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 - Diversity in a Polymicrobial Community Revealed by Analysis of Viromes, Endolysins and CRISPR Spacers. JF - PLoS One Y1 - 2016 A1 - Davison, Michelle A1 - Todd Treangen A1 - Koren, Sergey A1 - Pop, Mihai A1 - Bhaya, Devaki AB -

The polymicrobial biofilm communities in Mushroom and Octopus Spring in Yellowstone National Park (YNP) are well characterized, yet little is known about the phage populations. Dominant species, Synechococcus sp. JA-2-3B'a(2-13), Synechococcus sp. JA-3-3Ab, Chloroflexus sp. Y-400-fl, and Roseiflexus sp. RS-1, contain multiple CRISPR-Cas arrays, suggesting complex interactions with phage predators. To analyze phage populations from Octopus Spring biofilms, we sequenced a viral enriched fraction. To assemble and analyze phage metagenomic data, we developed a custom module, VIRITAS, implemented within the MetAMOS framework. This module bins contigs into groups based on tetranucleotide frequencies and CRISPR spacer-protospacer matching and ORF calling. Using this pipeline we were able to assemble phage sequences into contigs and bin them into three clusters that corroborated with their potential host range. The virome contained 52,348 predicted ORFs; some were clearly phage-like; 9319 ORFs had a recognizable Pfam domain while the rest were hypothetical. Of the recognized domains with CRISPR spacer matches, was the phage endolysin used by lytic phage to disrupt cells. Analysis of the endolysins present in the thermophilic cyanophage contigs revealed a subset of characterized endolysins as well as a Glyco_hydro_108 (PF05838) domain not previously associated with sequenced cyanophages. A search for CRISPR spacer matches to all identified phage endolysins demonstrated that a majority of endolysin domains were targets. This strategy provides a general way to link host and phage as endolysins are known to be widely distributed in bacteriophage. Endolysins can also provide information about host cell wall composition and have the additional potential to be used as targets for novel therapeutics.

VL - 11 CP - 9 M3 - 10.1371/journal.pone.0160574 ER - TY - JOUR T1 - Genome-scale study reveals reduced metabolic adaptability in patients with non-alcoholic fatty liver disease JF - Nature Communications Y1 - 2016 A1 - ötyläinen, Tuulia A1 - Jerby, Livnat A1 - äjä, Elina M. A1 - Mattila, Ismo A1 - äntti, Sirkku A1 - Auvinen, Petri A1 - Gastaldelli, Amalia A1 - ärvinen, Hannele A1 - Ruppin, Eytan A1 - šič, Matej VL - 7 UR - http://www.nature.com/doifinder/10.1038/ncomms9994 J1 - Nat Comms M3 - 10.1038/ncomms9994 ER - TY - JOUR T1 - Identification and genomic analysis of a novel group C orthobunyavirus isolated from a mosquito captured near Iquitos, Peru JF - PLoS Negl Trop Dis Y1 - 2016 A1 - Todd Treangen A1 - Schoeler, George A1 - Phillippy, Adam M A1 - Bergman, Nicholas H A1 - Turell, Michael J VL - 10 ER - TY - JOUR T1 - A joint analysis of transcriptomic and metabolomic data uncovers enhanced enzyme-metabolite coupling in breast cancer. JF - Sci Rep Y1 - 2016 A1 - Auslander, Noam A1 - Yizhak, Keren A1 - Weinstock, Adam A1 - Budhu, Anuradha A1 - Tang, Wei A1 - Wang, Xin Wei A1 - Ambs, Stefan A1 - Ruppin, Eytan AB -

Disrupted regulation of cellular processes is considered one of the hallmarks of cancer. We analyze metabolomic and transcriptomic profiles jointly collected from breast cancer and hepatocellular carcinoma patients to explore the associations between the expression of metabolic enzymes and the levels of the metabolites participating in the reactions they catalyze. Surprisingly, both breast cancer and hepatocellular tumors exhibit an increase in their gene-metabolites associations compared to noncancerous adjacent tissues. Following, we build predictors of metabolite levels from the expression of the enzyme genes catalyzing them. Applying these predictors to a large cohort of breast cancer samples we find that depleted levels of key cancer-related metabolites including glucose, glycine, serine and acetate are significantly associated with improved patient survival. Thus, we show that the levels of a wide range of metabolites in breast cancer can be successfully predicted from the transcriptome, going beyond the limited set of those measured.

VL - 6 M3 - 10.1038/srep29662 ER - TY - CONF T1 - Limitations of Current Approaches for Reference-Free, Graph-Based Variant Detection T2 - the 7th ACM International ConferenceProceedings of the 7th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics - BCB '16 Y1 - 2016 A1 - Bateman, Amelia A1 - Todd Treangen A1 - Pop, Mihai JA - the 7th ACM International ConferenceProceedings of the 7th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics - BCB '16 PB - ACM Press CY - Seattle, WA, USANew York, New York, USA SN - 9781450342254 UR - http://dl.acm.org/citation.cfm?doid=2975167http://dl.acm.org/citation.cfm?doid=2975167.2985653 M3 - 10.1145/297516710.1145/2975167.2985653 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 - Mash: fast genome and metagenome distance estimation using MinHash JF - Genome Biology Y1 - 2016 A1 - Ondov, Brian D. A1 - Todd Treangen A1 - Melsted, áll A1 - Mallonee, Adam B. A1 - Bergman, Nicholas H. A1 - Koren, Sergey A1 - Phillippy, Adam M. UR - http://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0997-xhttp://link.springer.com/content/pdf/10.1186/s13059-016-0997-x CP - 1Suppl 19 J1 - Genome Biol M3 - 10.1186/s13059-016-0997-x 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 - ABST T1 - Algorithms in Bioinformatics: 15th International Workshop, WABI 2015 Y1 - 2015 A1 - Pop, Mihai A1 - Touzet, Hélène ED - Istrail, Sorin ED - Pevzner, Pavel ED - Waterman, Michael S JA - Lecture Notes in Bioinformatics PB - Springer SN - 978-3-662-48220-9 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 - 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 - Evolutionary Conservation of Bacterial Essential Metabolic Genes across All Bacterial Culture Media Y1 - 2015 A1 - Ish-Am, Oren A1 - Kristensen, David M. A1 - Ruppin, Eytan ED - Thangaraj, Kumarasamy JA - PLOS ONE VL - 10 UR - http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0123785 CP - 4 J1 - PLoS ONE M3 - 10.1371/journal.pone.0123785 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 - JOUR T1 - Microbiota that affect risk for shigellosis in children in low-income countries JF - Emerg Infect DisEmerg Infect Dis Y1 - 2015 A1 - Lindsay, B. A1 - Oundo, J. A1 - Hossain, M. A. A1 - Antonio, M. A1 - Tamboura, B. A1 - Walker, A. W. A1 - Paulson, J. N. A1 - Parkhill, J. A1 - Omore, R. A1 - Faruque, A. S. A1 - Das, S. K. A1 - Ikumapayi, U. N. A1 - Adeyemi, M. A1 - Sanogo, D. A1 - Saha, D. A1 - Sow, S. A1 - Farag, T. H. A1 - Nasrin, D. A1 - Li, S. A1 - Panchalingam, S. A1 - Levine, M. M. A1 - Kotloff, K. A1 - Magder, L. S. A1 - Hungerford, L. A1 - Sommerfelt, H. A1 - Pop, M. A1 - Nataro, J. P. A1 - Stine, O. C. AB - Pathogens in the gastrointestinal tract exist within a vast population of microbes. We examined associations between pathogens and composition of gut microbiota as they relate to Shigella spp./enteroinvasive Escherichia coli infection. We analyzed 3,035 stool specimens (1,735 nondiarrheal and 1,300 moderate-to-severe diarrheal) from the Global Enteric Multicenter Study for 9 enteropathogens. Diarrheal specimens had a higher number of enteropathogens (diarrheal mean 1.4, nondiarrheal mean 0.95; p<0.0001). Rotavirus showed a negative association with Shigella spp. in cases of diarrhea (odds ratio 0.31, 95% CI 0.17-0.55) and had a large combined effect on moderate-to-severe diarrhea (odds ratio 29, 95% CI 3.8-220). In 4 Lactobacillus taxa identified by 16S rRNA gene sequencing, the association between pathogen and disease was decreased, which is consistent with the possibility that Lactobacillus spp. are protective against Shigella spp.-induced diarrhea. Bacterial diversity of gut microbiota was associated with diarrhea status, not high levels of the Shigella spp. ipaH gene. VL - 21 SN - 1080-6059 (Electronic)
1080-6040 (Linking) N1 - Lindsay, Brianna
Oundo, Joe
Hossain, M Anowar
Antonio, Martin
Tamboura, Boubou
Walker, Alan W
Paulson, Joseph N
Parkhill, Julian
Omore, Richard
Faruque, Abu S G
Das, Suman Kumar
Ikumapayi, Usman N
Adeyemi, Mitchell
Sanogo, Doh
Saha, Debasish
Sow, Samba
Farag, Tamer H
Nasrin, Dilruba
Li, Shan
Panchalingam, Sandra
Levine, Myron M
Kotloff, Karen
Magder, Laurence S
Hungerford, Laura
Sommerfelt, Halvor
Pop, Mihai
Nataro, James P
Stine, O Colin
U19 090873/PHS HHS/United States
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.
United States
Emerg Infect Dis. 2015 Feb;21(2):242-50. doi: 10.3201/eid2101.140795. U2 - PMC4313639 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 - 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 - 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 - Automated ensemble assembly and validation of microbial genomes. JF - BMC Bioinformatics Y1 - 2014 A1 - Koren, Sergey A1 - Todd Treangen A1 - Hill, Christopher M A1 - Pop, Mihai A1 - Phillippy, Adam M KW - Genome, Bacterial KW - Genome, Microbial KW - Genomics KW - Mycobacterium tuberculosis KW - Rhodobacter sphaeroides KW - Sequence Analysis, DNA KW - software AB -

BACKGROUND: The continued democratization of DNA sequencing has sparked a new wave of development of genome assembly and assembly validation methods. As individual research labs, rather than centralized centers, begin to sequence the majority of new genomes, it is important to establish best practices for genome assembly. However, recent evaluations such as GAGE and the Assemblathon have concluded that there is no single best approach to genome assembly. Instead, it is preferable to generate multiple assemblies and validate them to determine which is most useful for the desired analysis; this is a labor-intensive process that is often impossible or unfeasible.

RESULTS: To encourage best practices supported by the community, we present iMetAMOS, an automated ensemble assembly pipeline; iMetAMOS encapsulates the process of running, validating, and selecting a single assembly from multiple assemblies. iMetAMOS packages several leading open-source tools into a single binary that automates parameter selection and execution of multiple assemblers, scores the resulting assemblies based on multiple validation metrics, and annotates the assemblies for genes and contaminants. We demonstrate the utility of the ensemble process on 225 previously unassembled Mycobacterium tuberculosis genomes as well as a Rhodobacter sphaeroides benchmark dataset. On these real data, iMetAMOS reliably produces validated assemblies and identifies potential contamination without user intervention. In addition, intelligent parameter selection produces assemblies of R. sphaeroides comparable to or exceeding the quality of those from the GAGE-B evaluation, affecting the relative ranking of some assemblers.

