TY - Generic T1 - Draft Genome Sequences from a Novel Clade of Bacillus cereus sensu lato Strains Isolated from the International Space Station Y1 - 2017 A1 - Kasthuri Venkateswaran A1 - Aleksandra Checinska-Sielaff A1 - Joy Klubnik A1 - Todd Treangen A1 - M.J. Rosovitz A1 - Nicholas H. Bergman JA - Genome Announcements VL - 1 ER - TY - JOUR T1 - The fruRBA Operon Is Necessary for Group A Streptococcal Growth in Fructose and for Resistance to Neutrophil Killing during Growth in Whole Human Blood JF - Infection and Immunity Y1 - 2016 A1 - Valdes, Kayla M. A1 - Sundar, Ganesh S. A1 - Vega, Luis A. A1 - Belew, Ashton T. A1 - Islam, Emrul A1 - Binet, Rachel A1 - El-Sayed, Najib M. A1 - Le Breton, Yoann A1 - McIver, Kevin S. ED - Camilli, A. VL - 84 UR - http://iai.asm.org/lookup/doi/10.1128/IAI.01296-15 CP - 4 J1 - Infect. Immun. M3 - 10.1128/IAI.01296-15 ER - TY - JOUR T1 - Individual-specific changes in the human gut microbiota after challenge with enterotoxigenic Escherichia coli and subsequent ciprofloxacin treatment JF - BMC Genomics Y1 - 2016 A1 - Pop, Mihai A1 - Paulson, Joseph N. A1 - Chakraborty, Subhra A1 - Astrovskaya, Irina A1 - Lindsay, Brianna R. A1 - Li, Shan A1 - Bravo, éctor Corrada A1 - Harro, Clayton A1 - Parkhill, Julian A1 - Walker, Alan W. A1 - Walker, Richard I. A1 - Sack, David A. A1 - Stine, O. Colin VL - 17183412111831230710512122489914142853341501081566039108377115651846133171373920352123327102188151723 UR - http://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-016-2777-0http://link.springer.com/content/pdf/10.1186/s12864-016-2777-0 CP - 1326124105778571763174155114260523Suppl 1611Suppl 26-7Suppl 197591Pt 11321131 Suppl241Database issue1612210375335 J1 - BMC Genomics M3 - 10.1186/s12864-016-2777-0 ER - TY - JOUR T1 - Longitudinal analysis of the lung microbiota of cynomolgous macaques during long-term SHIV infection JF - Microbiome Y1 - 2016 A1 - Morris, Alison A1 - Paulson, Joseph N. A1 - Talukder, Hisham A1 - Tipton, Laura A1 - Kling, Heather A1 - Cui, Lijia A1 - Fitch, Adam A1 - Pop, Mihai A1 - Norris, Karen A. A1 - Ghedin, Elodie VL - 4320384718719152130282021211818418719223326578105723 UR - http://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-016-0183-0http://link.springer.com/content/pdf/10.1186/s40168-016-0183-0 CP - 158836212108125732558101131110121arXiv:1006.3316 J1 - Microbiome M3 - 10.1186/s40168-016-0183-0 ER - TY - JOUR T1 - Metagenomic Assembly: Overview, Challenges and Applications JF - Yale J Biol Med Y1 - 2016 A1 - Jay S. Ghurye A1 - Victoria Cepeda-Espinoza A1 - Mihai Pop VL - 89 UR - https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5045144/ CP - 3 ER - TY - RPRT T1 - Scaffolding of long read assemblies using long range contact information Y1 - 2016 A1 - Ghurye, Jay A1 - Pop, Mihai A1 - Koren, Sergey A1 - Chin, Chen-Shan UR - http://biorxiv.org/lookup/doi/10.1101/083964 M3 - 10.1101/083964 ER - TY - JOUR T1 - Therapeutic relevance of the protein phosphatase 2A in cancer JF - Oncotarget.com Y1 - 2016 A1 - Cunningham, Chelsea E. A1 - Li, Shuangshuang A1 - Vizeacoumar, Frederick S. A1 - Bhanumathy, Kalpana Kalyanasundaram A1 - Lee, Joo Sang A1 - Parameswaran, Sreejit A1 - Furber, Levi A1 - Abuhussein, Omar A1 - Paul, James M. A1 - McDonald, Megan A1 - Templeton, Shaina D. A1 - Shukla, Hersh A1 - El Zawily, Amr M. A1 - Boyd, Frederick A1 - Alli, Nezeka A1 - Mousseau, Darrell D. A1 - Geyer, Ron A1 - Bonham, Keith A1 - Anderson, Deborah H. A1 - Yan, Jiong A1 - Yu-Lee, Li-Yuan A1 - Weaver, Beth A. A1 - Uppalapati, Maruti A1 - Ruppin, Eytan A1 - Sablina, Anna A1 - Freywald, Andrew A1 - Vizeacoumar, Franco J. UR - https://www.oncotarget.com/article/11399 J1 - Oncotarget M3 - 10.18632/oncotarget.11399 ER - TY - JOUR T1 - Transcriptome Remodeling in Trypanosoma cruzi and Human Cells during Intracellular Infection. JF - PLoS Pathog Y1 - 2016 A1 - Li, Yuan A1 - Shah-Simpson, Sheena A1 - Okrah, Kwame A1 - Belew, A Trey A1 - Choi, Jungmin A1 - Caradonna, Kacey L A1 - Padmanabhan, Prasad A1 - Ndegwa, David M A1 - Temanni, M Ramzi A1 - Corrada Bravo, Hector A1 - El-Sayed, Najib M A1 - Burleigh, Barbara A AB -

Intracellular colonization and persistent infection by the kinetoplastid protozoan parasite, Trypanosoma cruzi, underlie the pathogenesis of human Chagas disease. To obtain global insights into the T. cruzi infective process, transcriptome dynamics were simultaneously captured in the parasite and host cells in an infection time course of human fibroblasts. Extensive remodeling of the T. cruzi transcriptome was observed during the early establishment of intracellular infection, coincident with a major developmental transition in the parasite. Contrasting this early response, few additional changes in steady state mRNA levels were detected once mature T. cruzi amastigotes were formed. Our findings suggest that transcriptome remodeling is required to establish a modified template to guide developmental transitions in the parasite, whereas homeostatic functions are regulated independently of transcriptomic changes, similar to that reported in related trypanosomatids. Despite complex mechanisms for regulation of phenotypic expression in T. cruzi, transcriptomic signatures derived from distinct developmental stages mirror known or projected characteristics of T. cruzi biology. Focusing on energy metabolism, we were able to validate predictions forecast in the mRNA expression profiles. We demonstrate measurable differences in the bioenergetic properties of the different mammalian-infective stages of T. cruzi and present additional findings that underscore the importance of mitochondrial electron transport in T. cruzi amastigote growth and survival. Consequences of T. cruzi colonization for the host include dynamic expression of immune response genes and cell cycle regulators with upregulation of host cholesterol and lipid synthesis pathways, which may serve to fuel intracellular T. cruzi growth. Thus, in addition to the biological inferences gained from gene ontology and functional enrichment analysis of differentially expressed genes in parasite and host, our comprehensive, high resolution transcriptomic dataset provides a substantially more detailed interpretation of T. cruzi infection biology and offers a basis for future drug and vaccine discovery efforts.

VL - 12 CP - 4 M3 - 10.1371/journal.ppat.1005511 ER - TY - JOUR T1 - Bayesian integration of genetics and epigenetics detects causal regulatory SNPs underlying expression variability JF - Nature Communications Y1 - 2015 A1 - Das, Avinash A1 - Morley, Michael A1 - Moravec, Christine S. A1 - Tang, W. H. W. A1 - Hakonarson, Hakon A1 - Ashley, Euan A. A1 - Brandimarto, Jeffrey A1 - Hu, Ray A1 - Li, Mingyao A1 - Li, Hongzhe A1 - Liu, Yichuan A1 - Qu, Liming A1 - Sanchez, Pablo A1 - Margulies, Kenneth B. A1 - Cappola, Thomas P. A1 - Jensen, Shane A1 - Hannenhalli, Sridhar VL - 6 UR - http://www.nature.com/doifinder/10.1038/ncomms9555 J1 - Nat Comms M3 - 10.1038/ncomms9555 ER - TY - CONF T1 - Chromatin and genomic determinants of alternative splicing T2 - BCB '15 Proceedings of the 6th ACM Conference on Bioinformatics, Computational Biology and Health Informatics Y1 - 2015 A1 - Kun Wang A1 - Kan Cao A1 - Sridhar Hannenhalli JA - BCB '15 Proceedings of the 6th ACM Conference on Bioinformatics, Computational Biology and Health Informatics PB - ACM ER - TY - JOUR T1 - Drugs that reverse disease transcriptomic signatures are more effective in a mouse model of dyslipidemia. JF - Mol Syst Biol Y1 - 2015 A1 - Wagner, Allon A1 - Cohen, Noa A1 - Kelder, Thomas A1 - Amit, Uri A1 - Liebman, Elad A1 - Steinberg, David M A1 - Radonjic, Marijana A1 - Ruppin, Eytan AB -

High-throughput omics have proven invaluable in studying human disease, and yet day-to-day clinical practice still relies on physiological, non-omic markers. The metabolic syndrome, for example, is diagnosed and monitored by blood and urine indices such as blood cholesterol levels. Nevertheless, the association between the molecular and the physiological manifestations of the disease, especially in response to treatment, has not been investigated in a systematic manner. To this end, we studied a mouse model of diet-induced dyslipidemia and atherosclerosis that was subject to various drug treatments relevant to the disease in question. Both physiological data and gene expression data (from the liver and white adipose) were analyzed and compared. We find that treatments that restore gene expression patterns to their norm are associated with the successful restoration of physiological markers to their baselines. This holds in a tissue-specific manner—treatments that reverse the transcriptomic signatures of the disease in a particular tissue are associated with positive physiological effects in that tissue. Further, treatments that introduce large non-restorative gene expression alterations are associated with unfavorable physiological outcomes. These results provide a sound basis to in silico methods that rely on omic metrics for drug repurposing and drug discovery by searching for compounds that reverse a disease’s omic signatures. Moreover, they highlight the need to develop drugs that restore the global cellular state to its healthy norm rather than rectify particular disease phenotypes.

VL - 11 CP - 3 ER - TY - Generic T1 - The effects of telomere shortening on cancer cells: a network model of proteomic and microRNA analysis. Y1 - 2015 A1 - Uziel, O A1 - Yosef, N A1 - Sharan, R A1 - Ruppin, E A1 - Kupiec, M A1 - Kushnir, M A1 - Beery, E A1 - Cohen-Diker, T A1 - Nordenberg, J A1 - Lahav, M KW - Gene Expression Regulation, Neoplastic KW - Gene Regulatory Networks KW - HUMANS KW - MicroRNAs KW - Neoplasms KW - Oligonucleotides KW - Proteome KW - proteomics KW - Telomere Shortening KW - Tumor Cells, Cultured AB -

Previously, we have shown that shortening of telomeres by telomerase inhibition sensitized cancer cells to cisplatinum, slowed their migration, increased DNA damage and impaired DNA repair. The mechanism behind these effects is not fully characterized. Its clarification could facilitate novel therapeutics development and may obviate the time consuming process of telomere shortening achieved by telomerase inhibition. Here we aimed to decipher the microRNA and proteomic profiling of cancer cells with shortened telomeres and identify the key mediators in telomere shortening-induced damage to those cells. Of 870 identified proteins, 98 were differentially expressed in shortened-telomere cells. 47 microRNAs were differentially expressed in these cells; some are implicated in growth arrest or act as oncogene repressors. The obtained data was used for a network construction, which provided us with nodal candidates that may mediate the shortened-telomere dependent features. These proteins' expression was experimentally validated, supporting their potential central role in this system.

JA - Genomics VL - 105 CP - 1 M3 - 10.1016/j.ygeno.2014.10.013 ER - TY - Generic T1 - Epiviz: a view inside the design of an integrated visual analysis software for genomics Y1 - 2015 A1 - Chelaru, Florin A1 - Corrada Bravo, éctor JA - BMC Bioinformatics VL - 16 UR - http://www.biomedcentral.com/1471-2105/16/S11/S4 CP - Suppl 11 J1 - BMC BioinformaticsBMC Bioinformatics M3 - 10.1186/1471-2105-16-S11-S4 ER - TY - JOUR T1 - Essential Genes in the Core Genome of the Human Pathogen Streptococcus pyogenes. JF - Sci Rep Y1 - 2015 A1 - Le Breton, Yoann A1 - Belew, Ashton T A1 - Valdes, Kayla M A1 - Islam, Emrul A1 - Curry, Patrick A1 - Tettelin, Hervé A1 - Shirtliff, Mark E A1 - El-Sayed, Najib M A1 - McIver, Kevin S AB -

Streptococcus pyogenes (Group A Streptococcus, GAS) remains a major public health burden worldwide, infecting over 750 million people leading to over 500,000 deaths annually. GAS pathogenesis is complex, involving genetically distinct GAS strains and multiple infection sites. To overcome fastidious genetic manipulations and accelerate pathogenesis investigations in GAS, we developed a mariner-based system (Krmit) for en masse monitoring of complex mutant pools by transposon sequencing (Tn-seq). Highly saturated transposant libraries (Krmit insertions in ca. every 25 nucleotides) were generated in two distinct GAS clinical isolates, a serotype M1T1 invasive strain 5448 and a nephritogenic serotype M49 strain NZ131, and analyzed using a Bayesian statistical model to predict GAS essential genes, identifying sets of 227 and 241 of those genes in 5448 and NZ131, respectively. A large proportion of GAS essential genes corresponded to key cellular processes and metabolic pathways, and 177 were found conserved within the GAS core genome established from 20 available GAS genomes. Selected essential genes were validated using conditional-expression mutants. Finally, comparison to previous essentiality analyses in S. sanguinis and S. pneumoniae revealed significant overlaps, providing valuable insights for the development of new antimicrobials to treat infections by GAS and other pathogenic streptococci.

VL - 5 M3 - 10.1038/srep09838 ER - TY - Generic T1 - Evaluation of BLAST-based edge-weighting metrics used for homology inference with the Markov Clustering algorithm. Y1 - 2015 A1 - Gibbons, Theodore R A1 - Mount, Stephen M A1 - Cooper, Endymion D A1 - Delwiche, Charles F AB -

BACKGROUND: Clustering protein sequences according to inferred homology is a fundamental step in the analysis of many large data sets. Since the publication of the Markov Clustering (MCL) algorithm in 2002, it has been the centerpiece of several popular applications. Each of these approaches generates an undirected graph that represents sequences as nodes connected to each other by edges weighted with a BLAST-based metric. MCL is then used to infer clusters of homologous proteins by analyzing these graphs. The various approaches differ only by how they weight the edges, yet there has been very little direct examination of the relative performance of alternative edge-weighting metrics. This study compares the performance of four BLAST-based edge-weighting metrics: the bit score, bit score ratio (BSR), bit score over anchored length (BAL), and negative common log of the expectation value (NLE). Performance is tested using the Extended CEGMA KOGs (ECK) database, which we introduce here.

RESULTS: All metrics performed similarly when analyzing full-length sequences, but dramatic differences emerged as progressively larger fractions of the test sequences were split into fragments. The BSR and BAL successfully rescued subsets of clusters by strengthening certain types of alignments between fragmented sequences, but also shifted the largest correct scores down near the range of scores generated from spurious alignments. This penalty outweighed the benefits in most test cases, and was greatly exacerbated by increasing the MCL inflation parameter, making these metrics less robust than the bit score or the more popular NLE. Notably, the bit score performed as well or better than the other three metrics in all scenarios.

CONCLUSIONS: The results provide a strong case for use of the bit score, which appears to offer equivalent or superior performance to the more popular NLE. The insight that MCL-based clustering methods can be improved using a more tractable edge-weighting metric will greatly simplify future implementations. We demonstrate this with our own minimalist Python implementation: Porthos, which uses only standard libraries and can process a graph with 25 m + edges connecting the 60 k + KOG sequences in half a minute using less than half a gigabyte of memory.

JA - BMC Bioinformatics VL - 16 M3 - 10.1186/s12859-015-0625-x ER - TY - Generic T1 - Fumarate induces redox-dependent senescence by modifying glutathione metabolism. Y1 - 2015 A1 - Zheng, Liang A1 - Cardaci, Simone A1 - Jerby, Livnat A1 - MacKenzie, Elaine D A1 - Sciacovelli, Marco A1 - Johnson, T Isaac A1 - Gaude, Edoardo A1 - King, Ayala A1 - Leach, Joshua D G A1 - Edrada-Ebel, RuAngelie A1 - Hedley, Ann A1 - Morrice, Nicholas A A1 - Kalna, Gabriela A1 - Blyth, Karen A1 - Ruppin, Eytan A1 - Frezza, Christian A1 - Gottlieb, Eyal AB -

Mutations in the tricarboxylic acid (TCA) cycle enzyme fumarate hydratase (FH) are associated with a highly malignant form of renal cancer. We combined analytical chemistry and metabolic computational modelling to investigate the metabolic implications of FH loss in immortalized and primary mouse kidney cells. Here, we show that the accumulation of fumarate caused by the inactivation of FH leads to oxidative stress that is mediated by the formation of succinicGSH, a covalent adduct between fumarate and glutathione. Chronic succination of GSH, caused by the loss of FH, or by exogenous fumarate, leads to persistent oxidative stress and cellular senescence in vitro and in vivo. Importantly, the ablation of p21, a key mediator of senescence, in Fh1-deficient mice resulted in the transformation of benign renal cysts into a hyperplastic lesion, suggesting that fumarate-induced senescence needs to be bypassed for the initiation of renal cancers.

JA - Nat Commun VL - 6 M3 - 10.1038/ncomms7001 ER - TY - Generic T1 - The generation of macrophages with anti-inflammatory activity in the absence of STAT6 signaling. Y1 - 2015 A1 - Fleming, Bryan D A1 - Chandrasekaran, Prabha A1 - Dillon, Laura A L A1 - Dalby, Elizabeth A1 - Suresh, Rahul A1 - Sarkar, Arup A1 - El-Sayed, Najib M A1 - Mosser, David M AB -

Macrophages readily change their phenotype in response to exogenous stimuli. In this work, macrophages were stimulated under a variety of experimental conditions, and phenotypic alterations were correlated with changes in gene expression. We identified 3 transcriptionally related populations of macrophages with immunoregulatory activity. They were generated by stimulating cells with TLR ligands in the presence of 3 different "reprogramming" signals: high-density ICs, PGE2, or Ado. All 3 of these cell populations produced high levels of transcripts for IL-10 and growth and angiogenic factors. They also secreted reduced levels of inflammatory cytokines IL-1β, IL-6, and IL-12. All 3 macrophage phenotypes could partially rescue mice from lethal endotoxemia, and therefore, we consider each to have anti-inflammatory activity. This ability to regulate innate-immune responses occurred equally well in macrophages from STAT6-deficient mice. The lack of STAT6 did not affect the ability of macrophages to change cytokine production reciprocally or to rescue mice from lethal endotoxemia. Furthermore, treatment of macrophages with IL-4 failed to induce similar phenotypic or transcriptional alterations. This work demonstrates that there are multiple ways to generate macrophages with immunoregulatory activity. These anti-inflammatory macrophages are transcriptionally and functionally related to each other and are quite distinct from macrophages treated with IL-4.

JA - J Leukoc Biol VL - 98 CP - 3 M3 - 10.1189/jlb.2A1114-560R ER - TY - JOUR T1 - Glutamine synthetase activity fuels nucleotide biosynthesis and supports growth of glutamine-restricted glioblastoma JF - Nature Cell Biology Y1 - 2015 A1 - Tardito, Saverio A1 - Oudin, ïs A1 - Ahmed, Shafiq U. A1 - Fack, Fred A1 - Keunen, Olivier A1 - Zheng, Liang A1 - Miletic, Hrvoje A1 - Sakariassen, Øystein A1 - Weinstock, Adam A1 - Wagner, Allon A1 - Lindsay, Susan L. A1 - Hock, Andreas K. A1 - Barnett, Susan C. A1 - Ruppin, Eytan A1 - ørkve, Svein Harald A1 - Lund-Johansen, Morten A1 - Chalmers, Anthony J. A1 - Bjerkvig, Rolf A1 - Niclou, Simone P. A1 - Gottlieb, Eyal VL - 17 UR - http://www.nature.com/doifinder/10.1038/ncb3272 CP - 12 J1 - Nat Cell Biol M3 - 10.1038/ncb3272 ER - TY - JOUR T1 - Independent Emergence of Artemisinin Resistance Mutations Among Plasmodium falciparum in Southeast Asia JF - Journal of Infectious Diseases Y1 - 2015 A1 - Takala-Harrison, S. A1 - Jacob, C. G. A1 - Arze, C. A1 - Michael P. Cummings A1 - Silva, J. C. A1 - Dondorp, A. M. A1 - Fukuda, M. M. A1 - Hien, T. T. A1 - Mayxay, M. A1 - Noedl, H. A1 - Nosten, F. A1 - Kyaw, M. P. A1 - Nhien, N. T. T. A1 - Imwong, M. A1 - Bethell, D. A1 - Se, Y. A1 - Lon, C. A1 - Tyner, S. D. A1 - Saunders, D. L. A1 - Ariey, F. A1 - Mercereau-Puijalon, O. A1 - Menard, D. A1 - Newton, P. N. A1 - Khanthavong, M. A1 - Hongvanthong, B. A1 - Starzengruber, P. A1 - Fuehrer, H.-P. A1 - Swoboda, P. A1 - Khan, W. A. A1 - Phyo, A. P. A1 - Nyunt, M. M. A1 - Nyunt, M. H. A1 - Brown, T. S. A1 - Adams, M. A1 - Pepin, C. S. A1 - Bailey, J. A1 - Tan, J. C. A1 - Ferdig, M. T. A1 - Clark, T. G. A1 - Miotto, O. A1 - MacInnis, B. A1 - Kwiatkowski, D. P. A1 - White, N. J. A1 - Ringwald, P. A1 - Plowe, CV VL - 211 M3 - 10.1093/infdis/jiu491 ER - TY - Generic T1 - Modeling cancer metabolism on a genome scale Y1 - 2015 A1 - Yizhak, K. A1 - Chaneton, B. A1 - Gottlieb, E. A1 - Ruppin, E. JA - Molecular Systems Biology VL - 11 UR - http://msb.embopress.org/cgi/doi/10.15252/msb.20145307 CP - 6 J1 - Molecular Systems Biology M3 - 10.15252/msb.20145307 ER - TY - JOUR T1 - A molecular phylogeny for the oldest (nonditrysian) lineages of extant Lepidoptera, with implications for classification, comparative morphology and life-history evolution JF - Systematic Entomology Y1 - 2015 A1 - Regier, Jerome C A1 - Mitter, Charles A1 - KRISTENSEN, NIELS P. A1 - Davis, Donald R. A1 - VAN NIEUKERKEN, ERIK J. A1 - ROTA, JADRANKA A1 - Simonsen, Thomas J. A1 - Mitter, Kim T. A1 - Kawahara, Akito Y. A1 - Yen, Shen-Horn A1 - Michael P. Cummings A1 - Zwick, Andreas M3 - 10.1111/syen.12129 ER - TY - Generic T1 - Orchestrating high-throughput genomic analysis with Bioconductor. Y1 - 2015 A1 - Huber, Wolfgang A1 - Carey, Vincent J A1 - Gentleman, Robert A1 - Anders, Simon A1 - Carlson, Marc A1 - Carvalho, Benilton S A1 - Bravo, Héctor Corrada A1 - Davis, Sean A1 - Gatto, Laurent A1 - Girke, Thomas A1 - Gottardo, Raphael A1 - Hahne, Florian A1 - Hansen, Kasper D A1 - Irizarry, Rafael A A1 - Lawrence, Michael A1 - Love, Michael I A1 - MacDonald, James A1 - Obenchain, Valerie A1 - Oleś, Andrzej K A1 - Pagès, Hervé A1 - Reyes, Alejandro A1 - Shannon, Paul A1 - Smyth, Gordon K A1 - Tenenbaum, Dan A1 - Waldron, Levi A1 - Morgan, Martin KW - Computational Biology KW - Gene Expression Profiling KW - Genomics KW - High-Throughput Screening Assays KW - Programming Languages KW - software KW - User-Computer Interface AB -

Bioconductor is an open-source, open-development software project for the analysis and comprehension of high-throughput data in genomics and molecular biology. The project aims to enable interdisciplinary research, collaboration and rapid development of scientific software. Based on the statistical programming language R, Bioconductor comprises 934 interoperable packages contributed by a large, diverse community of scientists. Packages cover a range of bioinformatic and statistical applications. They undergo formal initial review and continuous automated testing. We present an overview for prospective users and contributors.

JA - Nat Methods VL - 12 CP - 2 M3 - 10.1038/nmeth.3252 ER - TY - Generic T1 - Phenotype-Dependent Coexpression Gene Clusters: Application to Normal and Premature Ageing Y1 - 2015 A1 - Wang, Kun A1 - Das, Avinash A1 - Xiong, Zheng-Mei A1 - Cao, Kan A1 - Hannenhalli, Sridhar JA - IEEE/ACM Transactions on Computational Biology and Bioinformatics VL - 12 UR - http://ieeexplore.ieee.org/lpdocs/epic03/wrapper.htm?arnumber=6948331http://xplorestaging.ieee.org/iel7/8857/7035191/06948331.pdf?arnumber=6948331 CP - 1 J1 - IEEE/ACM Trans. Comput. Biol. and Bioinf. M3 - 10.1109/TCBB.2014.2359446 ER - TY - JOUR T1 - Plasmodium falciparum field isolates from areas of repeated emergence of drug resistant malaria show no evidence of hypermutator phenotype JF - Infection, Genetics and Evolution Y1 - 2015 A1 - Brown, Tyler S. A1 - Jacob, Christopher G A1 - Silva, Joana C A1 - Takala-Harrison, Shannon A1 - Djimdé, Abdoulaye A1 - Dondorp, Arjen M A1 - Fukuda, Mark A1 - Noedl, Harald A1 - Nyunt, Myaing Myaing A1 - Kyaw, Myat Phone A1 - Mayxay, Mayfong A1 - Hien, Tran Tinh A1 - Plowe, Christopher V A1 - Michael P. Cummings VL - 30 M3 - 10.1016/j.meegid.2014.12.010 ER - TY - JOUR T1 - Relationships within Cladobranchia (Gastropoda: Nudibranchia) based on RNA-Seq data: an initial investigation JF - Royal Society Open Science Y1 - 2015 A1 - Goodheart, Jessica A1 - Bazinet, Adam L. A1 - Collins, Allen G. A1 - CUMMINGS, MICHAEL P. VL - 23547143619757560685451171766 UR - http://rsos.royalsocietypublishing.org/lookup/doi/10.1098/rsos.150196 CP - 9 J1 - R. Soc. open sci. M3 - 10.1098/rsos.150196 ER - TY - Generic T1 - RNA-Seq identifies novel myocardial gene expression signatures of heart failure. Y1 - 2015 A1 - Liu, Yichuan A1 - Morley, Michael A1 - Brandimarto, Jeffrey A1 - Hannenhalli, Sridhar A1 - Hu, Yu A1 - Ashley, Euan A A1 - Tang, W H Wilson A1 - Moravec, Christine S A1 - Margulies, Kenneth B A1 - Cappola, Thomas P A1 - Li, Mingyao AB -

Heart failure is a complex clinical syndrome and has become the most common reason for adult hospitalization in developed countries. Two subtypes of heart failure, ischemic heart disease (ISCH) and dilated cardiomyopathy (DCM), have been studied using microarray platforms. However, microarray has limited resolution. Here we applied RNA sequencing (RNA-Seq) to identify gene signatures for heart failure from six individuals, including three controls, one ISCH and two DCM patients. Using genes identified from this small RNA-Seq dataset, we were able to accurately classify heart failure status in a much larger set of 313 individuals. The identified genes significantly overlapped with genes identified via genome-wide association studies for cardiometabolic traits and the promoters of those genes were enriched for binding sites for transcriptions factors. Our results indicate that it is possible to use RNA-Seq to classify disease status for complex diseases such as heart failure using an extremely small training dataset.

JA - Genomics VL - 105 CP - 2 M3 - 10.1016/j.ygeno.2014.12.002 ER - TY - JOUR T1 - Robust Parameter Estimation for Biological Systems: A Study on the Dynamics of Microbial Communities JF - arXiv preprint arXiv:1509.06926 Y1 - 2015 A1 - Matthias Chung A1 - Justin Krueger A1 - Mihai Pop ER - TY - JOUR T1 - Systematics and biogeography of Pleurobranchus  Cuvier, 1804, sea slugs (Heterobranchia: Nudipleura: Pleurobranchidae) JF - Zoological Journal of the Linnean Society Y1 - 2015 A1 - Goodheart, Jessica A1 - Camacho-García, Yolanda A1 - Padula, Vinicius A1 - Schrödl, Michael A1 - Cervera, Juan L. A1 - Gosliner, Terrence M. A1 - Valdés, Ángel AB - Species of Pleurobranchus (Mollusca: Gastropoda: Heterobranchia: Nudipleura: Pleurobranchidae) are commonly found worldwide, but there is a substantial amount of confusion regarding the ranges and identification of individual species. Difficulties in phylogenetic reconstruction and identification of pleurobranchids using morphological traits has resulted in complex classification schemes, with several species having disjunct ranges across physical and biogeographical barriers (including the tropical Indo-Pacific, the eastern Pacific, and the Atlantic). A sizeable number of species of Pleurobranchus has been described; however, many of these species are morphologically and biogeographically similar to others, and probably constitute synonyms. This paper provides a phylogenetic framework of classification for Pleurobranchus based on the mitochondrial genes cytochrome c oxidase I (COI) and 16S rDNA and the nuclear gene histone 3 (H3) using Bayesian and maximum likelihood approaches. Molecular phylogenies obtained recovered most of the well-established species of Pleurobranchus and some morphological characters were found to have taxonomic value for delimiting species in this group. Automatic barcode gap discovery (ABGD) analyses substantiated the distinctiveness of units/species recovered in the phylogenetic analyses, with some exceptions. Morphological descriptions for the 14 species recovered in the molecular phylogeny and discussions on the biogeography and colour variation are included. UR - http://doi.wiley.com/10.1111/zoj.12237 J1 - Zool J Linn Soc M3 - 10.1111/zoj.12237 ER - TY - Generic T1 - Conservation in first introns is positively associated with the number of exons within genes and the presence of regulatory epigenetic signals Y1 - 2014 A1 - Park, Seung A1 - Hannenhalli, Sridhar A1 - Choi, Sun JA - BMC Genomics VL - 15 UR - http://www.biomedcentral.com/1471-2164/15/526 CP - 1 J1 - BMC GenomicsBMC Genomics M3 - 10.1186/1471-2164-15-526 ER - TY - Generic T1 - Determinants of expression variability Y1 - 2014 A1 - Alemu, E. Y. A1 - Carl, J. W. A1 - Corrada Bravo, H. A1 - Hannenhalli, S. JA - Nucleic Acids Research VL - 42 UR - http://nar.oxfordjournals.org/lookup/doi/10.1093/nar/gkt1364 CP - 6 J1 - Nucleic Acids Research M3 - 10.1093/nar/gkt1364 ER - TY - Generic T1 - Epiviz: interactive visual analytics for functional genomics data. Y1 - 2014 A1 - Chelaru, Florin A1 - Smith, Llewellyn A1 - Goldstein, Naomi A1 - Bravo, Héctor Corrada KW - algorithms KW - Chromosome mapping KW - Data Mining KW - database management systems KW - Databases, Genetic KW - Genomics KW - Internet KW - software KW - User-Computer Interface AB -

Visualization is an integral aspect of genomics data analysis. Algorithmic-statistical analysis and interactive visualization are most effective when used iteratively. Epiviz (http://epiviz.cbcb.umd.edu/), a web-based genome browser, and the Epivizr Bioconductor package allow interactive, extensible and reproducible visualization within a state-of-the-art data-analysis platform.

JA - Nat Methods VL - 11 CP - 9 M3 - 10.1038/nmeth.3038 ER - TY - Generic T1 - An evaluation of Monte-Carlo logic and logicFS motivated by a study of the regulation of gene expression in heart failure Y1 - 2014 A1 - Lu, Yun A1 - Hannenhalli, Sridhar A1 - Cappola, Tom A1 - Putt, Mary JA - Journal of Applied Statistics VL - 41 UR - http://www.tandfonline.com/doi/abs/10.1080/02664763.2014.898133 CP - 9 J1 - Journal of Applied Statistics M3 - 10.1080/02664763.2014.898133 ER - TY - JOUR T1 - A Gateway for Phylogenetic Analysis Powered by Grid Computing Featuring GARLI 2.0 JF - Syst Biol Y1 - 2014 A1 - Adam L. Bazinet A1 - Zwickl, Derrick J. A1 - Michael P. Cummings AB -

We introduce molecularevolution.org, a publicly available gateway for high-throughput, maximum likelihood phylogenetic analysis powered by grid computing. The gateway features a garli 2.0 web service that enables a user to quickly and easily submit thousands of maximum likelihood tree searches or bootstrap searches that are executed in parallel on distributed computing resources. The garli web service allows one to easily specify partitioned substitution models using a graphical interface, and it performs sophisticated post-processing of phylogenetic results. Although the garli web service has been used by the research community for over three years, here we formally announce the availability of the service, describe its capabilities, highlight new features and recent improvements, and provide details about how the grid system efficiently delivers high-quality phylogenetic results.

ER - TY - Generic T1 - Minfi: a flexible and comprehensive Bioconductor package for the analysis of Infinium DNA methylation microarrays. Y1 - 2014 A1 - Aryee, Martin J A1 - Jaffe, Andrew E A1 - Corrada-Bravo, Hector A1 - Ladd-Acosta, Christine A1 - Feinberg, Andrew P A1 - Hansen, Kasper D A1 - Irizarry, Rafael A KW - Aged KW - algorithms KW - Colonic Neoplasms KW - DNA Methylation KW - Genome KW - High-Throughput Nucleotide Sequencing KW - HUMANS KW - Oligonucleotide Array Sequence Analysis KW - Polymorphism, Single Nucleotide KW - software AB -

MOTIVATION: The recently released Infinium HumanMethylation450 array (the '450k' array) provides a high-throughput assay to quantify DNA methylation (DNAm) at ∼450 000 loci across a range of genomic features. Although less comprehensive than high-throughput sequencing-based techniques, this product is more cost-effective and promises to be the most widely used DNAm high-throughput measurement technology over the next several years.

RESULTS: Here we describe a suite of computational tools that incorporate state-of-the-art statistical techniques for the analysis of DNAm data. The software is structured to easily adapt to future versions of the technology. We include methods for preprocessing, quality assessment and detection of differentially methylated regions from the kilobase to the megabase scale. We show how our software provides a powerful and flexible development platform for future methods. We also illustrate how our methods empower the technology to make discoveries previously thought to be possible only with sequencing-based methods.

AVAILABILITY AND IMPLEMENTATION: http://bioconductor.org/packages/release/bioc/html/minfi.html.

CONTACT: khansen@jhsph.edu; rafa@jimmy.harvard.edu

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

JA - Bioinformatics VL - 30 CP - 10 M3 - 10.1093/bioinformatics/btu049 ER - TY - JOUR T1 - A molecular phylogeny and revised classification for the oldest ditrysian moth lineages (Lepidoptera: Tineoidea), with implications for ancestral feeding habits of the mega-diverse Ditrysia JF - Systematic Entomology Y1 - 2014 A1 - Regier, Jerome C A1 - Mitter, Charles A1 - Davis, Donald R. A1 - HARRISON, TERRY L. A1 - Sohn, Jae-Cheon A1 - Michael P. Cummings A1 - Zwick, Andreas A1 - Mitter, Kim T. VL - 40 M3 - 10.1111/syen.12110 ER - TY - JOUR T1 - A new rhesus macaque assembly and annotation for next-generation sequencing analyses JF - Biology direct Y1 - 2014 A1 - Zimin, Aleksey V A1 - Cornish, Adam S A1 - Maudhoo, Mnirnal D A1 - Gibbs, Robert M A1 - Zhang, Xiongfei A1 - Pandey, Sanjit A1 - Meehan, Daniel T A1 - Wipfler, Kristin A1 - Bosinger, Steven E A1 - Johnson, Zachary P A1 - Todd Treangen VL - 9 ER - TY - JOUR T1 - Predicting cancer-specific vulnerability via data-driven detection of synthetic lethality. JF - Cell Y1 - 2014 A1 - Jerby-Arnon, Livnat A1 - Pfetzer, Nadja A1 - Waldman, Yedael Y A1 - McGarry, Lynn A1 - James, Daniel A1 - Shanks, Emma A1 - Seashore-Ludlow, Brinton A1 - Weinstock, Adam A1 - Geiger, Tamar A1 - Clemons, Paul A A1 - Gottlieb, Eyal A1 - Ruppin, Eytan KW - Breast Neoplasms KW - Cell Line, Tumor KW - Computational Biology KW - Data Mining KW - Genes, Tumor Suppressor KW - HUMANS KW - Neoplasms KW - Oncogenes KW - RNA, Small Interfering KW - workflow AB -

Synthetic lethality occurs when the inhibition of two genes is lethal while the inhibition of each single gene is not. It can be harnessed to selectively treat cancer by identifying inactive genes in a given cancer and targeting their synthetic lethal (SL) partners. We present a data-driven computational pipeline for the genome-wide identification of SL interactions in cancer by analyzing large volumes of cancer genomic data. First, we show that the approach successfully captures known SL partners of tumor suppressors and oncogenes. We then validate SL predictions obtained for the tumor suppressor VHL. Next, we construct a genome-wide network of SL interactions in cancer and demonstrate its value in predicting gene essentiality and clinical prognosis. Finally, we identify synthetic lethality arising from gene overactivation and use it to predict drug efficacy. These results form a computational basis for exploiting synthetic lethality to uncover cancer-specific susceptibilities.

VL - 158 CP - 5 M3 - 10.1016/j.cell.2014.07.027 ER - TY - Generic T1 - RNA-sequencing of the brain transcriptome implicates dysregulation of neuroplasticity, circadian rhythms and GTPase binding in bipolar disorder. Y1 - 2014 A1 - Akula, N A1 - Barb, J A1 - Jiang, X A1 - Wendland, J R A1 - Choi, K H A1 - Sen, S K A1 - Hou, L A1 - Chen, D T W A1 - Laje, G A1 - Johnson, K A1 - Lipska, B K A1 - Kleinman, J E A1 - Corrada-Bravo, H A1 - Detera-Wadleigh, S A1 - Munson, P J A1 - McMahon, F J KW - Adult KW - Aged KW - Bipolar Disorder KW - Circadian Rhythm KW - Female KW - Genome-Wide Association Study KW - GTP Phosphohydrolases KW - HUMANS KW - Male KW - Meta-Analysis as Topic KW - Microarray Analysis KW - Middle Aged KW - Neuronal Plasticity KW - Polymerase Chain Reaction KW - Prefrontal Cortex KW - Principal Component Analysis KW - Sequence Analysis, RNA KW - Transcriptome KW - Young Adult AB -

RNA-sequencing (RNA-seq) is a powerful technique to investigate the complexity of gene expression in the human brain. We used RNA-seq to survey the brain transcriptome in high-quality postmortem dorsolateral prefrontal cortex from 11 individuals diagnosed with bipolar disorder (BD) and from 11 age- and gender-matched controls. Deep sequencing was performed, with over 350 million reads per specimen. At a false discovery rate of <5%, we detected five differentially expressed (DE) genes and 12 DE transcripts, most of which have not been previously implicated in BD. Among these, Prominin 1/CD133 and ATP-binding cassette-sub-family G-member2 (ABCG2) have important roles in neuroplasticity. We also show for the first time differential expression of long noncoding RNAs (lncRNAs) in BD. DE transcripts include those of serine/arginine-rich splicing factor 5 (SRSF5) and regulatory factor X4 (RFX4), which along with lncRNAs have a role in mammalian circadian rhythms. The DE genes were significantly enriched for several Gene Ontology categories. Of these, genes involved with GTPase binding were also enriched for BD-associated SNPs from previous genome-wide association studies, suggesting that differential expression of these genes is not simply a consequence of BD or its treatment. Many of these findings were replicated by microarray in an independent sample of 60 cases and controls. These results highlight common pathways for inherited and non-inherited influences on disease risk that may constitute good targets for novel therapies.

JA - Mol Psychiatry VL - 19 CP - 11 M3 - 10.1038/mp.2013.170 ER - TY - JOUR T1 - RNA-sequencing of the brain transcriptome implicates dysregulation of neuroplasticity, circadian rhythms and GTPase binding in bipolar disorder JF - Molecular psychiatry Y1 - 2014 A1 - Akula, N. A1 - Barb, J. A1 - Jiang, X. A1 - Wendland, J. R. A1 - Choi, K. H. A1 - Sen, S. K. A1 - Hou, L. A1 - Chen, D. T. W. A1 - Laje, G. A1 - Johnson, K. A1 - Lipska, B. K. A1 - Kleinman, J. E. A1 - Héctor Corrada Bravo A1 - Detera-Wadleigh, S. A1 - Munson, P. J. A1 - McMahon, F. J. AB - RNA-sequencing (RNA-seq) is a powerful technique to investigate the complexity of gene expression in the human brain. We used RNA-seq to survey the brain transcriptome in high-quality postmortem dorsolateral prefrontal cortex from 11 individuals diagnosed with bipolar disorder (BD) and from 11 age- and gender-matched controls. Deep sequencing was performed, with over 350 million reads per specimen. At a false discovery rate of <5%, we detected five differentially expressed (DE) genes and 12 DE transcripts, most of which have not been previously implicated in BD. Among these, Prominin 1/CD133 and ATP-binding cassette-sub-family G-member2 (ABCG2) have important roles in neuroplasticity. We also show for the first time differential expression of long noncoding RNAs (lncRNAs) in BD. DE transcripts include those of serine/arginine-rich splicing factor 5 (SRSF5) and regulatory factor X4 (RFX4), which along with lncRNAs have a role in mammalian circadian rhythms. The DE genes were significantly enriched for several Gene Ontology categories. Of these, genes involved with GTPase binding were also enriched for BD-associated SNPs from previous genome-wide association studies, suggesting that differential expression of these genes is not simply a consequence of BD or its treatment. Many of these findings were replicated by microarray in an independent sample of 60 cases and controls. These results highlight common pathways for inherited and non-inherited influences on disease risk that may constitute good targets for novel therapies.Molecular Psychiatry advance online publication, 7 January 2014; doi:10.1038/mp.2013.170. N1 - http://www.ncbi.nlm.nih.gov/pubmed/24393808?dopt=Abstract ER - TY - CHAP T1 - AWTY, BAMBE, BEAGLE, BEAST, BEAUti, Bio++, DataMonkey, DendroPy, DnaSP, ENCprime/SeqCount, FigTree, GARLI, genealogical sorting index (gsi), HyPhy, IMa2, jModelTest, JELLYFISH, LAMARC, MacClade, MEGA, Mesquite T2 - Dictionary of Bioinformatics Y1 - 2013 A1 - Michael P. Cummings ED - Hancock, J. ED - Zvelebil, M. JA - Dictionary of Bioinformatics PB - Wiley-Liss CY - Hoboken ER - TY - JOUR T1 - Can RNA-Seq resolve the rapid radiation of advanced moths and butterflies (Hexapoda: Lepidoptera: Apoditrysia)? An exploratory study JF - PLoS One Y1 - 2013 A1 - Adam L. Bazinet A1 - Michael P. Cummings A1 - Mitter, Kim T. A1 - Mitter, Charles W. AB -

Recent molecular phylogenetic studies of the insect order Lepidoptera have robustly resolved family-level divergences within most superfamilies, and most divergences among the relatively species-poor early-arising superfamilies. In sharp contrast, relationships among the superfamilies of more advanced moths and butterflies that comprise the mega-diverse clade Apoditrysia (ca. 145,000 spp.) remain mostly poorly supported. This uncertainty, in turn, limits our ability to discern the origins, ages and evolutionary consequences of traits hypothesized to promote the spectacular diversification of Apoditrysia. Low support along the apoditrysian "backbone" probably reflects rapid diversification. If so, it may be feasible to strengthen resolution by radically increasing the gene sample, but case studies have been few. We explored the potential of next-generation sequencing to conclusively resolve apoditrysian relationships. We used transcriptome RNA-Seq to generate 1579 putatively orthologous gene sequences across a broad sample of 40 apoditrysians plus four outgroups, to which we added two taxa from previously published data. Phylogenetic analysis of a 46-taxon, 741-gene matrix, resulting from a strict filter that eliminated ortholog groups containing any apparent paralogs, yielded dramatic overall increase in bootstrap support for deeper nodes within Apoditrysia as compared to results from previous and concurrent 19-gene analyses. High support was restricted mainly to the huge subclade Obtectomera broadly defined, in which 11 of 12 nodes subtending multiple superfamilies had bootstrap support of 100%. The strongly supported nodes showed little conflict with groupings from previous studies, and were little affected by changes in taxon sampling, suggesting that they reflect true signal rather than artifacts of massive gene sampling. In contrast, strong support was seen at only 2 of 11 deeper nodes among the "lower", non-obtectomeran apoditrysians. These represent a much harder phylogenetic problem, for which one path to resolution might include further increase in gene sampling, together with improved orthology assignments.

VL - 8 ER - TY - JOUR T1 - Contribution of nucleosome binding preferences and co-occurring DNA sequences to transcription factor binding JF - BMC Genomics Y1 - 2013 A1 - He, Ximiao A1 - Chatterjee, Raghunath A1 - John, Sam A1 - Bravo, Hector A1 - Sathyanarayana, B K A1 - Biddie, Simon C A1 - FitzGerald, Peter C A1 - Stamatoyannopoulos, John A A1 - Hager, Gordon L A1 - Vinson, Charles VL - 14 UR - http://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-14-428 CP - 1 J1 - BMC GenomicsBMC Genomics M3 - 10.1186/1471-2164-14-428 ER - TY - JOUR T1 - A decision-theory approach to interpretable set analysis for high-dimensional data JF - BiometricsBiometrics Y1 - 2013 A1 - Boca, Simina M. A1 - Héctor Corrada Bravo A1 - Caffo, Brian A1 - Leek, Jeffrey T. A1 - Parmigiani, Giovanni AB - A key problem in high-dimensional significance analysis is to find pre-defined sets that show enrichment for a statistical signal of interest; the classic example is the enrichment of gene sets for differentially expressed genes. Here, we propose a new decision-theory approach to the analysis of gene sets which focuses on estimating the fraction of non-null variables in a set. We introduce the idea of "atoms," non-overlapping sets based on the original pre-defined set annotations. Our approach focuses on finding the union of atoms that minimizes a weighted average of the number of false discoveries and missed discoveries. We introduce a new false discovery rate for sets, called the atomic false discovery rate (afdr), and prove that the optimal estimator in our decision-theory framework is to threshold the afdr. These results provide a coherent and interpretable framework for the analysis of sets that addresses the key issues of overlapping annotations and difficulty in interpreting p values in both competitive and self-contained tests. We illustrate our method and compare it to a popular existing method using simulated examples, as well as gene-set and brain ROI data analyses. VL - 69 N1 - http://www.ncbi.nlm.nih.gov/pubmed/23909925?dopt=Abstract ER - TY - JOUR T1 - Genetic loci associated with delayed clearance of Plasmodium falciparum following artemisinin treatment in Southeast Asia 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 - 2013 A1 - Takala-Harrison, Shannon A1 - Clark, Taane G. A1 - Jacob, Christopher G. A1 - Michael P. Cummings A1 - Miotto, Olivo A1 - Dondorp, Arjen M. A1 - Fukuda, Mark M. A1 - Nosten, Francois A1 - Noedl, Harald A1 - Imwong, Mallika A1 - Bethell, Delia A1 - Se, Youry A1 - Lon, Chanthap A1 - Tyner, Stuart D. A1 - Saunders, David L. A1 - Socheat, Duong A1 - Ariey, Frederic A1 - Phyo, Aung Pyae A1 - Starzengruber, Peter A1 - Fuehrer, Hans-Peter A1 - Swoboda, Paul A1 - Stepniewska, Kasia A1 - Flegg, Jennifer A1 - Arze, Cesar A1 - Cerqueira, Gustavo C. A1 - Silva, Joana C. A1 - Ricklefs, Stacy M. A1 - Porcella, Stephen F. A1 - Stephens, Robert M. A1 - Adams, Matthew A1 - Kenefic, Leo J. A1 - Campino, Susana A1 - Auburn, Sarah A1 - Macinnis, Bronwyn A1 - Kwiatkowski, Dominic P. A1 - Su, Xin-Zhuan A1 - White, Nicholas J. A1 - Ringwald, Pascal A1 - Plowe, Christopher V. AB - The recent emergence of artemisinin-resistant Plasmodium falciparum malaria in western Cambodia could threaten prospects for malaria elimination. Identification of the genetic basis of resistance would provide tools for molecular surveillance, aiding efforts to contain resistance. Clinical trials of artesunate efficacy were conducted in Bangladesh, in northwestern Thailand near the Myanmar border, and at two sites in western Cambodia. Parasites collected from trial participants were genotyped at 8,079 single nucleotide polymorphisms (SNPs) using a P. falciparum-specific SNP array. Parasite genotypes were examined for signatures of recent positive selection and association with parasite clearance phenotypes to identify regions of the genome associated with artemisinin resistance. Four SNPs on chromosomes 10 (one), 13 (two), and 14 (one) were significantly associated with delayed parasite clearance. The two SNPs on chromosome 13 are in a region of the genome that appears to be under strong recent positive selection in Cambodia. The SNPs on chromosomes 10 and 13 lie in or near genes involved in postreplication repair, a DNA damage-tolerance pathway. Replication and validation studies are needed to refine the location of loci responsible for artemisinin resistance and to understand the mechanism behind it; however, two SNPs on chromosomes 10 and 13 may be useful markers of delayed parasite clearance in surveillance for artemisinin resistance in Southeast Asia. VL - 110 ER - TY - JOUR T1 - Genome sequence of the attenuated Carbosap vaccine strain of Bacillus anthracis JF - Genome announcements Y1 - 2013 A1 - Harrington, Robin A1 - Ondov, Brian D A1 - Radune, Diana A1 - Friss, Mary Beth A1 - Klubnik, Joy A1 - Diviak, Lynn A1 - Hnath, Jonathan A1 - Cendrowski, Stephen R A1 - Blank, Thomas E A1 - Karaolis, David A1 - Todd Treangen VL - 1 ER - TY - CONF T1 - Identification of gene clusters with phenotype-dependent expression with application to normal and premature ageing T2 - Proceedings of the International Conference on Bioinformatics, Computational Biology and Biomedical Informatics Y1 - 2013 A1 - Kun Wang A1 - Avinash Das A1 - Zheng-Mei Xiong A1 - Kan Cao A1 - Sridhar Hannenhalli JA - Proceedings of the International Conference on Bioinformatics, Computational Biology and Biomedical Informatics PB - ACM CY - Wshington DC, USA U1 - 2506652 ER - TY - JOUR T1 - A large-scale, higher-level, molecular phylogenetic study of the insect order Lepidoptera (moths and butterflies) JF - PLoS OnePLoS One Y1 - 2013 A1 - Regier, Jerome C. A1 - Mitter, Charles A1 - Zwick, Andreas A1 - Adam L. Bazinet A1 - Michael P. Cummings A1 - Kawahara, Akito Y. A1 - Sohn, Jae-Cheon A1 - Zwickl, Derrick J. A1 - Cho, Soowon A1 - Davis, Donald R. A1 - Baixeras, Joaquin A1 - Brown, John A1 - Parr, Cynthia A1 - Weller, Susan A1 - Lees, David C. A1 - Mitter, Kim T. KW - Animals KW - Butterflies KW - Moths KW - Phylogeny AB -

BACKGROUND: Higher-level relationships within the Lepidoptera, and particularly within the species-rich subclade Ditrysia, are generally not well understood, although recent studies have yielded progress. We present the most comprehensive molecular analysis of lepidopteran phylogeny to date, focusing on relationships among superfamilies.

METHODOLOGY PRINCIPAL FINDINGS: 483 taxa spanning 115 of 124 families were sampled for 19 protein-coding nuclear genes, from which maximum likelihood tree estimates and bootstrap percentages were obtained using GARLI. Assessment of heuristic search effectiveness showed that better trees and higher bootstrap percentages probably remain to be discovered even after 1000 or more search replicates, but further search proved impractical even with grid computing. Other analyses explored the effects of sampling nonsynonymous change only versus partitioned and unpartitioned total nucleotide change; deletion of rogue taxa; and compositional heterogeneity. Relationships among the non-ditrysian lineages previously inferred from morphology were largely confirmed, plus some new ones, with strong support. Robust support was also found for divergences among non-apoditrysian lineages of Ditrysia, but only rarely so within Apoditrysia. Paraphyly for Tineoidea is strongly supported by analysis of nonsynonymous-only signal; conflicting, strong support for tineoid monophyly when synonymous signal was added back is shown to result from compositional heterogeneity. CONCLUSIONS SIGNIFICANCE: Support for among-superfamily relationships outside the Apoditrysia is now generally strong. Comparable support is mostly lacking within Apoditrysia, but dramatically increased bootstrap percentages for some nodes after rogue taxon removal, and concordance with other evidence, strongly suggest that our picture of apoditrysian phylogeny is approximately correct. This study highlights the challenge of finding optimal topologies when analyzing hundreds of taxa. It also shows that some nodes get strong support only when analysis is restricted to nonsynonymous change, while total change is necessary for strong support of others. Thus, multiple types of analyses will be necessary to fully resolve lepidopteran phylogeny.

VL - 8 ER - TY - JOUR T1 - A molecular phylogeny for Yponomeutoidea (Insecta, Lepidoptera, Ditrysia) and its implications for classification, biogeography and\ the evolution of host plant use JF - PLoS One Y1 - 2013 A1 - J. C. Sohn A1 - Regier, J. C. A1 - Mitter, C. A1 - D. Davis A1 - J. F. Landry A1 - Zwick, A. A1 - Michael P. Cummings ER - TY - JOUR T1 - Primate transcript and protein expression levels evolve under compensatory selection pressures. JF - Science Y1 - 2013 A1 - Khan, Zia A1 - Ford, Michael J A1 - Cusanovich, Darren A A1 - Mitrano, Amy A1 - Pritchard, Jonathan K A1 - Gilad, Yoav KW - Animals KW - Evolution, Molecular KW - Gene Expression Regulation KW - HUMANS KW - Macaca mulatta KW - Pan troglodytes KW - Protein Biosynthesis KW - RNA, Messenger KW - Selection, Genetic KW - Species Specificity KW - Transcription, Genetic AB -

Changes in gene regulation have likely played an important role in the evolution of primates. Differences in messenger RNA (mRNA) expression levels across primates have often been documented; however, it is not yet known to what extent measurements of divergence in mRNA levels reflect divergence in protein expression levels, which are probably more important in determining phenotypic differences. We used high-resolution, quantitative mass spectrometry to collect protein expression measurements from human, chimpanzee, and rhesus macaque lymphoblastoid cell lines and compared them to transcript expression data from the same samples. We found dozens of genes with significant expression differences between species at the mRNA level yet little or no difference in protein expression. Overall, our data suggest that protein expression levels evolve under stronger evolutionary constraint than mRNA levels.

