Nucleic acid arrays to monitor water and other ecosystems
First Claim
1. A method for monitoring an ecosystem of interest comprising:
- (a) generating an array comprising a plurality of oligonucleotides immobilized at known locations on a substrate, wherein each location on the substrate comprises an oligonucleotide having a sequence derived from a single, predetermined microbial operational taxonomic unit (OTU), and wherein the array comprises at least one oligonucleotide having the sequence as set forth in SEQ ID NO;
25, SEQ ID NO;
26, SEQ ID NO;
32, SEQ ID NO;
40, SEQ ID NO;
98, or SEQ ID NO;
100, or SEQ ID NO;
106, the complement of the sequence as set forth in SEQ ID NO;
25, 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;
(b) preparing a nucleic acid sample from the ecosystem of interest;
(c) hybridizing the nucleic acid sample to the array;
(d) measuring hybridization of the nucleic acid sample to the array; and
(e) correlating hybridization of the nucleic acid sample to the array with at least one parameter that comprises at least part of the ecosystem of interest.
2 Assignments
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
24 Claims
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1. A method for monitoring an ecosystem of interest comprising:
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(a) generating an array comprising a plurality of oligonucleotides immobilized at known locations on a substrate, wherein each location on the substrate comprises an oligonucleotide having a sequence derived from a single, predetermined microbial operational taxonomic unit (OTU), and wherein the array comprises at least one oligonucleotide having the sequence as set forth in SEQ ID NO;
25, SEQ ID NO;
26, SEQ ID NO;
32, SEQ ID NO;
40, SEQ ID NO;
98, or SEQ ID NO;
100, or SEQ ID NO;
106, the complement of the sequence as set forth in SEQ ID NO;
25, 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;(b) preparing a nucleic acid sample from the ecosystem of interest; (c) hybridizing the nucleic acid sample to the array; (d) measuring hybridization of the nucleic acid sample to the array; and (e) correlating hybridization of the nucleic acid sample to the array with at least one parameter that comprises at least part of the ecosystem of interest. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19)
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13. A method for analyzing a pattern to evaluate the status of an ecosystem of interest comprising:
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measuring hybridization of a nucleic acid sample isolated from the ecosystem of interest to an array of oligonucleotides immobilized at known locations on a substrate, wherein each location on the array comprises an oligonucleotide having a sequence that is derived from a single, predetermined microbial operational taxonomic unit (OTU), and wherein the array comprises at least one oligonucleotide having the sequence as set forth in SEQ ID NO;
25, 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 the sequence as set forth in SEQ ID NO;
25, 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; andcorrelating a pattern of hybridization of the nucleic acid sample to the array with at least one parameter that comprises at least part of the ecosystem of interest. - View Dependent Claims (14, 15, 16, 17, 20, 21, 22, 23, 24)
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Specification