The Experts below are selected from a list of 109296 Experts worldwide ranked by ideXlab platform
James R Cole - One of the best experts on this subject based on the ideXlab platform.
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ribosomal database project data and tools for high throughput rRNA Analysis
Nucleic Acids Research, 2014Co-Authors: James R Cole, Jordan A Fish, Donna M Mcgarrell, Yanni Sun, Titus C Brown, Andrea Porrasalfaro, Benli Chai, Cheryl R. Kuske, Qiong Wang, James M TiedjeAbstract:Ribosomal Database Project (RDP; http://rdp.cme.msu.edu/) provides the research community with aligned and annotated rRNA gene sequence data, along with tools to allow researchers to analyze their own rRNA gene sequences in the RDP framework. RDP data and tools are utilized in fields as diverse as human health, microbial ecology, environmental microbiology, nucleic acid chemistry, taxonomy and phylogenetics. In addition to aligned and annotated collections of bacterial and archaeal small subunit rRNA genes, RDP now includes a collection of fungal large subunit rRNA genes. RDP tools, including Classifier and Aligner, have been updated to work with this new fungal collection. The use of high-throughput sequencing to characterize environmental microbial populations has exploded in the past several years, and as sequence technologies have improved, the sizes of environmental datasets have increased. With release 11, RDP is providing an expanded set of tools to facilitate Analysis of high-throughput data, including both single-stranded and paired-end reads. In addition, most tools are now available as open source packages for download and local use by researchers with high-volume needs or who would like to develop custom Analysis pipelines.
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the ribosomal database project improved alignments and new tools for rRNA Analysis
Nucleic Acids Research, 2009Co-Authors: James R Cole, Jordan A Fish, Donna M Mcgarrell, Benli Chai, Qiong Wang, Erick Cardenas, Ryan J Farris, A S Kulamsyedmohideen, Terry L Marsh, George M GarrityAbstract:The Ribosomal Database Project (RDP) provides researchers with quality-controlled bacterial and archaeal small subunit rRNA alignments and Analysis tools. An improved alignment strategy uses the Infernal secondary structure aware aligner to provide a more consistent higher quality alignment and faster processing of user sequences. Substantial new Analysis features include a new Pyrosequencing Pipeline that provides tools to support Analysis of ultra high-throughput rRNA sequencing data. This pipeline offers a collection of tools that automate the data processing and simplify the computationally intensive Analysis of large sequencing libraries. In addition, a new Taxomatic visualization tool allows rapid visualization of taxonomic inconsistencies and suggests corrections, and a new class Assignment Generator provides instructors with a lesson plan and individualized teaching materials. Details about RDP data and analytical functions can be found at http://rdp.cme.msu.edu/.
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the ribosomal database project rdp ii sequences and tools for high throughput rRNA Analysis
Nucleic Acids Research, 2004Co-Authors: James R Cole, Donna M Mcgarrell, Benli Chai, Qiong Wang, Ryan J Farris, George M Garrity, S A Kulam, James M TiedjeAbstract:The Ribosomal Database Project (RDP-II) provides the research community with aligned and annotated rRNA gene sequences, along with Analysis services and a phylogenetically consistent taxonomic framework for these data. Updated monthly, these services are made available through the RDP-II website (http://rdp.cme.msu.edu/). RDP-II release 9.21 (August 2004) contains 101 632 bacterial small subunit rRNA gene sequences in aligned and annotated format. High-throughput tools for initial taxonomic placement, identification of related sequences, probe and primer testing, data navigation and subalignment download are provided. The RDP-II email address for questions or comments is ude.usm@ffatspdr.
James M Tiedje - One of the best experts on this subject based on the ideXlab platform.
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ribosomal database project data and tools for high throughput rRNA Analysis
Nucleic Acids Research, 2014Co-Authors: James R Cole, Jordan A Fish, Donna M Mcgarrell, Yanni Sun, Titus C Brown, Andrea Porrasalfaro, Benli Chai, Cheryl R. Kuske, Qiong Wang, James M TiedjeAbstract:Ribosomal Database Project (RDP; http://rdp.cme.msu.edu/) provides the research community with aligned and annotated rRNA gene sequence data, along with tools to allow researchers to analyze their own rRNA gene sequences in the RDP framework. RDP data and tools are utilized in fields as diverse as human health, microbial ecology, environmental microbiology, nucleic acid chemistry, taxonomy and phylogenetics. In addition to aligned and annotated collections of bacterial and archaeal small subunit rRNA genes, RDP now includes a collection of fungal large subunit rRNA genes. RDP tools, including Classifier and Aligner, have been updated to work with this new fungal collection. The use of high-throughput sequencing to characterize environmental microbial populations has exploded in the past several years, and as sequence technologies have improved, the sizes of environmental datasets have increased. With release 11, RDP is providing an expanded set of tools to facilitate Analysis of high-throughput data, including both single-stranded and paired-end reads. In addition, most tools are now available as open source packages for download and local use by researchers with high-volume needs or who would like to develop custom Analysis pipelines.
