TY - Generic T1 - Uncovering Genomic Reassortments among Influenza Strains by Enumerating Maximal Bicliques T2 - IEEE International Conference on Bioinformatics and Biomedicine, 2008. BIBM '08 Y1 - 2008 A1 - Nagarajan, N. A1 - Kingsford, Carl KW - avian hosted influenza genome KW - Bioinformatics KW - Capacitive sensors KW - Delay KW - diseases KW - Event detection KW - general bipartite graphs KW - genomic reassortments KW - Genomics KW - graph theory KW - high probability inconsistencies KW - History KW - human hosted influenza genome KW - incompatibility graph KW - Influenza KW - influenza strain KW - maximal biclique KW - maximal biclique enumeration KW - microorganisms KW - phylogenetic trees KW - Phylogeny KW - Public healthcare KW - quadratic delay algorithm KW - reassortment KW - reassortment event detection KW - Tree graphs KW - viral genome evolutionary history KW - virulence AB - The evolutionary histories of viral genomes have received significant recent attention due to their importance in understanding virulence and the corresponding ramifications to public health. We present a novel framework to detect reassortment events in influenza based on the comparison of two distributions of phylogenetic trees, rather than a pair of, possibly unreliable, consensus trees. We show how to detect all high-probability inconsistencies between two distributions of trees by enumerating maximal bicliques within a defined incompatibility graph. In the process, we give the first quadratic delay algorithm for enumerating maximal bicliques within general bipartite graphs. We demonstrate the utility of our approach by applying it to several sets of influenza genomes (both human- and avian-hosted) and successfully identify all known reassortment events and a few novel candidate reassortments. In addition, on simulated datasets, our approach correctly finds implanted reassortments and rarely detects reassortments where none were introduced. JA - IEEE International Conference on Bioinformatics and Biomedicine, 2008. BIBM '08 PB - IEEE SN - 978-0-7695-3452-7 ER - TY - JOUR T1 - Septaplex PCR assay for rapid identification of Vibrio cholerae including detection of virulence and int SXT genes JF - FEMS Microbiology LettersFEMS Microbiology Letters Y1 - 2006 A1 - Mantri, Chinmay K. A1 - Mohapatra, Saswat S. A1 - Ramamurthy, Thandavarayan A1 - Ghosh, Raikamal A1 - Rita R. Colwell A1 - Singh, Durg V. KW - DETECTION KW - intsxt KW - septaplex PCR KW - Vibrio cholerae KW - virulence AB - In this study, we describe a septaplex PCR assay for rapid identification of Vibrio cholerae including detection of the virulence and intsxt genes. Conditions were optimized to amplify fragments of ISRrRNA (encoding for 16S–23S rRNA gene, Intergenic spacer regions), O1rfb (O1 serogroup specific rfb), O139rfb (O139 serogroup specific rfb), ctxA (cholera toxin subunit A), tcpA (toxin coregulated pilus), and intsxt (sxt integron) simultaneously in a single PCR. The septaplex PCR was evaluated using 211 strains of V. cholerae and six water samples for in situ testing. PCR results were correlated with genotype data obtained by individual PCR and slot-blot assays. The one-step PCR described here can be used to identify V. cholerae accurately and rapidly. Also, the virulence and intsxt genes can be simultaneously detected, providing a useful method for monitoring pathogenic, intsxt-positive and nonpathogenic, intsxt-negative V. cholerae serogroups both in the environment and clinical settings. VL - 265 SN - 1574-6968 ER - TY - JOUR T1 - Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial "pan-genome" JF - Proceedings of the National Academy of Sciences of the United States of AmericaProceedings of the National Academy of Sciences of the United States of America Y1 - 2005 A1 - Tettelin, Hervé A1 - Masignani, Vega A1 - Cieslewicz, Michael J. A1 - Donati, Claudio A1 - Medini, Duccio A1 - Ward, Naomi L. A1 - Angiuoli, Samuel V. A1 - Crabtree, Jonathan A1 - Jones, Amanda L. A1 - Durkin, A. Scott A1 - DeBoy, Robert T. A1 - Davidsen, Tanja M. A1 - Mora, Marirosa A1 - Scarselli, Maria A1 - Margarit y Ros, Immaculada A1 - Peterson, Jeremy D. A1 - Hauser, Christopher R. A1 - Sundaram, Jaideep P. A1 - Nelson, William C. A1 - Madupu, Ramana A1 - Brinkac, Lauren M. A1 - Dodson, Robert J. A1 - Rosovitz, Mary J. A1 - Sullivan, Steven A. A1 - Daugherty, Sean C. A1 - Haft, Daniel H. A1 - J. Selengut A1 - Gwinn, Michelle L. A1 - Zhou, Liwei A1 - Zafar, Nikhat A1 - Khouri, Hoda A1 - Radune, Diana A1 - Dimitrov, George A1 - Watkins, Kisha A1 - O'Connor, Kevin J. B. A1 - Smith, Shannon A1 - Utterback, Teresa R. A1 - White, Owen A1 - Rubens, Craig E. A1 - Grandi, Guido A1 - Madoff, Lawrence C. A1 - Kasper, Dennis L. A1 - Telford, John L. A1 - Wessels, Michael R. A1 - Rappuoli, Rino A1 - Fraser, Claire M. KW - Amino Acid Sequence KW - Bacterial Capsules KW - Base Sequence KW - Gene expression KW - Genes, Bacterial KW - Genetic Variation KW - Genome, Bacterial KW - Molecular Sequence Data KW - Phylogeny KW - sequence alignment KW - Sequence Analysis, DNA KW - Streptococcus agalactiae KW - virulence AB - The development of efficient and inexpensive genome sequencing methods has revolutionized the study of human bacterial pathogens and improved vaccine design. Unfortunately, the sequence of a single genome does not reflect how genetic variability drives pathogenesis within a bacterial species and also limits genome-wide screens for vaccine candidates or for antimicrobial targets. We have generated the genomic sequence of six strains representing the five major disease-causing serotypes of Streptococcus agalactiae, the main cause of neonatal infection in humans. Analysis of these genomes and those available in databases showed that the S. agalactiae species can be described by a pan-genome consisting of a core genome shared by all isolates, accounting for approximately 80% of any single genome, plus a dispensable genome consisting of partially shared and strain-specific genes. Mathematical extrapolation of the data suggests that the gene reservoir available for inclusion in the S. agalactiae pan-genome is vast and that unique genes will continue to be identified even after sequencing hundreds of genomes. VL - 102 N1 - http://www.ncbi.nlm.nih.gov/pubmed/16172379?dopt=Abstract ER - TY - JOUR T1 - Whole-genome sequence analysis of Pseudomonas syringae pv. phaseolicola 1448A reveals divergence among pathovars in genes involved in virulence and transposition JF - Journal of bacteriologyJournal of bacteriology Y1 - 2005 A1 - Joardar, Vinita A1 - Lindeberg, Magdalen A1 - Jackson, Robert W. A1 - J. Selengut A1 - Dodson, Robert A1 - Brinkac, Lauren M. A1 - Daugherty, Sean C. A1 - Deboy, Robert A1 - Durkin, A. Scott A1 - Giglio, Michelle Gwinn A1 - Madupu, Ramana A1 - Nelson, William C. A1 - Rosovitz, M. J. A1 - Sullivan, Steven A1 - Crabtree, Jonathan A1 - Creasy, Todd A1 - Davidsen, Tanja A1 - Haft, Dan H. A1 - Zafar, Nikhat A1 - Zhou, Liwei A1 - Halpin, Rebecca A1 - Holley, Tara A1 - Khouri, Hoda A1 - Feldblyum, Tamara A1 - White, Owen A1 - Fraser, Claire M. A1 - Chatterjee, Arun K. A1 - Cartinhour, Sam A1 - Schneider, David J. A1 - Mansfield, John A1 - Collmer, Alan A1 - Buell, C. Robin KW - Bacterial Proteins KW - DNA, Bacterial KW - Genes, Bacterial KW - Genome, Bacterial KW - Molecular Sequence Data KW - Pseudomonas syringae KW - Species Specificity KW - virulence AB - Pseudomonas syringae pv. phaseolicola, a gram-negative bacterial plant pathogen, is the causal agent of halo blight of bean. In this study, we report on the genome sequence of P. syringae pv. phaseolicola isolate 1448A, which encodes 5,353 open reading frames (ORFs) on one circular chromosome (5,928,787 bp) and two plasmids (131,950 bp and 51,711 bp). Comparative analyses with a phylogenetically divergent pathovar, P. syringae pv. tomato DC3000, revealed a strong degree of conservation at the gene and genome levels. In total, 4,133 ORFs were identified as putative orthologs in these two pathovars using a reciprocal best-hit method, with 3,941 ORFs present in conserved, syntenic blocks. Although these two pathovars are highly similar at the physiological level, they have distinct host ranges; 1448A causes disease in beans, and DC3000 is pathogenic on tomato and Arabidopsis. Examination of the complement of ORFs encoding virulence, fitness, and survival factors