VL - 342 CP - 6162 M3 - 10.1126/science.1242379 ER - TY - Generic T1 - Primate Transcript and Protein Expression Levels Evolve Under Compensatory Selection Pressures Y1 - 2013 A1 - Khan, Z. A1 - Ford, M. J. A1 - Cusanovich, D. A. A1 - Mitrano, A. A1 - Pritchard, J. K. A1 - Gilad, Y. JA - Science VL - 342 UR - http://www.sciencemag.org/cgi/doi/10.1126/science.1242379 CP - 6162 J1 - Science M3 - 10.1126/science.1242379 ER - TY - JOUR T1 - Three independent determinants of protein evolutionary rate JF - J Mol EvolJ Mol EvolJ Mol Evol Y1 - 2013 A1 - Choi, S. S. A1 - Sridhar Hannenhalli KW - *Evolution, Molecular KW - *Mutation Rate KW - Animals KW - Genes/physiology KW - Genetic Fitness KW - HUMANS KW - Models, Genetic KW - Protein Biosynthesis/genetics KW - Protein Folding KW - Protein Interaction Domains and Motifs/genetics KW - Proteins/chemistry/*genetics/metabolism AB - One of the most widely accepted ideas related to the evolutionary rates of proteins is that functionally important residues or regions evolve slower than other regions, a reasonable outcome of which should be a slower evolutionary rate of the proteins with a higher density of functionally important sites. Oddly, the role of functional importance, mainly measured by essentiality, in determining evolutionary rate has been challenged in recent studies. Several variables other than protein essentiality, such as expression level, gene compactness, protein-protein interactions, etc., have been suggested to affect protein evolutionary rate. In the present review, we try to refine the concept of functional importance of a gene, and consider three factors-functional importance, expression level, and gene compactness, as independent determinants of evolutionary rate of a protein, based not only on their known correlation with evolutionary rate but also on a reasonable mechanistic model. We suggest a framework based on these mechanistic models to correctly interpret the correlations between evolutionary rates and the various variables as well as the interrelationships among the variables. VL - 76 SN - 1432-1432 (Electronic)
0022-2844 (Linking) N1 - Choi, Sun Shim
Hannenhalli, Sridhar
eng
R01GM085226/GM/NIGMS NIH HHS/
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Review
Germany
2013/02/13 06:00
J Mol Evol. 2013 Mar;76(3):98-111. doi: 10.1007/s00239-013-9543-6. Epub 2013 Feb 12. J1 - Journal of molecular evolutionJournal of molecular evolution ER - TY - JOUR T1 - BEAGLE: An Application Programming Interface and High-Performance Computing Library for Statistical Phylogenetics JF - Systematic BiologySyst BiolSystematic BiologySyst Biol Y1 - 2012 A1 - Ayres, Daniel L. A1 - Darling, Aaron A1 - Zwickl, Derrick J. A1 - Beerli, Peter A1 - Holder, Mark T. A1 - Lewis, Paul O. A1 - Huelsenbeck, John P. A1 - Ronquist, Fredrik A1 - Swofford, David L. A1 - Michael P. Cummings A1 - Rambaut, Andrew A1 - Suchard, Marc A. KW - Bayesian phylogenetics KW - gpu KW - maximum likelihood KW - parallel computing AB - Phylogenetic inference is fundamental to our understanding of most aspects of the origin and evolution of life, and in recent years, there has been a concentration of interest in statistical approaches such as Bayesian inference and maximum likelihood estimation. Yet, for large data sets and realistic or interesting models of evolution, these approaches remain computationally demanding. High-throughput sequencing can yield data for thousands of taxa, but scaling to such problems using serial computing often necessitates the use of nonstatistical or approximate approaches. The recent emergence of graphics processing units (GPUs) provides an opportunity to leverage their excellent floating-point computational performance to accelerate statistical phylogenetic inference. A specialized library for phylogenetic calculation would allow existing software packages to make more effective use of available computer hardware, including GPUs. Adoption of a common library would also make it easier for other emerging computing architectures, such as field programmable gate arrays, to be used in the future. We present BEAGLE, an application programming interface (API) and library for high-performance statistical phylogenetic inference. The API provides a uniform interface for performing phylogenetic likelihood calculations on a variety of compute hardware platforms. The library includes a set of efficient implementations and can currently exploit hardware including GPUs using NVIDIA CUDA, central processing units (CPUs) with Streaming SIMD Extensions and related processor supplementary instruction sets, and multicore CPUs via OpenMP. To demonstrate the advantages of a common API, we have incorporated the library into several popular phylogenetic software packages. The BEAGLE library is free open source software licensed under the Lesser GPL and available from http://beagle-lib.googlecode.com. An example client program is available as public domain software. VL - 61 SN - 1063-5157, 1076-836X ER - TY - JOUR T1 - A comparative evaluation of sequence classification programs JF - BMC BioinformaticsBMC Bioinformatics Y1 - 2012 A1 - Adam L. Bazinet A1 - Michael P. Cummings AB - Background A fundamental problem in modern genomics is to taxonomically or functionally classify DNA sequence fragments derived from environmental sampling (i.e., metagenomics). Several different methods have been proposed for doing this effectively and efficiently, and many have been implemented in software. In addition to varying their basic algorithmic approach to classification, some methods screen sequence reads for ’barcoding genes’ like 16S rRNA, or various types of protein-coding genes. Due to the sheer number and complexity of methods, it can be difficult for a researcher to choose one that is well-suited for a particular analysis. Results We divided the very large number of programs that have been released in recent years for solving the sequence classification problem into three main categories based on the general algorithm they use to compare a query sequence against a database of sequences. We also evaluated the performance of the leading programs in each category on data sets whose taxonomic and functional composition is known. Conclusions We found significant variability in classification accuracy, precision, and resource consumption of sequence classification programs when used to analyze various metagenomics data sets. However, we observe some general trends and patterns that will be useful to researchers who use sequence classification programs. VL - 13 ER - TY - JOUR T1 - Deep Sequencing of the Oral Microbiome Reveals Signatures of Periodontal Disease JF - PloS onePLoS One Y1 - 2012 A1 - Liu, B. A1 - Faller, L. L. A1 - Klitgord, N. A1 - Mazumdar, V. A1 - Ghodsi, M. A1 - Sommer, D. D. A1 - Gibbons, T. R. A1 - Todd Treangen A1 - Chang, Y. C. A1 - Li, S. A1 - others, PB - Public Library of Science VL - 7 ER - TY - JOUR T1 - Epigenomic model of cardiac enhancers with application to Genome wideassociation studies JF - Pacific Symposium on BiocomputingPacific Symposium on Biocomputing Y1 - 2012 A1 - Avinash, D. Sahu A1 - R. Aniba A1 - Y. C. Chang A1 - Sridhar Hannenhalli ER - TY - JOUR T1 - Exploiting sparseness in de novo genome assembly JF - BMC bioinformaticsBMC Bioinformatics Y1 - 2012 A1 - Chengxi Ye A1 - Ma, Z. S. A1 - Cannon, C. H. A1 - M. Pop A1 - Yu, D. W. PB - BioMed Central Ltd VL - 13 ER - TY - JOUR T1 - A framework for human microbiome research JF - NatureNature Y1 - 2012 A1 - Methé, B. A. A1 - Nelson, K. E. A1 - M. Pop A1 - Creasy, H. H. A1 - Giglio, M. G. A1 - Huttenhower, C. A1 - Gevers, D. A1 - Petrosino, J. F. A1 - Abubucker, S. A1 - Badger, J. H. A1 - others, VL - 486 ER - TY - JOUR T1 - A framework for human microbiome research JF - Nature Y1 - 2012 A1 - Human Microbiome Project Consortium A1 - Todd Treangen VL - 486 ER - TY - JOUR T1 - Functional genomics of trypanosomatids. JF - Parasite Immunol Y1 - 2012 A1 - Choi, J A1 - El-Sayed, N M KW - Animals KW - Genome, Protozoan KW - Genomics KW - HUMANS KW - Proteome KW - Protozoan Proteins KW - Transcriptome KW - Trypanosomatina AB -

The decoding of the Tritryp reference genomes nearly 7 years ago provided a first peek into the biology of pathogenic trypanosomatids and a blueprint that has paved the way for genome-wide studies. Although 60-70% of the predicted protein coding genes in Trypanosoma brucei, Trypanosoma cruzi and Leishmania major remain unannotated, the functional genomics landscape is rapidly changing. Facilitated by the advent of next-generation sequencing technologies, improved structural and functional annotation and genes and their products are emerging. Information is also growing for the interactions between cellular components as transcriptomes, regulatory networks and metabolomes are characterized, ushering in a new era of systems biology. Simultaneously, the launch of comparative sequencing of multiple strains of kinetoplastids will finally lead to the investigation of a vast, yet to be explored, evolutionary and pathogenomic space.

VL - 34 CP - 2-3 M3 - 10.1111/j.1365-3024.2011.01347.x ER - TY - JOUR T1 - Genomic analysis of ICEVchBan8: An atypical genetic element in Vibrio cholerae JF - FEBS LettersFEBS Letters Y1 - 2012 A1 - Taviani, Elisa A1 - Spagnoletti, Matteo A1 - Ceccarelli, Daniela A1 - Haley, Bradd J. A1 - Hasan, Nur A. A1 - Chen, Arlene A1 - Colombo, Mauro M. A1 - Huq, Anwar A1 - Rita R. Colwell KW - Genomic islands KW - Integrative conjugative elements KW - Lateral gene transfer KW - Vibrio cholerae AB - Genomic islands (GIs) and integrative conjugative elements (ICEs) are major players in bacterial evolution since they encode genes involved in adaptive functions of medical or environmental importance. Here we performed the genomic analysis of ICEVchBan8, an unusual ICE found in the genome of a clinical non-toxigenic Vibrio cholerae O37 isolate. ICEVchBan8 shares most of its genetic structure with SXT/R391 ICEs. However, this ICE codes for a different integration/excision module is located at a different insertion site, and part of its genetic cargo shows homology to other pathogenicity islands of V. cholerae. SN - 0014-5793 ER - TY - JOUR T1 - Genomic analysis of sleep deprivation reveals translational regulation in the hippocampus JF - Physiological GenomicsPhysiological Genomics Y1 - 2012 A1 - Christopher, G. Vecsey A1 - Lucia, Peixoto A1 - Jennifer, H. K. Choi A1 - Mathieu, Wimmer A1 - Devan, Jaganath A1 - Pepe, J. Hernandez A1 - Jennifer, Blackwell A1 - Karuna, Meda A1 - Alan, J. Park A1 - Sridhar Hannenhalli A1 - Abel, Ted ER - TY - JOUR T1 - InterPro in 2011: new developments in the family and domain prediction database JF - Nucleic acids researchNucleic Acids Research Y1 - 2012 A1 - Hunter, Sarah A1 - Jones, Philip A1 - Mitchell, Alex A1 - Apweiler, Rolf A1 - Attwood, Teresa K. A1 - Bateman, Alex A1 - Bernard, Thomas A1 - Binns, David A1 - Bork, Peer A1 - Burge, Sarah A1 - de Castro, Edouard A1 - Coggill, Penny A1 - Corbett, Matthew A1 - Das, Ujjwal A1 - Daugherty, Louise A1 - Duquenne, Lauranne A1 - Finn, Robert D. A1 - Fraser, Matthew A1 - Gough, Julian A1 - Haft, Daniel A1 - Hulo, Nicolas A1 - Kahn, Daniel A1 - Kelly, Elizabeth A1 - Letunic, Ivica A1 - Lonsdale, David A1 - Lopez, Rodrigo A1 - Madera, Martin A1 - Maslen, John A1 - McAnulla, Craig A1 - McDowall, Jennifer A1 - McMenamin, Conor A1 - Mi, Huaiyu A1 - Mutowo-Muellenet, Prudence A1 - Mulder, Nicola A1 - Natale, Darren A1 - Orengo, Christine A1 - Pesseat, Sebastien A1 - Punta, Marco A1 - Quinn, Antony F. A1 - Rivoire, Catherine A1 - Sangrador-Vegas, Amaia A1 - J. Selengut A1 - Sigrist, Christian J. A. A1 - Scheremetjew, Maxim A1 - Tate, John A1 - Thimmajanarthanan, Manjulapramila A1 - Thomas, Paul D. A1 - Wu, Cathy H. A1 - Yeats, Corin A1 - Yong, Siew-Yit KW - Databases, Protein KW - Protein Structure, Tertiary KW - Proteins KW - Sequence Analysis, Protein KW - software KW - Terminology as Topic KW - User-Computer Interface AB - InterPro (http://www.ebi.ac.uk/interpro/) is a database that integrates diverse information about protein families, domains and functional sites, and makes it freely available to the public via Web-based interfaces and services. Central to the database are diagnostic models, known as signatures, against which protein sequences can be searched to determine their potential function. InterPro has utility in the large-scale analysis of whole genomes and meta-genomes, as well as in characterizing individual protein sequences. Herein we give an overview of new developments in the database and its associated software since 2009, including updates to database content, curation processes and Web and programmatic interfaces. VL - 40 N1 - http://www.ncbi.nlm.nih.gov/pubmed/22096229?dopt=Abstract ER - TY - JOUR T1 - InterPro in 2011: new developments in the family and domain prediction database. JF - Nucleic Acids Res Y1 - 2012 A1 - Hunter, Sarah A1 - Jones, Philip A1 - Mitchell, Alex A1 - Apweiler, Rolf A1 - Attwood, Teresa K A1 - Bateman, Alex A1 - Bernard, Thomas A1 - Binns, David A1 - Bork, Peer A1 - Burge, Sarah A1 - de Castro, Edouard A1 - Coggill, Penny A1 - Corbett, Matthew A1 - Das, Ujjwal A1 - Daugherty, Louise A1 - Duquenne, Lauranne A1 - Finn, Robert D A1 - Fraser, Matthew A1 - Gough, Julian A1 - Haft, Daniel A1 - Hulo, Nicolas A1 - Kahn, Daniel A1 - Kelly, Elizabeth A1 - Letunic, Ivica A1 - Lonsdale, David A1 - Lopez, Rodrigo A1 - Madera, Martin A1 - Maslen, John A1 - McAnulla, Craig A1 - McDowall, Jennifer A1 - McMenamin, Conor A1 - Mi, Huaiyu A1 - Mutowo-Muellenet, Prudence A1 - Mulder, Nicola A1 - Natale, Darren A1 - Orengo, Christine A1 - Pesseat, Sebastien A1 - Punta, Marco A1 - Quinn, Antony F A1 - Rivoire, Catherine A1 - Sangrador-Vegas, Amaia A1 - Selengut, Jeremy D A1 - Sigrist, Christian J A A1 - Scheremetjew, Maxim A1 - Tate, John A1 - Thimmajanarthanan, Manjulapramila A1 - Thomas, Paul D A1 - Wu, Cathy H A1 - Yeats, Corin A1 - Yong, Siew-Yit KW - Databases, Protein KW - Protein Structure, Tertiary KW - Proteins KW - Sequence Analysis, Protein KW - software KW - Terminology as Topic KW - User-Computer Interface AB -

InterPro (http://www.ebi.ac.uk/interpro/) is a database that integrates diverse information about protein families, domains and functional sites, and makes it freely available to the public via Web-based interfaces and services. Central to the database are diagnostic models, known as signatures, against which protein sequences can be searched to determine their potential function. InterPro has utility in the large-scale analysis of whole genomes and meta-genomes, as well as in characterizing individual protein sequences. Herein we give an overview of new developments in the database and its associated software since 2009, including updates to database content, curation processes and Web and programmatic interfaces.

VL - 40 CP - Database issue M3 - 10.1093/nar/gkr948 ER - TY - JOUR T1 - A molecular phylogeny for the leaf-roller moths (Lepidoptera: Tortricidae) and its implications for classification and life history evolution. JF - PloS one Y1 - 2012 A1 - Regier, Jerome C A1 - Brown, John W A1 - Mitter, Charles A1 - Baixeras, Joaquin A1 - Cho, Soowon A1 - Michael P. Cummings A1 - Zwick, Andreas AB - Tortricidae, one of the largest families of microlepidopterans, comprise about 10,000 described species worldwide, including important pests, biological control agents and experimental models. Understanding of tortricid phylogeny, the basis for a predictive classification, is currently provisional. We present the first detailed molecular estimate of relationships across the tribes and subfamilies of Tortricidae, assess its concordance with previous morphological evidence, and re-examine postulated evolutionary trends in host plant use and biogeography. VL - 7 ER - TY - JOUR T1 - A molecular phylogeny for the pyraloid moths (Lepidoptera: Pyraloidea) and its implications for higher-level classification JF - Systematic Entomology Y1 - 2012 A1 - Regier, Jerome C. A1 - Mitter, Charles A1 - SOLIS, M. ALMA A1 - HAYDEN, JAMES E. A1 - LANDRY, BERNARD A1 - NUSS, MATTHIAS A1 - Simonsen, Thomas J. A1 - Yen, Shen-Horn A1 - Zwick, Andreas A1 - Michael P. Cummings VL - 37 UR - http://doi.wiley.com/10.1111/sen.2012.37.issue-4http://doi.wiley.com/10.1111/j.1365-3113.2012.00641.x CP - 4 M3 - 10.1111/sen.2012.37.issue-410.1111/j.1365-3113.2012.00641.x ER - TY - JOUR T1 - Occurrence of protozoans & their limnological relationships in some ponds of Mathbaria, Bangladesh JF - University Journal of Zoology, Rajshahi UniversityUniversity Journal of Zoology, Rajshahi University Y1 - 2012 A1 - Mozumder, P. K. A1 - Banu, M. A. A1 - Naser, M. N. A1 - Ali, M. S. A1 - Alam, M. A1 - Sack, R. B. A1 - Rita R. Colwell A1 - Huq, A. VL - 29 SN - 1023-6104 ER - TY - Generic T1 - Plasmodium falciparum merozoite surface protein 1 blocks the proinflammatory protein S100P. Y1 - 2012 A1 - Waisberg, Michael A1 - Cerqueira, Gustavo C A1 - Yager, Stephanie B A1 - Francischetti, Ivo M B A1 - Lu, Jinghua A1 - Gera, Nidhi A1 - Srinivasan, Prakash A1 - Miura, Kazutoyo A1 - Rada, Balazs A1 - Lukszo, Jan A1 - Barbian, Kent D A1 - Leto, Thomas L A1 - Porcella, Stephen F A1 - Narum, David L A1 - El-Sayed, Najib A1 - Miller, Louis H A1 - Pierce, Susan K KW - Amino Acid Sequence KW - Animals KW - Calcium-Binding Proteins KW - Chromatography, Gel KW - Electrophoresis, Polyacrylamide Gel KW - Enzyme-Linked Immunosorbent Assay KW - HUMANS KW - Merozoite Surface Protein 1 KW - Microscopy, Confocal KW - Molecular Sequence Data KW - Neoplasm Proteins KW - Plasmodium falciparum KW - Sequence Homology, Amino Acid KW - Surface Plasmon Resonance AB -

The malaria parasite, Plasmodium falciparum, and the human immune system have coevolved to ensure that the parasite is not eliminated and reinfection is not resisted. This relationship is likely mediated through a myriad of host-parasite interactions, although surprisingly few such interactions have been identified. Here we show that the 33-kDa fragment of P. falciparum merozoite surface protein 1 (MSP1(33)), an abundant protein that is shed during red blood cell invasion, binds to the proinflammatory protein, S100P. MSP1(33) blocks S100P-induced NFκB activation in monocytes and chemotaxis in neutrophils. Remarkably, S100P binds to both dimorphic alleles of MSP1, estimated to have diverged >27 Mya, suggesting an ancient, conserved relationship between these parasite and host proteins that may serve to attenuate potentially damaging inflammatory responses.

JA - Proc Natl Acad Sci U S A VL - 109 CP - 14 M3 - 10.1073/pnas.1202689109 ER - TY - JOUR T1 - Quantitative measurement of allele-specific protein expression in a diploid yeast hybrid by LC-MS JF - Molecular Systems Biology Y1 - 2012 A1 - Khan, Zia A1 - Bloom, Joshua S A1 - Amini, Sasan A1 - Singh, Mona A1 - Perlman, David H A1 - Caudy, Amy A A1 - Kruglyak, Leonid VL - 8 UR - http://msb.embopress.org/cgi/doi/10.1038/msb.2012.34 J1 - Mol Syst Biol M3 - 10.1038/msb.2012.34 ER - TY - Generic T1 - Quantitative measurement of allele-specific protein expression in a diploid yeast hybrid by LC-MS. Y1 - 2012 A1 - Khan, Zia A1 - Bloom, Joshua S A1 - Amini, Sasan A1 - Singh, Mona A1 - Perlman, David H A1 - Caudy, Amy A A1 - Kruglyak, Leonid KW - Alleles KW - Chromatography, Liquid KW - Fungal Proteins KW - Gene Expression Profiling KW - Gene Expression Regulation, Fungal KW - HUMANS KW - Mass Spectrometry KW - proteomics KW - Regression Analysis KW - Saccharomyces KW - Saccharomyces cerevisiae KW - Saccharomyces cerevisiae Proteins KW - Species Specificity AB -

Understanding the genetic basis of gene regulatory variation is a key goal of evolutionary and medical genetics. Regulatory variation can act in an allele-specific manner (cis-acting) or it can affect both alleles of a gene (trans-acting). Differential allele-specific expression (ASE), in which the expression of one allele differs from another in a diploid, implies the presence of cis-acting regulatory variation. While microarrays and high-throughput sequencing have enabled genome-wide measurements of transcriptional ASE, methods for measurement of protein ASE (pASE) have lagged far behind. We describe a flexible, accurate, and scalable strategy for measurement of pASE by liquid chromatography-coupled mass spectrometry (LC-MS). We apply this approach to a hybrid between the yeast species Saccharomyces cerevisiae and Saccharomyces bayanus. Our results provide the first analysis of the relative contribution of cis-acting and trans-acting regulatory differences to protein expression divergence between yeast species.

JA - Mol Syst Biol VL - 8 M3 - 10.1038/msb.2012.34 ER - TY - JOUR T1 - Role of Shrimp Chitin in the Ecology of Toxigenic Vibrio cholerae and Cholera Transmission JF - Frontiers in MicrobiologyFront MicrobiolFrontiers in MicrobiologyFront Microbiol Y1 - 2012 A1 - Nahar, Shamsun A1 - Sultana, Marzia A1 - Naser, M. Niamul A1 - Nair, Gopinath B. A1 - Watanabe, Haruo A1 - Ohnishi, Makoto A1 - Yamamoto, Shouji A1 - Endtz, Hubert A1 - Cravioto, Alejandro A1 - Sack, R. Bradley A1 - Hasan, Nur A. A1 - Sadique, Abdus A1 - Huq, Anwar A1 - Rita R. Colwell A1 - Alam, Munirul AB - Seasonal plankton blooms correlate with occurrence of cholera in Bangladesh, although the mechanism of how dormant Vibrio cholerae, enduring interepidemic period in biofilms and plankton, initiates seasonal cholera is not fully understood. In this study, laboratory microcosms prepared with estuarine Mathbaria water (MW) samples supported active growth of toxigenic V. cholerae O1 up to 7 weeks as opposed to 6 months when microcosms were supplemented with dehydrated shrimp chitin chips (CC) as the single source of nutrient. Bacterial counting and detection of wbe and ctxA genes were done employing culture, direct fluorescent antibody (DFA) assay, and multiplex-polymerase chain reaction methods. In MW microcosm, the aqueous phase became clear as the non-culturable cells settled, whereas the aqueous phase of the MW–CC microcosm became turbid from bacterial growth stimulated by chitin. Bacterial chitin degradation and biofilm formation proceeded from an initial steady state to a gradually declining bacterial culturable count. V. cholerae within the microenvironments of chitin and chitin-associated biofilms remained metabolically active even in a high acidic environment without losing either viability or virulence. It is concluded that the abundance of chitin that occurs during blooms plays an important role in the aquatic life cycle of V. cholerae and, ultimately, in the seasonal transmission of cholera. VL - 2 SN - 1664-302X ER - TY - JOUR T1 - Structure, function and diversity of the healthy human microbiome JF - NatureNature Y1 - 2012 A1 - Huttenhower, C. A1 - Gevers, D. A1 - Knight, R. A1 - Abubucker, S. A1 - Badger, J. H. A1 - Chinwalla, A. T. A1 - Creasy, H. H. A1 - Earl, A. M. A1 - Fitzgerald, M. G. A1 - Fulton, R. S. A1 - others, VL - 486 ER - TY - JOUR T1 - Structure, function and diversity of the healthy human microbiome JF - Nature Y1 - 2012 A1 - Human Microbiome Project Consortium A1 - Todd Treangen VL - 486 ER - TY - JOUR T1 - Temporal and Spatial Variability in the Distribution of Vibrio vulnificus in the Chesapeake Bay: A Hindcast Study JF - EcoHealthEcoHealth Y1 - 2012 A1 - Banakar, V. A1 - Constantin de Magny, G. A1 - Jacobs, J. A1 - Murtugudde, R. A1 - Huq, A. A1 - J. Wood, R. A1 - Rita R. Colwell AB - Vibrio vulnificus, an estuarine bacterium, is the causative agent of seafood-related gastroenteritis, primary septicemia, and wound infections worldwide. It occurs as part of the normal microflora of coastal marine environments and can be isolated from water, sediment, and oysters. Hindcast prediction was undertaken to determine spatial and temporal variability in the likelihood of occurrence of V. vulnificus in surface waters of the Chesapeake Bay. Hindcast predictions were achieved by forcing a multivariate habitat suitability model with simulated sea surface temperature and salinity in the Bay for the period between 1991 and 2005 and the potential hotspots of occurrence of V. vulnificus in the Chesapeake Bay were identified. The likelihood of occurrence of V. vulnificus during high and low rainfall years was analyzed. From results of the study, it is concluded that hindcast prediction yields an improved understanding of environmental conditions associated with occurrence of V. vulnificus in the Chesapeake Bay. ER - TY - Generic T1 - Transcript expression analysis of putative Trypanosoma brucei GPI-anchored surface proteins during development in the tsetse and mammalian hosts. Y1 - 2012 A1 - Savage, Amy F A1 - Cerqueira, Gustavo C A1 - Regmi, Sandesh A1 - Wu, Yineng A1 - El Sayed, Najib M A1 - Aksoy, Serap KW - Animals KW - Computational Biology KW - Gastrointestinal Tract KW - Gene Expression Profiling KW - GPI-Linked Proteins KW - HUMANS KW - Male KW - Membrane Proteins KW - Protozoan Proteins KW - Real-Time Polymerase Chain Reaction KW - Salivary Glands KW - Trypanosoma brucei brucei KW - Trypanosomiasis, African KW - Tsetse Flies AB -

Human African Trypanosomiasis is a devastating disease caused by the parasite Trypanosoma brucei. Trypanosomes live extracellularly in both the tsetse fly and the mammal. Trypanosome surface proteins can directly interact with the host environment, allowing parasites to effectively establish and maintain infections. Glycosylphosphatidylinositol (GPI) anchoring is a common posttranslational modification associated with eukaryotic surface proteins. In T. brucei, three GPI-anchored major surface proteins have been identified: variant surface glycoproteins (VSGs), procyclic acidic repetitive protein (PARP or procyclins), and brucei alanine rich proteins (BARP). The objective of this study was to select genes encoding predicted GPI-anchored proteins with unknown function(s) from the T. brucei genome and characterize the expression profile of a subset during cyclical development in the tsetse and mammalian hosts. An initial in silico screen of putative T. brucei proteins by Big PI algorithm identified 163 predicted GPI-anchored proteins, 106 of which had no known functions. Application of a second GPI-anchor prediction algorithm (FragAnchor), signal peptide and trans-membrane domain prediction software resulted in the identification of 25 putative hypothetical proteins. Eighty-one gene products with hypothetical functions were analyzed for stage-regulated expression using semi-quantitative RT-PCR. The expression of most of these genes were found to be upregulated in trypanosomes infecting tsetse salivary gland and proventriculus tissues, and 38% were specifically expressed only by parasites infecting salivary gland tissues. Transcripts for all of the genes specifically expressed in salivary glands were also detected in mammalian infective metacyclic trypomastigotes, suggesting a possible role for these putative proteins in invasion and/or establishment processes in the mammalian host. These results represent the first large-scale report of the differential expression of unknown genes encoding predicted T. brucei surface proteins during the complete developmental cycle. This knowledge may form the foundation for the development of future novel transmission blocking strategies against metacyclic parasites.

JA - PLoS Negl Trop Dis VL - 6 CP - 6 M3 - 10.1371/journal.pntd.0001708 ER - TY - JOUR T1 - Vibrio Cholerae Classical Biotype Strains Reveal Distinct Signatures in Mexico JF - Journal of Clinical MicrobiologyJ. Clin. Microbiol.Journal of Clinical MicrobiologyJ. Clin. Microbiol. Y1 - 2012 A1 - Alam, Munirul A1 - Islam, M. Tarequl A1 - Rashed, Shah Manzur A1 - Johura, Fatema-Tuz A1 - Bhuiyan, Nurul A. A1 - Delgado, Gabriela A1 - Morales, Rosario A1 - Mendez, Jose Luis A1 - Navarro, Armando A1 - Watanabe, Haruo A1 - Hasan, Nur- A. A1 - Rita R. Colwell A1 - Cravioto, Alejandro AB - Vibrio cholerae O1 Classical (CL) biotype caused the 5th and 6th, and probably the earlier cholera pandemics, before the El Tor (ET) biotype initiated the 7th pandemic in Asia in the 1970's by completely displacing the CL biotype. Although the CL biotype was thought to be extinct in Asia, and it had never been reported from Latin America, V. cholerae CL and ET biotypes, including hybrid ET were found associated with endemic cholera in Mexico between 1991 and 1997. In this study, CL biotype strains isolated from endemic cholera in Mexico, between 1983 and 1997 were characterized in terms of major phenotypic and genetic traits, and compared with CL biotype strains isolated in Bangladesh between 1962 and 1989. According to sero- and bio-typing data, all V. cholerae strains tested had the major phenotypic and genotypic characteristics specific for the CL biotype. Antibiograms revealed the majority of the Bangladeshi strains to be resistant to trimethoprim/sulfamethoxazole, furazolidone, ampicillin, and gentamycin, while the Mexican strains were sensitive to all of these drugs, as well as to ciprofloxacin, erythromycin, and tetracycline. Pulsed-field gel electrophoresis (PFGE) of NotI-digested genomic DNA revealed characteristic banding patterns for all the CL biotype strains, although the Mexican strains differed with the Bangladeshi strains in 1-2 DNA bands. The difference may be subtle, but consistent, as confirmed by the sub-clustering patterns in the PFGE-based dendrogram, and can serve as regional signature, suggesting pre-1991 existence and evolution of the CL biotype strains in the Americas, independent from that of Asia. SN - 0095-1137, 1098-660X ER - TY - JOUR T1 - Widespread evidence of viral miRNAs targeting host pathways JF - BMC GenomicsBMC Genomics Y1 - 2012 A1 - Joseph Carl, Joanne Trgovcich A1 - Sridhar Hannenhalli ER - TY - Generic T1 - Accurate proteome-wide protein quantification from high-resolution 15N mass spectra Y1 - 2011 A1 - Khan, Zia A1 - Amini, Sasan A1 - Bloom, Joshua S A1 - Ruse, Cristian A1 - Caudy, Amy A A1 - Kruglyak, Leonid A1 - Singh, Mona A1 - Perlman, David H A1 - Tavazoie, Saeed JA - Genome Biology VL - 12 UR - http://genomebiology.com/2012/12/12/R122 CP - 12 J1 - Genome BiolGenome Biology M3 - 10.1186/gb-2011-12-12-r122 ER - TY - JOUR T1 - Accurate proteome-wide protein quantification from high-resolution 15N mass spectra. JF - Genome Biol Y1 - 2011 A1 - Khan, Zia A1 - Amini, Sasan A1 - Bloom, Joshua S A1 - Ruse, Cristian A1 - Caudy, Amy A A1 - Kruglyak, Leonid A1 - Singh, Mona A1 - Perlman, David H A1 - Tavazoie, Saeed KW - algorithms KW - Amino Acid Sequence KW - Bacterial Proteins KW - Escherichia coli KW - Isotope Labeling KW - Mass Spectrometry KW - Molecular Sequence Data KW - Nitrogen Isotopes KW - Proteome KW - proteomics KW - Sensitivity and Specificity KW - software AB -

In quantitative mass spectrometry-based proteomics, the metabolic incorporation of a single source of 15N-labeled nitrogen has many advantages over using stable isotope-labeled amino acids. However, the lack of a robust computational framework for analyzing the resulting spectra has impeded wide use of this approach. We have addressed this challenge by introducing a new computational methodology for analyzing 15N spectra in which quantification is integrated with identification. Application of this method to an Escherichia coli growth transition reveals significant improvement in quantification accuracy over previous methods.

VL - 12 CP - 12 M3 - 10.1186/gb-2011-12-12-r122 ER - TY - JOUR T1 - Aquatic Realm and Cholera JF - Epidemiological and Molecular Aspects on CholeraEpidemiological and Molecular Aspects on Cholera Y1 - 2011 A1 - Huq, A. A1 - Grim, C. J. A1 - Rita R. Colwell AB - Cholera is an ancient disease that can be severe and life threatening. It occurs predominantly in areas of the world where populations lack safe drinking water. Epidemics of cholera are linked with malnutrition, poor sanitation, and conditions resulting from natural disasters such as severe flooding. According to a report published by WHO in 2000 [1], cholera remains a major public health problem and is becoming increasingly important since the number of countries in which cholera is endemic continues to increase. Unfortunately, outbreaks of the disease continue into the twenty-first century with ominous portent in the wake of global climate change [1]. Yet cholera is a preventable disease if people have access to safe drinking water and are properly educated how to protect themselves from the risk of infection with vibrios. Cholera also is an easily treatable disease. Oral rehydration therapy, a solution containing glucose and appropriate salts, has proven to be effective for treatment of most cholera victims [2]. Nevertheless, each year, tens of thousands of people are victims of the disease, bringing this “curse of humankind” to modern civilization. Present understanding of cholera is based on studies conducted over the past three decades and significant new information has been gained concerning environmental factors associated with this disease, especially how to detect the bacterium and where it lives in the natural environment, outside the human gut, and what triggers the annual outbreaks that occur with remarkable regularity. Environmental research on Vibrio cholerae and cholera has provided insights for prediction and prevention of the disease it causes, while the race for effective vaccines against cholera continues. ER - TY - JOUR T1 - Can Deliberately Incomplete Gene Sample Augmentation Improve a Phylogeny Estimate for the Advanced Moths and Butterflies (Hexapoda: Lepidoptera)? JF - Systematic BiologySyst BiolSystematic BiologySyst Biol Y1 - 2011 A1 - Cho, Soowon A1 - Zwick, Andreas A1 - Regier, Jerome C. A1 - Mitter, Charles A1 - Michael P. Cummings A1 - Yao, Jianxiu A1 - Du, Zaile A1 - Zhao, Hong A1 - Kawahara, Akito Y. A1 - Weller, Susan A1 - Davis, Donald R. A1 - Baixeras, Joaquin A1 - Brown, John W. A1 - Parr, Cynthia KW - Ditrysia KW - gene sampling KW - Hexapoda KW - Lepidoptera KW - missing data KW - molecular phylogenetics KW - nuclear genes KW - taxon sampling AB - This paper addresses the question of whether one can economically improve the robustness of a molecular phylogeny estimate by increasing gene sampling in only a subset of taxa, without having the analysis invalidated by artifacts arising from large blocks of missing data. Our case study stems from an ongoing effort to resolve poorly understood deeper relationships in the large clade Ditrysia ( > 150,000 species) of the insect order Lepidoptera (butterflies and moths). Seeking to remedy the overall weak support for deeper divergences in an initial study based on five nuclear genes (6.6 kb) in 123 exemplars, we nearly tripled the total gene sample (to 26 genes, 18.4 kb) but only in a third (41) of the taxa. The resulting partially augmented data matrix (45% intentionally missing data) consistently increased bootstrap support for groupings previously identified in the five-gene (nearly) complete matrix, while introducing no contradictory groupings of the kind that missing data have been predicted to produce. Our results add to growing evidence that data sets differing substantially in gene and taxon sampling can often be safely and profitably combined. The strongest overall support for nodes above the family level came from including all nucleotide changes, while partitioning sites into sets undergoing mostly nonsynonymous versus mostly synonymous change. In contrast, support for the deepest node for which any persuasive molecular evidence has yet emerged (78–85% bootstrap) was weak or nonexistent unless synonymous change was entirely excluded, a result plausibly attributed to compositional heterogeneity. This node (Gelechioidea + Apoditrysia), tentatively proposed by previous authors on the basis of four morphological synapomorphies, is the first major subset of ditrysian superfamilies to receive strong statistical support in any phylogenetic study. A “more-genes-only” data set (41 taxa×26 genes) also gave strong signal for a second deep grouping (Macrolepidoptera) that was obscured, but not strongly contradicted, in more taxon-rich analyses. VL - 60 SN - 1063-5157, 1076-836X ER - TY - JOUR T1 - Clonal transmission, dual peak, and off-season cholera in Bangladesh JF - Infection Ecology & EpidemiologyInfection Ecology & Epidemiology Y1 - 2011 A1 - Alam, M. A1 - Islam, A. A1 - Bhuiyan, N. A. A1 - Rahim, N. A1 - Hossain, A. A1 - Khan, G. Y. A1 - Ahmed, D. A1 - Watanabe, H. A1 - Izumiya, H. A1 - Faruque, A. S. G. A1 - Rita R. Colwell VL - 1 ER - TY - JOUR T1 - A computational statistics approach for estimating the spatial range of morphogen gradients. JF - Development Y1 - 2011 A1 - Kanodia, Jitendra S A1 - Kim, Yoosik A1 - Tomer, Raju A1 - Khan, Zia A1 - Chung, Kwanghun A1 - Storey, John D A1 - Lu, Hang A1 - Keller, Philipp J A1 - Shvartsman, Stanislav Y KW - Animals KW - Biostatistics KW - Cleavage Stage, Ovum KW - Computational Biology KW - Computer simulation KW - Drosophila KW - Drosophila Proteins KW - Embryo, Nonmammalian KW - Gene Expression Regulation, Developmental KW - Genes, Developmental KW - Imaging, Three-Dimensional KW - In Situ Hybridization, Fluorescence KW - Morphogenesis KW - Osmolar Concentration KW - Tissue Distribution AB -

A crucial issue in studies of morphogen gradients relates to their range: the distance over which they can act as direct regulators of cell signaling, gene expression and cell differentiation. To address this, we present a straightforward statistical framework that can be used in multiple developmental systems. We illustrate the developed approach by providing a point estimate and confidence interval for the spatial range of the graded distribution of nuclear Dorsal, a transcription factor that controls the dorsoventral pattern of the Drosophila embryo.

VL - 138 CP - 22 M3 - 10.1242/dev.071571 ER - TY - Generic T1 - A computational statistics approach for estimating the spatial range of morphogen gradients Y1 - 2011 A1 - Kanodia, J. S. A1 - Kim, Y. A1 - Tomer, R. A1 - Khan, Z. A1 - Chung, K. A1 - Storey, J. D. A1 - Lu, H. A1 - Keller, P. J. A1 - Shvartsman, S. Y. JA - Development VL - 138 UR - http://dev.biologists.org/cgi/doi/10.1242/dev.071571 CP - 22 J1 - Development M3 - 10.1242/dev.071571 ER - TY - Generic T1 - Computing the Tree of Life: Leveraging the Power of Desktop and Service Grids T2 - Parallel and Distributed Processing Workshops and Phd Forum (IPDPSW), 2011 IEEE International Symposium on Y1 - 2011 A1 - Adam L. Bazinet A1 - Michael P. Cummings KW - (artificial KW - (mathematics) KW - analysis KW - BOINC KW - COMPUTATION KW - computational KW - computing KW - data KW - Estimation KW - evolutionary KW - GARLI KW - genetic KW - Grid KW - GRIDS KW - handling KW - heterogeneous KW - History KW - HPC KW - information KW - intelligence) KW - interface KW - interfaces KW - Internet KW - jobs KW - lattice KW - learning KW - life KW - likelihood KW - load KW - machine KW - maximum KW - method KW - model KW - molecular KW - phylogenetic KW - portal KW - Portals KW - power KW - project KW - resource KW - Science KW - sequence KW - service KW - services KW - sets KW - software KW - substantial KW - system KW - systematics KW - tree KW - TREES KW - user KW - Web AB - The trend in life sciences research, particularly in molecular evolutionary systematics, is toward larger data sets and ever-more detailed evolutionary models, which can generate substantial computational loads. Over the past several years we have developed a grid computing system aimed at providing researchers the computational power needed to complete such analyses in a timely manner. Our grid system, known as The Lattice Project, was the first to combine two models of grid computing - the service model, which mainly federates large institutional HPC resources, and the desktop model, which harnesses the power of PCs volunteered by the general public. Recently we have developed a "science portal" style web interface that makes it easier than ever for phylogenetic analyses to be completed using GARLI, a popular program that uses a maximum likelihood method to infer the evolutionary history of organisms on the basis of genetic sequence data. This paper describes our approach to scheduling thousands of GARLI jobs with diverse requirements to heterogeneous grid resources, which include volunteer computers running BOINC software. A key component of this system provides a priori GARLI runtime estimates using machine learning with random forests. JA - Parallel and Distributed Processing Workshops and Phd Forum (IPDPSW), 2011 IEEE International Symposium on ER - TY - JOUR T1 - Direct targeting of Sec23a by miR-200s influences cancer cell secretome and promotes metastatic colonization. JF - Nat Med Y1 - 2011 A1 - Korpal, Manav A1 - Ell, Brian J A1 - Buffa, Francesca M A1 - Ibrahim, Toni A1 - Blanco, Mario A A1 - Celià-Terrassa, Toni A1 - Mercatali, Laura A1 - Khan, Zia A1 - Goodarzi, Hani A1 - Hua, Yuling A1 - Wei, Yong A1 - Hu, Guohong A1 - Garcia, Benjamin A A1 - Ragoussis, Jiannis A1 - Amadori, Dino A1 - Harris, Adrian L A1 - Kang, Yibin KW - Animals KW - Cadherins KW - Cell Line, Tumor KW - Female KW - Gene Expression Profiling KW - Gene Expression Regulation, Neoplastic KW - HUMANS KW - Mass Spectrometry KW - Mice KW - Mice, Inbred BALB C KW - Microarray Analysis KW - MicroRNAs KW - Neoplasm Metastasis KW - Statistics, Nonparametric KW - Vesicular Transport Proteins AB -

Although the role of miR-200s in regulating E-cadherin expression and epithelial-to-mesenchymal transition is well established, their influence on metastatic colonization remains controversial. Here we have used clinical and experimental models of breast cancer metastasis to discover a pro-metastatic role of miR-200s that goes beyond their regulation of E-cadherin and epithelial phenotype. Overexpression of miR-200s is associated with increased risk of metastasis in breast cancer and promotes metastatic colonization in mouse models, phenotypes that cannot be recapitulated by E-cadherin expression alone. Genomic and proteomic analyses revealed global shifts in gene expression upon miR-200 overexpression toward that of highly metastatic cells. miR-200s promote metastatic colonization partly through direct targeting of Sec23a, which mediates secretion of metastasis-suppressive proteins, including Igfbp4 and Tinagl1, as validated by functional and clinical correlation studies. Overall, these findings suggest a pleiotropic role of miR-200s in promoting metastatic colonization by influencing E-cadherin-dependent epithelial traits and Sec23a-mediated tumor cell secretome.

VL - 17 CP - 9 M3 - 10.1038/nm.2401 ER - TY - JOUR T1 - Gene Coexpression Network Topology of Cardiac Development, Hypertrophy, and FailureClinical Perspective JF - Circulation: cardiovascular geneticsCirculation: Cardiovascular Genetics Y1 - 2011 A1 - Dewey, F. E. A1 - Perez, M. V. A1 - Wheeler, M. T. A1 - Watt, C. A1 - Spin, J. A1 - Langfelder, P. A1 - Horvath, S. A1 - Sridhar Hannenhalli A1 - Cappola, T. P. A1 - Ashley, E. A. PB - Lippincott Williams & Wilkins VL - 4 ER - TY - JOUR T1 - Haem oxygenase is synthetically lethal with the tumour suppressor fumarate hydratase. JF - Nature Y1 - 2011 A1 - Frezza, Christian A1 - Zheng, Liang A1 - Folger, Ori A1 - Rajagopalan, Kartik N A1 - MacKenzie, Elaine D A1 - Jerby, Livnat A1 - Micaroni, Massimo A1 - Chaneton, Barbara A1 - Adam, Julie A1 - Hedley, Ann A1 - Kalna, Gabriela A1 - Tomlinson, Ian P M A1 - Pollard, Patrick J A1 - Watson, Dave G A1 - Deberardinis, Ralph J A1 - Shlomi, Tomer A1 - Ruppin, Eytan A1 - Gottlieb, Eyal KW - Animals KW - Bilirubin KW - Cell Line KW - Cells, Cultured KW - Citric Acid Cycle KW - Computer simulation KW - Fumarate Hydratase KW - Fumarates KW - Genes, Lethal KW - Genes, Tumor Suppressor KW - Glutamine KW - Heme KW - Heme Oxygenase (Decyclizing) KW - Kidney Neoplasms KW - Leiomyomatosis KW - Mice KW - Mitochondria KW - Mutation KW - NAD KW - Neoplastic Syndromes, Hereditary KW - Skin Neoplasms KW - Uterine Neoplasms AB -

Fumarate hydratase (FH) is an enzyme of the tricarboxylic acid cycle (TCA cycle) that catalyses the hydration of fumarate into malate. Germline mutations of FH are responsible for hereditary leiomyomatosis and renal-cell cancer (HLRCC). It has previously been demonstrated that the absence of FH leads to the accumulation of fumarate, which activates hypoxia-inducible factors (HIFs) at normal oxygen tensions. However, so far no mechanism that explains the ability of cells to survive without a functional TCA cycle has been provided. Here we use newly characterized genetically modified kidney mouse cells in which Fh1 has been deleted, and apply a newly developed computer model of the metabolism of these cells to predict and experimentally validate a linear metabolic pathway beginning with glutamine uptake and ending with bilirubin excretion from Fh1-deficient cells. This pathway, which involves the biosynthesis and degradation of haem, enables Fh1-deficient cells to use the accumulated TCA cycle metabolites and permits partial mitochondrial NADH production. We predicted and confirmed that targeting this pathway would render Fh1-deficient cells non-viable, while sparing wild-type Fh1-containing cells. This work goes beyond identifying a metabolic pathway that is induced in Fh1-deficient cells to demonstrate that inhibition of haem oxygenation is synthetically lethal when combined with Fh1 deficiency, providing a new potential target for treating HLRCC patients.

VL - 477 CP - 7363 M3 - 10.1038/nature10363 ER - TY - JOUR T1 - Identification of Schistosoma mansoni microRNAs. JF - BMC Genomics Y1 - 2011 A1 - Simões, Mariana C A1 - Lee, Jonathan A1 - Djikeng, Appolinaire A1 - Cerqueira, Gustavo C A1 - Zerlotini, Adhemar A1 - da Silva-Pereira, Rosiane A A1 - Dalby, Andrew R A1 - LoVerde, Philip A1 - El-Sayed, Najib M A1 - Oliveira, Guilherme KW - Animals KW - Computational Biology KW - Genome, Helminth KW - MicroRNAs KW - Schistosoma mansoni AB -

BACKGROUND: MicroRNAs (miRNAs) constitute a class of single-stranded RNAs which play a crucial role in regulating development and controlling gene expression by targeting mRNAs and triggering either translation repression or messenger RNA (mRNA) degradation. miRNAs are widespread in eukaryotes and to date over 14,000 miRNAs have been identified by computational and experimental approaches. Several miRNAs are highly conserved across species. In Schistosoma, the full set of miRNAs and their expression patterns during development remain poorly understood. Here we report on the development and implementation of a homology-based detection strategy to search for miRNA genes in Schistosoma mansoni. In addition, we report results on the experimental detection of miRNAs by means of cDNA cloning and sequencing of size-fractionated RNA samples.

RESULTS: Homology search using the high-throughput pipeline was performed with all known miRNAs in miRBase. A total of 6,211 mature miRNAs were used as reference sequences and 110 unique S. mansoni sequences were returned by BLASTn analysis. The existing mature miRNAs that produced these hits are reported, as well as the locations of the homologous sequences in the S. mansoni genome. All BLAST hits aligned with at least 95% of the miRNA sequence, resulting in alignment lengths of 19-24 nt. Following several filtering steps, 15 potential miRNA candidates were identified using this approach. By sequencing small RNA cDNA libraries from adult worm pairs, we identified 211 novel miRNA candidates in the S. mansoni genome. Northern blot analysis was used to detect the expression of the 30 most frequent sequenced miRNAs and to compare the expression level of these miRNAs between the lung stage schistosomula and adult worm stages. Expression of 11 novel miRNAs was confirmed by northern blot analysis and some presented a stage-regulated expression pattern. Three miRNAs previously identified from S. japonicum were also present in S. mansoni.

CONCLUSION: Evidence for the presence of miRNAs in S. mansoni is presented. The number of miRNAs detected by homology-based computational methods in S. mansoni is limited due to the lack of close relatives in the miRNA repository. In spite of this, the computational approach described here can likely be applied to the identification of pre-miRNA hairpins in other organisms. Construction and analysis of a small RNA library led to the experimental identification of 14 novel miRNAs from S. mansoni through a combination of molecular cloning, DNA sequencing and expression studies. Our results significantly expand the set of known miRNAs in multicellular parasites and provide a basis for understanding the structural and functional evolution of miRNAs in these metazoan parasites.

