression that is at least about two-fold different from a level of expression of the at least one polynucleotide in cells of a plant not exposed to a cold stress, or detecting a level of expression that is less than about two-fold different from a level of expression of the at least one polynucleotide in cells of a plant known to be exposed to a cold stress, indicates the test plant has been exposed to a cold stress, or wherein

detecting a level of expression that is less than at least about two-fold different from a level of expression of the at least one polynucleotide in cells of a plant not exposed to a cold stress, or detecting a level of expression that is at least two-fold different from a level of expression of the at least one polynucleotide in cells of a plant known to be exposed to a cold stress, indicates the test plant has not been exposed to a cold stress.

Claim 35

A method for determining whether a test plant has been exposed to a saline stress, the method comprising

• detecting a level of expression of at least one polynucleotide comprising a nucleotide sequence as set forth in SEQ ID NOS:2226-2427 in cells of the test plant, wherein

detecting a level of expression that is at least about two-fold different from a level of expression of the at least one polynucleotide in cells of a plant not exposed to a saline stress, or detecting a level of expression that is less than about two-fold different from a level of expression of the at least one polynucleotide in cells of a plant known to be exposed to a saline stress, indicates the test plant has been exposed to a saline stress, or wherein

detecting a level of expression that is less than about two-fold different from a level of expression of the at least one polynucleotide in cells of a plant not exposed to a saline stress, or detecting a level of expression that is at least about two-fold different from a level of expression of the at least one polynucleotide in cells of a plant known to be exposed to a saline stress, indicates the test plant has not been exposed to a saline stress.

Claim 36

A method for determining whether a test plant has been exposed to an osmotic stress, the method comprising

• detecting a level of expression of at least one polynucleotide comprising a nucleotide sequence as set forth in SEQ ID NOS:2428-2585 in cells of the test plant, wherein

detecting a level of expression that is at least about two-fold different from a level of expression of the at least one polynucleotide in cells of a plant not exposed to an osmotic stress, or detecting a level of expression that is less than about two-fold different from a level of expression of the at least one polynucleotide in cells of a plant known to be exposed to an osmotic stress, indicates the test plant has been exposed to a osmotic stress, or wherein

detecting a level of expression that is less than about two-fold different from level of expression of the at least one polynucleotide in cells of a plant not exposed to an osmotic stress, or detecting a level of expression that is at least about two-fold different from a level of expression of the at least one polynucleotide in cells of a plant known to be exposed to an osmotic stress, indicates the test plant has not been exposed to a osmotic stress.

Claim 37

A method for determining whether a test plant has been exposed to a cold stress and an osmotic stress, the method comprising

• detecting a level of expression of at least one polynucleotide comprising a nucleotide sequence as set forth in SEQ ID NOS:1699-1969 in cells of the test plant, wherein

detecting a level of expression that is at least about two-fold different from a level of expression of the at least one polynucleotide in cells of a plant not exposed to a cold stress and an osmotic stress, or detecting a level of expression that is less than about two-fold different from a level of expression of the at least one polynucleotide in cells of a plant known to be exposed to a cold stress and an osmotic stress, indicates the test plant has been exposed to a cold stress and an osmotic stress, or wherein

detecting a level of expression that is less than about two-fold different from as a level of expression of the at least one polynucleotide in cells of a plant not exposed to a cold stress and an osmotic stress, or detecting a level of expression that is at least about two-fold different from a level of expression of the at least one polynucleotide in cells of a plant known to be exposed to a cold stress and an osmotic stress, indicates the test plant has not been exposed to a cold stress and an osmotic stress.

Claim 38

A method for determining whether a test plant has been exposed to a cold stress and a saline stress, the method comprising

• detecting a level of expression of at least one polynucleotide comprising a nucleotide sequence as set forth in SEQ ID NOS:1970-2226 in cells of the test plant, wherein

detecting a level of expression that is at least about two-fold different from a level of expression of the at least one polynucleotide in cells of a plant not exposed to a cold stress and a saline stress, or detecting a level of expression that is less than about two-fold different from as a level of expression of the at least one polynucleotide in cells of a plant known to be exposed to a cold stress and a saline stress, indicates the test plant has been exposed to a cold stress and a saline stress, or wherein

detecting a level of expression that is less than about two-fold different from as a level of expression of the at least one polynucleotide in cells of a plant not exposed to a cold stress and a saline stress, or detecting a level of expression that is at least about two-fold different from a level of expression of the at least one polynucleotide in cells of a plant known to be exposed to a cold stress and a saline stress, indicates the test plant has not been exposed to a cold stress and a saline stress.

Claim 39

A method for determining whether a test plant has been exposed to a saline stress and an osmotic stress, the method comprising

• detecting a level of expression of at least one polynucleotide comprising a nucleotide sequence as set forth in SEQ ID NOS:2586-2703 in cells of the test plant, wherein

detecting a level of expression that is at least about two-fold different from a level of expression of the at least one polynucleotide in cells of a plant not exposed to a saline stress and an osmotic stress, or detecting a level of expression that is less than about two-fold different from a level of expression of the at least one polynucleotide in cells of a plant known to be exposed to a saline stress and an osmotic stress, indicates the test plant has been exposed to a saline stress and an osmotic stress, or wherein

detecting a level of expression that is less than about two-fold different from a level of expression of the at least one polynucleotide in cells of a plant not exposed to a saline stress and an osmotic stress, or detecting a level of expression that is at least about two-fold different from a level of expression of the at least one polynucleotide in cells of a plant known to be exposed to saline stress and an osmotic stress, indicates the test plant has not been exposed to a saline stress and an osmotic stress.

Claim 40

A method for determining whether a test plant has been exposed to a cold stress, the method comprising

• detecting a level of expression of at least one polynucleotide comprising a nucleotide sequence as set forth SEQ ID NOS:1-155, 157-229, 230-232, 234-557, 559-572, 574-605, 607-634, 636-634, 636-786, 788812, and 814-1261 in cells of the test plant, wherein

detecting a level of expression that is at least about two-fold different from a level of expression of the at least one polynucleotide in cells of a plant not exposed to a cold stress, or detecting a level of expression that is less than about two-fold different from a level of expression of the at least one polynucleotide in cells of a plant known to be exposed to a cold stress, indicates the test plant has been exposed to a cold stress, or wherein

detecting a level of expression that is less than about two-fold different from a level of expression of the at least one polynucleotide in cells of a plant not exposed to a cold stress, or detecting a level of expression that is at least about two-fold different from a level of expression of the at least one polynucleotide in cells of a plant known to be exposed to a cold stress, indicates the test plant has not been exposed to a cold stress.

Claim 41

A method for determining whether a test plant has been exposed to a cold stress, a saline stress and an osmotic stress, the method comprising

• detecting a level of expression of at least one polynucleotide comprising a nucleotide sequence as set forth in SEQ ID NOS:1262-1698 in cells of the test plant, wherein

detecting a level of expression that is at least about two-fold different from a level of expression of the at least one polynucleotide in cells of a plant not exposed to a cold stress, a saline stress and an osmotic stress, or detecting a level of expression that is less than about two-fold different from a level of expression of the at least one polynucleotide in cells of a plant known to be exposed to a cold stress, a saline stress and an osmotic stress, indicates the test plant has been exposed to a cold stress, a saline stress and an osmotic stress, or wherein

detecting a level of expression that is less than about two-fold different from a level of expression of the at least one polynucleotide in cells of a plant not exposed to a cold stress, a saline stress and an osmotic stress, or detecting a level of expression that is at least about two-fold different from a level of expression of the at least one polynucleotide in cells of a plant known to be exposed to a cold stress, a saline stress and an osmotic stress, indicates the test plant has not been exposed to a cold stress, a saline stress and an osmotic stress.

Claim 42

A method of producing a transgenic plant comprising plant cells that exhibit altered responsiveness to at least one stress condition, the method comprising

• introducing a polynucleotide portion of a plant stress-regulated gene into a plant cell genome, wherein the polynucleotide portion of the stress-regulated gene does not comprise a nucleotide sequence as set forth in any of SEQ ID NOS:156, 229, 233, 558, 573, 606, 635, 787, 813, 1263, 1386, 1391, 1405, 1445, 1484, 1589, 1609, 1634, 1726, 1866, 1918 or 1928, whereby the polynucleotide portion of the plant stress-regulated gene modulates a response of the plant cells to at least one stress condition, thereby producing a transgenic plant comprising plant cells that exhibit altered responsiveness to the stress condition.

Claim 46

A method of producing a transgenic plant comprising plant cells that exhibit altered responsiveness to a combination of at least two stress conditions, the method comprising

• introducing a polynucleotide portion of a plant stress-regulated gene into a plant cell genome, whereby the polynucleotide portion of the plant stress-regulated gene modulates a response of the plant cells to a combination of at least two stress conditions, thereby producing a transgenic plant comprising plant cells that exhibit altered responsiveness to the stress conditions.

Claim 85

A method of selecting a plant having an altered resistance to an abiotic stress condition or a combination of abiotic stress conditions, the method comprising:

a) contacting nucleic acid molecules representative of expressed polynucleotides in a plant cell of a plant to be examined for having an altered resistance to an abiotic stress with a nucleic acid probes that selectively hybridizes under stringent conditions to a plant stress-regulated gene comprising a nucleotide sequence as set forth in any of SEQ ID NO:1-5379;

b) detecting a level of selective hybridization of the nucleic acid probes to a nucleic acid molecule representative of an expressed polynucleotide in the plant cell, wherein the level of selective hybridization corresponds to the level of the expressed polynucleotide in the plant cell, which is indicative of resistance of the plant to an abiotic stress; and

c) selecting a plant having a level of expression of a polynucleotide indicative of altered resistance to an abiotic stress condition.

A method of modulating the responsiveness of a plant cell to a stress condition, the method comprising

• introducing a polynucleotide portion of a plant stress-regulated gene into the plant cell, wherein said gene comprises a nucleotide sequence of a polynucleotide as set forth in any of SEQ ID NOS:1-155, 157-228, 230-232, 234-557, 559-572, 574-605, 607-634, 636-786, 788-812, 814-1262, 1264-1386, 1387-1390, 1392-1404, 1406-1444, 1446-1483, 1485-1588, 1590-1608, 1610-1633, 1634-1725, 1727-1865, 1867-1917, 1919-1927, 1929-2855, 2857-2928, 2930-2932, 2934-3256, 3258-3271, 3273-3304, 3306-3323, 3325-3333, 3335-3485, 3487-3511, 3313-3956, 3958-4078, 4080-4097, 4099-4136, 4138-4175, 4177-4279, 4281-4299, 4301-4324, 4326-4414, 4416-4552, 4554-4602, and 4604-5379, thereby modulating the responsiveness of the plant cell to a stress condition.

A method of expressing a heterologous nucleotide sequence in a plant cell, the method comprising

• introducing into the plant cell a plant stress-regulated regulatory element operatively linked to the heterologous nucleotide sequence, wherein said regulatory element comprises a nucleotide sequence as set forth in any of SEQ ID NOS:2704-2855, 2857-2928, 2930-2932, 2934-3256, 3258-3271, 3273-3304, 3306-3323, 3325-3333, 3335-3485, 3487-3511, 3313-3956, 3958-4078, 4080-4097, 4099-4136, 4138-4175, 4177-4279, 4281-4299, 4301-4324, 4326-4414, 4416-4552, 4554-4602, and 4604-5379, whereby, upon exposure of the plant cell to stress condition, the heterologous nucleotide sequence is expressed in the plant cell.

A method of modulating the activity of a biological pathway in a plant cell involving a plant stress-regulated polypeptide, the method comprising

• introducing a polynucleotide portion of a plant stress-regulated gene into the plant cell, wherein the plant stress-regulated gene comprises a nucleotide sequence as set forth in any of SEQ ID NOS:1-155, 157-228, 230-232, 234-557, 559-572, 574-605, 607-634, 636-786, 788-812, 814-1262, 1264-1386, 1387-1390, 1392-1404, 1406-1444, 1446-1483, 1485-1588, 1590-1608, 1610-1633, 1634-1725, 1727-1865,1867-1917, 1919-1927, 1929-2855, 2857-2928, 2930-2932, 2934-3256, 3258-3271, 3273-3304, 3306-3323, 3325-3333, 3335-3485, 3487-3511, 3313-3956, 3958-4078, 4080-4097, 4099-4136, 4138-4175, 4177-4279, 4281-4299, 4301-4324, 4326-4414, 4416-4552, 4554-4602, and 4604-5379, thereby modulating the activity of the biological pathway.

