Sample records for colibactin genomic island

  1. Complete Genome Sequence of a Klebsiella pneumoniae Isolate with Chromosomally Encoded Carbapenem Resistance and Colibactin Synthesis Loci.

    PubMed

    Conlan, Sean; Deming, Clayton; Tsai, Yu-Chih; Lau, Anna F; Dekker, John P; Korlach, Jonas; Segre, Julia A

    2014-01-01

    Klebsiella pneumoniae is an important nosocomial pathogen, and multidrug-resistant strains have become a worldwide concern. Here, we report the complete genome of a K. pneumoniae isolate with chromosomally integrated blaKPC genes and a colibactin synthesis locus. PMID:25540345

  2. Interplay between Siderophores and Colibactin Genotoxin Biosynthetic Pathways in Escherichia coli

    PubMed Central

    Martin, Patricia; Marcq, Ingrid; Magistro, Giuseppe; Penary, Marie; Garcie, Christophe; Payros, Delphine; Boury, Michèle; Olier, Maïwenn; Nougayrède, Jean-Philippe; Audebert, Marc; Chalut, Christian; Schubert, Sören; Oswald, Eric

    2013-01-01

    In Escherichia coli, the biosynthetic pathways of several small iron-scavenging molecules known as siderophores (enterobactin, salmochelins and yersiniabactin) and of a genotoxin (colibactin) are known to require a 4?-phosphopantetheinyl transferase (PPTase). Only two PPTases have been clearly identified: EntD and ClbA. The gene coding for EntD is part of the core genome of E. coli, whereas ClbA is encoded on the pks pathogenicity island which codes for colibactin. Interestingly, the pks island is physically associated with the high pathogenicity island (HPI) in a subset of highly virulent E. coli strains. The HPI carries the gene cluster required for yersiniabactin synthesis except for a gene coding its cognate PPTase. Here we investigated a potential interplay between the synthesis pathways leading to the production of siderophores and colibactin, through a functional interchangeability between EntD and ClbA. We demonstrated that ClbA could contribute to siderophores synthesis. Inactivation of both entD and clbA abolished the virulence of extra-intestinal pathogenic E. coli (ExPEC) in a mouse sepsis model, and the presence of either functional EntD or ClbA was required for the survival of ExPEC in vivo. This is the first report demonstrating a connection between multiple phosphopantetheinyl-requiring pathways leading to the biosynthesis of functionally distinct secondary metabolites in a given microorganism. Therefore, we hypothesize that the strict association of the pks island with HPI has been selected in highly virulent E. coli because ClbA is a promiscuous PPTase that can contribute to the synthesis of both the genotoxin and siderophores. The data highlight the complex regulatory interaction of various virulence features with different functions. The identification of key points of these networks is not only essential to the understanding of ExPEC virulence but also an attractive and promising target for the development of anti-virulence therapy strategies. PMID:23853582

  3. Genomic islands in pathogenic and environmental microorganisms

    Microsoft Academic Search

    Ulrich Dobrindt; Bianca Hochhut; Ute Hentschel; Jörg Hacker

    2004-01-01

    Horizontal gene transfer is an important mechanism for the evolution of microbial genomes. Pathogenicity islands — mobile genetic elements that contribute to rapid changes in virulence potential — are known to have contributed to genome evolution by horizontal gene transfer in many bacterial pathogens. Increasing evidence indicates that equivalent elements in non-pathogenic species — genomic islands — are important in

  4. Ecological fitness, genomic islands and bacterial pathogenicity

    PubMed Central

    Hacker, Jörg; Carniel, Elisabeth

    2001-01-01

    The compositions of bacterial genomes can be changed rapidly and dramatically through a variety of processes including horizontal gene transfer. This form of change is key to bacterial evolution, as it leads to ‘evolution in quantum leaps’. Horizontal gene transfer entails the incorporation of genetic elements transferred from another organism—perhaps in an earlier generation—directly into the genome, where they form ‘genomic islands’, i.e. blocks of DNA with signatures of mobile genetic elements. Genomic islands whose functions increase bacterial fitness, either directly or indirectly, have most likely been positively selected and can be termed ‘fitness islands’. Fitness islands can be divided into several subtypes: ‘ecological islands’ in environmental bacteria and ‘saprophytic islands’, ‘symbiosis islands’ or ‘pathogenicity islands’ (PAIs) in microorganisms that interact with living hosts. Here we discuss ways in which PAIs contribute to the pathogenic potency of bacteria, and the idea that genetic entities similar to genomic islands may also be present in the genomes of eukaryotes. PMID:11375927

  5. COMPUTATIONAL PREDICTION AND CHARACTERIZATION OF GENOMIC ISLANDS

    E-print Network

    Hammerton, James

    COMPUTATIONAL PREDICTION AND CHARACTERIZATION OF GENOMIC ISLANDS: INSIGHTS INTO BACTERIAL islands: insights into bacterial pathogenicity Examining Committee: Chair: Dr. Paul C.H. Li Associate will be described; as well as an observation that recently discovered phage defence elements, CRISPRs, are over

  6. Comparative Analysis of Mobilizable Genomic Islands

    PubMed Central

    Daccord, Aurélie; Ceccarelli, Daniela; Rodrigue, Sébastien

    2013-01-01

    Mobilizable genomic islands (MGIs) are small genomic islands of less than 35 kbp containing an integrase gene and a sequence that resembles the origin of transfer (oriT) of an integrating conjugative element (ICE). MGIs have been shown to site-specifically integrate and excise from the chromosome of bacterial hosts and hijack the conjugative machinery of a coresident ICE to disseminate. To date, MGIs have been described in three strains belonging to three different Vibrio species. In this study, we report the discovery of 11 additional putative MGIs found in various species of Vibrio, Alteromonas, Pseudoalteromonas, and Methylophaga. We designed an MGI capture system that allowed us to relocate chromosomal MGIs onto a low-copy-number plasmid and facilitate their isolation and sequencing. Comparative genomics and phylogenetic analyses of these mobile genetic elements revealed their mosaic structure and their evolution through recombination and acquisition of exogenous DNA. MGIs were found to belong to a larger family of genomic islands (GIs) sharing a similar integrase gene and often integrated into the same integration site yet exhibiting a different mechanism of regulation of excision and mobilization. We found that MGIs can excise only when an ICE of the SXT/R391 family is coresident in the same cell, while GIs still excise regardless. PMID:23204461

  7. Genome Island: A Virtual Science Environment in Second Life

    ERIC Educational Resources Information Center

    Clark, Mary Anne

    2009-01-01

    Mary Anne CLark describes the organization and uses of Genome Island, a virtual laboratory complex constructed in Second Life. Genome Island was created for teaching genetics to university undergraduates but also provides a public space where anyone interested in genetics can spend a few minutes, or a few hours, interacting with genetic…

  8. IslandViewer 3: more flexible, interactive genomic island discovery, visualization and analysis.

    PubMed

    Dhillon, Bhavjinder K; Laird, Matthew R; Shay, Julie A; Winsor, Geoffrey L; Lo, Raymond; Nizam, Fazmin; Pereira, Sheldon K; Waglechner, Nicholas; McArthur, Andrew G; Langille, Morgan G I; Brinkman, Fiona S L

    2015-07-01

    IslandViewer (http://pathogenomics.sfu.ca/islandviewer) is a widely used web-based resource for the prediction and analysis of genomic islands (GIs) in bacterial and archaeal genomes. GIs are clusters of genes of probable horizontal origin, and are of high interest since they disproportionately encode genes involved in medically and environmentally important adaptations, including antimicrobial resistance and virulence. We now report a major new release of IslandViewer, since the last release in 2013. IslandViewer 3 incorporates a completely new genome visualization tool, IslandPlot, enabling for the first time interactive genome analysis and gene search capabilities using synchronized circular, horizontal and vertical genome views. In addition, more curated virulence factors and antimicrobial resistance genes have been incorporated, and homologs of these genes identified in closely related genomes using strict filters. Pathogen-associated genes have been re-calculated for all pre-computed complete genomes. For user-uploaded genomes to be analysed, IslandViewer 3 can also now handle incomplete genomes, with an improved queuing system on compute nodes to handle user demand. Overall, IslandViewer 3 represents a significant new version of this GI analysis software, with features that may make it more broadly useful for general microbial genome analysis and visualization. PMID:25916842

  9. IslandViewer 3: more flexible, interactive genomic island discovery, visualization and analysis

    PubMed Central

    Dhillon, Bhavjinder K.; Laird, Matthew R.; Shay, Julie A.; Winsor, Geoffrey L.; Lo, Raymond; Nizam, Fazmin; Pereira, Sheldon K.; Waglechner, Nicholas; McArthur, Andrew G.; Langille, Morgan G.I.; Brinkman, Fiona S.L.

    2015-01-01

    IslandViewer (http://pathogenomics.sfu.ca/islandviewer) is a widely used web-based resource for the prediction and analysis of genomic islands (GIs) in bacterial and archaeal genomes. GIs are clusters of genes of probable horizontal origin, and are of high interest since they disproportionately encode genes involved in medically and environmentally important adaptations, including antimicrobial resistance and virulence. We now report a major new release of IslandViewer, since the last release in 2013. IslandViewer 3 incorporates a completely new genome visualization tool, IslandPlot, enabling for the first time interactive genome analysis and gene search capabilities using synchronized circular, horizontal and vertical genome views. In addition, more curated virulence factors and antimicrobial resistance genes have been incorporated, and homologs of these genes identified in closely related genomes using strict filters. Pathogen-associated genes have been re-calculated for all pre-computed complete genomes. For user-uploaded genomes to be analysed, IslandViewer 3 can also now handle incomplete genomes, with an improved queuing system on compute nodes to handle user demand. Overall, IslandViewer 3 represents a significant new version of this GI analysis software, with features that may make it more broadly useful for general microbial genome analysis and visualization. PMID:25916842

  10. CpG island density and its correlations with genomic features in mammalian genomes

    Microsoft Academic Search

    Leng Han; Bing Su; Wen-Hsiung Li; Zhongming Zhao

    2008-01-01

    ABSTRACT: BACKGROUND: CpG islands, which are clusters of CpG dinucleotides in GC-rich regions, are considered gene markers and represent an important feature of mammalian genomes. Previous studies of CpG islands have largely been on specific loci or within one genome. To date, there seems to be no comparative analysis of CpG islands and their density at the DNA sequence level

  11. The Association of Virulence Factors with Genomic Islands

    Microsoft Academic Search

    Shannan J. Ho Sui; Amber Fedynak; William W. L. Hsiao; Morgan G. I. Langille; Fiona S. L. Brinkman; Niyaz Ahmed

    2009-01-01

    BackgroundIt has been noted that many bacterial virulence factor genes are located within genomic islands (GIs; clusters of genes in a prokaryotic genome of probable horizontal origin). However, such studies have been limited to single genera or isolated observations. We have performed the first large-scale analysis of multiple diverse pathogens to examine this association. We additionally identified genes found predominantly

  12. A large scale comparative genomic analysis reveals insertion sites for newly acquired genomic islands in bacterial genomes

    PubMed Central

    2011-01-01

    Background Bacterial virulence enhancement and drug resistance are major threats to public health worldwide. Interestingly, newly acquired genomic islands (GIs) from horizontal transfer between different bacteria strains were found in Vibrio cholerae, Streptococcus suis, and Mycobacterium tuberculosis, which caused outbreak of epidemic diseases in recently years. Results Using a large-scale comparative genomic analysis of 1088 complete genomes from all available bacteria (1009) and Archaea (79), we found that newly acquired GIs are often anchored around switch sites of GC-skew (sGCS). After calculating correlations between relative genomic distances of genomic islands to sGCSs and the evolutionary distances of the genomic islands themselves, we found that newly acquired genomic islands are closer to sGCSs than the old ones, indicating that regions around sGCSs are hotspots for genomic island insertion. Conclusions Based on our results, we believe that genomic regions near sGCSs are hotspots for horizontal transfer of genomic islands, which may significantly affect key properties of epidemic disease-causing pathogens, such as virulence and adaption to new environments. PMID:21672261

  13. SIGI: score-based identification of genomic islands

    PubMed Central

    Merkl, Rainer

    2004-01-01

    Background Genomic islands can be observed in many microbial genomes. These stretches of DNA have a conspicuous composition with regard to sequence or encoded functions. Genomic islands are assumed to be frequently acquired via horizontal gene transfer. For the analysis of genome structure and the study of horizontal gene transfer, it is necessary to reliably identify and characterize these islands. Results A scoring scheme on codon frequencies Score_G1G2(cdn) = log(f_G2(cdn) / f_G1(cdn)) was utilized. To analyse genes of a species G1 and to test their relatedness to species G2, scores were determined by applying the formula to log-odds derived from mean codon frequencies of the two genomes. A non-redundant set of nearly 400 codon usage tables comprising microbial species was derived; its members were used alternatively at position G2. Genes having at least one score value above a species-specific and dynamically determined cut-off value were analysed further. By means of cluster analysis, genes were identified that comprise clusters of statistically significant size. These clusters were predicted as genomic islands. Finally and individually for each of these genes, the taxonomical relation among those species responsible for significant scores was interpreted. The validity of the approach and its limitations were made plausible by an extensive analysis of natural genes and synthetic ones aimed at modelling the process of gene amelioration. Conclusions The method reliably allows to identify genomic island and the likely origin of alien genes. PMID:15113412

  14. Genomic islands predict functional adaptation in marine actinobacteria

    Microsoft Academic Search

    Kevin Penn; Caroline Jenkins; Markus Nett; Daniel Udwary; Erin Gontang; Ryan McGlinchey; Brian Foster; Alla Lapidus; Sheila Podell; Eric Allen; Bradley Moore; Paul Jensen

    2009-01-01

    Linking functional traits to bacterial phylogeny remains a fundamental but elusive goal of microbial ecology 1. Without this information, it becomes impossible to resolve meaningful units of diversity and the mechanisms by which bacteria interact with each other and adapt to environmental change. Ecological adaptations among bacterial populations have been linked to genomic islands, strain-specific regions of DNA that house

  15. Patterns and architecture of genomic islands in marine bacteria

    PubMed Central

    2012-01-01

    Background Genomic Islands (GIs) have key roles since they modulate the structure and size of bacterial genomes displaying a diverse set of laterally transferred genes. Despite their importance, GIs in marine bacterial genomes have not been explored systematically to uncover possible trends and to analyze their putative ecological significance. Results We carried out a comprehensive analysis of GIs in 70 selected marine bacterial genomes detected with IslandViewer to explore the distribution, patterns and functional gene content in these genomic regions. We detected 438 GIs containing a total of 8152 genes. GI number per genome was strongly and positively correlated with the total GI size. In 50% of the genomes analyzed the GIs accounted for approximately 3% of the genome length, with a maximum of 12%. Interestingly, we found transposases particularly enriched within Alphaproteobacteria GIs, and site-specific recombinases in Gammaproteobacteria GIs. We described specific Homologous Recombination GIs (HR-GIs) in several genera of marine Bacteroidetes and in Shewanella strains among others. In these HR-GIs, we recurrently found conserved genes such as the ?-subunit of DNA-directed RNA polymerase, regulatory sigma factors, the elongation factor Tu and ribosomal protein genes typically associated with the core genome. Conclusions Our results indicate that horizontal gene transfer mediated by phages, plasmids and other mobile genetic elements, and HR by site-specific recombinases play important roles in the mobility of clusters of genes between taxa and within closely related genomes, modulating the flexible pool of the genome. Our findings suggest that GIs may increase bacterial fitness under environmental changing conditions by acquiring novel foreign genes and/or modifying gene transcription and/or transduction. PMID:22839777

  16. Expression Islands Clustered on the Symbiosis Island of the Mesorhizobium loti Genome

    PubMed Central

    Uchiumi, Toshiki; Ohwada, Takuji; Itakura, Manabu; Mitsui, Hisayuki; Nukui, Noriyuki; Dawadi, Pramod; Kaneko, Takakazu; Tabata, Satoshi; Yokoyama, Tadashi; Tejima, Kouhei; Saeki, Kazuhiko; Omori, Hirofumi; Hayashi, Makoto; Maekawa, Takaki; Sriprang, Rutchadaporn; Murooka, Yoshikatsu; Tajima, Shigeyuki; Simomura, Kenshiro; Nomura, Mika; Suzuki, Akihiro; Shimoda, Yoshikazu; Sioya, Kouki; Abe, Mikiko; Minamisawa, Kiwamu

    2004-01-01

    Rhizobia are symbiotic nitrogen-fixing soil bacteria that are associated with host legumes. The establishment of rhizobial symbiosis requires signal exchanges between partners in microaerobic environments that result in mutualism for the two partners. We developed a macroarray for Mesorhizobium loti MAFF303099, a microsymbiont of the model legume Lotus japonicus, and monitored the transcriptional dynamics of the bacterium during symbiosis, microaerobiosis, and starvation. Global transcriptional profiling demonstrated that the clusters of genes within the symbiosis island (611 kb), a transmissible region distinct from other chromosomal regions, are collectively expressed during symbiosis, whereas genes outside the island are downregulated. This finding implies that the huge symbiosis island functions as clustered expression islands to support symbiotic nitrogen fixation. Interestingly, most transposase genes on the symbiosis island were highly upregulated in bacteroids, as were nif, fix, fdx, and rpoN. The genome region containing the fixNOPQ genes outside the symbiosis island was markedly upregulated as another expression island under both microaerobic and symbiotic conditions. The symbiosis profiling data suggested that there was activation of amino acid metabolism, as well as nif-fix gene expression. In contrast, genes for cell wall synthesis, cell division, DNA replication, and flagella were strongly repressed in differentiated bacteroids. A highly upregulated gene in bacteroids, mlr5932 (encoding 1-aminocyclopropane-1-carboxylate deaminase), was disrupted and was confirmed to be involved in nodulation enhancement, indicating that disruption of highly expressed genes is a useful strategy for exploring novel gene functions in symbiosis. PMID:15060047

  17. Variation in genomic islands contribute to genome plasticity in cupriavidus metallidurans

    PubMed Central

    2012-01-01

    Background Different Cupriavidus metallidurans strains isolated from metal-contaminated and other anthropogenic environments were genotypically and phenotypically compared with C. metallidurans type strain CH34. The latter is well-studied for its resistance to a wide range of metals, which is carried for a substantial part by its two megaplasmids pMOL28 and pMOL30. Results Comparative genomic hybridization (CGH) indicated that the extensive arsenal of determinants involved in metal resistance was well conserved among the different C. metallidurans strains. Contrary, the mobile genetic elements identified in type strain CH34 were not present in all strains but clearly showed a pattern, although, not directly related to a particular biotope nor location (geographical). One group of strains carried almost all mobile genetic elements, while these were much less abundant in the second group. This occurrence was also reflected in their ability to degrade toluene and grow autotrophically on hydrogen gas and carbon dioxide, which are two traits linked to separate genomic islands of the Tn4371-family. In addition, the clear pattern of genomic islands distribution allowed to identify new putative genomic islands on chromosome 1 and 2 of C. metallidurans CH34. Conclusions Metal resistance determinants are shared by all C. metallidurans strains and their occurrence is apparently irrespective of the strain's isolation type and place. Cupriavidus metallidurans strains do display substantial differences in the diversity and size of their mobile gene pool, which may be extensive in some (including the type strain) while marginal in others. PMID:22443515

  18. Genomic islands in the pathogenic filamentous fungus Aspergillus fumigatus.

    PubMed

    Fedorova, Natalie D; Khaldi, Nora; Joardar, Vinita S; Maiti, Rama; Amedeo, Paolo; Anderson, Michael J; Crabtree, Jonathan; Silva, Joana C; Badger, Jonathan H; Albarraq, Ahmed; Angiuoli, Sam; Bussey, Howard; Bowyer, Paul; Cotty, Peter J; Dyer, Paul S; Egan, Amy; Galens, Kevin; Fraser-Liggett, Claire M; Haas, Brian J; Inman, Jason M; Kent, Richard; Lemieux, Sebastien; Malavazi, Iran; Orvis, Joshua; Roemer, Terry; Ronning, Catherine M; Sundaram, Jaideep P; Sutton, Granger; Turner, Geoff; Venter, J Craig; White, Owen R; Whitty, Brett R; Youngman, Phil; Wolfe, Kenneth H; Goldman, Gustavo H; Wortman, Jennifer R; Jiang, Bo; Denning, David W; Nierman, William C

    2008-04-01

    We present the genome sequences of a new clinical isolate of the important human pathogen, Aspergillus fumigatus, A1163, and two closely related but rarely pathogenic species, Neosartorya fischeri NRRL181 and Aspergillus clavatus NRRL1. Comparative genomic analysis of A1163 with the recently sequenced A. fumigatus isolate Af293 has identified core, variable and up to 2% unique genes in each genome. While the core genes are 99.8% identical at the nucleotide level, identity for variable genes can be as low 40%. The most divergent loci appear to contain heterokaryon incompatibility (het) genes associated with fungal programmed cell death such as developmental regulator rosA. Cross-species comparison has revealed that 8.5%, 13.5% and 12.6%, respectively, of A. fumigatus, N. fischeri and A. clavatus genes are species-specific. These genes are significantly smaller in size than core genes, contain fewer exons and exhibit a subtelomeric bias. Most of them cluster together in 13 chromosomal islands, which are enriched for pseudogenes, transposons and other repetitive elements. At least 20% of A. fumigatus-specific genes appear to be functional and involved in carbohydrate and chitin catabolism, transport, detoxification, secondary metabolism and other functions that may facilitate the adaptation to heterogeneous environments such as soil or a mammalian host. Contrary to what was suggested previously, their origin cannot be attributed to horizontal gene transfer (HGT), but instead is likely to involve duplication, diversification and differential gene loss (DDL). The role of duplication in the origin of lineage-specific genes is further underlined by the discovery of genomic islands that seem to function as designated "gene dumps" and, perhaps, simultaneously, as "gene factories". PMID:18404212

  19. Identification of a Perchlorate Reduction Genomic Island with Novel Regulatory and Metabolic Genes ?

    PubMed Central

    Melnyk, Ryan A.; Engelbrektson, Anna; Clark, Iain C.; Carlson, Hans K.; Byrne-Bailey, Kathy; Coates, John D.

    2011-01-01

    A comparative analysis of the genomes of four dissimilatory (per)chlorate-reducing bacteria has revealed a genomic island associated with perchlorate reduction. In addition to the characterized metabolic genes for perchlorate reductase and chlorite dismutase, the island contains multiple conserved uncharacterized genes possibly involved in electron transport and regulation. PMID:21856823

  20. Compositional searching of CpG islands in the human genome Pedro Luis Luque-Escamilla

    E-print Network

    Martínez Aroza, José

    Compositional searching of CpG islands in the human genome Pedro Luis Luque-Escamilla Department received 31 January 2005; published 29 June 2005 We report on an entropic edge detector based on the local calculation of the Jensen-Shannon divergence with application to the search for CpG islands. CpG islands

  1. The phn Island: A New Genomic Island Encoding Catabolism of Polynuclear Aromatic Hydrocarbons

    PubMed Central

    Hickey, William J.; Chen, Shicheng; Zhao, Jiangchao

    2012-01-01

    Bacteria are key in the biodegradation of polycyclic aromatic hydrocarbons (PAH), which are widespread environmental pollutants. At least six genotypes of PAH degraders are distinguishable via phylogenies of the ring-hydroxylating dioxygenase (RHD) that initiates bacterial PAH metabolism. A given RHD genotype can be possessed by a variety of bacterial genera, suggesting horizontal gene transfer (HGT) is an important process for dissemination of PAH-degrading genes. But, mechanisms of HGT for most RHD genotypes are unknown. Here, we report in silico and functional analyses of the phenanthrene-degrading bacterium Delftia sp. Cs1-4, a representative of the phnAFK2 RHD group. The phnAFK2 genotype predominates PAH degrader communities in some soils and sediments, but, until now, their genomic biology has not been explored. In the present study, genes for the entire phenanthrene catabolic pathway were discovered on a novel ca. 232?kb genomic island (GEI), now termed the phn island. This GEI had characteristics of an integrative and conjugative element with a mobilization/stabilization system similar to that of SXT/R391-type GEI. But, it could not be grouped with any known GEI, and was the first member of a new GEI class. The island also carried genes predicted to encode: synthesis of quorum sensing signal molecules, fatty acid/polyhydroxyalkanoate biosynthesis, a type IV secretory system, a PRTRC system, DNA mobilization functions and >50 hypothetical proteins. The 50% G?+?C content of the phn gene cluster differed significantly from the 66.7% G?+?C level of the island as a whole and the strain Cs1-4 chromosome, indicating a divergent phylogenetic origin for the phn genes. Collectively, these studies added new insights into the genetic elements affecting the PAH biodegradation capacity of microbial communities specifically, and the potential vehicles of HGT in general. PMID:22493593

  2. Genomic analysis of Pseudomonas putida: genes in a genome island are crucial for nicotine degradation

    PubMed Central

    Tang, Hongzhi; Yao, Yuxiang; Wang, Lijuan; Yu, Hao; Ren, Yiling; Wu, Geng; Xu, Ping

    2012-01-01

    Nicotine is an important chemical compound in nature that has been regarded as an environmental toxicant causing various preventable diseases. Several bacterial species are adapted to decompose this heterocyclic compound, including Pseudomonas and Arthrobacter. Pseudomonas putida S16 is a bacterium that degrades nicotine through the pyrrolidine pathway, similar to that present in animals. The corresponding late steps of the nicotine degradation pathway in P. putida S16 was first proposed and demonstrated to be from 2,5-dihydroxy-pyridine through the intermediates N-formylmaleamic acid, maleamic acid, maleic acid, and fumaric acid. Genomics of strain S16 revealed that genes located in the largest genome island play a major role in nicotine degradation and may originate from other strains, as suggested by the constructed phylogenetic tree and the results of comparative genomic analysis. The deletion of gene hpo showed that this gene is essential for nicotine degradation. This study defines the mechanism of nicotine degradation. PMID:22530095

  3. Genomic analysis of Pseudomonas putida: genes in a genome island are crucial for nicotine degradation.

    PubMed

    Tang, Hongzhi; Yao, Yuxiang; Wang, Lijuan; Yu, Hao; Ren, Yiling; Wu, Geng; Xu, Ping

    2012-01-01

    Nicotine is an important chemical compound in nature that has been regarded as an environmental toxicant causing various preventable diseases. Several bacterial species are adapted to decompose this heterocyclic compound, including Pseudomonas and Arthrobacter. Pseudomonas putida S16 is a bacterium that degrades nicotine through the pyrrolidine pathway, similar to that present in animals. The corresponding late steps of the nicotine degradation pathway in P. putida S16 was first proposed and demonstrated to be from 2,5-dihydroxy-pyridine through the intermediates N-formylmaleamic acid, maleamic acid, maleic acid, and fumaric acid. Genomics of strain S16 revealed that genes located in the largest genome island play a major role in nicotine degradation and may originate from other strains, as suggested by the constructed phylogenetic tree and the results of comparative genomic analysis. The deletion of gene hpo showed that this gene is essential for nicotine degradation. This study defines the mechanism of nicotine degradation. PMID:22530095

  4. Identification of Horizontally-transferred Genomic Islands and Genome Segmentation Points by Using the GC Profile Method

    PubMed Central

    Zhang, Ren; Ou, Hong-Yu; Gao, Feng; Luo, Hao

    2014-01-01

    The nucleotide composition of genomes undergoes dramatic variations among all three kingdoms of life. GC content, an important characteristic for a genome, is related to many important functions, and therefore GC content and its distribution are routinely reported for sequenced genomes. Traditionally, GC content distribution is assessed by computing GC contents in windows that slide along the genome. Disadvantages of this routinely used window-based method include low resolution and low sensitivity. Additionally, different window sizes result in different GC content distribution patterns within the same genome. We proposed a windowless method, the GC profile, for displaying GC content variations across the genome. Compared to the window-based method, the GC profile has the following advantages: 1) higher sensitivity, because of variation-amplifying procedures; 2) higher resolution, because boundaries between domains can be determined at one single base pair; 3) uniqueness, because the GC profile is unique for a given genome and 4) the capacity to show both global and regional GC content distributions. These characteristics are useful in identifying horizontally-transferred genomic islands and homogenous GC-content domains. Here, we review the applications of the GC profile in identifying genomic islands and genome segmentation points, and in serving as a platform to integrate with other algorithms for genome analysis. A web server generating GC profiles and implementing relevant genome segmentation algorithms is available at: www.zcurve.net. PMID:24822029

  5. Genome Sequence of Banana Streak MY Virus from the Pacific Ocean Island of Tonga.

    PubMed

    Stainton, Daisy; Halafihi, Mana'ia; Collings, David A; Varsani, Arvind

    2015-01-01

    Banana streak disease is caused by a variety of banana-infecting badnaviruses. A genome of the episomal form of a banana streak MY virus was recovered from an infected banana plant sampled on Vava'u Island, Tonga, and shares >98% pairwise identity with the six other genomes available in public databases. PMID:26021925

  6. Sulphur islands in the Escherichia coli genome: markers of the cell’s architecture?

    Microsoft Academic Search

    Eduardo P. C. Rocha; Agnieszka Sekowska; Antoine Danchin

    2000-01-01

    Two highly contrasted images depict genomes: at first sight, genes appear to be distributed randomly along the chromosome. In contrast, their organisation into operons (or pathogenicity islands) suggests that, at least locally, related functions are in physical proximity. Analysis of the codon usage bias in orthologous genes in the genome of bacteria which diverged a long time ago suggested that

  7. Genome Sequence of Banana Streak MY Virus from the Pacific Ocean Island of Tonga

    PubMed Central

    Stainton, Daisy; Halafihi, Mana’ia; Collings, David A.

    2015-01-01

    Banana streak disease is caused by a variety of banana-infecting badnaviruses. A genome of the episomal form of a banana streak MY virus was recovered from an infected banana plant sampled on Vava’u Island, Tonga, and shares >98% pairwise identity with the six other genomes available in public databases. PMID:26021925

  8. Mitochondrial Genomes Suggest Rapid Evolution of Dwarf California Channel Islands Foxes (Urocyon littoralis)

    PubMed Central

    Hofman, Courtney A.; Rick, Torben C.; Hawkins, Melissa T. R.; Funk, W. Chris; Ralls, Katherine; Boser, Christina L.; Collins, Paul W.; Coonan, Tim; King, Julie L.; Morrison, Scott A.; Newsome, Seth D.; Sillett, T. Scott; Fleischer, Robert C.; Maldonado, Jesus E.

    2015-01-01

    Island endemics are typically differentiated from their mainland progenitors in behavior, morphology, and genetics, often resulting from long-term evolutionary change. To examine mechanisms for the origins of island endemism, we present a phylogeographic analysis of whole mitochondrial genomes from the endangered island fox (Urocyon littoralis), endemic to California’s Channel Islands, and mainland gray foxes (U. cinereoargenteus). Previous genetic studies suggested that foxes first appeared on the islands >16,000 years ago, before human arrival (~13,000 cal BP), while archaeological and paleontological data supported a colonization >7000 cal BP. Our results are consistent with initial fox colonization of the northern islands probably by rafting or human introduction ~9200–7100 years ago, followed quickly by human translocation of foxes from the northern to southern Channel Islands. Mitogenomes indicate that island foxes are monophyletic and most closely related to gray foxes from northern California that likely experienced a Holocene climate-induced range shift. Our data document rapid morphological evolution of island foxes (in ~2000 years or less). Despite evidence for bottlenecks, island foxes have generated and maintained multiple mitochondrial haplotypes. This study highlights the intertwined evolutionary history of island foxes and humans, and illustrates a new approach for investigating the evolutionary histories of other island endemics. PMID:25714775

  9. Comparative genomic hybridizations reveal absence of large Streptomyces coelicolor genomic islands in Streptomyces lividans

    PubMed Central

    Jayapal, Karthik P; Lian, Wei; Glod, Frank; Sherman, David H; Hu, Wei-Shou

    2007-01-01

    Background The genomes of Streptomyces coelicolor and Streptomyces lividans bear a considerable degree of synteny. While S. coelicolor is the model streptomycete for studying antibiotic synthesis and differentiation, S. lividans is almost exclusively considered as the preferred host, among actinomycetes, for cloning and expression of exogenous DNA. We used whole genome microarrays as a comparative genomics tool for identifying the subtle differences between these two chromosomes. Results We identified five large S. coelicolor genomic islands (larger than 25 kb) and 18 smaller islets absent in S. lividans chromosome. Many of these regions show anomalous GC bias and codon usage patterns. Six of them are in close vicinity of tRNA genes while nine are flanked with near perfect repeat sequences indicating that these are probable recent evolutionary acquisitions into S. coelicolor. Embedded within these segments are at least four DNA methylases and two probable methyl-sensing restriction endonucleases. Comparison with S. coelicolor transcriptome and proteome data revealed that some of the missing genes are active during the course of growth and differentiation in S. coelicolor. In particular, a pair of methylmalonyl CoA mutase (mcm) genes involved in polyketide precursor biosynthesis, an acyl-CoA dehydrogenase implicated in timing of actinorhodin synthesis and bldB, a developmentally significant regulator whose mutation causes complete abrogation of antibiotic synthesis belong to this category. Conclusion Our findings provide tangible hints for elucidating the genetic basis of important phenotypic differences between these two streptomycetes. Importantly, absence of certain genes in S. lividans identified here could potentially explain the relative ease of DNA transformations and the conditional lack of actinorhodin synthesis in S. lividans. PMID:17623098

  10. Comparative analysis of Klebsiella pneumoniae genomes identifies a phospholipase D family protein as a novel virulence factor

    PubMed Central

    2014-01-01

    Background Klebsiella pneumoniae strains are pathogenic to animals and humans, in which they are both a frequent cause of nosocomial infections and a re-emerging cause of severe community-acquired infections. K. pneumoniae isolates of the capsular serotype K2 are among the most virulent. In order to identify novel putative virulence factors that may account for the severity of K2 infections, the genome sequence of the K2 reference strain Kp52.145 was determined and compared to two K1 and K2 strains of low virulence and to the reference strains MGH 78578 and NTUH-K2044. Results In addition to diverse functions related to host colonization and virulence encoded in genomic regions common to the four strains, four genomic islands specific for Kp52.145 were identified. These regions encoded genes for the synthesis of colibactin toxin, a putative cytotoxin outer membrane protein, secretion systems, nucleases and eukaryotic-like proteins. In addition, an insertion within a type VI secretion system locus included sel1 domain containing proteins and a phospholipase D family protein (PLD1). The pld1 mutant was avirulent in a pneumonia model in mouse. The pld1 mRNA was expressed in vivo and the pld1 gene was associated with K. pneumoniae isolates from severe infections. Analysis of lipid composition of a defective E. coli strain complemented with pld1 suggests an involvement of PLD1 in cardiolipin metabolism. Conclusions Determination of the complete genome of the K2 reference strain identified several genomic islands comprising putative elements of pathogenicity. The role of PLD1 in pathogenesis was demonstrated for the first time and suggests that lipid metabolism is a novel virulence mechanism of K. pneumoniae. PMID:24885329

  11. Comparative genomic analysis shows that Streptococcus suis meningitis isolate SC070731 contains a unique 105K genomic island.

    PubMed

    Wu, Zongfu; Wang, Weixue; Tang, Min; Shao, Jing; Dai, Chen; Zhang, Wei; Fan, Hongjie; Yao, Huochun; Zong, Jie; Chen, Dai; Wang, Junning; Lu, Chengping

    2014-02-10

    Streptococcus suis (SS) is an important swine pathogen worldwide that occasionally causes serious infections in humans. SS infection may result in meningitis in pigs and humans. The pathogenic mechanisms of SS are poorly understood. Here, we provide the complete genome sequence of S. suis serotype 2 (SS2) strain SC070731 isolated from a pig with meningitis. The chromosome is 2,138,568bp in length. There are 1933 predicted protein coding sequences and 96.7% (57/59) of the known virulence-associated genes are present in the genome. Strain SC070731 showed similar virulence with SS2 virulent strains HA9801 and ZY05719, but was more virulent than SS2 virulent strain P1/7 in the zebrafish infection model. Comparative genomic analysis revealed a unique 105K genomic island in strain SC070731 that is absent in seven other sequenced SS2 strains. Further analysis of the 105K genomic island indicated that it contained a complete nisin locus similar to the nisin U locus in S. uberis strain 42, a prophage similar to S. oralis phage PH10 and several antibiotic resistance genes. Several proteins in the 105K genomic island, including nisin and RelBE toxin-antitoxin system, contribute to the bacterial fitness and virulence in other pathogenic bacteria. Further investigation of newly identified gene products, including four putative new virulence-associated surface proteins, will improve our understanding of SS pathogenesis. PMID:24316490

  12. Host and invader impact of transfer of the clc genomic island into Pseudomonas aeruginosa PAO1

    PubMed Central

    Gaillard, Muriel; Pernet, Nataskha; Vogne, Christelle; Hagenbüchle, Otto; van der Meer, Jan Roelof

    2008-01-01

    Genomic islands, large potentially mobile regions of bacterial chromosomes, are a major contributor to bacteria evolution. Here, we investigated the fitness cost and phenotypic differences between the bacterium Pseudomonas aeruginosa PAO1 and a derivative carrying one integrated copy of the clc element, a 103-kb genomic island [and integrative and conjugative element (ICE)] originating in Pseudomonas sp. strain B13 and a close relative of genomic islands found in clinical and environmental isolates of P. aeruginosa. By using a combination of whole genome transcriptome profiling, phenotypic arrays, competition experiments, and biofilm formation studies, only few differences became apparent, such as reduced biofilm growth and fourfold stationary phase repression of genes involved in acetoin metabolism in PAO1 containing the clc element. In contrast, PAO1 carrying the clc element acquired the capacity to grow on 3-chlorobenzoate and 2-aminophenol as sole carbon and energy substrates. No fitness loss >1% was detectable in competition experiments between PAO1 and PAO1 carrying the clc element. The genes from the clc element were not silent in PAO1, and excision was observed, although transfer of clc from PAO1 to other recipient bacteria was reduced by two orders of magnitude. Our results indicate that newly acquired mobile DNA not necessarily invoke an important fitness cost on their host. Absence of immediate detriment to the host may have contributed to the wide distribution of genomic islands like clc in bacterial genomes. PMID:18448680

  13. Genomic islands link secondary metabolism to functional adaptation in marine Actinobacteria.

    PubMed

    Penn, Kevin; Jenkins, Caroline; Nett, Markus; Udwary, Daniel W; Gontang, Erin A; McGlinchey, Ryan P; Foster, Brian; Lapidus, Alla; Podell, Sheila; Allen, Eric E; Moore, Bradley S; Jensen, Paul R

    2009-10-01

    Genomic islands have been shown to harbor functional traits that differentiate ecologically distinct populations of environmental bacteria. A comparative analysis of the complete genome sequences of the marine Actinobacteria Salinispora tropica and Salinispora arenicola reveals that 75% of the species-specific genes are located in 21 genomic islands. These islands are enriched in genes associated with secondary metabolite biosynthesis providing evidence that secondary metabolism is linked to functional adaptation. Secondary metabolism accounts for 8.8% and 10.9% of the genes in the S. tropica and S. arenicola genomes, respectively, and represents the major functional category of annotated genes that differentiates the two species. Genomic islands harbor all 25 of the species-specific biosynthetic pathways, the majority of which occur in S. arenicola and may contribute to the cosmopolitan distribution of this species. Genome evolution is dominated by gene duplication and acquisition, which in the case of secondary metabolism provide immediate opportunities for the production of new bioactive products. Evidence that secondary metabolic pathways are exchanged horizontally, coupled with earlier evidence for fixation among globally distributed populations, supports a functional role and suggests that the acquisition of natural product biosynthetic gene clusters represents a previously unrecognized force driving bacterial diversification. Species-specific differences observed in clustered regularly interspaced short palindromic repeat sequences suggest that S. arenicola may possess a higher level of phage immunity, whereas a highly duplicated family of polymorphic membrane proteins provides evidence for a new mechanism of marine adaptation in Gram-positive bacteria. PMID:19474814

  14. Predicting a novel pathogenicity island in Helicobacter pylori by genomic barcoding

    PubMed Central

    Wang, Guo-Qing; Xu, Jian-Ting; Xu, Guang-Yu; Zhang, Yang; Li, Fan; Suo, Jian

    2013-01-01

    AIM: To apply a new, integrated technique for visualizing bacterial genomes to identify novel pathogenicity islands in Helicobacter pylori (H. pylori). METHODS: A genomic barcode imaging method (converting frequency matrices to grey-scale levels) was designed to visually distinguish origin-specific genomic regions in H. pylori. The complete genome sequences of the six H. pylori strains published in the National Center for Biotechnological Information prokaryotic genome database were scanned, and compared to the genome barcodes of Escherichia coli (E. coli) O157:H7 strain EDL933 and a random nucleotide sequence. The following criteria were applied to identify potential pathogenicity islands (PAIs): (1) barcode distance distinct from that of the general background; (2) length greater than 10000 continuous base pairs; and (3) containing genes with known virulence-related functions (as determined by PfamScan and Blast2GO). RESULTS: Comparison of the barcode images generated for the 26695, HPAG1, J99, Shi470, G27 and P12 H. pylori genomes with those for the E. coli and random sequence controls revealed that H. pylori genomes contained fewer anomalous regions. Among the H. pylori-specific continuous anomalous regions (longer than 20 kbp in each strain’s genome), two fit the criteria for identifying candidate PAIs. The bioinformatic-based functional analyses revealed that one of the two anomalous regions was the known pathogenicity island cag-PAI, this finding also served as proof-of-principle for the utility of the genomic barcoding approach for identifying PAIs, and characterized the other as a novel PAI, which was designated as tfs3-PAI. Furthermore, the cag-PAI and tfs3-PAI harbored genes encoding type IV secretion system proteins and were predicted to have potential for functional synergy. CONCLUSION: Genomic barcode imaging represents an effective bioinformatic-based approach for scanning bacterial genomes, such as H. pylori, to identify candidate PAIs. PMID:23946608

  15. CRISPR-based screening of genomic island excision events in bacteria.

    PubMed

    Selle, Kurt; Klaenhammer, Todd R; Barrangou, Rodolphe

    2015-06-30

    Genomic analysis of Streptococcus thermophilus revealed that mobile genetic elements (MGEs) likely contributed to gene acquisition and loss during evolutionary adaptation to milk. Clustered regularly interspaced short palindromic repeats-CRISPR-associated genes (CRISPR-Cas), the adaptive immune system in bacteria, limits genetic diversity by targeting MGEs including bacteriophages, transposons, and plasmids. CRISPR-Cas systems are widespread in streptococci, suggesting that the interplay between CRISPR-Cas systems and MGEs is one of the driving forces governing genome homeostasis in this genus. To investigate the genetic outcomes resulting from CRISPR-Cas targeting of integrated MGEs, in silico prediction revealed four genomic islands without essential genes in lengths from 8 to 102 kbp, totaling 7% of the genome. In this study, the endogenous CRISPR3 type II system was programmed to target the four islands independently through plasmid-based expression of engineered CRISPR arrays. Targeting lacZ within the largest 102-kbp genomic island was lethal to wild-type cells and resulted in a reduction of up to 2.5-log in the surviving population. Genotyping of Lac(-) survivors revealed variable deletion events between the flanking insertion-sequence elements, all resulting in elimination of the Lac-encoding island. Chimeric insertion sequence footprints were observed at the deletion junctions after targeting all of the four genomic islands, suggesting a common mechanism of deletion via recombination between flanking insertion sequences. These results established that self-targeting CRISPR-Cas systems may direct significant evolution of bacterial genomes on a population level, influencing genome homeostasis and remodeling. PMID:26080436

  16. CRISPR-based screening of genomic island excision events in bacteria

    PubMed Central

    Selle, Kurt; Klaenhammer, Todd R.; Barrangou, Rodolphe

    2015-01-01

    Genomic analysis of Streptococcus thermophilus revealed that mobile genetic elements (MGEs) likely contributed to gene acquisition and loss during evolutionary adaptation to milk. Clustered regularly interspaced short palindromic repeats–CRISPR-associated genes (CRISPR-Cas), the adaptive immune system in bacteria, limits genetic diversity by targeting MGEs including bacteriophages, transposons, and plasmids. CRISPR-Cas systems are widespread in streptococci, suggesting that the interplay between CRISPR-Cas systems and MGEs is one of the driving forces governing genome homeostasis in this genus. To investigate the genetic outcomes resulting from CRISPR-Cas targeting of integrated MGEs, in silico prediction revealed four genomic islands without essential genes in lengths from 8 to 102 kbp, totaling 7% of the genome. In this study, the endogenous CRISPR3 type II system was programmed to target the four islands independently through plasmid-based expression of engineered CRISPR arrays. Targeting lacZ within the largest 102-kbp genomic island was lethal to wild-type cells and resulted in a reduction of up to 2.5-log in the surviving population. Genotyping of Lac? survivors revealed variable deletion events between the flanking insertion-sequence elements, all resulting in elimination of the Lac-encoding island. Chimeric insertion sequence footprints were observed at the deletion junctions after targeting all of the four genomic islands, suggesting a common mechanism of deletion via recombination between flanking insertion sequences. These results established that self-targeting CRISPR-Cas systems may direct significant evolution of bacterial genomes on a population level, influencing genome homeostasis and remodeling. PMID:26080436

  17. Detection and characterization of variant Salmonella genomic island 1s from Salmonella Derby isolates.

    PubMed

    Akiba, Masato; Nakamura, Kotaro; Shinoda, David; Yoshii, Noriyo; Ito, Hiroya; Uchida, Ikuo; Nakazawa, Muneo

    2006-10-01

    The purpose of this study is to investigate the distribution and structure of Salmonella genomic island 1 (SGI1) among Salmonella enterica serovar Derby isolates from swine and their rearing environment. Three variants of SGI1s, specifically SGI1-A, C, and I, were identified by PCR mapping. The results of macro-restriction analysis and DNA sequencing of SGI1 flanking regions revealed that there are at least two genomic lineages of Derby strains bearing SGI1s. PMID:17060705

  18. MobilomeFINDER: web-based tools for in silico and experimental discovery of bacterial genomic islands

    PubMed Central

    Ou, Hong-Yu; He, Xinyi; Harrison, Ewan M.; Kulasekara, Bridget R.; Thani, Ali Bin; Kadioglu, Aras; Lory, Stephen; Hinton, Jay C. D.; Barer, Michael R.; Rajakumar, Kumar

    2007-01-01

    MobilomeFINDER (http://mml.sjtu.edu.cn/MobilomeFINDER) is an interactive online tool that facilitates bacterial genomic island or ‘mobile genome’ (mobilome) discovery; it integrates the ArrayOme and tRNAcc software packages. ArrayOme utilizes a microarray-derived comparative genomic hybridization input data set to generate ‘inferred contigs’ produced by merging adjacent genes classified as ‘present’. Collectively these ‘fragments’ represent a hypothetical ‘microarray-visualized genome (MVG)’. ArrayOme permits recognition of discordances between physical genome and MVG sizes, thereby enabling identification of strains rich in microarray-elusive novel genes. Individual tRNAcc tools facilitate automated identification of genomic islands by comparative analysis of the contents and contexts of tRNA sites and other integration hotspots in closely related sequenced genomes. Accessory tools facilitate design of hotspot-flanking primers for in silico and/or wet-science-based interrogation of cognate loci in unsequenced strains and analysis of islands for features suggestive of foreign origins; island-specific and genome-contextual features are tabulated and represented in schematic and graphical forms. To date we have used MobilomeFINDER to analyse several Enterobacteriaceae, Pseudomonas aeruginosa and Streptococcus suis genomes. MobilomeFINDER enables high-throughput island identification and characterization through increased exploitation of emerging sequence data and PCR-based profiling of unsequenced test strains; subsequent targeted yeast recombination-based capture permits full-length sequencing and detailed functional studies of novel genomic islands. PMID:17537813

  19. Genome-wide screening of pathogenicity islands in Mycobacterium tuberculosis based on the genomic barcode visualization.

    PubMed

    Xie, Jiao; Zhou, Fengfeng; Xu, Guangyu; Mai, Guoqin; Hu, Jie; Wang, Guoqing; Li, Fan

    2014-09-01

    Mycobacterium tuberculosis (M. tuberculosis) is one of the most widely spread human pathogenic bacteria, and it frequently exchanges pathogenesis genes among its strains or with other pathogenic microbes. The purpose of this study was to screen the pathogenicity islands (PAIs) in M. tuberculosis using the genomic barcode visualization technique and to characterize the functions of the detected PAIs. By visually screening the barcode image of the M. tuberculosis chromosomes, three candidate PAIs were detected as MPI-1, MPI-2 and MPI-3, among which MPI-2 and MPI-3 were known to harbor pathogenesis genes, and MPI-1 represents a novel candidate. Based on the functional annotations of Pfam domains and GO categories, both MPI-2 and MPI-3 carry genes encoding PE/PPE family proteins, MPI-2 encodes the type VII secretion system, and MPI-3 encodes genes for mycolic acid synthesis in the cell wall. Some of these genes were already widely used in early diagnosis or treatment of M. tuberculosis. The novel candidate PAI MPI-1 encodes CRISPR-C as family proteins, which are known to be associated with persistent infection of M. tuberculosis. Our data represents a molecular basis and protocol for comprehensive annotating the pathogenic systems of M. tuberculosis, and will also facilitate the development of diagnosis and vaccination techniques of M. tuberculosis. PMID:25108673

  20. Comparative genomics reveals long, evolutionarily-conserved, low-complexity islands in yeast proteins

    E-print Network

    Epstein, Susan L.

