The Experts below are selected from a list of 911718 Experts worldwide ranked by ideXlab platform
Darren M. Reynolds - One of the best experts on this subject based on the ideXlab platform.
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Comparative Analysis of 37 Acinetobacter Bacteriophages.
Viruses, 2017Co-Authors: Dann Turner, Hans-w. Ackermann, Rob Lavigne, J. Sutton, Andrew M Kropinski, Darren M. ReynoldsAbstract:Members of the genus Acinetobacter are ubiquitous in the environment and the multiple-drug resistant species A. baumannii is of significant clinical concern. This clinical relevance is currently driving research on bacterial viruses infecting A. baumannii, in an effort to implement phage therapy and phage-derived antimicrobials. Initially, a total of 42 Acinetobacter phage genome sequences were available in the international nucleotide sequence databases, corresponding to a total of 2.87 Mbp of sequence information and representing all three families of the order Caudovirales and a single member of the Leviviridae. A Comparative bioinformatics Analysis of 37 Acinetobacter phages revealed that they form six discrete clusters and two singletons based on genomic organisation and nucleotide sequence identity. The assignment of these phages to clusters was further supported by proteomic relationships established using OrthoMCL. The 4067 proteins encoded by the 37 phage genomes formed 737 groups and 974 orphans. Notably, over half of the proteins encoded by the Acinetobacter phages are of unknown function. The Comparative Analysis and clustering presented enables an updated taxonomic framing of these clades.
Dann Turner - One of the best experts on this subject based on the ideXlab platform.
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Comparative Analysis of 37 Acinetobacter Bacteriophages.
Viruses, 2017Co-Authors: Dann Turner, Hans-w. Ackermann, Rob Lavigne, J. Sutton, Andrew M Kropinski, Darren M. ReynoldsAbstract:Members of the genus Acinetobacter are ubiquitous in the environment and the multiple-drug resistant species A. baumannii is of significant clinical concern. This clinical relevance is currently driving research on bacterial viruses infecting A. baumannii, in an effort to implement phage therapy and phage-derived antimicrobials. Initially, a total of 42 Acinetobacter phage genome sequences were available in the international nucleotide sequence databases, corresponding to a total of 2.87 Mbp of sequence information and representing all three families of the order Caudovirales and a single member of the Leviviridae. A Comparative bioinformatics Analysis of 37 Acinetobacter phages revealed that they form six discrete clusters and two singletons based on genomic organisation and nucleotide sequence identity. The assignment of these phages to clusters was further supported by proteomic relationships established using OrthoMCL. The 4067 proteins encoded by the 37 phage genomes formed 737 groups and 974 orphans. Notably, over half of the proteins encoded by the Acinetobacter phages are of unknown function. The Comparative Analysis and clustering presented enables an updated taxonomic framing of these clades.
Bogomolnaya L. - One of the best experts on this subject based on the ideXlab platform.
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Isoforms of Serratia marcescens nuclease. Comparative Analysis of substrate specificity
2020Co-Authors: Filimonova M., Garusov A., Smetanina T., Andreeva M., Bogomolnaya L.Abstract:Comparative Analysis of the specificity of Serratia marcescens nuclease isoforms has been carried out. Mononucleotides separated by anion-exchange chromatography in the presence of 7 M urea from partially hydrolyzed RNA with nucleases Sm1 and Sm2 were identified by reverse-phase HPLC. Both enzymes were found to split phosphodiester bonds at nearly all nucleic acid bases. However, nuclease Sm1 demonstrated preferential cleavage of phosphodiester bonds near uracil and nuclease Sm2 near guanine. A possible role of the N-terminal tripeptide fragment in the nuclease mechanism is discussed
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Isoforms of Serratia marcescens nuclease. Comparative Analysis of the substrate specificity
2020Co-Authors: Filimonova M., Garusov A., Smetanina T., Andreeva M., Bogomolnaya L.Abstract:Comparative Analysis of the specificity of Serratia marcescens nuclease isoforms has been carried out. Mononucleotides separated by anion-exchange chromatography with presence of 7 M urea from partially hydrolyzed RNA were identified by reversed-phase HPLC. Both enzymes were found to split phosphodiester bonds at nearly all bases in the nucleic acid chain. However nuclease Sm1 demonstrated a preferred cleavage of phosphodiester bonds near uracil and nuclease Sm2 - near guanine. A possible role of N-terminal tripeptide fragment in nucleases mechanism is discussed
Ward F Odenwald - One of the best experts on this subject based on the ideXlab platform.
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Flavivirus and Filovirus EvoPrinters: New alignment tools for the Comparative Analysis of viral evolution.