A method of identifying a polynucleotide that modulates a stress response in a plant cell, the methods comprising:

a) contacting an array of probes representative of a plant cell genome and nucleic acid molecules expressed in plant cell exposed to the stress;

b) detecting a nucleic acid molecule that is expressed at a level different from a level of expression in the absence of the stress;

c) introducing the nucleic acid molecule of step b) into a plant cell; and

d) detecting a modulated response of the plant cell of step c) to a stress, thereby identifying a polynucleotide that modulates a stress response in a plant cell.

A transgenic plant, which contains a transgene comprising a polynucleotide portion of plant stress-regulated gene, wherein the gene comprises

• a nucleotide sequence as set forth in any of SEQ ID NOS:1-155, 157-228, 230-232, 234-SS7, 559-572, 574-605, 607-634, 636-786, 788-812, 814-1262, 1264-1386, 1387-1390, 1392-1404, 1406-1444, 1446-1483, 1485-1588, 1590-1608, 1610-1633, 1634-1725, 1727-1865, 1867-1917, 1919-1927, 1929-2855, 2857-2928, 2930-2932, 2934-3256, 3258-3271, 3273-3304, 3306-3323, 3325-3333, 3335-3485, 3487-3511, 3313-3956, 3958-4078, 4080-4097, 4099-4136, 4138-4175, 4177-4279, 4281-4299, 4301-4324, 4326-4414, 4416-4552, 4554-4602, and 4604-5379.

A plant stress-regulated gene regulatory element, wherein the gene comprises

• a nucleotide sequence as set forth in any of SEQ ID NOS:1-155, 157228, 230-232, 234-557, 559-572, 574-605, 607-634, 636-786, 788-812, 814-1262, 1264-1386, 1387-1390, 1392-1404, 1406-1444, 1446-1483, 1485-1588, 1590-1608, 1610-1633, 1634-1725, 1727-1865, 1867-1917, 1919-1927, 1929-2855, 2857-2928, 2930-2932, 2934-3256, 3258-3271, 3273-3304, 3306-3323, 3325-3333, 3335-3485, 3487-3511, 3313-3956, 3958-4078, 4080-4097, 4099-4136, 4138-4175, 4177-4279, 4281-4299, 4301-4324, 4326-4414, 4416-4552, 4554-4602, and 4604-5379.

A method for identifying a polynucleotide involved in a stress response of a plant, the method comprising:

a) contacting nucleic acid molecules representative of expressed polynucleotides in plant cells of a plant exposed to a stress condition or combination of stress conditions with an array of probes representative of the plant cell genome; and

b) detecting a nucleic acid molecule that exhibits at least a two-fold change in the level of expression as compared to the level of the nucleic acid molecule in a corresponding plant cell of a plant that was not exposed to the stress condition, thereby identifying a polynucleotide involved in a stress response of the plant.

A computer readable medium having stored thereon computer executable instructions for performing a method comprising:

a) receiving data on expression in a cell of a plant of a nucleic acid molecule having at least 70% sequence identity to a nucleotide sequence comprising any of SEQ ID NO. 1-5379; and

b) comparing the data on expression of the nucleic acid molecule with data on expression of the nucleic acid in a cell of a plant that has not been exposed to an abiotic stress, of a plant that has been exposed to an abiotic stress condition or combination of abiotic stress conditions, or of a combination of such plants.

A computer-readable medium having stored thereon a data structure comprising:

• sequence data for at least one nucleic acid molecule having at least 70% nucleic acid sequence identity to a polynucleotide having a nucleotide sequence as set forth in any of SEQ ID NO. 1-5379 or a nucleotide sequence complementary thereto; and

• a module receiving the nucleic acid molecule sequence data, which compares the nucleic acid molecule sequence data to a least one other nucleic acid sequence.

An isolated nucleic acid molecule comprising a polynucleotide selected from the group consisting of:

a) any one of the nucleotide sequences selected from the group consisting of SEQ ID NOs. 1-4;

b) a functional portion of any of the sequences of a);

c) a polynucleotide that is substantially similar to a sequence of a) or b);

d) a sequence of at least 15 nucletides that hybridizes under stringent conditions to a polynucleotide of a), b) or c);

e) the complement of any sequence of a), b), c) or d);

f) the reverse complement of any sequence of a), b), c) or d);

g) a polynucleotide encoding any polypeptide selected from the group consisting of SEQ ID NOs. 5-8; and

h) an allelic variant of any of the above.

An isolated polypeptide comprising:

a) any one of the amino acid sequences selected from the group consisting of SEQ ID NOs. 5-8;

b) a functional portion of a);

c) an amino acid sequence substantially similar to any sequence of a) or b);

d) an amino acid sequence of a)-c) wherein there has been at least one conservative amino acid substitution;

e) an allelic variant of any of a)-d).

A method for altering the tolerance of a plant to an abiotic stress comprising

• introducing into said plant a recombinant nucleic acid construct comprising at least one of the polynucleotides selected from the group consisting of SEQ ID NOs. 1-4.

A method for altering the tolerance of a plant to an abiotic stress comprising

• introducing into said plant a recombinant nucleic acid construct comprising a polynucleotide of at least 15 nucleotides in length that hybridizes under high stringency conditions to the complement of a sequence selected from the group consisting of SEQ ID NOs. 1-4.

A method for altering the tolerance of a plant to an abiotic stress comprising

• introducing into said plant a recombinant nucleic acid construct, wherein

said construct encodes a molecule which alters expression of an abiotic stress regulated coding region selected from the group consisting of SEQ ID NOs. 1-4, or the complement thereof.

A method for selecting an agent that alters abiotic stress regulated polynucleotide expression in a plant cell comprising:

• contacting at least one plant cell with a test agent;

• subjecting said plant cell to an abiotic stress before, during or after contacting said plant cell with said test agent;

• obtaining an expression profile of said plant cell wherein said expression profile comprises expression data for at least one abiotic stress regulated sequence selected from the group consisting of SEQ ID NOs. 1-4.;

• comparing the expression profile of said cell to the expression profile obtained from at least one plant cell not exposed to said agent, but exposed to said abiotic stress;

• selecting said agent if said agent alters expression of said abiotic stress regulated sequence.

An isolated nucleic acid molecule comprising a polynucleotide selected from the group consisting of:

a) any one of the nucleotide sequences selected from the group consisting of SEQ ID NOs. 1-4131, 8263-8353, 8445-8829 and 17505-17506;
b) a functional portion of any of the sequences of a);
c) a polynucleotide that is substantially similar to a sequence of a) or b);
d) a sequence of at least 15 nucletides that hybridizes under stringent conditions to a polynucleotide of a), b) or c);
e) the complement of any sequence of a), b), c) or d);
f) the reverse complement of any sequence of a), b), c) or d);
g) a polynucleotide encoding any polypeptide selected from the group consisting of SEQ ID NOs. 4132-8262, 8354-8444, and 8830-9214; and
h) an allelic variant of any of the above.

An isolated polypeptide comprising:

a) any one of the amino acid sequences selected from the group consisting of SEQ ID NOs. 4132-8262, 8354-8444, and 8830-9214;
b) a functional portion of a);
c) an amino acid sequence to any sequence of a) or b);
d) an amino acid sequence of a)-c) wherein there has been at least one conservative amino acid substitution;
e) an allelic variant of any of a)-d).

A method for determining whether a test plant has been exposed to at least one abiotic stress condition comprising,

• determining expression of a plurality of polynucleotides selected from the group consisting of SEQ ID NOs. 1-4131, 8263-8353, 8445-8829 and 17505-17506 in said test plant to produce an expression profile, and

• comparing said expression profile of said test plant to an expression profile for the same plurality of polynucleotides in a reference plant exposed to at least one abiotic stress.

A method for altering the tolerance of a plant to an abiotic stress comprising

• introducing into said plant a recombinant nucleic acid construct comprising at least one of the polynucleotides selected from the group consisting of SEQ lD NOs. 1-4131, 8263-8353, 8445-8829, and 11374-17506.

A method for altering the tolerance of a plant to an abiotic stress comprising

• introducing into said plant a recombinant nucleic acid construct comprising a polynucleotide of at least 15 nucleotides in length that hybridizes under high stringency conditions to the complement of a sequence selected from the group consisting of SEQ ID NOs. 1-4131, 8263-8353, 8445-8829, and 17505-17506.

A method for altering the tolerance of a plant to an abiotic stress comprising

• introducing into said plant a recombinant nucleic acid construct, wherein said construct encodes a molecule which alters expression of an abiotic stress regulated coding region selected from the group consisting of SEQ ID NOs. 1-4131, 8263-8353, 8445-8829, and 17505-17506, or the complement thereof.

A method for selecting an agent that alters abiotic stress regulated polynucleotide expression in a plant cell comprising:

• contacting at least one plant cell with a test agent;

• subjecting said plant cell to an abiotic stress before, during or after contacting said plant cell with said test agent;

• obtaining an expression profile of said plant cell wherein said expression profile comprises expression data for at least one abiotic stress regulated sequence selected from the group consisting of SEQ ID NOs. 1-4131, 8263-8353, 8445-8829, and 17505-17506.;

• comparing the expression profile of said cell to the expression profile obtained from at least one plant cell not exposed to said agent, but exposed to said abiotic stress;

• selecting said agent if said agent alters expression of said abiotic stress regulated sequence.

A computer readable medium having stored thereon computer executable instructions for performing a method comprising,

• receiving data on expression in a test plant of at least one polynucleotide having at least 70% sequence identity to a nucleotide sequence selected from the group consisting of SEQ ID NOs. 1-4131, 8263-8353, 8445-8829, and 17505-17506, or the complement thereof and

• comparing expression data from said test plant to expressin data for the same at least one nucleic acid molecule in a plant which has been exposed to at least one abiotic stress.

A computer-readable medium having stored thereon a data structure comprising,

• sequence data for at least one polynucleotide having at least 70% nucleic acid sequence identity to a polynucleotide selected from the group consisting of SEQ ID NOs. 1-4131, 8263-8353, 8445-8829, and 17505-17506, or the complement thereof; and

• a module receiving the nucleic acid molecule sequence data which compares the nucleic acid molecule sequence data to at least one other nucleic acid sequence.

A method for identifying a homolog or ortholog to an abiotic stress responsive polynucleotide comprising:

a) determining the nucleotide sequence of a plurality of isolated polynucleotides to create a set of nucleotide sequences;
b) translating the nucleotide sequences in the set to derive one or more putative amino acid sequences, based on one or more of the possible reading frames of the nucleotide sequences and their complementary sequences;
c) selecting an amino acid sequence of an abiotic stress-responsive protein and comparing the amino acid sequence of the abiotic stress-responsive protein with at least one of the putative amino acid sequences;
d) identifying putative amino acid sequences having homology with at least a region of the amino acid sequence of the abiotic stress-responsive protein; and
e) correlating putative amino acid sequences having said homology to translated nucleotide sequences of b).

A method for altering the expression of a polynucleotide in response to an abiotic stress comprising

• operably linking said polynucleotide to a regulatory region selected from the group consisting of SEQ ID NOs. 13374-17504.

A fused gene comprising

a promoter sequence derived from a gene of Alcaligenes eutrophus strain CH34, SV661, DS185, AE453, or A5, said gene being a regulatory gene involved in the expression of either the resistance to one or several metals or the catabolism of one or several xenobiotic compounds, said promoter from said regulatory gene being an inducible promoter and is inducible in the presence of said metals or xenobiotic compounds, or both, and

downstream of the promoter, a five gene lux (CDABE) operon said genes coding for subunit .alpha. and .beta. of luciferase, a fatty acid reductase, an acyltransferase and an acylprotein synthase, said operon being under the operational control of said promoter, wherein at least one of said genes produces a detectable signal.

A process for preparing a bacterial cellular host wherein said bacterial cellular host emits light in the presence of zinc with a detection limit of 1 ppm and dynamic ravage between 1 and 23 ppm zinc comprising the steps of:

(a) digesting with SalI a plasmid pBR325 comprising a czc fragment of plasmid pMOL30 from Alcaligenes eutrophus strain CH34 and surrounding EcoRI fragment to obtain a promoter and a gene encoding resistance to zinc;
(b) inserting said promoter and said gene encoding resistance to zinc of step
(a) into a plasmid pUCD615 (in E. coli CM600 deposited at the C.N.C.M., Institut Pasteur, rue du Docteur Roux, 75015 Paris, on Feb. 28, 1991, under No. I-1050), at its multiple cloning site, and comprising the lux operon of Vibrio fischeri, to obtain a replicable plasmid;
(c) transforming the replicable plasmid of (b) in E. coli;
(d) selecting the inserted plasmid on ampicillin plates with various concentrations of zinc; and
(e) detecting the light producing E. coli in the presence of zinc.