    1 Comparative genomics reveals long, evolutionarily-conserved, low- complexity islands in yeast, 695 Park Avenue, New York, New York 10021, USA *Corresponding author: Wei-Gang Qiu Department of Biological Sciences Hunter College, City University of New York 695 Park Avenue, New York, New York 10021 Tel

  1. Phage-mediated horizontal transfer of a Staphylococcus aureus virulence-associated genomic island.

    PubMed

    Moon, Bo Youn; Park, Joo Youn; Hwang, Sun Yung; Robinson, D Ashley; Thomas, Jonathan C; Fitzgerald, J Ross; Park, Yong Ho; Seo, Keun Seok

    2015-01-01

    Staphylococcus aureus is a major pathogen of humans and animals. The capacity of S. aureus to adapt to different host species and tissue types is strongly influenced by the acquisition of mobile genetic elements encoding determinants involved in niche adaptation. The genomic islands ?Sa? and ?Sa? are found in almost all S. aureus strains and are characterized by extensive variation in virulence gene content. However the basis for the diversity and the mechanism underlying mobilization of the genomic islands between strains are unexplained. Here, we demonstrated that the genomic island, ?Sa?, encoding an array of virulence factors including staphylococcal superantigens, proteases, and leukotoxins, in addition to bacteriocins, was transferrable in vitro to human and animal strains of multiple S. aureus clones via a resident prophage. The transfer of the ?Sa? appears to have been accomplished by multiple conversions of transducing phage particles carrying overlapping segments of the ?Sa?. Our findings solve a long-standing mystery regarding the diversification and spread of the genomic island ?Sa?, highlighting the central role of bacteriophages in the pathogenic evolution of S. aureus. PMID:25891795

  2. Genomic Evidence for Island Population Conversion Resolves Conflicting Theories of Polar Bear Evolution

    PubMed Central

    Cahill, James A.; Green, Richard E.; Fulton, Tara L.; Stiller, Mathias; Jay, Flora; Ovsyanikov, Nikita; Salamzade, Rauf; St. John, John; Stirling, Ian; Slatkin, Montgomery; Shapiro, Beth

    2013-01-01

    Despite extensive genetic analysis, the evolutionary relationship between polar bears (Ursus maritimus) and brown bears (U. arctos) remains unclear. The two most recent comprehensive reports indicate a recent divergence with little subsequent admixture or a much more ancient divergence followed by extensive admixture. At the center of this controversy are the Alaskan ABC Islands brown bears that show evidence of shared ancestry with polar bears. We present an analysis of genome-wide sequence data for seven polar bears, one ABC Islands brown bear, one mainland Alaskan brown bear, and a black bear (U. americanus), plus recently published datasets from other bears. Surprisingly, we find clear evidence for gene flow from polar bears into ABC Islands brown bears but no evidence of gene flow from brown bears into polar bears. Importantly, while polar bears contributed <1% of the autosomal genome of the ABC Islands brown bear, they contributed 6.5% of the X chromosome. The magnitude of sex-biased polar bear ancestry and the clear direction of gene flow suggest a model wherein the enigmatic ABC Island brown bears are the descendants of a polar bear population that was gradually converted into brown bears via male-dominated brown bear admixture. We present a model that reconciles heretofore conflicting genetic observations. We posit that the enigmatic ABC Islands brown bears derive from a population of polar bears likely stranded by the receding ice at the end of the last glacial period. Since then, male brown bear migration onto the island has gradually converted these bears into an admixed population whose phenotype and genotype are principally brown bear, except at mtDNA and X-linked loci. This process of genome erosion and conversion may be a common outcome when climate change or other forces cause a population to become isolated and then overrun by species with which it can hybridize. PMID:23516372

  3. Genomic evidence for island population conversion resolves conflicting theories of polar bear evolution.

    PubMed

    Cahill, James A; Green, Richard E; Fulton, Tara L; Stiller, Mathias; Jay, Flora; Ovsyanikov, Nikita; Salamzade, Rauf; St John, John; Stirling, Ian; Slatkin, Montgomery; Shapiro, Beth

    2013-01-01

    Despite extensive genetic analysis, the evolutionary relationship between polar bears (Ursus maritimus) and brown bears (U. arctos) remains unclear. The two most recent comprehensive reports indicate a recent divergence with little subsequent admixture or a much more ancient divergence followed by extensive admixture. At the center of this controversy are the Alaskan ABC Islands brown bears that show evidence of shared ancestry with polar bears. We present an analysis of genome-wide sequence data for seven polar bears, one ABC Islands brown bear, one mainland Alaskan brown bear, and a black bear (U. americanus), plus recently published datasets from other bears. Surprisingly, we find clear evidence for gene flow from polar bears into ABC Islands brown bears but no evidence of gene flow from brown bears into polar bears. Importantly, while polar bears contributed <1% of the autosomal genome of the ABC Islands brown bear, they contributed 6.5% of the X chromosome. The magnitude of sex-biased polar bear ancestry and the clear direction of gene flow suggest a model wherein the enigmatic ABC Island brown bears are the descendants of a polar bear population that was gradually converted into brown bears via male-dominated brown bear admixture. We present a model that reconciles heretofore conflicting genetic observations. We posit that the enigmatic ABC Islands brown bears derive from a population of polar bears likely stranded by the receding ice at the end of the last glacial period. Since then, male brown bear migration onto the island has gradually converted these bears into an admixed population whose phenotype and genotype are principally brown bear, except at mtDNA and X-linked loci. This process of genome erosion and conversion may be a common outcome when climate change or other forces cause a population to become isolated and then overrun by species with which it can hybridize. PMID:23516372

  4. Complete mitochondrial genomes of Tuatara endemic to different islands of New Zealand.

    PubMed

    Mohandesan, Elmira; Subramanian, Sankar; Millar, Craig D; Lambert, David M

    2015-02-01

    Tuatara are the sister taxon to the Squamata (including lizards and snakes) and are regarded as the most distinctive surviving reptilian genus. They are currently inhabits on offshore islands around New Zealand and have been recognized as a species in need of active conservation management. In this study, we report a total number of five nearly complete mitochondrial genomes, which were sequenced by Sanger and Next Generation DNA sequencing methods. Our phylogenomic analysis revealed distinct clustering of tuatara populations from the north and south islands of New Zealand. PMID:24156717

  5. Strain-specific genes of Helicobacter pylori: genome evolution driven by a novel type IV secretion system and genomic island transfer

    PubMed Central

    Fischer, Wolfgang; Windhager, Lukas; Rohrer, Stefanie; Zeiller, Matthias; Karnholz, Arno; Hoffmann, Reinhard; Zimmer, Ralf; Haas, Rainer

    2010-01-01

    The availability of multiple bacterial genome sequences has revealed a surprising extent of variability among strains of the same species. The human gastric pathogen Helicobacter pylori is known as one of the most genetically diverse species. We have compared the genome sequence of the duodenal ulcer strain P12 and six other H. pylori genomes to elucidate the genetic repertoire and genome evolution mechanisms of this species. In agreement with previous findings, we estimate that the core genome comprises about 1200 genes and that H. pylori possesses an open pan-genome. Strain-specific genes are preferentially located at potential genome rearrangement sites or in distinct plasticity zones, suggesting two different mechanisms of genome evolution. The P12 genome contains three plasticity zones, two of which encode type IV secretion systems and have typical features of genomic islands. We demonstrate for the first time that one of these islands is capable of self-excision and horizontal transfer by a conjugative process. We also show that excision is mediated by a protein of the XerD family of tyrosine recombinases. Thus, in addition to its natural transformation competence, conjugative transfer of genomic islands has to be considered as an important source of genetic diversity in H. pylori. PMID:20478826

  6. Long-Range Autocorrelations of CpG Islands in the Human Genome

    PubMed Central

    Koester, Benjamin; Rea, Thomas J.; Templeton, Alan R.; Szalay, Alexander S.; Sing, Charles F.

    2012-01-01

    In this paper, we use a statistical estimator developed in astrophysics to study the distribution and organization of features of the human genome. Using the human reference sequence we quantify the global distribution of CpG islands (CGI) in each chromosome and demonstrate that the organization of the CGI across a chromosome is non-random, exhibits surprisingly long range correlations (10 Mb) and varies significantly among chromosomes. These correlations of CGI summarize functional properties of the genome that are not captured when considering variation in any particular separate (and local) feature. The demonstration of the proposed methods to quantify the organization of CGI in the human genome forms the basis of future studies. The most illuminating of these will assess the potential impact on phenotypic variation of inter-individual variation in the organization of the functional features of the genome within and among chromosomes, and among individuals for particular chromosomes. PMID:22253817

  7. Genomic tests of the species-pump hypothesis: Recent island connectivity cycles drive population divergence but not speciation in Caribbean crickets across the Virgin Islands.

    PubMed

    Papadopoulou, Anna; Knowles, L Lacey

    2015-06-01

    Harnessing the power of genomic scans, we test the debated "species pump" hypothesis that implicates repeated cycles of island connectivity and isolation as drivers of divergence. This question has gone understudied given the limited resolution of past molecular markers for studying such dynamic phenomena. With an average of 32,000 SNPs from the genome of 136 individuals from 10 populations of a Caribbean flightless ground cricket species (Amphiacusta sanctaecrucis) and a complementary set of statistical approaches, we infer a stepping-stone colonization model and high levels of genetic differentiation across the Virgin Islands, which have been periodically interconnected until 8 ka. Estimates of divergence times from models based on the site frequency spectrum coincide with a period of repeated connection and fragmentation of the islands at 75-130 ka. These results are consistent with a role of island connectivity cycles in promoting genomic divergence and indicate that the genetic distinctiveness of island populations has persisted despite subsequent and extended interisland connections identified from bathymetric data. We discuss these findings in the broader context of Caribbean biogeography, and more specifically why high levels of genomic divergence across the Virgin Islands associated with repeated connectivity cycles do not actually translate into species diversification. PMID:25903255

  8. Bacterial evolution by genomic island transfer occurs via DNA transformation in planta.

    PubMed

    Lovell, Helen C; Mansfield, John W; Godfrey, Scott A C; Jackson, Robert W; Hancock, John T; Arnold, Dawn L

    2009-09-29

    Our understanding of the evolution of microbial pathogens has been advanced by the discovery of "islands" of DNA that differ from core genomes and contain determinants of virulence. The acquisition of genomic islands (GIs) by horizontal gene transfer (HGT) is thought to have played a major role in microbial evolution. There are, however, few practical demonstrations of the acquisition of genes that control virulence, and, significantly, all have been achieved outside the animal or plant host. Loss of a GI from the bean pathogen Pseudomonas syringae pv. phaseolicola (Pph) is driven by exposure to the stress imposed by the plant's resistance response. Here, we show that the complete episomal island, which carries pathogenicity genes including the effector avrPphB, transfers between strains of Pph by transformation in planta and inserts at a specific att site in the genome of the recipient. Our results show that the evolution of bacterial pathogens by HGT may be achieved via transformation, the simplest mechanism of DNA exchange. This process is activated by exposure to plant defenses, when the pathogen is in greatest need of acquiring new genetic traits to alleviate the antimicrobial stress imposed by plant innate immunity. PMID:19747826

  9. Draft Genome Sequence of Sphingomonas sp. Strain Ant20, Isolated from Oil-Contaminated Soil on Ross Island, Antarctica

    PubMed Central

    Ronca, Sandra; Frossard, Aline; Guerrero, Leandro D.; Makhalanyane, Thulani P.; Aislabie, Jackie M.

    2015-01-01

    Here, we present the draft genome of Sphingomonas sp. strain Ant20, isolated from oil-polluted soil near Scott Base, Ross Island, Antarctica. The genome of this aromatic hydrocarbon-degrading bacterium provides valuable information on the microbially mediated biodegradation of aromatic compounds in cold-climate systems. PMID:25573925

  10. Heritability and genome-wide linkage analysis of migraine in the genetic isolate of Norfolk Island.

    PubMed

    Cox, Hannah C; Lea, Rod A; Bellis, Claire; Nyholt, Dale R; Dyer, Thomas D; Haupt, Larisa M; Charlesworth, Jac; Matovinovic, Elizabeth; Blangero, John; Griffiths, Lyn R

    2012-02-15

    Migraine is a common neurovascular disorder with a complex envirogenomic aetiology. In an effort to identify migraine susceptibility genes, we conducted a study of the isolated population of Norfolk Island, Australia. A large portion of the permanent inhabitants of Norfolk Island are descended from 18th Century English sailors involved in the infamous mutiny on the Bounty and their Polynesian consorts. In total, 600 subjects were recruited including a large pedigree of 377 individuals with lineage to the founders. All individuals were phenotyped for migraine using International Classification of Headache Disorders-II criterion. All subjects were genotyped for a genome-wide panel of microsatellite markers. Genotype and phenotype data for the pedigree were analysed using heritability and linkage methods implemented in the programme SOLAR. Follow-up association analysis was performed using the CLUMP programme. A total of 154 migraine cases (25%) were identified indicating the Norfolk Island population is high-risk for migraine. Heritability estimation of the 377-member pedigree indicated a significant genetic component for migraine (h(2)=0.53, P=0.016). Linkage analysis showed peaks on chromosome 13q33.1 (P=0.003) and chromosome 9q22.32 (P=0.008). Association analysis of the key microsatellites in the remaining 223 unrelated Norfolk Island individuals showed evidence of association, which strengthen support for the linkage findings (P?0.05). In conclusion, a genome-wide linkage analysis and follow-up association analysis of migraine in the genetic isolate of Norfolk Island provided evidence for migraine susceptibility loci on chromosomes 9q22.22 and 13q33.1. PMID:22197687

  11. Genomic island genes in a coastal marine Synechococcus strain confer enhanced tolerance to copper and oxidative stress.

    PubMed

    Stuart, Rhona K; Brahamsha, Bianca; Busby, Kayla; Palenik, Brian

    2013-06-01

    Highly variable regions called genomic islands are found in the genomes of marine picocyanobacteria, and have been predicted to be involved in niche adaptation and the ecological success of these microbes. These picocyanobacteria are typically highly sensitive to copper stress and thus, increased copper tolerance could confer a selective advantage under some conditions seen in the marine environment. Through targeted gene inactivation of genomic island genes that were known to be upregulated in response to copper stress in Synechococcus sp. strain CC9311, we found two genes (sync_1495 and sync_1217) conferred tolerance to both methyl viologen and copper stress in culture. The prevalence of one gene, sync_1495, was then investigated in natural samples, and had a predictable temporal variability in abundance at a coastal monitoring site with higher abundance in winter months. Together, this shows that genomic island genes can confer an adaptive advantage to specific stresses in marine Synechococcus, and may help structure their population diversity. PMID:23344240

  12. Variants of a genomic island in Aeromonas salmonicida subsp. salmonicida link isolates with their geographical origins.

    PubMed

    Emond-Rheault, Jean-Guillaume; Vincent, Antony T; Trudel, Mélanie V; Brochu, Francis; Boyle, Brian; Tanaka, Katherine H; Attéré, Sabrina A; Jubinville, Éric; Loch, Thomas P; Winters, Andrew D; Faisal, Mohamed; Frenette, Michel; Derome, Nicolas; Charette, Steve J

    2015-01-30

    Aeromonas salmonicida subsp. salmonicida is a fish pathogen. Analysis of its genomic characteristics is required to determine the worldwide distribution of the various populations of this bacterium. Genomic alignments between the 01-B526 pathogenic strain and the A449 reference strain have revealed a 51-kb chromosomal insertion in 01-B526. This insertion (AsaGEI1a) has been identified as a new genomic island (GEI) bearing prophage genes. PCR assays were used to detect this GEI in a collection of 139 A. salmonicida subsp. salmonicida isolates. Three forms of this GEI (AsaGEI1a, AsaGEI1b, AsaGEI2a) are now known based on this analysis and the sequencing of the genomes of seven additional isolates. A new prophage (prophage 3) associated with AsaGEI2a was also discovered. Each GEI appeared to be strongly associated with a specific geographic region. AsaGEI1a and AsaGEI2a were exclusively found in North American isolates, except for one European isolate bearing AsaGEI2a. The majority of the isolates bearing AsaGEI1b or no GEI were from Europe. Prophage 3 has also a particular geographic distribution and was found only in North American isolates. We demonstrated that A. salmonicida subsp. salmonicida possesses unsuspected elements of genomic heterogeneity that could be used as indicators to determine the geographic origins of isolates of this bacterium. PMID:25480167

  13. A Genomic Island in Salmonella enterica ssp. salamae Provides New Insights on the Genealogy of the Locus of Enterocyte Effacement

    PubMed Central

    Chandry, P. Scott; Gladman, Simon; Moore, Sean C.; Seemann, Torsten; Crandall, Keith A.; Fegan, Narelle

    2012-01-01

    The genomic island encoding the locus of enterocyte effacement (LEE) is an important virulence factor of the human pathogenic Escherichia coli. LEE typically encodes a type III secretion system (T3SS) and secreted effectors capable of forming attaching and effacing lesions. Although prominent in the pathogenic E. coli such as serotype O157:H7, LEE has also been detected in Citrobacter rodentium, E. albertii, and although not confirmed, it is likely to also be in Shigella boydii. Previous phylogenetic analysis of LEE indicated the genomic island was evolving through stepwise acquisition of various components. This study describes a new LEE region from two strains of Salmonella enterica subspecies salamae serovar Sofia along with a phylogenetic analysis of LEE that provides new insights into the likely evolution of this genomic island. The Salmonella LEE contains 36 of the 41 genes typically observed in LEE within a genomic island of 49, 371 bp that encodes a total of 54 genes. A phylogenetic analysis was performed on the entire T3SS and four T3SS genes (escF, escJ, escN, and escV) to elucidate the genealogy of LEE. Phylogenetic analysis inferred that the previously known LEE islands are members of a single lineage distinct from the new Salmonella LEE lineage. The previously known lineage of LEE diverged between islands found in Citrobacter and those in Escherichia and Shigella. Although recombination and horizontal gene transfer are important factors in the genealogy of most genomic islands, the phylogeny of the T3SS of LEE can be interpreted with a bifurcating tree. It seems likely that the LEE island entered the Enterobacteriaceae through horizontal gene transfer as a single unit, rather than as separate subsections, which was then subjected to the forces of both mutational change and recombination. PMID:22860002

  14. Two Novel Salmonella Genomic Island 1 Variants in Proteus mirabilis Isolates from Swine Farms in China.

    PubMed

    Lei, Chang-Wei; Zhang, An-Yun; Liu, Bi-Hui; Wang, Hong-Ning; Yang, Li-Qin; Guan, Zhong-Bin; Xu, Chang-Wen; Zhang, Dong-Dong; Yang, Yong-Qiang

    2015-07-01

    Four different Salmonella genomic island 1 (SGI1) variants, including two novel variants, were characterized in one Salmonella enterica serovar Rissen sequence type ST1917 isolate and three Proteus mirabilis isolates from swine farms in China. One novel variant was derived from SGI1-B with the backbone gene S021 disrupted by a 12.72-kb IS26 composite transposon containing the dfrA17-aadA5 cassettes and macrolide inactivation gene cluster mphA-mrx-mphR. The other one was an integron-free SGI1 and contained a 183-bp truncated S025 next to IS6100 and S044. PMID:25918148

  15. Versatile Insertion Plasmids for Targeted Genome Manipulations in Bacteria: Isolation, Deletion, and Rescue of the Pathogenicity Island LEE of the Escherichia coli O157:H7 Genome

    Microsoft Academic Search

    GYORGY POSFAI; MICHAEL D. KOOB; HEATHER A. KIRKPATRICK; FREDERICK R. BLATTNER

    1997-01-01

    A system of versatile insertion plasmids was constructed that permits efficient delivery of the target sites of an ultra-rare-cutting endonuclease and the recombinase FLP into preselected sites of the bacterial genome. With the help of this system, the pathogenicity island LEE of the Escherichia coli O157:H7 genome was excised and isolated in vitro, deleted in vivo, rescued as a plasmid,

  16. The New Macrolide-Lincosamide-Streptogramin B Resistance Gene erm(45) Is Located within a Genomic Island in Staphylococcus fleurettii.

    PubMed

    Wipf, Juliette R K; Schwendener, Sybille; Nielsen, Jesper Boye; Westh, Henrik; Perreten, Vincent

    2015-06-01

    Genome alignment of a macrolide, lincosamide, and streptogramin B (MLSB)-resistant Staphylococcus fleurettii strain with an MLSB-susceptible S. fleurettii strain revealed a novel 11,513-bp genomic island carrying the new erythromycin resistance methylase gene erm(45). This gene was shown to confer inducible MLSB resistance when cloned into Staphylococcus aureus. The erm(45)-containing island was integrated into the housekeeping gene guaA in S. fleurettii and was able to form a circular intermediate but was not transmissible to S. aureus. PMID:25779586

  17. Features and Trend of Loss of Promoter-Associated CpG Islands in the Human and Mouse Genomes

    Microsoft Academic Search

    Cizhong Jiang; Leng Han; Bing Su; Wen-Hsiung Li; Zhongming Zhao

    2007-01-01

    CpG islands (CGIs) are often considered as gene markers, but the number of CGIs varies among mammalian genomes that have similar numbers of genes. In this study, we investigated the distribution of CGIs in the promoter regions of 3,197 human-mouse orthologous gene pairs and found that the mouse genome has notably fewer CGIs in the promoter regions and less pronounced

  18. A putative genomic island, PGI-1, in Ralstonia solanacearum biovar 2 revealed by subtractive hybridization

    PubMed Central

    Stevens, Patricia

    2010-01-01

    Ralstonia solanacearum biovar 2, a key bacterial pathogen of potato, has recently established in temperate climate waters. On the basis of isolates obtained from diseased (potato) plants, its genome has been assumed to be virtually clonal, but information on environmental isolates has been lacking. Based on differences in pulsed-field gel electrophoresis patterns, we compared the genomes of two biovar 2 strains with different life histories. Thus, genomic DNA of the novel environmental strain KZR-5 (The Netherlands) was compared to that of reference potato strain 715 (Bangladesh) by suppressive subtractive hybridization. Various strain-specific sequences were found, all being homologous to those found in the genome of reference potato strain 1609. Approximately 20% of these were related to genes involved in recombinational processes. We found a deletion of a 17.6-Kb region, denoted as a putative genomic island PGI-1, in environmental strain KZR-5. The deleted region was, at both extremes, flanked by a composite of two insertion sequence (IS) elements, identified as ISRso2 and ISRso3. The PGI-1 region contained open reading frames that putatively encoded a (p)ppGpp synthetase, a transporter protein, a transcriptional regulator, a cellobiohydrolase, a site-specific integrase/recombinase, a phage-related protein and seven hypothetical proteins. As yet, no phenotype could be assigned to the loss of PGI-1. The ecological behavior of strain KZR-5 was compared to that of reference strain 715. Strain KZR-5 showed enhanced tolerance to 4°C as compared to the reference strain, but was not affected in its virulence on tomato. PMID:20467813

  19. The Genome Sequence of Streptomyces lividans 66 Reveals a Novel tRNA-Dependent Peptide Biosynthetic System within a Metal-Related Genomic Island

    PubMed Central

    Cruz-Morales, Pablo; Vijgenboom, Erik; Iruegas-Bocardo, Fernanda; Girard, Geneviève; Yáñez-Guerra, Luis Alfonso; Ramos-Aboites, Hilda E.; Pernodet, Jean-Luc; Anné, Jozef; van Wezel, Gilles P.; Barona-Gómez, Francisco

    2013-01-01

    The complete genome sequence of the original isolate of the model actinomycete Streptomyces lividans 66, also referred to as 1326, was deciphered after a combination of next-generation sequencing platforms and a hybrid assembly pipeline. Comparative analysis of the genomes of S. lividans 66 and closely related strains, including S. coelicolor M145 and S. lividans TK24, was used to identify strain-specific genes. The genetic diversity identified included a large genomic island with a mosaic structure, present in S. lividans 66 but not in the strain TK24. Sequence analyses showed that this genomic island has an anomalous (G + C) content, suggesting recent acquisition and that it is rich in metal-related genes. Sequences previously linked to a mobile conjugative element, termed plasmid SLP3 and defined here as a 94 kb region, could also be identified within this locus. Transcriptional analysis of the response of S. lividans 66 to copper was used to corroborate a role of this large genomic island, including two SLP3-borne “cryptic” peptide biosynthetic gene clusters, in metal homeostasis. Notably, one of these predicted biosynthetic systems includes an unprecedented nonribosomal peptide synthetase—tRNA-dependent transferase biosynthetic hybrid organization. This observation implies the recruitment of members of the leucyl/phenylalanyl-tRNA-protein transferase family to catalyze peptide bond formation within the biosynthesis of natural products. Thus, the genome sequence of S. lividans 66 not only explains long-standing genetic and phenotypic differences but also opens the door for further in-depth comparative genomic analyses of model Streptomyces strains, as well as for the discovery of novel natural products following genome-mining approaches. PMID:23709624

  20. Molecular Detection of Genomic Islands Associated With Class 1 and 2 Integron in Haemophilus influenzae Isolated in Iran

    PubMed Central

    Boroumand, Mojgan; Irani, Shiva; Siadat, Seyed Davar; Bouzari, Saied

    2015-01-01

    Background: High levels of multidrug resistance are usually associated with mobile genetic elements that encode specific resistance genes. Integrons are important genetic elements involved in spreading antibiotic multi-resistance. In special cases, large exogenous segments in bacterial genomes form genomic islands, and one of the functions of these genomic islands is antibiotic resistance. Due to geographical heterogeneity in antibiotic resistance pattern, it is mandatory to determine resistance patterns that are region-specific rather than generalized. Objectives: The objective of this study was to detect class 1 and 2 integrons in clinical isolates of Haemophilus influenzae. Patients and Methods: Antibiogram tests were carried out for twenty clinical isolates collected from different patients admitted to the Milad hospital. The PCR reactions were performed using universal primers specified for Int1 and Int2 genes attributed to class 1 and 2 integrons. Also amplification of integrase genes related to genomic islands was investigated by designing specific primers. Results: Of the twenty isolates, all (100%) were resistant to clindamycin, chloramphenicol and tetracycline, 95% to amoxicillin, 50% to ceftriaxone, 45% to ciprofloxacin and 5% to azithromycin. Also, all isolates (100%) were sensitive to trimethoprim/sulfamethoxazole. Class 1 and 2 integrons were not detected in any of the isolates; however the integrase gene attributed to genomic islands was identified in twelve isolates. Conclusions: Antibiotic resistance gene cassettes may be carried on integron or other genetic elements. The purpose of this study was to detect integron or genomic islands involved in antibiotic resistance profile of the isolates of H. influenzae collected in this study. PMID:26034545

  1. Functional analysis of a lipolytic protein encoded in phytoplasma phage based genomic island.

    PubMed

    Gedvilaite, Alma; Jomantiene, Rasa; Dabrisius, Jonas; Norkiene, Milda; Davis, Robert E

    2014-01-01

    Wall-less bacteria known as phytoplasmas are obligate transkingdom parasites and pathogens of plants and insect vectors. These unusual bacteria possess some of the smallest genomes known among pathogenic bacteria, and have never been successfully isolated in artificial culture. Disease symptoms induced by phytoplasmas in infected plants include abnormal growth and often severe yellowing of leaves, but mechanisms involved in phytoplasma parasitism and pathogenicity are little understood. A phage based genomic island (sequence variable mosaic, SVM) in the genome of Malaysian periwinkle yellows (MPY) phytoplasma harbors a gene encoding membrane-targeted proteins, including a putative phospholipase (PL), potentially important in pathogen-host interactions. Since some phytoplasmal disease symptoms could possibly be accounted for, at least in part, by damage and/or degradation of host cell membranes, we hypothesize that the MPY phytoplasma putative PL is an active enzyme. To test this hypothesis, functional analysis of the MPY putative pl gene-encoded protein was carried out in vitro after its expression in bacterial and yeast hosts. The results demonstrated that the heterologously expressed phytoplasmal putative PL is an active lipolytic enzyme and could possibly act as a pathogenicity factor in the plant, and/or insect, host. PMID:24168924

  2. Genome sequence of Staphylococcus aureus strain Newman and comparative analysis of staphylococcal genomes: polymorphism and evolution of two major pathogenicity islands.

    PubMed

    Baba, Tadashi; Bae, Taeok; Schneewind, Olaf; Takeuchi, Fumihiko; Hiramatsu, Keiichi

    2008-01-01

    Strains of Staphylococcus aureus, an important human pathogen, display up to 20% variability in their genome sequence, and most sequence information is available for human clinical isolates that have not been subjected to genetic analysis of virulence attributes. S. aureus strain Newman, which was also isolated from a human infection, displays robust virulence properties in animal models of disease and has already been extensively analyzed for its molecular traits of staphylococcal pathogenesis. We report here the complete genome sequence of S. aureus Newman, which carries four integrated prophages, as well as two large pathogenicity islands. In agreement with the view that S. aureus Newman prophages contribute important properties to pathogenesis, fewer virulence factors are found outside of the prophages than for the highly virulent strain MW2. The absence of drug resistance genes reflects the general antibiotic-susceptible phenotype of S. aureus Newman. Phylogenetic analyses reveal clonal relationships between the staphylococcal strains Newman, COL, NCTC8325, and USA300 and a greater evolutionary distance to strains MRSA252, MW2, MSSA476, N315, Mu50, JH1, JH9, and RF122. However, polymorphism analysis of two large pathogenicity islands distributed among these strains shows that the two islands were acquired independently from the evolutionary pathway of the chromosomal backbones of staphylococcal genomes. Prophages and pathogenicity islands play central roles in S. aureus virulence and evolution. PMID:17951380

  3. Complete mitochondrial genome of the Tioman Island rock gecko, Cnemaspis limi (Sauria, Gekkota, Gekkonidae).

    PubMed

    Yan, Jie; Tian, Chao; Zhou, Jianli; Bauer, Aaron M; Lee Grismer, L; Zhou, Kaiya

    2014-06-01

    We sequenced the complete mitochondrial genome of the Tioman Island rock gecko, Cnemaspis limi, which is known as an endemic species to Malaysia. The complete mitogenome is 16,680?bp in size, consisting of 37 genes coding for 13 proteins, 22 transfer RNAs, two ribosomal RNAs and one control region. The A?+?T content of the overall base composition of H-strand is 53.09% (T: 23.20%, C: 32.48%, A: 29.89% and G: 14.43%). The major non-coding region (control region) is 1254?bp in length with the A?+?T content of 55.09% and four replicates of a 76-bp repeat within this region. PMID:23631365

  4. Orphan CpG islands identify numerous conserved promoters in the mammalian genome.

    PubMed

    Illingworth, Robert S; Gruenewald-Schneider, Ulrike; Webb, Shaun; Kerr, Alastair R W; James, Keith D; Turner, Daniel J; Smith, Colin; Harrison, David J; Andrews, Robert; Bird, Adrian P

    2010-09-01

    CpG islands (CGIs) are vertebrate genomic landmarks that encompass the promoters of most genes and often lack DNA methylation. Querying their apparent importance, the number of CGIs is reported to vary widely in different species and many do not co-localise with annotated promoters. We set out to quantify the number of CGIs in mouse and human genomes using CXXC Affinity Purification plus deep sequencing (CAP-seq). We also asked whether CGIs not associated with annotated transcripts share properties with those at known promoters. We found that, contrary to previous estimates, CGI abundance in humans and mice is very similar and many are at conserved locations relative to genes. In each species CpG density correlates positively with the degree of H3K4 trimethylation, supporting the hypothesis that these two properties are mechanistically interdependent. Approximately half of mammalian CGIs (>10,000) are "orphans" that are not associated with annotated promoters. Many orphan CGIs show evidence of transcriptional initiation and dynamic expression during development. Unlike CGIs at known promoters, orphan CGIs are frequently subject to DNA methylation during development, and this is accompanied by loss of their active promoter features. In colorectal tumors, however, orphan CGIs are not preferentially methylated, suggesting that cancer does not recapitulate a developmental program. Human and mouse genomes have similar numbers of CGIs, over half of which are remote from known promoters. Orphan CGIs nevertheless have the characteristics of functional promoters, though they are much more likely than promoter CGIs to become methylated during development and hence lose these properties. The data indicate that orphan CGIs correspond to previously undetected promoters whose transcriptional activity may play a functional role during development. PMID:20885785

  5. Gene Acquisition at the Insertion Site for SCCmec, the Genomic Island Conferring Methicillin Resistance in Staphylococcus aureus

    Microsoft Academic Search

    Michael J. Noto; Barry N. Kreiswirth; Alastair B. Monk; Gordon L. Archer

    2008-01-01

    Staphylococcus aureus becomes resistant to methicillin by acquiring a genomic island, known as staphylo- coccal chromosome cassette mec (SCCmec), which contains the methicillin resistance determinant, mecA. SCCmec is site-specifically integrated into the staphylococcal chromosome at a locus known as the SCCmec attachment site (attB). In an effort to gain a better understanding of the potential that methicillin-sensitive S. aureus (MSSA)

  6. A novel family of integrases associated with prophages and genomic islands integrated within the tRNA-dihydrouridine synthase A (dusA) gene

    PubMed Central

    Farrugia, Daniel N.; Elbourne, Liam D. H.; Mabbutt, Bridget C.; Paulsen, Ian T.

    2015-01-01

    Genomic islands play a key role in prokaryotic genome plasticity. Genomic islands integrate into chromosomal loci such as transfer RNA genes and protein coding genes, whilst retaining various cargo genes that potentially bestow novel functions on the host organism. A gene encoding a putative integrase was identified at a single site within the 5? end of the dusA gene in the genomes of over 200 bacteria. This integrase was discovered to be a component of numerous genomic islands, which appear to share a target site within the dusA gene. dusA encodes the tRNA-dihydrouridine synthase A enzyme, which catalyses the post-transcriptional reduction of uridine to dihydrouridine in tRNA. Genomic islands encoding homologous dusA-associated integrases were found at a much lower frequency within the related dusB and dusC genes, and non-dus genes. Excision of these dusA-associated islands from the chromosome as circularized intermediates was confirmed by polymerase chain reaction. Analysis of the dusA-associated islands indicated that they were highly diverse, with the integrase gene representing the only universal common feature. PMID:25883135

  7. Genome-wide SNP analysis reveals population structure and demographic history of the ryukyu islanders in the southern part of the Japanese archipelago.

    PubMed

    Sato, Takehiro; Nakagome, Shigeki; Watanabe, Chiaki; Yamaguchi, Kyoko; Kawaguchi, Akira; Koganebuchi, Kae; Haneji, Kuniaki; Yamaguchi, Tetsutaro; Hanihara, Tsunehiko; Yamamoto, Ken; Ishida, Hajime; Mano, Shuhei; Kimura, Ryosuke; Oota, Hiroki

    2014-11-01

    The Ryukyu Islands are located to the southwest of the Japanese archipelago. Archaeological evidence has revealed the existence of prehistoric cultural differentiation between the northern Ryukyu islands of Amami and Okinawa, and the southern Ryukyu islands of Miyako and Yaeyama. To examine a genetic subdivision in the Ryukyu Islands, we conducted genome-wide single nucleotide polymorphism typing of inhabitants from the Okinawa Islands, the Miyako Islands, and the Yaeyama Islands. Principal component and cluster analyses revealed genetic differentiation among the island groups, especially between Okinawa and Miyako. No genetic affinity was observed between aboriginal Taiwanese and any of the Ryukyu populations. The genetic differentiation observed between the inhabitants of the Okinawa Islands and the Miyako Islands is likely to have arisen due to genetic drift rather than admixture with people from neighboring regions. Based on the observed genetic differences, the divergence time between the inhabitants of Okinawa and Miyako islands was dated to the Holocene. These findings suggest that the Pleistocene inhabitants, whose bones have been found on the southern Ryukyu Islands, did not make a major genetic contribution, if any, to the present-day inhabitants of the southern Ryukyu Islands. PMID:25086001

  8. Symbiosis island shuffling with abundant insertion sequences in the genomes of extra-slow-growing strains of soybean bradyrhizobia.

    PubMed

    Iida, Takayuki; Itakura, Manabu; Anda, Mizue; Sugawara, Masayuki; Isawa, Tsuyoshi; Okubo, Takashi; Sato, Shusei; Chiba-Kakizaki, Kaori; Minamisawa, Kiwamu

    2015-06-15

    Extra-slow-growing bradyrhizobia from root nodules of field-grown soybeans harbor abundant insertion sequences (ISs) and are termed highly reiterated sequence-possessing (HRS) strains. We analyzed the genome organization of HRS strains with the focus on IS distribution and symbiosis island structure. Using pulsed-field gel electrophoresis, we consistently detected several plasmids (0.07 to 0.4 Mb) in the HRS strains (NK5, NK6, USDA135, 2281, USDA123, and T2), whereas no plasmids were detected in the non-HRS strain USDA110. The chromosomes of the six HRS strains (9.7 to 10.7 Mb) were larger than that of USDA110 (9.1 Mb). Using MiSeq sequences of 6 HRS and 17 non-HRS strains mapped to the USDA110 genome, we found that the copy numbers of ISRj1, ISRj2, ISFK1, IS1632, ISB27, ISBj8, and IS1631 were markedly higher in HRS strains. Whole-genome sequencing showed that the HRS strain NK6 had four small plasmids (136 to 212 kb) and a large chromosome (9,780 kb). Strong colinearity was found between 7.4-Mb core regions of the NK6 and USDA110 chromosomes. USDA110 symbiosis islands corresponded mainly to five small regions (S1 to S5) within two variable regions, V1 (0.8 Mb) and V2 (1.6 Mb), of the NK6 chromosome. The USDA110 nif gene cluster (nifDKENXSBZHQW-fixBCX) was split into two regions, S2 and S3, where ISRj1-mediated rearrangement occurred between nifS and nifB. ISs were also scattered in NK6 core regions, and ISRj1 insertion often disrupted some genes important for survival and environmental responses. These results suggest that HRS strains of soybean bradyrhizobia were subjected to IS-mediated symbiosis island shuffling and core genome degradation. PMID:25862225

  9. Vibrio cholerae VttRA and VttRB Regulatory Influences Extend beyond the Type 3 Secretion System Genomic Island

    PubMed Central

    Chaand, Mudit

    2013-01-01

    A subset of non-O1/non-O139 serogroup strains of Vibrio cholerae cause disease using type 3 secretion system (T3SS)-mediated mechanisms. An ?50-kb genomic island carries genes encoding the T3SS structural apparatus, effector proteins, and two transmembrane transcriptional regulators, VttRA and VttRB, which are ToxR homologues. Previous experiments demonstrated that VttRA and VttRB are necessary for colonization in vivo and promote bile-dependent T3SS gene expression in vitro. To better understand the scope of genes that are potential targets of VttRA and VttRB regulation, we performed deep RNA sequencing using O39 serogroup strain AM-19226 and derivatives carrying deletions in vttRA and vttRB grown in bile. Comparison of the transcript profiles from ?vttRA and ?vttRB mutant strains to the isogenic parent strain confirmed that VttRA and VttRB regulate expression of some T3SS island genes and provided additional information about relative expression levels and operon organization. Interestingly, the data also suggested that additional genes, located outside the T3SS island and encoding functions involved in motility, chemotaxis, type 6 secretion, transcriptional regulation, and stress responses, may also by regulated by VttRA and VttRB. We verified transcript levels for selected genes by quantitative reverse transcription (RT)-PCR and then focused additional studies on motility and biofilm formation. The results suggest that VttRA and VttRB act as part of a complex transcriptional network that coordinates virulence gene expression with multiple cellular phenotypes. VttRA and VttRB therefore represent horizontally acquired transcriptional regulators with the ability to influence global gene expression in addition to modulating gene expression within the T3SS genomic island. PMID:23524608

  10. Genome Sequence of Exiguobacterium antarcticum B7, Isolated from a Biofilm in Ginger Lake, King George Island, Antarctica

    PubMed Central

    Carneiro, Adriana Ribeiro; Ramos, Rommel Thiago Jucá; Dall'Agnol, Hivana; Pinto, Anne Cybelle; de Castro Soares, Siomar; Santos, Anderson Rodrigues; Guimarães, Luis Carlos; Almeida, Sintia Silva; Baraúna, Rafael Azevedo; das Graças, Diego Assis; Franco, Luciano Chaves; Ali, Amjad; Hassan, Syed Shah; Nunes, Catarina Isabel P.; Barbosa, Maria Silvanira; Fiaux, Karina Kelly; Aburjaile, Flávia Figueira; Barbosa, Eudes Guilherme Vieira; Bakhtiar, Syeda Marriam; Vilela, Daniella; Nóbrega, Felipe; dos Santos, Adriana Lopes; Carepo, Marta Sofia P.; Azevedo, Vasco; Schneider, Maria Paula Cruz; Pellizari, Vivian Helena

    2012-01-01

    Exiguobacterium antarcticum is a psychotropic bacterium isolated for the first time from microbial mats of Lake Fryxell in Antarctica. Many organisms of the genus Exiguobacterium are extremophiles and have properties of biotechnological interest, e.g., the capacity to adapt to cold, which make this genus a target for discovering new enzymes, such as lipases and proteases, in addition to improving our understanding of the mechanisms of adaptation and survival at low temperatures. This study presents the genome of E. antarcticum B7, isolated from a biofilm sample of Ginger Lake on King George Island, Antarctic peninsula. PMID:23144424

  11. Complete genome sequence and comparative genomic analysis of Mycobacterium massiliense JCM 15300 in the Mycobacterium abscessus group reveal a conserved genomic island MmGI-1 related to putative lipid metabolism.

    PubMed

    Sekizuka, Tsuyoshi; Kai, Masanori; Nakanaga, Kazue; Nakata, Noboru; Kazumi, Yuko; Maeda, Shinji; Makino, Masahiko; Hoshino, Yoshihiko; Kuroda, Makoto

    2014-01-01

    Mycobacterium abscessus group subsp., such as M. massiliense, M. abscessus sensu stricto and M. bolletii, are an environmental organism found in soil, water and other ecological niches, and have been isolated from respiratory tract infection, skin and soft tissue infection, postoperative infection of cosmetic surgery. To determine the unique genetic feature of M. massiliense, we sequenced the complete genome of M. massiliense type strain JCM 15300 (corresponding to CCUG 48898). Comparative genomic analysis was performed among Mycobacterium spp. and among M. abscessus group subspp., showing that additional ß-oxidation-related genes and, notably, the mammalian cell entry (mce) operon were located on a genomic island, M. massiliense Genomic Island 1 (MmGI-1), in M. massiliense. In addition, putative anaerobic respiration system-related genes and additional mycolic acid cyclopropane synthetase-related genes were found uniquely in M. massiliense. Japanese isolates of M. massiliense also frequently possess the MmGI-1 (14/44, approximately 32%) and three unique conserved regions (26/44; approximately 60%, 34/44; approximately 77% and 40/44; approximately 91%), as well as isolates of other countries (Malaysia, France, United Kingdom and United States). The well-conserved genomic island MmGI-1 may play an important role in high growth potential with additional lipid metabolism, extra factors for survival in the environment or synthesis of complex membrane-associated lipids. ORFs on MmGI-1 showed similarities to ORFs of phylogenetically distant M. avium complex (MAC), suggesting that horizontal gene transfer or genetic recombination events might have occurred within MmGI-1 among M. massiliense and MAC. PMID:25503461

  12. Complete Genome Sequence and Comparative Genomic Analysis of Mycobacterium massiliense JCM 15300 in the Mycobacterium abscessus Group Reveal a Conserved Genomic Island MmGI-1 Related to Putative Lipid Metabolism

    PubMed Central

    Nakanaga, Kazue; Nakata, Noboru; Kazumi, Yuko; Maeda, Shinji; Makino, Masahiko; Hoshino, Yoshihiko; Kuroda, Makoto

    2014-01-01

    Mycobacterium abscessus group subsp., such as M. massiliense, M. abscessus sensu stricto and M. bolletii, are an environmental organism found in soil, water and other ecological niches, and have been isolated from respiratory tract infection, skin and soft tissue infection, postoperative infection of cosmetic surgery. To determine the unique genetic feature of M. massiliense, we sequenced the complete genome of M. massiliense type strain JCM 15300 (corresponding to CCUG 48898). Comparative genomic analysis was performed among Mycobacterium spp. and among M. abscessus group subspp., showing that additional ß-oxidation-related genes and, notably, the mammalian cell entry (mce) operon were located on a genomic island, M. massiliense Genomic Island 1 (MmGI-1), in M. massiliense. In addition, putative anaerobic respiration system-related genes and additional mycolic acid cyclopropane synthetase-related genes were found uniquely in M. massiliense. Japanese isolates of M. massiliense also frequently possess the MmGI-1 (14/44, approximately 32%) and three unique conserved regions (26/44; approximately 60%, 34/44; approximately 77% and 40/44; approximately 91%), as well as isolates of other countries (Malaysia, France, United Kingdom and United States). The well-conserved genomic island MmGI-1 may play an important role in high growth potential with additional lipid metabolism, extra factors for survival in the environment or synthesis of complex membrane-associated lipids. ORFs on MmGI-1 showed similarities to ORFs of phylogenetically distant M. avium complex (MAC), suggesting that horizontal gene transfer or genetic recombination events might have occurred within MmGI-1 among M. massiliense and MAC. PMID:25503461

  13. Stability of a Pseudomonas putida KT2440 Bacteriophage-Carried Genomic Island and Its Impact on Rhizosphere Fitness

    PubMed Central

    Quesada, Jose M.; Soriano, María Isabel

    2012-01-01

    The stability of seven genomic islands of Pseudomonas putida KT2440 with predicted potential for mobilization was studied in bacterial populations associated with the rhizosphere of corn plants by multiplex PCR. DNA rearrangements were detected for only one of them (GI28), which was lost at high frequency. This genomic island of 39.4 kb, with 53 open reading frames, shows the characteristic organization of genes belonging to tailed phages. We present evidence indicating that it corresponds to the lysogenic state of a functional bacteriophage that we have designated Pspu28. Integrated and rarely excised forms of Pspu28 coexist in KT2440 populations. Pspu28 is self-transmissible, and an excisionase is essential for its removal from the bacterial chromosome. The excised Pspu28 forms a circular element that can integrate into the chromosome at a specific location, att sites containing a 17-bp direct repeat sequence. Excision/insertion of Pspu28 alters the promoter sequence and changes the expression level of PP_1531, which encodes a predicted arsenate reductase. Finally, we show that the presence of Pspu28 in the lysogenic state has a negative effect on bacterial fitness in the rhizosphere under conditions of intraspecific competition, thus explaining why clones having lost this mobile element are recovered from that environment. PMID:22843519

  14. Genomic Comparison of cag Pathogenicity Island (PAI)Positive and Negative Helicobacter pylori Strains: Identification of Novel Markers for cag PAIPositive Strains

    Microsoft Academic Search

    Courtney E. Terry; Lisa M. McGinnis; Katharine C. Madigan; Ping Cao; George W. Liechti; Richard M. Peek; M. H. Forsyth

    2005-01-01

    In an analysis of Helicobacter pylori genomic DNA by macroarray methodology, genomic DNA from a panel of cag pathogenicity island (PAI)-negative H. pylori clinical isolates failed to hybridize with 27 genes located outside the cag PAI in a cag PAI-positive reference strain. PCR analyses confirmed that HP0217 (encoding a lipopolysaccharide biosynthetic protein) and HP1079 (encoding a protein of unknown function)

  15. [The origin of polyploid genomes of bluegrasses Poa L. and gene flow between Northern Pacific and sub-Antarctic islands].

    PubMed

    Rodionov, A V; Nosov, N N; Kim, E S; Machs, E M; Punina, E O; Probatova, N S

    2010-12-01

    The involvement of present-day diploid bluegrass species in the formation of polyploid genomes was investigated using comparison of sequences of internal transcribed spacers ITS1 and ITS2, and the 5.8S rDNA sequence. It was demonstrated that highly polyploid New Zealand bluegrasses, P. cita (2n = 84; ca. 96 to 100), P. chathamica (2n = 112), and P. litorosa (2n = 263 to 266) formed separate highly supported clade together with tetraploids (2n = 28) P. intrusa, P. anceps, and P. trioides (Austrofestuca littoralis). Among the diploid species (2n = 14), the closest relatives of these species, as well as of the polyploid species of section Poa, are the genomes of Eurasian species P. remota, P. chaixcii (sect. Homalopoa), P densa (Bolbophorum), and P. sibirica (sect. Macropoa). Nuclear genomes of polyploid Stenopoa, Tichopoa, Oreinos, and Secundae are definitely related to the genome of Arctic species P. pseudabbreviata (sect. Abbreviatae). On the contrary, judging by the genes for nuclear 45S rRNA, genomes of diploid P. trivialis (sect. Pandemos), P. annua, and P. supina (sect. Ochlopoa both) are only remotely related to the genomes of highly polyploid species (distances p between them and other bluegrass species from different sections of subgenus Poa constitute 6-10% and 11-15%, respectively). The conclusion on the relationships between highly polyploid and diploid bluegrass species was tested using analysis of synapomorphic mutations in the 5.8S rRNA gene. It was demonstrated that genomes of Poa eminens (2n = 42) and P. schischkinii (2n = 70) (sect. Arctopoa both) were noticeably different in ITS regions from the genomes of the members of the type subgenus Poa. A comparison of the Arctopoa ITS regions showed that the differences between them constituted only 0.2%. At the same time, p distances between the Arctopoa ITS and those from the species belonging to other sections of the genus Poa varied from 5 to 14%. South American species P chonotica (sect. Andinae) (=Ncoraepoa chonotica) (2n = 42) was found to be related to Arctagrostis, Festucella, and Hookerochloa, being at the same time quite distant from the other species of the genus Poa. Polymorphic in chromosome number highly polyploid species of Northern Hemisphere, P. arctica (2n = 42 to 106), P. turneri (2n = 42, 63 to 64), and P. smirnovii (2n = 42, 70) (sect. Malacanthae) are relative to a large group of tetraploid (2n = 28) endemic bluegrass species from New Zealand and sub-Antarctic islands (P. novae-zelandiae and allied species). PMID:21434413

  16. Pyrosequencing-based comparative genome analysis of the nosocomial pathogen Enterococcus faecium and identification of a large transferable pathogenicity island

    PubMed Central

    2010-01-01

    Background The Gram-positive bacterium Enterococcus faecium is an important cause of nosocomial infections in immunocompromized patients. Results We present a pyrosequencing-based comparative genome analysis of seven E. faecium strains that were isolated from various sources. In the genomes of clinical isolates several antibiotic resistance genes were identified, including the vanA transposon that confers resistance to vancomycin in two strains. A functional comparison between E. faecium and the related opportunistic pathogen E. faecalis based on differences in the presence of protein families, revealed divergence in plant carbohydrate metabolic pathways and oxidative stress defense mechanisms. The E. faecium pan-genome was estimated to be essentially unlimited in size, indicating that E. faecium can efficiently acquire and incorporate exogenous DNA in its gene pool. One of the most prominent sources of genomic diversity consists of bacteriophages that have integrated in the genome. The CRISPR-Cas system, which contributes to immunity against bacteriophage infection in prokaryotes, is not present in the sequenced strains. Three sequenced isolates carry the esp gene, which is involved in urinary tract infections and biofilm formation. The esp gene is located on a large pathogenicity island (PAI), which is between 64 and 104 kb in size. Conjugation experiments showed that the entire esp PAI can be transferred horizontally and inserts in a site-specific manner. Conclusions Genes involved in environmental persistence, colonization and virulence can easily be aquired by E. faecium. This will make the development of successful treatment strategies targeted against this organism a challenge for years to come. PMID:20398277

  17. The Master Activator of IncA/C Conjugative Plasmids Stimulates Genomic Islands and Multidrug Resistance Dissemination

    PubMed Central

    Luo, Peng; Rodrigue, Sébastien; Burrus, Vincent

    2014-01-01

    Dissemination of antibiotic resistance genes occurs mostly by conjugation, which mediates DNA transfer between cells in direct contact. Conjugative plasmids of the IncA/C incompatibility group have become a substantial threat due to their broad host-range, the extended spectrum of antimicrobial resistance they confer, their prevalence in enteric bacteria and their very efficient spread by conjugation. However, their biology remains largely unexplored. Using the IncA/C conjugative plasmid pVCR94?X as a prototype, we have investigated the regulatory circuitry that governs IncA/C plasmids dissemination and found that the transcriptional activator complex AcaCD is essential for the expression of plasmid transfer genes. Using chromatin immunoprecipitation coupled with exonuclease digestion (ChIP-exo) and RNA sequencing (RNA-seq) approaches, we have identified the sequences recognized by AcaCD and characterized the AcaCD regulon. Data mining using the DNA motif recognized by AcaCD revealed potential AcaCD-binding sites upstream of genes involved in the intracellular mobility functions (recombination directionality factor and mobilization genes) in two widespread classes of genomic islands (GIs) phylogenetically unrelated to IncA/C plasmids. The first class, SGI1, confers and propagates multidrug resistance in Salmonella enterica and Proteus mirabilis, whereas MGIVmi1 in Vibrio mimicus belongs to a previously uncharacterized class of GIs. We have demonstrated that through expression of AcaCD, IncA/C plasmids specifically trigger the excision and mobilization of the GIs at high frequencies. This study provides new evidence of the considerable impact of IncA/C plasmids on bacterial genome plasticity through their own mobility and the mobilization of genomic islands. PMID:25340549

  18. Systematic evaluation of genome-wide methylated DNA enrichment using a CpG island array

    Microsoft Academic Search

    Liu Yang; Kunlin Zhang; Wei Dai; Ximiao He; Qian Zhao; Jing Wang; Zhong Sheng Sun

    2011-01-01

    BACKGROUND: Recent progress in high-throughput technologies has greatly contributed to the development of DNA methylation profiling. Although there are several reports that describe methylome detection of whole genome bisulfite sequencing, the high cost and heavy demand on bioinformatics analysis prevents its extensive application. Thus, current strategies for the study of mammalian DNA methylomes is still based primarily on genome-wide methylated

  19. Prediction of Genomic Methylation Status on CpG Islands Using DNA Sequence Features

    Microsoft Academic Search

    YOICHI YAMADA; KENJI SATOU

    2008-01-01

    In mammals, cytosines of most CpG dinucleotides in their genomes except gene promoters are subject to modification by methyl group (methylation). A number of genes in a mammal are regulated developmental- specifically or tissue-specifically by the methylation. Mammalian DNA methylation contributes to regulation of gene expression, repression of parasitic sequences, inactivation of X chromosome in female, genomic imprinting, etc. Aberrant

  20. Genome Sequence of Nitratireductor basaltis Strain UMTGB225, a Marine Bacterium Isolated from a Green Barrel Tunicate in Bidong Island, Malaysia

    PubMed Central

    Gan, Huan You; Gan, Han Ming; Saari, Nur Azna; Usup, Gires

    2014-01-01

    Nitratireductor basaltis strain UMTGB225 is a Gram-negative bacterium isolated from a marine tunicate found in Bidong Island, Terengganu, Malaysia. In this study, the genome of Nitratireductor basaltis UMTGB225 was sequenced to gain insight into the role of this bacterium and its association with tunicate hosts in a coral reef habitat. PMID:25301654

  1. Interactions of Neuropathogenic Escherichia coli K1 (RS218) and Its Derivatives Lacking Genomic Islands with Phagocytic Acanthamoeba castellanii and Nonphagocytic Brain Endothelial Cells

    PubMed Central

    Yousuf, Farzana Abubakar; Yousuf, Zuhair; Iqbal, Junaid; Siddiqui, Ruqaiyyah; Khan, Hafsa; Khan, Naveed Ahmed

    2014-01-01

    Here we determined the role of various genomic islands in E. coli K1 interactions with phagocytic A. castellanii and nonphagocytic brain microvascular endothelial cells. The findings revealed that the genomic islands deletion mutants of RS218 related to toxins (peptide toxin, ?-hemolysin), adhesins (P fimbriae, F17-like fimbriae, nonfimbrial adhesins, Hek, and hemagglutinin), protein secretion system (T1SS for hemolysin), invasins (IbeA, CNF1), metabolism (D-serine catabolism, dihydroxyacetone, glycerol, and glyoxylate metabolism) showed reduced interactions with both A. castellanii and brain microvascular endothelial cells. Interestingly, the deletion of RS218-derived genomic island 21 containing adhesins (P fimbriae, F17-like fimbriae, nonfimbrial adhesins, Hek, and hemagglutinin), protein secretion system (T1SS for hemolysin), invasins (CNF1), metabolism (D-serine catabolism) abolished E. coli K1-mediated HBMEC cytotoxicity in a CNF1-independent manner. Therefore, the characterization of these genomic islands should reveal mechanisms of evolutionary gain for E. coli K1 pathogenicity. PMID:24818136

  2. Complete genome sequence of Leptospirillum ferrooxidans strain C2-3, isolated from a fresh volcanic ash deposit on the island of Miyake, Japan.