VL - 12 M3 - 10.1186/1471-2164-12-47 ER - TY - JOUR T1 - The Importance of Chitin in the Marine Environment JF - Marine BiotechnologyMarine Biotechnology Y1 - 2011 A1 - Souza, C. P. A1 - Almeida, B. C. A1 - Rita R. Colwell A1 - Rivera, I. N. G. AB - Chitin is the most abundant renewable polymer in the oceans and is an important source of carbon and nitrogen for marine organisms. The process of chitin degradation is a key step in the cycling of nutrients in the oceans and chitinolytic bacteria play a significant role in this process. These bacteria are autochthonous to both marine and freshwater ecosystems and produce chitinases that degrade chitin, an insoluble polysaccharide, to a biologically useful form. In this brief review, a description of the structure of chitin and diversity of chitinolytic bacteria in the oceans is provided, in the context of the significance of chitin degradation for marine life. ER - TY - JOUR T1 - Increased gene sampling provides stronger support for higher-level groups within gracillariid leaf mining moths and relatives (Lepidoptera: Gracillariidae) JF - BMC Evol BiolBMC Evol Biol Y1 - 2011 A1 - Kawahara, A. Y. A1 - Ohshima, I. A1 - Kawakita, A. A1 - Regier, J. C. A1 - Mitter, C. A1 - Michael P. Cummings A1 - Davis, D. R. A1 - Wagner, D. L. A1 - De Prinis, J. A1 - Lopez-Vaamonde, C. VL - 11:182 ER - TY - JOUR T1 - Increased gene sampling yields robust support for higher‐level clades within Bombycoidea (Lepidoptera) JF - Systematic EntomologySystematic Entomology Y1 - 2011 A1 - Zwick, Andreas A1 - Regier, Jerome C. A1 - Mitter, Charles A1 - Michael P. Cummings AB - This study has as its primary aim the robust resolution of higher-level relationships within the lepidopteran superfamily Bombycoidea. Our study builds on an earlier analysis of five genes (∼6.6 kbp) sequenced for 50 taxa from Bombycoidea and its sister group Lasiocampidae, plus representatives of other macrolepidoteran superfamilies. The earlier study failed to yield strong support for the monophyly of and basal splits within Bombycoidea, among others. Therefore, in an effort to increase support specifically for higher-level nodes, we generated 11.7 kbp of additional data from 20 genes for 24 of 50 bombycoid and lasiocampid taxa. The data from the genes are all derived from protein-coding nuclear genes previously used to resolve other lepidopteran relationships. With these additional data, all but a few higher-level nodes are strongly supported. Given our decision to minimize project costs by augmenting genes for only 24 of the 50 taxa, we explored whether the resulting pattern of missing data in the combined-gene matrix introduced a nonphylogenetic bias, a possibility reported by others. This was achieved by comparing node support values (i.e. nonparametric bootstrap values) based on likelihood and parsimony analyses of three datasets that differ in their number of taxa and level of missing data: 50 taxa/5 genes (dataset A), 50 taxa/25 genes (dataset B) and 24 taxa/25 genes (dataset C). Whereas datasets B and C provided similar results for common nodes, both frequently yielded higher node support relative to dataset A, arguing that: (i) more data yield increased node support and (ii) partial gene augmentation does not introduce an obvious nonphylogenetic bias. A comparison of single-gene bootstrap analyses identified four nodes for which one or two of the 25 genes provided modest to strong support for a grouping not recovered by the combined-gene result. As a summary proposal, two of these four groupings (one each within Bombycoidea and Lasiocampidae) were deemed sufficiently problematic to regard them as unresolved trichotomies. Since the alternative groupings were always highly localized on the tree, we did not judge a combined-gene analysis to present a problem outside those regions. Based on our robustly resolved results, we have revised the classification of Bombycoidea: the family Bombycidae is restricted to its nominate subfamily, and its tribe Epiini is elevated to subfamily rank (Epiinae stat.rev.), whereas the bombycid subfamily Phiditiinae is reinstated as a separate family (Phiditiidae stat.rev.). The bombycid subfamilies Oberthueriinae Kuznetzov & Stekolnikov, 1985, syn.nov. and Prismostictinae Forbes, 1955, syn.nov., and the family Mirinidae Kozlov, 1985, syn.nov. are established as subjective junior synonyms of Endromidae Boisduval, 1828. The family Anthelidae (Lasiocampoidea) is reincluded in the superfamily Bombycoidea. VL - 36 SN - 1365-3113 ER - TY - JOUR T1 - Interaction of Vibrio cholerae non-O1/non-O139 with Copepods, Cladocerans and Competing Bacteria in the Large Alkaline Lake Neusiedler See, Austria JF - Microbial ecologyMicrobial ecology Y1 - 2011 A1 - Kirschner, A. K. T. A1 - Schauer, S. A1 - Steinberger, B. A1 - Wilhartitz, I. A1 - Grim, C. J. A1 - Huq, A. A1 - Rita R. Colwell A1 - Herzig, A. A1 - Sommer, R. AB - Vibrio cholerae is a human pathogen and natural inhabitant of aquatic environments. Serogroups O1/O139 have been associated with epidemic cholera, while non-O1/non-O139 serogroups usually cause human disease other than classical cholera. V. cholerae non-O1/non-O139 from the Neusiedler See, a large Central European lake, have caused ear and wound infections, including one case of fatal septicaemia. Recent investigations demonstrated rapid planktonic growth of V. cholerae non-O1/non-O139 and correlation with zooplankton biomass. The aim of this study was to elucidate the interaction of autochthonous V. cholerae with two dominant crustacean zooplankton species in the lake and investigate the influence of the natural bacterial community on this interaction. An existing data set was evaluated for statistical relationships between zooplankton species and V. cholerae and co-culture experiments were performed in the laboratory. A new fluorescence in situ hybridisation protocol was applied for quantification of V. cholerae non-O1/non-O139 cells, which significantly reduced analysis time. The experiments clearly demonstrated a significant relationship of autochthonous V. cholerae non-O1/non-O139 with cladocerans by promoting growth of V. cholerae non-O1/non-O139 in the water and on the surfaces of the cladocerans. In contrast, copepods had a negative effect on the growth of V. cholerae non-O1/non-O139 via competing bacteria from their surfaces. Thus, beside other known factors, biofilm formation by V. cholerae on crustacean zooplankton appears to be zooplankton taxon specific and may be controlled by the natural bacterial community. VL - 61 ER - TY - JOUR T1 - Long-term effects of ocean warming on the prokaryotic community: evidence from the vibrios JF - The ISME JournalThe ISME journal Y1 - 2011 A1 - Vezzulli, Luigi A1 - Brettar, Ingrid A1 - Pezzati, Elisabetta A1 - Reid, Philip C. A1 - Rita R. Colwell A1 - Höfle, Manfred G. A1 - Pruzzo, Carla KW - ecophysiology KW - ecosystems KW - environmental biotechnology KW - geomicrobiology KW - ISME J KW - microbe interactions KW - microbial communities KW - microbial ecology KW - microbial engineering KW - microbial epidemiology KW - microbial genomics KW - microorganisms AB - The long-term effects of ocean warming on prokaryotic communities are unknown because of lack of historical data. We overcame this gap by applying a retrospective molecular analysis to the bacterial community on formalin-fixed samples from the historical Continuous Plankton Recorder archive, which is one of the longest and most geographically extensive collections of marine biological samples in the world. We showed that during the last half century, ubiquitous marine bacteria of the Vibrio genus, including Vibrio cholerae, increased in dominance within the plankton-associated bacterial community of the North Sea, where an unprecedented increase in bathing infections related to these bacteria was recently reported. Among environmental variables, increased sea surface temperature explained 45% of the variance in Vibrio data, supporting the view that ocean warming is favouring the spread of vibrios and may be the cause of the globally increasing trend in their associated diseases. VL - 6 SN - 1751-7362 ER - TY - Generic T1 - MDMap: A system for data-driven layout and exploration of molecular dynamics simulations T2 - Biological Data Visualization (BioVis), 2011 IEEE Symposium on Y1 - 2011 A1 - Patro, R. A1 - Ip, Cheuk Yiu A1 - Bista, S. A1 - Cho, S. S. A1 - Thirumalai, D. A1 - Varshney, Amitabh KW - Biology KW - biomolecular KW - computing KW - data KW - digital KW - driven KW - DYNAMICS KW - exploration KW - folding KW - graph KW - landscapes KW - Layout KW - MDMap KW - method KW - molecular KW - processes KW - simulation KW - Simulations KW - space KW - state KW - Stochastic KW - THEORY KW - time-varying KW - Trajectory KW - transition AB - Contemporary molecular dynamics simulations result in a glut of simulation data, making analysis and discovery a difficult and burdensome task. We present MDMap, a system designed to summarize long-running molecular dynamics (MD) simulations. We represent a molecular dynamics simulation as a state transition graph over a set of intermediate (stable and semi-stable) states. The transitions amongst the states together with their frequencies represent the flow of a biomolecule through the trajectory space. MDMap automatically determines potential intermediate conformations and the transitions amongst them by analyzing the conformational space explored by the MD simulation. MDMap is an automated system to visualize MD simulations as state-transition diagrams, and can replace the current tedious manual layouts of biomolecular folding landscapes with an automated tool. The layout of the representative states and the corresponding transitions among them is presented to the user as a visual synopsis of the long-running MD simulation. We compare and contrast multiple presentations of the state transition diagrams, such as conformational embedding, and spectral, hierarchical, and force-directed graph layouts. We believe this system could provide a road-map for the visualization of other stochastic time-varying simulations in a variety of different domains. JA - Biological Data Visualization (BioVis), 2011 IEEE Symposium on ER - TY - JOUR T1 - Metagenomic 16S rDNA Targeted PCR-DGGE in Determining Bacterial Diversity in Aquatic Ecosystem JF - Bangladesh Journal of MicrobiologyBangladesh Journal of Microbiology Y1 - 2011 A1 - Hasan, Nur A. A1 - Chowdhury, W. Bari A1 - Rahim, Niaz A1 - Sultana, Marzia A1 - Shabnam, S. Antara A1 - Mai, Volker A1 - Ali, Afsar A1 - Morris, Glen J. A1 - Sack, R. Bradley A1 - Huq, Anwar A1 - Rita R. Colwell A1 - Endtz, Hubert Ph A1 - Cravioto, Alejandro A1 - Alam, Munirul AB - Bacterial numbers in surface water samples, collected randomly from six different water bodies, were estimated by acridine orange direct counting (AODC) and conventional culture-based heterotrophic plate counting (HPC). Bacterial genomic DNA was prepared from water samples by employing methods used for stool samples, including the population dynamics, were determined by primer extension of the 16S rDNA (V6/V8 region) using polymerase chain reaction (PCR), followed by denaturing gradient gel electrophoresis (DGGE), a metagenomic tool that is capable of separating unrelated DNAs based on the differences in their sequences and GC contents. The bacterial numbers in water samples ranged from 103 – 106 CFU/ mL for HPC and 104 – 107 cells/ mL for AODC, showing that a great majority of bacteria prevail as uncultivable which do not respond to culture methods that are used widely for tracking bacterial pathogens. The acridine orange-stained bacteria varied in sizes and shapes, and appeared either as planktonic (solitary) cells or as clusters of biofilms, showing the presence of diverse community under the epifluorescence microscope. The DGGE of the ca. 457 bp amplicons, as confirmed by agarose gel electrophoresis, produced bands that ranged in intensities and numbers from 18 to 31, with each band possibly indicating the presence of one or more closely related bacterial species. The enrichment of pathogenic bacteria in the aquatic ecosystem is known to precede the seasonal diarrhoeal outbreaks; therefore, bacterial community dynamics determined by Metagenomic 16S PCR-DGGE during pre-epidemic enrichment appears promising in predicting the upcoming diarrheal outbreaks. VL - 27 SN - 1011-9981 ER - TY - JOUR T1 - Population Dynamics of Vibrio Cholerae and Cholera in the Bangladesh Sundarbans: Role of Zooplankton Diversity JF - Applied and Environmental MicrobiologyAppl. Environ. Microbiol.Applied and Environmental MicrobiologyAppl. Environ. Microbiol. Y1 - 2011 A1 - De Magny, Guillaume Constantin A1 - Mozumder, Pronob K. A1 - Grim, Christopher J. A1 - Hasan, Nur A. A1 - Naser, M. Niamul A1 - Alam, Munirul A1 - Sack, Bradley A1 - Huq, Anwar A1 - Rita R. Colwell AB - Vibrio cholerae, a bacterium autochthonous to the aquatic environment, is the causative agent of cholera, a severe watery, life-threatening diarrhoeal disease occurring predominantly in developing countries. V. cholerae, including both serogroup O1 and O139, i.e. found in association with crustacean zooplankton, mainly copepods, and notably in ponds, rivers, and estuarine systems globally. The incidence of cholera and occurrence of V. cholerae pathogenic strains with zooplankton were studied in two areas of Bangladesh: Bakerganj and Mathbaria. Chitinous zooplankton communities of several bodies of water were analyzed in order to understand the interaction of zooplankton population composition with the population dynamics of pathogenic V. cholerae and incidence of cholera. Two dominant zooplankton groups were found to be consistently associated with detection of V. cholerae and/or occurrence of cholera cases, namely rotifers, and cladocerans, in addition to copepods. Local differences indicate there are subtle ecological factors that can influence interactions between V. cholerae, its plankton hosts, and the incidence of cholera. SN - 0099-2240, 1098-5336 ER - TY - JOUR T1 - Role of Zooplankton Diversity in Vibrio Cholerae Population Dynamics and in the Incidence of Cholera in the Bangladesh Sundarbans JF - Applied and Environmental MicrobiologyAppl. Environ. Microbiol.Applied and Environmental MicrobiologyAppl. Environ. Microbiol. Y1 - 2011 A1 - De Magny, Guillaume Constantin A1 - Mozumder, Pronob K. A1 - Grim, Christopher J. A1 - Hasan, Nur A. A1 - Naser, M. Niamul A1 - Alam, Munirul A1 - Sack, R. Bradley A1 - Huq, Anwar A1 - Rita R. Colwell AB - Vibrio cholerae, a bacterium autochthonous to the aquatic environment, is the causative agent of cholera, a severe watery, life-threatening diarrheal disease occurring predominantly in developing countries. V. cholerae, including both serogroups O1 and O139, is found in association with crustacean zooplankton, mainly copepods, and notably in ponds, rivers, and estuarine systems globally. The incidence of cholera and occurrence of pathogenic V. cholerae strains with zooplankton were studied in two areas of Bangladesh: Bakerganj and Mathbaria. Chitinous zooplankton communities of several bodies of water were analyzed in order to understand the interaction of the zooplankton population composition with the population dynamics of pathogenic V. cholerae and incidence of cholera. Two dominant zooplankton groups were found to be consistently associated with detection of V. cholerae and/or occurrence of cholera cases, namely, rotifers and cladocerans, in addition to copepods. Local differences indicate there are subtle ecological factors that can influence interactions between V. cholerae, its plankton hosts, and the incidence of cholera. VL - 77 SN - 0099-2240, 1098-5336 ER - TY - JOUR T1 - Temperature regulation of virulence factors in the pathogen Vibrio coralliilyticus JF - The ISME JournalThe ISME journal Y1 - 2011 A1 - Kimes, Nikole E. A1 - Grim, Christopher J. A1 - Johnson, Wesley R. A1 - Hasan, Nur A. A1 - Tall, Ben D. A1 - Kothary, Mahendra H. A1 - Kiss, Hajnalka A1 - Munk, A. Christine A1 - Tapia, Roxanne A1 - Green, Lance A1 - Detter, Chris A1 - Bruce, David C. A1 - Brettin, Thomas S. A1 - Rita R. Colwell A1 - Morris, Pamela J. KW - ecophysiology KW - ecosystems KW - environmental biotechnology KW - geomicrobiology KW - ISME J KW - microbe interactions KW - microbial communities KW - microbial ecology KW - microbial engineering KW - microbial epidemiology KW - microbial genomics KW - microorganisms AB - Sea surface temperatures (SST) are rising because of global climate change. As a result, pathogenic Vibrio species that infect humans and marine organisms during warmer summer months are of growing concern. Coral reefs, in particular, are already experiencing unprecedented degradation worldwide due in part to infectious disease outbreaks and bleaching episodes that are exacerbated by increasing SST. For example, Vibrio coralliilyticus, a globally distributed bacterium associated with multiple coral diseases, infects corals at temperatures above 27 °C. The mechanisms underlying this temperature-dependent pathogenicity, however, are unknown. In this study, we identify potential virulence mechanisms using whole genome sequencing of V. coralliilyticus ATCC (American Type Culture Collection) BAA-450. Furthermore, we demonstrate direct temperature regulation of numerous virulence factors using proteomic analysis and bioassays. Virulence factors involved in motility, host degradation, secretion, antimicrobial resistance and transcriptional regulation are upregulated at the higher virulent temperature of 27 °C, concurrent with phenotypic changes in motility, antibiotic resistance, hemolysis, cytotoxicity and bioluminescence. These results provide evidence that temperature regulates multiple virulence mechanisms in V. coralliilyticus, independent of abundance. The ecological and biological significance of this temperature-dependent virulence response is reinforced by climate change models that predict tropical SST to consistently exceed 27 °C during the spring, summer and fall seasons. We propose V. coralliilyticus as a model Gram-negative bacterium to study temperature-dependent pathogenicity in Vibrio-related diseases. VL - 6 SN - 1751-7362 ER - TY - JOUR T1 - Vibrio Cholerae O1 Detection in Estuarine and Coastal Zooplankton JF - Journal of Plankton ResearchJ. Plankton Res.Journal of Plankton ResearchJ. Plankton Res. Y1 - 2011 A1 - Martinelli Filho, José E. A1 - Lopes, Rubens M. A1 - Rivera, Irma N. G. A1 - Rita R. Colwell KW - DFA KW - estuary KW - plankton KW - Southwest Atlantic AB - Vibrio cholerae is an autochthonous marine bacterium, and its association with diverse planktonic crustaceans has been extensively investigated; however, the presence of V. cholerae on individuals of most phyla of planktonic animals is still incompletely understood. The objective of this study was to analyze the distribution of V. cholerae serogroup O1 associated with specific zooplankton taxa in an estuary and the adjacent continental shelf of the southeastern Brazilian coast. The occurrence of the bacterium was assessed in zooplankton samples, specifically on the most abundant taxa, using direct fluorescence assay (DFA) and direct viable count–direct fluorescence assay (DVC–DFA) methods. Vibrio cholerae O1 was detected in 88% of samples collected from the Santos-Bertioga estuary and in 67% of samples from the shelf. The salinity of the estuarine water ranged from 21.8 to 34.6, significantly lower than the shelf water which was 32.1–36.1. Salinity was the only environmental variable measured that displayed a significant correlation with the presence of V. cholerae (P< 0.05). Vibrio cholerae O1 was detected in chaetognaths, pluteus larvae of echinoderms and planktonic fish eggs (Engraulidae), all new sites for this bacterium. VL - 33 SN - 0142-7873, 1464-3774 ER - TY - JOUR T1 - Warming Oceans, Phytoplankton, and River Discharge: Implications for Cholera Outbreaks JF - The American Journal of Tropical Medicine and HygieneAm J Trop Med HygThe American Journal of Tropical Medicine and HygieneAm J Trop Med Hyg Y1 - 2011 A1 - Jutla, Antarpreet S. A1 - Akanda, Ali S. A1 - Griffiths, Jeffrey K. A1 - Rita R. Colwell A1 - Islam, Shafiqul AB - Phytoplankton abundance is inversely related to sea surface temperature (SST). However, a positive relationship is observed between SST and phytoplankton abundance in coastal waters of Bay of Bengal. This has led to an assertion that in a warming climate, rise in SST may increase phytoplankton blooms and, therefore, cholera outbreaks. Here, we explain why a positive SST-phytoplankton relationship exists in the Bay of Bengal and the implications of such a relationship on cholera dynamics. We found clear evidence of two independent physical drivers for phytoplankton abundance. The first one is the widely accepted phytoplankton blooming produced by the upwelling of cold, nutrient-rich deep ocean waters. The second, which explains the Bay of Bengal findings, is coastal phytoplankton blooming during high river discharges with terrestrial nutrients. Causal mechanisms should be understood when associating SST with phytoplankton and subsequent cholera outbreaks in regions where freshwater discharge are a predominant mechanism for phytoplankton production. VL - 85 SN - 0002-9637 ER - TY - JOUR T1 - Broader incorporation of bioinformatics in education: opportunities and challenges JF - Brief BioinformBrief Bioinform Y1 - 2010 A1 - Michael P. Cummings A1 - Temple, G. G. AB - The major opportunities for broader incorporation of bioinformatics in education can be placed into three general categories: general applicability of bioinformatics in life science and related curricula; inherent fit of bioinformatics for promoting student learning in most biology programs; and the general experience and associated comfort students have with computers and technology. Conversely, the major challenges for broader incorporation of bioinformatics in education can be placed into three general categories: required infrastructure and logistics; instructor knowledge of bioinformatics and continuing education; and the breadth of bioinformatics, and the diversity of students and educational objectives. Broader incorporation of bioinformatics at all education levels requires overcoming the challenges to using transformative computer- requiring learning activities, assisting faculty in collecting assessment data on mastery of student learning outcomes, as well as creating more faculty development opportunities that span diverse skill levels, with an emphasis placed on providing resource materials that are kept up-to-date as the field and tools change. VL - 11 ER - TY - JOUR T1 - Comparative genomic analysis reveals evidence of two novel Vibrio species closely related to V. cholerae JF - BMC MicrobiologyBMC Microbiology Y1 - 2010 A1 - Bradd, H. A1 - Christopher, G. A1 - Nur, H. A1 - Seon-Young, C. A1 - Jongsik, C. A1 - Thomas, B. A1 - David, B. A1 - Jean, C. A1 - Chris, D. J. A1 - Cliff, H. A1 - Rita R. Colwell AB - In recent years genome sequencing has been used to characterize new bacterial species, a method of analysis available as a result of improved methodology and reduced cost. Included in a constantly expanding list of Vibrio species are several that have been reclassified as novel members of the Vibrionaceae. The description of two putative new Vibrio species, Vibrio sp. RC341 and Vibrio sp. RC586 for which we propose the names V. metecus and V. parilis, respectively, previously characterized as non-toxigenic environmental variants of V. cholerae is presented in this study. Results Based on results of whole-genome average nucleotide identity (ANI), average amino acid identity (AAI), rpoB similarity, MLSA, and phylogenetic analysis, the new species are concluded to be phylogenetically closely related to V. cholerae and V. mimicus. Vibrio sp. RC341 and Vibrio sp. RC586 demonstrate features characteristic of V. cholerae and V. mimicus, respectively, on differential and selective media, but their genomes show a 12 to 15% divergence (88 to 85% ANI and 92 to 91% AAI) compared to the sequences of V. cholerae and V. mimicus genomes (ANI <95% and AAI <96% indicative of separate species). Vibrio sp. RC341 and Vibrio sp. RC586 share 2104 ORFs (59%) and 2058 ORFs (56%) with the published core genome of V. cholerae and 2956 (82%) and 3048 ORFs (84%) with V. mimicus MB-451, respectively. The novel species share 2926 ORFs with each other (81% Vibrio sp. RC341 and 81% Vibrio sp. RC586). Virulence-associated factors and genomic islands of V. cholerae and V. mimicus, including VSP-I and II, were found in these environmental Vibrio spp. Conclusions Results of this analysis demonstrate these two environmental vibrios, previously characterized as variant V. cholerae strains, are new species which have evolved from ancestral lineages of the V. cholerae and V. mimicus clade. The presence of conserved integration loci for genomic islands as well as evidence of horizontal gene transfer between these two new species, V. cholerae, and V. mimicus suggests genomic islands and virulence factors are transferred between these species. VL - 10 ER - TY - JOUR T1 - Comparative Genomics of Clinical and Environmental Vibrio Mimicus JF - Proceedings of the National Academy of SciencesPNASProceedings of the National Academy of SciencesPNAS Y1 - 2010 A1 - Hasan, Nur A. A1 - Grim, Christopher J. A1 - Haley, Bradd J. A1 - Jongsik, Chun A1 - Alam, Munirul A1 - Taviani, Elisa A1 - Mozammel, Hoq A1 - Munk, A. Christine A1 - Rita R. Colwell AB - Whether Vibrio mimicus is a variant of Vibrio cholerae or a separate species has been the subject of taxonomic controversy. A genomic analysis was undertaken to resolve the issue. The genomes of V. mimicus MB451, a clinical isolate, and VM223, an environmental isolate, comprise ca. 4,347,971 and 4,313,453 bp and encode 3,802 and 3,290 ORFs, respectively. As in other vibrios, chromosome I (C-I) predominantly contains genes necessary for growth and viability, whereas chromosome II (C-II) bears genes for adaptation to environmental change. C-I harbors many virulence genes, including some not previously reported in V. mimicus, such as mannose-sensitive hemagglutinin (MSHA), and enterotoxigenic hemolysin (HlyA); C-II encodes a variant of Vibrio pathogenicity island 2 (VPI-2), and Vibrio seventh pandemic island II (VSP-II) cluster of genes. Extensive genomic rearrangement in C-II indicates it is a hot spot for evolution and genesis of speciation for the genus Vibrio. The number of virulence regions discovered in this study (VSP-II, MSHA, HlyA, type IV pilin, PilE, and integron integrase, IntI4) with no notable difference in potential virulence genes between clinical and environmental strains suggests these genes also may play a role in the environment and that pathogenic strains may arise in the environment. Significant genome synteny with prototypic pre-seventh pandemic strains of V. cholerae was observed, and the results of phylogenetic analysis support the hypothesis that, in the course of evolution, V. mimicus and V. cholerae diverged from a common ancestor with a prototypic sixth pandemic genomic backbone. VL - 107 SN - 0027-8424, 1091-6490 ER - TY - JOUR T1 - Computational Approaches for Genome Assembly Validation JF - Biological Data MiningBiological Data Mining Y1 - 2010 A1 - Choi, J. H. A1 - Tang, H. A1 - Kim, S. A1 - M. Pop ER - TY - JOUR T1 - Conversion of viable but nonculturable Vibrio cholerae to the culturable state by co‐culture with eukaryotic cells JF - Microbiology and ImmunologyMicrobiology and Immunology Y1 - 2010 A1 - Senoh, Mitsutoshi A1 - Ghosh‐Banerjee, Jayeeta A1 - Ramamurthy, Thandavarayan A1 - Hamabata, Takashi A1 - Kurakawa, Takashi A1 - Takeda, Makoto A1 - Rita R. Colwell A1 - Nair, G. Balakrish A1 - Takeda, Yoshifumi KW - conversion to culturability KW - co‐culture KW - eukaryotic cell KW - viable but nonculturable (VBNC) Vibrio cholerae AB - VBNC Vibrio cholerae O139 VC-280 obtained by incubation in 1% solution of artificial sea water IO at 4°C for 74 days converted to the culturable state when co-cultured with CHO cells. Other eukaryotic cell lines, including HT-29, Caco-2, T84, HeLa, and Intestine 407, also supported conversion of VBNC cells to the culturable state. Conversion of VBNC V. cholerae O1 N16961 and V. cholerae O139 VC-280/pG13 to the culturable state, under the same conditions, was also confirmed. When VBNC V. cholerae O139 VC-280 was incubated in 1% IO at 4°C for up to 91 days, the number of cells converted by co-culture with CHO cells declined with each additional day of incubation and after 91 days conversion was not observed. VL - 54 SN - 1348-0421 ER - TY - JOUR T1 - Discovery of novel Vibrio cholerae VSP‐II genomic islands using comparative genomic analysis JF - FEMS Microbiology LettersFEMS Microbiology Letters Y1 - 2010 A1 - Taviani, Elisa A1 - Grim, Christopher J. A1 - Choi, Jinna A1 - Jongsik, Chun A1 - Haley, Bradd A1 - Hasan, Nur A. A1 - Huq, Anwar A1 - Rita R. Colwell KW - Vibrio cholerae KW - Vibrio mimicus KW - VPS‐II AB - This report describes Vibrio seventh pandemic island II (VSP-II) and three novel variants revealed by comparative genomics of 23 Vibrio cholerae strains and their presence among a large and diverse collection of V. cholerae isolates. Three VSP-II variants were reported previously and our results demonstrate the presence of three novel VSP-II in clinical and environmental V. cholerae marked by major deletions and genetic rearrangements. A new VSP-II cluster was found in the seventh pandemic V. cholerae O1 El Tor strain CIRS101, which is dominant (95%) among the recent (2004–2007) seven pandemic V. cholerae O1 El Tor isolates from two endemic sites, but was not found in older strains from the same region. Two other variants were found in V. cholerae TMA21 and RC385, two environmental strains from coastal Brazil and the Chesapeake Bay, respectively, the latter being prevalent among environmental V. cholerae non-O1/non-O139 and Vibrio mimicus. The results of this study indicate that the VSP-II island has undergone significant rearrangement through a complex evolutionary pathway in V. cholerae. Interestingly, one of the new VSP-II revealed the presence of ‘old’ and ‘new’V. cholerae O1 El Tor pandemic clones circulating in some of the areas where cholera is endemic. VL - 308 SN - 1574-6968 ER - TY - JOUR T1 - Diversity and distribution of cholix toxin, a novel ADP‐ribosylating factor from Vibrio cholerae JF - Environmental Microbiology ReportsEnvironmental Microbiology Reports Y1 - 2010 A1 - Purdy, Alexandra E. A1 - Balch, Deborah A1 - Lizárraga‐Partida, Marcial Leonardo A1 - Islam, Mohammad Sirajul A1 - Martinez‐Urtaza, Jaime A1 - Huq, Anwar A1 - Rita R. Colwell A1 - Bartlett, Douglas H. AB - Non-toxigenic non-O1, non-O139 Vibrio cholerae strains isolated from both environmental and clinical settings carry a suite of virulence factors aside from cholera toxin. Among V. cholerae strains isolated from coastal waters of southern California, this includes cholix toxin, an ADP-ribosylating factor that is capable of halting protein synthesis in eukaryotic cells. The prevalence of the gene encoding cholix toxin, chxA, was assessed among a collection of 155 diverse V. cholerae strains originating from both clinical and environmental settings in Bangladesh and Mexico and other countries around the globe. The chxA gene was present in 47% of 83 non-O1, non-O139 strains and 16% of 72 O1/O139 strains screened as part of this study. A total of 86 chxA gene sequences were obtained, and phylogenetic analysis revealed that they fall into two distinct clades. These two clades were also observed in the phylogenies of several housekeeping genes, suggesting that the divergence observed in chxA extends to other regions of the V. cholerae genome, and most likely has arisen from vertical descent rather than horizontal transfer. Our results clearly indicate that ChxA is a major toxin of V. cholerae with a worldwide distribution that is preferentially associated with non-pandemic strains. VL - 2 SN - 1758-2229 ER - TY - JOUR T1 - Effect on Human Cells of Environmental Vibrio Parahaemolyticus Strains Carrying Type III Secretion System 2 JF - Infection and ImmunityInfect. Immun.Infection and ImmunityInfect. Immun. Y1 - 2010 A1 - Caburlotto, Greta A1 - Lleò, Maria M. A1 - Hilton, Tamara A1 - Huq, Anwar A1 - Rita R. Colwell A1 - Kaper, James B. AB - Vibrio parahaemolyticus is an inhabitant of estuarine and marine environments that causes seafood-borne gastroenteritis worldwide. Recently, a type 3 secretion system (T3SS2) able to secrete and translocate virulence factors into the eukaryotic cell has been identified in a pathogenicity island (VP-PAI) located on the smaller chromosome. These virulence-related genes have previously been detected only in clinical strains. Classical virulence genes for this species (tdh, trh) are rarely detected in environmental strains, which are usually considered to lack virulence potential. However, during screening of a collection of environmental V. parahaemolyticus isolates obtained in the North Adriatic Sea in Italy, a number of marine strains carrying virulence-related genes, including genes involved in the T3SS2, were detected. In this study, we investigated the pathogenic potential of these marine V. parahaemolyticus strains by studying their adherence ability, their cytotoxicity, their effect on zonula occludin protein 1 (ZO-1) of the tight junctions, and their effect on transepithelial resistance (TER) in infected Caco-2 cells. By performing a reverse transcription-PCR, we also tested the expression of the T3SS2 genes vopT and vopB2, encoding an effector and a translocon protein, respectively. Our results indicate that, similarly to clinical strains, marine V. parahaemolyticus strains carrying vopT and vopB2 and that other genes included in the VP-PAI are capable of adhering to human cells and of causing cytoskeletal disruption and loss of membrane integrity in infected cells. On the basis of data presented here, environmental V. parahaemolyticus strains should be included in coastal water surveillance plans, as they may represent a risk for human health. VL - 78 SN - 0019-9567, 1098-5522 ER - TY - JOUR T1 - Environmental reservoirs of Vibrio cholerae and their role in cholera JF - Environmental Microbiology ReportsEnvironmental Microbiology Reports Y1 - 2010 A1 - Vezzulli, Luigi A1 - Pruzzo, Carla A1 - Huq, Anwar A1 - Rita R. Colwell AB - In the aquatic environment, Vibrio cholerae has been reported to be associated with a variety of living organisms, including animals with an exoskeleton of chitin, aquatic plants, protozoa, bivalves, waterbirds, as well as abiotic substrates (e.g. sediments). Most of these are well-known or putative environmental reservoirs for the bacterium, defined as places where the pathogen lives over time, with the potential to be released and to cause human infection. Environmental reservoirs also serve as V. cholerae disseminators and vectors. They can be responsible for the start of an epidemic, may be critical to cholera endemicity, and affect the evolution of pathogen virulence. To date, in addition to the generally recognized role of zooplankton as the largest environmental reservoir for V. cholerae, other environmental reservoirs play some role in cholera epidemiology by favouring persistence of the pathogen during inter-epidemic periods. Little is known about the ecological factors affecting V. cholerae survival in association with aquatic substrates. Studies aimed at these aspects, i.e. understanding how environmental reservoirs interact, are affected by climate, and contribute to disease epidemiology, will be useful for understanding global implications of V. cholerae and the disease cholera. VL - 2 SN - 1758-2229 ER - TY - CHAP T1 - Evolutionary framework for Lepidoptera model systems T2 - Genetics and Molecular Biology of LepidopteraGenetics and Molecular Biology of Lepidoptera Y1 - 2010 A1 - Roe, A. A1 - Weller, S. A1 - Baixeras, J. A1 - Brown, J. W. A1 - Michael P. Cummings A1 - Davis, D. R. A1 - Horak, M. A1 - Kawahara, A. Y. A1 - Mitter, C. A1 - Parr, C. S. A1 - Regier, J. C. A1 - Rubinoff, D. A1 - Simonsen, T. J. A1 - Wahlberg, N. A1 - Zwick, A. ED - Goldsmith, M. ED - Marec, F. AB - “Model systems” are specific organisms upon which detailed studies have been conducted examining a fundamental biological question. If the studies are robust, their results can be extrapolated among an array of organisms that possess features in common with the subject organism. The true power of model systems lies in the ability to extrapolate these details across larger groups of organisms. In order to generalize these results, comparative studies are essential and require that model systems be placed into their evolutionary or phylogenetic context. This chapter examines model systems in the insect order Lepidoptera from the perspective of several different superfamilies. Historically, many species of Lepidoptera have been essential in the development of invaluable model systems in the fields of development biology, genetics, molecular biology, physiology, co-evolution, population dynamics, and ecology. JA - Genetics and Molecular Biology of LepidopteraGenetics and Molecular Biology of Lepidoptera PB - Taylor & Francis CY - Boca Raton ER - TY - JOUR T1 - Finishing genomes with limited resources: lessons from an ensemble of microbial genomes JF - BMC GenomicsBMC Genomics Y1 - 2010 A1 - Nagarajan, Niranjan A1 - Cook, Christopher A1 - Di Bonaventura, Maria Pia A1 - Ge, Hong A1 - Richards, Allen A1 - Bishop-Lilly, Kimberly A. A1 - DeSalle, Robert A1 - Read, Timothy D. A1 - M. Pop AB - While new sequencing technologies have ushered in an era where microbial genomes can be easily sequenced, the goal of routinely producing high-quality draft and finished genomes in a cost-effective fashion has still remained elusive. Due to shorter read lengths and limitations in library construction protocols, shotgun sequencing and assembly based on these technologies often results in fragmented assemblies. Correspondingly, while draft assemblies can be obtained in days, finishing can take many months and hence the time and effort can only be justified for high-priority genomes and in large sequencing centers. In this work, we revisit this issue in light of our own experience in producing finished and nearly-finished genomes for a range of microbial species in a small-lab setting. These genomes were finished with surprisingly little investments in terms of time, computational effort and lab work, suggesting that the increased access to sequencing might also eventually lead to a greater proportion of finished genomes from small labs and genomics cores. VL - 11 SN - 1471-2164 ER - TY - JOUR T1 - Genome Sequence of Hybrid Vibrio Cholerae O1 MJ-1236, B-33, and CIRS101 and Comparative Genomics with V. Cholerae JF - Journal of BacteriologyJ. Bacteriol.Journal of BacteriologyJ. Bacteriol. Y1 - 2010 A1 - Grim, Christopher J. A1 - Hasan, Nur A. A1 - Taviani, Elisa A1 - Haley, Bradd A1 - Jongsik, Chun A1 - Brettin, Thomas S. A1 - Bruce, David C. A1 - Detter, J. Chris A1 - Han, Cliff S. A1 - Chertkov, Olga A1 - Challacombe, Jean A1 - Huq, Anwar A1 - Nair, G. Balakrish A1 - Rita R. Colwell AB - The genomes of Vibrio cholerae O1 Matlab variant MJ-1236, Mozambique O1 El Tor variant B33, and altered O1 El Tor CIRS101 were sequenced. All three strains were found to belong to the phylocore group 1 clade of V. cholerae, which includes the 7th-pandemic O1 El Tor and serogroup O139 isolates, despite displaying certain characteristics of the classical biotype. All three strains were found to harbor a hybrid variant of CTXΦ and an integrative conjugative element (ICE), leading to their establishment as successful clinical clones and the displacement of prototypical O1 El Tor. The absence of strain- and group-specific genomic islands, some of which appear to be prophages and phage-like elements, seems to be the most likely factor in the recent establishment of dominance of V. cholerae CIRS101 over the other two hybrid strains. VL - 192 SN - 0021-9193, 1098-5530 ER - TY - JOUR T1 - Genome-wide analysis reveals novel genes essential for heme homeostasis in Caenorhabditis elegans. JF - PLoS Genet Y1 - 2010 A1 - Severance, Scott A1 - Rajagopal, Abbhirami A1 - Rao, Anita U A1 - Cerqueira, Gustavo C A1 - Mitreva, Makedonka A1 - El-Sayed, Najib M A1 - Krause, Michael A1 - Hamza, Iqbal KW - Animals KW - Caenorhabditis elegans KW - Dose-Response Relationship, Drug KW - Gene Expression Profiling KW - Gene Expression Regulation KW - genes KW - Genome-Wide Association Study KW - Heme KW - Homeostasis KW - HUMANS KW - Leishmania KW - Nematoda KW - Trypanosoma AB -

Heme is a cofactor in proteins that function in almost all sub-cellular compartments and in many diverse biological processes. Heme is produced by a conserved biosynthetic pathway that is highly regulated to prevent the accumulation of heme--a cytotoxic, hydrophobic tetrapyrrole. Caenorhabditis elegans and related parasitic nematodes do not synthesize heme, but instead require environmental heme to grow and develop. Heme homeostasis in these auxotrophs is, therefore, regulated in accordance with available dietary heme. We have capitalized on this auxotrophy in C. elegans to study gene expression changes associated with precisely controlled dietary heme concentrations. RNA was isolated from cultures containing 4, 20, or 500 microM heme; derived cDNA probes were hybridized to Affymetrix C. elegans expression arrays. We identified 288 heme-responsive genes (hrgs) that were differentially expressed under these conditions. Of these genes, 42% had putative homologs in humans, while genomes of medically relevant heme auxotrophs revealed homologs for 12% in both Trypanosoma and Leishmania and 24% in parasitic nematodes. Depletion of each of the 288 hrgs by RNA-mediated interference (RNAi) in a transgenic heme-sensor worm strain identified six genes that regulated heme homeostasis. In addition, seven membrane-spanning transporters involved in heme uptake were identified by RNAi knockdown studies using a toxic heme analog. Comparison of genes that were positive in both of the RNAi screens resulted in the identification of three genes in common that were vital for organismal heme homeostasis in C. elegans. Collectively, our results provide a catalog of genes that are essential for metazoan heme homeostasis and demonstrate the power of C. elegans as a genetic animal model to dissect the regulatory circuits which mediate heme trafficking in both vertebrate hosts and their parasites, which depend on environmental heme for survival.

VL - 6 CP - 7 M3 - 10.1371/journal.pgen.1001044 ER - TY - JOUR T1 - Genomic characterization of the Yersinia genus JF - Genome BiologyGenome Biology Y1 - 2010 A1 - Chen, Peter E. A1 - Cook, Christopher A1 - Stewart, Andrew C. A1 - Nagarajan, Niranjan A1 - Sommer, Dan D. A1 - M. Pop A1 - Thomason, Brendan A1 - Thomason, Maureen P. K. A1 - Lentz, Shannon A1 - Nolan, Nichole A1 - Sozhamannan, Shanmuga A1 - Sulakvelidze, Alexander A1 - Mateczun, Alfred A1 - Du, Lei A1 - Zwick, Michael E. A1 - Read, Timothy D. AB - New DNA sequencing technologies have enabled detailed comparative genomic analyses of entire genera of bacterial pathogens. Prior to this study, three species of the enterobacterial genus Yersinia that cause invasive human diseases (Yersinia pestis, Yersinia pseudotuberculosis, and Yersinia enterocolitica) had been sequenced. However, there were no genomic data on the Yersinia species with more limited virulence potential, frequently found in soil and water environments. VL - 11 SN - 1465-6906 ER - TY - JOUR T1 - Identification of Pathogenic Vibrio Species by Multilocus PCR-Electrospray Ionization Mass Spectrometry and Its Application to Aquatic Environments of the Former Soviet Republic of Georgia JF - Applied and Environmental MicrobiologyAppl. Environ. Microbiol.Applied and Environmental MicrobiologyAppl. Environ. Microbiol. Y1 - 2010 A1 - Whitehouse, Chris A. A1 - Baldwin, Carson A1 - Sampath, Rangarajan A1 - Blyn, Lawrence B. A1 - Melton, Rachael A1 - Li, Feng A1 - Hall, Thomas A. A1 - Harpin, Vanessa A1 - Matthews, Heather A1 - Tediashvili, Marina A1 - Jaiani, Ekaterina A1 - Kokashvili, Tamar A1 - Janelidze, Nino A1 - Grim, Christopher A1 - Rita R. Colwell A1 - Huq, Anwar AB - The Ibis T5000 is a novel diagnostic platform that couples PCR and mass spectrometry. In this study, we developed an assay that can identify all known pathogenic Vibrio species and field-tested it using natural water samples from both freshwater lakes and the Georgian coastal zone of the Black Sea. Of the 278 total water samples screened, 9 different Vibrio species were detected, 114 (41%) samples were positive for V. cholerae, and 5 (0.8%) samples were positive for the cholera toxin A gene (ctxA). All ctxA-positive samples were from two freshwater lakes, and no ctxA-positive samples from any of the Black Sea sites were detected. VL - 76 SN - 0099-2240, 1098-5336 ER - TY - JOUR T1 - A model for using a concept inventory as a tool for students' assessment and faculty professional development. JF - CBE Life Sci Educ Y1 - 2010 A1 - Marbach-Ad, Gili A1 - McAdams, Katherine C A1 - Benson, Spencer A1 - Briken, Volker A1 - Cathcart, Laura A1 - Chase, Michael A1 - El-Sayed, Najib M A1 - Frauwirth, Kenneth A1 - Fredericksen, Brenda A1 - Joseph, Sam W A1 - Lee, Vincent A1 - McIver, Kevin S A1 - Mosser, David A1 - Quimby, B Booth A1 - Shields, Patricia A1 - Song, Wenxia A1 - Stein, Daniel C A1 - Stewart, Richard A1 - Thompson, Katerina V A1 - Smith, Ann C KW - Curriculum KW - Faculty KW - Models, Theoretical KW - Research KW - Students KW - Teaching AB -

This essay describes how the use of a concept inventory has enhanced professional development and curriculum reform efforts of a faculty teaching community. The Host Pathogen Interactions (HPI) teaching team is composed of research and teaching faculty with expertise in HPI who share the goal of improving the learning experience of students in nine linked undergraduate microbiology courses. To support evidence-based curriculum reform, we administered our HPI Concept Inventory as a pre- and postsurvey to approximately 400 students each year since 2006. The resulting data include student scores as well as their open-ended explanations for distractor choices. The data have enabled us to address curriculum reform goals of 1) reconciling student learning with our expectations, 2) correlating student learning with background variables, 3) understanding student learning across institutions, 4) measuring the effect of teaching techniques on student learning, and 5) demonstrating how our courses collectively form a learning progression. The analysis of the concept inventory data has anchored and deepened the team's discussions of student learning. Reading and discussing students' responses revealed the gap between our understanding and the students' understanding. We provide evidence to support the concept inventory as a tool for assessing student understanding of HPI concepts and faculty development.

VL - 9 CP - 4 M3 - 10.1187/cbe.10-05-0069 ER - TY - JOUR T1 - Occurrence of the Vibrio cholerae seventh pandemic VSP-I island and a new variant JF - OMICS: A Journal of Integrative BiologyOMICS: A Journal of Integrative Biology Y1 - 2010 A1 - Grim, Christopher J. A1 - Choi, Jinna A1 - Jongsik, Chun A1 - Jeon, Yoon-Seong A1 - Taviani, Elisa A1 - Hasan, Nur A. A1 - Haley, Bradd A1 - Huq, Anwar A1 - Rita R. Colwell VL - 14 SN - 1536-2310, 1557-8100 ER - TY - JOUR T1 - The pre‐seventh pandemic Vibrio cholerae BX 330286 El Tor genome: evidence for the environment as a genome reservoir JF - Environmental Microbiology ReportsEnvironmental Microbiology Reports Y1 - 2010 A1 - Haley, Bradd J. A1 - Grim, Christopher J. A1 - Hasan, Nur A. A1 - Taviani, Elisa A1 - Jongsik, Chun A1 - Brettin, Thomas S. A1 - Bruce, David C. A1 - Challacombe, Jean F. A1 - Detter, J. Chris A1 - Han, Cliff S. A1 - Huq, Anwar A1 - Nair, G. Balakrish A1 - Rita R. Colwell AB - Vibrio cholerae O1 El Tor BX 330286 was isolated from a water sample in Australia in 1986, 9 years after an indigenous outbreak of cholera occurred in that region. This environmental strain encodes virulence factors highly similar to those of clinical strains, suggesting an ability to cause disease in humans. We demonstrate its high similarity in gene content and genome-wide nucleotide sequence to clinical V. cholerae strains, notably to pre-seventh pandemic O1 El Tor strains isolated in 1910 (V. cholerae NCTC 8457) and 1937 (V. cholerae MAK 757), as well as seventh pandemic strains isolated after 1960 globally. Here we demonstrate that this strain represents a transitory clone with shared characteristics between pre-seventh and seventh pandemic strains of V. cholerae. Interestingly, this strain was isolated 25 years after the beginning of the seventh pandemic, suggesting the environment as a genome reservoir in areas where cholera does not occur in sporadic, endemic or epidemic form. VL - 2 SN - 1758-2229 ER - TY - JOUR T1 - Serodiversity and ecological distribution of Vibrio parahaemolyticus in the Venetian Lagoon, Northeast Italy JF - Environmental Microbiology ReportsEnvironmental Microbiology Reports Y1 - 2010 A1 - Caburlotto, Greta A1 - Haley, Bradd J. A1 - Lleò, Maria M. A1 - Huq, Anwar A1 - Rita R. Colwell AB - Vibrio parahaemolyticus is a natural inhabitant of estuarine and marine environments constituting part of the autochthonous microflora. This species is associated with human gastroenteritis caused by ingestion of contaminated water and undercooked seafood. During the past several years, the number of V. parahaemolyticus gastroenteritis cases have increased worldwide, causing over half of all food-poisoning outbreaks of bacterial origin. Vibrio populations in water are known to be influenced by environmental factors. Notably, it has been shown that in different parts of the world the distribution of V. parahaemolyticus in the marine environment is related to the water temperature. In this study, we identified environmental determinants affecting distribution of V. parahaemolyticus in the Venetian Lagoon, in the Italian North Adriatic Sea. Data obtained revealed that sea surface temperature constitutes the key factor influencing occurrence of V. parahaemolyticus, but salinity and chlorophyll concentration are also important. Serotyping of a collection of V. parahaemolyticus environmental isolates revealed high serodiversity, with serotypes O3:KUT and O1:KUT, belonging to the ‘pandemic group’, occurring with higher frequency. From our results, we conclude that there is no correlation between serotype and specific geographic site or season of the year. However, certain serotypes were isolated in the Lagoon during the entire 18 months of the study, strongly suggesting persistence in this environment. VL - 2 SN - 1758-2229 ER - TY - JOUR T1 - Validating the systematic position of ıt Plationus Segers, Murugan & Dumont, 1993 (Rotifera: Brachionidae) using sequences of the large subunit of the nuclear ribosomal DNA and of cytochrome C oxidase JF - HydrobiologiaHydrobiologia Y1 - 2010 A1 - Reyna-Fabian, M. E. A1 - Laclette, J. P. A1 - Michael P. Cummings A1 - García-Varela, M. KW - Cox1 KW - likelihood KW - LSU KW - maximum KW - Phylogeny KW - Plationus AB - Members of the family Brachionidae are free-living organisms that range in size from 170 to 250 microns. They comprise part of the zooplankton in freshwater and marine systems worldwide. Morphologically, members of the family are characterized by a single piece loricated body without furrows, grooves, sulci or dorsal head shields, and a malleate trophi. Differences in these structures have been traditionally used to recognize 217 species that are classified into seven genera. However, the validity of the species, Plationus patulus, P. patulus macracanthus P. polyacanthus, and P. felicitas have been confused because they were alternatively assigned in Brachionus or Platyias, when considering only morphological and ecological characters. Based on scanning electron microscope (SEM) images of the trophi, these taxa were assigned in a new genus, Plationus. In this study, we examined the systematic position of P. patulus and P. patulus macracanthus using DNA sequences of two genes: the cytochrome oxidase subunit 1 (cox1) and domains D2 and D3 of the large subunit of the nuclear ribosomal RNA (LSU). In addition, the cox1 and LSU sequences representing five genera of Brachionidae (Anuraeopsis, Brachionus, Keratella, Plationus, and Platyias) plus four species of three families from the order Ploima were used as the outgroup. The maximum likelihood (ML) analyses were conducted for each individual gene as well as for the combined (cox1 + LSU) data set. The ML tree from the combined data set yielded the family Brachionidae as a monophyletic group with weak bootstrap support (< 50%). Five main clades in this tree had high (> 85%) bootstrap support. The first clade was composed of three populations of P. patulus + P. patulus macracanthus. The second clade was composed of a single species of Platyias. The third clade was composed of six species of Brachionus. The fourth clade included a single species of the genus Anuraeopsis, and the fifth clade was composed of three species of the genus Keratella. The genetic divergence between Plationus and Platyias ranged from 18.4 to 19.2% for cox1, and from 4.5 to 4.9% for LSU, and between Brachionus and Plationus, it ranged from 16.9 to 23.1% (cox1), and from 7.3 to 9.1% (LSU). Morphological evidence, the amount of genetic divergence, the systematic position of Plationus within the family Brachionidae, and the position of Plationus as a sister group of Brachionus and Platyias support the validity of Plationus patulus and P. patulus macracanthus into the genus Plationus. VL - 644 ER - TY - JOUR T1 - Analysis of clonally related environmental Vibrio cholerae O1 El Tor isolated before 1992 from Varanasi, India reveals origin of SXT‐ICEs belonging to O139 and O1 serogroups JF - Environmental Microbiology ReportsEnvironmental Microbiology Reports Y1 - 2009 A1 - Mohapatra, Saswat S. A1 - Mantri, Chinmay K. A1 - Mohapatra, Harapriya A1 - Rita R. Colwell A1 - Singh, Durg V. AB - In this study, we report the presence of SXT in environmental Vibrio cholerae O1 El Tor strains isolated before 1992 from Varanasi, India. All isolates, except one, were resistant to Tm, and/or Sul, Sm, Fr, Na and Am. None contained plasmids. PCR and DNA sequencing revealed the presence of SXT containing dfrA1 and/or sulII, strAB in six isolates and dfr18, sulII and strAB in five isolates. Three clinical V. cholerae O1 isolated during 1992 contained the antibiotic resistance gene cassette aadA1 in the class 1 integron. Conjugation experiments, followed by PCR analysis of transconjugants, provided evidence of the transferable nature of SXT and associated antibiotic resistance genes, and its integration into the prfC site. Results of phylogenetic analysis of the intSXT gene of clonally similar V. cholerae showed a clear difference between dfr18+ and dfrA1+V. cholerae O1 isolates. This is the first report of the occurrence of SXT harbouring sulII, strAB, dfr18 and/or dfrA1 genes in environmental V. cholerae O1 isolated prior to 1992 from Varanasi, India, and suggests emergence of SXT+ antibiotic-resistant V. cholerae O139 and O1 from an environmental V. cholerae progenitor by acquisition of SXT and antibiotic-resistant gene clusters. VL - 2 SN - 1758-2229 ER - TY - JOUR T1 - Automated classification of bird and amphibian calls using machine learning: A comparison of methods JF - Ecological Informatics Y1 - 2009 A1 - Acevedo, Miguel A. A1 - Corrada-Bravo, Carlos J. A1 - Corrada-Bravo, Hector A1 - Villanueva-Rivera, Luis J. A1 - Aide, T. Mitchell VL - 4 UR - http://linkinghub.elsevier.com/retrieve/pii/S1574954109000351http://api.elsevier.com/content/article/PII:S1574954109000351?httpAccept=text/xmlhttp://api.elsevier.com/content/article/PII:S1574954109000351?httpAccept=text/plain CP - 4 J1 - Ecological Informatics M3 - 10.1016/j.ecoinf.2009.06.005 ER - TY - JOUR T1 - Biological agent detection technologies JF - Molecular Ecology ResourcesMolecular Ecology Resources Y1 - 2009 A1 - Jakupciak, John P. A1 - Rita R. Colwell KW - barcoding KW - biological agent KW - DETECTION KW - identification KW - sequencing AB - The challenge for first responders, physicians in the emergency room, public health personnel, as well as for food manufacturers, distributors and retailers is accurate and reliable identification of pathogenic agents and their corresponding diseases. This is the weakest point in biological agent detection capability today.There is intense research for new molecular detection technologies that could be used for very accurate detection of pathogens that would be a concern to first responders. These include the need for sensors for multiple applications as varied as understanding the ecology of pathogenic micro-organisms, forensics, environmental sampling for detect-to-treat applications, biological sensors for ‘detect to warn’ in infrastructure protection, responses to reports of ‘suspicious powders’, and customs and borders enforcement, to cite a few examples. The benefits of accurate detection include saving millions of dollars annually by reducing disruption of the workforce and the national economy and improving delivery of correct countermeasures to those who are most in need of the information to provide protective and/or response measures. VL - 9 SN - 1755-0998 ER - TY - JOUR T1 - Comparative genomics reveals mechanism for short-term and long-term clonal transitions in pandemic Vibrio cholerae JF - Proceedings of the National Academy of SciencesProceedings of the National Academy of Sciences Y1 - 2009 A1 - Chun, J. A1 - Grim, C. J. A1 - Hasan, N. A. A1 - Lee, J. H. A1 - Choi, S. Y. A1 - Haley, B. J. A1 - Taviani, E. A1 - Jeon, Y. S. A1 - Kim, D. W. A1 - Lee, J. H. A1 - Rita R. Colwell AB - Vibrio cholerae, the causative agent of cholera, is a bacterium autochthonous to the aquatic environment, and a serious public health threat. V. cholerae serogroup O1 is responsible for the previous two cholera pandemics, in which classical and El Tor biotypes were dominant in the sixth and the current seventh pandemics, respectively. Cholera researchers continually face newly emerging and reemerging pathogenic clones carrying diverse combinations of phenotypic and genotypic properties, which significantly hampered control of the disease. To elucidate evolutionary mechanisms governing genetic diversity of pandemic V. cholerae, we compared the genome sequences of 23 V. cholerae strains isolated from a variety of sources over the past 98 years. The genome-based phylogeny revealed 12 distinct V. cholerae lineages, of which one comprises both O1 classical and El Tor biotypes. All seventh pandemic clones share nearly identical gene content. Using analogy to influenza virology, we define the transition from sixth to seventh pandemic strains as a “shift” between pathogenic clones belonging to the same O1 serogroup, but from significantly different phyletic lineages. In contrast, transition among clones during the present pandemic period is characterized as a “drift” between clones, differentiated mainly by varying composition of laterally transferred genomic islands, resulting in emergence of variants, exemplified by V. cholerae O139 and V. cholerae O1 El Tor hybrid clones. Based on the comparative genomics it is concluded that V. cholerae undergoes extensive genetic recombination via lateral gene transfer, and, therefore, genome assortment, not serogroup, should be used to define pathogenic V. cholerae clones. VL - 106 SN - 0027-8424, 1091-6490 ER - TY - JOUR T1 - Detection of toxigenic Vibrio cholerae O1 in freshwater lakes of the former Soviet Republic of Georgia JF - Environmental Microbiology ReportsEnvironmental Microbiology Reports Y1 - 2009 A1 - Grim, Christopher J. A1 - Jaiani, Ekaterina A1 - Whitehouse, Chris A. A1 - Janelidze, Nino A1 - Kokashvili, Tamuna A1 - Tediashvili, Marina A1 - Rita R. Colwell A1 - Huq, Anwar AB - Three freshwater lakes, Lisi Lake, Kumisi Lake and Tbilisi Sea, near Tbilisi, Georgia, were studied from January 2006 to December 2007 to determine the presence of Vibrio cholerae employing both bacteriological culture method and direct detection methods, namely PCR and direct fluorescent antibody (DFA). For PCR, DNA extracted from water samples was tested for presence of V. cholerae and genes coding for selected virulence factors. Vibrio cholerae non-O1/non-O139 was routinely isolated by culture from all three lakes; whereas V. cholerae O1 and O139 were not. Water samples collected during the summer months from Lisi Lake and Kumisi Lake were positive for both V. cholerae and V. cholerae ctxA, tcpA, zot, ompU and toxR by PCR. Water samples collected during the same period from both Lisi and Kumisi Lake were also positive for V. cholerae serogroup O1 by DFA. All of the samples were negative for V. cholerae serotype O139. The results of this study provide evidence for an environmental presence of toxigenic V. cholerae O1, which may represent a potential source of illness as these lakes serve as recreational water in Tbilisi, Georgia. VL - 2 SN - 1758-2229 ER - TY - JOUR T1 - Determination of relationships among non-toxigenic Vibrio cholerae O1 biotype El Tor strains from housekeeping gene sequences and ribotype patterns JF - Research in MicrobiologyResearch in Microbiology Y1 - 2009 A1 - Mohapatra, Saswat S. A1 - Ramachandran, Dhanya A1 - Mantri, Chinmay K. A1 - Rita R. Colwell A1 - Singh, Durg V. KW - Housekeeping genes KW - Ribotyping KW - sequencing KW - Vibrio cholerae AB - Sequencing of three housekeeping genes, mdh, dnaE and recA, and ribotyping for seven non-toxigenic Vibrio cholerae O1 strains isolated from different geographic sources indicate a phylogenetic relationship among the strains. Results of MLST and ribotyping indicate a clear difference between three toxigenic strains (N16961, O395, and 569B) and three non-toxigenic strains from India (GS1, GS2, and GW87) and one Guam strain (X392), the latter of which were similar in both MLST and ribotyping, while two other non-toxigenic strains from the USA and India (2740-80 and OR69) appeared to be more closely related to toxigenic strains than to non-toxigenic strains, although this was not supported by ribotyping. These results provide clues to the emergence of toxigenic strains from a non-toxigenic progenitor by acquisition of virulence gene clusters. Results of split decomposition analysis suggest that widespread recombination occurs among the three housekeeping genes and that recombination plays an important role in the emergence of toxigenic strains of V. cholerae O1. VL - 160 SN - 0923-2508 ER - TY - JOUR T1 - Diversity and Seasonality of Bioluminescent Vibrio Cholerae Populations in Chesapeake Bay JF - Applied and Environmental MicrobiologyAppl. Environ. Microbiol.Applied and Environmental MicrobiologyAppl. Environ. Microbiol. Y1 - 2009 A1 - Zo, Young-Gun A1 - Chokesajjawatee, Nipa A1 - Grim, Christopher A1 - Arakawa, Eiji A1 - Watanabe, Haruo A1 - Rita R. Colwell AB - Association of luminescence with phenotypic and genotypic traits and with environmental parameters was determined for 278 strains of Vibrio cholerae isolated from the Chesapeake Bay during 1998 to 2000. Three clusters of luminescent strains (A, B, and C) and two nonluminescent clusters (X and Y) were identified among 180 clonal types. V. cholerae O1 strains isolated during pandemics and endemic cholera in the Ganges Delta were related to cluster Y. Heat-stable enterotoxin (encoded by stn) and the membrane protein associated with bile resistance (encoded by ompU) were found to be linked to luminescence in strains of cluster A. Succession from nonluminescent to luminescent populations of V. cholerae occurred during spring to midsummer. Occurrence of cluster A strains in water with neutral pH was contrasted with that of cluster Y strains in water with a pH of >8. Cluster A was found to be associated with a specific calanoid population cooccurring with cyclopoids. Cluster B was related to cluster Y, with its maximal prevalence at pH 8. Occurrence of cluster B strains was more frequent with warmer water temperatures and negatively correlated with maturity of the copepod community. It is concluded that each cluster of luminescent V. cholerae strains occupies a distinct ecological niche. Since the dynamics of these niche-specific subpopulations are associated with zooplankton community composition, the ecology of luminescent V. cholerae is concluded to be related to its interaction with copepods and related crustacean species. VL - 75 SN - 0099-2240, 1098-5336 ER - TY - JOUR T1 - Evidence for Coregulation of Myocardial Gene Expression by MEF2 and NFAT in Human Heart FailureCLINICAL PERSPECTIVE JF - Circulation: Cardiovascular GeneticsCirculation: Cardiovascular Genetics Y1 - 2009 A1 - Putt, M. E. A1 - Sridhar Hannenhalli A1 - Lu, Y. A1 - Haines, P. A1 - Chandrupatla, H. R. A1 - Morrisey, E. E. A1 - Margulies, K. B. A1 - Cappola, T. P. PB - Am Heart Assoc VL - 2 ER - TY - JOUR T1 - Extreme polymorphism in a vaccine antigen and risk of clinical malaria: implications for vaccine development JF - Sci Transl MedSci Transl Med Y1 - 2009 A1 - Takala, S. L. A1 - Coulibaly, D. A1 - Thera, M. A. A1 - Batchelor, A. H. A1 - Michael P. Cummings A1 - Escalante, A. A. A1 - Ouattara, A. A1 - Traoré, K. A1 - Niangaly, A. A1 - Djimdé, A. A. A1 - Doumbo, O. K. A1 - Plowe, C. V. AB - Vaccines directed against the blood stages of Plasmodium falciparum malaria are intended to prevent the parasite from invading and replicating within host cells. No blood-stage malaria vaccine has shown clinical efficacy in humans. Most malaria vaccine antigens are parasite surface proteins that have evolved extensive genetic diversity, and this diversity could allow malaria parasites to escape vaccine-induced immunity. We examined the extent and within-host dynamics of genetic diversity in the blood-stage malaria vaccine antigen apical membrane antigen-1 in a longitudinal study in Mali. Two hundred and fourteen unique apical membrane antigen-1 haplotypes were identified among 506 human infections, and amino acid changes near a putative invasion machinery binding site were strongly associated with the development of clinical symptoms, suggesting that these residues may be important to consider in designing polyvalent apical membrane antigen-1 vaccines and in assessing vaccine efficacy in field trials. This extreme diversity may pose a serious obstacle to an effective polyvalent recombinant subunit apical membrane antigen-1 vaccine. VL - 1 ER - TY - JOUR T1 - Gene Profiling of Human Adipose Tissue During Evoked Inflammation In Vivo JF - DiabetesDiabetesDiabetesDiabetes Y1 - 2009 A1 - Shah, Rachana A1 - Lu, Yun A1 - Hinkle, Christine C. A1 - McGillicuddy, Fiona C. A1 - Kim, Roy A1 - Sridhar Hannenhalli A1 - Cappola, Thomas P. A1 - Heffron, Sean A1 - Wang, XingMei A1 - Mehta, Nehal N. A1 - Putt, Mary A1 - Reilly, Muredach P. AB - OBJECTIVE Adipose inflammation plays a central role in obesity-related metabolic and cardiovascular complications. However, few human adipose-secreted proteins are known to mediate these processes. We hypothesized that microarray mRNA profiling of human adipose during evoked inflammation could identify novel adipocytokines.RESEARCH DESIGN AND METHODS Healthy human volunteers (n = 14) were treated with intravenous endotoxin (3 ng/kg lipopolysaccharide [LPS]) and underwent subcutaneous adipose biopsies before and after LPS. On Affymetrix U133Plus 2.0 arrays, adipose mRNAs modulated >1.5-fold (with P < 0.00001) were selected. SignalP 3.0 and SecretomeP 2.0 identified genes predicted to encode secreted proteins. Of these, 86 candidates were chosen for validation in adipose from an independent human endotoxemia protocol (N = 7, with 0.6 ng/kg LPS) and for exploration of cellular origin in primary human adipocytes and macrophages in vitro. RESULTS Microarray identified 776 adipose genes modulated by LPS; 298 were predicted to be secreted. Of detectable prioritized genes, 82 of 85 (96% [95% CI 90–99]) were upregulated (fold changes >1.0) during the lower-dose (LPS 0.6 ng/kg) validation study and 51 of 85 (59% [49–70]) were induced greater than 1.5-fold. Treatment of primary adipocytes with LPS and macrophage polarization to M1 proinflammatory phenotype increased expression by 1.5-fold for 58 and 73% of detectable genes, respectively. CONCLUSIONS We demonstrate that evoked inflammation of human adipose in vivo modulated expression of multiple genes likely secreted by adipocytes and monocytes. These included established adipocytokines and chemokines implicated in recruitment and activation of lymphocytes, adhesion molecules, antioxidants, and several novel genes with unknown function. Such candidates may represent biomarkers and therapeutic targets for obesity-related complications. VL - 58 SN - 0012-1797, 1939-327X ER - TY - JOUR T1 - Genome assortment, not serogroup, defines Vibrio cholerae pandemic strains JF - NatureNature Y1 - 2009 A1 - Brettin, Thomas S. A1 - Bruce, David C. A1 - Challacombe, Jean F. A1 - Detter, John C. A1 - Han, Cliff S. A1 - Munik, A. C. A1 - Chertkov, Olga A1 - Meincke, Linda A1 - Saunders, Elizabeth A1 - Choi, Seon Y. A1 - Haley, Bradd J. A1 - Taviani, Elisa A1 - Jeon, Yoon-Seong A1 - Kim, Dong Wook A1 - Lee, Jae-Hak A1 - Walters, Ronald A. A1 - Hug, Anwar A1 - Rita R. Colwell KW - 59 KW - CHOLERA KW - genes KW - Genetics KW - GENOTYPE KW - ISLANDS KW - ORIGIN KW - PHENOTYPE KW - PUBLIC HEALTH KW - recombination KW - STRAINS KW - Toxins AB - Vibrio cholerae, the causative agent of cholera, is a bacterium autochthonous to the aquatic environment, and a serious public health threat. V. cholerae serogroup O1 is responsible for the previous two cholera pandemics, in which classical and El Tor biotypes were dominant in the 6th and the current 7th pandemics, respectively. Cholera researchers continually face newly emerging and re-emerging pathogenic clones carrying combinations of new serogroups as well as of phenotypic and genotypic properties. These genotype and phenotype changes have hampered control of the disease. Here we compare the complete genome sequences of 23 strains of V. cholerae isolated from a variety of sources and geographical locations over the past 98 years in an effort to elucidate the evolutionary mechanisms governing genetic diversity and genesis of new pathogenic clones. The genome-based phylogeny revealed 12 distinct V. cholerae phyletic lineages, of which one, designated the V. cholerae core genome (CG), comprises both O1 classical and EI Tor biotypes. All 7th pandemic clones share nearly identical gene content, i.e., the same genome backbone. The transition from 6th to 7th pandemic strains is defined here as a 'shift' between pathogenic clones belonging to the same O1 serogroup, but from significantly different phyletic lineages within the CG clade. In contrast, transition among clones during the present 7th pandemic period can be characterized as a 'drift' between clones, differentiated mainly by varying composition of laterally transferred genomic islands, resulting in emergence of variants, exemplified by V.cholerae serogroup O139 and V.cholerae O1 El Tor hybrid clones that produce cholera toxin of classical biotype. Based on the comprehensive comparative genomics presented in this study it is concluded that V. cholerae undergoes extensive genetic recombination via lateral gene transfer, and, therefore, genome assortment, not serogroup, should be used to define pathogenic V. cholerae clones. ER - TY - JOUR T1 - The genome of the blood fluke Schistosoma mansoni. JF - Nature Y1 - 2009 A1 - Berriman, Matthew A1 - Haas, Brian J A1 - LoVerde, Philip T A1 - Wilson, R Alan A1 - Dillon, Gary P A1 - Cerqueira, Gustavo C A1 - Mashiyama, Susan T A1 - Al-Lazikani, Bissan A1 - Andrade, Luiza F A1 - Ashton, Peter D A1 - Aslett, Martin A A1 - Bartholomeu, Daniella C A1 - Blandin, Gaëlle A1 - Caffrey, Conor R A1 - Coghlan, Avril A1 - Coulson, Richard A1 - Day, Tim A A1 - Delcher, Art A1 - DeMarco, Ricardo A1 - Djikeng, Appolinaire A1 - Eyre, Tina A1 - Gamble, John A A1 - Ghedin, Elodie A1 - Gu, Yong A1 - Hertz-Fowler, Christiane A1 - Hirai, Hirohisha A1 - Hirai, Yuriko A1 - Houston, Robin A1 - Ivens, Alasdair A1 - Johnston, David A A1 - Lacerda, Daniela A1 - Macedo, Camila D A1 - McVeigh, Paul A1 - Ning, Zemin A1 - Oliveira, Guilherme A1 - Overington, John P A1 - Parkhill, Julian A1 - Pertea, Mihaela A1 - Pierce, Raymond J A1 - Protasio, Anna V A1 - Quail, Michael A A1 - Rajandream, Marie-Adèle A1 - Rogers, Jane A1 - Sajid, Mohammed A1 - Salzberg, Steven L A1 - Stanke, Mario A1 - Tivey, Adrian R A1 - White, Owen A1 - Williams, David L A1 - Wortman, Jennifer A1 - Wu, Wenjie A1 - Zamanian, Mostafa A1 - Zerlotini, Adhemar A1 - Fraser-Liggett, Claire M A1 - Barrell, Barclay G A1 - El-Sayed, Najib M KW - Animals KW - Biological Evolution KW - Exons KW - Genes, Helminth KW - Genome, Helminth KW - Host-Parasite Interactions KW - Introns KW - Molecular Sequence Data KW - Physical Chromosome Mapping KW - Schistosoma mansoni KW - Schistosomiasis mansoni AB -

Schistosoma mansoni is responsible for the neglected tropical disease schistosomiasis that affects 210 million people in 76 countries. Here we present analysis of the 363 megabase nuclear genome of the blood fluke. It encodes at least 11,809 genes, with an unusual intron size distribution, and new families of micro-exon genes that undergo frequent alternative splicing. As the first sequenced flatworm, and a representative of the Lophotrochozoa, it offers insights into early events in the evolution of the animals, including the development of a body pattern with bilateral symmetry, and the development of tissues into organs. Our analysis has been informed by the need to find new drug targets. The deficits in lipid metabolism that make schistosomes dependent on the host are revealed, and the identification of membrane receptors, ion channels and more than 300 proteases provide new insights into the biology of the life cycle and new targets. Bioinformatics approaches have identified metabolic chokepoints, and a chemogenomic screen has pinpointed schistosome proteins for which existing drugs may be active. The information generated provides an invaluable resource for the research community to develop much needed new control tools for the treatment and eradication of this important and neglected disease.