A process for preparing a bacterial cellular host wherein said bacterial cellular host emits light in the presence of cobalt with a detection limit of 1 ppm and dynamic range between 1 and 23 ppm cobalt comprising the steps of:

(a) digesting with SalI a plasmid pBR325 comprising a czc fragment of plasmid pMOL30 from Alcaligenes eutrophus strain CH34 and surrounding EcoRI fragment to obtain a promoter and a gene encoding resistance to cobalt;
(b) inserting said promoter and said gene encoding resistance to cobalt of step (a) into a plasmid pUCD615 (in E. coli CM600 deposited at the C.N.C.M. Institut Pasteur, 28 rue du Docteur Roux, 75015 Paris, on Feb. 28, 1991, under No. I-1050), at its multiple cloning site, and comprising the lux operon of Vibrio fischeri, to obtain a replicable plasmid;
(c) transforming the replicable plasmid of (b) in E. coli;
(d) selecting the inserted plasmid on ampicillin plates with various concentrations of cobalt; and
(e) detecting the light producing E. coli in the presence of cobalt.

Fused gene containing:

-  a promoter sequence obtainable from (a) gene(s) of Alcaligenes eutrophus and encoding either the resistance to one or several metal(s) or the catabolism of one or several xenobiotic compound(s), said promoter being inducible in the presence of said metal(s) or xenobiotic compound(s), or both,
- and downstream of the promoter, a five gene IuxCDABE operon, said genes coding respectively for a fatty acid reductase, an acyl transferase, two subunits Q and 3 of the luciferase and an acylprotein synthase, said lux operon being under the operational control of said Alcaligenes eutrophus promoter.

Transconjugants forming biosensors emitting light in the presence of metals or xenobiotics characterized in that they are obtained by the conjugation of Alcaligenes eutrophus and E. coli, wherein

- Alcaligenes eutrophus contains a gene encoding the resistance to a metal or encoding the catabolism of a xenobiotic compound, and possibly a marker of the presence of the gene,
-   E. coli contains a transposon containing the luxCDABE operon of Vibrio fischeri without its own promoter and possibly a marker of the presence of said gene.

A fused gene comprising

a promoter sequence derived from a gene of Alcaligenes eutrophus strain CH34, SV661, DS185, AE453, or A5, said gene being a regulatory gene involved in the expression of either the resistance to one or several metals or the catabolism of one or several xenobiotic compounds, said promoter from said regulatory gene being an inducible promoter and is inducible in the presence of said metals or xenobiotic compounds, or both, and

downstream of the promoter, a five gene lux (CDABE) operon said genes coding for subunit α and β of luciferase, a fatty acid reductase, an acyltransferase and an acylprotein synthase, said operon being under the operational control of said promoter, wherein at least one of said genes produces a detectable signal.

A process for preparing a bacterial cellular host wherein said bacterial cellular host emits light in the presence of zinc with a detection limit of 1 ppm and dynamic range between 1 and 23 ppm zinc comprising the steps of:

(a) digesting with SalI a plasmid pBR325 comprising a czc fragment of plasmid pMOL30 from Alcaligenes eutrophus strain CH34 and surrounding EcoRI fragment to obtain a promoter and a gene encoding resistance to zinc;

(b) inserting said promoter and said gene encoding resistance to zinc of step (a) into a plasmid pUCD615 (in E. coli CM600 deposited at the C.N.C.M., Institut Pasteur, 28 rue du Docteur Roux, 75015 Paris, on Feb. 28, 1991, under No. I-1050), at its multiple cloning site, and comprising the lux operon of Vibrio fischeri, to obtain a replicable plasmid;

(c) transforming the replicable plasmid of (b) in E. coli;

(d) selecting the inserted plasmid on ampicillin plates with various concentrations of zinc; and

(e) detecting the light producing E. coli in the presence of zinc.

A process for preparing a bacterial cellular host wherein said bacterial cellular host emits light in the presence of cobalt with a detection limit of 1 ppm and dynamic range between 1 and 23 ppm cobalt comprising the steps of:

(a) digesting with SalI a plasmid pBR325 comprising a czc fragment of plasmid pMOL30 from Alcaligenes eutrophus strain CH34 and surrounding EcoRI fragment to obtain a promoter and a gene encoding resistance to cobalt;
(b) inserting said promoter and said gene encoding resistance to cobalt of step (a) into a plasmid pUCD615 (in E. coli CM600 deposited at the C.N.C.M. Institut Pasteur, 28 rue du Docteur Roux, 75015 Paris, on Feb. 28, 1991, under No. I-1050), at its multiple cloning site, and comprising the lux operon of Vibrio fischeri, to obtain a replicable plasmid;
(c) transforming the replicable plasmid of (b) in E. coli;
(d) selecting the inserted plasmid on ampicillin plates with various concentrations of cobalt; and
(e) detecting the light producing E. coli in the presence of cobalt.

Fused gene containing :

- the promoter sequence of (a) gene(s) encoding the resistance to one or several metal(s) or encoding the catabolism of one or several xenobiotic compound(s), said promoter being inducible in the presence of said metal(s) or xenobiotic compound(s), or both,

- and downstream the promoter, a gene producing a detectable signal such as light emitting gene, said gene being under the control of said promoter, said gene producing a detectable signal being located at a position such that the induction of the promoter causes the transcription of the gene producing a detectable signal and such that there is no terminator between the promoter and the gene producing a detectable signal, said gene being such that it enables to recycle fatty acid (which has been generated during the reaction responsible for the detectable signal) into aldehyde.

A recombinant nucleic acid sequence comprising an SOS regulated promoter with an induction ratio higher than 40, said promoter being operatively linked to a reporter encoding nucleic acid sequence encoding a reporter resulting in a signal that can be assayed as light production.

A method for determining the presence of multiple genotoxic compounds in a sample, said method comprising the steps of

- culturing a host microorganism, said host microorganism comprising a nucleic acid sequence comprising an SOS regulated promoter, said promoter being operatively linked to a reporter encoding nucleic acid sequence encoding a reporter resulting in a signal that can be assayed as light production,
- measuring the luminescence of the culture, said measuring occurring at various points in time, preferably continuously and determining the signal to noise ratio at said points in time, plotting the data, said data representing the kinetics of genotoxicity of said sample with multiple peaks being indicative of multiple genotoxicity compounds with different induction kinetics.

A method for determining the presence of a genotoxic compound in a sample, said method comprising the steps of

- culturing a host microorganism, said host microorganism comprising a nucleic acid sequence comprising an SOS regulated promoter with an induction ratio higher than 40, said promoter being operatively linked to a reporter encoding nucleic acid sequence encoding a reporter resulting in a signal that can be assayed as light production,
- measuring the luminescence of the culture at multiple points in time, preferably continuously and
- determining whether the luminescence of the culture has changed, increased luminescence being indicative of the presence of a genotoxic compound.

A recombinant nucleic acid sequence comprising an SOS regulated promoter with an induction ratio higher than 40, said promoter being operatively linked to a reporter encoding nucleic acid sequence encoding a reporter resulting in a signal that can be assayed as light production.

A method for determining the presence of multiple genotoxic compounds in a sample, said method comprising the steps of

- culturing a host microorganism, said host microorganism
comprising a nucleic acid sequence comprising an SOS regulated promoter, said promoter being operatively linked to a reporter encoding nucleic acid sequence encoding a reporter resulting in a signal that can be assayed as light production,
- measuring the luminescence of the culture, said
measuring occurring at various points in time, preferably continuously and determining the signal to noise ratio at said points in time, plotting the data, said data representing the kinetics of genotoxicity of said sample with multiple peaks being indicative of multiple genotoxicity compounds with different induction kinetics.

A method for determining the presence of a genotoxic compound in a sample, said method comprising the steps of

- culturing a host microorganism, said host microorganism comprising a nucleic acid sequence comprising an SOS regulated promoter with an induction ratio higher than 20, said promoter being operatively linked to a reporter encoding nucleic acid sequence encoding a reporter resulting in a signal that can be assayed as light production,
- measuring the luminescence of the culture at multiple points in time, preferably continuously and
- determining whether the luminescence of the culture has changed, increased luminescence being indicative of the presence of a genotoxic compound.

A recombinant nucleic acid sequence comprising an SOS regulated promoter with an induction ratio higher than 40, said promoter being operatively linked to a reporter encoding nucleic acid sequence encoding a reporter resulting in a signal that can be assayed as light production, wherein the promoter is Rec N (seq. id. no. 3).

A recombinant nucleic acid sequence comprising an SOS regulated promoter with an induction ratio higher than 40, said promoter being operatively linked to a reporter encoding nucleic acid sequence encoding a reporter resulting in a signal that can be assayed as light production, wherein the promoter is a mutated RecN promoter with the following nucleic acid sequence id. no. 9.

A recombinant nucleic acid sequence comprising an SOS regulated promoter with an induction ratio higher than 40, said promoter being operatively linked to a reporter encoding nucleic acid sequence encoding a reporter resulting in a signal that can be assayed as light production, wherein the promoter is a mutated RecN promoter with the following nucleic acid sequence id. no. 10.

A recombinant nucleic acid sequence comprising an SOS regulated promoter with an induction ratio higher than 40, said promoter being operatively linked to a reporter encoding nucleic acid sequence encoding a reporter resulting in a signal that can be assayed as light production.

A method for determining the presence of multiple genotoxic compounds in a sample, said method comprising the steps of

- culturing a host microorganism, said host microorganism comprising a nucleic acid sequence comprising an SOS regulated promoter, said promoter being operatively linked to a reporter encoding nucleic acid sequence encoding a reporter resulting in a signal that can be assayed as light production,
- measuring the luminescence of the culture, said measuring occurring at various points in time, preferably continuously and determining the signal to noise ratio at said points in time, plotting the data, said data representing the kinetics of genotoxicity of said sample with multiple peaks being indicative of multiple genotoxicity compounds with different induction kinetics.

A method for determining the presence of a genotoxic compound in a sample, said method comprising the steps of

- culturing a host microorganism, said host microorganism comprising a nucleic acid sequence comprising an SOS regulated promoter with an induction ratio higher than 20, said promoter being operatively linked to a reporter encoding nucleic acid sequence encoding a reporter resulting in a signal that can be assayed as light production,
- measuring the luminescence of the culture at multiple points in time, preferably continuously and
- determining whether the luminescence of the culture has changed, increased luminescence being indicative of the presence of a genotoxic compound.

A recombinant gene comprising

• an SOS gene expressed when a DNA is damaged and a gene expressing luciferase activity positioned downstream of the SOS gene.

A host microorganism transformed with a recombinant gene comprising

• an SOS gene expressed when a DNA is damaged and a gene expressing luciferase activity positioned downstream of the SOS gene.

A method for detecting or quantitating a mutagenic substance in a sample, comprising the steps of:

• culturing a host microorganism transformed with a recombinant gene comprising an SOS gene expressed when a DNA is damaged and a gene expressing luciferase activity positioned downstream of the SOS gene, in a medium to which the sample is added; and

• measuring a luminescence generated by expression of the gene expressing luciferase activity.

A recombinant gene comprising

• an SOS gene expressed when a DNA is damaged and genes expressing luciferase activity and an enzyme which catalyzes the production of a substrate for the luciferase, positioned downstream of the SOS gene.

A host microorganism transformed with a recombinant gene comprising

• an SOS gene expressed when a DNA is damaged and genes expressing luciferase activity and an enzyme which catalyzes the production of a substrate for the luciferase positioned downstream of the SOS gene.

A method for detecting or quantitating a mutagenic substance in a sample, comprising the steps of:

• culturing a host microorganism transformed with a recombinant gene comprising an SOS gene expressed when a DNA is damaged and genes expressing luciferase activity and an enzyme which catalyzes the production of a substrate for luciferase, positioned downstream of the SOS gene, in a medium to which the sample is added; and

• measuring a luminescence generated by expression of the genes expressing luciferase activity and an enzyme which catalyzes the production of a substrate for luciferase.

A method for identifying a mutagenic substance, comprising the steps of:

• culturing Escherichia or Salmonella transformed with recombinant DNA comprising

(i) an Escherichia or Salmonella SOS gene and
(ii) a gene encoding luciferase isolated from Photobacterium phosphoreum, Photobacterium leiognethi, Vibrio splendidus, Vibrio cholerae, Photinus pyralis, Vibrio harveyi or Vibrio fischeria; wherein
said gene encoding luciferase is positioned downstream of said SOS gene such that when said SOS gene is expressed, then said gene encoding luciferase is also expressed;

• contacting said culture with a substance to be tested wherein said Escherichia or Salmonella in said culture is provided with a luciferase substrate; and

• determining whether said substance is mutagenic by measuring the amount of luminescence in said culture.

A yeast cell comprising:

(a) a nucleic acid encoding LuxA and a nucleic acid encoding LuxB, the nucleic acid encoding LuxA and the nucleic acid encoding LuxB both being operatively linked to at least a first promoter and at least one estrogen response element; and
(b) at least one receptor capable of binding an estrogenic agent and the at least one estrogen response element.