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the ribosomal database project rdp ii sequences and tools for high throughput rRNA Analysis
Nucleic Acids Research, 2004Co-Authors: James R Cole, Donna M Mcgarrell, Benli Chai, Qiong Wang, Ryan J Farris, George M Garrity, S A Kulam, James M TiedjeAbstract:The Ribosomal Database Project (RDP-II) provides the research community with aligned and annotated rRNA gene sequences, along with Analysis services and a phylogenetically consistent taxonomic framework for these data. Updated monthly, these services are made available through the RDP-II website (http://rdp.cme.msu.edu/). RDP-II release 9.21 (August 2004) contains 101 632 bacterial small subunit rRNA gene sequences in aligned and annotated format. High-throughput tools for initial taxonomic placement, identification of related sequences, probe and primer testing, data navigation and subalignment download are provided. The RDP-II email address for questions or comments is ude.usm@ffatspdr.
Alastair Mcgregor - One of the best experts on this subject based on the ideXlab platform.
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clinical characteristics and treatment outcomes in a cohort of patients with pyogenic and amoebic liver abscess
BMC Infectious Diseases, 2019Co-Authors: Lorna Neill, Frances Edwards, Simon M Collin, David P Harrington, Dominic Wakerley, Alastair McgregorAbstract:We describe the clinical features of a cohort of patients with liver abscesses and investigate relationships between clinical, radiological and microbiological findings and mortality. Retrospective review of pyogenic (PLA) or amoebic liver abscesses (ALA) diagnosed and treated at a major infectious diseases department in London over 9 years. One hundred forty-one patient records were identified; 132 (93.6%) had PLA and 9 (6.4%) ALA. No organism was identified in 38.6% (51/132); a single bacterial species was isolated in 47.0% (62/132) of PLA, ≥ 2 in 14.4% (19/132). There was weak evidence of variation in abscess size by type of microorganism, with streptococcal PLA typically larger (p = 0.03 for Streptococcus milleri group, p = 0.05 for non-milleri streptococci). Patients with ALA were younger (median 41, IQR 37–51 years) than those with PLA (median 68, IQR 50.5–78 years) (p = 0.003) and all were male (9/9, 100%, (p = 0.03)), with a history of recent travel in the majority (6/9, 66.7% (p = 0.003)). C-reactive protein was higher in ALA than in PLA (p = 0.06). In the entire cohort, loculation (HR = 2.51 (95% CI 1.00–6.32), p = 0.04) and baseline ALP (HR = 4.78 (95% CI 1.19–19.2) per log10 increase, p = 0.03) were associated with mortality. 16S ribosomal RNA (rRNA) Analysis was used in a subset of culture-negative cases and increased the diagnostic yield by 13%. Clinical or radiological features cannot be used to distinguish between PLA and ALA, or help identify the bacterial cause of PLA. However, ALA is more common in young, male patients with a history of travel. 16S rRNA Analysis of abscess fluid has a role in improving microbiological diagnosis in culture-negative cases.
George M Garrity - One of the best experts on this subject based on the ideXlab platform.
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the ribosomal database project improved alignments and new tools for rRNA Analysis
Nucleic Acids Research, 2009Co-Authors: James R Cole, Jordan A Fish, Donna M Mcgarrell, Benli Chai, Qiong Wang, Erick Cardenas, Ryan J Farris, A S Kulamsyedmohideen, Terry L Marsh, George M GarrityAbstract:The Ribosomal Database Project (RDP) provides researchers with quality-controlled bacterial and archaeal small subunit rRNA alignments and Analysis tools. An improved alignment strategy uses the Infernal secondary structure aware aligner to provide a more consistent higher quality alignment and faster processing of user sequences. Substantial new Analysis features include a new Pyrosequencing Pipeline that provides tools to support Analysis of ultra high-throughput rRNA sequencing data. This pipeline offers a collection of tools that automate the data processing and simplify the computationally intensive Analysis of large sequencing libraries. In addition, a new Taxomatic visualization tool allows rapid visualization of taxonomic inconsistencies and suggests corrections, and a new class Assignment Generator provides instructors with a lesson plan and individualized teaching materials. Details about RDP data and analytical functions can be found at http://rdp.cme.msu.edu/.