VL - 460 CP - 7253 M3 - 10.1038/nature08160 ER - TY - JOUR T1 - Genomic organization and expression profile of the mucin-associated surface protein (masp) family of the human pathogen Trypanosoma cruzi. JF - Nucleic Acids Res Y1 - 2009 A1 - Bartholomeu, Daniella C A1 - Cerqueira, Gustavo C A1 - Leão, Ana Carolina A A1 - daRocha, Wanderson D A1 - Pais, Fabiano S A1 - Macedo, Camila A1 - Djikeng, Appolinaire A1 - Teixeira, Santuza M R A1 - El-Sayed, Najib M KW - 3' Flanking Region KW - 5' Flanking Region KW - Amino Acid Sequence KW - Animals KW - Base Sequence KW - Conserved Sequence KW - Gene Expression Profiling KW - Genes, Protozoan KW - Genome, Protozoan KW - Membrane Proteins KW - Molecular Sequence Data KW - Mucins KW - Multigene Family KW - Protozoan Proteins KW - RNA, Messenger KW - Trypanosoma cruzi AB -

A novel large multigene family was recently identified in the human pathogen Trypanosoma cruzi, causative agent of Chagas disease, and corresponds to approximately 6% of the parasite diploid genome. The predicted gene products, mucin-associated surface proteins (MASPs), are characterized by highly conserved N- and C-terminal domains and a strikingly variable and repetitive central region. We report here an analysis of the genomic organization and expression profile of masp genes. Masps are not randomly distributed throughout the genome but instead are clustered with genes encoding mucin and other surface protein families. Masp transcripts vary in size, are preferentially expressed during the trypomastigote stage and contain highly conserved 5' and 3' untranslated regions. A sequence analysis of a trypomastigote cDNA library reveals the expression of multiple masp variants with a bias towards a particular masp subgroup. Immunofluorescence assays using antibodies generated against a MASP peptide reveals that the expression of particular MASPs at the cell membrane is limited to subsets of the parasite population. Western blots of phosphatidylinositol-specific phospholipase C (PI-PLC)-treated parasites suggest that MASP may be GPI-anchored and shed into the medium culture, thus contributing to the large repertoire of parasite polypeptides that are exposed to the host immune system.

VL - 37 CP - 10 M3 - 10.1093/nar/gkp172 ER - TY - CHAP T1 - The Genus Vibrio and Related Genera T2 - Practical handbook of microbiologyPractical handbook of microbiology Y1 - 2009 A1 - Rita R. Colwell A1 - Chun, J. ED - Goldman, Emanuel ED - Green, Lorrence H. JA - Practical handbook of microbiologyPractical handbook of microbiology PB - CRC Press SN - 9780849393655 ER - TY - Generic T1 - Measuring differential gene expression by short read sequencing: quantitative comparison to 2-channel gene expression microarrays Y1 - 2009 A1 - Bloom, Joshua S A1 - Khan, Zia A1 - Kruglyak, Leonid A1 - Singh, Mona A1 - Caudy, Amy A JA - BMC Genomics VL - 10 UR - http://www.biomedcentral.com/1471-2164/10/221 CP - 1 J1 - BMC GenomicsBMC Genomics M3 - 10.1186/1471-2164-10-221 ER - TY - JOUR T1 - Measuring differential gene expression by short read sequencing: quantitative comparison to 2-channel gene expression microarrays. JF - BMC Genomics Y1 - 2009 A1 - Bloom, Joshua S A1 - Khan, Zia A1 - Kruglyak, Leonid A1 - Singh, Mona A1 - Caudy, Amy A KW - algorithms KW - DNA, Complementary KW - DNA, Fungal KW - Gene Expression Profiling KW - Oligonucleotide Array Sequence Analysis KW - Saccharomyces cerevisiae KW - sequence alignment KW - Sequence Analysis, DNA AB -

BACKGROUND: High-throughput cDNA synthesis and sequencing of poly(A)-enriched RNA is rapidly emerging as a technology competing to replace microarrays as a quantitative platform for measuring gene expression.

RESULTS: Consequently, we compared full length cDNA sequencing to 2-channel gene expression microarrays in the context of measuring differential gene expression. Because of its comparable cost to a gene expression microarray, our study focused on the data obtainable from a single lane of an Illumina 1 G sequencer. We compared sequencing data to a highly replicated microarray experiment profiling two divergent strains of S. cerevisiae.

CONCLUSION: Using a large number of quantitative PCR (qPCR) assays, more than previous studies, we found that neither technology is decisively better at measuring differential gene expression. Further, we report sequencing results from a diploid hybrid of two strains of S. cerevisiae that indicate full length cDNA sequencing can discover heterozygosity and measure quantitative allele-specific expression simultaneously.

VL - 10 M3 - 10.1186/1471-2164-10-221 ER - TY - JOUR T1 - Microbial oceanography in a sea of opportunity JF - NatureNature Y1 - 2009 A1 - Bowler, Chris A1 - Karl, David M. A1 - Rita R. Colwell KW - Astronomy KW - astrophysics KW - Biochemistry KW - Bioinformatics KW - Biology KW - biotechnology KW - cancer KW - cell cycle KW - cell signalling KW - climate change KW - Computational Biology KW - development KW - developmental biology KW - DNA KW - drug discovery KW - earth science KW - ecology KW - environmental science KW - Evolution KW - evolutionary biology KW - functional genomics KW - Genetics KW - Genomics KW - geophysics KW - immunology KW - interdisciplinary science KW - life KW - marine biology KW - materials science KW - medical research KW - medicine KW - metabolomics KW - molecular biology KW - molecular interactions KW - nanotechnology KW - Nature KW - neurobiology KW - neuroscience KW - palaeobiology KW - pharmacology KW - Physics KW - proteomics KW - quantum physics KW - RNA KW - Science KW - science news KW - science policy KW - signal transduction KW - structural biology KW - systems biology KW - transcriptomics AB - Plankton use solar energy to drive the nutrient cycles that make the planet habitable for larger organisms. We can now explore the diversity and functions of plankton using genomics, revealing the gene repertoires associated with survival in the oceans. Such studies will help us to appreciate the sensitivity of ocean systems and of the ocean's response to climate change, improving the predictive power of climate models. VL - 459 SN - 0028-0836 ER - TY - JOUR T1 - Modeling and visualization of human activities for multicamera networks JF - EURASIP Journal on Image and Video ProcessingEURASIP Journal on Image and Video Processing Y1 - 2009 A1 - Sankaranarayanan, A. C. A1 - Patro, R. A1 - Turaga, P. A1 - Varshney, Amitabh A1 - Chellappa, Rama VL - 2009 ER - TY - JOUR T1 - New records of phytoplankton for Bangladesh. 9. Some rare and a new species JF - Bangladesh Journal of Plant TaxonomyBangladesh Journal of Plant Taxonomy Y1 - 2009 A1 - Khondker, Moniruzzaman A1 - Bhuiyan, Rauf Ahmed A1 - Yeasmin, Jenat A1 - Alam, Munirul A1 - Sack, R. Bradley A1 - Huq, Anwar A1 - Rita R. Colwell AB - Ten taxa belonging to Chlorophyceae, Cyanophyceae, Bacillariophyceae and Euglenophyceae, and one with an uncertain taxonomic position have been described in this paper. Of these, 10 taxa have been found to be globally rare and new records for Bangladesh, whereas Strombomonas islamii Khondker sp. nov. has been described as new to science. VL - 16 SN - 1028-2092 ER - TY - JOUR T1 - Predicting the distribution of Vibrio spp. in the Chesapeake Bay: a Vibrio cholerae case study JF - EcoHealthEcoHealth Y1 - 2009 A1 - Constantin de Magny, G. A1 - Long, W. A1 - Brown, C. W. A1 - Hood, R. R. A1 - Huq, A. A1 - Murtugudde, R. A1 - Rita R. Colwell AB - Vibrio cholerae, the causative agent of cholera, is a naturally occurring inhabitant of the Chesapeake Bay and serves as a predictor for other clinically important vibrios, including Vibrio parahaemolyticus and Vibrio vulnificus. A system was constructed to predict the likelihood of the presence of V. cholerae in surface waters of the Chesapeake Bay, with the goal to provide forecasts of the occurrence of this and related pathogenic Vibrio spp. Prediction was achieved by driving an available multivariate empirical habitat model estimating the probability of V. cholerae within a range of temperatures and salinities in the Bay, with hydrodynamically generated predictions of ambient temperature and salinity. The experimental predictions provided both an improved understanding of the in situ variability of V. cholerae, including identification of potential hotspots of occurrence, and usefulness as an early warning system. With further development of the system, prediction of the probability of the occurrence of related pathogenic vibrios in the Chesapeake Bay, notably V. parahaemolyticus and V. vulnificus, will be possible, as well as its transport to any geographical location where sufficient relevant data are available. VL - 6 ER - TY - JOUR T1 - Resistin gene variation is associated with systemic inflammation but not plasma adipokine levels, metabolic syndrome or coronary atherosclerosis in nondiabetic Caucasians JF - Clinical EndocrinologyClinical Endocrinology Y1 - 2009 A1 - Qasim, Atif N. A1 - Metkus, Thomas S. A1 - Tadesse, Mahlet A1 - Lehrke, Michael A1 - Restine, Stephanie A1 - Wolfe, Megan L. A1 - Sridhar Hannenhalli A1 - Cappola, Thomas A1 - Rader, Daniel J. A1 - Reilly, Muredach P. AB - Objective Resistin causes insulin resistance and diabetes in mice whereas in humans it is linked to inflammation and atherosclerosis. Few human genetic studies of resistin in inflammation and atherosclerosis have been performed. We hypothesized that the –420C>G putative gain-of-function resistin variant would be associated with inflammatory markers and atherosclerosis but not with metabolic syndrome or adipokines in humans.Design and methods We examined the association of three resistin polymorphisms, –852A>G, –420C>G and +157C>T, and related haplotypes with plasma resistin, cytokines, C-reactive protein (CRP), adipokines, plasma lipoproteins, metabolic syndrome and coronary artery calcification (CAC) in nondiabetic Caucasians (n = 851). Results Resistin levels were higher, dose-dependently, with the –420G allele (CC 5·9 ± 2·7 ng/ml, GC 6·5 ± 4·0 ng/ml and GG 7·2 ± 4·8 ng/ml, trend P = 0·04) after age and gender adjustment [fold higher for GC + GG vs. CC; 1·07 (1·00–1·15), P < 0·05)]. The –852A>G single nucleotide polymorphism (SNP) was associated with higher soluble tumour necrosis factor-receptor 2 (sol-TNFR2) levels in fully adjusted models [1·06 (95% CI 1·01–1·11), P = 0·01)]. The estimated resistin haplotype (GGT) was associated with sol-TNFR2 (P = 0·04) and the AGT haplotype was related to CRP (P = 0·04) in the fully adjusted models. Resistin SNPs and haplotypes were not associated with body mass index (BMI), fasting glucose, insulin resistance, metabolic syndrome, adipokines or CAC scores. Conclusions Despite modest associations with plasma resistin and inflammatory biomarkers, resistin 5′ variants were not associated with metabolic parameters or coronary calcification. This suggests that resistin is an inflammatory cytokine in humans but has little influence on adiposity, metabolic syndrome or atherosclerosis. VL - 70 SN - 1365-2265 ER - TY - JOUR T1 - RNA Colony Blot Hybridization Method for Enumeration of Culturable Vibrio Cholerae and Vibrio Mimicus Bacteria JF - Applied and Environmental MicrobiologyAppl. Environ. Microbiol.Applied and Environmental MicrobiologyAppl. Environ. Microbiol. Y1 - 2009 A1 - Grim, Christopher J. A1 - Zo, Young-Gun A1 - Hasan, Nur A. A1 - Ali, Afsar A1 - Chowdhury, Wasimul B. A1 - Islam, Atiqul A1 - Rashid, Mohammed H. A1 - Alam, Munirul A1 - Morris, J. Glenn A1 - Huq, Anwar A1 - Rita R. Colwell AB - A species-specific RNA colony blot hybridization protocol was developed for enumeration of culturable Vibrio cholerae and Vibrio mimicus bacteria in environmental water samples. Bacterial colonies on selective or nonselective plates were lysed by sodium dodecyl sulfate, and the lysates were immobilized on nylon membranes. A fluorescently labeled oligonucleotide probe targeting a phylogenetic signature sequence of 16S rRNA of V. cholerae and V. mimicus was hybridized to rRNA molecules immobilized on the nylon colony lift blots. The protocol produced strong positive signals for all colonies of the 15 diverse V. cholerae-V. mimicus strains tested, indicating 100% sensitivity of the probe for the targeted species. For visible colonies of 10 nontarget species, the specificity of the probe was calculated to be 90% because of a weak positive signal produced by Grimontia (Vibrio) hollisae, a marine bacterium. When both the sensitivity and specificity of the assay were evaluated using lake water samples amended with a bioluminescent V. cholerae strain, no false-negative or false-positive results were found, indicating 100% sensitivity and specificity for culturable bacterial populations in freshwater samples when G. hollisae was not present. When the protocol was applied to laboratory microcosms containing V. cholerae attached to live copepods, copepods were found to carry approximately 10,000 to 50,000 CFU of V. cholerae per copepod. The protocol was also used to analyze pond water samples collected in an area of cholera endemicity in Bangladesh over a 9-month period. Water samples collected from six ponds demonstrated a peak in abundance of total culturable V. cholerae bacteria 1 to 2 months prior to observed increases in pathogenic V. cholerae and in clinical cases recorded by the area health clinic. The method provides a highly specific and sensitive tool for monitoring the dynamics of V. cholerae in the environment. The RNA blot hybridization protocol can also be applied to detection of other gram-negative bacteria for taxon-specific enumeration. VL - 75 SN - 0099-2240, 1098-5336 ER - TY - JOUR T1 - Serogroup, Virulence, and Genetic Traits of Vibrio Parahaemolyticus in the Estuarine Ecosystem of Bangladesh JF - Applied and Environmental MicrobiologyAppl. Environ. Microbiol.Applied and Environmental MicrobiologyAppl. Environ. Microbiol. Y1 - 2009 A1 - Alam, Munirul A1 - Chowdhury, Wasimul B. A1 - Bhuiyan, N. A. A1 - Islam, Atiqul A1 - Hasan, Nur A. A1 - Nair, G. Balakrish A1 - Watanabe, H. A1 - Siddique, A. K. A1 - Huq, Anwar A1 - Sack, R. Bradley A1 - Akhter, M. Z. A1 - Grim, Christopher J. A1 - Kam, K. M. A1 - Luey, C. K. Y. A1 - Endtz, Hubert P. A1 - Cravioto, Alejandro A1 - Rita R. Colwell AB - Forty-two strains of Vibrio parahaemolyticus were isolated from Bay of Bengal estuaries and, with two clinical strains, analyzed for virulence, phenotypic, and molecular traits. Serological analysis indicated O8, O3, O1, and K21 to be the major O and K serogroups, respectively, and O8:K21, O1:KUT, and O3:KUT to be predominant. The K antigen(s) was untypeable, and pandemic serogroup O3:K6 was not detected. The presence of genes toxR and tlh were confirmed by PCR in all but two strains, which also lacked toxR. A total of 18 (41%) strains possessed the virulence gene encoding thermostable direct hemolysin (TDH), and one had the TDH-related hemolysin (trh) gene, but not tdh. Ten (23%) strains exhibited Kanagawa phenomenon that surrogates virulence, of which six, including the two clinical strains, possessed tdh. Of the 18 tdh-positive strains, 17 (94%), including the two clinical strains, had the seromarker O8:K21, one was O9:KUT, and the single trh-positive strain was O1:KUT. None had the group-specific or ORF8 pandemic marker gene. DNA fingerprinting employing pulsed-field gel electrophoresis (PFGE) of SfiI-digested DNA and cluster analysis showed divergence among the strains. Dendrograms constructed using PFGE (SfiI) images from a soft database, including those of pandemic and nonpandemic strains of diverse geographic origin, however, showed that local strains formed a cluster, i.e., “clonal cluster,” as did pandemic strains of diverse origin. The demonstrated prevalence of tdh-positive and diarrheagenic serogroup O8:K21 strains in coastal villages of Bangladesh indicates a significant human health risk for inhabitants. VL - 75 SN - 0099-2240, 1098-5336 ER - TY - JOUR T1 - Three genomes from the phylum Acidobacteria provide insight into the lifestyles of these microorganisms in soils JF - Applied and environmental microbiologyApplied and environmental microbiology Y1 - 2009 A1 - Ward, Naomi L. A1 - Challacombe, Jean F. A1 - Janssen, Peter H. A1 - Henrissat, Bernard A1 - Coutinho, Pedro M. A1 - Wu, Martin A1 - Xie, Gary A1 - Haft, Daniel H. A1 - Sait, Michelle A1 - Badger, Jonathan A1 - Barabote, Ravi D. A1 - Bradley, Brent A1 - Brettin, Thomas S. A1 - Brinkac, Lauren M. A1 - Bruce, David A1 - Creasy, Todd A1 - Daugherty, Sean C. A1 - Davidsen, Tanja M. A1 - DeBoy, Robert T. A1 - Detter, J. Chris A1 - Dodson, Robert J. A1 - Durkin, A. Scott A1 - Ganapathy, Anuradha A1 - Gwinn-Giglio, Michelle A1 - Han, Cliff S. A1 - Khouri, Hoda A1 - Kiss, Hajnalka A1 - Kothari, Sagar P. A1 - Madupu, Ramana A1 - Nelson, Karen E. A1 - Nelson, William C. A1 - Paulsen, Ian A1 - Penn, Kevin A1 - Ren, Qinghu A1 - Rosovitz, M. J. A1 - J. Selengut A1 - Shrivastava, Susmita A1 - Sullivan, Steven A. A1 - Tapia, Roxanne A1 - Thompson, L. Sue A1 - Watkins, Kisha L. A1 - Yang, Qi A1 - Yu, Chunhui A1 - Zafar, Nikhat A1 - Zhou, Liwei A1 - Kuske, Cheryl R. KW - Anti-Bacterial Agents KW - bacteria KW - Biological Transport KW - Carbohydrate Metabolism KW - Cyanobacteria KW - DNA, Bacterial KW - Fungi KW - Genome, Bacterial KW - Macrolides KW - Molecular Sequence Data KW - Nitrogen KW - Phylogeny KW - Proteobacteria KW - Sequence Analysis, DNA KW - Sequence Homology KW - Soil Microbiology AB - The complete genomes of three strains from the phylum Acidobacteria were compared. Phylogenetic analysis placed them as a unique phylum. They share genomic traits with members of the Proteobacteria, the Cyanobacteria, and the Fungi. The three strains appear to be versatile heterotrophs. Genomic and culture traits indicate the use of carbon sources that span simple sugars to more complex substrates such as hemicellulose, cellulose, and chitin. The genomes encode low-specificity major facilitator superfamily transporters and high-affinity ABC transporters for sugars, suggesting that they are best suited to low-nutrient conditions. They appear capable of nitrate and nitrite reduction but not N(2) fixation or denitrification. The genomes contained numerous genes that encode siderophore receptors, but no evidence of siderophore production was found, suggesting that they may obtain iron via interaction with other microorganisms. The presence of cellulose synthesis genes and a large class of novel high-molecular-weight excreted proteins suggests potential traits for desiccation resistance, biofilm formation, and/or contribution to soil structure. Polyketide synthase and macrolide glycosylation genes suggest the production of novel antimicrobial compounds. Genes that encode a variety of novel proteins were also identified. The abundance of acidobacteria in soils worldwide and the breadth of potential carbon use by the sequenced strains suggest significant and previously unrecognized contributions to the terrestrial carbon cycle. Combining our genomic evidence with available culture traits, we postulate that cells of these isolates are long-lived, divide slowly, exhibit slow metabolic rates under low-nutrient conditions, and are well equipped to tolerate fluctuations in soil hydration. VL - 75 N1 - http://www.ncbi.nlm.nih.gov/pubmed/19201974?dopt=Abstract ER - TY - JOUR T1 - Three genomes from the phylum Acidobacteria provide insight into the lifestyles of these microorganisms in soils. JF - Appl Environ Microbiol Y1 - 2009 A1 - Ward, Naomi L A1 - Challacombe, Jean F A1 - Janssen, Peter H A1 - Henrissat, Bernard A1 - Coutinho, Pedro M A1 - Wu, Martin A1 - Xie, Gary A1 - Haft, Daniel H A1 - Sait, Michelle A1 - Badger, Jonathan A1 - Barabote, Ravi D A1 - Bradley, Brent A1 - Brettin, Thomas S A1 - Brinkac, Lauren M A1 - Bruce, David A1 - Creasy, Todd A1 - Daugherty, Sean C A1 - Davidsen, Tanja M A1 - DeBoy, Robert T A1 - Detter, J Chris A1 - Dodson, Robert J A1 - Durkin, A Scott A1 - Ganapathy, Anuradha A1 - Gwinn-Giglio, Michelle A1 - Han, Cliff S A1 - Khouri, Hoda A1 - Kiss, Hajnalka A1 - Kothari, Sagar P A1 - Madupu, Ramana A1 - Nelson, Karen E A1 - Nelson, William C A1 - Paulsen, Ian A1 - Penn, Kevin A1 - Ren, Qinghu A1 - Rosovitz, M J A1 - Selengut, Jeremy D A1 - Shrivastava, Susmita A1 - Sullivan, Steven A A1 - Tapia, Roxanne A1 - Thompson, L Sue A1 - Watkins, Kisha L A1 - Yang, Qi A1 - Yu, Chunhui A1 - Zafar, Nikhat A1 - Zhou, Liwei A1 - Kuske, Cheryl R KW - Anti-Bacterial Agents KW - bacteria KW - Biological Transport KW - Carbohydrate Metabolism KW - Cyanobacteria KW - DNA, Bacterial KW - Fungi KW - Genome, Bacterial KW - Macrolides KW - Molecular Sequence Data KW - Nitrogen KW - Phylogeny KW - Proteobacteria KW - Sequence Analysis, DNA KW - Sequence Homology KW - Soil Microbiology AB -

The complete genomes of three strains from the phylum Acidobacteria were compared. Phylogenetic analysis placed them as a unique phylum. They share genomic traits with members of the Proteobacteria, the Cyanobacteria, and the Fungi. The three strains appear to be versatile heterotrophs. Genomic and culture traits indicate the use of carbon sources that span simple sugars to more complex substrates such as hemicellulose, cellulose, and chitin. The genomes encode low-specificity major facilitator superfamily transporters and high-affinity ABC transporters for sugars, suggesting that they are best suited to low-nutrient conditions. They appear capable of nitrate and nitrite reduction but not N(2) fixation or denitrification. The genomes contained numerous genes that encode siderophore receptors, but no evidence of siderophore production was found, suggesting that they may obtain iron via interaction with other microorganisms. The presence of cellulose synthesis genes and a large class of novel high-molecular-weight excreted proteins suggests potential traits for desiccation resistance, biofilm formation, and/or contribution to soil structure. Polyketide synthase and macrolide glycosylation genes suggest the production of novel antimicrobial compounds. Genes that encode a variety of novel proteins were also identified. The abundance of acidobacteria in soils worldwide and the breadth of potential carbon use by the sequenced strains suggest significant and previously unrecognized contributions to the terrestrial carbon cycle. Combining our genomic evidence with available culture traits, we postulate that cells of these isolates are long-lived, divide slowly, exhibit slow metabolic rates under low-nutrient conditions, and are well equipped to tolerate fluctuations in soil hydration.

VL - 75 CP - 7 M3 - 10.1128/AEM.02294-08 ER - TY - JOUR T1 - Toward reconstructing the evolution of advanced moths and butterflies (Lepidoptera: Ditrysia): an initial molecular study JF - BMC Evol BiolBMC Evol Biol Y1 - 2009 A1 - Regier, J. C. A1 - Zwick, A. A1 - Michael P. Cummings A1 - Kawahara, A. Y. A1 - Cho, S. A1 - Weller, S. A1 - Roe, A. A1 - Baixeras, J. A1 - Brown, J. W. A1 - Parr, C. A1 - Davis, D. R. A1 - Epstein, M. A1 - Hallwachs, W. A1 - Hausmann, A. A1 - Janzen, D. H. A1 - Kitching, I. J. A1 - Solis, M. A. A1 - Yen, S. H. A1 - Adam L. Bazinet A1 - Mitter, C. AB - BACKGROUND: In the mega-diverse insect order Lepidoptera (butterflies and moths; 165,000 described species), deeper relationships are little understood within the clade Ditrysia, to which 98% of the species belong. To begin addressing this problem, we tested the ability of five protein-coding nuclear genes (6.7 kb total), and character subsets therein, to resolve relationships among 123 species representing 27 (of 33) superfamilies and 55 (of 100) families of Ditrysia under maximum likelihood analysis. RESULTS: Our trees show broad concordance with previous morphological hypotheses of ditrysian phylogeny, although most relationships among superfamilies are weakly supported. There are also notable surprises, such as a consistently closer relationship of Pyraloidea than of butterflies to most Macrolepidoptera. Monophyly is significantly rejected by one or more character sets for the putative clades Macrolepidoptera as currently defined (P < 0.05) and Macrolepidoptera excluding Noctuoidea and Bombycoidea sensu lato (P < or = 0.005), and nearly so for the superfamily Drepanoidea as currently defined (P < 0.08). Superfamilies are typically recovered or nearly so, but usually without strong support. Relationships within superfamilies and families, however, are often robustly resolved. We provide some of the first strong molecular evidence on deeper splits within Pyraloidea, Tortricoidea, Geometroidea, Noctuoidea and others.Separate analyses of mostly synonymous versus non-synonymous character sets revealed notable differences (though not strong conflict), including a marked influence of compositional heterogeneity on apparent signal in the third codon position (nt3). As available model partitioning methods cannot correct for this variation, we assessed overall phylogeny resolution through separate examination of trees from each character set. Exploration of "tree space" with GARLI, using grid computing, showed that hundreds of searches are typically needed to find the best-feasible phylogeny estimate for these data. CONCLUSION: Our results (a) corroborate the broad outlines of the current working phylogenetic hypothesis for Ditrysia, (b) demonstrate that some prominent features of that hypothesis, including the position of the butterflies, need revision, and (c) resolve the majority of family and subfamily relationships within superfamilies as thus far sampled. Much further gene and taxon sampling will be needed, however, to strongly resolve individual deeper nodes. VL - 9 ER - TY - JOUR T1 - Using Satellite Images of Environmental Changes to Predict Infectious Disease Outbreaks JF - Emerging Infectious DiseasesEmerg Infect DisEmerging Infectious DiseasesEmerg Infect Dis Y1 - 2009 A1 - Ford, Timothy E. A1 - Rita R. Colwell A1 - Rose, Joan B. A1 - Morse, Stephen S. A1 - Rogers, David J. A1 - Yates, Terry L. AB - A strong global satellite imaging system is essential for predicting outbreaks., Recent events clearly illustrate a continued vulnerability of large populations to infectious diseases, which is related to our changing human-constructed and natural environments. A single person with multidrug-resistant tuberculosis in 2007 provided a wake-up call to the United States and global public health infrastructure, as the health professionals and the public realized that today’s ease of airline travel can potentially expose hundreds of persons to an untreatable disease associated with an infectious agent. Ease of travel, population increase, population displacement, pollution, agricultural activity, changing socioeconomic structures, and international conflicts worldwide have each contributed to infectious disease events. Today, however, nothing is larger in scale, has more potential for long-term effects, and is more uncertain than the effects of climate change on infectious disease outbreaks, epidemics, and pandemics. We discuss advances in our ability to predict these events and, in particular, the critical role that satellite imaging could play in mounting an effective response. VL - 15 SN - 1080-6040 ER - TY - JOUR T1 - Viable but not cultivable bacteria JF - Uncultivated MicroorganismsUncultivated Microorganisms Y1 - 2009 A1 - Rita R. Colwell AB - A well-studied, long-term survival mechanism employed by Gram-positive bacteria is formation of endospores. For Gram-negative bacteria, the assumption has been that a survival state does not exist. However, a dormancy state has been described for Gram-negative bacteria and designated as the viable but nonculturable (VBNC) strategy of nonspore-forming cells. A variety of environmental factors are involved in induction of the viable but nonculturable state and Vibrio cholerae provides a useful paradigm for the VBNC phenomenon. It is now accepted that plate counts cannot be relied upon to enumerate or detect VBNC cells. Therefore, direct methods employing fluorescent staining, molecular genetic probes, and other molecular methods have proven both useful and reliable in detecting and enumerating both culturable and nonculturable cells. A predictive model for cholera has been developed, based on ground truth data gathered using these molecular methods and combining them with data obtained by remote sensing, employing satellites. It is clear that microbiology in the twenty-first century has been enhanced by these new tools and paradigms. ER - TY - JOUR T1 - Biofilms in water, its role and impact in human disease transmission JF - Current Opinion in BiotechnologyCurrent Opinion in Biotechnology Y1 - 2008 A1 - Huq, Anwar A1 - Whitehouse, Chris A. A1 - Grim, Christopher J. A1 - Alam, Munirul A1 - Rita R. Colwell AB - Understanding the mechanism of biofilm formation is the first step in determining its function and, thereby, its impact and role in the environment. Extensive studies accomplished during the past few years have elucidated the genetics and biochemistry of biofilm formation. Cell-to-cell communication, that is, quorum sensing, is a key factor in the initiation of biofilm. Occurrence of viable but nonculturable bacteria, including Vibrio cholerae in biofilms has been reported and most likely such cells were overlooked previously because appropriate methods of detection were not employed. For this reason discovery and investigation of this important bacterial ecological niche in the environment were impeded. VL - 19 SN - 0958-1669 ER - TY - JOUR T1 - The Complete Genome Sequence of Thermococcus Onnurineus NA1 Reveals a Mixed Heterotrophic and Carboxydotrophic Metabolism JF - Journal of BacteriologyJ. Bacteriol.Journal of BacteriologyJ. Bacteriol. Y1 - 2008 A1 - Lee, Hyun Sook A1 - Kang, Sung Gyun A1 - Bae, Seung Seob A1 - Lim, Jae Kyu A1 - Cho, Yona A1 - Kim, Yun Jae A1 - Jeon, Jeong Ho A1 - Cha, Sun-Shin A1 - Kwon, Kae Kyoung A1 - Kim, Hyung-Tae A1 - Park, Cheol-Joo A1 - Lee, Hee-Wook A1 - Kim, Seung Il A1 - Jongsik, Chun A1 - Rita R. Colwell A1 - Kim, Sang-Jin A1 - Lee, Jung-Hyun AB - Members of the genus Thermococcus, sulfur-reducing hyperthermophilic archaea, are ubiquitously present in various deep-sea hydrothermal vent systems and are considered to play a significant role in the microbial consortia. We present the complete genome sequence and feature analysis of Thermococcus onnurineus NA1 isolated from a deep-sea hydrothermal vent area, which reveal clues to its physiology. Based on results of genomic analysis, T. onnurineus NA1 possesses the metabolic pathways for organotrophic growth on peptides, amino acids, or sugars. More interesting was the discovery that the genome encoded unique proteins that are involved in carboxydotrophy to generate energy by oxidation of CO to CO2, thereby providing a mechanistic basis for growth with CO as a substrate. This lithotrophic feature in combination with carbon fixation via RuBisCO (ribulose 1,5-bisphosphate carboxylase/oxygenase) introduces a new strategy with a complementing energy supply for T. onnurineus NA1 potentially allowing it to cope with nutrient stress in the surrounding of hydrothermal vents, providing the first genomic evidence for the carboxydotrophy in Thermococcus. VL - 190 SN - 0021-9193, 1098-5530 ER - TY - JOUR T1 - Covariability of Vibrio Cholerae Microdiversity and Environmental Parameters JF - Applied and Environmental MicrobiologyAppl. Environ. Microbiol.Applied and Environmental MicrobiologyAppl. Environ. Microbiol. Y1 - 2008 A1 - Zo, Young-Gun A1 - Chokesajjawatee, Nipa A1 - Arakawa, Eiji A1 - Watanabe, Haruo A1 - Huq, Anwar A1 - Rita R. Colwell AB - Fine-scale diversity of natural bacterial assemblages has been attributed to neutral radiation because correspondence between bacterial phylogenetic signals in the natural environment and environmental parameters had not been detected. Evidence that such correspondence occurs is provided for Vibrio cholerae, establishing a critical role for environmental parameters in bacterial diversity. VL - 74 SN - 0099-2240, 1098-5336 ER - TY - JOUR T1 - Determination of Clonality and Relatedness of Vibrio Cholerae Isolates by Genomic Fingerprinting, Using Long-Range Repetitive Element Sequence-Based PCR JF - Applied and Environmental MicrobiologyAppl. Environ. Microbiol.Applied and Environmental MicrobiologyAppl. Environ. Microbiol. Y1 - 2008 A1 - Chokesajjawatee, Nipa A1 - Zo, Young-Gun A1 - Rita R. Colwell AB - A high-throughput method which is applicable for rapid screening, identification, and delineation of isolates of Vibrio cholerae, sensitive to genome variation, and capable of providing phylogenetic inferences enhances environmental monitoring of this bacterium. We have developed and optimized a method for genomic fingerprinting of V. cholerae based on long-range PCR. The method uses a primer set directed to enterobacterial repetitive intergenic consensus sequences, a high-fidelity DNA polymerase, and analysis via conventional agarose gel electrophoresis. Long (∼10 kb), highly reproducible amplicons were generated from V. cholerae isolates, including those from different geographical locations and historical strains isolated during the period 1931-2000. The amplicons yielded reduced variability in their densitometric band patterns to ≤10% and clonal distinction at <90% similarity. Rapid band-matching analysis was accomplished for fingerprints with ≥90% similarity, discriminating O serotypes and biotypes (classical versus El Tor) as well as pathogenic and nonpathogenic strains. Compared to genome similarity measured by DNA-DNA hybridization, the results showed good correlation (r = 0.7; P < 0.001), with five times less measurement error and without bias. The method permits both phylogenetic inference and clonal differentiation of individual V. cholerae strains, enables robust, high-throughput analysis, and does not require specialized equipment to perform. With access to a curated public database furnished with appropriate analytical software applications, the method should prove useful in large-scale multilaboratory surveys, especially those designed to detect specific pathogens in the natural environment. VL - 74 SN - 0099-2240, 1098-5336 ER - TY - JOUR T1 - The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus). JF - Nature Y1 - 2008 A1 - Ming, Ray A1 - Hou, Shaobin A1 - Feng, Yun A1 - Yu, Qingyi A1 - Dionne-Laporte, Alexandre A1 - Saw, Jimmy H A1 - Senin, Pavel A1 - Wang, Wei A1 - Ly, Benjamin V A1 - Lewis, Kanako L T A1 - Salzberg, Steven L A1 - Feng, Lu A1 - Jones, Meghan R A1 - Skelton, Rachel L A1 - Murray, Jan E A1 - Chen, Cuixia A1 - Qian, Wubin A1 - Shen, Junguo A1 - Du, Peng A1 - Eustice, Moriah A1 - Tong, Eric A1 - Tang, Haibao A1 - Lyons, Eric A1 - Paull, Robert E A1 - Michael, Todd P A1 - Wall, Kerr A1 - Rice, Danny W A1 - Albert, Henrik A1 - Wang, Ming-Li A1 - Zhu, Yun J A1 - Schatz, Michael A1 - Nagarajan, Niranjan A1 - Acob, Ricelle A A1 - Guan, Peizhu A1 - Blas, Andrea A1 - Wai, Ching Man A1 - Ackerman, Christine M A1 - Ren, Yan A1 - Liu, Chao A1 - Wang, Jianmei A1 - Wang, Jianping A1 - Na, Jong-Kuk A1 - Shakirov, Eugene V A1 - Haas, Brian A1 - Thimmapuram, Jyothi A1 - Nelson, David A1 - Wang, Xiyin A1 - Bowers, John E A1 - Gschwend, Andrea R A1 - Delcher, Arthur L A1 - Singh, Ratnesh A1 - Suzuki, Jon Y A1 - Tripathi, Savarni A1 - Neupane, Kabi A1 - Wei, Hairong A1 - Irikura, Beth A1 - Paidi, Maya A1 - Jiang, Ning A1 - Zhang, Wenli A1 - Presting, Gernot A1 - Windsor, Aaron A1 - Navajas-Pérez, Rafael A1 - Torres, Manuel J A1 - Feltus, F Alex A1 - Porter, Brad A1 - Li, Yingjun A1 - Burroughs, A Max A1 - Luo, Ming-Cheng A1 - Liu, Lei A1 - Christopher, David A A1 - Mount, Stephen M A1 - Moore, Paul H A1 - Sugimura, Tak A1 - Jiang, Jiming A1 - Schuler, Mary A A1 - Friedman, Vikki A1 - Mitchell-Olds, Thomas A1 - Shippen, Dorothy E A1 - dePamphilis, Claude W A1 - Palmer, Jeffrey D A1 - Freeling, Michael A1 - Paterson, Andrew H A1 - Gonsalves, Dennis A1 - Wang, Lei A1 - Alam, Maqsudul KW - Arabidopsis KW - Carica KW - Contig Mapping KW - Databases, Genetic KW - Genes, Plant KW - Genome, Plant KW - Molecular Sequence Data KW - Plants, Genetically Modified KW - sequence alignment KW - Sequence Analysis, DNA KW - Transcription Factors KW - Tropical Climate AB -

Papaya, a fruit crop cultivated in tropical and subtropical regions, is known for its nutritional benefits and medicinal applications. Here we report a 3x draft genome sequence of 'SunUp' papaya, the first commercial virus-resistant transgenic fruit tree to be sequenced. The papaya genome is three times the size of the Arabidopsis genome, but contains fewer genes, including significantly fewer disease-resistance gene analogues. Comparison of the five sequenced genomes suggests a minimal angiosperm gene set of 13,311. A lack of recent genome duplication, atypical of other angiosperm genomes sequenced so far, may account for the smaller papaya gene number in most functional groups. Nonetheless, striking amplifications in gene number within particular functional groups suggest roles in the evolution of tree-like habit, deposition and remobilization of starch reserves, attraction of seed dispersal agents, and adaptation to tropical daylengths. Transgenesis at three locations is closely associated with chloroplast insertions into the nuclear genome, and with topoisomerase I recognition sites. Papaya offers numerous advantages as a system for fruit-tree functional genomics, and this draft genome sequence provides the foundation for revealing the basis of Carica's distinguishing morpho-physiological, medicinal and nutritional properties.

VL - 452 CP - 7190 M3 - 10.1038/nature06856 ER - TY - JOUR T1 - Dual role colonization factors connecting Vibrio cholerae's lifestyles in human and aquatic environments open new perspectives for combating infectious diseases JF - Current Opinion in BiotechnologyCurrent Opinion in Biotechnology Y1 - 2008 A1 - Vezzulli, Luigi A1 - Guzmán, Carlos A. A1 - Rita R. Colwell A1 - Pruzzo, Carla AB - Vibrio cholerae exhibits two distinctive lifestyles, one inside the milieu of the human intestine and the other in the aquatic environment. Recently, the existence of V. cholerae ligands involved in colonization of both human intestine and environmental chitin surfaces via the same binding specificity has been shown. Such molecules, here named ‘dual role colonization factors (DRCFs)’, are example of a tight connection between the two V. cholerae's lifestyles. It is suggested that DRCFs and, more generally, bacterial factors and pathways having roles in pathogenesis and in the out of the human body life may be promising targets for development of novel prophylactic or therapeutic interventions that may also affect V. cholerae fitness in its environmental reservoirs. VL - 19 SN - 0958-1669 ER - TY - JOUR T1 - Environmental signatures associated with cholera epidemics JF - Proceedings of the National Academy of SciencesProceedings of the National Academy of Sciences Y1 - 2008 A1 - Constantin de Magny, G. A1 - Murtugudde, R. A1 - Sapiano, M. R. P. A1 - Nizam, A. A1 - Brown, C. W. A1 - Busalacchi, A. J. A1 - Yunus, M. A1 - Nair, G. B. A1 - Gil, A. I. A1 - Lanata, C. F. A1 - Rita R. Colwell AB - The causative agent of cholera, Vibrio cholerae, has been shown to be autochthonous to riverine, estuarine, and coastal waters along with its host, the copepod, a significant member of the zooplankton community. Temperature, salinity, rainfall and plankton have proven to be important factors in the ecology of V. cholerae, influencing the transmission of the disease in those regions of the world where the human population relies on untreated water as a source of drinking water. In this study, the pattern of cholera outbreaks during 1998–2006 in Kolkata, India, and Matlab, Bangladesh, and the earth observation data were analyzed with the objective of developing a prediction model for cholera. Satellite sensors were used to measure chlorophyll a concentration (CHL) and sea surface temperature (SST). In addition, rainfall data were obtained from both satellite and in situ gauge measurements. From the analyses, a statistically significant relationship between the time series for cholera in Kolkata, India, and CHL and rainfall anomalies was determined. A statistically significant one month lag was observed between CHL anomaly and number of cholera cases in Matlab, Bangladesh. From the results of the study, it is concluded that ocean and climate patterns are useful predictors of cholera epidemics, with the dynamics of endemic cholera being related to climate and/or changes in the aquatic ecosystem. When the ecology of V. cholerae is considered in predictive models, a robust early warning system for cholera in endemic regions of the world can be developed for public health planning and decision making.ecology epidemiology microbiology remote sensing VL - 105 SN - 0027-8424, 1091-6490 ER - TY - JOUR T1 - Environmental Vibrio spp., isolated in Mozambique, contain a polymorphic group of integrative conjugative elements and class 1 integrons JF - FEMS Microbiology EcologyFEMS Microbiology Ecology Y1 - 2008 A1 - Taviani, Elisa A1 - Ceccarelli, Daniela A1 - Lazaro, Nivalda A1 - Bani, Stefania A1 - Cappuccinelli, Piero A1 - Rita R. Colwell A1 - Colombo, Mauro M. KW - ICE KW - integron KW - Mozambique KW - Vibrio AB - Circulation of mobile genetic elements linked to drug resistance spread was studied in Vibrio strains isolated from surface urban water (river and sea) and shellfish samples in 2002–2003 in Maputo, Mozambique. Class 1 integrons and integrating conjugative elements (ICE) were investigated by PCR and mating experiments in strains of major health interest: 10 Vibrio cholerae, six Vibrio parahaemolyticus, two Vibrio alginolyticus and one Vibrio fluvialis. Resistance to at least two antibiotics (predominantly β-lactams) was detected in all the strains, with additional resistances to sulfamethoxazole, spectinomycin, streptomycin and/or trimethoprim. Class 1 integrons contributed partially to the expression of drug resistance and were found in five isolates: four V. cholerae (blaP1 cassette, one strain also contained the dfrA15 cassette) and one V. alginolyticus (aadA2 cassette). ICEs, apparently devoid of resistance genes, were found in eight V. cholerae, three V. parahaemolyticus and one V. fluvialis isolates. A wide variability was observed by molecular characterization of ICEs. Five ICEs were included in the SXT/R391 family and seven ICEs were not classified. Our results indicate that the SXT/R391 family and related ICEs comprise a large class of polymorphic genetic elements widely circulating in environmental Vibrio strains in Africa, beside those evidently linked to drug resistance in clinical isolates. VL - 64 SN - 1574-6941 ER - TY - CHAP T1 - Expanding the reach of Grid computing: combining Globus- and BOINC-based systems T2 - Grids for Bioinformatics and Computational BiologyGrids for Bioinformatics and Computational Biology Y1 - 2008 A1 - Myers, D. S. A1 - Adam L. Bazinet A1 - Michael P. Cummings ED - Talbi, E. G. ED - Zomaya, A. Y. JA - Grids for Bioinformatics and Computational BiologyGrids for Bioinformatics and Computational Biology T3 - Wiley Book Series on Bioinformatics: Computational Techniques and Engineering PB - Wiley-Interscience CY - Hoboken ER - TY - JOUR T1 - A GENEALOGICAL APPROACH TO QUANTIFYING LINEAGE DIVERGENCE JF - EvolutionEvolution Y1 - 2008 A1 - Michael P. Cummings A1 - Neel, Maile C. A1 - Shaw, Kerry L. KW - Ancestral polymorphism KW - congruence KW - exclusivity KW - genealogy KW - lineage sorting KW - monophyly KW - paraphyly KW - Phylogeny KW - polyphyly KW - speciation KW - species AB - We introduce a statistic, the genealogical sorting index (gsi), for quantifying the degree of exclusive ancestry of labeled groups on a rooted genealogy and demonstrate its application. The statistic is simple, intuitive, and easily calculated. It has a normalized range to facilitate comparisons among different groups, trees, or studies and it provides information on individual groups rather than a composite measure for all groups. It naturally handles polytomies and accommodates measures of uncertainty in phylogenetic relationships. We use coalescent simulations to explore the behavior of the gsi across a range of divergence times, with the mean value increasing to 1, the maximum value when exclusivity within a group reached monophyly. Simulations also demonstrate that the power to reject the null hypothesis of mixed genealogical ancestry increased markedly as sample size increased, and that the gsi provides a statistically more powerful measure of divergence than FST. Applications to data from published studies demonstrated that the gsi provides a useful way to detect significant exclusivity even when groups are not monophyletic. Although we describe this statistic in the context of divergence, it is more broadly applicable to quantify and assess the significance of clustering of observations in labeled groups on any tree. VL - 62 SN - 1558-5646 ER - TY - JOUR T1 - Global impact of Vibrio cholerae interactions with chitin JF - Environmental MicrobiologyEnvironmental Microbiology Y1 - 2008 A1 - Pruzzo, Carla A1 - Vezzulli, Luigi A1 - Rita R. Colwell AB - The interaction of Vibrio cholerae with chitin exemplifies for microbial ecology a successful bacteria–substrate interaction with complex and significant influence on the lifestyle of the bacterium. Chitin is one of the most abundant polymers on earth and possibly the most abundant in the aquatic environment, where its association with V. cholerae has provided the microorganism with a number of advantages, including food availability, adaptation to environmental nutrient gradients, tolerance to stress and protection from predators. Emergent properties of V. cholerae–chitin interactions occur at multiple hierarchical levels in the environment and include cell metabolic and physiological responses e.g. chemotaxis, cell multiplication, induction of competence, biofilm formation, commensal and symbiotic relationship with higher organisms, cycling of nutrients, and pathogenicity for humans and aquatic animals. As factors mediating virulence of V. cholerae for humans and aquatic animals derive from mechanisms of adaptation to its environment, at different levels of hierarchical scale, V. cholerae interactions with chitin represent a useful model for examination of the role of primary habitat selection in the development of traits that have been identified as virulence factors in human disease. VL - 10 SN - 1462-2920 ER - TY - CHAP T1 - The Lattice Project: a Grid research and production environment combining multiple Grid computing models T2 - Distributed & Grid Computing — Science Made Transparent for Everyone. Principles, Applications and Supporting CommunitiesDistributed & Grid Computing — Science Made Transparent for Everyone. Principles, Applications and Supporting Communities Y1 - 2008 A1 - Adam L. Bazinet A1 - Michael P. Cummings ED - Weber, M. H. W. JA - Distributed & Grid Computing — Science Made Transparent for Everyone. Principles, Applications and Supporting CommunitiesDistributed & Grid Computing — Science Made Transparent for Everyone. Principles, Applications and Supporting Communities PB - Rechenkraft.net CY - Marburg ER - TY - CHAP T1 - The marine environment and human health: the cholera model T2 - Global Climate Change and Extreme Weather Events: Understanding the Contributions to Infectious Disease EmergenceGlobal Climate Change and Extreme Weather Events: Understanding the Contributions to Infectious Disease Emergence Y1 - 2008 A1 - Rita R. Colwell ED - Relman, David JA - Global Climate Change and Extreme Weather Events: Understanding the Contributions to Infectious Disease EmergenceGlobal Climate Change and Extreme Weather Events: Understanding the Contributions to Infectious Disease Emergence PB - National Academies Press SN - 9780309124027 ER - TY - JOUR T1 - Maternal depletion of CTCF reveals multiple functions during oocyte and preimplantation embryo development JF - DevelopmentDevelopment Y1 - 2008 A1 - Wan, L. B. A1 - Pan, H. A1 - Sridhar Hannenhalli A1 - Cheng, Y. A1 - Ma, J. A1 - Fedoriw, A. A1 - Lobanenkov, V. A1 - Latham, K. E. A1 - Schultz, R. M. A1 - Bartolomei, M. S. PB - The Company of Biologists Limited VL - 135 ER - TY - JOUR T1 - The minimum information about a genome sequence (MIGS) specification JF - Nature biotechnologyNature biotechnology Y1 - 2008 A1 - Field, Dawn A1 - Garrity, George A1 - Gray, Tanya A1 - Morrison, Norman A1 - J. Selengut A1 - Sterk, Peter A1 - Tatusova, Tatiana A1 - Thomson, Nicholas A1 - Allen, Michael J. A1 - Angiuoli, Samuel V. A1 - Ashburner, Michael A1 - Axelrod, Nelson A1 - Baldauf, Sandra A1 - Ballard, Stuart A1 - Boore, Jeffrey A1 - Cochrane, Guy A1 - Cole, James A1 - Dawyndt, Peter A1 - De Vos, Paul A1 - DePamphilis, Claude A1 - Edwards, Robert A1 - Faruque, Nadeem A1 - Feldman, Robert A1 - Gilbert, Jack A1 - Gilna, Paul A1 - Glöckner, Frank Oliver A1 - Goldstein, Philip A1 - Guralnick, Robert A1 - Haft, Dan A1 - Hancock, David A1 - Hermjakob, Henning A1 - Hertz-Fowler, Christiane A1 - Hugenholtz, Phil A1 - Joint, Ian A1 - Kagan, Leonid A1 - Kane, Matthew A1 - Kennedy, Jessie A1 - Kowalchuk, George A1 - Kottmann, Renzo A1 - Kolker, Eugene A1 - Kravitz, Saul A1 - Kyrpides, Nikos A1 - Leebens-Mack, Jim A1 - Lewis, Suzanna E. A1 - Li, Kelvin A1 - Lister, Allyson L. A1 - Lord, Phillip A1 - Maltsev, Natalia A1 - Markowitz, Victor A1 - Martiny, Jennifer A1 - Methe, Barbara A1 - Mizrachi, Ilene A1 - Moxon, Richard A1 - Nelson, Karen A1 - Parkhill, Julian A1 - Proctor, Lita A1 - White, Owen A1 - Sansone, Susanna-Assunta A1 - Spiers, Andrew A1 - Stevens, Robert A1 - Swift, Paul A1 - Taylor, Chris A1 - Tateno, Yoshio A1 - Tett, Adrian A1 - Turner, Sarah A1 - Ussery, David A1 - Vaughan, Bob A1 - Ward, Naomi A1 - Whetzel, Trish A1 - San Gil, Ingio A1 - Wilson, Gareth A1 - Wipat, Anil KW - Chromosome mapping KW - Databases, Factual KW - information dissemination KW - Information Storage and Retrieval KW - Information Theory KW - Internationality AB - With the quantity of genomic data increasing at an exponential rate, it is imperative that these data be captured electronically, in a standard format. Standardization activities must proceed within the auspices of open-access and international working bodies. To tackle the issues surrounding the development of better descriptions of genomic investigations, we have formed the Genomic Standards Consortium (GSC). Here, we introduce the minimum information about a genome sequence (MIGS) specification with the intent of promoting participation in its development and discussing the resources that will be required to develop improved mechanisms of metadata capture and exchange. As part of its wider goals, the GSC also supports improving the 'transparency' of the information contained in existing genomic databases. VL - 26 N1 - http://www.ncbi.nlm.nih.gov/pubmed/18464787?dopt=Abstract ER - TY - JOUR T1 - A molecular footprint of limb loss: sequence variation of the autopodial identity gene Hoxa-13 JF - J Mol EvolJ Mol Evol Y1 - 2008 A1 - Kohlsdorf, T. A1 - Michael P. Cummings A1 - Lynch, V. J. A1 - Stopper, G. F. A1 - Takahashi, K. A1 - Wagner, G. P. AB - The homeobox gene Hoxa-13 codes for a transcription factor involved in multiple functions, including body axis and hand/foot development in tetrapods. In this study we investigate whether the loss of one function (e.g., limb loss in snakes) left a molecular footprint in exon 1 of Hoxa-13 that could be associated with the release of functional constraints caused by limb loss. Fragments of the Hoxa-13 exon 1 were sequenced from 13 species and analyzed, with additional published sequences of the same region, using relative rates and likelihood-ratio tests. Five amino acid sites in exon 1 of Hoxa-13 were detected as evolving under positive selection in the stem lineage of snakes. To further investigate whether there is an association between limb loss and sequence variation in Hoxa-13, we used the random forest method on an alignment that included shark, basal fish lineages, and "eu-tetrapods" such as mammals, turtle, alligator, and birds. The random forest method approaches the problem as one of classification, where we seek to predict the presence or absence of autopodium based on amino acid variation in Hoxa-13 sequences. Different alignments tested were associated with similar error rates (18.42%). The random forest method suggested that phenotypic states (autopodium present and absent) can often be correctly predicted based on Hoxa-13 sequences. Basal, nontetrapod gnat-hostomes that never had an autopodium were consistently classified as limbless together with the snakes, while eu-tetrapods without any history of limb loss in their phylogeny were also consistently classified as having a limb. Misclassifications affected mostly lizards, which, as a group, have a history of limb loss and limb re-evolution, and the urodele and caecilian in our sample. We conclude that a molecular footprint can be detected in Hoxa-13 that is associated with the lack of an autopodium; groups with classification ambiguity (lizards) are characterized by a history of repeated limb loss and possible limb re-evolution. VL - 67 ER - TY - JOUR T1 - New records of phytoplankton for Bangladesh. 2. Cryptophyceae and Synurophyceae JF - Bangladesh Journal of BotanyBangladesh Journal of Botany Y1 - 2008 A1 - Khondker, Moniruzzaman A1 - Bhuiyan, Rauf Ahmed A1 - Yeasmin, Jenat A1 - Alam, Munirul A1 - Sack, R. Bradley A1 - Huq, Anwar A1 - Rita R. Colwell AB - This study presents two species of Rhodomonas, four species of Chroomonas, six species of Cryptomonas and Cryptochrysis minor, Cyanomonas coeruleus, Chrysodidymus synuroideus and Mallomonas akrokomos. These species have been reported from some ponds of Mathbaria in Pirojpur and Bakerganj of Barisal district in Bangladesh. VL - 36 SN - 0253-5416 ER - TY - JOUR T1 - New records of phytoplankton for Bangladesh. 5. Euglena, Euglenocapsa JF - Bangladesh Journal of Plant TaxonomyBangladesh Journal of Plant Taxonomy Y1 - 2008 A1 - Khondker, Moniruzzaman A1 - Bhuiyan, Rauf Ahmed A1 - Yeasmin, Jenat A1 - Alam, Munirul A1 - Sack, R. Bradley A1 - Huq, Anwar A1 - Rita R. Colwell AB - This study presents 20 taxa of the genus Euglena and one species of the rare euglenoid genus Euglenocapsa. All these taxa are reported for the first time from some pond ecosystems of Mathbaria in Pirojpur and Bakerganj of Barisal districts of Bangladesh. VL - 15 SN - 1028-2092 ER - TY - JOUR T1 - New records of phytoplankton for Bangladesh. 7. Phacus spp JF - Bangladesh Journal of BotanyBangladesh Journal of Botany Y1 - 2008 A1 - Khondker, Moniruzzaman A1 - Bhuiyan, Rauf Ahmed A1 - Yeasmin, Jenat A1 - Alam, Munirul A1 - Sack, R. Bradley A1 - Huq, Anwar A1 - Rita R. Colwell AB - Thirteen species of Phacus hitherto not reported from Bangladesh have been described and illustrated. Freshwater ponds at southern districts of Pirojpur and Barisal revealed these presence of the species. VL - 37 SN - 0253-5416 ER - TY - JOUR T1 - New records of phytoplankton for Bangladesh. 8. Trachelomonas Ehr. (Euglenophyceae) JF - Bangladesh Journal of BotanyBangladesh Journal of Botany Y1 - 2008 A1 - Khondker, Moniruzzaman A1 - Bhuiyan, Rauf Ahmed A1 - Yeasmin, Jenat A1 - Alam, Munirul A1 - Sack, R. Bradley A1 - Huq, Anwar A1 - Rita R. Colwell AB - Investigation of pelagic plankton communities from some freshwater ponds of Pirojpur and Barisal districts revealed the presence of 17 species under the genus Trachelomonas Ehr. for the first time in Bangladesh. VL - 37 SN - 0253-5416 ER - TY - JOUR T1 - Occurrence and Expression of Luminescence in Vibrio Cholerae JF - Applied and Environmental MicrobiologyAppl. Environ. Microbiol.Applied and Environmental MicrobiologyAppl. Environ. Microbiol. Y1 - 2008 A1 - Grim, Christopher J. A1 - Taviani, Elisa A1 - Alam, Munirul A1 - Huq, Anwar A1 - Sack, R. Bradley A1 - Rita R. Colwell AB - Several species of the genus Vibrio, including Vibrio cholerae, are bioluminescent or contain bioluminescent strains. Previous studies have reported that only 10% of V. cholerae strains are luminescent. Analysis of 224 isolates of non-O1/non-O139 V. cholerae collected from Chesapeake Bay, MD, revealed that 52% (116/224) were luminescent when an improved assay method was employed and 58% (130/224) of isolates harbored the luxA gene. In contrast, 334 non-O1/non-O139 V. cholerae strains isolated from two rural provinces in Bangladesh yielded only 21 (6.3%) luminescent and 35 (10.5%) luxA+ isolates. An additional 270 clinical and environmental isolates of V. cholerae serogroups O1 and O139 were tested, and none were luminescent or harbored luxA. These results indicate that bioluminescence may be a trait specific for non-O1/non-O139 V. cholerae strains that frequently occur in certain environments. Luminescence expression patterns of V. cholerae were also investigated, and isolates could be grouped based on expression level. Several strains with defective expression of the lux operon, including natural K variants, were identified. VL - 74 SN - 0099-2240, 1098-5336 ER - TY - JOUR T1 - Resolving arthropod phylogeny: exploring phylogenetic signal within 41 kb of protein-coding nuclear gene sequence JF - Syst BiolSyst Biol Y1 - 2008 A1 - Regier, J. C. A1 - Shultz, J. W. A1 - Ganley, A. R. D. A1 - Hussey, A. A1 - Shi, D. A1 - Ball, B. A1 - Zwick, A. A1 - Stajich, J. E. A1 - Michael P. Cummings A1 - Martin, J. W. A1 - Cunningham, C. W. AB - This study attempts to resolve relationships among and within the four basal arthropod lineages (Pancrustacea, Myriapoda, Euchelicerata, Pycnogonida) and to assess the widespread expectation that remaining phylogenetic problems will yield to increasing amounts of sequence data. Sixty-eight regions of 62 protein-coding nuclear genes (approximately 41 kilobases (kb)/taxon) were sequenced for 12 taxonomically diverse arthropod taxa and a tardigrade outgroup. Parsimony, likelihood, and Bayesian analyses of total nucleotide data generally strongly supported the monophyly of each of the basal lineages represented by more than one species. Other relationships within the Arthropoda were also supported, with support levels depending on method of analysis and inclusion/exclusion of synonymous changes. Removing third codon positions, where the assumption of base compositional homogeneity was rejected, altered the results. Removing the final class of synonymous mutations–first codon positions encoding leucine and arginine, which were also compositionally heterogeneous–yielded a data set that was consistent with a hypothesis of base compositional homogeneity. Furthermore, under such a data-exclusion regime, all 68 gene regions individually were consistent with base compositional homogeneity. Restricting likelihood analyses to nonsynonymous change recovered trees with strong support for the basal lineages but not for other groups that were variably supported with more inclusive data sets. In a further effort to increase phylogenetic signal, three types of data exploration were undertaken. (1) Individual genes were ranked by their average rate of nonsynonymous change, and three rate categories were assigned–fast, intermediate, and slow. Then, bootstrap analysis of each gene was performed separately to see which taxonomic groups received strong support. Five taxonomic groups were strongly supported independently by two or more genes, and these genes mostly belonged to the slow or intermediate categories, whereas groups supported only by a single gene region tended to be from genes of the fast category, arguing that fast genes provide a less consistent signal. (2) A sensitivity analysis was performed in which increasing numbers of genes were excluded, beginning with the fastest. The number of strongly supported nodes increased up to a point and then decreased slightly. Recovery of Hexapoda required removal of fast genes. Support for Mandibulata (Pancrustacea + Myriapoda) also increased, at times to "strong" levels, with removal of the fastest genes. (3) Concordance selection was evaluated by clustering genes according to their ability to recover Pancrustacea, Euchelicerata, or Myriapoda and analyzing the three clusters separately. All clusters of genes recovered the three concordance clades but were at times inconsistent in the relationships recovered among and within these clades, a result that indicates that the a priori concordance criteria may bias phylogenetic signal in unexpected ways. In a further attempt to increase support of taxonomic relationships, sequence data from 49 additional taxa for three slow genes (i.e., EF-1 alpha, EF-2, and Pol II) were combined with the various 13-taxon data sets. The 62-taxon analyses supported the results of the 13-taxon analyses and provided increased support for additional pancrustacean clades found in an earlier analysis including only EF-1 alpha, EF-2, and Pol II. VL - 57 ER - TY - JOUR T1 - Schistosoma mansoni: Microarray analysis of gene expression induced by host sex. JF - Exp Parasitol Y1 - 2008 A1 - Waisberg, M A1 - Lobo, F P A1 - Cerqueira, G C A1 - Passos, L K J A1 - Carvalho, O S A1 - El-Sayed, N M A1 - Franco, G R KW - Animals KW - Biomphalaria KW - Female KW - Gene expression KW - Host-Parasite Interactions KW - Male KW - Mice KW - Oligonucleotide Array Sequence Analysis KW - Reverse Transcriptase Polymerase Chain Reaction KW - RNA, Helminth KW - Schistosoma mansoni KW - Schistosomiasis mansoni KW - Sex Factors AB -

Schistosoma mansoni is a digenetic trematode and a human parasite responsible for high social and economic impact. Although some authors have studied the effect of host hormones on parasites, not much is known about the effects of host sex on gene expression in Schistosomes. In order to study gene transcripts associated with the host sex, we compared the gene expression profiles of both male and female unisexual adult S. mansoni parasites raised on either male or female hosts, using DNA microarrays. Our results show that host sex caused differential expression of at least 11 genes in female parasites and of 134 in male parasites. Of the differentially expressed genes in female worms, 10 were preferentially expressed in female worms from male mice, while of the 134 differentially expressed genes in male parasites, 79 (59%) were preferentially expressed in worms from female mice. Further investigation of the role of each of those genes will help understand better their importance in the pathogenesis of Schistosomiasis.