CONCLUSIONS: Ensemble assembly with iMetAMOS provides users with multiple, validated assemblies for each genome. Although computationally limited to small or mid-sized genomes, this approach is the most effective and reproducible means for generating high-quality assemblies and enables users to select an assembly best tailored to their specific needs.

VL - 15 M3 - 10.1186/1471-2105-15-126 ER - TY - JOUR T1 - Complete genome sequence of the quality control strain Staphylococcus aureus subsp. aureus ATCC 25923 JF - Genome announcements Y1 - 2014 A1 - Treangen, Todd J A1 - Maybank, Rosslyn A A1 - Enke, Sana A1 - Friss, Mary Beth A1 - Diviak, Lynn F A1 - Karaolis, David KR A1 - Koren, Sergey A1 - Ondov, Brian A1 - Phillippy, Adam M A1 - Bergman, Nicholas H VL - 2 ER - TY - JOUR T1 - CTCF binding site sequence differences are associated with unique regulatory and functional trends during embryonic stem cell differentiation JF - Nucleic Acids ResNucleic Acids ResNucleic Acids Res Y1 - 2014 A1 - Plasschaert, R. N. A1 - Vigneau, S. A1 - Tempera, I. A1 - Gupta, R. A1 - Maksimoska, J. A1 - Everett, L. A1 - Davuluri, R. A1 - Mamorstein, R. A1 - Lieberman, P. M. A1 - Schultz, D. A1 - Sridhar Hannenhalli A1 - Bartolomei, M. S. KW - *Gene Expression Regulation KW - *Regulatory Elements, Transcriptional KW - Animals KW - Binding Sites KW - Cell Differentiation/*genetics KW - Cells, Cultured KW - Embryonic Stem Cells/cytology/*metabolism KW - Mice KW - Nucleotide Motifs KW - Protein Binding KW - Repressor Proteins/*metabolism AB - CTCF (CCCTC-binding factor) is a highly conserved multifunctional DNA-binding protein with thousands of binding sites genome-wide. Our previous work suggested that differences in CTCF's binding site sequence may affect the regulation of CTCF recruitment and its function. To investigate this possibility, we characterized changes in genome-wide CTCF binding and gene expression during differentiation of mouse embryonic stem cells. After separating CTCF sites into three classes (LowOc, MedOc and HighOc) based on similarity to the consensus motif, we found that developmentally regulated CTCF binding occurs preferentially at LowOc sites, which have lower similarity to the consensus. By measuring the affinity of CTCF for selected sites, we show that sites lost during differentiation are enriched in motifs associated with weaker CTCF binding in vitro. Specifically, enrichment for T at the 18(th) position of the CTCF binding site is associated with regulated binding in the LowOc class and can predictably reduce CTCF affinity for binding sites. Finally, by comparing changes in CTCF binding with changes in gene expression during differentiation, we show that LowOc and HighOc sites are associated with distinct regulatory functions. Our results suggest that the regulatory control of CTCF is dependent in part on specific motifs within its binding site. VL - 42 SN - 1362-4962 (Electronic)
0305-1048 (Linking) N1 - Plasschaert, Robert N
Vigneau, Sebastien
Tempera, Italo
Gupta, Ravi
Maksimoska, Jasna
Everett, Logan
Davuluri, Ramana
Mamorstein, Ronen
Lieberman, Paul M
Schultz, David
Hannenhalli, Sridhar
Bartolomei, Marisa S
eng
K99AI099153/AI/NIAID NIH HHS/
P30 CA10815/CA/NCI NIH HHS/
R01 CA140652/CA/NCI NIH HHS/
R01-GM052880/GM/NIGMS NIH HHS/
R01CA140652/CA/NCI NIH HHS/
R01GM085226/GM/NIGMS NIH HHS/
R01HD042026/HD/NICHD NIH HHS/
T32GM008216/GM/NIGMS NIH HHS/
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
England
2013/10/15 06:00
Nucleic Acids Res. 2014 Jan;42(2):774-89. doi: 10.1093/nar/gkt910. Epub 2013 Oct 10. U2 - 3902912 J1 - Nucleic acids researchNucleic acids research ER - TY - Generic T1 - Diarrhea in young children from low-income countries leads to large-scale alterations in intestinal microbiota composition. Y1 - 2014 A1 - Pop, Mihai A1 - Walker, Alan W A1 - Paulson, Joseph A1 - Lindsay, Brianna A1 - Antonio, Martin A1 - Hossain, M Anowar A1 - Oundo, Joseph A1 - Tamboura, Boubou A1 - Mai, Volker A1 - Astrovskaya, Irina A1 - Corrada Bravo, Hector A1 - Rance, Richard A1 - Stares, Mark A1 - Levine, Myron M A1 - Panchalingam, Sandra A1 - Kotloff, Karen A1 - Ikumapayi, Usman N A1 - Ebruke, Chinelo A1 - Adeyemi, Mitchell A1 - Ahmed, Dilruba A1 - Ahmed, Firoz A1 - Alam, Meer Taifur A1 - Amin, Ruhul A1 - Siddiqui, Sabbir A1 - Ochieng, John B A1 - Ouma, Emmanuel A1 - Juma, Jane A1 - Mailu, Euince A1 - Omore, Richard A1 - Morris, J Glenn A1 - Breiman, Robert F A1 - Saha, Debasish A1 - Parkhill, Julian A1 - Nataro, James P A1 - Stine, O Colin KW - Bangladesh KW - Base Sequence KW - Case-Control Studies KW - Child, Preschool KW - Diarrhea, Infantile KW - Dysentery KW - Feces KW - Female KW - Gambia KW - HUMANS KW - Infant KW - Infant, Newborn KW - Intestines KW - Kenya KW - Male KW - Mali KW - Microbiota KW - Molecular Typing KW - Poverty KW - RNA, Bacterial KW - RNA, Ribosomal, 16S AB -

BACKGROUND: Diarrheal diseases continue to contribute significantly to morbidity and mortality in infants and young children in developing countries. There is an urgent need to better understand the contributions of novel, potentially uncultured, diarrheal pathogens to severe diarrheal disease, as well as distortions in normal gut microbiota composition that might facilitate severe disease.

RESULTS: We use high throughput 16S rRNA gene sequencing to compare fecal microbiota composition in children under five years of age who have been diagnosed with moderate to severe diarrhea (MSD) with the microbiota from diarrhea-free controls. Our study includes 992 children from four low-income countries in West and East Africa, and Southeast Asia. Known pathogens, as well as bacteria currently not considered as important diarrhea-causing pathogens, are positively associated with MSD, and these include Escherichia/Shigella, and Granulicatella species, and Streptococcus mitis/pneumoniae groups. In both cases and controls, there tend to be distinct negative correlations between facultative anaerobic lineages and obligate anaerobic lineages. Overall genus-level microbiota composition exhibit a shift in controls from low to high levels of Prevotella and in MSD cases from high to low levels of Escherichia/Shigella in younger versus older children; however, there was significant variation among many genera by both site and age.

CONCLUSIONS: Our findings expand the current understanding of microbiota-associated diarrhea pathogenicity in young children from developing countries. Our findings are necessarily based on correlative analyses and must be further validated through epidemiological and molecular techniques.

JA - Genome Biol VL - 15 CP - 6 M3 - 10.1186/gb-2014-15-6-r76 ER - TY - JOUR T1 - The Harvest suite for rapid core-genome alignment and visualization of thousands of intraspecific microbial genomes JF - Genome biology Y1 - 2014 A1 - Todd Treangen A1 - Ondov, Brian D A1 - Koren, Sergey A1 - Phillippy, Adam M VL - 15 ER - TY - Generic T1 - Large hypomethylated blocks as a universal defining epigenetic alteration in human solid tumors. Y1 - 2014 A1 - Timp, Winston A1 - Bravo, Héctor Corrada A1 - McDonald, Oliver G A1 - Goggins, Michael A1 - Umbricht, Chris A1 - Zeiger, Martha A1 - Feinberg, Andrew P A1 - Irizarry, Rafael A AB -

BACKGROUND: One of the most provocative recent observations in cancer epigenetics is the discovery of large hypomethylated blocks, including single copy genes, in colorectal cancer, that correspond in location to heterochromatic LOCKs (large organized chromatin lysine-modifications) and LADs (lamin-associated domains).

METHODS: Here we performed a comprehensive genome-scale analysis of 10 breast, 28 colon, nine lung, 38 thyroid, 18 pancreas cancers, and five pancreas neuroendocrine tumors as well as matched normal tissue from most of these cases, as well as 51 premalignant lesions. We used a new statistical approach that allows the identification of large hypomethylated blocks on the Illumina HumanMethylation450 BeadChip platform.

RESULTS: We find that hypomethylated blocks are a universal feature of common solid human cancer, and that they occur at the earliest stage of premalignant tumors and progress through clinical stages of thyroid and colon cancer development. We also find that the disrupted CpG islands widely reported previously, including hypermethylated island bodies and hypomethylated shores, are enriched in hypomethylated blocks, with flattening of the methylation signal within and flanking the islands. Finally, we found that genes showing higher between individual gene expression variability are enriched within these hypomethylated blocks.

CONCLUSION: Thus hypomethylated blocks appear to be a universal defining epigenetic alteration in human cancer, at least for common solid tumors.

