The Experts below are selected from a list of 65742 Experts worldwide ranked by ideXlab platform
Seokhwan Hwang - One of the best experts on this subject based on the ideXlab platform.
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primer and Probe Sets for group specific quantification of the genera nitrosomonas and nitrosospira using real time pcr
Biotechnology and Bioengineering, 2008Co-Authors: Juntaek Lim, Seung Gu Shin, Seokhwan HwangAbstract:Use of quantitative real-time PCR (QPCR) with TaqMan Probes is increasingly popular in various environmental works to detect and quantify a specific microorganism or a group of target microorganism. Although many aspects of conducting a QPCR assay have become very easy to perform, a proper design of oligonucleotide sequences comprising primers and a Probe is still considered as one of the most important aspects of a QPCR application. This work was conducted to design group specific primer and Probe Sets for the detection of ammonia oxidizing bacteria (AOB) using a real-time PCR with a TaqMan system. The genera Nitrosomonas and Nitrosospira were grouped into five clusters based on similarity of their 16S rRNA gene sequences. Five group-specific AOB primer and Probe Sets were designed. These Sets separately detect four subgroups of Nitrosomonas (Nitrosomonas europaea-, Nitrosococcus mobilis-, Nitrosomonas nitrosa-, and Nitrosomonas cryotolerans-clusters) along with the genus Nitrosospira. Target-group specificity of each primer and Probe Set was initially investigated by analyzing potential false results in silico, followed by a series of experimental tests for QPCR efficiency and detection limit. In general, each primer and Probe Set was very specific to the target group and sensitive to detect target DNA as low as two 16S rRNA gene copies per reaction mixture. QPCR efficiency, higher than 93.5%, could be achieved for all primer and Probe Sets. The primer and Probe Sets designed in this study can be used to detect and quantify the beta-proteobacterial AOB in biological nitrification processes and various environments.
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group specific primer and Probe Sets to detect methanogenic communities using quantitative real time polymerase chain reaction
Biotechnology and Bioengineering, 2005Co-Authors: Changsoo Lee, Jaai Kim, Seokhwan HwangAbstract:Real-time polymerase chain reaction (PCR) is a highly sensitive method that can be used for the detection and quantification of microbial populations without cultivating them in anaerobic processes and environmental samples. This work was conducted to design primer and Probe Sets for the detection of methanogens using a real-time PCR with the TaqMan system. Six group-specific methanogenic primer and Probe Sets were designed. These Sets separately detect four orders (Methanococcales, Methanobacteriales, Methanomicrobiales, and Methanosarcinales) along with two families (Methanosarcinaceae and Methanosaetaceae) of the order Methanosarcinales. We also designed the universal primer and Probe Sets that specifically detect the 16S rDNA of prokaryotes and of the domain Bacteria and Archaea, and which are fully compatible with the TaqMan real-time PCR system. Target-group specificity of each primer and Probe Set was empirically verified by testing DNA isolated from 28 archaeal cultures and by analyzing potential false results. In general, each primer and Probe Set was very specific to the target group. The primer and Probe Sets designed in this study can be used to detect and quantify the order-level (family-level in the case of Methanosarcinales) methanogenic groups in anaerobic biological processes and various environments.
Kyoko Sawabe - One of the best experts on this subject based on the ideXlab platform.
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high throughput genotyping of a full voltage gated sodium channel gene via genomic dna using target capture sequencing and analytical pipeline monas to discover novel insecticide resistance mutations
PLOS Neglected Tropical Diseases, 2019Co-Authors: Kentaro Itokawa, Tsuyoshi Sekizuka, Yoshihide Maekawa, Koji Yatsu, Osamu Komagata, Masaaki Sugiura, Tomonori Sasaki, Takashi Tomita, Makoto Kuroda, Kyoko SawabeAbstract:In insects, the voltage-gated sodium channel (VGSC) is the primary target site of pyrethroid insecticides. Various amino acid substitutions in the VGSC protein, which are selected under insecticide pressure, are known to confer insecticide resistance. In the genome, the VGSC gene consists of more than 30 exons sparsely distributed across a large genomic region, which often exceeds 100 kbp. Due to this complex genomic structure, it is often challenging to genotype full coding nucleotide sequences (CDSs) of VGSC from individual genomic DNA (gDNA). In this study, we designed biotinylated oligonucleotide Probes from CDSs of VGSC of Asian tiger mosquito, Aedes albopictus. The Probe Set effectively concentrated (>80,000-fold) all targeted regions of gene VGSC from pooled barcoded Illumina libraries each constructed from individual A. albopictus gDNAs. The Probe Set also captured all orthologous VGSC CDSs, except some tiny exons, from the gDNA of other Culicinae mosquitos, A. aegypti and Culex pipiens complex, with comparable efficiency as a result of the high nucleotide-level conservation of VGSC. To improve efficiency of the downstream bioinformatic process, we developed an automated pipeline—MoNaS (Mosquito Na+ channel mutation Search)—which calls amino acid substitutions in the VGSC from NGS reads and compares those to known resistance mutations. The proposed method and our bioinformatic tool should facilitate the discovery of novel amino acid variants conferring insecticide resistance on VGSC and population genetic studies on resistance alleles (with respect to the origin, selection, and migration etc.) in both clinically and agriculturally important insect pests.
