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Using expression arrays for copy number detection: an example from E. coli

Dmitriy Skvortsov, Diana Abdueva, Michael E Stitzer, Steven E Finkel, Simon Tavaré
2007 BMC Bioinformatics  
While many of the methods and algorithms developed for the analysis microarrays have focused on expression analysis, the same technology can be used to detect genetic alterations, using for example standard  ...  Microarray-based comparative genomic hybridization (array CGH) has enabled the high-resolution detection of DNA copy number aberrations.  ...  We describe an unconventional approach for copy number detection using commercially available E. coli high-density expression arrays that includes raw data normalization, background correction, data transformation  ... 
doi:10.1186/1471-2105-8-203 pmid:17570850 pmcid:PMC1914360 fatcat:2lwkntj3qvcctksd25l53vfa7e

Detection of CRISPR adaptation

Anna Shiriaeva, Ivan Fedorov, Danylo Vyhovskyi, Konstantin Severinov
2020 Biochemical Society Transactions  
Once adapted, spacers provide immunity through the recognition of complementary nucleic acid sequences, channeling them for destruction.  ...  CRISPR adaptation is a multistep process which comprises selection, generation, and incorporation of prespacers into arrays.  ...  (A) To create an E. coli strain suitable for detection of primed adaptation by SENECA, parental E. coli KD263 cells containing Figure 4 . 4 SupPCR increases the sensitivity of detection of CRISPR adaptation  ... 
doi:10.1042/bst20190662 pmid:32010936 pmcid:PMC7054753 fatcat:xwc4s3v7sbajpkhhsxnpxuvud4

Electrochemical biosensors for pathogen detection

Ellen Cesewski, Blake N. Johnson
2020 Biosensors & bioelectronics  
Recent advances in electrochemical biosensors for pathogen detection are reviewed.  ...  Future directions and challenges of electrochemical biosensors for pathogen detection are discussed, including wearable and conformal biosensors, detection of plant pathogens, multiplexed detection, reusable  ...  Acknowledgments: The authors are grateful for the generous support of the United States National Science Foundation (CBET-1650601 and CMMI-1739318), which provided funding for the reported work.  ... 
doi:10.1016/j.bios.2020.112214 pmid:32364936 pmcid:PMC7152911 fatcat:h5bob7wnprbwlb56mkgsmztcgm

Challenges of Microarray Applications for Microbial Detection and Gene Expression Profiling in Food

Yanhong Liu Yan Wang
2011 Journal of Microbial & Biochemical Technology  
Citation: Liu Y, Wang Y, Gang J (2011) Challenges of microarray applications for microbial detection and gene expression profiling in food. J Microbial  ...  Citation: Liu Y, Wang Y, Gang J (2011) Challenges of microarray applications for microbial detection and gene expression profiling in food. J Microbial Biochem Technol S2:001.  ...  Luchansky, and James Smith (USDA, Agricultural Research Services, Eastern Regional Research Center, Wyndmoor, PA) for critical reading of the manuscript and helpful discussions  ... 
doi:10.4172/1948-5948.s2-001 fatcat:scqm3fsnpjhz7brmao5v375twe

Food Microbial Pathogen Detection and Analysis Using DNA Microarray Technologies

Avraham Rasooly, Keith E. Herold
2008 Foodborne pathogens and disease  
Culture-based methods used for microbial detection and identification are simple to use, relatively inexpensive, and sensitive.  ...  and characterization of multiple pathogens and many genes in a single array assay.  ...  The minimum detection limit was esti-mated to be about 100 fg of E. coli genomic DNA or 1.4Â10 2 copies of the 23S rRNA gene (Lee et al., 2006) .  ... 
doi:10.1089/fpd.2008.0119 pmid:18673074 pmcid:PMC3186690 fatcat:sjpkkm4xyzgqjarlqsmag4ktsm

A Laboratory-Developed TaqMan Array Card for Simultaneous Detection of 19 Enteropathogens

