@article {49839, title = {Sequestration of nematocysts by divergent cnidarian predators: mechanism, function, and evolution}, journal = {Invertebrate Biology}, volume = {136}, year = {2017}, month = {Jan-03-2017}, pages = {75 - 91}, doi = {10.1111/ivb.2017.136.issue-110.1111/ivb.12154}, url = {http://doi.wiley.com/10.1111/ivb.2017.136.issue-1http://doi.wiley.com/10.1111/ivb.12154http://onlinelibrary.wiley.com/wol1/doi/10.1111/ivb.12154/fullpdfhttps://api.wiley.com/onlinelibrary/tdm/v1/articles/10.1111\%2Fivb.12154}, author = {Goodheart, Jessica and Bely, Alexandra E.} } @book {49820, title = {Better Identification of Repeats in Metagenomic Scaffolding}, volume = {9838}, year = {2016}, pages = {174 - 184}, publisher = {Springer International Publishing}, organization = {Springer International Publishing}, address = {Cham}, isbn = {978-3-319-43680-7}, issn = {0302-9743}, doi = {10.1007/978-3-319-43681-410.1007/978-3-319-43681-4_14}, url = {http://link.springer.com/10.1007/978-3-319-43681-4http://link.springer.com/content/pdf/10.1007/978-3-319-43681-4}, author = {Ghurye, Jay and Pop, Mihai} } @article {49773, title = {Capturing the most wanted taxa through cross-sample correlations}, journal = {The ISME Journal}, year = {2016}, month = {Apr-03-2016}, issn = {1751-7362}, doi = {10.1038/ismej.2016.35}, url = {http://www.nature.com/doifinder/10.1038/ismej.2016.35}, author = {Almeida, Mathieu and Pop, Mihai and Le Chatelier, Emmanuelle and Prifti, Edi and Pons, Nicolas and Ghozlane, Amine and Ehrlich, S Dusko} } @article {49657, title = {Genome-scale study reveals reduced metabolic adaptability in patients with non-alcoholic fatty liver disease}, journal = {Nature Communications}, volume = {7}, year = {2016}, month = {Mar-02-2016}, pages = {8994}, doi = {10.1038/ncomms9994}, url = {http://www.nature.com/doifinder/10.1038/ncomms9994}, author = {{\"o}tyl{\"a}inen, Tuulia and Jerby, Livnat and {\"a}j{\"a}, Elina M. and Mattila, Ismo and {\"a}ntti, Sirkku and Auvinen, Petri and Gastaldelli, Amalia and {\"a}rvinen, Hannele and Ruppin, Eytan and {\v s}i{\v c}, Matej} } @article {49730, title = {Genome-scale study reveals reduced metabolic adaptability in patients with non-alcoholic fatty liver disease.}, journal = {Nat Commun}, volume = {7}, year = {2016}, month = {2016}, pages = {8994}, abstract = {

Non-alcoholic fatty liver disease (NAFLD) is a major risk factor leading to chronic liver disease and type 2 diabetes. Here we chart liver metabolic activity and functionality in NAFLD by integrating global transcriptomic data, from human liver biopsies, and metabolic flux data, measured across the human splanchnic vascular bed, within a genome-scale model of human metabolism. We show that an increased amount of liver fat induces mitochondrial metabolism, lipolysis, glyceroneogenesis and a switch from lactate to glycerol as substrate for gluconeogenesis, indicating an intricate balance of exacerbated opposite metabolic processes in glycemic regulation. These changes were associated with reduced metabolic adaptability on a network level in the sense that liver fat accumulation puts increasing demands on the liver to adaptively regulate metabolic responses to maintain basic liver functions. We propose that failure to meet excessive metabolic challenges coupled with reduced metabolic adaptability may lead to a vicious pathogenic cycle leading to the co-morbidities of NAFLD.

}, issn = {2041-1723}, doi = {10.1038/ncomms9994}, author = {Hy{\"o}tyl{\"a}inen, Tuulia and Jerby, Livnat and Pet{\"a}j{\"a}, Elina M and Mattila, Ismo and J{\"a}ntti, Sirkku and Auvinen, Petri and Gastaldelli, Amalia and Yki-J{\"a}rvinen, Hannele and Ruppin, Eytan and Ore{\v s}i{\v c}, Matej} } @article {49840, title = {Identification guide to the heterobranch sea slugs (Mollusca: Gastropoda) from Bocas del Toro, Panama}, journal = {Marine Biodiversity Records}, volume = {96737453830254034557880541418411912544728739317415779780725696418782226404216145163412560451520488424050829677}, year = {2016}, month = {Jan-12-2016}, doi = {10.1186/s41200-016-0048-z}, url = {http://mbr.biomedcentral.com/articles/10.1186/s41200-016-0048-zhttp://link.springer.com/content/pdf/10.1186/s41200-016-0048-z}, author = {Goodheart, Jessica and Ellingson, Ryan A. and Vital, Xochitl G. and {\~a}o Filho, Hilton C. and McCarthy, Jennifer B. and Medrano, Sabrina M. and Bhave, Vishal J. and {\'\i}a-M{\'e}ndez, Kimberly and {\'e}nez, Lina M. and {\'o}pez, Gina and Hoover, Craig A. and Awbrey, Jaymes D. and De Jesus, Jessika M. and Gowacki, William and Krug, Patrick J. and {\'e}s, {\'A}ngel} } @article {49821, title = {Longitudinal analysis of the lung microbiota of cynomolgous macaques during long-term SHIV infection}, journal = {Microbiome}, volume = {4320384718719152130282021211818418719223326578105723}, year = {2016}, month = {Jan-12-2016}, doi = {10.1186/s40168-016-0183-0}, url = {http://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-016-0183-0http://link.springer.com/content/pdf/10.1186/s40168-016-0183-0}, author = {Morris, Alison and Paulson, Joseph N. and Talukder, Hisham and Tipton, Laura and Kling, Heather and Cui, Lijia and Fitch, Adam and Pop, Mihai and Norris, Karen A. and Ghedin, Elodie} } @article {49823, title = {Metagenomic Assembly: Overview, Challenges and Applications}, journal = {Yale J Biol Med}, volume = {89}, year = {2016}, chapter = {353}, url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5045144/}, author = {Jay S. Ghurye and Victoria Cepeda-Espinoza and Mihai Pop} } @article {49818, title = {A pathway-centric view of spatial proximity in the 3D nucleome across cell lines}, journal = {Scientific Reports}, volume = {6}, year = {2016}, month = {Mar-12-2017}, pages = {39279}, doi = {10.1038/srep39279}, url = {http://www.nature.com/articles/srep39279}, author = {Karathia, Hiren and Kingsford, Carl and Girvan, Michelle and Hannenhalli, Sridhar} } @article {49822, title = {Scaffolding of long read assemblies using long range contact information}, year = {2016}, doi = {10.1101/083964}, url = {http://biorxiv.org/lookup/doi/10.1101/083964}, author = {Ghurye, Jay and Pop, Mihai and Koren, Sergey and Chin, Chen-Shan} } @article {49729, title = {Systems-Wide Prediction of Enzyme Promiscuity Reveals a New Underground Alternative Route for Pyridoxal 5{\textquoteright}-Phosphate Production in E. coli.}, journal = {PLoS Comput Biol}, volume = {12}, year = {2016}, month = {2016 Jan}, pages = {e1004705}, abstract = {

Recent insights suggest that non-specific and/or promiscuous enzymes are common and active across life. Understanding the role of such enzymes is an important open question in biology. Here we develop a genome-wide method, PROPER, that uses a permissive PSI-BLAST approach to predict promiscuous activities of metabolic genes. Enzyme promiscuity is typically studied experimentally using multicopy suppression, in which over-expression of a promiscuous {\textquoteright}replacer{\textquoteright} gene rescues lethality caused by inactivation of a {\textquoteright}target{\textquoteright} gene. We use PROPER to predict multicopy suppression in Escherichia coli, achieving highly significant overlap with published cases (hypergeometric p = 4.4e-13). We then validate three novel predicted target-replacer gene pairs in new multicopy suppression experiments. We next go beyond PROPER and develop a network-based approach, GEM-PROPER, that integrates PROPER with genome-scale metabolic modeling to predict promiscuous replacements via alternative metabolic pathways. GEM-PROPER predicts a new indirect replacer (thiG) for an essential enzyme (pdxB) in production of pyridoxal 5{\textquoteright}-phosphate (the active form of Vitamin B6), which we validate experimentally via multicopy suppression. We perform a structural analysis of thiG to determine its potential promiscuous active site, which we validate experimentally by inactivating the pertaining residues and showing a loss of replacer activity. Thus, this study is a successful example where a computational investigation leads to a network-based identification of an indirect promiscuous replacement of a key metabolic enzyme, which would have been extremely difficult to identify directly.

}, issn = {1553-7358}, doi = {10.1371/journal.pcbi.1004705}, author = {Oberhardt, Matthew A and Zarecki, Raphy and Reshef, Leah and Xia, Fangfang and Duran-Frigola, Miquel and Schreiber, Rachel and Henry, Christopher S and Ben-Tal, Nir and Dwyer, Daniel J and Gophna, Uri and Ruppin, Eytan} } @article {49799, title = {System-wide Clinical Proteomics of Breast Cancer Reveals Global Remodeling of Tissue Homeostasis.}, journal = {Cell Syst}, volume = {2}, year = {2016}, month = {2016 Mar 23}, pages = {172-84}, abstract = {

The genomic and transcriptomic landscapes of breast cancer have been extensively studied, but the proteomes of breast tumors are far less characterized. Here, we use high-resolution, high-accuracy mass spectrometry to perform a deep analysis of luminal-type breast cancer progression using clinical breast samples from primary tumors, matched lymph node metastases, and healthy breast epithelia. We used a super-SILAC mix to quantify over 10,000 proteins with high accuracy, enabling us to identify key proteins and pathways associated with tumorigenesis and metastatic spread. We found high expression levels of proteins associated with protein synthesis and degradation in cancer tissues, accompanied by metabolic alterations that may facilitate energy production in cancer cells within their natural environment. In addition, we found proteomic differences between breast cancer stages and minor differences between primary tumors and their matched lymph node metastases. These results highlight the potential of proteomic technology in the elucidation of clinically relevant cancer signatures.

}, issn = {2405-4712}, doi = {10.1016/j.cels.2016.02.001}, author = {Pozniak, Yair and Balint-Lahat, Nora and Rudolph, Jan Daniel and Lindskog, Cecilia and Katzir, Rotem and Avivi, Camilla and Pont{\'e}n, Fredrik and Ruppin, Eytan and Barshack, Iris and Geiger, Tamar} } @article {49817, title = {Therapeutic relevance of the protein phosphatase 2A in cancer}, journal = {Oncotarget.com}, year = {2016}, month = {Jul-09-2017}, doi = {10.18632/oncotarget.11399}, url = {https://www.oncotarget.com/article/11399}, author = {Cunningham, Chelsea E. and Li, Shuangshuang and Vizeacoumar, Frederick S. and Bhanumathy, Kalpana Kalyanasundaram and Lee, Joo Sang and Parameswaran, Sreejit and Furber, Levi and Abuhussein, Omar and Paul, James M. and McDonald, Megan and Templeton, Shaina D. and Shukla, Hersh and El Zawily, Amr M. and Boyd, Frederick and Alli, Nezeka and Mousseau, Darrell D. and Geyer, Ron and Bonham, Keith and Anderson, Deborah H. and Yan, Jiong and Yu-Lee, Li-Yuan and Weaver, Beth A. and Uppalapati, Maruti and Ruppin, Eytan and Sablina, Anna and Freywald, Andrew and Vizeacoumar, Franco J.} } @article {49570, title = {Evaluation of BLAST-based edge-weighting metrics used for homology inference with the Markov Clustering algorithm.}, volume = {16}, year = {2015}, month = {2015}, pages = {218}, abstract = {

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

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

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

}, issn = {1471-2105}, doi = {10.1186/s12859-015-0625-x}, author = {Gibbons, Theodore R and Mount, Stephen M and Cooper, Endymion D and Delwiche, Charles F} } @article {49579, title = {Fumarate induces redox-dependent senescence by modifying glutathione metabolism.}, volume = {6}, year = {2015}, month = {2015}, pages = {6001}, abstract = {

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

}, issn = {2041-1723}, doi = {10.1038/ncomms7001}, author = {Zheng, Liang and Cardaci, Simone and Jerby, Livnat and MacKenzie, Elaine D and Sciacovelli, Marco and Johnson, T Isaac and Gaude, Edoardo and King, Ayala and Leach, Joshua D G and Edrada-Ebel, RuAngelie and Hedley, Ann and Morrice, Nicholas A and Kalna, Gabriela and Blyth, Karen and Ruppin, Eytan and Frezza, Christian and Gottlieb, Eyal} } @article {49734, title = {Genomic variation. Impact of regulatory variation from RNA to protein.}, journal = {Science}, volume = {347}, year = {2015}, month = {2015 Feb 6}, pages = {664-7}, abstract = {

The phenotypic consequences of expression quantitative trait loci (eQTLs) are presumably due to their effects on protein expression levels. Yet the impact of genetic variation, including eQTLs, on protein levels remains poorly understood. To address this, we mapped genetic variants that are associated with eQTLs, ribosome occupancy (rQTLs), or protein abundance (pQTLs). We found that most QTLs are associated with transcript expression levels, with consequent effects on ribosome and protein levels. However, eQTLs tend to have significantly reduced effect sizes on protein levels, which suggests that their potential impact on downstream phenotypes is often attenuated or buffered. Additionally, we identified a class of cis QTLs that affect protein abundance with little or no effect on messenger RNA or ribosome levels, which suggests that they may arise from differences in posttranslational regulation.

}, keywords = {3{\textquoteright} Flanking Region, 5{\textquoteright} Flanking Region, Cell Line, Exons, Gene Expression Regulation, Genetic Variation, HUMANS, PHENOTYPE, Protein Biosynthesis, Quantitative Trait Loci, Ribosomes, RNA, Messenger, Transcription, Genetic}, issn = {1095-9203}, doi = {10.1126/science.1260793}, author = {Battle, Alexis and Khan, Zia and Wang, Sidney H and Mitrano, Amy and Ford, Michael J and Pritchard, Jonathan K and Gilad, Yoav} } @article {49659, title = {Glutamine synthetase activity fuels nucleotide biosynthesis and supports growth of glutamine-restricted glioblastoma}, journal = {Nature Cell Biology}, volume = {17}, year = {2015}, month = {Nov-11-2016}, pages = {1556 - 1568}, issn = {1465-7392}, doi = {10.1038/ncb3272}, url = {http://www.nature.com/doifinder/10.1038/ncb3272}, author = {Tardito, Saverio and Oudin, {\"\i}s and Ahmed, Shafiq U. and Fack, Fred and Keunen, Olivier and Zheng, Liang and Miletic, Hrvoje and Sakariassen, {\O}ystein and Weinstock, Adam and Wagner, Allon and Lindsay, Susan L. and Hock, Andreas K. and Barnett, Susan C. and Ruppin, Eytan and {\o}rkve, Svein Harald and Lund-Johansen, Morten and Chalmers, Anthony J. and Bjerkvig, Rolf and Niclou, Simone P. and Gottlieb, Eyal} } @article {49723, title = {Harnessing the landscape of microbial culture media to predict new organism-media pairings.}, journal = {Nat Commun}, volume = {6}, year = {2015}, month = {2015}, pages = {8493}, abstract = {

Culturing microorganisms is a critical step in understanding and utilizing microbial life. Here we map the landscape of existing culture media by extracting natural-language media recipes into a Known Media Database (KOMODO), which includes >18,000 strain-media combinations, >3300 media variants and compound concentrations (the entire collection of the Leibniz Institute DSMZ repository). Using KOMODO, we show that although media are usually tuned for individual strains using biologically common salts, trace metals and vitamins/cofactors are the most differentiating components between defined media of strains within a genus. We leverage KOMODO to predict new organism-media pairings using a transitivity property (74\% growth in new in vitro experiments) and a phylogeny-based collaborative filtering tool (83\% growth in new in vitro experiments and stronger growth on predicted well-scored versus poorly scored media). These resources are integrated into a web-based platform that predicts media given an organism{\textquoteright}s 16S rDNA sequence, facilitating future cultivation efforts.

}, issn = {2041-1723}, doi = {10.1038/ncomms9493}, author = {Oberhardt, Matthew A and Zarecki, Raphy and Gronow, Sabine and Lang, Elke and Klenk, Hans-Peter and Gophna, Uri and Ruppin, Eytan} } @article {49540, title = {Impact of regulatory variation from RNA to protein}, volume = {347}, year = {2015}, month = {Jun-02-2015}, pages = {664 - 667}, issn = {0036-8075}, doi = {10.1126/science.1260793}, url = {http://www.sciencemag.org/cgi/doi/10.1126/science.1260793}, author = {Battle, A. and Khan, Z. and Wang, S. H. and Mitrano, A. and Ford, M. J. and Pritchard, J. K. and Gilad, Y.} } @article {49573, title = {Modeling cancer metabolism on a genome scale}, volume = {11}, year = {2015}, month = {Jan-06-2015}, pages = {817 - 817}, doi = {10.15252/msb.20145307}, url = {http://msb.embopress.org/cgi/doi/10.15252/msb.20145307}, author = {Yizhak, K. and Chaneton, B. and Gottlieb, E. and Ruppin, E.} } @article {49606, title = {Orchestrating high-throughput genomic analysis with Bioconductor.}, volume = {12}, year = {2015}, month = {2015 Feb}, pages = {115-21}, abstract = {

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.

}, keywords = {Computational Biology, Gene Expression Profiling, Genomics, High-Throughput Screening Assays, Programming Languages, software, User-Computer Interface}, issn = {1548-7105}, doi = {10.1038/nmeth.3252}, author = {Huber, Wolfgang and Carey, Vincent J and Gentleman, Robert and Anders, Simon and Carlson, Marc and Carvalho, Benilton S and Bravo, H{\'e}ctor Corrada and Davis, Sean and Gatto, Laurent and Girke, Thomas and Gottardo, Raphael and Hahne, Florian and Hansen, Kasper D and Irizarry, Rafael A and Lawrence, Michael and Love, Michael I and MacDonald, James and Obenchain, Valerie and Ole{\'s}, Andrzej K and Pag{\`e}s, Herv{\'e} and Reyes, Alejandro and Shannon, Paul and Smyth, Gordon K and Tenenbaum, Dan and Waldron, Levi and Morgan, Martin} } @article {49577, title = {Proteomics-based metabolic modeling reveals that fatty acid oxidation (FAO) controls endothelial cell (EC) permeability.}, volume = {14}, year = {2015}, month = {2015 Mar}, pages = {621-34}, abstract = {

Endothelial cells (ECs) play a key role to maintain the functionality of blood vessels. Altered EC permeability causes severe impairment in vessel stability and is a hallmark of pathologies such as cancer and thrombosis. Integrating label-free quantitative proteomics data into genome-wide metabolic modeling, we built up a model that predicts the metabolic fluxes in ECs when cultured on a tridimensional matrix and organize into a vascular-like network. We discovered how fatty acid oxidation increases when ECs are assembled into a fully formed network that can be disrupted by inhibiting CPT1A, the fatty acid oxidation rate-limiting enzyme. Acute CPT1A inhibition reduces cellular ATP levels and oxygen consumption, which are restored by replenishing the tricarboxylic acid cycle. Remarkably, global phosphoproteomic changes measured upon acute CPT1A inhibition pinpointed altered calcium signaling. Indeed, CPT1A inhibition increases intracellular calcium oscillations. Finally, inhibiting CPT1A induces hyperpermeability in vitro and leakage of blood vessel in vivo, which were restored blocking calcium influx or replenishing the tricarboxylic acid cycle. Fatty acid oxidation emerges as central regulator of endothelial functions and blood vessel stability and druggable pathway to control pathological vascular permeability.

}, issn = {1535-9484}, doi = {10.1074/mcp.M114.045575}, author = {Patella, Francesca and Schug, Zachary T and Persi, Erez and Neilson, Lisa J and Erami, Zahra and Avanzato, Daniele and Maione, Federica and Hernandez-Fernaud, Juan R and Mackay, Gillian and Zheng, Liang and Reid, Steven and Frezza, Christian and Giraudo, Enrico and Fiorio Pla, Alessandra and Anderson, Kurt and Ruppin, Eytan and Gottlieb, Eyal and Zanivan, Sara} } @article {49620, title = {Relationships within Cladobranchia (Gastropoda: Nudibranchia) based on RNA-Seq data: an initial investigation}, journal = {Royal Society Open Science}, volume = {23547143619757560685451171766}, year = {2015}, month = {Nov-09-2016}, pages = {150196}, doi = {10.1098/rsos.150196}, url = {http://rsos.royalsocietypublishing.org/lookup/doi/10.1098/rsos.150196}, author = {Goodheart, Jessica and Bazinet, Adam L. and Collins, Allen G. and CUMMINGS, MICHAEL P.} } @article {49508, title = {Systematics and biogeography of Pleurobranchus Cuvier, 1804, sea slugs (Heterobranchia: Nudipleura: Pleurobranchidae)}, journal = {Zoological Journal of the Linnean Society}, year = {2015}, month = {Jan-03-2015}, pages = {n/a - n/a}, abstract = {Species of Pleurobranchus (Mollusca: Gastropoda: Heterobranchia: Nudipleura: Pleurobranchidae) are commonly found worldwide, but there is a substantial amount of confusion regarding the ranges and identification of individual species. Difficulties in phylogenetic reconstruction and identification of pleurobranchids using morphological traits has resulted in complex classification schemes, with several species having disjunct ranges across physical and biogeographical barriers (including the tropical Indo-Pacific, the eastern Pacific, and the Atlantic). A sizeable number of species of Pleurobranchus has been described; however, many of these species are morphologically and biogeographically similar to others, and probably constitute synonyms. This paper provides a phylogenetic framework of classification for Pleurobranchus based on the mitochondrial genes cytochrome c oxidase I (COI) and 16S rDNA and the nuclear gene histone 3 (H3) using Bayesian and maximum likelihood approaches. Molecular phylogenies obtained recovered most of the well-established species of Pleurobranchus and some morphological characters were found to have taxonomic value for delimiting species in this group. Automatic barcode gap discovery (ABGD) analyses substantiated the distinctiveness of units/species recovered in the phylogenetic analyses, with some exceptions. Morphological descriptions for the 14 species recovered in the molecular phylogeny and discussions on the biogeography and colour variation are included.}, doi = {10.1111/zoj.12237}, url = {http://doi.wiley.com/10.1111/zoj.12237}, author = {Goodheart, Jessica and Camacho-Garc{\'\i}a, Yolanda and Padula, Vinicius and Schr{\"o}dl, Michael and Cervera, Juan L. and Gosliner, Terrence M. and Vald{\'e}s, {\'A}ngel} } @article {38584, title = {CTCF binding site sequence differences are associated with unique regulatory and functional trends during embryonic stem cell differentiation}, journal = {Nucleic Acids ResNucleic Acids ResNucleic Acids Res}, volume = {42}, number = {2}, year = {2014}, note = {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{\textquoteright}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.}, month = {Jan}, pages = {774-89}, abstract = {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{\textquoteright}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.}, keywords = {*Gene Expression Regulation, *Regulatory Elements, Transcriptional, Animals, Binding Sites, Cell Differentiation/*genetics, Cells, Cultured, Embryonic Stem Cells/cytology/*metabolism, Mice, Nucleotide Motifs, Protein Binding, Repressor Proteins/*metabolism}, isbn = {1362-4962 (Electronic)
0305-1048 (Linking)}, author = {Plasschaert, R. N. and Vigneau, S. and Tempera, I. and Gupta, R. and Maksimoska, J. and Everett, L. and Davuluri, R. and Mamorstein, R. and Lieberman, P. M. and Schultz, D. and Sridhar Hannenhalli and Bartolomei, M. S.} } @article {49602, title = {Epiviz: interactive visual analytics for functional genomics data.}, volume = {11}, year = {2014}, month = {2014 Sep}, pages = {938-40}, abstract = {

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

}, keywords = {algorithms, Chromosome mapping, Data Mining, database management systems, Databases, Genetic, Genomics, Internet, software, User-Computer Interface}, issn = {1548-7105}, doi = {10.1038/nmeth.3038}, author = {Chelaru, Florin and Smith, Llewellyn and Goldstein, Naomi and Bravo, H{\'e}ctor Corrada} } @article {49585, title = {Glycan Degradation (GlyDeR) Analysis Predicts Mammalian Gut Microbiota Abundance and Host Diet-Specific Adaptations}, volume = {5}, year = {2014}, month = {May-08-2016}, pages = {e01526-14 - e01526-14}, doi = {10.1128/mBio.01526-14}, url = {http://mbio.asm.org/cgi/doi/10.1128/mBio.01526-14}, author = {Eilam, O. and Zarecki, R. and Oberhardt, M. and Ursell, L. K. and Kupiec, M. and Knight, R. and Gophna, U. and Ruppin, E.} } @article {49604, title = {Large hypomethylated blocks as a universal defining epigenetic alteration in human solid tumors.}, volume = {6}, year = {2014}, month = {2014}, pages = {61}, abstract = {

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.

}, issn = {1756-994X}, doi = {10.1186/s13073-014-0061-y}, author = {Timp, Winston and Bravo, H{\'e}ctor Corrada and McDonald, Oliver G and Goggins, Michael and Umbricht, Chris and Zeiger, Martha and Feinberg, Andrew P and Irizarry, Rafael A} } @article {49588, title = {Maximal Sum of Metabolic Exchange Fluxes Outperforms Biomass Yield as a Predictor of Growth Rate of Microorganisms}, volume = {9}, year = {2014}, month = {Mar-05-2016}, pages = {e98372}, doi = {10.1371/journal.pone.0098372}, url = {http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0098372}, author = {Zarecki, Raphy and Oberhardt, Matthew A. and Yizhak, Keren and Wagner, Allon and Shtifman Segal, Ella and Freilich, Shiri and Henry, Christopher S. and Gophna, Uri and Ruppin, Eytan}, editor = {Fong, Stephen S.} } @article {49583, title = {Network-level architecture and the evolutionary potential of underground metabolism}, volume = {111}, year = {2014}, month = {Dec-08-2014}, pages = {11762 - 11767}, issn = {0027-8424}, doi = {10.1073/pnas.1406102111}, url = {http://www.pnas.org/cgi/doi/10.1073/pnas.1406102111}, author = {Notebaart, R. A. and Szappanos, B. and Kintses, B. and Pal, F. and Gyorkei, A. and Bogos, B. and Lazar, V. and Spohn, R. and Bogos, B. and Wagner, A. and Ruppin, E. and Pal, C. and Papp, B.} } @article {49862, title = {A new rhesus macaque assembly and annotation for next-generation sequencing analyses}, journal = {Biology direct}, volume = {9}, year = {2014}, pages = {20}, author = {Zimin, Aleksey V and Cornish, Adam S and Maudhoo, Mnirnal D and Gibbs, Robert M and Zhang, Xiongfei and Pandey, Sanjit and Meehan, Daniel T and Wipfler, Kristin and Bosinger, Steven E and Johnson, Zachary P and Todd Treangen} } @article {49587, title = {A Novel Nutritional Predictor Links Microbial Fastidiousness with Lowered Ubiquity, Growth Rate, and Cooperativeness}, journal = {PLoS Computational Biology}, volume = {10}, year = {2014}, month = {May-07-2015}, pages = {e1003726}, doi = {10.1371/journal.pcbi.1003726}, url = {http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003726}, author = {Zarecki, Raphy and Oberhardt, Matthew A. and Reshef, Leah and Gophna, Uri and Ruppin, Eytan}, editor = {Maranas, Costas D.} } @article {49724, title = {Phenotype-based cell-specific metabolic modeling reveals metabolic liabilities of cancer.}, journal = {Elife}, volume = {3}, year = {2014}, month = {2014}, abstract = {

Utilizing molecular data to derive functional physiological models tailored for specific cancer cells can facilitate the use of individually tailored therapies. To this end we present an approach termed PRIME for generating cell-specific genome-scale metabolic models (GSMMs) based on molecular and phenotypic data. We build >280 models of normal and cancer cell-lines that successfully predict metabolic phenotypes in an individual manner. We utilize this set of cell-specific models to predict drug targets that selectively inhibit cancerous but not normal cell proliferation. The top predicted target, MLYCD, is experimentally validated and the metabolic effects of MLYCD depletion investigated. Furthermore, we tested cell-specific predicted responses to the inhibition of metabolic enzymes, and successfully inferred the prognosis of cancer patients based on their PRIME-derived individual GSMMs. These results lay a computational basis and a counterpart experimental proof of concept for future personalized metabolic modeling applications, enhancing the search for novel selective anticancer therapies.

}, keywords = {algorithms, Antineoplastic Agents, Biomarkers, Tumor, Carboxy-Lyases, Cell Line, Tumor, Cell Proliferation, Citric Acid Cycle, Fatty Acids, Gene Knockdown Techniques, Genome, Human, HUMANS, Lymphocytes, Models, Biological, Neoplasms, Oxidation-Reduction, PHENOTYPE, Precision Medicine}, issn = {2050-084X}, doi = {10.7554/eLife.03641}, author = {Yizhak, Keren and Gaude, Edoardo and Le D{\'e}v{\'e}dec, Sylvia and Waldman, Yedael Y and Stein, Gideon Y and van de Water, Bob and Frezza, Christian and Ruppin, Eytan} } @article {49726, title = {Predicting cancer-specific vulnerability via data-driven detection of synthetic lethality.}, journal = {Cell}, volume = {158}, year = {2014}, month = {2014 Aug 28}, pages = {1199-209}, abstract = {

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

}, keywords = {Breast Neoplasms, Cell Line, Tumor, Computational Biology, Data Mining, Genes, Tumor Suppressor, HUMANS, Neoplasms, Oncogenes, RNA, Small Interfering, workflow}, issn = {1097-4172}, doi = {10.1016/j.cell.2014.07.027}, author = {Jerby-Arnon, Livnat and Pfetzer, Nadja and Waldman, Yedael Y and McGarry, Lynn and James, Daniel and Shanks, Emma and Seashore-Ludlow, Brinton and Weinstock, Adam and Geiger, Tamar and Clemons, Paul A and Gottlieb, Eyal and Ruppin, Eytan} } @article {49737, title = {Stable isotope labeling of phosphoproteins for large-scale phosphorylation rate determination.}, journal = {Mol Cell Proteomics}, volume = {13}, year = {2014}, month = {2014 Apr}, pages = {1106-18}, abstract = {

Signals that control responses to stimuli and cellular function are transmitted through the dynamic phosphorylation of thousands of proteins by protein kinases. Many techniques have been developed to study phosphorylation dynamics, including several mass spectrometry (MS)-based methods. Over the past few decades, substantial developments have been made in MS techniques for the large-scale identification of proteins and their post-translational modifications. Nevertheless, all of the current MS-based techniques for quantifying protein phosphorylation dynamics rely on the measurement of changes in peptide abundance levels, and many methods suffer from low confidence in phosphopeptide identification due to poor fragmentation. Here we have optimized an approach for the stable isotope labeling of amino acids by phosphate using [γ-{\textonesuperior}$^{8}$O$_{4}$]ATP in nucleo to determine global site-specific phosphorylation rates. The advantages of this metabolic labeling technique are increased confidence in phosphorylated peptide identification, direct labeling of phosphorylation sites, measurement phosphorylation rates, and the identification of actively phosphorylated sites in a cell-like environment. In this study we calculated approximate rate constants for over 1,000 phosphorylation sites based on labeling progress curves. We measured a wide range of phosphorylation rate constants from 0.34 min$^{-}${\textonesuperior} to 0.001 min$^{-}${\textonesuperior}. Finally, we applied stable isotope labeling of amino acids by phosphate to identify sites that have different phosphorylation kinetics during G1/S and M phase. We found that most sites had very similar phosphorylation rates under both conditions; however, a small subset of sites on proteins involved in the mitotic spindle were more actively phosphorylated during M phase, whereas proteins involved in DNA replication and transcription were more actively phosphorylated during G1/S phase. The data have been deposited to the ProteomeXchange with the identifier PXD000680.

