The Experts below are selected from a list of 18978 Experts worldwide ranked by ideXlab platform
William S. Talbot - One of the best experts on this subject based on the ideXlab platform.
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rapid mapping of zebrafish mutations with snps and Oligonucleotide Microarrays
Genome Research, 2002Co-Authors: Heather L. Stickney, Ian G. Woods, Caleb C. Holtzer, Peter D. Kelly, Richard M. Myers, Jeremy Schmutz, Mark Dickson, William S. TalbotAbstract:Large-scale genetic screens in zebrafish have identified thousands of mutations in hundreds of essential genes. The genetic mapping of these mutations is necessary to link DNA sequences to the gene functions defined by mutant phenotypes. Here, we report two advances that will accelerate the mapping of zebrafish mutations: (1) The construction of a first generation single nucleotide polymorphism (SNP) map of the zebrafish genome comprising 2035 SNPs and 178 small insertions/deletions, and (2) the development of a method for mapping mutations in which hundreds of SNPs can be scored in parallel with an Oligonucleotide microarray. We have demonstrated the utility of the microarray technique in crosses with haploid and diploid embryos by mapping two known mutations to their previously identified locations. We have also used this approach to localize four previously unmapped mutations. We expect that mapping with SNPs and Oligonucleotide Microarrays will accelerate the molecular analysis of zebrafish mutations. [Supplemental material is available online at www.genome.org. The sequence data described in this paper have been submitted to dbSNP under accession nos. 5103507–5105537. The following individuals kindly provided reagents, samples, or unpublished information as indicated in the paper: J. Postlethwait, C.-B. Chien, C. Kimmel, L. Maves, and M. Westerfield.]
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Rapid mapping of zebrafish mutations with SNPs and Oligonucleotide Microarrays
Genome Research, 2002Co-Authors: Heather L. Stickney, Ian G. Woods, Caleb C. Holtzer, Mark C. Dickson, Peter D. Kelly, Richard M. Myers, Jeremy Schmutz, William S. TalbotAbstract:Large-scale genetic screens in zebrafish have identified thousands of mutations in hundreds of essential genes. The genetic mapping of these mutations is necessary to link DNA sequences to the gene functions defined by mutant phenotypes. Here, we report two advances that will accelerate the mapping of zebrafish mutations: (1) The construction of a first generation single nucleotide polymorphism (SNP) map of the zebrafish genome comprising 2035 SNPs and 178 small insertions/deletions, and (2) the development of a method for mapping mutations in which hundreds of SNPs can be scored in parallel with an Oligonucleotide microarray. We have demonstrated the utility of the microarray technique in crosses with haploid and diploid embryos by mapping two known mutations to their previously identified locations. We have also used this approach to localize four previously unmapped mutations. We expect that mapping with SNPs and Oligonucleotide Microarrays will accelerate the molecular analysis of zebrafish mutations.
David A Stahl - One of the best experts on this subject based on the ideXlab platform.
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optimization of single base pair mismatch discrimination in Oligonucleotide Microarrays
Applied and Environmental Microbiology, 2003Co-Authors: Hidetoshi Urakawa, Said El Fantroussi, John J Kelly, Peter A Noble, Hauke Smidt, James C Smoot, Erik H Tribou, David A StahlAbstract:The discrimination between perfect-match and single-base-pair-mismatched nucleic acid duplexes was investigated by using Oligonucleotide DNA Microarrays and nonequilibrium dissociation rates (melting profiles). DNA and RNA versions of two synthetic targets corresponding to the 16S rRNA sequences of Staphylococcus epidermidis (38 nucleotides) and Nitrosomonas eutropha (39 nucleotides) were hybridized to perfect-match probes (18-mer and 19-mer) and to a set of probes having all possible single-base-pair mismatches. The melting profiles of all probe-target duplexes were determined in parallel by using an imposed temperature step gradient. We derived an optimum wash temperature for each probe and target by using a simple formula to calculate a discrimination index for each temperature of the step gradient. This optimum corresponded to the output of an independent analysis using a customized neural network program. These results together provide an experimental and analytical framework for optimizing mismatch discrimination among all probes on a DNA microarray.
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direct profiling of environmental microbial populations by thermal dissociation analysis of native rrnas hybridized to Oligonucleotide Microarrays
Applied and Environmental Microbiology, 2003Co-Authors: Said El Fantroussi, Hidetoshi Urakawa, Anne E Bernhard, John J Kelly, Peter A Noble, Hauke Smidt, Gennadiy Yershov, David A StahlAbstract:Oligonucleotide Microarrays were used to profile directly extracted rRNA from environmental microbial populations without PCR amplification. In our initial inspection of two distinct estuarine study sites, the hybridization patterns were reproducible and varied between estuarine sediments of differing salinities. The determination of a thermal dissociation curve (i.e., melting profile) for each probe-target duplex provided information on hybridization specificity, which is essential for confirming adequate discrimination between target and nontarget sequences.