    PubMed

    Fujimura, Reiko; Sato, Yoshinori; Nishizawa, Tomoyasu; Oshima, Kenshiro; Kim, Seok-Won; Hattori, Masahira; Kamijo, Takashi; Ohta, Hiroyuki

    2012-08-01

    A diazotrophic, acidophilic, iron-oxidizing bacterium, Leptospirillum ferrooxidans, known to be difficult to cultivate, was isolated from a fresh volcanic ash deposit on the island of Miyake, Japan. Here, we report the complete genome sequence of a cultured strain, C2-3. PMID:22815442

  3. Draft Genome Sequence of the Filamentous Cyanobacterium Leptolyngbya sp. Strain Heron Island J, Exhibiting Chromatic Acclimation

    PubMed Central

    Paul, Robin; Jinkerson, Robert E.; Buss, Kristina; Steel, Jason; Mohr, Remus; Hess, Wolfgang R.; Chen, Min

    2014-01-01

    Leptolyngbya sp. strain Heron Island is a cyanobacterium exhibiting chromatic acclimation. However, this strain has strong interactions with other bacteria, making it impossible to obtain axenic cultures for sequencing. A protocol involving an analysis of tetranucleotide frequencies, G+C content, and BLAST searches has been described for separating the cyanobacterial scaffolds from those of its cooccurring bacteria. PMID:24503993

  4. The complete genomes of subgenotype IA hepatitis A virus strains from four different islands in Indonesia form a phylogenetic cluster.

    PubMed

    Mulyanto; Wibawa, I Dewa Nyoman; Suparyatmo, Joseph Benedictus; Amirudin, Rifai; Ohnishi, Hiroshi; Takahashi, Masaharu; Nishizawa, Tsutomu; Okamoto, Hiroaki

    2014-05-01

    Despite the high endemicity of hepatitis A virus (HAV) in Indonesia, genetic information on those HAV strains is limited. Serum samples obtained from 76 individuals during outbreaks of hepatitis A in Jember (East Java) in 2006 and Tangerang (West Java) in 2007 and those from 82 patients with acute hepatitis in Solo (Central Java), Denpasar on Bali Island, Mataram on Lombok Island, and Makassar on Sulawesi Island in 2003 or 2007 were tested for the presence of HAV RNA by reverse transcription PCR with primers targeting the VP1-2B region (481 nucleotides, primer sequences at both ends excluded). Overall, 34 serum samples had detectable HAV RNA, including at least one viremic sample from each of the six regions. These 34 strains were 96.3-100 % identical to each other and formed a phylogenetic cluster within genotype IA. Six representative HAV isolates from each region shared 98.3-98.9 % identity over the entire genome and constituted a IA sublineage with a bootstrap value of 100 %, consisting of only Indonesian strains. HAV strains recovered from Japanese patients who were presumed to have contracted HAV infection while visiting Indonesia were closest to the Indonesian IA HAV strains obtained in the present study, with a high identity of 99.5-99.7 %, supporting the Indonesian origin of the imported strains. These results indicate that genetic analysis of HAV strains indigenous to HAV-endemic countries, including Indonesia, are useful for tracing infectious sources in imported cases of acute hepatitis A and for defining the epidemiological features of HAV infection in that country. PMID:24212885

  5. Gene-rich islands for fiber development in the cotton genome

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Cotton fiber is an economically important seed trichome and the world's leading natural fiber used in the manufacture of textiles. As a step towards elucidating the genomic organization and distribution of gene networks responsible for cotton fiber development, we investigated the distribution of f...

  6. Population genomic analysis uncovers African and European admixture in Drosophila melanogaster populations from the south-eastern United States and Caribbean Islands.

    PubMed

    Kao, Joyce Y; Zubair, Asif; Salomon, Matthew P; Nuzhdin, Sergey V; Campo, Daniel

    2015-04-01

    Drosophila melanogaster is postulated to have colonized North America in the past several 100 years in two waves. Flies from Europe colonized the east coast United States while flies from Africa inhabited the Caribbean, which if true, make the south-east US and Caribbean Islands a secondary contact zone for African and European D. melanogaster. This scenario has been proposed based on phenotypes and limited genetic data. In our study, we have sequenced individual whole genomes of flies from populations in the south-east US and Caribbean Islands and examined these populations in conjunction with population sequences from the west coast US, Africa, and Europe. We find that west coast US populations are closely related to the European population, likely reflecting a rapid westward expansion upon first settlements into North America. We also find genomic evidence of African and European admixture in south-east US and Caribbean populations, with a clinal pattern of decreasing proportions of African ancestry with higher latitude. Our genomic analysis of D. melanogaster populations from the south-east US and Caribbean Islands provides more evidence for the Caribbean Islands as the source of previously reported novel African alleles found in other east coast US populations. We also find the border between the south-east US and the Caribbean island to be the admixture hot zone where distinctly African-like Caribbean flies become genomically more similar to European-like south-east US flies. Our findings have important implications for previous studies examining the generation of east coast US clines via selection. PMID:25735402

  7. GENOMICS

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Genomics is the science of taking a holistic approach to studying the genome. A useful analogy of genomics is that it is like looking at the entire forest, rather than individual trees. Genomics is more a thought process than a science and truly came to fruition when high throughput genetic technolo...

  8. Genomic Comparison of cag Pathogenicity Island (PAI)-Positive and -Negative Helicobacter pylori Strains: Identification of Novel Markers for cag PAI-Positive Strains

    PubMed Central

    Terry, Courtney E.; McGinnis, Lisa M.; Madigan, Katharine C.; Cao, Ping; Cover, Timothy L.; Liechti, George W.; Peek, Richard M.; Forsyth, Mark H.

    2005-01-01

    In an analysis of Helicobacter pylori genomic DNA by macroarray methodology, genomic DNA from a panel of cag pathogenicity island (PAI)-negative H. pylori clinical isolates failed to hybridize with 27 genes located outside the cag PAI in a cag PAI-positive reference strain. PCR analyses confirmed that HP0217 (encoding a lipopolysaccharide biosynthetic protein) and HP1079 (encoding a protein of unknown function) were present significantly more frequently in cagA-positive strains than in cagA-negative strains. A low G+C content of these two genes suggests they were acquired by horizontal transfer events. PMID:15908415

  9. Structure of a short-chain dehydrogenase/reductase (SDR) within a genomic island from a clinical strain of Acinetobacter baumannii

    PubMed Central

    Shah, Bhumika S.; Tetu, Sasha G.; Harrop, Stephen J.; Paulsen, Ian T.; Mabbutt, Bridget C.

    2014-01-01

    Over 15% of the genome of an Australian clinical isolate of Acinetobacter baumannii occurs within genomic islands. An uncharacterized protein encoded within one island feature common to this and other International Clone II strains has been studied by X-ray crystallography. The 2.4?Å resolution structure of SDR-WM99c reveals it to be a new member of the classical short-chain dehydrogenase/reductase (SDR) superfamily. The enzyme contains a nucleotide-binding domain and, like many other SDRs, is tetrameric in form. The active site contains a catalytic tetrad (Asn117, Ser146, Tyr159 and Lys163) and water molecules occupying the presumed NADP cofactor-binding pocket. An adjacent cleft is capped by a relatively mobile helical subdomain, which is well positioned to control substrate access. PMID:25286932

  10. A novel strategy for the identification of genomic islands by comparative analysis of the contents and contexts of tRNA sites in closely related bacteria

    Microsoft Academic Search

    Hong-Yu Ou; Ling-Ling Chen; James Lonnen; Roy R. Chaudhuri; Ali Bin Thani; Rebecca Smith; Natalie J. Garton; Jay Hinton; Mark Pallen; Michael R. Barer; Kumar Rajakumar

    2006-01-01

    We devised software tools to systematically investig- ate the contents and contexts of bacterial tRNA and tmRNA genes, which are known insertion hotspots for genomic islands (GIs). The strategy, based on MAUVE-facilitated multigenome comparisons, was used to examine 87 Escherichia coli MG1655 tRNA and tmRNA genes and their orthologues in E.coli EDL933, E.coli CFT073 and Shigella flexneri Sf301. Our approach

  11. Genome-Wide Analysis of the Salmonella Fis Regulon and Its Regulatory Mechanism on Pathogenicity Islands

    PubMed Central

    Wang, Quan; Wang, Lei

    2013-01-01

    Fis, one of the most important nucleoid-associated proteins, functions as a global regulator of transcription in bacteria that has been comprehensively studied in Escherichia coli K12. Fis also influences the virulence of Salmonella enterica and pathogenic E. coli by regulating their virulence genes, however, the relevant mechanism is unclear. In this report, using combined RNA-seq and chromatin immunoprecipitation (ChIP)-seq technologies, we first identified 1646 Fis-regulated genes and 885 Fis-binding targets in the S. enterica serovar Typhimurium, and found a Fis regulon different from that in E. coli. Fis has been reported to contribute to the invasion ability of S. enterica. By using cell infection assays, we found it also enhances the intracellular replication ability of S. enterica within macrophage cell, which is of central importance for the pathogenesis of infections. Salmonella pathogenicity islands (SPI)-1 and SPI-2 are crucial for the invasion and survival of S. enterica in host cells. Using mutation and overexpression experiments, real-time PCR analysis, and electrophoretic mobility shift assays, we demonstrated that Fis regulates 63 of the 94 Salmonella pathogenicity island (SPI)-1 and SPI-2 genes, by three regulatory modes: i) binds to SPI regulators in the gene body or in upstream regions; ii) binds to SPI genes directly to mediate transcriptional activation of themselves and downstream genes; iii) binds to gene encoding OmpR which affects SPI gene expression by controlling SPI regulators SsrA and HilD. Our results provide new insights into the impact of Fis on SPI genes and the pathogenicity of S. enterica. PMID:23717649

  12. Draft Genome Sequences of Thalassobacter Strains 1CONIMAR09 and 16PALIMAR09, Two Members of the Roseobacter Lineage Isolated from Coastal Areas of the Mediterranean Sea around Mallorca Island.

    PubMed

    Mas-Lladó, Maria; Piña-Villalonga, Joana Maria; Brunet-Galmés, Isabel; Nogales, Balbina; Bosch, Rafael

    2015-01-01

    We report the draft genome sequence of two new members of the Roseobacter lineage, Thalassobacter strains 1CONIMAR09 and 16PALIMAR09, which were isolated from the seawater coast of Mallorca Island. Each genome harbored putative genes for obtaining energy by chemolithotrophy and making aerobic anoxygenic photosynthesis. PMID:25744993

  13. Fraser Island Lady Elliot Island

    E-print Network

    Wang, Yan

    Hinchinbrook Island Lizard Island Double Island Green Island Fitzroy Island North and South Stradbroke Islands Moreton Island GOLD COAST Gulf of Carpenteria Thursday Island Torres Strait Horn Island Maroochydore

  14. Testing models of speciation from genome sequences: divergence and asymmetric admixture in Island South-East Asian Sus species during the Plio-Pleistocene climatic fluctuations

    PubMed Central

    Frantz, Laurent A F; Madsen, Ole; Megens, Hendrik-Jan; Groenen, Martien A M; Lohse, Konrad

    2014-01-01

    In many temperate regions, ice ages promoted range contractions into refugia resulting in divergence (and potentially speciation), while warmer periods led to range expansions and hybridization. However, the impact these climatic oscillations had in many parts of the tropics remains elusive. Here, we investigate this issue using genome sequences of three pig (Sus) species, two of which are found on islands of the Sunda-shelf shallow seas in Island South-East Asia (ISEA). A previous study revealed signatures of interspecific admixture between these Sus species (Genome biology,14, 2013, R107). However, the timing, directionality and extent of this admixture remain unknown. Here, we use a likelihood-based model comparison to more finely resolve this admixture history and test whether it was mediated by humans or occurred naturally. Our analyses suggest that interspecific admixture between Sunda-shelf species was most likely asymmetric and occurred long before the arrival of humans in the region. More precisely, we show that these species diverged during the late Pliocene but around 23% of their genomes have been affected by admixture during the later Pleistocene climatic transition. In addition, we show that our method provides a significant improvement over D-statistics which are uninformative about the direction of admixture. PMID:25294645

  15. A Genomic Island, Termed High-Pathogenicity Island, Is Present in Certain Non-O157 Shiga Toxin-Producing Escherichia coli Clonal Lineages

    Microsoft Academic Search

    H. KARCH; S. SCHUBERT; D. ZHANG; W. ZHANG; H. SCHMIDT; T. OLSCHLAGER; J. HACKER

    1999-01-01

    Shiga toxin-producing Escherichia coli (STEC) strains cause a wide spectrum of diseases in humans. In this study, we tested 206 STEC strains isolated from patients for potential virulence genes including stx, eae, and enterohemorrhagic E. coli hly. In addition, all strains were examined for the presence of another genetic element, the high-pathogenicity island (HPI). The HPI was first described in

  16. Novel insertion sequence- and transposon-mediated genetic rearrangements in genomic island SGI1 of Salmonella enterica serovar Kentucky.

    PubMed

    Doublet, Benoît; Praud, Karine; Bertrand, Sophie; Collard, Jean-Marc; Weill, François-Xavier; Cloeckaert, Axel

    2008-10-01

    Salmonella genomic island 1 (SGI1) is an integrative mobilizable element that harbors a multidrug resistance (MDR) gene cluster. Since its identification in epidemic Salmonella enterica serovar Typhimurium DT104 strains, variant SGI1 MDR gene clusters conferring different MDR phenotypes have been identified in several S. enterica serovars and classified as SGI1-A to -O. A study was undertaken to characterize SGI1 from serovar Kentucky strains isolated from travelers returning from Africa. Several strains tested were found to contain the partially characterized variant SGI1-K, recently described in a serovar Kentucky strain isolated in Australia. This variant contained only one cassette array, aac(3)-Id-aadA7, and an adjacent mercury resistance module. Here, the uncharacterized part of SGI1-K was sequenced. Downstream of the mer module similar to that found in Tn21, a mosaic genetic structure was found, comprising (i) part of Tn1721 containing the tetracycline resistance genes tetR and tet(A); (ii) part of Tn5393 containing the streptomycin resistance genes strAB, IS1133, and a truncated tnpR gene; and (iii) a Tn3-like region containing the tnpR gene and the beta-lactamase bla(TEM-1) gene flanked by two IS26 elements in opposite orientations. The rightmost IS26 element was shown to be inserted into the S044 open reading frame of the SGI1 backbone. This variant MDR region was named SGI1-K1 according to the previously described variant SGI1-K. Other SGI1-K MDR regions due to different IS26 locations, inversion, and partial deletions were characterized and named SGI1-K2 to -K5. Two new SGI1 variants named SGI1-P1 and -P2 contained only the Tn3-like region comprising the beta-lactamase bla(TEM-1) gene flanked by the two IS26 elements inserted into the SGI1 backbone. Three other new variants harbored only one IS26 element inserted in place of the MDR region of SGI1 and were named SGI1-Q1 to -Q3. Thus, in serovar Kentucky, the SGI1 MDR region undergoes recombinational and insertional events of transposon and insertion sequences, resulting in a higher diversity of MDR gene clusters than previously reported and consequently a higher diversity of MDR phenotypes. PMID:18676889

  17. Genome-Wide Profiling of DNA Methylation Reveals a Class of Normally Methylated CpG Island Promoters

    PubMed Central

    Shen, Lanlan; Kondo, Yutaka; Guo, Yi; Zhang, Jiexin; Zhang, Li; Ahmed, Saira; Shu, Jingmin; Chen, Xinli; Waterland, Robert A; Issa, Jean-Pierre J

    2007-01-01

    The role of CpG island methylation in normal development and cell differentiation is of keen interest, but remains poorly understood. We performed comprehensive DNA methylation profiling of promoter regions in normal peripheral blood by methylated CpG island amplification in combination with microarrays. This technique allowed us to simultaneously determine the methylation status of 6,177 genes, 92% of which include dense CpG islands. Among these 5,549 autosomal genes with dense CpG island promoters, we have identified 4.0% genes that are nearly completely methylated in normal blood, providing another exception to the general rule that CpG island methylation in normal tissue is limited to X inactivation and imprinted genes. We examined seven genes in detail, including ANKRD30A, FLJ40201, INSL6, SOHLH2, FTMT, C12orf12, and DPPA5. Dense promoter CpG island methylation and gene silencing were found in normal tissues studied except testis and sperm. In both tissues, bisulfite cloning and sequencing identified cells carrying unmethylated alleles. Interestingly, hypomethylation of several genes was associated with gene activation in cancer. Furthermore, reactivation of silenced genes could be induced after treatment with a DNA demethylating agent or in a cell line lacking DNMT1 and/or DNMT3b. Sequence analysis identified five motifs significantly enriched in this class of genes, suggesting that cis-regulatory elements may facilitate preferential methylation at these promoter CpG islands. We have identified a group of non-X–linked bona fide promoter CpG islands that are densely methylated in normal somatic tissues, escape methylation in germline cells, and for which DNA methylation is a primary mechanism of tissue-specific gene silencing. PMID:17967063

  18. Site-specific Relaxase Activity of a VirD2-like Protein Encoded within the tfs4 Genomic Island of Helicobacter pylori*

    PubMed Central

    Grove, Jane I.; Alandiyjany, Maher N.; Delahay, Robin M.

    2013-01-01

    Four different type IV secretion systems are variously represented in the genomes of different Helicobacter pylori strains. Two of these, encoded by tfs3 and tfs4 gene clusters are contained within self-transmissible genomic islands. Although chromosomal excision of tfs4 circular intermediates is reported to be dependent upon the function of a tfs4-encoded XerD tyrosine-like recombinase, other factors required for transfer to a recipient cell have not been demonstrated. Here, we characterize the functional activity of a putative tfs4-encoded VirD2-like relaxase protein. Tfs4 VirD2 was purified as a fusion to maltose-binding protein and demonstrated to bind and nick both supercoiled duplex DNA and oligonucleotides in vitro in a manner dependent upon the presence of Mg2+ but independently of any auxiliary proteins. Unusually, concentration-dependent nicking of duplex DNA appeared to require only transient protein-DNA interaction. Although phylogenetically distinct from established relaxase families, site-specific cleavage of oligonucleotides by Tfs4 VirD2 required the nick region sequence 5?-ATCCTG-3? common to transfer origins (oriT) recognized by MOBP conjugative relaxases. Cleavage resulted in covalent attachment of MBP-VirD2 to the 5?-cleaved end, consistent with conventional relaxase activity. Identification of an oriT-like sequence upstream of tfs4 virD2 and demonstration of VirD2 protein-protein interaction with a putative VirC1 relaxosome component indicate that transfer initiation of the tfs4 genomic island is analogous to mechanisms underlying mobilization of other integrated mobile elements, such as integrating conjugative elements, requiring site-specific targeting of relaxase activity to a cognate oriT sequence. PMID:23900838

  19. AsaGEI2b: a new variant of a genomic island identified in the Aeromonas salmonicida subsp. salmonicida JF3224 strain isolated from a wild fish in Switzerland.

    PubMed

    Emond-Rheault, Jean-Guillaume; Vincent, Antony T; Trudel, Mélanie V; Frey, Joachim; Frenette, Michel; Charette, Steve J

    2015-07-01

    Aeromonas salmonicida subsp. salmonicida is the causal agent of furunculosis in salmonids. We recently identified a group of genomic islands (AsaGEI) in this bacterium. AsaGEI2a, one of these genomic islands, has almost exclusively been identified in isolates from North America. To date, Aeromonas salmonicida subsp. salmonicida JF3224, a strain isolated from a wild brown trout (Salmo trutta) caught in Switzerland, was the only European isolate that appeared to bear AsaGEI2a. We analyzed the genome of JF3224 and showed that the genomic island in JF3224 is a new variant of AsaGEI, which we have called AsaGEI2b. While AsaGEI2b shares the same integrase gene and insertion site as AsaGEI2a, it is very different in terms of many other features. Additional genomic investigations combined with PCR genotyping revealed that JF3224 is sensitive to growth at 25°C, leading to insertion sequence-dependent rearrangement of the locus on the pAsa5 plasmid that encodes a type three secretion system, which is essential for the virulence of the bacterium. The analysis of the JF3224 genome confirmed that AsaGEIs are accurate indicators of the geographic origins of A. salmonicida subsp. salmonicida isolates and is another example of the susceptibility of the pAsa5 plasmid to DNA rearrangements. PMID:26048417

  20. Sequence Analysis of Staphylococcus hyicus ATCC 11249T, an Etiological Agent of Exudative Epidermitis in Swine, Reveals a Type VII Secretion System Locus and a Novel 116-Kilobase Genomic Island Harboring Toxin-Encoding Genes

    PubMed Central

    Foecking, Mark F.; Hsieh, Hsin-Yeh; Adkins, Pamela R. F.; Stewart, George C.; Middleton, John R.

    2015-01-01

    Staphylococcus hyicus is the primary etiological agent of exudative epidermitis in swine. Analysis of the complete genome sequence of the type strain revealed a locus encoding a type VII secretion system and a large chromosomal island harboring the genes encoding exfoliative toxin ExhA and an EDIN toxin homolog. PMID:25700402

  1. Pyrosequencing-based comparative genome analysis of the nosocomial pathogen Enterococcus faecium and identification of a large transferable pathogenicity island

    Microsoft Academic Search

    Willem van Schaik; Janetta Top; David R. Riley; Jos Boekhorst; Joyce E. P. Vrijenhoek; Claudia M. E. Schapendonk; Antoni P. A. Hendrickx; Isaäc J. Nijman; Marc J. M. Bonten; Hervé Tettelin; Rob J. L. Willems

    2010-01-01

    BACKGROUND: The Gram-positive bacterium Enterococcus faecium is an important cause of nosocomial infections in immunocompromized patients. RESULTS: We present a pyrosequencing-based comparative genome analysis of seven E. faecium strains that were isolated from various sources. In the genomes of clinical isolates several antibiotic resistance genes were identified, including the vanA transposon that confers resistance to vancomycin in two strains. A

  2. Characterization of Salmonella enterica serovar Typhimurium isolates harboring a chromosomally encoded CMY-2 beta-lactamase gene located on a multidrug resistance genomic island.

    PubMed

    Shahada, Francis; Sekizuka, Tsuyoshi; Kuroda, Makoto; Kusumoto, Masahiro; Ohishi, Daiki; Matsumoto, Atsuko; Okazaki, Hizuru; Tanaka, Kiyoshi; Uchida, Ikuo; Izumiya, Hidemasa; Watanabe, Haruo; Tamamura, Yukino; Iwata, Taketoshi; Akiba, Masato

    2011-09-01

    Since 2004, extended-spectrum cephalosporin (ESC)-resistant Salmonella enterica serovar Typhimurium (S. Typhimurium) isolates have been detected from cattle in the northern major island of Japan, Hokkaido. Resistance to ESCs was found to be mediated by CMY-2 type ?-lactamase among 22 epidemiologically unrelated isolates showing indistinguishable pulsed-field gel electrophoresis patterns. Southern blot analysis using I-CeuI-digested genomic DNA demonstrated that the CMY-2 ?-lactamase gene (bla(CMY-2)) was integrated in a 2.5-Mb chromosomal fragment. Genetic analysis of S. Typhimurium isolate L-3553 indicated that bla(CMY-2) was located on a unique 125-kb genomic island, GI-VII-6, which consists of 140 open reading frames. Pairwise alignment of GI-VII-6 and Escherichia coli plasmid pAR060302 (size, 167 kb) revealed that a large proportion of GI-VII-6 (99%) shows a high sequence similarity (>99%) with pAR060302. GI-VII-6 contains 11 antimicrobial resistance genes including sul1, qacE?1, aadA2, and dfrA12 in the aadA2 region; sugE1 and bla(CMY-2) in the bla(CMY-2) region; and sul2, strA, strB, tet(A), and floR in the floR region. Two directly repeated IS26 copies were present at both ends of GI-VII-6. Junction regions of GI-VII-6 were flanked by an 8-bp direct repeat, indicating that GI-VII-6 was acquired by transposition involving IS26 transposase. PCR scanning revealed that the overall structure of GI-VII-6 was almost identical in the 22 isolates. Phylogenetic analysis suggested that S. Typhimurium isolates harboring GI-VII-6 belong to a different genomic lineage than other whole-genome-sequenced S. Typhimurium strains. These data indicate that a particular clone of S. Typhimurium harboring GI-VII-6 has spread among the cattle population in Hokkaido, Japan. PMID:21709089

  3. Genome Sequence of Staphylococcus aureus Strain Newman and Comparative Analysis of Staphylococcal Genomes: Polymorphism and Evolution of Two Major Pathogenicity Islands

    Microsoft Academic Search

    Tadashi Baba; Taeok Bae; Olaf Schneewind; Fumihiko Takeuchi; Keiichi Hiramatsu

    2008-01-01

    Strains of Staphylococcus aureus, an important human pathogen, display up to 20% variability in their genome sequence, and most sequence information is available for human clinical isolates that have not been subjected to genetic analysis of virulence attributes. S. aureus strain Newman, which was also isolated from a human infection, displays robust virulence properties in animal models of disease and

  4. A small non-coding RNA of the invasion gene island (SPI-1) represses outer membrane protein synthesis from the Salmonella core genome.

    PubMed

    Pfeiffer, Verena; Sittka, Alexandra; Tomer, Raju; Tedin, Karsten; Brinkmann, Volker; Vogel, Jörg

    2007-12-01

    The Salmonella pathogenicity island (SPI-1) encodes approximately 35 proteins involved in assembly of a type III secretion system (T3SS) which endows Salmonella with the ability to invade eukaryotic cells. We have discovered a novel SPI-1 gene, invR, which expresses an abundant small non-coding RNA (sRNA). The invR gene, which we identified in a global search for new Salmonella sRNA genes, is activated by the major SPI-1 transcription factor, HilD, under conditions that favour host cell invasion. The RNA chaperone, Hfq, is essential for the in vivo stability of the approximately 80 nt InvR RNA. Hfq binds InvR with high affinity in vitro, and InvR co-immunoprecipitates with FLAG epitope-tagged Hfq in Salmonella extracts. Surprisingly, deletion/overexpression of invR revealed no phenotype in SPI-1 regulation. In contrast, we find that InvR represses the synthesis of the abundant OmpD porin encoded by the Salmonella core genome. As invR is conserved in the early branching Salmonella bongori, we speculate that porin repression by InvR may have aided successful establishment of the SPI-1 T3SS after horizontal acquisition in the Salmonella lineage. This study identifies the first regulatory RNA of an enterobacterial pathogenicity island, and new roles for Hfq and HilD in SPI-1 gene expression. PMID:17971080

  5. Can AFLP genome scans detect small islands of differentiation? The case of shell sculpture variation in the periwinkle Echinolittorina hawaiiensis.

    PubMed

    Tice, K A; Carlon, D B

    2011-08-01

    Genome scans have identified candidate regions of the genome undergoing selection in a wide variety of organisms, yet have rarely been applied to broadly dispersing marine organisms experiencing divergent selection pressures, where high recombination rates can reduce the extent of linkage disequilibrium (LD) and the ability to detect genomic regions under selection. The broadly dispersing periwinkle Echinolittorina hawaiiensis exhibits a heritable shell sculpture polymorphism that is correlated with environmental variation. To elucidate the genetic basis of phenotypic variation, a genome scan using over 1000 AFLP loci was conducted on smooth and sculptured snails from divergent habitats at four replicate sites. Approximately 5% of loci were identified as outliers with Dfdist, whereas no outliers were identified by BayeScan. Closer examination of the Dfdist outliers supported the conclusion that these loci were false positives. These results highlight the importance of controlling for Type I error using multiple outlier detection approaches, multitest corrections and replicate population comparisons. Assuming shell phenotypes have a genetic basis, our failure to detect outliers suggests that the life history of the target species needs to be considered when designing a genome scan. PMID:21605221

  6. Extensively drug-resistant pseudomonas aeruginosa isolates containing blaVIM-2 and elements of Salmonella genomic island 2: a new genetic resistance determinant in Northeast Ohio.

    PubMed

    Perez, Federico; Hujer, Andrea M; Marshall, Steven H; Ray, Amy J; Rather, Philip N; Suwantarat, Nuntra; Dumford, Donald; O'Shea, Patrick; Domitrovic, T Nicholas J; Salata, Robert A; Chavda, Kalyan D; Chen, Liang; Kreiswirth, Barry N; Vila, Alejandro J; Haussler, Susanne; Jacobs, Michael R; Bonomo, Robert A

    2014-10-01

    Carbapenems are a mainstay of treatment for infections caused by Pseudomonas aeruginosa. Carbapenem resistance mediated by metallo-?-lactamases (MBLs) remains uncommon in the United States, despite the worldwide emergence of this group of enzymes. Between March 2012 and May 2013, we detected MBL-producing P. aeruginosa in a university-affiliated health care system in northeast Ohio. We examined the clinical characteristics and outcomes of patients, defined the resistance determinants and structure of the genetic element harboring the blaMBL gene through genome sequencing, and typed MBL-producing P. aeruginosa isolates using pulsed-field gel electrophoresis (PFGE), repetitive sequence-based PCR (rep-PCR), and multilocus sequence typing (MLST). Seven patients were affected that were hospitalized at three community hospitals, a long-term-care facility, and a tertiary care center; one of the patients died as a result of infection. Isolates belonged to sequence type 233 (ST233) and were extensively drug resistant (XDR), including resistance to all fluoroquinolones, aminoglycosides, and ?-lactams; two isolates were nonsusceptible to colistin. The blaMBL gene was identified as blaVIM-2 contained within a class 1 integron (In559), similar to the cassette array previously detected in isolates from Norway, Russia, Taiwan, and Chicago, IL. Genomic sequencing and assembly revealed that In559 was part of a novel 35-kb region that also included a Tn501-like transposon and Salmonella genomic island 2 (SGI2)-homologous sequences. This analysis of XDR strains producing VIM-2 from northeast Ohio revealed a novel recombination event between Salmonella and P. aeruginosa, heralding a new antibiotic resistance threat in this region's health care system. PMID:25070102

  7. Prokaryotic Genomes Eurkaryotic Genomes

    E-print Network

    Qiu, Weigang

    Prokaryotic Genomes Eurkaryotic Genomes Chapter 6. Genomics and Gene Identification Weigang Qiu Weigang Qiu Chapter 6. Genomics and Gene Identification #12;Prokaryotic Genomes Eurkaryotic Genomes Outline 1 Prokaryotic Genomes 2 Eurkaryotic Genomes Weigang Qiu Chapter 6. Genomics and Gene

  8. Genome Bioinformatics

    NSDL National Science Digital Library

    This no-frills UC-Santa Cruz Genome Bioinformatics Web site contains searchable "working drafts of the human genome and the mouse genome," which each represent "immense collaborative efforts" within the biomedical research community. Those who are active in genome research may find this Web site useful, especially for the multi-faceted genome browser that "provides a rapid and reliable display of any requested portion of genomes at any scale, together with dozens of aligned annotation tracks (known genes, predicted genes, ESTs, mRNAs, CpG islands, assembly gaps and coverage, chromosomal bands, mouse homologies, and more)." Users may also access Blat alignments, a table browser (provides tabular representation of the data as an alternative to the graphical display of the genome browser), downloadable versions of the data set, and more. The site also contains a helpful FAQ page and a News section that alerts the user to corrected errors, new features, etc. The extensive list of links leads to dozens of other genome databases, browsers, and related tools.

  9. The fast milk acidifying phenotype of Streptococcus thermophilus can be acquired by natural transformation of the genomic island encoding the cell-envelope proteinase PrtS

    PubMed Central

    2011-01-01

    Background In industrial fermentation processes, the rate of milk acidification by Streptococcus thermophilus is of major technological importance. The cell-envelope proteinase PrtS was previously shown to be a key determinant of the milk acidification activity in this species. The PrtS enzyme is tightly anchored to the cell wall via a mechanism involving the typical sortase A (SrtA) and initiates the breakdown of milk casein into small oligopeptides. The presence or absence of PrtS divides the S. thermophilus strains into two phenotypic groups i.e. the slow and the fast acidifying strains. The aim of this study was to improve the milk acidification rate of slow S. thermophilus strains, and hence optimise the fermentation process of dairy products. Results In the present work, we developed for the first time a strategy based on natural transformation to confer the rapid acidification phenotype to slow acidifying starter strains of S. thermophilus. First, we established by gene disruption that (i) prtS, encoding the cell-envelope proteinase, is a key factor responsible for rapid milk acidification in fast acidifying strains, and that (ii) srtA, encoding sortase A, is not absolutely required to express the PrtS activity. Second, a 15-kb PCR product encompassing the prtS genomic island was transfered by natural transformation using the competence-inducing peptide in three distinct prtS-defective genetic backgrounds having or not a truncated sortase A gene. We showed that in all cases the milk acidification rate of transformants was significantly increased, reaching a level similar to that of wild-type fast acidifying strains. Furthermore, it appeared that the prtS-encoded activity does not depend on the prtS copy number or on its chromosomal integration locus. Conclusion We have successfully used natural competence to transfer the prtS locus encoding the cell-envelope proteinase in three slow acidifying strains of S. thermophilus, allowing their conversion into fast acidifying derivatives. The efficient protocol developed in this article will provide the dairy industry with novel and optimised S. thermophilus starter strains. PMID:21995822

  10. Complete and Assembled Genome Sequence of Staphylococcus aureus RKI4, a Food-Poisoning Strain Exhibiting a Novel S. aureus Pathogenicity Island Carrying seb

    PubMed Central

    Stevens, Marc J. A.; Stephan, Roger

    2015-01-01

    The genome of Staphylococcus aureus RKI4, a strain isolated from feces of a patient in a case of staphylococcal food poisoning, was sequenced using combined Illumina and single-molecule real-time sequencing. Hierarchical assembly of the genome resulted in a 2,725,654-bp chromosome and a 17,905-bp mobile genetic element. PMID:26139727

  11. Island Biogeography

    NSDL National Science Digital Library

    John Jungck (BioQUEST Curriculum Consortium; Biology)

    2005-12-16

    This excel workbook demonstrates the principles of the MacArthur-Wilson theory of Island Biogeography. It allows the user to define the mainland species pool, area of the island, and distance of the island from the mainland. Graphical output included species richness equilibrium at varying island size and distance. The workbook also allows the user to calculate a species-area function for data entered into the data input page. Several datasets on island area and species richness are included for various types of islands and species. Variables and formulas are defined in the accompanying tutorial.

  12. Engineering a Reduced Escherichia coli Genome

    Microsoft Academic Search

    Vitaliy Kolisnychenko; Guy Plunkett; Christopher D. Herring; Tamás Fehér; János Pósfai; Frederick R. Blattner; György Pósfai

    2002-01-01

    Our goal is to construct an improved Escherichia coli to serve both as a better model organism and as a more useful technological tool for genome science. We developed techniques for precise genomic surgery and applied them to deleting the largest K-islands of E. coli, identified by comparative genomics as recent horizontal acquisitions to the genome. They are loaded with

  13. Identifying Pathogenicity Islands in Bacterial Pathogenomics Using Computational Approaches

    PubMed Central

    Che, Dongsheng; Hasan, Mohammad Shabbir; Chen, Bernard

    2014-01-01

    High-throughput sequencing technologies have made it possible to study bacteria through analyzing their genome sequences. For instance, comparative genome sequence analyses can reveal the phenomenon such as gene loss, gene gain, or gene exchange in a genome. By analyzing pathogenic bacterial genomes, we can discover that pathogenic genomic regions in many pathogenic bacteria are horizontally transferred from other bacteria, and these regions are also known as pathogenicity islands (PAIs). PAIs have some detectable properties, such as having different genomic signatures than the rest of the host genomes, and containing mobility genes so that they can be integrated into the host genome. In this review, we will discuss various pathogenicity island-associated features and current computational approaches for the identification of PAIs. Existing pathogenicity island databases and related computational resources will also be discussed, so that researchers may find it to be useful for the studies of bacterial evolution and pathogenicity mechanisms. PMID:25437607

  14. Genome Sequence of Paenibacillus polymyxa Strain CICC 10580, Isolated from the Fruit of Noni (Morinda citrifolia L.) Grown in the Paracel Islands.

    PubMed

    Xu, Youqiang; Liu, Yang; Yao, Su; Li, Jinxia; Cheng, Chi

    2014-01-01

    Noni is a plant reported to have nutritional and therapeutic properties. Paenibacillus polymyxa CICC 10580 is a strain that was isolated from the fruit of noni and showed comprehensive antagonistic activity against many pathogens. Its genome was sequenced and assembled (6.10 Mb). The coding sequences (CDSs) correlated with antagonistic activity were annotated. PMID:25169860

  15. Genome Sequence of Paenibacillus polymyxa Strain CICC 10580, Isolated from the Fruit of Noni (Morinda citrifolia L.) Grown in the Paracel Islands

    PubMed Central

    Xu, Youqiang; Yao, Su; Li, Jinxia

    2014-01-01

    Noni is a plant reported to have nutritional and therapeutic properties. Paenibacillus polymyxa CICC 10580 is a strain that was isolated from the fruit of noni and showed comprehensive antagonistic activity against many pathogens. Its genome was sequenced and assembled (6.10 Mb). The coding sequences (CDSs) correlated with antagonistic activity were annotated. PMID:25169860

  16. Earth Island

    NSDL National Science Digital Library

    The Earth Island Web site is maintained by the Earth Island Institute (EII). EII also publishes the Earth Island Journal quarterly. The current issue of the journal can be browsed by section or by subject, and offers current news, world reports, and feature articles on a wide range of environmental subject areas. Earth Island also undertakes a number of projects that are discussed at the site as well as in a portion of the journal. The entire site is searchable. This is an excellent site for those interested in keeping up on environmental issues.

  17. The genome sequence of the tomato-pathogenic actinomycete Clavibacter michiganensis subsp. michiganensis NCPPB382 reveals a large island involved in pathogenicity.

    PubMed

    Gartemann, Karl-Heinz; Abt, Birte; Bekel, Thomas; Burger, Annette; Engemann, Jutta; Flügel, Monika; Gaigalat, Lars; Goesmann, Alexander; Gräfen, Ines; Kalinowski, Jörn; Kaup, Olaf; Kirchner, Oliver; Krause, Lutz; Linke, Burkhard; McHardy, Alice; Meyer, Folker; Pohle, Sandra; Rückert, Christian; Schneiker, Susanne; Zellermann, Eva-Maria; Pühler, Alfred; Eichenlaub, Rudolf; Kaiser, Olaf; Bartels, Daniela

    2008-03-01

    Clavibacter michiganensis subsp. michiganensis is a plant-pathogenic actinomycete that causes bacterial wilt and canker of tomato. The nucleotide sequence of the genome of strain NCPPB382 was determined. The chromosome is circular, consists of 3.298 Mb, and has a high G+C content (72.6%). Annotation revealed 3,080 putative protein-encoding sequences; only 26 pseudogenes were detected. Two rrn operons, 45 tRNAs, and three small stable RNA genes were found. The two circular plasmids, pCM1 (27.4 kbp) and pCM2 (70.0 kbp), which carry pathogenicity genes and thus are essential for virulence, have lower G+C contents (66.5 and 67.6%, respectively). In contrast to the genome of the closely related organism Clavibacter michiganensis subsp. sepedonicus, the genome of C. michiganensis subsp. michiganensis lacks complete insertion elements and transposons. The 129-kb chp/tomA region with a low G+C content near the chromosomal origin of replication was shown to be necessary for pathogenicity. This region contains numerous genes encoding proteins involved in uptake and metabolism of sugars and several serine proteases. There is evidence that single genes located in this region, especially genes encoding serine proteases, are required for efficient colonization of the host. Although C. michiganensis subsp. michiganensis grows mainly in the xylem of tomato plants, no evidence for pronounced genome reduction was found. C. michiganensis subsp. michiganensis seems to have as many transporters and regulators as typical soil-inhabiting bacteria. However, the apparent lack of a sulfate reduction pathway, which makes C. michiganensis subsp. michiganensis dependent on reduced sulfur compounds for growth, is probably the reason for the poor survival of C. michiganensis subsp. michiganensis in soil. PMID:18192381

  18. Island Hopping

    ERIC Educational Resources Information Center

    Bennett, Gayle

    2009-01-01

    At some institutions, it may feel as though faculty live on one island and advancement staff on another. The islands form part of an archipelago, and they exchange ambassadors and send emissaries occasionally, but interactions are limited. It may even seem as though the two groups speak different languages, deal in different currencies, and abide…

  19. Nihoa Island

    NSDL National Science Digital Library

    2007-08-09

    This video segment adapted from the NOW-RAMP 2002 Expedition documents a research expedition to Nihoa Island. It showcases Nihoa's unique birds and plants, the threat posed by invading grasshoppers, and restoration efforts.

  20. Pathogenicity island mobility and gene content.

    SciTech Connect

    Williams, Kelly Porter

    2013-10-01

    Key goals towards national biosecurity include methods for analyzing pathogens, predicting their emergence, and developing countermeasures. These goals are served by studying bacterial genes that promote pathogenicity and the pathogenicity islands that mobilize them. Cyberinfrastructure promoting an island database advances this field and enables deeper bioinformatic analysis that may identify novel pathogenicity genes. New automated methods and rich visualizations were developed for identifying pathogenicity islands, based on the principle that islands occur sporadically among closely related strains. The chromosomally-ordered pan-genome organizes all genes from a clade of strains; gaps in this visualization indicate islands, and decorations of the gene matrix facilitate exploration of island gene functions. A %E2%80%9Clearned phyloblocks%E2%80%9D method was developed for automated island identification, that trains on the phylogenetic patterns of islands identified by other methods. Learned phyloblocks better defined termini of previously identified islands in multidrug-resistant Klebsiella pneumoniae ATCC BAA-2146, and found its only antibiotic resistance island.

  1. Island biology: looking towards the future.

    PubMed

    Kueffer, Christoph; Drake, Donald R; Fernández-Palacios, José María

    2014-10-01

    Oceanic islands are renowned for the profound scientific insights that their fascinating biotas have provided to biologists during the past two centuries. Research presented at Island Biology 2014-an international conference, held in Honolulu, Hawaii (7-11 July 2014), which attracted 253 presenters and 430 participants from at least 35 countries(1)-demonstrated that islands are reclaiming a leading role in ecology and evolution, especially for synthetic studies at the intersections of macroecology, evolution, community ecology and applied ecology. New dynamics in island biology are stimulated by four major developments. We are experiencing the emergence of a truly global and comprehensive island research community incorporating previously neglected islands and taxa. Macroecology and big-data analyses yield a wealth of global-scale synthetic studies and detailed multi-island comparisons, while other modern research approaches such as genomics, phylogenetic and functional ecology, and palaeoecology, are also dispersing to islands. And, increasingly tight collaborations between basic research and conservation management make islands places where new conservation solutions for the twenty-first century are being tested. Islands are home to a disproportionate share of the world's rare (and extinct) species, and there is an urgent need to develop increasingly collaborative and innovative research to address their conservation requirements. PMID:25339655

  2. A genome-wide analysis of CpG dinucleotides in the human genome distinguishes two

    E-print Network

    Brutlag, Doug

    A genome-wide analysis of CpG dinucleotides in the human genome distinguishes two distinct classes, 2005 A striking feature of the human genome is the dearth of CpG dinucleotides (CpGs) interrupted occasionally by CpG islands (CGIs), regions with relatively high content of the dinucleotide. CGIs

  3. Analysis of the allohexaploid bread wheat genome (Triticum aestivum) using comparative whole genome shotgun sequencing

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The large 17 Gb allopolyploid genome of bread wheat is a major challenge for genome analysis because it is composed of three closely- related and independently maintained genomes, with genes dispersed as small “islands” separated by vast tracts of repetitive DNA. We used a novel comparative genomi...

  4. Microbial Genomics

    NSDL National Science Digital Library

    Web page with links to microbes in the Joint Genome Institute (JGI) system than have finished genomes and draft genomes. There are also links to JGI home page, genome portal home, and the human genome project.

  5. Markov models of genome segmentation

    NASA Astrophysics Data System (ADS)

    Thakur, Vivek; Azad, Rajeev K.; Ramaswamy, Ram

    2007-01-01

    We introduce Markov models for segmentation of symbolic sequences, extending a segmentation procedure based on the Jensen-Shannon divergence that has been introduced earlier. Higher-order Markov models are more sensitive to the details of local patterns and in application to genome analysis, this makes it possible to segment a sequence at positions that are biologically meaningful. We show the advantage of higher-order Markov-model-based segmentation procedures in detecting compositional inhomogeneity in chimeric DNA sequences constructed from genomes of diverse species, and in application to the E. coli K12 genome, boundaries of genomic islands, cryptic prophages, and horizontally acquired regions are accurately identified.

  6. Streamlined Island

    NASA Technical Reports Server (NTRS)

    2003-01-01

    MGS MOC Release No. MOC2-514, 15 October 2003

    This Mars Global Surveyor (MGS) Mars Orbiter Camera (MOC) picture shows a streamlined island in Marte Vallis, a large outflow channel system that crosses the 180oW meridian between the Elysium and Amazonis regions of Mars. The flow patterns on the floor of Marte Vallis might be the remains of lava flows or mud flows. Marte is the Spanish word for Mars. Most of the largest valleys on the red planet are named for 'Mars' in various languages. This island is located near 21.8oN, 175.3oW. The picture covers an area 3 km (1.9 mi) wide and is illuminated by sunlight from the lower left.

  7. Thermal Islands

    NSDL National Science Digital Library

    In this problem-based learning unit, students learn about the causes and impacts of urban heat islands. Numerous studies have shown how concrete pavements and buildings retain heat in cities, making cities several degrees warmer than the surrounding countryside. Students investigate the role of cities in our climate, specifically how the urban heat island affects climate. Instructions to access NASA data are provided along with additional resources and activities. This module was developed for use in the Earth System Science Education Alliance (ESSEA) professional development courses for middle and high school teachers and is also available to teachers to adapt for general classroom use. See Related & Supplemental URLs for a demo course showing how this module is integrated into an ESSEA course for teachers.