}, keywords = {cell cycle, HEK293 Cells, HeLa Cells, HUMANS, Isotope Labeling, Kinetics, Peptide Mapping, Phosphoproteins, Phosphorylation, proteomics, Tandem Mass Spectrometry}, issn = {1535-9484}, doi = {10.1074/mcp.O113.036145}, author = {Molden, Rosalynn C and Goya, Jonathan and Khan, Zia and Garcia, Benjamin A} } @article {38192, title = {De novo likelihood-based measures for comparing genome assemblies}, journal = {BMC research notes}, volume = {6}, year = {2013}, publisher = {BioMed Central Ltd}, author = {Ghodsi, Mohammadreza and Christopher M. Hill and Irina Astrovskaya and Lin, Henry and Sommer, Dan D. and Koren, Sergey and M. Pop} } @article {38306, title = {Genome sequencing of four strains of Rickettsia prowazekii, the causative agent of epidemic typhus, including one flying squirrel isolate}, journal = {Genome announcementsGenome announcements}, volume = {1}, year = {2013}, publisher = {American Society for Microbiology}, isbn = {2169-8287}, author = {Bishop-Lilly, Kimberly A. and Ge, Hong and Butani, Amy and Osborne, Brian and Verratti, Kathleen and Mokashi, Vishwesh and Nagarajan, Niranjan and M. Pop and Read, Timothy D. and Richards, Allen L.} } @article {49535, title = {Genomic analysis of sequence-dependent DNA curvature in Leishmania.}, volume = {8}, year = {2013}, month = {2013}, pages = {e63068}, abstract = {

Leishmania major is a flagellated protozoan parasite of medical importance. Like other members of the Trypanosomatidae family, it possesses unique mechanisms of gene expression such as constitutive polycistronic transcription of directional gene clusters, gene amplification, mRNA trans-splicing, and extensive editing of mitochondrial transcripts. The molecular signals underlying most of these processes remain under investigation. In order to investigate the role of DNA secondary structure signals in gene expression, we carried out a genome-wide in silico analysis of the intrinsic DNA curvature. The L. major genome revealed a lower frequency of high intrinsic curvature regions as well as inter- and intra- chromosomal distribution heterogeneity, when compared to prokaryotic and eukaryotic organisms. Using a novel method aimed at detecting region-integrated intrinsic curvature (RIIC), high DNA curvature was found to be associated with regions implicated in transcription initiation. Those include divergent strand-switch regions between directional gene clusters and regions linked to markers of active transcription initiation such as acetylated H3 histone, TRF4 and SNAP50. These findings suggest a role for DNA curvature in transcription initiation in Leishmania supporting the relevance of DNA secondary structures signals.

}, keywords = {Chromosome mapping, Comparative Genomic Hybridization, Computational Biology, DNA, Protozoan, Genome, Protozoan, Genomics, HUMANS, Leishmania, Nucleic Acid Conformation}, issn = {1932-6203}, doi = {10.1371/journal.pone.0063068}, author = {Smircich, Pablo and Forteza, Diego and El-Sayed, Najib M and Garat, Beatriz} } @article {38354, title = {Intrinsically disordered proteins and conformational noise: Implications in cancer}, journal = {Cell CycleCell Cycle}, volume = {12}, year = {2013}, note = {cc}, type = {10.4161/cc10.4161/cc.23178}, author = {Mahmoudabadi, Gita and Rajagopalan, Krithika and Getzenberg, Robert H. and Sridhar Hannenhalli and Rangarajan, Govindan and Kulkarni, Prakash} } @article {49738, title = {Primate transcript and protein expression levels evolve under compensatory selection pressures.}, journal = {Science}, volume = {342}, year = {2013}, month = {2013 Nov 29}, pages = {1100-4}, abstract = {

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

}, keywords = {Animals, Evolution, Molecular, Gene Expression Regulation, HUMANS, Macaca mulatta, Pan troglodytes, Protein Biosynthesis, RNA, Messenger, Selection, Genetic, Species Specificity, Transcription, Genetic}, issn = {1095-9203}, doi = {10.1126/science.1242379}, author = {Khan, Zia and Ford, Michael J and Cusanovich, Darren A and Mitrano, Amy and Pritchard, Jonathan K and Gilad, Yoav} } @article {49545, title = {Primate Transcript and Protein Expression Levels Evolve Under Compensatory Selection Pressures}, volume = {342}, year = {2013}, month = {May-11-2015}, pages = {1100 - 1104}, issn = {0036-8075}, doi = {10.1126/science.1242379}, url = {http://www.sciencemag.org/cgi/doi/10.1126/science.1242379}, author = {Khan, Z. and Ford, M. J. and Cusanovich, D. A. and Mitrano, A. and Pritchard, J. K. and Gilad, Y.} } @article {49506, title = {Re-evaluation of the Doriopsilla areolata Bergh, 1880 (Mollusca: Opisthobranchia) subspecies complex in the eastern Atlantic Ocean and its relationship to South African Doriopsilla miniata (Alder \& Hancock, 1864) based on molecular data}, journal = {Marine Biodiversity}, volume = {43}, year = {2013}, month = {Jan-06-2013}, pages = {113 - 120}, issn = {1867-1616}, doi = {10.1007/s12526-012-0136-1}, url = {http://link.springer.com/10.1007/s12526-012-0136-1http://link.springer.com/content/pdf/10.1007/s12526-012-0136-1}, author = {Goodheart, Jessica and Vald{\'e}s, {\'A}ngel} } @book {49516, title = {Sea Slug Systematics: Using Molecular and Morphological Tools to Infer Species Relationships in Opisthobracnchs}, year = {2013}, publisher = {California State Polytechnic University, Pomona}, organization = {California State Polytechnic University, Pomona}, url = {https://books.google.com/books?id=LZw3nwEACAAJ}, author = {Goodheart, Jessica and California State Polytechnic University, Pomona. Department of Biological Sciences} } @article {38509, title = {Somatic alterations contributing to metastasis of a castration-resistant prostate cancer}, journal = {Human mutationHuman mutation}, volume = {34}, year = {2013}, note = {http://www.ncbi.nlm.nih.gov/pubmed/23636849?dopt=Abstract}, type = {10.1002/humu.22346}, abstract = {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.}, author = {Nickerson, Michael L. and Im, Kate M. and Misner, Kevin J. and Tan, Wei and Lou, Hong and Gold, Bert and Wells, David W. and H{\'e}ctor Corrada Bravo and Fredrikson, Karin M. and Harkins, Timothy T. and Milos, Patrice and Zbar, Berton and Linehan, W. Marston and Yeager, Meredith and Andresson, Thorkell and Dean, Michael and Bova, G. Steven} } @conference {38585, title = {Topological properties of chromosome conformation graphs reflect spatial proximities within chromatin}, booktitle = {Proceedings of the International Conference on Bioinformatics, Computational Biology and Biomedical Informatics}, year = {2013}, pages = {306-315}, publisher = {ACM}, organization = {ACM}, address = {Wshington DC, USA}, author = {Hao Wang and Geet Duggal and Rob Patro and Michelle Girvan and Sridhar Hannenhalli and Carl Kingsford} } @article {38107, title = {AGORA: Assembly Guided by Optical Restriction Alignment}, journal = {BMC bioinformaticsBMC Bioinformatics}, volume = {13}, year = {2012}, publisher = {BioMed Central Ltd}, author = {Lin, H. C. and Goldstein, S. and L. Mendelowitz and Zhou, S. and Wetzel, J. and Schwartz, D. C. and M. Pop} } @article {49741, title = {BclAF1 restriction factor is neutralized by proteasomal degradation and microRNA repression during human cytomegalovirus infection.}, journal = {Proc Natl Acad Sci U S A}, volume = {109}, year = {2012}, month = {2012 Jun 12}, pages = {9575-80}, abstract = {

Cell proteins can restrict the replication of viruses. Here, we identify the cellular BclAF1 protein as a human cytomegalovirus restriction factor and describe two independent mechanisms the virus uses to decrease its steady-state levels. Immediately following infection, the viral pp71 and UL35 proteins, which are delivered to cells within virions, direct the proteasomal degradation of BclAF1. Although BclAF1 reaccumulates through the middle stages of infection, it is subsequently down-regulated at late times by miR-UL112-1, a virus-encoded microRNA. In the absence of BclAF1 neutralization, viral gene expression and replication are inhibited. These data identify two temporally and mechanistically distinct functions used by human cytomegalovirus to down-regulate a cellular antiviral protein.

}, keywords = {Cytomegalovirus, Cytomegalovirus Infections, Genes, Immediate-Early, HUMANS, Hydrolysis, MicroRNAs, Proteasome Endopeptidase Complex, Repressor Proteins, Tumor Suppressor Proteins}, issn = {1091-6490}, doi = {10.1073/pnas.1207496109}, author = {Lee, Song Hee and Kalejta, Robert F and Kerry, Julie and Semmes, Oliver John and O{\textquoteright}Connor, Christine M and Khan, Zia and Garcia, Benjamin A and Shenk, Thomas and Murphy, Eain} } @article {49551, title = {BclAF1 restriction factor is neutralized by proteasomal degradation and microRNA repression during human cytomegalovirus infection}, volume = {109}, year = {2012}, month = {Dec-06-2012}, pages = {9575 - 9580}, issn = {0027-8424}, doi = {10.1073/pnas.1207496109}, url = {http://www.pnas.org/cgi/doi/10.1073/pnas.1207496109}, author = {Lee, S. H. and Kalejta, R. F. and Kerry, J. and Semmes, O. J. and O{\textquoteright}Connor, C. M. and Khan, Z. and Garcia, B. A. and Shenk, T. and Murphy, E.} } @article {49550, title = {BclAF1 restriction factor is neutralized by proteasomal degradation and microRNA repression during human cytomegalovirus infection}, journal = {Proceedings of the National Academy of Sciences}, volume = {109}, year = {2012}, month = {Dec-06-2012}, pages = {9575 - 9580}, issn = {0027-8424}, doi = {10.1073/pnas.1207496109}, url = {http://www.pnas.org/cgi/doi/10.1073/pnas.1207496109}, author = {Lee, S. H. and Kalejta, R. F. and Kerry, J. and Semmes, O. J. and O{\textquoteright}Connor, C. M. and Khan, Z. and Garcia, B. A. and Shenk, T. and Murphy, E.} } @article {38133, title = {Bioinformatics for the Human Microbiome Project}, journal = {PLOS Computational BiologyPLOS Computational Biology}, volume = {8}, year = {2012}, publisher = {Public Library of Science}, isbn = {1553-7358}, author = {Gevers, Dirk and M. Pop and Schloss, Patrick D. and Huttenhower, Curtis} } @article {38195, title = {Deep Sequencing of the Oral Microbiome Reveals Signatures of Periodontal Disease}, journal = {PloS onePLoS One}, volume = {7}, year = {2012}, publisher = {Public Library of Science}, author = {Liu, B. and Faller, L. L. and Klitgord, N. and Mazumdar, V. and Ghodsi, M. and Sommer, D. D. and Gibbons, T. R. and Todd Treangen and Chang, Y. C. and Li, S. and others,} } @article {38264, title = {A framework for human microbiome research}, journal = {NatureNature}, volume = {486}, year = {2012}, author = {Meth{\'e}, B. A. and Nelson, K. E. and M. Pop and Creasy, H. H. and Giglio, M. G. and Huttenhower, C. and Gevers, D. and Petrosino, J. F. and Abubucker, S. and Badger, J. H. and others,} } @article {49740, title = {Global secretome analysis identifies novel mediators of bone metastasis.}, journal = {Cell Res}, volume = {22}, year = {2012}, month = {2012 Sep}, pages = {1339-55}, abstract = {

Bone is the one of the most common sites of distant metastasis of solid tumors. Secreted proteins are known to influence pathological interactions between metastatic cancer cells and the bone stroma. To comprehensively profile secreted proteins associated with bone metastasis, we used quantitative and non-quantitative mass spectrometry to globally analyze the secretomes of nine cell lines of varying bone metastatic ability from multiple species and cancer types. By comparing the secretomes of parental cells and their bone metastatic derivatives, we identified the secreted proteins that were uniquely associated with bone metastasis in these cell lines. We then incorporated bioinformatic analyses of large clinical metastasis datasets to obtain a list of candidate novel bone metastasis proteins of several functional classes that were strongly associated with both clinical and experimental bone metastasis. Functional validation of selected proteins indicated that in vivo bone metastasis can be promoted by high expression of (1) the salivary cystatins CST1, CST2, and CST4; (2) the plasminogen activators PLAT and PLAU; or (3) the collagen functionality proteins PLOD2 and COL6A1. Overall, our study has uncovered several new secreted mediators of bone metastasis and therefore demonstrated that secretome analysis is a powerful method for identification of novel biomarkers and candidate therapeutic targets.

}, keywords = {Animals, Biomarkers, Tumor, Bone Neoplasms, Cell Line, Tumor, Collagen Type VI, Computational Biology, HUMANS, Mass Spectrometry, Mice, Neoplasms, Plasminogen Activators, Procollagen-Lysine, 2-Oxoglutarate 5-Dioxygenase, Proteome, proteomics, Salivary Cystatins}, issn = {1748-7838}, doi = {10.1038/cr.2012.89}, author = {Blanco, Mario Andres and LeRoy, Gary and Khan, Zia and Ale{\v c}kovi{\'c}, Ma{\v s}a and Zee, Barry M and Garcia, Benjamin A and Kang, Yibin} } @article {49549, title = {Global secretome analysis identifies novel mediators of bone metastasis}, volume = {22}, year = {2012}, month = {Dec-09-2012}, pages = {1339 - 1355}, issn = {1001-0602}, doi = {10.1038/cr.2012.89}, url = {http://www.nature.com/doifinder/10.1038/cr.2012.89}, author = {Blanco, Mario Andres and LeRoy, Gary and Khan, Zia and {\v c}kovi{\'c}, {\v s}a and Zee, Barry M and Garcia, Benjamin A and Kang, Yibin} } @article {38352, title = {InterPro in 2011: new developments in the family and domain prediction database}, journal = {Nucleic acids researchNucleic Acids Research}, volume = {40}, year = {2012}, note = {http://www.ncbi.nlm.nih.gov/pubmed/22096229?dopt=Abstract}, type = {10.1093/nar/gkr948}, abstract = {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.}, keywords = {Databases, Protein, Protein Structure, Tertiary, Proteins, Sequence Analysis, Protein, software, Terminology as Topic, User-Computer Interface}, author = {Hunter, Sarah and Jones, Philip and Mitchell, Alex and Apweiler, Rolf and Attwood, Teresa K. and Bateman, Alex and Bernard, Thomas and Binns, David and Bork, Peer and Burge, Sarah and de Castro, Edouard and Coggill, Penny and Corbett, Matthew and Das, Ujjwal and Daugherty, Louise and Duquenne, Lauranne and Finn, Robert D. and Fraser, Matthew and Gough, Julian and Haft, Daniel and Hulo, Nicolas and Kahn, Daniel and Kelly, Elizabeth and Letunic, Ivica and Lonsdale, David and Lopez, Rodrigo and Madera, Martin and Maslen, John and McAnulla, Craig and McDowall, Jennifer and McMenamin, Conor and Mi, Huaiyu and Mutowo-Muellenet, Prudence and Mulder, Nicola and Natale, Darren and Orengo, Christine and Pesseat, Sebastien and Punta, Marco and Quinn, Antony F. and Rivoire, Catherine and Sangrador-Vegas, Amaia and J. Selengut and Sigrist, Christian J. A. and Scheremetjew, Maxim and Tate, John and Thimmajanarthanan, Manjulapramila and Thomas, Paul D. and Wu, Cathy H. and Yeats, Corin and Yong, Siew-Yit} } @article {49765, title = {InterPro in 2011: new developments in the family and domain prediction database.}, journal = {Nucleic Acids Res}, volume = {40}, year = {2012}, month = {2012 Jan}, pages = {D306-12}, abstract = {

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.

}, keywords = {Databases, Protein, Protein Structure, Tertiary, Proteins, Sequence Analysis, Protein, software, Terminology as Topic, User-Computer Interface}, issn = {1362-4962}, doi = {10.1093/nar/gkr948}, author = {Hunter, Sarah and Jones, Philip and Mitchell, Alex and Apweiler, Rolf and Attwood, Teresa K and Bateman, Alex and Bernard, Thomas and Binns, David and Bork, Peer and Burge, Sarah and de Castro, Edouard and Coggill, Penny and Corbett, Matthew and Das, Ujjwal and Daugherty, Louise and Duquenne, Lauranne and Finn, Robert D and Fraser, Matthew and Gough, Julian and Haft, Daniel and Hulo, Nicolas and Kahn, Daniel and Kelly, Elizabeth and Letunic, Ivica and Lonsdale, David and Lopez, Rodrigo and Madera, Martin and Maslen, John and McAnulla, Craig and McDowall, Jennifer and McMenamin, Conor and Mi, Huaiyu and Mutowo-Muellenet, Prudence and Mulder, Nicola and Natale, Darren and Orengo, Christine and Pesseat, Sebastien and Punta, Marco and Quinn, Antony F and Rivoire, Catherine and Sangrador-Vegas, Amaia and Selengut, Jeremy D and Sigrist, Christian J A and Scheremetjew, Maxim and Tate, John and Thimmajanarthanan, Manjulapramila and Thomas, Paul D and Wu, Cathy H and Yeats, Corin and Yong, Siew-Yit} } @article {49531, title = {Plasmodium falciparum merozoite surface protein 1 blocks the proinflammatory protein S100P.}, volume = {109}, year = {2012}, month = {2012 Apr 3}, pages = {5429-34}, abstract = {

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

}, keywords = {Amino Acid Sequence, Animals, Calcium-Binding Proteins, Chromatography, Gel, Electrophoresis, Polyacrylamide Gel, Enzyme-Linked Immunosorbent Assay, HUMANS, Merozoite Surface Protein 1, Microscopy, Confocal, Molecular Sequence Data, Neoplasm Proteins, Plasmodium falciparum, Sequence Homology, Amino Acid, Surface Plasmon Resonance}, issn = {1091-6490}, doi = {10.1073/pnas.1202689109}, author = {Waisberg, Michael and Cerqueira, Gustavo C and Yager, Stephanie B and Francischetti, Ivo M B and Lu, Jinghua and Gera, Nidhi and Srinivasan, Prakash and Miura, Kazutoyo and Rada, Balazs and Lukszo, Jan and Barbian, Kent D and Leto, Thomas L and Porcella, Stephen F and Narum, David L and El-Sayed, Najib and Miller, Louis H and Pierce, Susan K} } @article {38510, title = {Speeding Up Particle Trajectory Simulations under Moving Force Fields using GPUs}, journal = {Journal of Computing and Information Science in EngineeringJournal of Computing and Information Science in Engineering}, year = {2012}, abstract = {In this paper, we introduce a GPU-based framework forsimulating particle trajectories under both static and dynamic force fields. By exploiting the highly parallel nature of the problem and making efficient use of the available hardware, our simulator exhibits a significant speedup over its CPU- based analog. We apply our framework to a specific experi- mental simulation: the computation of trapping probabilities associated with micron-sized silica beads in optical trapping workbenches. When evaluating large numbers of trajectories (4096), we see approximately a 356 times speedup of the GPU-based simulator over its CPU-based counterpart.}, author = {Patro, R. and Dickerson, J. P. and Bista, S. and Gupta, S. K. and Varshney, Amitabh} } @article {38516, title = {Structure, function and diversity of the healthy human microbiome}, journal = {NatureNature}, volume = {486}, year = {2012}, author = {Huttenhower, C. and Gevers, D. and Knight, R. and Abubucker, S. and Badger, J. H. and Chinwalla, A. T. and Creasy, H. H. and Earl, A. M. and Fitzgerald, M. G. and Fulton, R. S. and others,} } @article {38102, title = {Accurate and fast estimation of taxonomic profiles from metagenomic shotgun sequences}, journal = {BMC GenomicsBMC Genomics}, volume = {12}, year = {2011}, type = {10.1186/1471-2164-12-S2-S4}, abstract = {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.}, isbn = {1471-2164}, author = {Liu, Bo and Gibbons, Theodore and Ghodsi, Mohammad and Todd Treangen and M. Pop} } @article {38118, title = {Aquatic Realm and Cholera}, journal = {Epidemiological and Molecular Aspects on CholeraEpidemiological and Molecular Aspects on Cholera}, year = {2011}, type = {10.1007/978-1-60327-265-0_18}, abstract = {Cholera is an ancient disease that can be severe and life threatening. It occurs predominantly in areas of the world where populations lack safe drinking water. Epidemics of cholera are linked with malnutrition, poor sanitation, and conditions resulting from natural disasters such as severe flooding. According to a report published by WHO in 2000 [1], cholera remains a major public health problem and is becoming increasingly important since the number of countries in which cholera is endemic continues to increase. Unfortunately, outbreaks of the disease continue into the twenty-first century with ominous portent in the wake of global climate change [1]. Yet cholera is a preventable disease if people have access to safe drinking water and are properly educated how to protect themselves from the risk of infection with vibrios. Cholera also is an easily treatable disease. Oral rehydration therapy, a solution containing glucose and appropriate salts, has proven to be effective for treatment of most cholera victims [2]. Nevertheless, each year, tens of thousands of people are victims of the disease, bringing this {\textquotedblleft}curse of humankind{\textquotedblright} to modern civilization. Present understanding of cholera is based on studies conducted over the past three decades and significant new information has been gained concerning environmental factors associated with this disease, especially how to detect the bacterium and where it lives in the natural environment, outside the human gut, and what triggers the annual outbreaks that occur with remarkable regularity. Environmental research on Vibrio cholerae and cholera has provided insights for prediction and prevention of the disease it causes, while the race for effective vaccines against cholera continues.}, author = {Huq, A. and Grim, C. J. and Rita R. Colwell} } @article {49556, title = {Direct targeting of Sec23a by miR-200s influences cancer cell secretome and promotes metastatic colonization}, volume = {17}, year = {2011}, month = {Jul-08-2011}, pages = {1101 - 1108}, issn = {1078-8956}, doi = {10.1038/nm.2401}, url = {http://www.nature.com/doifinder/10.1038/nm.2401}, author = {Korpal, Manav and Ell, Brian J and Buffa, Francesca M and Ibrahim, Toni and Blanco, Mario A and {\`a}-Terrassa, Toni and Mercatali, Laura and Khan, Zia and Goodarzi, Hani and Hua, Yuling and Wei, Yong and Hu, Guohong and Garcia, Benjamin A and Ragoussis, Jiannis and Amadori, Dino and Harris, Adrian L and Kang, Yibin} } @article {49746, title = {Direct targeting of Sec23a by miR-200s influences cancer cell secretome and promotes metastatic colonization.}, journal = {Nat Med}, volume = {17}, year = {2011}, month = {2011 Sep}, pages = {1101-8}, abstract = {

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

}, keywords = {Animals, Cadherins, Cell Line, Tumor, Female, Gene Expression Profiling, Gene Expression Regulation, Neoplastic, HUMANS, Mass Spectrometry, Mice, Mice, Inbred BALB C, Microarray Analysis, MicroRNAs, Neoplasm Metastasis, Statistics, Nonparametric, Vesicular Transport Proteins}, issn = {1546-170X}, doi = {10.1038/nm.2401}, author = {Korpal, Manav and Ell, Brian J and Buffa, Francesca M and Ibrahim, Toni and Blanco, Mario A and Celi{\`a}-Terrassa, Toni and Mercatali, Laura and Khan, Zia and Goodarzi, Hani and Hua, Yuling and Wei, Yong and Hu, Guohong and Garcia, Benjamin A and Ragoussis, Jiannis and Amadori, Dino and Harris, Adrian L and Kang, Yibin} } @article {38213, title = {DNACLUST: accurate and efficient clustering of phylogenetic marker genes}, journal = {BMC BioinformaticsBMC Bioinformatics}, volume = {12}, year = {2011}, type = {10.1186/1471-2105-12-271}, abstract = {Clustering is a fundamental operation in the analysis of biological sequence data. New DNA sequencing technologies have dramatically increased the rate at which we can generate data, resulting in datasets that cannot be efficiently analyzed by traditional clustering methods.}, isbn = {1471-2105}, author = {Ghodsi, Mohammadreza and Liu, Bo and M. Pop} } @article {49727, title = {Haem oxygenase is synthetically lethal with the tumour suppressor fumarate hydratase.}, journal = {Nature}, volume = {477}, year = {2011}, month = {2011 Sep 8}, pages = {225-8}, abstract = {

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.

}, keywords = {Animals, Bilirubin, Cell Line, Cells, Cultured, Citric Acid Cycle, Computer simulation, Fumarate Hydratase, Fumarates, Genes, Lethal, Genes, Tumor Suppressor, Glutamine, Heme, Heme Oxygenase (Decyclizing), Kidney Neoplasms, Leiomyomatosis, Mice, Mitochondria, Mutation, NAD, Neoplastic Syndromes, Hereditary, Skin Neoplasms, Uterine Neoplasms}, issn = {1476-4687}, doi = {10.1038/nature10363}, author = {Frezza, Christian and Zheng, Liang and Folger, Ori and Rajagopalan, Kartik N and MacKenzie, Elaine D and Jerby, Livnat and Micaroni, Massimo and Chaneton, Barbara and Adam, Julie and Hedley, Ann and Kalna, Gabriela and Tomlinson, Ian P M and Pollard, Patrick J and Watson, Dave G and Deberardinis, Ralph J and Shlomi, Tomer and Ruppin, Eytan and Gottlieb, Eyal} } @article {38350, title = {Interaction of Vibrio cholerae non-O1/non-O139 with Copepods, Cladocerans and Competing Bacteria in the Large Alkaline Lake Neusiedler See, Austria}, journal = {Microbial ecologyMicrobial ecology}, volume = {61}, year = {2011}, type = {10.1007/s00248-010-9764-9}, abstract = {Vibrio cholerae is a human pathogen and natural inhabitant of aquatic environments. Serogroups O1/O139 have been associated with epidemic cholera, while non-O1/non-O139 serogroups usually cause human disease other than classical cholera. V. cholerae non-O1/non-O139 from the Neusiedler See, a large Central European lake, have caused ear and wound infections, including one case of fatal septicaemia. Recent investigations demonstrated rapid planktonic growth of V. cholerae non-O1/non-O139 and correlation with zooplankton biomass. The aim of this study was to elucidate the interaction of autochthonous V. cholerae with two dominant crustacean zooplankton species in the lake and investigate the influence of the natural bacterial community on this interaction. An existing data set was evaluated for statistical relationships between zooplankton species and V. cholerae and co-culture experiments were performed in the laboratory. A new fluorescence in situ hybridisation protocol was applied for quantification of V. cholerae non-O1/non-O139 cells, which significantly reduced analysis time. The experiments clearly demonstrated a significant relationship of autochthonous V. cholerae non-O1/non-O139 with cladocerans by promoting growth of V. cholerae non-O1/non-O139 in the water and on the surfaces of the cladocerans. In contrast, copepods had a negative effect on the growth of V. cholerae non-O1/non-O139 via competing bacteria from their surfaces. Thus, beside other known factors, biofilm formation by V. cholerae on crustacean zooplankton appears to be zooplankton taxon specific and may be controlled by the natural bacterial community.}, author = {Kirschner, A. K. T. and Schauer, S. and Steinberger, B. and Wilhartitz, I. and Grim, C. J. and Huq, A. and Rita R. Colwell and Herzig, A. and Sommer, R.} } @article {38440, title = {Population Dynamics of Vibrio Cholerae and Cholera in the Bangladesh Sundarbans: Role of Zooplankton Diversity}, journal = {Applied and Environmental MicrobiologyAppl. Environ. Microbiol.Applied and Environmental MicrobiologyAppl. Environ. Microbiol.}, year = {2011}, type = {10.1128/AEM.01472-10}, abstract = {Vibrio cholerae, a bacterium autochthonous to the aquatic environment, is the causative agent of cholera, a severe watery, life-threatening diarrhoeal disease occurring predominantly in developing countries. V. cholerae, including both serogroup O1 and O139, i.e. found in association with crustacean zooplankton, mainly copepods, and notably in ponds, rivers, and estuarine systems globally. The incidence of cholera and occurrence of V. cholerae pathogenic strains with zooplankton were studied in two areas of Bangladesh: Bakerganj and Mathbaria. Chitinous zooplankton communities of several bodies of water were analyzed in order to understand the interaction of zooplankton population composition with the population dynamics of pathogenic V. cholerae and incidence of cholera. Two dominant zooplankton groups were found to be consistently associated with detection of V. cholerae and/or occurrence of cholera cases, namely rotifers, and cladocerans, in addition to copepods. Local differences indicate there are subtle ecological factors that can influence interactions between V. cholerae, its plankton hosts, and the incidence of cholera.}, isbn = {0099-2240, 1098-5336}, author = {De Magny, Guillaume Constantin and Mozumder, Pronob K. and Grim, Christopher J. and Hasan, Nur A. and Naser, M. Niamul and Alam, Munirul and Sack, Bradley and Huq, Anwar and Rita R. Colwell} } @article {49728, title = {Predicting selective drug targets in cancer through metabolic networks.}, journal = {Mol Syst Biol}, volume = {7}, year = {2011}, month = {2011}, pages = {501}, abstract = {

The interest in studying metabolic alterations in cancer and their potential role as novel targets for therapy has been rejuvenated in recent years. Here, we report the development of the first genome-scale network model of cancer metabolism, validated by correctly identifying genes essential for cellular proliferation in cancer cell lines. The model predicts 52 cytostatic drug targets, of which 40\% are targeted by known, approved or experimental anticancer drugs, and the rest are new. It further predicts combinations of synthetic lethal drug targets, whose synergy is validated using available drug efficacy and gene expression measurements across the NCI-60 cancer cell line collection. Finally, potential selective treatments for specific cancers that depend on cancer type-specific downregulation of gene expression and somatic mutations are compiled.