JA - Genome Med VL - 6 CP - 8 M3 - 10.1186/s13073-014-0061-y 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 - CONF T1 - De novo likelihood-based measures for comparing metagenomic assemblies T2 - 2013 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) Y1 - 2013 A1 - Hill, Christopher M A1 - Irina Astrovskaya A1 - Huang, Howard A1 - Koren, Sergey A1 - Memon, Atif A1 - Todd Treangen A1 - Pop, Mihai JA - 2013 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) PB - IEEE CY - Shanghai, China 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 - JOUR T1 - MetAMOS: a modular and open source metagenomic assembly and analysis pipeline JF - Genome BiolGenome Biol Y1 - 2013 A1 - Todd Treangen A1 - Koren, S. A1 - Sommer, D. D. A1 - Liu, B. A1 - Irina Astrovskaya A1 - Ondov, B. A1 - Darling, A. E. A1 - Phillippy, A. M. A1 - M. Pop AB - ABSTRACT: We describe MetAMOS, an open source and modular metagenomic assembly and analysis pipeline. MetAMOS represents an important step towards fully automated metagenomic analysis, starting with next-generation sequencing reads and producing genomic scaffolds, open-reading frames and taxonomic or functional annotations. MetAMOS can aid in reducing assembly errors, commonly encountered when assembling metagenomic samples, and improves taxonomic assignment accuracy while also reducing computational cost. MetAMOS can be downloaded from: https://github.com/treangen/MetAMOS. VL - 14 SN - 1465-6914 (Electronic)1465-6906 (Linking) N1 - Treangen, Todd JKoren, SergeySommer, Daniel DLiu, BoAstrovskaya, IrinaOndov, BrianDarling, Aaron EPhillippy, Adam MPop, MihaiGenome Biol. 2013 Jan 15;14(1):R2.
Genome biology ER - TY - JOUR T1 - Quantitative PCR for Detection of Shigella Improves Ascertainment of Shigella Burden in Children with Moderate-to-Severe Diarrhea in Low-Income Countries JF - Journal of Clinical MicrobiologyJournal of Clinical Microbiology Y1 - 2013 A1 - Lindsay, Brianna A1 - Ochieng, John B. A1 - Ikumapayi, Usman N. A1 - Toure, Aliou A1 - Ahmed, Dilruba A1 - Li, Shan A1 - Panchalingam, Sandra A1 - Levine, Myron M. A1 - Kotloff, Karen A1 - Rasko, David A. PB - American Society for Microbiology VL - 51 SN - 0095-1137 ER - TY - JOUR T1 - Somatic alterations contributing to metastasis of a castration-resistant prostate cancer JF - Human mutationHuman mutation Y1 - 2013 A1 - Nickerson, Michael L. A1 - Im, Kate M. A1 - Misner, Kevin J. A1 - Tan, Wei A1 - Lou, Hong A1 - Gold, Bert A1 - Wells, David W. A1 - Héctor Corrada Bravo A1 - Fredrikson, Karin M. A1 - Harkins, Timothy T. A1 - Milos, Patrice A1 - Zbar, Berton A1 - Linehan, W. Marston A1 - Yeager, Meredith A1 - Andresson, Thorkell A1 - Dean, Michael A1 - Bova, G. Steven AB - Metastatic castration-resistant prostate cancer (mCRPC) is a lethal disease, and molecular markers that differentiate indolent from aggressive subtypes are needed. We sequenced the exomes of five metastatic tumors and healthy kidney tissue from an index case with mCRPC to identify lesions associated with disease progression and metastasis. An Ashkenazi Jewish (AJ) germline founder mutation, del185AG in BRCA1, was observed and AJ ancestry was confirmed. Sixty-two somatic variants altered proteins in tumors, including cancer-associated genes, TMPRSS2-ERG, PBRM1, and TET2. The majority (n = 53) of somatic variants were present in all metastases and only a subset (n = 31) was observed in the primary tumor. Integrating tumor next-generation sequencing and DNA copy number showed somatic loss of BRCA1 and TMPRSS2-ERG. We sequenced 19 genes with deleterious mutations in the index case in additional mCRPC samples and detected a frameshift, two somatic missense alterations, tumor loss of heterozygosity, and combinations of germline missense SNPs in TET2. In summary, genetic analysis of metastases from an index case permitted us to infer a chronology for the clonal spread of disease based on sequential accrual of somatic lesions. The role of TET2 in mCRPC deserves additional analysis and may define a subset of metastatic disease. VL - 34 N1 - http://www.ncbi.nlm.nih.gov/pubmed/23636849?dopt=Abstract ER - TY - JOUR T1 - Survey of Culture, GoldenGate Assay, Universal Biosensor Assay, and 16S rRNA Gene Sequencing as Alternative Methods of Bacterial Pathogen Detection JF - Journal of Clinical MicrobiologyJournal of Clinical Microbiology Y1 - 2013 A1 - Lindsay, Brianna A1 - M. Pop A1 - Antonio, Martin A1 - Walker, Alan W. A1 - Mai, Volker A1 - Ahmed, Dilruba A1 - Oundo, Joseph A1 - Tamboura, Boubou A1 - Panchalingam, Sandra A1 - Levine, Myron M. PB - American Society for Microbiology VL - 51 SN - 0095-1137 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 - A framework for human microbiome research JF - Nature Y1 - 2012 A1 - Human Microbiome Project Consortium A1 - Todd Treangen VL - 486 ER - TY - JOUR T1 - GAGE: A critical evaluation of genome assemblies and assembly algorithms JF - Genome researchGenome Research Y1 - 2012 A1 - Salzberg, S. L. A1 - Phillippy, A. M. A1 - Zimin, A. A1 - Puiu, D. A1 - Magoc, T. A1 - Koren, S. A1 - Todd Treangen A1 - Schatz, M. C. A1 - Delcher, A. L. A1 - Roberts, M. A1 - others, PB - Cold Spring Harbor Lab VL - 22 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 - Identification of Coli Surface Antigen 23, a Novel Adhesin of Enterotoxigenic Escherichia coli JF - Infection and immunityInfection and immunity Y1 - 2012 A1 - Del Canto, F. A1 - Botkin, D. J. A1 - Valenzuela, P. A1 - Popov, V. A1 - Ruiz-Perez, F. A1 - Nataro, J. P. A1 - Levine, M. M. A1 - Stine, O. C. A1 - M. Pop A1 - Torres, A. G. A1 - others, PB - American Society for Microbiology VL - 80 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 - Irreconcilable differences: divorcing geographic mutation and recombination rates within a global MRSA clone JF - Genome Biology Y1 - 2012 A1 - Phillippy, Adam A1 - Todd Treangen VL - 13 ER - TY - JOUR T1 - MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space JF - Systematic Biology Y1 - 2012 A1 - F. Ronquist A1 - Teslenko, M. A1 - van der Mark, P. A1 - Ayres, D. L. A1 - Darling, A. A1 - Hohna, S. A1 - B. Larget A1 - Liu, L. A1 - Suchard, M. A. A1 - J. P. Huelsenbeck VL - 61 M3 - 10.1093/sysbio/sys029 ER - TY - JOUR T1 - Myocardin-like Protein (MKL)-2 Regulates TGF-beta Signaling JF - Embryonic Stem Cells and the Developing Vasculature DevelopmentEmbryonic Stem Cells and the Developing Vasculature Development Y1 - 2012 A1 - Li, Jian A1 - Nina, Bowens A1 - Lan, Cheng A1 - Mary, Chen A1 - Sridhar Hannenhalli A1 - Xiaohong, Zhu A1 - Thomas, P. Cappola A1 - Parmacek, Michael S. 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 - Whole genome analysis of Leptospira licerasiae provides insight into leptospiral evolution and pathogenicity JF - PLoS neglected tropical diseasesPLoS neglected tropical diseases Y1 - 2012 A1 - Ricaldi, Jessica N. A1 - Fouts, Derrick E. A1 - J. Selengut A1 - Harkins, Derek M. A1 - Patra, Kailash P. A1 - Moreno, Angelo A1 - Lehmann, Jason S. A1 - Purushe, Janaki A1 - Sanka, Ravi A1 - Torres, Michael A1 - Webster, Nicholas J. A1 - Vinetz, Joseph M. A1 - Matthias, Michael A. KW - DNA, Bacterial KW - Evolution, Molecular KW - Gene Transfer, Horizontal KW - Genome, Bacterial KW - Genomic islands KW - HUMANS KW - Leptospira KW - Molecular Sequence Data KW - Multigene Family KW - Prophages KW - Sequence Analysis, DNA KW - Virulence factors AB - The whole genome analysis of two strains of the first intermediately pathogenic leptospiral species to be sequenced (Leptospira licerasiae strains VAR010 and MMD0835) provides insight into their pathogenic potential and deepens our understanding of leptospiral evolution. Comparative analysis of eight leptospiral genomes shows the existence of a core leptospiral genome comprising 1547 genes and 452 conserved genes restricted to infectious species (including L. licerasiae) that are likely to be pathogenicity-related. Comparisons of the functional content of the genomes suggests that L. licerasiae retains several proteins related to nitrogen, amino acid and carbohydrate metabolism which might help to explain why these Leptospira grow well in artificial media compared with pathogenic species. L. licerasiae strains VAR010(T) and MMD0835 possess two prophage elements. While one element is circular and shares homology with LE1 of L. biflexa, the second is cryptic and homologous to a previously identified but unnamed region in L. interrogans serovars Copenhageni and Lai. We also report a unique O-antigen locus in L. licerasiae comprised of a 6-gene cluster that is unexpectedly short compared with L. interrogans in which analogous regions may include >90 such genes. Sequence homology searches suggest that these genes were acquired by lateral gene transfer (LGT). Furthermore, seven putative genomic islands ranging in size from 5 to 36 kb are present also suggestive of antecedent LGT. How Leptospira become naturally competent remains to be determined, but considering the phylogenetic origins of the genes comprising the O-antigen cluster and other putative laterally transferred genes, L. licerasiae must be able to exchange genetic material with non-invasive environmental bacteria. The data presented here demonstrate that L. licerasiae is genetically more closely related to pathogenic than to saprophytic Leptospira and provide insight into the genomic bases for its infectiousness and its unique antigenic characteristics. VL - 6 N1 - http://www.ncbi.nlm.nih.gov/pubmed/23145189?dopt=Abstract ER - TY - JOUR T1 - Whole genome analysis of Leptospira licerasiae provides insight into leptospiral evolution and pathogenicity. JF - PLoS Negl Trop Dis Y1 - 2012 A1 - Ricaldi, Jessica N A1 - Fouts, Derrick E A1 - Selengut, Jeremy D A1 - Harkins, Derek M A1 - Patra, Kailash P A1 - Moreno, Angelo A1 - Lehmann, Jason S A1 - Purushe, Janaki A1 - Sanka, Ravi A1 - Torres, Michael A1 - Webster, Nicholas J A1 - Vinetz, Joseph M A1 - Matthias, Michael A KW - DNA, Bacterial KW - Evolution, Molecular KW - Gene Transfer, Horizontal KW - Genome, Bacterial KW - Genomic islands KW - HUMANS KW - Leptospira KW - Molecular Sequence Data KW - Multigene Family KW - Prophages KW - Sequence Analysis, DNA KW - Virulence factors AB -

The whole genome analysis of two strains of the first intermediately pathogenic leptospiral species to be sequenced (Leptospira licerasiae strains VAR010 and MMD0835) provides insight into their pathogenic potential and deepens our understanding of leptospiral evolution. Comparative analysis of eight leptospiral genomes shows the existence of a core leptospiral genome comprising 1547 genes and 452 conserved genes restricted to infectious species (including L. licerasiae) that are likely to be pathogenicity-related. Comparisons of the functional content of the genomes suggests that L. licerasiae retains several proteins related to nitrogen, amino acid and carbohydrate metabolism which might help to explain why these Leptospira grow well in artificial media compared with pathogenic species. L. licerasiae strains VAR010(T) and MMD0835 possess two prophage elements. While one element is circular and shares homology with LE1 of L. biflexa, the second is cryptic and homologous to a previously identified but unnamed region in L. interrogans serovars Copenhageni and Lai. We also report a unique O-antigen locus in L. licerasiae comprised of a 6-gene cluster that is unexpectedly short compared with L. interrogans in which analogous regions may include >90 such genes. Sequence homology searches suggest that these genes were acquired by lateral gene transfer (LGT). Furthermore, seven putative genomic islands ranging in size from 5 to 36 kb are present also suggestive of antecedent LGT. How Leptospira become naturally competent remains to be determined, but considering the phylogenetic origins of the genes comprising the O-antigen cluster and other putative laterally transferred genes, L. licerasiae must be able to exchange genetic material with non-invasive environmental bacteria. The data presented here demonstrate that L. licerasiae is genetically more closely related to pathogenic than to saprophytic Leptospira and provide insight into the genomic bases for its infectiousness and its unique antigenic characteristics.