VL - 120 CP - 4 M3 - 10.1016/j.exppara.2008.09.005 ER - TY - JOUR T1 - Seasonal Cholera from Multiple Small Outbreaks, Rural Bangladesh JF - Emerging Infectious DiseasesEmerg Infect DisEmerging Infectious DiseasesEmerg Infect Dis Y1 - 2008 A1 - Stine, O. Colin A1 - Alam, Munirul A1 - Tang, Li A1 - Nair, G. Balakrish A1 - Siddique, A. Kasem A1 - Faruque, Shah M. A1 - Huq, Anwar A1 - Rita R. Colwell A1 - Sack, R. Bradley A1 - Morris, J. Glenn AB - Clinical and environmental Vibrio cholerae organisms collected from February 2004 through April 2005 were systematically isolated from 2 rural Bangladeshi locales. Their genetic relatedness was evaluated at 5 loci that contained a variable number of tandem repeats (VNTR). The observed minimal overlap in VNTR patterns between the 2 communities was consistent with sequential, small outbreaks from local sources. VL - 14 SN - 1080-6040 ER - TY - JOUR T1 - Sequence diversity and evolution of multigene families in Trypanosoma cruzi JF - Molecular and Biochemical ParasitologyMolecular and Biochemical Parasitology Y1 - 2008 A1 - Cerqueira, Gustavo C. A1 - Bartholomeu, Daniella C. A1 - DaRocha, Wanderson D. A1 - Hou, Lihua A1 - Freitas-Silva, Danielle M. A1 - Machado, Carlos Renato A1 - Najib M. El‐Sayed A1 - Teixeira, Santuza M. R. KW - Amastin KW - Gene conversion KW - Genetic diversity KW - Multigene families KW - Trypanosoma cruzi AB - Several copies of genes belonging to three multigene families present in the genome of Trypanosoma cruzi were sequenced and comparatively analyzed across six different strains of the parasite belonging to the T. cruzi I lineage (Colombiana, Silvio X10 and Dm28c), the T. cruzi II lineage (Esmeraldo and JG) and a hybrid strain (CL Brener). For all three gene families analyzed, our results support the division in T. cruzi I and II lineages. Furthermore, in agreement with its hybrid nature, sequences derived from the CL Brener clone clustered together with T. cruzi II sequences as well as with a third group of sequences. Paralogous sequences encoding Amastin, an amastigote surface glycoprotein and TcAG48, an antigenic RNA binding protein, which are clustered in the parasite genome, present higher intragenomic variability in T. cruzi II and CL Brener strains, when compared to T. cruzi I strains. Paralogous sequences derived from the TcADC gene family, which encode various isoforms of adenylyl cyclases and are dispersed throughout the T. cruzi genome, exhibit similar degree of variability in all strains, except in the CL Brener strain, in which the sequences were more divergent. Several factors including mutation rates and gene conversion mechanisms, acting differently within the T. cruzi population, may contribute to create such distinct levels of sequence diversity in multigene families that are clustered in the T. cruzi genome. VL - 157 SN - 0166-6851 ER - TY - JOUR T1 - Silent Sputnik JF - BioScienceBioScience Y1 - 2008 A1 - Rita R. Colwell VL - 58 SN - 0006-3568 ER - TY - JOUR T1 - A simple binomial test for estimating sequencing errors in public repository 16S rRNA sequences JF - Journal of Microbiological MethodsJournal of Microbiological Methods Y1 - 2008 A1 - Zo, Young-Gun A1 - Rita R. Colwell KW - 16S rRNA KW - Binomial model KW - Sequence similarity coefficient KW - Sequencing error KW - SSU rRNA AB - Sequences in public databases may contain a number of sequencing errors. A double binomial model describing the distribution of indel-excluded similarity coefficients (S) among repeatedly sequenced 16S rRNA was previously developed and it produced a confidence interval of S useful for testing sequence identity among sequences of 400-bp length. We characterized patterns in sequencing errors found in nearly complete 16S rRNA sequences of Vibrionaceae as highly variable in reported sequence length and containing a small number of indels. To accommodate these characteristics, a simple binomial model for distribution of the similarity coefficient (H) that included indels was derived from the double binomial model for S. The model showed good fit to empirical data. By using either a pre-determined or bootstrapping estimated standard probability of base matching, we were able to use the exact binomial test to determine the relative level of sequencing error for a given pair of duplicated sequences. A limitation of the method is the requirement that duplicated sequences for the same template sequence be paired, but this can be overcome by using only conserved regions of 16S rRNA sequences and pairing a given sequence with its highest scoring BLAST search hit from the nr database of GenBank. VL - 72 SN - 0167-7012 ER - TY - JOUR T1 - Transesterification activity of a novel lipase from Acinetobacter venetianus RAG-1 JF - Antonie van LeeuwenhoekAntonie van Leeuwenhoek Y1 - 2008 A1 - Snellman, E. A. A1 - Rita R. Colwell AB - Transesterification activity and the industrial potential of a novel lipase prepared from Acinetobacter ventiatus RAG-1 were evaluated. Purified lipase samples were dialyzed against pH 9.0 buffer in a single optimization step prior to lyophilization. The enzyme and organic phase were pre-equilibrated (separately) to the same thermodynamic water activities (a w) ranging from a w 0.33 to 0.97. Production of 1-octyl butyrate by lipase-catalyzed transesterification of vinyl butyrate with 1-octanol in hexane was monitored by gas chromatography. Production of 1-octyl butyrate and initial rate of reaction depended on water activity. Product synthesis and rate of transesterification increased sharply with increase from a w 0.33 to 0.55. Highest product concentration (218 mM) and rate of reaction (18.7 μmol h−1 · 10 μg protein) were measured at a w 0.86. Transesterification activity in hexane represented 32% of comparable hydrolytic activity in aqueous buffer. VL - 94 ER - TY - JOUR T1 - Vibrio cholerae non‐O1, non‐O139 strains isolated before 1992 from Varanasi, India are multiple drug resistant, contain intSXT, dfr18 and aadA5 genes JF - Environmental MicrobiologyEnvironmental Microbiology Y1 - 2008 A1 - Mohapatra, Harapriya A1 - Mohapatra, Saswat S. A1 - Mantri, Chinmay K. A1 - Rita R. Colwell A1 - Singh, Durg V. AB - In this study, we report the presence of the SXT element and Class I integron in Vibrio cholerae non-O1, non-O139 strains isolated from Varanasi, India. Isolates were resistant to cotrimoxazole, trimethoprim and/or streptomycin, furazolidone and ampicillin. None contained plasmids. Polymerase chain reaction (PCR) and DNA sequencing revealed the presence of antibiotic resistance gene cassettes, aadA1, aadA2, aadA5 and dfrA15, in the Class I integron and SXT, an integrative conjugative element containing dfr18, sulII and strAB, in three and six of the isolates respectively. Conjugation experiments, followed by PCR analysis of transconjugants, provided evidence for the transferable nature of intSXT and associated antibiotic resistance gene cassettes. This is the first report of the occurrence of SXT ICE, dfr18, sulII, strAB and aadA5 genes in environmental V. cholerae non-O1, non-O139 strains from Varanasi, India, that had been isolated before 1992. VL - 10 SN - 1462-2920 ER - TY - JOUR T1 - Association of Vibrio Cholerae O1 El Tor and O139 Bengal with the Copepods Acartia Tonsa and Eurytemora Affinis JF - Applied and Environmental MicrobiologyAppl. Environ. Microbiol.Applied and Environmental MicrobiologyAppl. Environ. Microbiol. Y1 - 2007 A1 - Rawlings, Tonya K. A1 - Ruiz, Gregory M. A1 - Rita R. Colwell AB - The association of Vibrio cholerae with zooplankton has been suggested as an important factor in transmission of human epidemic cholera, and the ability to colonize zooplankton surfaces may play a role in the temporal variation and predominance of the two different serogroups (V. cholerae O1 El Tor and O139) in the aquatic environment. To date, interactions between specific serogroups and species of plankton remain poorly understood. Laboratory microcosm experiments were carried out to compare quantitatively the colonization of two copepod species, Acartia tonsa and Eurytemora affinis, by each of the epidemic serogroups. V. cholerae O1 consistently achieved higher abundances than V. cholerae O139 in colonizing adults of each copepod species as well as the multiple life stages of E. affinis. This difference in colonization may be significant in the general predominance of V. cholerae O1 in cholera epidemics in rural Bangladesh where water supplies are taken directly from the environment. VL - 73 SN - 0099-2240, 1098-5336 ER - TY - JOUR T1 - Biased data reduce efficiency and effectiveness of conservation reserve networks JF - Ecology LettersEcology Letters Y1 - 2007 A1 - Grand, Joanna A1 - Michael P. Cummings A1 - Rebelo, Tony G. A1 - Ricketts, Taylor H. A1 - Neel, Maile C. KW - Bias KW - biodiversity conservation KW - complementarity KW - efficiency KW - marxan KW - rarity KW - reserve networks KW - reserve selection algorithms KW - species detection AB - Complementarity-based reserve selection algorithms efficiently prioritize sites for biodiversity conservation, but they are data-intensive and most regions lack accurate distribution maps for the majority of species. We explored implications of basing conservation planning decisions on incomplete and biased data using occurrence records of the plant family Proteaceae in South Africa. Treating this high-quality database as ‘complete’, we introduced three realistic sampling biases characteristic of biodiversity databases: a detectability sampling bias and two forms of roads sampling bias. We then compared reserve networks constructed using complete, biased, and randomly sampled data. All forms of biased sampling performed worse than both the complete data set and equal-effort random sampling. Biased sampling failed to detect a median of 1–5% of species, and resulted in reserve networks that were 9–17% larger than those designed with complete data. Spatial congruence and the correlation of irreplaceability scores between reserve networks selected with biased and complete data were low. Thus, reserve networks based on biased data require more area to protect fewer species and identify different locations than those selected with randomly sampled or complete data. VL - 10 SN - 1461-0248 ER - TY - JOUR T1 - Bio-STEER: A Semantic Web workflow tool for Grid computing in the life sciences JF - Future Generation Comp SystFuture Generation Comp Syst Y1 - 2007 A1 - Lee, S. A1 - Wang, T. D. A1 - Hashmi, N. A1 - Michael P. Cummings KW - client/server KW - distributed KW - ENVIRONMENTS KW - integrated KW - interface KW - management KW - semantics KW - services KW - systems KW - user KW - web-base KW - workflow AB - Life science research is becoming evermore computationally intensive. Hence, from a computational resource perspective, Grid computing provides a logical approach to meeting many of the computational needs of life science research. However, there are several barriers to the widespread use of Grid computing in life sciences. In this paper, we attempt to address one particular barrier: the difficulty of using Grid computing by life scientists. Life science research often involves connecting multiple applications together to form a workflow. This process of constructing a workflow is complex. When combined with the difficulty of using Grid services, composing a meaningful workflow using Grid services can present a challenge to life scientists. Our proposed solution is a Semantic Web-enabled computing environment, called Bio-STEER. In BioSTEER, bioinformatics Grid services are mapped to Semantic Web services, described in OWL-S. We also defined an ontology in OWL to model bioinformatics applications. A graphical user interface helps to construct a scientific workflow by showing a list of services that are semantically sound: that is, the output of one service is semantically compatible with the input of the connecting service. Bio-STEER can help users take full advantaue of Grid services through a user-friendly graphical user interface (GUI), which allows them to easily construct the workflows they need. (c) 2006 Elsevier B.V. All rights reserved. VL - 23 ER - TY - Generic T1 - Bridging art and science with creativity support tools T2 - Proceedings of the 6th ACM SIGCHI conference on Creativity & cognition Y1 - 2007 A1 - Shneiderman, Ben A1 - Rita R. Colwell A1 - Diamond, Sara A1 - Greenhalgh, Paul A1 - Wulf, William JA - Proceedings of the 6th ACM SIGCHI conference on Creativity & cognition T3 - C&C '07 PB - ACM CY - New York, NY, USA SN - 978-1-59593-712-4 ER - TY - JOUR T1 - Cofactor-independent phosphoglycerate mutase is an essential gene in procyclic form Trypanosoma brucei JF - Parasitology researchParasitology research Y1 - 2007 A1 - Djikeng, A. A1 - Raverdy, S. A1 - Foster, Jeffrey S. A1 - Bartholomeu, D. A1 - Zhang, Y. A1 - Najib M. El‐Sayed A1 - Carlow, C. VL - 100 ER - TY - JOUR T1 - Creating a nationwide wireless detection sensor network for chemical, biological and radiological threats JF - Gentag White PaperGentag White Paper Y1 - 2007 A1 - Rita R. Colwell A1 - Peeters, J. ER - TY - JOUR T1 - Draft genome of the filarial nematode parasite Brugia malayi JF - ScienceScience Y1 - 2007 A1 - Ghedin, E. A1 - Wang, S. A1 - Spiro, D. A1 - Caler, E. A1 - Zhao, Q. A1 - Crabtree, J. A1 - Allen, J. E. A1 - Delcher, A. L. A1 - Guiliano, D. B. A1 - Miranda-Saavedra, D. A1 - others, PB - American Association for the Advancement of Science VL - 317 ER - TY - JOUR T1 - Evolution of genes and genomes on the Drosophila phylogeny JF - NatureNature Y1 - 2007 A1 - Clark, Andrew G. A1 - Eisen, Michael B. A1 - Smith, Douglas R. A1 - Bergman, Casey M. A1 - Oliver, Brian A1 - Markow, Therese A. A1 - Kaufman, Thomas C. A1 - Kellis, Manolis A1 - Gelbart, William A1 - Iyer, Venky N. A1 - Pollard, Daniel A. A1 - Sackton, Timothy B. A1 - Larracuente, Amanda M. A1 - Singh, Nadia D. A1 - Abad, Jose P. A1 - Abt, Dawn N. A1 - Adryan, Boris A1 - Aguade, Montserrat A1 - Akashi, Hiroshi A1 - Anderson, Wyatt W. A1 - Aquadro, Charles F. A1 - Ardell, David H. A1 - Arguello, Roman A1 - Artieri, Carlo G. A1 - Barbash, Daniel A. A1 - Barker, Daniel A1 - Barsanti, Paolo A1 - Batterham, Phil A1 - Batzoglou, Serafim A1 - Begun, Dave A1 - Bhutkar, Arjun A1 - Blanco, Enrico A1 - Bosak, Stephanie A. A1 - Bradley, Robert K. A1 - Brand, Adrianne D. A1 - Brent, Michael R. A1 - Brooks, Angela N. A1 - Brown, Randall H. A1 - Butlin, Roger K. A1 - Caggese, Corrado A1 - Calvi, Brian R. A1 - Carvalho, A. Bernardo de A1 - Caspi, Anat A1 - Castrezana, Sergio A1 - Celniker, Susan E. A1 - Chang, Jean L. A1 - Chapple, Charles A1 - Chatterji, Sourav A1 - Chinwalla, Asif A1 - Civetta, Alberto A1 - Clifton, Sandra W. A1 - Comeron, Josep M. A1 - Costello, James C. A1 - Coyne, Jerry A. A1 - Daub, Jennifer A1 - David, Robert G. A1 - Delcher, Arthur L. A1 - Delehaunty, Kim A1 - Do, Chuong B. A1 - Ebling, Heather A1 - Edwards, Kevin A1 - Eickbush, Thomas A1 - Evans, Jay D. A1 - Filipski, Alan A1 - Findei, A1 - Sven A1 - Freyhult, Eva A1 - Fulton, Lucinda A1 - Fulton, Robert A1 - Garcia, Ana C. L. A1 - Gardiner, Anastasia A1 - Garfield, David A. A1 - Garvin, Barry E. A1 - Gibson, Greg A1 - Gilbert, Don A1 - Gnerre, Sante A1 - Godfrey, Jennifer A1 - Good, Robert A1 - Gotea, Valer A1 - Gravely, Brenton A1 - Greenberg, Anthony J. A1 - Griffiths-Jones, Sam A1 - Gross, Samuel A1 - Guigo, Roderic A1 - Gustafson, Erik A. A1 - Haerty, Wilfried A1 - Hahn, Matthew W. A1 - Halligan, Daniel L. A1 - Halpern, Aaron L. A1 - Halter, Gillian M. A1 - Han, Mira V. A1 - Heger, Andreas A1 - Hillier, LaDeana A1 - Hinrichs, Angie S. A1 - Holmes, Ian A1 - Hoskins, Roger A. A1 - Hubisz, Melissa J. A1 - Hultmark, Dan A1 - Huntley, Melanie A. A1 - Jaffe, David B. A1 - Jagadeeshan, Santosh A1 - Jeck, William R. A1 - Johnson, Justin A1 - Jones, Corbin D. A1 - Jordan, William C. A1 - Karpen, Gary H. A1 - Kataoka, Eiko A1 - Keightley, Peter D. A1 - Kheradpour, Pouya A1 - Kirkness, Ewen F. A1 - Koerich, Leonardo B. A1 - Kristiansen, Karsten A1 - Kudrna, Dave A1 - Kulathinal, Rob J. A1 - Kumar, Sudhir A1 - Kwok, Roberta A1 - Lander, Eric A1 - Langley, Charles H. A1 - Lapoint, Richard A1 - Lazzaro, Brian P. A1 - Lee, So-Jeong A1 - Levesque, Lisa A1 - Li, Ruiqiang A1 - Lin, Chiao-Feng A1 - Lin, Michael F. A1 - Lindblad-Toh, Kerstin A1 - Llopart, Ana A1 - Long, Manyuan A1 - Low, Lloyd A1 - Lozovsky, Elena A1 - Lu, Jian A1 - Luo, Meizhong A1 - Machado, Carlos A. A1 - Makalowski, Wojciech A1 - Marzo, Mar A1 - Matsuda, Muneo A1 - Matzkin, Luciano A1 - McAllister, Bryant A1 - McBride, Carolyn S. A1 - McKernan, Brendan A1 - McKernan, Kevin A1 - Mendez-Lago, Maria A1 - Minx, Patrick A1 - Mollenhauer, Michael U. A1 - Montooth, Kristi A1 - Stephen M. Mount A1 - Mu, Xu A1 - Myers, Eugene A1 - Negre, Barbara A1 - Newfeld, Stuart A1 - Nielsen, Rasmus A1 - Noor, Mohamed A. F. A1 - O'Grady, Patrick A1 - Pachter, Lior A1 - Papaceit, Montserrat A1 - Parisi, Matthew J. A1 - Parisi, Michael A1 - Parts, Leopold A1 - Pedersen, Jakob S. A1 - Pesole, Graziano A1 - Phillippy, Adam M. A1 - Ponting, Chris P. A1 - M. Pop A1 - Porcelli, Damiano A1 - Powell, Jeffrey R. A1 - Prohaska, Sonja A1 - Pruitt, Kim A1 - Puig, Marta A1 - Quesneville, Hadi A1 - Ram, Kristipati Ravi A1 - Rand, David A1 - Rasmussen, Matthew D. A1 - Reed, Laura K. A1 - Reenan, Robert A1 - Reily, Amy A1 - Remington, Karin A. A1 - Rieger, Tania T. A1 - Ritchie, Michael G. A1 - Robin, Charles A1 - Rogers, Yu-Hui A1 - Rohde, Claudia A1 - Rozas, Julio A1 - Rubenfield, Marc J. A1 - Ruiz, Alfredo A1 - Russo, Susan A1 - Salzberg, Steven L. A1 - Sanchez-Gracia, Alejandro A1 - Saranga, David J. A1 - Sato, Hajime A1 - Schaeffer, Stephen W. A1 - Schatz, Michael C. A1 - Schlenke, Todd A1 - Schwartz, Russell A1 - Segarra, Carmen A1 - Singh, Rama S. A1 - Sirot, Laura A1 - Sirota, Marina A1 - Sisneros, Nicholas B. A1 - Smith, Chris D. A1 - Smith, Temple F. A1 - Spieth, John A1 - Stage, Deborah E. A1 - Stark, Alexander A1 - Stephan, Wolfgang A1 - Strausberg, Robert L. A1 - Strempel, Sebastian A1 - Sturgill, David A1 - Sutton, Granger A1 - Sutton, Granger G. A1 - Tao, Wei A1 - Teichmann, Sarah A1 - Tobari, Yoshiko N. A1 - Tomimura, Yoshihiko A1 - Tsolas, Jason M. A1 - Valente, Vera L. S. A1 - Venter, Eli A1 - Venter, J. Craig A1 - Vicario, Saverio A1 - Vieira, Filipe G. A1 - Vilella, Albert J. A1 - Villasante, Alfredo A1 - Walenz, Brian A1 - Wang, Jun A1 - Wasserman, Marvin A1 - Watts, Thomas A1 - Wilson, Derek A1 - Wilson, Richard K. A1 - Wing, Rod A. A1 - Wolfner, Mariana F. A1 - Wong, Alex A1 - Wong, Gane Ka-Shu A1 - Wu, Chung- I. A1 - Wu, Gabriel A1 - Yamamoto, Daisuke A1 - Yang, Hsiao-Pei A1 - Yang, Shiaw-Pyng A1 - Yorke, James A. A1 - Yoshida, Kiyohito A1 - Zdobnov, Evgeny A1 - Zhang, Peili A1 - Zhang, Yu A1 - Zimin, Aleksey V. A1 - Baldwin, Jennifer A1 - Abdouelleil, Amr A1 - Abdulkadir, Jamal A1 - Abebe, Adal A1 - Abera, Brikti A1 - Abreu, Justin A1 - Acer, St Christophe A1 - Aftuck, Lynne A1 - Alexander, Allen A1 - An, Peter A1 - Anderson, Erica A1 - Anderson, Scott A1 - Arachi, Harindra A1 - Azer, Marc A1 - Bachantsang, Pasang A1 - Barry, Andrew A1 - Bayul, Tashi A1 - Berlin, Aaron A1 - Bessette, Daniel A1 - Bloom, Toby A1 - Blye, Jason A1 - Boguslavskiy, Leonid A1 - Bonnet, Claude A1 - Boukhgalter, Boris A1 - Bourzgui, Imane A1 - Brown, Adam A1 - Cahill, Patrick A1 - Channer, Sheridon A1 - Cheshatsang, Yama A1 - Chuda, Lisa A1 - Citroen, Mieke A1 - Collymore, Alville A1 - Cooke, Patrick A1 - Costello, Maura A1 - D'Aco, Katie A1 - Daza, Riza A1 - Haan, Georgius De A1 - DeGray, Stuart A1 - DeMaso, Christina A1 - Dhargay, Norbu A1 - Dooley, Kimberly A1 - Dooley, Erin A1 - Doricent, Missole A1 - Dorje, Passang A1 - Dorjee, Kunsang A1 - Dupes, Alan A1 - Elong, Richard A1 - Falk, Jill A1 - Farina, Abderrahim A1 - Faro, Susan A1 - Ferguson, Diallo A1 - Fisher, Sheila A1 - Foley, Chelsea D. A1 - Franke, Alicia A1 - Friedrich, Dennis A1 - Gadbois, Loryn A1 - Gearin, Gary A1 - Gearin, Christina R. A1 - Giannoukos, Georgia A1 - Goode, Tina A1 - Graham, Joseph A1 - Grandbois, Edward A1 - Grewal, Sharleen A1 - Gyaltsen, Kunsang A1 - Hafez, Nabil A1 - Hagos, Birhane A1 - Hall, Jennifer A1 - Henson, Charlotte A1 - Hollinger, Andrew A1 - Honan, Tracey A1 - Huard, Monika D. A1 - Hughes, Leanne A1 - Hurhula, Brian A1 - Husby, M. Erii A1 - Kamat, Asha A1 - Kanga, Ben A1 - Kashin, Seva A1 - Khazanovich, Dmitry A1 - Kisner, Peter A1 - Lance, Krista A1 - Lara, Marcia A1 - Lee, William A1 - Lennon, Niall A1 - Letendre, Frances A1 - LeVine, Rosie A1 - Lipovsky, Alex A1 - Liu, Xiaohong A1 - Liu, Jinlei A1 - Liu, Shangtao A1 - Lokyitsang, Tashi A1 - Lokyitsang, Yeshi A1 - Lubonja, Rakela A1 - Lui, Annie A1 - MacDonald, Pen A1 - Magnisalis, Vasilia A1 - Maru, Kebede A1 - Matthews, Charles A1 - McCusker, William A1 - McDonough, Susan A1 - Mehta, Teena A1 - Meldrim, James A1 - Meneus, Louis A1 - Mihai, Oana A1 - Mihalev, Atanas A1 - Mihova, Tanya A1 - Mittelman, Rachel A1 - Mlenga, Valentine A1 - Montmayeur, Anna A1 - Mulrain, Leonidas A1 - Navidi, Adam A1 - Naylor, Jerome A1 - Negash, Tamrat A1 - Nguyen, Thu A1 - Nguyen, Nga A1 - Nicol, Robert A1 - Norbu, Choe A1 - Norbu, Nyima A1 - Novod, Nathaniel A1 - O'Neill, Barry A1 - Osman, Sahal A1 - Markiewicz, Eva A1 - Oyono, Otero L. A1 - Patti, Christopher A1 - Phunkhang, Pema A1 - Pierre, Fritz A1 - Priest, Margaret A1 - Raghuraman, Sujaa A1 - Rege, Filip A1 - Reyes, Rebecca A1 - Rise, Cecil A1 - Rogov, Peter A1 - Ross, Keenan A1 - Ryan, Elizabeth A1 - Settipalli, Sampath A1 - Shea, Terry A1 - Sherpa, Ngawang A1 - Shi, Lu A1 - Shih, Diana A1 - Sparrow, Todd A1 - Spaulding, Jessica A1 - Stalker, John A1 - Stange-Thomann, Nicole A1 - Stavropoulos, Sharon A1 - Stone, Catherine A1 - Strader, Christopher A1 - Tesfaye, Senait A1 - Thomson, Talene A1 - Thoulutsang, Yama A1 - Thoulutsang, Dawa A1 - Topham, Kerri A1 - Topping, Ira A1 - Tsamla, Tsamla A1 - Vassiliev, Helen A1 - Vo, Andy A1 - Wangchuk, Tsering A1 - Wangdi, Tsering A1 - Weiand, Michael A1 - Wilkinson, Jane A1 - Wilson, Adam A1 - Yadav, Shailendra A1 - Young, Geneva A1 - Yu, Qing A1 - Zembek, Lisa A1 - Zhong, Danni A1 - Zimmer, Andrew A1 - Zwirko, Zac A1 - Jaffe, David B. A1 - Alvarez, Pablo A1 - Brockman, Will A1 - Butler, Jonathan A1 - Chin, CheeWhye A1 - Gnerre, Sante A1 - Grabherr, Manfred A1 - Kleber, Michael A1 - Mauceli, Evan A1 - MacCallum, Iain AB - Comparative analysis of multiple genomes in a phylogenetic framework dramatically improves the precision and sensitivity of evolutionary inference, producing more robust results than single-genome analyses can provide. The genomes of 12 Drosophila species, ten of which are presented here for the first time (sechellia, simulans, yakuba, erecta, ananassae, persimilis, willistoni, mojavensis, virilis and grimshawi), illustrate how rates and patterns of sequence divergence across taxa can illuminate evolutionary processes on a genomic scale. These genome sequences augment the formidable genetic tools that have made Drosophila melanogaster a pre-eminent model for animal genetics, and will further catalyse fundamental research on mechanisms of development, cell biology, genetics, disease, neurobiology, behaviour, physiology and evolution. Despite remarkable similarities among these Drosophila species, we identified many putatively non-neutral changes in protein-coding genes, non-coding RNA genes, and cis-regulatory regions. These may prove to underlie differences in the ecology and behaviour of these diverse species. VL - 450 SN - 0028-0836 N1 - [szlig] ER - TY - JOUR T1 - Evolution of genes and genomes on the Drosophila phylogeny. JF - Nature Y1 - 2007 A1 - Clark, Andrew G A1 - Eisen, Michael B A1 - Smith, Douglas R A1 - Bergman, Casey M A1 - Oliver, Brian A1 - Markow, Therese A A1 - Kaufman, Thomas C A1 - Kellis, Manolis A1 - Gelbart, William A1 - Iyer, Venky N A1 - Pollard, Daniel A A1 - Sackton, Timothy B A1 - Larracuente, Amanda M A1 - Singh, Nadia D A1 - Abad, Jose P A1 - Abt, Dawn N A1 - Adryan, Boris A1 - Aguade, Montserrat A1 - Akashi, Hiroshi A1 - Anderson, Wyatt W A1 - Aquadro, Charles F A1 - Ardell, David H A1 - Arguello, Roman A1 - Artieri, Carlo G A1 - Barbash, Daniel A A1 - Barker, Daniel A1 - Barsanti, Paolo A1 - Batterham, Phil A1 - Batzoglou, Serafim A1 - Begun, Dave A1 - Bhutkar, Arjun A1 - Blanco, Enrico A1 - Bosak, Stephanie A A1 - Bradley, Robert K A1 - Brand, Adrianne D A1 - Brent, Michael R A1 - Brooks, Angela N A1 - Brown, Randall H A1 - Butlin, Roger K A1 - Caggese, Corrado A1 - Calvi, Brian R A1 - Bernardo de Carvalho, A A1 - Caspi, Anat A1 - Castrezana, Sergio A1 - Celniker, Susan E A1 - Chang, Jean L A1 - Chapple, Charles A1 - Chatterji, Sourav A1 - Chinwalla, Asif A1 - Civetta, Alberto A1 - Clifton, Sandra W A1 - Comeron, Josep M A1 - Costello, James C A1 - Coyne, Jerry A A1 - Daub, Jennifer A1 - David, Robert G A1 - Delcher, Arthur L A1 - Delehaunty, Kim A1 - Do, Chuong B A1 - Ebling, Heather A1 - Edwards, Kevin A1 - Eickbush, Thomas A1 - Evans, Jay D A1 - Filipski, Alan A1 - Findeiss, Sven A1 - Freyhult, Eva A1 - Fulton, Lucinda A1 - Fulton, Robert A1 - Garcia, Ana C L A1 - Gardiner, Anastasia A1 - Garfield, David A A1 - Garvin, Barry E A1 - Gibson, Greg A1 - Gilbert, Don A1 - Gnerre, Sante A1 - Godfrey, Jennifer A1 - Good, Robert A1 - Gotea, Valer A1 - Gravely, Brenton A1 - Greenberg, Anthony J A1 - Griffiths-Jones, Sam A1 - Gross, Samuel A1 - Guigo, Roderic A1 - Gustafson, Erik A A1 - Haerty, Wilfried A1 - Hahn, Matthew W A1 - Halligan, Daniel L A1 - Halpern, Aaron L A1 - Halter, Gillian M A1 - Han, Mira V A1 - Heger, Andreas A1 - Hillier, LaDeana A1 - Hinrichs, Angie S A1 - Holmes, Ian A1 - Hoskins, Roger A A1 - Hubisz, Melissa J A1 - Hultmark, Dan A1 - Huntley, Melanie A A1 - Jaffe, David B A1 - Jagadeeshan, Santosh A1 - Jeck, William R A1 - Johnson, Justin A1 - Jones, Corbin D A1 - Jordan, William C A1 - Karpen, Gary H A1 - Kataoka, Eiko A1 - Keightley, Peter D A1 - Kheradpour, Pouya A1 - Kirkness, Ewen F A1 - Koerich, Leonardo B A1 - Kristiansen, Karsten A1 - Kudrna, Dave A1 - Kulathinal, Rob J A1 - Kumar, Sudhir A1 - Kwok, Roberta A1 - Lander, Eric A1 - Langley, Charles H A1 - Lapoint, Richard A1 - Lazzaro, Brian P A1 - Lee, So-Jeong A1 - Levesque, Lisa A1 - Li, Ruiqiang A1 - Lin, Chiao-Feng A1 - Lin, Michael F A1 - Lindblad-Toh, Kerstin A1 - Llopart, Ana A1 - Long, Manyuan A1 - Low, Lloyd A1 - Lozovsky, Elena A1 - Lu, Jian A1 - Luo, Meizhong A1 - Machado, Carlos A A1 - Makalowski, Wojciech A1 - Marzo, Mar A1 - Matsuda, Muneo A1 - Matzkin, Luciano A1 - McAllister, Bryant A1 - McBride, Carolyn S A1 - McKernan, Brendan A1 - McKernan, Kevin A1 - Mendez-Lago, Maria A1 - Minx, Patrick A1 - Mollenhauer, Michael U A1 - Montooth, Kristi A1 - Mount, Stephen M A1 - Mu, Xu A1 - Myers, Eugene A1 - Negre, Barbara A1 - Newfeld, Stuart A1 - Nielsen, Rasmus A1 - Noor, Mohamed A F A1 - O'Grady, Patrick A1 - Pachter, Lior A1 - Papaceit, Montserrat A1 - Parisi, Matthew J A1 - Parisi, Michael A1 - Parts, Leopold A1 - Pedersen, Jakob S A1 - Pesole, Graziano A1 - Phillippy, Adam M A1 - Ponting, Chris P A1 - Pop, Mihai A1 - Porcelli, Damiano A1 - Powell, Jeffrey R A1 - Prohaska, Sonja A1 - Pruitt, Kim A1 - Puig, Marta A1 - Quesneville, Hadi A1 - Ram, Kristipati Ravi A1 - Rand, David A1 - Rasmussen, Matthew D A1 - Reed, Laura K A1 - Reenan, Robert A1 - Reily, Amy A1 - Remington, Karin A A1 - Rieger, Tania T A1 - Ritchie, Michael G A1 - Robin, Charles A1 - Rogers, Yu-Hui A1 - Rohde, Claudia A1 - Rozas, Julio A1 - Rubenfield, Marc J A1 - Ruiz, Alfredo A1 - Russo, Susan A1 - Salzberg, Steven L A1 - Sanchez-Gracia, Alejandro A1 - Saranga, David J A1 - Sato, Hajime A1 - Schaeffer, Stephen W A1 - Schatz, Michael C A1 - Schlenke, Todd A1 - Schwartz, Russell A1 - Segarra, Carmen A1 - Singh, Rama S A1 - Sirot, Laura A1 - Sirota, Marina A1 - Sisneros, Nicholas B A1 - Smith, Chris D A1 - Smith, Temple F A1 - Spieth, John A1 - Stage, Deborah E A1 - Stark, Alexander A1 - Stephan, Wolfgang A1 - Strausberg, Robert L A1 - Strempel, Sebastian A1 - Sturgill, David A1 - Sutton, Granger A1 - Sutton, Granger G A1 - Tao, Wei A1 - Teichmann, Sarah A1 - Tobari, Yoshiko N A1 - Tomimura, Yoshihiko A1 - Tsolas, Jason M A1 - Valente, Vera L S A1 - Venter, Eli A1 - Venter, J Craig A1 - Vicario, Saverio A1 - Vieira, Filipe G A1 - Vilella, Albert J A1 - Villasante, Alfredo A1 - Walenz, Brian A1 - Wang, Jun A1 - Wasserman, Marvin A1 - Watts, Thomas A1 - Wilson, Derek A1 - Wilson, Richard K A1 - Wing, Rod A A1 - Wolfner, Mariana F A1 - Wong, Alex A1 - Wong, Gane Ka-Shu A1 - Wu, Chung-I A1 - Wu, Gabriel A1 - Yamamoto, Daisuke A1 - Yang, Hsiao-Pei A1 - Yang, Shiaw-Pyng A1 - Yorke, James A A1 - Yoshida, Kiyohito A1 - Zdobnov, Evgeny A1 - Zhang, Peili A1 - Zhang, Yu A1 - Zimin, Aleksey V A1 - Baldwin, Jennifer A1 - Abdouelleil, Amr A1 - Abdulkadir, Jamal A1 - Abebe, Adal A1 - Abera, Brikti A1 - Abreu, Justin A1 - Acer, St Christophe A1 - Aftuck, Lynne A1 - Alexander, Allen A1 - An, Peter A1 - Anderson, Erica A1 - Anderson, Scott A1 - Arachi, Harindra A1 - Azer, Marc A1 - Bachantsang, Pasang A1 - Barry, Andrew A1 - Bayul, Tashi A1 - Berlin, Aaron A1 - Bessette, Daniel A1 - Bloom, Toby A1 - Blye, Jason A1 - Boguslavskiy, Leonid A1 - Bonnet, Claude A1 - Boukhgalter, Boris A1 - Bourzgui, Imane A1 - Brown, Adam A1 - Cahill, Patrick A1 - Channer, Sheridon A1 - Cheshatsang, Yama A1 - Chuda, Lisa A1 - Citroen, Mieke A1 - Collymore, Alville A1 - Cooke, Patrick A1 - Costello, Maura A1 - D'Aco, Katie A1 - Daza, Riza A1 - De Haan, Georgius A1 - DeGray, Stuart A1 - DeMaso, Christina A1 - Dhargay, Norbu A1 - Dooley, Kimberly A1 - Dooley, Erin A1 - Doricent, Missole A1 - Dorje, Passang A1 - Dorjee, Kunsang A1 - Dupes, Alan A1 - Elong, Richard A1 - Falk, Jill A1 - Farina, Abderrahim A1 - Faro, Susan A1 - Ferguson, Diallo A1 - Fisher, Sheila A1 - Foley, Chelsea D A1 - Franke, Alicia A1 - Friedrich, Dennis A1 - Gadbois, Loryn A1 - Gearin, Gary A1 - Gearin, Christina R A1 - Giannoukos, Georgia A1 - Goode, Tina A1 - Graham, Joseph A1 - Grandbois, Edward A1 - Grewal, Sharleen A1 - Gyaltsen, Kunsang A1 - Hafez, Nabil A1 - Hagos, Birhane A1 - Hall, Jennifer A1 - Henson, Charlotte A1 - Hollinger, Andrew A1 - Honan, Tracey A1 - Huard, Monika D A1 - Hughes, Leanne A1 - Hurhula, Brian A1 - Husby, M Erii A1 - Kamat, Asha A1 - Kanga, Ben A1 - Kashin, Seva A1 - Khazanovich, Dmitry A1 - Kisner, Peter A1 - Lance, Krista A1 - Lara, Marcia A1 - Lee, William A1 - Lennon, Niall A1 - Letendre, Frances A1 - LeVine, Rosie A1 - Lipovsky, Alex A1 - Liu, Xiaohong A1 - Liu, Jinlei A1 - Liu, Shangtao A1 - Lokyitsang, Tashi A1 - Lokyitsang, Yeshi A1 - Lubonja, Rakela A1 - Lui, Annie A1 - MacDonald, Pen A1 - Magnisalis, Vasilia A1 - Maru, Kebede A1 - Matthews, Charles A1 - McCusker, William A1 - McDonough, Susan A1 - Mehta, Teena A1 - Meldrim, James A1 - Meneus, Louis A1 - Mihai, Oana A1 - Mihalev, Atanas A1 - Mihova, Tanya A1 - Mittelman, Rachel A1 - Mlenga, Valentine A1 - Montmayeur, Anna A1 - Mulrain, Leonidas A1 - Navidi, Adam A1 - Naylor, Jerome A1 - Negash, Tamrat A1 - Nguyen, Thu A1 - Nguyen, Nga A1 - Nicol, Robert A1 - Norbu, Choe A1 - Norbu, Nyima A1 - Novod, Nathaniel A1 - O'Neill, Barry A1 - Osman, Sahal A1 - Markiewicz, Eva A1 - Oyono, Otero L A1 - Patti, Christopher A1 - Phunkhang, Pema A1 - Pierre, Fritz A1 - Priest, Margaret A1 - Raghuraman, Sujaa A1 - Rege, Filip A1 - Reyes, Rebecca A1 - Rise, Cecil A1 - Rogov, Peter A1 - Ross, Keenan A1 - Ryan, Elizabeth A1 - Settipalli, Sampath A1 - Shea, Terry A1 - Sherpa, Ngawang A1 - Shi, Lu A1 - Shih, Diana A1 - Sparrow, Todd A1 - Spaulding, Jessica A1 - Stalker, John A1 - Stange-Thomann, Nicole A1 - Stavropoulos, Sharon A1 - Stone, Catherine A1 - Strader, Christopher A1 - Tesfaye, Senait A1 - Thomson, Talene A1 - Thoulutsang, Yama A1 - Thoulutsang, Dawa A1 - Topham, Kerri A1 - Topping, Ira A1 - Tsamla, Tsamla A1 - Vassiliev, Helen A1 - Vo, Andy A1 - Wangchuk, Tsering A1 - Wangdi, Tsering A1 - Weiand, Michael A1 - Wilkinson, Jane A1 - Wilson, Adam A1 - Yadav, Shailendra A1 - Young, Geneva A1 - Yu, Qing A1 - Zembek, Lisa A1 - Zhong, Danni A1 - Zimmer, Andrew A1 - Zwirko, Zac A1 - Jaffe, David B A1 - Alvarez, Pablo A1 - Brockman, Will A1 - Butler, Jonathan A1 - Chin, CheeWhye A1 - Gnerre, Sante A1 - Grabherr, Manfred A1 - Kleber, Michael A1 - Mauceli, Evan A1 - MacCallum, Iain KW - Animals KW - Codon KW - DNA Transposable Elements KW - Drosophila KW - Drosophila Proteins KW - Evolution, Molecular KW - Gene Order KW - Genes, Insect KW - Genome, Insect KW - Genome, Mitochondrial KW - Genomics KW - Immunity KW - Multigene Family KW - Phylogeny KW - Reproduction KW - RNA, Untranslated KW - sequence alignment KW - Sequence Analysis, DNA KW - Synteny AB -

Comparative analysis of multiple genomes in a phylogenetic framework dramatically improves the precision and sensitivity of evolutionary inference, producing more robust results than single-genome analyses can provide. The genomes of 12 Drosophila species, ten of which are presented here for the first time (sechellia, simulans, yakuba, erecta, ananassae, persimilis, willistoni, mojavensis, virilis and grimshawi), illustrate how rates and patterns of sequence divergence across taxa can illuminate evolutionary processes on a genomic scale. These genome sequences augment the formidable genetic tools that have made Drosophila melanogaster a pre-eminent model for animal genetics, and will further catalyse fundamental research on mechanisms of development, cell biology, genetics, disease, neurobiology, behaviour, physiology and evolution. Despite remarkable similarities among these Drosophila species, we identified many putatively non-neutral changes in protein-coding genes, non-coding RNA genes, and cis-regulatory regions. These may prove to underlie differences in the ecology and behaviour of these diverse species.

VL - 450 CP - 7167 M3 - 10.1038/nature06341 ER - TY - JOUR T1 - GATA and Nkx factors synergistically regulate tissue-specific gene expression and development in vivo JF - DevelopmentDevelopment Y1 - 2007 A1 - Zhang, Yuzhen A1 - Rath, Nibedita A1 - Sridhar Hannenhalli A1 - Wang, Zhishan A1 - Cappola, Thomas A1 - Kimura, Shioko A1 - Atochina-Vasserman, Elena A1 - Lu, Min Min A1 - Beers, Michael F. A1 - Morrisey, Edward E. AB - In vitro studies have suggested that members of the GATA and Nkx transcription factor families physically interact, and synergistically activate pulmonary epithelial- and cardiac-gene promoters. However, the relevance of this synergy has not been demonstrated in vivo. We show that Gata6-Titf1 (Gata6-Nkx2.1) double heterozygous (G6-Nkx DH) embryos and mice have severe defects in pulmonary epithelial differentiation and distal airway development, as well as reduced phospholipid production. The defects in G6-Nkx DH embryos and mice are similar to those observed in human neonates with respiratory distress syndromes, including bronchopulmonary dysplasia, and differential gene expression analysis reveals essential developmental pathways requiring synergistic regulation by both Gata6 and Titf1 (Nkx2.1). These studies indicate that Gata6 and Nkx2.1 act in a synergistic manner to direct pulmonary epithelial differentiation and development in vivo, providing direct evidence that interactions between these two transcription factor families are crucial for the development of the tissues in which they are co-expressed. VL - 134 ER - TY - JOUR T1 - Genome Analysis Linking Recent European and African Influenza (H5N1) Viruses JF - Emerging Infectious DiseasesEmerg Infect DisEmerging Infectious DiseasesEmerg Infect Dis Y1 - 2007 A1 - Salzberg, Steven L. A1 - Kingsford, Carl A1 - Cattoli, Giovanni A1 - Spiro, David J. A1 - Janies, Daniel A. A1 - Aly, Mona Mehrez A1 - Brown, Ian H. A1 - Couacy-Hymann, Emmanuel A1 - De Mia, Gian Mario A1 - Dung, Do Huu A1 - Guercio, Annalisa A1 - Joannis, Tony A1 - Ali, Ali Safar Maken A1 - Osmani, Azizullah A1 - Padalino, Iolanda A1 - Saad, Magdi D. A1 - Savić, Vladimir A1 - Sengamalay, Naomi A. A1 - Yingst, Samuel A1 - Zaborsky, Jennifer A1 - Zorman-Rojs, Olga A1 - Ghedin, Elodie A1 - Capua, Ilaria AB - Although linked, these viruses are distinct from earlier outbreak strains., To better understand the ecology and epidemiology of the highly pathogenic avian influenza virus in its transcontinental spread, we sequenced and analyzed the complete genomes of 36 recent influenza A (H5N1) viruses collected from birds in Europe, northern Africa, and southeastern Asia. These sequences, among the first complete genomes of influenza (H5N1) viruses outside Asia, clearly depict the lineages now infecting wild and domestic birds in Europe and Africa and show the relationships among these isolates and other strains affecting both birds and humans. The isolates fall into 3 distinct lineages, 1 of which contains all known non-Asian isolates. This new Euro-African lineage, which was the cause of several recent (2006) fatal human infections in Egypt and Iraq, has been introduced at least 3 times into the European-African region and has split into 3 distinct, independently evolving sublineages. One isolate provides evidence that 2 of these sublineages have recently reassorted. VL - 13 SN - 1080-6040 ER - TY - JOUR T1 - Grid Services Base Library: A high-level, procedural application programming interface for writing Globus-based Grid services JF - Future Generation Comp SystFuture Generation Comp Syst Y1 - 2007 A1 - Adam L. Bazinet A1 - Myers, D. S. A1 - Fuetsch, J. A1 - Michael P. Cummings AB - The Grid Services Base Library (GSBL) is a procedural application programming interface (API) that abstracts many of the high-level functions performed by Globus Grid services, thus dramatically lowering the barriers to writing Grid services. The library has been extensively tested and used for computational biology research in a Globus Toolkit-based Grid system, in which no fewer than twenty Grid services written with this API are deployed. VL - 23 ER - TY - JOUR T1 - Members of a large retroposon family are determinants of post-transcriptional gene expression in Leishmania. JF - PLoS Pathog Y1 - 2007 A1 - Bringaud, Frederic A1 - Müller, Michaela A1 - Cerqueira, Gustavo Coutinho A1 - Smith, Martin A1 - Rochette, Annie A1 - el-Sayed, Najib M A A1 - Papadopoulou, Barbara A1 - Ghedin, Elodie KW - 3' Untranslated Regions KW - Animals KW - Base Sequence KW - Biological Evolution KW - Down-Regulation KW - Gene Expression Regulation KW - Genome, Protozoan KW - Leishmania KW - Leishmania major KW - Molecular Sequence Data KW - Retroelements KW - RNA, Messenger KW - sequence alignment KW - Trypanosoma brucei brucei KW - Trypanosoma cruzi AB -

Trypanosomatids are unicellular protists that include the human pathogens Leishmania spp. (leishmaniasis), Trypanosoma brucei (sleeping sickness), and Trypanosoma cruzi (Chagas disease). Analysis of their recently completed genomes confirmed the presence of non-long-terminal repeat retrotransposons, also called retroposons. Using the 79-bp signature sequence common to all trypanosomatid retroposons as bait, we identified in the Leishmania major genome two new large families of small elements--LmSIDER1 (785 copies) and LmSIDER2 (1,073 copies)--that fulfill all the characteristics of extinct trypanosomatid retroposons. LmSIDERs are approximately 70 times more abundant in L. major compared to T. brucei and are found almost exclusively within the 3'-untranslated regions (3'UTRs) of L. major mRNAs. We provide experimental evidence that LmSIDER2 act as mRNA instability elements and that LmSIDER2-containing mRNAs are generally expressed at lower levels compared to the non-LmSIDER2 mRNAs. The considerable expansion of LmSIDERs within 3'UTRs in an organism lacking transcriptional control and their role in regulating mRNA stability indicate that Leishmania have probably recycled these short retroposons to globally modulate the expression of a number of genes. To our knowledge, this is the first example in eukaryotes of the domestication and expansion of a family of mobile elements that have evolved to fulfill a critical cellular function.

VL - 3 CP - 9 M3 - 10.1371/journal.ppat.0030136 ER - TY - JOUR T1 - Microarray analysis of gene expression induced by sexual contact in Schistosoma mansoni JF - BMC GenomicsBMC Genomics Y1 - 2007 A1 - Waisberg, Michael A1 - Lobo, Francisco A1 - Cerqueira, Gustavo A1 - Passos, Liana A1 - Carvalho, Omar A1 - Franco, Gloria A1 - Najib M. El‐Sayed AB - BACKGROUND:The parasitic trematode Schistosoma mansoni is one of the major causative agents of Schistosomiasis, a disease that affects approximately 200 million people, mostly in developing countries. Since much of the pathology is associated with eggs laid by the female worm, understanding the mechanisms involved in oogenesis and sexual maturation is an important step towards the discovery of new targets for effective drug therapy. It is known that the adult female worm only develops fully in the presence of a male worm and that the rates of oviposition and maturation of eggs are significantly increased by mating. In order to study gene transcripts associated with sexual maturation and oviposition, we compared the gene expression profiles of sexually mature and immature parasites using DNA microarrays.RESULTS:For each experiment, three amplified RNA microarray hybridizations and their dye swaps were analyzed. Our results show that 265 transcripts are differentially expressed in adult females and 53 in adult males when mature and immature worms are compared. Of the genes differentially expressed, 55% are expressed at higher levels in paired females while the remaining 45% are more expressed in unpaired ones and 56.6% are expressed at higher levels in paired male worms while the remaining 43.4% are more expressed in immature parasites. Real-time RT-PCR analysis validated the microarray results. Several new maturation associated transcripts were identified. Genes that were up-regulated in single-sex females were mostly related to energy generation (i.e. carbohydrate and protein metabolism, generation of precursor metabolites and energy, cellular catabolism, and organelle organization and biogenesis) while genes that were down-regulated related to RNA metabolism, reactive oxygen species metabolism, electron transport, organelle organization and biogenesis and protein biosynthesis.CONCLUSION:Our results confirm previous observations related to gene expression induced by sexual maturation in female schistosome worms. They also increase the list of S. mansoni maturation associated transcripts considerably, therefore opening new and exciting avenues for the study of the conjugal biology and development of new drugs against schistosomes. VL - 8 SN - 1471-2164 ER - TY - JOUR T1 - New developments in the InterPro database. JF - Nucleic Acids Res Y1 - 2007 A1 - Mulder, Nicola J A1 - Apweiler, Rolf A1 - Attwood, Teresa K A1 - Bairoch, Amos A1 - Bateman, Alex A1 - Binns, David A1 - Bork, Peer A1 - Buillard, Virginie A1 - Cerutti, Lorenzo A1 - Copley, Richard A1 - Courcelle, Emmanuel A1 - Das, Ujjwal A1 - Daugherty, Louise A1 - Dibley, Mark A1 - Finn, Robert A1 - Fleischmann, Wolfgang A1 - Gough, Julian A1 - Haft, Daniel A1 - Hulo, Nicolas A1 - Hunter, Sarah A1 - Kahn, Daniel A1 - Kanapin, Alexander A1 - Kejariwal, Anish A1 - Labarga, Alberto A1 - Langendijk-Genevaux, Petra S A1 - Lonsdale, David A1 - Lopez, Rodrigo A1 - Letunic, Ivica A1 - Madera, Martin A1 - Maslen, John A1 - McAnulla, Craig A1 - McDowall, Jennifer A1 - Mistry, Jaina A1 - Mitchell, Alex A1 - Nikolskaya, Anastasia N A1 - Orchard, Sandra A1 - Orengo, Christine A1 - Petryszak, Robert A1 - Selengut, Jeremy D A1 - Sigrist, Christian J A A1 - Thomas, Paul D A1 - Valentin, Franck A1 - Wilson, Derek A1 - Wu, Cathy H A1 - Yeats, Corin KW - Databases, Protein KW - Internet KW - Protein Structure, Tertiary KW - Proteins KW - Sequence Analysis, Protein KW - Systems Integration KW - User-Computer Interface AB -

InterPro is an integrated resource for protein families, domains and functional sites, which integrates the following protein signature databases: PROSITE, PRINTS, ProDom, Pfam, SMART, TIGRFAMs, PIRSF, SUPERFAMILY, Gene3D and PANTHER. The latter two new member databases have been integrated since the last publication in this journal. There have been several new developments in InterPro, including an additional reading field, new database links, extensions to the web interface and additional match XML files. InterPro has always provided matches to UniProtKB proteins on the website and in the match XML file on the FTP site. Additional matches to proteins in UniParc (UniProt archive) are now available for download in the new match XML files only. The latest InterPro release (13.0) contains more than 13 000 entries, covering over 78% of all proteins in UniProtKB. The database is available for text- and sequence-based searches via a webserver (http://www.ebi.ac.uk/interpro), and for download by anonymous FTP (ftp://ftp.ebi.ac.uk/pub/databases/interpro). The InterProScan search tool is now also available via a web service at http://www.ebi.ac.uk/Tools/webservices/WSInterProScan.html.

