Multiplexed waterborne pathogen detection using DNA microarrays by Timothy M. Straub

Cover of: Multiplexed waterborne pathogen detection using DNA microarrays | Timothy M. Straub

Published by AWWA Research Foundation/American Water Works Association/IWA Pub. in Denver, CO .

Written in English

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  • Pathogenic microorganisms -- Detection,
  • Water -- Microbiology

Edition Notes

Includes bibliographical references (p. 39-41).

Book details

Statementprepared by Timothy M. Straub ; sponsored by Awwa Research Foundation.
ContributionsAWWA Research Foundation.
LC ClassificationsTD384 S77 2006
The Physical Object
Paginationxvii, 45 p. :
Number of Pages45
ID Numbers
Open LibraryOL23629164M
LC Control Number2007276234

Download Multiplexed waterborne pathogen detection using DNA microarrays

Develops and demonstrates the simultaneous detection and genotyping capabilities of nucleic acid microarrays for different groups of pathogens. Designs a DNA microarray that targets several well characterized virulence genes from E.

coli OH7 and Cryptosporidium parvum. Published in A POWERFUL TOOL FOR PATHOGEN DETECTION | [email protected] 3 BENEFITS OF DNA MICROARRAYS DNA microarray offers several unique advantages when applied to the field of microbial detection and identification. This includes: 1.

Multiplexed Array Layout – the dynamic nature of DNA microarrays allows for a highly flexible platform File Size: KB. Multiplexed Identification of Blood-Borne Bacterial Pathogens by Use of a Novel 16S rRNA Gene PCR-Ligase Detection Reaction-Capillary Electrophoresis Assay † Maneesh R.

Pingle, 1 Kathleen Granger, 1 Philip Feinberg, 1 Rebecca Shatsky, 2 Bram Sterling, 1 Mark Rundell, 1 Eric Spitzer, 3 Davise Larone, 1, 2 Linnie Golightly, 1, 4 and Francis Barany 1, *Cited by:   These results demonstrate the feasibility of using DNA microarrays in the detection of waterborne pathogens within mixed populations but also raise the problem of PCR bias in such experiments.

A small-oligonucleotide microarray prototype was designed with probes specific for the universal 16S rRNA and cpn60 genes of several pathogens that are usually encountered in by: DNA microarrays were reported for the detection and identification of several pathogens.

In these arrays, a DNA probe or short oligonucleotide is immobilised at fixed positions on a substrate and used to capture the target molecule through hybridisation of the amplified DNA, offering in this way higher capacity for multiplexing, as well as the possibility of miniaturisation and automation [33].Cited by:   Abstract.

DNA microarrays have emerged as a viable platform for detection of pathogenic organisms in clinical and environmental samples. These microbial detection arrays occupy a middle ground between low cost, narrowly focused assays such as multiplex PCR and more expensive, broad-spectrum technologies like high-throughput by:   To enable highly multiplexed detection with high sample throughput, we developed a set of 1, solution-based colour codes using ratios of 4.

The use of microarrays is highly appreciated for parallel detection and identification of microbial pathogens. DNA microarrays have been used for pathogen detection in environmental samples (Call et al. ), in wastewater (Kelly et al. ), for detecting waterborne pathogens (Lee et al.

), specific groups of microorganisms in complex systems (Sahm et al. ) and for Cited by: 3. This study demonstrates the use of the Luminex LabMAP system as a rapid and flexible platform for the simultaneous, multiplexed detection of DNA or protein from common bacterial pathogens.

The LabMAP nucleic acid assay could be completed in 30 to 40 min post-amplification and was sensitive with a detection limit of 10 6 to 10 7 genome equivalents in the hybridization by: In this work, the multiplexed CL imaging assay was designed on a DNA microarray with proximity binding-induced HCR amplification for sensitive screen detection of protein biomarkers.

Amino modified hairpin DNAs (C1, C2 and C3) containing a functional fragment of 20 bases, a stem of 24 bases and a loop of 18 bases were spotted on the sensing Cited by: These results demonstrate the feasibility of using DNA microarrays in the detection of waterborne pathogens within mixed populations but also raise the problem of PCR bias in such experiments.