}, keywords = {Cell Line, Tumor, Cell Proliferation, Computational Biology, Cytostatic Agents, Down-Regulation, Drug Delivery Systems, Gene Expression Regulation, Neoplastic, HUMANS, Metabolic Networks and Pathways, Models, Biological, Neoplasms, RNA, Small Interfering}, issn = {1744-4292}, doi = {10.1038/msb.2011.35}, author = {Folger, Ori and Jerby, Livnat and Frezza, Christian and Gottlieb, Eyal and Ruppin, Eytan and Shlomi, Tomer} } @article {38473, title = {Role of Zooplankton Diversity in Vibrio Cholerae Population Dynamics and in the Incidence of Cholera in the Bangladesh Sundarbans}, journal = {Applied and Environmental MicrobiologyAppl. Environ. Microbiol.Applied and Environmental MicrobiologyAppl. Environ. Microbiol.}, volume = {77}, year = {2011}, type = {10.1128/AEM.01472-10}, abstract = {Vibrio cholerae, a bacterium autochthonous to the aquatic environment, is the causative agent of cholera, a severe watery, life-threatening diarrheal disease occurring predominantly in developing countries. V. cholerae, including both serogroups O1 and O139, is found in association with crustacean zooplankton, mainly copepods, and notably in ponds, rivers, and estuarine systems globally. The incidence of cholera and occurrence of pathogenic V. cholerae strains with zooplankton were studied in two areas of Bangladesh: Bakerganj and Mathbaria. Chitinous zooplankton communities of several bodies of water were analyzed in order to understand the interaction of the zooplankton population composition with the population dynamics of pathogenic V. cholerae and incidence of cholera. Two dominant zooplankton groups were found to be consistently associated with detection of V. cholerae and/or occurrence of cholera cases, namely, rotifers and cladocerans, in addition to copepods. Local differences indicate there are subtle ecological factors that can influence interactions between V. cholerae, its plankton hosts, and the incidence of cholera.}, isbn = {0099-2240, 1098-5336}, author = {De Magny, Guillaume Constantin and Mozumder, Pronob K. and Grim, Christopher J. and Hasan, Nur A. and Naser, M. Niamul and Alam, Munirul and Sack, R. Bradley and Huq, Anwar and Rita R. Colwell} } @article {38524, title = {Temperature regulation of virulence factors in the pathogen Vibrio coralliilyticus}, journal = {The ISME JournalThe ISME journal}, volume = {6}, year = {2011}, type = {10.1038/ismej.2011.154}, abstract = {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 {\textdegree}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 {\textdegree}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 {\textdegree}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.}, keywords = {ecophysiology, ecosystems, environmental biotechnology, geomicrobiology, ISME J, microbe interactions, microbial communities, microbial ecology, microbial engineering, microbial epidemiology, microbial genomics, microorganisms}, isbn = {1751-7362}, author = {Kimes, Nikole E. and Grim, Christopher J. and Johnson, Wesley R. and Hasan, Nur A. and Tall, Ben D. and Kothary, Mahendra H. and Kiss, Hajnalka and Munk, A. Christine and Tapia, Roxanne and Green, Lance and Detter, Chris and Bruce, David C. and Brettin, Thomas S. and Rita R. Colwell and Morris, Pamela J.} } @article {38570, title = {Warming Oceans, Phytoplankton, and River Discharge: Implications for Cholera Outbreaks}, journal = {The American Journal of Tropical Medicine and HygieneAm J Trop Med HygThe American Journal of Tropical Medicine and HygieneAm J Trop Med Hyg}, volume = {85}, year = {2011}, type = {10.4269/ajtmh.2011.11-0181}, abstract = {Phytoplankton abundance is inversely related to sea surface temperature (SST). However, a positive relationship is observed between SST and phytoplankton abundance in coastal waters of Bay of Bengal. This has led to an assertion that in a warming climate, rise in SST may increase phytoplankton blooms and, therefore, cholera outbreaks. Here, we explain why a positive SST-phytoplankton relationship exists in the Bay of Bengal and the implications of such a relationship on cholera dynamics. We found clear evidence of two independent physical drivers for phytoplankton abundance. The first one is the widely accepted phytoplankton blooming produced by the upwelling of cold, nutrient-rich deep ocean waters. The second, which explains the Bay of Bengal findings, is coastal phytoplankton blooming during high river discharges with terrestrial nutrients. Causal mechanisms should be understood when associating SST with phytoplankton and subsequent cholera outbreaks in regions where freshwater discharge are a predominant mechanism for phytoplankton production.}, isbn = {0002-9637}, author = {Jutla, Antarpreet S. and Akanda, Ali S. and Griffiths, Jeffrey K. and Rita R. Colwell and Islam, Shafiqul} } @article {38109, title = {Alignment and clustering of phylogenetic markers - implications for microbial diversity studies}, journal = {BMC BioinformaticsBMC Bioinformatics}, volume = {11}, year = {2010}, type = {10.1186/1471-2105-11-152}, abstract = {Molecular studies of microbial diversity have provided many insights into the bacterial communities inhabiting the human body and the environment. A common first step in such studies is a survey of conserved marker genes (primarily 16S rRNA) to characterize the taxonomic composition and diversity of these communities. To date, however, there exists significant variability in analysis methods employed in these studies.}, isbn = {1471-2105}, author = {White, James R. and Navlakha, Saket and Nagarajan, Niranjan and Ghodsi, Mohammad-Reza and Kingsford, Carl and M. Pop} } @article {49648, title = {The Alveolate Perkinsus marinus: biological insights from EST gene discovery.}, journal = {BMC Genomics}, volume = {11}, year = {2010}, month = {2010}, pages = {228}, abstract = {

BACKGROUND: Perkinsus marinus, a protozoan parasite of the eastern oyster Crassostrea virginica, has devastated natural and farmed oyster populations along the Atlantic and Gulf coasts of the United States. It is classified as a member of the Perkinsozoa, a recently established phylum considered close to the ancestor of ciliates, dinoflagellates, and apicomplexans, and a key taxon for understanding unique adaptations (e.g. parasitism) within the Alveolata. Despite intense parasite pressure, no disease-resistant oysters have been identified and no effective therapies have been developed to date.

RESULTS: To gain insight into the biological basis of the parasite{\textquoteright}s virulence and pathogenesis mechanisms, and to identify genes encoding potential targets for intervention, we generated>31,000 5{\textquoteright} expressed sequence tags (ESTs) derived from four trophozoite libraries generated from two P. marinus strains. Trimming and clustering of the sequence tags yielded 7,863 unique sequences, some of which carry a spliced leader. Similarity searches revealed that 55\% of these had hits in protein sequence databases, of which 1,729 had their best hit with proteins from the chromalveolates (E-value

CONCLUSIONS: Our transcriptome analysis of P. marinus, the first for any member of the Perkinsozoa, contributes new insight into its biology and taxonomic position. It provides a very informative, albeit preliminary, glimpse into the expression of genes encoding functionally relevant proteins as potential targets for chemotherapy, and evidence for the presence of a relict plastid. Further, although P. marinus sequences display significant similarity to those from both apicomplexans and dinoflagellates, the presence of trans-spliced transcripts confirms the previously established affinities with the latter. The EST analysis reported herein, together with the recently completed sequence of the P. marinus genome and the development of transfection methodology, should result in improved intervention strategies against dermo disease.

}, keywords = {Alveolata, Animals, Expressed Sequence Tags, Ostreidae, Phylogeny}, issn = {1471-2164}, doi = {10.1186/1471-2164-11-228}, author = {Joseph, Sandeep J and Fern{\'a}ndez-Robledo, Jos{\'e} A and Gardner, Malcolm J and El-Sayed, Najib M and Kuo, Chih-Horng and Schott, Eric J and Wang, Haiming and Kissinger, Jessica C and Vasta, Gerardo R} } @article {38160, title = {Comparative Genomics of Clinical and Environmental Vibrio Mimicus}, journal = {Proceedings of the National Academy of SciencesPNASProceedings of the National Academy of SciencesPNAS}, volume = {107}, year = {2010}, type = {10.1073/pnas.1013825107}, abstract = {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.}, isbn = {0027-8424, 1091-6490}, author = {Hasan, Nur A. and Grim, Christopher J. and Haley, Bradd J. and Jongsik, Chun and Alam, Munirul and Taviani, Elisa and Mozammel, Hoq and Munk, A. Christine and Rita R. Colwell} } @article {38178, title = {Conversion of viable but nonculturable Vibrio cholerae to the culturable state by co-culture with eukaryotic cells}, journal = {Microbiology and ImmunologyMicrobiology and Immunology}, volume = {54}, year = {2010}, type = {10.1111/j.1348-0421.2010.00245.x}, abstract = {VBNC Vibrio cholerae O139 VC-280 obtained by incubation in 1\% solution of artificial sea water IO at 4{\textdegree}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{\textdegree}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.}, keywords = {conversion to culturability, co-culture, eukaryotic cell, viable but nonculturable (VBNC) Vibrio cholerae}, isbn = {1348-0421}, author = {Senoh, Mitsutoshi and Ghosh-Banerjee, Jayeeta and Ramamurthy, Thandavarayan and Hamabata, Takashi and Kurakawa, Takashi and Takeda, Makoto and Rita R. Colwell and Nair, G. Balakrish and Takeda, Yoshifumi} } @article {38207, title = {Discovery of novel Vibrio cholerae VSP-II genomic islands using comparative genomic analysis}, journal = {FEMS Microbiology LettersFEMS Microbiology Letters}, volume = {308}, year = {2010}, type = {10.1111/j.1574-6968.2010.02008.x}, abstract = {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{\textendash}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 {\textquoteleft}old{\textquoteright} and {\textquoteleft}new{\textquoteright}V. cholerae O1 El Tor pandemic clones circulating in some of the areas where cholera is endemic.}, keywords = {Vibrio cholerae, Vibrio mimicus, VPS-II}, isbn = {1574-6968}, author = {Taviani, Elisa and Grim, Christopher J. and Choi, Jinna and Jongsik, Chun and Haley, Bradd and Hasan, Nur A. and Huq, Anwar and Rita R. Colwell} } @inbook {38246, title = {Evolutionary framework for Lepidoptera model systems}, booktitle = {Genetics and Molecular Biology of LepidopteraGenetics and Molecular Biology of Lepidoptera}, year = {2010}, publisher = {Taylor \& Francis}, organization = {Taylor \& Francis}, address = {Boca Raton}, abstract = {{\textquotedblleft}Model systems{\textquotedblright} are specific organisms upon which detailed studies have been conducted examining a fundamental biological question. If the studies are robust, their results can be extrapolated among an array of organisms that possess features in common with the subject organism. The true power of model systems lies in the ability to extrapolate these details across larger groups of organisms. In order to generalize these results, comparative studies are essential and require that model systems be placed into their evolutionary or phylogenetic context. This chapter examines model systems in the insect order Lepidoptera from the perspective of several different superfamilies. Historically, many species of Lepidoptera have been essential in the development of invaluable model systems in the fields of development biology, genetics, molecular biology, physiology, co-evolution, population dynamics, and ecology.}, author = {Roe, A. and Weller, S. and Baixeras, J. and Brown, J. W. and Michael P. Cummings and Davis, D. R. and Horak, M. and Kawahara, A. Y. and Mitter, C. and Parr, C. S. and Regier, J. C. and Rubinoff, D. and Simonsen, T. J. and Wahlberg, N. and Zwick, A.}, editor = {Goldsmith, M. and Marec, F.} } @article {38263, title = {Finishing genomes with limited resources: lessons from an ensemble of microbial genomes}, journal = {BMC GenomicsBMC Genomics}, volume = {11}, year = {2010}, type = {10.1186/1471-2164-11-242}, abstract = {While new sequencing technologies have ushered in an era where microbial genomes can be easily sequenced, the goal of routinely producing high-quality draft and finished genomes in a cost-effective fashion has still remained elusive. Due to shorter read lengths and limitations in library construction protocols, shotgun sequencing and assembly based on these technologies often results in fragmented assemblies. Correspondingly, while draft assemblies can be obtained in days, finishing can take many months and hence the time and effort can only be justified for high-priority genomes and in large sequencing centers. In this work, we revisit this issue in light of our own experience in producing finished and nearly-finished genomes for a range of microbial species in a small-lab setting. These genomes were finished with surprisingly little investments in terms of time, computational effort and lab work, suggesting that the increased access to sequencing might also eventually lead to a greater proportion of finished genomes from small labs and genomics cores.}, isbn = {1471-2164}, author = {Nagarajan, Niranjan and Cook, Christopher and Di Bonaventura, Maria Pia and Ge, Hong and Richards, Allen and Bishop-Lilly, Kimberly A. and DeSalle, Robert and Read, Timothy D. and M. Pop} } @article {38301, title = {Genome Sequence of Hybrid Vibrio Cholerae O1 MJ-1236, B-33, and CIRS101 and Comparative Genomics with V. Cholerae}, journal = {Journal of BacteriologyJ. Bacteriol.Journal of BacteriologyJ. Bacteriol.}, volume = {192}, year = {2010}, type = {10.1128/JB.00040-10}, abstract = {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.}, isbn = {0021-9193, 1098-5530}, author = {Grim, Christopher J. and Hasan, Nur A. and Taviani, Elisa and Haley, Bradd and Jongsik, Chun and Brettin, Thomas S. and Bruce, David C. and Detter, J. Chris and Han, Cliff S. and Chertkov, Olga and Challacombe, Jean and Huq, Anwar and Nair, G. Balakrish and Rita R. Colwell} } @article {38335, title = {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}, journal = {Applied and Environmental MicrobiologyAppl. Environ. Microbiol.Applied and Environmental MicrobiologyAppl. Environ. Microbiol.}, volume = {76}, year = {2010}, type = {10.1128/AEM.01919-09}, abstract = {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.}, isbn = {0099-2240, 1098-5336}, author = {Whitehouse, Chris A. and Baldwin, Carson and Sampath, Rangarajan and Blyn, Lawrence B. and Melton, Rachael and Li, Feng and Hall, Thomas A. and Harpin, Vanessa and Matthews, Heather and Tediashvili, Marina and Jaiani, Ekaterina and Kokashvili, Tamar and Janelidze, Nino and Grim, Christopher and Rita R. Colwell and Huq, Anwar} } @inbook {38338, title = {Identifying Differentially Abundant Metabolic Pathways in Metagenomic Datasets}, booktitle = {Bioinformatics Research and ApplicationsBioinformatics Research and Applications}, series = {Lecture Notes in Computer Science}, volume = {6053}, year = {2010}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {Enabled by rapid advances in sequencing technology, metagenomic studies aim to characterize entire communities of microbes bypassing the need for culturing individual bacterial members. One major goal of such studies is to identify specific functional adaptations of microbial communities to their habitats. Here we describe a powerful analytical method (MetaPath) that can identify differentially abundant pathways in metagenomic data-sets, relying on a combination of metagenomic sequence data and prior metabolic pathway knowledge. We show that MetaPath outperforms other common approaches when evaluated on simulated datasets. We also demonstrate the power of our methods in analyzing two, publicly available, metagenomic datasets: a comparison of the gut microbiome of obese and lean twins; and a comparison of the gut microbiome of infant and adult subjects. We demonstrate that the subpathways identified by our method provide valuable insights into the biological activities of the microbiome.}, isbn = {978-3-642-13077-9}, author = {Liu, Bo and M. Pop}, editor = {Borodovsky, Mark and Gogarten, Johann and Przytycka, Teresa and Rajasekaran, Sanguthevar} } @proceedings {38374, title = {MetaPhyler: Taxonomic profiling for metagenomic sequences}, year = {2010}, month = {2010}, publisher = {IEEE}, type = {10.1109/BIBM.2010.5706544}, abstract = {A major goal of metagenomics is to characterize the microbial diversity 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 16S rRNA gene between even closely related organisms, and due to PCR artifacts. The taxonomic composition can also be determined from whole-metagenome sequencing data by matching individual sequences against a database of reference genes. One major limitation of prior methods used for this purpose is the use of a universal classification threshold for all genes at all taxonomic levels. We propose that better classification results can be obtained by tuning the taxonomic classifier to each matching length, reference gene, and taxonomic level. We present a novel taxonomic profiler MetaPhyler, which uses marker genes as a taxonomic reference. Results on simulated datasets demonstrate that MetaPhyler outperforms other tools commonly used in this context (CARMA, Megan and PhymmBL). We also present interesting results obtained by applying MetaPhyler to a real metagenomic dataset.}, keywords = {Bioinformatics, CARMA comparison, Databases, Genomics, Linear regression, marker genes, matching length, Megan comparison, metagenomic sequences, metagenomics, MetaPhyler, microbial diversity, microorganisms, molecular biophysics, molecular configurations, Pattern classification, pattern matching, phylogenetic classification, Phylogeny, PhymmBL comparison, reference gene database, Sensitivity, sequence matching, taxonomic classifier, taxonomic level, taxonomic profiling, whole metagenome sequencing data}, isbn = {978-1-4244-8306-8}, author = {Liu, Bo and Gibbons, T. and Ghodsi, M. and M. Pop} } @article {38413, title = {Occurrence of the Vibrio cholerae seventh pandemic VSP-I island and a new variant}, journal = {OMICS: A Journal of Integrative BiologyOMICS: A Journal of Integrative Biology}, volume = {14}, year = {2010}, type = {10.1089/omi.2009.0087}, isbn = {1536-2310, 1557-8100}, author = {Grim, Christopher J. and Choi, Jinna and Jongsik, Chun and Jeon, Yoon-Seong and Taviani, Elisa and Hasan, Nur A. and Haley, Bradd and Huq, Anwar and Rita R. Colwell} } @article {38448, title = {The pre-seventh pandemic Vibrio cholerae BX 330286 El Tor genome: evidence for the environment as a genome reservoir}, journal = {Environmental Microbiology ReportsEnvironmental Microbiology Reports}, volume = {2}, year = {2010}, type = {10.1111/j.1758-2229.2010.00141.x}, abstract = {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.}, isbn = {1758-2229}, author = {Haley, Bradd J. and Grim, Christopher J. and Hasan, Nur A. and Taviani, Elisa and Jongsik, Chun and Brettin, Thomas S. and Bruce, David C. and Challacombe, Jean F. and Detter, J. Chris and Han, Cliff S. and Huq, Anwar and Nair, G. Balakrish and Rita R. Colwell} } @article {38522, title = {Tackling the widespread and critical impact of batch effects in high-throughput data}, journal = {Nature reviews. GeneticsNature reviews. Genetics}, volume = {11}, year = {2010}, note = {http://www.ncbi.nlm.nih.gov/pubmed/20838408?dopt=Abstract}, type = {10.1038/nrg2825}, abstract = {High-throughput technologies are widely used, for example to assay genetic variants, gene and protein expression, and epigenetic modifications. One often overlooked complication with such studies is batch effects, which occur because measurements are affected by laboratory conditions, reagent lots and personnel differences. This becomes a major problem when batch effects are correlated with an outcome of interest and lead to incorrect conclusions. Using both published studies and our own analyses, we argue that batch effects (as well as other technical and biological artefacts) are widespread and critical to address. We review experimental and computational approaches for doing so.}, keywords = {biotechnology, Computational Biology, Genomics, Oligonucleotide Array Sequence Analysis, Periodicals as Topic, Research Design, Sequence Analysis, DNA}, author = {Leek, Jeffrey T. and Scharpf, Robert B. and H{\'e}ctor Corrada Bravo and Simcha, David and Langmead, Benjamin and Johnson, W. Evan and Geman, Donald and Baggerly, Keith and Irizarry, Rafael A.} } @article {38561, title = {Validating the systematic position of {\i}t Plationus Segers, Murugan \& Dumont, 1993 (Rotifera: Brachionidae) using sequences of the large subunit of the nuclear ribosomal DNA and of cytochrome C oxidase}, journal = {HydrobiologiaHydrobiologia}, volume = {644}, year = {2010}, type = {DOI 10.1007/s10750-010-0203-1}, abstract = {Members of the family Brachionidae are free-living organisms that range in size from 170 to 250 microns. They comprise part of the zooplankton in freshwater and marine systems worldwide. Morphologically, members of the family are characterized by a single piece loricated body without furrows, grooves, sulci or dorsal head shields, and a malleate trophi. Differences in these structures have been traditionally used to recognize 217 species that are classified into seven genera. However, the validity of the species, Plationus patulus, P. patulus macracanthus P. polyacanthus, and P. felicitas have been confused because they were alternatively assigned in Brachionus or Platyias, when considering only morphological and ecological characters. Based on scanning electron microscope (SEM) images of the trophi, these taxa were assigned in a new genus, Plationus. In this study, we examined the systematic position of P. patulus and P. patulus macracanthus using DNA sequences of two genes: the cytochrome oxidase subunit 1 (cox1) and domains D2 and D3 of the large subunit of the nuclear ribosomal RNA (LSU). In addition, the cox1 and LSU sequences representing five genera of Brachionidae (Anuraeopsis, Brachionus, Keratella, Plationus, and Platyias) plus four species of three families from the order Ploima were used as the outgroup. The maximum likelihood (ML) analyses were conducted for each individual gene as well as for the combined (cox1 + LSU) data set. The ML tree from the combined data set yielded the family Brachionidae as a monophyletic group with weak bootstrap support (< 50\%). Five main clades in this tree had high (> 85\%) bootstrap support. The first clade was composed of three populations of P. patulus + P. patulus macracanthus. The second clade was composed of a single species of Platyias. The third clade was composed of six species of Brachionus. The fourth clade included a single species of the genus Anuraeopsis, and the fifth clade was composed of three species of the genus Keratella. The genetic divergence between Plationus and Platyias ranged from 18.4 to 19.2\% for cox1, and from 4.5 to 4.9\% for LSU, and between Brachionus and Plationus, it ranged from 16.9 to 23.1\% (cox1), and from 7.3 to 9.1\% (LSU). Morphological evidence, the amount of genetic divergence, the systematic position of Plationus within the family Brachionidae, and the position of Plationus as a sister group of Brachionus and Platyias support the validity of Plationus patulus and P. patulus macracanthus into the genus Plationus.}, keywords = {Cox1, likelihood, LSU, maximum, Phylogeny, Plationus}, author = {Reyna-Fabian, M. E. and Laclette, J. P. and Michael P. Cummings and Garc{\'\i}a-Varela, M.} } @article {49645, title = {Assessing Student Understanding of Host Pathogen Interactions Using a Concept Inventory}, journal = {J. Microbiol. Biol. Ed.}, volume = {10}, year = {2009}, pages = {43-50}, author = {Marbach-Ad, G. and Briken, V. and El-Sayed, N.M. and Frauwirth, K. and Fredericksen, B. and Hutcheson, S. and Gao, L.-Y. and Joseph, S. and Lee, V. and McIver, K.S. and Mosser, D. and Quimby, B.B. and Shields, P. and Song, W. and Stein, D.C. and Yuan, R.T. and Smith, A.C.} } @article {38163, title = {Comparative genomics reveals mechanism for short-term and long-term clonal transitions in pandemic Vibrio cholerae}, journal = {Proceedings of the National Academy of SciencesProceedings of the National Academy of Sciences}, volume = {106}, year = {2009}, type = {10.1073/pnas.0907787106}, abstract = {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 {\textquotedblleft}shift{\textquotedblright} 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 {\textquotedblleft}drift{\textquotedblright} 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.}, isbn = {0027-8424, 1091-6490}, author = {Chun, J. and Grim, C. J. and Hasan, N. A. and Lee, J. H. and Choi, S. Y. and Haley, B. J. and Taviani, E. and Jeon, Y. S. and Kim, D. W. and Lee, J. H. and Rita R. Colwell} } @article {38198, title = {Detection of toxigenic Vibrio cholerae O1 in freshwater lakes of the former Soviet Republic of Georgia}, journal = {Environmental Microbiology ReportsEnvironmental Microbiology Reports}, volume = {2}, year = {2009}, type = {10.1111/j.1758-2229.2009.00073.x}, abstract = {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.}, isbn = {1758-2229}, author = {Grim, Christopher J. and Jaiani, Ekaterina and Whitehouse, Chris A. and Janelidze, Nino and Kokashvili, Tamuna and Tediashvili, Marina and Rita R. Colwell and Huq, Anwar} } @article {38211, title = {Diversity and Seasonality of Bioluminescent Vibrio Cholerae Populations in Chesapeake Bay}, journal = {Applied and Environmental MicrobiologyAppl. Environ. Microbiol.Applied and Environmental MicrobiologyAppl. Environ. Microbiol.}, volume = {75}, year = {2009}, type = {10.1128/AEM.02894-07}, abstract = {Association of luminescence with phenotypic and genotypic traits and with environmental parameters was determined for 278 strains of Vibrio cholerae isolated from the Chesapeake Bay during 1998 to 2000. Three clusters of luminescent strains (A, B, and C) and two nonluminescent clusters (X and Y) were identified among 180 clonal types. V. cholerae O1 strains isolated during pandemics and endemic cholera in the Ganges Delta were related to cluster Y. Heat-stable enterotoxin (encoded by stn) and the membrane protein associated with bile resistance (encoded by ompU) were found to be linked to luminescence in strains of cluster A. Succession from nonluminescent to luminescent populations of V. cholerae occurred during spring to midsummer. Occurrence of cluster A strains in water with neutral pH was contrasted with that of cluster Y strains in water with a pH of >8. Cluster A was found to be associated with a specific calanoid population cooccurring with cyclopoids. Cluster B was related to cluster Y, with its maximal prevalence at pH 8. Occurrence of cluster B strains was more frequent with warmer water temperatures and negatively correlated with maturity of the copepod community. It is concluded that each cluster of luminescent V. cholerae strains occupies a distinct ecological niche. Since the dynamics of these niche-specific subpopulations are associated with zooplankton community composition, the ecology of luminescent V. cholerae is concluded to be related to its interaction with copepods and related crustacean species.}, isbn = {0099-2240, 1098-5336}, author = {Zo, Young-Gun and Chokesajjawatee, Nipa and Grim, Christopher and Arakawa, Eiji and Watanabe, Haruo and Rita R. Colwell} } @article {49646, title = {The genome of the blood fluke Schistosoma mansoni.}, journal = {Nature}, volume = {460}, year = {2009}, month = {2009 Jul 16}, pages = {352-8}, abstract = {

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.

}, keywords = {Animals, Biological Evolution, Exons, Genes, Helminth, Genome, Helminth, Host-Parasite Interactions, Introns, Molecular Sequence Data, Physical Chromosome Mapping, Schistosoma mansoni, Schistosomiasis mansoni}, issn = {1476-4687}, doi = {10.1038/nature08160}, author = {Berriman, Matthew and Haas, Brian J and LoVerde, Philip T and Wilson, R Alan and Dillon, Gary P and Cerqueira, Gustavo C and Mashiyama, Susan T and Al-Lazikani, Bissan and Andrade, Luiza F and Ashton, Peter D and Aslett, Martin A and Bartholomeu, Daniella C and Blandin, Ga{\"e}lle and Caffrey, Conor R and Coghlan, Avril and Coulson, Richard and Day, Tim A and Delcher, Art and DeMarco, Ricardo and Djikeng, Appolinaire and Eyre, Tina and Gamble, John A and Ghedin, Elodie and Gu, Yong and Hertz-Fowler, Christiane and Hirai, Hirohisha and Hirai, Yuriko and Houston, Robin and Ivens, Alasdair and Johnston, David A and Lacerda, Daniela and Macedo, Camila D and McVeigh, Paul and Ning, Zemin and Oliveira, Guilherme and Overington, John P and Parkhill, Julian and Pertea, Mihaela and Pierce, Raymond J and Protasio, Anna V and Quail, Michael A and Rajandream, Marie-Ad{\`e}le and Rogers, Jane and Sajid, Mohammed and Salzberg, Steven L and Stanke, Mario and Tivey, Adrian R and White, Owen and Williams, David L and Wortman, Jennifer and Wu, Wenjie and Zamanian, Mostafa and Zerlotini, Adhemar and Fraser-Liggett, Claire M and Barrell, Barclay G and El-Sayed, Najib M} } @inbook {38318, title = {The Genus Vibrio and Related Genera}, booktitle = {Practical handbook of microbiologyPractical handbook of microbiology}, year = {2009}, publisher = {CRC Press}, organization = {CRC Press}, isbn = {9780849393655}, author = {Rita R. Colwell and Chun, J.}, editor = {Goldman, Emanuel and Green, Lorrence H.} } @proceedings {38343, title = {Inexact Local Alignment Search over Suffix Arrays}, year = {2009}, month = {2009}, publisher = {IEEE}, type = {10.1109/BIBM.2009.25}, abstract = {We describe an algorithm for finding approximate seeds for DNA homology searches. In contrast to previous algorithms that use exact or spaced seeds, our approximate seeds may contain insertions and deletions. We present a generalized heuristic for finding such seeds efficiently and prove that the heuristic does not affect sensitivity. We show how to adapt this algorithm to work over the memory efficient suffix array with provably minimal overhead in running time. We demonstrate the effectiveness of our algorithm on two tasks: whole genome alignment of bacteria and alignment of the DNA sequences of 177 genes that are orthologous in human and mouse. We show our algorithm achieves better sensitivity and uses less memory than other commonly used local alignment tools.}, keywords = {bacteria, Bioinformatics, biology computing, Computational Biology, Costs, DNA, DNA homology searches, DNA sequences, Educational institutions, generalized heuristic, genes, Genetics, genome alignment, Genomics, human, inexact local alignment search, inexact seeds, local alignment, local alignment tools, memory efficient suffix array, microorganisms, molecular biophysics, mouse, Organisms, Sensitivity and Specificity, sequences, suffix array, USA Councils}, isbn = {978-0-7695-3885-3}, author = {Ghodsi, M. and M. Pop} } @article {49781, title = {InterPro: the integrative protein signature database.}, journal = {Nucleic Acids Res}, volume = {37}, year = {2009}, month = {2009 Jan}, pages = {D211-5}, abstract = {

The InterPro database (http://www.ebi.ac.uk/interpro/) integrates together predictive models or {\textquoteright}signatures{\textquoteright} 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/).

}, keywords = {Databases, Protein, Proteins, Sequence Analysis, Protein, Systems Integration}, issn = {1362-4962}, doi = {10.1093/nar/gkn785}, author = {Hunter, Sarah and Apweiler, Rolf and Attwood, Teresa K and Bairoch, Amos and Bateman, Alex and Binns, David and Bork, Peer and Das, Ujjwal and Daugherty, Louise and Duquenne, Lauranne and Finn, Robert D and Gough, Julian and Haft, Daniel and Hulo, Nicolas and Kahn, Daniel and Kelly, Elizabeth and Laugraud, Aur{\'e}lie and Letunic, Ivica and Lonsdale, David and Lopez, Rodrigo and Madera, Martin and Maslen, John and McAnulla, Craig and McDowall, Jennifer and Mistry, Jaina and Mitchell, Alex and Mulder, Nicola and Natale, Darren and Orengo, Christine and Quinn, Antony F and Selengut, Jeremy D and Sigrist, Christian J A and Thimma, Manjula and Thomas, Paul D and Valentin, Franck and Wilson, Derek and Wu, Cathy H and Yeats, Corin} } @article {38353, title = {InterPro: the integrative protein signature database}, journal = {Nucleic acids researchNucleic Acids Research}, volume = {37}, year = {2009}, note = {http://www.ncbi.nlm.nih.gov/pubmed/18940856?dopt=Abstract}, type = {10.1093/nar/gkn785}, abstract = {The InterPro database (http://www.ebi.ac.uk/interpro/) integrates together predictive models or {\textquoteright}signatures{\textquoteright} 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/).}, keywords = {Databases, Protein, Proteins, Sequence Analysis, Protein, Systems Integration}, author = {Hunter, Sarah and Apweiler, Rolf and Attwood, Teresa K. and Bairoch, Amos and Bateman, Alex and Binns, David and Bork, Peer and Das, Ujjwal and Daugherty, Louise and Duquenne, Lauranne and Finn, Robert D. and Gough, Julian and Haft, Daniel and Hulo, Nicolas and Kahn, Daniel and Kelly, Elizabeth and Laugraud, Aur{\'e}lie and Letunic, Ivica and Lonsdale, David and Lopez, Rodrigo and Madera, Martin and Maslen, John and McAnulla, Craig and McDowall, Jennifer and Mistry, Jaina and Mitchell, Alex and Mulder, Nicola and Natale, Darren and Orengo, Christine and Quinn, Antony F. and J. Selengut and Sigrist, Christian J. A. and Thimma, Manjula and Thomas, Paul D. and Valentin, Franck and Wilson, Derek and Wu, Cathy H. and Yeats, Corin} } @article {49557, title = {Protein quantification across hundreds of experimental conditions}, volume = {106}, year = {2009}, month = {Mar-09-2010}, pages = {15544 - 15548}, issn = {0027-8424}, doi = {10.1073/pnas.0904100106}, url = {http://www.pnas.org/cgi/doi/10.1073/pnas.0904100106}, author = {Khan, Z. and Bloom, J. S. and Garcia, B. A. and Singh, M. and Kruglyak, L.} } @article {49747, title = {Protein quantification across hundreds of experimental conditions.}, journal = {Proc Natl Acad Sci U S A}, volume = {106}, year = {2009}, month = {2009 Sep 15}, pages = {15544-8}, abstract = {

Quantitative studies of protein abundance rarely span more than a small number of experimental conditions and replicates. In contrast, quantitative studies of transcript abundance often span hundreds of experimental conditions and replicates. This situation exists, in part, because extracting quantitative data from large proteomics datasets is significantly more difficult than reading quantitative data from a gene expression microarray. To address this problem, we introduce two algorithmic advances in the processing of quantitative proteomics data. First, we use space-partitioning data structures to handle the large size of these datasets. Second, we introduce techniques that combine graph-theoretic algorithms with space-partitioning data structures to collect relative protein abundance data across hundreds of experimental conditions and replicates. We validate these algorithmic techniques by analyzing several datasets and computing both internal and external measures of quantification accuracy. We demonstrate the scalability of these techniques by applying them to a large dataset that comprises a total of 472 experimental conditions and replicates.