VL - 35 CP - Database issue M3 - 10.1093/nar/gkl841 ER - TY - JOUR T1 - New records of phytoplankton for Bangladesh. 3. Volvocales JF - Bangladesh Journal of Plant TaxonomyBangladesh Journal of Plant Taxonomy Y1 - 2007 A1 - Khondker, Moniruzzaman A1 - Bhuiyan, Rauf Ahmed A1 - Yeasmin, Jenat A1 - Alam, Munirul A1 - Sack, R. Bradley A1 - Huq, Anwar A1 - Rita R. Colwell AB - This study presents 21 species of Chlamydomonas, four species of Carteria, two species of each of Nephroselmis, Pyramidomonas and Scherffelia, and Collodictyon triciliatum, Polytoma minus, Tetrachloridium ? allorgei and Tetraselmis cordiformis. These species have been reported from some ponds of Mathbaria of Pirojpur and Bakerganj of Barisal districts in Bangladesh. VL - 14 SN - 1028-2092 ER - TY - JOUR T1 - New records of phytoplankton for Bangladesh. 4. Chlorococcales JF - Bangladesh Journal of Plant TaxonomyBangladesh Journal of Plant Taxonomy Y1 - 2007 A1 - Khondker, Moniruzzaman A1 - Bhuiyan, Rauf Ahmed A1 - Yeasim, Jenat A1 - Alam, Munirul A1 - Sack, R. Bradley A1 - Huq, Anwar A1 - Rita R. Colwell AB - This study presents three species from each of Schroederia, Monoraphidium and Ankistrodesmus, two species and one variety of Dictyosphaerium, two varieties of Pediastrum, and Tetraedron arthrodesmiforme var. contorta, Chlorotetraedron polymorphum, Myrmecia aquatica, Oocystis tainoensis, Nephrocytium spirale, Kirchneriella irregularis, Coelastrum indicum and Scenedesmus similagineus. These taxa have been reported from some ponds of Mathbaria of Pirojpur and Bakerganj of Barisal Districts in Bangladesh. VL - 14 SN - 1028-2092 ER - TY - JOUR T1 - Recovery in culture of viable but nonculturable Vibrio parahaemolyticus: regrowth or resuscitation? JF - The ISME JournalThe ISME journal Y1 - 2007 A1 - Coutard, Fran A1 - ois, A1 - Crassous, Philippe A1 - Droguet, Micka A1 - l, A1 - Gobin, Eric A1 - Rita R. Colwell A1 - Pommepuy, Monique A1 - Hervio-Heath, Dominique KW - ecophysiology KW - ecosystems KW - environmental biotechnology KW - geomicrobiology KW - ISME J KW - microbe interactions KW - microbial communities KW - microbial ecology KW - microbial engineering KW - microbial epidemiology KW - microbial genomics KW - microorganisms AB - The objective of this study was to explore the recovery of culturability of viable but nonculturable (VBNC) Vibrio parahaemolyticus after temperature upshift and to determine whether regrowth or resuscitation occurred. A clinical strain of V. parahaemolyticus Vp5 was rendered VBNC by exposure to artificial seawater (ASW) at 4°C. Aliquots of the ASW suspension of cells (0.1, 1 and 10 ml) were subjected to increased temperatures of 20°C and 37°C. Culturability of the cells in the aliquots was monitored for colony formation on a rich medium and changes in morphology were measured by scanning (SEM) and transmission (TEM) electron microscopy. Samples of VBNC cells were fixed and examined by SEM, revealing a heterogeneous population comprising small cells and larger, flattened cells. Forty-eight hours after temperature upshift to 20°C or 37°C, both elongation and division by binary fission of the cells were observed, employing SEM and TEM, but only in the 10-ml aliquots. The results suggest that a portion of VBNC cells is able to undergo cell division. It is concluded that a portion of VBNC cells of V. parahaemolyticus subjected to cold temperatures remain viable. After temperature upshift, regrowth of those cells, rather than resuscitation of all bacteria of the initial inoculum, appears to be responsible for recovery of culturability of VBNC cells of V. parahaemolyticus. Nutrient in filtrates of VBNC cells is hypothesized to allow growth of the temperature-responsive cells, with cell division occurring via binary fission, but also including an atypical, asymmetric cell division. VL - 1 SN - 1751-7362 N1 - [ccedil]
[euml] ER - TY - JOUR T1 - Schistosoma mansoni genome: Closing in on a final gene set JF - Experimental ParasitologyExperimental Parasitology Y1 - 2007 A1 - Haas, Brian J. A1 - Berriman, Matthew A1 - Hirai, Hirohisa A1 - Cerqueira, Gustavo G. A1 - LoVerde, Philip T. A1 - Najib M. El‐Sayed KW - Annotation KW - Gene finding KW - Genome KW - Schistosoma mansoni AB - The Schistosoma mansoni genome sequencing consortium has recently released the latest versions of the genome assembly as well as an automated preliminary gene structure annotation. The combined datasets constitute a vast resource for researchers to exploit in a variety of post-genomic studies with an emphasis of transcriptomic and proteomic tools. Here we present an innovative method used for combining diverse sources of evidence including ab initio gene predictions, protein and transcript sequence homologies, and cross-genome sequence homologies between S. mansoni and Schistosoma japonicum to define a comprehensive list of protein-coding genes. VL - 117 SN - 0014-4894 ER - TY - JOUR T1 - Ultrastructure of coccoid viable but non‐culturable Vibrio cholerae JF - Environmental MicrobiologyEnvironmental Microbiology Y1 - 2007 A1 - Chaiyanan, Saipin A1 - Chaiyanan, Sitthipan A1 - Grim, Christopher A1 - Maugel, Timothy A1 - Huq, Anwar A1 - Rita R. Colwell AB - Morphology of viable but non-culturable Vibrio cholerae was monitored for 2 years by scanning and transmission electron microscopy. Morphological changes included very small coccoid forms, after extended incubation at 4°C and room temperature, and sequential transformation from curved rods to irregular (∼1 μm) rods to ∼0.8 μm coccoid cells and, ultimately, to tiny coccoid forms (0.07–0.4 μm). Irregular rod-shaped and coccoid cells were equally distributed in microcosms during the first 30–60 days of incubation at both temperatures, but only coccoid cells were observed after incubation for 60 days at 4°C. When V. cholerae O1 and O139, maintained for 30–60 days at both temperatures, were heated to 45°C for 60 s, after serial passage through 0.45 μm and 0.1 μm filters, and plating on Luria–Bertania (LB) agar, only cells larger than 1 μm yielded colonies on LB agar. Approximately 0.1% of heat-treated cultures were culturable. Cell division in the smallest coccoid cells was observed, yielding daughter cells of equal size, whereas other coccoid cells revealed bleb-like, cell wall evagination, followed by transfer of nuclear material. Coccoid cells of V. cholerae O1 and O139 incubated at 4°C for more than 1 year remained substrate responsive and antigenic. VL - 9 SN - 1462-2920 ER - TY - JOUR T1 - Viable but nonculturable Vibrio cholerae O1 in biofilms in the aquatic environment and their role in cholera transmission JF - Proceedings of the National Academy of SciencesProceedings of the National Academy of Sciences Y1 - 2007 A1 - Alam, M. A1 - Sultana, M. A1 - Nair, G. B. A1 - Siddique, A. K. A1 - Hasan, N. A. A1 - Sack, R. B. A1 - Sack, D. A. A1 - Ahmed, K. U. A1 - Sadique, A. A1 - Watanabe, H. A1 - Rita R. Colwell AB - Vibrio cholerae persists in aquatic environments predominantly in a nonculturable state. In this study coccoid, nonculturable V. cholerae O1 in biofilms maintained for 495 days in Mathbaria, Bangladesh, pond water became culturable upon animal passage. Culturability, biofilm formation, and the wbe, ctxA, and rstR2 genes were monitored by culture, direct fluorescent antibody (DFA), and multiplex PCR. DFA counts were not possible after formation of biofilm. Furthermore, wbe, but not ctxA, were amplifiable, even after incubation for 54 and 68 days at room temperature (≈25°C) and 4°C, respectively, when no growth was detectable. Slower biofilm formation and extended culturability were observed for cultures incubated at 4°C, compared with ≈25°C, suggesting biofilm production to be temperature dependent and linked to loss of culturability. Small colonies appearing after incubation in microcosms for 54 and 68 days at 25°C and 4°C, respectively, were wbe positive and ctxA and rstR2 negative, indicating loss of bacteriophage CTXΦ. The coccoid V. cholerae O1 observed as free cells in microcosms incubated for 495 days could not be cultured, but biofilms in the same microcosms yielded culturable cells. It is concluded that biofilms can act as a reservoir for V. cholerae O1 between epidemics because of its long-term viability in biofilms. In contrast to biofilms produced in Mathbaria pond water, V. cholerae O1 in biofilms present in cholera stools and incubated under identical conditions as the Mathbaria pond water biofilms could not be cultured after 2 months, indicating that those V. cholerae cells freshly discharged into the environment are significantly less robust than cells adapted to environmental conditions.Bangladesh bacteriophage CTXΦ DFA multiplex-PCR ctxA VL - 104 SN - 0027-8424, 1091-6490 ER - TY - JOUR T1 - Analysis of fat body transcriptome from the adult tsetse fly, Glossina morsitans morsitans. JF - Insect Mol Biol Y1 - 2006 A1 - Attardo, G M A1 - Strickler-Dinglasan, P A1 - Perkin, S A H A1 - Caler, E A1 - Bonaldo, M F A1 - Soares, M B A1 - El-Sayeed, N A1 - Aksoy, S KW - Adipose Tissue KW - Animals KW - Base Sequence KW - Computational Biology KW - DNA Primers KW - Egg Proteins KW - Expressed Sequence Tags KW - Female KW - Gene Expression Profiling KW - Insect Vectors KW - Male KW - Molecular Sequence Data KW - Reverse Transcriptase Polymerase Chain Reaction KW - Sequence Analysis, DNA KW - Sex Factors KW - Tsetse Flies AB -

Tsetse flies (Diptera: Glossinidia) are vectors of pathogenic African trypanosomes. To develop a foundation for tsetse physiology, a normalized expressed sequence tag (EST) library was constructed from fat body tissue of immune-stimulated Glossina morsitans morsitans. Analysis of 20,257 high-quality ESTs yielded 6372 unique genes comprised of 3059 tentative consensus (TC) sequences and 3313 singletons (available at http://aksoylab.yale.edu). We analysed the putative fat body transcriptome based on homology to other gene products with known functions available in the public domain. In particular, we describe the immune-related products, reproductive function related yolk proteins and milk-gland protein, iron metabolism regulating ferritins and transferrin, and tsetse's major energy source proline biosynthesis. Expression analysis of the three yolk proteins indicates that all are detected in females, while only the yolk protein with similarity to lipases, is expressed in males. Milk gland protein, apparently important for larval nutrition, however, is primarily synthesized by accessory milk gland tissue.

VL - 15 CP - 4 M3 - 10.1111/j.1365-2583.2006.00649.x ER - TY - JOUR T1 - Comparative genomics of emerging human ehrlichiosis agents JF - PLoS geneticsPLoS genetics Y1 - 2006 A1 - Dunning Hotopp, Julie C. A1 - Lin, Mingqun A1 - Madupu, Ramana A1 - Crabtree, Jonathan A1 - Angiuoli, Samuel V. A1 - Eisen, Jonathan A. A1 - Eisen, Jonathan A1 - Seshadri, Rekha A1 - Ren, Qinghu A1 - Wu, Martin A1 - Utterback, Teresa R. A1 - Smith, Shannon A1 - Lewis, Matthew A1 - Khouri, Hoda A1 - Zhang, Chunbin A1 - Niu, Hua A1 - Lin, Quan A1 - Ohashi, Norio A1 - Zhi, Ning A1 - Nelson, William A1 - Brinkac, Lauren M. A1 - Dodson, Robert J. A1 - Rosovitz, M. J. A1 - Sundaram, Jaideep A1 - Daugherty, Sean C. A1 - Davidsen, Tanja A1 - Durkin, Anthony S. A1 - Gwinn, Michelle A1 - Haft, Daniel H. A1 - J. Selengut A1 - Sullivan, Steven A. A1 - Zafar, Nikhat A1 - Zhou, Liwei A1 - Benahmed, Faiza A1 - Forberger, Heather A1 - Halpin, Rebecca A1 - Mulligan, Stephanie A1 - Robinson, Jeffrey A1 - White, Owen A1 - Rikihisa, Yasuko A1 - Tettelin, Hervé KW - Animals KW - Biotin KW - DNA Repair KW - Ehrlichia KW - Ehrlichiosis KW - Genome KW - Genomics KW - HUMANS KW - Models, Biological KW - Phylogeny KW - Rickettsia KW - Ticks AB - Anaplasma (formerly Ehrlichia) phagocytophilum, Ehrlichia chaffeensis, and Neorickettsia (formerly Ehrlichia) sennetsu are intracellular vector-borne pathogens that cause human ehrlichiosis, an emerging infectious disease. We present the complete genome sequences of these organisms along with comparisons to other organisms in the Rickettsiales order. Ehrlichia spp. and Anaplasma spp. display a unique large expansion of immunodominant outer membrane proteins facilitating antigenic variation. All Rickettsiales have a diminished ability to synthesize amino acids compared to their closest free-living relatives. Unlike members of the Rickettsiaceae family, these pathogenic Anaplasmataceae are capable of making all major vitamins, cofactors, and nucleotides, which could confer a beneficial role in the invertebrate vector or the vertebrate host. Further analysis identified proteins potentially involved in vacuole confinement of the Anaplasmataceae, a life cycle involving a hematophagous vector, vertebrate pathogenesis, human pathogenesis, and lack of transovarial transmission. These discoveries provide significant insights into the biology of these obligate intracellular pathogens. VL - 2 N1 - http://www.ncbi.nlm.nih.gov/pubmed/16482227?dopt=Abstract ER - TY - JOUR T1 - Comprehensive analysis of alternative splicing in rice and comparative analyses with Arabidopsis. JF - BMC Genomics Y1 - 2006 A1 - Campbell, Matthew A A1 - Haas, Brian J A1 - Hamilton, John P A1 - Mount, Stephen M A1 - Buell, C Robin KW - Alternative Splicing KW - Arabidopsis KW - DNA, Complementary KW - Expressed Sequence Tags KW - Oryza AB -

BACKGROUND: Recently, genomic sequencing efforts were finished for Oryza sativa (cultivated rice) and Arabidopsis thaliana (Arabidopsis). Additionally, these two plant species have extensive cDNA and expressed sequence tag (EST) libraries. We employed the Program to Assemble Spliced Alignments (PASA) to identify and analyze alternatively spliced isoforms in both species.

RESULTS: A comprehensive analysis of alternative splicing was performed in rice that started with >1.1 million publicly available spliced ESTs and over 30,000 full length cDNAs in conjunction with the newly enhanced PASA software. A parallel analysis was performed with Arabidopsis to compare and ascertain potential differences between monocots and dicots. Alternative splicing is a widespread phenomenon (observed in greater than 30% of the loci with transcript support) and we have described nine alternative splicing variations. While alternative splicing has the potential to create many RNA isoforms from a single locus, the majority of loci generate only two or three isoforms and transcript support indicates that these isoforms are generally not rare events. For the alternate donor (AD) and acceptor (AA) classes, the distance between the splice sites for the majority of events was found to be less than 50 basepairs (bp). In both species, the most frequent distance between AA is 3 bp, consistent with reports in mammalian systems. Conversely, the most frequent distance between AD is 4 bp in both plant species, as previously observed in mouse. Most alternative splicing variations are localized to the protein coding sequence and are predicted to significantly alter the coding sequence.

CONCLUSION: Alternative splicing is widespread in both rice and Arabidopsis and these species share many common features. Interestingly, alternative splicing may play a role beyond creating novel combinations of transcripts that expand the proteome. Many isoforms will presumably have negative consequences for protein structure and function, suggesting that their biological role involves post-transcriptional regulation of gene expression.

VL - 7 M3 - 10.1186/1471-2164-7-327 ER - TY - CHAP T1 - Detection, Isolation, and Identification of Vibrio cholerae from the Environment T2 - Current Protocols in MicrobiologyCurrent Protocols in Microbiology Y1 - 2006 A1 - Huq, Anwar A1 - Grim, Christopher A1 - Rita R. Colwell A1 - Nair, G. Balakrish KW - culturable KW - DETECTION KW - Environment KW - identification KW - isolation KW - nonculturable KW - viable KW - Vibrio cholerae JA - Current Protocols in MicrobiologyCurrent Protocols in Microbiology PB - John Wiley & Sons, Inc. SN - 9780471729259 ER - TY - JOUR T1 - Effect of transport at ambient temperature on detection and isolation of Vibrio cholerae from environmental samples JF - Applied and environmental microbiologyApplied and environmental microbiology Y1 - 2006 A1 - Alam, M. A1 - Sadique, A. A1 - Bhuiyan, N. A. A1 - Nair, G. B. A1 - Siddique, A. K. A1 - Sack, D. A. A1 - Ahsan, S. A1 - Huq, A. A1 - Sack, R. B. A1 - Rita R. Colwell A1 - others, AB - It has long been assumed that prolonged holding of environmental samples at the ambient air temperature prior to bacteriological analysis is detrimental to isolation and detection of Vibrio cholerae, the causative agent of pandemic cholera. The present study was aimed at understanding the effect of transporting environmental samples at the ambient air temperature on isolation and enumeration of V. cholerae. For water and plankton samples held at ambient temperatures ranging from 31°C to 35°C for 20 h, the total counts did not increase significantly but the number of culturable V. cholerae increased significantly compared to samples processed within 1 h of collection, as measured by culture, acridine orange direct count, direct fluorescent-antibody-direct viable count (DFA-DVC), and multiplex PCR analyses. For total coliform counts, total bacterial counts, and DFA-DVC counts, the numbers did not increase significantly, but the culturable plate counts for V. cholerae increased significantly after samples were held at the ambient temperature during transport to the laboratory for analysis. An increase in the recovery of V. cholerae O1 and improved detection of V. cholerae O1 rfb and ctxA also occurred when samples were enriched after they were kept for 20 h at the ambient temperature during transport. Improved detection and isolation of toxigenic V. cholerae from freshwater ecosystems can be achieved by holding samples at the ambient temperature, an observation that has significant implications for tracking this pathogen in diverse aquatic environments. VL - 72 ER - TY - JOUR T1 - Evolution of non-LTR retrotransposons in the trypanosomatid genomes: Leishmania major has lost the active elements JF - Molecular and Biochemical ParasitologyMolecular and Biochemical Parasitology Y1 - 2006 A1 - Bringaud, Frederic A1 - Ghedin, Elodie A1 - Blandin, Gaëlle A1 - Bartholomeu, Daniella C. A1 - Caler, Elisabet A1 - Levin, Mariano J. A1 - Baltz, Théo A1 - Najib M. El‐Sayed KW - Degenerate retroelement KW - Evolution KW - Ingi KW - L1Tc KW - Leishmania major KW - Non-LTR retrotransposon KW - Retroposon KW - Trypanosoma brucei KW - Trypanosoma cruzi AB - The ingi and L1Tc non-LTR retrotransposons - which constitute the ingi clade - are abundant in the genome of the trypanosomatid species Trypanosoma brucei and Trypanosoma cruzi, respectively. The corresponding retroelements, however, are not present in the genome of a closely related trypanosomatid, Leishmania major. To study the evolution of non-LTR retrotransposons in trypanosomatids, we have analyzed all ingi/L1Tc elements and highly degenerate ingi/L1Tc-related sequences identified in the recently completed T. brucei, T. cruzi and L. major genomes. The coding sequences of 242 degenerate ingi/L1Tc-related elements (DIREs) in all three genomes were reconstituted by removing the numerous frame shifts. Three independent phylogenetic analyses conducted on the conserved domains encoded by these elements show that all DIREs, including the 52 L. major DIREs, form a monophyletic group belonging to the ingi clade. This indicates that the trypanosomatid ancestor contained active mobile elements that have been retained in the Trypanosoma species, but were lost from L. major genome, where only remnants (DIRE) are detectable. All 242 DIREs analyzed group together according to their species origin with the exception of 11 T. cruzi DIREs which are close to the T. brucei ingi/DIRE families. Considering the absence of known horizontal transfer between the African T. brucei and the South-American T. cruzi, this suggests that this group of elements evolved at a lower rate when compared to the other trypanosomatid elements. Interestingly, the only nucleotide sequence conserved between ingi and L1Tc (the first 79 residues) is also present at the 5'-extremity of all the full length DIREs and suggests a possible role for this conserved motif, as well as for DIREs. VL - 145 SN - 0166-6851 ER - TY - JOUR T1 - Functional Analysis of Hes-1 in Preadipocytes JF - Molecular EndocrinologyMolecular EndocrinologyMolecular EndocrinologyMolecular Endocrinology Y1 - 2006 A1 - Ross, David A. A1 - Sridhar Hannenhalli A1 - Tobias, John W. A1 - Cooch, Neil A1 - Shiekhattar, Ramin A1 - Kadesch, Tom AB - Notch signaling blocks differentiation of 3T3-L1 preadipocytes, and this can be mimicked by constitutive expression of the Notch target gene Hes-1. Although considered initially to function only as a repressor, recent evidence indicates that Hes-1 can also activate transcription. We show here that the domains of Hes-1 needed to block adipogenesis coincide with those necessary for transcriptional repression. HRT1, another basic-helix-loop-helix protein and potential Hes-1 partner, was also induced by Notch in 3T3-L1 cells but did not block adipogenesis, suggesting that Hes-1 functions primarily as a homodimer or possibly as a heterodimer with an unknown partner. Purification of Hes-1 identified the Groucho/transducin-like enhancer of split family of corepressors as the only significant Hes-1 interacting proteins in vivo. An evaluation of global gene expression in preadipocytes identified approximately 200 Hes-1-responsive genes comprising roughly equal numbers of up-regulated and down-regulated genes. However, promoter analyses indicated that the down-regulated genes were significantly more likely to contain Hes-1 binding sites, indicating that Hes-1 is more likely to repress transcription of its direct targets. We conclude that Notch most likely blocks adipogenesis through the induction of Hes-1 homodimers, which repress transcription of key target genes. VL - 20 SN - 0888-8809, 1944-9917 ER - TY - Generic T1 - Microbial diversity in the era of genomics T2 - SYMPOSIA-SOCIETY FOR GENERAL MICROBIOLOGY Y1 - 2006 A1 - Rita R. Colwell JA - SYMPOSIA-SOCIETY FOR GENERAL MICROBIOLOGY VL - 66 ER - TY - JOUR T1 - Molecular Characterization of Serine-, Alanine-, and Proline-Rich Proteins of Trypanosoma cruzi and Their Possible Role in Host Cell Infection JF - Infect. Immun.Infect. Immun. Y1 - 2006 A1 - Baida, Renata C. P. A1 - Santos, Marcia R. M. A1 - Carmo, Mirian S. A1 - Yoshida, Nobuko A1 - Ferreira, Danielle A1 - Ferreira, Alice Teixeira A1 - El Sayed, Najib M. A1 - Andersson, Björn A1 - da Silveira, Jose Franco AB - We previously reported the isolation of a novel protein gene family, termed SAP (serine-, alanine-, and proline-rich protein), from Trypanosoma cruzi. Aided by the availability of the completed genome sequence of T. cruzi, we have now identified 39 full-length sequences of SAP, six pseudogenes and four partial genes. SAPs share a central domain of about 55 amino acids and can be divided into four groups based on their amino (N)- and carboxy (C)-terminal sequences. Some SAPs have conserved N- and C-terminal domains encoding a signal peptide and a glycosylphosphatidylinositol anchor addition site, respectively. Analysis of the expression of SAPs in metacyclic trypomastigotes by two-dimensional electrophoresis and immunoblotting revealed that they are likely to be posttranslationally modified in vivo. We have also demonstrated that some SAPs are shed into the extracellular medium. The recombinant SAP exhibited an adhesive capacity toward mammalian cells, where binding was dose dependent and saturable, indicating a possible ligand-receptor interaction. SAP triggered the host cell Ca2+ response required for parasite internalization. A cell invasion assay performed in the presence of SAP showed inhibition of internalization of the metacyclic forms of the CL strain. Taken together, these results show that SAP is involved in the invasion of mammalian cells by metacyclic trypomastigotes, and they confirm the hypothesis that infective trypomastigotes exploit an arsenal of surface glycoproteins and shed proteins to induce signaling events required for their internalization. VL - 74 ER - TY - BOOK T1 - Oceans And Health: Pathogens In The Marine Environment Y1 - 2006 A1 - Belkin, Shimshon A1 - Rita R. Colwell KW - Electronic books KW - Marine microbiology KW - Medical / Epidemiology KW - Medical / Microbiology KW - Nature / Animals / Marine Life KW - Pathogenic microorganisms KW - Science / Environmental Science KW - Science / Life Sciences / Biology KW - Science / Life Sciences / Marine Biology KW - Science / Life Sciences / Microbiology KW - Seawater/ microbiology AB - The release of non-disinfected wastewaters into the marine environment is a common worldwide practice, in under-developed as well as in highly developed countries. Consequently, the seas are constantly infused with wastewater bacteria, among them highly pathogenic ones. In view of the public health significance of this phenomenon, it is surprising how little is actually known concerning the fate of such bacteria once they enter the sea. While numerous studies have addressed the effects of various environmental parameters on colony formation, many of them actually ignore the fact that bacteria can retain viability and infectivity while losing colony-forming ability. Only in recent years have efforts also been directed at unraveling the mechanisms determining bacterial sensitivity or survival under these conditions. This, therefore, is one subject of Oceans and Health: Pathogens in the Marine Environment: the survival, infectivity, pathogenicity and viability of enteric bacteria in the sea. Chapters also detail the public health aspects of wastewater release, civil engineering and economic considerations, other sources of pathogens, and much more. PB - Springer SN - 9780387237084 ER - TY - JOUR T1 - Retroviral DNA integration: viral and cellular determinants of target-site selection JF - PLoS pathogensPLoS pathogens Y1 - 2006 A1 - Lewinski, M. K. A1 - Yamashita, M. A1 - Emerman, M. A1 - Ciuffi, A. A1 - Marshall, H. A1 - Crawford, G. A1 - Collins, F. A1 - Shinn, P. A1 - Leipzig, J. A1 - Sridhar Hannenhalli A1 - others, PB - Public Library of Science VL - 2 ER - TY - JOUR T1 - Seasonal Cholera Caused by Vibrio Cholerae Serogroups O1 and O139 in the Coastal Aquatic Environment of Bangladesh JF - Applied and Environmental MicrobiologyAppl. Environ. Microbiol.Applied and Environmental MicrobiologyAppl. Environ. Microbiol. Y1 - 2006 A1 - Alam, Munirul A1 - Hasan, Nur A. A1 - Sadique, Abdus A1 - Bhuiyan, N. A. A1 - Ahmed, Kabir U. A1 - Nusrin, Suraia A1 - Nair, G. Balakrish A1 - Siddique, A. K. A1 - Sack, R. Bradley A1 - Sack, David A. A1 - Huq, Anwar A1 - Rita R. Colwell AB - Since Vibrio cholerae O139 first appeared in 1992, both O1 El Tor and O139 have been recognized as the epidemic serogroups, although their geographic distribution, endemicity, and reservoir are not fully understood. To address this lack of information, a study of the epidemiology and ecology of V. cholerae O1 and O139 was carried out in two coastal areas, Bakerganj and Mathbaria, Bangladesh, where cholera occurs seasonally. The results of a biweekly clinical study (January 2004 to May 2005), employing culture methods, and of an ecological study (monthly in Bakerganj and biweekly in Mathbaria from March 2004 to May 2005), employing direct and enrichment culture, colony blot hybridization, and direct fluorescent-antibody methods, showed that cholera is endemic in both Bakerganj and Mathbaria and that V. cholerae O1, O139, and non-O1/non-O139 are autochthonous to the aquatic environment. Although V. cholerae O1 and O139 were isolated from both areas, most noteworthy was the isolation of V. cholerae O139 in March, July, and September 2004 in Mathbaria, where seasonal cholera was clinically linked only to V. cholerae O1. In Mathbaria, V. cholerae O139 emerged as the sole cause of a significant outbreak of cholera in March 2005. V. cholerae O1 reemerged clinically in April 2005 and established dominance over V. cholerae O139, continuing to cause cholera in Mathbaria. In conclusion, the epidemic potential and coastal aquatic reservoir for V. cholerae O139 have been demonstrated. Based on the results of this study, the coastal ecosystem of the Bay of Bengal is concluded to be a significant reservoir for the epidemic serogroups of V. cholerae. VL - 72 SN - 0099-2240, 1098-5336 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 - Toxigenic Vibrio Cholerae in the Aquatic Environment of Mathbaria, Bangladesh JF - Applied and Environmental MicrobiologyAppl. Environ. Microbiol.Applied and Environmental MicrobiologyAppl. Environ. Microbiol. Y1 - 2006 A1 - Alam, Munirul A1 - Sultana, Marzia A1 - Nair, G. Balakrish A1 - Sack, R. Bradley A1 - Sack, David A. A1 - Siddique, A. K. A1 - Ali, Afsar A1 - Huq, Anwar A1 - Rita R. Colwell AB - Toxigenic Vibrio cholerae, rarely isolated from the aquatic environment between cholera epidemics, can be detected in what is now understood to be a dormant stage, i.e., viable but nonculturable when standard bacteriological methods are used. In the research reported here, biofilms have proved to be a source of culturable V. cholerae, even in nonepidemic periods. Biweekly environmental surveillance for V. cholerae was carried out in Mathbaria, an area of cholera endemicity adjacent to the Bay of Bengal, with the focus on V. cholerae O1 and O139 Bengal. A total of 297 samples of water, phytoplankton, and zooplankton were collected between March and December 2004, yielding eight V. cholerae O1 and four O139 Bengal isolates. A combination of culture methods, multiplex-PCR, and direct fluorescent antibody (DFA) counting revealed the Mathbaria aquatic environment to be a reservoir for V. cholerae O1 and O139 Bengal. DFA results showed significant clumping of the bacteria during the interepidemic period for cholera, and the fluorescent micrographs revealed large numbers of V. cholerae O1 in thin films of exopolysaccharides (biofilm). A similar clumping of V. cholerae O1 was also observed in samples collected from Matlab, Bangladesh, where cholera also is endemic. Thus, the results of the study provided in situ evidence for V. cholerae O1 and O139 in the aquatic environment, predominantly as viable but nonculturable cells and culturable cells in biofilm consortia. The biofilm community is concluded to be an additional reservoir of cholera bacteria in the aquatic environment between seasonal epidemics of cholera in Bangladesh. VL - 72 SN - 0099-2240, 1098-5336 ER - TY - JOUR T1 - Transcriptional Genomics Associates FOX Transcription Factors With Human Heart Failure JF - CirculationCirculation Y1 - 2006 A1 - Sridhar Hannenhalli A1 - Putt, Mary E. A1 - Gilmore, Joan M. A1 - Wang, Junwen A1 - Parmacek, Michael S. A1 - Epstein, Jonathan A. A1 - Morrisey, Edward E. A1 - Margulies, Kenneth B. A1 - Cappola, Thomas P. AB - Background— Specific transcription factors (TFs) modulate cardiac gene expression in murine models of heart failure, but their relevance in human subjects remains untested. We developed and applied a computational approach called transcriptional genomics to test the hypothesis that a discrete set of cardiac TFs is associated with human heart failure.Methods and Results— RNA isolates from failing (n=196) and nonfailing (n=16) human hearts were hybridized with Affymetrix HU133A arrays, and differentially expressed heart failure genes were determined. TF binding sites overrepresented in the −5-kb promoter sequences of these heart failure genes were then determined with the use of public genome sequence databases. Binding sites for TFs identified in murine heart failure models (MEF2, NKX, NF-AT, and GATA) were significantly overrepresented in promoters of human heart failure genes (P<0.002; false discovery rate 2% to 4%). In addition, binding sites for FOX TFs showed substantial overrepresentation in both advanced human and early murine heart failure (P<0.002 and false discovery rate <4% for each). A role for FOX TFs was supported further by expression of FOXC1, C2, P1, P4, and O1A in failing human cardiac myocytes at levels similar to established hypertrophic TFs and by abundant FOXP1 protein in failing human cardiac myocyte nuclei.Conclusions— Our results provide the first evidence that specific TFs identified in murine models (MEF2, NKX, NFAT, and GATA) are associated with human heart failure. Moreover, these data implicate specific members of the FOX family of TFs (FOXC1, C2, P1, P4, and O1A) not previously suggested in heart failure pathogenesis. These findings provide a crucial link between animal models and human disease and suggest a specific role for FOX signaling in modulating the hypertrophic response of the heart to stress in humans. VL - 114 ER - TY - JOUR T1 - Trypanosoma cruzi mitochondrial maxicircles display species- and strain-specific variation and a conserved element in the non-coding region. JF - BMC Genomics Y1 - 2006 A1 - Westenberger, Scott J A1 - Cerqueira, Gustavo C A1 - El-Sayed, Najib M A1 - Zingales, Bianca A1 - Campbell, David A A1 - Sturm, Nancy R KW - Amino Acid Sequence KW - Animals KW - Animals, Inbred Strains KW - Base Composition KW - Conserved Sequence KW - DNA, Kinetoplast KW - Frameshifting, Ribosomal KW - Gene Deletion KW - Gene Order KW - Genetic Variation KW - Leishmania KW - Models, Biological KW - Molecular Sequence Data KW - Muscle Proteins KW - NADH Dehydrogenase KW - Open Reading Frames KW - Regulatory Elements, Transcriptional KW - RNA Editing KW - Sequence Homology, Amino Acid KW - Species Specificity KW - Trypanosoma brucei brucei KW - Trypanosoma cruzi KW - Ubiquitin-Protein Ligases KW - Untranslated Regions AB -

BACKGROUND: The mitochondrial DNA of kinetoplastid flagellates is distinctive in the eukaryotic world due to its massive size, complex form and large sequence content. Comprised of catenated maxicircles that contain rRNA and protein-coding genes and thousands of heterogeneous minicircles encoding small guide RNAs, the kinetoplast network has evolved along with an extreme form of mRNA processing in the form of uridine insertion and deletion RNA editing. Many maxicircle-encoded mRNAs cannot be translated without this post-transcriptional sequence modification.

RESULTS: We present the complete sequence and annotation of the Trypanosoma cruzi maxicircles for the CL Brener and Esmeraldo strains. Gene order is syntenic with Trypanosoma brucei and Leishmania tarentolae maxicircles. The non-coding components have strain-specific repetitive regions and a variable region that is unique for each strain with the exception of a conserved sequence element that may serve as an origin of replication, but shows no sequence identity with L. tarentolae or T. brucei. Alternative assemblies of the variable region demonstrate intra-strain heterogeneity of the maxicircle population. The extent of mRNA editing required for particular genes approximates that seen in T. brucei. Extensively edited genes were more divergent among the genera than non-edited and rRNA genes. Esmeraldo contains a unique 236-bp deletion that removes the 5'-ends of ND4 and CR4 and the intergenic region. Esmeraldo shows additional insertions and deletions outside of areas edited in other species in ND5, MURF1, and MURF2, while CL Brener has a distinct insertion in MURF2.

CONCLUSION: The CL Brener and Esmeraldo maxicircles represent two of three previously defined maxicircle clades and promise utility as taxonomic markers. Restoration of the disrupted reading frames might be accomplished by strain-specific RNA editing. Elements in the non-coding region may be important for replication, transcription, and anchoring of the maxicircle within the kinetoplast network.

VL - 7 M3 - 10.1186/1471-2164-7-60 ER - TY - JOUR T1 - Trypanosoma cruzi mitochondrial maxicircles display species- and strain-specific variation and a conserved element in the non-coding region JF - BMC GenomicsBMC Genomics Y1 - 2006 A1 - Westenberger, Scott A1 - Cerqueira, Gustavo A1 - Najib M. El‐Sayed A1 - Zingales, Bianca A1 - Campbell, David A1 - Sturm, Nancy AB - BACKGROUND:The mitochondrial DNA of kinetoplastid flagellates is distinctive in the eukaryotic world due to its massive size, complex form and large sequence content. Comprised of catenated maxicircles that contain rRNA and protein-coding genes and thousands of heterogeneous minicircles encoding small guide RNAs, the kinetoplast network has evolved along with an extreme form of mRNA processing in the form of uridine insertion and deletion RNA editing. Many maxicircle-encoded mRNAs cannot be translated without this post-transcriptional sequence modification.RESULTS:We present the complete sequence and annotation of the Trypanosoma cruzi maxicircles for the CL Brener and Esmeraldo strains. Gene order is syntenic with Trypanosoma brucei and Leishmania tarentolae maxicircles. The non-coding components have strain-specific repetitive regions and a variable region that is unique for each strain with the exception of a conserved sequence element that may serve as an origin of replication, but shows no sequence identity with L. tarentolae or T. brucei. Alternative assemblies of the variable region demonstrate intra-strain heterogeneity of the maxicircle population. The extent of mRNA editing required for particular genes approximates that seen in T. brucei. Extensively edited genes were more divergent among the genera than non-edited and rRNA genes. Esmeraldo contains a unique 236-bp deletion that removes the 5'-ends of ND4 and CR4 and the intergenic region. Esmeraldo shows additional insertions and deletions outside of areas edited in other species in ND5, MURF1, and MURF2, while CL Brener has a distinct insertion in MURF2.CONCLUSION:The CL Brener and Esmeraldo maxicircles represent two of three previously defined maxicircle clades and promise utility as taxonomic markers. Restoration of the disrupted reading frames might be accomplished by strain-specific RNA editing. Elements in the non-coding region may be important for replication, transcription, and anchoring of the maxicircle within the kinetoplast network. VL - 7 SN - 1471-2164 ER - TY - JOUR T1 - Cholera: the killer from the deep JF - The BiochemistThe Biochemist Y1 - 2005 A1 - Rita R. Colwell AB - The current international attention to the importance ofcombating infectious diseases can provide the opportunity for a multidisciplinary approach that joins medicine with many other scientific and technological disciplines. Science and technology are major forces that have the potential to balance the world’s inequities. The connection between cholera and the environment provides a paradigm for this perspective. ER - TY - JOUR T1 - Comparative Genomics of Trypanosomatid Parasitic Protozoa JF - ScienceScience Y1 - 2005 A1 - Najib M. El‐Sayed A1 - Myler, Peter J. A1 - Blandin, Gaëlle A1 - Berriman, Matthew A1 - Crabtree, Jonathan A1 - Aggarwal, Gautam A1 - Caler, Elisabet A1 - Renauld, Hubert A1 - Worthey, Elizabeth A. A1 - Hertz-Fowler, Christiane A1 - Ghedin, Elodie A1 - Peacock, Christopher A1 - Bartholomeu, Daniella C. A1 - Haas, Brian J. A1 - Tran, Anh-Nhi A1 - Wortman, Jennifer R. A1 - Alsmark, U. Cecilia M. A1 - Angiuoli, Samuel A1 - Anupama, Atashi A1 - Badger, Jonathan A1 - Bringaud, Frederic A1 - Cadag, Eithon A1 - Carlton, Jane M. A1 - Cerqueira, Gustavo C. A1 - Creasy, Todd A1 - Delcher, Arthur L. A1 - Djikeng, Appolinaire A1 - Embley, T. Martin A1 - Hauser, Christopher A1 - Ivens, Alasdair C. A1 - Kummerfeld, Sarah K. A1 - Pereira-Leal, Jose B. A1 - Nilsson, Daniel A1 - Peterson, Jeremy A1 - Salzberg, Steven L. A1 - Shallom, Joshua A1 - Silva, Joana C. A1 - Sundaram, Jaideep A1 - Westenberger, Scott A1 - White, Owen A1 - Melville, Sara E. A1 - Donelson, John E. A1 - Andersson, Björn A1 - Stuart, Kenneth D. A1 - Hall, Neil AB - A comparison of gene content and genome architecture of Trypanosoma brucei, Trypanosoma cruzi, and Leishmania major, three related pathogens with different life cycles and disease pathology, revealed a conserved core proteome of about 6200 genes in large syntenic polycistronic gene clusters. Many species-specific genes, especially large surface antigen families, occur at nonsyntenic chromosome-internal and subtelomeric regions. Retroelements, structural RNAs, and gene family expansion are often associated with syntenic discontinuities that—along with gene divergence, acquisition and loss, and rearrangement within the syntenic regions—have shaped the genomes of each parasite. Contrary to recent reports, our analyses reveal no evidence that these species are descended from an ancestor that contained a photosynthetic endosymbiont. VL - 309 ER - TY - JOUR T1 - Critical Factors Influencing the Occurrence of Vibrio Cholerae in the Environment of Bangladesh JF - Applied and Environmental MicrobiologyAppl. Environ. Microbiol.Applied and Environmental MicrobiologyAppl. Environ. Microbiol. Y1 - 2005 A1 - Huq, Anwar A1 - Sack, R. Bradley A1 - Nizam, Azhar A1 - Longini, Ira M. A1 - Nair, G. Balakrish A1 - Ali, Afsar A1 - Morris, J. Glenn A1 - Khan, M. N. Huda A1 - Siddique, A. Kasem A1 - Yunus, Mohammed A1 - Albert, M. John A1 - Sack, David A. A1 - Rita R. Colwell AB - The occurrence of outbreaks of cholera in Africa in 1970 and in Latin America in 1991, mainly in coastal communities, and the appearance of the new serotype Vibrio cholerae O139 in India and subsequently in Bangladesh have stimulated efforts to understand environmental factors influencing the growth and geographic distribution of epidemic Vibrio cholerae serotypes. Because of the severity of recent epidemics, cholera is now being considered by some infectious disease investigators as a “reemerging” disease, prompting new work on the ecology of vibrios. Epidemiological and ecological surveillance for cholera has been under way in four rural, geographically separated locations in Bangladesh for the past 4 years, during which both clinical and environmental samples were collected at biweekly intervals. The clinical epidemiology portion of the research has been published (Sack et al., J. Infect. Dis. 187:96-101, 2003). The results of environmental sampling and analysis of the environmental and clinical data have revealed significant correlations of water temperature, water depth, rainfall, conductivity, and copepod counts with the occurrence of cholera toxin-producing bacteria (presumably V. cholerae). The lag periods between increases or decreases in units of factors, such as temperature and salinity, and occurrence of cholera correlate with biological parameters, e.g., plankton population blooms. The new information on the ecology of V. cholerae is proving useful in developing environmental models for the prediction of cholera epidemics. VL - 71 SN - 0099-2240, 1098-5336 ER - TY - JOUR T1 - Data sharing in ecology and evolution JF - Trends in Ecology & EvolutionTrends in Ecology & Evolution Y1 - 2005 A1 - Parr, Cynthia S. A1 - Michael P. Cummings VL - 20 SN - 0169-5347 ER - TY - JOUR T1 - A framework for set-oriented computation in inductive logic programming and its application in generalizing inverse entailment JF - Inductive Logic ProgrammingInductive Logic Programming Y1 - 2005 A1 - Héctor Corrada Bravo A1 - Page, D. A1 - Ramakrishnan, R. A1 - Shavlik, J. A1 - Costa, V. S. 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 - The genome of the African trypanosome Trypanosoma brucei JF - ScienceScience Y1 - 2005 A1 - Berriman, M. A1 - Ghedin, E. A1 - Hertz-Fowler, C. A1 - Blandin, G. A1 - Renauld, H. A1 - Bartholomeu, D. C. A1 - Lennard, N. J. A1 - Caler, E. A1 - Hamlin, N. E. A1 - Haas, B. A1 - others, VL - 309 ER - TY - JOUR T1 - Genome-Wide Analysis of Chromosomal Features Repressing Human Immunodeficiency Virus Transcription JF - Journal of VirologyJ. Virol.Journal of VirologyJ. Virol. Y1 - 2005 A1 - Lewinski, M. K. A1 - Bisgrove, D. A1 - Shinn, P. A1 - Chen, H. A1 - Hoffmann, C. A1 - Sridhar Hannenhalli A1 - Verdin, E. A1 - Berry, C. C. A1 - Ecker, J. R. A1 - Bushman, F. D. AB - We have investigated regulatory sequences in noncoding human DNA that are associated with repression of an integrated human immunodeficiency virus type 1 (HIV-1) promoter. HIV-1 integration results in the formation of precise and homogeneous junctions between viral and host DNA, but integration takes place at many locations. Thus, the variation in HIV-1 gene expression at different integration sites reports the activity of regulatory sequences at nearby chromosomal positions. Negative regulation of HIV transcription is of particular interest because of its association with maintaining HIV in a latent state in cells from infected patients. To identify chromosomal regulators of HIV transcription, we infected Jurkat T cells with an HIV-based vector transducing green fluorescent protein (GFP) and separated cells into populations containing well-expressed (GFP-positive) or poorly expressed (GFP-negative) proviruses. We then determined the chromosomal locations of the two classes by sequencing 971 junctions between viral and cellular DNA. Possible effects of endogenous cellular transcription were characterized by transcriptional profiling. Low-level GFP expression correlated with integration in (i) gene deserts, (ii) centromeric heterochromatin, and (iii) very highly expressed cellular genes. These data provide a genome-wide picture of chromosomal features that repress transcription and suggest models for transcriptional latency in cells from HIV-infected patients. VL - 79 SN - 0022-538X, 1098-5514 ER - TY - JOUR T1 - Genome-wide analysis of retroviral DNA integration JF - Nat Rev MicroNat Rev MicroNat Rev MicroNat Rev Micro Y1 - 2005 A1 - Bushman, Frederic A1 - Lewinski, Mary A1 - Ciuffi, Angela A1 - Barr, Stephen A1 - Leipzig, Jeremy A1 - Sridhar Hannenhalli A1 - Hoffmann, Christian VL - 3 SN - 1740-1526 ER - TY - JOUR T1 - Global microbial ecology of Vibrio cholerae JF - Oceans and health: pathogens in the marine environmentOceans and health: pathogens in the marine environment Y1 - 2005 A1 - Rita R. Colwell AB - The disease cholera can no longer be considered a simple equation of bacteria and human host, but represents a complex network that includes global weather patterns, aquatic reservoirs, phages, zooplankton, collective behavior of surface-attached cells, an adaptable genome, and the deep sea inter alia. This interesting characterization emerges from a view of biological systems termed biocomplexity (Colwell, 2002a, b). The holistic approach to understanding cholera integrates contributions from experts in many fields, with multiple points of view, in models for prediction, prevention, and treatment of the disease that Vibrio cholerae causes. The spiral form shown in Figure 12.1 symbolizes the nonlinear manner in which the many parts of such a model interact. It also shows that these interactions often occur across many different scales. ER - TY - JOUR T1 - Grid computing JF - EDUCAUSE ReviewEDUCAUSE Review Y1 - 2005 A1 - Michael P. Cummings A1 - Huskamp, J. C. VL - 40 ER - TY - JOUR T1 - Magic bullets and golden rules: data sampling in molecular phylogenetics JF - Zoology (Jena)Zoology (Jena) Y1 - 2005 A1 - Michael P. Cummings A1 - Meyer, A. AB - Data collection for molecular phylogenetic studies is based on samples of both genes and taxa. In an ideal world, with no limitations to resources, as many genes could be sampled as deemed necessary to address phylogenetic problems. Given limited resources in the real world, inadequate (in terms of choice of genes or number of genes) sequences or restricted taxon sampling can adversely affect the reliability or information gained in phylogenetics. Recent empirical and simulation-based studies of data sampling in molecular phylogenetics have reached differing conclusions on how to deal with these problems. Some advocated sampling more genes, others more taxa. There is certainly no 'magic bullet' that will fit all phylogenetic problems, and no specific 'golden rules' have been deduced, other than that single genes may not always contain sufficient phylogenetic information. However, several general conclusions and suggestions can be made. One suggestion is that the determination of a multiple, but moderate number (e.g., 6-10) of gene sequences might take precedence over sequencing a larger set of genes and thereby permit the sampling of more taxa for a phylogenetic study. VL - 108 ER - TY - JOUR T1 - Pathogenic Vibrio species in the marine and estuarine environment JF - Oceans and health: pathogens in the marine environmentOceans and health: pathogens in the marine environment Y1 - 2005 A1 - Pruzzo, C. A1 - Huq, A. A1 - Rita R. Colwell A1 - Donelli, G. AB - The genus Vibrio includes more than 30 species, at least 12 of which are pathogenic to humans and/or have been associated with foodborne diseases (Chakraborty et al., 1997). Among these species, Vibrio cholerae, serogroups O1 and O139, are the most important, since they are associated with epidemic and pandemic diarrhea outbreaks in many parts of the world (Centers for Disease Control and Prevention, 1995; Kaper et al., 1995). However, other species of vibrios capable of causing diarrheal disease in humans have received greater attention in the last decade. These include Vibrio parahaemolyticus, a leading cause of foodborne disease outbreaks in Japan and Korea (Lee et al., 2001), Vibrio vulnificus, Vibrio alginolyticus, Vibrio damsela, Vibrio fluvialis, Vibrio furnissii, Vibrio hollisae, Vibrio metschnikovii, and Vibrio mimicus (Altekruse et al., 2000; Høi et al., 1997). In the USA, Vibrio species have been estimated to be the cause of about 8000 illnesses annually (Mead et al., 1999). ER - TY - JOUR T1 - Telomere and subtelomere of Trypanosoma cruzi chromosomes are enriched in (pseudo)genes of retrotransposon hot spot and trans-sialidase-like gene families: the origins of T. cruzi telomeres. JF - Gene Y1 - 2005 A1 - Kim, Dong A1 - Chiurillo, Miguel Angel A1 - El-Sayed, Najib A1 - Jones, Kristin A1 - Santos, Márcia R M A1 - Porcile, Patricio E A1 - Andersson, Björn A1 - Myler, Peter A1 - da Silveira, Jose Franco A1 - Ramírez, José Luis KW - Amino Acid Sequence KW - Animals KW - Base Sequence KW - Chromosomes KW - Chromosomes, Artificial, Bacterial KW - DNA, Protozoan KW - Genes, Protozoan KW - Glycoproteins KW - Molecular Sequence Data KW - Multigene Family KW - Neuraminidase KW - Pseudogenes KW - Retroelements KW - Sequence Homology, Amino Acid KW - Sequence Homology, Nucleic Acid KW - Telomere KW - Trypanosoma cruzi AB -

Here, we sequenced two large telomeric regions obtained from the pathogen protozoan Trypanosoma cruzi. These sequences, together with in silico assembled contigs, allowed us to establish the general features of telomeres and subtelomeres of this parasite. Our findings can be summarized as follows: We confirmed the presence of two types of telomeric ends; subtelomeric regions appeared to be enriched in (pseudo)genes of RHS (retrotransposon hot spot), TS (trans-sialidase)-like proteins, and putative surface protein DGF-1 (dispersed gene family-1). Sequence analysis of the ts-like genes located at the telomeres suggested that T. cruzi chromosomal ends could have been the site for generation of new gp85 variants, an important adhesin molecule involved in the invasion of mammalian cells by T. cruzi. Finally, a mechanism for generation of T. cruzi telomere by chromosome breakage and telomere healing is proposed.

VL - 346 M3 - 10.1016/j.gene.2004.10.014 ER - TY - JOUR T1 - Temperature-Driven Campylobacter Seasonality in England and Wales JF - Applied and Environmental MicrobiologyAppl. Environ. Microbiol.Applied and Environmental MicrobiologyAppl. Environ. Microbiol. Y1 - 2005 A1 - Louis, Valérie R. A1 - Gillespie, Iain A. A1 - O'Brien, Sarah J. A1 - Russek-Cohen, Estelle A1 - Pearson, Andrew D. A1 - Rita R. Colwell AB - Campylobacter incidence in England and Wales between 1990 and 1999 was examined in conjunction with weather conditions. Over the 10-year interval, the average annual rate was determined to be 78.4 ± 15.0 cases per 100,000, with an upward trend. Rates were higher in males than in females, regardless of age, and highest in children less than 5 years old. Major regional differences were detected, with the highest rates in Wales and the southwest and the lowest in the southeast. The disease displayed a seasonal pattern, and increased campylobacter rates were found to be correlated with temperature. The most marked seasonal effect was observed for children under the age of 5. The seasonal pattern of campylobacter infections indicated a linkage with environmental factors rather than food sources. Therefore, public health interventions should not be restricted to food-borne approaches, and the epidemiology of the seasonal peak in human campylobacter infections may best be understood through studies in young children. VL - 71 SN - 0099-2240, 1098-5336 ER - TY - JOUR T1 - Transcriptional profiling of the hyperthermophilic methanarchaeon Methanococcus jannaschii in response to lethal heat and non-lethal cold shock. JF - Environ Microbiol Y1 - 2005 A1 - Boonyaratanakornkit, Boonchai B A1 - Simpson, Anjana J A1 - Whitehead, Timothy A A1 - Fraser, Claire M A1 - el-Sayed, Najib M A A1 - Clark, Douglas S KW - Adaptation, Physiological KW - Archaeal Proteins KW - Cold Temperature KW - Gene Expression Profiling KW - Gene Expression Regulation, Archaeal KW - Heat-Shock Proteins KW - Hot Temperature KW - Methanococcus KW - Temperature KW - Transcription, Genetic AB -

Temperature shock of the hyperthermophilic methanarchaeon Methanococcus jannaschii from its optimal growth temperature of 85 degrees C to 65 degrees C and 95 degrees C resulted in different transcriptional responses characteristic of both the direction of shock (heat or cold shock) and whether the shock was lethal. Specific outcomes of lethal heat shock to 95 degrees C included upregulation of genes encoding chaperones, and downregulation of genes encoding subunits of the H+ transporting ATP synthase. A gene encoding an alpha subunit of a putative prefoldin was also upregulated, which may comprise a novel element in the protein processing pathway in M. jannaschii. Very different responses were observed upon cold shock to 65 degrees C. These included upregulation of a gene encoding an RNA helicase and other genes involved in transcription and translation, and upregulation of genes coding for proteases and transport proteins. Also upregulated was a gene that codes for an 18 kDa FKBP-type PPIase, which may facilitate protein folding at low temperatures. Transcriptional profiling also revealed several hypothetical proteins that respond to temperature stress conditions.

VL - 7 CP - 6 M3 - 10.1111/j.1462-2920.2005.00751.x ER - TY - JOUR T1 - Transcriptional profiling of the hyperthermophilic methanarchaeon Methanococcus jannaschii in response to lethal heat and non‐lethal cold shock JF - Environmental MicrobiologyEnvironmental Microbiology Y1 - 2005 A1 - Boonyaratanakornkit, Boonchai B. A1 - Simpson, Anjana J. A1 - Whitehead, Timothy A. A1 - Fraser, Claire M. A1 - Najib M. El‐Sayed A1 - Clark, Douglas S. AB - Temperature shock of the hyperthermophilic methanarchaeon Methanococcus jannaschii from its optimal growth temperature of 85°C to 65°C and 95°C resulted in different transcriptional responses characteristic of both the direction of shock (heat or cold shock) and whether the shock was lethal. Specific outcomes of lethal heat shock to 95°C included upregulation of genes encoding chaperones, and downregulation of genes encoding subunits of the H+ transporting ATP synthase. A gene encoding an α subunit of a putative prefoldin was also upregulated, which may comprise a novel element in the protein processing pathway in M. jannaschii. Very different responses were observed upon cold shock to 65°C. These included upregulation of a gene encoding an RNA helicase and other genes involved in transcription and translation, and upregulation of genes coding for proteases and transport proteins. Also upregulated was a gene that codes for an 18 kDa FKBP-type PPIase, which may facilitate protein folding at low temperatures. Transcriptional profiling also revealed several hypothetical proteins that respond to temperature stress conditions. VL - 7 SN - 1462-2920 ER - TY - JOUR T1 - What the genome sequence is revealing about trypanosome antigenic variation. JF - Biochem Soc Trans Y1 - 2005 A1 - Barry, J D A1 - Marcello, L A1 - Morrison, L J A1 - Read, A F A1 - Lythgoe, K A1 - Jones, N A1 - Carrington, M A1 - Blandin, G A1 - Böhme, U A1 - Caler, E A1 - Hertz-Fowler, C A1 - Renauld, H A1 - El-Sayed, N A1 - Berriman, M KW - Animals KW - Antigens, Protozoan KW - Evolution, Molecular KW - Genetic Variation KW - Genome KW - Trypanosomatina KW - Variant Surface Glycoproteins, Trypanosoma AB -

African trypanosomes evade humoral immunity through antigenic variation, whereby they switch expression of the gene encoding their VSG (variant surface glycoprotein) coat. Switching proceeds by duplication of silent VSG genes into a transcriptionally active locus. The genome project has revealed that most of the silent archive consists of hundreds of subtelomeric VSG tandem arrays, and that most of these are not functional genes. Precedent suggests that they can contribute combinatorially to the formation of expressed, functional genes through segmental gene conversion. These findings from the genome project have major implications for evolution of the VSG archive and for transmission of the parasite in the field.