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high throughput genotyping of a full voltage gated sodium channel gene via genomic dna using target capture sequencing and analytical pipeline monas to discover novel insecticide resistance mutations
bioRxiv, 2019Co-Authors: Kentaro Itokawa, Tsuyoshi Sekizuka, Yoshihide Maekawa, Koji Yatsu, Osamu Komagata, Masaaki Sugiura, Tomonori Sasaki, Takashi Tomita, Makoto Kuroda, Kyoko SawabeAbstract:In insects, voltage-gated sodium channel (VGSC) is the primary target site of pyrethroid insecticides. Various amino acid substitutions in the VGSC protein, which are selected under insecticide pressure, are known to confer insecticide resistance. In the genome, the VGSC gene consists of more than 30 exons sparsely distributed across a large genomic region, which often exceeds 100 kbp. Due to this complex genomic structure of VGSC gene, it is often challenging to genotype full coding nucleotide sequences (CDSs) of VGSC from individual genomic DNA (gDNA). In this study, we designed biotinylated oligonucleotide Probes from annotated CDSs of VGSC of Asian tiger mosquito, Aedes albopictus . The Probe Set effectively concentrated (>80,000-fold) all targeted regions of gene VGSC from pooled barcoded Illumina libraries each constructed from individual A. albopictus gDNAs. The Probe Set also captured all homologous VGSC CDSs except some tiny exons from the gDNA of other Culicinae mosquitos, A. aegypti and Culex pipiens complex, with comparable efficiency as a result of the high nucleotide-level conservation of VGSC . To enhance efficiency of the downstream bioinformatic process, we developed an automated pipeline to genotype VGSC after capture sequencing-MoNaS ( Mo squito Na + channel mutation S earch)-which calls amino acid substitutions and compares those to known resistance mutations. The proposed method and our bioinformatic tool should facilitate the discovery of novel amino acid variants conferring insecticide resistance on VGSC and population genetics studies on resistance alleles (with respect to the origin, selection, and migration etc.) in both clinically and agriculturally important insect pests.
Kentaro Itokawa - One of the best experts on this subject based on the ideXlab platform.
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high throughput genotyping of a full voltage gated sodium channel gene via genomic dna using target capture sequencing and analytical pipeline monas to discover novel insecticide resistance mutations
PLOS Neglected Tropical Diseases, 2019Co-Authors: Kentaro Itokawa, Tsuyoshi Sekizuka, Yoshihide Maekawa, Koji Yatsu, Osamu Komagata, Masaaki Sugiura, Tomonori Sasaki, Takashi Tomita, Makoto Kuroda, Kyoko SawabeAbstract:In insects, the voltage-gated sodium channel (VGSC) is the primary target site of pyrethroid insecticides. Various amino acid substitutions in the VGSC protein, which are selected under insecticide pressure, are known to confer insecticide resistance. In the genome, the VGSC gene consists of more than 30 exons sparsely distributed across a large genomic region, which often exceeds 100 kbp. Due to this complex genomic structure, it is often challenging to genotype full coding nucleotide sequences (CDSs) of VGSC from individual genomic DNA (gDNA). In this study, we designed biotinylated oligonucleotide Probes from CDSs of VGSC of Asian tiger mosquito, Aedes albopictus. The Probe Set effectively concentrated (>80,000-fold) all targeted regions of gene VGSC from pooled barcoded Illumina libraries each constructed from individual A. albopictus gDNAs. The Probe Set also captured all orthologous VGSC CDSs, except some tiny exons, from the gDNA of other Culicinae mosquitos, A. aegypti and Culex pipiens complex, with comparable efficiency as a result of the high nucleotide-level conservation of VGSC. To improve efficiency of the downstream bioinformatic process, we developed an automated pipeline—MoNaS (Mosquito Na+ channel mutation Search)—which calls amino acid substitutions in the VGSC from NGS reads and compares those to known resistance mutations. The proposed method and our bioinformatic tool should facilitate the discovery of novel amino acid variants conferring insecticide resistance on VGSC and population genetic studies on resistance alleles (with respect to the origin, selection, and migration etc.) in both clinically and agriculturally important insect pests.