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single base pair discrimination of terminal mismatches by using Oligonucleotide Microarrays and neural network analyses
Applied and Environmental Microbiology, 2002Co-Authors: Hidetoshi Urakawa, Said El Fantroussi, John J Kelly, Peter A Noble, David A StahlAbstract:The effects of single-base-pair near-terminal and terminal mismatches on the dissociation temperature (Td) and signal intensity of short DNA duplexes were determined by using Oligonucleotide Microarrays and neural network (NN) analyses. Two perfect-match probes and 29 probes having a single-base-pair mismatch at positions 1 to 5 from the 5′ terminus of the probe were designed to target one of two short sequences representing 16S rRNA. Nonequilibrium dissociation rates (i.e., melting profiles) of all probe-target duplexes were determined simultaneously. Analysis of variance revealed that position of the mismatch, type of mismatch, and formamide concentration significantly affected the Td and signal intensity. Increasing the concentration of formamide in the washing buffer decreased the Td and signal intensity, and it decreased the variability of the signal. Although Tds of probe-target duplexes with mismatches in the first or second position were not significantly different from one another, duplexes with mismatches in the third to fifth positions had significantly lower Tds than those with mismatches in the first or second position. The trained NNs predicted the Td with high accuracies (R2 = 0.93). However, the NNs predicted the signal intensity only moderately accurately (R2 = 0.67), presumably due to increased noise in the signal intensity at low formamide concentrations. Sensitivity analysis revealed that the concentration of formamide explained most (75%) of the variability in Tds, followed by position of the mismatch (19%) and type of mismatch (6%). The results suggest that position of the mismatch at or near the 5′ terminus plays a greater role in determining the Td and signal intensity of duplexes than the type of mismatch.
Hidetoshi Urakawa - One of the best experts on this subject based on the ideXlab platform.
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Direct Profiling of rRNA in Saline Wastewater Treatment Samples Using an Oligonucleotide Microarray
Microbes and Environments, 2007Co-Authors: Hidetoshi Urakawa, Junpei Matsumoto, Tatsuhiko Hoshino, Satoshi TsunedaAbstract:Fifteen Oligonucleotide probes, targeting a broad range of microorganisms, were spotted on a DNA microarray. Specificity and reproducibility were evaluated using fluorescently labeled rRNA from 16 bacterial and eukaryal strains. The Oligonucleotide microarray was then used to analyze activated sludge samples of saline industrial wastewater in which microbial communities had been characterized previously using 16S rRNA clone libraries. The results obtained were partially consistent with the results of cloning, and demonstrate the possibility of using Oligonucleotide Microarrays for the monitoring and characterization of saline industrial wastewater populations.
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optimization of single base pair mismatch discrimination in Oligonucleotide Microarrays
Applied and Environmental Microbiology, 2003Co-Authors: Hidetoshi Urakawa, Said El Fantroussi, John J Kelly, Peter A Noble, Hauke Smidt, James C Smoot, Erik H Tribou, David A StahlAbstract:The discrimination between perfect-match and single-base-pair-mismatched nucleic acid duplexes was investigated by using Oligonucleotide DNA Microarrays and nonequilibrium dissociation rates (melting profiles). DNA and RNA versions of two synthetic targets corresponding to the 16S rRNA sequences of Staphylococcus epidermidis (38 nucleotides) and Nitrosomonas eutropha (39 nucleotides) were hybridized to perfect-match probes (18-mer and 19-mer) and to a set of probes having all possible single-base-pair mismatches. The melting profiles of all probe-target duplexes were determined in parallel by using an imposed temperature step gradient. We derived an optimum wash temperature for each probe and target by using a simple formula to calculate a discrimination index for each temperature of the step gradient. This optimum corresponded to the output of an independent analysis using a customized neural network program. These results together provide an experimental and analytical framework for optimizing mismatch discrimination among all probes on a DNA microarray.
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direct profiling of environmental microbial populations by thermal dissociation analysis of native rrnas hybridized to Oligonucleotide Microarrays
Applied and Environmental Microbiology, 2003Co-Authors: Said El Fantroussi, Hidetoshi Urakawa, Anne E Bernhard, John J Kelly, Peter A Noble, Hauke Smidt, Gennadiy Yershov, David A StahlAbstract:Oligonucleotide Microarrays were used to profile directly extracted rRNA from environmental microbial populations without PCR amplification. In our initial inspection of two distinct estuarine study sites, the hybridization patterns were reproducible and varied between estuarine sediments of differing salinities. The determination of a thermal dissociation curve (i.e., melting profile) for each probe-target duplex provided information on hybridization specificity, which is essential for confirming adequate discrimination between target and nontarget sequences.