Microbial water quality assessment and the rapid detection of pathogenic microorganisms remain great challenges in ecotoxicology, public health maintenance, and, more recently, bioterrorism Cited by: Using a DNA microarray employing 10 functional genes as detection targets, the sensitivity of the microarray was determined to be approximately μg of E.

coli genomic DNA, or 2 × 10 8 copies of the target gene. The sensitivity of the microarray was enhanced by approximately six orders of magnitude when the target 23S rRNA gene sequences were PCR amplified with a novel universal primer set Cited by: The major cause of most outbreaks of waterborne diseases is the infections associated with microbial contamination.Several pathogens (as listed in Table 1) are present in water such as bacteria, viruses, and parasites (including protozoa).As of now, more than types of contaminants (including bacteria, viruses, parasitic protozoa, and a few fungi/helminth species have been identified to Cited by: 5.

DNA microarrays in pathogen detection. Probe selection and design is usually an important first step in microarray-based pathogen detection, and many issues associated with probe design for DNA microarrays can impact the overall fidelity of the assay, in particular with regard to levels of specificity and sensitivity attained.

These issues and Cited by: Wang L, Li PCH () Flexible microarray construction and fast DNA hybridization conducted on a microfluidic chip for greenhouse plant fungal pathogen detection. J Agric Food Chem – CrossRef PubMed Google ScholarCited by: A Au particle-on-wire system that can be used as a specific, sensitive, and multiplex DNA sensor is developed.

A pattern formed by multiple Au nanowire sensors provides positional address and identification for each sensor. By using this system, multiplex sensing of target DNAs was possible in a quantitative manner with a detection limit of 10 by: Waterborne Pathogen Detection by Use of Oligonucleotide-Based Microarrays Article (PDF Available) in Applied and Environmental Microbiology 71(12) January with 75 Reads.

Request PDF | Microarrays/DNA Chips for the Detection of Waterborne Pathogens | DNA microarrays are useful for the simultaneous detection of microorganisms in water samples.

Specific probes. This paper reviews multiplexed foodborne pathogen microorganisms detection methods based on electrochemical sensors incorporating microarrays and other platforms. These devices usually involve antibody-antigen and DNA hybridization specific interactions, although other approaches such as the monitoring of oxygen consumption are also by: Microarrays for detection of human enteric viru ses in community wastewaters using cell culture coupled with multiple targets including DNA and RNA viruses have also been developed [81].

The. Pathogen detection and the identification of fecal contamination sources are challenging in environmental waters. Factors including pathogen diversity and ubiquity of fecal indicator bacteria hamper risk assessment and remediation of contamination sources.

A custom microarray targeting pathogens (viruses, bacteria, protozoa), microbial source tracking (MST) markers, and antibiotic Cited by: @article{osti_, title = {Towards a unified system for detecting waterborne pathogens}, author = {Straub, Tim M and Chandler, Darrell P}, abstractNote = {Currently, there is no single method to collect, process, and analyze a water sample for all pathogenic microorganisms of interest.

Some of the difficulties in developing a universal method include the physical differences between the. Request PDF | DNA Microarrays for Pathogen Detection | The application of DNA microarrays for pathogen detection has become a widespread field of research which. Detection of pathogenic microorganisms in environmental samples is a difficult process.

Concentration of the organisms of interest also co-concentrates inhibitors of many end-point detection methods, notably, nucleic acid methods. In addition, sensitive, highly multiplexed pathogen detection.

Microarray analysis of microbial pathogens has potential uses in research, food safety, medical, agricultural, regulatory, public health, and industrial settings.

In this article, we describe the main technical elements of microarray technology and the application and potential use of DNA microarrays for food microbial by: A microbial diagnostic microarray technique for the sensitive detection and identification of pathogenic bacteria in a background of non‐pathogens.

Anal Biochem. ; – et al. Kostrzynska M., Bachand A. Application of DNA microarray technology for detection, identification and characterisation of food‐borne by: Protein microarrays are powerful tools for high-throughput and simultaneous detection of different target molecules in complex biological samples.

However, the sensitivity of conventional fluorescence-labeling protein detection methods is limited by the availability of signal molecules for binding to the target molecule. Here, we built a multifunctional fluorescent protein nanowire (FNw) by Cited by: 4. Complete genomic sequences of microbial pathogens and hosts offer sophisticated new strategies for studying host-pathogen interactions.

