Nucleic acid arrays to monitor water and other ecosystems
First Claim
1. A device comprising an array, wherein the array comprises a plurality of oligonucleotides covalently immobilized at known locations of the array, and wherein each location on the array comprises an oligonucleotide having a sequence as set forth in any one of SEQ ID NO:
- 26, SEQ ID NO;
32, SEQ ID NO;
40, SEQ ID NO;
98, SEQ ID NO;
100 and SEQ ID NO;
106 or the complement of SEQ ID NO;
26, SEQ ID NO;
32, SEQ ID NO;
40, SEQ ID NO;
98, SEQ ID NO;
100 and SEQ ID NO;
106.
1 Assignment
0 Petitions
Accused Products
Abstract
Disclosed are arrays for monitoring ecosystems, such as bodies of water, and methods and systems for making such arrays. In one embodiment, the array may include a plurality of oligonucleotides immobilized at known locations on a substrate, such that each location on the array is an oligonucleotide having a sequence derived from a single, predetermined operational taxonomic unit (OTU). The sequences immobilized on the array may be from known, or unknown organisms. Also disclosed are methods for identifying and isolating bioindicators diagnostic of specific ecosystems. The arrays and bioindicators of the invention may be used for rapid, and continual monitoring of ecosystems.
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Citations
34 Claims
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1. A device comprising an array, wherein the array comprises a plurality of oligonucleotides covalently immobilized at known locations of the array, and wherein each location on the array comprises an oligonucleotide having a sequence as set forth in any one of SEQ ID NO:
- 26, SEQ ID NO;
32, SEQ ID NO;
40, SEQ ID NO;
98, SEQ ID NO;
100 and SEQ ID NO;
106 or the complement of SEQ ID NO;
26, SEQ ID NO;
32, SEQ ID NO;
40, SEQ ID NO;
98, SEQ ID NO;
100 and SEQ ID NO;
106. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 28, 30, 31)
- 26, SEQ ID NO;
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11. A system for monitoring an ecosystem comprising:
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(a) an array comprising a plurality oligonucleotides covalently immobilized at known locations of the array, such that each location on the array comprises an oligonucleotide having a sequence as set forth in any one of SEQ ID NO;
26, SEQ ID NO;
32, SEQ ID NO;
40, SEQ ID NO;
98, SEQ ID NO;
100 or SEQ ID NO;
106, or the complement of SEQ ID NO;
26, SEQ ID NO;
32, SEQ ID NO;
40, SEQ ID NO;
98, SEQ ID NO;
100 or SEQ ID NO;
106; and(b) polymerase chain reaction primers for amplifying DNA isolated from an ecosystem to generate oligonucleotides complementary to at least some of the plurality of oligonucleotides of the array to generate an amplified nucleic acid sample from the ecosystem. - View Dependent Claims (12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 29, 32)
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21. A system for monitoring water quality comprising an array, wherein the array comprises a plurality of oligonucleotides covalently immobilized at known locations of the array, and wherein each location on the array comprises an oligonucleotide having a sequence that is derived from a single, predetermined microbial operational taxonomic unit;
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a plurality of oligonucleotides having a detectable label covalently attached thereto for hybridizing to the array wherein at least one of the detectably labeled oligonucleotides comprises the sequence as set forth in any one of SEQ ID NO;
26, SEQ ID NO;
32, SEQ ID NO;
40, SEQ ID NO;
98, SEQ ID NO;
100 or SEQ ID NO;
106, or the complement of SEQ ID NO;
26, SEQ ID NO;
32, SEQ ID NO;
40, SEQ ID NO;
98, SEQ ID NO;
100 or SEQ ID NO;
106. - View Dependent Claims (22, 24, 25, 26, 27, 33, 34)
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Specification