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the ribosomal database project rdp ii sequences and tools for high throughput rRNA Analysis
Nucleic Acids Research, 2004Co-Authors: James R Cole, Donna M Mcgarrell, Benli Chai, Qiong Wang, Ryan J Farris, George M Garrity, S A Kulam, James M TiedjeAbstract:The Ribosomal Database Project (RDP-II) provides the research community with aligned and annotated rRNA gene sequences, along with Analysis services and a phylogenetically consistent taxonomic framework for these data. Updated monthly, these services are made available through the RDP-II website (http://rdp.cme.msu.edu/). RDP-II release 9.21 (August 2004) contains 101 632 bacterial small subunit rRNA gene sequences in aligned and annotated format. High-throughput tools for initial taxonomic placement, identification of related sequences, probe and primer testing, data navigation and subalignment download are provided. The RDP-II email address for questions or comments is ude.usm@ffatspdr.
Juergen Wiegel - One of the best experts on this subject based on the ideXlab platform.
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isolation and characterization of desulfitobacterium dehalogenans gen nov sp nov an anaerobic bacterium which reductively dechlorinates chlorophenolic compounds
International Journal of Systematic and Evolutionary Microbiology, 1994Co-Authors: Ilya Utkin, Carl R Woese, Juergen WiegelAbstract:An organism that is able to reductively ortho-dechlorinate 2,4-dichlorophenol and 3-chloro-4-hydroxyphenylacetate (3-Cl-4-OHPA) was isolated from a methanogenic lake sediment. This organism, an anaerobic, motile, Gram-type-positive, rod-shaped bacterium, grew in the presence of 0.1% yeast extract when pyruvate, lactate, formate, or hydrogen was used as the electron donor for reductive dehalogenation of 3-Cl-4-OHPA. Sulfite, thiosulfate, and sulfur were reduced to sulfide, nitrate was reduced to nitrite, and fumarate was reduced to succinate. Dissimilatory reduction of sulfate could not be demonstrated, and no adenylylsulfate reductase was detected with an immunoassay. The organism fermented two pyruvate molecules to one lactate molecule, one acetate molecule, and one carbon dioxide molecule. The pH and temperature optima for both growth and dechlorination of 3-Cl-4-OHPA were 7.5 and 38°C, respectively. The doubling time under these conditions was approximately 3.5 h. On the basis of the results of a 16S rRNA Analysis and the inability of the organism to use sulfate as an electron acceptor, strain JW/IU-DC1 is described as the type strain of the new taxon Desulfitobacterium dehalogenans gen. nov., sp. nov.
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isolation and characterization of a moderately thermophilic anaerobic alkaliphile clostridium paradoxum sp nov
International Journal of Systematic and Evolutionary Microbiology, 1993Co-Authors: Linda Mandelco, Juergen WiegelAbstract:Alkaliphilic, moderately thermophilic anaerobic bacteria able to grow above pH 10.5 and 55°C were isolated from various sewage plants in the United States. The strains were motile with two to six peritrichous flagella and formed round to slightly oval terminal spores in terminally distended and slightly enlarged cells. Sporulated cells remained motile. The pH range for growth was between 7.0 and 11.1, with an optimum of around 10.1 At pH 10.1 the temperature range for growth was between 30 and 63°C, with an optimum of 56°C. The shortest observed doubling time (glucose) was around 16 min at 56°C and pH 10.1. No dissimilatory sulfate reduction was detected. The organism utilized glucose, fructose, sucrose, maltose, and pyruvate but required yeast extract or tryptone for growth. Optimal NaCI concentrations for growth were between 50 and 200 mM. The guanine-plus-cytosine content was 30.0 ± 0.10 mol%. On the basis of unique properties and 16S rRNA Analysis, the strains are placed in a new species, Clostridium paradoxum, referring to the unusual retainment of motility by sporulated cells. Strain JW-YL-7 (DSM 7308) is designated as the type strain.