VL - 6 CP - 10 M3 - 10.1371/journal.pntd.0001853 ER - TY - JOUR T1 - Accurate and fast estimation of taxonomic profiles from metagenomic shotgun sequences JF - BMC GenomicsBMC Genomics Y1 - 2011 A1 - Liu, Bo A1 - Gibbons, Theodore A1 - Ghodsi, Mohammad A1 - Todd Treangen A1 - M. Pop AB - A major goal of metagenomics is to characterize the microbial composition of an environment. The most popular approach relies on 16S rRNA sequencing, however this approach can generate biased estimates due to differences in the copy number of the gene between even closely related organisms, and due to PCR artifacts. The taxonomic composition can also be determined from metagenomic shotgun sequencing data by matching individual reads against a database of reference sequences. One major limitation of prior computational methods used for this purpose is the use of a universal classification threshold for all genes at all taxonomic levels. VL - 12 SN - 1471-2164 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 - Bambus 2: Scaffolding Metagenomes JF - Bioinformatics Y1 - 2011 A1 - Koren, Sergey A1 - Todd Treangen A1 - M. Pop AB - Motivation: Sequencing projects increasingly target samples from non-clonal sources. In particular, metagenomics has enabled scientists to begin to characterize the structure of microbial communities. The software tools developed for assembling and analyzing sequencing data for clonal organisms are, however, unable to adequately process data derived from non-clonal sources.Results: We present a new scaffolder, Bambus 2, to address some of the challenges encountered when analyzing metagenomes. Our approach relies on a combination of a novel method for detecting genomic repeats and algorithms that analyze assembly graphs to identify biologically meaningful genomic variants. We compare our software to current assemblers using simulated and real data. We demonstrate that the repeat detection algorithms have higher sensitivity than current approaches without sacrificing specificity. In metagenomic datasets, the scaffolder avoids false joins between distantly related organisms while obtaining long-range contiguity. Bambus 2 represents a first step toward automated metagenomic assembly. Availability: Bambus 2 is open source and available from http://amos.sf.net. Contact: mpop@umiacs.umd.edu Supplementary Information: Supplementary data are available at Bioinformatics online. VL - 27 SN - 1367-4803, 1460-2059 ER - TY - JOUR T1 - Complete Columbian mammoth mitogenome suggests interbreeding with woolly mammoths JF - Genome biology Y1 - 2011 A1 - Enk, Jacob A1 - Devault, Alison A1 - Debruyne, Regis A1 - King, Christine E A1 - Todd Treangen A1 - O'Rourke, Dennis A1 - Salzberg, Steven L A1 - Fisher, Daniel A1 - MacPhee, Ross A1 - Poinar, Hendrik VL - 12 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 - Direct targeting of Sec23a by miR-200s influences cancer cell secretome and promotes metastatic colonization Y1 - 2011 A1 - Korpal, Manav A1 - Ell, Brian J A1 - Buffa, Francesca M A1 - Ibrahim, Toni A1 - Blanco, Mario A A1 - à-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 JA - Nature Medicine VL - 17 UR - http://www.nature.com/doifinder/10.1038/nm.2401 CP - 9 J1 - Nat Med M3 - 10.1038/nm.2401 ER - TY - JOUR T1 - Effective detection of rare variants in pooled DNA samples using Cross-pool tailcurve analysis JF - Genome Biology Y1 - 2011 A1 - Niranjan, Tejasvi S A1 - Adamczyk, Abby A1 - Bravo, Hector A1 - Taub, Margaret A A1 - Wheelan, Sarah J A1 - Irizarry, Rafael A1 - Wang, Tao VL - 12 UR - http://genomebiology.biomedcentral.com/articles/10.1186/gb-2011-12-9-r93 CP - 9 J1 - Genome BiolGenome Biology M3 - 10.1186/gb-2011-12-9-r93 ER - TY - JOUR T1 - The genome and its implications. JF - Adv Parasitol Y1 - 2011 A1 - Teixeira, Santuza M A1 - El-Sayed, Najib M A1 - Araújo, Patrícia R KW - Animals KW - Antigens, Protozoan KW - Chagas Disease KW - Chromosomes KW - Comparative Genomic Hybridization KW - DNA, Protozoan KW - Gene Expression Regulation KW - Genetic Variation KW - Genome, Protozoan KW - Host-Parasite Interactions KW - HUMANS KW - Species Specificity KW - Synteny KW - Transcription, Genetic KW - Transfection KW - Trypanosoma cruzi AB -

Trypanosoma cruzi has a heterogeneous population composed of a pool of strains that circulate in the domestic and sylvatic cycles. Genome sequencing of the clone CL Brener revealed a highly repetitive genome of about 110Mb containing an estimated 22,570 genes. Because of its hybrid nature, sequences representing the two haplotypes have been generated. In addition, a repeat content close to 50% made the assembly of the estimated 41 pairs of chromosomes quite challenging. Similar to other trypanosomatids, the organization of T. cruzi chromosomes was found to be very peculiar, with protein-coding genes organized in long polycistronic transcription units encoding 20 or more proteins in one strand separated by strand switch regions. Another remarkable feature of the T. cruzi genome is the massive expansion of surface protein gene families. Because of the high genetic diversity of the T. cruzi population, sequencing of additional strains and comparative genomic and transcriptome analyses are in progress. Five years after its publication, the genome data have proven to be an essential tool for the study of T. cruzi and increasing efforts to translate this knowledge into the development of new modes of intervention to control Chagas disease are underway.

VL - 75 M3 - 10.1016/B978-0-12-385863-4.00010-1 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 - Horizontal transfer, not duplication, drives the expansion of protein families in prokaryotes JF - PLoS Genet Y1 - 2011 A1 - Todd Treangen A1 - Eduardo Rocha VL - 7 ER - TY - JOUR T1 - Increased methylation variation in epigenetic domains across cancer types JF - Nature Genetics Y1 - 2011 A1 - Hansen, Kasper Daniel A1 - Timp, Winston A1 - Bravo, Héctor Corrada A1 - Sabunciyan, Sarven A1 - Langmead, Benjamin A1 - McDonald, Oliver G A1 - Wen, Bo A1 - Wu, Hao A1 - Liu, Yun A1 - Diep, Dinh A1 - Briem, Eirikur A1 - Zhang, Kun A1 - Irizarry, Rafael A A1 - Feinberg, Andrew P VL - 43 UR - http://www.nature.com/doifinder/10.1038/ng.865 CP - 8 J1 - Nat Genet M3 - 10.1038/ng.865 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 - A Model for Early Prediction of Facial Nerve Recovery After Vestibular Schwannoma Surgery JF - Otology & Neurotology Y1 - 2011 A1 - Rivas, Alejandro A1 - Boahene, Kofi D. A1 - Bravo, Héctor Corrada A1 - Tan, Marietta A1 - Tamargo, Rafael J. A1 - Francis, Howard W. VL - 32 UR - http://content.wkhealth.com/linkback/openurl?sid=WKPTLP:landingpage&an=00129492-201107000-00019 CP - 5 J1 - Otology & Neurotology M3 - 10.1097/MAO.0b013e31821b0afd ER - TY - JOUR T1 - Next Generation Sequence Assembly with AMOS JF - Current Protocols in BioinformaticsCurrent Protocols in Bioinformatics Y1 - 2011 A1 - Todd Treangen A1 - Sommer, D. D. A1 - Angly, F. E. A1 - Koren, S. A1 - M. Pop PB - Wiley Online Library VL - 11 ER - TY - JOUR T1 - Regulation of Lung Endoderm Progenitor Cell Behavior by miR302/367 JF - DevelopmentDevelopmentDevelopmentDevelopment Y1 - 2011 A1 - Tian, Ying A1 - Zhang, Yuzhen A1 - Hurd, Laura A1 - Sridhar Hannenhalli A1 - Liu, Feiyan A1 - Lu, Min Min A1 - Morrisey, Edward E. KW - Lung KW - MicroRNA KW - mouse KW - Progenitor AB - The temporal and spatial control of organ-specific endoderm progenitor development is poorly understood. miRNAs affect cell function by regulating programmatic changes in protein expression levels. We show that the miR302/367 cluster is a target of the transcription factor Gata6 in mouse lung endoderm and regulates multiple aspects of early lung endoderm progenitor development. miR302/367 is expressed at early stages of lung development, but its levels decline rapidly as development proceeds. Gain- and loss-of-function studies show that altering miR302/367 expression disrupts the balance of lung endoderm progenitor proliferation and differentiation, as well as apical-basal polarity. Increased miR302/367 expression results in the formation of an undifferentiated multi-layered lung endoderm, whereas loss of miR302/367 activity results in decreased proliferation and enhanced lung endoderm differentiation. miR302/367 coordinates the balance between proliferation and differentiation, in part, through direct regulation of Rbl2 and Cdkn1a, whereas apical-basal polarity is controlled by regulation of Tiam1 and Lis1. Thus, miR302/367 directs lung endoderm development by coordinating multiple aspects of progenitor cell behavior, including proliferation, differentiation and apical-basal polarity. VL - 138 SN - 0950-1991, 1477-9129 ER - TY - JOUR T1 - Repetitive DNA and next-generation sequencing: computational challenges and solutions JF - Nature Reviews Genetics Y1 - 2011 A1 - Todd Treangen A1 - Salzberg, Steven L 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 - 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 - CHAP T1 - Genetics of Trypanosoma cruzi in American Trypanosomiasis: Chagas Disease One hundred Years of Research Y1 - 2010 A1 - Bartholomeu, D. A1 - Buck, G. A1 - Teixeira, S. A1 - El-Sayed, N.M. PB - Elsevier Press CY - Burlington 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 - 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 - Hopx and Hdac2 Interact to Modulate Gata4 Acetylation and Embryonic Cardiac Myocyte Proliferation JF - Developmental CellDevelopmental Cell Y1 - 2010 A1 - Trivedi, Chinmay M. A1 - Zhu, Wenting A1 - Wang, Qiaohong A1 - Jia, Cheng A1 - Kee, Hae Jin A1 - Li, Li A1 - Sridhar Hannenhalli A1 - Epstein, Jonathan A. AB - SummaryRegulation of chromatin structure via histone modification has recently received intense attention. Here, we demonstrate that the chromatin-modifying enzyme histone deacetylase 2 (Hdac2) functions with a small homeodomain factor, Hopx, to mediate deacetylation of Gata4, which is expressed by cardiac progenitor cells and plays critical roles in the regulation of cardiogenesis. In the absence of Hopx and Hdac2 in mouse embryos, Gata4 hyperacetylation is associated with a marked increase in cardiac myocyte proliferation, upregulation of Gata4 target genes, and perinatal lethality. Hdac2 physically interacts with Gata4, and this interaction is stabilized by Hopx. The ability of Gata4 to transactivate cell cycle genes is impaired by Hopx/Hdac2-mediated deacetylation, and this effect is abrogated by loss of Hdac2-Gata4 interaction. These results suggest that Gata4 is a nonhistone target of Hdac2-mediated deacetylation and that Hdac2, Hopx, and Gata4 coordinately regulate cardiac myocyte proliferation during embryonic development. VL - 19 SN - 1534-5807 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 - Overcoming bias and systematic errors in next generation sequencing data JF - Genome medicineGenome medicine Y1 - 2010 A1 - Taub, Margaret A. A1 - Héctor Corrada Bravo A1 - Irizarry, Rafael A. AB - Considerable time and effort has been spent in developing analysis and quality assessment methods to allow the use of microarrays in a clinical setting. As is the case for microarrays and other high-throughput technologies, data from new high-throughput sequencing technologies are subject to technological and biological biases and systematic errors that can impact downstream analyses. Only when these issues can be readily identified and reliably adjusted for will clinical applications of these new technologies be feasible. Although much work remains to be done in this area, we describe consistently observed biases that should be taken into account when analyzing high-throughput sequencing data. In this article, we review current knowledge about these biases, discuss their impact on analysis results, and propose solutions. VL - 2 N1 - http://www.ncbi.nlm.nih.gov/pubmed/21144010?dopt=Abstract 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 - 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 - 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 - Genesis, effects and fates of repeats in prokaryotic genomes JF - FEMS microbiology reviews Y1 - 2009 A1 - Todd Treangen A1 - Abraham, Anne-Laure A1 - Touchon, Marie A1 - Rocha, Eduardo PC VL - 33 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 - JOUR T1 - InterPro: the integrative protein signature database. JF - Nucleic Acids Res Y1 - 2009 A1 - Hunter, Sarah A1 - Apweiler, Rolf A1 - Attwood, Teresa K A1 - Bairoch, Amos A1 - Bateman, Alex A1 - Binns, David A1 - Bork, Peer A1 - Das, Ujjwal A1 - Daugherty, Louise A1 - Duquenne, Lauranne A1 - Finn, Robert D A1 - Gough, Julian A1 - Haft, Daniel A1 - Hulo, Nicolas A1 - Kahn, Daniel A1 - Kelly, Elizabeth A1 - Laugraud, Aurélie A1 - Letunic, Ivica A1 - Lonsdale, David A1 - Lopez, Rodrigo A1 - Madera, Martin A1 - Maslen, John A1 - McAnulla, Craig A1 - McDowall, Jennifer A1 - Mistry, Jaina A1 - Mitchell, Alex A1 - Mulder, Nicola A1 - Natale, Darren A1 - Orengo, Christine A1 - Quinn, Antony F A1 - Selengut, Jeremy D A1 - Sigrist, Christian J A A1 - Thimma, Manjula A1 - Thomas, Paul D A1 - Valentin, Franck A1 - Wilson, Derek A1 - Wu, Cathy H A1 - Yeats, Corin KW - Databases, Protein KW - Proteins KW - Sequence Analysis, Protein KW - Systems Integration AB -