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single base pair discrimination of terminal mismatches by using Oligonucleotide Microarrays and neural network analyses
Applied and Environmental Microbiology, 2002Co-Authors: Hidetoshi Urakawa, Said El Fantroussi, John J Kelly, Peter A Noble, David A StahlAbstract:The effects of single-base-pair near-terminal and terminal mismatches on the dissociation temperature (Td) and signal intensity of short DNA duplexes were determined by using Oligonucleotide Microarrays and neural network (NN) analyses. Two perfect-match probes and 29 probes having a single-base-pair mismatch at positions 1 to 5 from the 5′ terminus of the probe were designed to target one of two short sequences representing 16S rRNA. Nonequilibrium dissociation rates (i.e., melting profiles) of all probe-target duplexes were determined simultaneously. Analysis of variance revealed that position of the mismatch, type of mismatch, and formamide concentration significantly affected the Td and signal intensity. Increasing the concentration of formamide in the washing buffer decreased the Td and signal intensity, and it decreased the variability of the signal. Although Tds of probe-target duplexes with mismatches in the first or second position were not significantly different from one another, duplexes with mismatches in the third to fifth positions had significantly lower Tds than those with mismatches in the first or second position. The trained NNs predicted the Td with high accuracies (R2 = 0.93). However, the NNs predicted the signal intensity only moderately accurately (R2 = 0.67), presumably due to increased noise in the signal intensity at low formamide concentrations. Sensitivity analysis revealed that the concentration of formamide explained most (75%) of the variability in Tds, followed by position of the mismatch (19%) and type of mismatch (6%). The results suggest that position of the mismatch at or near the 5′ terminus plays a greater role in determining the Td and signal intensity of duplexes than the type of mismatch.
Heather L. Stickney - One of the best experts on this subject based on the ideXlab platform.
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rapid mapping of zebrafish mutations with snps and Oligonucleotide Microarrays
Genome Research, 2002Co-Authors: Heather L. Stickney, Ian G. Woods, Caleb C. Holtzer, Peter D. Kelly, Richard M. Myers, Jeremy Schmutz, Mark Dickson, William S. TalbotAbstract:Large-scale genetic screens in zebrafish have identified thousands of mutations in hundreds of essential genes. The genetic mapping of these mutations is necessary to link DNA sequences to the gene functions defined by mutant phenotypes. Here, we report two advances that will accelerate the mapping of zebrafish mutations: (1) The construction of a first generation single nucleotide polymorphism (SNP) map of the zebrafish genome comprising 2035 SNPs and 178 small insertions/deletions, and (2) the development of a method for mapping mutations in which hundreds of SNPs can be scored in parallel with an Oligonucleotide microarray. We have demonstrated the utility of the microarray technique in crosses with haploid and diploid embryos by mapping two known mutations to their previously identified locations. We have also used this approach to localize four previously unmapped mutations. We expect that mapping with SNPs and Oligonucleotide Microarrays will accelerate the molecular analysis of zebrafish mutations. [Supplemental material is available online at www.genome.org. The sequence data described in this paper have been submitted to dbSNP under accession nos. 5103507–5105537. The following individuals kindly provided reagents, samples, or unpublished information as indicated in the paper: J. Postlethwait, C.-B. Chien, C. Kimmel, L. Maves, and M. Westerfield.]
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Rapid mapping of zebrafish mutations with SNPs and Oligonucleotide Microarrays
Genome Research, 2002Co-Authors: Heather L. Stickney, Ian G. Woods, Caleb C. Holtzer, Mark C. Dickson, Peter D. Kelly, Richard M. Myers, Jeremy Schmutz, William S. TalbotAbstract:Large-scale genetic screens in zebrafish have identified thousands of mutations in hundreds of essential genes. The genetic mapping of these mutations is necessary to link DNA sequences to the gene functions defined by mutant phenotypes. Here, we report two advances that will accelerate the mapping of zebrafish mutations: (1) The construction of a first generation single nucleotide polymorphism (SNP) map of the zebrafish genome comprising 2035 SNPs and 178 small insertions/deletions, and (2) the development of a method for mapping mutations in which hundreds of SNPs can be scored in parallel with an Oligonucleotide microarray. We have demonstrated the utility of the microarray technique in crosses with haploid and diploid embryos by mapping two known mutations to their previously identified locations. We have also used this approach to localize four previously unmapped mutations. We expect that mapping with SNPs and Oligonucleotide Microarrays will accelerate the molecular analysis of zebrafish mutations.
Xiaochuan Zhou - One of the best experts on this subject based on the ideXlab platform.
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In situ synthesis of Oligonucleotide Microarrays
Biopolymers, 2004Co-Authors: Erdogan Gulari, Xiaochuan ZhouAbstract:This contribution presents a brief overall look of the methods for the preparation of various types of DNA Microarrays and a thorough examination of the methods for in situ synthesis of Oligonucleotide Microarrays.
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in situ synthesis of Oligonucleotide Microarrays
Biopolymers, 2004Co-Authors: Erdogan Gulari, Xiaochuan ZhouAbstract:This contribution presents a brief overall look of the methods for the preparation of various types of DNA Microarrays and a thorough examination of the methods for in situ synthesis of Oligonucleotide Microarrays. © 2004 Wiley Periodicals, Inc. Biopolymers, 2004