J. Liu, J. Gratz, C. Amour, G. Kibiki, S. Becker, L. Janaki, J. J. Verweij, M. Taniuchi, S. U. Sobuz, R. Haque, D. M. Haverstick, E. R. Houpt
2012 Journal of Clinical Microbiology  
The TaqMan Array Card (TAC) system is a 384-well singleplex real-time PCR format that has been used to detect multiple infection targets.  ...  Here we developed an enteric TaqMan Array Card to detect 19 enteropathogens, including viruses (adenovirus, astrovirus, norovirus GII, rotavirus, and sapovirus), bacteria (Campylobacter jejuni/C. coli,  ...  We thank the staff and participants of the MAL-ED Network Project for their important contributions.  ... 
doi:10.1128/jcm.02658-12 pmid:23175269 pmcid:PMC3553916 fatcat:g7ypyisvqjcdhj7ukc4uwlc7du

The Yeast Two-Hybrid System for Detecting Interacting Proteins [chapter]

Ilya G. Serebriiskii, Erica A. Golemis, Peter Uetz
2005 The Proteomics Protocols Handbook  
Detailed protocols are provided for both library and array screens.  ...  One of the most popular and most effective methods for the detection of protein-protein interactions is the yeast two-hybrid system, sometimes called the interaction trap.  ...  U n c o r r e c t e d P r o o f C o p y Uncorrected Proof Copy as a bait in an interactor hunt to isolate the cDNA for protein B (which is now going to be made into a bait), construct a plasmid for expressing  ... 
doi:10.1385/1-59259-890-0:653 fatcat:rggfh5vgjvdrda6hgbv4osio5y

Detecting Gene Copy Number Fluctuations in Tumor Cells by Microarray Analysis of Genomic Representations

R. Lucito
2000 Genome Research  
We demonstrate that arrays of DNA probes derived from low-complexity representations can be used to detect amplifications, deletions, and polymorphic differences when hybridized to representations of genomic  ...  In this work, we explore the use of representations in conjunction with DNA microarray technology to measure gene copy number changes in cancer.  ...  M.W. is an American Cancer Society research professor. We thank C. Yen and M. Nakamura for valuable information and reagents, and L. Rodgers for help with informatics. Also, special thanks to D.  ... 
doi:10.1101/gr.138300 pmid:11076858 pmcid:PMC310939 fatcat:7d66kahuu5bt5jc5argvvwoihm

Electrochemical Detection of Pathogenic Bacteria-Recent Strategies, Advances and Challenges

Sabine Kuss, Hatem M. A. Amin, Richard G. Compton
2018 Chemistry - An Asian Journal  
Bacterial infections represent one of the leading causes of mortality worldwide, nevertheless the design and development of rapid, cost-efficient and reliable detection methods for pathogens remains challenging  ...  Amin gratefully acknowledges the German Research Foundation (DFG) for funding (grant number AB 702/1-1).  ...  Acknowledgements The authors thank the support from the European Commission under the Marie Curie Programme (grant number 702009).  ... 
doi:10.1002/asia.201800798 pmid:30051968 fatcat:d5tuifvuavc7voc3kjy3q3rawm

A Comparison of Two-Hybrid Approaches for Detecting Protein–Protein Interactions [chapter]

J. Mehla, J.H. Caufield, N. Sakhawalkar, P. Uetz
2017 Methods in Enzymology  
A number of variants of yeast and bacterial two-hybrid systems exist, rendering them ideal for modern, flexible proteomics-driven studies.  ...  In this chapter, we provide detailed protocols for yeast and bacterial two-hybrid systems as well as a comparison of outcomes for each approach using our own and published data.  ...  The master copy of the array should only be used to make fresh copies on YEPDA agar plates for mating.  ... 
doi:10.1016/bs.mie.2016.10.020 pmid:28137570 pmcid:PMC5737774 fatcat:vrsskowwrva47lef4xlqtld7si