The InterPro database (http://www.ebi.ac.uk/interpro/) integrates together predictive models or 'signatures' representing protein domains, families and functional sites from multiple, diverse source databases: Gene3D, PANTHER, Pfam, PIRSF, PRINTS, ProDom, PROSITE, SMART, SUPERFAMILY and TIGRFAMs. Integration is performed manually and approximately half of the total approximately 58,000 signatures available in the source databases belong to an InterPro entry. Recently, we have started to also display the remaining un-integrated signatures via our web interface. Other developments include the provision of non-signature data, such as structural data, in new XML files on our FTP site, as well as the inclusion of matchless UniProtKB proteins in the existing match XML files. The web interface has been extended and now links out to the ADAN predicted protein-protein interaction database and the SPICE and Dasty viewers. The latest public release (v18.0) covers 79.8% of UniProtKB (v14.1) and consists of 16 549 entries. InterPro data may be accessed either via the web address above, via web services, by downloading files by anonymous FTP or by using the InterProScan search software (http://www.ebi.ac.uk/Tools/InterProScan/).

VL - 37 CP - Database issue M3 - 10.1093/nar/gkn785 ER - TY - JOUR T1 - InterPro: the integrative protein signature database JF - Nucleic acids researchNucleic Acids Research Y1 - 2009 A1 - Hunter, Sarah A1 - Apweiler, Rolf A1 - Attwood, Teresa K. A1 - Bairoch, Amos A1 - Bateman, Alex A1 - Binns, David A1 - Bork, Peer A1 - Das, Ujjwal A1 - Daugherty, Louise A1 - Duquenne, Lauranne A1 - Finn, Robert D. A1 - Gough, Julian A1 - Haft, Daniel A1 - Hulo, Nicolas A1 - Kahn, Daniel A1 - Kelly, Elizabeth A1 - Laugraud, Aurélie A1 - Letunic, Ivica A1 - Lonsdale, David A1 - Lopez, Rodrigo A1 - Madera, Martin A1 - Maslen, John A1 - McAnulla, Craig A1 - McDowall, Jennifer A1 - Mistry, Jaina A1 - Mitchell, Alex A1 - Mulder, Nicola A1 - Natale, Darren A1 - Orengo, Christine A1 - Quinn, Antony F. A1 - J. Selengut A1 - Sigrist, Christian J. A. A1 - Thimma, Manjula A1 - Thomas, Paul D. A1 - Valentin, Franck A1 - Wilson, Derek A1 - Wu, Cathy H. A1 - Yeats, Corin KW - Databases, Protein KW - Proteins KW - Sequence Analysis, Protein KW - Systems Integration AB - The InterPro database (http://www.ebi.ac.uk/interpro/) integrates together predictive models or 'signatures' representing protein domains, families and functional sites from multiple, diverse source databases: Gene3D, PANTHER, Pfam, PIRSF, PRINTS, ProDom, PROSITE, SMART, SUPERFAMILY and TIGRFAMs. Integration is performed manually and approximately half of the total approximately 58,000 signatures available in the source databases belong to an InterPro entry. Recently, we have started to also display the remaining un-integrated signatures via our web interface. Other developments include the provision of non-signature data, such as structural data, in new XML files on our FTP site, as well as the inclusion of matchless UniProtKB proteins in the existing match XML files. The web interface has been extended and now links out to the ADAN predicted protein-protein interaction database and the SPICE and Dasty viewers. The latest public release (v18.0) covers 79.8% of UniProtKB (v14.1) and consists of 16 549 entries. InterPro data may be accessed either via the web address above, via web services, by downloading files by anonymous FTP or by using the InterProScan search software (http://www.ebi.ac.uk/Tools/InterProScan/). VL - 37 N1 - http://www.ncbi.nlm.nih.gov/pubmed/18940856?dopt=Abstract 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 - CONF T1 - Novel computational methods for large scale genome comparison T2 - 2nd International Workshop on Practical Applications of Computational Biology and Bioinformatics (IWPACBB 2008) Y1 - 2009 A1 - Todd Treangen A1 - Messeguer, Xavier JA - 2nd International Workshop on Practical Applications of Computational Biology and Bioinformatics (IWPACBB 2008) PB - Springer ER - TY - JOUR T1 - A Novel Heuristic for Local Multiple Alignment of Interspersed DNA Repeats JF - IEEE/ACM Transactions on Computational Biology and Bioinformatics Y1 - 2009 A1 - Todd Treangen A1 - Darling, A.E. A1 - Achaz, G. A1 - Ragan, M.A. A1 - Messeguer, X. A1 - Rocha, E.P.C. VL - 6 UR - http://ieeexplore.ieee.org/document/4770094/http://xplorestaging.ieee.org/ielx5/8857/4907697/04770094.pdf?arnumber=4770094 CP - 2 J1 - IEEE/ACM Trans. Comput. Biol. and Bioinf. M3 - 10.1109/TCBB.2009.9 ER - TY - JOUR T1 - A novel heuristic for local multiple alignment of interspersed DNA repeats JF - IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB) Y1 - 2009 A1 - Todd Treangen A1 - Darling, Aaron E A1 - Achaz, Guillaume A1 - Ragan, Mark A A1 - Messeguer, Xavier A1 - Rocha, Eduardo PC 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 - 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 - Ultrafast and memory-efficient alignment of short DNA sequences to the human genome JF - Genome BiologyGenome Biology Y1 - 2009 A1 - Langmead, Ben A1 - Trapnell, Cole A1 - M. Pop A1 - Salzberg, Steven L. AB - Bowtie is an ultrafast, memory-efficient alignment program for aligning short DNA sequence reads to large genomes. For the human genome, Burrows-Wheeler indexing allows Bowtie to align more than 25 million reads per CPU hour with a memory footprint of approximately 1.3 gigabytes. Bowtie extends previous Burrows-Wheeler techniques with a novel quality-aware backtracking algorithm that permits mismatches. Multiple processor cores can be used simultaneously to achieve even greater alignment speeds. Bowtie is open source http://bowtie.cbcb.umd.edu. VL - 10 SN - 1465-6906 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 - 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 - The impact of the neisserial DNA uptake sequences on genome evolution and stability JF - Genome biology Y1 - 2008 A1 - Todd Treangen A1 - Ambur, Ole Herman A1 - Tonjum, Tone A1 - Rocha, Eduardo PC VL - 9 ER - TY - BOOK T1 - Lecture Notes in Computer ScienceBioinformatics Research and ApplicationsGapped Extension for Local Multiple Alignment of Interspersed DNA Repeats Y1 - 2008 A1 - Todd Treangen A1 - Darling, Aaron E. A1 - Ragan, Mark A. A1 - Messeguer, Xavier PB - Springer Berlin Heidelberg CY - Berlin, Heidelberg VL - 4983 SN - 978-3-540-79449-3 UR - http://www.springerlink.com/index/10.1007/978-3-540-79450-9http://link.springer.com/10.1007/978-3-540-79450-9_8http://www.springerlink.com/index/pdf/10.1007/978-3-540-79450-9_8 M3 - 10.1007/978-3-540-79450-910.1007/978-3-540-79450-9_8 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 - 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 - 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 - Analyzing patterns of microbial evolution using the mauve genome alignment system JF - Comparative Genomics Y1 - 2007 A1 - Darling, Aaron E A1 - Todd Treangen A1 - Messeguer, Xavier A1 - Perna, Nicole T 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 - Genome sequence and identification of candidate vaccine antigens from the animal pathogen Dichelobacter nodosus. JF - Nat Biotechnol Y1 - 2007 A1 - Myers, Garry S A A1 - Parker, Dane A1 - Al-Hasani, Keith A1 - Kennan, Ruth M A1 - Seemann, Torsten A1 - Ren, Qinghu A1 - Badger, Jonathan H A1 - Selengut, Jeremy D A1 - DeBoy, Robert T A1 - Tettelin, Hervé A1 - Boyce, John D A1 - McCarl, Victoria P A1 - Han, Xiaoyan A1 - Nelson, William C A1 - Madupu, Ramana A1 - Mohamoud, Yasmin A1 - Holley, Tara A1 - Fedorova, Nadia A1 - Khouri, Hoda A1 - Bottomley, Steven P A1 - Whittington, Richard J A1 - Adler, Ben A1 - Songer, J Glenn A1 - Rood, Julian I A1 - Paulsen, Ian T KW - Animals KW - Antigens KW - Chromosome mapping KW - Dichelobacter nodosus KW - Foot Rot KW - Genome, Bacterial KW - Sequence Analysis, DNA AB -

Dichelobacter nodosus causes ovine footrot, a disease that leads to severe economic losses in the wool and meat industries. We sequenced its 1.4-Mb genome, the smallest known genome of an anaerobe. It differs markedly from small genomes of intracellular bacteria, retaining greater biosynthetic capabilities and lacking any evidence of extensive ongoing genome reduction. Comparative genomic microarray studies and bioinformatic analysis suggested that, despite its small size, almost 20% of the genome is derived from lateral gene transfer. Most of these regions seem to be associated with virulence. Metabolic reconstruction indicated unsuspected capabilities, including carbohydrate utilization, electron transfer and several aerobic pathways. Global transcriptional profiling and bioinformatic analysis enabled the prediction of virulence factors and cell surface proteins. Screening of these proteins against ovine antisera identified eight immunogenic proteins that are candidate antigens for a cross-protective vaccine.