A method for detecting the presence of an estrogenic agent in a sample, the method comprising:

(a) providing a sample;
(b) providing at least one yeast cell comprising a nucleic acid encoding
LuxA and a nucleic acid encoding LuxB, the nucleic acid encoding LuxA and the nucleic acid encoding LuxB both being operatively linked to at least a first promoter and at least one estrogen response element, and at least one receptor capable of binding an estrogenic agent and the at least one estrogen response element;
(c) contacting the at least one cell with the sample, wherein the cell emits bioluminescence when the estrogenic agent is present; and
(d) analyzing the cell for bioluminescence.

Claim 1
An apparatus for the detection of an estrogen or a xenoestrogen, comprising:

• an integrated circuit chip, wherein

said chip comprises an integrated light detection system, and

• a biosensor comprising a collection of eukaryotic cells harboring a recombinant lux gene from a high temperature microorganism wherein

said gene is operably linked with a heterologous promoter, wherein

a detectable light-emitting lux gene product is expressed in the presence of said estrogen or xenoestrogen, light from said light-emitting lux gene product being detected by said light detection system.

Claim 1
An apparatus for the detection of an estrogen or a xenoestrogen, comprising:

• an integrated circuit chip, wherein

said chip comprises an integrated light detection system, and

• a biosensor comprising a collection of eukaryotic cells harboring a recombinant lux gene from a high temperature microorganism

wherein said gene is operably linked with a heterologous promoter, wherein

a detectable light-emitting lux gene product is expressed in the presence of said estrogen or xenoestrogen, light from said light-emitting lux gene product being detected by said light detection system.

A cell which is obtained by transfer of

• a promoter containing a heat shock factor binding DNA sequence and

• a transcriptional regulatory sequence necessary on an occasion of stress induction as a transcriptional regulatory factor binding site, as well as

• a reporter gene under the control of said promoter into a chromosome,

said reporter gene
- being connected, on the downstream side thereof, to the SV40pA signal without any intervening intron, and
- which is used for detecting chemicals or natural toxins which disrupt or disturb homeostasis in organisms, by measuring said reporter gene protein inducing activity.

A cell which is obtained by transfer of

• a promoter containing a heat shock factor binding DNA sequence and

• a transcriptional regulatory sequence which functions in response to stress induction of a protein as a transcriptional regulatory factor binding site, as well as

• a reporter gene under the control of said promoter into a chromosome,

said reporter gene

- being connected, on the downstream side thereof, to the SV40pA signal without any intervening intron, and
- which is usable for detecting chemicals or natural toxins which disrupt or disturb homeostasis in organisms, by measuring a protein inducing activity of said reporter gene, wherein

• the promoter containing the heat shock factor binding DNA sequence and the transcriptional regulatory sequence which functions on the occasion of stress induction of a protein as the transcriptional regulatory factor binding site, is an HSP47 promoter containing the heat shock factor binding DNA sequence and an SP1 factor binding sequence.

YH9-RC deposited under KCTC 0730BP reacts with toxic substances to show change in the degree of luminescence.

A method for detecting toxic substances comprising

    the step of determining the existence and the concentration of toxic substances using a microorganism, wherein

• the microorganism is YH9-RC deposited under KCTC 0730BP, and

• an aldehyde is added as a substrate so that the microorganism can emit light.

A kit for analyzing toxic substances comprising

• a toxic substance sample,

• a microorganism which reacts with the toxic substance to show change in the degree of luminescence,

• a reactor where the sample reacts with the microorganism, and

• a light-detection apparatus which can detect light emitted from the microorganism, wherein

the microorganism is YH9-RC deposited under KCTC 0730BP, and an aldehyde is introduced into the reactor so that the microorganism can emit light.

YH9-RC deposited under KCTC 0730BP reacts with toxic substances to show change in the degree of luminescence.

A method for detecting toxic substances comprising

    the step of determining the existence and the concentration of toxic substances using a microorganism, wherein

• the microorganism is YH9-RC deposited under KCTC 0730BP, and

• an aldehyde is added as a substrate so that the microorganism can emit light.

A kit for analyzing toxic substances comprising

• a toxic substance sample,

• a microorganism which reacts with the toxic substance to show change in the degree of luminescence,

• a reactor where the sample reacts with the microorganism, and

• a light-detection apparatus which can detect light emitted from the microorganism, wherein

the microorganism is YH9-RC deposited under KCTC 0730BP, and an aldehyde is introduced into the reactor so that the microorganism can emit light.

A transgenic nematode

• selected from the group consisting of PC71, deposited as ATCC Accession Designation No. 209318, PC72, deposited as ATCC Accession Designation No. 209319, and PC73, deposited as ATCC Accession Designation No. 209320,

• said nematode having a gene construct stably integrated into its genome, and gene construct comprising the nematode hsp16 promoter operably linked to the lacZ gene, wherein the lacZ gene is expressed when said nematode is exposed to a toxin.

A kit comprising:

(a) a test chamber containing a liquid growth medium and at least one transgenic nematode selected from the group consisting of PC71, deposited as ATCC Accession Designation No. 209318, PC72, deposited as ATCC Accession Designation No. 209319, and PC73, deposited as ATCC Accession Designation No. 209320, said nematode having a gene construct stably integrated into its genome, said gene construct comprising a nematode hsp16 promoter operably linked to the lacZ gene, wherein the lacZ gene is expressed when said nematode is exposed to a toxin; and

(b) means for detecting expression of the lacZ gene.

Process to detect toxic substances in the environment based on the use of a biosensor, characterized in that it includes the stages consisting in:

• placing in an environment to be biomonitorized, such as air, ground, food, clothes, etc. a biosensor consisting of cells of a wild type strain or of genetically engineered strains of Dictyostelium in conditions apt to development;

• leaving for 20 hr the cells in such an environment;

• evaluating the morphology of the developing cells aggreagates or the expression of reporter genes.

A method of providing transgenic fish to the ornamental fish market, comprising the steps of:

(a) obtaining an ornamental transgenic fish comprising one or more chimeric fluorescence genes positioned under the control of a promoter, wherein

• the transgenic fish expresses one or more fluorescent proteins encoded by the one or more fluorescence genes at a level sufficient such that said fish fluoresces upon exposure to one or more of a blue light, ultraviolet light or sunlight; and

(b) distributing said fish to the ornamental fish market.

Claim 1

A zebrafish cytokeratin gene promoter which is capable of directing a structural gene to be predominantly expressed in skin epithelia when it is inserted in front of the structural gene and introduced into fish embryos.

Claim 2

A zebrafish muscle creatine kinase gene promoter which is capable of directing a structural gene to be specifically expressed in muscles when it is inserted in front of the structural gene and introduced into fish embryos.

Claim 3

A zebrafish fast skeletal muscle isoform of myosin light chain 2 gene promoter which is capable of directing a structural gene to be predominantly expressed in skeletal muscles when it is inserted in front of the structural gene and introduced into fish embryos.

Claim 4

A zebrafish acidic ribosomal protein PG gene promoter which is capable of directing a structural gene to be expressed ubiquitously in all tissues when it is inserted in front of the structural gene and introduced into fish embryos.

Claim 10

A transgenic fish comprising a DNA that encodes a fluorescent protein under control of a promoter that causes said DNA
(1) to be expressed in predominantly skin epithelia,
(2) to be specifically expressed in muscles,
(3) to be predominantly expressed in skeletal muscles, or
(4) to be expressed ubiquitously in all tissues.

Claim 14

A recombinant DNA vector comprising a promoter DNA that hybridizes under stringent conditions to a polynucleotide of any one of SEQ ID NOS:7, 8, 9, or 22, operatively linked to a structural gene encoding a fluorescent or chemiluminescent protein.

Claim 16

A transgenic fish comprising a chimeric gene in turn comprising a promoter DNA that hybridizes under stringent conditions to a polynucleotide of any one of SEQ ID NOS:7, 8, 9, or 22, operatively linked to a structural gene encoding a fluorescent or a chemiluminescent protein.

Claim 17

A method for sensing a steroid hormone or a steroid hormone derivative in a water sample comprising:
(a) contacting a fish expressing a fluorescent or chemiluminescent protein under control of an estrogen- or other steroid hormone-inducible promoter with a sample of water; and
(b) measuring the amount of fluorescent or chemiluminescent light from said fish.

Claim 18

A method for sensing heavy metals, such as zinc, copper, cadmium, mecury etc., in a water sample comprising:
(a) contacting a fish expressing a fluorescent or chemiluminescent protein under control of a heavy metal-inducible promoter with a sample of water; and
(b) measuring the amount of fluorescent or chemiluminescent light from said fish.

A method of detecting the presence of an environmental insult comprising:

(a) exposing a transformed detector E. coli to an environmental insult, the transformed detector E. coli being genetically engineered to contain an expressible heterologous luxCDABE gene complex under the control of a stress-inducible promoter sequence wherein the promoter sequence is responsive to a regulatory circuit; and
(b) measuring an increase in luminescence of the transformed detector E. coli, the increase indicating the presence of an environmental insult.

A method of detecting stress in a population of transformed E. coli comprising:

(a) exposing a population of transformed detector E. coli to an environmental insult, the transformed detector E. coli being genetically engineered to contain an expressible heterologous luxCDABE gene complex under the control of a stress-inducible promoter sequence wherein the promoter sequence is responsive to a global regulatory circuit; and
(b) measuring an increase in luminescence of the transformed detector E. coli, the increase indicating stress.

A transformed bioluminescent E coli capable of an increase in bioluminescence upon exposure to a sublethal level of environmental insult, the transformed bioluminescent E. coli comprising:

(a) a stress inducible promoter sequence wherein the promoter sequence is responsive to a regulatory circuit; and
(b) an expressible heterologous luxCDABE gone complex under the control of the stress inducible promoter sequence.

A method of detecting the presence of a environmental insult comprising:

(a) exposing a transformed detector E. coli to a sublethal environmental insult, the transformed detector E. coli being genetically engineered to contain an expressible heterologous luxCDABE gone complex under the control of a stress-inducible promoter sequence wherein the promoter sequence is responsive to a regulatory circuit; and
(b) measuring an increase in luminescence of the transformed detector E. coli, the increase indicating the presence of an environmental insult.

E. coli selected from the group consisting of:

(i) TV1076 having ATCC Number 69314 comprising a tolC- mutation and an expressible heterologous lux gene complex under the control of a grpE stress inducible promoter sequence;
(ii) WM1302 having ATCC Number 69316 comprising a tolC- mutation and an expressible heterologous lux gene complex under the control of a dnaK stress inducible promoter sequence;
(iii) TV1060 having ATCC Number 69142 comprising an expressible heterologous lux gene complex under control of a grpE stress inducible promoter sequence;
(iv) TV1061 having ATCC Number 69315 comprising an expressible heterologous lux gene complex under control of a grpE stress inducible promoter sequence;
(v) WM1021 having ATCC Number 69141 comprising an expressible heterologous lux gene complex under control of a dnaK stress inducible promoter sequence;
(vi) WM1026 having ATCC Number 69143 comprising an expressible heterologous lux gene complex under control of a dnaK stress inducible promoter sequence; and
(vii) WM1202 having ATCC Number 69313 comprising an expressible heterologous lux gene complex under control of a dnaK stress inducible promoter sequence.

A nucleic acid molecule, comprising:

(a) a stress inducible promoter sequence wherein said promoter sequence is responsive to a regulatory circuit; and
(b) an expressible bacterial luxCDABE gene complex under control of said promoter sequence.

A method of detecting environmental stress comprising:

(a) exposing a detector organism to an environmental insult, said organism being genetically engineered to contain an expressible lux gene complex under the control of a stress inducible promoter sequence wherein the promoter sequence is responsive to a global regulatory circuit; and
(b) measuring a change in luminescence of said detector organism.

A method of detecting environmental stress comprising:

(a) exposing a detector organism to a sublethal environmental insult, said organism being genetically engineered to contain an expressible lux gene complex under the control of a stress inducible promoter sequence wherein the promoter sequence is responsive to a global regulatory circuit; and
(b) measuring an increase in luminescence of said detector organism.

A method of detecting stress on a microorganism population, comprising:

(a) exposing a detector organism to an environmental insult, said organism being genetically engineered to contain an expressible heterologous lux gene complex under the control of a stress inducible promoter sequence wherein the promoter sequence is responsive to a global regulatory circuit; and
(b) measuring a change in luminescence of said detector organism.

A transformed bioluminescent microorganism capable of an increase in bioluminescence upon exposure to a sublethal level of environmental insult, said microorganism comprising:

(a) a stress inducible promoter sequence wherein the promoter sequence is responsive to a global regulatory circuit; and
(b) an expressible lux gene complex under the control of said stress inducible promoter sequence.