Public Library of Science (PLoS), 2017Co-Authors: Thomas Brody, Amarendra S Yavatkar, Dong Sun Park, Alexander Kuzin, Jermaine Ross, Ward F OdenwaldAbstract:Flavivirus and Filovirus infections are serious epidemic threats to human populations. Multi-genome Comparative Analysis of these evolving pathogens affords a view of their essential, conserved sequence elements as well as progressive evolutionary changes. While phylogenetic Analysis has yielded important insights, the growing number of available genomic sequences makes comparisons between hundreds of viral strains challenging. We report here a new approach for the Comparative Analysis of these hemorrhagic fever viruses that can superimpose an unlimited number of one-on-one alignments to identify important features within genomes of interest.We have adapted EvoPrinter alignment algorithms for the rapid Comparative Analysis of Flavivirus or Filovirus sequences including Zika and Ebola strains. The user can input a full genome or partial viral sequence and then view either individual comparisons or generate color-coded readouts that superimpose hundreds of one-on-one alignments to identify unique or shared identity SNPs that reveal ancestral relationships between strains. The user can also opt to select a database genome in order to access a library of pre-aligned genomes of either 1,094 Flaviviruses or 460 Filoviruses for rapid Comparative Analysis with all database entries or a select subset. Using EvoPrinter search and alignment programs, we show the following: 1) superimposing alignment data from many related strains identifies lineage identity SNPs, which enable the assessment of sublineage complexity within viral outbreaks; 2) whole-genome SNP profile screens uncover novel Dengue2 and Zika recombinant strains and their parental lineages; 3) differential SNP profiling identifies host cell A-to-I hyper-editing within Ebola and Marburg viruses, and 4) hundreds of superimposed one-on-one Ebola genome alignments highlight ultra-conserved regulatory sequences, invariant amino acid codons and evolutionarily variable protein-encoding domains within a single genome.EvoPrinter allows for the assessment of lineage complexity within Flavivirus or Filovirus outbreaks, identification of recombinant strains, highlights sequences that have undergone host cell A-to-I editing, and identifies unique input and database SNPs within highly conserved sequences. EvoPrinter's ability to superimpose alignment data from hundreds of strains onto a single genome has allowed us to identify unique Zika virus sublineages that are currently spreading in South, Central and North America, the Caribbean, and in China. This new set of integrated alignment programs should serve as a useful addition to existing tools for the Comparative Analysis of these viruses
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Flavivirus and Filovirus EvoPrinters: New alignment tools for the Comparative Analysis of viral evolution
2017Co-Authors: Thomas Brody, Amarendra S Yavatkar, Dong Sun Park, Alexander Kuzin, Jermaine Ross, Ward F OdenwaldAbstract:BackgroundFlavivirus and Filovirus infections are serious epidemic threats to human populations. Multi-genome Comparative Analysis of these evolving pathogens affords a view of their essential, conserved sequence elements as well as progressive evolutionary changes. While phylogenetic Analysis has yielded important insights, the growing number of available genomic sequences makes comparisons between hundreds of viral strains challenging. We report here a new approach for the Comparative Analysis of these hemorrhagic fever viruses that can superimpose an unlimited number of one-on-one alignments to identify important features within genomes of interest.Methodology/Principal findingWe have adapted EvoPrinter alignment algorithms for the rapid Comparative Analysis of Flavivirus or Filovirus sequences including Zika and Ebola strains. The user can input a full genome or partial viral sequence and then view either individual comparisons or generate color-coded readouts that superimpose hundreds of one-on-one alignments to identify unique or shared identity SNPs that reveal ancestral relationships between strains. The user can also opt to select a database genome in order to access a library of pre-aligned genomes of either 1,094 Flaviviruses or 460 Filoviruses for rapid Comparative Analysis with all database entries or a select subset. Using EvoPrinter search and alignment programs, we show the following: 1) superimposing alignment data from many related strains identifies lineage identity SNPs, which enable the assessment of sublineage complexity within viral outbreaks; 2) whole-genome SNP profile screens uncover novel Dengue2 and Zika recombinant strains and their parental lineages; 3) differential SNP profiling identifies host cell A-to-I hyper-editing within Ebola and Marburg viruses, and 4) hundreds of superimposed one-on-one Ebola genome alignments highlight ultra-conserved regulatory sequences, invariant amino acid codons and evolutionarily variable protein-encoding domains within a single genome.Conclusions/SignificanceEvoPrinter allows for the assessment of lineage complexity within Flavivirus or Filovirus outbreaks, identification of recombinant strains, highlights sequences that have undergone host cell A-to-I editing, and identifies unique input and database SNPs within highly conserved sequences. EvoPrinter’s ability to superimpose alignment data from hundreds of strains onto a single genome has allowed us to identify unique Zika virus sublineages that are currently spreading in South, Central and North America, the Caribbean, and in China. This new set of integrated alignment programs should serve as a useful addition to existing tools for the Comparative Analysis of these viruses.
J. Sutton - One of the best experts on this subject based on the ideXlab platform.
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Comparative Analysis of 37 Acinetobacter Bacteriophages.
Viruses, 2017Co-Authors: Dann Turner, Hans-w. Ackermann, Rob Lavigne, J. Sutton, Andrew M Kropinski, Darren M. ReynoldsAbstract:Members of the genus Acinetobacter are ubiquitous in the environment and the multiple-drug resistant species A. baumannii is of significant clinical concern. This clinical relevance is currently driving research on bacterial viruses infecting A. baumannii, in an effort to implement phage therapy and phage-derived antimicrobials. Initially, a total of 42 Acinetobacter phage genome sequences were available in the international nucleotide sequence databases, corresponding to a total of 2.87 Mbp of sequence information and representing all three families of the order Caudovirales and a single member of the Leviviridae. A Comparative bioinformatics Analysis of 37 Acinetobacter phages revealed that they form six discrete clusters and two singletons based on genomic organisation and nucleotide sequence identity. The assignment of these phages to clusters was further supported by proteomic relationships established using OrthoMCL. The 4067 proteins encoded by the 37 phage genomes formed 737 groups and 974 orphans. Notably, over half of the proteins encoded by the Acinetobacter phages are of unknown function. The Comparative Analysis and clustering presented enables an updated taxonomic framing of these clades.