VL - 25 CP - 5 M3 - 10.1038/nbt1302 ER - TY - JOUR T1 - Genome sequence and identification of candidate vaccine antigens from the animal pathogen Dichelobacter nodosus JF - Nature biotechnologyNature biotechnology Y1 - 2007 A1 - Myers, Garry S. A. A1 - Parker, Dane A1 - Al-Hasani, Keith A1 - Kennan, Ruth M. A1 - Seemann, Torsten A1 - Ren, Qinghu A1 - Badger, Jonathan H. A1 - J. Selengut A1 - DeBoy, Robert T. A1 - Tettelin, Hervé A1 - Boyce, John D. A1 - McCarl, Victoria P. A1 - Han, Xiaoyan A1 - Nelson, William C. A1 - Madupu, Ramana A1 - Mohamoud, Yasmin A1 - Holley, Tara A1 - Fedorova, Nadia A1 - Khouri, Hoda A1 - Bottomley, Steven P. A1 - Whittington, Richard J. A1 - Adler, Ben A1 - Songer, J. Glenn A1 - Rood, Julian I. A1 - Paulsen, Ian T. KW - Animals KW - Antigens KW - Chromosome mapping KW - Dichelobacter nodosus KW - Foot Rot KW - Genome, Bacterial KW - Sequence Analysis, DNA AB - Dichelobacter nodosus causes ovine footrot, a disease that leads to severe economic losses in the wool and meat industries. We sequenced its 1.4-Mb genome, the smallest known genome of an anaerobe. It differs markedly from small genomes of intracellular bacteria, retaining greater biosynthetic capabilities and lacking any evidence of extensive ongoing genome reduction. Comparative genomic microarray studies and bioinformatic analysis suggested that, despite its small size, almost 20% of the genome is derived from lateral gene transfer. Most of these regions seem to be associated with virulence. Metabolic reconstruction indicated unsuspected capabilities, including carbohydrate utilization, electron transfer and several aerobic pathways. Global transcriptional profiling and bioinformatic analysis enabled the prediction of virulence factors and cell surface proteins. Screening of these proteins against ovine antisera identified eight immunogenic proteins that are candidate antigens for a cross-protective vaccine. VL - 25 N1 - http://www.ncbi.nlm.nih.gov/pubmed/17468768?dopt=Abstract ER - TY - JOUR T1 - High-throughput sequence alignment using Graphics Processing Units JF - BMC BioinformaticsBMC Bioinformatics Y1 - 2007 A1 - Schatz, Michael C. A1 - Trapnell, Cole A1 - Delcher, Arthur L. A1 - Varshney, Amitabh VL - 8 SN - 1471-2105 ER - TY - JOUR T1 - MetaProm: a neural network based meta-predictor for alternative human promoter prediction JF - BMC genomicsBMC Genomics Y1 - 2007 A1 - Wang, J. A1 - Ungar, L. H. A1 - Tseng, H. A1 - Sridhar Hannenhalli PB - BioMed Central Ltd VL - 8 ER - TY - BOOK T1 - Methods in Molecular BiologyComparative GenomicsAnalyzing Patterns of Microbial Evolution Using the Mauve Genome Alignment System Y1 - 2007 A1 - Darling, Aaron E A1 - Todd Treangen A1 - Messeguer, Xavier A1 - Perna, Nicole T ED - Walker, John M. ED - Bergman, Nicholas H. PB - Humana Press CY - Totowa, NJ VL - 396 SN - 978-1-934115-37-4 UR - http://www.springerlink.com/index/10.1007/978-1-59745-515-2http://www.springerlink.com/index/pdf/10.1007/978-1-59745-515-2http://link.springer.com/10.1007/978-1-59745-515-2_10http://www.springerlink.com/index/pdf/10.1007/978-1-59745-515-2_10 M3 - 10.1007/978-1-59745-515-210.1007/978-1-59745-515-2_10 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 - 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 - 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 - JOUR T1 - Metagenomic Analysis of the Human Distal Gut Microbiome JF - ScienceScienceScienceScience Y1 - 2006 A1 - Gill, Steven R. A1 - M. Pop A1 - DeBoy, Robert T. A1 - Eckburg, Paul B. A1 - Turnbaugh, Peter J. A1 - Samuel, Buck S. A1 - Gordon, Jeffrey I. A1 - Relman, David A. A1 - Fraser-Liggett, Claire M. A1 - Nelson, Karen E. AB - The human intestinal microbiota is composed of 1013 to 1014 microorganisms whose collective genome (“microbiome”) contains at least 100 times as many genes as our own genome. We analyzed ∼78 million base pairs of unique DNA sequence and 2062 polymerase chain reaction–amplified 16S ribosomal DNA sequences obtained from the fecal DNAs of two healthy adults. Using metabolic function analyses of identified genes, we compared our human genome with the average content of previously sequenced microbial genomes. Our microbiome has significantly enriched metabolism of glycans, amino acids, and xenobiotics; methanogenesis; and 2-methyl-d-erythritol 4-phosphate pathway–mediated biosynthesis of vitamins and isoprenoids. Thus, humans are superorganisms whose metabolism represents an amalgamation of microbial and human attributes. VL - 312 SN - 0036-8075, 1095-9203 ER - TY - JOUR T1 - M-GCAT: interactively and efficiently constructing large-scale multiple genome comparison frameworks in closely related species JF - BMC bioinformatics Y1 - 2006 A1 - Todd Treangen A1 - Messeguer, Xavier VL - 7 ER - TY - BOOK T1 - Procrastination Leads to Efficient Filtration for Local Multiple Alignment Y1 - 2006 A1 - Darling, Aaron E. A1 - Todd Treangen A1 - Zhang, Louxin A1 - Kuiken, Carla A1 - Messeguer, Xavier A1 - Perna, Nicole T. PB - Springer Berlin Heidelberg CY - Berlin, Heidelberg VL - 4175 SN - 978-3-540-39583-6 UR - http://www.springerlink.com/index/10.1007/11851561http://www.springerlink.com/index/pdf/10.1007/11851561http://link.springer.com/10.1007/11851561_12http://www.springerlink.com/index/pdf/10.1007/11851561_12 M3 - 10.1007/1185156110.1007/11851561_12 ER - TY - CONF T1 - Procrastination leads to efficient filtration for local multiple alignment T2 - International Workshop on Algorithms in Bioinformatics Y1 - 2006 A1 - Darling, Aaron E A1 - Todd Treangen A1 - Zhang, Louxin A1 - Kuiken, Carla A1 - Messeguer, Xavier A1 - Perna, Nicole T JA - International Workshop on Algorithms in Bioinformatics PB - Springer Berlin Heidelberg 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 - eGenomics: Cataloguing our Complete Genome Collection JF - Comparative and functional genomicsComparative and functional genomics Y1 - 2005 A1 - Field, Dawn A1 - Garrity, George A1 - Morrison, Norman A1 - J. Selengut A1 - Sterk, Peter A1 - Tatusova, Tatiana A1 - Thomson, Nick VL - 6 N1 - http://www.ncbi.nlm.nih.gov/pubmed/18629208?dopt=Abstract ER - TY - JOUR T1 - The genetic map and comparative analysis with the physical map of Trypanosoma brucei JF - Nucleic acids researchNucleic Acids Research Y1 - 2005 A1 - MacLeod, A. A1 - Tweedie, A. A1 - McLellan, S. A1 - Taylor, S. A1 - Hall, N. A1 - Berriman, M. A1 - Najib M. El‐Sayed A1 - Hope, M. A1 - Turner, C. M. R. A1 - Tait, A. VL - 33 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 sequence of Trypanosoma cruzi, etiologic agent of Chagas disease JF - ScienceScience Y1 - 2005 A1 - Najib M. El‐Sayed A1 - Myler, P. J. A1 - Bartholomeu, D. C. A1 - Nilsson, D. A1 - Aggarwal, G. A1 - Tran, A. N. A1 - Ghedin, E. A1 - Worthey, E. A. A1 - Delcher, A. L. A1 - Blandin, G. A1 - others, PB - American Association for the Advancement of Science VL - 309 ER - TY - JOUR T1 - Comparison of the genome of the oral pathogen Treponema denticola with other spirochete genomes JF - Proceedings of the National Academy of Sciences of the United States of AmericaProceedings of the National Academy of Sciences of the United States of America Y1 - 2004 A1 - Seshadri, Rekha A1 - Myers, Garry S. A. A1 - Tettelin, Hervé A1 - Eisen, Jonathan A. A1 - Heidelberg, John F. A1 - Dodson, Robert J. A1 - Davidsen, Tanja M. A1 - DeBoy, Robert T. A1 - Fouts, Derrick E. A1 - Haft, Dan H. A1 - J. Selengut A1 - Ren, Qinghu A1 - Brinkac, Lauren M. A1 - Madupu, Ramana A1 - Kolonay, Jamie A1 - Durkin, A. Scott A1 - Daugherty, Sean C. A1 - Shetty, Jyoti A1 - Shvartsbeyn, Alla A1 - Gebregeorgis, Elizabeth A1 - Geer, Keita A1 - Tsegaye, Getahun A1 - Malek, Joel A1 - Ayodeji, Bola A1 - Shatsman, Sofiya A1 - McLeod, Michael P. A1 - Smajs, David A1 - Howell, Jerrilyn K. A1 - Pal, Sangita A1 - Amin, Anita A1 - Vashisth, Pankaj A1 - McNeill, Thomas Z. A1 - Xiang, Qin A1 - Sodergren, Erica A1 - Baca, Ernesto A1 - Weinstock, George M. A1 - Norris, Steven J. A1 - Fraser, Claire M. A1 - Paulsen, Ian T. KW - ATP-Binding Cassette Transporters KW - Bacterial Proteins KW - Base Sequence KW - Borrelia burgdorferi KW - Genes, Bacterial KW - Genome, Bacterial KW - Leptospira interrogans KW - Models, Genetic KW - Molecular Sequence Data KW - Mouth KW - Sequence Homology, Amino Acid KW - Treponema KW - Treponema pallidum AB - We present the complete 2,843,201-bp genome sequence of Treponema denticola (ATCC 35405) an oral spirochete associated with periodontal disease. Analysis of the T. denticola genome reveals factors mediating coaggregation, cell signaling, stress protection, and other competitive and cooperative measures, consistent with its pathogenic nature and lifestyle within the mixed-species environment of subgingival dental plaque. Comparisons with previously sequenced spirochete genomes revealed specific factors contributing to differences and similarities in spirochete physiology as well as pathogenic potential. The T. denticola genome is considerably larger in size than the genome of the related syphilis-causing spirochete Treponema pallidum. The differences in gene content appear to be attributable to a combination of three phenomena: genome reduction, lineage-specific expansions, and horizontal gene transfer. Genes lost due to reductive evolution appear to be largely involved in metabolism and transport, whereas some of the genes that have arisen due to lineage-specific expansions are implicated in various pathogenic interactions, and genes acquired via horizontal gene transfer are largely phage-related or of unknown function. VL - 101 N1 - http://www.ncbi.nlm.nih.gov/pubmed/15064399?dopt=Abstract ER - TY - JOUR T1 - The genome sequence of the anaerobic, sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough JF - Nature biotechnologyNature biotechnology Y1 - 2004 A1 - Heidelberg, John F. A1 - Seshadri, Rekha A1 - Haveman, Shelley A. A1 - Hemme, Christopher L. A1 - Paulsen, Ian T. A1 - Kolonay, James F. A1 - Eisen, Jonathan A. A1 - Ward, Naomi A1 - Methe, Barbara A1 - Brinkac, Lauren M. 