E. coli selected from the group consisting of:

(i) TV1076 having ATCC Number 69314 comprising a tolC- mutation and an expressible heterologous lux gene complex under the control of a grpE stress inducible promoter sequence;
(ii) WM1302 having ATCC Number 69316 comprising a tolC- mutation and an expressible heterologous lux gene complex under the control of a dnaK stress inducible promoter sequence;
(iii) TV1060 having ATCC Number 69142 comprising an expressible heterologous lux gene complex under control of a grpE stress inducible promoter sequence;
(iv) TV1061 having ATCC Number 69315 comprising an expressible heterologous lux gene complex under control of a grpE stress inducible promoter sequence;
(v) WM1021 having ATCC Number 69141 comprising an expressible heterologous lux gene complex under control of a dnaK stress inducible promoter sequence;
(vi) WM1026 having ATCC Number 69143 comprising an expressible heterologous lux gene complex under control of a dnaK stress inducible promoter sequence; and
(vii) WM1202 having ATCC Number 69313 comprising an expressible heterologous lux gene complex under control of a dnaK stress inducible promoter sequence.

Nucleic acid molecules, comprising:

(a) a stress inducible promoter sequence wherein the promoter sequence is responsive to a global regulatory circuit; and
(b) an expressible bacterial lux gene complex under control of said promoter sequence.

A method of detecting the presence of an environmental insult comprising:

(a) exposing a transformed detector E. coli to an environmental insult, the transformed detector E. coli being genetically engineered to contain an expressible heterologous luxCDABE gene complex under the control of a stress-inducible promoter sequence wherein the promoter sequence is responsive to a regulatory circuit; and
(b) measuring an increase in luminescence of the transformed detector E. coli, the increase indicating the presence of an environmental insult.

A method of detecting stress in a population of transformed E. coli comprising:

(a) exposing a population of transformed detector E. coli to an environmental insult, the transformed detector E. coli being genetically engineered to contain an expressible heterologous luxCDABE gene complex under the control of a stress-inducible promoter sequence wherein the promoter sequence is responsive to a global regulatory circuit; and
(b) measuring an increase in luminescence of the transformed detector E. coli, the increase indicating stress.

A transformed bioluminescent E coli capable of an increase in bioluminescence upon exposure to a sublethal level of environmental insult, the transformed bioluminescent E. coli comprising:

(a) a stress inducible promoter sequence wherein the promoter sequence is responsive to a regulatory circuit; and
(b) an expressible heterologous luxCDABE gene complex under the control the stress inducible promoter sequence.

A method of detecting the presence of a environmental insult comprising:

(a) exposing a transformed detector E. coli to a sublethal environmental insult, the transformed detector E. coli being genetically engineered to contain an expressible heterologous luxCDABE gene complex under the control of a stress-inducible promoter sequence wherein the promoter sequence is responsive to a regulatory circuit; and
(b) measuring an increase in luminescence of the transformed detector E. coli, the increase indicating the presence of an environmental insult.

E. coli selected from the group consisting of:

(i) TV1076 having ATCC Number 69314 comprising a tolC- mutation and an expressible heterologous lux gene complex under the control of a grpE stress inducible promoter sequence;
(ii) WM1302 having ATCC Number 69316 comprising a tolC- mutation and an expressible heterologous lux gene complex under the control of a dnaK stress inducible promoter sequence;
(iii) TV1060 having ATCC Number 69142 comprising an expressible heterologous lux gene complex under control of a grpE stress inducible promoter sequence;
(iv) TV1061 having ATCC Number 69315 comprising an expressible heterologous lux gene complex under control of a grpE stress inducible promoter sequence;
(v) WM1021 having ATCC Number 69141 comprising an expressible heterologous lux gene complex under control of a dnaK stress inducible promoter sequence;
(vi) WM1026 having ATCC Number 69143 comprising an expressible heterologous lux gene complex under control of a dnaK stress inducible promoter sequence; and
(vii) WM1202 having ATCC Number 69313 comprising an expressible heterologous lux gene complex under control of a dnaK stress inducible promoter sequence.

A nucleic acid molecule, comprising:
(a) a stress inducible promoter sequence wherein said promoter sequence is responsive to a regulatory circuit; and
(b) an expressible bacterial luxCDABE gene complex under control of said promoter sequence.

A method of detecting environmental stress comprising:

(a) exposing a detector organism to an environmental insult, said organism being genetically engineered to contain an expressible lux gene complex under the control of a stress inducible promoter sequence; and
(b) measuring a change in luminescence of said detector organism.

A method of detecting environmental stress comprising:

(a) exposing a detector organism to a sublethal environmental insult, said organism being genetically engineered to contain an expressible lux gene complex under the control of a stress inducible promoter sequence; and
(b) measuring an increase in luminescence of said detector organism.

A method of detecting stress on a microorganism population, comprising:

(a)  exposing a detector organism to an environmental insult, said organism being genetically engineered to contain an expressible heterologous lux gene complex under the control of a stress inducible promoter sequence; and
(b)  measuring a change in luminescence of said detector organism.

A transformed bioluminescent microorganism capable of an increase in bioluminescence upon exposure to a sublethal level of environmental insult, said microorganism comprising:

(a) a stress inducible promoter sequence; and
(b) an expressible lux gene complex under the control of said stress inducible promoter sequence.

E. coli selected from the group consisting of:

(i) TV1076 having ATCC Number 69314 comprising a tolC mutation and an expressible heterologous lux gene complex under the control of a grpE stress inducible promoter sequence;
(ii) WM1302 having ATCC Number 69316 comprising a tolC mutation and an expressible heterologous lux gene complex under the control of a dnaK stress inducible promoter sequence;
(iii) TV1O6O having ATCC Number 69142 comprising an expressible heterologous lux gene complex under control of a grpE stress inducible promoter sequence;
(iv) TV1061 having ATCC Number 69315 comprising an expressible heterologous lux gene complex under control of a grpE stress inducible promoter sequence;
(v) W141021 having ATCC Number 69141 comprising an expressible heterologous lux gene complex under control of a dnaK stress inducible promoter sequence;
(vi) WM1026 having ATTC Number 69143 comprising an expressible heterologous lux gene complex under control of a dnaK stress inducible promoter sequence; and
(vii) Wb41202 having ATCC Number 69313 comprising an expressible heterologous lux gene complex under control of a dnaK stress inducible promoter sequence.

Nucleic acid molecules, comprising:

(a) a stress inducible promoter sequence; and
(b) an expressible bacterial lux gene complex under control of said promoter sequence.

A method for determining a heavy metal in a sample comprising;

a) providing a cell comprising a recombinant DNA plasmid, said plasmid comprising a gene coding for an insect luciferase or a green fluorescent protein (GFP) marker protein, wherein the copy number of said plasmid is under the control of a promoter regulatable by a heavy metal, and wherein said promoter controls the origin of replication of said plasmid;
b) contacting said cell with a sample which contains said heavy metal;
c) allowing said heavy metal to affect said cell, whereafter the amount of said marker protein is determined;
d) comparing the amount of said marker protein with a control in which no metal was present or in which the heavy metal was present in a known amount, whereby the presence and/or amount of said heavy metal is determined.

A method for the determination of a heavy metal in a sample, comprising:

a) providing a cell comprising a recombinant DNA plasmid, said plasmid comprising a gene coding for an insect luciferase or a green fluorescent protein (GFP) marker protein, and having a copy number between 1 and 2000/cell, wherein the expression of said marker protein sequence being (missing?: under the control of a promoter regulatable by?) a heavy metal, and wherein said promoter controls the origin of the replication of said plasmid;
b) contacting said cell with a sample which contains said heavy metal;
c) allowing said heavy metal to affect said cell, whereafter the amount of said marker protein is determined;
d) comparing the amount of said marker protein with a control in which no metal was present or in which it was present in a known amount, whereby the presence and amount of said heavy metal is determined.

The plasmid pMV1 (DSM Deposit No. 8708).

The plasmid pMV3 (DSM Deposit No. 8893).

The plasmid pTOO21 (DSM Deposit No. 9666).

The plasmid pTOO23 (DSM Deposit No. 9667).

A method for determining a metal in a sample, characterized in that

a)    a recombinant DNA plasmid the copy number of which is under the control of a promotor regulatable by the metal is transferred into a cell;
b)    the cell containing the recombinant DNA plasmid is contacted with the sample which contains a metal, for example by incubating them together, in which case the passing of the metal into the cell either is passive or there is a mechanism for it in the cell;
c)    the metal is allowed to affect for a suitable time the cell which contains the recombinant DNA plasmid, whereafter the amount of recombinant DNA plasmid is determined by either physical or chemical means;
d)    the amount of recombinant DNA plasmid is compared by chemical or physical methods with a control test in which no metal was present and/or it was present in a known amount in a reaction, whereby the presence and/or amount of the metal can be determined.

A method for the determination of a metal in a sample, characterized in that

a)    a recombinant DNA plasmid having a constant copy number between 1 and 2000/cell is transferred into a cell, and the plasmid contains as a marker protein a DNA sequence coding for a virus, procaryotic cell or eucaryotic cell protein, or a portion thereof, essential in terms of its biological activity, the expression of the DNA sequence being under the control of a promoter regulatable by means of the metal and being controlled by negative and/or positive feedback;
b)    the cell containing the recombinant DNA plasmid is contacted with a sample which contains metal, for example by incubating them together, in which case the passing of the metal into the cell either is passive or there is a separate mechanism for it in the cell;
c)    the metal is allowed to affect for a suitable time the cell which contains the recombinant DNA plasmid, whereafter the amount of protein coded for by recombinant DNA plasmid is determined by either physical or chemical means;
d)    the amount of the protein coded for by the recombinant DNA plasmid is compared by chemical or physical means with a control test in which no metal was present and/or it was present in a known amount in a reaction, whereby the presence and/or amount of the metal can be determined.

The plasmid pMV1, which has been deposited with the depository DSM under deposit number 8708.

The plasmid pMV3, which has been deposited with the depository DSM under deposit number 8893.

The plasmid pTOO21, which has been deposited with the depository DSM under deposit number 9666.

The plasmid pTOO23, which has been deposited with the depository DSM under deposit number 9667.

A method for determining the presence or amount of a factor in a sample to be tested, wherein the factor affects directly or indirectly the DNA, RNA and/or proteins of the cell or the synthesis mechanisms thereof, characterized in

a) incubating a sample to be tested with a population of transformed cells for a period sufficient to allow said factor, if present in the sample, to affect said cells, said cells being transformed with a recombinant-DNA plasmid, the replication of said plasmid being subject to a regulatable promoter, which can be induced by an exogenous stimulus independent of replication of the cells;
b) then applying said exogenous stimulus to said cells to induce replication of said plasmid, whereupon the copy number of the plasmid will begin to increase in the cell, if the factor has not affected the plasmid by inhibiting the replication; and
c) the change in the copy number of the recombinant-DNA plasmid in the cell is determined directly or indirectly, and compared with a reference test in which the factor was not present or in which it was present in a known amount, and thereby the presence or the amount of the factor is determined.

A method for determining the presence or amount of a factor in a sample to be tested, wherein the factor affects directly or indirectly the DNA, RNA and/or proteins of the cell or the synthesis mechanisms thereof, characterized in

a) incubatiang a sample to be tested with a population of transformed cells for a period sufficient to allow said factor, if present in the sample, to affect said cells, said cells being transformed with a high copy number recombinant DNA plasmid containing a DNA sequence encoding a marker protein or a part thereof essential to the biological activity of said protein, said sequence being coupled to a regulatable promoter such that expression of said marker protein is inducible by an exogenous stimulus;
b) then applying said exogenous stimulus to said population of cells to induce expression of said marker protein, whereby the amount of the marker protein in the cell starts to grow, if the factor has not affected the protein synthesis directly or indirectly;
c) determining the amount of the marker protein expressed by said population of cells, and comparing said amount with a reference test in which the factor was not present or in which it was present in a known amount, and thereby the presence or the amount of the factor is determined.

A method for determining the presence or amount of at least one inhibitory factor in the sample to be tested, wherein the inhibitory factor inhibits one or more of DNA synthesis, transcription of DNA, translation of RNA, cell wall synthesis, cell membrane function or metabolic functions which participate in or influence these processes, said method comprising:

a) incubating a sample to be tested with a population of transformed cells for a period sufficient to allow an inhibitory factor, if present in the sample, to affect said cells, said cells being transformed with a recombinant DNA plasmid, and replication of said plasmid being inducible by an exogenous stimulus independent of replication of the cells and further wherein said cells are sensitive to inhibition by the inhibitory factor;
b) then applying said exogenous stimulus to said cells in an amount sufficient to induce replication of said plasmid in the absence of the inhibitory factor; and
c) determining the amount of DNA produced by said population of cells, the amount of the inhibitory factor in said sample being correlated with a reduction in the amount of DNA produced compared to the amount of DNA produced by a like cell population by application of a like amount of exogenous stimulus in the absence of said sample.