  8. DNA methylation and the analysis of CpG Islands

    E-print Network

    Czygrinow, Andrzej

    DNA methylation and the analysis of CpG Islands in genomes M. F. Wojciechowski MAT 351 25 March 2005 #12;#12;Nucleotides #12;Base pairing * * #12;DNA methylation In mammalian genomes, methylation residues represent a target for covalent modification of DNA Cytosine is one of two bases found commonly

  9. DNA clustering and genome complexity.

    PubMed

    Dios, Francisco; Barturen, Guillermo; Lebrón, Ricardo; Rueda, Antonio; Hackenberg, Michael; Oliver, José L

    2014-12-01

    Early global measures of genome complexity (power spectra, the analysis of fluctuations in DNA walks or compositional segmentation) uncovered a high degree of complexity in eukaryotic genome sequences. The main evolutionary mechanisms leading to increases in genome complexity (i.e. gene duplication and transposon proliferation) can all potentially produce increases in DNA clustering. To quantify such clustering and provide a genome-wide description of the formed clusters, we developed GenomeCluster, an algorithm able to detect clusters of whatever genome element identified by chromosome coordinates. We obtained a detailed description of clusters for ten categories of human genome elements, including functional (genes, exons, introns), regulatory (CpG islands, TFBSs, enhancers), variant (SNPs) and repeat (Alus, LINE1) elements, as well as DNase hypersensitivity sites. For each category, we located their clusters in the human genome, then quantifying cluster length and composition, and estimated the clustering level as the proportion of clustered genome elements. In average, we found a 27% of elements in clusters, although a considerable variation occurs among different categories. Genes form the lowest number of clusters, but these are the longest ones, both in bp and the average number of components, while the shortest clusters are formed by SNPs. Functional and regulatory elements (genes, CpG islands, TFBSs, enhancers) show the highest clustering level, as compared to DNase sites, repeats (Alus, LINE1) or SNPs. Many of the genome elements we analyzed are known to be composed of clusters of low-level entities. In addition, we found here that the clusters generated by GenomeCluster can be in turn clustered into high-level super-clusters. The observation of 'clusters-within-clusters' parallels the 'domains within domains' phenomenon previously detected through global statistical methods in eukaryotic sequences, and reveals a complex human genome landscape dominated by hierarchical clustering. PMID:25182383

  10. Alcatraz Island

    NSDL National Science Digital Library

    2005-01-01

    â??The Rockâ?, the oft-used vernacular phrase used to describe Alcatraz, is perhaps one of the Bay Areaâ??s most dramatic landscapes, and certainly itâ??s best known island. Over the past several hundred years, it has served at times as a place for protest by Native Americans and a place of incarceration for some of Americaâ??s most hardened (and colorful) criminals. The National Park Service recently created this rather well-done online exhibit that allows users to view objects from Alcatrazâ??s past (such as escape materials and historic photographs) and also to allow them to take a virtual tour of the prison and its grounds. Visitors can also listen to a number of compelling sound clips that discuss the infamous â??Battle of Alcatrazâ? and the cellhouse rules. The site also features a number of thematic slide shows, including one that addresses the occupation of the island by members of the American Indian Movement from 1969 to 1971.

  11. Tenarife Island, Canary Island Archipelago, Atlantic Ocean

    NASA Technical Reports Server (NTRS)

    1991-01-01

    Tenarife Island is one of the most volcanically active of the Canary Island archipelago, Atlantic Ocean, just off the NW coast of Africa, (28.5N, 16.5W). The old central caldera, nearly filled in by successive volcanic activity culminating in two stratocones. From those two peaks, a line of smaller cinder cones extend to the point of the island. Extensive gullies dissect the west side of the island and some forests still remain on the east side.

  12. Island Formation: Constructing a Coral Island

    ERIC Educational Resources Information Center

    Austin, Heather; Edd, Amelia

    2009-01-01

    The process of coral island formation is often difficult for middle school students to comprehend. Coral island formation is a dynamic process, and students should have the opportunity to experience this process in a synergistic context. The authors provide instructional guidelines for constructing a coral island. Students play an interactive role…

  13. Genomic Testing

    MedlinePLUS

    ... About CDC.gov . Public Health Genomics Share Compartir Genomic Testing Fact Sheet: Identifying Opportunities to Improve Health and Transform Healthcare [PDF 139.91 KB] Genomic Tests by Levels of Evidence Guidelines, Policies and ...

  14. Rhode Island Transportation

    E-print Network

    Rhode Island, University of

    Rhode Island Transportation Fact Book Highlights Transportation Center #12;Transportation in Rhode Island University of Rhode Island Transportation Center 2 Road Conditions / Road Ownership Public Road Length by Ownership 2008 Road Conditions 2008 9% 17% 45% 18% 11% Rhode Island Road Condition (2008

  15. Genome Research

    NSDL National Science Digital Library

    Genome Research, the Web version of Cold Spring Harbor Laboratory's printed journal, focuses on "genome studies in all species, including genetic and physical mapping, DNA sequencing, genome-based analyses of biological processes, gene discovery, comparative genome analyses, evolution studies, forensics, informatics, statistical and mathematical methods, genome structure and function, and technological innovations and applications." Online issues are available from April 1997; tables of contents and abstracts begin August 1995. The free access period for Genome Research ends December 31, 1998. Genome Research is made available through Stanford University's HighWire Press.

  16. Galapagos Islands Flyby

    NSDL National Science Digital Library

    Dave Pape

    1994-03-13

    This animation shows the power of computer graphics to explore data in the sense of virtual reality. In this scene, standard tools are applied to fly around the Galapagos Islands and the ocean floor surrounding the islands.

  17. Overwash on Assateague Island

    USGS Multimedia Gallery

    Overwash on Assateague Island. Overwash occurs when waves overtop the main sand dune and redistribute the sand along new patterns. Overwash has contributed to the gradual movement of Assateague Island to the south....

  18. Henderson Island, Pacific Ocean

    NASA Technical Reports Server (NTRS)

    1983-01-01

    Henderson Island (24.5S, 128.5W) Pacific Ocean southeast of the Tuamotu Archipelago, is a good example of the many barren islands that but for lack of a source of water could be another lush tropical paradise. The crew of HMS Bounty, in searching for a refuge, sailed past this island but rejected it in favor of nearby Pitcairn Island because of the lack of resources and water.

  19. Falkland Islands, UK

    NASA Technical Reports Server (NTRS)

    1991-01-01

    This view of the Falkland Islands (52.0S, 58.5W) was taken with a dual camera mount. Compare this scene with STS048-109-043 to analyze the unique properties of each film type. Seldom seen cloud free, the Falkland Islands lie off the southern coast of Argentina. The cold Falklands Ocean Current keeps the islands chilly, ideal for sheep herding and fishing, the two main industries. Colonies of seals and penguins also thrive on the islands.

  20. Arctic ice islands

    SciTech Connect

    Sackinger, W.M.; Jeffries, M.O.; Lu, M.C.; Li, F.C.

    1988-01-01

    The development of offshore oil and gas resources in the Arctic waters of Alaska requires offshore structures which successfully resist the lateral forces due to moving, drifting ice. Ice islands are floating, a tabular icebergs, up to 60 meters thick, of solid ice throughout their thickness. The ice islands are thus regarded as the strongest ice features in the Arctic; fixed offshore structures which can directly withstand the impact of ice islands are possible but in some locations may be so expensive as to make oilfield development uneconomic. The resolution of the ice island problem requires two research steps: (1) calculation of the probability of interaction between an ice island and an offshore structure in a given region; and (2) if the probability if sufficiently large, then the study of possible interactions between ice island and structure, to discover mitigative measures to deal with the moving ice island. The ice island research conducted during the 1983-1988 interval, which is summarized in this report, was concerned with the first step. Monte Carlo simulations of ice island generation and movement suggest that ice island lifetimes range from 0 to 70 years, and that 85% of the lifetimes are less then 35 years. The simulation shows a mean value of 18 ice islands present at any time in the Arctic Ocean, with a 90% probability of less than 30 ice islands. At this time, approximately 34 ice islands are known, from observations, to exist in the Arctic Ocean, not including the 10-meter thick class of ice islands. Return interval plots from the simulation show that coastal zones of the Beaufort and Chukchi Seas, already leased for oil development, have ice island recurrences of 10 to 100 years. This implies that the ice island hazard must be considered thoroughly, and appropriate safety measures adopted, when offshore oil production plans are formulated for the Alaskan Arctic offshore. 132 refs., 161 figs., 17 tabs.

  1. Island Fox Paradox

    NSDL National Science Digital Library

    Sharon Levy (Freelancer; )

    2010-05-03

    Channel Island foxes, long the top predator in their ecosystem, show little fear of humans. Wild foxes often accost visitors on San Nicolas, the island with the most abundant fox population in the island chain. Now, archaeologists have new evidence that suggests foxes were carried to the islands by indigenous people thousands of years ago, and that humans shaped the evolution of the entire species. Do species introduced by native people thousands of years ago deserve protection?

  2. Islands in Amazonia

    Microsoft Academic Search

    G. T. Prance

    1996-01-01

    There are a number of habitats within the lowland Amazonian rainforest ecosystem that are functional islands. Those that are discussed are savannas, white sand campinas and caatingas, inselbergs and sandstone table mountains or tepuis. Each of these habitats is a series of isolated islands of vegetation and in some cases speciation has taken place between islands, especially the older tepuis,

  3. Overwash on Assateague Island

    USGS Multimedia Gallery

    Overwash on Assateague Island. When waves wash over the main sand dune on the island, that creates a phenomenon called overwash, where the sand is moved along the path of the wave. Overwash has contributed to the gradual movement of Assateague Island to the south....

  4. Diomede Islands, Bering Straight

    NASA Technical Reports Server (NTRS)

    2008-01-01

    The Diomede Islands consisting of the western island Big Diomede (also known as Imaqliq, Nunarbuk or Ratmanov Island), and the eastern island Little Diomede (also known as Krusenstern Island or Inaliq), are two rocky islands located in the middle of the Bering Strait between Russia and Alaska. The islands are separated by an international border and the International Date Line which is approximately 1.5 km from each island; you can look from Alaska into tomorrow in Russia. At the closest land approach between the United States, which controls Little Diomede, and Russia, which controls Big Diomede, they are 3 km apart. Little Diomede Island constitutes the Alaskan City of Diomede, while Big Diomede Island is Russia's easternmost point. The first European to reach the islands was the Russian explorer Semyon Dezhnev in 1648. The text of the 1867 treaty finalizing the sale of Alaska uses the islands to designate the border between the two nations.

    The image was acquired July 8, 2000, covers an area of 13.5 x 10.8 km, and is located at 65.8 degrees north latitude, 169 degrees west longitude.

    The U.S. science team is located at NASA's Jet Propulsion Laboratory, Pasadena, Calif. The Terra mission is part of NASA's Science Mission Directorate.

  5. How Are Islands Formed?

    NSDL National Science Digital Library

    2001-01-01

    This lesson provides students with information about how islands are formed, including a basic knowledge of plate tectonics. Using the islands of Hawaii as an example, students learn about the earth processes that cause the formation of islands over time, including volcanoes and hot spots.

  6. Avifauna: Turnover on Islands

    Microsoft Academic Search

    Ernst Mayr

    1965-01-01

    The percentage of endemic species of birds on islands increases with island area at a double logarithmic rate. This relation is apparently due to extinction, which is more rapid the smaller the island. The turnover resulting from extinction and replacement appears to be far more rapid than hitherto suspected.

  7. Complete Genome Sequence of Antarctic Bacterium Psychrobacter sp. Strain G

    PubMed Central

    Che, Shuai; Song, Lai; Song, Weizhi; Yang, Meng

    2013-01-01

    Here, we report the complete genome sequence of Psychrobacter sp. strain G, isolated from King George Island, Antarctica, which can produce lipolytic enzymes at low temperatures. The genomics information of this strain will facilitate the study of the physiology, cold adaptation properties, and evolution of this genus. PMID:24051316

  8. Complete Genome Sequence of Lactococcus lactis subsp. cremoris A76

    PubMed Central

    Quinquis, Benoit; Ehrlich, Stanislas Dusko; Sorokin, Alexei

    2012-01-01

    We report the complete genome sequence of Lactococcus lactis subsp. cremoris A76, a dairy strain isolated from a cheese production outfit. Genome analysis detected two contiguous islands fitting to the L. lactis subsp. lactis rather than to the L. lactis subsp. cremoris lineage. This indicates the existence of genetic exchange between the diverse subspecies, presumably related to the technological process. PMID:22328746

  9. Complete genome sequence of Lactococcus lactis subsp. cremoris A76.

    PubMed

    Bolotin, Alexander; Quinquis, Benoit; Ehrlich, Stanislas Dusko; Sorokin, Alexei

    2012-03-01

    We report the complete genome sequence of Lactococcus lactis subsp. cremoris A76, a dairy strain isolated from a cheese production outfit. Genome analysis detected two contiguous islands fitting to the L. lactis subsp. lactis rather than to the L. lactis subsp. cremoris lineage. This indicates the existence of genetic exchange between the diverse subspecies, presumably related to the technological process. PMID:22328746

  10. Genome duplications (polyploidy) / ancientGenome duplications (polyploidy) / ancient genome duplications (genome duplications (paleopolyploidypaleopolyploidy))

    E-print Network

    Utrecht, Universiteit

    Genome duplications (polyploidy) / ancientGenome duplications (polyploidy) / ancient genome duplications (genome duplications (paleopolyploidypaleopolyploidy)) Mechanism? e.g. a diploid cell undergoes;Paramecium genome duplicationsParamecium genome duplications #12;Comparison of two scaffolds originating from

  11. Genome duplications (polyploidy) / ancientGenome duplications (polyploidy) / ancient genome duplications (genome duplications (paleopolyploidypaleopolyploidy))

    E-print Network

    Utrecht, Universiteit

    Genome duplications (polyploidy) / ancientGenome duplications (polyploidy) / ancient genome duplications (genome duplications (paleopolyploidypaleopolyploidy)) e.g. a diploid cell undergoes failed genome duplicationsParamecium genome duplications #12;Comparison of two scaffolds originating from a

  12. Complete Genome Sequence of the Nicotine-Degrading Pseudomonas putida Strain S16

    PubMed Central

    Yu, Hao; Tang, Hongzhi; Wang, Lijuan; Yao, Yuxiang; Wu, Geng; Xu, Ping

    2011-01-01

    Pseudomonas putida S16 is an efficient degrader of nicotine. The complete genome of strain S16 (5,984,790 bp in length) includes genes related to catabolism of aromatic and heterocyclic compounds. The genes of enzymes in the core genome and a genomic island encode the proteins responsible for nicotine catabolism. PMID:21914868

  13. The Flores Island tsunamis

    Microsoft Academic Search

    Harry Yeh; Fumihiko Imamura; Costas Synolakis; Yoshinobu Tsuji; Philip Liu; Shaozhong Shi

    1993-01-01

    On December 12, 1992, at 5:30 A.M. GMT, an earthquake of magnitude Ms 7.5 struck the eastern region of Flores Island, Indonesia (Figure 1), a volcanic island located just at the transition between the Sunda and Banda Island arc systems. The local newspaper reported that 25-m high tsunamis struck the town of Maumere, causing substantial casualties and property damage. On

  14. Ober's Island, One of the Review Islands on Rainy Lake, ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    Ober's Island, One of the Review Islands on Rainy Lake, bounded on the south by The Hawk Island and on the north by The Crow Island. These islands are located seven miles east of Ranier, Minnesota, three miles west of Voyageur National Park, and one mile south of the international border of the United States of America and Canada. The legal description of Mallard Island is Lot 6, Section 19, T-17-N, R-22-W, Koochiching County, Minnesota, Ranier, Koochiching County, MN

  15. inGeno – an integrated genome and ortholog viewer for improved genome to genome comparisons

    PubMed Central

    Liang, Chunguang; Dandekar, Thomas

    2006-01-01

    Background Systematic genome comparisons are an important tool to reveal gene functions, pathogenic features, metabolic pathways and genome evolution in the era of post-genomics. Furthermore, such comparisons provide important clues for vaccines and drug development. Existing genome comparison software often lacks accurate information on orthologs, the function of similar genes identified and genome-wide reports and lists on specific functions. All these features and further analyses are provided here in the context of a modular software tool "inGeno" written in Java with Biojava subroutines. Results InGeno provides a user-friendly interactive visualization platform for sequence comparisons (comprehensive reciprocal protein – protein comparisons) between complete genome sequences and all associated annotations and features. The comparison data can be acquired from several different sequence analysis programs in flexible formats. Automatic dot-plot analysis includes output reduction, filtering, ortholog testing and linear regression, followed by smart clustering (local collinear blocks; LCBs) to reveal similar genome regions. Further, the system provides genome alignment and visualization editor, collinear relationships and strain-specific islands. Specific annotations and functions are parsed, recognized, clustered, logically concatenated and visualized and summarized in reports. Conclusion As shown in this study, inGeno can be applied to study and compare in particular prokaryotic genomes against each other (gram positive and negative as well as close and more distantly related species) and has been proven to be sensitive and accurate. This modular software is user-friendly and easily accommodates new routines to meet specific user-defined requirements. PMID:17054788

  16. Hydrologic data for Block Island, Rhode Island

    USGS Publications Warehouse

    Burns, Emily

    1993-01-01

    This report was compiled as part of a study to assess the hydrogeology and the quality and quantity of fresh ground water on Block Island, Rhode Island. Hydrologic data were collected on Block Island during 1988-91. The data are pre- sented in illustrations and tables. Data collec- ted include precipitation, surfae-water, ground- water, lithologic, and well-construction and dis- charge information. Precipitation data include total monthly precipitation values from 11 rain gages and water-quality analyses of 14 precipi- tation samples from one station. Surface-water data include water-level measurements at 12 ponds, water-quality data for five ponds, and field specific-conductance measurements at 56 surface- water sites (streams, ponds, and springs). Ground- water data include water-level measurements at 159 wells, water-quality data at 150 wells, and field specific-conductance data at 52 wells. Lithologic logs for 375 wells and test borings, and construc- tion and location data for 570 wells, springs, and test borings are included. In addition, the data set contains data on water quality of water samples, collected by the Rhode Island Department of Health during 1976-91, from Fresh and Sands Ponds and from wells at the Block Island Water Company well field north of Sands Pond.

  17. Evolution of paralogous genes: Reconstruction of genome rearrangements through comparison of multiple genomes within Staphylococcus aureus.

    PubMed

    Tsuru, Takeshi; Kawai, Mikihiko; Mizutani-Ui, Yoko; Uchiyama, Ikuo; Kobayashi, Ichizo

    2006-06-01

    Analysis of evolution of paralogous genes in a genome is central to our understanding of genome evolution. Comparison of closely related bacterial genomes, which has provided clues as to how genome sequences evolve under natural conditions, would help in such an analysis. With species Staphylococcus aureus, whole-genome sequences have been decoded for seven strains. We compared their DNA sequences to detect large genome polymorphisms and to deduce mechanisms of genome rearrangements that have formed each of them. We first compared strains N315 and Mu50, which make one of the most closely related strain pairs, at the single-nucleotide resolution to catalogue all the middle-sized (more than 10 bp) to large genome polymorphisms such as indels and substitutions. These polymorphisms include two paralogous gene sets, one in a tandem paralogue gene cluster for toxins in a genomic island and the other in a ribosomal RNA operon. We also focused on two other tandem paralogue gene clusters and type I restriction-modification (RM) genes on the genomic islands. Then we reconstructed rearrangement events responsible for these polymorphisms, in the paralogous genes and the others, with reference to the other five genomes. For the tandem paralogue gene clusters, we were able to infer sequences for homologous recombination generating the change in the repeat number. These sequences were conserved among the repeated paralogous units likely because of their functional importance. The sequence specificity (S) subunit of type I RM systems showed recombination, likely at the homology of a conserved region, between the two variable regions for sequence specificity. We also noticed novel alleles in the ribosomal RNA operons and suggested a role for illegitimate recombination in their formation. These results revealed importance of recombination involving long conserved sequence in the evolution of paralogous genes in the genome. PMID:16601000

  18. Marine and Island Ecology.

    ERIC Educational Resources Information Center

    Stephens, Lawrence J.; And Others

    1988-01-01

    Describes an ecology course which provides students with an opportunity to observe aquatic and terrestrial life in the Bahamas. States that students learn scientific methodology by measuring physical and chemical aspects of the island habitats. Provides information on the island, course description and objectives, transportation, facilities, and…

  19. Genome synthesis and genomic functional cores

    E-print Network

    Radulescu, Ovidiu

    Genome synthesis and genomic functional cores Alessandra Carbone Département d.fr #12;Plan 1. algorithms + statistics to analyse microbial genomes without using biological information 2. space of genomes : from phylogeny to environmental classification 3. essential metabolic

  20. 75 FR 51098 - Protection Island and San Juan Islands National Wildlife Refuges, Jefferson, Island, San Juan...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-08-18

    ...Wildlife Service [FWS-R1-R-2010-N131; 1265-0000-10137-S3] Protection Island and San Juan Islands National Wildlife Refuges, Jefferson, Island, San Juan, Skagit, and Whatcom Counties, WA AGENCY: Fish and Wildlife...

  1. Baculovirus genomics.

    PubMed

    van Oers, Monique M; Vlak, Just M

    2007-10-01

    Baculovirus genomes are covalently closed circles of double stranded-DNA varying in size between 80 and 180 kilobase-pair. The genomes of more than fourty-one baculoviruses have been sequenced to date. The majority of these (37) are pathogenic to lepidopteran hosts; three infect sawflies (Hymenoptera) and one has a mosquito host (Diptera). With this information, general patterns of genome structure and gene content became apparent. Baculovirus open reading frames are tightly packed with minimal intergenic regions and the coding sequences are almost equally distributed over both strands. Baculovirus genes form single transcription units, with early and late transcribed ORFs scattered along the genome. A set of twenty nine core genes is conserved and therefore is characteristic for baculoviruses. Most baculovirus genomes contain multiple homologous regions with repeated sequences and often palindromic motifs, which play a crucial role as enhancers of early transcription and most likely in viral DNA replication. Baculovirus genomes have a certain degree of plasticity, as evidenced from the genomic variations within virus isolates from the field. Recombination events and transposon insertions appear to play a role in the uptake of new genes from co-infecting viruses or from the insect host. This review deals with the structural and functional properties of baculovirus genomes including both conserved and variable genes. PMID:17979665

  2. Aquaculture Genomics

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The genomics chapter covers the basics of genome mapping and sequencing and the current status of several relevant species. The chapter briefly describes the development and use of (cDNA, BAC, etc.) libraries for mapping and obtaining specific sequence information. Other topics include comparative ...

  3. Tracing Lifestyle Adaptation in Prokaryotic Genomes

    PubMed Central

    Altermann, Eric

    2012-01-01

    Lifestyle adaptation of microbes due to changes in their ecological niches or acquisition of new environments is a major driving force for genetic changes in their respective genomes. Moving into more specialized niches often results in the acquisition of new gene sets via horizontal gene transfer to utilize previously unavailable metabolites, while genetic ballast is shed by gene loss and/or gene inactivation. In some cases, larger genome rearrangements can be observed, such as the incorporation of whole genetic islands, providing a range of new phenotypic capabilities. Until recently these changes could not be comprehensively followed and identified due to the lack of complete microbial genome sequences. The advent of high-throughput DNA sequencing has dramatically changed the scientific landscape and today microbial genomes have become increasingly abundant. Currently, more than 2,900 genomes are published and more than 11,000 genome projects are listed in the Genomes Online Database‡. Although this wealth of information provides many new opportunities to assess microbial functionality, it also creates a new array of challenges when a comparison between multiple microbial genomes is required. Here, functional genome distribution (FGD) is introduced, analyzing the diversity between microbes based on their predicted ORFeome. FGD is therefore a comparative genomics approach, emphasizing the assessments of gene complements. To further facilitate the comparison between two or more genomes, degrees of amino-acid similarities between ORFeomes can be visualized in the Artemis comparison tool, graphically depicting small and large scale genome rearrangements, insertion and deletion events, and levels of similarity between individual open reading frames. FGD provides a new tool for comparative microbial genomics and the interpretation of differences in the genetic makeup of bacteria. PMID:22363326

  4. Comparative genomic analysis of Lactobacillus rhamnosus GG reveals pili containing a human- mucus binding protein

    Microsoft Academic Search

    M. Kankainen; L. Paulin; S. Tynkkynen; I. von Ossowski; J. Reunanen; P. Partanen; R. Satokari; S. Vesterlund; A. P. A. Hendrickx; S. Lebeer; S. C. J. de Keersmaecker; J. Vanderleyden; T. Hamalainen; S. Laukkanen; N. Salovuori; J. Ritari; E. Alatalo; R. Korpela; T. Mattila-Sandholm; A. Lassig; K. Hatakka; K. T. Kinnunen; H. Karjalainen; M. Saxelin; K. Laakso; A. Surakka; A. Palva; T. Salusjarvi; P. Auvinen; W. M. de Vos

    2009-01-01

    To unravel the biological function of the widely used probiotic bacterium Lactobacillus rhamnosus GG, we compared its 3.0-Mbp genome sequence with the similarly sized genome of L. rhamnosus LC705, an adjunct starter culture exhibiting reduced binding to mucus. Both genomes demonstrated high sequence identity and synteny. However, for both strains, genomic islands, 5 in GG and 4 in LC705, punctuated

  5. Ober's Island: The Mallard Ober's Island, One of the ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    Ober's Island: The Mallard - Ober's Island, One of the Review Islands on Rainy Lake, bounded on the south by The Hawk Island and on the north by The Crow Island. These islands are located seven miles east of Ranier, Minnesota, three miles west of Voyageur National Park, and one mile south of the international border of the United States of America and Canada. The legal description of Mallard Island is Lot 6, Section 19, T-17-N, R-22-W, Koochiching County, Minnesota, Ranier, Koochiching County, MN

  6. Your Genome

    NSDL National Science Digital Library

    2002-01-01

    This Web siteby the Wellcome Trust Sanger Institute provides information about genome science for various levels of awareness. Although the advanced section is not yet complete, the beginner and intermediate touch on genes, DNA, RNA, and the Human Genome Project. If your curiosity is not satisfied by the Web site, there is a form for submitting questions directly to the Sanger Institute. Two nice features are the links (with descriptions and organized by level) and a timeline of genome science from the 1950's to the present.

  7. 123Genomics

    NSDL National Science Digital Library

    The providers of this searchable metasite have, over the years, accumulated hundreds of genomics-related bookmarks which they now share freely. The eighteen major categories at 123 genomics each contain dozens of links to bioinformatics- and genomics-related science news, research labs, databases, scientific societies, protocol guides, etc. Examples of the category headings include Microarrays, Molecular Pathways, Sequence Databases, Journals and Publications, and Diseases and Disorders. This simply designed site provides enough good resources to keep most graduate students and researchers of bioinformatics happy and well informed.

  8. The Plant Cell, Vol. 14, 26592679, November 2002, www.plantcell.org 2002 American Society of Plant Biologists GENOMICS ARTICLE

    E-print Network

    dePamphilis, Claude

    lineages of the plant kingdom. With these se- quences and the genome sequence of the cyanobacterium of Plant Biologists GENOMICS ARTICLE The Chlamydomonas reinhardtii Plastid Chromosome: Islands of Genes significance. Among other sequenced chlorophyte plastid genomes, only that of the green alga Chlorella vulgaris

  9. Genome-wide expression dynamics of a marine virus and host reveal features of co-evolution

    E-print Network

    Church, George M.

    LETTERS Genome-wide expression dynamics of a marine virus and host reveal features of co to reciprocal genome evolution through a dynamic co- evolutionary process1­5 . Phage-mediated transfer of host genes-- often located in genome islands--has had a major impact on microbial evolution1

  10. Conservation Strategy for Sable Island

    E-print Network

    Jones, Ian L.

    Towards a Conservation Strategy for Sable Island Environment Canada, Canadian Wildlife Service, Atlantic Region #12;SABLE ISLAND CONSERVATION STRATEGY page - i March, 1998 A CONSERVATION STRATEGY FOR SABLE ISLAND PREPARED BY This Conservation Strategy for Sable Island was prepared for Environment Canada

  11. Genomics Glossary

    NSDL National Science Digital Library

    Chitty, Mary Glen.

    Because genomics is an interdisciplinary science that unites biology, chemistry, physics, and mathematics, its language is diverse and includes terms not always found in dictionaries. This site from Cambridge Healthtech Institute of Massachusetts was designed to help scientists keep on top of this complex language. Loads of terms in categories such as basic genetics, functional and structural genomics, informatics, and genomic-related technology are defined here. Users can access the glossary terms either through a short index of major subject headings or by a longer alphabetically-arranged subject list. The Genomics Glossary deserves bonus points for including links to related resources in the text of its definitions. For example, within the definition of "polymerase chain reaction" are links to sites at Yale Medical School and the National Library of Medicine. In addition, links to pages on nomenclature, a bibliography of Web and print resources, and a FAQ page are available at this fantastic Website.

  12. The tad locus: postcards from the widespread colonization island.

    PubMed

    Tomich, Mladen; Planet, Paul J; Figurski, David H

    2007-05-01

    The Tad (tight adherence) macromolecular transport system, which is present in many bacterial and archaeal species, represents an ancient and major new subtype of type II secretion. The tad genes are present on a genomic island named the widespread colonization island (WCI), and encode the machinery that is required for the assembly of adhesive Flp (fimbrial low-molecular-weight protein) pili. The tad genes are essential for biofilm formation, colonization and pathogenesis in the genera Aggregatibacter (Actinobacillus), Haemophilus, Pasteurella, Pseudomonas, Yersinia, Caulobacter and perhaps others. Here we review the structure, function and evolution of the Tad secretion system. PMID:17435791

  13. Island Watershed Activity.

    ERIC Educational Resources Information Center

    Benson, Rod

    2003-01-01

    Describes a 90-minute "Island Watershed" activity to help earth science students understand the concept of the water cycle. Introduces a surface waters unit appropriate for students in grades 7-10. Includes watershed project guidelines. (Author/KHR)

  14. Small islands adrift

    NASA Astrophysics Data System (ADS)

    Petherick, Anna

    2015-07-01

    With the charismatic former president of the Maldives, Mohamed Nasheed, behind bars on a widely derided terrorism charge, Anna Petherick asks whether small island states can really make themselves heard in Paris.

  15. The Island Institute

    NSDL National Science Digital Library

    Since 1983, the Island Institute has employed a wide range of individuals, including photographers, artists, policy experts, and others, all in the name of maintaining the viability of the fifteen year-round island communities in the Gulf of Maine. They have become well-known for their outreach efforts, and their website will be of great value to anyone interested in this region, or how various island communities remain economically, culturally, and ecologically sustainable. Resources located on the Institute's homepage include information about fellowship opportunities and links to full and annual reports on the Atlantic herring spawning project. Visitors who are hoping to get a sense of the flavor of this unique region should definitely peruse their monthly publication, "The Working Waterfront." Recent articles include opinion pieces on fish hatcheries, the lobster business, and news profiles of local islanders.

  16. Deoxyribonucleic acid methylation profiling of single human blastocysts by methylated CpG-island amplification coupled with CpG-island microarray

    PubMed Central

    Huntriss, John; Hemmings, Karen; Baskaran, Praveen; Hazelwood, Lee; Elder, Kay; Virtanen, Carl; Miller, David; Picton, Helen M.

    2015-01-01

    Objective To study whether methylated CpG-island (CGI) amplification coupled with microarray (MCAM) can be used to generate DNA (deoxyribonucleic acid) methylation profiles from single human blastocysts. Design A pilot microarray study with methylated CpG-island amplification applied to human blastocyst genomic DNA and hybridized on CpG-island microarrays. Setting University research laboratory. Patient(s) Five cryopreserved sibling 2-pronuclear zygotes that were surplus to requirements for clinical treatment by in vitro fertilization were donated with informed consent from a patient attending Bourn Hall Clinic, Cambridge, United Kingdom. Intervention(s) None. Main Outcome Measure(s) Successful generation of genome-wide DNA methylation profiles at CpG islands from individual human blastocysts, with common genomic regions of DNA methylation identified between embryos. Result(s) Between 472 and 734 CpG islands were methylated in each blastocyst, with 121 CpG islands being commonly methylated in all 5 blastocysts. A further 159 CGIs were commonly methylated in 4 of the 5 tested blastocysts. Methylation was observed at a number of CGIs within imprinted-gene, differentially methylated regions (DMRs), including placental and preimplantation-specific DMRs. Conclusion(s) The MCAM method is capable of providing comprehensive DNA methylation data in individual human blastocysts. PMID:25914096

  17. Genome Sequence of Vibrio cholerae Strain O1 Ogawa El Tor, Isolated in Mexico, 2013

    PubMed Central

    Hernández-Monroy, Irma; López-Martínez, Irma; Ortiz-Alcántara, Joanna; González-Durán, Elizabeth; Ruiz-Matus, Cuitláhuac; Kuri-Morales, Pablo; Ramírez-González, José Ernesto

    2014-01-01

    We present the draft genome sequence of Vibrio cholerae InDRE 3140 recovered in 2013 during a cholera outbreak in Mexico. The genome showed the Vibrio 7th pandemic islands VSP1 and VSP2, the pathogenic islands VPI-1 and VPI-2, the integrative and conjugative element SXT/R391 (ICE-SXT), and both prophages CTX? and RS1?. PMID:25359919

  18. Small variable segments constitute a major type of diversity of bacterial genomes at the species level

    Microsoft Academic Search

    Fabrice Touzain; Erick Denamur; Claudine Médigue; Valérie Barbe; Meriem El Karoui; Marie-Agnès Petit

    2010-01-01

    Background  Analysis of large scale diversity in bacterial genomes has mainly focused on elements such as pathogenicity islands, or more\\u000a generally, genomic islands. These comprise numerous genes and confer important phenotypes, which are present or absent depending\\u000a on strains. We report that despite this widely accepted notion, most diversity at the species level is composed of much smaller\\u000a DNA segments, 20

  19. Genome Sequence of Vibrio cholerae Strain O1 Ogawa El Tor, Isolated in Mexico, 2013.

    PubMed

    Díaz-Quiñonez, José Alberto; Hernández-Monroy, Irma; López-Martínez, Irma; Ortiz-Alcántara, Joanna; González-Durán, Elizabeth; Ruiz-Matus, Cuitláhuac; Kuri-Morales, Pablo; Ramírez-González, José Ernesto

    2014-01-01

    We present the draft genome sequence of Vibrio cholerae InDRE 3140 recovered in 2013 during a cholera outbreak in Mexico. The genome showed the Vibrio 7th pandemic islands VSP1 and VSP2, the pathogenic islands VPI-1 and VPI-2, the integrative and conjugative element SXT/R391 (ICE-SXT), and both prophages CTX? and RS1?. PMID:25359919

  20. Galveston Island and erosion 

    E-print Network

    Bolleter, Jim Mason

    1985-01-01

    ABSTRACT Galveston Island and Erosion. (May 1985) Jim Mason Bolleter, B. S. , Texas AM University Chairman of Advisory Committee: Dr. A. R. Benton Jr. Mid-term changes in the beach vegetation line on Galveston Island, I as well as the erosional effects... of recent hurri canes and tropical . storms, wer e documented with multi -date aerial photography. While ~ localized accretion has occurred on East Beach due to the shadowing effect of the South Jetty, West beach has fluctuated between erosion Major...

  1. Melville Island, Australia

    NASA Technical Reports Server (NTRS)

    1992-01-01

    Melville Island, just off the coast of Darwin, Northern Territory, Australia (11.5S, 131.0E) is a sparsely inhabited tropical island with heavy woodland concentrations. The widespread and prominant smoke plumes were most likely set to renew pasture under open canopy woodland. Soil erosion is almost non- existant as can be seen by the clear and clean river flow. The offshore sediments are coastal current borne deposits from King Sound to the west.

  2. The complete genome sequence of the carcinogenic bacterium Helicobacter hepaticus.

    PubMed

    Suerbaum, Sebastian; Josenhans, Christine; Sterzenbach, Torsten; Drescher, Bernd; Brandt, Petra; Bell, Monica; Droge, Marcus; Fartmann, Berthold; Fischer, Hans-Peter; Ge, Zhongming; Horster, Andrea; Holland, Rudi; Klein, Kerstin; Konig, Jochen; Macko, Ludwig; Mendz, George L; Nyakatura, Gerald; Schauer, David B; Shen, Zeli; Weber, Jacqueline; Frosch, Matthias; Fox, James G

    2003-06-24

    Helicobacter hepaticus causes chronic hepatitis and liver cancer in mice. It is the prototype enterohepatic Helicobacter species and a close relative of Helicobacter pylori, also a recognized carcinogen. Here we report the complete genome sequence of H. hepaticus ATCC51449. H. hepaticus has a circular chromosome of 1,799,146 base pairs, predicted to encode 1,875 proteins. A total of 938, 953, and 821 proteins have orthologs in H. pylori, Campylobacter jejuni, and both pathogens, respectively. H. hepaticus lacks orthologs of most known H. pylori virulence factors, including adhesins, the VacA cytotoxin, and almost all cag pathogenicity island proteins, but has orthologs of the C. jejuni adhesin PEB1 and the cytolethal distending toxin (CDT). The genome contains a 71-kb genomic island (HHGI1) and several genomic islets whose G+C content differs from the rest of the genome. HHGI1 encodes three basic components of a type IV secretion system and other virulence protein homologs, suggesting a role of HHGI1 in pathogenicity. The genomic variability of H. hepaticus was assessed by comparing the genomes of 12 H. hepaticus strains with the sequenced genome by microarray hybridization. Although five strains, including all those known to have caused liver disease, were indistinguishable from ATCC51449, other strains lacked between 85 and 229 genes, including large parts of HHGI1, demonstrating extensive variation of genome content within the species. PMID:12810954

  3. Selecting Genomes for Reconstruction of Ancestral Genomes

    E-print Network

    Zhang, Louxin

    Selecting Genomes for Reconstruction of Ancestral Genomes Guoliang Li1 , Jian Ma2 , and Louxin. It is often impossible to sequence all descendent genomes to reconstruct an ancestral genome. In addition, more genomes do not neces- sarily give a higher accuracy for the reconstruction of ancestral character

  4. The broad host range pathogen Pseudomonas aeruginosa strain PA14 carries two pathogenicity islands harboring plant and animal virulence genes

    Microsoft Academic Search

    Jianxin He; Regina L. Baldini; Eric Déziel; Maude Saucier; Qunhao Zhang; Nicole T. Liberati; Daniel Lee; Jonathan Urbach; Howard M. Goodman; Laurence G. Rahme

    2004-01-01

    The ubiquitous bacterium Pseudomonas aeruginosa is the quintessential opportunistic pathogen. Certain isolates infect a broad range of host organisms, from plants to humans. The pathogenic promiscuity of particular variants may reflect an increased virulence gene repertoire beyond the core P. aeruginosa genome. We have identified and characterized two P. aeruginosa pathogenicity islands (PAPI-1 and PAPI-2) in the genome of PA14,

  5. Island species radiation and karyotypic stasis in Pachycladon allopolyploids

    PubMed Central

    2010-01-01

    Background Pachycladon (Brassicaceae, tribe Camelineae) is a monophyletic genus of ten morphologically and ecogeographically differentiated, and presumably allopolyploid species occurring in the South Island of New Zealand and in Tasmania. All Pachycladon species possess ten chromosome pairs (2n = 20). The feasibility of comparative chromosome painting (CCP) in crucifer species allows the origin and genome evolution in this genus to be elucidated. We focus on the origin and genome evolution of Pachycladon as well as on its genomic relationship to other crucifer species, particularly to the allopolyploid Australian Camelineae taxa. As species radiation on islands is usually characterized by chromosomal stasis, i.e. uniformity of chromosome numbers/ploidy levels, the role of major karyotypic reshuffling during the island adaptive and species radiation in Pachycladon is investigated through whole-genome CCP analysis. Results The four analyzed Pachycladon species possess an identical karyotype structure. The consensual ancestral karyotype is most likely common to all Pachycladon species and corroborates the monophyletic origin of the genus evidenced by previous phylogenetic analyses. The ancestral Pachycladon karyotype (n = 10) originated through an allopolyploidization event between two genomes structurally resembling the Ancestral Crucifer Karyotype (ACK, n = 8). The primary allopolyploid (apparently with n = 16) has undergone genome reshuffling by descending dysploidy toward n = 10. Chromosome "fusions" were mediated by inversions, translocations and centromere inactivation/loss. Pachycladon chromosome 3 (PC3) resulted from insertional fusion, described in grasses. The allopolyploid ancestor originated in Australia, from the same or closely related ACK-like parental species as the Australian Camelineae allopolyploids. However, the two whole-genome duplication (WGD) events were independent, with the Pachycladon WGD being significantly younger. The long-distance dispersal of the diploidized Pachycladon ancestor to New Zealand was followed by the Pleistocene species radiation in alpine habitats and characterized by karyotypic stasis. Conclusions Karyotypic stasis in Pachycladon suggests that the insular species radiation in this genus proceeded through homoploid divergence rather than through species-specific gross chromosomal repatterning. The ancestral Pachycladon genome originated in Australia through an allopolyploidization event involving two closely related parental genomes, and spread to New Zealand by a long-distance dispersal. We argue that the chromosome number decrease mediated by inter-genomic reshuffling (diploidization) could provide the Pachycladon allopolyploid founder with an adaptive advantage to colonize montane/alpine habitats. The ancestral Pachycladon karyotype remained stable during the Pleistocene adaptive radiation into ten different species. PMID:21114825

  6. Imaging genomics

    PubMed Central

    Thompson, Paul M.; Martin, Nicholas G.; Wright, Margaret J.

    2010-01-01

    Purpose of review Imaging genomics is an emerging field that is rapidly identifying genes that influence the brain, cognition, and risk for disease. Worldwide, thousands of individuals are being scanned with high-throughput genotyping (genome-wide scans), and new imaging techniques [high angular resolution diffusion imaging and resting state functional magnetic resonance imaging (MRI)] that provide fine-grained measures of the brain’s structural and functional connectivity. Along with clinical diagnosis and cognitive testing, brain imaging offers highly reproducible measures that can be subjected to genetic analysis. Recent findings Recent studies of twin, pedigree, and population-based datasets have discovered several candidate genes that consistently show small to moderate effects on brain measures. Many studies measure single phenotypes from the images, such as hippocampal volume, but voxel-wise genomic methods can plot the profile of genetic association at each 3D point in the brain. This exploits the full arsenal of imaging statistics to discover and replicate gene effects. Summary Imaging genomics efforts worldwide are now working together to discover and replicate many promising leads. By studying brain phenotypes closer to causative gene action, larger gene effects are detectable with realistic sample sizes obtainable from meta-analysis of smaller studies. Imaging genomics has broad applications to dementia, mental illness, and public health. PMID:20581684

  7. Modeling Catastrophic Barrier Island Dynamics

    NASA Astrophysics Data System (ADS)

    Whitley, J. W.; McNamara, D.

    2012-12-01

    Barrier islands, thin strips of sand lying parallel to the mainland coastline, along the U.S. Atlantic and Gulf Coasts appear to have maintained their form for thousands of years in the face of rising sea level. The mechanisms that allow barrier islands to remain robust are transport of sediment from the ocean side of barriers to the top and backside during storms, termed island overwash, and the growth and alongshore propagation of tidal deltas near barrier island inlets. Dynamically these processes provide the necessary feedbacks to maintain a barrier island in an attractor that withstands rising sea level within a phase space of barrier island geometrical characteristics. Current barrier island configurations along the Atlantic and Gulf coasts exist among a wide range of storm climate and underlying geologic conditions and therefore the environment that forces overwash and tidal delta dynamics varies considerably. It has been suggested that barrier islands in certain locations such as those between Avon and Buxton (losing 76% of island width since 1852) and Chandeleur islands (losing 85% of its surface area since 2005) along the Atlantic and Gulf coasts, respectively, may be subject to a catastrophic shift in barrier island attractor states - more numerous inlets cutting barriers in some locations and the complete disappearance of barrier islands in other locations. In contrast to common models for barrier islands that neglect storm dynamics and often only consider cross-shore response, we use an alongshore extended model for barrier island dynamics including beach erosion, island overwash and inlet cutting during storms, and beach accretion, tidal delta growth and dune and vegetation growth between storms to explore the response of barrier islands to a wide range of environmental forcing. Results will be presented that show how barrier island attractor states are altered with variations in the rate of sea level rise, storminess, and underlying geology. We will also investigate the conditions necessary for a barrier island attractor similar to those found along the Atlantic and Gulf coasts to become unstable.

  8. Arts & Genomics

    NSDL National Science Digital Library

    Based at the University of Leiden in the Netherlands, The Arts & Genomics Centre is interested in expanding the "public debate on (future) goals, means, possibilities and use of results of genomics, from the specific point of view of bio-genetic art." The homepage provides ample information about their most recent initiatives, which have included a symposium on food, art and science and a video on their VivoArts program, which attempts to bring together biology and various contemporary arts. Moving on, the "Research" section of the site includes project documents and proposals that deal with their representational space program and the "Imagining Genomics" initiative. The site is rounded out by a collection of links to other germane sites and online resources.

  9. Insular organization of gene space in grass genomes.

    PubMed

    Gottlieb, Andrea; Müller, Hans-Georg; Massa, Alicia N; Wanjugi, Humphrey; Deal, Karin R; You, Frank M; Xu, Xiangyang; Gu, Yong Q; Luo, Ming-Cheng; Anderson, Olin D; Chan, Agnes P; Rabinowicz, Pablo; Devos, Katrien M; Dvorak, Jan

    2013-01-01

    Wheat and maize genes were hypothesized to be clustered into islands but the hypothesis was not statistically tested. The hypothesis is statistically tested here in four grass species differing in genome size, Brachypodium distachyon, Oryza sativa, Sorghum bicolor, and Aegilops tauschii. Density functions obtained under a model where gene locations follow a homogeneous Poisson process and thus are not clustered are compared with a model-free situation quantified through a non-parametric density estimate. A simple homogeneous Poisson model for gene locations is not rejected for the small O. sativa and B. distachyon genomes, indicating that genes are distributed largely uniformly in those species, but is rejected for the larger S. bicolor and Ae. tauschii genomes, providing evidence for clustering of genes into islands. It is proposed to call the gene islands "gene insulae" to distinguish them from other types of gene clustering that have been proposed. An average S. bicolor and Ae. tauschii insula is estimated to contain 3.7 and 3.9 genes with an average intergenic distance within an insula of 2.1 and 16.5 kb, respectively. Inter-insular distances are greater than 8 and 81 kb and average 15.1 and 205 kb, in S. bicolor and Ae. tauschii, respectively. A greater gene density observed in the distal regions of the Ae. tauschii chromosomes is shown to be primarily caused by shortening of inter-insular distances. The comparison of the four grass genomes suggests that gene locations are largely a function of a homogeneous Poisson process in small genomes. Nonrandom insertions of LTR retroelements during genome expansion creates gene insulae, which become less dense and further apart with the increase in genome size. High concordance in relative lengths of orthologous intergenic distances among the investigated genomes including the maize genome suggests functional constraints on gene distribution in the grass genomes. PMID:23326580

  10. Recombinant protein production in an Escherichia coli reduced genome strain

    Microsoft Academic Search

    Shamik S. Sharma; Frederick R. Blattner; Sarah W. Harcum

    2007-01-01

    Recently, efforts have been made to improve the properties of Escherichia coli as a recombinant host by ‘genomic surgery’—deleting large segments of the E. coli K12 MG1655 genome without scars. These excised segments included K-islands, which contain a high proportion of transposons, insertion sequences, cryptic phage, damaged, and unknown-function genes. The resulting multiple-deletion strain, designated E. coli MDS40, has a

  11. Comparing Genomes of Helicobacter pylori Strains from the High-Altitude Desert of Ladakh, India

    Microsoft Academic Search

    Farhana Kauser; M. Abid Hussain; Irshad Ahmed; Naheed Ahmad; Aejaz Habeeb; Aleem A. Khan; Niyaz Ahmed

    2005-01-01

    The genomic diversity of Helicobacter pylori from the vast Indian subcontinent is largely unknown. We compared the genomes of 10 H. pylori strains from Ladakh, North India. Molecular analysis was carried out to identify rearrangements within and outside the cag pathogenicity island (cag PAI) and DNA sequence divergence in candidate genes. Analyses of virulence genes (such as the cag PAI

  12. Physiological Genomics

    NSDL National Science Digital Library

    1969-12-31

    Five journals with free (or recently extended) online trial periods were recently announced; online content includes full text, figures, and tables. The American Physiological Society has announced free, online access to Physiological Genomics through December 31, 2001; full text and abstracts are available from 1999. The journal is published in conjunction with Stanford University's HighWire Press.

  13. HEAT ISLAND REDUCTION STRATEGIES GUIDEBOOK

    EPA Science Inventory

    This heat island reduction strategies guidebook provides an overview of urban heat islands and steps communities can take to reduce them. In particular, this guidebook provides background basics and answers the questions: ?What is a heat island?? ?What are its impacts?" "What ar...

  14. Density compensation in island avifaunas

    Microsoft Academic Search

    S. Joseph Wright

    1980-01-01

    This paper analyzes factors which determine the extent of density compensation on islands; i.e., is the summed population density of all species on an island equal to the summed mainland density? A graphical analysis allows quantitative comparisons of density compensation studies. Two hypotheses which are generally applicable predict the extent of density compensation on islands: (1) Niche theory predicts that

  15. Genome-wide study of correlations between genomic features and their relationship with the regulation of gene expression

    PubMed Central

    Kravatsky, Yuri V.; Chechetkin, Vladimir R.; Tchurikov, Nikolai A.; Kravatskaya, Galina I.

    2015-01-01

    The broad class of tasks in genetics and epigenetics can be reduced to the study of various features that are distributed over the genome (genome tracks). The rapid and efficient processing of the huge amount of data stored in the genome-scale databases cannot be achieved without the software packages based on the analytical criteria. However, strong inhomogeneity of genome tracks hampers the development of relevant statistics. We developed the criteria for the assessment of genome track inhomogeneity and correlations between two genome tracks. We also developed a software package, Genome Track Analyzer, based on this theory. The theory and software were tested on simulated data and were applied to the study of correlations between CpG islands and transcription start sites in the Homo sapiens genome, between profiles of protein-binding sites in chromosomes of Drosophila melanogaster, and between DNA double-strand breaks and histone marks in the H. sapiens genome. Significant correlations between transcription start sites on the forward and the reverse strands were observed in genomes of D. melanogaster, Caenorhabditis elegans, Mus musculus, H. sapiens, and Danio rerio. The observed correlations may be related to the regulation of gene expression in eukaryotes. Genome Track Analyzer is freely available at http://ancorr.eimb.ru/. PMID:25627242

  16. Three Mile Island

    Microsoft Academic Search

    M. S. Wood; S. M. Shultz

    1988-01-01

    This bibliography is divided into the following categories: Accident Overviews, Sequence and Causes; International Commentary and Reaction; Emergency Preparedness and Disaster Planning; Health Effects; Radioactive Releases and the Environment; Accident Investigations\\/Commissions; Nuclear Industry: Safety, Occupational, and Financial Issues; Media and Communications; Cleanup; Sociopolitical Response and Commentary; Restart; Legal Ramifications; Federal Documents: President's Commission on the Accident at Three Mile Island;

  17. Three Mile Island revisited

    Microsoft Academic Search

    B. L. Lipford; N. M. Cole; T. J. Friderichs

    1991-01-01

    As a result of the accident in March 1979, the Three Mile Island Unit 2 (TMI-2) reactor vessel sustained significant internal damage. Approximately half of the reactor core suffered some degree of melting, with 10 to 20 tons of molten core material relocating inside the vessel and flowing down onto the reactor vessel's lower head. The resulting damage and the

  18. URBAN EXTENTS Falkland Islands

    E-print Network

    Columbia University

    URBAN EXTENTS BRAZIL CHILE PARAGUAY URUGUAY GRUMPv1 Falkland Islands A t l a n t i c O c e a n P Tropical (CIAT). Global Rural-Urban Mapping Project (GRUMP), Population Density. Palisades, NY: CIESIN Equal Area Projection Urban Extent Administrative Units National Boundaries Note: National boundaries

  19. Atsena Otie Key Island

    USGS Multimedia Gallery

    Atsena Otie Key is one of thirteen islands on Florida's Gulf Coast that make up Cedar Keys National Wildlife Refuge. Nearby waters support a multi-million dollar clam-farming industry. USGS documented pre-oil coastal conditions near the Refuge with baseline petrochemical measurements and aerial phot...