revealed a substantial, but not complete, overlap between these two pathovars. Another distinguishing feature between the two pathovars is their distinctive sets of transposable elements. With access to a fifth complete pseudomonad genome sequence, we were able to identify 3,567 ORFs that likely comprise the core Pseudomonas genome and 365 ORFs that are P. syringae specific. VL - 187 N1 - http://www.ncbi.nlm.nih.gov/pubmed/16159782?dopt=Abstract ER - TY - JOUR T1 - Structural flexibility in the Burkholderia mallei genome JF - Proceedings of the National Academy of Sciences of the United States of AmericaProceedings of the National Academy of Sciences of the United States of America Y1 - 2004 A1 - Nierman, William C. A1 - DeShazer, David A1 - Kim, H. Stanley A1 - Tettelin, Hervé A1 - Nelson, Karen E. A1 - Feldblyum, Tamara A1 - Ulrich, Ricky L. A1 - Ronning, Catherine M. A1 - Brinkac, Lauren M. A1 - Daugherty, Sean C. A1 - Davidsen, Tanja D. A1 - DeBoy, Robert T. A1 - Dimitrov, George A1 - Dodson, Robert J. A1 - Durkin, A. Scott A1 - Gwinn, Michelle L. A1 - Haft, Daniel H. A1 - Khouri, Hoda A1 - Kolonay, James F. A1 - Madupu, Ramana A1 - Mohammoud, Yasmin A1 - Nelson, William C. A1 - Radune, Diana A1 - Romero, Claudia M. A1 - Sarria, Saul A1 - J. Selengut A1 - Shamblin, Christine A1 - Sullivan, Steven A. A1 - White, Owen A1 - Yu, Yan A1 - Zafar, Nikhat A1 - Zhou, Liwei A1 - Fraser, Claire M. KW - Animals KW - Base Composition KW - Base Sequence KW - Burkholderia mallei KW - Chromosomes, Bacterial KW - Cricetinae KW - Genome, Bacterial KW - Glanders KW - Liver KW - Mesocricetus KW - Molecular Sequence Data KW - Multigene Family KW - Oligonucleotide Array Sequence Analysis KW - Open Reading Frames KW - virulence AB - The complete genome sequence of Burkholderia mallei ATCC 23344 provides insight into this highly infectious bacterium's pathogenicity and evolutionary history. B. mallei, the etiologic agent of glanders, has come under renewed scientific investigation as a result of recent concerns about its past and potential future use as a biological weapon. Genome analysis identified a number of putative virulence factors whose function was supported by comparative genome hybridization and expression profiling of the bacterium in hamster liver in vivo. The genome contains numerous insertion sequence elements that have mediated extensive deletions and rearrangements of the genome relative to Burkholderia pseudomallei. The genome also contains a vast number (>12,000) of simple sequence repeats. Variation in simple sequence repeats in key genes can provide a mechanism for generating antigenic variation that may account for the mammalian host's inability to mount a durable adaptive immune response to a B. mallei infection. VL - 101 N1 - http://www.ncbi.nlm.nih.gov/pubmed/15377793?dopt=Abstract ER - TY - JOUR T1 - Whole genome comparisons of serotype 4b and 1/2a strains of the food-borne pathogen Listeria monocytogenes reveal new insights into the core genome components of this species JF - Nucleic acids researchNucleic Acids Research Y1 - 2004 A1 - Nelson, Karen E. A1 - Fouts, Derrick E. A1 - Mongodin, Emmanuel F. A1 - Ravel, Jacques A1 - DeBoy, Robert T. A1 - Kolonay, James F. A1 - Rasko, David A. A1 - Angiuoli, Samuel V. A1 - Gill, Steven R. A1 - Paulsen, Ian T. A1 - Peterson, Jeremy A1 - White, Owen A1 - Nelson, William C. A1 - Nierman, William A1 - Beanan, Maureen J. A1 - Brinkac, Lauren M. A1 - Daugherty, Sean C. A1 - Dodson, Robert J. A1 - Durkin, A. Scott A1 - Madupu, Ramana A1 - Haft, Daniel H. A1 - J. Selengut A1 - Van Aken, Susan A1 - Khouri, Hoda A1 - Fedorova, Nadia A1 - Forberger, Heather A1 - Tran, Bao A1 - Kathariou, Sophia A1 - Wonderling, Laura D. A1 - Uhlich, Gaylen A. A1 - Bayles, Darrell O. A1 - Luchansky, John B. A1 - Fraser, Claire M. KW - Base Composition KW - Chromosomes, Bacterial KW - DNA Transposable Elements KW - Food Microbiology KW - Genes, Bacterial KW - Genome, Bacterial KW - Genomics KW - Listeria monocytogenes KW - Meat KW - Open Reading Frames KW - Physical Chromosome Mapping KW - Polymorphism, Single Nucleotide KW - Prophages KW - Serotyping KW - Species Specificity KW - Synteny KW - virulence AB - The genomes of three strains of Listeria monocytogenes that have been associated with food-borne illness in the USA were subjected to whole genome comparative analysis. A total of 51, 97 and 69 strain-specific genes were identified in L.monocytogenes strains F2365 (serotype 4b, cheese isolate), F6854 (serotype 1/2a, frankfurter isolate) and H7858 (serotype 4b, meat isolate), respectively. Eighty-three genes were restricted to serotype 1/2a and 51 to serotype 4b strains. These strain- and serotype-specific genes probably contribute to observed differences in pathogenicity, and the ability of the organisms to survive and grow in their respective environmental niches. The serotype 1/2a-specific genes include an operon that encodes the rhamnose biosynthetic pathway that is associated with teichoic acid biosynthesis, as well as operons for five glycosyl transferases and an adenine-specific DNA methyltransferase. A total of 8603 and 105 050 high quality single nucleotide polymorphisms (SNPs) were found on the draft genome sequences of strain H7858 and strain F6854, respectively, when compared with strain F2365. Whole genome comparative analyses revealed that the L.monocytogenes genomes are essentially syntenic, with the majority of genomic differences consisting of phage insertions, transposable elements and SNPs. VL - 32 N1 - http://www.ncbi.nlm.nih.gov/pubmed/15115801?dopt=Abstract ER - TY - JOUR T1 - The complete genome sequence of the Arabidopsis and tomato pathogen Pseudomonas syringae pv. tomato DC3000 JF - Proceedings of the National Academy of Sciences of the United States of AmericaProceedings of the National Academy of Sciences of the United States of America Y1 - 2003 A1 - Buell, C. Robin A1 - Joardar, Vinita A1 - Lindeberg, Magdalen A1 - J. Selengut A1 - Paulsen, Ian T. A1 - Gwinn, Michelle L. A1 - Dodson, Robert J. A1 - DeBoy, Robert T. A1 - Durkin, A. Scott A1 - Kolonay, James F. A1 - Madupu, Ramana A1 - Daugherty, Sean A1 - Brinkac, Lauren A1 - Beanan, Maureen J. A1 - Haft, Daniel H. A1 - Nelson, William C. A1 - Davidsen, Tanja A1 - Zafar, Nikhat A1 - Zhou, Liwei A1 - Liu, Jia A1 - Yuan, Qiaoping A1 - Khouri, Hoda A1 - Fedorova, Nadia A1 - Tran, Bao A1 - Russell, Daniel A1 - Berry, Kristi A1 - Utterback, Teresa A1 - Aken, Susan E. van A1 - Feldblyum, Tamara V. A1 - D'Ascenzo, Mark A1 - Deng, Wen-Ling A1 - Ramos, Adela R. A1 - Alfano, James R. A1 - Cartinhour, Samuel A1 - Chatterjee, Arun K. A1 - Delaney, Terrence P. A1 - Lazarowitz, Sondra G. A1 - Martin, Gregory B. A1 - Schneider, David J. A1 - Tang, Xiaoyan A1 - Bender, Carol L. A1 - White, Owen A1 - Fraser, Claire M. A1 - Collmer, Alan KW - Arabidopsis KW - Base Sequence KW - Biological Transport KW - Genome, Bacterial KW - Lycopersicon esculentum KW - Molecular Sequence Data KW - Plant Growth Regulators KW - Plasmids KW - Pseudomonas KW - Reactive Oxygen Species KW - Siderophores KW - virulence AB - We report the complete genome sequence of the model bacterial pathogen Pseudomonas syringae pathovar tomato DC3000 (DC3000), which is pathogenic on tomato and Arabidopsis thaliana. The DC3000 genome (6.5 megabases) contains a circular chromosome and two plasmids, which collectively encode 5,763 ORFs. We identified 298 established and putative virulence genes, including several clusters of genes encoding 31 confirmed and 19 predicted type III secretion system effector proteins. Many of the virulence genes were members of paralogous families and also were proximal to mobile elements, which collectively comprise 7% of the DC3000 genome. The bacterium possesses a large repertoire of transporters for the acquisition of nutrients, particularly sugars, as well as genes implicated in attachment to plant surfaces. Over 12% of the genes are dedicated to regulation, which may reflect the need for rapid adaptation to the diverse environments encountered during epiphytic growth and pathogenesis. Comparative analyses confirmed a high degree of similarity with two sequenced pseudomonads, Pseudomonas putida and Pseudomonas aeruginosa, yet revealed 1,159 genes unique to DC3000, of which 811 lack a known function. VL - 100 N1 - http://www.ncbi.nlm.nih.gov/pubmed/12928499?dopt=Abstract ER -