A method for determining the presence or amount of at least one inhibitory factor in the sample to be tested, wherein the inhibitory factor inhibits one of more of DNA synthesis, transcription of DNA, translation of RNA, cell wall synthesis, cell membrane function or metabolic functions which participate in or influence these processes, said method comprising:

a) incubating a sample to be tested with a population of transformed cells for a period sufficient to allow the inhibitory factor, if present in the sample, to affect said cells, said cells being transformed with a high copy number recombinant DNA plasmid containing a sequence encoding a marker protein which is detectable when expressed, said sequence being coupled to a regulatable promoter such that expression of said marker protein is inducible by an exogenous stimulus;
b) then applying said exogenous stimulus to said population of cells in an amount sufficient to induce expression of said marker protein in the absence of the inhibitory factor; and
c) determining the amount of said marker protein expressed by said population of cells, the amount of the inhibitory factor in the sample being correlated with a reduction in the amount of said marker protein produced compared to the amount of said marker protein produced by a like cell population by application of a like amount of exogenous stimulus in the absence of the sample.

A method for determining the presence of at least one inhibitory factor selected from the group consisting of ampicillin, chloramphenicol, oxytetracycline, streptomycin, erythromycin, ofloxacin, ciprofloxacin, actinomycin and trimethoprim in a sample of a biological fluid selected from the group consisting of blood, plasma, serum, urine, semen and milk, said method comprising:

a) obtaining a population of cells transformed with a high copy number recombinant DNA plasmid containing a sequence encoding luciferase, wherein said sequence is coupled to a regulatable promoter such that expression of said sequence is inducible by application of a chemical inducer to cells containing said plasmid;
b) incubating said sample with said cell population in a medium suitable for growth of said cells for a period sufficient to allow said inhibitory factor if present to affect said cells;
c) then applying said chemical inducer to said cells in an amount which in the absence of said inhibitory factor is sufficient to induce expression of said sequence; and
d) determining the amount of luciferase expressed by said cell population, the amount of said inhibitory factor in said sample being correlated with the reduction in the amount of luciferase produced relative to the amount of luciferase produced by a like cell population by application of a like amount of said chemical inducer in the absence of said sample.

A method for determining a factor affecting a cell, the factor affecting the DNA, the RNA and/or proteins of the cell or the synthesis machineries thereof, characterized in that

a) into the cell is transferred a recombinant DNA plasmid, in which the starting point or points of the machinery responsible for the replication are subject to a regulatable promoter, which can be controlled either by a positive or a negative feedback;
b) the cell containing the recombinant DNA plasmid is brought into contact with the affecting factor;
c) the affecting factor is allowed to affect the cell containing the recombinant DNA plasmid for a suitable time, and subsequently the promoter regulating the starting point of the machinery responsible for the replication of the recombinant DNA plasmid is activated, whereby the copy number of the plasmid starts growing in the cell, unless the affecting factor has not affected the plasmid in a manner inhibiting the replication;
d) the shift of the copy number of the recombinant DNA plasmid is determined directly or indirectly.

A method for determining a factor affecting the cell, the factor affecting directly or indirecty the DNA, RNA and/or proteins of the cell or their synthesis machineries, characterized in that

a) to the cell is transferred a recombinant DNA plasmid, present in many copies in the cell and the plasmid contains as a marker protein a protein of a virus, a procaryotic cell or an eucaryotic cell or a DNA sequence encoding a part essential with regard to its biological activity, the expression of which is subject to a regulatable promoter and is controlled either by a negative or a positive feedback;
b) the cell containing the recombinant DNA plasmid is brought into contact with the affecting factor;
c) the affecting factor is allowed to affect the cell containing the recombinant DNA plasmid for a suitable time, after which the regulatable promoter controlling the expression of the marker protein of the recombinant DNA plasmid is activated, whereby the amount of marker protein in the cell starts to grow, unless the affecting factor has affected the protein synthesis directly or indirectly;
d) the change of the amount/activity of the marker protein encoded by the recombinant DNA plasmid is measured.

A biologically based test system for the detection of inorganic and organic pollutants in water samples comprising

• a genetically modified bacterium producing a marker protein upon induction of a regulatory protein, wherein
• the activity of said regulatory protein is induced by the presence of said pollutant, characterized in that said genetically modified bacterium comprises at least one additional DNA binding site for the regulatory protein.

A biologically based test system for the detection of inorganic and organic pollutants in water samples, comprising

• a genetically modified bacterium producing a marker protein upon induction of a regulatory protein, wherein
• the activity of said regulatory protein is induced by the presence of said pollutant, wherein said genetically modified bacterium comprises at least one additional DNA binding site for the regulatory protein.

A  biologically based test system for the detection of inorganic and organic pollutants in water samples comprising

• a genetically modified bacterium producing a marker protein upon induction of a regulatory protein, wherein
• the activity of said regulatory protein is induced by the presence of said pollutant, characterized in that said genetically modified bacterium comprises at least one additional DNA binding site for the regulatory protein.

Claim 1

A method of detecting explosives buried beneath the surface of the ground, comprising:

1. spraying a biological sensor comprising a recombinant bacterial organism that responds to contact with said explosives by producing a detectable signal, on the surface of the ground in an area believed to be contaminated by said buried explosives, so that the biological sensor contacts soil of said surface of said ground believed to contain the buried explosives;
2. allowing a sufficient time to pass to enable the biological sensor to react with explosive residue in said soil to produce a visually detectable signal; and
3. examining said surface of the ground believed to contain said buried explosives for said visually detectable signal.

Claim 15

A method of detecting explosives buried beneath the surface of the ground, comprising the steps of:

1) spraying a biological sensor comprising a recombinant bacterial organism that responds to contact with said explosives by producing a detectable signal on the surface of the ground in an area believed to contain said buried explosives, wherein said surface of said ground is believed to be contaminated by vapors from said explosives, under conditions such that said biological sensor contacts the soil of said surface of said ground believed to contain the buried explosives;

2) allowing a sufficient time to pass to enable the biological sensor to react with explosive residue from said buried explosives in said soil to produce a visually detectable signal; and

3) examining said soil of said ground surface believed to contain said buried explosives for said visually detectable signal.

Claim 22

A method of detecting explosive residue in soil comprising the steps of:

a) providing:

    i) a biological sensor comprising a recombinant bacterial strain, and
    ii) a soil sample suspected of containing detectable levels of explosive residue; and

b) contacting said soil sample with said biological sensor under conditions such that a detectable signal is produced in the presence of said detectable levels of explosive residue.

Claim 29

A method of detecting explosive residue in soil comprising the steps of:

a) providing:

   i) a biological sensor comprising a recombinant bacterial strain, wherein said recombinant bacterial strain is selected from the group consisting of recombinant Pseudomonas, Escherichia and Bacillus, and
   ii) a soil sample suspected of containing detectable levels of explosive residue; and

b) contacting said soil sample with said biological sensor under conditions such that a detectable signal is produced in the presence of said detectable levels of explosive residue.

Claim 30

A biological sensor for detecting explosives comprising a recombinant bacterial strain that responds to contacting a chemical from an explosive by producing a detectable signal, wherein said recombinant bacterial strain is selected from the group consisting of recombinant Bacillus, Pseudomonas, and Escherichia coli.

Claim 35

A biological sensor for detecting explosives comprising a recombinant bacterial strain that responds to contacting a chemical from an explosive by producing a detectable signal, wherein

• said recombinant bacterial strain is selected from the group consisting of recombinant Bacillus, Pseudomonas, and Escherichia coli, and wherein
• said chemical from said explosive is selected from the group consisting of trinitrotoluene, hexahydro-1,3,5-trinitro-1,3,5-triazine and octahydro-1,3,5-trinitro-1,3,5,7-tetrazocine.

A reporter system giving rise to a directly monitorable phenotypic trait in a plant in the presence of solely an outer stimulus, said reporter system comprising

• a gene which is not part of the natural plant genome encoding a product which is involved in the development of said directly monitorable phenotypic trait in response to the presence of said outer stimulus.

A reporter system giving rise to a directly monitorable phenotypic trait in a plant in the presence of solely an outer stimulus, said reporter system comprising

• a gene which is not part of the natural plant genome encoding a product which is involved in the development of said directly monitorable phenotypic trait in response to the presence of said outer stimulus.

 A reporter system capable of giving rise to a directly monitorable phenotypic trait in a plant in the presence of an outer stimulus, said reporter system comprising

• a gene encoding a product which is involved in the development of said directly monitorable phenotypic trait in response to the presence of said outer stimulus.

GSH1 promoter (glutamate-cysteine ligase chloroplast isoform)
GSH2 promoter (glutathione synthase)
PCS1 promoter (gene bank accession AF461180)
PCS2 promoter (gene bank accession AY044049)
GST30 promoter (glutathione S-transferase)
CAD1 promoter (phytochelatin synthase)

CHS (chalcone synthase)
LUC (luciferase)
GFP (green fluorescent protein)

35S

GSH1
GSH2
CAD1
Nramp1 (gene bank accession AF165125)
Nramp2 (gene bank accession AF141240)
PCS1
PCS2

Nr1 promoter (nitrate reductase 1)
Nr2 promoter (nitrate reductase 2)
Nii promoter (nitrite reductase)
Ntr-2-1 promoter (high-affinity nitrate transporter ACH2)

CHS
LUC
GFP

35S

Nr1
Nr2
Nii
Ntr-2-1
XenA (xenobiotic reductase A)
XenB (xenobiotic reductase B)
Onr (pentaerythriol tetranitrate reductase)

Claim 1

A nucleic acid construct comprising:

• a gene encoding a product involved in the biosynthesis of a plant pigment, said gene being operably linked to an inducible sensor system, wherein the sensor system is responsive to the presence of a contaminant.

Claim 26

A transgenic plant cell comprising a transgene comprising:

• a gene encoding a product involved in the biosynthesis of a plant pigment, said gene being operably linked to an inducible sensor system, wherein the sensor system is responsive to the presence of a contaminant.

Claim 49

A transgenic plant exhibiting a change in color phenotype when exposed to a contaminant, the transgenic plant comprising a transgene comprising:

• a gene encoding a product involved in the biosynthesis of a plant pigment, said gene being operably linked to an inducible sensor system which is responsive to the presence of a contaminant.

Claim 75

A transgenic plant exhibiting different changes in color phenotype when exposed to different contaminants, the transgenic plant comprising more than one transgene, each transgene comprising:

• a gene encoding a product involved in the biosynthesis of a plant pigment, said gene being operably linked to an inducible sensor system which is responsive to the presence of a particular contaminant and whose induction by that particular contaminant is associated with a specific change in color phenotype.

Claim 76

A method for preparing a transgenic plant exhibiting a change in color phenotype when exposed to a contaminant, the method comprising:
   1. introducing a nucleic acid construct into a plant cell or protoplast to obtain a stably transformed plant cell or protoplast, the construct comprising:

• a gene encoding a product involved in the biosynthesis of a plant pigment, said gene being operably linked to an inducible sensor system, wherein the sensor system is responsive to the presence of the contaminant;

   2. regenerating a whole plant from the stably transformed plant cell or protoplast to obtain a transgenic plant comprising a transgene comprising:

• a gene encoding a product involved in the biosynthesis of a plant pigment, said gene being operably linked to an inducible sensor system, wherein the sensor system is responsive to the presence of the contaminant; and

   3. exposing the transgenic plant to the contaminant.

Claim 105

A method for detecting the presence of a contaminant in an area, the method comprising:
   1. introducing, in the area to be tested, seeds from a transgenic plant comprising a transgene comprising:

• a gene encoding a product involved in the biosynthesis of a plant pigment, said gene being operably linked to an inducible sensor system, wherein the sensor system is responsive to the presence of the contaminant;

   2. growing transgenic plants from the seeds;
   3. monitoring the color phenotype of the resulting plants; and
   4. determining that the contaminant is present in the area tested if a change in color phenotype was observed in the resulting plants.

Claim 131

A method for detecting the presence of contaminants in an area, the method comprising:
   1. introducing, in the area to be tested, seeds from a transgenic plant comprising more than one transgene, each transgene comprising:

• a gene encoding a product involved in the biosynthesis of a plant pigment, said gene being operably linked to an inducible sensor system which is responsive to the presence of a particular contaminant and whose induction by that particular contaminant is associated with a specific change in color phenotype;

   2. growing transgenic plants from the seeds;
   3. monitoring the color phenotype of the resulting plants; and
   4. determining that a particular contaminant is present in the area tested if the associated change in color phenotype was observed in the resulting plants.