DNA microarrays exploit primary sequence data to measure transcript levels and detect sequence polymorphisms, for every gene, simultaneously. The design and construction of a DNA microarray for any given microbial genome are straightforward.

(). Challenges and Opportunities for Pathogen Detection Using DNA Microarrays. Critical Reviews in Microbiology: Vol. 31, No. 2, pp. Cited by: DNA-based microarrays may contain hundreds to thousands of different, selective probe molecules, which are designed to hybridize with their respective target DNA; i.e., the DNA of those microorganisms to be detected in a single by: 7.

DNA microarrays have been used for pathogen detection in environmental samples (Call et al. ), in wastewater (Kelly et al. ), for detecting waterborne pathogens (Lee et al.

), specific. Multiplexed error-robust fluorescence in situ hybridization (MERFISH) allows simultaneous imaging of numerous RNA species in their native cellular environment and hence spatially resolved single Cited by: 1. Multiplexed detection and differentiation of pathogens in the Enterobacteriaceae family by direct hybridization of mRNA to microarrays.

Presented at the American Society for Microbiology th General Meeting, New Orleans, LA, @article{osti_, title = {Detecting and genotyping Escherichia coli OH7 using multiplexed PCR and nucleic acid microarrays}, author = {Call, Douglas R and Brockman, Fred J and Chandler, Darrell P}, abstractNote = {Rapid detection and characterization of food borne pathogens such as Escherichia coli OH7 is crucial for epidemiological investigations and food safety surveillance.

To prepare nucleic acid samples for amplification, pathogen-derived DNA was enriched using a Cot Human DNA subtraction technique, and RNA was enriched using Ambion’s MICROBEnrich Kit.

The pathogen-enriched nucleic acid was amplified using a whole. A majority of existing microRNA detection technologies such as RT-PCR or microarray-based miRNA assays are not suitable for single cell analysis [15,16].The PreAmp workflow (ABI/Thermo Fisher, Waltham, MA, USA) adds an intermediate step between RT and real-time PCR to pre-amplify cDNA prior to qPCR detection [].However, it is mainly for single-plex real-time PCR, and each PCR tube contains Cited by: 1.

Detection of emerging microbial contaminants in source and finished drinking water with DNA microarrays. Presented at the Drinking Water Program Review, Science To Achieve Results (STAR) Program, U.S.

Environmental Protection Agency, Silver Spring, MD, The ability to survey the DNA or RNA hybridization response profiles of many genes simultaneously makes microarray technology attractive for the detection of any waterborne pathogen as well.

In traditional expression array experiments, all genes come from a. Keywords: DNA microarrays, detection, diagnostics, identification, pathogens, plant pathogens Abstract The scientific backgrounds and principles, types and technical aspects of obtaining experimental data for DNA microarrays were described.

Utilization of this technology in biological research which includes pathogen detection was also described. Abstract. DNA microarrays bring practical benefits to the field of food safety in regard to pathogen detection and characterization.

This chapter is a review of how DNA microarray technology has been applied to the identification of pathogens, assessment of their diversity, analysis of their responses to different forms of stress, and studies on how specific metabolic pathways might contribute Author: Guillermo López-Campos, Joaquín V.

Martínez-Suárez, Mónica Aguado-Urda, Victoria López-Alonso. @article{osti_, title = {Detecting and Genotyping Escherichia coli OH7 using multiplexed PCR and nucleic acid microarrays}, author = {Call, Douglas R.

and Brockman, Fred J. and Chandler, Darrell P.}, abstractNote = {Rapid detection and characterization of food borne pathogens such as Escherichia coli OH7 is crucial for epidemiological investigations and food safety surveillance.

We have developed a novel high-throughput PCR-ligase detection reaction-capillary electrophoresis (PCR-LDR-CE) assay for the multiplexed identification of 20 blood-borne pathogens (Staphylococcus epidermidis, Staphylococcus aureus, Bacillus cereus, Enterococcus faecalis, Enterococcus faecium, Listeria monocytogenes, Streptococcus pneumoniae, Streptococcus Cited by:   Inexpensive, portable, and easy-to-use devices for rapid detection of microbial pathogens are needed to ensure safety of water and food.

In this study, a disposable polymer microfluidic chip for quantitative detection of multiple pathogens using isothermal nucleic acid amplification was developed. The chip contains an array of 15 interconnected reaction wells with Cited by:

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