}, keywords = {algorithms, Animals, Automatic Data Processing, Chromatography, Liquid, Databases, Factual, Fungal Proteins, HUMANS, Isotopes, Mice, Proteins, proteomics, Tandem Mass Spectrometry}, issn = {1091-6490}, doi = {10.1073/pnas.0904100106}, author = {Khan, Zia and Bloom, Joshua S and Garcia, Benjamin A and Singh, Mona and Kruglyak, Leonid} } @article {38468, title = {RNA Colony Blot Hybridization Method for Enumeration of Culturable Vibrio Cholerae and Vibrio Mimicus Bacteria}, journal = {Applied and Environmental MicrobiologyAppl. Environ. Microbiol.Applied and Environmental MicrobiologyAppl. Environ. Microbiol.}, volume = {75}, year = {2009}, type = {10.1128/AEM.02007-08}, abstract = {A species-specific RNA colony blot hybridization protocol was developed for enumeration of culturable Vibrio cholerae and Vibrio mimicus bacteria in environmental water samples. Bacterial colonies on selective or nonselective plates were lysed by sodium dodecyl sulfate, and the lysates were immobilized on nylon membranes. A fluorescently labeled oligonucleotide probe targeting a phylogenetic signature sequence of 16S rRNA of V. cholerae and V. mimicus was hybridized to rRNA molecules immobilized on the nylon colony lift blots. The protocol produced strong positive signals for all colonies of the 15 diverse V. cholerae-V. mimicus strains tested, indicating 100\% sensitivity of the probe for the targeted species. For visible colonies of 10 nontarget species, the specificity of the probe was calculated to be 90\% because of a weak positive signal produced by Grimontia (Vibrio) hollisae, a marine bacterium. When both the sensitivity and specificity of the assay were evaluated using lake water samples amended with a bioluminescent V. cholerae strain, no false-negative or false-positive results were found, indicating 100\% sensitivity and specificity for culturable bacterial populations in freshwater samples when G. hollisae was not present. When the protocol was applied to laboratory microcosms containing V. cholerae attached to live copepods, copepods were found to carry approximately 10,000 to 50,000 CFU of V. cholerae per copepod. The protocol was also used to analyze pond water samples collected in an area of cholera endemicity in Bangladesh over a 9-month period. Water samples collected from six ponds demonstrated a peak in abundance of total culturable V. cholerae bacteria 1 to 2 months prior to observed increases in pathogenic V. cholerae and in clinical cases recorded by the area health clinic. The method provides a highly specific and sensitive tool for monitoring the dynamics of V. cholerae in the environment. The RNA blot hybridization protocol can also be applied to detection of other gram-negative bacteria for taxon-specific enumeration.}, isbn = {0099-2240, 1098-5336}, author = {Grim, Christopher J. and Zo, Young-Gun and Hasan, Nur A. and Ali, Afsar and Chowdhury, Wasimul B. and Islam, Atiqul and Rashid, Mohammed H. and Alam, Munirul and Morris, J. Glenn and Huq, Anwar and Rita R. Colwell} } @article {38498, title = {Serogroup, Virulence, and Genetic Traits of Vibrio Parahaemolyticus in the Estuarine Ecosystem of Bangladesh}, journal = {Applied and Environmental MicrobiologyAppl. Environ. Microbiol.Applied and Environmental MicrobiologyAppl. Environ. Microbiol.}, volume = {75}, year = {2009}, type = {10.1128/AEM.00266-09}, abstract = {Forty-two strains of Vibrio parahaemolyticus were isolated from Bay of Bengal estuaries and, with two clinical strains, analyzed for virulence, phenotypic, and molecular traits. Serological analysis indicated O8, O3, O1, and K21 to be the major O and K serogroups, respectively, and O8:K21, O1:KUT, and O3:KUT to be predominant. The K antigen(s) was untypeable, and pandemic serogroup O3:K6 was not detected. The presence of genes toxR and tlh were confirmed by PCR in all but two strains, which also lacked toxR. A total of 18 (41\%) strains possessed the virulence gene encoding thermostable direct hemolysin (TDH), and one had the TDH-related hemolysin (trh) gene, but not tdh. Ten (23\%) strains exhibited Kanagawa phenomenon that surrogates virulence, of which six, including the two clinical strains, possessed tdh. Of the 18 tdh-positive strains, 17 (94\%), including the two clinical strains, had the seromarker O8:K21, one was O9:KUT, and the single trh-positive strain was O1:KUT. None had the group-specific or ORF8 pandemic marker gene. DNA fingerprinting employing pulsed-field gel electrophoresis (PFGE) of SfiI-digested DNA and cluster analysis showed divergence among the strains. Dendrograms constructed using PFGE (SfiI) images from a soft database, including those of pandemic and nonpandemic strains of diverse geographic origin, however, showed that local strains formed a cluster, i.e., {\textquotedblleft}clonal cluster,{\textquotedblright} as did pandemic strains of diverse origin. The demonstrated prevalence of tdh-positive and diarrheagenic serogroup O8:K21 strains in coastal villages of Bangladesh indicates a significant human health risk for inhabitants.}, isbn = {0099-2240, 1098-5336}, author = {Alam, Munirul and Chowdhury, Wasimul B. and Bhuiyan, N. A. and Islam, Atiqul and Hasan, Nur A. and Nair, G. Balakrish and Watanabe, H. and Siddique, A. K. and Huq, Anwar and Sack, R. Bradley and Akhter, M. Z. and Grim, Christopher J. and Kam, K. M. and Luey, C. K. Y. and Endtz, Hubert P. and Cravioto, Alejandro and Rita R. Colwell} } @article {38528, title = {Three genomes from the phylum Acidobacteria provide insight into the lifestyles of these microorganisms in soils}, journal = {Applied and environmental microbiologyApplied and environmental microbiology}, volume = {75}, year = {2009}, note = {http://www.ncbi.nlm.nih.gov/pubmed/19201974?dopt=Abstract}, type = {10.1128/AEM.02294-08}, abstract = {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.}, keywords = {Anti-Bacterial Agents, bacteria, Biological Transport, Carbohydrate Metabolism, Cyanobacteria, DNA, Bacterial, Fungi, Genome, Bacterial, Macrolides, Molecular Sequence Data, Nitrogen, Phylogeny, Proteobacteria, Sequence Analysis, DNA, Sequence Homology, Soil Microbiology}, author = {Ward, Naomi L. and Challacombe, Jean F. and Janssen, Peter H. and Henrissat, Bernard and Coutinho, Pedro M. and Wu, Martin and Xie, Gary and Haft, Daniel H. and Sait, Michelle and Badger, Jonathan and Barabote, Ravi D. and Bradley, Brent and Brettin, Thomas S. and Brinkac, Lauren M. and Bruce, David and Creasy, Todd and Daugherty, Sean C. and Davidsen, Tanja M. and DeBoy, Robert T. and Detter, J. Chris and Dodson, Robert J. and Durkin, A. Scott and Ganapathy, Anuradha and Gwinn-Giglio, Michelle and Han, Cliff S. and Khouri, Hoda and Kiss, Hajnalka and Kothari, Sagar P. and Madupu, Ramana and Nelson, Karen E. and Nelson, William C. and Paulsen, Ian and Penn, Kevin and Ren, Qinghu and Rosovitz, M. J. and J. Selengut and Shrivastava, Susmita and Sullivan, Steven A. and Tapia, Roxanne and Thompson, L. Sue and Watkins, Kisha L. and Yang, Qi and Yu, Chunhui and Zafar, Nikhat and Zhou, Liwei and Kuske, Cheryl R.} } @article {49780, title = {Three genomes from the phylum Acidobacteria provide insight into the lifestyles of these microorganisms in soils.}, journal = {Appl Environ Microbiol}, volume = {75}, year = {2009}, month = {2009 Apr}, pages = {2046-56}, abstract = {

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.

}, keywords = {Anti-Bacterial Agents, bacteria, Biological Transport, Carbohydrate Metabolism, Cyanobacteria, DNA, Bacterial, Fungi, Genome, Bacterial, Macrolides, Molecular Sequence Data, Nitrogen, Phylogeny, Proteobacteria, Sequence Analysis, DNA, Sequence Homology, Soil Microbiology}, issn = {1098-5336}, doi = {10.1128/AEM.02294-08}, author = {Ward, Naomi L and Challacombe, Jean F and Janssen, Peter H and Henrissat, Bernard and Coutinho, Pedro M and Wu, Martin and Xie, Gary and Haft, Daniel H and Sait, Michelle and Badger, Jonathan and Barabote, Ravi D and Bradley, Brent and Brettin, Thomas S and Brinkac, Lauren M and Bruce, David and Creasy, Todd and Daugherty, Sean C and Davidsen, Tanja M and DeBoy, Robert T and Detter, J Chris and Dodson, Robert J and Durkin, A Scott and Ganapathy, Anuradha and Gwinn-Giglio, Michelle and Han, Cliff S and Khouri, Hoda and Kiss, Hajnalka and Kothari, Sagar P and Madupu, Ramana and Nelson, Karen E and Nelson, William C and Paulsen, Ian and Penn, Kevin and Ren, Qinghu and Rosovitz, M J and Selengut, Jeremy D and Shrivastava, Susmita and Sullivan, Steven A and Tapia, Roxanne and Thompson, L Sue and Watkins, Kisha L and Yang, Qi and Yu, Chunhui and Zafar, Nikhat and Zhou, Liwei and Kuske, Cheryl R} } @article {38130, title = {Biofilms in water, its role and impact in human disease transmission}, journal = {Current Opinion in BiotechnologyCurrent Opinion in Biotechnology}, volume = {19}, year = {2008}, type = {10.1016/j.copbio.2008.04.005}, abstract = {Understanding the mechanism of biofilm formation is the first step in determining its function and, thereby, its impact and role in the environment. Extensive studies accomplished during the past few years have elucidated the genetics and biochemistry of biofilm formation. Cell-to-cell communication, that is, quorum sensing, is a key factor in the initiation of biofilm. Occurrence of viable but nonculturable bacteria, including Vibrio cholerae in biofilms has been reported and most likely such cells were overlooked previously because appropriate methods of detection were not employed. For this reason discovery and investigation of this important bacterial ecological niche in the environment were impeded.}, isbn = {0958-1669}, author = {Huq, Anwar and Whitehouse, Chris A. and Grim, Christopher J. and Alam, Munirul and Rita R. Colwell} } @article {49676, title = {The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus).}, journal = {Nature}, volume = {452}, year = {2008}, month = {2008 Apr 24}, pages = {991-6}, abstract = {

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 {\textquoteright}SunUp{\textquoteright} 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{\textquoteright}s distinguishing morpho-physiological, medicinal and nutritional properties.

}, keywords = {Arabidopsis, Carica, Contig Mapping, Databases, Genetic, Genes, Plant, Genome, Plant, Molecular Sequence Data, Plants, Genetically Modified, sequence alignment, Sequence Analysis, DNA, Transcription Factors, Tropical Climate}, issn = {1476-4687}, doi = {10.1038/nature06856}, author = {Ming, Ray and Hou, Shaobin and Feng, Yun and Yu, Qingyi and Dionne-Laporte, Alexandre and Saw, Jimmy H and Senin, Pavel and Wang, Wei and Ly, Benjamin V and Lewis, Kanako L T and Salzberg, Steven L and Feng, Lu and Jones, Meghan R and Skelton, Rachel L and Murray, Jan E and Chen, Cuixia and Qian, Wubin and Shen, Junguo and Du, Peng and Eustice, Moriah and Tong, Eric and Tang, Haibao and Lyons, Eric and Paull, Robert E and Michael, Todd P and Wall, Kerr and Rice, Danny W and Albert, Henrik and Wang, Ming-Li and Zhu, Yun J and Schatz, Michael and Nagarajan, Niranjan and Acob, Ricelle A and Guan, Peizhu and Blas, Andrea and Wai, Ching Man and Ackerman, Christine M and Ren, Yan and Liu, Chao and Wang, Jianmei and Wang, Jianping and Na, Jong-Kuk and Shakirov, Eugene V and Haas, Brian and Thimmapuram, Jyothi and Nelson, David and Wang, Xiyin and Bowers, John E and Gschwend, Andrea R and Delcher, Arthur L and Singh, Ratnesh and Suzuki, Jon Y and Tripathi, Savarni and Neupane, Kabi and Wei, Hairong and Irikura, Beth and Paidi, Maya and Jiang, Ning and Zhang, Wenli and Presting, Gernot and Windsor, Aaron and Navajas-P{\'e}rez, Rafael and Torres, Manuel J and Feltus, F Alex and Porter, Brad and Li, Yingjun and Burroughs, A Max and Luo, Ming-Cheng and Liu, Lei and Christopher, David A and Mount, Stephen M and Moore, Paul H and Sugimura, Tak and Jiang, Jiming and Schuler, Mary A and Friedman, Vikki and Mitchell-Olds, Thomas and Shippen, Dorothy E and dePamphilis, Claude W and Palmer, Jeffrey D and Freeling, Michael and Paterson, Andrew H and Gonsalves, Dennis and Wang, Lei and Alam, Maqsudul} } @article {38217, title = {Dual role colonization factors connecting Vibrio cholerae{\textquoteright}s lifestyles in human and aquatic environments open new perspectives for combating infectious diseases}, journal = {Current Opinion in BiotechnologyCurrent Opinion in Biotechnology}, volume = {19}, year = {2008}, type = {10.1016/j.copbio.2008.04.002}, abstract = {Vibrio cholerae exhibits two distinctive lifestyles, one inside the milieu of the human intestine and the other in the aquatic environment. Recently, the existence of V. cholerae ligands involved in colonization of both human intestine and environmental chitin surfaces via the same binding specificity has been shown. Such molecules, here named {\textquoteleft}dual role colonization factors (DRCFs){\textquoteright}, are example of a tight connection between the two V. cholerae{\textquoteright}s lifestyles. It is suggested that DRCFs and, more generally, bacterial factors and pathways having roles in pathogenesis and in the out of the human body life may be promising targets for development of novel prophylactic or therapeutic interventions that may also affect V. cholerae fitness in its environmental reservoirs.}, isbn = {0958-1669}, author = {Vezzulli, Luigi and Guzm{\'a}n, Carlos A. and Rita R. Colwell and Pruzzo, Carla} } @article {38232, title = {Environmental signatures associated with cholera epidemics}, journal = {Proceedings of the National Academy of SciencesProceedings of the National Academy of Sciences}, volume = {105}, year = {2008}, type = {10.1073/pnas.0809654105}, abstract = {The causative agent of cholera, Vibrio cholerae, has been shown to be autochthonous to riverine, estuarine, and coastal waters along with its host, the copepod, a significant member of the zooplankton community. Temperature, salinity, rainfall and plankton have proven to be important factors in the ecology of V. cholerae, influencing the transmission of the disease in those regions of the world where the human population relies on untreated water as a source of drinking water. In this study, the pattern of cholera outbreaks during 1998{\textendash}2006 in Kolkata, India, and Matlab, Bangladesh, and the earth observation data were analyzed with the objective of developing a prediction model for cholera. Satellite sensors were used to measure chlorophyll a concentration (CHL) and sea surface temperature (SST). In addition, rainfall data were obtained from both satellite and in situ gauge measurements. From the analyses, a statistically significant relationship between the time series for cholera in Kolkata, India, and CHL and rainfall anomalies was determined. A statistically significant one month lag was observed between CHL anomaly and number of cholera cases in Matlab, Bangladesh. From the results of the study, it is concluded that ocean and climate patterns are useful predictors of cholera epidemics, with the dynamics of endemic cholera being related to climate and/or changes in the aquatic ecosystem. When the ecology of V. cholerae is considered in predictive models, a robust early warning system for cholera in endemic regions of the world can be developed for public health planning and decision making.ecology epidemiology microbiology remote sensing}, isbn = {0027-8424, 1091-6490}, author = {Constantin de Magny, G. and Murtugudde, R. and Sapiano, M. R. P. and Nizam, A. and Brown, C. W. and Busalacchi, A. J. and Yunus, M. and Nair, G. B. and Gil, A. I. and Lanata, C. F. and Rita R. Colwell} } @article {38308, title = {Genome-Wide Analysis of Natural Selection on Human Cis-Elements}, journal = {PLoS ONEPLoS ONEPLoS ONEPLoS ONE}, volume = {3}, year = {2008}, type = {10.1371/journal.pone.0003137}, abstract = {It has been speculated that the polymorphisms in the non-coding portion of the human genome underlie much of the phenotypic variability among humans and between humans and other primates. If so, these genomic regions may be undergoing rapid evolutionary change, due in part to natural selection. However, the non-coding region is a heterogeneous mix of functional and non-functional regions. Furthermore, the functional regions are comprised of a variety of different types of elements, each under potentially different selection regimes.Using the HapMap and Perlegen polymorphism data that map to a stringent set of putative binding sites in human proximal promoters, we apply the Derived Allele Frequency distribution test of neutrality to provide evidence that many human-specific and primate-specific binding sites are likely evolving under positive selection. We also discuss inherent limitations of publicly available human SNP datasets that complicate the inference of selection pressures. Finally, we show that the genes whose proximal binding sites contain high frequency derived alleles are enriched for positive regulation of protein metabolism and developmental processes. Thus our genome-scale investigation provides evidence for positive selection on putative transcription factor binding sites in human proximal promoters.}, author = {Sethupathy, Praveen and Giang, Hoa and Plotkin, Joshua B. and Sridhar Hannenhalli} } @article {38324, title = {Guest Editors{\textquoteright} Introduction to the Special Section on Algorithms in Bioinformatics (WABI{\textquoteright}07)}, journal = {IEEE/ACM Transactions on Computational Biology and BioinformaticsIEEE/ACM Transactions on Computational Biology and Bioinformatics}, year = {2008}, publisher = {IEEE Computer Society}, author = {Giancarlo, R. and Sridhar Hannenhalli} } @article {38383, title = {The minimum information about a genome sequence (MIGS) specification}, journal = {Nature biotechnologyNature biotechnology}, volume = {26}, year = {2008}, note = {http://www.ncbi.nlm.nih.gov/pubmed/18464787?dopt=Abstract}, type = {10.1038/nbt1360}, abstract = {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 {\textquoteright}transparency{\textquoteright} of the information contained in existing genomic databases.}, keywords = {Chromosome mapping, Databases, Factual, information dissemination, Information Storage and Retrieval, Information Theory, Internationality}, author = {Field, Dawn and Garrity, George and Gray, Tanya and Morrison, Norman and J. Selengut and Sterk, Peter and Tatusova, Tatiana and Thomson, Nicholas and Allen, Michael J. and Angiuoli, Samuel V. and Ashburner, Michael and Axelrod, Nelson and Baldauf, Sandra and Ballard, Stuart and Boore, Jeffrey and Cochrane, Guy and Cole, James and Dawyndt, Peter and De Vos, Paul and DePamphilis, Claude and Edwards, Robert and Faruque, Nadeem and Feldman, Robert and Gilbert, Jack and Gilna, Paul and Gl{\"o}ckner, Frank Oliver and Goldstein, Philip and Guralnick, Robert and Haft, Dan and Hancock, David and Hermjakob, Henning and Hertz-Fowler, Christiane and Hugenholtz, Phil and Joint, Ian and Kagan, Leonid and Kane, Matthew and Kennedy, Jessie and Kowalchuk, George and Kottmann, Renzo and Kolker, Eugene and Kravitz, Saul and Kyrpides, Nikos and Leebens-Mack, Jim and Lewis, Suzanna E. and Li, Kelvin and Lister, Allyson L. and Lord, Phillip and Maltsev, Natalia and Markowitz, Victor and Martiny, Jennifer and Methe, Barbara and Mizrachi, Ilene and Moxon, Richard and Nelson, Karen and Parkhill, Julian and Proctor, Lita and White, Owen and Sansone, Susanna-Assunta and Spiers, Andrew and Stevens, Robert and Swift, Paul and Taylor, Chris and Tateno, Yoshio and Tett, Adrian and Turner, Sarah and Ussery, David and Vaughan, Bob and Ward, Naomi and Whetzel, Trish and San Gil, Ingio and Wilson, Gareth and Wipat, Anil} } @article {38411, title = {Occurrence and Expression of Luminescence in Vibrio Cholerae}, journal = {Applied and Environmental MicrobiologyAppl. Environ. Microbiol.Applied and Environmental MicrobiologyAppl. Environ. Microbiol.}, volume = {74}, year = {2008}, type = {10.1128/AEM.01537-07}, abstract = {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.}, isbn = {0099-2240, 1098-5336}, author = {Grim, Christopher J. and Taviani, Elisa and Alam, Munirul and Huq, Anwar and Sack, R. Bradley and Rita R. Colwell} } @article {38463, title = {Resolving arthropod phylogeny: exploring phylogenetic signal within 41 kb of protein-coding nuclear gene sequence}, journal = {Syst BiolSyst Biol}, volume = {57}, year = {2008}, type = {10.1080/10635150802570791}, abstract = {This study attempts to resolve relationships among and within the four basal arthropod lineages (Pancrustacea, Myriapoda, Euchelicerata, Pycnogonida) and to assess the widespread expectation that remaining phylogenetic problems will yield to increasing amounts of sequence data. Sixty-eight regions of 62 protein-coding nuclear genes (approximately 41 kilobases (kb)/taxon) were sequenced for 12 taxonomically diverse arthropod taxa and a tardigrade outgroup. Parsimony, likelihood, and Bayesian analyses of total nucleotide data generally strongly supported the monophyly of each of the basal lineages represented by more than one species. Other relationships within the Arthropoda were also supported, with support levels depending on method of analysis and inclusion/exclusion of synonymous changes. Removing third codon positions, where the assumption of base compositional homogeneity was rejected, altered the results. Removing the final class of synonymous mutations{\textendash}first codon positions encoding leucine and arginine, which were also compositionally heterogeneous{\textendash}yielded a data set that was consistent with a hypothesis of base compositional homogeneity. Furthermore, under such a data-exclusion regime, all 68 gene regions individually were consistent with base compositional homogeneity. Restricting likelihood analyses to nonsynonymous change recovered trees with strong support for the basal lineages but not for other groups that were variably supported with more inclusive data sets. In a further effort to increase phylogenetic signal, three types of data exploration were undertaken. (1) Individual genes were ranked by their average rate of nonsynonymous change, and three rate categories were assigned{\textendash}fast, intermediate, and slow. Then, bootstrap analysis of each gene was performed separately to see which taxonomic groups received strong support. Five taxonomic groups were strongly supported independently by two or more genes, and these genes mostly belonged to the slow or intermediate categories, whereas groups supported only by a single gene region tended to be from genes of the fast category, arguing that fast genes provide a less consistent signal. (2) A sensitivity analysis was performed in which increasing numbers of genes were excluded, beginning with the fastest. The number of strongly supported nodes increased up to a point and then decreased slightly. Recovery of Hexapoda required removal of fast genes. Support for Mandibulata (Pancrustacea + Myriapoda) also increased, at times to "strong" levels, with removal of the fastest genes. (3) Concordance selection was evaluated by clustering genes according to their ability to recover Pancrustacea, Euchelicerata, or Myriapoda and analyzing the three clusters separately. All clusters of genes recovered the three concordance clades but were at times inconsistent in the relationships recovered among and within these clades, a result that indicates that the a priori concordance criteria may bias phylogenetic signal in unexpected ways. In a further attempt to increase support of taxonomic relationships, sequence data from 49 additional taxa for three slow genes (i.e., EF-1 alpha, EF-2, and Pol II) were combined with the various 13-taxon data sets. The 62-taxon analyses supported the results of the 13-taxon analyses and provided increased support for additional pancrustacean clades found in an earlier analysis including only EF-1 alpha, EF-2, and Pol II.}, author = {Regier, J. C. and Shultz, J. W. and Ganley, A. R. D. and Hussey, A. and Shi, D. and Ball, B. and Zwick, A. and Stajich, J. E. and Michael P. Cummings and Martin, J. W. and Cunningham, C. W.} } @article {38472, title = {Role of transposable elements in trypanosomatids}, journal = {Microbes and InfectionMicrobes and Infection}, volume = {10}, year = {2008}, type = {16/j.micinf.2008.02.009}, abstract = {Transposable elements constitute 2-5\% of the genome content in trypanosomatid parasites. Some of them are involved in critical cellular functions, such as the regulation of gene expression in Leishmania spp. In this review, we highlight the remarkable role extinct transposable elements can play as the source of potential new functions.}, keywords = {Cellular function, Domestication, Evolution, Gene expression, Leishmania, Regulation of mRNA stability, Retroposon, Transposable element, Trypanosoma}, isbn = {1286-4579}, author = {Bringaud, Frederic and Ghedin, Elodie and Najib M. El-Sayed and Papadopoulou, Barbara} } @article {38499, title = {Sex and age dimorphism of myocardial gene expression in nonischemic human heart failure}, journal = {Circulation: Cardiovascular GeneticsCirculation: Cardiovascular Genetics}, volume = {1}, year = {2008}, publisher = {Am Heart Assoc}, author = {Fermin, D. R. and Barac, A. and Lee, S. and Polster, S. P. and Sridhar Hannenhalli and Bergemann, T. L. and Grindle, S. and Dyke, D. B. and Pagani, F. and Miller, L. W. and others,} } @book {38108, title = {Algorithms in Bioinformatics: 7th International Workshop, WABI 2007, Philadelphia, PA, USA, September 8-9, 2007, Proceedings}, volume = {4645}, year = {2007}, publisher = {Springer}, organization = {Springer}, author = {Giancarlo, R. and Sridhar Hannenhalli} } @article {38129, title = {Biased data reduce efficiency and effectiveness of conservation reserve networks}, journal = {Ecology LettersEcology Letters}, volume = {10}, year = {2007}, type = {10.1111/j.1461-0248.2007.01025.x}, abstract = {Complementarity-based reserve selection algorithms efficiently prioritize sites for biodiversity conservation, but they are data-intensive and most regions lack accurate distribution maps for the majority of species. We explored implications of basing conservation planning decisions on incomplete and biased data using occurrence records of the plant family Proteaceae in South Africa. Treating this high-quality database as {\textquoteleft}complete{\textquoteright}, we introduced three realistic sampling biases characteristic of biodiversity databases: a detectability sampling bias and two forms of roads sampling bias. We then compared reserve networks constructed using complete, biased, and randomly sampled data. All forms of biased sampling performed worse than both the complete data set and equal-effort random sampling. Biased sampling failed to detect a median of 1{\textendash}5\% of species, and resulted in reserve networks that were 9{\textendash}17\% larger than those designed with complete data. Spatial congruence and the correlation of irreplaceability scores between reserve networks selected with biased and complete data were low. Thus, reserve networks based on biased data require more area to protect fewer species and identify different locations than those selected with randomly sampled or complete data.}, keywords = {Bias, biodiversity conservation, complementarity, efficiency, marxan, rarity, reserve networks, reserve selection algorithms, species detection}, isbn = {1461-0248}, author = {Grand, Joanna and Michael P. Cummings and Rebelo, Tony G. and Ricketts, Taylor H. and Neel, Maile C.} } @proceedings {38139, title = {Bridging art and science with creativity support tools}, year = {2007}, month = {2007}, publisher = {ACM}, type = {10.1145/1254960.1255044}, address = {New York, NY, USA}, isbn = {978-1-59593-712-4}, author = {Shneiderman, Ben and Rita R. Colwell and Diamond, Sara and Greenhalgh, Paul and Wulf, William} } @article {38147, title = {Characterization of Ehp, a Secreted Complement Inhibitory Protein from Staphylococcus aureus}, journal = {Journal of Biological ChemistryJournal of Biological Chemistry}, volume = {282}, year = {2007}, type = {10.1074/jbc.M704247200}, abstract = {We report here the discovery and characterization of Ehp, a new secreted Staphylococcus aureus protein that potently inhibits the alternative complement activation pathway. Ehp was identified through a genomic scan as an uncharacterized secreted protein from S. aureus, and immunoblotting of conditioned S. aureus culture medium revealed that the Ehp protein was secreted at the highest levels during log-phase bacterial growth. The mature Ehp polypeptide is composed of 80 residues and is 44\% identical to the complement inhibitory domain of S. aureus Efb (extracellular fibrinogen-binding protein). We observed preferential binding by Ehp to native and hydrolyzed C3 relative to fully active C3b and found that Ehp formed a subnanomolar affinity complex with these various forms of C3 by binding to its thioester-containing C3d domain. Site-directed mutagenesis demonstrated that Arg75 and Asn82 are important in forming the Ehp{\textperiodcentered}C3d complex, but loss of these side chains did not completely disrupt Ehp/C3d binding. This suggested the presence of a second C3d-binding site in Ehp, which was mapped to the proximity of Ehp Asn63. Further molecular level details of the Ehp/C3d interaction were revealed by solving the 2.7-{\r A} crystal structure of an Ehp{\textperiodcentered}C3d complex in which the low affinity site had been mutationally inactivated. Ehp potently inhibited C3b deposition onto sensitized surfaces by the alternative complement activation pathway. This inhibition was directly related to Ehp/C3d binding and was more potent than that seen for Efb-C. An altered conformation in Ehp-bound C3 was detected by monoclonal antibody C3-9, which is specific for a neoantigen exposed in activated forms of C3. Our results suggest that increased inhibitory potency of Ehp relative to Efb-C is derived from the second C3-binding site in this new protein.}, author = {Hammel, Michal and Sfyroera, Georgia and Pyrpassopoulos, Serapion and Ricklin, Daniel and Ramyar, Kasra X. and M. Pop and Jin, Zhongmin and Lambris, John D. and Geisbrecht, Brian V.} } @article {38215, title = {Draft genome of the filarial nematode parasite Brugia malayi}, journal = {ScienceScience}, volume = {317}, year = {2007}, publisher = {American Association for the Advancement of Science}, author = {Ghedin, E. and Wang, S. and Spiro, D. and Caler, E. and Zhao, Q. and Crabtree, J. and Allen, J. E. and Delcher, A. L. and Guiliano, D. B. and Miranda-Saavedra, D. and others,} } @article {38242, title = {Evolution of genes and genomes on the Drosophila phylogeny}, journal = {NatureNature}, volume = {450}, year = {2007}, note = {[szlig]}, type = {10.1038/nature06341}, abstract = {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.}, isbn = {0028-0836}, author = {Clark, Andrew G. and Eisen, Michael B. and Smith, Douglas R. and Bergman, Casey M. and Oliver, Brian and Markow, Therese A. and Kaufman, Thomas C. and Kellis, Manolis and Gelbart, William and Iyer, Venky N. and Pollard, Daniel A. and Sackton, Timothy B. and Larracuente, Amanda M. and Singh, Nadia D. and Abad, Jose P. and Abt, Dawn N. and Adryan, Boris and Aguade, Montserrat and Akashi, Hiroshi and Anderson, Wyatt W. and Aquadro, Charles F. and Ardell, David H. and Arguello, Roman and Artieri, Carlo G. and Barbash, Daniel A. and Barker, Daniel and Barsanti, Paolo and Batterham, Phil and Batzoglou, Serafim and Begun, Dave and Bhutkar, Arjun and Blanco, Enrico and Bosak, Stephanie A. and Bradley, Robert K. and Brand, Adrianne D. and Brent, Michael R. and Brooks, Angela N. and Brown, Randall H. and Butlin, Roger K. and Caggese, Corrado and Calvi, Brian R. and Carvalho, A. Bernardo de and Caspi, Anat and Castrezana, Sergio and Celniker, Susan E. and Chang, Jean L. and Chapple, Charles and Chatterji, Sourav and Chinwalla, Asif and Civetta, Alberto and Clifton, Sandra W. and Comeron, Josep M. and Costello, James C. and Coyne, Jerry A. and Daub, Jennifer and David, Robert G. and Delcher, Arthur L. and Delehaunty, Kim and Do, Chuong B. and Ebling, Heather and Edwards, Kevin and Eickbush, Thomas and Evans, Jay D. and Filipski, Alan and Findei, and Sven and Freyhult, Eva and Fulton, Lucinda and Fulton, Robert and Garcia, Ana C. L. and Gardiner, Anastasia and Garfield, David A. and Garvin, Barry E. and Gibson, Greg and Gilbert, Don and Gnerre, Sante and Godfrey, Jennifer and Good, Robert and Gotea, Valer and Gravely, Brenton and Greenberg, Anthony J. and Griffiths-Jones, Sam and Gross, Samuel and Guigo, Roderic and Gustafson, Erik A. and Haerty, Wilfried and Hahn, Matthew W. and Halligan, Daniel L. and Halpern, Aaron L. and Halter, Gillian M. and Han, Mira V. and Heger, Andreas and Hillier, LaDeana and Hinrichs, Angie S. and Holmes, Ian and Hoskins, Roger A. and Hubisz, Melissa J. and Hultmark, Dan and Huntley, Melanie A. and Jaffe, David B. and Jagadeeshan, Santosh and Jeck, William R. and Johnson, Justin and Jones, Corbin D. and Jordan, William C. and Karpen, Gary H. and Kataoka, Eiko and Keightley, Peter D. and Kheradpour, Pouya and Kirkness, Ewen F. and Koerich, Leonardo B. and Kristiansen, Karsten and Kudrna, Dave and Kulathinal, Rob J. and Kumar, Sudhir and Kwok, Roberta and Lander, Eric and Langley, Charles H. and Lapoint, Richard and Lazzaro, Brian P. and Lee, So-Jeong and Levesque, Lisa and Li, Ruiqiang and Lin, Chiao-Feng and Lin, Michael F. and Lindblad-Toh, Kerstin and Llopart, Ana and Long, Manyuan and Low, Lloyd and Lozovsky, Elena and Lu, Jian and Luo, Meizhong and Machado, Carlos A. and Makalowski, Wojciech and Marzo, Mar and Matsuda, Muneo and Matzkin, Luciano and McAllister, Bryant and McBride, Carolyn S. and McKernan, Brendan and McKernan, Kevin and Mendez-Lago, Maria and Minx, Patrick and Mollenhauer, Michael U. and Montooth, Kristi and Stephen M. Mount and Mu, Xu and Myers, Eugene and Negre, Barbara and Newfeld, Stuart and Nielsen, Rasmus and Noor, Mohamed A. F. and O{\textquoteright}Grady, Patrick and Pachter, Lior and Papaceit, Montserrat and Parisi, Matthew J. and Parisi, Michael and Parts, Leopold and Pedersen, Jakob S. and Pesole, Graziano and Phillippy, Adam M. and Ponting, Chris P. and M. Pop and Porcelli, Damiano and Powell, Jeffrey R. and Prohaska, Sonja and Pruitt, Kim and Puig, Marta and Quesneville, Hadi and Ram, Kristipati Ravi and Rand, David and Rasmussen, Matthew D. and Reed, Laura K. and Reenan, Robert and Reily, Amy and Remington, Karin A. and Rieger, Tania T. and Ritchie, Michael G. and Robin, Charles and Rogers, Yu-Hui and Rohde, Claudia and Rozas, Julio and Rubenfield, Marc J. and Ruiz, Alfredo and Russo, Susan and Salzberg, Steven L. and Sanchez-Gracia, Alejandro and Saranga, David J. and Sato, Hajime and Schaeffer, Stephen W. and Schatz, Michael C. and Schlenke, Todd and Schwartz, Russell and Segarra, Carmen and Singh, Rama S. and Sirot, Laura and Sirota, Marina and Sisneros, Nicholas B. and Smith, Chris D. and Smith, Temple F. and Spieth, John and Stage, Deborah E. and Stark, Alexander and Stephan, Wolfgang and Strausberg, Robert L. and Strempel, Sebastian and Sturgill, David and Sutton, Granger and Sutton, Granger G. and Tao, Wei and Teichmann, Sarah and Tobari, Yoshiko N. and Tomimura, Yoshihiko and Tsolas, Jason M. and Valente, Vera L. S. and Venter, Eli and Venter, J. Craig and Vicario, Saverio and Vieira, Filipe G. and Vilella, Albert J. and Villasante, Alfredo and Walenz, Brian and Wang, Jun and Wasserman, Marvin and Watts, Thomas and Wilson, Derek and Wilson, Richard K. and Wing, Rod A. and Wolfner, Mariana F. and Wong, Alex and Wong, Gane Ka-Shu and Wu, Chung- I. and Wu, Gabriel and Yamamoto, Daisuke and Yang, Hsiao-Pei and Yang, Shiaw-Pyng and Yorke, James A. and Yoshida, Kiyohito and Zdobnov, Evgeny and Zhang, Peili and Zhang, Yu and Zimin, Aleksey V. and Baldwin, Jennifer and Abdouelleil, Amr and Abdulkadir, Jamal and Abebe, Adal and Abera, Brikti and Abreu, Justin and Acer, St Christophe and Aftuck, Lynne and Alexander, Allen and An, Peter and Anderson, Erica and Anderson, Scott and Arachi, Harindra and Azer, Marc and Bachantsang, Pasang and Barry, Andrew and Bayul, Tashi and Berlin, Aaron and Bessette, Daniel and Bloom, Toby and Blye, Jason and Boguslavskiy, Leonid and Bonnet, Claude and Boukhgalter, Boris and Bourzgui, Imane and Brown, Adam and Cahill, Patrick and Channer, Sheridon and Cheshatsang, Yama and Chuda, Lisa and Citroen, Mieke and Collymore, Alville and Cooke, Patrick and Costello, Maura and D{\textquoteright}Aco, Katie and Daza, Riza and Haan, Georgius De and DeGray, Stuart and DeMaso, Christina and Dhargay, Norbu and Dooley, Kimberly and Dooley, Erin and Doricent, Missole and Dorje, Passang and Dorjee, Kunsang and Dupes, Alan and Elong, Richard and Falk, Jill and Farina, Abderrahim and Faro, Susan and Ferguson, Diallo and Fisher, Sheila and Foley, Chelsea D. and Franke, Alicia and Friedrich, Dennis and Gadbois, Loryn and Gearin, Gary and Gearin, Christina R. and Giannoukos, Georgia and Goode, Tina and Graham, Joseph and Grandbois, Edward and Grewal, Sharleen and Gyaltsen, Kunsang and Hafez, Nabil and Hagos, Birhane and Hall, Jennifer and Henson, Charlotte and Hollinger, Andrew and Honan, Tracey and Huard, Monika D. and Hughes, Leanne and Hurhula, Brian and Husby, M. Erii and Kamat, Asha and Kanga, Ben and Kashin, Seva and Khazanovich, Dmitry and Kisner, Peter and Lance, Krista and Lara, Marcia and Lee, William and Lennon, Niall and Letendre, Frances and LeVine, Rosie and Lipovsky, Alex and Liu, Xiaohong and Liu, Jinlei and Liu, Shangtao and Lokyitsang, Tashi and Lokyitsang, Yeshi and Lubonja, Rakela and Lui, Annie and MacDonald, Pen and Magnisalis, Vasilia and Maru, Kebede and Matthews, Charles and McCusker, William and McDonough, Susan and Mehta, Teena and Meldrim, James and Meneus, Louis and Mihai, Oana and Mihalev, Atanas and Mihova, Tanya and Mittelman, Rachel and Mlenga, Valentine and Montmayeur, Anna and Mulrain, Leonidas and Navidi, Adam and Naylor, Jerome and Negash, Tamrat and Nguyen, Thu and Nguyen, Nga and Nicol, Robert and Norbu, Choe and Norbu, Nyima and Novod, Nathaniel and O{\textquoteright}Neill, Barry and Osman, Sahal and Markiewicz, Eva and Oyono, Otero L. and Patti, Christopher and Phunkhang, Pema and Pierre, Fritz and Priest, Margaret and Raghuraman, Sujaa and Rege, Filip and Reyes, Rebecca and Rise, Cecil and Rogov, Peter and Ross, Keenan and Ryan, Elizabeth and Settipalli, Sampath and Shea, Terry and Sherpa, Ngawang and Shi, Lu and Shih, Diana and Sparrow, Todd and Spaulding, Jessica and Stalker, John and Stange-Thomann, Nicole and Stavropoulos, Sharon and Stone, Catherine and Strader, Christopher and Tesfaye, Senait and Thomson, Talene and Thoulutsang, Yama and Thoulutsang, Dawa and Topham, Kerri and Topping, Ira and Tsamla, Tsamla and Vassiliev, Helen and Vo, Andy and Wangchuk, Tsering and Wangdi, Tsering and Weiand, Michael and Wilkinson, Jane and Wilson, Adam and Yadav, Shailendra and Young, Geneva and Yu, Qing and Zembek, Lisa and Zhong, Danni and Zimmer, Andrew and Zwirko, Zac and Jaffe, David B. and Alvarez, Pablo and Brockman, Will and Butler, Jonathan and Chin, CheeWhye and Gnerre, Sante and Grabherr, Manfred and Kleber, Michael and Mauceli, Evan and MacCallum, Iain} } @article {49677, title = {Evolution of genes and genomes on the Drosophila phylogeny.}, journal = {Nature}, volume = {450}, year = {2007}, month = {2007 Nov 8}, pages = {203-18}, abstract = {