A method of detecting the presence of a sublethal environmental insult with a lyophilized biological reagent, said reagent comprising

• a detector prokaryote microorganism containing an expressible luxCDABE gene complex under the control of a stress inducible promoter sequence, the method comprising the steps of:

(i) rehydrating the lyophilized biological reagent in a suitable amount of water wherein a baseline bioluminescence is produced;
(ii) immediately contacting the rehydrated reagent with a sample suspected of containing an environmental insult to form a reagent mixture;
(iii) incubating the mixture for at least 20 minutes and at a temperature of up to 30°C and;
(iv) detecting a change in bioluminescence from the mixture.

A lyophilized biological reagent comprising

• a transformed bacteria containing an expressible luxCDABE gene complex under the control of a stress inducible promoter sequence.

 A kit for detecting the presence of a sublethal environmental insult comprising the following in packaged combination:

(i) an aliquoted lyophilized biological reagent comprising;
     (a) a detector prokaryotic microorganism cell containing a DNA fragment comprising a stress inducible promoter operably linked to the luxCDABE gene complex;
     (b) a suitable buffer, and
     (c) a cryoprotective reagent;
(ii) a rehydrating reagent; and
(iii) a suitable growth media.

A method of detecting the presence of an environmental insult with a lyophilized biological reagent said reagent comprising a detector organism containing an expressible lux gene complex under the control of a stress inducible promoter sequence, the method comprising the steps of:

(i) rehydrating the lyophilized biological reagent in a suitable amount of water wherein a baseline bioluminescence is produced;
(ii) immediately contacting the rehydrated reagent with a sample suspected of containing an environmental insult to form a reagent mixture;
(iii) incubating the mixture for at least 20 minutes and at a temperature of up to 300˚C and;
(iv) detecting a change in bioluminescence from the mixture.

A lyophilized biological reagent comprising a transformed bacteria containing an expressible lux gene complex under the control of a stress inducible promoter sequence.

A kit for detecting the presence of an environmental insult comprising the following in packaged combination:

(i) an aliquoted lyophilized biological reagent comprising;
(a) a detector cell containing a DNA fragment comprising a stress promoter gene operably linked to the lux gene complex;
(b) a suitable buffer; and
(c) a cryoprotective reagent;
(ii) a rehydrating reagent; and
(iii) a suitable growth media.

A method of detecting the presence of a sublethal environmental insult with a lyophilized biological reagent said reagent comprising

• a detector prokaryotic microorganism containing an expressible luxCDABE gene complex under the control of a stress inducible promoter sequence, the method comprising the steps of:

(i) rehydrating the lyophilized biological reagent in a suitable amount of water wherein a baseline bioluminescence is produced;
(ii) immediately contacting the rehydrated reagent with a sample suspected of containing an environment insult to form a reagent mixture;
(iii) incubating the mixture for at least 20 minutes and at a temperature of up to 30° C. and;
(iv) detecting an increase in bioluminescence from the mixture.

A lyophilized biological reagent comprising

• bacteria transformed with an expressible luxCDABE gene complex under the control of a stress inducible promoter sequence.

A kit for detecting the presence of a sublethal environmental insult comprising the following in packaged combination:

(i) an aliquoted lyophilized biological reagent comprising;
     (a) a detector prokaryotic microorganism cell containing a DNA fragment comprising a stress promoter gene operably linked to a luxCDABE gene complex;
     (b) a suitable buffer; and
     (c) a cryo protective reagent;
(ii) a rehydrating reagent; and
(iii) a suitable growth media.

A method of detecting the presence of an environmental insult with a lyophilized biological reagent said reagent comprising a detector organism containing an expressible lux gene complex under the control of a stress inducible promoter sequence, the method comprising the steps of:

(i) rehydrating the lyophilized biological reagent in a suitable amount of water wherein a baseline bioluminescence is produced;
(ii) immediately contacting the rehydrated reagent with a sample suspected of containing an environmental insult to form a reagent mixture;
(iii) incubating the mixture for at least 20 minutes and at a temperature of up to 30˚C and;
(iv) detecting a change in bioluminescence from the mixture.

A lyophilized biological reagent comprising a transformed bacteria containing an expressible lux gene complex under the control of a stress inducible promoter sequence.

A kit for detecting the presence of an environmental insult comprising the following in packaged combination:

(i) an aliquoted lyophilized biological reagent comprising;
     (a) a detector cell containing a DNA fragment comprising a stress promoter gene operably linked to the lux gene complex;
     (b) a suitable buffer; and
     (c) a cryoprotective reagent;
(ii) a rehydrating reagent; and
(iii) a suitable growth media.

Claim 1

A method of measuring contaminants in water comprising:

a. introducing into a transgenic zebrafish organism a DNA construct having the sequence of at least one regulatory response element gene operatively linked to a DNA molecule encoding at least one reporter gene such that the at least one regulatory element of the gene controls the expression of the at least one reporter gene;
b. exposing the transgenic zebrafish to a water sample to be tested for a time sufficient to allow contaminants become bioconcentrated within the zebrafish;
c. exposing the transgenic zebrafish to conditions permitting expression of the at least one reporter gene; and
d. detecting the expression of the at least one reporter gene; and
e. correlating the detected expression to known standards and thereby determining the quantity of contaminants in the water sample.

A method of measuring contaminants in water comprising:

a. introducing into a transgenic zebrafish organism a DNA construct having the sequence of two or more regulatory response element genes operatively linked to a DNA molecule encoding at least one reporter gene such that a regulatory elements of the gene controls expression of the reporter gene;
b. exposing the transgenic zebrafish to a water sample to be tested for a time sufficient to allow contaminants become bioconcentrated within the zebrafish
c. exposing the transgenic zebrafish to conditions permitting expression of the reporter genes; and
d. detecting the expression of the reporter genes; and
e. correlating the detected expression to known standards and thereby determining the quantity of contaminants in the water sample.

Claim 1

A method of measuring contaminants in water comprising:

a. introducing into a transgenic zebrafish organism a DNA construct having the sequence of at least one regulatory response element gene operatively linked to a DNA molecule encoding at least one reporter gene such that the at least one regulatory element of the gene controls the expression of the at least one reporter gene;
b. exposing the transgenic zebrafish to a water sample to be tested for a time sufficient to allow contaminants become bioconcentrated within the zebrafish;
c. exposing the transgenic zebrafish to conditions permitting expression of the at least one reporter gene; and
d. detecting the expression of the at least one reporter gene; and
e. correlating the detected expression to known standards and thereby determining the quantity of contaminants in the water sample.

A method of measuring contaminants in water comprising:

a. introducing into a transgenic zebrafish organism a DNA construct having the sequence of two or more regulatory response element genes operatively linked to a DNA molecule encoding at least one reporter gene such that a regulatory elements of the gene controls expression of the reporter gene;
b. exposing the transgenic zebrafish to a water sample to be tested for a time sufficient to allow contaminants become bioconcentrated within the zebrafish
c. exposing the transgenic zebrafish to conditions permitting expression of the reporter genes; and
d. detecting the expression of the reporter genes; and
e. correlating the detected expression to known standards and thereby determining the quantity of contaminants in the water sample.

Claim 1
Biosensor system comprising

• a cell or organism harbouring a DNA molecule enabling said cell or organism to express p-hydroxyphenyl-pyruvic acid dioxygenase under the control of a promotor which is inducible by the presence of substances or conditions to be analyzed.

Claim 10
An isolated DNA molecule comprising a nucleotide sequence providing an expression cassette capable of directing the expression of p-hydroxyphenyl-pyruvic acid dioxygenase, wherein said expression cassette comprises from 5' to 3':
(a) an inducible promoter capable of expressing a downstream coding sequence;
(b) a DNA sequence coding for the expression of p-hydroxyphenyl-pyruvic acid dioxygenase; and
(c) a 3' termination sequence,
characterized in that the inducible promoter (a) is selected from the group consisting of zntA, cadA, merA, nic, chr, ars, fliC, corA, dmpR, xylR, xylS, pqiAB, SoxRS, zrt, zip, ycfl, cup1-1, cup1-2, gefl, ftr1, hal1, gre1, and aad4.

Claim 16
Process for studying and/or monitoring the activity of a promoter or functional part thereof by the steps of using of

• a vector which comprises a DNA sequence coding for the expression of p-hydroxyphenyl-pyruvic acid dioxygenase under the control of said promoter or functional part thereof and

• a transcriptional terminator, wherein

the DNA sequence is, for the transformation of a host cell or organism, cultivating the transformants and monitoring the activity of said promoter or functional part thereof by measuring the content of ochronotic pigment accumulated in the culture medium.

Zinc

E. coli zntA

Arabidopsis hpd

E. coli TOP10

Zinc

E. coli zntA

Synechocystis hpd

E. coli Bl21(DE3)RIL

Copper

S. cerevisiae CUP1-2

Arabidopsis hpd

S. cerevisiae INVSc1

Zinc

TOP10

A device for detecting a selected analyte, comprising:

• a stably transformed bacterium containing a promoterless lux gene cassette having a regulatory element for a selected analyte inserted in front of the lux gene cassette;
• a support matrix onto which the bacterium is attached; and
• an encapsulating material to contain said bacterium attached to the support matrix wherein the encapsulated bacterium emits visibly detectable light in the presence of the selected analyte.

A genetically modified bacterium responsive to divalent mercury, said bacterium containing a merRo/p-lux gene stably integrated into the bacterial chromosome wherein said bacterium produces a bioluminescent protein in the presence of divalent mercury.

A method for detecting mercury comprising

• contacting a sample suspected of containing mercury II ion with a bioreporter bacterium genetically modified to contain a merRo/pA-lux gene; and
• detecting the presence of the mercury ion when a visibly detectable luminescence is produced.

A device for detecting a selected analyte, comprising:

a stably transformed bacterium containing a promoterless lux gene cassette having a regulatory element for a selected analyte inserted in front of the lux gene cassette;
a support matrix onto which the bacterium is attached; and
an encapsulating material to contain said bacterium attached to the support matrix wherein the encapsulated bacterium emits visibly detectable light in the presence of the selected analyte.

A genetically modified bacterium responsive to divalent mercury, said bacterium containing a merRo/p-lux gene stably integrated into the bacterial chromosome wherein said bacterium produces a bioluminescent protein in the presence of divalent mercury.

A method for detecting mercury comprising

• contacting a sample suspected of containing mercury II ion with a bioreporter bacterium genetically modified to contain a merRo/pA-lux gene; and detecting the presence of the mercury ion when a visibly detectable luminescence is produced.

A portable system for detecting a selected analyte, comprising:

• a stably transformed bacterium containing a promoterless lux gene cassette having a regulatory element for a selected analyte inserted in front of the lux gene cassette;
• a support matrix onto which the bacterium is attached ;
• an encapsulating material to contain said bacterium attached to the support matrix, wherein the encapsulated bacterium emits visibly detectable light in the presence of the selected analyte, and
• a portable detection device.

A genetically modified bacterium responsive to divalent mercury, said bacterium being encapsulated and containing a gene stably integrated into bacterial chromosome, wherein said bacterium produces a bioluminescent protein in the presence of divalent mercury.

A mobile method for detecting mercury in water samples comprising

• providing a plurality of stably transformed bioreporter bacterium genetically modified to contain a merRo/p-lux gene, said bacterium attached to a support matrix and disposed within protective packaging for preserving hydration of said bacterium;
• removing said protective packaging;
• contacting a water comprising sample suspected of containing mercury II ion with said detecting the presence of the mercury ion when a visibly detectable luminescence is produced, said detecting using a portable detection device.

A reporter bacterium, comprising

• a bacterium that occurs naturally in a biological sludge and that contains a nucleic acid that encodes a reporter protein not found in the naturally occurring bacterium.

 A bioluminescent reporter bacterium, obtained by the process comprising:

• contacting a bacteria-containing sample of a biological sludge with a donor bacterium, wherein

the donor bacterium contains a nucleic acid that encodes a bioluminescent reporter protein that does not naturally occur in biological sludge bacteria under conditions whereby mating can occur.

A bioluminescent reporter bacterium, obtained by the process comprising:

• delivering to an isolated bacterium, that occurs naturally in a biological sludge, a nucleic acid construct which contains a nucleic acid that encodes a bioluminescent reporter protein that does not occur naturally in the bacterium, under conditions whereby the nucleic acid encoding the bioluminescent reporter protein is taken up by a bacterium in the sludge sample.

A method for making a bioluminescent reporter bacterium, comprising:

• contacting a bacteria-containing sample of a biological sludge with a bacterium that contains a nucleic acid that encodes a bioluminescent reporter protein that does not naturally occur in biological sludge bacteria, under conditions whereby the nucleic acid encoding the reporter protein is taken up by a bacterium in the sludge sample.