  20. Japan: Shikoku Island

    Atmospheric Science Data Center

    2013-04-16

    ... energy balance, and directly sampled airborne dust and pollution particles while the Multi-angle Imaging SpectroRadiometer (MISR) and ... for Atmospheric Research (NCAR) C-130 aircraft probed the environment near Oki island, in the upper left part of the images. At the same ...

  1. Siberian Expedition: Wrangel Island

    NSDL National Science Digital Library

    This web site chronicles an American Museum of Natural History research expedition in 1998 to Siberia's Wrangel Island to collect woolly mammoth bones and test the theory that lethal disease caused the mammal's extinction. Information on the team members and journal excerpts are included as well as information on the expedition's objectives and the important tools used by the team.

  2. Kiritimati, Kiribati (Christmas Island)

    NASA Technical Reports Server (NTRS)

    2002-01-01

    Pronounced 'Ki-ris-mas,' Kiritimati Island has a large infilled lagoon that gives it the largest land area (125 square miles, 321 square km) of any atoll in the world. Captain Cook named the atoll Christmas Island when he arrived on Christmas Eve in 1777. Used for nuclear testing in the 1950s and 1960s, the island is now valued for its marine and wildlife resources. It is particularly important as a seabird nesting site-with an estimated 6 million birds using or breeding on the island, including several million Sooty Terns. Rainfall on Kiritimati is linked to El Nino patterns, with long droughts experienced between the wetter El Nino years. This image is based on a mosaic of four digital photographs taken on 16 January 2002 from the Space Station Alpha as part of the Crew Earth Observations Project. The underlying data have 10 meter spatial resolution. Coral reefs are one of the areas selected as a scientific theme for this project (see also the recent Earth Observatory article, Mapping the Decline of Coral Reefs. The mosaic, based on images ISS004-ESC-6249 to 6252, was provided by the Earth Sciences and Image Analysis Laboratory at Johnson Space Center. Additional images taken by astronauts and cosmonauts can be viewed at the NASA-JSC Gateway to Astronaut Photography of Earth.

  3. Hawaii's Sugar Islands.

    ERIC Educational Resources Information Center

    Hawaiian Sugar Planters' Association, Aiea, HI.

    A warm and sunny subtropical climate helps make Hawaii an important sugar producer. History records that sugarcane was already present when Captain James Cook discovered the islands in 1778, and that the first successful sugarcane plantation was started in 1835 by Ladd and Company at Koloa. The first recorded export of Hawaiian sugar was in 1837,…

  4. Genomic diversity and versatility of Lactobacillus plantarum, a natural metabolic engineer

    PubMed Central

    2011-01-01

    In the past decade it has become clear that the lactic acid bacterium Lactobacillus plantarum occupies a diverse range of environmental niches and has an enormous diversity in phenotypic properties, metabolic capacity and industrial applications. In this review, we describe how genome sequencing, comparative genome hybridization and comparative genomics has provided insight into the underlying genomic diversity and versatility of L. plantarum. One of the main features appears to be genomic life-style islands consisting of numerous functional gene cassettes, in particular for carbohydrates utilization, which can be acquired, shuffled, substituted or deleted in response to niche requirements. In this sense, L. plantarum can be considered a “natural metabolic engineer”. PMID:21995294

  5. Colonization of an island volcano, Long Island, Papua New Guinea, and an emergent island,

    E-print Network

    , in its caldera lake. VI. The pioneer arthropod community of Motmot John S. Edwards1 and Ian W. B Wisdom which occupies the caldera of Long Island, Papua New Guinea. Methods Arthropod sampling by means studies on the pioneer biota of an emergent island, Motmot, in Long Island's freshwater caldera lake, Lake

  6. Genome informatics and vaccine targets in Corynebacterium urealyticum using two whole genomes, comparative genomics, and reverse vaccinology

    PubMed Central

    2015-01-01

    Background Corynebacterium urealyticum is an opportunistic pathogen that normally lives on skin and mucous membranes in humans. This high Gram-positive bacteria can cause acute or encrusted cystitis, encrusted pyelitis, and pyelonephritis in immunocompromised patients. The bacteria is multi-drug resistant, and knowledge about the genes that contribute to its virulence is very limited. Two complete genome sequences were used in this comparative genomic study: C. urealyticum DSM 7109 and C. urealyticum DSM 7111. Results We used comparative genomics strategies to compare the two strains, DSM 7109 and DSM 7111, and to analyze their metabolic pathways, genome plasticity, and to predict putative antigenic targets. The genomes of these two strains together encode 2,115 non-redundant coding sequences, 1,823 of which are common to both genomes. We identified 188 strain-specific genes in DSM 7109 and 104 strain-specific genes in DSM 7111. The high number of strain-specific genes may be a result of horizontal gene transfer triggered by the large number of transposons in the genomes of these two strains. Screening for virulence factors revealed the presence of the spaDEF operon that encodes pili forming proteins. Therefore, spaDEF may play a pivotal role in facilitating the adhesion of the pathogen to the host tissue. Application of the reverse vaccinology method revealed 19 putative antigenic proteins that may be used in future studies as candidate drug or vaccine targets. Conclusions The genome features and the presence of virulence factors in genomic islands in the two strains of C. urealyticum provide insights in the lifestyle of this opportunistic pathogen and may be useful in developing future therapeutic strategies. PMID:26041051

  7. Silencing Genomes

    NSDL National Science Digital Library

    2007-06-12

    While we may have complete genome sequences for humans and some animals, scientists are now entering the "post genome" era. The challenges of this era include determining the physiological functions of the thousands of new genes "for which little is known beyond their sequences." The use of RNAi, along with bioinformatics, can provide scientists with the tools to determine these functions in living organisms. This interactive and informative site, created by Cold Spring Harbor Laboratory, allows visitors to learn about the ways in which RNAi functions. Visitors can make their way through the seven interactive features here, which include "Inducing RNAi by Feeding" and "Creating an RNAi Feeding Strain". Additionally, the site has a "Resources" area which contains more materials on RNAi (such as interviews with scientists and such), along with videos of different strains in action.

  8. Ancient genomics

    PubMed Central

    Der Sarkissian, Clio; Allentoft, Morten E.; Ávila-Arcos, María C.; Barnett, Ross; Campos, Paula F.; Cappellini, Enrico; Ermini, Luca; Fernández, Ruth; da Fonseca, Rute; Ginolhac, Aurélien; Hansen, Anders J.; Jónsson, Hákon; Korneliussen, Thorfinn; Margaryan, Ashot; Martin, Michael D.; Moreno-Mayar, J. Víctor; Raghavan, Maanasa; Rasmussen, Morten; Velasco, Marcela Sandoval; Schroeder, Hannes; Schubert, Mikkel; Seguin-Orlando, Andaine; Wales, Nathan; Gilbert, M. Thomas P.; Willerslev, Eske; Orlando, Ludovic

    2015-01-01

    The past decade has witnessed a revolution in ancient DNA (aDNA) research. Although the field's focus was previously limited to mitochondrial DNA and a few nuclear markers, whole genome sequences from the deep past can now be retrieved. This breakthrough is tightly connected to the massive sequence throughput of next generation sequencing platforms and the ability to target short and degraded DNA molecules. Many ancient specimens previously unsuitable for DNA analyses because of extensive degradation can now successfully be used as source materials. Additionally, the analytical power obtained by increasing the number of sequence reads to billions effectively means that contamination issues that have haunted aDNA research for decades, particularly in human studies, can now be efficiently and confidently quantified. At present, whole genomes have been sequenced from ancient anatomically modern humans, archaic hominins, ancient pathogens and megafaunal species. Those have revealed important functional and phenotypic information, as well as unexpected adaptation, migration and admixture patterns. As such, the field of aDNA has entered the new era of genomics and has provided valuable information when testing specific hypotheses related to the past. PMID:25487338

  9. Genomic Science in Understanding Cholera Outbreaks and Evolution of Vibrio cholerae as a Human Pathogen

    PubMed Central

    Mekalanos, John J.

    2014-01-01

    Modern genomic and bioinformatic approaches have been applied to interrogate the V. cholerae genome, the role of genomic elements in cholera disease, and the origin, relatedness, and dissemination of epidemic strains. A universal attribute of choleragenic strains includes a repertoire of pathogenicity islands and virulence genes, namely the CTX–? prophage and Toxin Co-regulated Pilus (TCP) in addition to other virulent genetic elements including those referred to as Seventh Pandemic Islands. During the last decade, the advent of Next Generation Sequencing (NGS) has provided highly resolved and often complete genomic sequences of epidemic isolates in addition to both clinical and environmental strains isolated from geographically unconnected regions. Genomic comparisons of these strains, as was completed during and following the Haitian outbreak in 2010, reveals that most epidemic strains appear closely related, regardless of region of origin. Non-O1 clinical or environmental strains may also possess some virulence islands, but phylogenic analysis of the core genome suggests they are more diverse and distantly related than those isolated during epidemics. Like Haiti, genomic studies that examine both the Vibrio core- and pan-genome in addition to Single Nucleotide Polymorphisms (SNPs) conclude that a number of epidemics are caused by strains that closely resemble those in Asia, and often appear to originate there and then spread globally. The accumulation of SNPs in the epidemic strains over time can then be applied to better understand the evolution of the V. cholerae genome as an etiological agent. PMID:24590676

  10. Pine Island Iceberg Formation

    NSDL National Science Digital Library

    Lori Perkins

    2002-01-10

    This animation is a sequence showing the formation of the Pine Island iceberg and the glacial seaward flow upstream from the crack. It is a series of MISR images from the Terra satellite on top of the continental Radarsat view of Antarctica. The Pine Island Glacier is the largest discharger of ice in Antarctica and the continents fastest moving glacier. Even so, when a large crack formed across the glacier in mid 2000, it was surprising how fast the crack expanded, 15 meters per day, and how soon the resulting iceberg broke off, mid-November, 2001. This iceberg, called B-21, is 42 kilometers by 17 kilometers and contains seven years of glacier outflow released to the sea in a single event.

  11. Kodiak Island, Alaska

    NASA Technical Reports Server (NTRS)

    2002-01-01

    Running vertically between Alaska on the right and Russia on the left, the Bering Strait is mostly free of ice in this true-color MODIS image acquired from data captured on May 31, 2001. To the lower right of the image, a phytoplankton bloom appears to be occurring at the mouth of Norton Sound, and is coloring the darker water a bright bluish green. At the bottom center of the image is snow-covered St. Lawrence Island.

  12. Dauphin Island Sea Lab

    NSDL National Science Digital Library

    Dauphin Island Sea Lab is Alabama's marine education and research center. Lab also provides a public aquarium that focuses solely on the native eco-systems of the Mobile Bay estuary. Site provides information on graduate programs, undergraduate opportunities, faculty, facilities, and news and events. Explore the Education and Aquarium sections for teacher resources and information on workshops, student summer camps, and academic-year programs.

  13. Poetic Waves: Angel Island

    NSDL National Science Digital Library

    2005-01-01

    While many visitors to San Francisco may be familiar with Alcatraz Island, they may be less familiar with the story of Angel Island, which is also located nearby. From 1910 to 1940, the island served as immigration station for newly arrived Asian American immigrants to the United States. While here, these people began to bond over their shared experiences, and also started to learn about the difficult time that they would face in this new land. This multimedia website pays tribute to their experiences through offering compelling information about this place through audio narration and music. As the title of the site suggests, visitors can read some of the poetry the immigrants carved into the barracks where they lived when they were being processed upon arrival. The website accurately suggests that â??â?¦there is no direct connection between them except for the languages, the time period, and place.â? Of course, visitors may wish to continue their visit to the site, by taking the online tour of the facility, which includes the hospital building, the pier, and the barracks.

  14. Islands behind Islands: An Unappreciated Coastal Landform Category

    Microsoft Academic Search

    J. A. G. Cooper; O. H. Pilkey; D. A. Lewis

    COOPER, J.A.G., PILKEY, O.H., and LEWIS, D.A. 2007. Islands behind islands: an unappreciated coastal landform category. Journal of Coastal Research, SI 50 (Proceedings of the 9th International Coastal Symposium), 907 - 911. Gold Coast, Australia, ISSN 0749-0208 The 15,000 plus barrier islands in sheltered or fetch-limited, nearshore marine waters have not achieved recognition as a distinct and important landform. As

  15. The Human Genome From human genome to other

    E-print Network

    Linial, Michal

    The Human Genome Project From human genome to other genomes and to gene function June 2000 From genome to health Structural Genomics initiative #12;What is the Human Genome Project? · U.S. govt that arise from genome research #12;The Human Genome Project Project began in 1990 as a $3 billion, 15-year

  16. Genomic Species Are Ecological Species as Revealed by Comparative Genomics in Agrobacterium tumefaciens

    PubMed Central

    Lassalle, Florent; Campillo, Tony; Vial, Ludovic; Baude, Jessica; Costechareyre, Denis; Chapulliot, David; Shams, Malek; Abrouk, Danis; Lavire, Céline; Oger-Desfeux, Christine; Hommais, Florence; Guéguen, Laurent; Daubin, Vincent; Muller, Daniel; Nesme, Xavier

    2011-01-01

    The definition of bacterial species is based on genomic similarities, giving rise to the operational concept of genomic species, but the reasons of the occurrence of differentiated genomic species remain largely unknown. We used the Agrobacterium tumefaciens species complex and particularly the genomic species presently called genomovar G8, which includes the sequenced strain C58, to test the hypothesis of genomic species having specific ecological adaptations possibly involved in the speciation process. We analyzed the gene repertoire specific to G8 to identify potential adaptive genes. By hybridizing 25 strains of A. tumefaciens on DNA microarrays spanning the C58 genome, we highlighted the presence and absence of genes homologous to C58 in the taxon. We found 196 genes specific to genomovar G8 that were mostly clustered into seven genomic islands on the C58 genome—one on the circular chromosome and six on the linear chromosome—suggesting higher plasticity and a major adaptive role of the latter. Clusters encoded putative functional units, four of which had been verified experimentally. The combination of G8-specific functions defines a hypothetical species primary niche for G8 related to commensal interaction with a host plant. This supports that the G8 ancestor was able to exploit a new ecological niche, maybe initiating ecological isolation and thus speciation. Searching genomic data for synapomorphic traits is a powerful way to describe bacterial species. This procedure allowed us to find such phenotypic traits specific to genomovar G8 and thus propose a Latin binomial, Agrobacterium fabrum, for this bona fide genomic species. PMID:21795751

  17. 75 FR 61993 - Amendment of Class E Airspace; Kwajalein Island, Marshall Islands, RMI

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-10-07

    ...2120-AA66 Amendment of Class E Airspace; Kwajalein Island, Marshall Islands, RMI AGENCY: Federal Aviation Administration (FAA...description of the Class E airspace areas for Kwajalein Island, Bucholz AAF, Marshall Islands, RMI. The...

  18. 77 FR 34894 - Safety Zone; Bostock 50th Anniversary Fireworks, Long Island Sound; Manursing Island, NY

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-06-12

    ...Zone; Bostock 50th Anniversary Fireworks, Long Island Sound; Manursing Island, NY AGENCY: Coast Guard, DHS. ACTION: Notice...temporary safety zone on the navigable waters of Long Island Sound in the vicinity of Manursing Island, NY...

  19. 75 FR 28643 - Pine Island, Matlacha Pass, Island Bay, and Caloosahatchee National Wildlife Refuges, Lee and...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-05-21

    ...FWS-R4-R-2010-N051; 40136-1265-0000-S3] Pine Island, Matlacha Pass, Island Bay, and Caloosahatchee National Wildlife Refuges...environmental assessment (Draft CCP/EA) for Pine Island, Matlacha Pass, Island Bay, and...

  20. 77 FR 51473 - Safety Zone; Bostock 50th Anniversary Fireworks, Long Island Sound; Manursing Island, NY

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-08-24

    ...Zone; Bostock 50th Anniversary Fireworks, Long Island Sound; Manursing Island, NY AGENCY: Coast Guard, DHS. ACTION: Final...temporary safety zone on the navigable waters of Long Island Sound in the vicinity of Manursing Island, NY...

  1. 50 CFR Appendix E to Part 622 - Caribbean Island/Island Group Management Areas

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ...2013-10-01 false Caribbean Island/Island Group Management Areas E Appendix...FISHERIES OF THE CARIBBEAN, GULF OF MEXICO, AND SOUTH ATLANTIC Pt. 622...Appendix E to Part 622—Caribbean Island/Island Group Management...

  2. 50 CFR Appendix E to Part 622 - Caribbean Island/Island Group Management Areas

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ...2014-10-01 false Caribbean Island/Island Group Management Areas E Appendix...FISHERIES OF THE CARIBBEAN, GULF OF MEXICO, AND SOUTH ATLANTIC Pt. 622...Appendix E to Part 622—Caribbean Island/Island Group Management...

  3. The Genetic Structure of Pacific Islanders

    PubMed Central

    Friedlaender, Jonathan S; Friedlaender, Françoise R; Reed, Floyd A; Kidd, Kenneth K; Kidd, Judith R; Chambers, Geoffrey K; Lea, Rodney A; Loo, Jun-Hun; Koki, George; Hodgson, Jason A; Merriwether, D. Andrew; Weber, James L

    2008-01-01

    Human genetic diversity in the Pacific has not been adequately sampled, particularly in Melanesia. As a result, population relationships there have been open to debate. A genome scan of autosomal markers (687 microsatellites and 203 insertions/deletions) on 952 individuals from 41 Pacific populations now provides the basis for understanding the remarkable nature of Melanesian variation, and for a more accurate comparison of these Pacific populations with previously studied groups from other regions. It also shows how textured human population variation can be in particular circumstances. Genetic diversity within individual Pacific populations is shown to be very low, while differentiation among Melanesian groups is high. Melanesian differentiation varies not only between islands, but also by island size and topographical complexity. The greatest distinctions are among the isolated groups in large island interiors, which are also the most internally homogeneous. The pattern loosely tracks language distinctions. Papuan-speaking groups are the most differentiated, and Austronesian or Oceanic-speaking groups, which tend to live along the coastlines, are more intermixed. A small “Austronesian” genetic signature (always <20%) was detected in less than half the Melanesian groups that speak Austronesian languages, and is entirely lacking in Papuan-speaking groups. Although the Polynesians are also distinctive, they tend to cluster with Micronesians, Taiwan Aborigines, and East Asians, and not Melanesians. These findings contribute to a resolution to the debates over Polynesian origins and their past interactions with Melanesians. With regard to genetics, the earlier studies had heavily relied on the evidence from single locus mitochondrial DNA or Y chromosome variation. Neither of these provided an unequivocal signal of phylogenetic relations or population intermixture proportions in the Pacific. Our analysis indicates the ancestors of Polynesians moved through Melanesia relatively rapidly and only intermixed to a very modest degree with the indigenous populations there. PMID:18208337

  4. The College of Staten Island Undergraduate Catalog

    E-print Network

    Rosen, Jay

    The College of Staten Island Undergraduate Catalog 2010-2011 2800 Victory Blvd Staten Island, NY 10314 718.982.2000 www.csi.cuny.edu Statement of Nondiscrimination The College of Staten Island of Staten Island/The City University of New York 2800 Victory Blvd, Staten Island, NY 10314 #12;About

  5. Public Health Genomics (PHG)

    Cancer.gov

    Public Health Genomics (PHG) is "a multidisciplinary field concerned with the effective and responsible translation of genome based knowledge and technologies to improve population health" (Bellagio Statement, 2006).

  6. Comparative Genomics and Transcriptomics of Propionibacterium acnes

    PubMed Central

    Brzuszkiewicz, Elzbieta; Weiner, January; Wollherr, Antje; Thürmer, Andrea; Hüpeden, Jennifer; Lomholt, Hans B.; Kilian, Mogens; Gottschalk, Gerhard; Daniel, Rolf; Mollenkopf, Hans-Joachim; Meyer, Thomas F.; Brüggemann, Holger

    2011-01-01

    The anaerobic Gram-positive bacterium Propionibacterium acnes is a human skin commensal that is occasionally associated with inflammatory diseases. Recent work has indicated that evolutionary distinct lineages of P. acnes play etiologic roles in disease while others are associated with maintenance of skin homeostasis. To shed light on the molecular basis for differential strain properties, we carried out genomic and transcriptomic analysis of distinct P. acnes strains. We sequenced the genome of the P. acnes strain 266, a type I-1a strain. Comparative genome analysis of strain 266 and four other P. acnes strains revealed that overall genome plasticity is relatively low; however, a number of island-like genomic regions, encoding a variety of putative virulence-associated and fitness traits differ between phylotypes, as judged from PCR analysis of a collection of P. acnes strains. Comparative transcriptome analysis of strains KPA171202 (type I-2) and 266 during exponential growth revealed inter-strain differences in gene expression of transport systems and metabolic pathways. In addition, transcript levels of genes encoding possible virulence factors such as dermatan-sulphate adhesin, polyunsaturated fatty acid isomerase, iron acquisition protein HtaA and lipase GehA were upregulated in strain 266. We investigated differential gene expression during exponential and stationary growth phases. Genes encoding components of the energy-conserving respiratory chain as well as secreted and virulence-associated factors were transcribed during the exponential phase, while the stationary growth phase was characterized by upregulation of genes involved in stress responses and amino acid metabolism. Our data highlight the genomic basis for strain diversity and identify, for the first time, the actively transcribed part of the genome, underlining the important role growth status plays in the inflammation-inducing activity of P. acnes. We argue that the disease-causing potential of different P. acnes strains is not only determined by the phylotype-specific genome content but also by variable gene expression. PMID:21738717

  7. 76 FR 16636 - Pine Island, Matlacha Pass, Island Bay, and Caloosahatchee NWRs, Lee County, FL; Final...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-03-24

    ...FWS-R4-R-2010-N240; 40136-1265-0000-S3] Pine Island, Matlacha Pass, Island Bay, and...for the environmental assessment for Pine Island, Matlacha Pass, Island Bay, and...notice, we finalize the CCP process for Pine Island, Matlacha Pass, Island Bay,...

  8. Island biogeography of the Anthropocene.

    PubMed

    Helmus, Matthew R; Mahler, D Luke; Losos, Jonathan B

    2014-09-25

    For centuries, biogeographers have examined the factors that produce patterns of biodiversity across regions. The study of islands has proved particularly fruitful and has led to the theory that geographic area and isolation influence species colonization, extinction and speciation such that larger islands have more species and isolated islands have fewer species (that is, positive species-area and negative species-isolation relationships). However, experimental tests of this theory have been limited, owing to the difficulty in experimental manipulation of islands at the scales at which speciation and long-distance colonization are relevant. Here we have used the human-aided transport of exotic anole lizards among Caribbean islands as such a test at an appropriate scale. In accord with theory, as anole colonizations have increased, islands impoverished in native species have gained the most exotic species, the past influence of speciation on island biogeography has been obscured, and the species-area relationship has strengthened while the species-isolation relationship has weakened. Moreover, anole biogeography increasingly reflects anthropogenic rather than geographic processes. Unlike the island biogeography of the past that was determined by geographic area and isolation, in the Anthropocene--an epoch proposed for the present time interval--island biogeography is dominated by the economic isolation of human populations. PMID:25254475

  9. Cognitive Constraints and Island Effects

    PubMed Central

    Hofmeister, Philip; Sag, Ivan A.

    2012-01-01

    Competence-based theories of island effects play a central role in generative grammar, yet the graded nature of many syntactic islands has never been properly accounted for. Categorical syntactic accounts of island effects have persisted in spite of a wealth of data suggesting that island effects are not categorical in nature and that non-structural manipulations that leave island structures intact can radically alter judgments of island violations. We argue here, building on work by Deane, Kluender, and others, that processing factors have the potential to account for this otherwise unexplained variation in acceptability judgments. We report the results of self-paced reading experiments and controlled acceptability studies which explore the relationship between processing costs and judgments of acceptability. In each of the three self-paced reading studies, the data indicate that the processing cost of different types of island violations can be significantly reduced to a degree comparable to that of non-island filler-gap constructions by manipulating a single non-structural factor. Moreover, this reduction in processing cost is accompanied by significant improvements in acceptability. This evidence favors the hypothesis that island-violating constructions involve numerous processing pressures that aggregate to drive processing difficulty above a threshold so that a perception of unacceptability ensues. We examine the implications of these findings for the grammar of filler-gap dependencies.* PMID:22661792

  10. Genomics of host-restricted pathogens of the genus bartonella.

    PubMed

    Engel, P; Dehio, C

    2009-01-01

    The alpha-proteobacterial genus Bartonella comprises numerous arthropod-borne pathogens that share a common host-restricted life-style, which is characterized by long-lasting intraerythrocytic infections in their specific mammalian reservoirs and transmission by blood-sucking arthropods. Infection of an incidental host (e.g. humans by a zoonotic species) may cause disease in the absence of intra-erythrocytic infection. The genome sequences of four Bartonella species are known, i.e. those of the human-specific pathogens Bartonella bacilliformis and Bartonella quintana, the feline-specific Bartonella henselae also causing incidental human infections, and the rat-specific species Bartonella tribocorum. The circular chromosomes of these bartonellae range in size from 1.44 Mb (encoding1,283 genes) to 2.62 Mb (encoding 2,136 genes). They share a mostly synthenic core genome of 959 genes that features characteristics of a host-integrated metabolism. The diverse accessory genomes highlight dynamic genome evolution at the species level, ranging from significant genome expansion in B. tribocorum due to gene duplication and lateral acquisition of prophages and genomic islands (such as type IV secretion systems that adopted prominent roles in host adaptation and specificity) to massive secondary genome reduction in B. quintana. Moreover, analysis of natural populations of B. henselae revealed genomic rearrangements, deletions and amplifications, evidencing marked genome dynamics at the strain level. PMID:19696500

  11. Establishment of new mutations under divergence and genome hitchhiking

    PubMed Central

    Feder, Jeffrey L.; Gejji, Richard; Yeaman, Sam; Nosil, Patrik

    2012-01-01

    Theoretical models addressing genome-wide patterns of divergence during speciation are needed to help us understand the evolutionary processes generating empirical patterns. Here, we examine a critical issue concerning speciation-with-gene flow: to what degree does physical linkage (r < 0.5) of new mutations to already diverged genes aid the build-up of genomic islands of differentiation? We used simulation and analytical approaches to partition the probability of establishment for a new divergently selected mutation when the mutation (i) is the first to arise in an undifferentiated genome (the direct effect of selection), (ii) arises unlinked to any selected loci (r = 0.5), but within a genome that has some already diverged genes (the effect of genome-wide reductions in gene flow for facilitating divergence, which we term ‘genome hitchhiking’), and (iii) arises in physical linkage to a diverged locus (divergence hitchhiking). We find that the strength of selection acting directly on a new mutation is generally the most important predictor for establishment, with divergence and genomic hitchhiking having smaller effects. We outline the specific conditions under which divergence and genome hitchhiking can aid mutation establishment. The results generate predictions about genome divergence at different points in the speciation process and avenues for further work. PMID:22201175

  12. PLANT GENOMICS The coffee genome provides insight

    E-print Network

    Napp, Nils

    PLANT GENOMICS The coffee genome provides insight into the convergent evolution of caffeine characteristic flavor, aroma, and the stimulating effects of caffeine. We generated a high-quality draft genome) involved in caffeine production, defense-related genes, and alkaloid and flavonoid enzymes involved

  13. Racquel Maronde Location: North Island and South Island, New Zealand

    E-print Network

    Minnesota, University of

    Racquel Maronde Location: North Island and South Island, New Zealand Term: January Term ESPM Track in New Zealand Visiting New Zealand was the most amazing experience of my life. You travel a lot and get to see every possible landscape of New Zealand - rainforests, mountains, caves, beaches, etc. The most we

  14. DNA Microarray Analysis of Genome Dynamics in Yersinia pestis: Insights into Bacterial Genome Microevolution and Niche Adaptation

    PubMed Central

    Zhou, Dongsheng; Han, Yanping; Song, Yajun; Tong, Zongzhong; Wang, Jin; Guo, Zhaobiao; Pei, Decui; Pang, Xin; Zhai, Junhui; Li, Min; Cui, Baizhong; Qi, Zhizhen; Jin, Lixia; Dai, Ruixia; Du, Zongmin; Bao, Jingyue; Zhang, Xiuqing; Yu, Jun; Wang, Jian; Huang, Peitang; Yang, Ruifu

    2004-01-01

    Genomics research provides an unprecedented opportunity for us to probe into the pathogenicity and evolution of the world's most deadly pathogenic bacterium, Yersinia pestis, in minute detail. In our present work, extensive microarray analysis in conjunction with PCR validation revealed that there are considerable genome dynamics, due to gene acquisition and loss, in natural populations of Y. pestis. We established a genomotyping system to group homologous isolates of Y. pestis, based on profiling or gene acquisition and loss in their genomes, and then drew an outline of parallel microevolution of the Y. pestis genome. The acquisition of a number of genomic islands and plasmids most likely induced Y. pestis to evolve rapidly from Yersinia pseudotuberculosis to a new, deadly pathogen. Horizontal gene acquisition also plays a key role in the dramatic evolutionary segregation of Y. pestis lineages (biovars and genomovars). In contrast to selective genome expansion by gene acquisition, genome reduction occurs in Y. pestis through the loss of DNA regions. We also theorized about the links between niche adaptation and genome microevolution. The transmission, colonization, and expansion of Y. pestis in the natural foci of endemic plague are parallel and directional and involve gradual adaptation to the complex of interactions between the environment, the hosts, and the pathogen itself. These adaptations are based on the natural selections against the accumulation of genetic changes within genome. Our data strongly support that the modern plague originated from Yunnan Province in China, due to the arising of biovar orientalis from biovar antiqua rather than mediaevalis. PMID:15262950

  15. Islands of the Arctic

    NASA Astrophysics Data System (ADS)

    Dowdeswell, Julian; Hambrey, Michael

    2002-11-01

    The Arctic islands are characterized by beautiful mountains and glaciers, in which the wildlife lives in delicate balance with its environment. It is a fragile region with a long history of exploration and exploitation that is now experiencing rapid environmental change. All of these themes are explored in Islands of the Arctic, a richly illustrated volume with superb photographs from the Canadian Arctic archipelago, Greenland, Svalbard and the Russian Arctic. It begins with the various processes shaping the landscape: glaciers, rivers and coastal processes, the role of ice in the oceans and the weather and climate. Julian Dowdeswell and Michael Hambrey describe the flora and fauna in addition to the human influences on the environment, from the sustainable approach of the Inuit, to the devastating damage inflicted by hunters and issues arising from the presence of military security installations. Finally, they consider the future prospects of the Arctic islands Julian Dowdeswell is Director of the Scott Polar Research Institute and Professor of Physical Geography at 0he University of Cambridge. He received the Polar Medal from Queen Elizabeth for his contributions to the study of glacier geophysics and the Gill Memorial Award from the Royal Geographical Society. He is chair of the Publications Committee of the International Glaciological Society and head of the Glaciers and Ice Sheets Division of the International Commission for Snow and Ice. Michael Hambrey is Director of the Centre for Glaciology at the University of Wales, Aberystwyth. A past recipient of the Polar Medal, he was also given the Earth Science Editors' Outstanding Publication Award for Glaciers (Cambridge University Press). Hambrey is also the author of Glacial Environments (British Columbia, 1994).

  16. 27 CFR 9.170 - Long Island.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ...section is “Long Island.” (b) Approved...boundary of the Long Island viticultural area are three United States Geological...Boundaries. The Long Island viticultural area includes...approximately 1,170 square miles or 749,146...

  17. 27 CFR 9.170 - Long Island.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ...section is “Long Island.” (b) Approved...boundary of the Long Island viticultural area are three United States Geological...Boundaries. The Long Island viticultural area includes...approximately 1,170 square miles or 749,146...

  18. 27 CFR 9.170 - Long Island.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ...section is “Long Island.” (b) Approved...boundary of the Long Island viticultural area are three United States Geological...Boundaries. The Long Island viticultural area includes...approximately 1,170 square miles or 749,146...

  19. 27 CFR 9.170 - Long Island.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ...section is “Long Island.” (b) Approved...boundary of the Long Island viticultural area are three United States Geological...Boundaries. The Long Island viticultural area includes...approximately 1,170 square miles or 749,146...

  20. 21 CFR 808.89 - Rhode Island.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 2014-04-01 2014-04-01 false Rhode Island. 808.89 Section 808.89 Food and Drugs...Specific State and Local Exemptions § 808.89 Rhode Island. The following Rhode Island medical device requirements are...

  1. 21 CFR 808.89 - Rhode Island.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 2010-04-01 2010-04-01 false Rhode Island. 808.89 Section 808.89 Food and Drugs...Specific State and Local Exemptions § 808.89 Rhode Island. The following Rhode Island medical device requirements are...

  2. 21 CFR 808.89 - Rhode Island.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 2012-04-01 2012-04-01 false Rhode Island. 808.89 Section 808.89 Food and Drugs...Specific State and Local Exemptions § 808.89 Rhode Island. The following Rhode Island medical device requirements are...

  3. 21 CFR 808.89 - Rhode Island.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 2011-04-01 2011-04-01 false Rhode Island. 808.89 Section 808.89 Food and Drugs...Specific State and Local Exemptions § 808.89 Rhode Island. The following Rhode Island medical device requirements are...

  4. 21 CFR 808.89 - Rhode Island.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 2013-04-01 2013-04-01 false Rhode Island. 808.89 Section 808.89 Food and Drugs...Specific State and Local Exemptions § 808.89 Rhode Island. The following Rhode Island medical device requirements are...

  5. Three Mile Island

    SciTech Connect

    Wood, M.S.; Shultz, S.M.

    1988-01-01

    This bibliography is divided into the following categories: Accident Overviews, Sequence and Causes; International Commentary and Reaction; Emergency Preparedness and Disaster Planning; Health Effects; Radioactive Releases and the Environment; Accident Investigations/Commissions; Nuclear Industry: Safety, Occupational, and Financial Issues; Media and Communications; Cleanup; Sociopolitical Response and Commentary; Restart; Legal Ramifications; Federal Documents: President's Commission on the Accident at Three Mile Island; Federal Documents: Nuclear Regulatory Commission; Federal Documents: United States Department of Energy; Federal Documents: Miscellaneous Reports; Pennsylvania State Documents; Federal and State Hearings; and Popular Literature.

  6. Three Mile Island assessments

    Microsoft Academic Search

    Daniels

    1983-01-01

    This paper describes the accident which occurred at Three Mile Island Unit Two (TMI-2) near Middletown, Pennsylvania, including the radioactivity released, consequences of off-site releases, and subsequent cleanup activities. Population dose estimates are presented from exposure to ⁸⁸Kr, ¹³³Xe, \\/sup 133m\\/Xe, ¹³⁵Xe, \\/sup 135m\\/Xe, and ¹³¹I. Based on animal studies and careful calculations, the health effects group has determined that

  7. Urban heat island

    NASA Technical Reports Server (NTRS)

    Kim, Hongsuk H.

    1991-01-01

    The phenomenon of urban heat island was investigated by the use of LANDSAT Thematic Mapper data sets collected over the metropolitan area of Washington DC (U.S.). By combining the retrieved spectral albedos and temperatures, urban modification on radiation budgets of five surface categories were analyzed. The surface radiation budget imagery of the area show that urban heating is attributable to a large heat flux from the rapidly heating surfaces of asphalt, bare soil and short grass. In summer, symptoms of diurnal heating begin to appear by mid morning and can be about 10 degrees warmer than nearby woodlands in summer.

  8. Pine Island Glacier, Antarctica

    NASA Technical Reports Server (NTRS)

    2001-01-01

    This pair of MISR images of the Pine Island Glacier in western Antarctica was acquired on December 12, 2000 during Terra orbit 5246. At left is a conventional, true-color image from the downward-looking (nadir) camera. The false-color image at right is a composite of red band data taken by the MISR forward 60-degree, nadir, and aftward 60-degree cameras, displayed in red, green, and blue colors, respectively. Color variations in the left (true-color) image highlight spectral differences. In the multi-angle composite, on the other hand, color variations act as a proxy for differences in the angular reflectance properties of the scene. In this representation, clouds show up as light purple. Blue to orange gradations on the surface indicate a transition in ice texture from smooth to rough. For example, the bright orange 'carrot-like' features are rough crevasses on the glacier's tongue. In the conventional nadir view, the blue ice labeled 'rough crevasses' and 'smooth blue ice' exhibit similar coloration, but the multi-angle composite reveals their different textures, with the smoother ice appearing dark purple instead of orange. This could be an indicator of different mechanisms by which this ice is exposed. The multi-angle view also reveals subtle roughness variations on the frozen sea ice between the glacier and the open water in Pine Island Bay.

    To the left of the 'icebergs' label are chunks of floating ice. Additionally, smaller icebergs embedded in the frozen sea ice are visible below and to the right of the label. These small icebergs are associated with dark streaks. Analysis of the illumination geometry suggests that these streaks are surface features, not shadows. Wind-driven motion and thinning of the sea ice in the vicinity of the icebergs is one possible explanation.

    Recently, Robert Bindschadler, a glaciologist at the NASA Goddard Space Flight Center discovered in Landsat 7 imagery a newly-formed crack traversing the Pine Island Glacier. This crack is visible as an off-vertical dark line in the MISR nadir view. In the multi-angle composite, the crack and other stress fractures show up very clearly in bright orange. Radar observations of Pine Island Glacier in the 1990's showed the glacier to be shrinking, and the newly discovered crack is expected to eventually lead to the calving of a major iceberg.

    MISR was built and is managed by NASA's Jet Propulsion Laboratory, Pasadena, CA, for NASA's Office of Earth Science, Washington, DC. The Terra satellite is managed by NASA's Goddard Space Flight Center, Greenbelt, MD. JPL is a division of the California Institute of Technology.

  9. Experimental Swap of Anopheles gambiae's Assortative Mating Preferences Demonstrates Key Role of X-Chromosome Divergence Island in Incipient Sympatric Speciation

    PubMed Central

    Aboagye-Antwi, Fred; Alhafez, Nahla; Weedall, Gareth D.; Brothwood, Jessica; Kandola, Sharanjit; Paton, Doug; Fofana, Abrahamane; Olohan, Lisa; Betancourth, Mauro Pazmiño; Ekechukwu, Nkiru E.; Baeshen, Rowida; Traorè, Sékou F.; Diabate, Abdoulaye; Tripet, Frédéric

    2015-01-01

    Although many theoretical models of sympatric speciation propose that genes responsible for assortative mating amongst incipient species should be associated with genomic regions protected from recombination, there are few data to support this theory. The malaria mosquito, Anopheles gambiae, is known for its sympatric cryptic species maintained by pre-mating reproductive isolation and its putative genomic islands of speciation, and is therefore an ideal model system for studying the genomic signature associated with incipient sympatric speciation. Here we selectively introgressed the island of divergence located in the pericentric region of the X chromosome of An. gambiae s.s. into its sister taxon An. coluzzii through 5 generations of backcrossing followed by two generations of crosses within the introgressed strains that resulted in An. coluzzii-like recombinant strains fixed for the M and S marker in the X chromosome island. The mating preference of recombinant strains was then tested by giving virgin recombinant individuals a choice of mates with X-islands matching and non-matching their own island type. We show through genetic analyses of transferred sperm that recombinant females consistently mated with matching island-type males thereby associating assortative mating genes with the X-island of divergence. Furthermore, full-genome sequencing confirmed that protein-coding differences between recombinant strains were limited to the experimentally swapped pericentromeric region. Finally, targeted-genome comparisons showed that a number of these unique differences were conserved in sympatric field populations, thereby revealing candidate speciation genes. The functional demonstration of a close association between speciation genes and the X-island of differentiation lends unprecedented support to island-of-speciation models of sympatric speciation facilitated by pericentric recombination suppression. PMID:25880677

  10. Gene flow-dependent genomic divergence between Anopheles gambiae M and S forms.

    PubMed

    Weetman, David; Wilding, Craig S; Steen, Keith; Pinto, João; Donnelly, Martin J

    2012-01-01

    Anopheles gambiae sensu stricto exists as two often-sympatric races termed the M and S molecular forms, characterized by fixed differences at an X-linked marker. Extreme divergence between M and S forms at pericentromeric "genomic islands" suggested that selection on variants therein could be driving interform divergence in the presence of ongoing gene flow, but recent work has detected much more widespread genomic differentiation. Whether such genomic islands are important in reproductive isolation or represent ancestral differentiation preserved by low recombination is currently unclear. A critical test of these competing hypotheses could be provided by comparing genomic divergence when rates of recent introgression vary. We genotyped 871 single nucleotide polymorphisms (SNPs) in A. gambiae sensu stricto from locations of M and S sympatry and allopatry, encompassing the full range of observed hybridization rates (0-25%). M and S forms were readily partitioned based on genomewide SNP variation in spite of evidence for ongoing introgression that qualitatively reflects hybridization rates. Yet both the level and the heterogeneity of genomic divergence varied markedly in line with levels of introgression. A few genomic regions of differentiation between M and S were common to each sampling location, the most pronounced being two centromere-proximal speciation islands identified previously but with at least one additional region outside of areas expected to exhibit reduced recombination. Our results demonstrate that extreme divergence at genomic islands does not simply represent segregating ancestral polymorphism in regions of low recombination and can be resilient to substantial gene flow. This highlights the potential for islands comprising a relatively small fraction of the genome to play an important role in early-stage speciation when reproductive isolation is limited. PMID:21836185

  11. Extreme chromosomal heterogeneity in a small-island population of Rumex acetosa.

    PubMed

    Parker, J S; Wilby, A S

    1989-02-01

    Chromosome analyses of 227 mature plants of the dioecious species Rumex acetosa collected on the small island of Skomer have revealed an extremely high level of unique and polymorphic variation. The three common polymorphisms in this species--supernumerary segments on chromosomes 1 and 6, and B-chromosomes--are widespread on the island and the frequency of supernumerary segment 1 is higher than in all 37 mainland populations previously studied. Novel variants, unknown elsewhere, occur in each polymorphism. Fourteen different chromosome rearrangements are unique to the island, and eleven of these were detected in 67 plants from a small area which had undergone a population crash in 1977. It is argued that the genome of R. acetosa is undergoing rapid reorganisation on this small island which may be associated with an enforced shift towards inbreeding in this dioecious species. PMID:2732084

  12. Reconstructing Austronesian population history in Island Southeast Asia

    PubMed Central

    Lipson, Mark; Loh, Po-Ru; Patterson, Nick; Moorjani, Priya; Ko, Ying-Chin; Stoneking, Mark; Berger, Bonnie; Reich, David

    2014-01-01

    Austronesian languages are spread across half the globe, from Easter Island to Madagascar. Evidence from linguistics and archaeology indicates that the ‘Austronesian expansion,’ which began 4,000–5,000 years ago, likely had roots in Taiwan, but the ancestry of present-day Austronesian-speaking populations remains controversial. Here, we analyse genome-wide data from 56 populations using new methods for tracing ancestral gene flow, focusing primarily on Island Southeast Asia. We show that all sampled Austronesian groups harbour ancestry that is more closely related to aboriginal Taiwanese than to any present-day mainland population. Surprisingly, western Island Southeast Asian populations have also inherited ancestry from a source nested within the variation of present-day populations speaking Austro-Asiatic languages, which have historically been nearly exclusive to the mainland. Thus, either there was once a substantial Austro-Asiatic presence in Island Southeast Asia, or Austronesian speakers migrated to and through the mainland, admixing there before continuing to western Indonesia. PMID:25137359

  13. Reconstructing Austronesian population history in Island Southeast Asia.

    PubMed

    Lipson, Mark; Loh, Po-Ru; Patterson, Nick; Moorjani, Priya; Ko, Ying-Chin; Stoneking, Mark; Berger, Bonnie; Reich, David

    2014-01-01

    Austronesian languages are spread across half the globe, from Easter Island to Madagascar. Evidence from linguistics and archaeology indicates that the 'Austronesian expansion,' which began 4,000-5,000 years ago, likely had roots in Taiwan, but the ancestry of present-day Austronesian-speaking populations remains controversial. Here, we analyse genome-wide data from 56 populations using new methods for tracing ancestral gene flow, focusing primarily on Island Southeast Asia. We show that all sampled Austronesian groups harbour ancestry that is more closely related to aboriginal Taiwanese than to any present-day mainland population. Surprisingly, western Island Southeast Asian populations have also inherited ancestry from a source nested within the variation of present-day populations speaking Austro-Asiatic languages, which have historically been nearly exclusive to the mainland. Thus, either there was once a substantial Austro-Asiatic presence in Island Southeast Asia, or Austronesian speakers migrated to and through the mainland, admixing there before continuing to western Indonesia. PMID:25137359

  14. Beyond the island: epigenetic biomarkers of colorectal and prostate cancer.

    PubMed

    Savio, Andrea J; Bapat, Bharati

    2015-01-01

    Epigenetic dysregulation is a common feature across all cancer types. Epigenetic mechanisms, from DNA methylation to histone modifications, allow for a vast number of cellular phenotypes to be created from the same genetic material. Just as certain genetic changes play a key role in tumor initiation and progression, epigenetic changes may also set the course of tumor development and be required for malignant transformation. The most frequently studied epigenetic changes investigated thus far are global genomic DNA hypomethylation along with specific hypermethylation, predominantly at promoter CpG islands of tumor suppressor genes. In addition to DNA methylation changes at CpG islands, there is an abundance of other epigenetic alterations occurring within cancer cells including DNA methylation alterations outside of CpG islands, non-CpG methylation, changes in cytosine oxidative species (hydroxymethylcytosine, formylcytosine, carboxylcytosine) levels, and histone modifications. This chapter examines epigenetic alterations beyond the island, and summarizes recent findings in DNA-based epigenetic regulation of the two most commonly diagnosed cancers in the Western world: colorectal cancer and prostate cancer. PMID:25421657

  15. GenomeFingerprinter: The Genome Fingerprint and the Universal Genome Fingerprint Analysis for Systematic Comparative Genomics

    PubMed Central

    Ai, Yuncan; Ai, Hannan; Meng, Fanmei; Zhao, Lei

    2013-01-01

    Background No attention has been paid on comparing a set of genome sequences crossing genetic components and biological categories with far divergence over large size range. We define it as the systematic comparative genomics and aim to develop the methodology. Results First, we create a method, GenomeFingerprinter, to unambiguously produce a set of three-dimensional coordinates from a sequence, followed by one three-dimensional plot and six two-dimensional trajectory projections, to illustrate the genome fingerprint of a given genome sequence. Second, we develop a set of concepts and tools, and thereby establish a method called the universal genome fingerprint analysis (UGFA). Particularly, we define the total genetic component configuration (TGCC) (including chromosome, plasmid, and phage) for describing a strain as a systematic unit, the universal genome fingerprint map (UGFM) of TGCC for differentiating strains as a universal system, and the systematic comparative genomics (SCG) for comparing a set of genomes crossing genetic components and biological categories. Third, we construct a method of quantitative analysis to compare two genomes by using the outcome dataset of genome fingerprint analysis. Specifically, we define the geometric center and its geometric mean for a given genome fingerprint map, followed by the Euclidean distance, the differentiate rate, and the weighted differentiate rate to quantitatively describe the difference between two genomes of comparison. Moreover, we demonstrate the applications through case studies on various genome sequences, giving tremendous insights into the critical issues in microbial genomics and taxonomy. Conclusions We have created a method, GenomeFingerprinter, for rapidly computing, geometrically visualizing, intuitively comparing a set of genomes at genome fingerprint level, and hence established a method called the universal genome fingerprint analysis, as well as developed a method of quantitative analysis of the outcome dataset. These have set up the methodology of systematic comparative genomics based on the genome fingerprint analysis. PMID:24205026

  16. Exploring Other Genomes: Bacteria.

    ERIC Educational Resources Information Center

    Flannery, Maura C.

    2001-01-01

    Points out the importance of genomes other than the human genome project and provides information on the identified bacterial genomes Pseudomonas aeuroginosa, Leprosy, Cholera, Meningitis, Tuberculosis, Bubonic Plague, and plant pathogens. Considers the computer's use in genome studies. (Contains 14 references.) (YDS)

  17. Highly asymmetric rice genomes

    Microsoft Academic Search

    Jing Ding; Hitoshi Araki; Qiang Wang; Pengfei Zhang; Sihai Yang; Jian-Qun Chen; Dacheng Tian

    2007-01-01

    BACKGROUND: Individuals in the same species are assumed to share the same genomic set. However, it is not unusual to find an orthologous gene only in small subset of the species, and recent genomic studies suggest that structural rearrangements are very frequent between genomes in the same species. Two recently sequenced rice genomes Oryza sativa L. var. Nipponbare and O.