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high throughput genotyping of a full voltage gated sodium channel gene via genomic dna using target capture sequencing and analytical pipeline monas to discover novel insecticide resistance mutations
bioRxiv, 2019Co-Authors: Kentaro Itokawa, Tsuyoshi Sekizuka, Yoshihide Maekawa, Koji Yatsu, Osamu Komagata, Masaaki Sugiura, Tomonori Sasaki, Takashi Tomita, Makoto Kuroda, Kyoko SawabeAbstract:In insects, voltage-gated sodium channel (VGSC) is the primary target site of pyrethroid insecticides. Various amino acid substitutions in the VGSC protein, which are selected under insecticide pressure, are known to confer insecticide resistance. In the genome, the VGSC gene consists of more than 30 exons sparsely distributed across a large genomic region, which often exceeds 100 kbp. Due to this complex genomic structure of VGSC gene, it is often challenging to genotype full coding nucleotide sequences (CDSs) of VGSC from individual genomic DNA (gDNA). In this study, we designed biotinylated oligonucleotide Probes from annotated CDSs of VGSC of Asian tiger mosquito, Aedes albopictus . The Probe Set effectively concentrated (>80,000-fold) all targeted regions of gene VGSC from pooled barcoded Illumina libraries each constructed from individual A. albopictus gDNAs. The Probe Set also captured all homologous VGSC CDSs except some tiny exons from the gDNA of other Culicinae mosquitos, A. aegypti and Culex pipiens complex, with comparable efficiency as a result of the high nucleotide-level conservation of VGSC . To enhance efficiency of the downstream bioinformatic process, we developed an automated pipeline to genotype VGSC after capture sequencing-MoNaS ( Mo squito Na + channel mutation S earch)-which calls amino acid substitutions and compares those to known resistance mutations. The proposed method and our bioinformatic tool should facilitate the discovery of novel amino acid variants conferring insecticide resistance on VGSC and population genetics studies on resistance alleles (with respect to the origin, selection, and migration etc.) in both clinically and agriculturally important insect pests.
Jonathan M. Elkins - One of the best experts on this subject based on the ideXlab platform.
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sgc gak 1 a chemical Probe for cyclin g associated kinase gak
Journal of Medicinal Chemistry, 2019Co-Authors: Christopher R. M. Asquith, James M. Bennett, Jonathan M. Elkins, Benedicttilman Berger, Jing Wan, Stephen J Capuzzi, Daniel J Crona, David H Drewry, Michael P EastAbstract:We describe SGC-GAK-1 (11), a potent, selective, and cell-active inhibitor of cyclin G-associated kinase (GAK), together with a structurally related negative control SGC-GAK-1N (14). 11 was highly selective in an in vitro kinome-wide screen, but cellular engagement assays defined RIPK2 as a collateral target. We identified 18 as a potent RIPK2 inhibitor lacking GAK activity. Together, this chemical Probe Set can be used to interrogate GAK cellular biology.
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sgc gak 1 a chemical Probe for cyclin g associated kinase gak
bioRxiv, 2018Co-Authors: Christopher R. M. Asquith, James M. Bennett, Jonathan M. Elkins, Benedicttilman Berger, Jing Wan, Michael P East, O Fedorov, P H C Godoi, Debra Hunter, S KnappAbstract:We describe SGC-GAK-1 (11), a potent, selective, and cell-active inhibitor of cyclin G associated kinase (GAK), together with a structurally-related negative control SGC-GAK-1N (14). SGC-GAK-1 is highly selective in a kinome-wide screen, but cellular engagement assays defined RIPK2 as a collateral target. We identified 18 as a potent inhibitor of RIPK2 lacking GAK activity. Together, the chemical Probe Set of 11, 14, and 18 can be used to interrogate the cellular biology of GAK inhibition.
Daniel P Normolle - One of the best experts on this subject based on the ideXlab platform.
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a multicenter study of a fluorescence in situ hybridization Probe Set for diagnosing high grade dysplasia and adenocarcinoma in barrett s esophagus
Digestive Diseases and Sciences, 2017Co-Authors: John M Poneros, Adam S Faye, Emily Barr G Fritcher, Sharmila Anandasabapathy, Robert S Bresalier, Norman E Marcon, Kim D Turgeon, Henry D Appelman, Daniel P Normolle, Larry MorrisonAbstract:Background and Aims Preliminary single-institution data suggest that fluorescence in situ hybridization (FISH) may be useful for detecting high-grade dysplasia (HGD) and esophageal adenocarcinoma (EA) in patients with Barrett’s esophagus (BE). This multicenter study aims to validate the measurement of polysomy (gain of at least two loci) by FISH as a way to discriminate degrees of dysplasia in BE specimens.
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a multicenter study of a fluorescence in situ hybridization Probe Set for diagnosing high grade dysplasia and adenocarcinoma in barrett s esophagus
Digestive Diseases and Sciences, 2017Co-Authors: John M Poneros, Adam S Faye, Emily Barr G Fritcher, Sharmila Anandasabapathy, Robert S Bresalier, Norman E Marcon, Kim D Turgeon, Henry D Appelman, Ananda Sen, Daniel P NormolleAbstract:Background and Aims Preliminary single-institution data suggest that fluorescence in situ hybridization (FISH) may be useful for detecting high-grade dysplasia (HGD) and esophageal adenocarcinoma (EA) in patients with Barrett’s esophagus (BE). This multicenter study aims to validate the measurement of polysomy (gain of at least two loci) by FISH as a way to discriminate degrees of dysplasia in BE specimens.