A method for making a bioluminescent reporter bacterium, comprising:

• delivering to an isolated bacterium, that occurs naturally in a biological sludge, a nucleic acid construct which contains a nucleic acid that encodes a bioluminescent reporter protein that does not occur naturally in the bacterium, under conditions whereby the nucleic acid encoding the reporter protein is taken up by the isolated sludge bacterium.

A method of making and using bioluminescent reporter bacteria, the method comprising the following steps:

a) obtaining bacteria from biological wastewater sludge of a wastewater treatment facility;
b) introducing into said bacteria a nucleic acid construct that encodes a bioluminescent reporter protein under conditions whereby the nucleic acid encoding the bioluminescent reporter protein is taken up by, and expressed in, said bacteria, and wherein the bioluminescent reporter protein does not naturally occur in said bacteria;
c) contacting the influent from the wastewater treatment facility with the bioluminescent reporter bacteria obtained by steps a) and b);
d) detecting the bioluminescent reporter protein expressed by the bioluminescent reporter bacteria; and
e) correlating the presence of toxicity with the reduction in expression of the bioluminescent reporter protein;

wherein the bioluminescent reporter bacteria are made from bacteria obtained from the same wastewater treatment facility at which the bioluminescent reporter bacteria are to be used for detecting toxicity, and are therefore specifically adapted to the conditions of said wastewater treatment facility.

A reporter bacterium, comprising

• a bacterium that occurs naturally in a biological sludge and that contains a nucleic acid that encodes a reporter protein not found in the naturally occurring bacterium.

 A bioluminescent reporter bacterium, obtained by the process comprising:

• contacting a bacteria-containing sample of a biological sludge with a donor bacterium, wherein

the donor bacterium contains a nucleic acid that encodes a bioluminescent reporter protein that does not naturally occur in biological sludge bacteria under conditions whereby mating can occur.

A bioluminescent reporter bacterium, obtained by the process comprising:

• delivering to an isolated bacterium, that occurs naturally in a biological sludge, a nucleic acid construct which contains a nucleic acid that encodes a bioluminescent reporter protein that does not occur naturally in the bacterium, under conditions whereby the nucleic acid encoding the bioluminescent reporter protein is taken up by a bacterium in the sludge sample.

A method for making a bioluminescent reporter bacterium, comprising:

• contacting a bacteria-containing sample of a biological sludge with a bacterium that contains a nucleic acid that encodes a bioluminescent reporter protein that does not naturally occur in biological sludge bacteria, under conditions whereby the nucleic acid encoding the reporter protein is taken up by a bacterium in the sludge sample.

A method for making a bioluminescent reporter bacterium, comprising:

• delivering to an isolated bacterium, that occurs naturally in a biological sludge, a nucleic acid construct which contains a nucleic acid that encodes a bioluminescent reporter protein that does not occur naturally in the bacterium, under conditions whereby the nucleic acid encoding the reporter protein is taken up by the isolated sludge bacterium.

A diagnostic system made of:

- a transformed micro-organism capable of an increased reporter activity upon exposure to an environmental insult, said micro-organism having a stress inducible promoter sequence being operatively linked to a reporter encoding nucleic acid sequence encoding a reporter molecule resulting in a signal that can be assayed, and of
- a transformed micro-organism having a constitutive and non stress inducible promoter sequence being operatively linked to a reporter encoding nucleic acid sequence encoding a reporter molecule resulting in a signal that can be assayed.

Method for determining the kinetics of genotoxicity of a compound into a sample, wherein the measuring of luminescence of both inducible and constitutive transformed micro-organisms occurs at multiple points in time, preferably continuously, and in addition carrying out the step of determining the signal-to-noise (S/N) ratio for the transformed micro-organisms at said point and time, dividing the S/N ratio of the inducible micro-organism by teat of the constitutive micro-organisms and plotting these data, said plotting representing the corrected kinetics ef genotoxicity of the genotoxic compound in the sample.

A diagnostic system made of :

a transformed micro-organism capable of an increased reporter activity upon exposure to an environmental insult, said micro-organism having a stress inducible promoter sequence being operatively linked to a reporter encoding nucleic acid sequence encoding a reporter molecule resulting in a signal that can be assayed, and of
a transformed micro-organism having a constitutive and non stress inducible promoter sequence being operatively linked to a reporter encoding nucleic acid sequence encoding a reporter molecule resulting in a signal that can be assayed.

Method for determining the kinetics of genotoxicity of a compound into a sample, wherein the measuring of luminescence of both inducible and constitutive transformed micro-organisms occurs at multiple points in time, preferably continuously, and in addition carrying out the step of determining the signal-to-noise (S/N) ratio for the transformed micro-organisms at said point and time, dividing the S/N ratio of the inducible micro-organism by that of the constitutive micro-organisms and plotting these data, said plotting representing the corrected kinetics of genotoxicity of the genotoxic compound in the sample.

A diagnostic system comprising:

1. a first transformed micro-organism capable of an increased reporter activity upon exposure to an environmental insult, said micro-organism having a stress inducible promoter sequence being operatively linked to a nucleic acid sequence encoding a reporter molecule resulting in a signal that can be assayed, and

1. a second transformed micro-organism having a constitutive and non-stress inducible promoter sequence being operatively linked to a nucleic acid sequence encoding a reporter molecule resulting in a signal that can be assayed, wherein

said second and first microorganisms are Salmonella typhimurium microorganisms selected from the group consisting of

• Ames test micro-organism, micro-organism designated by deposit number LMG P-18318, transformed TA98, transformed TA100, transformed TA102, transformed TA104, transformed TA1538, transformed TA7001 to transformed TA7005, and transformed TA7041 to transformed TA7046,

said micro-organisms being suitable to cooperatively detect said environmental insult while eliminating false positive and false negative result.

A diagnostic system made of

- a transformed micro-organism capable of an increased reporter activity upon exposure to an environmental insult, said micro-organism having a stress inducible promoter sequence being operatively linked to a reporter encoding nucleic acid sequence encoding a reporter molecule resulting in a signal that can be assayed, and of
- a transformed micro-organism having a constitutive and non stress inducible promoter sequence being operatively linked  to  a reporter encoding nucleic acid sequence encoding a reporter molecule resulting in a signal that can be assayed.

Method for determining the kinetics of genotoxicity of a compound into a sample, wherein the measuring of luminescence of both inducible and constitutive transformed micro-organisms occurs at multiple points in time, preferably continuously, and in addition carrying out the step of determining the signal-to-noise (S/N) ratio for the transformed micro-organisms at said point and time, dividing the S/N ratio of the inducible micro-organism by that of the constitutive micro-organisms and plotting these data, said plotting representing the corrected kinetics of genotoxicity of the genotoxic compound in the sample.

An isolated nucleic acid molecule encoding a green light emitting luciferase selected from the group consisting of:

a) a nucleic acid molecule comprising SEQ ID NO:1; and
b) a nucleic acid molecule that hybridizes to SEQ ID NO:1 under high stringency conditions comprising washing in a solution containing 0.1×SSC/0.1% SDS for 15 min at 68° C.; or
a nucleic acid molecule that is 100% complementary to (a) or (b)
wherein the encoded green light emitting luciferase emits green bioluminescence having a maximum lambda of approximately 549 nm when expressed in E coli.

An isolated nucleic acid molecule comprising a nucleotide sequence selected from the group consisting:

a) SEQ ID NO: 1;

b) the complement of SEQ ID NO: 1;

c) nucleic acid molecule which is greater than about 90 percent identical to the nucleic acid sequence of SEQ ID NO: 1 or the complement of SEQ ID NO: 1;

d) nucleic acid encoding a polypeptide having the amino acid sequence of SEQ ID NO: 3; and

e) nucleic acid encoding a polypeptide having an amino acid sequence which is greater than about 93 percent identical to the amino acid sequence of SEQ ID NO: 3.

An isolated nucleic acid molecule encoding a luciferase which hybridizes under high stringency conditions to a nucleotide sequence selected from the group consisting:

a) SEQ ID NO: 1; and

b) the complement of SEQ ID NO: 1.

An isolated nucleic acid molecule contained in deposit pB1-PvGR .

An isolated nucleic acid molecule encoding a red light emitting luciferase which hybridizes under high stringency conditions to a nucleotide sequence selected from the group consisting of:

(a) SEQ ID NO.3, and
(b) the complement of SEQ ID No.3,
wherein said high stringency conditions correspond to washing in prewarmed (68° C.) solution containing 0.1×SSC/0.1% SDS for 15 min at 68° C.,
wherein the encoded red light emitting luciferase emits red bioluminescence having a maximum lambda of approximately 622 nm when expressed in E coli.

A nucleic acid comprising a codon-optimized nucleotide sequence encoding a component of a bacterial luciferase system.

A cell comprising a nucleic acid comprising a codon-optimized nucleotide sequence encoding a component of a bacterial luciferase system.

A method comprising the step of introducing into a mammalian cell a nucleic acid comprising a codon-optimized nucleotide-sequence encoding a component of a bacterial luciferase system.

A nucleic acid comprising a codon-optimized nucleotide sequence encoding a component of a bacterial luciferase system.

A cell comprising a nucleic acid comprising a codon-optimized nucleotide sequence encoding a component of a bacterial luciferase system.

A method comprising the step of introducing into a mammalian cell a nucleic acid comprising a codon-optimized nucleotide-sequence encoding a component of a bacterial luciferase system.

Claim 1

A PETN reductase enzyme which catalyses the removal of nitrite from PETN characterised in having the amino acid sequence shown in Figure 4 or a derivative thereof.

Claim 28

An Enterobacter cloacae bacterial strain referred to as "PB2" and deposited as NCIMB 40718, and mutants and variants thereof capable of producing enzymic activity which degrades PETN in the presence of NADPH.

Claim 1

A pentaerythritol tetranitrate (PETN) reductase which catalyses the removal of nitrite from PETN, characterised in that

it comprises the amino acid sequence shown in Figure 4, or a derivative thereof, which

• derivative has PETN reductase activity that catalyses the removal of nitrite from PETN and which
• has insertions, deletions and/or substitutions of the amino acid sequence of Figure 4, and which
• is encodeable by a nucleic acid sequence which is at least 70% identical to the coding sequence of Figure 3.

Claim 30

An Enterobacter cloacae bacterial strain deposited as NCIMB 40718 and mutants and variants thereof capable of producing enzymatic activity degrading PETN in the presence of NADPH.

Claim 1

A PETN reductase enzyme which catalyses the removal of nitrite from PETN characterised in having the amino acid sequence as set forth in SEQ ID NO: 2.

Claim 13

A method of detecting PETN in a sample, comprising

(1) subjecting the sample to a reaction involving the removal of nitrite from PETN, the reaction being carried out in the presence of NADPH and PETN reductase enzyme, having the amino acid sequence as set forth in SEQ ID NO: 2 until NADP and nitrite are produced, and

(2) detecting the occurrence of said reaction.

Claim 24

An Enterobacter cloacae bacterial strain referred to as "PB2" and deposited as NCIMB 40718, and mutants thereof capable of producing enzymic activity which degrades PETN in the presence of NADPH.

Claim 1

A PETN reductase enzyme characterised in that:
(1) it catalyses the removal of nitrite from PETN; and
(2) it has reductase activity specifically at the nitrate ester linkage of PETN.

Claim 3

An enzyme having the amino acid sequence shown in Figure 4 or a derivative thereof.

Claim 4

The gene (designated onr) which encodes the enzyme, or a derivative thereof.

Claim 5

A DNA molecule including the nucleotide sequence of the onr gene as shown in Figure 3 or a derivative of that sequence.

Claim 6

An enzyme comprising substantially the transcribed product of the onr gene.

Claim 8

A recombinant DNA vector containing the onr gene or a derivative thereof.

Claim 9

A host cell transformed with the onr gene or a derivative thereof.

Claim 12

PETN reductase enzyme which is recombinantly produced.

Claim 13

A method for the production of PETN reductase enzyme or a derivative thereof which comprises the steps of:
1) transforming host cells with the onr gene or a derivative thereof,
2) suitably culturing said transformed host cells; and
3) extracting the enzyme from the growth medium or from the host cells after disruption thereof.

Claim 25

A biosensor for the detection of PETN in a sample which comprises

• means for contacting the sample with a PETN reductase enzyme in the presence of NADPH and
• means for detecting the occurrence of a reaction, catalysed by the enzyme, of PETN when PETN is present in the sample.

Claim 26

A biosensor for the detection of GTN and/or EGDN in a sample which comprises

• means for contacting the sample with a PETN reductase enzyme in the presence of NADPH and
• means for detecting the occurrence of a reaction, catalyzed by the enzyme, of GTN and/or EGDN when either or both is present in the sample.

Claim 32

An Enterobacter cloacae bacterial strain referred to as"PB2" and deposited as NCIMB 40718, and mutants and variants thereof capable of producing enzymic activity which degrades PETN in the presence of NADPH.