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.

}, keywords = {Animals, Codon, DNA Transposable Elements, Drosophila, Drosophila Proteins, Evolution, Molecular, Gene Order, Genes, Insect, Genome, Insect, Genome, Mitochondrial, Genomics, Immunity, Multigene Family, Phylogeny, Reproduction, RNA, Untranslated, sequence alignment, Sequence Analysis, DNA, Synteny}, issn = {1476-4687}, doi = {10.1038/nature06341}, author = {Clark, Andrew G and Eisen, Michael B and Smith, Douglas R and Bergman, Casey M and Oliver, Brian and Markow, Therese A and Kaufman, Thomas C and Kellis, Manolis and Gelbart, William and Iyer, Venky N and Pollard, Daniel A and Sackton, Timothy B and Larracuente, Amanda M and Singh, Nadia D and Abad, Jose P and Abt, Dawn N and Adryan, Boris and Aguade, Montserrat and Akashi, Hiroshi and Anderson, Wyatt W and Aquadro, Charles F and Ardell, David H and Arguello, Roman and Artieri, Carlo G and Barbash, Daniel A and Barker, Daniel and Barsanti, Paolo and Batterham, Phil and Batzoglou, Serafim and Begun, Dave and Bhutkar, Arjun and Blanco, Enrico and Bosak, Stephanie A and Bradley, Robert K and Brand, Adrianne D and Brent, Michael R and Brooks, Angela N and Brown, Randall H and Butlin, Roger K and Caggese, Corrado and Calvi, Brian R and Bernardo de Carvalho, A and Caspi, Anat and Castrezana, Sergio and Celniker, Susan E and Chang, Jean L and Chapple, Charles and Chatterji, Sourav and Chinwalla, Asif and Civetta, Alberto and Clifton, Sandra W and Comeron, Josep M and Costello, James C and Coyne, Jerry A and Daub, Jennifer and David, Robert G and Delcher, Arthur L and Delehaunty, Kim and Do, Chuong B and Ebling, Heather and Edwards, Kevin and Eickbush, Thomas and Evans, Jay D and Filipski, Alan and Findeiss, Sven and Freyhult, Eva and Fulton, Lucinda and Fulton, Robert and Garcia, Ana C L and Gardiner, Anastasia and Garfield, David A and Garvin, Barry E and Gibson, Greg and Gilbert, Don and Gnerre, Sante and Godfrey, Jennifer and Good, Robert and Gotea, Valer and Gravely, Brenton and Greenberg, Anthony J and Griffiths-Jones, Sam and Gross, Samuel and Guigo, Roderic and Gustafson, Erik A and Haerty, Wilfried and Hahn, Matthew W and Halligan, Daniel L and Halpern, Aaron L and Halter, Gillian M and Han, Mira V and Heger, Andreas and Hillier, LaDeana and Hinrichs, Angie S and Holmes, Ian and Hoskins, Roger A and Hubisz, Melissa J and Hultmark, Dan and Huntley, Melanie A and Jaffe, David B and Jagadeeshan, Santosh and Jeck, William R and Johnson, Justin and Jones, Corbin D and Jordan, William C and Karpen, Gary H and Kataoka, Eiko and Keightley, Peter D and Kheradpour, Pouya and Kirkness, Ewen F and Koerich, Leonardo B and Kristiansen, Karsten and Kudrna, Dave and Kulathinal, Rob J and Kumar, Sudhir and Kwok, Roberta and Lander, Eric and Langley, Charles H and Lapoint, Richard and Lazzaro, Brian P and Lee, So-Jeong and Levesque, Lisa and Li, Ruiqiang and Lin, Chiao-Feng and Lin, Michael F and Lindblad-Toh, Kerstin and Llopart, Ana and Long, Manyuan and Low, Lloyd and Lozovsky, Elena and Lu, Jian and Luo, Meizhong and Machado, Carlos A and Makalowski, Wojciech and Marzo, Mar and Matsuda, Muneo and Matzkin, Luciano and McAllister, Bryant and McBride, Carolyn S and McKernan, Brendan and McKernan, Kevin and Mendez-Lago, Maria and Minx, Patrick and Mollenhauer, Michael U and Montooth, Kristi and Mount, Stephen M and Mu, Xu and Myers, Eugene and Negre, Barbara and Newfeld, Stuart and Nielsen, Rasmus and Noor, Mohamed A F and O{\textquoteright}Grady, Patrick and Pachter, Lior and Papaceit, Montserrat and Parisi, Matthew J and Parisi, Michael and Parts, Leopold and Pedersen, Jakob S and Pesole, Graziano and Phillippy, Adam M and Ponting, Chris P and Pop, Mihai and Porcelli, Damiano and Powell, Jeffrey R and Prohaska, Sonja and Pruitt, Kim and Puig, Marta and Quesneville, Hadi and Ram, Kristipati Ravi and Rand, David and Rasmussen, Matthew D and Reed, Laura K and Reenan, Robert and Reily, Amy and Remington, Karin A and Rieger, Tania T and Ritchie, Michael G and Robin, Charles and Rogers, Yu-Hui and Rohde, Claudia and Rozas, Julio and Rubenfield, Marc J and Ruiz, Alfredo and Russo, Susan and Salzberg, Steven L and Sanchez-Gracia, Alejandro and Saranga, David J and Sato, Hajime and Schaeffer, Stephen W and Schatz, Michael C and Schlenke, Todd and Schwartz, Russell and Segarra, Carmen and Singh, Rama S and Sirot, Laura and Sirota, Marina and Sisneros, Nicholas B and Smith, Chris D and Smith, Temple F and Spieth, John and Stage, Deborah E and Stark, Alexander and Stephan, Wolfgang and Strausberg, Robert L and Strempel, Sebastian and Sturgill, David and Sutton, Granger and Sutton, Granger G and Tao, Wei and Teichmann, Sarah and Tobari, Yoshiko N and Tomimura, Yoshihiko and Tsolas, Jason M and Valente, Vera L S and Venter, Eli and Venter, J Craig and Vicario, Saverio and Vieira, Filipe G and Vilella, Albert J and Villasante, Alfredo and Walenz, Brian and Wang, Jun and Wasserman, Marvin and Watts, Thomas and Wilson, Derek and Wilson, Richard K and Wing, Rod A and Wolfner, Mariana F and Wong, Alex and Wong, Gane Ka-Shu and Wu, Chung-I and Wu, Gabriel and Yamamoto, Daisuke and Yang, Hsiao-Pei and Yang, Shiaw-Pyng and Yorke, James A and Yoshida, Kiyohito and Zdobnov, Evgeny and Zhang, Peili and Zhang, Yu and Zimin, Aleksey V and Baldwin, Jennifer and Abdouelleil, Amr and Abdulkadir, Jamal and Abebe, Adal and Abera, Brikti and Abreu, Justin and Acer, St Christophe and Aftuck, Lynne and Alexander, Allen and An, Peter and Anderson, Erica and Anderson, Scott and Arachi, Harindra and Azer, Marc and Bachantsang, Pasang and Barry, Andrew and Bayul, Tashi and Berlin, Aaron and Bessette, Daniel and Bloom, Toby and Blye, Jason and Boguslavskiy, Leonid and Bonnet, Claude and Boukhgalter, Boris and Bourzgui, Imane and Brown, Adam and Cahill, Patrick and Channer, Sheridon and Cheshatsang, Yama and Chuda, Lisa and Citroen, Mieke and Collymore, Alville and Cooke, Patrick and Costello, Maura and D{\textquoteright}Aco, Katie and Daza, Riza and De Haan, Georgius and DeGray, Stuart and DeMaso, Christina and Dhargay, Norbu and Dooley, Kimberly and Dooley, Erin and Doricent, Missole and Dorje, Passang and Dorjee, Kunsang and Dupes, Alan and Elong, Richard and Falk, Jill and Farina, Abderrahim and Faro, Susan and Ferguson, Diallo and Fisher, Sheila and Foley, Chelsea D and Franke, Alicia and Friedrich, Dennis and Gadbois, Loryn and Gearin, Gary and Gearin, Christina R and Giannoukos, Georgia and Goode, Tina and Graham, Joseph and Grandbois, Edward and Grewal, Sharleen and Gyaltsen, Kunsang and Hafez, Nabil and Hagos, Birhane and Hall, Jennifer and Henson, Charlotte and Hollinger, Andrew and Honan, Tracey and Huard, Monika D and Hughes, Leanne and Hurhula, Brian and Husby, M Erii and Kamat, Asha and Kanga, Ben and Kashin, Seva and Khazanovich, Dmitry and Kisner, Peter and Lance, Krista and Lara, Marcia and Lee, William and Lennon, Niall and Letendre, Frances and LeVine, Rosie and Lipovsky, Alex and Liu, Xiaohong and Liu, Jinlei and Liu, Shangtao and Lokyitsang, Tashi and Lokyitsang, Yeshi and Lubonja, Rakela and Lui, Annie and MacDonald, Pen and Magnisalis, Vasilia and Maru, Kebede and Matthews, Charles and McCusker, William and McDonough, Susan and Mehta, Teena and Meldrim, James and Meneus, Louis and Mihai, Oana and Mihalev, Atanas and Mihova, Tanya and Mittelman, Rachel and Mlenga, Valentine and Montmayeur, Anna and Mulrain, Leonidas and Navidi, Adam and Naylor, Jerome and Negash, Tamrat and Nguyen, Thu and Nguyen, Nga and Nicol, Robert and Norbu, Choe and Norbu, Nyima and Novod, Nathaniel and O{\textquoteright}Neill, Barry and Osman, Sahal and Markiewicz, Eva and Oyono, Otero L and Patti, Christopher and Phunkhang, Pema and Pierre, Fritz and Priest, Margaret and Raghuraman, Sujaa and Rege, Filip and Reyes, Rebecca and Rise, Cecil and Rogov, Peter and Ross, Keenan and Ryan, Elizabeth and Settipalli, Sampath and Shea, Terry and Sherpa, Ngawang and Shi, Lu and Shih, Diana and Sparrow, Todd and Spaulding, Jessica and Stalker, John and Stange-Thomann, Nicole and Stavropoulos, Sharon and Stone, Catherine and Strader, Christopher and Tesfaye, Senait and Thomson, Talene and Thoulutsang, Yama and Thoulutsang, Dawa and Topham, Kerri and Topping, Ira and Tsamla, Tsamla and Vassiliev, Helen and Vo, Andy and Wangchuk, Tsering and Wangdi, Tsering and Weiand, Michael and Wilkinson, Jane and Wilson, Adam and Yadav, Shailendra and Young, Geneva and Yu, Qing and Zembek, Lisa and Zhong, Danni and Zimmer, Andrew and Zwirko, Zac and Jaffe, David B and Alvarez, Pablo and Brockman, Will and Butler, Jonathan and Chin, CheeWhye and Gnerre, Sante and Grabherr, Manfred and Kleber, Michael and Mauceli, Evan and MacCallum, Iain} } @article {38258, title = {Features generated for computational splice-site prediction correspond to functional elements}, journal = {BMC BioinformaticsBMC Bioinformatics}, volume = {8}, year = {2007}, type = {10.1186/1471-2105-8-410}, abstract = {BackgroundAccurate selection of splice sites during the splicing of precursors to messenger RNA requires both relatively well-characterized signals at the splice sites and auxiliary signals in the adjacent exons and introns. We previously described a feature generation algorithm (FGA) that is capable of achieving high classification accuracy on human 3{\textquoteright} splice sites. In this paper, we extend the splice-site prediction to 5{\textquoteright} splice sites and explore the generated features for biologically meaningful splicing signals. Results We present examples from the observed features that correspond to known signals, both core signals (including the branch site and pyrimidine tract) and auxiliary signals (including GGG triplets and exon splicing enhancers). We present evidence that features identified by FGA include splicing signals not found by other methods. Conclusion Our generated features capture known biological signals in the expected sequence interval flanking splice sites. The method can be easily applied to other species and to similar classification problems, such as tissue-specific regulatory elements, polyadenylation sites, promoters, etc.}, isbn = {14712105}, author = {Dogan, Rezarta Islamaj and Getoor, Lise and Wilbur, W. John and Stephen M. Mount} } @article {49678, title = {Features generated for computational splice-site prediction correspond to functional elements.}, journal = {BMC Bioinformatics}, volume = {8}, year = {2007}, month = {2007}, pages = {410}, abstract = {

BACKGROUND: Accurate selection of splice sites during the splicing of precursors to messenger RNA requires both relatively well-characterized signals at the splice sites and auxiliary signals in the adjacent exons and introns. We previously described a feature generation algorithm (FGA) that is capable of achieving high classification accuracy on human 3{\textquoteright} splice sites. In this paper, we extend the splice-site prediction to 5{\textquoteright} splice sites and explore the generated features for biologically meaningful splicing signals.

RESULTS: We present examples from the observed features that correspond to known signals, both core signals (including the branch site and pyrimidine tract) and auxiliary signals (including GGG triplets and exon splicing enhancers). We present evidence that features identified by FGA include splicing signals not found by other methods.

CONCLUSION: Our generated features capture known biological signals in the expected sequence interval flanking splice sites. The method can be easily applied to other species and to similar classification problems, such as tissue-specific regulatory elements, polyadenylation sites, promoters, etc.

}, keywords = {Computational Biology, HUMANS, Predictive Value of Tests, RNA Splice Sites, RNA, Messenger}, issn = {1471-2105}, doi = {10.1186/1471-2105-8-410}, author = {Dogan, Rezarta Islamaj and Getoor, Lise and Wilbur, W John and Mount, Stephen M} } @article {38286, title = {Genome Analysis Linking Recent European and African Influenza (H5N1) Viruses}, journal = {Emerging Infectious DiseasesEmerg Infect DisEmerging Infectious DiseasesEmerg Infect Dis}, volume = {13}, year = {2007}, type = {10.3201/eid1305.070013}, abstract = {Although linked, these viruses are distinct from earlier outbreak strains., To better understand the ecology and epidemiology of the highly pathogenic avian influenza virus in its transcontinental spread, we sequenced and analyzed the complete genomes of 36 recent influenza A (H5N1) viruses collected from birds in Europe, northern Africa, and southeastern Asia. These sequences, among the first complete genomes of influenza (H5N1) viruses outside Asia, clearly depict the lineages now infecting wild and domestic birds in Europe and Africa and show the relationships among these isolates and other strains affecting both birds and humans. The isolates fall into 3 distinct lineages, 1 of which contains all known non-Asian isolates. This new Euro-African lineage, which was the cause of several recent (2006) fatal human infections in Egypt and Iraq, has been introduced at least 3 times into the European-African region and has split into 3 distinct, independently evolving sublineages. One isolate provides evidence that 2 of these sublineages have recently reassorted.}, isbn = {1080-6040}, author = {Salzberg, Steven L. and Kingsford, Carl and Cattoli, Giovanni and Spiro, David J. and Janies, Daniel A. and Aly, Mona Mehrez and Brown, Ian H. and Couacy-Hymann, Emmanuel and De Mia, Gian Mario and Dung, Do Huu and Guercio, Annalisa and Joannis, Tony and Ali, Ali Safar Maken and Osmani, Azizullah and Padalino, Iolanda and Saad, Magdi D. and Savi{\'c}, Vladimir and Sengamalay, Naomi A. and Yingst, Samuel and Zaborsky, Jennifer and Zorman-Rojs, Olga and Ghedin, Elodie and Capua, Ilaria} } @article {49642, title = {Members of a large retroposon family are determinants of post-transcriptional gene expression in Leishmania.}, journal = {PLoS Pathog}, volume = {3}, year = {2007}, month = {2007 Sep 7}, pages = {1291-307}, abstract = {

Trypanosomatids are unicellular protists that include the human pathogens Leishmania spp. (leishmaniasis), Trypanosoma brucei (sleeping sickness), and Trypanosoma cruzi (Chagas disease). Analysis of their recently completed genomes confirmed the presence of non-long-terminal repeat retrotransposons, also called retroposons. Using the 79-bp signature sequence common to all trypanosomatid retroposons as bait, we identified in the Leishmania major genome two new large families of small elements--LmSIDER1 (785 copies) and LmSIDER2 (1,073 copies)--that fulfill all the characteristics of extinct trypanosomatid retroposons. LmSIDERs are approximately 70 times more abundant in L. major compared to T. brucei and are found almost exclusively within the 3{\textquoteright}-untranslated regions (3{\textquoteright}UTRs) of L. major mRNAs. We provide experimental evidence that LmSIDER2 act as mRNA instability elements and that LmSIDER2-containing mRNAs are generally expressed at lower levels compared to the non-LmSIDER2 mRNAs. The considerable expansion of LmSIDERs within 3{\textquoteright}UTRs in an organism lacking transcriptional control and their role in regulating mRNA stability indicate that Leishmania have probably recycled these short retroposons to globally modulate the expression of a number of genes. To our knowledge, this is the first example in eukaryotes of the domestication and expansion of a family of mobile elements that have evolved to fulfill a critical cellular function.

}, keywords = {3{\textquoteright} Untranslated Regions, Animals, Base Sequence, Biological Evolution, Down-Regulation, Gene Expression Regulation, Genome, Protozoan, Leishmania, Leishmania major, Molecular Sequence Data, Retroelements, RNA, Messenger, sequence alignment, Trypanosoma brucei brucei, Trypanosoma cruzi}, issn = {1553-7374}, doi = {10.1371/journal.ppat.0030136}, author = {Bringaud, Frederic and M{\"u}ller, Michaela and Cerqueira, Gustavo Coutinho and Smith, Martin and Rochette, Annie and el-Sayed, Najib M A and Papadopoulou, Barbara and Ghedin, Elodie} } @article {49783, title = {New developments in the InterPro database.}, journal = {Nucleic Acids Res}, volume = {35}, year = {2007}, month = {2007 Jan}, pages = {D224-8}, abstract = {

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.

}, keywords = {Databases, Protein, Internet, Protein Structure, Tertiary, Proteins, Sequence Analysis, Protein, Systems Integration, User-Computer Interface}, issn = {1362-4962}, doi = {10.1093/nar/gkl841}, author = {Mulder, Nicola J and Apweiler, Rolf and Attwood, Teresa K and Bairoch, Amos and Bateman, Alex and Binns, David and Bork, Peer and Buillard, Virginie and Cerutti, Lorenzo and Copley, Richard and Courcelle, Emmanuel and Das, Ujjwal and Daugherty, Louise and Dibley, Mark and Finn, Robert and Fleischmann, Wolfgang and Gough, Julian and Haft, Daniel and Hulo, Nicolas and Hunter, Sarah and Kahn, Daniel and Kanapin, Alexander and Kejariwal, Anish and Labarga, Alberto and Langendijk-Genevaux, Petra S and Lonsdale, David and Lopez, Rodrigo and Letunic, Ivica and Madera, Martin and Maslen, John and McAnulla, Craig and McDowall, Jennifer and Mistry, Jaina and Mitchell, Alex and Nikolskaya, Anastasia N and Orchard, Sandra and Orengo, Christine and Petryszak, Robert and Selengut, Jeremy D and Sigrist, Christian J A and Thomas, Paul D and Valentin, Franck and Wilson, Derek and Wu, Cathy H and Yeats, Corin} } @article {38456, title = {Recovery in culture of viable but nonculturable Vibrio parahaemolyticus: regrowth or resuscitation?}, journal = {The ISME JournalThe ISME journal}, volume = {1}, year = {2007}, note = {[ccedil]
[euml]}, type = {10.1038/ismej.2007.1}, abstract = {The objective of this study was to explore the recovery of culturability of viable but nonculturable (VBNC) Vibrio parahaemolyticus after temperature upshift and to determine whether regrowth or resuscitation occurred. A clinical strain of V. parahaemolyticus Vp5 was rendered VBNC by exposure to artificial seawater (ASW) at 4{\textdegree}C. Aliquots of the ASW suspension of cells (0.1, 1 and 10 ml) were subjected to increased temperatures of 20{\textdegree}C and 37{\textdegree}C. Culturability of the cells in the aliquots was monitored for colony formation on a rich medium and changes in morphology were measured by scanning (SEM) and transmission (TEM) electron microscopy. Samples of VBNC cells were fixed and examined by SEM, revealing a heterogeneous population comprising small cells and larger, flattened cells. Forty-eight hours after temperature upshift to 20{\textdegree}C or 37{\textdegree}C, both elongation and division by binary fission of the cells were observed, employing SEM and TEM, but only in the 10-ml aliquots. The results suggest that a portion of VBNC cells is able to undergo cell division. It is concluded that a portion of VBNC cells of V. parahaemolyticus subjected to cold temperatures remain viable. After temperature upshift, regrowth of those cells, rather than resuscitation of all bacteria of the initial inoculum, appears to be responsible for recovery of culturability of VBNC cells of V. parahaemolyticus. Nutrient in filtrates of VBNC cells is hypothesized to allow growth of the temperature-responsive cells, with cell division occurring via binary fission, but also including an atypical, asymmetric cell division.}, keywords = {ecophysiology, ecosystems, environmental biotechnology, geomicrobiology, ISME J, microbe interactions, microbial communities, microbial ecology, microbial engineering, microbial epidemiology, microbial genomics, microorganisms}, isbn = {1751-7362}, author = {Coutard, Fran and ois, and Crassous, Philippe and Droguet, Micka and l, and Gobin, Eric and Rita R. Colwell and Pommepuy, Monique and Hervio-Heath, Dominique} } @article {49681, title = {Spliceosomal small nuclear RNA genes in 11 insect genomes.}, journal = {RNA}, volume = {13}, year = {2007}, month = {2007 Jan}, pages = {5-14}, abstract = {

The removal of introns from the primary transcripts of protein-coding genes is accomplished by the spliceosome, a large macromolecular complex of which small nuclear RNAs (snRNAs) are crucial components. Following the recent sequencing of the honeybee (Apis mellifera) genome, we used various computational methods, ranging from sequence similarity search to RNA secondary structure prediction, to search for putative snRNA genes (including their promoters) and to examine their pattern of conservation among 11 available insect genomes (A. mellifera, Tribolium castaneum, Bombyx mori, Anopheles gambiae, Aedes aegypti, and six Drosophila species). We identified candidates for all nine spliceosomal snRNA genes in all the analyzed genomes. All the species contain a similar number of snRNA genes, with the exception of A. aegypti, whose genome contains more U1, U2, and U5 genes, and A. mellifera, whose genome contains fewer U2 and U5 genes. We found that snRNA genes are generally more closely related to homologs within the same genus than to those in other genera. Promoter regions for all spliceosomal snRNA genes within each insect species share similar sequence motifs that are likely to correspond to the PSEA (proximal sequence element A), the binding site for snRNA activating protein complex, but these promoter elements vary in sequence among the five insect families surveyed here. In contrast to the other insect species investigated, Dipteran genomes are characterized by a rapid evolution (or loss) of components of the U12 spliceosome and a striking loss of U12-type introns.

}, keywords = {Animals, Base Sequence, Bees, Computational Biology, Diptera, Evolution, Molecular, Genes, Insect, Genome, Insect, Molecular Sequence Data, Nucleic Acid Conformation, Phylogeny, Promoter Regions, Genetic, RNA Splicing, RNA, Small Nuclear, Sequence Analysis, RNA, Spliceosomes}, issn = {1355-8382}, doi = {10.1261/rna.259207}, author = {Mount, Stephen M and Gotea, Valer and Lin, Chiao-Feng and Hernandez, Kristina and Makalowski, Wojciech} } @article {49679, title = {SplicePort--an interactive splice-site analysis tool.}, journal = {Nucleic Acids Res}, volume = {35}, year = {2007}, month = {2007 Jul}, pages = {W285-91}, abstract = {

SplicePort is a web-based tool for splice-site analysis that allows the user to make splice-site predictions for submitted sequences. In addition, the user can also browse the rich catalog of features that underlies these predictions, and which we have found capable of providing high classification accuracy on human splice sites. Feature selection is optimized for human splice sites, but the selected features are likely to be predictive for other mammals as well. With our interactive feature browsing and visualization tool, the user can view and explore subsets of features used in splice-site prediction (either the features that account for the classification of a specific input sequence or the complete collection of features). Selected feature sets can be searched, ranked or displayed easily. The user can group features into clusters and frequency plot WebLogos can be generated for each cluster. The user can browse the identified clusters and their contributing elements, looking for new interesting signals, or can validate previously observed signals. The SplicePort web server can be accessed at http://www.cs.umd.edu/projects/SplicePort and http://www.spliceport.org.