  18. Genome evolution in yeasts

    Microsoft Academic Search

    Bernard Dujon; David Sherman; Gilles Fischer; Pascal Durrens; Serge Casaregola; Ingrid Lafontaine; Jacky de Montigny; Christian Marck; Cécile Neuvéglise; Emmanuel Talla; Nicolas Goffard; Lionel Frangeul; Michel Aigle; Véronique Anthouard; Anna Babour; Valérie Barbe; Stéphanie Barnay; Sylvie Blanchin; Jean-Marie Beckerich; Emmanuelle Beyne; Claudine Bleykasten; Anita Boisramé; Jeanne Boyer; Laurence Cattolico; Fabrice Confanioleri; Antoine de Daruvar; Laurence Despons; Emmanuelle Fabre; Cécile Fairhead; Hélène Ferry-Dumazet; Alexis Groppi; Florence Hantraye; Christophe Hennequin; Nicolas Jauniaux; Philippe Joyet; Rym Kachouri; Alix Kerrest; Romain Koszul; Marc Lemaire; Isabelle Lesur; Laurence Ma; Héloïse Muller; Jean-Marc Nicaud; Macha Nikolski; Sophie Oztas; Odile Ozier-Kalogeropoulos; Stefan Pellenz; Serge Potier; Guy-Franck Richard; Marie-Laure Straub; Audrey Suleau; Dominique Swennen; Fredj Tekaia; Micheline Wésolowski-Louvel; Eric Westhof; Bénédicte Wirth; Maria Zeniou-Meyer; Ivan Zivanovic; Monique Bolotin-Fukuhara; Agnès Thierry; Christiane Bouchier; Bernard Caudron; Claude Scarpelli; Claude Gaillardin; Jean Weissenbach; Patrick Wincker; Jean-Luc Souciet

    2004-01-01

    Identifying the mechanisms of eukaryotic genome evolution by comparative genomics is often complicated by the multiplicity of events that have taken place throughout the history of individual lineages, leaving only distorted and superimposed traces in the genome of each living organism. The hemiascomycete yeasts, with their compact genomes, similar lifestyle and distinct sexual and physiological properties, provide a unique opportunity

  19. Plasmodium genomics: latest milestone

    Microsoft Academic Search

    Arnab Pain; Christiane Hertz-Fowler

    2009-01-01

    Our knowledge on comparative genomics of the malaria parasites has advanced a step forward with the publication of the genomes of two primate-infecting malaria parasites: Plasmodium vivax and Plasmodium knowlesi. Even though the genomes of these organisms are the fifth and sixth Plasmodium genomes to be sequenced, respectively, both have revealed previously unknown features, which are discussed in this month's

  20. Personal Genomics, Personalized Medicine,

    E-print Network

    Napp, Nils

    Personal Genomics, Personalized Medicine, & YOU Carrie Iwema, PhD, MLS 21st May 2012 AAAS/Science Translational Medicine panel discussion; MLA 2012 #12;Timeline: Human Genome Sequence HSLS, U.Pitt 1995 2014 2000 2003 2007 2007 2010 Human Genome Draft Sequence Complete Human Reference Genome Individual Human

  1. Genome Medicine 2009, 11

    E-print Network

    Genome Medicine 2009, 11::39 Research AA kkeerrnneell--bbaasseedd iinntteeggrraattiioonn ooff of fusing more than one source of genome-wide data, such as the genome, transcriptome, proteome support in which many genome-wide data sources are combined. Integration occurs within the patient domain

  2. WIND DATA REPORT Deer Island Outfall

    E-print Network

    Massachusetts at Amherst, University of

    WIND DATA REPORT Deer Island Outfall August 18, 2003 ­ December 4, 2003 Prepared for Massachusetts........................................................................................................................ 16 TABLE OF FIGURES Figure 1 - Site location at Deer Island Outfall site. ......................

  3. Ontology for Genome Comparison and Genomic Rearrangements

    PubMed Central

    Flanagan, Keith; Stevens, Robert; Pocock, Matthew; Lee, Pete

    2004-01-01

    We present an ontology for describing genomes, genome comparisons, their evolution and biological function. This ontology will support the development of novel genome comparison algorithms and aid the community in discussing genomic evolution. It provides a framework for communication about comparative genomics, and a basis upon which further automated analysis can be built. The nomenclature defined by the ontology will foster clearer communication between biologists, and also standardize terms used by data publishers in the results of analysis programs. The overriding aim of this ontology is the facilitation of consistent annotation of genomes through computational methods, rather than human annotators. To this end, the ontology includes definitions that support computer analysis and automated transfer of annotations between genomes, rather than relying upon human mediation. PMID:18629137

  4. The Theory of Island Biogeography

    E-print Network

    Landweber, Laura

    The Theory of Island Biogeography Robert H. MacArthur and Edward O. Wilson The young biologists" dominated by the collection of data. In The Theory of Island Biogeography they set out to change that by devel- oping a general mathema- tical theory that would make sense of a key ecological problem

  5. Rethinking Easter Island's ecological catastrophe

    Microsoft Academic Search

    Terry L. Hunt

    2007-01-01

    Rapa Nui (Easter Island) has become a paragon for prehistoric human induced ecological catastrophe and cultural collapse. A popular narrative recounts an obsession for monumental statuary that led to the island's ecological devastation and the collapse of the ancient civilization. Scholars offer this story as a parable of today's global environmental problems. In this paper, I review new and emerging

  6. south georgia & the falkland islands

    E-print Network

    Bou-Zeid, Elie

    ANTARCTICA south georgia & the falkland islands Aboard the Clipper Adventurer January 13 ­ February Carcass Island Dear Princetonian © Peter Harrison is Antarctic expedition is ideally timed during into the natural wonders and historic legacy along the way. For Antarctica history buffs, birders, photographers

  7. Okhotskia: International Sakhalin Island Project

    NSDL National Science Digital Library

    This website presents the International Sakhalin Island Project (ISIP), "an international collaboration of American, Russian, and Japanese scientists to survey the plants, lichens, mosses, liverworts, fungi, insects, spiders, freshwater and terrestrial mollusks, freshwater fishes, amphibians, and reptiles of Sakhalin Island." The website was developed primarily "to provide easy access to project results and databases, both for participants and other interested scientists." Site visitors can link to the project proposal- submitted by the University of Washington, Russian Academy of Sciences, and Hokkaido University- for descriptions of project objectives, anticipated future research, references cited, and more. Links are also provided to project Results including ISIP databases, publications, and NSF reports for ISIP and the Phase One Okhotskia project: the International Kuril Island Project (IKIP). The Sakhalin Island Info page is currently under construction but will eventually feature sections on Lichens, Macrofungi, Mayflies (Ephemeroptera), and many more. The website also offers a small photo gallery with beautiful photographs from Sakhalin Island.

  8. Okhotskia: International Sakhalin Island Project

    NSDL National Science Digital Library

    This website presents the International Sakhalin Island Project (ISIP), "an international collaboration of American, Russian, and Japanese scientists to survey the plants, lichens, mosses, liverworts, fungi, insects, spiders, freshwater and terrestrial mollusks, freshwater fishes, amphibians, and reptiles of Sakhalin Island." The website was developed primarily "to provide easy access to project results and databases, both for participants and other interested scientists." Site visitors can link to the project proposal submitted by the University of Washington, Russian Academy of Sciences, and Hokkaido University for descriptions of project objectives, anticipated future research, references cited, and more. Links are also provided to project Results including ISIP databases, publications, and NSF reports for ISIP and the Phase One Okhotskia project: the International Kuril Island Project (IKIP). The Sakhalin Island Info page is currently under construction but will ev entually feature sections on Lichens, Macrofungi, Mayflies (Ephemeroptera), and many more. The website also offers a small photo gallery with beautiful photographs from Sakhalin Island.

  9. From Genomes of Species

    NSDL National Science Digital Library

    R. Brian Watts (C�©gep de la Gasp�©sie et des ��les, Gasp�©; )

    2005-12-01

    The teacher resource will help students gain an understanding of genomic research on model organisms, understand the implications of such genomic research to our knowledge of the human genome, be able to explain the potential such research has for understanding, treating, and possibly curing human genetic conditions, be able to summarize the current state of comparative genomic research, and examine the potential of proteomic research as a companion to comparative genomics.

  10. Island tameness: living on islands reduces flight initiation distance

    PubMed Central

    Cooper, William E.; Pyron, R. Alexander; Garland, Theodore

    2014-01-01

    One of Darwin's most widely known conjectures is that prey are tame on remote islands, where mammalian predators are absent. Many species appear to permit close approach on such islands, but no comparative studies have demonstrated reduced wariness quantified as flight initiation distance (FID; i.e. predator–prey distance when the prey begins to flee) in comparison with mainland relatives. We used the phylogenetic comparative method to assess influence of distance from the mainland and island area on FID of 66 lizard species. Because body size and predator approach speed affect predation risk, we included these as independent variables. Multiple regression showed that FID decreases as distance from mainland increases and is shorter in island than mainland populations. Although FID increased as area increased in some models, collinearity made it difficult to separate effects of area from distance and island occupancy. FID increases as SVL increases and approach speed increases; these effects are statistically independent of effects of distance to mainland and island occupancy. Ordinary least-squares models fit the data better than phylogenetic regressions, indicating little or no phylogenetic signal in residual FID after accounting for the independent variables. Our results demonstrate that island tameness is a real phenomenon in lizards. PMID:24403345

  11. Tracing the legacy of the early Hainan Islanders - a perspective from mitochondrial DNA

    PubMed Central

    2011-01-01

    Background Hainan Island is located around the conjunction of East Asia and Southeast Asia, and during the Last Glacial Maximum (LGM) was connected with the mainland. This provided an opportunity for the colonization of Hainan Island by modern human in the Upper Pleistocene. Whether the ancient dispersal left any footprints in the contemporary gene pool of Hainan islanders is debatable. Results We collected samples from 285 Li individuals and analyzed mitochondrial DNA (mtDNA) variations of hypervariable sequence I and II (HVS-I and II), as well as partial coding regions. By incorporating previously reported data, the phylogeny of Hainan islanders was reconstructed. We found that Hainan islanders showed a close relationship with the populations in mainland southern China, especially from Guangxi. Haplotype sharing analyses suggested that the recent gene flow from the mainland might play important roles in shaping the maternal pool of Hainan islanders. More importantly, haplogroups M12, M7e, and M7c1* might represent the genetic relics of the ancient population that populated this region; thus, 14 representative complete mtDNA genomes were further sequenced. Conclusions The detailed phylogeographic analyses of haplogroups M12, M7e, and M7c1* indicated that the early peopling of Hainan Island by modern human could be traced back to the early Holocene and/or even the late Upper Pleistocene, around 7 - 27 kya. These results correspond to both Y-chromosome and archaeological studies. PMID:21324107

  12. Genome Maps, a new generation genome browser

    PubMed Central

    Medina, Ignacio; Salavert, Francisco; Sanchez, Rubén; de Maria, Alejandro; Alonso, Roberto; Escobar, Pablo; Bleda, Marta; Dopazo, Joaquín

    2013-01-01

    Genome browsers have gained importance as more genomes and related genomic information become available. However, the increase of information brought about by new generation sequencing technologies is, at the same time, causing a subtle but continuous decrease in the efficiency of conventional genome browsers. Here, we present Genome Maps, a genome browser that implements an innovative model of data transfer and management. The program uses highly efficient technologies from the new HTML5 standard, such as scalable vector graphics, that optimize workloads at both server and client sides and ensure future scalability. Thus, data management and representation are entirely carried out by the browser, without the need of any Java Applet, Flash or other plug-in technology installation. Relevant biological data on genes, transcripts, exons, regulatory features, single-nucleotide polymorphisms, karyotype and so forth, are imported from web services and are available as tracks. In addition, several DAS servers are already included in Genome Maps. As a novelty, this web-based genome browser allows the local upload of huge genomic data files (e.g. VCF or BAM) that can be dynamically visualized in real time at the client side, thus facilitating the management of medical data affected by privacy restrictions. Finally, Genome Maps can easily be integrated in any web application by including only a few lines of code. Genome Maps is an open source collaborative initiative available in the GitHub repository (https://github.com/compbio-bigdata-viz/genome-maps). Genome Maps is available at: http://www.genomemaps.org. PMID:23748955

  13. Genome Maps, a new generation genome browser.

    PubMed

    Medina, Ignacio; Salavert, Francisco; Sanchez, Rubén; de Maria, Alejandro; Alonso, Roberto; Escobar, Pablo; Bleda, Marta; Dopazo, Joaquín

    2013-07-01

    Genome browsers have gained importance as more genomes and related genomic information become available. However, the increase of information brought about by new generation sequencing technologies is, at the same time, causing a subtle but continuous decrease in the efficiency of conventional genome browsers. Here, we present Genome Maps, a genome browser that implements an innovative model of data transfer and management. The program uses highly efficient technologies from the new HTML5 standard, such as scalable vector graphics, that optimize workloads at both server and client sides and ensure future scalability. Thus, data management and representation are entirely carried out by the browser, without the need of any Java Applet, Flash or other plug-in technology installation. Relevant biological data on genes, transcripts, exons, regulatory features, single-nucleotide polymorphisms, karyotype and so forth, are imported from web services and are available as tracks. In addition, several DAS servers are already included in Genome Maps. As a novelty, this web-based genome browser allows the local upload of huge genomic data files (e.g. VCF or BAM) that can be dynamically visualized in real time at the client side, thus facilitating the management of medical data affected by privacy restrictions. Finally, Genome Maps can easily be integrated in any web application by including only a few lines of code. Genome Maps is an open source collaborative initiative available in the GitHub repository (https://github.com/compbio-bigdata-viz/genome-maps). Genome Maps is available at: http://www.genomemaps.org. PMID:23748955

  14. Comparative Analysis of the First Complete Enterococcus faecium Genome

    PubMed Central

    Lam, Margaret M. C.; Seemann, Torsten; Bulach, Dieter M.; Gladman, Simon L.; Chen, Honglei; Haring, Volker; Moore, Robert J.; Ballard, Susan; Grayson, M. Lindsay; Johnson, Paul D. R.; Howden, Benjamin P.

    2012-01-01

    Vancomycin-resistant enterococci (VRE) are one of the leading causes of nosocomial infections in health care facilities around the globe. In particular, infections caused by vancomycin-resistant Enterococcus faecium are becoming increasingly common. Comparative and functional genomic studies of E. faecium isolates have so far been limited owing to the lack of a fully assembled E. faecium genome sequence. Here we address this issue and report the complete 3.0-Mb genome sequence of the multilocus sequence type 17 vancomycin-resistant Enterococcus faecium strain Aus0004, isolated from the bloodstream of a patient in Melbourne, Australia, in 1998. The genome comprises a 2.9-Mb circular chromosome and three circular plasmids. The chromosome harbors putative E. faecium virulence factors such as enterococcal surface protein, hemolysin, and collagen-binding adhesin. Aus0004 has a very large accessory genome (38%) that includes three prophage and two genomic islands absent among 22 other E. faecium genomes. One of the prophage was present as inverted 50-kb repeats that appear to have facilitated a 683-kb chromosomal inversion across the replication terminus, resulting in a striking replichore imbalance. Other distinctive features include 76 insertion sequence elements and a single chromosomal copy of Tn1549 containing the vanB vancomycin resistance element. A complete E. faecium genome will be a useful resource to assist our understanding of this emerging nosocomial pathogen. PMID:22366422

  15. CpG islands and the regulation of transcription

    PubMed Central

    Deaton, Aimée M.; Bird, Adrian

    2011-01-01

    Vertebrate CpG islands (CGIs) are short interspersed DNA sequences that deviate significantly from the average genomic pattern by being GC-rich, CpG-rich, and predominantly nonmethylated. Most, perhaps all, CGIs are sites of transcription initiation, including thousands that are remote from currently annotated promoters. Shared DNA sequence features adapt CGIs for promoter function by destabilizing nucleosomes and attracting proteins that create a transcriptionally permissive chromatin state. Silencing of CGI promoters is achieved through dense CpG methylation or polycomb recruitment, again using their distinctive DNA sequence composition. CGIs are therefore generically equipped to influence local chromatin structure and simplify regulation of gene activity. PMID:21576262

  16. West Nile virus in the British Virgin Islands.

    PubMed

    Anthony, S J; Garner, M M; Palminteri, L; Navarrete-Macias, I; Sanchez-Leon, M D; Briese, T; Daszak, P; Lipkin, W I

    2014-06-01

    West Nile virus (WNV) first emerged in the US in 1999 and has since spread across the Americas. Here, we report the continued expansion of WNV to the British Virgin Islands following its emergence in a flock of free-roaming flamingos. Histologic review of a single chick revealed lesions consistent with WNV infection, subsequently confirmed with PCR, immunohistochemistry and in situ hybridization. Full genome analysis revealed 99% sequence homology to strains circulating in the US over the past decade. This study highlights the need for rapid necropsy of wild bird carcasses to fully understand the impact of WNV on wild populations. PMID:24504904

  17. SRTM Anaglyph: Fiji Islands

    NASA Technical Reports Server (NTRS)

    2000-01-01

    The Sovereign Democratic Republic of the Fiji Islands, commonly known as Fiji, is an independent nation consisting of some 332 islands surrounding the Koro Sea in the South Pacific Ocean. This topographic image shows Viti Levu, the largest island in the group. With an area of 10,429 square kilometers (about 4000 square miles), it comprises more than half the area of the Fiji Islands. Suva, the capital city, lies on the southeast shore. The Nakauvadra, the rugged mountain range running from north to south, has several peaks rising above 900 meters (about 3000 feet). Mount Tomanivi, in the upper center, is the highest peak at 1324 meters (4341 feet). The distinct circular feature on the north shore is the Tavua Caldera, the remnant of a large shield volcano that was active about 4 million years ago. Gold has been mined on the margin of the caldera since the 1930s. The Nadrau plateau is the low relief highland in the center of the mountain range. The coastal plains in the west, northwest and southeast account for only 15 percent of Viti Levu's area but are the main centers of agriculture and settlement.

    This shaded relief anaglyph image was generated using preliminary topographic data from the Shuttle Radar Topography Mission. A computer-generated artificial light source illuminates the elevation data from the top (north) to produce a pattern of light and shadows. Slopes facing the light appear bright, while those facing away are shaded. The stereoscopic effect was created by first draping the shaded relief image back over the topographic data and then generating two differing perspectives, one for each eye. When viewed through special glasses, the result is a vertically exaggerated view of the Earth's surface in its full three dimensions. Anaglyph glasses cover the left eye with a red filter and cover the right eye with a blue filter.

    This image was acquired by SRTM aboard the Space Shuttle Endeavour, launched on February 11, 2000. SRTM used the same radar instrument that comprised the Spaceborne Imaging Radar-C/X-Band Synthetic Aperture Radar (SIR-C/X-SAR) that flew twice on the Space Shuttle Endeavour in 1994. SRTM was designed to collect three-dimensional measurements of the Earth's surface. To collect the 3-D data, engineers added a 60-meter-long (about 200 feet) mast, installed additional C-band and X-band antennas, and improved tracking and navigation devices. The mission is a cooperative project between the National Aeronautics and Space Administration (NASA), the National Imagery and Mapping Agency (NIMA) of the U.S. Department of Defense (DoD), and the German and Italian space agencies. It is managed by NASA's Jet Propulsion Laboratory, Pasadena, CA, for NASA's Earth Science Enterprise, Washington, DC.

    Size: 192 km (119 miles) x 142 km (88 miles) Location: 17.8 deg. South lat., 178.0 deg. East lon. Orientation: North at top Date Acquired: February 19, 2000 Image: NASA/JPL/NIMA

  18. Global Collembola on Deception Island

    PubMed Central

    Greenslade, Penelope; Potapov, Mikhail; Russell, David; Convey, Peter

    2012-01-01

    Three new non-indigenous springtail species are recorded in recent collections made on Deception Island, South Shetland Islands, maritime Antarctic: Deuteraphorura (Deuteraphorura) cebennaria (Gisin) (Collembola: Onychiuridae), Mesaphorura macrochaeta Rusek (Tullbergiidae), and Proisotoma minuta Axelson (Isotomidae). One of these, D. (D.) cebennaria, is described. Additionally, two new indigenous species, Mesaphorura macrochaeta Rusek and Proisotoma minuta Axelson, are also recorded. The total number of Collembola species now known from the island is 14, comprised of eight native species and six non-indigenous species. This number of non-indigenous species recorded at Deception Island compares with only a single non-indigenous springtail recorded at any other maritime or continental Antarctic location. The reason underlying this high level of occurrence of non-indigenous species on Deception Island is likely to be a combination of the island's high level of human visitation and the presence of relatively benign terrestrial habitats associated with areas of geothermal activity. Two of the new records represent species recently assessed as being of the highest risk to become invaders in the less extreme environments of the subantarctic, thereby emphasising the importance and urgency of adopting and applying effective biosecurity measures to protect the unique and vulnerable ecosystems of this region. Also documented are the impacts on the soil fauna of the island from human trampling, which drastically reduced densities of both native and non-indigenous species to 1% of the abundance typical of non-trampled sites. PMID:23438196

  19. Genomic Encyclopedia of Fungi

    SciTech Connect

    Grigoriev, Igor

    2012-08-10

    Genomes of fungi relevant to energy and environment are in focus of the Fungal Genomic Program at the US Department of Energy Joint Genome Institute (JGI). Its key project, the Genomics Encyclopedia of Fungi, targets fungi related to plant health (symbionts, pathogens, and biocontrol agents) and biorefinery processes (cellulose degradation, sugar fermentation, industrial hosts), and explores fungal diversity by means of genome sequencing and analysis. Over 150 fungal genomes have been sequenced by JGI to date and released through MycoCosm (www.jgi.doe.gov/fungi), a fungal web-portal, which integrates sequence and functional data with genome analysis tools for user community. Sequence analysis supported by functional genomics leads to developing parts list for complex systems ranging from ecosystems of biofuel crops to biorefineries. Recent examples of such parts suggested by comparative genomics and functional analysis in these areas are presented here.

  20. JGI Fungal Genomics Program

    SciTech Connect

    Grigoriev, Igor V.

    2011-03-14

    Genomes of energy and environment fungi are in focus of the Fungal Genomic Program at the US Department of Energy Joint Genome Institute (JGI). Its key project, the Genomics Encyclopedia of Fungi, targets fungi related to plant health (symbionts, pathogens, and biocontrol agents) and biorefinery processes (cellulose degradation, sugar fermentation, industrial hosts), and explores fungal diversity by means of genome sequencing and analysis. Over 50 fungal genomes have been sequenced by JGI to date and released through MycoCosm (www.jgi.doe.gov/fungi), a fungal web-portal, which integrates sequence and functional data with genome analysis tools for user community. Sequence analysis supported by functional genomics leads to developing parts list for complex systems ranging from ecosystems of biofuel crops to biorefineries. Recent examples of such 'parts' suggested by comparative genomics and functional analysis in these areas are presented here

  1. Strategies for genome reduction in microbial genomes.

    PubMed

    Sakharkar, Kishore R; Chow, Vincent T K

    2005-01-01

    Niche dependent differential gene loss and overlapping genes have been proposed as means of achieving genome reduction by retaining indispensable genes and compressing maximum amount of information in available sequence space. Herein, we analyzed the differential gene loss and overlapping genes in bacterial genomes with different lifestyles. Our results clearly suggest that gene loss and overlapping genes could be a result of evolutionary pressure to minimize genome size. Comparative analysis of the genomes shows that the genomes display marked similarities in patterns of protein length and frequency. It is clear from our analysis that habitat is a major factor contributing to genome reduction. These comparisons increase our knowledge of the forces that drive the extreme specialization of the bacteria and its association to the host. PMID:16901090

  2. Clean Waters of Rhode Island Primary Investigators

    E-print Network

    Rhode Island, University of

    Clean Waters of Rhode Island Primary Investigators Harold Knickle Donald Gray #12;Final Report Clean Waters of Rhode Island By Harold Knickle and Donald Gray Department of Chemical Engineering University of Rhode Island Kingston, Rhode Island 02881 May 2007 #12;Abstract There were two thrusts

  3. Origin of barrier islands on sandy coasts

    Microsoft Academic Search

    1990-01-01

    Many barrier islands on the coasts of the Gulf of Mexico contain one or more nuclei; island growth has taken place more or less seaward from these nuclei, which are the oldest parts of the islands. The nuclei were, at one time, separate islands; the oldest beach ridges wrap around them on two or three sides, showing that they were

  4. Integrating sequence, evolution and functional genomics in regulatory genomics

    PubMed Central

    Vingron, Martin; Brazma, Alvis; Coulson, Richard; van Helden, Jacques; Manke, Thomas; Palin, Kimmo; Sand, Olivier; Ukkonen, Esko

    2009-01-01

    With genome analysis expanding from the study of genes to the study of gene regulation, 'regulatory genomics' utilizes sequence information, evolution and functional genomics measurements to unravel how regulatory information is encoded in the genome. PMID:19226437

  5. What is a genome?

    PubMed

    Stencel, A; Crespi, B

    2013-07-01

    The field of genomics is expanding rapidly, yet the meanings of the word ‘genome’ have yet to be conceptualized in explicit, coherent and useful frameworks. We develop and apply an evolutionary conceptualization of the genome,which represents a logical extension of the evolutionary definition of a gene developed by George C.Williams. An evolutionary genome thus represents a set of genetic material, in a lineage, that due to common interests tends to favour the same or similar phenotypes.This conceptualization provides novel perspectives on genome functions, boundaries and evolution, which should help to guide theoretical and empirical genomics research. PMID:23967454

  6. Recognition of CpG Island Chromatin by KDM2A Requires Direct and Specific Interaction with Linker DNA

    PubMed Central

    Zhou, Jin C.; Blackledge, Neil P.; Farcas, Anca M.

    2012-01-01

    Up to 70% of human genes are associated with regions of nonmethylated DNA called CpG islands (S. Saxonov, P. Berg, and D. L. Brutlag, Proc. Natl. Acad. Sci. U. S. A. 103:1412–1417, 2006). Usually associated with the 5? end of genes, CpG islands are thought to impact gene expression. We previously demonstrated that the histone demethylase KDM2A is specifically recruited to CpG islands to define a unique chromatin architecture and highlight gene regulatory regions in large and complex mammalian genomes. This targeting relies on a zinc finger CXXC DNA binding domain (ZF-CXXC), but how this demethylase interfaces with CpG island chromatin in vivo remains unknown. Here we demonstrate, using defined chromatin templates in vitro and chromatin profiling in vivo, that nucleosomes are a major barrier to KDM2A binding and that CpG islands are directly interpreted by the ZF-CXXC domain through specific interaction with linker DNA. Furthermore, KDM2A appears to be constrained to CpG islands not only by their nonmethylated state but also by a combination of methylated DNA and nucleosome occlusion elsewhere in the genome. Our observations suggest that both DNA sequence and chromatin structure are defining factors in interpreting CpG island chromatin and translation of the CpG signal. More generally, these features of CpG island recognition suggest that chromatin structure and accessibility play a major role in defining how transcription factors recognize DNA and regulatory elements genome-wide. PMID:22083960

  7. The Three Mile Island Disaster.

    ERIC Educational Resources Information Center

    Crosby, Emeral

    1980-01-01

    For the past decade, education has been experiencing meltdown, explosions, radiation leaks, heat pollution, and management crises, just like the Three Mile Island disaster. This article offers suggestions on how to deal with these problems. (Author/LD)

  8. Vanishing Island: Sea Level Rise

    NSDL National Science Digital Library

    Massy Halbert

    This video features interviews with native people living on atoll islands in Micronesia, so viewers are able to understand the real, current threats that these people are facing due to climate change.

  9. Wild Ponies on Assateague Island

    USGS Multimedia Gallery

    Wild ponies on Assateague Island. Wild ponies have lived on Assateague since the 1600s, although how they were introduced to Assateague is still debated. There are now around 300 or so wild ponies in Maryland and Virginia....

  10. Synthesizing knowledge of ocean islands

    NASA Astrophysics Data System (ADS)

    Jefferson, Anne J.; Lees, Jonathan M.; McClinton, Tim

    2011-11-01

    AGU Chapman Conference on the Galápagos as a Laboratory for the Earth Sciences; Puerto Ayora, Galápagos, Ecuador, 25-30 July 2011 An inspiration for Darwin's theory of evolution, the Galápagos Islands and surrounding waters are a natural laboratory for a wide range of Earth science topics. The Galápagos are perfectly situated for geophysical and geochemical investigations of deep-Earth processes at a hot spot, and proximity to a spreading center allows exploration of hot spot-ridge interactions. Several highly active volcanoes show rapid deformation facilitating investigation of melt transport paths and volcanic structure. The islands exhibit a range of ages, eruptive styles, and climatic zones that allow analysis of hydrogeologic and geomorphic processes. The Galápagos Islands are a World Heritage Site and are an ideal setting for developing an integrated biological and geological understanding of ocean island evolution.

  11. Genome Instability in Lactobacillus rhamnosus GG

    PubMed Central

    Molenaar, Douwe; van IJcken, Wilfred; Venema, Koen

    2013-01-01

    We describe here a comparative genome analysis of three dairy product isolates of Lactobacillus rhamnosus GG (LGG) and the ATCC 53103 reference strain to the published genome sequence of L. rhamnosus GG. The analysis showed that in two of three isolates, major DNA segments were missing from the genomic islands LGGISL1,2. The deleted DNA segments consist of 34 genes in one isolate and 84 genes in the other and are flanked by identical insertion elements. Among the missing genes are the spaCBA genes, which encode pilin subunits involved in adhesion to mucus and persistence of the strains in the human intestinal tract. Subsequent quantitative PCR analyses of six commercial probiotic products confirmed that two more products contain a heterogeneous population of L. rhamnosus GG variants, including genotypes with or without spaC. These results underline the relevance for quality assurance and control measures targeting genome stability in probiotic strains and justify research assessing the effect of genetic rearrangements in probiotics on the outcome of in vitro and in vivo efficacy studies. PMID:23354703

  12. Upolu Island, Western Samoa

    NASA Technical Reports Server (NTRS)

    2000-01-01

    Island nations in the South Pacific Ocean experience natural disasters associated with typhoons, and with their proximity to the Pacific Ocean's 'Ring of Fire.' This radar image shows the western end of the island of Upolu in the nation of Western Samoa. Disaster managers use digital elevation models (DEMs) generated from radar data to assist in research toward disaster mitigation and management. Geologists also use DEM data of volcanic features, such as the circular craters in this image, to study eruption rates and volumes, and volcanic landform evolution.

    Black areas near the top of the image are areas where steep topography causes holes in the data; these holes can be filled in by collecting data at other look directions. Color represents topography and intensity represents across-section of the radar backscatter. Since rough areas return more of the incident signal, they appear brighter on the image than relatively smooth areas, such as the ocean surface at the top of the image.

    This image was acquired by the AIRborne Synthetic Aperture (AIRSAR) radar instrument aboard a DC-8 aircraft operated out of NASA's Dryden Flight Research Center. AIRSAR collects fully polarimetric data at three wavelengths; C-band (0.057 meter), L-band (0.25 meter) and P-band (0.68 meter). AIRSAR also collects cross-track and along track interferometric data that results in topographic measurements and motion detection, respectively.

    This image was collected during the Pacific Rim mission, a three-month mission from July to October 2000 that collected data at over 200 sites in eighteen countries and territories around the Pacific Rim. AIRSAR is managed by NASA's Jet Propulsion Laboratory, Pasadena, CA, for NASA's Earth Science Enterprise,Washington, D.C.

    Size: 10 km (6.2 miles) x 10 km (6.2 miles) Location: 14.02 deg. North lat., 171.52 deg. West Orientation: North at top Date Acquired: August 10, 2000

  13. Upolu Island, Western Samoa

    NASA Technical Reports Server (NTRS)

    2000-01-01

    Island nations in the South Pacific Ocean experience natural disasters associated with typhoons, and with their proximity to the Pacific Ocean's 'Ring of Fire.' This radar image shows most of the northern coast of the island of Upolu in the nation of Western Samoa. Disaster managers use digital elevation models (DEMs) generated from radar data to assist in research toward disaster mitigation and management. Geologists also use DEM data of volcanic features, such as the line of circular craters in this image, to study eruption rates and volumes, and volcanic landform evolution. The capital of Western Samoa, Apia, is in the lower left of the image.

    Angular black areas in the image are areas where steep topography causes holes in the data; these holes can be filled in by collecting data at other look directions. Color represents topography and intensity represents across-section of the radar backscatter. Since rough areas return more of the incident signal, they appear brighter on the image than relatively smooth areas, such as the ocean surface , along the left side of the image.

    This image was acquired by the AIRborne Synthetic Aperture (AIRSAR) radar instrument aboard a DC-8 aircraft operated out of NASA's Dryden Flight Research Center. AIRSAR collects fully polarimetric data at three wavelengths; C-band (0.057 meter), L-band (0.25 meter) and P-band (0.68 meter). AIRSAR also collects cross-track and along track interferometric data that results in topographic measurements and motion detection, respectively.

    This image was collected during the Pacific Rim mission, a three-month mission from July to October 2000 that collected data at over 200 sites in eighteen countries and territories around the Pacific Rim. AIRSAR is managed by NASA's Jet Propulsion Laboratory, Pasadena, CA, for NASA's Earth Science Enterprise,Washington, D.C.

    Size: 10 km (6.2 miles) x 63 km (37.3 miles) Location: 14.16 deg. North lat., 171.75 deg. West Orientation: North towards the left side of image Date Acquired: August 10, 2000

  14. Genomic Careers: Interactive Videos

    MedlinePLUS

    ... Institute in Bethesda, Maryland. 06:55 - Bioethicist Using Genomics - Dr. Carlton Haywood Jr. Bioethicist at the Johns ... Health in Bethesda, Maryland. 06:08 - Bioethicist Using Genomics - Dr. Ruth Faden Director of the Berman Institute ...

  15. GENOMICS AND ENVIRONMENTAL RESEARCH

    EPA Science Inventory

    The impact of recently developed and emerging genomics technologies on environmental sciences has significant implications for human and ecological risk assessment issues. The linkage of data generated from genomics, transcriptomics, proteomics, metabalomics, and ecology can be ...

  16. Human Genome Center

    NSDL National Science Digital Library

    Human Genome Center At Lawrence Berkeley Lab (LBL), Berkeley, California: offering information about projects in Biology, Informatics and Instrumentation, photos of LBL robotic instruments, software, and online access to one LBL genomic database.

  17. Cancer Genomics Overview

    Cancer.gov

    Genomic information about cancer is leading to better diagnoses and treatment strategies that are tailored to patients’ tumors. Precision medicine is the application of genomic insights to a therapeutic approach adapted specifically for each patient.

  18. Comparative genomic workflow

    E-print Network

    Rajapakse, Jagath

    his article describes a workflow for identifying conserved patterns in noncoding regions of vertebrate genomes, with an intention of investigating possible functions of the conserved regions. The annotations of genomes are ...

  19. Comparative genomics of Helicobacter pylori isolates recovered from ulcer disease patients in England

    Microsoft Academic Search

    Farhana Kauser; M Abid Hussain; Irshad Ahmed; Sriramula Srinivas; S Manjulata Devi; Ahmed A Majeed; K Rajender Rao; Aleem A Khan; Leonardo A Sechi; Niyaz Ahmed

    2005-01-01

    BACKGROUND: Genomic diversity of H. pylori from many different human populations is largely unknown. We compared genomes of 65 H. pylori strains from Nottingham, England. Molecular analysis was carried out to identify rearrangements within and outside the cag-pathogenicity-island (cag PAI) and DNA sequence divergence in candidate genes. Phylogenetic analysis was carried out based on various high-resolution genotyping techniques. RESULTS: Analyses

  20. Complete genome sequence of the plant commensal Pseudomonas fluorescens Pf5

    Microsoft Academic Search

    Jacques Ravel; Donald Y Kobayashi; Garry S A Myers; Dmitri V Mavrodi; Robert T DeBoy; Rekha Seshadri; Qinghu Ren; Ramana Madupu; Robert J Dodson; A Scott Durkin; Lauren M Brinkac; Sean C Daugherty; Stephen A Sullivan; Mary J Rosovitz; Michelle L Gwinn; Liwei Zhou; Davd J Schneider; Samuel W Cartinhour; William C Nelson; Janice Weidman; Kisha Watkins; Kevin Tran; Hoda Khouri; Elizabeth A Pierson; Leland S Pierson; Linda S Thomashow; Ian T Paulsen; Joyce E Loper

    2005-01-01

    Pseudomonas fluorescens Pf-5 is a plant commensal bacterium that inhabits the rhizosphere and produces secondary metabolites that suppress soilborne plant pathogens. The complete sequence of the 7.1-Mb Pf-5 genome was determined. We analyzed repeat sequences to identify genomic islands that, together with other approaches, suggested P. fluorescens Pf-5's recent lateral acquisitions include six secondary metabolite gene clusters, seven phage regions

  1. Major Structural Differences and Novel Potential Virulence Mechanisms from the Genomes of Multiple Campylobacter Species

    Microsoft Academic Search

    Derrick E. Fouts; Emmanuel F. Mongodin; Robert E. Mandrell; William G. Miller; David A. Rasko; Jacques Ravel; Lauren M. Brinkac; Robert T. DeBoy; Craig T. Parker; Sean C. Daugherty; Robert J. Dodson; A. Scott Durkin; Ramana Madupu; Steven A. Sullivan; Jyoti U. Shetty; Mobolanle A. Ayodeji; Alla Shvartsbeyn; Michael C. Schatz; Jonathan H. Badger; Claire M. Fraser; Karen E. Nelson

    2005-01-01

    Sequencing and comparative genome analysis of four strains of Campylobacter including C. lari RM2100, C. upsaliensis RM3195, and C. coli RM2228 has revealed major structural differences that are associated with the insertion of phage- and plasmid-like genomic islands, as well as major variations in the lipooligosaccharide complex. Poly G tracts are longer, are greater in number, and show greater variability

  2. A hybrid neural network system for prediction and recognition of promoter regions in human genome

    Microsoft Academic Search

    CHEN Chuan-bo

    2005-01-01

    This paper proposes a high specificity and sensitivity algorithm called PromPredictor for recognizing promoter re- gions in the human genome. PromPredictor extracts compositional features and CpG islands information from genomic sequence, feeding these features as input for a hybrid neural network system (HNN) and then applies the HNN for prediction. It combines a novel promoter recognition model, coding theory, feature

  3. SOUTHERN SEASCRUISE IN LUXURY ABOARD CRYSTAL SYMPHONY Easter Island | Pitcairn Island | Moora | Tahiti

    E-print Network

    Liu, Taosheng

    SOUTHERN SEASCRUISE IN LUXURY ABOARD CRYSTAL SYMPHONY Easter Island | Pitcairn Island | Mooréa ethnologist, 1859-1920, "Easter Island," 1912 "Tahiti is lovely; the climate is perfect... The world actually

  4. 76 FR 19781 - Protection Island and San Juan Islands National Wildlife Refuges, Jefferson, San Juan, Skagit...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-04-08

    ...Service [FWS-R1-R-2010-N222; 10137-1265-0000 S3] Protection Island and San Juan Islands National Wildlife Refuges, Jefferson, San Juan, Skagit, Island, and Whatcom Counties, WA; Final Comprehensive Conservation Plan,...

  5. 78 FR 63860 - Amendment of Class D Airspace; Kwajalein Island, Marshall Islands, RMI

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-10-25

    ...2120-AA66 Amendment of Class D Airspace; Kwajalein Island, Marshall Islands, RMI AGENCY: Federal Aviation Administration (FAA...SUMMARY: This action amends the Kwajalein Island Class D airspace description by amending the...

  6. Structural genomics: beyond the Human Genome Project

    Microsoft Academic Search

    Stephen K Burley; Steven C Almo; Jeffrey B Bonanno; Malcolm Capel; Mark R Chance; Terry Gaasterland; Dawei Lin; Andrej Šali; F. William Studier; Subramanyam Swaminathan

    1999-01-01

    With access to whole genome sequences for various organisms and imminent completion of the Human Genome Project, the entire process of discovery in molecular and cellular biology is poised to change. Massively parallel measurement strategies promise to revolutionize how we study and ultimately understand the complex biochemical circuitry responsible for controlling normal development, physiologic homeostasis and disease processes. This information

  7. Genome Data Analysis Centers

    Cancer.gov

    The use of novel technologies, the need to integrate different data types and the immense quantity of data generated by The Cancer Genome Atlas (TCGA) Research Network has led to an expansion of the TCGA Research Network to include new centers devoted to data analysis. The Genome Data Analysis Centers (GDACs) work hand-in-hand with the Genome Characterization Centers (GCCs) to develop state-of-the-art tools that assist researchers with processing and integrating data analyses across the entire genome.

  8. Exploiting the genome

    SciTech Connect

    Block, S.; Cornwall, J.; Dyson, F.; Koonin, S.; Lewis, N.; Schwitters, R.

    1998-09-11

    In 1997, JASON conducted a DOE-sponsored study of the human genome project with special emphasis on the areas of technology, quality assurance and quality control, and informatics. The present study has two aims: first, to update the 1997 Report in light of recent developments in genome sequencing technology, and second, to consider possible roles for the DOE in the ''post-genomic" era, following acquisition of the complete human genome sequence.

  9. UCSC genome browser tutorial

    Microsoft Academic Search

    Ann S. Zweig; Donna Karolchik; Robert M. Kuhn; David Haussler; W. James Kent

    2008-01-01

    The University of California Santa Cruz (UCSC) Genome Bioinformatics website consists of a suite of free, open-source, on-line tools that can be used to browse, analyze, and query genomic data. These tools are available to anyone who has an Internet browser and an interest in genomics. The website provides a quick and easy-to-use visual display of genomic data. It places

  10. Three Mile Island revisited

    SciTech Connect

    Lipford, B.L.; Cole, N.M.; Friderichs, T.J. (MPR Associates Inc., Washington, DC (US))

    1991-01-01

    As a result of the accident in March 1979, the Three Mile Island Unit 2 (TMI-2) reactor vessel sustained significant internal damage. Approximately half of the reactor core suffered some degree of melting, with 10 to 20 tons of molten core material relocating inside the vessel and flowing down onto the reactor vessel's lower head. The resulting damage and the margin to failure of the lower head are of interest to the nuclear industry. In early 1988 the owner and operator of the TMI facility, had completed a large portion of the defueling work in the reactor core region and was preparing to remove the lower structural internals in order to defuel the area within the lower head. At that point the U.S. Nuclear Regulatory Commission's Office of Nuclear Regulatory Research (NRC-Res) in Washington, D.C., initiated a project to remove metallurgical specimens from the reactor vessel's lower head region. The goal was to determine the extent of damage to the pressure-retaining boundary in the lower head and to learn what happened during the accident.

  11. Genomic organization of the neurofibromatosis 1 gene ( NF1)

    Microsoft Academic Search

    Ying Li; Peter O'connell; Heidi Huntsman Breidenbach; Richard Cawthon; Jeff Stevens; Gangfeng Xu; Shannon Neil; Margaret Robertson; Ray White; David Viskochil

    1995-01-01

    Neurofibromatosis 1 maps to chromosome band 17q11.2, and the NF1 locus has been partially characterized. Even though the full-length NF1 cDNA has been sequenced, the complete genomic structure of the NF1 gene has not been elucidated. The 5? end of NF1 is embedded in a CpG island containing a NotI restriction site, and the remainder of the gene lies in

  12. Insights on antibiotic resistance of Staphylococcus aureus from its whole genome: genomic island SCC

    Microsoft Academic Search

    Teruyo Ito; Keiko Okuma; Xiao Xue Ma; Harumi Yuzawa; Keiichi Hiramatsu

    2003-01-01

    Staphylococci are ubiquitous colonizers of the skin and mucous membranes and Staphylococus aureus is the most pathogenic species. The spread of antibiotic resistance among S. aureus strains is a major concern in the treatment of staphylococcal infections. Acquisition of resistance may involve mutation of a bacterial gene on the chromosome or transfer of a resistance gene from other organisms by

  13. Mitochondrial-DNA sequence variation, and the genetic affinity of Peromyscus from the Triangle Island, British Columbia, Canada 

    E-print Network

    Arianpour, Roozbeh

    2013-02-22

    To determine the genetic and specific affinity of deer mice (Peromyscus) inhabiting Triangle Island, British Colombia, Canada, a 1,439 base-pair (bp) fragment of the mitochondrial genome (containing the ND3, ND4L, and a portion of the ND4 genes...

  14. Mutations in Salmonella Pathogenicity Island 2 (SPI2) Genes Affecting Transcription of SPI1 Genes and Resistance to Antimicrobial Agents

    Microsoft Academic Search

    JORG DEIWICK; THOMAS NIKOLAUS; JAQUELINE E. SHEA; COLIN GLEESON; DAVID W. HOLDEN; MICHAEL HENSEL

    1998-01-01

    The Salmonella typhimurium genome contains two pathogenicity islands (SPI) with genes encoding type III secretion systems for virulence proteins. SPI1 is required for the penetration of the epithelial layer of the intestine. SPI2 is important for the subsequent proliferation of bacteria in the spleens of infected hosts. Although most mutations in SPI2 lead to a strong reduction of virulence, they

  15. Mitochondrial-DNA sequence variation, and the genetic affinity of Peromyscus from the Triangle Island, British Columbia, Canada

    E-print Network

    Arianpour, Roozbeh

    2013-02-22

    To determine the genetic and specific affinity of deer mice (Peromyscus) inhabiting Triangle Island, British Colombia, Canada, a 1,439 base-pair (bp) fragment of the mitochondrial genome (containing the ND3, ND4L, and a portion of the ND4 genes...

  16. Bird predation by domestic cats on Hahajima Island, Bonin Islands, Japan

    Microsoft Academic Search

    Kazuto Kawakami; Hiroyoshi Higuchi

    \\u000a The Bonin Islands are oceanic islands situated in the northwest Pacific Ocean 1,000 km south of the Japanese main island of\\u000a Honshu. These islands lacked terrestrial mammalian carnivores until human colonization in 1830. Early immigrants introduced\\u000a domestic cats Felis earns to the islands, some of which escaped from the island's residential area. Even by 1877 there were already reports of

  17. Evolutionary genomics of Entamoeba

    Microsoft Academic Search

    Gareth D. Weedall; Neil Hall

    2011-01-01

    Entamoeba histolytica is a human pathogen that causes amoebic dysentery and leads to significant morbidity and mortality worldwide. Understanding the genome and evolution of the parasite will help explain how, when and why it causes disease. Here we review current knowledge about the evolutionary genomics of Entamoeba: how differences between the genomes of different species may help explain different phenotypes,

  18. Genomics & Medicine Doug Brutlag

    E-print Network

    Brutlag, Doug

    Genomics & Medicine Doug Brutlag Department of Biochemistry & BioMedical Informatics (by courtesyProtein PhenotypePhenotype (Symptoms)(Symptoms) DNADNA #12;Central Paradigm of Medicine DNADNA RNARNA Protein, Bioinformatics & Medicine BioinformaticsBioinformaticsGenomicsGenomics Identify Drug TargetsIdentify Drug Targets

  19. INTRODUCTION TO GENOMIC MEDICINE

    E-print Network

    INTRODUCTION TO GENOMIC MEDICINE Genomics play a role in 21st century research and clinical practice and Washington University School of Medicine is at the forefront of this evolving field related to genomic medicine. Tentative Schedule: WHEN: WHERE: WHO CAN ATTEND? INTRODUCTION January 31

  20. LEGUME COMPARATIVE GENOMICS

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Comparisons among increasing numbers of plant genome sequences are uncovering features that seem likely to hold for most, if not all, higher plant genomes. Gene collinearity (synteny) is frequently conserved across long genomic regions and very long times, with limited synteny evident even between s...

  1. Introduction into Plant Genomics

    Microsoft Academic Search

    A. V. Zelenin; E. D. Badaeva; O. V. Muravenko

    2001-01-01

    The success in complete sequencing of “small” genomes and development of new technologies that markedly speed up the cloning and sequencing processes open the way to intense development of plant genomics and complete sequencing of DNA of some species. It is assumed that success in plant genomics will result in revolutionary changes in biotechnology and plant breeding. However, the enormous

  2. The human genome project

    Microsoft Academic Search

    Thomas D. Yager; Thomas E. Zewert; Leroy E. Hood

    1994-01-01

    The Human Genome Project (HGP) is a coordinated worldwide effort to precisely map the human genome and the genomes of selected model organisms. The first explicit proposal for this project dates from 1985 although its foundations (both conceptual and technological) can be traced back many years in genetics, molecular biology, and biotechnology. The HGP has matured rapidly and is producing

  3. Office of Cancer Genomics |

    Cancer.gov

    The mission of the NCI’s Office of Cancer Genomics (OCG) is to enhance the understanding of the molecular mechanisms of cancer, advance and accelerate genomics science and technology development, and efficiently translate the genomics data to improve cancer prevention, early detection, diagnosis and treatment.

  4. Whole Genome Selection

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Whole genome selection (WGS) is an approach to using DNA markers that are distributed throughout the entire genome. Genes affecting most economically-important traits are distributed throughout the genome and there are relatively few that have large effects with many more genes with progressively sm...

  5. Comparative Apicomplexan genomics

    Microsoft Academic Search

    Arnab Pain; Lisa Crossman; Julian Parkhill

    2005-01-01

    The power of comparative genomics has, until recently, been limited to model organisms and prokaryotes, mainly because of the cost and difficulty of sequencing eukaryotic genomes. However, as costs fall and technology advances, comparative genomics are more widely applied. In addition to a member of the Chloroflexi, two specific examples from the parasitic world are also discussed this week, both

  6. GENOME OF CROCODILEPOX VIRUS

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Here we present the genome sequence, with analysis, of a poxvirus infecting Nile crocodiles (Crocodylus niloticus) (CRV). The genome is 190054 bp (62% G+C) and encodes 173 open reading frames (ORFs) of 53 to 1941 amino acids. The central genomic region contains genes conserved and generally colinea...

  7. Genome BBiioollooggyy 2008, 99

    E-print Network

    Weng, Zhiping

    Genome BBiioollooggyy 2008, 99::302 Meeting report IInn ssiilliiccoo mmeeeettss iinn vviivvoo School, Worcester, MA 01605, USA. ¶Center for Genomic Regulation, C/Dr. Aiguader 88, 08005 Barcelona.guigo@crg.es Published: 25 February 2008 Genome BBiioollooggyy 2008, 99::302 (doi:10.1186/gb-2008-9-2-302) The electronic

  8. Genome BBiioollooggyy 2008, 99

    E-print Network

    Genome BBiioollooggyy 2008, 99::245 Minireview DDiiaattoomm ggeennoommeess ccoommee ooff aaggee The results of two published genome sequences from marine diatoms provide basic insights into how in the contemporary ocean. Published: 2 January 2009 Genome BBiioollooggyy 2008, 99::245 (doi:10.1186/gb-2008

  9. Treeline Dynamics on Southern Vancouver Island, British Columbia

    E-print Network

    Smith, Dan

    Vancouver Island marmot. Keywords: dendroecology, subalpine meadows, seedling establishment, tree rings, Vancouver Island, Vancouver Island marmot. *Corresponding author Western Geography, 10/11(2000/01), pp. 43

  10. OUTERBRIDGE CROSSING BRIDGE IN PERSPECTIVE, STATEN ISLAND ON RIGHT ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    OUTERBRIDGE CROSSING BRIDGE IN PERSPECTIVE, STATEN ISLAND ON RIGHT - Outerbridge Crossing Bridge, Spanning Arthur Kill from New Jersey to Staten Island, Staten Island (subdivision), Richmond County, NY

  11. Mammals evolve faster on smaller islands.

    PubMed

    Millien, Virginie

    2011-07-01

    Island mammals often display remarkable evolutionary changes in size and morphology. Both theory and empirical data support the hypothesis that island mammals evolve at faster rates than their mainland congeners. It is also often assumed that the island effect is stronger and that evolution is faster on the smallest islands. I used a dataset assembled from the literature to test these assumptions for the first time. I show that mammals on smaller islands do indeed evolve more rapidly than mammals on larger islands, and also evolve by a greater amount. These results fit well the theory of an evolutionary burst due to the opening of new ecological opportunities on islands. This evolutionary burst is expected to be the strongest on the smallest islands where the contrast between the island and the mainland environments is the most dramatic. PMID:21729049

  12. Bryophytes from Simeonof Island in the Shumagin Islands, southwestern Alaska

    USGS Publications Warehouse

    Schofield, W.B.; Talbot, S. S.; Talbot, S.L.