A Functional Gene Array for Detection of Bacterial Virulence Elements

Crystal Jaing, Shea Gardner, Kevin McLoughlin, Nisha Mulakken, Michelle Alegria-Hartman, Phillip Banda, Peter Williams, Pauline Gu, Mark Wagner, Chitra Manohar, Tom Slezak, Ching-Hong Yang
2008 PLoS ONE  
Our first generation array targets genes from Escherichia coli strains K12 and CFT073, Enterococcus faecalis and Staphylococcus aureus.  ...  In combination with whole-genome amplification, the array detects femtogram concentrations of purified DNA, either spiked in to an aerosol sample background, or in combinations from one or more of the  ...  of the arrays.  ... 
doi:10.1371/journal.pone.0002163 pmid:18478124 pmcid:PMC2367441 fatcat:qkqht6tn6bcmfgq5tvwaaf3k7q

Waterborne Pathogens: Detection Methods and Challenges

Flor Ramírez-Castillo, Abraham Loera-Muro, Mario Jacques, Philippe Garneau, Francisco Avelar-González, Josée Harel, Alma Guerrero-Barrera
2015 Pathogens  
This review also focuses in the main molecular techniques for detection of waterborne pathogens and the use of QMRA approach to protect public health.  ...  Quantitative microbial risk assessment (QMRA) is a helpful tool to evaluate the scenarios for pathogen contamination that involve surveillance, detection methods, analysis and decision-making.  ...  Abraham Loera Muro and Mario Jacques included the fluorescence in situ hybridization detection of Actinobacillus pleuropneumoniae isolated from water sources.  ... 
doi:10.3390/pathogens4020307 pmid:26011827 pmcid:PMC4493476 fatcat:whyptdv3xfddfbmafvlxmyphtm

Design of a transcriptional biosensor for the portable, on-demand detection of cyanuric acid [article]

Xiangyang Liu, Adam D Silverman, Khalid K Alam, Erik Iverson, Julius B Lucks, Michael C Jewett, Srivatsan Raman
2019 bioRxiv   pre-print
regulation from both hosts, which enabled E. coli to function as whole-cell biosensor for CYA.  ...  Here, we engineer a portable biosensor for cyanuric acid (CYA), an analyte of interest for human and environmental health, using a LysR-type transcription regulator (LTTR) from Pseudomonas within the context  ...  ACKNOWLEDGEMENTS The authors would like to acknowledge members of the Raman, Jewett and Lucks Labs for helpful discussions. S.R. and X.L. were supported by the University of Wisconsin-  ... 
doi:10.1101/736355 fatcat:obeyevxurbeqrcdnoak5j4khde

Dark matter in the genome: evidence of widespread transcription detected by microarray tiling experiments

Jason M. Johnson, Stephen Edwards, Daniel Shoemaker, Eric E. Schadt
2005 Trends in Genetics  
In this article, we discuss different explanations for this phenomenon.  ...  This technology thus offers an important source of genomic sequence annotation that is complementary to cDNA sequencing and computational gene-finding methods.  ...  Parrish for helpful discussions and article review. We are also grateful for the thoughtful and helpful comments received from the journal referees.  ... 
doi:10.1016/j.tig.2004.12.009 pmid:15661355 fatcat:4qcxbssmcfau3ntxmtefxpi2ri

Quantitative Detection of Microbial Genes by Using DNA Microarrays

J.-C. Cho, J. M. Tiedje
2002 Applied and Environmental Microbiology  
This approach for designing quantitative microarrays and the inferred equation from this study provide a simple and convenient way to estimate the target gene concentration from the hybridization signal  ...  This method was tested using nitrate reductase (nirS), naphthalene dioxygenase (nahA), and Escherichia coli O157 O-antigen biosynthesis genes as model genes and lambda DNA as the reference DNA.  ...  We thank Alison Murray and Jizhong Zhou for helpful discussion and Syed Hashsham for use of microarray facilities. This research was supported by NSF grant no.  ... 
doi:10.1128/aem.68.3.1425-1430.2002 pmid:11872496 pmcid:PMC123775 fatcat:cvqgwmwporhypjgutyt5fpb6f4
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