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 - Fouts, Derrick A1 - Haft, Daniel H. A1 - J. Selengut A1 - Peterson, Jeremy D. A1 - Davidsen, Tanja M. A1 - Zafar, Nikhat A1 - Zhou, Liwei A1 - Radune, Diana A1 - Dimitrov, George A1 - Hance, Mark A1 - Tran, Kevin A1 - Khouri, Hoda A1 - Gill, John A1 - Utterback, Terry R. A1 - Feldblyum, Tamara V. A1 - Wall, Judy D. A1 - Voordouw, Gerrit A1 - Fraser, Claire M. KW - Desulfovibrio vulgaris KW - Energy Metabolism KW - Genome, Bacterial KW - Molecular Sequence Data AB - Desulfovibrio vulgaris Hildenborough is a model organism for studying the energy metabolism of sulfate-reducing bacteria (SRB) and for understanding the economic impacts of SRB, including biocorrosion of metal infrastructure and bioremediation of toxic metal ions. The 3,570,858 base pair (bp) genome sequence reveals a network of novel c-type cytochromes, connecting multiple periplasmic hydrogenases and formate dehydrogenases, as a key feature of its energy metabolism. The relative arrangement of genes encoding enzymes for energy transduction, together with inferred cellular location of the enzymes, provides a basis for proposing an expansion to the 'hydrogen-cycling' model for increasing energy efficiency in this bacterium. Plasmid-encoded functions include modification of cell surface components, nitrogen fixation and a type-III protein secretion system. This genome sequence represents a substantial step toward the elucidation of pathways for reduction (and bioremediation) of pollutants such as uranium and chromium and offers a new starting point for defining this organism's complex anaerobic respiration. VL - 22 N1 - http://www.ncbi.nlm.nih.gov/pubmed/15077118?dopt=Abstract ER - TY - BOOK T1 - Lecture Notes in Computer ScienceComputer Vision - ECCV 2004An MCMC-Based Particle Filter for Tracking Multiple Interacting Targets Y1 - 2004 A1 - Khan, Zia A1 - Balch, Tucker A1 - Dellaert, Frank ED - Kanade, Takeo ED - Kittler, Josef ED - Kleinberg, Jon M. ED - Mattern, Friedemann ED - Mitchell, John C. ED - Nierstrasz, Oscar ED - Pandu Rangan, C. ED - Steffen, Bernhard ED - Sudan, Madhu ED - Terzopoulos, Demetri ED - Tygar, Dough ED - Vardi, Moshe Y. ED - Weikum, Gerhard ED - Pajdla, ás ED - Matas, ří PB - Springer Berlin Heidelberg CY - Berlin, Heidelberg VL - 3024 SN - 978-3-540-21981-1 UR - http://www.springerlink.com/index/10.1007/b97873http://www.springerlink.com/index/pdf/10.1007/b97873http://link.springer.com/10.1007/978-3-540-24673-2_23http://www.springerlink.com/index/pdf/10.1007/978-3-540-24673-2_23 M3 - 10.1007/b9787310.1007/978-3-540-24673-2_23 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 - JOUR T1 - Structural flexibility in the Burkholderia mallei genome JF - Proceedings of the National Academy of Sciences of the United States of AmericaProceedings of the National Academy of Sciences of the United States of America Y1 - 2004 A1 - Nierman, William C. A1 - DeShazer, David A1 - Kim, H. Stanley A1 - Tettelin, Hervé A1 - Nelson, Karen E. A1 - Feldblyum, Tamara A1 - Ulrich, Ricky L. A1 - Ronning, Catherine M. A1 - Brinkac, Lauren M. A1 - Daugherty, Sean C. A1 - Davidsen, Tanja D. A1 - DeBoy, Robert T. A1 - Dimitrov, George A1 - Dodson, Robert J. A1 - Durkin, A. Scott A1 - Gwinn, Michelle L. A1 - Haft, Daniel H. A1 - Khouri, Hoda A1 - Kolonay, James F. A1 - Madupu, Ramana A1 - Mohammoud, Yasmin A1 - Nelson, William C. A1 - Radune, Diana A1 - Romero, Claudia M. A1 - Sarria, Saul A1 - J. Selengut A1 - Shamblin, Christine A1 - Sullivan, Steven A. A1 - White, Owen A1 - Yu, Yan A1 - Zafar, Nikhat A1 - Zhou, Liwei A1 - Fraser, Claire M. KW - Animals KW - Base Composition KW - Base Sequence KW - Burkholderia mallei KW - Chromosomes, Bacterial KW - Cricetinae KW - Genome, Bacterial KW - Glanders KW - Liver KW - Mesocricetus KW - Molecular Sequence Data KW - Multigene Family KW - Oligonucleotide Array Sequence Analysis KW - Open Reading Frames KW - virulence AB - The complete genome sequence of Burkholderia mallei ATCC 23344 provides insight into this highly infectious bacterium's pathogenicity and evolutionary history. B. mallei, the etiologic agent of glanders, has come under renewed scientific investigation as a result of recent concerns about its past and potential future use as a biological weapon. Genome analysis identified a number of putative virulence factors whose function was supported by comparative genome hybridization and expression profiling of the bacterium in hamster liver in vivo. The genome contains numerous insertion sequence elements that have mediated extensive deletions and rearrangements of the genome relative to Burkholderia pseudomallei. The genome also contains a vast number (>12,000) of simple sequence repeats. Variation in simple sequence repeats in key genes can provide a mechanism for generating antigenic variation that may account for the mammalian host's inability to mount a durable adaptive immune response to a B. mallei infection. VL - 101 N1 - http://www.ncbi.nlm.nih.gov/pubmed/15377793?dopt=Abstract ER - TY - JOUR T1 - 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 - Whole genome comparisons of serotype 4b and 1/2a strains of the food-borne pathogen Listeria monocytogenes reveal new insights into the core genome components of this species JF - Nucleic acids researchNucleic Acids Research Y1 - 2004 A1 - Nelson, Karen E. A1 - Fouts, Derrick E. A1 - Mongodin, Emmanuel F. A1 - Ravel, Jacques A1 - DeBoy, Robert T. A1 - Kolonay, James F. A1 - Rasko, David A. A1 - Angiuoli, Samuel V. A1 - Gill, Steven R. A1 - Paulsen, Ian T. A1 - Peterson, Jeremy A1 - White, Owen A1 - Nelson, William C. A1 - Nierman, William A1 - Beanan, Maureen J. A1 - Brinkac, Lauren M. A1 - Daugherty, Sean C. A1 - Dodson, Robert J. A1 - Durkin, A. Scott A1 - Madupu, Ramana A1 - Haft, Daniel H. A1 - J. Selengut A1 - Van Aken, Susan A1 - Khouri, Hoda A1 - Fedorova, Nadia A1 - Forberger, Heather A1 - Tran, Bao A1 - Kathariou, Sophia A1 - Wonderling, Laura D. A1 - Uhlich, Gaylen A. A1 - Bayles, Darrell O. A1 - Luchansky, John B. A1 - Fraser, Claire M. KW - Base Composition KW - Chromosomes, Bacterial KW - DNA Transposable Elements KW - Food Microbiology KW - Genes, Bacterial KW - Genome, Bacterial KW - Genomics KW - Listeria monocytogenes KW - Meat KW - Open Reading Frames KW - Physical Chromosome Mapping KW - Polymorphism, Single Nucleotide KW - Prophages KW - Serotyping KW - Species Specificity KW - Synteny KW - virulence AB - The genomes of three strains of Listeria monocytogenes that have been associated with food-borne illness in the USA were subjected to whole genome comparative analysis. A total of 51, 97 and 69 strain-specific genes were identified in L.monocytogenes strains F2365 (serotype 4b, cheese isolate), F6854 (serotype 1/2a, frankfurter isolate) and H7858 (serotype 4b, meat isolate), respectively. Eighty-three genes were restricted to serotype 1/2a and 51 to serotype 4b strains. These strain- and serotype-specific genes probably contribute to observed differences in pathogenicity, and the ability of the organisms to survive and grow in their respective environmental niches. The serotype 1/2a-specific genes include an operon that encodes the rhamnose biosynthetic pathway that is associated with teichoic acid biosynthesis, as well as operons for five glycosyl transferases and an adenine-specific DNA methyltransferase. A total of 8603 and 105 050 high quality single nucleotide polymorphisms (SNPs) were found on the draft genome sequences of strain H7858 and strain F6854, respectively, when compared with strain F2365. Whole genome comparative analyses revealed that the L.monocytogenes genomes are essentially syntenic, with the majority of genomic differences consisting of phage insertions, transposable elements and SNPs. VL - 32 N1 - http://www.ncbi.nlm.nih.gov/pubmed/15115801?dopt=Abstract ER - TY - JOUR T1 - 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 - 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 - 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 - Genome of Geobacter sulfurreducens: metal reduction in subsurface environments JF - Science (New York, N.Y.)Science (New York, N.Y.) Y1 - 2003 A1 - Methé, B. A. A1 - Nelson, K. E. A1 - Eisen, J. A. A1 - Paulsen, I. T. A1 - Nelson, W. A1 - Heidelberg, J. F. A1 - Wu, D. A1 - Wu, M. A1 - Ward, N. A1 - Beanan, M. J. A1 - Dodson, R. J. A1 - Madupu, R. A1 - Brinkac, L. M. A1 - Daugherty, S. C. A1 - DeBoy, R. T. A1 - Durkin, A. S. A1 - Gwinn, M. A1 - Kolonay, J. F. A1 - Sullivan, S. A. A1 - Haft, D. H. A1 - J. Selengut A1 - Davidsen, T. M. A1 - Zafar, N. A1 - White, O. A1 - Tran, B. A1 - Romero, C. A1 - Forberger, H. A. A1 - Weidman, J. A1 - Khouri, H. A1 - Feldblyum, T. V. A1 - Utterback, T. R. A1 - Van Aken, S. E. A1 - Lovley, D. R. A1 - Fraser, C. M. KW - Acetates KW - Acetyl Coenzyme A KW - Aerobiosis KW - Anaerobiosis KW - Bacterial Proteins KW - Carbon KW - Chemotaxis KW - Chromosomes, Bacterial KW - Cytochromes c KW - Electron Transport KW - Energy Metabolism KW - Genes, Bacterial KW - Genes, Regulator KW - Genome, Bacterial KW - Geobacter KW - Hydrogen KW - Metals KW - Movement KW - Open Reading Frames KW - Oxidation-Reduction KW - Phylogeny AB - The complete genome sequence of Geobacter sulfurreducens, a delta-proteobacterium, reveals unsuspected capabilities, including evidence of aerobic metabolism, one-carbon and complex carbon metabolism, motility, and chemotactic behavior. These characteristics, coupled with the possession of many two-component sensors and many c-type cytochromes, reveal an ability to create alternative, redundant, electron transport networks and offer insights into the process of metal ion reduction in subsurface environments. As well as playing roles in the global cycling of metals and carbon, this organism clearly has the potential for use in bioremediation of radioactive metals and in the generation of electricity. VL - 302 N1 - http://www.ncbi.nlm.nih.gov/pubmed/14671304?dopt=Abstract 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 - Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies. JF - Nucleic Acids Res Y1 - 2003 A1 - Haas, Brian J A1 - Delcher, Arthur L A1 - Mount, Stephen M A1 - Wortman, Jennifer R A1 - Smith, Roger K A1 - Hannick, Linda I A1 - Maiti, Rama A1 - Ronning, Catherine M A1 - Rusch, Douglas B A1 - Town, Christopher D A1 - Salzberg, Steven L A1 - White, Owen KW - algorithms KW - Alternative Splicing KW - Arabidopsis KW - DNA, Complementary KW - Expressed Sequence Tags KW - Genome, Plant KW - Introns KW - Plant Proteins KW - RNA, Plant KW - sequence alignment KW - software KW - Transcription, Genetic KW - Untranslated Regions AB -