    2004-01-01

    Simeonof Island is located south of the Alaska Peninsula in the hyperoceanic sector of the middle boreal subzone. We examined the bryoflora of Simeonof Island to determine species composition in an area where no previous collections had been reported. This field study was conducted in sites selected to represent the spectrum of environmental variation within Simeonof Island. Data were analyzed using published reports to compare bryophyte distribution patterns at three levels, the Northern Hemisphere, North America, and Alaska. A total of 271 bryophytes were identified: 202 mosses and 69 liverworts. The annotated list of species for Simeonof Island expands the known range for many species and fills distribution gaps within Hulte??n's Western Pacific Coast district. Maps and notes on the distribution of 14 significant distribution records are presented. Compared with bryophyte distribution in the Northern Hemisphere, the bryoflora of Simeonof Island primarily includes taxa of boreal (55%), temperate (20%), arctic (10%), and cosmopolitan (8%) distribution; 6% of the moss flora are western North America endemics. A description of the bryophytes present in the vegetation and habitat types is provided as is a quantitative analysis of the most frequently occurring bryophytes in crowberry heath.

  13. Histone methylation marks play important roles in predicting the methylation status of CpG islands.

    PubMed

    Fan, Shicai; Zhang, Michael Q; Zhang, Xuegong

    2008-09-26

    The methylation status of CpG islands is highly correlated with gene expression. Current methods for computational prediction of DNA methylation only utilize DNA sequence features. In this study, besides 35 DNA sequence features, we added four histone methylation marks to predict the methylation status of CpG islands, and improved the accuracy to 89.94%. Also we applied our model to predict the methylation pattern of all the CpG islands in the human genome, and the results are consistent with the previous reports. Our results imply the important roles of histone methylation marks in affecting the methylation status of CpG islands. H3K4me enriched in the methylation-resistant CpG islands could disrupt the contacts between nucleosomes, unravel chromatin and make DNA sequences accessible. And the established open environment may be a prerequisite for or a consequence of the function implementation of zinc finger proteins that could protect CpG islands from DNA methylation. PMID:18656446

  14. Comparative genomics of Lactobacillus.

    PubMed

    Kant, Ravi; Blom, Jochen; Palva, Airi; Siezen, Roland J; de Vos, Willem M

    2011-05-01

    The genus Lactobacillus includes a diverse group of bacteria consisting of many species that are associated with fermentations of plants, meat or milk. In addition, various lactobacilli are natural inhabitants of the intestinal tract of humans and other animals. Finally, several Lactobacillus strains are marketed as probiotics as their consumption can confer a health benefit to host. Presently, 154 Lactobacillus species are known and a growing fraction of these are subject to draft genome sequencing. However, complete genome sequences are needed to provide a platform for detailed genomic comparisons. Therefore, we selected a total of 20 genomes of various Lactobacillus strains for which complete genomic sequences have been reported. These genomes had sizes varying from 1.8 to 3.3?Mb and other characteristic features, such as G+C content that ranged from 33% to 51%. The Lactobacillus pan genome was found to consist of approximately 14?000 protein-encoding genes while all 20 genomes shared a total of 383 sets of orthologous genes that defined the Lactobacillus core genome (LCG). Based on advanced phylogeny of the proteins encoded by this LCG, we grouped the 20 strains into three main groups and defined core group genes present in all genomes of a single group, signature group genes shared in all genomes of one group but absent in all other Lactobacillus genomes, and Group-specific ORFans present in core group genes of one group and absent in all other complete genomes. The latter are of specific value in defining the different groups of genomes. The study provides a platform for present individual comparisons as well as future analysis of new Lactobacillus genomes. PMID:21375712

  15. Comparative genomics of Lactobacillus

    PubMed Central

    Kant, Ravi; Blom, Jochen; Palva, Airi; Siezen, Roland J.; de Vos, Willem M.

    2011-01-01

    Summary The genus Lactobacillus includes a diverse group of bacteria consisting of many species that are associated with fermentations of plants, meat or milk. In addition, various lactobacilli are natural inhabitants of the intestinal tract of humans and other animals. Finally, several Lactobacillus strains are marketed as probiotics as their consumption can confer a health benefit to host. Presently, 154 Lactobacillus species are known and a growing fraction of these are subject to draft genome sequencing. However, complete genome sequences are needed to provide a platform for detailed genomic comparisons. Therefore, we selected a total of 20 genomes of various Lactobacillus strains for which complete genomic sequences have been reported. These genomes had sizes varying from 1.8 to 3.3?Mb and other characteristic features, such as G+C content that ranged from 33% to 51%. The Lactobacillus pan genome was found to consist of approximately 14?000 protein?encoding genes while all 20 genomes shared a total of 383 sets of orthologous genes that defined the Lactobacillus core genome (LCG). Based on advanced phylogeny of the proteins encoded by this LCG, we grouped the 20 strains into three main groups and defined core group genes present in all genomes of a single group, signature group genes shared in all genomes of one group but absent in all other Lactobacillus genomes, and Group?specific ORFans present in core group genes of one group and absent in all other complete genomes. The latter are of specific value in defining the different groups of genomes. The study provides a platform for present individual comparisons as well as future analysis of new Lactobacillus genomes. PMID:21375712

  16. HLA in anthropology: the enigma of Easter Island.

    PubMed

    Sanchez-Mazas, Alicia; Thorsby, Erik

    2013-01-01

    In this article, we first present four significant cases where human leukocyte antigen (HLA) studies have been useful for the reconstruction of human peopling history on the worldwide scale; i.e., the spread of modern humans from East Africa, the colonization of East Asia along two geographic routes, the co-evolution of genes and languages in Africa, and the peopling of Europe through a main northward migration. These examples show that natural selection did not erase the genetic signatures of our past migrations in the HLA genetic diversity patterns observed today. In the second part, we summarize our studies on Easter Island. Using genomic HLA typing, we could trace an introduction of HLA alleles of native American (Amerindian) origin to Easter Island before the Peruvian slave trades; i.e., before the 1860s, and provide suggestive evidence that they may have already been introduced in prehistoric time. Our results give further support to an initial Polynesian population of the island, but also reveal an early contribution by Amerindians. Together, our data illustrate the usefulness of typing for HLA alleles to complement genetic analyses in anthropological investigations. PMID:25095505

  17. A genome blogger manifesto

    PubMed Central

    2012-01-01

    Cheap prices for genomic testing have revolutionized consumers’ access to personal genomics. Exploration of personal genomes poses significant challenges for customers wishing to learn beyond provider customer reports. A vibrant community has spontaneously appeared blogging experiences and data as a way to learn about their personal genomes. No set of values has publicly been described to date encapsulating ideals and code of conduct for this community. Here I present a first attempt to address this vacuum based on my own personal experiences as genome blogger. PMID:23587446

  18. A genome blogger manifesto.

    PubMed

    Corpas, Manuel

    2012-01-01

    Cheap prices for genomic testing have revolutionized consumers' access to personal genomics. Exploration of personal genomes poses significant challenges for customers wishing to learn beyond provider customer reports. A vibrant community has spontaneously appeared blogging experiences and data as a way to learn about their personal genomes. No set of values has publicly been described to date encapsulating ideals and code of conduct for this community. Here I present a first attempt to address this vacuum based on my own personal experiences as genome blogger. PMID:23587446

  19. Perspective View of Umnak Island, Aleutian Islands, Alaska (#2)

    NASA Technical Reports Server (NTRS)

    2001-01-01

    This image is a perspective view of Umnak Island, one of Alaska's Aleutian Islands. The active Okmok volcano appears in the center of the island.

    The image was created by draping a Landsat 7 Thematic Mapper image over a digital elevation mosaic derived from Airsar data.

    This work was conducted as part of a NASA-funded Alaska Digital Elevation Model Project at the Alaska Synthetic Aperture Radar Facility (ASF) at the University of Alaska Geophysical Institute in Fairbanks, Alaska.

    Airsar collected the Alaska data as part of its PacRim 2000 Mission, which took the instrument to French Polynesia, American and Western Samoa, Fiji, New Zealand, Australia, New Guinea, Indonesia, Malaysia, Cambodia, Philippines, Taiwan, South Korea, Japan, Northern Marianas, Guam, Palau, Hawaii and Alaska. Airsar, part of NASA's Airborne Science Program, is managed for NASA's Earth Science Enterprise by JPL. JPL is a division of the California Institute of Technology in Pasadena.

  20. Perspective View of Umnak Island, Aleutian Islands, Alaska (#1)

    NASA Technical Reports Server (NTRS)

    2001-01-01

    This image is a perspective view of Umnak Island, one of Alaska's Aleutian Islands. The active Okmok volcano appears in the center of the island.

    The image was created by draping a Landsat 7 Thematic Mapper image over a digital elevation mosaic derived from Airsar data.

    This work was conducted as part of a NASA-funded Alaska Digital Elevation Model Project at the Alaska Synthetic Aperture Radar Facility (ASF) at the University of Alaska Geophysical Institute in Fairbanks, Alaska.

    Airsar collected the Alaska data as part of its PacRim 2000 Mission, which took the instrument to French Polynesia, American and Western Samoa, Fiji, New Zealand, Australia, New Guinea, Indonesia, Malaysia, Cambodia, Philippines, Taiwan, South Korea, Japan, Northern Marianas, Guam, Palau, Hawaii and Alaska. Airsar, part of NASA's Airborne Science Program, is managed for NASA's Earth Science Enterprise by JPL. JPL is a division of the California Institute of Technology in Pasadena.

  1. Bacterial Genome Instability

    PubMed Central

    Darmon, Elise

    2014-01-01

    SUMMARY Bacterial genomes are remarkably stable from one generation to the next but are plastic on an evolutionary time scale, substantially shaped by horizontal gene transfer, genome rearrangement, and the activities of mobile DNA elements. This implies the existence of a delicate balance between the maintenance of genome stability and the tolerance of genome instability. In this review, we describe the specialized genetic elements and the endogenous processes that contribute to genome instability. We then discuss the consequences of genome instability at the physiological level, where cells have harnessed instability to mediate phase and antigenic variation, and at the evolutionary level, where horizontal gene transfer has played an important role. Indeed, this ability to share DNA sequences has played a major part in the evolution of life on Earth. The evolutionary plasticity of bacterial genomes, coupled with the vast numbers of bacteria on the planet, substantially limits our ability to control disease. PMID:24600039

  2. Transposable element islands facilitate adaptation to novel environments in an invasive species

    PubMed Central

    Schrader, Lukas; Kim, Jay W.; Ence, Daniel; Zimin, Aleksey; Klein, Antonia; Wyschetzki, Katharina; Weichselgartner, Tobias; Kemena, Carsten; Stökl, Johannes; Schultner, Eva; Wurm, Yannick; Smith, Christopher D.; Yandell, Mark; Heinze, Jürgen; Gadau, Jürgen; Oettler, Jan

    2014-01-01

    Adaptation requires genetic variation, but founder populations are generally genetically depleted. Here we sequence two populations of an inbred ant that diverge in phenotype to determine how variability is generated. Cardiocondyla obscurior has the smallest of the sequenced ant genomes and its structure suggests a fundamental role of transposable elements (TEs) in adaptive evolution. Accumulations of TEs (TE islands) comprising 7.18% of the genome evolve faster than other regions with regard to single-nucleotide variants, gene/exon duplications and deletions and gene homology. A non-random distribution of gene families, larvae/adult specific gene expression and signs of differential methylation in TE islands indicate intragenomic differences in regulation, evolutionary rates and coalescent effective population size. Our study reveals a tripartite interplay between TEs, life history and adaptation in an invasive species. PMID:25510865

  3. Thermal island destabilization and the Greenwald limit

    NASA Astrophysics Data System (ADS)

    White, R. B.; Gates, D. A.; Brennan, D. P.

    2015-02-01

    Magnetic reconnection is ubiquitous in the magnetosphere, the solar corona, and in toroidal fusion research discharges. In a fusion device, a magnetic island saturates at a width which produces a minimum in the magnetic energy of the configuration. At saturation, the modified current density profile, a function of the flux in the island, is essentially flat, the growth rate proportional to the difference in the current at the O-point and the X-point. Further modification of the current density profile in the island interior causes a change in the island stability and additional growth or contraction of the saturated island. Because field lines in an island are isolated from the outside plasma, an island can heat or cool preferentially depending on the balance of Ohmic heating and radiation loss in the interior, changing the resistivity and hence the current in the island. A simple model of island destabilization due to radiation cooling of the island is constructed, and the effect of modification of the current within an island is calculated. An additional destabilization effect is described, and it is shown that a small imbalance of heating can lead to exponential growth of the island. A destabilized magnetic island near the plasma edge can lead to plasma loss, and because the radiation is proportional to plasma density and charge, this effect can cause an impurity dependent density limit.

  4. 3. Photograph of a photograph in possession of Rock Island ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    3. Photograph of a photograph in possession of Rock Island Arsenal Historical Office. SOUTH ELEVATION IN UNALTERED CONDITION. DATED MARCH 19, 1945. - Rock Island Arsenal, Building No. 61, Rodman Avenue & First Street, Rock Island, Rock Island County, IL

  5. 4. Photograph of a photograph in possession of Rock Island ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    4. Photograph of a photograph in possession of Rock Island Arsenal Historical Office. LOOKING NORTH AFTER ADDITION OF CONICAL ROOF. ORIGINALLY PUBLISHED 1887. - Rock Island Arsenal, Building No. 53, North Avenue North of Midpoint, Rock Island, Rock Island County, IL

  6. 11. Photograph of a photograph in possession of Rock Island ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    11. Photograph of a photograph in possession of Rock Island Arsenal Historical Office. BASEMENT, SHOWING ORIGINAL OPEN INTERIOR PLAN. DATED APRIL 7, 1942. - Rock Island Arsenal, Building No. 56, North Avenue & East Avenue, Rock Island, Rock Island County, IL

  7. 10. Photograph of a photograph in possession of Rock Island ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    10. Photograph of a photograph in possession of Rock Island Arsenal Historical Office. INTERIOR, LOOKING WEST. DATED OCTOBER 2, 1945. - Rock Island Arsenal, Building No. 138, Second Avenue between South Avenue & Ramsey Street, Rock Island, Rock Island County, IL

  8. 5. Photograph of a photograph in possession of Rock Island ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    5. Photograph of a photograph in possession of Rock Island Arsenal Historical Office. INTERIOR AFTER REMODELING INTO OFFICE SPACE. DATED FEBRUARY 13, 1943. - Rock Island Arsenal, Building No. 67, Rodman Avenue & Fourth Street, Rock Island, Rock Island County, IL

  9. 8. Photograph of a photograph in possession of Rock Island ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    8. Photograph of a photograph in possession of Rock Island Arsenal Historical Office. SOUTH ELEVATON IN UNALTERED CONDITION. ORIGINALLY PUBLISHED 1898. - Rock Island Arsenal, Building No. 68, Rodman Avenue between Fourth Street & East Avenue, Rock Island, Rock Island County, IL

  10. 10. Photograph of a photograph in possession of Rock Island ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    10. Photograph of a photograph in possession of Rock Island Arsenal Historical Office. SOUTH AND WEST ELEVATIONS IN UNALTERED CONDITION. DATED APRIL 18, 1941. - Rock Island Arsenal, Building No. 56, North Avenue & East Avenue, Rock Island, Rock Island County, IL

  11. 3. Photograph of a photograph in possession of Rock Island ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    3. Photograph of a photograph in possession of Rock Island Arsenal Historical Office. NORTH ELEVATION IN UNALTERED CONDITION. DATED NOVEMBER 21, 1944. - Rock Island Arsenal, Building No. 103, Rodman Avenue & First Street, Rock Island, Rock Island County, IL

  12. 4. Photograph of a photograph in possession of Rock Island ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    4. Photograph of a photograph in possession of Rock Island Arsenal Historical Office. NORTH AND WEST ELEVATIONS. DATED NOVEMBER 21, 1944. - Rock Island Arsenal, Building No. 108, Rodman Avenue between Third & Fourth Streets, Rock Island, Rock Island County, IL

  13. 4. Photograph of a photograph in possession of Rock Island ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    4. Photograph of a photograph in possession of Rock Island Arsenal Historical Office. NORTH ELEVATION IN UNALTERED CONDITION. DATED NOVEMBER 21, 1944. - Rock Island Arsenal, Building No. 109, Rodman Avenue & Fourth Street, Rock Island, Rock Island County, IL

  14. 5. Photograph of a photograph in possession of Rock Island ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    5. Photograph of a photograph in possession of Rock Island Arsenal Historical Office. WEST ELEVATION IN UNALTERED CONDITION. ORIGINALLY PUBLISHED 1898. - Rock Island Arsenal, Building No. 280, Sylvan Drive, Rock Island, Rock Island County, IL

  15. 9. Photograph of photograph in possession of Rock Island Arsenal ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    9. Photograph of photograph in possession of Rock Island Arsenal Historical Office. WEST AND NORTH ELEVATIONS. ORIGINALLY PUBLISHED 1887. - Rock Island Arsenal, Building No. 90, East Avenue between North Avenue & King Drive, Rock Island, Rock Island County, IL

  16. 7. Photograph of a photograph in possession of Rock Island ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    7. Photograph of a photograph in possession of Rock Island Arsenal Historical Office. SOUTH AND EAST ELEVATIONS. DATED MARCH 19, 1945. - Rock Island Arsenal, Building No. 62, Rodman Avenue between First & Second Streets, Rock Island, Rock Island County, IL

  17. WAKE ISLAND AIRFIELD TERMINAL, BUILDING 1502 LOOKING SOUTHEAST AT NORTHWEST ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    WAKE ISLAND AIRFIELD TERMINAL, BUILDING 1502 LOOKING SOUTHEAST AT NORTHWEST FAÇADE AND BLAST WALL, DATE UNKNOWN - Wake Island Airfield, Terminal Building, West Side of Wake Avenue, Wake Island, Wake Island, UM

  18. 11. Photograph of a photograph in possession of Rock Island ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    11. Photograph of a photograph in possession of Rock Island Arsenal Historical Office. SOUTH AND EAST ELEVATIONS. ORIGINALLY PUBLISHED 1898. - Rock Island Arsenal, Building No. 360, Gillespie Avenue between Rodman Avenue & North Avenue, Rock Island, Rock Island County, IL

  19. 21. Photograph of a photograph in possession of Rock Island ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    21. Photograph of a photograph in possession of Rock Island Arsenal Historical Office. ORIGINAL HORIZONTAL SHAFTING OF GENERAL ELECTRIC GENERATORS. ORIGINALLY PUBLISHED IN 1905. - Rock Island Arsenal, Building No. 160, Sylvan Drive, Rock Island, Rock Island County, IL

  20. Pacific Island Ecosystems Research Center

    NSDL National Science Digital Library

    The Pacific Island Ecosystems Research Center (PIERC) is part of the Biological Division of the United States Geological Survey (USGS). The mission of PIERC is to provide the scientific understanding and technologies needed to support the sound management and conservation of our Nation's biological resources occurring within the cultural, sociological, and political contexts of the State of Hawaii. The geographical isolation of the Hawaiian Islands has resulted in the evolution of a highly endemic biota, while human colonization has severely impacted native plant and animal populations. The PIERC website provides information and research studies about the Hawaiian Islands ecosystem, as well as staff projects that are currently in progress. Topics include birds, mammals, ecosystem diversity, genetics, wildlife health, plant ecology, and marine biology. There is an education section with outdoor activities, online activities, and a coloring book. Links are provided for further information.

  1. Rhode Island Critical Resource Atlas

    NSDL National Science Digital Library

    Geographic Information System (GIS) technology is used to assist planners, scientists, geographers, and others to visualize data sets. This particular project created draws on data from the state of Rhode Island's Geographic Information System (RIGIS) database in order to assist land managers and other interested parties. The project was created with support from the Environmental Protection Agency, the University of Rhode Island Cooperative Extension, and a number of other organizations. On the site, visitors can click on maps of forests and wetlands, land use patterns, groundwater resources, soil hydrology, and biodiversity. On the site's homepage, visitors can also use the "Towns" drop down menu to look at information for different cities throughout the state. Additionally, the "Watershed Atlas" area provides detailed maps of the twelve watersheds located in Rhode Island.

  2. Draft genome sequence of Alcaligenes faecalis subsp. faecalis NCIB 8687 (CCUG 2071).

    PubMed

    Phung, Le T; Trimble, William L; Meyer, Folker; Gilbert, Jack A; Silver, Simon

    2012-09-01

    Alcaligenes faecalis subsp. faecalis NCIB 8687, the betaproteobacterium from which arsenite oxidase had its structure solved and the first "arsenate gene island" identified, provided a draft genome of 3.9 Mb in 186 contigs (with the largest 15 comprising 90% of the total) for this opportunistic pathogen species. PMID:22933773

  3. Draft Genome Sequence of Enterococcus faecalis Strain PF3, Isolated from Adélie Penguin Feces from Antarctica

    PubMed Central

    Spence, Robert J.; Pavasovic, Ana; Smith, James J.

    2014-01-01

    Enterococcus faecalis is one of the leading causes of nosocomial infections and is a common commensal organism in humans and other animals. In this study, we report a draft genome sequence for the E. faecalis strain PF3, isolated from Adélie penguin feces collected from Warriner Island, Antarctica. PMID:24459271

  4. Draft Genome Sequence of Enterococcus faecalis Strain PF3, Isolated from Adelie Penguin Feces from Antarctica.

    PubMed

    Spence, Robert J; Pavasovic, Ana; Smith, James J; Prentis, Peter J

    2014-01-01

    Enterococcus faecalis is one of the leading causes of nosocomial infections and is a common commensal organism in humans and other animals. In this study, we report a draft genome sequence for the E. faecalis strain PF3, isolated from Adélie penguin feces collected from Warriner Island, Antarctica. PMID:24459271

  5. Complete Genome Sequence of the Urethral Catheter Isolate Myroides sp. A21

    PubMed Central

    Burghartz, Melanie; Bunk, Boyke; Spröer, Cathrin; Voget, Sonja; Daniel, Rolf; Overmann, Jörg

    2015-01-01

    Myroides sp. A21, isolated from a urethral catheterized patient without symptoms of a urinary tract infection in Germany, proved to be extensively drug resistant. Here, we report the 4.16-Mb complete genome sequence of strain A21, carrying unusual pathogenicity islands and explaining the features of multidrug resistance. PMID:25745004

  6. Draft Genome Sequence of Pantoea anthophila Strain 11-2 from Hypersaline Lake Laysan, Hawaii

    PubMed Central

    Hou, Shaobin; Phan, Nolwenn; Malone Moss, Jennifer S.; Donachie, Stuart P.; Alam, Maqsudul

    2015-01-01

    Most Pantoea spp. have been isolated from plant sources or clinical samples. However, we cultivated Pantoea anthophila 11-2 from hypersaline water from the lake on Laysan, Northwestern Hawaiian Islands. Draft genome sequencing of 11-2 provides a molecular basis for studies in evolution and pathogenicity in Pantoea spp. PMID:25977417

  7. The diploid D genome cottons (Gossypium spp.) of the new world

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The diploid D genome cottons (Gossypium spp.) of the New World are part of a great reservoir of important genes for improving fiber quality, pest and disease resistance, and drought and salt tolerance in the modern cultivated Upland/Acala (G. hirsutum) and Pima [also known as Sea Island or Egyptian ...

  8. The Big Island of Hawaii

    NASA Technical Reports Server (NTRS)

    2002-01-01

    Boasting snow-covered mountain peaks and tropical forest, the Island of Hawaii, the largest of the Hawaiian Islands, is stunning at any altitude. This false-color composite (processed to simulate true color) image of Hawaii was constructed from data gathered between 1999 and 2001 by the Enhanced Thematic Mapper plus (ETM+) instrument, flying aboard the Landsat 7 satellite. The Landsat data were processed by the National Oceanographic and Atmospheric Administration (NOAA) to develop a landcover map. This map will be used as a baseline to chart changes in land use on the islands. Types of change include the construction of resorts along the coastal areas, and the conversion of sugar plantations to other crop types. Hawaii was created by a 'hotspot' beneath the ocean floor. Hotspots form in areas where superheated magma in the Earth's mantle breaks through the Earth's crust. Over the course of millions of years, the Pacific Tectonic Plate has slowly moved over this hotspot to form the entire Hawaiian Island archipelago. The black areas on the island (in this scene) that resemble a pair of sun-baked palm fronds are hardened lava flows formed by the active Mauna Loa Volcano. Just to the north of Mauna Loa is the dormant grayish Mauna Kea Volcano, which hasn't erupted in an estimated 3,500 years. A thin greyish plume of smoke is visible near the island's southeastern shore, rising from Kilauea-the most active volcano on Earth. Heavy rainfall and fertile volcanic soil have given rise to Hawaii's lush tropical forests, which appear as solid dark green areas in the image. The light green, patchy areas near the coasts are likely sugar cane plantations, pineapple farms, and human settlements. Courtesy of the NOAA Coastal Services Center Hawaii Land Cover Analysis project

  9. Plant Genomes Central: Integrated Resources for Plant Genomics

    E-print Network

    Levin, Judith G.

    . First, it integrates all of the genetic maps for each plant species genome with observed sequence search page and a special BLAST page for plant genomes · Large-Scale Sequencing Projects contains linksPlant Genomes Central: Integrated Resources for Plant Genomics Plant Genomes Central (PGC

  10. Dynamic Genomes of Eukaryotes and the Maintenance of Genomic Integrity

    E-print Network

    Katz, Laura

    Dynamic Genomes of Eukaryotes and the Maintenance of Genomic Integrity Eukaryotes specify a genome to be inherited stably, enabling dynamic rearrangements and amplifications of other genomic elements Laura Wegener Parfrey and Laura A. Katz M any biologists assume that eu- karyotic genomes are transmit- ted stably

  11. Critical island-size, stability and island morphology in nanoparticle island self-assembly

    NASA Astrophysics Data System (ADS)

    Amar, Jacques; Hubartt, Bradley

    2015-03-01

    The critical island-size, stability, and morphology of 2D colloidal Au nanoparticle (NP) islands formed at the toluene-air interface during drop-drying are studied using molecular dynamics and energetics calculations. Our calculations were carried out using an empirical potential which takes into account interactions between the dodecanethiol ligands and the toluene solvent, ligand-ligand interactions, and the van der Waals interaction between the Au cores. Good agreement with experimental results is obtained for the dependence of the critical island-size on NP diameter. Our results for the critical length-scale for smoothing via edge-diffusion are also consistent with the limited facet size and island-relaxation observed in experiments. The relatively high rate of NP diffusion on an island obtained in our simulations as well as the low calculated activation barrier for interlayer diffusion are also consistent with experimental observations that second-layer growth does not occur until after the first layer is complete. Supported by NSF CHE-1012896 and DMR-1410840

  12. LONG ISLAND SOUND STUDY CCMP, 1994

    EPA Science Inventory

    The Comprehensive Conservation and Management Plan for Long Island Sound characterizes the priority problems affecting the Sound and identifies specific commitments and recommendations developed by the Long Island Sound Study (LISS) Management Conference. The CCMP provides a hist...

  13. Asthma and Native Hawaiians/Pacific Islanders

    MedlinePLUS

    ... twice as likely to have asthma as non-Hispanic whites. National data for this population is very ... had asthma, 2012 Native Hawaiian/Pacific Islander Non-Hispanic White Native Hawaiian/Pacific Islander/ Non-Hispanic White ...

  14. WIND DATA REPORT Deer Island Parking Lot

    E-print Network

    Massachusetts at Amherst, University of

    WIND DATA REPORT Deer Island Parking Lot May 1, 2003 ­ July 15, 2003 Prepared for Massachusetts........................................................................................................................ 16 TABLE OF FIGURES Figure 1 - Site location at Deer Island Parking Lot site................

  15. Obesity and Native Hawaiians/Pacific Islanders

    MedlinePLUS

    Obesity and Native Hawaiians/Pacific Islanders Native Hawaiians/Pacific Islanders were almost four times more likely to ... data available at this time. HEALTH IMPACT OF OBESITY More than 80 percent of people with type ...

  16. Native Hawaiian & Other Pacific Islander Populations

    MedlinePLUS

    ... origins in any of the original peoples of Hawaii, Guam, Samoa, or other Pacific Islands. According to ... or Other Pacific Islander populations in 2011 were Hawaii (359,000) and California (329,000) . The Native ...

  17. Profile: Native Hawaiians and Pacific Islanders

    MedlinePLUS

    ... origins in any of the original peoples of Hawaii, Guam, Samoa or other Pacific Islands. According to ... 000 Native Hawaiians or Pacific Islanders reside in Hawaii. Some other states that have a significant Native ...

  18. Modulation of virulence within a pathogenicity island in vancomycin-resistant Enterococcus faecalis.

    PubMed

    Shankar, Nathan; Baghdayan, Arto S; Gilmore, Michael S

    2002-06-13

    Enterococci are members of the healthy human intestinal flora, but are also leading causes of highly antibiotic-resistant, hospital-acquired infection. We examined the genomes of a strain of Enterococcus faecalis that caused an infectious outbreak in a hospital ward in the mid-1980s (ref. 2), and a strain that was identified as the first vancomycin-resistant isolate in the United States, and found that virulence determinants were clustered on a large pathogenicity island, a genetic element previously unknown in this genus. The pathogenicity island, which varies only subtly between strains, is approximately 150 kilobases in size, has a lower G + C content than the rest of the genome, and is flanked by terminal repeats. Here we show that subtle variations within the structure of the pathogenicity island enable strains harbouring the element to modulate virulence, and that these variations occur at high frequency. Moreover, the enterococcal pathogenicity island, in addition to coding for most known auxiliary traits that enhance virulence of the organism, includes a number of additional, previously unstudied genes that are rare in non-infection-derived isolates, identifying a class of new targets associated with disease which are not essential for the commensal behaviour of the organism. PMID:12066186

  19. 33 CFR 110.6 - Portland Harbor, Portland, Maine (between Little Diamond Island and Great Diamond Island).

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ...Portland Harbor, Portland, Maine (between Little Diamond Island and Great Diamond Island). 110.6 Section 110.6 Navigation...Portland Harbor, Portland, Maine (between Little Diamond Island and Great Diamond Island)....

  20. 33 CFR 110.6 - Portland Harbor, Portland, Maine (between Little Diamond Island and Great Diamond Island).

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ...Portland Harbor, Portland, Maine (between Little Diamond Island and Great Diamond Island). 110.6 Section 110.6 Navigation...Portland Harbor, Portland, Maine (between Little Diamond Island and Great Diamond Island)....

  1. Numerical Simulations of the Island-Induced Circulations over the Island of Hawaii during HaRP

    E-print Network

    Chen, Yi-Leng

    Numerical Simulations of the Island-Induced Circulations over the Island of Hawaii during HaRP YANG island-scale circulations over the island of Hawaii during the Hawaiian Rainband Project (HaRP, 11 July

  2. 46 CFR 7.85 - St. Simons Island, GA to Little Talbot Island, FL.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ...2012-10-01 false St. Simons Island, GA to Little Talbot Island, FL. 7.85 Section... § 7.85 St. Simons Island, GA to Little Talbot Island, FL. (a) A line drawn from...thence to the northeasternmost extremity of Little Talbot...

  3. Circulation in Block Island Sound, Rhode Island Sound, and Adjacent Waters, with Emphasis on Subsurface Flows

    E-print Network

    Codiga, Daniel L.

    Circulation in Block Island Sound, Rhode Island Sound, and Adjacent Waters, with Emphasis on Subsurface Flows Daniel L. Codiga, Graduate School of Oceanography, University of Rhode Island EXECUTIVE SUMMARY Presentation for Rhode Island Sea Grant Ronald C. Baird Symposium 2008 Abstract Subsurface flows

  4. ELEVATED FOSSIL CORAL DEPOSITS IN THE HAWAIIAN ISLANDS: A MEASURE OF ISLAND UPLIFT IN THE QUATERNARY

    E-print Network

    Luther, Douglas S.

    ELEVATED FOSSIL CORAL DEPOSITS IN THE HAWAIIAN ISLANDS: A MEASURE OF ISLAND UPLIFT Gary McMurtry Johanna Resig #12;ABSTRACT The origin of emerged marine fossils in the Hawaiian Islands waves swept up to 326 m on Lanai and neighboring islands depositing marine fossils 105 ka; (3

  5. Origins and antiquity of the island fox ( Urocyon littoralis) on California's Channel Islands

    Microsoft Academic Search

    Torben C. Rick; Jon M. Erlandson; René L. Vellanoweth; Todd J. Braje; Paul W. Collins; Daniel A. Guthrie; Thomas W. Stafford Jr.

    2009-01-01

    The island fox (Urocyon littoralis) is one of few reportedly endemic terrestrial mammals on California's Channel Islands. Questions remain about how and when foxes first colonized the islands, with researchers speculating on a natural, human-assisted, or combined dispersal during the late Pleistocene and\\/or Holocene. A natural dispersal of foxes to the northern Channel Islands has been supported by reports of

  6. Speciation by genome duplication: Repeated origins and genomic composition of the recently formed allopolyploid species Mimulus peregrinus.

    PubMed

    Vallejo-Marín, Mario; Buggs, Richard J A; Cooley, Arielle M; Puzey, Joshua R

    2015-06-01

    Whole genome duplication (polyploidization) is a mechanism of "instantaneous" species formation that has played a major role in the evolutionary history of plants. Much of what we know about the early evolution of polyploids is based upon studies of a handful of recently formed species. A new polyploid hybrid (allopolyploid) species Mimulus peregrinus, formed within the last 140 years, was recently discovered on the Scottish mainland and corroborated by chromosome counts. Here, using targeted, high-depth sequencing of 1200 genic regions, we confirm the parental origins of this new species from M. x robertsii, a sterile triploid hybrid between the two introduced species M. guttatus and M. luteus that are naturalized and widespread in the United Kingdom. We also report a new population of M. peregrinus on the Orkney Islands and demonstrate that populations on the Scottish mainland and Orkney Islands arose independently via genome duplication from local populations of M. x robertsii. Our data raise the possibility that some alleles are already being lost in the evolving M. peregrinus genomes. The recent origins of a new species of the ecological model genus Mimulus via allopolyploidization provide a powerful opportunity to explore the early stages of hybridization and genome duplication in naturally evolved lineages. PMID:25929999

  7. Flooding of regular islands by chaotic states

    E-print Network

    A. Bäcker; R. Ketzmerick; A. G. Monastra

    2005-02-02

    We introduce a criterion for the existence of regular states in systems with a mixed phase space. If this condition is not fulfilled chaotic eigenstates substantially extend into a regular island. Wave packets started in the chaotic sea progressively flood the island. The extent of flooding by eigenstates and wave packets increases logarithmically with the size of the chaotic sea and the time, respectively. This new effect can be observed for island chains with just 10 islands.

  8. University of Rhode IslandUniversity of Rhode IslandUniversity of Rhode IslandUniversity of Rhode Island Graduate School of OceanographyGraduate School of OceanographyGraduate School of OceanographyGraduate School of Oceanography

    E-print Network

    Rhode Island, University of

    University of Rhode IslandUniversity of Rhode IslandUniversity of Rhode IslandUniversity of Rhode of Rhode Island ­ Graduate School of Oceanography. © Copyright 2002-2008 by University of Rhode Island by the University of Rhode Island ­ Graduate School of Oceanography is warranted against defective components

  9. University of Rhode IslandUniversity of Rhode IslandUniversity of Rhode IslandUniversity of Rhode Island Graduate School of OceanographyGraduate School of OceanographyGraduate School of OceanographyGraduate School of Oceanography

    E-print Network

    Rhode Island, University of

    University of Rhode IslandUniversity of Rhode IslandUniversity of Rhode IslandUniversity of Rhode Island ­ Graduate School of Oceanography. © Copyright 2002-2007 by University of Rhode Island ­ Graduate by the University of Rhode Island ­ Graduate School of Oceanography is warranted against defective components

  10. The Complete Genome Sequence of Mycoplasma bovis Strain Hubei-1

    PubMed Central

    Li, Yuan; Zheng, Huajun; Liu, Yang; Jiang, Yanwei; Xin, Jiuqing; Chen, Wei; Song, Zhiqiang

    2011-01-01

    Infection by Mycoplasma bovis (M. bovis) can induce diseases, such as pneumonia and otitis media in young calves and mastitis and arthritis in older animals. Here, we report the finished and annotated genome sequence of M. bovis strain Hubei-1, a strain isolated in 2008 that caused calf pneumonia on a Chinese farm. The genome of M. bovis strain Hubei-1 contains a single circular chromosome of 953,114 bp with a 29.37% GC content. We identified 803 open reading frames (ORFs) that occupy 89.5% of the genome. While 34 ORFs were Hubei-1 specific, 662 ORFs had orthologs in the M. bovis type strain PG45 genome. Genome analysis validated lateral gene transfer between M. bovis and the Mycoplasma mycoides subspecies mycoides, while phylogenetic analysis found that the closest M. bovis neighbor is Mycoplasma agalactiae. Glycerol may be the main carbon and energy source of M. bovis, and most of the biosynthesis pathways were incomplete. We report that 47 lipoproteins, 12 extracellular proteins and 18 transmembrane proteins are phase-variable and may help M. bovis escape the immune response. Besides lipoproteins and phase-variable proteins, genomic analysis found two possible pathogenicity islands, which consist of four genes and 11 genes each, and several other virulence factors including hemolysin, lipoate protein ligase, dihydrolipoamide dehydrogenase, extracellular cysteine protease and 5?-nucleotidase. PMID:21731639

  11. Streamlined Islands in Ares Valles

    NASA Technical Reports Server (NTRS)

    2002-01-01

    (Released 10 June 2002) The Science Although liquid water is not stable on the surface of Mars today, there is substantial geologic evidence that large quantities of water once flowed across the surface in the distant past. Streamlined islands, shown here, are one piece of evidence for this ancient water. The tremendous force of moving water, possibly from a catastrophic flood, carved these teardrop-shaped islands within a much larger channel called Ares Valles. The orientation of the islands can be used as an indicator of the direction the water flowed. The islands have a blunt end that is usually associated with an obstacle, commonly an impact crater. The crater is resistant to erosion and creates a geologic barrier around which the water must flow. As the water flows past the obstacle, its erosive power is directed outward, leaving the area in the lee of the obstacle relatively uneroded. However, some scientists have also argued that the area in the lee of the obstacle might be a depositional zone, where material is dropped out of the water as it briefly slows. The ridges observed on the high-standing terrain in the leeward parts of the islands may be benches carved into the rock that mark the height of the water at various times during the flood, or they might be indicative of layering in the leeward rock. As the water makes its way downstream, the interference of the water flow by the obstacle is reduced, and the water that was diverted around the obstacle rejoins itself at the narrow end of the island. Therefore, the direction of the water flow is parallel to the orientation of the island, and the narrow end of the island points downstream. In addition to the streamlined islands, the channel floor exhibits fluting that is also suggestive of flowing water. The flutes (also known as longitudinal grooves) are also parallel to the direction of flow, indicating that the water flow was turbulent and probably quite fast, which is consistent with the hypothesized catastrophic floods that came through Ares Valles. The Story In symbolism only, these guppy-shaped islands and current-like flutes of land beside them may conjure up a mental image of a flowing Martian river. This picture would only be half-right. Scientifically, no fish ever swam this channel, but these landforms do reveal that catastrophic floods of rushing water probably patterned the land in just this way. Geologists who study flood areas believe that a tremendous force of moving water probably carved both the islands and the small, parallel, 'current-like' ridges around them. The blunt end of the islands (the 'heads' of the 'fish') are probably ancient impact craters that posed obstacles to the water as it rushed down the channel in torrents. Because a crater is resistant to erosion, it creates a geologic barrier around which the water must flow. As the water makes its way downstream, the crater's interference with the water flow is reduced, so the water that was diverted around the obstacle rejoins at the narrow end of the island (the 'tail' of the 'fish'). Therefore, from this information, you can tell that the water flowed from the southeast to the northwest. As a rule of thumb for the future, you can say that the narrow end of the island points downstream. The result may be the island behind the crater, but geologists disagree about the exact process by which the island forms. Some scientists argue that the erosive power of the water is directed outward, leaving the area behind, or in the lee of, the obstacle relatively untouched. Other scientists argue that the water slows when it encounters the crater obstacle, and small particles of sand and 'dirt' drop out of the water and are deposited in the lee. There's another small associated uncertainty too. Look closely at the edges of the islands and notice how the land is terraced. These ledges might mark the height of the water at various times during the flood . . . or they might be an indication that layering occurred. It all depends on your hypothesis. Like the stream

  12. Planning the Genome Institute's Future

    E-print Network

    Botstein, David

    floors of a house, resting on a foundation of the Human Genome Project, with "Genomics to Society" on top planning that society will realize the scientific and public health benefits of the Human Genome Project. It has been a genome community tradi- tion since before there was a Human Genome Project, and NHGRI

  13. Horse Genome Project

    NSDL National Science Digital Library

    What's in a horse? As it turns out, what's in a horse is quite important, and the Horse Genome Project at the University of Kentucky is currently defining the genome of this animal. The Project is a cooperative international effort which involves some 100 scientists working in 20 countries. On the left-hand side of the page, visitors can make their way through five sections, including "The People", "The Horses", "Genomics 101", and "Applications of Genome Study". "The Horses" area is a good place to start, as it gives an overview of the animals being used in the project. In "Genomics 101", interested parties will find an overview of some basic terms used in the field, such as gene, allele, and mutation. The "Applications of Genome Study" area focuses in on how their work will be used to benefit the health and welfare of horses.

  14. Past, Present, Future Erosion at Locke Island

    SciTech Connect

    Bjornstad, Bruce N.

    2006-08-08

    This report describes and documents the erosion that has occurred along the northeast side of Locke Island over the last 10 to 20 years. The principal cause of this erosion is the massive Locke Island landslide complex opposite the Columbia River along the White Bluffs, which constricts the flow of the river and deflects the river's thalweg southward against the island.

  15. November 2011 UNIVERSITY OF RHODE ISLAND

    E-print Network

    Rhode Island, University of

    November 2011 UNIVERSITY OF RHODE ISLAND Eligibility for InState Tuition and Fees Based Upon Rhode Island High School Attendance Guidance for Students and Families If you are a student, including an undocumented student, who currently attends or plans to attend the University of Rhode Island

  16. ANNUAL FISH PASSAGE REPORT ROCK ISLAND DAM

    E-print Network

    ANNUAL FISH PASSAGE REPORT ROCK ISLAND DAM COLUMBIA RIVER, WASHINGTON, 1959 :y .iiJA/i-3ri ^' WUUUi. ANNUAL FISH PASSAGE REPORT - ROCK ISLAND DAM COLUMBIA RIVER, WASHINGTON, 1959 by Paul D. Zimmer, Clifton and observations 10 Summary 13 #12;#12;ANNUAL FISH PASSAGE REPORT - ROCK ISLAND DAM COLUMBIA RIVER, WASHINGTON

  17. ANNUAL FISH PASSAGE REPORT ROCK ISLAND DAM

    E-print Network

    42) ANNUAL FISH PASSAGE REPORT ROCK ISLAND DAM COLUMBIA RIVER, WASHINGTON 1961 Marine Biological. McKeman, Director ANNUAL FISH PASSAGE REPORT - ROCK ISLAND DAM COLUMBIA RIVER, WASHINGTON, 1961--Fisheries No. 421 Washington, D. C. April 1962 #12;Rock Island Dam, Columbia River, Washington ii #12;CONTENTS

  18. Island wakes in the Southern California Bight

    Microsoft Academic Search

    R. M. A. Caldeira; P. Marchesiello; N. P. Nezlin; P. M. DiGiacomo; J. C. McWilliams

    2005-01-01

    Wind- and current-induced island wakes were investigated using a multiplatform approach of in situ, remote sensing, and numerical model simulations for the Southern California Bight (SCB). Island wind wakes are a result of sheltering from the wind, with weak wind mixing, strong heat storage, and consequent high sea surface temperature (SST). Wind wakes around Santa Catalina Island are most persistent

  19. Heat island development in Mexico City

    Microsoft Academic Search

    Ernesto Jauregui

    1997-01-01

    The present paper describes the climatology of the near surface urban heat island of Mexico City, using hourly data from two recently installed automatic stations at a rural and an urban site. The results show that the nocturnal heat island was more frequent (75% of the time for the period examined) than daytime cases (25%). The maximum nocturnal heat island

  20. Threats to Avifauna on Oceanic Islands

    Microsoft Academic Search

    HEATHER S. TREVINO; AMY L. SKIBIEL; TIM J. KARELS; F. STEPHEN DOBSON

    2007-01-01

    Results of the study by Blackburn et al. (2004a) of avifauna on oceanic islands suggest that distance from the mainland and time since European colonization have major influences on species extinctions and that island area is a significant but secondary contributing factor. After augmenting the data of the study on geographical properties for some of the islands they examined, we

  1. Extensive linkage disequilibrium and parallel adaptive divergence across threespine stickleback genomes.

    PubMed

    Hohenlohe, Paul A; Bassham, Susan; Currey, Mark; Cresko, William A

    2012-02-01

    Population genomic studies are beginning to provide a more comprehensive view of dynamic genome-scale processes in evolution. Patterns of genomic architecture, such as genomic islands of increased divergence, may be important for adaptive population differentiation and speciation. We used next-generation sequencing data to examine the patterns of local and long-distance linkage disequilibrium (LD) across oceanic and freshwater populations of threespine stickleback, a useful model for studies of evolution and speciation. We looked for associations between LD and signatures of divergent selection, and assessed the role of recombination rate variation in generating LD patterns. As predicted under the traditional biogeographic model of unidirectional gene flow from ancestral oceanic to derived freshwater stickleback populations, we found extensive local and long-distance LD in fresh water. Surprisingly, oceanic populations showed similar patterns of elevated LD, notably between large genomic regions previously implicated in adaptation to fresh water. These results support an alternative biogeographic model for the stickleback radiation, one of a metapopulation with appreciable bi-directional gene flow combined with strong divergent selection between oceanic and freshwater populations. As predicted by theory, these processes can maintain LD within and among genomic islands of divergence. These findings suggest that the genomic architecture in oceanic stickleback populations may provide a mechanism for the rapid re-assembly and evolution of multi-locus genotypes in newly colonized freshwater habitats, and may help explain genetic mapping of parallel phenotypic variation to similar loci across independent freshwater populations. PMID:22201169

  2. Meeting Highlights: Genome Informatics

    PubMed Central

    Ashurst, Jennifer

    2003-01-01

    We bring you the highlights of the second Joint Cold Spring Harbor Laboratory and Wellcome Trust ‘Genome Informatics’ Conference, organized by Ewan Birney, Suzanna Lewis and Lincoln Stein. There were sessions on in silico data discovery, comparative genomics, annotation pipelines, functional genomics and integrative biology. The conference included a keynote address by Sydney Brenner, who was awarded the 2002 Nobel Prize in Physiology or Medicine (jointly with John Sulston and H. Robert Horvitz) a month later. PMID:18629014

  3. De novo methylation of the MyoD1 CpG island during the establishment of immortal cell lines.

    PubMed Central

    Jones, P A; Wolkowicz, M J; Rideout, W M; Gonzales, F A; Marziasz, C M; Coetzee, G A; Tapscott, S J

    1990-01-01

    CpG dinucleotides are unevenly distributed in the vertebrate genome. Bulk DNA is depleted of CpGs and most of the cytosines in the dinucleotide in this fraction are methylated. On the other hand, CpG islands, which are often associated with genes, are unmethylated at testable sites in all normal tissues with the exception of genes on the inactive X chromosome. We used Hpa II/Msp I analysis and ligation-mediated polymerase chain reaction to examine the methylation of the MyoD1 CpG island in adult mouse tissues, early cultures of mouse embryo cells, and immortal fibroblastic cell lines. The island was almost devoid of methylation at CCGG sites in adult mouse tissues and in low-passage mouse embryo fibroblasts. In marked contrast, the island was methylated in 10T 1/2 cells and in six other immortal cell lines showing that methylation of this CpG island had occurred during escape from senescence. The island became even more methylated in chemically transformed derivatives of 10T 1/2 cells. Thus, CpG islands not methylated in normal tissues may become modified to an abnormally high degree during immortalization and transformation. Images PMID:2385586

  4. Integrated genome analysis suggests that most conserved non-coding sequences are regulatory factor binding sites

    PubMed Central

    Hemberg, Martin; Gray, Jesse M.; Cloonan, Nicole; Kuersten, Scott; Grimmond, Sean; Greenberg, Michael E.; Kreiman, Gabriel

    2012-01-01

    More than 98% of a typical vertebrate genome does not code for proteins. Although non-coding regions are sprinkled with short (<200 bp) islands of evolutionarily conserved sequences, the function of most of these unannotated conserved islands remains unknown. One possibility is that unannotated conserved islands could encode non-coding RNAs (ncRNAs); alternatively, unannotated conserved islands could serve as promoter-distal regulatory factor binding sites (RFBSs) like enhancers. Here we assess these possibilities by comparing unannotated conserved islands in the human and mouse genomes to transcribed regions and to RFBSs, relying on a detailed case study of one human and one mouse cell type. We define transcribed regions by applying a novel transcript-calling algorithm to RNA-Seq data obtained from total cellular RNA, and we define RFBSs using ChIP-Seq and DNAse-hypersensitivity assays. We find that unannotated conserved islands are four times more likely to coincide with RFBSs than with unannotated ncRNAs. Thousands of conserved RFBSs can be categorized as insulators based on the presence of CTCF or as enhancers based on the presence of p300/CBP and H3K4me1. While many unannotated conserved RFBSs are transcriptionally active to some extent, the transcripts produced tend to be unspliced, non-polyadenylated and expressed at levels 10 to 100-fold lower than annotated coding or ncRNAs. Extending these findings across multiple cell types and tissues, we propose that most conserved non-coding genomic DNA in vertebrate genomes corresponds to promoter-distal regulatory elements. PMID:22684627

  5. Genome sequence of adherent-invasive Escherichia coli and comparative genomic analysis with other E. coli pathotypes

    PubMed Central

    2010-01-01

    Background Adherent and invasive Escherichia coli (AIEC) are commonly found in ileal lesions of Crohn's Disease (CD) patients, where they adhere to intestinal epithelial cells and invade into and survive in epithelial cells and macrophages, thereby gaining access to a typically restricted host niche. Colonization leads to strong inflammatory responses in the gut suggesting that AIEC could play a role in CD immunopathology. Despite extensive investigation, the genetic determinants accounting for the AIEC phenotype remain poorly defined. To address this, we present the complete genome sequence of an AIEC, revealing the genetic blueprint for this disease-associated E. coli pathotype. Results We sequenced the complete genome of E. coli NRG857c (O83:H1), a clinical isolate of AIEC from the ileum of a Crohn's Disease patient. Our sequence data confirmed a phylogenetic linkage between AIEC and extraintestinal pathogenic E. coli causing urinary tract infections and neonatal meningitis. The comparison of the NRG857c AIEC genome with other pathogenic and commensal E. coli allowed for the identification of unique genetic features of the AIEC pathotype, including 41 genomic islands, and unique genes that are found only in strains exhibiting the adherent and invasive phenotype. Conclusions Up to now, the virulence-like features associated with AIEC are detectable only phenotypically. AIEC genome sequence data will facilitate the identification of genetic determinants implicated in invasion and intracellular growth, as well as enable functional genomic studies of AIEC gene expression during health and disease. PMID:21108814

  6. Comparative Genomics of 12 Strains of Erwinia amylovora Identifies a Pan-Genome with a Large Conserved Core

    PubMed Central

    Mann, Rachel A.; Smits, Theo H. M.; Bühlmann, Andreas; Blom, Jochen; Goesmann, Alexander; Frey, Jürg E.; Plummer, Kim M.; Beer, Steven V.; Luck, Joanne; Duffy, Brion; Rodoni, Brendan

    2013-01-01

    The plant pathogen Erwinia amylovora can be divided into two host-specific groupings; strains infecting a broad range of hosts within the Rosaceae subfamily Spiraeoideae (e.g., Malus, Pyrus, Crataegus, Sorbus) and strains infecting Rubus (raspberries and blackberries). Comparative genomic analysis of 12 strains representing distinct populations (e.g., geographic, temporal, host origin) of E. amylovora was used to describe the pan-genome of this major pathogen. The pan-genome contains 5751 coding sequences and is highly conserved relative to other phytopathogenic bacteria comprising on average 89% conserved, core genes. The chromosomes of Spiraeoideae-infecting strains were highly homogeneous, while greater genetic diversity was observed between Spiraeoideae- and Rubus-infecting strains (and among individual Rubus-infecting strains), the majority of which was attributed to variable genomic islands. Based on genomic distance scores and phylogenetic analysis, the Rubus-infecting strain ATCC BAA-2158 was genetically more closely related to the Spiraeoideae-infecting strains of E. amylovora than it was to the other Rubus-infecting strains. Analysis of the accessory genomes of Spiraeoideae- and Rubus-infecting strains has identified putative host-specific determinants including variation in the effector protein HopX1Ea and a putative secondary metabolite pathway only present in Rubus-infecting strains. PMID:23409014

  7. Human Genome Resources

    NSDL National Science Digital Library

    In an effort to track the progress of and provide access to the work of the Human Genome Project (see the October 14, 1998 Scout Report for Science & Engineering), the National Center for Biotechnology Information (NCBI) of the National Library of Medicine (NLM) has expanded their Web resource. An international research program "designed to construct detailed genetic and physical maps of the human genome." The Human Genome Resources page provides a wealth of relevant resources, from background information on the project, to specific sequences for each human chromosome (click on the desired chromosome), to Genome Maps of other organisms.