VL - 33 CP - Pt 5 M3 - 10.1042/BST20050986 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 - Generic T1 - Abstracting workflows: unifying bioinformatics task conceptualization and specification through Semantic Web services T2 - W3C Workshop on Semantic Web for Life Sciences Y1 - 2004 A1 - Hashmi, N. A1 - Lee, S. A1 - Michael P. Cummings JA - W3C Workshop on Semantic Web for Life Sciences CY - Cambridge, Massachusetts USA ER - TY - JOUR T1 - Acinetobacter lipases: molecular biology, biochemical properties and biotechnological potential JF - Journal of industrial microbiology & biotechnologyJournal of industrial microbiology & biotechnology Y1 - 2004 A1 - Snellman, E. A. A1 - Rita R. Colwell AB - Lipases (EC 3.1.1.3) have received increased attention recently, evidenced by the increasing amount of information about lipases in the current literature. The renewed interest in this enzyme class is due primarily to investigations of their role in pathogenesis and their increasing use in biotechnological applications [38]. Also, many microbial lipases are available as commercial products, the majority of which are used in detergents, cosmetic production, food flavoring, and organic synthesis. Lipases are valued biocatalysts because they act under mild conditions, are highly stable in organic solvents, show broad substrate specificity, and usually show high regio- and/or stereo-selectivity in catalysis. A number of lipolytic strains of Acinetobacter have been isolated from a variety of sources and their lipases possess many biochemical properties similar to those that have been developed for biotechnological applications. This review discusses the biology of lipase expression in Acinetobacter, with emphasis on those aspects relevant to potential biotechnology applications. VL - 31 ER - TY - RPRT T1 - Applying permutation tests to tree-based statistical models: extending the R package rpart Y1 - 2004 A1 - Michael P. Cummings A1 - Myers, D. S. A1 - Mangelson, M. AB - Tree-based statistical models are useful for evaluating relationships between predictor and response variables and for generating predictions when the response is unknown. However, current methods of constructing tree-based models do not provide a probabilistic assessment of the models produced. Here we describe our work to use permutation tests to quantitatively estimate the probability of tree-based statistical models. We have extended the rpart (recursive partitioning) package of the R system for statistical data analysis. This extension, rpart.permutation, executes the permutations in parallel, using MPI (Message Passing Interface) to greatly decrease the time necessary to complete the analysis. PB - University of Maryland Institute for Advanced Computer Studies VL - 2004-24 ER - TY - CHAP T1 - BAMBE, DnaSP, ENCprime/SeqCount, LAMARC, MacClade, MEGA, Modeltest, MrBayes, PAML, PAUP*, PHYLIP, r8s, readseq, Seq-Gen, Sites, TreeView T2 - Dictionary of Bioinformatics Y1 - 2004 A1 - Michael P. Cummings ED - Hancock, JM ED - Zvelebil, MJ JA - Dictionary of Bioinformatics PB - Wiley-Liss CY - Hoboken ER - TY - JOUR T1 - A book like its cover JF - HeredityHeredity Y1 - 2004 A1 - Michael P. Cummings KW - animal and plant breeding KW - biometrical and statistical genetics KW - cytogenetics KW - ecological KW - eukaryotes KW - Genetics KW - Genomics KW - human population genetics KW - population and evolutionary genetics KW - post-genomics AB - An official journal of the Genetics Society, Heredity publishes high-quality articles describing original research and theoretical insights in all areas of genetics. Research papers are complimented by News & Commentary articles and reviews, keeping researchers and students abreast of hot topics in the field. VL - 93 SN - 0018-067X ER - TY - JOUR T1 - A book like its cover –- The Phylogenetic Handbook: A Practical Approach to DNA and Protein Phylogeny, Edited by M. Salemi and A.-M. Vandamme JF - Heredity Y1 - 2004 A1 - Michael P. Cummings VL - 93 ER - TY - JOUR T1 - Divergent Gene Copies in the Asexual Class Bdelloidea (Rotifera) Separated Before the Bdelloid Radiation or Within Bdelloid Families JF - Proceedings of the National Academy of Sciences of the United States of AmericaPNASProceedings of the National Academy of Sciences of the United States of AmericaPNAS Y1 - 2004 A1 - Welch, David B. Mark A1 - Michael P. Cummings A1 - Hillis, David M. A1 - Meselson, Matthew AB - Rotifers of the asexual class Bdelloidea are unusual in possessing two or more divergent copies of every gene that has been examined. Phylogenetic analysis of the heat-shock gene hsp82 and the TATA-box-binding protein gene tbp in multiple bdelloid species suggested that for each gene, each copy belonged to one of two lineages that began to diverge before the bdelloid radiation. Such gene trees are consistent with the two lineages having descended from former alleles that began to diverge after meiotic segregation ceased or from subgenomes of an alloploid ancestor of the bdelloids. However, the original analyses of bdelloid gene-copy divergence used only a single outgroup species and were based on parsimony and neighbor joining. We have now used maximum likelihood and Bayesian inference methods and, for hsp82, multiple outgroups in an attempt to produce more robust gene trees. Here we report that the available data do not unambiguously discriminate between gene trees that root the origin of hsp82 and tbp copy divergence before the bdelloid radiation and those which indicate that the gene copies began to diverge within bdelloid families. The remarkable presence of multiple diverged gene copies in individual genomes is nevertheless consistent with the loss of sex in an ancient ancestor of bdelloids. VL - 101 SN - 0027-8424, 1091-6490 ER - TY - JOUR T1 - Few amino acid positions in ıt rpoB are associated with most of the rifampin resistance in ıt Mycobacterium tuberculosis JF - BMC BioinformaticsBMC Bioinformatics Y1 - 2004 A1 - Michael P. Cummings A1 - Segal, M. R. AB - BACKGROUND: Mutations in rpoB, the gene encoding the beta subunit of DNA-dependent RNA polymerase, are associated with rifampin resistance in Mycobacterium tuberculosis. Several studies have been conducted where minimum inhibitory concentration (MIC, which is defined as the minimum concentration of the antibiotic in a given culture medium below which bacterial growth is not inhibited) of rifampin has been measured and partial DNA sequences have been determined for rpoB in different isolates of M. tuberculosis. However, no model has been constructed to predict rifampin resistance based on sequence information alone. Such a model might provide the basis for quantifying rifampin resistance status based exclusively on DNA sequence data and thus eliminate the requirements for time consuming culturing and antibiotic testing of clinical isolates. RESULTS: Sequence data for amino acid positions 511-533 of rpoB and associated MIC of rifampin for different isolates of M. tuberculosis were taken from studies examining rifampin resistance in clinical samples from New York City and throughout Japan. We used tree-based statistical methods and random forests to generate models of the relationships between rpoB amino acid sequence and rifampin resistance. The proportion of variance explained by a relatively simple tree-based cross-validated regression model involving two amino acid positions (526 and 531) is 0.679. The first partition in the data, based on position 531, results in groups that differ one hundredfold in mean MIC (1.596 micrograms/ml and 159.676 micrograms/ml). The subsequent partition based on position 526, the most variable in this region, results in a > 354-fold difference in MIC. When considered as a classification problem (susceptible or resistant), a cross-validated tree-based model correctly classified most (0.884) of the observations and was very similar to the regression model. Random forest analysis of the MIC data as a continuous variable, a regression problem, produced a model that explained 0.861 of the variance. The random forest analysis of the MIC data as discrete classes produced a model that correctly classified 0.942 of the observations with sensitivity of 0.958 and specificity of 0.885. CONCLUSIONS: Highly accurate regression and classification models of rifampin resistance can be made based on this short sequence region. Models may be better with improved (and consistent) measurements of MIC and more sequence data. VL - 5 ER - TY - CHAP T1 - Free-Living to Freewheeling: The Evolution of Vibrio cholerae from Innocence to Infamy T2 - Infectious Disease and Host-Pathogen EvolutionInfectious Disease and Host-Pathogen Evolution Y1 - 2004 A1 - Rita R. Colwell A1 - Faruque, S. M. A1 - Nair, G. B. ED - Dronamraju, Krishna R. JA - Infectious Disease and Host-Pathogen EvolutionInfectious Disease and Host-Pathogen Evolution PB - Cambridge University Press SN - 9780521820660 ER - TY - JOUR T1 - Genome sequence of Silicibacter pomeroyi reveals adaptations to the marine environment JF - NatureNature Y1 - 2004 A1 - Moran, Mary Ann A1 - Buchan, Alison A1 - González, José M. A1 - Heidelberg, John F. A1 - Whitman, William B. A1 - Kiene, Ronald P. A1 - Henriksen, James R. A1 - King, Gary M. A1 - Belas, Robert A1 - Fuqua, Clay A1 - Brinkac, Lauren A1 - Lewis, Matt A1 - Johri, Shivani A1 - Weaver, Bruce A1 - Pai, Grace A1 - Eisen, Jonathan A. A1 - Rahe, Elisha A1 - Sheldon, Wade M. A1 - Ye, Wenying A1 - Miller, Todd R. A1 - Carlton, Jane A1 - Rasko, David A. A1 - Paulsen, Ian T. A1 - Ren, Qinghu A1 - Daugherty, Sean C. A1 - DeBoy, Robert T. A1 - Dodson, Robert J. A1 - Durkin, A. Scott A1 - Madupu, Ramana A1 - Nelson, William C. A1 - Sullivan, Steven A. A1 - Rosovitz, M. J. A1 - Haft, Daniel H. A1 - J. Selengut A1 - Ward, Naomi KW - Adaptation, Physiological KW - Carrier Proteins KW - Genes, Bacterial KW - Genome, Bacterial KW - marine biology KW - Molecular Sequence Data KW - Oceans and Seas KW - Phylogeny KW - plankton KW - RNA, Ribosomal, 16S KW - Roseobacter KW - Seawater AB - Since the recognition of prokaryotes as essential components of the oceanic food web, bacterioplankton have been acknowledged as catalysts of most major biogeochemical processes in the sea. Studying heterotrophic bacterioplankton has been challenging, however, as most major clades have never been cultured or have only been grown to low densities in sea water. Here we describe the genome sequence of Silicibacter pomeroyi, a member of the marine Roseobacter clade (Fig. 1), the relatives of which comprise approximately 10-20% of coastal and oceanic mixed-layer bacterioplankton. This first genome sequence from any major heterotrophic clade consists of a chromosome (4,109,442 base pairs) and megaplasmid (491,611 base pairs). Genome analysis indicates that this organism relies upon a lithoheterotrophic strategy that uses inorganic compounds (carbon monoxide and sulphide) to supplement heterotrophy. Silicibacter pomeroyi also has genes advantageous for associations with plankton and suspended particles, including genes for uptake of algal-derived compounds, use of metabolites from reducing microzones, rapid growth and cell-density-dependent regulation. This bacterium has a physiology distinct from that of marine oligotrophs, adding a new strategy to the recognized repertoire for coping with a nutrient-poor ocean. VL - 432 N1 - http://www.ncbi.nlm.nih.gov/pubmed/15602564?dopt=Abstract ER - TY - JOUR T1 - Infectious disease and environment: cholera as a paradigm for waterborne disease JF - International MicrobiologyInternational Microbiology Y1 - 2004 A1 - Rita R. Colwell VL - 7 SN - 1139-6709 ER - TY - JOUR T1 - Occurrence and distribution of Vibrio cholerae in the coastal environment of Peru JF - Environmental MicrobiologyEnvironmental Microbiology Y1 - 2004 A1 - Gil, Ana I. A1 - Louis, Valérie R. A1 - Rivera, Irma N. G. A1 - Lipp, Erin A1 - Huq, Anwar A1 - Lanata, Claudio F. A1 - Taylor, David N. A1 - Russek‐Cohen, Estelle A1 - Choopun, Nipa A1 - Sack, R. Bradley A1 - Rita R. Colwell AB - The occurrence and distribution of Vibrio cholerae in sea water and plankton along the coast of Peru were studied from October 1997 to June 2000, and included the 1997–98 El Niño event. Samples were collected at four sites in coastal waters off Peru at monthly intervals. Of 178 samples collected and tested, V. cholerae O1 was cultured from 10 (5.6%) samples, and V. cholerae O1 was detected by direct fluorescent antibody assay in 26 out of 159 samples tested (16.4%). Based on the number of cholera cases reported in Peru from 1997 to 2000, a significant correlation was observed between cholera incidence and elevated sea surface temperature (SST) along the coast of Peru (P < 0.001). From the results of this study, coastal sea water and zooplankton are concluded to be a reservoir for V. cholerae in Peru. The climate–cholera relationship observed for the 1997–98 El Niño year suggests that an early warning system for cholera risk can be established for Peru and neighbouring Latin American countries. VL - 6 SN - 1462-2920 ER - TY - JOUR T1 - Pandemic strains of O3:K6 Vibrio parahaemolyticus in the aquatic environment of Bangladesh JF - Canadian Journal of MicrobiologyCanadian Journal of Microbiology Y1 - 2004 A1 - Islam, M. S. A1 - Tasmin, Rizwana A1 - Khan, Sirajul I. s l a m A1 - Bakht, Habibul B. M. A1 - Mahmood, Zahid H. a y a t A1 - Rahman, M. Z. i a u r A1 - Bhuiyan, Nurul A. m i n A1 - Nishibuchi, Mitsuaki A1 - Nair, G. B. a l a k r i s h A1 - Sack, R. B. r a d l e y A1 - Huq, Anwar A1 - Rita R. Colwell A1 - Sack, David A. AB - A total of 1500 environmental strains of Vibrio parahaemolyticus, isolated from the aquatic environment of Bangladesh, were screened for the presence of a major V. parahaemolyticus virulence factor, the thermostable direct haemolysin (tdh) gene, by the colony blot hybridization method using a digoxigenin-labeled tdh gene probe. Of 1500 strains, 5 carried the tdh sequence, which was further confirmed by PCR using primers specific for the tdh gene. Examination by PCR confirmed that the 5 strains were V. parahamolyticus and lacked the thermostable direct haemolysin-related haemolysin (trh) gene, the alternative major virulence gene known to be absent in pandemic strains. All 5 strains gave positive Kanagawa phenomenon reaction with characteristic beta-haemolysis on Wagatsuma agar medium. Southern blot analysis of the HindIII-digested chromosomal DNA demonstrated, in all 5 strains, the presence of 2 tdh genes common to strains positive for Kanagawa phenomenon. However, the 5 strains were found to belong to 3 different serotypes (O3:K29, O4:K37, and O3:K6). The 2 with pandemic serotype O3:K6 gave positive results in group-specific PCR and ORF8 PCR assays, characteristics unique to the pandemic clone. Clonal variations among the 5 isolates were analyzed by comparing RAPD and ribotyping patterns. Results showed different patterns for the 3 serotypes, but the pattern was identical among the O3:K6 strains. This is the first report on the isolation of pandemic O3:K6 strains of V. parahaemolyticus from the aquatic environment of Bangladesh. VL - 50 ER - TY - CHAP T1 - PHYLIP (Phylogeny Inference Package) Y1 - 2004 A1 - Michael P. Cummings ED - Hancock, John M. ED - Zvelebil, Marketa J. PB - John Wiley & Sons, Inc. CY - Hoboken, NJ, USA M3 - 10.1002/0471650129.dob0534 ER - TY - JOUR T1 - Polylysogeny and prophage induction by secondary infection in Vibrio cholerae JF - Environmental MicrobiologyEnvironmental Microbiology Y1 - 2004 A1 - Espeland, Eric M. A1 - Lipp, Erin K. A1 - Huq, Anwar A1 - Rita R. Colwell AB - Strains of Vibrio cholerae O1, biotypes El Tor and classical, were infected with a known temperate phage (ΦP15) and monitored over a 15-day period for prophage induction. Over the course of the experiment two morphologically and three genomically distinct virus-like particles were observed from the phage-infected El Tor strain by transmission electron microscopy and field inversion gel electrophoresis, respectively, whereas only one phage, ΦP15, was observed from the infected classical strain. In the uninfected El Tor culture one prophage was spontaneously induced after 6 days. No induction in either strain was observed after treatment with mitomycin C. Data indicate that El Tor biotypes of V. cholerae may be polylysogenic and that secondary infection can promote multiple prophage induction. These traits may be important in the transfer of genetic material among V. cholerae by providing an environmentally relevant route for multiple prophage propagation and transmission. VL - 6 SN - 1462-2920 ER - TY - JOUR T1 - Section-level relationships of North American ıt Agalinis (Orobanchaceae) based on DNA sequence analysis of three chloroplast gene regions JF - BMC Evol BiolBMC Evol Biol Y1 - 2004 A1 - Neel, M. C. A1 - Michael P. Cummings AB - BACKGROUND: The North American Agalinis are representatives of a taxonomically difficult group that has been subject to extensive taxonomic revision from species level through higher sub-generic designations (e.g., subsections and sections). Previous presentations of relationships have been ambiguous and have not conformed to modern phylogenetic standards (e.g., were not presented as phylogenetic trees). Agalinis contains a large number of putatively rare taxa that have some degree of taxonomic uncertainty. We used DNA sequence data from three chloroplast genes to examine phylogenetic relationships among sections within the genus Agalinis Raf. (=Gerardia), and between Agalinis and closely related genera within Orobanchaceae. RESULTS: Maximum likelihood analysis of sequences data from rbcL, ndhF, and matK gene regions (total aligned length 7323 bp) yielded a phylogenetic tree with high bootstrap values for most branches. Likelihood ratio tests showed that all but a few branch lengths were significantly greater than zero, and an additional likelihood ratio test rejected the molecular clock hypothesis. Comparisons of substitution rates between gene regions based on linear models of pairwise distance estimates between taxa show both ndhF and matK evolve more rapidly than rbcL, although the there is substantial rate heterogeneity within gene regions due in part to rate differences among codon positions. CONCLUSIONS: Phylogenetic analysis supports the monophyly of Agalinis, including species formerly in Tomanthera, and this group is sister to a group formed by the genera Aureolaria, Brachystigma, Dasistoma, and Seymeria. Many of the previously described sections within Agalinis are polyphyletic, although many of the subsections appear to form natural groups. The analysis reveals a single evolutionary event leading to a reduction in chromosome number from n = 14 to n = 13 based on the sister group relationship of section Erectae and section Purpureae subsection Pedunculares. Our results establish the evolutionary distinctiveness of A. tenella from the more widespread and common A. obtusifolia. However, further data are required to clearly resolve the relationship between A. acuta and A. tenella. VL - 4 ER - TY - JOUR T1 - A semidefinite programming approach to side chain positioning with new rounding strategies JF - INFORMS Journal on ComputingINFORMS Journal on Computing Y1 - 2004 A1 - Chazelle, B. A1 - Kingsford, Carl A1 - Singh, M. VL - 16 ER - TY - JOUR T1 - Simple statistical models predict C-to-U edited sites in plant mitochondrial RNA JF - BMC BioinformaticsBMC Bioinformatics Y1 - 2004 A1 - Michael P. Cummings A1 - Myers, D. S. AB - BACKGROUND: RNA editing is the process whereby an RNA sequence is modified from the sequence of the corresponding DNA template. In the mitochondria of land plants, some cytidines are converted to uridines before translation. Despite substantial study, the molecular biological mechanism by which C-to-U RNA editing proceeds remains relatively obscure, although several experimental studies have implicated a role for cis-recognition. A highly non-random distribution of nucleotides is observed in the immediate vicinity of edited sites (within 20 nucleotides 5' and 3'), but no precise consensus motif has been identified. RESULTS: Data for analysis were derived from the the complete mitochondrial genomes of Arabidopsis thaliana, Brassica napus, and Oryza sativa; additionally, a combined data set of observations across all three genomes was generated. We selected datasets based on the 20 nucleotides 5' and the 20 nucleotides 3' of edited sites and an equivalently sized and appropriately constructed null-set of non-edited sites. We used tree-based statistical methods and random forests to generate models of C-to-U RNA editing based on the nucleotides surrounding the edited/non-edited sites and on the estimated folding energies of those regions. Tree-based statistical methods based on primary sequence data surrounding edited/non-edited sites and estimates of free energy of folding yield models with optimistic re-substitution-based estimates of approximately 0.71 accuracy, approximately 0.64 sensitivity, and approximately 0.88 specificity. Random forest analysis yielded better models and more exact performance estimates with approximately 0.74 accuracy, approximately 0.72 sensitivity, and approximately 0.81 specificity for the combined observations. CONCLUSIONS: Simple models do moderately well in predicting which cytidines will be edited to uridines, and provide the first quantitative predictive models for RNA edited sites in plant mitochondria. Our analysis shows that the identity of the nucleotide -1 to the edited C and the estimated free energy of folding for a 41 nt region surrounding the edited C are the most important variables that distinguish most edited from non-edited sites. However, the results suggest that primary sequence data and simple free energy of folding calculations alone are insufficient to make highly accurate predictions. VL - 5 ER - TY - CHAP T1 - A Tangled Bank: Reflections on the Tree of Life and Human Health T2 - Assembling the Tree of LifeAssembling the Tree of Life Y1 - 2004 A1 - Rita R. Colwell JA - Assembling the Tree of LifeAssembling the Tree of Life PB - Oxford University Press SN - 9780195172348 ER - TY - JOUR T1 - Variation of toxigenic Vibrio cholerae O1 in the aquatic environment of Bangladesh and its correlation with the clinical strains JF - Microbiology and immunologyMicrobiology and Immunology Y1 - 2004 A1 - Islam, M. S. A1 - Talukder, K. A. A1 - Khan, N. H. A1 - Mahmud, Z. H. A1 - Rahman, M. Z. A1 - Nair, G. B. A1 - Siddique, A. K. M. A1 - Yunus, M. A1 - Sack, D. A. A1 - Sack, R. B. A1 - Rita R. Colwell VL - 48 ER - TY - JOUR T1 - Viable but Nonculturable Vibrio Cholerae O1 in the Aquatic Environment of Argentina JF - Applied and Environmental MicrobiologyAppl. Environ. Microbiol.Applied and Environmental MicrobiologyAppl. Environ. Microbiol. Y1 - 2004 A1 - Binsztein, Norma A1 - Costagliola, Marcela C. A1 - Pichel, Mariana A1 - Jurquiza, Verónica A1 - Ramírez, Fernando C. A1 - Akselman, Rut A1 - Vacchino, Marta A1 - Huq, Anwarul A1 - Rita R. Colwell AB - In Argentina, as in other countries of Latin America, cholera has occurred in an epidemic pattern. Vibrio cholerae O1 is native to the aquatic environment, and it occurs in both culturable and viable but nonculturable (VNC) forms, the latter during interepidemic periods. This is the first report of the presence of VNC V. cholerae O1 in the estuarine and marine waters of the Río de la Plata and the Argentine shelf of the Atlantic Ocean, respectively. Employing immunofluorescence and PCR methods, we were able to detect reservoirs of V. cholerae O1 carrying the virulence-associated genes ctxA and tcpA. The VNC forms of V. cholerae O1 were identified in samples of water, phytoplankton, and zooplankton; the latter organisms were mainly the copepods Acartia tonsa, Diaptomus sp., Paracalanus crassirostris, and Paracalanus parvus. We found that under favorable conditions, the VNC form of V. cholerae can revert to the pathogenic, transmissible state. We concluded that V. cholerae O1 is a resident of Argentinean waters, as has been shown to be the case in other geographic regions of the world. VL - 70 SN - 0099-2240, 1098-5336 ER - TY - JOUR T1 - A 4-Year Study of the Epidemiology of Vibrio Cholerae in Four Rural Areas of Bangladesh JF - Journal of Infectious DiseasesJ Infect Dis.Journal of Infectious DiseasesJ Infect Dis. Y1 - 2003 A1 - Sack, R. Bradley A1 - Siddique, A. Kasem A1 - Longini, Ira M. A1 - Nizam, Azhar A1 - Yunus, Md A1 - M. Sirajul Islam A1 - Morris A1 - Ali, Afsar A1 - Huq, Anwar A1 - Nair, G. Balakrish A1 - Qadri, Firdausi A1 - Faruque, Shah M. A1 - Sack, David A. A1 - Rita R. Colwell AB - How Vibrio cholerae spreads around the world and what determines its seasonal peaks in endemic areas are not known. These features of cholera have been hypothesized to be primarily the result of environmental factors associated with aquatic habitats that can now be identified. Since 1997, fortnightly surveillance in 4 widely separated geographic locations in Bangladesh has been performed to identify patients with cholera and to collect environmental data. A total of 5670 patients (53% <5 years of age) have been studied; 14.3% had cholera (10.4% due to V. cholerae O1 El Tor, 3.8% due to O139). Both serogroups were found in all locations; outbreaks were seasonal and often occurred simultaneously. Water-use patterns showed that bathing and washing clothes in tube-well water was significantly protective in two of the sites. These data will be correlated with environmental factors, to develop a model for prediction of cholera outbreaks VL - 187 SN - 0022-1899, 1537-6613 ER - TY - JOUR T1 - ANNUAL REVIEW & FORECAST REPORTS-THE OCEANS: TO PROTECT AND TO PLOW JF - Sea TechnologySea Technology Y1 - 2003 A1 - Rita R. Colwell VL - 44 ER - TY - JOUR T1 - Characterization of a Vibrio cholerae phage isolated from the coastal water of Peru JF - Environmental MicrobiologyEnvironmental Microbiology Y1 - 2003 A1 - Talledo, Miguel A1 - Rivera, Irma N. G. A1 - Lipp, Erin K. A1 - Neale, Angela A1 - Karaolis, David A1 - Huq, Anwar A1 - Rita R. Colwell AB - A Vibrio cholerae bacteriophage, family Myoviridae, was isolated from seawater collected from the coastal water of Lima, Peru. Genome size was estimated to be 29 kbp. The temperate phage was specific to V. cholerae and infected 12/13 V. cholerae O1 strains and half of the four non-O1/non-O139 strains tested in this study. Vibrio cholerae O139 strains were resistant to infection and highest infection rates were obtained in low nutrient media amended with NaCl or prepared using seawater as diluent. VL - 5 SN - 1462-2920 ER - TY - JOUR T1 - Comparing bootstrap and posterior probability values in the four-taxon case JF - Syst BiolSyst Biol Y1 - 2003 A1 - Michael P. Cummings A1 - Handley, S. A. A1 - Myers, D. S. A1 - Reed, D. L. A1 - Rokas, A. A1 - Winka, K. AB - Assessment of the reliability of a given phylogenetic hypothesis is an important step in phylogenetic analysis. Historically, the nonparametric bootstrap procedure has been the most frequently used method for assessing the support for specific phylogenetic relationships. The recent employment of Bayesian methods for phylogenetic inference problems has resulted in clade support being expressed in terms of posterior probabilities. We used simulated data and the four-taxon case to explore the relationship between nonparametric bootstrap values (as inferred by maximum likelihood) and posterior probabilities (as inferred by Bayesian analysis). The results suggest a complex association between the two measures. Three general regions of tree space can be identified: (1) the neutral zone, where differences between mean bootstrap and mean posterior probability values are not significant, (2) near the two-branch corner, and (3) deep in the two-branch corner. In the last two regions, significant differences occur between mean bootstrap and mean posterior probability values. Whether bootstrap or posterior probability values are higher depends on the data in support of alternative topologies. Examination of star topologies revealed that both bootstrap and posterior probability values differ significantly from theoretical expectations; in particular, there are more posterior probability values in the range 0.85-1 than expected by theory. Therefore, our results corroborate the findings of others that posterior probability values are excessively high. Our results also suggest that extrapolations from single topology branch-length studies are unlikely to provide any general conclusions regarding the relationship between bootstrap and posterior probability values. VL - 52 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 - TY - JOUR T1 - Direct Detection of Vibrio Cholerae and ctxA in Peruvian Coastal Water and Plankton by PCR JF - Applied and Environmental MicrobiologyAppl. Environ. Microbiol.Applied and Environmental MicrobiologyAppl. Environ. Microbiol. Y1 - 2003 A1 - Lipp, Erin K. A1 - Rivera, Irma N. G. A1 - Gil, Ana I. A1 - Espeland, Eric M. A1 - Choopun, Nipa A1 - Louis, Valérie R. A1 - Russek-Cohen, Estelle A1 - Huq, Anwar A1 - Rita R. Colwell AB - Seawater and plankton samples were collected over a period of 17 months from November 1998 to March 2000 along the coast of Peru. Total DNA was extracted from water and from plankton grouped by size into two fractions (64 μm to 202 μm and >202 μm). All samples were assayed for Vibrio cholerae, V. cholerae O1, V. cholerae O139, and ctxA by PCR. Of 50 samples collected and tested, 33 (66.0%) were positive for V. cholerae in at least one of the three fractions. Of these, 62.5% (n = 32) contained V. cholerae O1; ctxA was detected in 25% (n = 20) of the V. cholerae O1-positive samples. None were positive for V. cholerae O139. Thus, PCR was successfully employed in detecting toxigenic V. cholerae directly in seawater and plankton samples and provides evidence for an environmental reservoir for this pathogen in Peruvian coastal waters. VL - 69 SN - 0099-2240, 1098-5336 ER - TY - JOUR T1 - Effectiveness of conservation targets in capturing genetic diversity JF - Conserv BiolConserv Biol Y1 - 2003 A1 - Neel, M. C. A1 - Michael P. Cummings AB - Any conservation actions that preserve some populations and not others will have genetic consequences. We used empirical data from four rare plant taxa to assess these consequences in terms of how well allele numbers ( all alleles and alleles occurring at a frequency openface>0.05 in any population ) and expected heterozygosity are represented when different numbers of populations are conserved. We determined sampling distributions for these three measures of genetic diversity using Monte Carlo methods. We assessed the proportion of alleles included in the number of populations considered adequate for conservation, needed to capture all alleles, and needed to meet an accepted standard of genetic-diversity conservation of having a 90-95% probability of including all common alleles. We also assessed the number of populations necessary to obtain values of heterozygosity within +/-10% of the value obtained from all populations. Numbers of alleles were strongly affected by the number of populations sampled. Heterozygosity was only slightly less sensitive to numbers of populations than were alleles. On average, currently advocated conservation intensities represented 67-83% of all alleles and 85-93% of common alleles. The smallest number of populations to include all alleles ranged from 6 to 17 ( 42-57% ), but <0.2% of 1000 samples of these numbers of populations included them all. It was necessary to conserve 16-29 ( 53-93% ) of the sampled populations to meet the standard for common alleles. Between 20% and 64% of populations were needed to reliably represent species-level heterozygosity. Thus, higher percentages of populations are needed than are currently considered adequate to conserve genetic diversity if populations are selected without genetic data. VL - 17 ER - TY - JOUR T1 - Emergence and Evolution of Vibrio Cholerae O139 JF - Proceedings of the National Academy of SciencesPNASProceedings of the National Academy of SciencesPNAS Y1 - 2003 A1 - Faruque, Shah M. A1 - Sack, David A. A1 - Sack, R. Bradley A1 - Rita R. Colwell A1 - Takeda, Yoshifumi A1 - Nair, G. Balakrish AB - The emergence of Vibrio cholerae O139 Bengal during 1992–1993 was associated with large epidemics of cholera in India and Bangladesh and, initially, with a total displacement of the existing V. cholerae O1 strains. However, the O1 strains reemerged in 1994 and initiated a series of disappearance and reemergence of either of the two serogroups that was associated with temporal genetic and phenotypic changes sustained by the strains. Since the initial emergence of the O139 vibrios, new variants of the pathogen derived from multiple progenitors have been isolated and characterized. The clinical and epidemiological characteristics of these strains have been studied. Rapid genetic reassortment in O139 strains appears to be a response to the changing epidemiology of V. cholerae O1 and also a strategy for persistence in competition with strains of the O1 serogroup. The emergence of V. cholerae O139 has provided a unique opportunity to witness genetic changes in V. cholerae that may be associated with displacement of an existing serogroup by a newly emerging one and, thus, provide new insights into the epidemiology of cholera. The genetic changes and natural selection involving both environmental and host factors are likely to influence profoundly the genetics, epidemiology, and evolution of toxigenic V. cholerae, not only in the Ganges Delta region of India and Bangladesh, but also in other areas of endemic and epidemic cholera. VL - 100 SN - 0027-8424, 1091-6490 ER - TY - JOUR T1 - From terabytes to insights JF - Communications of the ACMCommunications of the ACM Y1 - 2003 A1 - Rita R. Colwell AB - For scientists and engineers tapping the NSF's high-performance cyberinfrastructure, the path to wisdom follows a route both miraculous and familiar. VL - 46 SN - 0001-0782 ER - TY - JOUR T1 - Genetic consequences of ecological reserve design guidelines: An empirical investigation JF - Conserv GenetConserv Genet Y1 - 2003 A1 - Neel, M. C. A1 - Michael P. Cummings KW - albens KW - Astragulus KW - Bernardino KW - conservation KW - design KW - diversity KW - Erigeron KW - Eriogonum KW - genetic KW - Genetics KW - goodmaniana KW - Mountains KW - ovalifolium KW - Oxytheca KW - parishii KW - plant KW - reserve KW - San KW - var. KW - vineum AB - We assessed the genetic diversity consequences of applying ecological reserve design guidelines to four federally-listed globally-rare plant species. Consequences were measured using two metrics: proportion of all alleles and of common alleles included in reserves. Common alleles were defined as those alleles having a frequency of greater than or equal to0.05 in at least one population. Four conservation professionals applied ecological reserve guidelines to choose specific populations of each species for inclusion in reserves of size 1 to N - 1, where N is the total number of populations of each species. Information regarding genetic diversity was not used in selecting populations. The resulting reserve designs were compared to random designs, and the agreement among experts was assessed using Kendall's coefficient of concordance. Application of ecological reserve design guidelines proved mostly ineffective in capturing more genetic diversity than is captured selecting populations randomly. Meeting established targets for genetic diversity, such as one advocated by the Center for Plant Conservation, required larger numbers of populations than are suggested to be sufficient. Relative performance of expert designs differed among species and was dependent on whether the proportion of all alleles or of common alleles was used as a measure of diversity. Furthermore there was no significant concordance among experts in order in which populations were incorporated into reserves as experts differed in priority they placed on individual guidelines. VL - 4 ER - TY - JOUR T1 - The genome sequence of Bacillus anthracis Ames and comparison to closely related bacteria JF - NatureNature Y1 - 2003 A1 - Read, Timothy D. A1 - Peterson, Scott N. A1 - Tourasse, Nicolas A1 - Baillie, Les W. A1 - Paulsen, Ian T. A1 - Nelson, Karen E. A1 - Tettelin, Herv A1 - Fouts, Derrick E. A1 - Eisen, Jonathan A. A1 - Gill, Steven R. A1 - Holtzapple, Erik K. A1 - kstad, Ole Andreas A1 - Helgason, Erlendur A1 - Rilstone, Jennifer A1 - Wu, Martin A1 - Kolonay, James F. A1 - Beanan, Maureen J. A1 - Dodson, Robert J. A1 - Brinkac, Lauren M. A1 - Gwinn, Michelle A1 - DeBoy, Robert T. A1 - Madpu, Ramana A1 - Daugherty, Sean C. A1 - Durkin, A. Scott A1 - Haft, Daniel H. A1 - Nelson, William C. A1 - Peterson, Jeremy D. A1 - M. Pop A1 - Khouri, Hoda M. A1 - Radune, Diana A1 - Benton, Jonathan L. A1 - Mahamoud, Yasmin A1 - Jiang, Lingxia A1 - Hance, Ioana R. A1 - Weidman, Janice F. A1 - Berry, Kristi J. A1 - Plaut, Roger D. A1 - Wolf, Alex M. A1 - Watkins, Kisha L. A1 - Nierman, William C. A1 - Hazen, Alyson A1 - Cline, Robin A1 - Redmond, Caroline A1 - Thwaite, Joanne E. A1 - White, Owen A1 - Salzberg, Steven L. A1 - Thomason, Brendan A1 - Friedlander, Arthur M. A1 - Koehler, Theresa M. A1 - Hanna, Philip C. A1 - Kolst, A1 - Anne-Brit A1 - Fraser, Claire M. AB - Bacillus anthracis is an endospore-forming bacterium that causes inhalational anthrax1. Key virulence genes are found on plasmids (extra-chromosomal, circular, double-stranded DNA molecules) pXO1 (ref. 2) and pXO2 (ref. 3). To identify additional genes that might contribute to virulence, we analysed the complete sequence of the chromosome of B. anthracis Ames (about 5.23 megabases). We found several chromosomally encoded proteins that may contribute to pathogenicity—including haemolysins, phospholipases and iron acquisition functions—and identified numerous surface proteins that might be important targets for vaccines and drugs. Almost all these putative chromosomal virulence and surface proteins have homologues in Bacillus cereus, highlighting the similarity of B. anthracis to near-neighbours that are not associated with anthrax4. By performing a comparative genome hybridization of 19 B. cereus and Bacillus thuringiensis strains against a B. anthracis DNA microarray, we confirmed the general similarity of chromosomal genes among this group of close relatives. However, we found that the gene sequences of pXO1 and pXO2 were more variable between strains, suggesting plasmid mobility in the group. The complete sequence of B. anthracis is a step towards a better understanding of anthrax pathogenesis. VL - 423 SN - 0028-0836 N1 - [eacute]
[Oslash] ER - TY - JOUR T1 - Method of DNA extraction and application of multiplex polymerase chain reaction to detect toxigenic Vibrio cholerae O1 and O139 from aquatic ecosystems JF - Environmental MicrobiologyEnvironmental Microbiology Y1 - 2003 A1 - Rivera, Irma N. G. A1 - Lipp, Erin K. A1 - Gil, Ana A1 - Choopun, Nipa A1 - Huq, Anwar A1 - Rita R. Colwell AB - Vibrio cholerae is a free-living bacterium found in water and in association with plankton. V. cholerae non-O1/non-O139 strains are frequently isolated from aquatic ecosystems worldwide. Less frequently isolated are V. cholerae O1 and V. cholerae O139, the aetiological agents of cholera. These strains have two main virulence-associated factors, cholera toxin (CT) and toxin co-regulated pilus (TCP). By extracting total DNA from aquatic samples, the presence of pathogenic strains can be determined quickly and used to improve a microbiological risk assessment for cholera in coastal areas. Some methods suggested for DNA extraction from water samples are not applicable to all water types. We describe here a method for DNA extraction from coastal water and a multiplex polymerase chain reaction (PCR) for O1 and O139 serogroups. DNA extraction was successfully accomplished from 117 sea water samples collected from coastal areas of Perú, Brazil and the USA. DNA concentration in all samples varied from 20 ng to 480 µg µl−1. The sensitivity of the DNA extraction method was 100 V. cholerae cells in 250 ml of water. The specificity of multiplex O1/O139 PCR was investigated by analysing 120 strains of V. cholerae, Vibrio and other Bacteria species. All V. cholerae O1 and O139 tested were positive. For cholera surveillance of aquatic environments and ballast water, total DNA extraction, followed by V. cholerae PCR, and O1/O139 serogroup and tcpA/ctxA genes by multiplex PCR offers an efficient system, permitting risk analysis for cholera in coastal areas. VL - 5 SN - 1462-2920 ER - TY - JOUR T1 - Necessity is the mother of invention: a simple grid computing system using commodity tools JF - J Parallel Distr ComJ Parallel Distr Com Y1 - 2003 A1 - Myers, D. S. A1 - Michael P. Cummings KW - Apache KW - computing KW - distributed KW - Grid KW - HTTP KW - java KW - Linux KW - Perl KW - SQL KW - Unix KW - XML-RPC AB - Access to sufficient resources is a barrier to scientific progress for many researchers facing large computational problems. Gaining access to large-scale resources (i.e., university-wide or federally supported computer centers) can be difficult, given their limited availability, particular architectures, and request/review/approval cycles. Simultaneously, researchers often find themselves with access to workstations and older clusters overlooked by their owners in favor of newer hardware. Software to tie these resources into a coherent Grid, however, has been problematic. Here, we describe our experiences building a Grid computing system to conduct a large-scale simulation study using "borrowed" computing resources distributed over a wide area. Using standard software components, we have produced a Grid computing system capable of coupling several hundred processors spanning multiple continents and administrative domains. We believe that this system fills an important niche between a closely coupled local system and a heavyweight, highly customized wide area system. (C) 2003 Elsevier Science (USA). All rights reserved. VL - 63 ER - TY - JOUR T1 - Pathogenic Potential of Environmental Vibrio Cholerae Strains Carrying Genetic Variants of the Toxin-Coregulated Pilus Pathogenicity Island JF - Infection and ImmunityInfect. Immun.Infection and ImmunityInfect. Immun. Y1 - 2003 A1 - Faruque, Shah M. A1 - Kamruzzaman, M. A1 - Meraj, Ismail M. A1 - Chowdhury, Nityananda A1 - Nair, G. Balakrish A1 - Sack, R. Bradley A1 - Rita R. Colwell A1 - Sack, David A. AB - The major virulence factors of toxigenic Vibrio cholerae are cholera toxin (CT), which is encoded by a lysogenic bacteriophage (CTXΦ), and toxin-coregulated pilus (TCP), an essential colonization factor which is also the receptor for CTXΦ. The genes for the biosynthesis of TCP are part of a larger genetic element known as the TCP pathogenicity island. To assess their pathogenic potential, we analyzed environmental strains of V. cholerae carrying genetic variants of the TCP pathogenicity island for colonization of infant mice, susceptibility to CTXΦ, and diarrheagenicity in adult rabbits. Analysis of 14 environmental strains, including 3 strains carrying a new allele of the tcpA gene, 9 strains carrying a new allele of the toxT gene, and 2 strains carrying conventional tcpA and toxT genes, showed that all strains colonized infant mice with various efficiencies in competition with a control El Tor biotype strain of V. cholerae O1. Five of the 14 strains were susceptible to CTXΦ, and these transductants produced CT and caused diarrhea in adult rabbits. These results suggested that the new alleles of the tcpA and toxT genes found in environmental strains of V. cholerae encode biologically active gene products. Detection of functional homologs of the TCP island genes in environmental strains may have implications for understanding the origin and evolution of virulence genes of V. cholerae. VL - 71 SN - 0019-9567, 1098-5522 ER - TY - JOUR T1 - Persistence of adhesive properties in Vibrio cholerae after long‐term exposure to sea water JF - Environmental MicrobiologyEnvironmental Microbiology Y1 - 2003 A1 - Pruzzo, Carla A1 - Tarsi, Renato A1 - Del Mar Lleò, Maria A1 - Signoretto, Caterina A1 - Zampini, Massimiliano A1 - Pane, Luigi A1 - Rita R. Colwell A1 - Canepari, Pietro AB - The effect of exposure to artificial sea water (ASW) on the ability of classical Vibrio cholerae O1 cells to interact with chitin-containing substrates and human intestinal cells was studied. Incubation of vibrios in ASW at 5°C and 18°C resulted in two kinds of cell responses: the viable but non-culturable (VBNC) state (i.e. <0.1 colony forming unit ml−1) at 5°C, and starvation (i.e. maintenance of culturability of the population) at 18°C. The latter remained rod shaped and, after 40 days’ incubation, presented a 47–58% reduction in the number of cells attached to chitin, a 48–53% reduction in the number of bacteria adhering to copepods, and a 48–54% reduction in the number of bacteria adhering to human cultured intestinal cells, compared to control cells not suspended in ASW. Bacteria suspended in ASW at 5°C became coccoid and, after 40 days, showed 34–42% fewer cells attached to chitin, 52–55% fewer adhering to copep-ods, and 45–48% fewer cells adhering to intestinal cell monolayers, compared to controls. Sarkosyl-insoluble membrane proteins that bind chitin particles were isolated and analysed by SDS-PAGE. After 40 days incubation in ASW at both 5°C and 18°C vibrios expressed chitin-binding ligands similar to bacteria harvested in the stationary growth phase. It is concluded that as vibrios do not lose adhesive properties after long-term exposure to ASW, it is important to include methods for VBNC bacteria when testing environmental and clinical samples for purposes of public health safety. VL - 5 SN - 1462-2920 ER - TY - JOUR T1 - Phylogenetic analysis reveals five independent transfers of the chloroplast gene ıt rbcL to the mitochondrial genome in angiosperms JF - Curr GenetCurr Genet Y1 - 2003 A1 - Michael P. Cummings A1 - Nugent, J. M. A1 - Olmstead, R. G. A1 - Palmer, J. D. AB - We used the chloroplast gene rbcL as a model to study the frequency and relative timing of transfer of chloroplast sequences to the mitochondrial genome. Southern blot survey of 20 mitochondrial DNAs confirmed three previously reported groups of plants containing rbcL in their mitochondrion, while PCR studies identified a new mitochondrial rbcL. Published and newly determined mitochondrial and chloroplast rbcL sequences were used to reconstruct rbcL phylogeny. The results imply five or six separate interorganellar transfers of rbcL among the angiosperms examined, and hundreds of successful transfers across all flowering plants. By taxonomic criteria, the crucifer transfer is the most ancient, two separate transfers within the grass family are of intermediate ancestry, and the morning-glory transfer is most recent. All five mitochondrial copies of rbcL examined exhibit insertion and/or deletion events that disrupt the reading frame (three are grossly truncated); and all are elevated in the proportion of nonsynonymous substitutions, providing clear evidence that these sequences are pseudogenes. VL - 43 ER - TY - JOUR T1 - Predictability of Vibrio Cholerae in Chesapeake Bay JF - Applied and Environmental MicrobiologyAppl. Environ. Microbiol.Applied and Environmental MicrobiologyAppl. Environ. Microbiol. Y1 - 2003 A1 - Louis, Valérie R. A1 - Russek-Cohen, Estelle A1 - Choopun, Nipa A1 - Rivera, Irma N. G. A1 - Gangle, Brian A1 - Jiang, Sunny C. A1 - Rubin, Andrea A1 - Patz, Jonathan A. A1 - Huq, Anwar A1 - Rita R. Colwell AB - Vibrio cholerae is autochthonous to natural waters and can pose a health risk when it is consumed via untreated water or contaminated shellfish. The correlation between the occurrence of V. cholerae in Chesapeake Bay and environmental factors was investigated over a 3-year period. Water and plankton samples were collected monthly from five shore sampling sites in northern Chesapeake Bay (January 1998 to February 2000) and from research cruise stations on a north-south transect (summers of 1999 and 2000). Enrichment was used to detect culturable V. cholerae, and 21.1% (n = 427) of the samples were positive. As determined by serology tests, the isolates, did not belong to serogroup O1 or O139 associated with cholera epidemics. A direct fluorescent-antibody assay was used to detect V. cholerae O1, and 23.8% (n = 412) of the samples were positive. V. cholerae was more frequently detected during the warmer months and in northern Chesapeake Bay, where the salinity is lower. Statistical models successfully predicted the presence of V. cholerae as a function of water temperature and salinity. Temperatures above 19°C and salinities between 2 and 14 ppt yielded at least a fourfold increase in the number of detectable V. cholerae. The results suggest that salinity variation in Chesapeake Bay or other parameters associated with Susquehanna River inflow contribute to the variability in the occurrence of V. cholerae and that salinity is a useful indicator. Under scenarios of global climate change, increased climate variability, accompanied by higher stream flow rates and warmer temperatures, could favor conditions that increase the occurrence of V. cholerae in Chesapeake Bay. VL - 69 SN - 0099-2240, 1098-5336 ER - TY - JOUR T1 - Reduction of Cholera in Bangladeshi Villages by Simple Filtration JF - Proceedings of the National Academy of SciencesPNASProceedings of the National Academy of SciencesPNAS Y1 - 2003 A1 - Rita R. Colwell A1 - Huq, Anwar A1 - M. Sirajul Islam A1 - K. M. A. Aziz A1 - Yunus, M. A1 - N. Huda Khan A1 - A. Mahmud A1 - Sack, R. Bradley A1 - Nair, G. B. A1 - J. Chakraborty A1 - Sack, David A. A1 - E. Russek-Cohen AB - Based on results of ecological studies demonstrating that Vibrio cholerae, the etiological agent of epidemic cholera, is commensal to zooplankton, notably copepods, a simple filtration procedure was developed whereby zooplankton, most phytoplankton, and particulates >20 μm were removed from water before use. Effective deployment of this filtration procedure, from September 1999 through July 2002 in 65 villages of rural Bangladesh, of which the total population for the entire study comprised ≈133,000 individuals, yielded a 48% reduction in cholera (P < 0.005) compared with the control. VL - 100 SN - 0027-8424, 1091-6490 ER - TY - JOUR T1 - The sequence and analysis of Trypanosoma brucei chromosome II. JF - Nucleic Acids Res Y1 - 2003 A1 - el-Sayed, Najib M A A1 - Ghedin, Elodie A1 - Song, Jinming A1 - MacLeod, Annette A1 - Bringaud, Frederic A1 - Larkin, Christopher A1 - Wanless, David A1 - Peterson, Jeremy A1 - Hou, Lihua A1 - Taylor, Sonya A1 - Tweedie, Alison A1 - Biteau, Nicolas A1 - Khalak, Hanif G A1 - Lin, Xiaoying A1 - Mason, Tanya A1 - Hannick, Linda A1 - Caler, Elisabet A1 - Blandin, Gaëlle A1 - Bartholomeu, Daniella A1 - Simpson, Anjana J A1 - Kaul, Samir A1 - Zhao, Hong A1 - Pai, Grace A1 - Van Aken, Susan A1 - Utterback, Teresa A1 - Haas, Brian A1 - Koo, Hean L A1 - Umayam, Lowell A1 - Suh, Bernard A1 - Gerrard, Caroline A1 - Leech, Vanessa A1 - Qi, Rong A1 - Zhou, Shiguo A1 - Schwartz, David A1 - Feldblyum, Tamara A1 - Salzberg, Steven A1 - Tait, Andrew A1 - Turner, C Michael R A1 - Ullu, Elisabetta A1 - White, Owen A1 - Melville, Sara A1 - Adams, Mark D A1 - Fraser, Claire M A1 - Donelson, John E KW - Animals KW - Antigens, Protozoan KW - Chromosome mapping KW - Chromosomes KW - DNA, Protozoan KW - Gene Duplication KW - Genes, Protozoan KW - Molecular Sequence Data KW - Pseudogenes KW - Recombination, Genetic KW - Sequence Analysis, DNA KW - Trypanosoma brucei brucei AB -

We report here the sequence of chromosome II from Trypanosoma brucei, the causative agent of African sleeping sickness. The 1.2-Mb pairs encode about 470 predicted genes organised in 17 directional clusters on either strand, the largest cluster of which has 92 genes lined up over a 284-kb region. An analysis of the GC skew reveals strand compositional asymmetries that coincide with the distribution of protein-coding genes, suggesting these asymmetries may be the result of transcription-coupled repair on coding versus non-coding strand. A 5-cM genetic map of the chromosome reveals recombinational 'hot' and 'cold' regions, the latter of which is predicted to include the putative centromere. One end of the chromosome consists of a 250-kb region almost exclusively composed of RHS (pseudo)genes that belong to a newly characterised multigene family containing a hot spot of insertion for retroelements. Interspersed with the RHS genes are a few copies of truncated RNA polymerase pseudogenes as well as expression site associated (pseudo)genes (ESAGs) 3 and 4, and 76 bp repeats. These features are reminiscent of a vestigial variant surface glycoprotein (VSG) gene expression site. The other end of the chromosome contains a 30-kb array of VSG genes, the majority of which are pseudogenes, suggesting that this region may be a site for modular de novo construction of VSG gene diversity during transposition/gene conversion events.

VL - 31 CP - 16 ER - TY - JOUR T1 - Analysis of 16S-23S rRNA intergenic spacer of Vibrio cholerae and Vibrio mimicus for detection of these species JF - METHODS IN MOLECULAR BIOLOGYMETHODS IN MOLECULAR BIOLOGY Y1 - 2002 A1 - Chun, J. A1 - Rivera, I. N. G. A1 - Rita R. Colwell VL - 179 ER - TY - JOUR T1 - Analysis of stage-specific gene expression in the bloodstream and the procyclic form of Trypanosoma brucei using a genomic DNA-microarray. JF - Mol Biochem Parasitol Y1 - 2002 A1 - Diehl, Susanne A1 - Diehl, Frank A1 - El-Sayed, Najib M A1 - Clayton, Christine A1 - Hoheisel, Jörg D KW - Animals KW - Blotting, Northern KW - Escherichia coli KW - Gene expression KW - Gene Expression Profiling KW - Genes, Protozoan KW - HUMANS KW - Life Cycle Stages KW - Molecular Sequence Data KW - Oligonucleotide Array Sequence Analysis KW - Polymerase Chain Reaction KW - Transcription, Genetic KW - Trypanosoma brucei brucei AB -

A microarray comprising 21,024 different PCR products spotted on glass slides was constructed for gene expression studies on Trypanosoma brucei. The arrayed fragments were generated from a T. brucei shotgun clone library, which had been prepared from randomly sheared and size-fractionated genomic DNA. For the identification of stage-specific gene activity, total RNA from in vitro cultures of the human, long slender form and the insect, procyclic form of the parasite was labelled and hybridised to the microarray. Approximately 75% of the genomic fragments produced a signal and about 2% exhibited significant differences between the transcript levels in the bloodstream and procyclic forms. A few results were confirmed by Northern blot analysis or reverse-transcription and PCR. Three hundred differentially regulated clones have been selected for sequencing. So far, of 33 clones that showed about 2-fold or more over-expression in bloodstream forms, 15 contained sequences similar to those of VSG expression sites and at least six others appeared non-protein-coding. Of 29 procyclic-specific clones, at least eight appeared not to be protein-coding. A surprisingly large proportion of known regulated genes was already identified in this small sample, and some new ones were found, illustrating the utility of genomic arrays.

VL - 123 CP - 2 ER - TY - JOUR T1 - Analysis of stage-specific gene expression in the bloodstream and the procyclic form of Trypanosoma brucei using a genomic DNA-microarray JF - Molecular and Biochemical ParasitologyMolecular and Biochemical Parasitology Y1 - 2002 A1 - Diehl, Susanne A1 - Diehl, Frank A1 - Najib M. El‐Sayed A1 - Clayton, Christine A1 - Hoheisel, Jörg D. KW - Expression KW - Gene KW - Microarray KW - Regulation KW - Trypanosoma brucei AB - A microarray comprising 21[punctuation space]024 different PCR products spotted on glass slides was constructed for gene expression studies on Trypanosoma brucei. The arrayed fragments were generated from a T. brucei shotgun clone library, which had been prepared from randomly sheared and size-fractionated genomic DNA. For the identification of stage-specific gene activity, total RNA from in vitro cultures of the human, long slender form and the insect, procyclic form of the parasite was labelled and hybridised to the microarray. Approximately 75% of the genomic fragments produced a signal and about 2% exhibited significant differences between the transcript levels in the bloodstream and procyclic forms. A few results were confirmed by Northern blot analysis or reverse-transcription and PCR. Three hundred differentially regulated clones have been selected for sequencing. So far, of 33 clones that showed about 2-fold or more over-expression in bloodstream forms, 15 contained sequences similar to those of VSG expression sites and at least six others appeared non-protein-coding. Of 29 procyclic-specific clones, at least eight appeared not to be protein-coding. A surprisingly large proportion of known regulated genes was already identified in this small sample, and some new ones were found, illustrating the utility of genomic arrays. VL - 123 SN - 0166-6851 ER - TY - JOUR T1 - Characterization of Pseudoalteromonas citrea and P. nigrifaciens Isolated from Different Ecological Habitats Based on REP-PCR Genomic Fingerprints JF - Systematic and Applied MicrobiologySystematic and Applied Microbiology Y1 - 2002 A1 - Ivanova, Elena P. A1 - Matte, Glavur R. A1 - Matte, Maria H. A1 - Coenye, Tom A1 - Huq, Anwarul A1 - Rita R. Colwell KW - biogeography KW - BOX-PCR KW - ERIC KW - Pseudoalteromonas KW - REP AB - SummaryDNA primers corresponding to conserved repetitive interspersed genomic motifs and PCR were used to show that REP, ERIC and BOX-like DNA sequences are present in marine, oxidative, Gram-negative Pseudoalteromonas strains. REP, ERIC and BOX-PCR were used for rapid molecular characterization of both the type species of the genus and environmental strains isolated from samples collected in different geographical areas. PCR-generated genomic fingerprint patterns were found to be both complex and strain specific. Analysis of the genotypic structure of phenotypically diverse P. citrea revealed a geographic clustering of Far Eastern brown-pigmented, agar-digesting strains of this species. Marine isolates of P. nigrifaciens with 67–70% DNA relatedness generated genomic patterns different from those of the type strain and formed a separate cluster. It is concluded that REP, ERIC and BOX-PCR are effective in generating strain specific patterns that can be used to elucidate geographic distribution, with these genomic patterns providing a valuable biogeographic criterion. VL - 25 SN - 0723-2020 ER - TY - CHAP T1 - Combinatorial Algorithms for Design of DNA Arrays T2 - Chip TechnologyChip Technology Y1 - 2002 A1 - Sridhar Hannenhalli A1 - Hubbell, Earl A1 - Lipshutz, Robert A1 - Pevzner, Pavel ED - Hoheisel, Jörg ED - Brazma, A. ED - Büssow, K. ED - Cantor, C. ED - Christians, F. ED - Chui, G. ED - Diaz, R. ED - Drmanac, R. ED - Drmanac, S. ED - Eickhoff, H. ED - Fellenberg, K. ED - Sridhar Hannenhalli ED - Hoheisel, J. ED - Hou, A. ED - Hubbell, E. ED - Jin, H. ED - Jin, P. ED - Jurinke, C. ED - Konthur, Z. ED - Köster, H. ED - Kwon, S. ED - Lacy, S. ED - Lehrach, H. ED - Lipshutz, R. ED - Little, D. ED - Lueking, A. ED - McGall, G. ED - Moeur, B. ED - Nordhoff, E. ED - Nyarsik, L. ED - Pevzner, P. ED - Robinson, A. ED - Sarkans, U. ED - Shafto, J. ED - Sohail, M. ED - Southern, E. ED - Swanson, D. ED - Ukrainczyk, T. ED - van den Boom, D. ED - Vilo, J. ED - Vingron, M. ED - Walter, G. ED - Xu, C. AB - Optimal design of DNA arrays requires the development of algorithms with two-fold goals: reducing the effects caused by unintended illumination ( border length minimization problem ) and reducing the complexity of masks ( mask decomposition problem ). We describe algorithms that reduce the number of rectangles in mask decomposition by 20–30% as compared to a standard array design under the assumption that the arrangement of oligonucleotides on the array is fixed. This algorithm produces provably optimal solution for all studied real instances of array design. We also address the difficult problem of finding an arrangement which minimizes the border length and come up with a new idea of threading that significantly reduces the border length as compared to standard designs. JA - Chip TechnologyChip Technology T3 - Advances in Biochemical Engineering/Biotechnology PB - Springer Berlin / Heidelberg VL - 77 SN - 978-3-540-43215-9 ER - TY - JOUR T1 - Detection of Cytotoxin-Hemolysin mRNA in Nonculturable Populations of Environmental and Clinical Vibrio Vulnificus Strains in Artificial Seawater JF - Applied and Environmental MicrobiologyAppl. Environ. Microbiol.Applied and Environmental MicrobiologyAppl. Environ. Microbiol. Y1 - 2002 A1 - Fischer-Le Saux, Marion A1 - Hervio-Heath, Dominique A1 - Loaec, Solen A1 - Rita R. Colwell A1 - Pommepuy, Monique AB - The objective of this study was to develop a molecular detection method that better estimates the potential risk associated with the presence of Vibrio vulnificus. For that purpose, we applied seminested reverse transcription-PCR (RT-PCR) to viable but nonculturable (VBNC) populations of V. vulnificus and targeted the cytotoxin-hemolysin virulence gene vvhA. Three strains, two environmental, IF Vv10 and IF Vv18, and one clinical, C7184, were used in this study. Artificial seawater, inoculated with mid-log-phase cells, was maintained at 4°C. VBNC cells resulted after 3, 6, and 14 days for C7184, IF Vv18, and IF Vv10, respectively. Our data indicate that seminested RT-PCR is sensitive for the detection of vvhA mRNA in artificial seawater when exclusively nonculturable bacteria are present. This is the first report of the expression of a toxin gene in VBNC V. vulnificus. Moreover, vvhA transcripts were shown to persist in nonculturable populations over a 4.5-month period, with a progressive decline of the signal over time. This result indicates that special attention should be given to the presence of potentially pathogenic VBNC cells in environmental samples when assessing public health risk. VL - 68 SN - 0099-2240, 1098-5336 ER - TY - JOUR T1 - The draft genome of Ciona intestinalis: insights into chordate and vertebrate origins. JF - Science Y1 - 2002 A1 - Dehal, Paramvir A1 - Satou, Yutaka A1 - Campbell, Robert K A1 - Chapman, Jarrod A1 - Degnan, Bernard A1 - De Tomaso, Anthony A1 - Davidson, Brad A1 - Di Gregorio, Anna A1 - Gelpke, Maarten A1 - Goodstein, David M A1 - Harafuji, Naoe A1 - Hastings, Kenneth E M A1 - Ho, Isaac A1 - Hotta, Kohji A1 - Huang, Wayne A1 - Kawashima, Takeshi A1 - Lemaire, Patrick A1 - Martinez, Diego A1 - Meinertzhagen, Ian A A1 - Necula, Simona A1 - Nonaka, Masaru A1 - Putnam, Nik A1 - Rash, Sam A1 - Saiga, Hidetoshi A1 - Satake, Masanobu A1 - Terry, Astrid A1 - Yamada, Lixy A1 - Wang, Hong-Gang A1 - Awazu, Satoko A1 - Azumi, Kaoru A1 - Boore, Jeffrey A1 - Branno, Margherita A1 - Chin-Bow, Stephen A1 - DeSantis, Rosaria A1 - Doyle, Sharon A1 - Francino, Pilar A1 - Keys, David N A1 - Haga, Shinobu A1 - Hayashi, Hiroko A1 - Hino, Kyosuke A1 - Imai, Kaoru S A1 - Inaba, Kazuo A1 - Kano, Shungo A1 - Kobayashi, Kenji A1 - Kobayashi, Mari A1 - Lee, Byung-In A1 - Makabe, Kazuhiro W A1 - Manohar, Chitra A1 - Matassi, Giorgio A1 - Medina, Monica A1 - Mochizuki, Yasuaki A1 - Mount, Steve A1 - Morishita, Tomomi A1 - Miura, Sachiko A1 - Nakayama, Akie A1 - Nishizaka, Satoko A1 - Nomoto, Hisayo A1 - Ohta, Fumiko A1 - Oishi, Kazuko A1 - Rigoutsos, Isidore A1 - Sano, Masako A1 - Sasaki, Akane A1 - Sasakura, Yasunori A1 - Shoguchi, Eiichi A1 - Shin-i, Tadasu A1 - Spagnuolo, Antoinetta A1 - Stainier, Didier A1 - Suzuki, Miho M A1 - Tassy, Olivier A1 - Takatori, Naohito A1 - Tokuoka, Miki A1 - Yagi, Kasumi A1 - Yoshizaki, Fumiko A1 - Wada, Shuichi A1 - Zhang, Cindy A1 - Hyatt, P Douglas A1 - Larimer, Frank A1 - Detter, Chris A1 - Doggett, Norman A1 - Glavina, Tijana A1 - Hawkins, Trevor A1 - Richardson, Paul A1 - Lucas, Susan A1 - Kohara, Yuji A1 - Levine, Michael A1 - Satoh, Nori A1 - Rokhsar, Daniel S KW - Alleles KW - Animals KW - Apoptosis KW - Base Sequence KW - Cellulose KW - Central Nervous System KW - Ciona intestinalis KW - Computational Biology KW - Endocrine System KW - Gene Dosage KW - Gene Duplication KW - genes KW - Genes, Homeobox KW - Genome KW - Heart KW - Immunity KW - Molecular Sequence Data KW - Multigene Family KW - Muscle Proteins KW - Organizers, Embryonic KW - Phylogeny KW - Polymorphism, Genetic KW - Proteins KW - Sequence Analysis, DNA KW - Sequence Homology, Nucleic Acid KW - Species Specificity KW - Thyroid Gland KW - Urochordata KW - Vertebrates AB -

The first chordates appear in the fossil record at the time of the Cambrian explosion, nearly 550 million years ago. The modern ascidian tadpole represents a plausible approximation to these ancestral chordates. To illuminate the origins of chordate and vertebrates, we generated a draft of the protein-coding portion of the genome of the most studied ascidian, Ciona intestinalis. The Ciona genome contains approximately 16,000 protein-coding genes, similar to the number in other invertebrates, but only half that found in vertebrates. Vertebrate gene families are typically found in simplified form in Ciona, suggesting that ascidians contain the basic ancestral complement of genes involved in cell signaling and development. The ascidian genome has also acquired a number of lineage-specific innovations, including a group of genes engaged in cellulose metabolism that are related to those in bacteria and fungi.

