Description:

DNA microarrays represent a potentially significant technology and analytical technique for the simultaneous detection of multiple pathogens in a single water sample, with the ability to incorporate live/dead discrimination via mRNA analysis. However, microarrays have not been applied to environmental samples (in general), and commercial array companies are focused solely on the high-throughput genotyping and drug discovery markets. We propose to overcome the limitations of culture and PCR-based analytical techniques through the development and use of DNA arrays specifically for natural, turbid and processed water supplies, using Cryptosporidium parvum and/or Helicobacter pylori as model organisms. Critical research questions and hypotheses include:

• Can state-of-the-art microarrays be successfully applied for the genetic analysis of relatively low-biomass source and finished water samples? What are the lower detection limits of DNA arrays in a water quality context? How are microarray detection limits and specificity affected by relatively large nucleic acid targets? Do co-extracted humic acids and environmental contaminants affect detection sensitivity or fluorescent readout strategies?

• Does surface charge modulation on tunable surfaces significantly enhance detection sensitivity and oligonucleotide specificity on microarrays? What are the practical consequences of tunable surface films relative to probe design, hybridization conditions, and detection sensitivity?

• What array formats and internal controls are required for quantitative analysis of C. parvum and/or H. pylori targets in raw water samples? How does microarray sensitivity, specificity and quantification ability compare to a standard IFA technique?

URLs/Downloads:

2002 Progress Report

Final Progress Report

chandler.html

2000 Progress Report

Record Details:

Record Type:PROJECT( ABSTRACT )

Start Date:03/01/2000

Completion Date:03/01/2003

Record ID: 18629

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Related Organizations:

Role :OWNER

Organization Name :METROPOLITAN WATER DISTRICT OF SOUTHERN CALIFORNIA

Mailing Address :350 South Grand Avenue

Citation :Los Angeles

State :CA

Zip Code :90054

Project Information:

Approach :Major tasks associated with this objective include 1) probe selection and design, 2) array fabrication and specificity testing in various genetic and chemical backgrounds (source, finished waters), 3) characterization of possible interactions between environmental samples (e.g. humic acids, particulates) and fluorescence labeling/readout methods, and 4) evaluation of microarray quantitative ability relative to currently accepted immunofluorescence assays (IFA).

Cost :$517,818.00

Research Component :ARSENIC

Risk Paradigm :EXPOSURE

Approach :Major tasks associated with this objective include 1) probe selection and design, 2) array fabrication and specificity testing in various genetic and chemical backgrounds (source, finished waters), 3) characterization of possible interactions between environmental samples (e.g. humic acids, particulates) and fluorescence labeling/readout methods, and 4) evaluation of microarray quantitative ability relative to currently accepted immunofluorescence assays (IFA).

Cost :$517,818.00

Research Component :Drinking Water

Risk Paradigm :RISK ASSESSMENT

Approach :Major tasks associated with this objective include 1) probe selection and design, 2) array fabrication and specificity testing in various genetic and chemical backgrounds (source, finished waters), 3) characterization of possible interactions between environmental samples (e.g. humic acids, particulates) and fluorescence labeling/readout methods, and 4) evaluation of microarray quantitative ability relative to currently accepted immunofluorescence assays (IFA).

Cost :$517,818.00

Research Component :OTHER

Risk Paradigm :RISK ASSESSMENT

Approach :Major tasks associated with this objective include 1) probe selection and design, 2) array fabrication and specificity testing in various genetic and chemical backgrounds (source, finished waters), 3) characterization of possible interactions between environmental samples (e.g. humic acids, particulates) and fluorescence labeling/readout methods, and 4) evaluation of microarray quantitative ability relative to currently accepted immunofluorescence assays (IFA).

Cost :$517,818.00

Research Component :M/DBP (MICROBIAL)

Risk Paradigm :RISK ASSESSMENT

Approach :Major tasks associated with this objective include 1) probe selection and design, 2) array fabrication and specificity testing in various genetic and chemical backgrounds (source, finished waters), 3) characterization of possible interactions between environmental samples (e.g. humic acids, particulates) and fluorescence labeling/readout methods, and 4) evaluation of microarray quantitative ability relative to currently accepted immunofluorescence assays (IFA).

Cost :$517,818.00

Research Component :ARSENIC

Risk Paradigm :RISK ASSESSMENT

Approach :Major tasks associated with this objective include 1) probe selection and design, 2) array fabrication and specificity testing in various genetic and chemical backgrounds (source, finished waters), 3) characterization of possible interactions between environmental samples (e.g. humic acids, particulates) and fluorescence labeling/readout methods, and 4) evaluation of microarray quantitative ability relative to currently accepted immunofluorescence assays (IFA).

Cost :$517,818.00

Research Component :Drinking Water

Risk Paradigm :EXPOSURE

Approach :Major tasks associated with this objective include 1) probe selection and design, 2) array fabrication and specificity testing in various genetic and chemical backgrounds (source, finished waters), 3) characterization of possible interactions between environmental samples (e.g. humic acids, particulates) and fluorescence labeling/readout methods, and 4) evaluation of microarray quantitative ability relative to currently accepted immunofluorescence assays (IFA).

Cost :$517,818.00

Research Component :OTHER

Risk Paradigm :EXPOSURE

Approach :Major tasks associated with this objective include 1) probe selection and design, 2) array fabrication and specificity testing in various genetic and chemical backgrounds (source, finished waters), 3) characterization of possible interactions between environmental samples (e.g. humic acids, particulates) and fluorescence labeling/readout methods, and 4) evaluation of microarray quantitative ability relative to currently accepted immunofluorescence assays (IFA).

Cost :$517,818.00

Research Component :M/DBP (MICROBIAL)

Risk Paradigm :EXPOSURE

Project IDs:

ID Code :R828039

Project type :EPA Grant