}, keywords = {Base Sequence, Chromosome mapping, Computational Biology, Computer simulation, DNA, Genome, HUMANS, Internet, Models, Genetic, Molecular Sequence Data, Pattern Recognition, Automated, RNA Splice Sites, sequence alignment, Sequence Analysis, DNA, User-Computer Interface}, issn = {1362-4962}, doi = {10.1093/nar/gkm407}, author = {Dogan, Rezarta Islamaj and Getoor, Lise and Wilbur, W John and Mount, Stephen M} } @article {38511, title = {SplicePort--An interactive splice-site analysis tool}, journal = {Nucleic Acids ResearchNucleic Acids Research}, volume = {35}, year = {2007}, type = {10.1093/nar/gkm407}, abstract = {SplicePort is a web-based tool for splice-site analysis that allows the user to make splice-site predictions for submitted sequences. In addition, the user can also browse the rich catalog of features that underlies these predictions, and which we have found capable of providing high classification accuracy on human splice sites. Feature selection is optimized for human splice sites, but the selected features are likely to be predictive for other mammals as well. With our interactive feature browsing and visualization tool, the user can view and explore subsets of features used in splice-site prediction (either the features that account for the classification of a specific input sequence or the complete collection of features). Selected feature sets can be searched, ranked or displayed easily. The user can group features into clusters and frequency plot WebLogos can be generated for each cluster. The user can browse the identified clusters and their contributing elements, looking for new interesting signals, or can validate previously observed signals. The SplicePort web server can be accessed at http://www.cs.umd.edu/projects/SplicePort and http://www.spliceport.org.}, isbn = {0305-1048, 1362-4962}, author = {Dogan, R. I. and Getoor, Lise and Wilbur, W. J. and Stephen M. Mount} } @article {38530, title = {TIGRFAMs and Genome Properties: tools for the assignment of molecular function and biological process in prokaryotic genomes}, journal = {Nucleic acids researchNucleic Acids Research}, volume = {35}, year = {2007}, note = {http://www.ncbi.nlm.nih.gov/pubmed/17151080?dopt=Abstract}, type = {10.1093/nar/gkl1043}, abstract = {TIGRFAMs is a collection of protein family definitions built to aid in high-throughput annotation of specific protein functions. Each family is based on a hidden Markov model (HMM), where both cutoff scores and membership in the seed alignment are chosen so that the HMMs can classify numerous proteins according to their specific molecular functions. Most TIGRFAMs models describe {\textquoteright}equivalog{\textquoteright} families, where both orthology and lateral gene transfer may be part of the evolutionary history, but where a single molecular function has been conserved. The Genome Properties system contains a queriable set of metabolic reconstructions, genome metrics and extractions of information from the scientific literature. Its genome-by-genome assertions of whether or not specific structures, pathways or systems are present provide high-level conceptual descriptions of genomic content. These assertions enable comparative genomics, provide a meaningful biological context to aid in manual annotation, support assignments of Gene Ontology (GO) biological process terms and help validate HMM-based predictions of protein function. The Genome Properties system is particularly useful as a generator of phylogenetic profiles, through which new protein family functions may be discovered. The TIGRFAMs and Genome Properties systems can be accessed at http://www.tigr.org/TIGRFAMs and http://www.tigr.org/Genome_Properties.}, keywords = {Archaeal Proteins, Bacterial Proteins, Databases, Protein, Genome, Bacterial, Genomics, Internet, Phylogeny, software, User-Computer Interface}, author = {J. Selengut and Haft, Daniel H. and Davidsen, Tanja and Ganapathy, Anurhada and Gwinn-Giglio, Michelle and Nelson, William C. and Richter, R. Alexander and White, Owen} } @article {38554, title = {Ultrastructure of coccoid viable but non-culturable Vibrio cholerae}, journal = {Environmental MicrobiologyEnvironmental Microbiology}, volume = {9}, year = {2007}, type = {10.1111/j.1462-2920.2006.01150.x}, abstract = {Morphology of viable but non-culturable Vibrio cholerae was monitored for 2~years by scanning and transmission electron microscopy. Morphological changes included very small coccoid forms, after extended incubation at 4{\textdegree}C and room temperature, and sequential transformation from curved rods to irregular (\~{}1~μm) rods to \~{}0.8~μm coccoid cells and, ultimately, to tiny coccoid forms (0.07{\textendash}0.4~μm). Irregular rod-shaped and coccoid cells were equally distributed in microcosms during the first 30{\textendash}60~days of incubation at both temperatures, but only coccoid cells were observed after incubation for 60~days at 4{\textdegree}C. When V.~cholerae O1 and O139, maintained for 30{\textendash}60~days at both temperatures, were heated to 45{\textdegree}C for 60~s, after serial passage through 0.45~μm and 0.1~μm filters, and plating on Luria{\textendash}Bertania (LB) agar, only cells larger than 1~μm yielded colonies on LB agar. Approximately 0.1\% of heat-treated cultures were culturable. Cell division in the smallest coccoid cells was observed, yielding daughter cells of equal size, whereas other coccoid cells revealed bleb-like, cell wall evagination, followed by transfer of nuclear material. Coccoid cells of V.~cholerae O1 and O139 incubated at 4{\textdegree}C for more than 1~year remained substrate responsive and antigenic.}, isbn = {1462-2920}, author = {Chaiyanan, Saipin and Chaiyanan, Sitthipan and Grim, Christopher and Maugel, Timothy and Huq, Anwar and Rita R. Colwell} } @article {38159, title = {Comparative genomic evidence for a close relationship between the dimorphic prosthecate bacteria Hyphomonas neptunium and Caulobacter crescentus}, journal = {Journal of bacteriologyJournal of bacteriology}, volume = {188}, year = {2006}, note = {http://www.ncbi.nlm.nih.gov/pubmed/16980487?dopt=Abstract}, type = {10.1128/JB.00111-06}, abstract = {The dimorphic prosthecate bacteria (DPB) are alpha-proteobacteria that reproduce in an asymmetric manner rather than by binary fission and are of interest as simple models of development. Prior to this work, the only member of this group for which genome sequence was available was the model freshwater organism Caulobacter crescentus. Here we describe the genome sequence of Hyphomonas neptunium, a marine member of the DPB that differs from C. crescentus in that H. neptunium uses its stalk as a reproductive structure. Genome analysis indicates that this organism shares more genes with C. crescentus than it does with Silicibacter pomeroyi (a closer relative according to 16S rRNA phylogeny), that it relies upon a heterotrophic strategy utilizing a wide range of substrates, that its cell cycle is likely to be regulated in a similar manner to that of C. crescentus, and that the outer membrane complements of H. neptunium and C. crescentus are remarkably similar. H. neptunium swarmer cells are highly motile via a single polar flagellum. With the exception of cheY and cheR, genes required for chemotaxis were absent in the H. neptunium genome. Consistent with this observation, H. neptunium swarmer cells did not respond to any chemotactic stimuli that were tested, which suggests that H. neptunium motility is a random dispersal mechanism for swarmer cells rather than a stimulus-controlled navigation system for locating specific environments. In addition to providing insights into bacterial development, the H. neptunium genome will provide an important resource for the study of other interesting biological processes including chromosome segregation, polar growth, and cell aging.}, keywords = {Alphaproteobacteria, Bacterial Outer Membrane Proteins, Caulobacter crescentus, cell cycle, Chemotaxis, DNA, Bacterial, Flagella, Genome, Bacterial, Microbial Viability, Molecular Sequence Data, Movement, Sequence Analysis, DNA, Sequence Homology, signal transduction}, author = {Badger, Jonathan H. and Hoover, Timothy R. and Brun, Yves V. and Weiner, Ronald M. and Laub, Michael T. and Alexandre, Gladys and Mr{\'a}zek, Jan and Ren, Qinghu and Paulsen, Ian T. and Nelson, Karen E. and Khouri, Hoda M. and Radune, Diana and Sosa, Julia and Dodson, Robert J. and Sullivan, Steven A. and Rosovitz, M. J. and Madupu, Ramana and Brinkac, Lauren M. and Durkin, A. Scott and Daugherty, Sean C. and Kothari, Sagar P. and Giglio, Michelle Gwinn and Zhou, Liwei and Haft, Daniel H. and J. Selengut and Davidsen, Tanja M. and Yang, Qi and Zafar, Nikhat and Ward, Naomi L.} } @article {38161, title = {Comparative genomics of emerging human ehrlichiosis agents}, journal = {PLoS geneticsPLoS genetics}, volume = {2}, year = {2006}, note = {http://www.ncbi.nlm.nih.gov/pubmed/16482227?dopt=Abstract}, type = {10.1371/journal.pgen.0020021}, abstract = {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.}, keywords = {Animals, Biotin, DNA Repair, Ehrlichia, Ehrlichiosis, Genome, Genomics, HUMANS, Models, Biological, Phylogeny, Rickettsia, Ticks}, author = {Dunning Hotopp, Julie C. and Lin, Mingqun and Madupu, Ramana and Crabtree, Jonathan and Angiuoli, Samuel V. and Eisen, Jonathan A. and Eisen, Jonathan and Seshadri, Rekha and Ren, Qinghu and Wu, Martin and Utterback, Teresa R. and Smith, Shannon and Lewis, Matthew and Khouri, Hoda and Zhang, Chunbin and Niu, Hua and Lin, Quan and Ohashi, Norio and Zhi, Ning and Nelson, William and Brinkac, Lauren M. and Dodson, Robert J. and Rosovitz, M. J. and Sundaram, Jaideep and Daugherty, Sean C. and Davidsen, Tanja and Durkin, Anthony S. and Gwinn, Michelle and Haft, Daniel H. and J. Selengut and Sullivan, Steven A. and Zafar, Nikhat and Zhou, Liwei and Benahmed, Faiza and Forberger, Heather and Halpin, Rebecca and Mulligan, Stephanie and Robinson, Jeffrey and White, Owen and Rikihisa, Yasuko and Tettelin, Herv{\'e}} } @inbook {38199, title = {Detection, Isolation, and Identification of Vibrio cholerae from the Environment}, booktitle = {Current Protocols in MicrobiologyCurrent Protocols in Microbiology}, year = {2006}, publisher = {John Wiley \& Sons, Inc.}, organization = {John Wiley \& Sons, Inc.}, keywords = {culturable, DETECTION, Environment, identification, isolation, nonculturable, viable, Vibrio cholerae}, isbn = {9780471729259}, author = {Huq, Anwar and Grim, Christopher and Rita R. Colwell and Nair, G. Balakrish} } @article {38243, title = {Evolution of non-LTR retrotransposons in the trypanosomatid genomes: Leishmania major has lost the active elements}, journal = {Molecular and Biochemical ParasitologyMolecular and Biochemical Parasitology}, volume = {145}, year = {2006}, type = {16/j.molbiopara.2005.09.017}, abstract = {The ingi and L1Tc non-LTR retrotransposons - which constitute the ingi clade - are abundant in the genome of the trypanosomatid species Trypanosoma brucei and Trypanosoma cruzi, respectively. The corresponding retroelements, however, are not present in the genome of a closely related trypanosomatid, Leishmania major. To study the evolution of non-LTR retrotransposons in trypanosomatids, we have analyzed all ingi/L1Tc elements and highly degenerate ingi/L1Tc-related sequences identified in the recently completed T. brucei, T. cruzi and L. major genomes. The coding sequences of 242 degenerate ingi/L1Tc-related elements (DIREs) in all three genomes were reconstituted by removing the numerous frame shifts. Three independent phylogenetic analyses conducted on the conserved domains encoded by these elements show that all DIREs, including the 52 L. major DIREs, form a monophyletic group belonging to the ingi clade. This indicates that the trypanosomatid ancestor contained active mobile elements that have been retained in the Trypanosoma species, but were lost from L. major genome, where only remnants (DIRE) are detectable. All 242 DIREs analyzed group together according to their species origin with the exception of 11 T. cruzi DIREs which are close to the T. brucei ingi/DIRE families. Considering the absence of known horizontal transfer between the African T. brucei and the South-American T. cruzi, this suggests that this group of elements evolved at a lower rate when compared to the other trypanosomatid elements. Interestingly, the only nucleotide sequence conserved between ingi and L1Tc (the first 79 residues) is also present at the 5{\textquoteright}-extremity of all the full length DIREs and suggests a possible role for this conserved motif, as well as for DIREs.}, keywords = {Degenerate retroelement, Evolution, Ingi, L1Tc, Leishmania major, Non-LTR retrotransposon, Retroposon, Trypanosoma brucei, Trypanosoma cruzi}, isbn = {0166-6851}, author = {Bringaud, Frederic and Ghedin, Elodie and Blandin, Ga{\"e}lle and Bartholomeu, Daniella C. and Caler, Elisabet and Levin, Mariano J. and Baltz, Th{\'e}o and Najib M. El-Sayed} } @article {49751, title = {How A.I. and multi-robot systems research will accelerate our understanding of social animal behavior}, volume = {94}, year = {2006}, pages = {1445-1463}, author = {Tucker Balch and Frank Dellaert and Adam Feldman and Andrew Guillory and Charles Isbell and Zia Khan and Andrew Stein and Hank Wilde} } @article {49561, title = {How Multirobot Systems Research will Accelerate our Understanding of Social Animal Behavior}, volume = {94}, year = {2006}, month = {Jan-07-2006}, pages = {1445 - 1463}, issn = {0018-9219}, doi = {10.1109/JPROC.2006.876969}, url = {http://ieeexplore.ieee.org/lpdocs/epic03/wrapper.htm?arnumber=1677955}, author = {Balch, T. and Dellaert, F. and Feldman, A. and Guillory, A. and Isbell, C.L. and Khan, Z. and Pratt, S.C. and Stein, A.N. and Wilde, H.} } @article {38371, title = {Metagenomic Analysis of the Human Distal Gut Microbiome}, journal = {ScienceScienceScienceScience}, volume = {312}, year = {2006}, type = {10.1126/science.1124234}, abstract = {The human intestinal microbiota is composed of 1013 to 1014 microorganisms whose collective genome ({\textquotedblleft}microbiome{\textquotedblright}) 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{\textendash}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{\textendash}mediated biosynthesis of vitamins and isoprenoids. Thus, humans are superorganisms whose metabolism represents an amalgamation of microbial and human attributes.}, isbn = {0036-8075, 1095-9203}, author = {Gill, Steven R. and M. Pop and DeBoy, Robert T. and Eckburg, Paul B. and Turnbaugh, Peter J. and Samuel, Buck S. and Gordon, Jeffrey I. and Relman, David A. and Fraser-Liggett, Claire M. and Nelson, Karen E.} } @article {38415, title = {An optimized system for expression and purification of secreted bacterial proteins}, journal = {Protein Expression and PurificationProtein Expression and Purification}, volume = {46}, year = {2006}, type = {10.1016/j.pep.2005.09.003}, abstract = {In this report, we describe an optimized system for the efficient overexpression, purification, and refolding of secreted bacterial proteins. Candidate secreted proteins were produced recombinantly in Escherichia coli as Tobacco Etch Virus protease-cleavable hexahistidine-c-myc eptiope fusion proteins. Without regard to their initial solubility, recombinant fusion proteins were extracted from whole cells with guanidium chloride, purified under denaturing conditions by immobilized metal affinity chromatography, and refolded by rapid dilution into a solution containing only Tris buffer and sodium chloride. Following concentration on the same resin under native conditions, each protein was eluted for further purification and/or characterization. Preliminary studies on a test set of 12 secreted proteins ranging in size from 13 to 130\&$\#$xa0;kDa yielded between 10 and 50\&$\#$xa0;mg of fusion protein per liter of induced culture at greater than 90\% purity, as judged by Coomassie-stained SDS{\textendash}PAGE. Of the nine proteins further purified, analytical gel filtration chromatography indicated that each was a monomer in solution and circular dichroism spectroscopy revealed that each had adopted a well-defined secondary structure. While there are many potential applications for this system, the results presented here suggest that it will be particularly useful for investigators employing structural approaches to understand protein function, as attested to by the crystal structures of three proteins purified using this methodology (B.V. Geisbrecht, B.Y. Hamaoka, B. Perman, A. Zemla, D.J. Leahy, J. Biol. Chem. 280 (2005) 17243{\textendash}17250).}, keywords = {Pathogens, Secreted proteins, Toxins, Virulence factors}, isbn = {1046-5928}, author = {Geisbrecht, Brian V. and Bouyain, Samuel and M. Pop} } @article {38488, title = {Septaplex PCR assay for rapid identification of Vibrio cholerae including detection of virulence and int SXT genes}, journal = {FEMS Microbiology LettersFEMS Microbiology Letters}, volume = {265}, year = {2006}, type = {10.1111/j.1574-6968.2006.00491.x}, abstract = {In this study, we describe a septaplex PCR assay for rapid identification of Vibrio cholerae including detection of the virulence and intsxt genes. Conditions were optimized to amplify fragments of ISRrRNA (encoding for 16S{\textendash}23S rRNA gene, Intergenic spacer regions), O1rfb (O1 serogroup specific rfb), O139rfb (O139 serogroup specific rfb), ctxA (cholera toxin subunit A), tcpA (toxin coregulated pilus), and intsxt (sxt integron) simultaneously in a single PCR. The septaplex PCR was evaluated using 211 strains of V. cholerae and six water samples for in situ testing. PCR results were correlated with genotype data obtained by individual PCR and slot-blot assays. The one-step PCR described here can be used to identify V. cholerae accurately and rapidly. Also, the virulence and intsxt genes can be simultaneously detected, providing a useful method for monitoring pathogenic, intsxt-positive and nonpathogenic, intsxt-negative V. cholerae serogroups both in the environment and clinical settings.}, keywords = {DETECTION, intsxt, septaplex PCR, Vibrio cholerae, virulence}, isbn = {1574-6968}, author = {Mantri, Chinmay K. and Mohapatra, Saswat S. and Ramamurthy, Thandavarayan and Ghosh, Raikamal and Rita R. Colwell and Singh, Durg V.} } @article {38537, title = {Transcriptional Genomics Associates FOX Transcription Factors With Human Heart Failure}, journal = {CirculationCirculation}, volume = {114}, year = {2006}, type = {10.1161/CIRCULATIONAHA.106.632430}, abstract = {Background{\textemdash} Specific transcription factors (TFs) modulate cardiac gene expression in murine models of heart failure, but their relevance in human subjects remains untested. We developed and applied a computational approach called transcriptional genomics to test the hypothesis that a discrete set of cardiac TFs is associated with human heart failure.Methods and Results{\textemdash} RNA isolates from failing (n=196) and nonfailing (n=16) human hearts were hybridized with Affymetrix HU133A arrays, and differentially expressed heart failure genes were determined. TF binding sites overrepresented in the -5-kb promoter sequences of these heart failure genes were then determined with the use of public genome sequence databases. Binding sites for TFs identified in murine heart failure models (MEF2, NKX, NF-AT, and GATA) were significantly overrepresented in promoters of human heart failure genes (P<0.002; false discovery rate 2\% to 4\%). In addition, binding sites for FOX TFs showed substantial overrepresentation in both advanced human and early murine heart failure (P<0.002 and false discovery rate <4\% for each). A role for FOX TFs was supported further by expression of FOXC1, C2, P1, P4, and O1A in failing human cardiac myocytes at levels similar to established hypertrophic TFs and by abundant FOXP1 protein in failing human cardiac myocyte nuclei.Conclusions{\textemdash} Our results provide the first evidence that specific TFs identified in murine models (MEF2, NKX, NFAT, and GATA) are associated with human heart failure. Moreover, these data implicate specific members of the FOX family of TFs (FOXC1, C2, P1, P4, and O1A) not previously suggested in heart failure pathogenesis. These findings provide a crucial link between animal models and human disease and suggest a specific role for FOX signaling in modulating the hypertrophic response of the heart to stress in humans.}, author = {Sridhar Hannenhalli and Putt, Mary E. and Gilmore, Joan M. and Wang, Junwen and Parmacek, Michael S. and Epstein, Jonathan A. and Morrisey, Edward E. and Margulies, Kenneth B. and Cappola, Thomas P.} } @article {38549, title = {The Trypanosoma cruzi L1Tc and NARTc non-LTR retrotransposons show relative site specificity for insertion}, journal = {Molecular biology and evolutionMolecular biology and evolution}, volume = {23}, year = {2006}, author = {Bringaud, F. and Bartholomeu, D. C. and Blandin, G. and Delcher, A. and Baltz, T. and Najib M. El-Sayed and Ghedin, E.} } @article {49639, title = {The Trypanosoma cruzi L1Tc and NARTc non-LTR retrotransposons show relative site specificity for insertion.}, journal = {Mol Biol Evol}, volume = {23}, year = {2006}, month = {2006 Feb}, pages = {411-20}, abstract = {

The trypanosomatid protozoan Trypanosoma cruzi contains long autonomous (L1Tc) and short nonautonomous (NARTc) non-long terminal repeat retrotransposons. NARTc (0.25 kb) probably derived from L1Tc (4.9 kb) by 3{\textquoteright}-deletion. It has been proposed that their apparent random distribution in the genome is related to the L1Tc-encoded apurinic/apyrimidinic endonuclease (APE) activity, which repairs modified residues. To address this question we used the T. cruzi (CL-Brener strain) genome data to analyze the distribution of all the L1Tc/NARTc elements present in contigs larger than 10 kb. This data set, which represents 0.91x sequence coverage of the haploid nuclear genome ( approximately 55 Mb), contains 419 elements, including 112 full-length L1Tc elements (14 of which are potentially functional) and 84 full-length NARTc. Approximately half of the full-length elements are flanked by a target site duplication, most of them (87\%) are 12 bp long. Statistical analyses of sequences flanking the full-length elements show the same highly conserved pattern upstream of both the L1Tc and NARTc retrotransposons. The two most conserved residues are a guanine and an adenine, which flank the site where first-strand cleavage is performed by the element-encoded endonuclease activity. This analysis clearly indicates that the L1Tc and NARTc elements display relative site specificity for insertion, which suggests that the APE activity is not responsible for first-strand cleavage of the target site.

}, keywords = {Animals, DNA, Protozoan, DNA-(Apurinic or Apyrimidinic Site) Lyase, Mutagenesis, Insertional, Retroelements, Sequence Deletion, Trypanosoma cruzi}, issn = {0737-4038}, doi = {10.1093/molbev/msj046}, author = {Bringaud, Frederic and Bartholomeu, Daniella C and Blandin, Ga{\"e}lle and Delcher, Arthur and Baltz, Th{\'e}o and el-Sayed, Najib M A and Ghedin, Elodie} } @article {38162, title = {Comparative Genomics of Trypanosomatid Parasitic Protozoa}, journal = {ScienceScience}, volume = {309}, year = {2005}, type = {10.1126/science.1112181}, abstract = {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{\textemdash}along with gene divergence, acquisition and loss, and rearrangement within the syntenic regions{\textemdash}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.}, author = {Najib M. El-Sayed and Myler, Peter J. and Blandin, Ga{\"e}lle and Berriman, Matthew and Crabtree, Jonathan and Aggarwal, Gautam and Caler, Elisabet and Renauld, Hubert and Worthey, Elizabeth A. and Hertz-Fowler, Christiane and Ghedin, Elodie and Peacock, Christopher and Bartholomeu, Daniella C. and Haas, Brian J. and Tran, Anh-Nhi and Wortman, Jennifer R. and Alsmark, U. Cecilia M. and Angiuoli, Samuel and Anupama, Atashi and Badger, Jonathan and Bringaud, Frederic and Cadag, Eithon and Carlton, Jane M. and Cerqueira, Gustavo C. and Creasy, Todd and Delcher, Arthur L. and Djikeng, Appolinaire and Embley, T. Martin and Hauser, Christopher and Ivens, Alasdair C. and Kummerfeld, Sarah K. and Pereira-Leal, Jose B. and Nilsson, Daniel and Peterson, Jeremy and Salzberg, Steven L. and Shallom, Joshua and Silva, Joana C. and Sundaram, Jaideep and Westenberger, Scott and White, Owen and Melville, Sara E. and Donelson, John E. and Andersson, Bj{\"o}rn and Stuart, Kenneth D. and Hall, Neil} } @article {38227, title = {eGenomics: Cataloguing our Complete Genome Collection}, journal = {Comparative and functional genomicsComparative and functional genomics}, volume = {6}, year = {2005}, note = {http://www.ncbi.nlm.nih.gov/pubmed/18629208?dopt=Abstract}, type = {10.1002/cfg.494}, author = {Field, Dawn and Garrity, George and Morrison, Norman and J. Selengut and Sterk, Peter and Tatusova, Tatiana and Thomson, Nick} } @article {38287, title = {Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial "pan-genome"}, journal = {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}, volume = {102}, year = {2005}, note = {http://www.ncbi.nlm.nih.gov/pubmed/16172379?dopt=Abstract}, type = {10.1073/pnas.0506758102}, abstract = {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.}, keywords = {Amino Acid Sequence, Bacterial Capsules, Base Sequence, Gene expression, Genes, Bacterial, Genetic Variation, Genome, Bacterial, Molecular Sequence Data, Phylogeny, sequence alignment, Sequence Analysis, DNA, Streptococcus agalactiae, virulence}, author = {Tettelin, Herv{\'e} and Masignani, Vega and Cieslewicz, Michael J. and Donati, Claudio and Medini, Duccio and Ward, Naomi L. and Angiuoli, Samuel V. and Crabtree, Jonathan and Jones, Amanda L. and Durkin, A. Scott and DeBoy, Robert T. and Davidsen, Tanja M. and Mora, Marirosa and Scarselli, Maria and Margarit y Ros, Immaculada and Peterson, Jeremy D. and Hauser, Christopher R. and Sundaram, Jaideep P. and Nelson, William C. and Madupu, Ramana and Brinkac, Lauren M. and Dodson, Robert J. and Rosovitz, Mary J. and Sullivan, Steven A. and Daugherty, Sean C. and Haft, Daniel H. and J. Selengut and Gwinn, Michelle L. and Zhou, Liwei and Zafar, Nikhat and Khouri, Hoda and Radune, Diana and Dimitrov, George and Watkins, Kisha and O{\textquoteright}Connor, Kevin J. B. and Smith, Shannon and Utterback, Teresa R. and White, Owen and Rubens, Craig E. and Grandi, Guido and Madoff, Lawrence C. and Kasper, Dennis L. and Telford, John L. and Wessels, Michael R. and Rappuoli, Rino and Fraser, Claire M.} } @article {38292, title = {The genome of the African trypanosome Trypanosoma brucei}, journal = {ScienceScience}, volume = {309}, year = {2005}, author = {Berriman, M. and Ghedin, E. and Hertz-Fowler, C. and Blandin, G. and Renauld, H. and Bartholomeu, D. C. and Lennard, N. J. and Caler, E. and Hamlin, N. E. and Haas, B. and others,} } @article {38305, title = {The genome sequence of Trypanosoma cruzi, etiologic agent of Chagas disease}, journal = {ScienceScience}, volume = {309}, year = {2005}, publisher = {American Association for the Advancement of Science}, author = {Najib M. El-Sayed and Myler, P. J. and Bartholomeu, D. C. and Nilsson, D. and Aggarwal, G. and Tran, A. N. and Ghedin, E. and Worthey, E. A. and Delcher, A. L. and Blandin, G. and others,} } @article {38450, title = {Promoter architecture and response to a positive regulator of archaeal transcription}, journal = {Molecular MicrobiologyMolecular Microbiology}, volume = {56}, year = {2005}, type = {10.1111/j.1365-2958.2005.04563.x}, abstract = {The archaeal transcription apparatus is chimeric: its core components (RNA polymerase and basal factors) closely resemble those of eukaryotic RNA polymerase II, but the putative archaeal transcriptional regulators are overwhelmingly of bacterial type. Particular interest attaches to how these bacterial-type effectors, especially activators, regulate a eukaryote-like transcription system. The hyperthermophilic archaeon Methanocaldococcus jannaschii encodes a potent transcriptional activator, Ptr2, related to the Lrp/AsnC family of bacterial regulators. Ptr2 activates rubredoxin 2 (rb2) transcription through a bipartite upstream activating site (UAS), and conveys its stimulatory effects on its cognate transcription machinery through direct recruitment of the TATA binding protein (TBP). A functional dissection of the highly constrained architecture of the rb2 promoter shows that a {\textquoteleft}one-site{\textquoteright} minimal UAS suffices for activation by Ptr2, and specifies the required placement of this site. The presence of such a simplified UAS upstream of the natural rubrerythrin (rbr) promoter also suffices for positive regulation by Ptr2 in vitro, and TBP recruitment remains the primary means of transcriptional activation at this promoter.}, isbn = {1365-2958}, author = {Ouhammouch, Mohamed and Langham, Geoffrey E. and Hausner, Winfried and Simpson, Anjana J. and Najib M. El-Sayed and Geiduschek, E. Peter} } @article {38525, title = {Temperature-Driven Campylobacter Seasonality in England and Wales}, journal = {Applied and Environmental MicrobiologyAppl. Environ. Microbiol.Applied and Environmental MicrobiologyAppl. Environ. Microbiol.}, volume = {71}, year = {2005}, type = {10.1128/AEM.71.1.85-92.2005}, abstract = {Campylobacter incidence in England and Wales between 1990 and 1999 was examined in conjunction with weather conditions. Over the 10-year interval, the average annual rate was determined to be 78.4 {\textpm} 15.0 cases per 100,000, with an upward trend. Rates were higher in males than in females, regardless of age, and highest in children less than 5 years old. Major regional differences were detected, with the highest rates in Wales and the southwest and the lowest in the southeast. The disease displayed a seasonal pattern, and increased campylobacter rates were found to be correlated with temperature. The most marked seasonal effect was observed for children under the age of 5. The seasonal pattern of campylobacter infections indicated a linkage with environmental factors rather than food sources. Therefore, public health interventions should not be restricted to food-borne approaches, and the epidemiology of the seasonal peak in human campylobacter infections may best be understood through studies in young children.}, isbn = {0099-2240, 1098-5336}, author = {Louis, Val{\'e}rie R. and Gillespie, Iain A. and O{\textquoteright}Brien, Sarah J. and Russek-Cohen, Estelle and Pearson, Andrew D. and Rita R. Colwell} } @article {38575, title = {Whole-genome sequence analysis of Pseudomonas syringae pv. phaseolicola 1448A reveals divergence among pathovars in genes involved in virulence and transposition}, journal = {Journal of bacteriologyJournal of bacteriology}, volume = {187}, year = {2005}, note = {http://www.ncbi.nlm.nih.gov/pubmed/16159782?dopt=Abstract}, type = {10.1128/JB.187.18.6488-6498.2005}, abstract = {Pseudomonas syringae pv. phaseolicola, a gram-negative bacterial plant pathogen, is the causal agent of halo blight of bean. In this study, we report on the genome sequence of P. syringae pv. phaseolicola isolate 1448A, which encodes 5,353 open reading frames (ORFs) on one circular chromosome (5,928,787 bp) and two plasmids (131,950 bp and 51,711 bp). Comparative analyses with a phylogenetically divergent pathovar, P. syringae pv. tomato DC3000, revealed a strong degree of conservation at the gene and genome levels. In total, 4,133 ORFs were identified as putative orthologs in these two pathovars using a reciprocal best-hit method, with 3,941 ORFs present in conserved, syntenic blocks. Although these two pathovars are highly similar at the physiological level, they have distinct host ranges; 1448A causes disease in beans, and DC3000 is pathogenic on tomato and Arabidopsis. Examination of the complement of ORFs encoding virulence, fitness, and survival factors revealed a substantial, but not complete, overlap between these two pathovars. Another distinguishing feature between the two pathovars is their distinctive sets of transposable elements. With access to a fifth complete pseudomonad genome sequence, we were able to identify 3,567 ORFs that likely comprise the core Pseudomonas genome and 365 ORFs that are P. syringae specific.}, keywords = {Bacterial Proteins, DNA, Bacterial, Genes, Bacterial, Genome, Bacterial, Molecular Sequence Data, Pseudomonas syringae, Species Specificity, virulence}, author = {Joardar, Vinita and Lindeberg, Magdalen and Jackson, Robert W. and J. Selengut and Dodson, Robert and Brinkac, Lauren M. and Daugherty, Sean C. and Deboy, Robert and Durkin, A. Scott and Giglio, Michelle Gwinn and Madupu, Ramana and Nelson, William C. and Rosovitz, M. J. and Sullivan, Steven and Crabtree, Jonathan and Creasy, Todd and Davidsen, Tanja and Haft, Dan H. and Zafar, Nikhat and Zhou, Liwei and Halpin, Rebecca and Holley, Tara and Khouri, Hoda and Feldblyum, Tamara and White, Owen and Fraser, Claire M. and Chatterjee, Arun K. and Cartinhour, Sam and Schneider, David J. and Mansfield, John and Collmer, Alan and Buell, C. Robin} } @article {38165, title = {Comparison of the genome of the oral pathogen Treponema denticola with other spirochete genomes}, journal = {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}, volume = {101}, year = {2004}, note = {http://www.ncbi.nlm.nih.gov/pubmed/15064399?dopt=Abstract}, type = {10.1073/pnas.0307639101}, abstract = {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.}, keywords = {ATP-Binding Cassette Transporters, Bacterial Proteins, Base Sequence, Borrelia burgdorferi, Genes, Bacterial, Genome, Bacterial, Leptospira interrogans, Models, Genetic, Molecular Sequence Data, Mouth, Sequence Homology, Amino Acid, Treponema, Treponema pallidum}, author = {Seshadri, Rekha and Myers, Garry S. A. and Tettelin, Herv{\'e} and Eisen, Jonathan A. and Heidelberg, John F. and Dodson, Robert J. and Davidsen, Tanja M. and DeBoy, Robert T. and Fouts, Derrick E. and Haft, Dan H. and J. Selengut and Ren, Qinghu and Brinkac, Lauren M. and Madupu, Ramana and Kolonay, Jamie and Durkin, A. Scott and Daugherty, Sean C. and Shetty, Jyoti and Shvartsbeyn, Alla and Gebregeorgis, Elizabeth and Geer, Keita and Tsegaye, Getahun and Malek, Joel and Ayodeji, Bola and Shatsman, Sofiya and McLeod, Michael P. and Smajs, David and Howell, Jerrilyn K. and Pal, Sangita and Amin, Anita and Vashisth, Pankaj and McNeill, Thomas Z. and Xiang, Qin and Sodergren, Erica and Baca, Ernesto and Weinstock, George M. and Norris, Steven J. and Fraser, Claire M. and Paulsen, Ian T.} } @article {49635, title = {Gene synteny and evolution of genome architecture in trypanosomatids.}, journal = {Mol Biochem Parasitol}, volume = {134}, year = {2004}, month = {2004 Apr}, pages = {183-91}, abstract = {

The trypanosomatid protozoa Trypanosoma brucei, Trypanosoma cruzi and Leishmania major are related human pathogens that cause markedly distinct diseases. Using information from genome sequencing projects currently underway, we have compared the sequences of large chromosomal fragments from each species. Despite high levels of divergence at the sequence level, these three species exhibit a striking conservation of gene order, suggesting that selection has maintained gene order among the trypanosomatids over hundreds of millions of years of evolution. The few sites of genome rearrangement between these species are marked by the presence of retrotransposon-like elements, suggesting that retrotransposons may have played an important role in shaping trypanosomatid genome organization. A degenerate retroelement was identified in L. major by examining the regions near breakage points of the synteny. This is the first such element found in L. major suggesting that retroelements were found in the common ancestor of all three species.