VL - 298 CP - 5601 M3 - 10.1126/science.1080049 ER - TY - JOUR T1 - Effects of Global Climate on Infectious Disease: The Cholera Model JF - Clinical Microbiology ReviewsClin. Microbiol. Rev.Clinical Microbiology ReviewsClin. Microbiol. Rev. Y1 - 2002 A1 - Lipp, Erin K. A1 - Huq, Anwar A1 - Rita R. Colwell AB - Recently, the role of the environment and climate in disease dynamics has become a subject of increasing interest to microbiologists, clinicians, epidemiologists, and ecologists. Much of the interest has been stimulated by the growing problems of antibiotic resistance among pathogens, emergence and/or reemergence of infectious diseases worldwide, the potential of bioterrorism, and the debate concerning climate change. Cholera, caused by Vibrio cholerae, lends itself to analyses of the role of climate in infectious disease, coupled to population dynamics of pathogenic microorganisms, for several reasons. First, the disease has a historical context linking it to specific seasons and biogeographical zones. In addition, the population dynamics of V. cholerae in the environment are strongly controlled by environmental factors, such as water temperature, salinity, and the presence of copepods, which are, in turn, controlled by larger-scale climate variability. In this review, the association between plankton and V. cholerae that has been documented over the last 20 years is discussed in support of the hypothesis that cholera shares properties of a vector-borne disease. In addition, a model for environmental transmission of cholera to humans in the context of climate variability is presented. The cholera model provides a template for future research on climate-sensitive diseases, allowing definition of critical parameters and offering a means of developing more sophisticated methods for prediction of disease outbreaks. VL - 15 SN - 0893-8512, 1098-6618 ER - TY - JOUR T1 - Evidence for a plastid origin of plant ethylene receptor genes. JF - Plant Physiol Y1 - 2002 A1 - Mount, Stephen M A1 - Chang, Caren KW - Amino Acid Sequence KW - Anabaena KW - Arabidopsis KW - Cyanobacteria KW - Molecular Sequence Data KW - Plant Proteins KW - Plastids KW - Protein Kinases KW - Receptors, Cell Surface KW - Sequence Homology, Amino Acid VL - 130 CP - 1 M3 - 10.1104/pp.005397 ER - TY - CHAP T1 - Fulfilling the promise of marine biotechnology T2 - Marine biotechnology in the twenty-first century: problems, promise, and productsMarine biotechnology in the twenty-first century: problems, promise, and products Y1 - 2002 A1 - Rita R. Colwell ED - National Research Council Committee on Marine Biotechnology: Biomedical Applications of Marine Natural, Products JA - Marine biotechnology in the twenty-first century: problems, promise, and productsMarine biotechnology in the twenty-first century: problems, promise, and products PB - National Academies Press SN - 9780309083423 N1 - (U S. ) ER - TY - JOUR T1 - Genome sequence and comparative analysis of the model rodent malaria parasite Plasmodium yoelii yoelii JF - NatureNature Y1 - 2002 A1 - Carlton, Jane M. A1 - Angiuoli, Samuel V. A1 - Suh, Bernard B. A1 - Kooij, Taco W. A1 - Pertea, Mihaela A1 - Silva, Joana C. A1 - Ermolaeva, Maria D. A1 - Allen, Jonathan E. A1 - J. Selengut A1 - Koo, Hean L. A1 - Peterson, Jeremy D. A1 - M. Pop A1 - Kosack, Daniel S. A1 - Shumway, Martin F. A1 - Bidwell, Shelby L. A1 - Shallom, Shamira J. A1 - Aken, Susan E. van A1 - Riedmuller, Steven B. A1 - Feldblyum, Tamara V. A1 - Cho, Jennifer K. A1 - Quackenbush, John A1 - Sedegah, Martha A1 - Shoaibi, Azadeh A1 - Cummings, Leda M. A1 - Florens, Laurence A1 - Yates, John R. A1 - Raine, J. Dale A1 - Sinden, Robert E. A1 - Harris, Michael A. A1 - Cunningham, Deirdre A. A1 - Preiser, Peter R. A1 - Bergman, Lawrence W. A1 - Vaidya, Akhil B. A1 - Lin, Leo H. van A1 - Janse, Chris J. A1 - Waters, Andrew P. A1 - Smith, Hamilton O. A1 - White, Owen R. A1 - Salzberg, Steven L. A1 - Venter, J. Craig A1 - Fraser, Claire M. A1 - Hoffman, Stephen L. A1 - Gardner, Malcolm J. A1 - Carucci, Daniel J. AB - Species of malaria parasite that infect rodents have long been used as models for malaria disease research. Here we report the whole-genome shotgun sequence of one species, Plasmodium yoelii yoelii, and comparative studies with the genome of the human malaria parasite Plasmodium falciparum clone 3D7. A synteny map of 2,212 P. y. yoelii contiguous DNA sequences (contigs) aligned to 14 P. falciparum chromosomes reveals marked conservation of gene synteny within the body of each chromosome. Of about 5,300 P. falciparum genes, more than 3,300 P. y. yoelii orthologues of predominantly metabolic function were identified. Over 800 copies of a variant antigen gene located in subtelomeric regions were found. This is the first genome sequence of a model eukaryotic parasite, and it provides insight into the use of such systems in the modelling of Plasmodium biology and disease. VL - 419 SN - 0028-0836 ER - TY - JOUR T1 - Genome sequence of the human malaria parasite Plasmodium falciparum JF - NatureNature Y1 - 2002 A1 - Gardner, Malcolm J. A1 - Hall, Neil A1 - Fung, Eula A1 - White, Owen A1 - Berriman, Matthew A1 - Hyman, Richard W. A1 - Carlton, Jane M. A1 - Pain, Arnab A1 - Nelson, Karen E. A1 - Bowman, Sharen A1 - Paulsen, Ian T. A1 - James, Keith A1 - Eisen, Jonathan A. A1 - Rutherford, Kim A1 - Salzberg, Steven L. A1 - Craig, Alister A1 - Kyes, Sue A1 - Chan, Man-Suen A1 - Nene, Vishvanath A1 - Shallom, Shamira J. A1 - Suh, Bernard A1 - Peterson, Jeremy A1 - Angiuoli, Sam A1 - Pertea, Mihaela A1 - Allen, Jonathan A1 - J. Selengut A1 - Haft, Daniel A1 - Mather, Michael W. A1 - Vaidya, Akhil B. A1 - Martin, David M. A. A1 - Fairlamb, Alan H. A1 - Fraunholz, Martin J. A1 - Roos, David S. A1 - Ralph, Stuart A. A1 - McFadden, Geoffrey I. A1 - Cummings, Leda M. A1 - Subramanian, G. Mani A1 - Mungall, Chris A1 - Venter, J. Craig A1 - Carucci, Daniel J. A1 - Hoffman, Stephen L. A1 - Newbold, Chris A1 - Davis, Ronald W. A1 - Fraser, Claire M. A1 - Barrell, Bart KW - Animals KW - Chromosome Structures KW - DNA Repair KW - DNA Replication KW - DNA, Protozoan KW - Evolution, Molecular KW - Genome, Protozoan KW - HUMANS KW - Malaria Vaccines KW - Malaria, Falciparum KW - Membrane Transport Proteins KW - Molecular Sequence Data KW - Plasmodium falciparum KW - Plastids KW - Proteome KW - Protozoan Proteins KW - Recombination, Genetic KW - Sequence Analysis, DNA AB - The parasite Plasmodium falciparum is responsible for hundreds of millions of cases of malaria, and kills more than one million African children annually. Here we report an analysis of the genome sequence of P. falciparum clone 3D7. The 23-megabase nuclear genome consists of 14 chromosomes, encodes about 5,300 genes, and is the most (A + T)-rich genome sequenced to date. Genes involved in antigenic variation are concentrated in the subtelomeric regions of the chromosomes. Compared to the genomes of free-living eukaryotic microbes, the genome of this intracellular parasite encodes fewer enzymes and transporters, but a large proportion of genes are devoted to immune evasion and host-parasite interactions. Many nuclear-encoded proteins are targeted to the apicoplast, an organelle involved in fatty-acid and isoprenoid metabolism. The genome sequence provides the foundation for future studies of this organism, and is being exploited in the search for new drugs and vaccines to fight malaria. VL - 419 N1 - http://www.ncbi.nlm.nih.gov/pubmed/12368864?dopt=Abstract ER - TY - JOUR T1 - Genomic profiles of clinical and environmental isolates of Vibrio cholerae O1 in cholera-endemic areas of Bangladesh JF - Proceedings of the National Academy of SciencesProceedings of the National Academy of Sciences Y1 - 2002 A1 - Zo, Y. G. A1 - Rivera, I. N. G. A1 - E. Russek-Cohen A1 - Islam, M. S. A1 - Siddique, A. K. A1 - Yunus, M. A1 - Sack, R. B. A1 - Huq, A. A1 - Rita R. Colwell AB - Diversity, relatedness, and ecological interactions of toxigenic Vibrio cholerae O1 populations in two distinctive habitats, the human intestine and the aquatic environment, were analyzed. Twenty environmental isolates and 42 clinical isolates were selected for study by matching serotype, geographic location of isolation in Bangladesh, and season of isolation. Genetic profiling was done by enterobacterial repetitive intergenic consensus sequence–PCR, optimized for profiling by using the fully sequenced V. cholerae El Tor N16961 genome. Five significant clonal clusters of haplotypes were found from 57 electrophoretic types. Isolates from different areas or habitats intermingled in two of the five significant clusters. Frequencies of haplotypes differed significantly only between the environmental populations (exact test; P < 0.05). Analysis of molecular variance yielded a population genetic structure reflecting the differentiating effects of geographic area, habitat, and sampling time. Although a parameter confounding the latter differences explained 9% of the total molecular variance in the entire population (P < 0.01), the net effect of habitat and time could not be separated because of the small number of environmental isolates included in the study. Five subpopulations from a single area were determined, and from these we were able to estimate a relative differentiating effect of habitat, which was small compared with the effect of temporal change. In conclusion, the resulting population structure supports the hypothesis that spatial and temporal fluctuations in the composition of toxigenic V. cholerae populations in the aquatic environment can cause shifts in the dynamics of the disease. VL - 99 SN - 0027-8424, 1091-6490 ER - TY - JOUR T1 - In vitro adhesion to human cells by viable but nonculturable Enterococcus faecalis JF - Current microbiologyCurrent microbiology Y1 - 2002 A1 - Pruzzo, C. A1 - Tarsi, R. A1 - Lleò, M. M. A1 - Signoretto, C. A1 - Zampini, M. A1 - Rita R. Colwell A1 - Canepari, P. AB - The ability of viable but nonculturable (VBNC) Enterococcus faecalis to adhere to Caco-2 and Girardi heart cultured cells and to urinary tract epithelial cells (ECs) was studied. Enterococci were harvested during the vegetative growth phase (early exponential and stationary), in the VBNC state, and after recovery of the ability to divide. VBNC bacteria maintained their adherence capability but the efficiency of attachment was reduced by about 50 to 70%, depending on the target cell employed. The decrease was transient, since enterococci that regained their culturability showed adherence values similar to those observed for actively growing cells. Analysis of the invasive properties of E. faecalis revealed that the VBNC state caused a decrease in the number of bacteria that entered the cultured HEK cells as a result of the reduction in the number of adhering bacteria. These results highlight the importance of studies of the VBNC phenomenon, with respect to both microbial survival in the environment and the impact on human health. VL - 45 ER - TY - JOUR T1 - Phylogenetic analysis based on 18S ribosomal RNA gene sequences supports the existence of class Polyacanthocephala (Acanthocephala) JF - Mol Phylogenet EvolMol Phylogenet Evol Y1 - 2002 A1 - García-Varela, M. A1 - Michael P. Cummings A1 - Pérez-Ponce de León, G. A1 - Gardner, S. L. A1 - Laclette, J. P. AB - Members of phylum Acanthocephala are parasites of vertebrates and arthropods and are distributed worldwide. The phylum has traditionally been divided into three classes, Archiacanthocephala, Palaeacanthocephala, and Eoacanthocephala; a fourth class, Polyacanthocephala, has been recently proposed. However, erection of this new class, based on morphological characters, has been controversial. We sequenced the near complete 18S rRNA gene of Polyacanthorhynchus caballeroi (Polyacanthocephala) and Rhadinorhynchus sp. (Palaeacanthocephala); these sequences were aligned with another 21 sequences of acanthocephalans representing the three widely recognized classes of the phylum and with 16 sequences from outgroup taxa. Phylogenetic relationships inferred by maximum-likelihood and maximum-parsimony analyses showed Archiacanthocephala as the most basal group within the phylum, whereas classes Polyacanthocephala + Eoacanthocephala formed a monophyletic clade, with Palaeacanthocephala as its sister group. These results are consistent with the view of Polyacanthocephala representing an independent class within Acanthocephala. VL - 23 ER - TY - JOUR T1 - Purification and properties of the extracellular lipase, LipA, of Acinetobacter sp. RAG‐1 JF - European Journal of BiochemistryEuropean Journal of Biochemistry Y1 - 2002 A1 - Snellman, Erick A. A1 - Sullivan, Elise R. A1 - Rita R. Colwell KW - Acinetobacter sp. RAG‐1 KW - LipA KW - lipase KW - protein purification KW - zymogram AB - An extracellular lipase, LipA, extracted from Acinetobacter sp. RAG-1 grown on hexadecane was purified and properties of the enzyme investigated. The enzyme is released into the growth medium during the transition to stationary phase. The lipase was harvested from cells grown to stationary phase, and purified with 22% yield and > 10-fold purification. The protein demonstrates little affinity for anion exchange resins, with contaminating proteins removed by passing crude supernatants over a Mono Q column. The lipase was bound to a butyl Sepharose column and eluted in a Triton X-100 gradient. The molecular mass (33 kDa) was determined employing SDS/PAGE. LipA was found to be stable at pH 5.8–9.0, with optimal activity at 9.0. The lipase remained active at temperatures up to 70 °C, with maximal activity observed at 55 °C. LipA is active against a wide range of fatty acid esters of p-nitrophenyl, but preferentially attacks medium length acyl chains (C6, C8). The enzyme demonstrates hydrolytic activity in emulsions of both medium and long chain triglycerides, as demonstrated by zymogram analysis. RAG-1 lipase is stabilized by Ca2+, with no loss in activity observed in preparations containing the cation, compared to a 70% loss over 30 h without Ca2+. The lipase is strongly inhibited by EDTA, Hg2+, and Cu2+, but shows no loss in activity after incubation with other metals or inhibitors examined in this study. The protein retains more than 75% of its initial activity after exposure to organic solvents, but is rapidly deactivated by pyridine. RAG-1 lipase offers potential for use as a biocatalyst. VL - 269 SN - 1432-1033 ER - TY - JOUR T1 - Sequence of Plasmodium falciparum chromosomes 2, 10, 11 and 14 JF - NatureNature Y1 - 2002 A1 - Gardner, Malcolm J. A1 - Shallom, Shamira J. A1 - Carlton, Jane M. A1 - Salzberg, Steven L. A1 - Nene, Vishvanath A1 - Shoaibi, Azadeh A1 - Ciecko, Anne A1 - Lynn, Jeffery A1 - Rizzo, Michael A1 - Weaver, Bruce A1 - Jarrahi, Behnam A1 - Brenner, Michael A1 - Parvizi, Babak A1 - Tallon, Luke A1 - Moazzez, Azita A1 - Granger, David A1 - Fujii, Claire A1 - Hansen, Cheryl A1 - Pederson, James A1 - Feldblyum, Tamara A1 - Peterson, Jeremy A1 - Suh, Bernard A1 - Angiuoli, Sam A1 - Pertea, Mihaela A1 - Allen, Jonathan A1 - J. Selengut A1 - White, Owen A1 - Cummings, Leda M. A1 - Smith, Hamilton O. A1 - Adams, Mark D. A1 - Venter, J. Craig A1 - Carucci, Daniel J. A1 - Hoffman, Stephen L. A1 - Fraser, Claire M. KW - Animals KW - Chromosomes KW - DNA, Protozoan KW - Genome, Protozoan KW - Plasmodium falciparum KW - Proteome KW - Protozoan Proteins KW - Sequence Analysis, DNA AB - The mosquito-borne malaria parasite Plasmodium falciparum kills an estimated 0.7-2.7 million people every year, primarily children in sub-Saharan Africa. Without effective interventions, a variety of factors-including the spread of parasites resistant to antimalarial drugs and the increasing insecticide resistance of mosquitoes-may cause the number of malaria cases to double over the next two decades. To stimulate basic research and facilitate the development of new drugs and vaccines, the genome of Plasmodium falciparum clone 3D7 has been sequenced using a chromosome-by-chromosome shotgun strategy. We report here the nucleotide sequences of chromosomes 10, 11 and 14, and a re-analysis of the chromosome 2 sequence. These chromosomes represent about 35% of the 23-megabase P. falciparum genome. VL - 419 N1 - http://www.ncbi.nlm.nih.gov/pubmed/12368868?dopt=Abstract ER - TY - JOUR T1 - Simple Procedure for Rapid Identification of Vibrio Cholerae from the Aquatic Environment JF - Applied and Environmental MicrobiologyAppl. Environ. Microbiol.Applied and Environmental MicrobiologyAppl. Environ. Microbiol. Y1 - 2002 A1 - Choopun, Nipa A1 - Louis, Valérie A1 - Huq, Anwar A1 - Rita R. Colwell AB - Biochemical tests commonly used to screen for Vibrio cholerae in environmental samples were evaluated, and we found that a combination of alkaline peptone enrichment followed by streaking on thiosulfate citrate bile salts sucrose agar and testing for arginine dihydrolase activity and esculin hydrolysis was an effective rapid technique to screen for aquatic environmental V. cholerae. This technique provided 100% sensitivity and ≥70% specificity. VL - 68 SN - 0099-2240, 1098-5336 ER - TY - JOUR T1 - A voyage of discovery: cholera, climate and complexity JF - Environmental MicrobiologyEnvironmental Microbiology Y1 - 2002 A1 - Rita R. Colwell VL - 4 SN - 1462-2920 ER - TY - JOUR T1 - Relating amino acid sequence to phenotype: analysis of peptide-binding data JF - BiometricsBiometrics Y1 - 2001 A1 - Segal, M. R. A1 - Michael P. Cummings A1 - Hubbard, A. E. AB - We illustrate data analytic concerns that arise in the context of relating genotype, as represented by amino acid sequence, to phenotypes (outcomes). The present application examines whether peptides that bind to a particular major histocompatibility complex (MHC) class I molecule have characteristic amino acid sequences. However, the concerns identified and addressed are considerably more general. It is recognized that simple rules for predicting binding based solely on preferences for specific amino acids in certain (anchor) positions of the peptide's amino acid sequence are generally inadequate and that binding is potentially influenced by all sequence positions as well as between-position interactions. The desire to elucidate these more complex prediction rules has spawned various modeling attempts, the shortcomings of which provide motivation for the methods adopted here. Because of (i) this need to model between-position interactions, (ii) amino acids constituting a highly (20) multilevel unordered categorical covariate, and (iii) there frequently being numerous such covariates (i.e., positions) comprising the sequence, standard regression/classification techniques are problematic due to the proliferation of indicator variables required for encoding the sequence position covariates and attendant interactions. These difficulties have led to analyses based on (continuous) properties (e.g., molecular weights) of the amino acids. However, there is potential information loss in such an approach if the properties used are incomplete and/or do not capture the mechanism underlying association with the phenotype. Here we demonstrate that handling unordered categorical covariates with numerous levels and accompanying interactions can be done effectively using classification trees and recently devised bump-hunting methods. We further tackle the question of whether observed associations are attributable to amino acid properties as well as addressing the assessment and implications of between-position covariation. VL - 57 ER - TY - JOUR T1 - A Case for Evolutionary Genomics and the Comprehensive Examination of Sequence Biodiversity JF - Molecular Biology and EvolutionMol Biol EvolMolecular Biology and EvolutionMol Biol Evol Y1 - 2000 A1 - Pollock, David D. A1 - Eisen, Jonathan A. A1 - Doggett, Norman A. A1 - Michael P. Cummings AB - Comparative analysis is one of the most powerful methods available for understanding the diverse and complex systems found in biology, but it is often limited by a lack of comprehensive taxonomic sampling. Despite the recent development of powerful genome technologies capable of producing sequence data in large quantities (witness the recently completed first draft of the human genome), there has been relatively little change in how evolutionary studies are conducted. The application of genomic methods to evolutionary biology is a challenge, in part because gene segments from different organisms are manipulated separately, requiring individual purification, cloning, and sequencing. We suggest that a feasible approach to collecting genome-scale data sets for evolutionary biology (i.e., evolutionary genomics) may consist of combination of DNA samples prior to cloning and sequencing, followed by computational reconstruction of the original sequences. This approach will allow the full benefit of automated protocols developed by genome projects to be realized; taxon sampling levels can easily increase to thousands for targeted genomes and genomic regions. Sequence diversity at this level will dramatically improve the quality and accuracy of phylogenetic inference, as well as the accuracy and resolution of comparative evolutionary studies. In particular, it will be possible to make accurate estimates of normal evolution in the context of constant structural and functional constraints (i.e., site-specific substitution probabilities), along with accurate estimates of changes in evolutionary patterns, including pairwise coevolution between sites, adaptive bursts, and changes in selective constraints. These estimates can then be used to understand and predict the effects of protein structure and function on sequence evolution and to predict unknown details of protein structure, function, and functional divergence. In order to demonstrate the practicality of these ideas and the potential benefit for functional genomic analysis, we describe a pilot project we are conducting to simultaneously sequence large numbers of vertebrate mitochondrial genomes. VL - 17 SN - 0737-4038, 1537-1719 ER - TY - JOUR T1 - The genome sequence of Drosophila melanogaster. JF - Science Y1 - 2000 A1 - Adams, M D A1 - Celniker, S E A1 - Holt, R A A1 - Evans, C A A1 - Gocayne, J D A1 - Amanatides, P G A1 - Scherer, S E A1 - Li, P W A1 - Hoskins, R A A1 - Galle, R F A1 - George, R A A1 - Lewis, S E A1 - Richards, S A1 - Ashburner, M A1 - Henderson, S N A1 - Sutton, G G A1 - Wortman, J R A1 - Yandell, M D A1 - Zhang, Q A1 - Chen, L X A1 - Brandon, R C A1 - Rogers, Y H A1 - Blazej, R G A1 - Champe, M A1 - Pfeiffer, B D A1 - Wan, K H A1 - Doyle, C A1 - Baxter, E G A1 - Helt, G A1 - Nelson, C R A1 - Gabor, G L A1 - Abril, J F A1 - Agbayani, A A1 - An, H J A1 - Andrews-Pfannkoch, C A1 - Baldwin, D A1 - Ballew, R M A1 - Basu, A A1 - Baxendale, J A1 - Bayraktaroglu, L A1 - Beasley, E M A1 - Beeson, K Y A1 - Benos, P V A1 - Berman, B P A1 - Bhandari, D A1 - Bolshakov, S A1 - Borkova, D A1 - Botchan, M R A1 - Bouck, J A1 - Brokstein, P A1 - Brottier, P A1 - Burtis, K C A1 - Busam, D A A1 - Butler, H A1 - Cadieu, E A1 - Center, A A1 - Chandra, I A1 - Cherry, J M A1 - Cawley, S A1 - Dahlke, C A1 - Davenport, L B A1 - Davies, P A1 - de Pablos, B A1 - Delcher, A A1 - Deng, Z A1 - Mays, A D A1 - Dew, I A1 - Dietz, S M A1 - Dodson, K A1 - Doup, L E A1 - Downes, M A1 - Dugan-Rocha, S A1 - Dunkov, B C A1 - Dunn, P A1 - Durbin, K J A1 - Evangelista, C C A1 - Ferraz, C A1 - Ferriera, S A1 - Fleischmann, W A1 - Fosler, C A1 - Gabrielian, A E A1 - Garg, N S A1 - Gelbart, W M A1 - Glasser, K A1 - Glodek, A A1 - Gong, F A1 - Gorrell, J H A1 - Gu, Z A1 - Guan, P A1 - Harris, M A1 - Harris, N L A1 - Harvey, D A1 - Heiman, T J A1 - Hernandez, J R A1 - Houck, J A1 - Hostin, D A1 - Houston, K A A1 - Howland, T J A1 - Wei, M H A1 - Ibegwam, C A1 - Jalali, M A1 - Kalush, F A1 - Karpen, G H A1 - Ke, Z A1 - Kennison, J A A1 - Ketchum, K A A1 - Kimmel, B E A1 - Kodira, C D A1 - Kraft, C A1 - Kravitz, S A1 - Kulp, D A1 - Lai, Z A1 - Lasko, P A1 - Lei, Y A1 - Levitsky, A A A1 - Li, J A1 - Li, Z A1 - Liang, Y A1 - Lin, X A1 - Liu, X A1 - Mattei, B A1 - McIntosh, T C A1 - McLeod, M P A1 - McPherson, D A1 - Merkulov, G A1 - Milshina, N V A1 - Mobarry, C A1 - Morris, J A1 - Moshrefi, A A1 - Mount, S M A1 - Moy, M A1 - Murphy, B A1 - Murphy, L A1 - Muzny, D M A1 - Nelson, D L A1 - Nelson, D R A1 - Nelson, K A A1 - Nixon, K A1 - Nusskern, D R A1 - Pacleb, J M A1 - Palazzolo, M A1 - Pittman, G S A1 - Pan, S A1 - Pollard, J A1 - Puri, V A1 - Reese, M G A1 - Reinert, K A1 - Remington, K A1 - Saunders, R D A1 - Scheeler, F A1 - Shen, H A1 - Shue, B C A1 - Sidén-Kiamos, I A1 - Simpson, M A1 - Skupski, M P A1 - Smith, T A1 - Spier, E A1 - Spradling, A C A1 - Stapleton, M A1 - Strong, R A1 - Sun, E A1 - Svirskas, R A1 - Tector, C A1 - Turner, R A1 - Venter, E A1 - Wang, A H A1 - Wang, X A1 - Wang, Z Y A1 - Wassarman, D A A1 - Weinstock, G M A1 - Weissenbach, J A1 - Williams, S M A1 - Worley, K C A1 - Wu, D A1 - Yang, S A1 - Yao, Q A A1 - Ye, J A1 - Yeh, R F A1 - Zaveri, J S A1 - Zhan, M A1 - Zhang, G A1 - Zhao, Q A1 - Zheng, L A1 - Zheng, X H A1 - Zhong, F N A1 - Zhong, W A1 - Zhou, X A1 - Zhu, S A1 - Zhu, X A1 - Smith, H O A1 - Gibbs, R A A1 - Myers, E W A1 - Rubin, G M A1 - Venter, J C KW - Animals KW - Biological Transport KW - Chromatin KW - Cloning, Molecular KW - Computational Biology KW - Contig Mapping KW - Cytochrome P-450 Enzyme System KW - DNA Repair KW - DNA Replication KW - Drosophila melanogaster KW - Euchromatin KW - Gene Library KW - Genes, Insect KW - Genome KW - Heterochromatin KW - Insect Proteins KW - Nuclear Proteins KW - Protein Biosynthesis KW - Sequence Analysis, DNA KW - Transcription, Genetic AB -

The fly Drosophila melanogaster is one of the most intensively studied organisms in biology and serves as a model system for the investigation of many developmental and cellular processes common to higher eukaryotes, including humans. We have determined the nucleotide sequence of nearly all of the approximately 120-megabase euchromatic portion of the Drosophila genome using a whole-genome shotgun sequencing strategy supported by extensive clone-based sequence and a high-quality bacterial artificial chromosome physical map. Efforts are under way to close the remaining gaps; however, the sequence is of sufficient accuracy and contiguity to be declared substantially complete and to support an initial analysis of genome structure and preliminary gene annotation and interpretation. The genome encodes approximately 13,600 genes, somewhat fewer than the smaller Caenorhabditis elegans genome, but with comparable functional diversity.

VL - 287 CP - 5461 ER - TY - JOUR T1 - Phylogenetic relationships of Acanthocephala based on analysis of 18S ribosomal RNA gene sequences JF - J Mol EvolJ Mol Evol Y1 - 2000 A1 - García-Varela, M. A1 - Pérez-Ponce de León, G. A1 - de la Torre, P. A1 - Michael P. Cummings A1 - Sarma, S. S. A1 - Laclette, J. P. AB - Acanthocephala (thorny-headed worms) is a phylum of endoparasites of vertebrates and arthropods, included among the most phylogenetically basal tripoblastic pseudocoelomates. The phylum is divided into three classes: Archiacanthocephala, Palaeacanthocephala, and Eoacanthocephala. These classes are distinguished by morphological characters such as location of lacunar canals, persistence of ligament sacs in females, number and type of cement glands in males, number and size of proboscis hooks, host taxonomy, and ecology. To understand better the phylogenetic relationships within Acanthocephala, and between Acanthocephala and Rotifera, we sequenced the nearly complete 18S rRNA genes of nine species from the three classes of Acanthocephala and four species of Rotifera from the classes Bdelloidea and Monogononta. Phylogenetic relationships were inferred by maximum-likelihood analyses of these new sequences and others previously determined. The analyses showed that Acanthocephala is the sister group to a clade including Eoacanthocephala and Palaeacanthocephala. Archiacanthocephala exhibited a slower rate of evolution at the nucleotide level, as evidenced by shorter branch lengths for the group. We found statistically significant support for the monophyly of Rotifera, represented in our analysis by species from the clade Eurotatoria, which includes the classes Bdelloidea and Monogononta. Eurotatoria also appears as the sister group to Acanthocephala. VL - 50 ER - TY - JOUR T1 - Phylogenetic relationships of ıt Phytophthora species based on ribosomal ITS I DNA sequence analysis with emphasis on Waterhouse groups V and VI JF - Mycol ResMycol Res Y1 - 2000 A1 - Förster, H. A1 - Michael P. Cummings A1 - Coffey, M. D. AB - Phylogenetic relationships among Phytophthora species were investigated by sequence analysis of the internal transcribed spacer region I of the ribosomal DNA repeat unit. The extensive collection of isolates included taxa from all six morphological groups recognized by Waterhouse (1963) including molecular groups previously identified using isozymes and mtDNA restriction fragment length polymorphisms. Similar to previous studies, the inferred relationships indicated that molecular groups of P. cryptooea/drechsleri-like and P. megasperma-like taxa are polyphyletic. Morphological groups V and VI, which are differentiated by the presence of amphigynous or paragynous antheridia, are not monophyletic: species of the two groups are interspersed in the tree. Species with papillate and semi-papillate sporangia (groups I-IV) clustered together and this cluster was distinct from those of species with non-papillate sporangia. There was no congruence between the mode of antheridial attachment, sporangial caducity, or homo- or heterothallic habit and the molecular grouping of the species. Our study provides evidence that the antheridial position together with homo- or heterothallic habit does not reflect phylogenetic relationships within Phytophthora. Consequently, confirming studies done previously (Cooke & Duncan 1997), this study provides evidence that the morphological characters used in Phytophthora taxonomy are of limited value for deducing phylogenetic relationships, because they exhibit convergent evolution. VL - 104 ER - TY - JOUR T1 - Genes and other samples of DNA sequence data for phylogenetic inference JF - The Biological BulletinThe Biological Bulletin Y1 - 1999 A1 - Michael P. Cummings A1 - Otto, S. P. A1 - Wakeley, J. VL - 196 ER - TY - JOUR T1 - Genetic nomenclature for Trypanosoma and Leishmania. JF - Mol Biochem Parasitol Y1 - 1998 A1 - Clayton, C A1 - Adams, M A1 - Almeida, R A1 - Baltz, T A1 - Barrett, M A1 - Bastien, P A1 - Belli, S A1 - Beverley, S A1 - Biteau, N A1 - Blackwell, J A1 - Blaineau, C A1 - Boshart, M A1 - Bringaud, F A1 - Cross, G A1 - Cruz, A A1 - Degrave, W A1 - Donelson, J A1 - El-Sayed, N A1 - Fu, G A1 - Ersfeld, K A1 - Gibson, W A1 - Gull, K A1 - Ivens, A A1 - Kelly, J A1 - Vanhamme, L KW - Animals KW - Leishmania KW - Terminology as Topic KW - Trypanosoma VL - 97 CP - 1-2 ER - TY - JOUR T1 - Nucleotide sequence diversity at the alcohol dehydrogenase 1 locus in wild barley (ıt Hordeum vulgare ssp. ıt spontaneum): an evaluation of the background selection hypothesis JF - Proc Natl Acad Sci USAProc Natl Acad Sci USA Y1 - 1998 A1 - Michael P. Cummings A1 - Clegg, M. T. AB - The background selection hypothesis predicts a reduction in nucleotide site diversity and an excess of rare variants, owing to linkage associations with deleterious alleles. This effect is expected to be amplified in species that are predominantly self-fertilizing. To examine the predictions of the background selection hypothesis in self-fertilizing species, we sequenced 1,362 bp of adh1, a gene for alcohol dehydrogenase (Adh; alcohol:NAD+ oxidoreductase, EC 1.1.1.1), in a sample of 45 accessions of wild barley, Hordeum vulgare ssp. spontaneum, drawn from throughout the species range. The region sequenced included 786 bp of exon sequence (part of exon 4, all of exons 5-9, and part of exon 10) and 576 bp of intron sequence (all of introns 4-9). There were 19 sites polymorphic for nucleotide substitutions, 8 in introns, and 11 in exons. Of the 11 nucleotide substitutions in codons, 4 were synonymous and 7 were nonsynonymous, occurring uniquely in the sample. There was no evidence of recombination in the region studied, and the estimated effective population size (Ne) based on synonymous sites was approximately 1.8-4.2 x 10(5). Several tests reveal that the pattern of nonsynonymous substitutions departs significantly from neutral expectations. However, the data do not appear to be consistent with recovery from a population bottleneck, recent population expansion, selective sweep, or strong positive selection. Though several features of the data are consistent with background selection, the distributions of polymorphic synonymous and intron sites are not perturbed toward a significant excess of rare alleles as would be predicted by background selection. VL - 95 ER - TY - JOUR T1 - Phylogenetic relationships of platyhelminthes based on 18S ribosomal gene sequences JF - Mol Phylogenet EvolMol Phylogenet Evol Y1 - 1998 A1 - Campos, A. A1 - Michael P. Cummings A1 - Reyes, J. L. A1 - Laclette, J. P. AB - Nucleotide sequences of 18S ribosomal RNA from 71 species of Platyhelminthes, the flatworms, were analyzed using maximum likelihood, and the resulting phylogenetic trees were compared with previous phylogenetic hypotheses. Analyses including 15 outgroup species belonging to eight other phyla show that Platyhelminthes are monophyletic with the exception of a sequence putatively from Acoela sp., Lecithoepitheliata, Polycladida, Tricladida, Trematoda (Aspidobothrii + Digenea), Monogenea, and Cestoda (Gyrocotylidea + Amphilinidea + Eucestoda) are monophyletic groups. Catenulids form the sister group to the rest of platyhelminths, whereas a complex clade formed by Acoela, Tricladida, "Dalyellioida", and perhaps "Typhloplanoida" is sister to Neodermata. "Typhloplanoida" does not appear to be monophyletic; Fecampiida does not appear to belong within "Dalyellioida," nor Kalyptorhynchia within "Typhloplanoida." Trematoda is the sister group to the rest of Neodermata, and Monogenea is sister group to Cestoda. Within Trematoda, Aspidobothrii is the sister group of Digenea and Heronimidae is the most basal family in Digenea. Our trees support the hypothesis that parasitism evolved at least twice in Platyhelminthes, once in the ancestor to Neodermata and again in the ancestor of Fecampiida, independently to the ancestor of putatively parasitic "Dalyellioida." VL - 10 ER - TY - JOUR T1 - Pigment composition of putatively achlorophyllous angiosperms JF - Plant Syst EvolPlant Syst Evol Y1 - 1998 A1 - Michael P. Cummings A1 - Welschmeyer, N. A. KW - Angiospermae KW - carotenoid KW - chlorophyll KW - high-performance liquid chromatography KW - Lennoaceae KW - Monotropaceae KW - Orchidaceae KW - Orobanchaceae KW - pigment AB - Chlorophyll and carotenoid pigment composition was determined for ten species of putatively achlorophyllous angiosperms using high-performance liquid chromatography. Four families were represented: Lennoaceae (Pholisma arenarium); Monotropaceae (Allotropa virgata, Monotropa uniflora, Pterospora andromedea, Sarcodes sanguinea); Orobanchaceae (Epifagus virginiana, Orobanche cooperi, O. uniflora); Orchidaceae (Cephalanthera austinae, Corallorhiza maculata). Chlorophyll a was detected in all tars, but chlorophyll b was only detected in Corallorhiza maculata. The relative amount of chlorophyll and chlorophyll-related pigments in these plants is greatly reduced compared to fully autotrophic angiosperms. VL - 210 ER - TY - JOUR T1 - Trends in the early careers of life scientists - Preface and executive summary JF - Mol Biol CellMol Biol Cell Y1 - 1998 A1 - Tilghman, S. A1 - Astin, H. S. A1 - Brinkley, W. A1 - Chilton, M. D. A1 - Michael P. Cummings A1 - Ehrenberg, R. G. A1 - Fox, M. F. A1 - Glenn, K. A1 - Green, P. J. A1 - Hans, S. A1 - Kelman, A. A1 - LaPidus, J. A1 - Levin, B. A1 - McIntosh, J. R. A1 - Riecken, H. A1 - Stephen, P. E. VL - 9 ER - TY - JOUR T1 - A computational model of acute focal cortical lesions JF - StrokeStroke Y1 - 1997 A1 - Goodall, S. A1 - Reggia, James A. A1 - Chen, Y. A1 - Ruppin, E. A1 - Whitney, C. VL - 28 ER - TY - JOUR T1 - The evolution of plant nuclear genes JF - Proc Natl Acad Sci USAProc Natl Acad Sci USA Y1 - 1997 A1 - Clegg, M. T. A1 - Michael P. Cummings A1 - Durbin, M. L. AB - We analyze the evolutionary dynamics of three of the best-studied plant nuclear multigene families. The data analyzed derive from the genes that encode the small subunit of ribulose-1,5-bisphosphate carboxylase (rbcS), the gene family that encodes the enzyme chalcone synthase (Chs), and the gene family that encodes alcohol dehydrogenases (Adh). In addition, we consider the limited evolutionary data available on plant transposable elements. New Chs and rbcS genes appear to be recruited at about 10 times the rate estimated for Adh genes, and this is correlated with a much smaller average gene family size for Adh genes. In addition, duplication and divergence in function appears to be relatively common for Chs genes in flowering plant evolution. Analyses of synonymous nucleotide substitution rates for Adh genes in monocots reject a linear relationship with clock time. Replacement substitution rates vary with time in a complex fashion, which suggests that adaptive evolution has played an important role in driving divergence following gene duplication events. Molecular population genetic studies of Adh and Chs genes reveal high levels of molecular diversity within species. These studies also reveal that inter- and intralocus recombination are important forces in the generation allelic novelties. Moreover, illegitimate recombination events appear to be an important factor in transposable element loss in plants. When we consider the recruitment and loss of new gene copies, the generation of allelic diversity within plant species, and ectopic exchange among transposable elements, we conclude that recombination is a pervasive force at all levels of plant evolution. VL - 94 ER - TY - JOUR T1 - Satellite DNA repeat sequence variation is low in three species of burying beetles in the genus ıt Nicrophorus (Coleoptera: Silphidae) JF - Mol Biol EvolMol Biol Evol Y1 - 1997 A1 - King, L. M. A1 - Michael P. Cummings AB - Three satellite DNA families were identified in three species of burying beetles, Nicrophorus orbicollis, N. marginatus, and N. americanus. Southern hybridization and nucleotide sequence analysis of individual randomly cloned repeats shows that these satellite DNA families are highly abundant in the genome, are composed of unique repeats, and are species-specific. The repeats do not have identifiable core elements or substructures that are similar in all three families, and most interspecific sequence similarity is confined to homopolymeric runs of A and T. Satellite DNA from N. marginatus and N. americanus show single-base-pair indels among repeats, but single-nucleotide substitutions characterize most of the repeat variability. Although the repeat units are of similar lengths (342, 350, and 354 bp) and A + T composition (65%, 71%, and 71%, respectively), the average nucleotide divergence among sequenced repeats is very low (0.18%, 1.22%, and 0.71%, respectively). Transition/transversion ratios from the consensus sequence are 0.20, 0.69, and 0.70, respectively. VL - 14 ER - TY - JOUR T1 - DNA sequence variation in the ribosomal internal transcribed spacer region of freshwater ıt Cladophora species (Chlorophyta) JF - J PhycolJ Phycol Y1 - 1996 A1 - Marks, J. C. A1 - Michael P. Cummings KW - algae KW - Chlorophyta KW - Cladophora KW - diversity KW - freshwater KW - genetic KW - internal KW - spacer KW - transcribed AB - Freshwater species of Cladophora (Chlorophyta) are globally distributed and occupy an unusually wide range of ecological habitats. Delineating species is difficult because most easily observed morphological traits are highly variable and because sexual reproduction has not been clearly documented. Synthesizing ecological data on freshwater Cladophora species is problematic because it is unclear whether freshwater Cladophora species comprise many genetically distinct species or a few ecologically and morphologically variable and / or plastic species. We determined nucleotide sequences of the internal transcribed spacer (ITS) region of the nuclear ribosomal cistron of freshwater Cladophora species from a wide range of habitats and geographic locations. We compared these sequences to those derived from culture collections of C. fracta and C. glomerata, the two most commonly reported freshwater Cladophora species. Cladophora fracta and C. glomerata had very similar ITS sequences (95.3%). All other sequences were identical to those from the C. fracta or C. glomerata culture collections with the exception of one California sample that was similar to both C. fracta (95.6%) and C. glomerata (92.4%). ITS genotypes did not correlate with morphology or geography. This analysis shows that common freshwater Cladophora species comprise very few (possibly one) ecologically and morphologically variable species. VL - 32 ER - TY - JOUR T1 - Evolutionary biology of parasitic platyhelminths: The role of molecular phylogenetics JF - Parasitol TodayParasitol Today Y1 - 1996 A1 - Blair, D. A1 - Campos, A. A1 - Michael P. Cummings A1 - Laclette, J. P. AB - As our appreciation of the diversity within the flatworms has grown, so too has our curiosity about the ways in which these varied creatures are related to one another. In particular, the parasitic groups (trematodes, cestodes and monogeneans have been the focus of enquiry. Until recently, morphology, anatomy and life histories have provided the raw data for building hypotheses on relationships. Now, ultrastructural evidence, and most recently, molecular data from nucleic acid sequences, have been brought to bear on the topic. Here, David Blair, Andrés Campos, Michael Cummings and Juan Pedro Laclette discuss the ways in which molecular data, in particular, are helping us recognize the various lineages of flatworms. VL - 12 ER - TY - CHAP T1 - Inferring phylogenies from DNA sequence data: The effects of sampling T2 - New Uses for New PhylogeniesNew Uses for New Phylogenies Y1 - 1996 A1 - Otto, S. P. A1 - Michael P. Cummings A1 - Wakeley, J. ED - Harvey, P. H. ED - Leigh Brown, A. J. ED - Maynard Smith, J. ED - Nee, S. JA - New Uses for New PhylogeniesNew Uses for New Phylogenies PB - Oxford University Press ER - TY - JOUR T1 - Genome Sequence Comparison and Scenarios for Gene Rearrangements: A Test Case JF - GenomicsGenomics Y1 - 1995 A1 - Sridhar Hannenhalli A1 - Chappey, Colombe A1 - Koonin, Eugene V. A1 - Pevzner, Pavel A. AB - As large portions of related genomes are being sequenced, methods for comparing complete or nearly complete genomes, as opposed to comparing individual genes, are becoming progressively more important. A major, widespread phenomenon in genome evolution is the rearrangement of genes and gene blocks. There is, however, no consistent method for genome sequence comparison combined with the reconstruction of the evolutionary history of highly rearranged genomes. We developed a schema for genome sequence comparison that includes three successive steps: (i) comparison of all proteins encoded in different genomes and generation of genomic similarity plots; (ii) construction of an alphabet of conserved genes and gene blocks; and (iii) generation of most parsimonious genome rearrangement scenarios. The approach is illustrated by a comparison of the herpesvirus genomes that constitute the largest set of relatively long, complete genome sequences available to date. Herpesviruses have from 70 to about 200 genes; comparison of the amino acid sequences encoded in these genes results in an alphabet of about 30 conserved genes comprising 7 conserved blocks that are rearranged in the genomes of different herpesviruses. Algorithms to analyze rearrangements of multiple genomes were developed and applied to the derivation of most parsimonious scenarios of herpesvirus evolution under different evolutionary models. The developed approaches to genome comparison will be applicable to the comparative analysis of bacterial and eukaryotic genomes as soon as their sequences become available. VL - 30 SN - 0888-7543 ER - TY - JOUR T1 - Genome sequence comparison and scenarios for gene rearrangements: A test case JF - GenomicsGenomics Y1 - 1995 A1 - Sridhar Hannenhalli A1 - Chappey, C. A1 - Koonin, E. V. A1 - Pevzner, P. A. A1 - others, PB - San Diego: Academic Press, c1987- VL - 30 ER - TY - JOUR T1 - Sampling properties of DNA sequence data in phylogenetic analysis JF - Mol Biol EvolMol Biol Evol Y1 - 1995 A1 - Michael P. Cummings A1 - Otto, S. P. A1 - Wakeley, J. AB - We inferred phylogenetic trees from individual genes and random samples of nucleotides from the mitochondrial genomes of 10 vertebrates and compared the results to those obtained by analyzing the whole genomes. Individual genes are poor samples in that they infrequently lead to the whole-genome tree. A large number of nucleotide sites is needed to exactly determine the whole-genome tree. A relatively small number of sites, however, often results in a tree close to the whole-genome tree. We found that blocks of contiguous sites were less likely to lead to the whole-genome tree than samples composed of sites drawn individually from throughout the genome. Samples of contiguous sites are not representative of the entire genome, a condition that violates a basic assumption of the bootstrap method as it is applied in phylogenetic studies. VL - 12 ER - TY - JOUR T1 - Slipped-strand mispairing in a plastid gene: ıt rpoC2 in grasses (Poaceae) JF - Mol Biol EvolMol Biol Evol Y1 - 1994 A1 - Michael P. Cummings A1 - King, L. M. A1 - Kellogg, E. A. AB - An exception to the generally conservative nature of plastid gene evolution is the gene coding for the beta" subunit of RNA polymerase, rpoC2. Previous work by others has shown that maize and rice have an insertion in the coding region of rpoC2, relative to spinach and tobacco. To assess the distribution of this extra coding sequence, we surveyed a broad phylogenetic sample comprising 55 species from 17 angiosperm families by using Southern hybridization. The extra coding sequence is restricted to the grasses (Poaceae). DNA sequence analysis of 11 species from all five subfamilies within the grass family demonstrates that the extra sequence in the coding region of rpoC2 is a repetitive array that exhibits more than a twofold increase in nucleotide substitution, as well as a large number of insertion/deletion events, relative to the adjacent flanking sequences. The structure of the array suggests that slipped-strand mispairing causes the repeated motifs and adds to the mechanisms through which the coding sequence of plastid genes are known to evolve. Phylogenetic analyses based on the sequence data from grass species support several relationships previously suggested by morphological work, but they are ambiguous about broad relationships within the family. VL - 11 ER - TY - JOUR T1 - Transmission patterns of eukaryotic transposable elements - arguments for and against horizontal transfer JF - Trends Ecol EvolTrends Ecol Evol Y1 - 1994 A1 - Michael P. Cummings AB - Recent studies have demonstrated that several classes of transposable elements are widely distributed within eukaryotes. Horizontal transmission of these transposable elements has often been invoked in order to explain the observed variation and relationships within and between species. These same patterns of variation and relationships, however, may originate from processes that do not involve the lateral transfer of genetic material across species. VL - 9 ER - TY - Generic T1 - A distributed algorithm for ear decomposition T2 - Fifth International Conference on Computing and Information, 1993. Proceedings ICCI '93 Y1 - 1993 A1 - Sridhar Hannenhalli A1 - Perumalla, K. A1 - Chandrasekharan, N. A1 - Sridhar, R. KW - Asynchronous communication KW - asynchronous communication network KW - Automata KW - Communication networks KW - computational complexity KW - Computer networks KW - Computer science KW - decomposition graph KW - distributed algorithm KW - distributed algorithms KW - Distributed computing KW - Ear KW - ear decomposition KW - graph theory KW - message-optimal KW - network decomposition KW - sorting KW - Testing KW - time-optimal AB - A distributed algorithm for finding an ear decomposition of an asynchronous communication network with n nodes and m links is presented. At the completion of the algorithm either the ears are correctly labeled or the nodes are informed that there exists no ear decomposition. First we present a novel algorithm to check the existence of an ear decomposition which uses O(m) messages. We also present two other algorithms, one which is time-optimal and the other which is message-optimal to determine the actual ears and their corresponding numbers after determining the existence of an ear decomposition JA - Fifth International Conference on Computing and Information, 1993. Proceedings ICCI '93 PB - IEEE SN - 0-8186-4212-2 ER - TY - JOUR T1 - copia-like retrotransposons are ubiquitous among plants JF - Proc Natl Acad Sci USAProc Natl Acad Sci USA Y1 - 1992 A1 - Voytas, D. F. A1 - Michael P. Cummings A1 - Koniczny, A. A1 - Ausubel, F. M. A1 - Rodermel, S. R. AB - Transposable genetic elements are assumed to be a feature of all eukaryotic genomes. Their identification, however, has largely been haphazard, limited principally to organisms subjected to molecular or genetic scrutiny. We assessed the phylogenetic distribution of copia-like retrotransposons, a class of transposable element that proliferates by reverse transcription, using a polymerase chain reaction assay designed to detect copia-like element reverse transcriptase sequences. copia-like retrotransposons were identified in 64 plant species as well as the photosynthetic protist Volvox carteri. The plant species included representatives from 9 of 10 plant divisions, including bryophytes, lycopods, ferns, gymnosperms, and angiosperms. DNA sequence analysis of 29 cloned PCR products and of a maize retrotransposon cDNA confirmed the identity of these sequences as copia-like reverse transcriptase sequences, thereby demonstrating that this class of retrotransposons is a ubiquitous component of plant genomes. VL - 89 ER - TY - JOUR T1 - Copia-like retrotransposons in plants: a brief introduction JF - The Plant Genetics NewsletterThe Plant Genetics Newsletter Y1 - 1992 A1 - Michael P. Cummings VL - 8 ER - TY - Generic T1 - Efficient algorithms for computing matching and chromatic polynomials on series-parallel graphs T2 - Fourth International Conference on Computing and Information, 1992. Proceedings. ICCI '92 Y1 - 1992 A1 - Chandrasekharan, N. A1 - Sridhar Hannenhalli KW - chromatic polynomials KW - computational complexity KW - Computer science KW - graph colouring KW - graph theory KW - matching polynomial KW - Polynomials KW - series-parallel graphs KW - Terminology KW - Tree data structures KW - Tree graphs AB - The authors present efficient algorithms for computing the matching polynomial and chromatic polynomial of a series-parallel graph in O(n3) and O(n2) time respectively. Their algorithm for computing the matching polynomial generalizes an existing result from Lovasz, Plummer (1986) and the chromatic polynomial algorithm improves the result given by Hunt, Ravi, Stearn (1988) from O(n4) time JA - Fourth International Conference on Computing and Information, 1992. Proceedings. ICCI '92 PB - IEEE SN - 0-8186-2812-X ER - TY - JOUR T1 - Patterns and processes of sequence evolution: plant organelle genomes and copia-like retrotransposons Y1 - 1992 A1 - Michael P. Cummings ER - TY - JOUR T1 - Review of Fundamentals of Molecular Evolution, by Li. W.-H. and D. Graur JF - CladisticsCladistics Y1 - 1991 A1 - Michael P. Cummings VL - 7 ER - TY - JOUR T1 - A superfamily of ıt Arabidopsis thaliana retrotransposons JF - GeneticsGenetics Y1 - 1991 A1 - Konieczny, A. A1 - Voytas, D. F. A1 - Michael P. Cummings A1 - Ausubel, F. M. AB - We describe a superfamily of Arabidopsis thaliana retrotransposable elements that consists of at least ten related families designated Ta1-Ta10. The Ta1 family has been described previously. Two genomic clones representing the Ta2 and Ta3 elements were isolated from an A. thaliana (race Landsberg erecta) lambda library using sequences derived from the reverse transcriptase region of Ta1 as hybridization probes. Nucleotide sequence analysis showed that the Ta1, Ta2 and Ta3 families share greater than 75% amino acid identity in pairwise comparisons of their reverse transcriptase and RNase H genes. In addition to Ta1, Ta2 and Ta3, we identified seven other related retrotransposon families in Landsberg erecta, Ta4-Ta10, using degenerate primers and the polymerase chain reaction to amplify a highly conserved region of retrotransposon-encoded reverse transcriptase. One to two copies of elements Ta2-Ta10 are present in the genomes of the A. thaliana races Landsberg erecta and Columbia indicating that the superfamily comprises at least 0.1% of the A. thaliana genome. The nucleotide sequences of the reverse transcriptase regions of the ten element families place them in the category of copia-like retrotransposons and phylogenetic analysis of the amino acid sequences suggests that horizontal transfer may have played a role in their evolution. VL - 127 ER - TY - JOUR T1 - Evolution of avocados as revealed by DNA restriction fragment variation JF - J HeredJ Hered Y1 - 1990 A1 - Furnier, G. R. A1 - Michael P. Cummings A1 - Clegg, M. T. AB - Individuals representing the genus ıt Persea, subgenus ıt Persea were assayed for restriction fragment length polymorphisms in their chloroplast genome, nuclear ribosomal DNA, and the genes coding for the enzyme cellulase. The subgenus ıt Persea appears to consist of ıt P. schiedeana and a separate taxon containing the remaining species. ıt P. americana does not appear to be a monophyletic group. If ıt P. americana is to be maintained as a species containing var. ıt americana, var. ıt drymifolia, and var. ıt guatemalensis, then our data suggest that it should also contain varieties corresponding to ıt P. floccosa, ıt P. nubigena, and ıt P. steyermarkii. ıt P. americana var. ıt guatemalensis appears to have originated as a hybrid between ıt P. steyermarkii and ıt P. nubigena. The root-rot-resistant cultivar G755A is a hybrid progeny of ıt P. schiedeana and ıt P. americana var. guatemalensis. The three varieties of ıt P. americana were all distinguished by mutations. VL - 81 ER - TY - JOUR T1 - The structure, distribution and evolution of the ıt Ta1 retrotransposable element family of ıt Arabidopsis thaliana JF - GeneticsGenetics Y1 - 1990 A1 - Voytas, D. F. A1 - Konieczny, A. A1 - Michael P. Cummings A1 - Ausubel, F. M. AB - The Ta1 elements are a low copy number, copia-like retrotransposable element family of Arabidopsis thaliana. Six Ta1 insertions comprise all of the Ta1 element copies found in three geographically diverse A. thaliana races. These six elements occupy three distinct target sites: Ta1-1 is located on chromosome 5 and is common to all three races (Col-0, Kas-1 and La-0). Ta1-2 is present in two races on chromosome 4 (Kas-1 and La-0), and Ta1-3, also located on chromosome 4, is present only in one race (La-0). The six Ta1 insertions share greater than 96% nucleotide identity, yet are likely to be incapable of further transposition due to deletions or nucleotide changes that alter either the coding capacity of the elements or conserved protein domains required for retrotransposition. Nucleotide sequence comparisons of these elements and the distribution of Ta1 among 12 additional A. thaliana geographical races suggest that Ta1-1 predated the global dispersal of A. thaliana. As the species spread throughout the world, two additional transposition events occurred which gave rise first to Ta1-2 and finally to Ta1-3. VL - 126 ER - TY - JOUR T1 - Surgery of the hip and knee in patients with rheumatoid arthritis. JF - J Bone Joint Surg Am Y1 - 1973 A1 - Conaty, J P KW - Acetabulum KW - Arthritis, Rheumatoid KW - Arthrodesis KW - Arthroplasty KW - Contracture KW - Debridement KW - Femur Head KW - Femur Head Necrosis KW - Hip KW - Hip Joint KW - HUMANS KW - Joint Prosthesis KW - Knee KW - Knee Joint KW - Osteotomy KW - Patella KW - Postoperative Complications KW - Recurrence KW - Synovial Membrane KW - Tibia VL - 55 CP - 2 ER -