The spliced alignment of expressed sequence data to genomic sequence has proven a key tool in the comprehensive annotation of genes in eukaryotic genomes. A novel algorithm was developed to assemble clusters of overlapping transcript alignments (ESTs and full-length cDNAs) into maximal alignment assemblies, thereby comprehensively incorporating all available transcript data and capturing subtle splicing variations. Complete and partial gene structures identified by this method were used to improve The Institute for Genomic Research Arabidopsis genome annotation (TIGR release v.4.0). The alignment assemblies permitted the automated modeling of several novel genes and >1000 alternative splicing variations as well as updates (including UTR annotations) to nearly half of the approximately 27 000 annotated protein coding genes. The algorithm of the Program to Assemble Spliced Alignments (PASA) tool is described, as well as the results of automated updates to Arabidopsis gene annotations.

VL - 31 CP - 19 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 - The sequence and analysis of Trypanosoma brucei chromosome II JF - Nucleic acids researchNucleic Acids Research Y1 - 2003 A1 - Najib M. El‐Sayed A1 - Ghedin, E. A1 - Song, J. A1 - MacLeod, A. A1 - Bringaud, F. A1 - Larkin, C. A1 - Wanless, D. A1 - Peterson, J. A1 - Hou, L. A1 - Taylor, S. A1 - others, VL - 31 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 - Sex-lethal splicing autoregulation in vivo: interactions between SEX-LETHAL, the U1 snRNP and U2AF underlie male exon skipping. JF - Development Y1 - 2003 A1 - Nagengast, Alexis A A1 - Stitzinger, Shane M A1 - Tseng, Chin-Hsiu A1 - Mount, Stephen M A1 - Salz, Helen K KW - Alternative Splicing KW - Amino Acid Sequence KW - Animals KW - Animals, Genetically Modified KW - Drosophila melanogaster KW - Drosophila Proteins KW - Exons KW - Female KW - Gene Expression Regulation, Developmental KW - Genes, Insect KW - Homeostasis KW - Male KW - Models, Genetic KW - Molecular Sequence Data KW - Nuclear Proteins KW - Point Mutation KW - Ribonucleoprotein, U1 Small Nuclear KW - Ribonucleoproteins KW - RNA Splicing KW - RNA-Binding Proteins KW - Sequence Homology, Amino Acid KW - Sex Differentiation AB -

Alternative splicing of the Sex-lethal pre-mRNA has long served as a model example of a regulated splicing event, yet the mechanism by which the female-specific SEX-LETHAL RNA-binding protein prevents inclusion of the translation-terminating male exon is not understood. Thus far, the only general splicing factor for which there is in vivo evidence for a regulatory role in the pathway leading to male-exon skipping is sans-fille (snf), a protein component of the spliceosomal U1 and U2 snRNPs. Its role, however, has remained enigmatic because of questions about whether SNF acts as part of an intact snRNP or a free protein. We provide evidence that SEX-LETHAL interacts with SANS-FILLE in the context of the U1 snRNP, through the characterization of a point mutation that interferes with both assembly into the U1 snRNP and complex formation with SEX-LETHAL. Moreover, we find that SEX-LETHAL associates with other integral U1 snRNP components, and we provide genetic evidence to support the biological relevance of these physical interactions. Similar genetic and biochemical approaches also link SEX-LETHAL with the heterodimeric splicing factor, U2AF. These studies point specifically to a mechanism by which SEX-LETHAL represses splicing by interacting with these key splicing factors at both ends of the regulated male exon. Moreover, because U2AF and the U1 snRNP are only associated transiently with the pre-mRNA during the course of spliceosome assembly, our studies are difficult to reconcile with the current model that proposes that the SEX-LETHAL blocks splicing at the second catalytic step, and instead argue that the SEX-LETHAL protein acts after splice site recognition, but before catalysis begins.

VL - 130 CP - 3 ER - TY - JOUR T1 - The transcription factor Eyes absent is a protein tyrosine phosphatase JF - NatureNature Y1 - 2003 A1 - Tootle, Tina L. A1 - Silver, Serena J. A1 - Davies, Erin L. A1 - Newman, Victoria A1 - Latek, Robert R. A1 - Mills, Ishara A. A1 - J. Selengut A1 - Parlikar, Beth E. W. A1 - Rebay, Ilaria KW - Amino Acid Motifs KW - Amino Acid Sequence KW - Animals KW - Antibodies, Phospho-Specific KW - Drosophila melanogaster KW - Drosophila Proteins KW - Embryonic Induction KW - eye KW - Eye Proteins KW - Gene Expression Regulation KW - Kinetics KW - Mice KW - Models, Molecular KW - Molecular Sequence Data KW - Mutation KW - Phosphorylation KW - Protein Conformation KW - Protein Tyrosine Phosphatases KW - Substrate Specificity KW - Transcription Factors AB - Post-translational modifications provide sensitive and flexible mechanisms to dynamically modulate protein function in response to specific signalling inputs. In the case of transcription factors, changes in phosphorylation state can influence protein stability, conformation, subcellular localization, cofactor interactions, transactivation potential and transcriptional output. Here we show that the evolutionarily conserved transcription factor Eyes absent (Eya) belongs to the phosphatase subgroup of the haloacid dehalogenase (HAD) superfamily, and propose a function for it as a non-thiol-based protein tyrosine phosphatase. Experiments performed in cultured Drosophila cells and in vitro indicate that Eyes absent has intrinsic protein tyrosine phosphatase activity and can autocatalytically dephosphorylate itself. Confirming the biological significance of this function, mutations that disrupt the phosphatase active site severely compromise the ability of Eyes absent to promote eye specification and development in Drosophila. Given the functional importance of phosphorylation-dependent modulation of transcription factor activity, this evidence for a nuclear transcriptional coactivator with intrinsic phosphatase activity suggests an unanticipated method of fine-tuning transcriptional regulation. VL - 426 N1 - http://www.ncbi.nlm.nih.gov/pubmed/14628053?dopt=Abstract 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 - 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 - 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 - Trypanosoma cruzi: RNA structure and post-transcriptional control of tubulin gene expression JF - Experimental ParasitologyExperimental Parasitology Y1 - 2002 A1 - Bartholomeu, Daniella C. A1 - Silva, Rosiane A. A1 - Galvão, Lucia M. C. A1 - Najib M. El‐Sayed A1 - Donelson, John E. A1 - Teixeira, Santuza M. R. AB - Changes in tubulin expression are among the biochemical and morphological adaptations that occur during the life cycle of Trypanosomatids. To investigate the mechanism responsible for the differential accumulation of tubulin mRNAs in Trypanosoma cruzi, we determine the sequences of [alpha]- and [beta]-tubulin transcripts and analyzed their expression during the life cycle of the parasite. Two [beta]-tubulin mRNAs of 1.9 and 2.3 kb were found to differ mainly by an additional 369 nucleotides at the end of the 3' untranslated region (UTR). Although their transcription rates are similar in epimastigotes and amastigotes, [alpha]- and [beta]-tubulin transcripts are 3- to 6-fold more abundant in epimastigotes than in trypomastigotes and amastigotes. Accordingly, the half-lives of [alpha]- and [beta]-tubulin mRNAs are significantly higher in epimastigotes than in amastigotes. Transient transfection experiments indicated that positive regulatory elements occur in the 3' UTR plus downstream intergenic region of the [alpha]-tubulin gene and that both positive and negative elements occur in the equivalent regions of the [beta]-tubulin gene.Index Descriptions and Abbreviations: Kinetoplastida; Trypanosoma cruzi; tubulin; gene regulation; PCR, polymerase chain reaction; UTR, untranslated region; IR, intergenic region; SL, spliced leader; BAC, bacterial artificial chromosome. VL - 102 SN - 0014-4894 ER - TY - JOUR T1 - Trypanosoma cruzi: RNA structure and post-transcriptional control of tubulin gene expression. JF - Exp Parasitol Y1 - 2002 A1 - Bartholomeu, Daniella C A1 - Silva, Rosiane A A1 - Galvão, Lucia M C A1 - el-Sayed, Najib M A A1 - Donelson, John E A1 - Teixeira, Santuza M R KW - Animals KW - Base Sequence KW - Blotting, Northern KW - DNA, Complementary KW - DNA, Protozoan KW - Gene Expression Regulation KW - Half-Life KW - Life Cycle Stages KW - Molecular Sequence Data KW - RNA Processing, Post-Transcriptional KW - RNA, Messenger KW - RNA, Protozoan KW - Transcription, Genetic KW - Transfection KW - Trypanosoma cruzi KW - Tubulin AB -

Changes in tubulin expression are among the biochemical and morphological adaptations that occur during the life cycle of Trypanosomatids. To investigate the mechanism responsible for the differential accumulation of tubulin mRNAs in Trypanosoma cruzi, we determine the sequences of alpha- and beta-tubulin transcripts and analyzed their expression during the life cycle of the parasite. Two beta-tubulin mRNAs of 1.9 and 2.3 kb were found to differ mainly by an additional 369 nucleotides at the end of the 3' untranslated region (UTR). Although their transcription rates are similar in epimastigotes and amastigotes, alpha- and beta-tubulin transcripts are 3- to 6-fold more abundant in epimastigotes than in trypomastigotes and amastigotes. Accordingly, the half-lives of alpha- and beta-tubulin mRNAs are significantly higher in epimastigotes than in amastigotes. Transient transfection experiments indicated that positive regulatory elements occur in the 3' UTR plus downstream intergenic region of the alpha-tubulin gene and that both positive and negative elements occur in the equivalent regions of the beta-tubulin gene.

VL - 102 CP - 3-4 ER - TY - JOUR T1 - Analysis of a donor gene region for a variant surface glycoprotein and its expression site in African trypanosomes JF - Nucleic acids researchNucleic Acids Research Y1 - 2001 A1 - LaCount, D. J. A1 - Najib M. El‐Sayed A1 - Kaul, S. A1 - Wanless, D. A1 - Turner, C. M. R. A1 - Donelson, J. E. VL - 29 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 - 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 - Management of an enlarging aortic aneurysm in the presence of radiation induced retroperitoneal fibrosis. JF - J Cardiovasc Surg (Torino) Y1 - 1989 A1 - Todd, G J A1 - Schwartz, A A1 - Rapoport, F KW - Aged KW - Aorta, Abdominal KW - Aortic Aneurysm KW - Blood Vessel Prosthesis KW - HUMANS KW - Lymphoma KW - Male KW - Radiation Injuries KW - Retroperitoneal Fibrosis KW - Retroperitoneal Neoplasms KW - T-Lymphocytes AB -

Despite a thoracoabdominal retroperitoneal approach to an enlarging symptomatic infrarenal aortic aneurysm, proximal aortic dissection was hazardous due to radiation induced retroperitoneal fibrosis. Iliac artery ligation and thoracic aorta to iliac artery bypass has resulted in successful management during 14 months of follow-up.

VL - 30 CP - 2 ER -