}, keywords = {Animals, Computational Biology, Evolution, Molecular, Gene Order, Genome, Protozoan, Genomics, Leishmania major, Multigene Family, Recombination, Genetic, Retroelements, Selection, Genetic, Synteny, Trypanosoma brucei brucei, Trypanosoma cruzi, Trypanosomatina}, issn = {0166-6851}, doi = {10.1016/j.molbiopara.2003.11.012}, author = {Ghedin, Elodie and Bringaud, Frederic and Peterson, Jeremy and Myler, Peter and Berriman, Matthew and Ivens, Alasdair and Andersson, Bj{\"o}rn and Bontempi, Esteban and Eisen, Jonathan and Angiuoli, Sam and Wanless, David and Von Arx, Anna and Murphy, Lee and Lennard, Nicola and Salzberg, Steven and Adams, Mark D and White, Owen and Hall, Neil and Stuart, Kenneth and Fraser, Claire M and el-Sayed, Najib M A} } @article {38302, title = {Genome sequence of Silicibacter pomeroyi reveals adaptations to the marine environment}, journal = {NatureNature}, volume = {432}, year = {2004}, note = {http://www.ncbi.nlm.nih.gov/pubmed/15602564?dopt=Abstract}, type = {10.1038/nature03170}, abstract = {Since the recognition of prokaryotes as essential components of the oceanic food web, bacterioplankton have been acknowledged as catalysts of most major biogeochemical processes in the sea. Studying heterotrophic bacterioplankton has been challenging, however, as most major clades have never been cultured or have only been grown to low densities in sea water. Here we describe the genome sequence of Silicibacter pomeroyi, a member of the marine Roseobacter clade (Fig. 1), the relatives of which comprise approximately 10-20\% of coastal and oceanic mixed-layer bacterioplankton. This first genome sequence from any major heterotrophic clade consists of a chromosome (4,109,442 base pairs) and megaplasmid (491,611 base pairs). Genome analysis indicates that this organism relies upon a lithoheterotrophic strategy that uses inorganic compounds (carbon monoxide and sulphide) to supplement heterotrophy. Silicibacter pomeroyi also has genes advantageous for associations with plankton and suspended particles, including genes for uptake of algal-derived compounds, use of metabolites from reducing microzones, rapid growth and cell-density-dependent regulation. This bacterium has a physiology distinct from that of marine oligotrophs, adding a new strategy to the recognized repertoire for coping with a nutrient-poor ocean.}, keywords = {Adaptation, Physiological, Carrier Proteins, Genes, Bacterial, Genome, Bacterial, marine biology, Molecular Sequence Data, Oceans and Seas, Phylogeny, plankton, RNA, Ribosomal, 16S, Roseobacter, Seawater}, author = {Moran, Mary Ann and Buchan, Alison and Gonz{\'a}lez, Jos{\'e} M. and Heidelberg, John F. and Whitman, William B. and Kiene, Ronald P. and Henriksen, James R. and King, Gary M. and Belas, Robert and Fuqua, Clay and Brinkac, Lauren and Lewis, Matt and Johri, Shivani and Weaver, Bruce and Pai, Grace and Eisen, Jonathan A. and Rahe, Elisha and Sheldon, Wade M. and Ye, Wenying and Miller, Todd R. and Carlton, Jane and Rasko, David A. and Paulsen, Ian T. and Ren, Qinghu and Daugherty, Sean C. and DeBoy, Robert T. and Dodson, Robert J. and Durkin, A. Scott and Madupu, Ramana and Nelson, William C. and Sullivan, Steven A. and Rosovitz, M. J. and Haft, Daniel H. and J. Selengut and Ward, Naomi} } @article {38303, title = {The genome sequence of the anaerobic, sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough}, journal = {Nature biotechnologyNature biotechnology}, volume = {22}, year = {2004}, note = {http://www.ncbi.nlm.nih.gov/pubmed/15077118?dopt=Abstract}, type = {10.1038/nbt959}, abstract = {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 {\textquoteright}hydrogen-cycling{\textquoteright} 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{\textquoteright}s complex anaerobic respiration.}, keywords = {Desulfovibrio vulgaris, Energy Metabolism, Genome, Bacterial, Molecular Sequence Data}, author = {Heidelberg, John F. and Seshadri, Rekha and Haveman, Shelley A. and Hemme, Christopher L. and Paulsen, Ian T. and Kolonay, James F. and Eisen, Jonathan A. and Ward, Naomi and Methe, Barbara and Brinkac, Lauren M. and Daugherty, Sean C. and DeBoy, Robert T. and Dodson, Robert J. and Durkin, A. Scott and Madupu, Ramana and Nelson, William C. and Sullivan, Steven A. and Fouts, Derrick and Haft, Daniel H. and J. Selengut and Peterson, Jeremy D. and Davidsen, Tanja M. and Zafar, Nikhat and Zhou, Liwei and Radune, Diana and Dimitrov, George and Hance, Mark and Tran, Kevin and Khouri, Hoda and Gill, John and Utterback, Terry R. and Feldblyum, Tamara V. and Wall, Judy D. and Voordouw, Gerrit and Fraser, Claire M.} } @article {38348, title = {The ingi and RIME non-LTR retrotransposons are not randomly distributed in the genome of Trypanosoma brucei}, journal = {Molecular biology and evolutionMolecular biology and evolution}, volume = {21}, year = {2004}, author = {Bringaud, F. and Biteau, N. and Zuiderwijk, E. and Berriman, M. and Najib M. El-Sayed and Ghedin, E. and Melville, S. E. and Hall, N. and Baltz, T.} } @article {49634, title = {The ingi and RIME non-LTR retrotransposons are not randomly distributed in the genome of Trypanosoma brucei.}, journal = {Mol Biol Evol}, volume = {21}, year = {2004}, month = {2004 Mar}, pages = {520-8}, abstract = {

The ingi (long and autonomous) and RIME (short and nonautonomous) non--long-terminal repeat retrotransposons are the most abundant mobile elements characterized to date in the genome of the African trypanosome Trypanosoma brucei. These retrotransposons were thought to be randomly distributed, but a detailed and comprehensive analysis of their genomic distribution had not been performed until now. To address this question, we analyzed the ingi/RIME sequences and flanking sequences from the ongoing T. brucei genome sequencing project (TREU927/4 strain). Among the 81 ingi/RIME elements analyzed, 60\% are complete, and 7\% of the ingi elements (approximately 15 copies per haploid genome) appear to encode for their own transposition. The size of the direct repeat flanking the ingi/RIME retrotransposons is conserved (i.e., 12-bp), and a strong 11-bp consensus pattern precedes the 5{\textquoteright}-direct repeat. The presence of a consensus pattern upstream of the retroelements was confirmed by the analysis of the base occurrence in 294 GSS containing 5{\textquoteright}-adjacent ingi/RIME sequences. The conserved sequence is present upstream of ingis and RIMEs, suggesting that ingi-encoded enzymatic activities are used for retrotransposition of RIMEs, which are short nonautonomous retroelements. In conclusion, the ingi and RIME retroelements are not randomly distributed in the genome of T. brucei and are preceded by a conserved sequence, which may be the recognition site of the ingi-encoded endonuclease.

}, keywords = {Amino Acid Sequence, Animals, Base Sequence, Consensus Sequence, Genome, Protozoan, Molecular Sequence Data, Retroelements, Sequence Analysis, Trypanosoma brucei brucei}, issn = {0737-4038}, doi = {10.1093/molbev/msh045}, author = {Bringaud, Frederic and Biteau, Nicolas and Zuiderwijk, Eduard and Berriman, Matthew and El-Sayed, Najib M and Ghedin, Elodie and Melville, Sara E and Hall, Neil and Baltz, Th{\'e}o} } @article {38408, title = {A Note on Efficient Computation of Haplotypes via Perfect Phylogeny}, journal = {Journal of Computational BiologyJournal of Computational Biology}, volume = {11}, year = {2004}, type = {10.1089/cmb.2004.11.858}, abstract = {The problem of inferring haplotype phase from a population of genotypes has received a lot of attention recently. This is partly due to the observation that there are many regions on human genomic DNA where genetic recombination is rare (Helmuth, 2001; Daly et al., 2001; Stephens et al., 2001; Friss et al., 2001). A Haplotype Map project has been announced by NIH to identify and characterize populations in terms of these haplotypes. Recently, Gusfield introduced the perfect phylogeny haplotyping problem, as an algorithmic implication of the no-recombination in long blocks observation, together with the standard population-genetic assumption of infinite sites. Gusfield{\textquoteright}s solution based on matroid theory was followed by direct θ(nm2 ) solutions that use simpler techniques (Bafna et al., 2003; Eskin et al., 2003), and also bound the number of solutions to the PPH problem. In this short note, we address two questions that were left open. First, can the algorithms of Bafna et al. (2003) and Eskin et al. (2003) be sped-up to O(nm + m2 ) time, which would imply an O(nm) time-bound for the PPH problem? Second, if there are multiple solutions, can we find one that is most parsimonious in terms of the number of distinct haplotypes.We give reductions that suggests that the answer to both questions is "no." For the first problem, we show that computing the output of the first step (in either method) is equivalent to Boolean matrix multiplication. Therefore, the best bound we can presently achieve is O(nmω{\textendash}1), where ω <= 2.52 is the exponent of matrix multiplication. Thus, any linear time solution to the PPH problem likely requires a different approach. For the second problem of computing a PPH solution that minimizes the number of distinct haplotypes, we show that the problem is NP-hard using a reduction from Vertex Cover (Garey and Johnson, 1979).}, isbn = {1066-5277, 1557-8666}, author = {Bafna, Vineet and Gusfield, Dan and Sridhar Hannenhalli and Yooseph, Shibu} } @article {38410, title = {Occurrence and distribution of Vibrio cholerae in the coastal environment of Peru}, journal = {Environmental MicrobiologyEnvironmental Microbiology}, volume = {6}, year = {2004}, type = {10.1111/j.1462-2920.2004.00601.x}, abstract = {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{\textendash}98 El Ni{\~n}o 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{\textendash}cholera relationship observed for the 1997{\textendash}98 El Ni{\~n}o year suggests that an early warning system for cholera risk can be established for Peru and neighbouring Latin American countries.}, isbn = {1462-2920}, author = {Gil, Ana I. and Louis, Val{\'e}rie R. and Rivera, Irma N. G. and Lipp, Erin and Huq, Anwar and Lanata, Claudio F. and Taylor, David N. and Russek-Cohen, Estelle and Choopun, Nipa and Sack, R. Bradley and Rita R. Colwell} } @article {38514, title = {Structural flexibility in the Burkholderia mallei genome}, journal = {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}, volume = {101}, year = {2004}, note = {http://www.ncbi.nlm.nih.gov/pubmed/15377793?dopt=Abstract}, type = {10.1073/pnas.0403306101}, abstract = {The complete genome sequence of Burkholderia mallei ATCC 23344 provides insight into this highly infectious bacterium{\textquoteright}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{\textquoteright}s inability to mount a durable adaptive immune response to a B. mallei infection.}, keywords = {Animals, Base Composition, Base Sequence, Burkholderia mallei, Chromosomes, Bacterial, Cricetinae, Genome, Bacterial, Glanders, Liver, Mesocricetus, Molecular Sequence Data, Multigene Family, Oligonucleotide Array Sequence Analysis, Open Reading Frames, virulence}, author = {Nierman, William C. and DeShazer, David and Kim, H. Stanley and Tettelin, Herv{\'e} and Nelson, Karen E. and Feldblyum, Tamara and Ulrich, Ricky L. and Ronning, Catherine M. and Brinkac, Lauren M. and Daugherty, Sean C. and Davidsen, Tanja D. and DeBoy, Robert T. and Dimitrov, George and Dodson, Robert J. and Durkin, A. Scott and Gwinn, Michelle L. and Haft, Daniel H. and Khouri, Hoda and Kolonay, James F. and Madupu, Ramana and Mohammoud, Yasmin and Nelson, William C. and Radune, Diana and Romero, Claudia M. and Sarria, Saul and J. Selengut and Shamblin, Christine and Sullivan, Steven A. and White, Owen and Yu, Yan and Zafar, Nikhat and Zhou, Liwei and Fraser, Claire M.} } @article {38574, title = {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}, journal = {Nucleic acids researchNucleic Acids Research}, volume = {32}, year = {2004}, note = {http://www.ncbi.nlm.nih.gov/pubmed/15115801?dopt=Abstract}, type = {10.1093/nar/gkh562}, abstract = {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.}, keywords = {Base Composition, Chromosomes, Bacterial, DNA Transposable Elements, Food Microbiology, Genes, Bacterial, Genome, Bacterial, Genomics, Listeria monocytogenes, Meat, Open Reading Frames, Physical Chromosome Mapping, Polymorphism, Single Nucleotide, Prophages, Serotyping, Species Specificity, Synteny, virulence}, author = {Nelson, Karen E. and Fouts, Derrick E. and Mongodin, Emmanuel F. and Ravel, Jacques and DeBoy, Robert T. and Kolonay, James F. and Rasko, David A. and Angiuoli, Samuel V. and Gill, Steven R. and Paulsen, Ian T. and Peterson, Jeremy and White, Owen and Nelson, William C. and Nierman, William and Beanan, Maureen J. and Brinkac, Lauren M. and Daugherty, Sean C. and Dodson, Robert J. and Durkin, A. Scott and Madupu, Ramana and Haft, Daniel H. and J. Selengut and Van Aken, Susan and Khouri, Hoda and Fedorova, Nadia and Forberger, Heather and Tran, Bao and Kathariou, Sophia and Wonderling, Laura D. and Uhlich, Gaylen A. and Bayles, Darrell O. and Luchansky, John B. and Fraser, Claire M.} } @article {38166, title = {Complete genome sequence and comparative analysis of the metabolically versatile Pseudomonas putida KT2440}, journal = {Environmental MicrobiologyEnvironmental Microbiology}, volume = {5}, year = {2003}, author = {Nelson, K. E. and Weinel, C. and Paulsen, I. T. and Dodson, R. J. and Hilbert, H. and Martins dos Santos, V. A. P. and Fouts, D. E. and Gill, S. R. and M. Pop and Holmes, M. and others,} } @article {38168, title = {The complete genome sequence of the Arabidopsis and tomato pathogen Pseudomonas syringae pv. tomato DC3000}, journal = {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}, volume = {100}, year = {2003}, note = {http://www.ncbi.nlm.nih.gov/pubmed/12928499?dopt=Abstract}, type = {10.1073/pnas.1731982100}, abstract = {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.}, keywords = {Arabidopsis, Base Sequence, Biological Transport, Genome, Bacterial, Lycopersicon esculentum, Molecular Sequence Data, Plant Growth Regulators, Plasmids, Pseudomonas, Reactive Oxygen Species, Siderophores, virulence}, author = {Buell, C. Robin and Joardar, Vinita and Lindeberg, Magdalen and J. Selengut and Paulsen, Ian T. and Gwinn, Michelle L. and Dodson, Robert J. and DeBoy, Robert T. and Durkin, A. Scott and Kolonay, James F. and Madupu, Ramana and Daugherty, Sean and Brinkac, Lauren and Beanan, Maureen J. and Haft, Daniel H. and Nelson, William C. and Davidsen, Tanja and Zafar, Nikhat and Zhou, Liwei and Liu, Jia and Yuan, Qiaoping and Khouri, Hoda and Fedorova, Nadia and Tran, Bao and Russell, Daniel and Berry, Kristi and Utterback, Teresa and Aken, Susan E. van and Feldblyum, Tamara V. and D{\textquoteright}Ascenzo, Mark and Deng, Wen-Ling and Ramos, Adela R. and Alfano, James R. and Cartinhour, Samuel and Chatterjee, Arun K. and Delaney, Terrence P. and Lazarowitz, Sondra G. and Martin, Gregory B. and Schneider, David J. and Tang, Xiaoyan and Bender, Carol L. and White, Owen and Fraser, Claire M. and Collmer, Alan} } @article {38206, title = {Direct Detection of Vibrio Cholerae and ctxA in Peruvian Coastal Water and Plankton by PCR}, journal = {Applied and Environmental MicrobiologyAppl. Environ. Microbiol.Applied and Environmental MicrobiologyAppl. Environ. Microbiol.}, volume = {69}, year = {2003}, type = {10.1128/AEM.69.6.3676-3680.2003}, abstract = {Seawater and plankton samples were collected over a period of 17 months from November 1998 to March 2000 along the coast of Peru. Total DNA was extracted from water and from plankton grouped by size into two fractions (64 μm to 202 μm and >202 μm). All samples were assayed for Vibrio cholerae, V. cholerae O1, V. cholerae O139, and ctxA by PCR. Of 50 samples collected and tested, 33 (66.0\%) were positive for V. cholerae in at least one of the three fractions. Of these, 62.5\% (n = 32) contained V. cholerae O1; ctxA was detected in 25\% (n = 20) of the V. cholerae O1-positive samples. None were positive for V. cholerae O139. Thus, PCR was successfully employed in detecting toxigenic V. cholerae directly in seawater and plankton samples and provides evidence for an environmental reservoir for this pathogen in Peruvian coastal waters.}, isbn = {0099-2240, 1098-5336}, author = {Lipp, Erin K. and Rivera, Irma N. G. and Gil, Ana I. and Espeland, Eric M. and Choopun, Nipa and Louis, Val{\'e}rie R. and Russek-Cohen, Estelle and Huq, Anwar and Rita R. Colwell} } @article {38291, title = {Genome of Geobacter sulfurreducens: metal reduction in subsurface environments}, journal = {Science (New York, N.Y.)Science (New York, N.Y.)}, volume = {302}, year = {2003}, note = {http://www.ncbi.nlm.nih.gov/pubmed/14671304?dopt=Abstract}, type = {10.1126/science.1088727}, abstract = {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.}, keywords = {Acetates, Acetyl Coenzyme A, Aerobiosis, Anaerobiosis, Bacterial Proteins, Carbon, Chemotaxis, Chromosomes, Bacterial, Cytochromes c, Electron Transport, Energy Metabolism, Genes, Bacterial, Genes, Regulator, Genome, Bacterial, Geobacter, Hydrogen, Metals, Movement, Open Reading Frames, Oxidation-Reduction, Phylogeny}, author = {Meth{\'e}, B. A. and Nelson, K. E. and Eisen, J. A. and Paulsen, I. T. and Nelson, W. and Heidelberg, J. F. and Wu, D. and Wu, M. and Ward, N. and Beanan, M. J. and Dodson, R. J. and Madupu, R. and Brinkac, L. M. and Daugherty, S. C. and DeBoy, R. T. and Durkin, A. S. and Gwinn, M. and Kolonay, J. F. and Sullivan, S. A. and Haft, D. H. and J. Selengut and Davidsen, T. M. and Zafar, N. and White, O. and Tran, B. and Romero, C. and Forberger, H. A. and Weidman, J. and Khouri, H. and Feldblyum, T. V. and Utterback, T. R. and Van Aken, S. E. and Lovley, D. R. and Fraser, C. M.} } @article {38300, title = {The genome sequence of Bacillus anthracis Ames and comparison to closely related bacteria}, journal = {NatureNature}, volume = {423}, year = {2003}, note = {[eacute]
[Oslash]}, type = {10.1038/nature01586}, abstract = {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{\textemdash}including haemolysins, phospholipases and iron acquisition functions{\textemdash}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.}, isbn = {0028-0836}, author = {Read, Timothy D. and Peterson, Scott N. and Tourasse, Nicolas and Baillie, Les W. and Paulsen, Ian T. and Nelson, Karen E. and Tettelin, Herv and Fouts, Derrick E. and Eisen, Jonathan A. and Gill, Steven R. and Holtzapple, Erik K. and kstad, Ole Andreas and Helgason, Erlendur and Rilstone, Jennifer and Wu, Martin and Kolonay, James F. and Beanan, Maureen J. and Dodson, Robert J. and Brinkac, Lauren M. and Gwinn, Michelle and DeBoy, Robert T. and Madpu, Ramana and Daugherty, Sean C. and Durkin, A. Scott and Haft, Daniel H. and Nelson, William C. and Peterson, Jeremy D. and M. Pop and Khouri, Hoda M. and Radune, Diana and Benton, Jonathan L. and Mahamoud, Yasmin and Jiang, Lingxia and Hance, Ioana R. and Weidman, Janice F. and Berry, Kristi J. and Plaut, Roger D. and Wolf, Alex M. and Watkins, Kisha L. and Nierman, William C. and Hazen, Alyson and Cline, Robin and Redmond, Caroline and Thwaite, Joanne E. and White, Owen and Salzberg, Steven L. and Thomason, Brendan and Friedlander, Arthur M. and Koehler, Theresa M. and Hanna, Philip C. and Kolst, and Anne-Brit and Fraser, Claire M.} } @article {38376, title = {Method of DNA extraction and application of multiplex polymerase chain reaction to detect toxigenic Vibrio cholerae O1 and O139 from aquatic ecosystems}, journal = {Environmental MicrobiologyEnvironmental Microbiology}, volume = {5}, year = {2003}, type = {10.1046/j.1462-2920.2003.00443.x}, abstract = {Vibrio cholerae is a free-living bacterium found in water and in association with plankton. V. cholerae non-O1/non-O139 strains are frequently isolated from aquatic ecosystems worldwide. Less frequently isolated are V. cholerae O1 and V. cholerae O139, the aetiological agents of cholera. These strains have two main virulence-associated factors, cholera toxin (CT) and toxin co-regulated pilus (TCP). By extracting total DNA from aquatic samples, the presence of pathogenic strains can be determined quickly and used to improve a microbiological risk assessment for cholera in coastal areas. Some methods suggested for DNA extraction from water samples are not applicable to all water types. We describe here a method for DNA extraction from coastal water and a multiplex polymerase chain reaction (PCR) for O1 and O139 serogroups. DNA extraction was successfully accomplished from 117 sea water samples collected from coastal areas of Per{\'u}, Brazil and the USA. DNA concentration in all samples varied from 20~ng to 480~{\textmu}g~{\textmu}l-1. The sensitivity of the DNA extraction method was 100 V. cholerae cells in 250~ml of water. The specificity of multiplex O1/O139 PCR was investigated by analysing 120 strains of V. cholerae, Vibrio and other Bacteria species. All V. cholerae O1 and O139 tested were positive. For cholera surveillance of aquatic environments and ballast water, total DNA extraction, followed by V. cholerae PCR, and O1/O139 serogroup and tcpA/ctxA genes by multiplex PCR offers an efficient system, permitting risk analysis for cholera in coastal areas.}, isbn = {1462-2920}, author = {Rivera, Irma N. G. and Lipp, Erin K. and Gil, Ana and Choopun, Nipa and Huq, Anwar and Rita R. Colwell} } @article {38445, title = {Predictability of Vibrio Cholerae in Chesapeake Bay}, journal = {Applied and Environmental MicrobiologyAppl. Environ. Microbiol.Applied and Environmental MicrobiologyAppl. Environ. Microbiol.}, volume = {69}, year = {2003}, type = {10.1128/AEM.69.5.2773-2785.2003}, abstract = {Vibrio cholerae is autochthonous to natural waters and can pose a health risk when it is consumed via untreated water or contaminated shellfish. The correlation between the occurrence of V. cholerae in Chesapeake Bay and environmental factors was investigated over a 3-year period. Water and plankton samples were collected monthly from five shore sampling sites in northern Chesapeake Bay (January 1998 to February 2000) and from research cruise stations on a north-south transect (summers of 1999 and 2000). Enrichment was used to detect culturable V. cholerae, and 21.1\% (n = 427) of the samples were positive. As determined by serology tests, the isolates, did not belong to serogroup O1 or O139 associated with cholera epidemics. A direct fluorescent-antibody assay was used to detect V. cholerae O1, and 23.8\% (n = 412) of the samples were positive. V. cholerae was more frequently detected during the warmer months and in northern Chesapeake Bay, where the salinity is lower. Statistical models successfully predicted the presence of V. cholerae as a function of water temperature and salinity. Temperatures above 19{\textdegree}C and salinities between 2 and 14 ppt yielded at least a fourfold increase in the number of detectable V. cholerae. The results suggest that salinity variation in Chesapeake Bay or other parameters associated with Susquehanna River inflow contribute to the variability in the occurrence of V. cholerae and that salinity is a useful indicator. Under scenarios of global climate change, increased climate variability, accompanied by higher stream flow rates and warmer temperatures, could favor conditions that increase the occurrence of V. cholerae in Chesapeake Bay.}, isbn = {0099-2240, 1098-5336}, author = {Louis, Val{\'e}rie R. and Russek-Cohen, Estelle and Choopun, Nipa and Rivera, Irma N. G. and Gangle, Brian and Jiang, Sunny C. and Rubin, Andrea and Patz, Jonathan A. and Huq, Anwar and Rita R. Colwell} } @article {38489, title = {The sequence and analysis of Trypanosoma brucei chromosome II}, journal = {Nucleic acids researchNucleic Acids Research}, volume = {31}, year = {2003}, author = {Najib M. El-Sayed and Ghedin, E. and Song, J. and MacLeod, A. and Bringaud, F. and Larkin, C. and Wanless, D. and Peterson, J. and Hou, L. and Taylor, S. and others,} } @article {49633, title = {The sequence and analysis of Trypanosoma brucei chromosome II.}, journal = {Nucleic Acids Res}, volume = {31}, year = {2003}, month = {2003 Aug 15}, pages = {4856-63}, abstract = {

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 {\textquoteright}hot{\textquoteright} and {\textquoteright}cold{\textquoteright} 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.

}, keywords = {Animals, Antigens, Protozoan, Chromosome mapping, Chromosomes, DNA, Protozoan, Gene Duplication, Genes, Protozoan, Molecular Sequence Data, Pseudogenes, Recombination, Genetic, Sequence Analysis, DNA, Trypanosoma brucei brucei}, issn = {1362-4962}, author = {el-Sayed, Najib M A and Ghedin, Elodie and Song, Jinming and MacLeod, Annette and Bringaud, Frederic and Larkin, Christopher and Wanless, David and Peterson, Jeremy and Hou, Lihua and Taylor, Sonya and Tweedie, Alison and Biteau, Nicolas and Khalak, Hanif G and Lin, Xiaoying and Mason, Tanya and Hannick, Linda and Caler, Elisabet and Blandin, Ga{\"e}lle and Bartholomeu, Daniella and Simpson, Anjana J and Kaul, Samir and Zhao, Hong and Pai, Grace and Van Aken, Susan and Utterback, Teresa and Haas, Brian and Koo, Hean L and Umayam, Lowell and Suh, Bernard and Gerrard, Caroline and Leech, Vanessa and Qi, Rong and Zhou, Shiguo and Schwartz, David and Feldblyum, Tamara and Salzberg, Steven and Tait, Andrew and Turner, C Michael R and Ullu, Elisabetta and White, Owen and Melville, Sara and Adams, Mark D and Fraser, Claire M and Donelson, John E} } @article {49687, title = {The draft genome of Ciona intestinalis: insights into chordate and vertebrate origins.}, journal = {Science}, volume = {298}, year = {2002}, month = {2002 Dec 13}, pages = {2157-67}, abstract = {

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.

}, keywords = {Alleles, Animals, Apoptosis, Base Sequence, Cellulose, Central Nervous System, Ciona intestinalis, Computational Biology, Endocrine System, Gene Dosage, Gene Duplication, genes, Genes, Homeobox, Genome, Heart, Immunity, Molecular Sequence Data, Multigene Family, Muscle Proteins, Organizers, Embryonic, Phylogeny, Polymorphism, Genetic, Proteins, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Species Specificity, Thyroid Gland, Urochordata, Vertebrates}, issn = {1095-9203}, doi = {10.1126/science.1080049}, author = {Dehal, Paramvir and Satou, Yutaka and Campbell, Robert K and Chapman, Jarrod and Degnan, Bernard and De Tomaso, Anthony and Davidson, Brad and Di Gregorio, Anna and Gelpke, Maarten and Goodstein, David M and Harafuji, Naoe and Hastings, Kenneth E M and Ho, Isaac and Hotta, Kohji and Huang, Wayne and Kawashima, Takeshi and Lemaire, Patrick and Martinez, Diego and Meinertzhagen, Ian A and Necula, Simona and Nonaka, Masaru and Putnam, Nik and Rash, Sam and Saiga, Hidetoshi and Satake, Masanobu and Terry, Astrid and Yamada, Lixy and Wang, Hong-Gang and Awazu, Satoko and Azumi, Kaoru and Boore, Jeffrey and Branno, Margherita and Chin-Bow, Stephen and DeSantis, Rosaria and Doyle, Sharon and Francino, Pilar and Keys, David N and Haga, Shinobu and Hayashi, Hiroko and Hino, Kyosuke and Imai, Kaoru S and Inaba, Kazuo and Kano, Shungo and Kobayashi, Kenji and Kobayashi, Mari and Lee, Byung-In and Makabe, Kazuhiro W and Manohar, Chitra and Matassi, Giorgio and Medina, Monica and Mochizuki, Yasuaki and Mount, Steve and Morishita, Tomomi and Miura, Sachiko and Nakayama, Akie and Nishizaka, Satoko and Nomoto, Hisayo and Ohta, Fumiko and Oishi, Kazuko and Rigoutsos, Isidore and Sano, Masako and Sasaki, Akane and Sasakura, Yasunori and Shoguchi, Eiichi and Shin-i, Tadasu and Spagnuolo, Antoinetta and Stainier, Didier and Suzuki, Miho M and Tassy, Olivier and Takatori, Naohito and Tokuoka, Miki and Yagi, Kasumi and Yoshizaki, Fumiko and Wada, Shuichi and Zhang, Cindy and Hyatt, P Douglas and Larimer, Frank and Detter, Chris and Doggett, Norman and Glavina, Tijana and Hawkins, Trevor and Richardson, Paul and Lucas, Susan and Kohara, Yuji and Levine, Michael and Satoh, Nori and Rokhsar, Daniel S} } @proceedings {38249, title = {Experimental Construction of Very Large Scale DNA Databases with Associative Search}, volume = {7}, year = {2002}, month = {2002}, author = {Reif, J. H. and LaBean, T. H. and Pirrung, M. and Rana, V. S. and Guo, B. and Kingsford, Carl and Wickham, G. S.} } @article {38295, title = {Genome sequence and comparative analysis of the model rodent malaria parasite Plasmodium yoelii yoelii}, journal = {NatureNature}, volume = {419}, year = {2002}, type = {10.1038/nature01099}, abstract = {Species of malaria parasite that infect rodents have long been used as models for malaria disease research. Here we report the whole-genome shotgun sequence of one species, Plasmodium yoelii yoelii, and comparative studies with the genome of the human malaria parasite Plasmodium falciparum clone 3D7. A synteny map of 2,212 P. y. yoelii contiguous DNA sequences (contigs) aligned to 14 P. falciparum chromosomes reveals marked conservation of gene synteny within the body of each chromosome. Of about 5,300 P. falciparum genes, more than 3,300 P. y. yoelii orthologues of predominantly metabolic function were identified. Over 800 copies of a variant antigen gene located in subtelomeric regions were found. This is the first genome sequence of a model eukaryotic parasite, and it provides insight into the use of such systems in the modelling of Plasmodium biology and disease.}, isbn = {0028-0836}, author = {Carlton, Jane M. and Angiuoli, Samuel V. and Suh, Bernard B. and Kooij, Taco W. and Pertea, Mihaela and Silva, Joana C. and Ermolaeva, Maria D. and Allen, Jonathan E. and J. Selengut and Koo, Hean L. and Peterson, Jeremy D. and M. Pop and Kosack, Daniel S. and Shumway, Martin F. and Bidwell, Shelby L. and Shallom, Shamira J. and Aken, Susan E. van and Riedmuller, Steven B. and Feldblyum, Tamara V. and Cho, Jennifer K. and Quackenbush, John and Sedegah, Martha and Shoaibi, Azadeh and Cummings, Leda M. and Florens, Laurence and Yates, John R. and Raine, J. Dale and Sinden, Robert E. and Harris, Michael A. and Cunningham, Deirdre A. and Preiser, Peter R. and Bergman, Lawrence W. and Vaidya, Akhil B. and Lin, Leo H. van and Janse, Chris J. and Waters, Andrew P. and Smith, Hamilton O. and White, Owen R. and Salzberg, Steven L. and Venter, J. Craig and Fraser, Claire M. and Hoffman, Stephen L. and Gardner, Malcolm J. and Carucci, Daniel J.} } @article {38304, title = {Genome sequence of the human malaria parasite Plasmodium falciparum}, journal = {NatureNature}, volume = {419}, year = {2002}, note = {http://www.ncbi.nlm.nih.gov/pubmed/12368864?dopt=Abstract}, type = {10.1038/nature01097}, abstract = {The parasite Plasmodium falciparum is responsible for hundreds of millions of cases of malaria, and kills more than one million African children annually. Here we report an analysis of the genome sequence of P. falciparum clone 3D7. The 23-megabase nuclear genome consists of 14 chromosomes, encodes about 5,300 genes, and is the most (A + T)-rich genome sequenced to date. Genes involved in antigenic variation are concentrated in the subtelomeric regions of the chromosomes. Compared to the genomes of free-living eukaryotic microbes, the genome of this intracellular parasite encodes fewer enzymes and transporters, but a large proportion of genes are devoted to immune evasion and host-parasite interactions. Many nuclear-encoded proteins are targeted to the apicoplast, an organelle involved in fatty-acid and isoprenoid metabolism. The genome sequence provides the foundation for future studies of this organism, and is being exploited in the search for new drugs and vaccines to fight malaria.}, keywords = {Animals, Chromosome Structures, DNA Repair, DNA Replication, DNA, Protozoan, Evolution, Molecular, Genome, Protozoan, HUMANS, Malaria Vaccines, Malaria, Falciparum, Membrane Transport Proteins, Molecular Sequence Data, Plasmodium falciparum, Plastids, Proteome, Protozoan Proteins, Recombination, Genetic, Sequence Analysis, DNA}, author = {Gardner, Malcolm J. and Hall, Neil and Fung, Eula and White, Owen and Berriman, Matthew and Hyman, Richard W. and Carlton, Jane M. and Pain, Arnab and Nelson, Karen E. and Bowman, Sharen and Paulsen, Ian T. and James, Keith and Eisen, Jonathan A. and Rutherford, Kim and Salzberg, Steven L. and Craig, Alister and Kyes, Sue and Chan, Man-Suen and Nene, Vishvanath and Shallom, Shamira J. and Suh, Bernard and Peterson, Jeremy and Angiuoli, Sam and Pertea, Mihaela and Allen, Jonathan and J. Selengut and Haft, Daniel and Mather, Michael W. and Vaidya, Akhil B. and Martin, David M. A. and Fairlamb, Alan H. and Fraunholz, Martin J. and Roos, David S. and Ralph, Stuart A. and McFadden, Geoffrey I. and Cummings, Leda M. and Subramanian, G. Mani and Mungall, Chris and Venter, J. Craig and Carucci, Daniel J. and Hoffman, Stephen L. and Newbold, Chris and Davis, Ronald W. and Fraser, Claire M. and Barrell, Bart} } @article {38334, title = {Identification of non-autonomous non-LTR retrotransposons in the genome of Trypanosoma cruzi}, journal = {Molecular and Biochemical ParasitologyMolecular and Biochemical Parasitology}, volume = {124}, year = {2002}, type = {16/S0166-6851(02)00167-6}, abstract = {As observed for most eukaryotic cells, trypanosomatids contains non-LTR retrotransposons randomly inserted in the nuclear genome. Autonomous retroelements which, code for their own transposition, have been characterized in Trypanosoma brucei (ingi) and Trypanosoma cruzi (L1Tc), whereas non-autonomous retroelements have only been characterized in T. brucei (RIME). Here, we have characterized in the genome of Trypanosoma cruzi four complete copies of a non-autonomous non-LTR retrotransposon, called NARTc. This 0.26 kb NARTc element has the characteristics of non-LTR retrotransposons: the presence a poly(dA) tail and of a short flanking duplicated motif. Analysis of the Genome Survey Sequence databases indicated that the Trypanosoma cruzi haploid genome contains about 140 NARTc copies and about twice as many L1Tc copies. Interestingly, the NARTc and L1Tc retroelements share, with the Trypanosoma brucei ingi and RIME retrotransposons, a common sequence (the first 45 bp with 91\% identity), whereas the remaining sequences are very divergent. This suggests that these four trypanosome non-LTR retrotransposons were derived from the same common ancester and the sequence of their 5{\textquoteright}-extremity may have a functional role. In addition, the genome of Leishmania major contains the same conserved motif present in the trypanosome retroelements, whicle no transposable elements have been detected so far in Leishmania sp.}, keywords = {Ingi, L1Tc, Non-LTR retrotransposon, RIME, Trypanosoma brucei, Trypanosoma cruzi}, isbn = {0166-6851}, author = {Bringaud, Frederic and Garc{\'\i}a-P{\'e}rez, Jos{\'e} Luis and Heras, Sara R. and Ghedin, Elodie and Najib M. El-Sayed and Andersson, Bj{\"o}rn and Baltz, Th{\'e}o and Lopez, Manuel C.} } @article {49630, title = {Identification of non-autonomous non-LTR retrotransposons in the genome of Trypanosoma cruzi.}, journal = {Mol Biochem Parasitol}, volume = {124}, year = {2002}, month = {2002 Sep-Oct}, pages = {73-8}, abstract = {

As observed for most eukaryotic cells, trypanosomatids contains non-LTR retrotransposons randomly inserted in the nuclear genome. Autonomous retroelements which, code for their own transposition, have been characterized in Trypanosoma brucei (ingi) and Trypanosoma cruzi (L1Tc), whereas non-autonomous retroelements have only been characterized in T. brucei (RIME). Here, we have characterized in the genome of Trypanosoma cruzi four complete copies of a non-autonomous non-LTR retrotransposon, called NARTc. This 0.26 kb NARTc element has the characteristics of non-LTR retrotransposons: the presence a poly(dA) tail and of a short flanking duplicated motif. Analysis of the Genome Survey Sequence databases indicated that the Trypanosoma cruzi haploid genome contains about 140 NARTc copies and about twice as many L1Tc copies. Interestingly, the NARTc and L1Tc retroelements share, with the Trypanosoma brucei ingi and RIME retrotransposons, a common sequence (the first 45 bp with 91\% identity), whereas the remaining sequences are very divergent. This suggests that these four trypanosome non-LTR retrotransposons were derived from the same common ancester and the sequence of their 5{\textquoteright}-extremity may have a functional role. In addition, the genome of Leishmania major contains the same conserved motif present in the trypanosome retroelements, whicle no transposable elements have been detected so far in Leishmania sp.

}, keywords = {Animals, Base Sequence, Computational Biology, Genome, Protozoan, Long Interspersed Nucleotide Elements, Molecular Sequence Data, Retroelements, Short Interspersed Nucleotide Elements, Trypanosoma cruzi}, issn = {0166-6851}, author = {Bringaud, Frederic and Garc{\'\i}a-P{\'e}rez, Jos{\'e} Luis and Heras, Sara R and Ghedin, Elodie and El-Sayed, Najib M and Andersson, Bj{\"o}rn and Baltz, Th{\'e}o and Lopez, Manuel C} } @article {38430, title = {Phylogenetic analysis based on 18S ribosomal RNA gene sequences supports the existence of class Polyacanthocephala (Acanthocephala)}, journal = {Mol Phylogenet EvolMol Phylogenet Evol}, volume = {23}, year = {2002}, type = {10.1016/S1055-7903(02)00020-9}, abstract = {Members of phylum Acanthocephala are parasites of vertebrates and arthropods and are distributed worldwide. The phylum has traditionally been divided into three classes, Archiacanthocephala, Palaeacanthocephala, and Eoacanthocephala; a fourth class, Polyacanthocephala, has been recently proposed. However, erection of this new class, based on morphological characters, has been controversial. We sequenced the near complete 18S rRNA gene of Polyacanthorhynchus caballeroi (Polyacanthocephala) and Rhadinorhynchus sp. (Palaeacanthocephala); these sequences were aligned with another 21 sequences of acanthocephalans representing the three widely recognized classes of the phylum and with 16 sequences from outgroup taxa. Phylogenetic relationships inferred by maximum-likelihood and maximum-parsimony analyses showed Archiacanthocephala as the most basal group within the phylum, whereas classes Polyacanthocephala + Eoacanthocephala formed a monophyletic clade, with Palaeacanthocephala as its sister group. These results are consistent with the view of Polyacanthocephala representing an independent class within Acanthocephala.}, author = {Garc{\'\i}a-Varela, M. and Michael P. Cummings and P{\'e}rez-Ponce de Le{\'o}n, G. and Gardner, S. L. and Laclette, J. P.} } @article {38492, title = {Sequence of Plasmodium falciparum chromosomes 2, 10, 11 and 14}, journal = {NatureNature}, volume = {419}, year = {2002}, note = {http://www.ncbi.nlm.nih.gov/pubmed/12368868?dopt=Abstract}, type = {10.1038/nature01094}, abstract = {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.}, keywords = {Animals, Chromosomes, DNA, Protozoan, Genome, Protozoan, Plasmodium falciparum, Proteome, Protozoan Proteins, Sequence Analysis, DNA}, author = {Gardner, Malcolm J. and Shallom, Shamira J. and Carlton, Jane M. and Salzberg, Steven L. and Nene, Vishvanath and Shoaibi, Azadeh and Ciecko, Anne and Lynn, Jeffery and Rizzo, Michael and Weaver, Bruce and Jarrahi, Behnam and Brenner, Michael and Parvizi, Babak and Tallon, Luke and Moazzez, Azita and Granger, David and Fujii, Claire and Hansen, Cheryl and Pederson, James and Feldblyum, Tamara and Peterson, Jeremy and Suh, Bernard and Angiuoli, Sam and Pertea, Mihaela and Allen, Jonathan and J. Selengut and White, Owen and Cummings, Leda M. and Smith, Hamilton O. and Adams, Mark D. and Venter, J. Craig and Carucci, Daniel J. and Hoffman, Stephen L. and Fraser, Claire M.} } @article {38551, title = {Trypanosoma cruzi: RNA structure and post-transcriptional control of tubulin gene expression}, journal = {Experimental ParasitologyExperimental Parasitology}, volume = {102}, year = {2002}, type = {16/S0014-4894(03)00034-1}, abstract = {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{\textquoteright} 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{\textquoteright} 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.}, isbn = {0014-4894}, author = {Bartholomeu, Daniella C. and Silva, Rosiane A. and Galv{\~a}o, Lucia M. C. and Najib M. El-Sayed and Donelson, John E. and Teixeira, Santuza M. R.} } @article {49632, title = {Trypanosoma cruzi: RNA structure and post-transcriptional control of tubulin gene expression.}, journal = {Exp Parasitol}, volume = {102}, year = {2002}, month = {2002 Nov-Dec}, pages = {123-33}, abstract = {

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{\textquoteright} 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{\textquoteright} 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.

}, keywords = {Animals, Base Sequence, Blotting, Northern, DNA, Complementary, DNA, Protozoan, Gene Expression Regulation, Half-Life, Life Cycle Stages, Molecular Sequence Data, RNA Processing, Post-Transcriptional, RNA, Messenger, RNA, Protozoan, Transcription, Genetic, Transfection, Trypanosoma cruzi, Tubulin}, issn = {0014-4894}, author = {Bartholomeu, Daniella C and Silva, Rosiane A and Galv{\~a}o, Lucia M C and el-Sayed, Najib M A and Donelson, John E and Teixeira, Santuza M R} } @proceedings {38226, title = {Efficient perspective-accurate silhouette computation and applications}, year = {2001}, month = {2001}, publisher = {ACM}, type = {10.1145/378583.378618}, address = {New York, NY, USA}, abstract = {Silhouettes are perceptually and geometrically salient features of geo metric models. Hence a number of graphics and visualization applications need to find them to aid further processing. The efficient computation of silhouettes, especially in the context of perspective projection, is known to be difficult. This paper presents a novel efficient and practical algorithm to compute silhouettes from a sequence of viewpoints under perspective projection. Parallel projection is a special case of this algorithm. Our approach is based on a point-plane duality in three dimensions, which allows an efficient computation of the \emph{changes} in the silhouette of a polygonal model between consecutive frames. In addition, we present several applications of our technique to problems from computer graphics and medical visualization. We also provide experimental data that show the efficiency of our approach. million vertices on an SGI Onyx workstation.}, keywords = {rendering, silhouette, simplification}, isbn = {1-58113-357-X}, author = {M. Pop and Duncan, Christian and Barequet, Gill and Goodrich, Michael and Huang, Wenjing and Kumar, Subodh} } @article {49692, title = {The genome sequence of Drosophila melanogaster.}, journal = {Science}, volume = {287}, year = {2000}, month = {2000 Mar 24}, pages = {2185-95}, abstract = {

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.

}, keywords = {Animals, Biological Transport, Chromatin, Cloning, Molecular, Computational Biology, Contig Mapping, Cytochrome P-450 Enzyme System, DNA Repair, DNA Replication, Drosophila melanogaster, Euchromatin, Gene Library, Genes, Insect, Genome, Heterochromatin, Insect Proteins, Nuclear Proteins, Protein Biosynthesis, Sequence Analysis, DNA, Transcription, Genetic}, issn = {0036-8075}, author = {Adams, M D and Celniker, S E and Holt, R A and Evans, C A and Gocayne, J D and Amanatides, P G and Scherer, S E and Li, P W and Hoskins, R A and Galle, R F and George, R A and Lewis, S E and Richards, S and Ashburner, M and Henderson, S N and Sutton, G G and Wortman, J R and Yandell, M D and Zhang, Q and Chen, L X and Brandon, R C and Rogers, Y H and Blazej, R G and Champe, M and Pfeiffer, B D and Wan, K H and Doyle, C and Baxter, E G and Helt, G and Nelson, C R and Gabor, G L and Abril, J F and Agbayani, A and An, H J and Andrews-Pfannkoch, C and Baldwin, D and Ballew, R M and Basu, A and Baxendale, J and Bayraktaroglu, L and Beasley, E M and Beeson, K Y and Benos, P V and Berman, B P and Bhandari, D and Bolshakov, S and Borkova, D and Botchan, M R and Bouck, J and Brokstein, P and Brottier, P and Burtis, K C and Busam, D A and Butler, H and Cadieu, E and Center, A and Chandra, I and Cherry, J M and Cawley, S and Dahlke, C and Davenport, L B and Davies, P and de Pablos, B and Delcher, A and Deng, Z and Mays, A D and Dew, I and Dietz, S M and Dodson, K and Doup, L E and Downes, M and Dugan-Rocha, S and Dunkov, B C and Dunn, P and Durbin, K J and Evangelista, C C and Ferraz, C and Ferriera, S and Fleischmann, W and Fosler, C and Gabrielian, A E and Garg, N S and Gelbart, W M and Glasser, K and Glodek, A and Gong, F and Gorrell, J H and Gu, Z and Guan, P and Harris, M and Harris, N L and Harvey, D and Heiman, T J and Hernandez, J R and Houck, J and Hostin, D and Houston, K A and Howland, T J and Wei, M H and Ibegwam, C and Jalali, M and Kalush, F and Karpen, G H and Ke, Z and Kennison, J A and Ketchum, K A and Kimmel, B E and Kodira, C D and Kraft, C and Kravitz, S and Kulp, D and Lai, Z and Lasko, P and Lei, Y and Levitsky, A A and Li, J and Li, Z and Liang, Y and Lin, X and Liu, X and Mattei, B and McIntosh, T C and McLeod, M P and McPherson, D and Merkulov, G and Milshina, N V and Mobarry, C and Morris, J and Moshrefi, A and Mount, S M and Moy, M and Murphy, B and Murphy, L and Muzny, D M and Nelson, D L and Nelson, D R and Nelson, K A and Nixon, K and Nusskern, D R and Pacleb, J M and Palazzolo, M and Pittman, G S and Pan, S and Pollard, J and Puri, V and Reese, M G and Reinert, K and Remington, K and Saunders, R D and Scheeler, F and Shen, H and Shue, B C and Sid{\'e}n-Kiamos, I and Simpson, M and Skupski, M P and Smith, T and Spier, E and Spradling, A C and Stapleton, M and Strong, R and Sun, E and Svirskas, R and Tector, C and Turner, R and Venter, E and Wang, A H and Wang, X and Wang, Z Y and Wassarman, D A and Weinstock, G M and Weissenbach, J and Williams, S M and Worley, K C and Wu, D and Yang, S and Yao, Q A and Ye, J and Yeh, R F and Zaveri, J S and Zhan, M and Zhang, G and Zhao, Q and Zheng, L and Zheng, X H and Zhong, F N and Zhong, W and Zhou, X and Zhu, S and Zhu, X and Smith, H O and Gibbs, R A and Myers, E W and Rubin, G M and Venter, J C} } @article {38433, title = {Phylogenetic relationships of Acanthocephala based on analysis of 18S ribosomal RNA gene sequences}, journal = {J Mol EvolJ Mol Evol}, volume = {50}, year = {2000}, abstract = {Acanthocephala (thorny-headed worms) is a phylum of endoparasites of vertebrates and arthropods, included among the most phylogenetically basal tripoblastic pseudocoelomates. The phylum is divided into three classes: Archiacanthocephala, Palaeacanthocephala, and Eoacanthocephala. These classes are distinguished by morphological characters such as location of lacunar canals, persistence of ligament sacs in females, number and type of cement glands in males, number and size of proboscis hooks, host taxonomy, and ecology. To understand better the phylogenetic relationships within Acanthocephala, and between Acanthocephala and Rotifera, we sequenced the nearly complete 18S rRNA genes of nine species from the three classes of Acanthocephala and four species of Rotifera from the classes Bdelloidea and Monogononta. Phylogenetic relationships were inferred by maximum-likelihood analyses of these new sequences and others previously determined. The analyses showed that Acanthocephala is the sister group to a clade including Eoacanthocephala and Palaeacanthocephala. Archiacanthocephala exhibited a slower rate of evolution at the nucleotide level, as evidenced by shorter branch lengths for the group. We found statistically significant support for the monophyly of Rotifera, represented in our analysis by species from the clade Eurotatoria, which includes the classes Bdelloidea and Monogononta. Eurotatoria also appears as the sister group to Acanthocephala.}, author = {Garc{\'\i}a-Varela, M. and P{\'e}rez-Ponce de Le{\'o}n, G. and de la Torre, P. and Michael P. Cummings and Sarma, S. S. and Laclette, J. P.} } @article {38390, title = {More surprises from Kinetoplastida}, journal = {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}, volume = {96}, year = {1999}, author = {Donelson, J. E. and Gardner, M. J. and Najib M. El-Sayed} } @article {38428, title = {Penumbral tissue damage following acute stroke: a computational investigation}, journal = {Progress in brain researchProgress in brain research}, volume = {121}, year = {1999}, author = {Ruppin, E. and Revett, K. and Ofer, E. and Goodall, S. and Reggia, James A.} } @article {49627, title = {Genetic nomenclature for Trypanosoma and Leishmania.}, journal = {Mol Biochem Parasitol}, volume = {97}, year = {1998}, month = {1998 Nov 30}, pages = {221-4}, keywords = {Animals, Leishmania, Terminology as Topic, Trypanosoma}, issn = {0166-6851}, author = {Clayton, C and Adams, M and Almeida, R and Baltz, T and Barrett, M and Bastien, P and Belli, S and Beverley, S and Biteau, N and Blackwell, J and Blaineau, C and Boshart, M and Bringaud, F and Cross, G and Cruz, A and Degrave, W and Donelson, J and El-Sayed, N and Fu, G and Ersfeld, K and Gibson, W and Gull, K and Ivens, A and Kelly, J and Vanhamme, L} } @article {38512, title = {Spreading depression in focal ischemia: A computational study}, journal = {Journal of Cerebral Blood Flow \& MetabolismJournal of Cerebral Blood Flow \& Metabolism}, volume = {18}, year = {1998}, author = {Revett, K. and Ruppin, E. and Goodall, S. and Reggia, James A.} } @article {38548, title = {Trends in the early careers of life scientists - Preface and executive summary}, journal = {Mol Biol CellMol Biol Cell}, volume = {9}, year = {1998}, author = {Tilghman, S. and Astin, H. S. and Brinkley, W. and Chilton, M. D. and Michael P. Cummings and Ehrenberg, R. G. and Fox, M. F. and Glenn, K. and Green, P. J. and Hans, S. and Kelman, A. and LaPidus, J. and Levin, B. and McIntosh, J. R. and Riecken, H. and Stephen, P. E.} } @article {38173, title = {A computational model of acute focal cortical lesions}, journal = {StrokeStroke}, volume = {28}, year = {1997}, author = {Goodall, S. and Reggia, James A. and Chen, Y. and Ruppin, E. and Whitney, C.} } @article {49697, title = {Localization of sequences required for size-specific splicing of a small Drosophila intron in vitro.}, journal = {J Mol Biol}, volume = {253}, year = {1995}, month = {1995 Oct 27}, pages = {426-37}, abstract = {

Many introns in Drosophila and other invertebrates are less than 80 nucleotides in length, too small to be recognized by the vertebrate splicing machinery. Comparison of nuclear splicing extracts from human HeLa and Drosophila Kc cells has revealed species-specificity, consistent with the observed size differences. Here we present additional results with the 68 nucleotide fifth intron of the Drosophila myosin heavy chain gene. As observed with the 74 nucleotide second intron of the Drosophila white gene, the wild-type myosin intron is accurately spliced in a homologous extract, and increasing the size by 16 nucleotides both eliminates splicing in the Drosophila extract and allows accurate splicing in the human extract. In contrast to previous results, however, an upstream cryptic 5{\textquoteright} splice site is activated when the wild-type myosin intron is tested in a human HeLa cell nuclear extract, resulting in the removal of a 98 nucleotide intron. The size dependence of splicing in Drosophila extracts is also intron-specific; we noted that a naturally larger (150 nucleotide) intron from the ftz gene is efficiently spliced in Kc cell extracts that do not splice enlarged introns (of 84, 90, 150 or 350 nucleotides) derived from the 74 nucleotide white intron. Here, we have exploited that observation, using a series of hybrid introns to show that a region of 46 nucleotides at the 3{\textquoteright} end of the white intron is sufficient to confer the species-specific size effect. At least two sequence elements within this region, yet distinct from previously described branchpoint and pyrimidine tract signals, are required for efficient splicing of small hybrid introns in vitro.

}, keywords = {Animals, Base Sequence, Cell Line, DNA, Drosophila, Genes, Insect, HeLa Cells, HUMANS, Introns, Molecular Sequence Data, Myosin Heavy Chains, RNA Splicing, Species Specificity}, issn = {0022-2836}, doi = {10.1006/jmbi.1995.0564}, author = {Guo, M and Mount, S M} } @article {49701, title = {Species-specific signals for the splicing of a short Drosophila intron in vitro.}, journal = {Mol Cell Biol}, volume = {13}, year = {1993}, month = {1993 Feb}, pages = {1104-18}, abstract = {

The effects of branchpoint sequence, the pyrimidine stretch, and intron size on the splicing efficiency of the Drosophila white gene second intron were examined in nuclear extracts from Drosophila and human cells. This 74-nucleotide intron is typical of many Drosophila introns in that it lacks a significant pyrimidine stretch and is below the minimum size required for splicing in human nuclear extracts. Alteration of sequences of adjacent to the 3{\textquoteright} splice site to create a pyrimidine stretch was necessary for splicing in human, but not Drosophila, extracts. Increasing the size of this intron with insertions between the 5{\textquoteright} splice site and the branchpoint greatly reduced the efficiency of splicing of introns longer than 79 nucleotides in Drosophila extracts but had an opposite effect in human extracts, in which introns longer than 78 nucleotides were spliced with much greater efficiency. The white-apricot copia insertion is immediately adjacent to the branchpoint normally used in the splicing of this intron, and a copia long terminal repeat insertion prevents splicing in Drosophila, but not human, extracts. However, a consensus branchpoint does not restore the splicing of introns containing the copia long terminal repeat, and alteration of the wild-type branchpoint sequence alone does not eliminate splicing. These results demonstrate species specificity of splicing signals, particularly pyrimidine stretch and size requirements, and raise the possibility that variant mechanisms not found in mammals may operate in the splicing of small introns in Drosophila and possibly other species.

}, keywords = {Animals, Base Sequence, Cell Nucleus, Consensus Sequence, DNA, DNA Transposable Elements, Drosophila, Drosophila Proteins, Electrophoresis, Polyacrylamide Gel, HeLa Cells, HUMANS, Introns, Molecular Sequence Data, Mutation, Peptide Hydrolases, Proteins, Regulatory Sequences, Nucleic Acid, Retroelements, RNA Splicing, Species Specificity}, issn = {0270-7306}, author = {Guo, M and Lo, P C and Mount, S M} } @article {49708, title = {Partial revertants of the transposable element-associated suppressible allele white-apricot in Drosophila melanogaster: structures and responsiveness to genetic modifiers.}, journal = {Genetics}, volume = {118}, year = {1988}, month = {1988 Feb}, pages = {221-34}, abstract = {

The eye color phenotype of white-apricot (wa), a mutant allele of the white locus caused by the insertion of the transposable element copia into a small intron, is suppressed by the extragenic suppressor suppressor-of-white-apricot (su(wa] and enhanced by the extragenic enhancers suppressor-of-forked su(f] and Enhancer-of-white-apricot (E(wa]. Derivatives of wa have been analyzed molecularly and genetically in order to correlate the structure of these derivatives with their response to modifiers. Derivatives in which the copia element is replaced precisely by a solo long terminal repeat (sLTR) were generated in vitro and returned to the germline by P-element mediated transformation; flies carrying this allele within a P transposon show a nearly wild-type phenotype and no response to either su(f) or su(wa). In addition, eleven partial phenotypic revertants of wa were analyzed. Of these, one appears to be a duplication of a large region which includes wa, three are new alleles of su(wa), two are sLTR derivatives whose properties confirm results obtained using transformation, and five are secondary insertions into the copia element within wa. One of these, waR84h, differs from wa by the insertion of the most 3{\textquoteright} 83 nucleotides of the I factor. The five insertion derivatives show a variety of phenotypes and modes of interaction with su[f) and su(wa). The eye pigmentation of waR84h is affected by su(f) and E(wa), but not su(wa). These results demonstrate that copia (as opposed to the interruption of white sequences) is essential for the wa phenotype and its response to genetic modifiers, and that there are multiple mechanisms for the alteration of the wa phenotype by modifiers.

}, keywords = {Alleles, Animals, Base Sequence, DNA Transposable Elements, Drosophila melanogaster, Enhancer Elements, Genetic, GENOTYPE, Molecular Sequence Data, Mutation, Suppression, Genetic}, issn = {0016-6731}, author = {Mount, S M and Green, M M and Rubin, G M} } @article {49716, title = {Small ribonucleoproteins from eukaryotes: structures and roles in RNA biogenesis.}, journal = {Cold Spring Harb Symp Quant Biol}, volume = {47 Pt 2}, year = {1983}, month = {1983}, pages = {893-900}, keywords = {Animals, Base Sequence, HeLa Cells, HUMANS, Mice, Molecular Weight, Nucleic Acid Conformation, Nucleic Acid Hybridization, Nucleoproteins, Ribonucleoproteins, Ribonucleoproteins, Small Nuclear, RNA Polymerase III, Transcription, Genetic}, issn = {0091-7451}, author = {Steitz, J A and Wolin, S L and Rinke, J and Pettersson, I and Mount, S M and Lerner, E A and Hinterberger, M and Gottlieb, E} } @article {49718, title = {Structure and function of small ribonucleoproteins from eukaryotic cells.}, journal = {Princess Takamatsu Symp}, volume = {12}, year = {1982}, month = {1982}, pages = {101-7}, abstract = {

Autoantibodies from patients with systemic lupus erythematosus and other related diseases have been used to identify and study small RNA-protein complexes from mammalian cells. Properties of three previously described and several new classes of small ribonucleoproteins (RNPs) are reviewed. The sequence of Drosophila U1 RNA reveals that the region proposed to pair with 5{\textquoteright} splice junctions is conserved, while that proposed to interact with 3{\textquoteright} junctions diverges; this forces some revision of the model for U1 small nuclear (sn)RNP participation in hnRNA splicing. Further characterization of the Ro and La small RNPs has shown that the Ro small cytoplasmic (sc)RNPs are a subclass of La RNPs. Both tRNA and 5S rRNA precursors are at least transiently associated with the La protein. This raises the possibility that the La protein may be an RNA polymerase III transcription factor.

}, keywords = {Antigen-Antibody Complex, Autoantibodies, HUMANS, Lupus Erythematosus, Systemic, Nucleoproteins, Ribonucleoproteins, RNA Polymerase III, Transcription, Genetic}, author = {Steitz, J A and Berg, C and Gottlieb, E and Hardin, J A and Hashimoto, C and Hendrick, J P and Hinterberger, M and Krikeles, M and Lerner, M R and Mount, S M} }