  8. The Geee! in Genome

    NSDL National Science Digital Library

    It's too late to catch the Geee! in Genome exhibit at the Canadian Museum of Nature, but virtual visitors can still check out the exhibit's excellent Web companion. The Web site, which is also available in French, is loaded with cool, interactive features on the everyday side of genomics. The Geee! in Genome Web site also contains a set of downloadable lesson plans and activities for grades 5 through 12. Together with the online features, these lesson plans offer a fun and engaging way to learn about genomics in the classroom.

  9. Genomics of Clostridium tetani.

    PubMed

    Brüggemann, Holger; Brzuszkiewicz, Elzbieta; Chapeton-Montes, Diana; Plourde, Lucile; Speck, Denis; Popoff, Michel R

    2015-05-01

    Genomic information about Clostridium tetani, the causative agent of the tetanus disease, is scarce. The genome of strain E88, a strain used in vaccine production, was sequenced about 10 years ago. One additional genome (strain 12124569) has recently been released. Here we report three new genomes of C. tetani and describe major differences among all five C. tetani genomes. They all harbor tetanus-toxin-encoding plasmids that contain highly conserved genes for TeNT (tetanus toxin), TetR (transcriptional regulator of TeNT) and ColT (collagenase), but substantially differ in other plasmid regions. The chromosomes share a large core genome that contains about 85% of all genes of a given chromosome. The non-core chromosome comprises mainly prophage-like genomic regions and genes encoding environmental interaction and defense functions (e.g. surface proteins, restriction-modification systems, toxin-antitoxin systems, CRISPR/Cas systems) and other fitness functions (e.g. transport systems, metabolic activities). This new genome information will help to assess the level of genome plasticity of the species C. tetani and provide the basis for detailed comparative studies. PMID:25638019

  10. Evolutionary genomics of Entamoeba.

    PubMed

    Weedall, Gareth D; Hall, Neil

    2011-01-01

    Entamoeba histolytica is a human pathogen that causes amoebic dysentery and leads to significant morbidity and mortality worldwide. Understanding the genome and evolution of the parasite will help explain how, when and why it causes disease. Here we review current knowledge about the evolutionary genomics of Entamoeba: how differences between the genomes of different species may help explain different phenotypes, and how variation among E. histolytica parasites reveals patterns of population structure. The imminent expansion of the amount genome data will greatly improve our knowledge of the genus and of pathogenic species within it. PMID:21288488

  11. Between two fern genomes.

    PubMed

    Sessa, Emily B; Banks, Jo Ann; Barker, Michael S; Der, Joshua P; Duffy, Aaron M; Graham, Sean W; Hasebe, Mitsuyasu; Langdale, Jane; Li, Fay-Wei; Marchant, D Blaine; Pryer, Kathleen M; Rothfels, Carl J; Roux, Stanley J; Salmi, Mari L; Sigel, Erin M; Soltis, Douglas E; Soltis, Pamela S; Stevenson, Dennis W; Wolf, Paul G

    2014-01-01

    Ferns are the only major lineage of vascular plants not represented by a sequenced nuclear genome. This lack of genome sequence information significantly impedes our ability to understand and reconstruct genome evolution not only in ferns, but across all land plants. Azolla and Ceratopteris are ideal and complementary candidates to be the first ferns to have their nuclear genomes sequenced. They differ dramatically in genome size, life history, and habit, and thus represent the immense diversity of extant ferns. Together, this pair of genomes will facilitate myriad large-scale comparative analyses across ferns and all land plants. Here we review the unique biological characteristics of ferns and describe a number of outstanding questions in plant biology that will benefit from the addition of ferns to the set of taxa with sequenced nuclear genomes. We explain why the fern clade is pivotal for understanding genome evolution across land plants, and we provide a rationale for how knowledge of fern genomes will enable progress in research beyond the ferns themselves. PMID:25324969

  12. Fungal Genomics Program

    SciTech Connect

    Grigoriev, Igor

    2012-03-12

    The JGI Fungal Genomics Program aims to scale up sequencing and analysis of fungal genomes to explore the diversity of fungi important for energy and the environment, and to promote functional studies on a system level. Combining new sequencing technologies and comparative genomics tools, JGI is now leading the world in fungal genome sequencing and analysis. Over 120 sequenced fungal genomes with analytical tools are available via MycoCosm (www.jgi.doe.gov/fungi), a web-portal for fungal biologists. Our model of interacting with user communities, unique among other sequencing centers, helps organize these communities, improves genome annotation and analysis work, and facilitates new larger-scale genomic projects. This resulted in 20 high-profile papers published in 2011 alone and contributing to the Genomics Encyclopedia of Fungi, which targets fungi related to plant health (symbionts, pathogens, and biocontrol agents) and biorefinery processes (cellulose degradation, sugar fermentation, industrial hosts). Our next grand challenges include larger scale exploration of fungal diversity (1000 fungal genomes), developing molecular tools for DOE-relevant model organisms, and analysis of complex systems and metagenomes.

  13. Genome@home

    NSDL National Science Digital Library

    With Genome@home, a project at Stanford University, computer owners can become de facto researchers in virtual genome protein design. By downloading and running the Genome@home protein sequence design client, users lend their idle computer time to run calculations for use with such projects as designing new medical drugs, understanding protein evolution, and determining the function of newly sequenced genes. The program can run during other applications without affecting computer performance. The Genome@home Web site also provides a mountain of scientific background information and other resources for understanding the overall project and learning what's been accomplished so far.

  14. Three Mile Island population registry

    Microsoft Academic Search

    M. K. Goldhaber; G. K. Tokuhata; E. Digon; G. G. Caldwell; G. F. Stein; G. Lutz; D. Gur

    2009-01-01

    Shortly after the March 28, 1979, accident at the Three Mile Island (TMI) nuclear plant outside Harrisburg, Pa., the Pennsylvania Department of Health, in conjunction with the Centers for Disease Control and the U.S. Bureau of the Census, conducted a census of the 35,930 persons residing within 5 miles of the plant. With the help of 150 enumerators, demographic and

  15. The Three Mile Island crisis

    Microsoft Academic Search

    P. S. Houts; P. D. Cleary; T. W. Hu

    1988-01-01

    Since the March 1979 accident at the Three Mile Island (TMI) nuclear power plant, many studies have assessed its impacts. Compiled and summarized in this book are the results of five related surveys, all aimed at the scientific assessment of the psycho-socio-economic behavior of the residents around the TMI facility. These studies are based on a randomly selected, large sample

  16. Pacific Islands Region News Release

    E-print Network

    Braun, contract marine mammal veterinarian for the Pacific Islands Fisheries Science Center. The mother at weaning. Hence, the need for additional food provided in a captive situation to increase their chances and NOAA Fisheries Service personnel where they will begin a week of marine debris cleanup on and around

  17. The Manitoulin Island Space Program.

    ERIC Educational Resources Information Center

    Shaffer, Dianna

    1991-01-01

    Describes a space education program in rural Manitoulin Island, Ontario. Reports that gifted and talented students examined space exploration, built models, met with astronauts, and designed multimedia presentations. Explains that the students also hosted a one-day conference on space for students, teachers, and parents and later visited…

  18. HISTORIC WETLANDS OF PRUDENCE ISLAND

    EPA Science Inventory

    Ten wetland sites around Narragansett Bay, Rhode Island have been selected for a multidisciplinary study. These wetland sites are being studied to develop indicators of "wetland health." The study includes assessing the ecological conditions of the wetlands in the past, and the c...

  19. Chaos in easter island ecology.

    PubMed

    Sprott, J C

    2011-10-01

    This paper demonstrates that a recently proposed dynamical model for the ecology of Easter Island admits periodic and chaotic attractors, not previously reported. Such behavior may more realistically depict the population dynamics of general ecosystems and illustrates the power of simple models to produce the kind of complex behavior that is ubiquitous in such systems. PMID:21933513

  20. Birds are islands for parasites.

    PubMed

    Koop, Jennifer A H; DeMatteo, Karen E; Parker, Patricia G; Whiteman, Noah K

    2014-08-01

    Understanding the mechanisms driving the extraordinary diversification of parasites is a major challenge in evolutionary biology. Co-speciation, one proposed mechanism that could contribute to this diversity is hypothesized to result from allopatric co-divergence of host-parasite populations. We found that island populations of the Galápagos hawk (Buteo galapagoensis) and a parasitic feather louse species (Degeeriella regalis) exhibit patterns of co-divergence across variable temporal and spatial scales. Hawks and lice showed nearly identical population genetic structure across the Galápagos Islands. Hawk population genetic structure is explained by isolation by distance among islands. Louse population structure is best explained by hawk population structure, rather than isolation by distance per se, suggesting that lice tightly track the recent population histories of their hosts. Among hawk individuals, louse populations were also highly structured, suggesting that hosts serve as islands for parasites from an evolutionary perspective. Altogether, we found that host and parasite populations may have responded in the same manner to geographical isolation across spatial scales. Allopatric co-divergence is likely one important mechanism driving the diversification of parasites. PMID:25099959

  1. A Fighter on Long Island.

    ERIC Educational Resources Information Center

    Stover, Del

    1991-01-01

    Superintendent Dan Domenech unsuccessfully battled New York's governor and legislature about a cut in state funding. Long Island has only 16 percent of the state's population but is being earmarked for 50 percent of the cuts. Domenech's earlier successes included a preschool for disadvantaged children, a full-day kindergarten, and a before- and…

  2. The flora of Antipodes Island

    Microsoft Academic Search

    E. J. Godley

    1989-01-01

    The history of botanical exploration of Antipodes Island begins in 1890 and is outlined up to 1985. The numbers of terrestrial species now known are algae (3), fungi (2), lichens (17), liverworts (37), mosses (21), lycopods (3), ferns (17), and flowering plants (52). Three of the latterare adventive (Poa annua, Stellaria media, Sonchus asper). The 20 species of indigenous monocotyledons

  3. An AscI Boundary Library for the Studies of Genetic and Epigenetic Alterations in CpG Islands

    PubMed Central

    Dai, Zunyan; Weichenhan, Dieter; Wu, Yue-Zhong; Hall, Julia L; Rush, Laura J.; Smith, Laura T.; Raval, Aparna; Yu, Li; Kroll, Daniela; Muehlisch, Joerg; Frühwald, Michael C.; de Jong, Pieter; Catanese, Joe; Davuluri, Ramana V.; Smiraglia, Dominic J.; Plass, Christoph

    2002-01-01

    Knudson's two-hit hypothesis postulates that genetic alterations in both alleles are required for the inactivation of tumor-suppressor genes. Genetic alterations include small or large deletions and mutations. Over the past years, it has become clear that epigenetic alterations such as DNA methylation are additional mechanisms for gene silencing. Restriction Landmark Genomic Scanning (RLGS) is a two-dimensional gel electrophoresis that assesses the methylation status of thousands of CpG islands. RLGS has been applied successfully to scan cancer genomes for aberrant DNA methylation patterns. So far, the majority of this work was done using NotI as the restriction landmark site. Here, we describe the development of RLGS using AscI as the restriction landmark site for genome-wide scans of cancer genomes. The availability of AscI as a restriction landmark for RLGS allows for scanning almost twice as many CpG islands in the human genome compared with using NotI only. We describe the development of an AscI–EcoRV boundary library that supports the cloning of novel methylated genes. Feasibility of this system is shown in three tumor types, medulloblastomas, lung cancers, and head and neck cancers. We report the cloning of 178 AscI RLGS fragments via two methods by use of this library. [Supplemental material is available online at http://www.genome.org.] PMID:12368252

  4. Nanoindentation response of piezoelectric nano-islands

    NASA Astrophysics Data System (ADS)

    Cheng, Guang; Sriram, Sharath; Bhaskaran, Madhu; Venkatesh, T. A.

    2014-09-01

    Through three-dimensional finite element modeling, it is demonstrated that the nanoindentation response of piezoelectric nano-islands is strongly dependent on the shape of the nano-island and the depth of indentation. For indentations that are relatively deep (i.e., greater than 5% of the height of the islands), the substrate's elastic and plastic properties have a strong influence on the indentation response of piezoelectric nano-islands with substrate plasticity resulting in a significant reduction in the mechanical and electrical indentation stiffness. The predictions of the finite element models compare well with experiments on nano-islands of strontium-doped lead zirconate titanate.

  5. Polar Bears International : Wrangel Island, Russia

    NSDL National Science Digital Library

    2007-12-12

    This site describes the ongoing research of the polar bears in the Russian High Arctic. Wrangel Island with neighboring small island, Herald Island, are the key reproductive areas for the Chukchi-Alaskan polar bear population. Marine areas and Wrangel and Herald islands provide optimum foraging habitats for polar bears, and polar bear densities in these marine habitats are high all year round. Approximately 350-500 pregnant female polar bears construct their maternity dens on Wrangel and Herald islands every fall, emerging with their cubs in spring. The research is described in terms of goals and objectives, structure, methods, equipment, staff, and implementations.

  6. Resources | Office of Cancer Genomics

    Cancer.gov

    The Center for Cancer Genomics (CCG) was established to unify the National Cancer Institute's activities in cancer genomics, with the goal of advancing genomics research and translating findings into the clinic to improve the precise diagnosis and treatment of cancers.

  7. Genomic analysis of mouse tumorigenesis

    E-print Network

    Tam, Mandy Chi-Mun

    2006-01-01

    The availability of the human and mouse genome sequences has spurred a growing interest in analyzing mouse models of human cancer using genomic techniques. Comparative genomic studies on mouse and human tumors can be ...

  8. A feast of protozoan genomes

    Microsoft Academic Search

    Christiane Hertz-Fowler; Matthew Berriman; Arnab Pain

    2005-01-01

    The recent completion of five new protozoan parasite genomes should lead to an improved understanding of their biology and, through comparative genomics, shed light on protozoan genome diversity and evolution.

  9. FUNCTIONAL GENOMICS Program of Study

    E-print Network

    Thomas, Andrew

    FUNCTIONAL GENOMICS Program of Study Research Areas Students Applying Correspondence Graduate Genomics. Students receive training in the biological, physical and computational sciences through of primary institutional affiliation. The Functional Genomics program is administered through the Graduate

  10. The Future of Microbial Genomics

    SciTech Connect

    Kyrpides, Nikos [Genome Biology group at the DOE Joint Genome Institute

    2010-06-02

    Nikos Kyrpides, head of the Genome Biology group at the DOE Joint Genome Institute discusses current challenges in the field of microbial genomics on June 2, 2010 at the "Sequencing, Finishing, Analysis in the Future" meeting in Santa Fe, NM

  11. A novel mutation in ferroportin1 is associated with haemochromatosis in a Solomon Islands patient

    PubMed Central

    Arden, K E; Wallace, D F; Dixon, J L; Summerville, L; Searle, J W; Anderson, G J; Ramm, G A; Powell, L W; Subramaniam, V N

    2003-01-01

    Background: A severe form of iron overload with the clinicopathological features of haemochromatosis inherited in an autosomal dominant manner has been described in the Solomon Islands. The genetic basis of the disorder has not been identified. The disorder has similarities to type 4 haemochromatosis, which is caused by mutations in ferroportin1. Aims: The aims of this study were to identify the genetic basis of iron overload in a patient from the Solomon Islands. Patient and methods: Genomic DNA was isolated from peripheral blood leucocytes of a Solomon Islands man with severe iron overload. The entire coding region and splice sites of the ferroportin1 gene was sequenced. Results and conclusions: A novel missense mutation (431A>C; N144T) was identified in exon 5 of the ferroportin1 gene. A novel restriction endonuclease based assay which identifies both the N144T and N144H mutations was developed which will simplify the diagnosis and screening of patients for iron overload in the Solomon Islands and other populations. This is the first identified mutation associated with haemochromatosis in the Solomon Islands population. PMID:12865285

  12. Barrier island bistability induced by biophysical interactions

    NASA Astrophysics Data System (ADS)

    Durán Vinent, Orencio; Moore, Laura J.

    2015-02-01

    Barrier islands represent about 10% of the world’s coastline, sustain rich ecosystems, host valuable infrastructure and protect mainland coasts from storms. Future climate-change-induced increases in the intensity and frequency of major hurricanes and accelerations in sea-level rise will have a significant impact on barrier islands--leading to increased coastal hazards and flooding--yet our understanding of island response to external drivers remains limited. Here, we find that island response is intrinsically bistable and controlled by previously unrecognized dynamics: the competing, and quantifiable, effects of storm erosion, sea-level rise, and the aeolian and biological processes that enable and drive dune recovery. When the biophysical processes driving dune recovery dominate, islands tend to be high in elevation and vulnerability to storms is minimized. Alternatively, when the effects of storm erosion dominate, islands may become trapped in a perpetual state of low elevation and maximum vulnerability to storms, even under mild storm conditions. When sea-level rise dominates, islands become unstable and face possible disintegration. This quantification of barrier island dynamics is supported by data from the Virginia Barrier Islands, USA and provides a broader context for considering island response to climate change and the likelihood of potentially abrupt transitions in island state.

  13. Alternative energy technologies for the Caribbean islands

    SciTech Connect

    Pytlinski, J.T. (Univ. of Puerto Rico, San Juan (Puerto Rico))

    1992-01-01

    All islands in the Caribbean except Puerto Rico can be classified as developing islands. Of these islands, all except Trinidad and Tobago are oil importers. Uncertainties concerning uninterrupted oil supply and increasing oil prices causes economic, social and political instability and jeopardizes further development of these islands. The paper discusses the energy situation of the Caribbean islands and presents alternative energy options. Several alternative energy projects financed by local, federal and international organizations are presented. Present and future uses of alternative energy technologies are described in different islands. Barrier which handicap developing and implementing alternative energy sources in the Caribbean are discussed. The potential and possible applications of alternative energy technologies such as: solar-thermal energy, photovoltaics, wind energy, ocean thermal energy conversion (OTEC), ocean currents and tides energy, biomass, peat energy, municipal solid wastes, bioconversion, hydropower, geothermal energy, nuclear energy and energy conservation are discussed in detail as means to alleviate the energy situation in the Caribbean islands.

  14. Magnetic island evolution in hot ion plasmas

    SciTech Connect

    Ishizawa, A.; Nakajima, N. [National Institute for Fusion Science, Toki 509-5292 (Japan); Waelbroeck, F. L.; Fitzpatrick, R.; Horton, W. [Institute for Fusion Studies, University of Texas at Austin, Austin, Texas 78712 (United States)

    2012-07-15

    Effects of finite ion temperature on magnetic island evolution are studied by means of numerical simulations of a reduced set of two-fluid equations which include ion as well as electron diamagnetism in slab geometry. The polarization current is found to be almost an order of magnitude larger in hot than in cold ion plasmas, due to the strong shear of ion velocity around the separatrix of the magnetic islands. As a function of the island width, the propagation speed decreases from the electron drift velocity (for islands thinner than the Larmor radius) to values close to the guiding-center velocity (for islands of order 10 times the Larmor radius). In the latter regime, the polarization current is destabilizing (i.e., it drives magnetic island growth). This is in contrast to cold ion plasmas, where the polarization current is generally found to have a healing effect on freely propagating magnetic island.

  15. 25 CFR 241.2 - Annette Islands Reserve; definition; exclusive fishery; licenses.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ...Proclamation of April 28, 1916 (39 Stat. 1777), as the waters within three thousand feet from the shore lines at mean low tide of Annette Island, Ham Island, Walker Island, Lewis Island, Spire Island, Hemlock Island, and adjacent rocks and...

  16. 25 CFR 241.2 - Annette Islands Reserve; definition; exclusive fishery; licenses.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ...Proclamation of April 28, 1916 (39 Stat. 1777), as the waters within three thousand feet from the shore lines at mean low tide of Annette Island, Ham Island, Walker Island, Lewis Island, Spire Island, Hemlock Island, and adjacent rocks and...

  17. 25 CFR 241.2 - Annette Islands Reserve; definition; exclusive fishery; licenses.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ...Proclamation of April 28, 1916 (39 Stat. 1777), as the waters within three thousand feet from the shore lines at mean low tide of Annette Island, Ham Island, Walker Island, Lewis Island, Spire Island, Hemlock Island, and adjacent rocks and...

  18. Methylation detection oligonucleotide microarray analysis: a high-resolution method for detection of CpG island methylation

    PubMed Central

    Kamalakaran, Sitharthan; Kendall, Jude; Zhao, Xiaoyue; Tang, Chunlao; Khan, Sohail; Ravi, Kandasamy; Auletta, Theresa; Riggs, Michael; Wang, Yun; Helland, Åslaug; Naume, Bjørn; Dimitrova, Nevenka; Børresen-Dale, Anne-Lise; Hicks, Jim; Lucito, Robert

    2009-01-01

    Methylation of CpG islands associated with genes can affect the expression of the proximal gene, and methylation of non-associated CpG islands correlates to genomic instability. This epigenetic modification has been shown to be important in many pathologies, from development and disease to cancer. We report the development of a novel high-resolution microarray that detects the methylation status of over 25 000 CpG islands in the human genome. Experiments were performed to demonstrate low system noise in the methodology and that the array probes have a high signal to noise ratio. Methylation measurements between different cell lines were validated demonstrating the accuracy of measurement. We then identified alterations in CpG islands, both those associated with gene promoters, as well as non-promoter-associated islands in a set of breast and ovarian tumors. We demonstrate that this methodology accurately identifies methylation profiles in cancer and in principle it can differentiate any CpG methylation alterations and can be adapted to analyze other species. PMID:19474344

  19. Shaded Relief Mosaic of Umnak Island, Aleutian Islands, Alaska

    NASA Technical Reports Server (NTRS)

    2001-01-01

    This image is a shaded relief mosaic of Umnak Island in Alaska's Aleutian Islands.

    It was created with Airsar data that was geocoded and combined into this mosaic as part of a NASA-funded Alaska Digital Elevation Model Project at the Alaska Synthetic Aperture Radar Facility (ASF) at the University of Alaska Geophysical Institute in Fairbanks, Alaska.

    Airsar collected the Alaska data as part of its PacRim 2000 Mission, which took the instrument to French Polynesia, American and Western Samoa, Fiji, New Zealand, Australia, New Guinea, Indonesia, Malaysia, Cambodia, Philippines, Taiwan, South Korea, Japan, Northern Marianas, Guam, Palau, Hawaii and Alaska. Airsar, part of NASA's Airborne Science Program, is managed for NASA's Earth Science Enterprise by JPL. JPL is a division of the California Institute of Technology in Pasadena.

  20. Barrier Island Failure During Hurricane Katrina

    NASA Astrophysics Data System (ADS)

    Sallenger, A.; Howd, P.; Stockdon, H.; Wright, C. W.; Fauver, L.; Guy, K.

    2006-12-01

    Classical models of barrier-island response to storms predict that wave runup can periodically overtop an island and transport sand from its seaside to its bayside, forcing the island to migrate landward. While this process can destroy fixed human developments, the island survives with little net change in form or dimensions. In contrast, we find that Louisiana's Chandeleur Islands during Hurricane Katrina were not periodically overtopped by waves, but were continuously inundated by storm surge. When such inundation occurs locally on a barrier island, it can force the erosion of a narrow breach that connects sea and bay. However, little is known about the response of a barrier island when it is entirely submerged. Here, we show that the Chandeleur Islands approached complete failure, losing 84% of their surface area. Their Gulf of Mexico shorelines retreated landward an average of 268 m, the largest retreat ever reported for a storm. Sand was stripped from the islands, reducing their peak elevation from >6 m to <3 m and exposing them to further degradation and potential failure by future hurricanes of less intensity than Katrina. Further, the islands that survived Katrina were marsh remnants composed of mud and vegetation that relatively small waves diminished following the storm. The Chandeleur Islands are prone to failure because of their location on the Mississippi delta where small sand supply and large sea-level rise (induced locally by land subsidence) limit natural rebuilding of the islands following a storm. The response of the delta's barrier islands during Hurricane Katrina provides a warning of how the world's barrier islands might respond to storm-surge inundation should predictions of accelerated global sea level rise prove accurate.

  1. Honey Bee Genome

    NSDL National Science Digital Library

    0000-00-00

    Human genome sequencing center at Baylor College of medicine has completed the honey bee genome (2006). It is available for download by chromosome. It can also be searched using NCBI megablast. Other links include the Nature press release and PDFs of several other related articles.

  2. GENOMICS OF ORAL BACTERIA

    Microsoft Academic Search

    Margaret J. Duncan

    Advances in bacterial genetics came with the discovery of the genetic code, followed by the development of recombinant DNA technologies. Now the field is undergoing a new revolution because of investigators' ability to sequence and assemble complete bacterial genomes. Over 200 genome projects have been completed or are in progress, and the oral microbi- ology research community has benefited through

  3. Genomics of Oral Bacteria

    Microsoft Academic Search

    Margaret J. Duncan

    2003-01-01

    Advances in bacterial genetics came with the discovery of the genetic code, followed by the development of recombinant DNA technologies. Now the field is undergoing a new revolution because of investigators’ ability to sequence and assemble complete bacterial genomes. Over 200 genome projects have been completed or are in progress, and the oral microbiology research community has benefited through projects

  4. Plant Functional Genomics

    NSDL National Science Digital Library

    Chris Somerville (Carnegie Institution of Washington; Department of Plant Biology)

    1999-07-16

    Nucleotide sequencing of the Arabidopsis genome is nearing completion, sequencing of the rice genome has begun, and large amounts of expressed sequence tag information are being obtained for many other plants. There are many opportunities to use this wealth of sequence information to accelerate progress toward a comprehensive understanding of the genetic mechanisms that control plant growth and development and responses to the environment.

  5. Species: Comparing Their Genome

    NSDL National Science Digital Library

    Howard Hughes Medical Institute (Howard Hughes Medical Institute; )

    2001-06-01

    The reprinted resource illustrates how mapping the genome of different species reveals that: all living things share parallel genes, the genome of other species can be used for human disease research, many diseases are caused by defective genes or proteins, and so far, the mouse offers the best insight into human disease.

  6. Unlocking the bovine genome

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The draft genome sequence of cattle (Bos taurus) has now been analyzed by the Bovine Genome Sequencing and Analysis Consortium and the Bovine HapMap Consortium, which together represent an extensive collaboration involving more than 300 scientists from 25 different countries. ...

  7. SGD: Saccharomyces Genome Database

    Microsoft Academic Search

    J. Michael Cherry; Caroline Adler; Catherine A. Ball; Stephen A. Chervitz; Selina S. Dwight; Erich T. Hester; Yankai Jia; Gail Juvik; Taiyun Roe; Mark Schroeder; Shuai Weng; David Botstein

    1998-01-01

    The Saccharomyces Genome Database (SGD) provides Internet access to the complete Saccharomyces cerevisiae genomic s equence, i ts g enes a nd t heir products, the p henotypes of i ts m utants, a nd t he literature supporting these data. The amount of information and t he n umber o f features p rovided b y SGD have i

  8. The Human Genome Project

    Microsoft Academic Search

    Maynard V. Olson

    1993-01-01

    The Human Genome Project in the United States is now well underway. Its programmatic direction was largely set by a National Research Council report issued in 1988. The broad framework supplied by this report has survived almost unchanged despite an upheaval in the technology of genome analysis. This upheaval has primarily affected physical and genetic mapping, the two dominant activities

  9. The Chicken Genome

    Microsoft Academic Search

    D. Burt

    2006-01-01

    The chicken has long been an important model organism for developmental biology, as well as a major source of protein with billions of birds used in meat and egg production each year. Chicken genomics has been transformed in recent years, with the characterisation of large EST collections and most recently with the assembly of the chicken genome sequence. Since the

  10. Genetics and Genomics

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Good progress is being made on genetics and genomics of sugar beet, however it is in process and the tools are now being generated and some results are being analyzed. The GABI BeetSeq project released a first draft of the sugar beet genome of KWS2320, a dihaploid (see http://bvseq.molgen.mpg.de/Gen...

  11. GENOMICS, HEALTH, AND SOCIETY

    Microsoft Academic Search

    CHEE KHOON CHAN

    2002-01-01

    On June 27, 2001, the World Health Organization conducted hearings in Geneva for a Special Report on Genomics & Health. Initially intended as a document to address the ethical, legal, and social implications of the gathering genomics resolution (ELSI), the terms of reference of the report were signifi- cantly modified to give primary emphasis to a scientific and technological assessment

  12. Breeding-assisted genomics.

    PubMed

    Poland, Jesse

    2015-04-01

    The revolution of inexpensive sequencing has ushered in an unprecedented age of genomics. The promise of using this technology to accelerate plant breeding is being realized with a vision of genomics-assisted breeding that will lead to rapid genetic gain for expensive and difficult traits. The reality is now that robust phenotypic data is an increasing limiting resource to complement the current wealth of genomic information. While genomics has been hailed as the discipline to fundamentally change the scope of plant breeding, a more symbiotic relationship is likely to emerge. In the context of developing and evaluating large populations needed for functional genomics, none excel in this area more than plant breeders. While genetic studies have long relied on dedicated, well-structured populations, the resources dedicated to these populations in the context of readily available, inexpensive genotyping is making this philosophy less tractable relative to directly focusing functional genomics on material in breeding programs. Through shifting effort for basic genomic studies from dedicated structured populations, to capturing the entire scope of genetic determinants in breeding lines, we can move towards not only furthering our understanding of functional genomics in plants, but also rapidly improving crops for increased food security, availability and nutrition. PMID:25795171

  13. Specialist fungi, versatile genomes

    Microsoft Academic Search

    Christiane Hertz-Fowler; Arnab Pain

    2007-01-01

    In recent years, the number of completely sequenced fungal genomes has steadily increased, with many more close to completion. This allows genomic comparisons to be made across several fungal genera that differ significantly with respect to their morphology, lifestyle and metabolic potential.

  14. ‘Genomics’: Buzzword or reality?

    Microsoft Academic Search

    Bertrand R. Jordan

    1999-01-01

    ‘Genomics’ has become a widely used term, covering a range of approaches that make use of the newly acquired wealth of genome data (both on man and on a number of model organisms) to gain new insights and accelerate research. This review attempts to present a clear and balanced view of developments in this field, to describe the four major

  15. | Office of Cancer Genomics

    Cancer.gov

    Dr. Louis Staudt, a member of the National Academy of Sciences, is a leading expert in lymphoma research within NCI’s intramural research program. He was recently named the Director of the Center for Cancer Genomics (CCG), the organization that encompasses the Office of Cancer Genomics. In this short interview, Dr. Staudt discusses the objectives, challenges, and future directions of the Center.

  16. Automated Microbial Genome Annotation

    SciTech Connect

    Land, Miriam [DOE Joint Genome Institute at Oak Ridge National Laboratory

    2009-05-29

    Miriam Land of the DOE Joint Genome Institute at Oak Ridge National Laboratory gives a talk on the current state and future challenges of moving toward automated microbial genome annotation at the "Sequencing, Finishing, Analysis in the Future" meeting in Santa Fe, NM

  17. Whole-Genome Sequence of CMY-2 ?-Lactamase-Producing Salmonella enterica Serovar Typhimurium Strain L-3553

    PubMed Central

    Sekizuka, Tsuyoshi; Lee, Ken-ichi; Kuroda, Makoto; Kusumoto, Masahiro; Iwata, Taketoshi; Uchida, Ikuo; Tanaka, Kiyoshi; Tamamura, Yukino

    2014-01-01

    Salmonella enterica serovar Typhimurium pulsed-field gel electrophoresis cluster VII has been isolated from cattle populations in Japan since the mid-2000s. Some cluster VII isolates exhibited extended-spectrum cephalosporin resistance defined by the blaCMY-2 gene located in a chromosomal genomic island, GI-VII-6. We determined the whole-genome sequence of strain L-3553 as the reference strain. PMID:25059867

  18. The UCSC Genome Browser

    PubMed Central

    Karolchik, Donna; Hinrichs, Angie S.; Kent, W. James

    2011-01-01

    The University of California Santa Cruz (UCSC) Genome Browser is a popular Web-based tool for quickly displaying a requested portion of a genome at any scale, accompanied by a series of aligned annotation “tracks.” The annotations generated by the UCSC Genome Bioinformatics Group and external collaborators include gene predictions, mRNA and expressed sequence tag alignments, simple nucleotide polymorphisms, expression and regulatory data, phenotype and variation data, and pairwise and multiple-species comparative genomics data. All information relevant to a region is presented in one window, facilitating biological analysis and interpretation. The database tables underlying the Genome Browser tracks can be viewed, downloaded, and manipulated using another Web-based application, the UCSC Table Browser. Users can upload personal datasets in a wide variety of formats as custom annotation tracks in both browsers for research or educational purposes. PMID:21975940

  19. Genomics in Education

    NSDL National Science Digital Library

    Elgin, Sarah C. R.

    Created by Professor Sarah C.R. Elgin at Washington University, the Genome Sequencing Video Tour is "aimed at increasing the scientific literacy of biology students in the technology of genomic sequence." Here, visitors can watch the entire tour, which include segments featuring an exploration of current genomic research in a pathogenic bacteria and an animated explanation of the chemistry of cycle sequencing. The site also includes several key resources that have been developed in collaboration with Washington University biology students. Visitors will find four different bioinformatics lab demonstrations here including "Investigating Eukaryotic Genome: Cloning and Sequencing a Fragment of Yeast DNA". Also, science teachers shouldn't miss the research-based course "Research Explorations in Genomics" available here, and they should also be sure to check out the information about their Summer Research Fellows program, which gives high school teachers the opportunity to learn about new research projects in a faculty member's lab.

  20. CDC: Public Health Genomics

    NSDL National Science Digital Library

    Created in 1997, the Office of Public Health Genomics (OPHG) was established "to integrate genomics into public health research, policy, and programs, which could improve interventions designed to prevent and control the country's leading chronic, infectious, environmental, and occupational diseases." Visitors to the site should start by looking over their "Focus Areas", which include "Genomics and Health", "Family Health History", and "Genetic Testing". The "Genomics and Health" area is a great place to begin looking through the site, as it contains materials that explain the relationship between genetic history and family health. Here visitors will find activities that explain and illuminate environmental health, hereditary blood disorders, and pediatric genetics. Also, the site includes a "For Health Professionals" area which is perfect for current public health practitioners and those teaching about these subjects. Rounding out the site is their "Genomics and Health Impact" blog, which is definitely worth a look.

  1. Microbial Genomes Multiply

    NASA Technical Reports Server (NTRS)

    Doolittle, Russell F.

    2002-01-01

    The publication of the first complete sequence of a bacterial genome in 1995 was a signal event, underscored by the fact that the article has been cited more than 2,100 times during the intervening seven years. It was a marvelous technical achievement, made possible by automatic DNA-sequencing machines. The feat is the more impressive in that complete genome sequencing has now been adopted in many different laboratories around the world. Four years ago in these columns I examined the situation after a dozen microbial genomes had been completed. Now, with upwards of 60 microbial genome sequences determined and twice that many in progress, it seems reasonable to assess just what is being learned. Are new concepts emerging about how cells work? Have there been practical benefits in the fields of medicine and agriculture? Is it feasible to determine the genomic sequence of every bacterial species on Earth? The answers to these questions maybe Yes, Perhaps, and No, respectively.

  2. Population genomics of the endangered giant Galápagos tortoise

    PubMed Central

    2013-01-01

    Background The giant Galápagos tortoise, Chelonoidis nigra, is a large-sized terrestrial chelonian of high patrimonial interest. The species recently colonized a small continental archipelago, the Galápagos Islands, where it has been facing novel environmental conditions and limited resource availability. To explore the genomic consequences of this ecological shift, we analyze the transcriptomic variability of five individuals of C. nigra, and compare it to similar data obtained from several continental species of turtles. Results Having clarified the timing of divergence in the Chelonoidis genus, we report in C. nigra a very low level of genetic polymorphism, signatures of a weakened efficacy of purifying selection, and an elevated mutation load in coding and regulatory sequences. These results are consistent with the hypothesis of an extremely low long-term effective population size in this insular species. Functional evolutionary analyses reveal a reduced diversity of immunity genes in C. nigra, in line with the hypothesis of attenuated pathogen diversity in islands, and an increased selective pressure on genes involved in response to stress, potentially related to the climatic instability of its environment and its elongated lifespan. Finally, we detect no population structure or homozygosity excess in our five-individual sample. Conclusions These results enlighten the molecular evolution of an endangered taxon in a stressful environment and point to island endemic species as a promising model for the study of the deleterious effects on genome evolution of a reduced long-term population size. PMID:24342523

  3. Draft Genome Sequences of Corynebacterium kroppenstedtii CNM633/14 and CNM632/14, Multidrug-Resistant and Antibiotic-Sensitive Isolates from Nodules of Granulomatous Mastitis Patients

    PubMed Central

    Soriano, Francisco; Ariza-Miguel, Jaime; Marrodan-Ciordia, Teresa; Acedo, Alberto; Hernandez, Marta; Tauch, Andreas

    2015-01-01

    Corynebacterium kroppenstedtii has been associated with infections of the female breast. Genome sequencing of two strains revealed a specific genomic island in the multidrug-resistant isolate CNM633/14 with similarity to the R plasmid pJA144188 of Corynebacterium resistens DSM 45100, being indicative of the horizontal transfer of antibiotic resistance genes to C. kroppenstedtii. PMID:25999560

  4. Okhotskia: International Kuril Island Project

    NSDL National Science Digital Library

    This website presents the International Kuril Island Project (IKIP), "an international collaboration of American, Russian, and Japanese scientists to survey the plants, insects, spiders, freshwater and terrestrial mollusks, freshwater fishes, amphibians, and reptiles of the Kuril Archipelago." The website was developed primarily "to provide easy access to project results and databases, both for participants and other interested scientists." Site visitors can link to the project proposal -- submitted by the University of Washington, Russian Academy of Sciences, and Hokkaido University -- to view text and images describing project Objectives, Rationale and Scope, Anticipated Future Research, and more. Links are also provided to project Results (including IKIP databases, publications, and presentations) and Island Info including sections on Vascular Plants, Stoneflies, Nesting Birds, and many more. Additionally, a very nicely organized photo gallery features maps and many beautiful photographs taken by project participants during collecting expeditions to the Kuril Archipelago.

  5. Tsunami Forecast for Galapagos Islands

    NASA Astrophysics Data System (ADS)

    Renteria, W.

    2012-04-01

    The objective of this study is to present a model for the short-term and long-term tsunami forecast for Galapagos Islands. For both cases the ComMIT/MOST(Titov,et al 2011) numerical model and methodology have been used. The results for the short-term model has been compared with the data from Lynett et al, 2011 surveyed from the impacts of the March/11 in the Galapagos Islands. For the case of long-term forecast, several scenarios have run along the Pacific, an extreme flooding map is obtained, the method is considered suitable for places with poor or without tsunami impact information, but under tsunami risk geographic location.

  6. Evolution of genome architecture.

    PubMed

    Koonin, Eugene V

    2009-02-01

    Charles Darwin believed that all traits of organisms have been honed to near perfection by natural selection. The empirical basis underlying Darwin's conclusions consisted of numerous observations made by him and other naturalists on the exquisite adaptations of animals and plants to their natural habitats and on the impressive results of artificial selection. Darwin fully appreciated the importance of heredity but was unaware of the nature and, in fact, the very existence of genomes. A century and a half after the publication of the "Origin", we have the opportunity to draw conclusions from the comparisons of hundreds of genome sequences from all walks of life. These comparisons suggest that the dominant mode of genome evolution is quite different from that of the phenotypic evolution. The genomes of vertebrates, those purported paragons of biological perfection, turned out to be veritable junkyards of selfish genetic elements where only a small fraction of the genetic material is dedicated to encoding biologically relevant information. In sharp contrast, genomes of microbes and viruses are incomparably more compact, with most of the genetic material assigned to distinct biological functions. However, even in these genomes, the specific genome organization (gene order) is poorly conserved. The results of comparative genomics lead to the conclusion that the genome architecture is not a straightforward result of continuous adaptation but rather is determined by the balance between the selection pressure, that is itself dependent on the effective population size and mutation rate, the level of recombination, and the activity of selfish elements. Although genes and, in many cases, multigene regions of genomes possess elaborate architectures that ensure regulation of expression, these arrangements are evolutionarily volatile and typically change substantially even on short evolutionary scales when gene sequences diverge minimally. Thus, the observed genome architectures are, mostly, products of neutral processes or epiphenomena of more general selective processes, such as selection for genome streamlining in successful lineages with large populations. Selection for specific gene arrangements (elements of genome architecture) seems only to modulate the results of these processes. PMID:18929678

  7. How to Trace Island Freeboard

    Microsoft Academic Search

    Ricardo Alexandre dos Santos Ramalho

    \\u000a The vertical movements affecting island edifices have a direct effect on the evolutionary history of those edifices. During\\u000a the seamount stage, the height of the edifice relative to the ocean’s surface—a parameter that mostly depends on the volcanic\\u000a activity and the uplift\\/subsidence of the edifice—has a strong impact on the dominant eruptive style. This happens because\\u000a the height of the

  8. The Three Mile Island crisis

    SciTech Connect

    Houts, P.S.; Cleary, P.D.; Hu, T.W.

    1988-01-01

    Since the March 1979 accident at the Three Mile Island (TMI) nuclear power plant, many studies have assessed its impacts. Compiled and summarized in this book are the results of five related surveys, all aimed at the scientific assessment of the psycho-socio-economic behavior of the residents around the TMI facility. These studies are based on a randomly selected, large sample of the population (with telephones) around TMI.

  9. Institute for Plant Genomics and Biotechnology GENOMICS AND BIOTECHNOLOGY

    E-print Network

    Institute for Plant Genomics and Biotechnology GENOMICS AND BIOTECHNOLOGY A multidisciplinary organization, the Institute for Plant Genomics and Biotechnology is a composed of faculty members representing projects at the Institute for Plant Genomics and Biotechnology include the development of transgenic plants

  10. Genome Analysis Genome-Wide Characterization of the Lignification

    E-print Network

    Gent, Universiteit

    , is indispensable for plant structure and defense. With the availability of the full genome sequence, large such as Arabidopsis, for which the genome sequence and efficient reverse genetics tools are available (ArabidopsisGenome Analysis Genome-Wide Characterization of the Lignification Toolbox in Arabidopsis1[w] Jeroen

  11. Human genome diversity: What about the other human genome project?

    Microsoft Academic Search

    Henry T. Greely

    2001-01-01

    Although the Human Genome Project has been successful, the Human Genome Diversity Project, proposed in 1991, has so far failed to thrive. One of the main values in studying the human genome, however, will come from examining its variations and their effects. To do that in a systematic way, an active Human Genome Diversity Project, or something very similar, will

  12. The medaka draft genome and insights into vertebrate genome evolution

    Microsoft Academic Search

    Masahiro Kasahara; Kiyoshi Naruse; Shin Sasaki; Yoichiro Nakatani; Wei Qu; Budrul Ahsan; Tomoyuki Yamada; Yukinobu Nagayasu; Koichiro Doi; Yasuhiro Kasai; Tomoko Jindo; Daisuke Kobayashi; Atsuko Shimada; Atsushi Toyoda; Yoko Kuroki; Asao Fujiyama; Takashi Sasaki; Atsushi Shimizu; Shuichi Asakawa; Nobuyoshi Shimizu; Shin-Ichi Hashimoto; Jun Yang; Yongjun Lee; Kouji Matsushima; Sumio Sugano; Mitsuru Sakaizumi; Takanori Narita; Kazuko Ohishi; Shinobu Haga; Fumiko Ohta; Hisayo Nomoto; Keiko Nogata; Tomomi Morishita; Tomoko Endo; Tadasu Shin-I; Hiroyuki Takeda; Shinichi Morishita; Yuji Kohara

    2007-01-01

    Teleosts comprise more than half of all vertebrate species and have adapted to a variety of marine and freshwater habitats. Their genome evolution and diversification are important subjects for the understanding of vertebrate evolution. Although draft genome sequences of two pufferfishes have been published, analysis of more fish genomes is desirable. Here we report a high-quality draft genome sequence of

  13. Comparative and Functional Genomics Comp Funct Genom 2003; 4: 3136.

    E-print Network

    Allen, John F.

    Comparative and Functional Genomics Comp Funct Genom 2003; 4: 31­36. Published online in Wiley and mitochondria contain genomes John F. Allen* Plant Biochemistry, Center for Chemistry and Chemical Engineering that the nucleotide sequences of mitochondrial and chloroplast genomes would provide the answer has proved unfounded

  14. Fuzzy Genome Sequence Assembly for Single and Environmental Genomes

    E-print Network

    Nicolescu, Monica

    Fuzzy Genome Sequence Assembly for Single and Environmental Genomes Sara Nasser, Adrienne Breland. Traditional methods obtain a microorganism's DNA by culturing it in- dividually. Recent advances in genomics microbial commu- nities are often very complex with tens and hundreds of species. Assembling these genomes

  15. Update on Genomic Studies of Algae Paths toward Algal Genomics

    E-print Network

    Update on Genomic Studies of Algae Paths toward Algal Genomics Arthur R. Grossman* The Carnegie of genomic information that is being used to help researchers understand the gene content of organisms, how the expression of genes. In this introductory manuscript, I discuss select algae and how genomics is impacting

  16. Comparative and Functional Genomics Comp Funct Genom 2003; 4: 239245.

    E-print Network

    Wurtele, Eve Syrkin

    Comparative and Functional Genomics Comp Funct Genom 2003; 4: 239­245. Published online 1 April://www.botany.iastate.edu/mash/metnetex/metabolicnetex.html) is pub- licly available software in development for analysis of genome-wide RNA, protein and metabolite in the post-genome era is to understand how interactions among molecules in a cell determine its form

  17. Genome Analysis The MaSuRCA genome Assembler

    E-print Network

    Yorke, James

    1 Genome Analysis The MaSuRCA genome Assembler Aleksey Zimin1,* , Guillaume Marçais1 , Daniela Puiu of the genome by short reads at a very low cost, which has prompted development of new assembly methods genome. We show that MaSuRCA performs on par or better than Allpaths-LG and sig- nificantly better than

  18. A global analysis of island pyrogeography

    NASA Astrophysics Data System (ADS)

    Trauernicht, C.; Murphy, B. P.

    2014-12-01

    Islands have provided insight into the ecological role of fire worldwide through research on the positive feedbacks between fire and nonnative grasses, particularly in the Hawaiian Islands. However, the global extent and frequency of fire on islands as an ecological disturbance has received little attention, possibly because 'natural fires' on islands are typically limited to infrequent dry lightning strikes and isolated volcanic events. But because most contemporary fires on islands are anthropogenic, islands provide ideal systems with which to understand the linkages between socio-economic development, shifting fire regimes, and ecological change. Here we use the density of satellite-derived (MODIS) active fire detections for the years 2000-2014 and global data sets of vegetation, climate, population density, and road development to examine the drivers of fire activity on islands at the global scale, and compare these results to existing pyrogeographic models derived from continental data sets. We also use the Hawaiian Islands as a case study to understand the extent to which novel fire regimes can pervade island ecosystems. The global analysis indicates that fire is a frequent disturbance across islands worldwide, strongly affected by human activities, indicating people can more readily override climatic drivers than on continental land masses. The extent of fire activity derived from local records in the Hawaiian Islands reveals that our global analysis likely underestimates the prevalence of fire among island systems and that the combined effects of human activity and invasion by nonnative grasses can create conditions for frequent and relatively large-scale fires. Understanding the extent of these novel fire regimes, and mitigating their impacts, is critical to reducing the current and rapid degradation of native island ecosystems worldwide.

  19. Floating Cities, Islands and States

    E-print Network

    Alexander Bolonkin

    2008-04-04

    Many small countries are in need of additional territory. They build landfills and expensive artificial islands. The ocean covers 71 per cent of the Earth surface. Those countries (or persons of wealth) starting the early colonization of the ocean may obtain advantages through additional territory or creating their own independent state. An old idea is building a big ship. The best solution to this problem, however, is the provision of floating cities, islands, and states. The author idea is to use for floating cities, islands, and states a cheap floating platform created from a natural ice field taken from the Arctic or Antarctic oceans. These cheap platforms protected by air-film (bottom and sides) and a conventional insulating cover (top) and having a cooling system can exist for an unlimited time. They can be increased in number or size at any time, float in warm oceans, travel to different continents and countries, serve as artificial airports, harbors and other marine improvements, as well as floating cities and industrial bases for virtually any use. Author researches and computes parameters of these ice floating platforms, other methods of building such floating territory, compares them and shows that the offered method is the most cheap and efficient means of ocean colonization.

  20. Generalized model of island biodiversity

    NASA Astrophysics Data System (ADS)

    Kessler, David A.; Shnerb, Nadav M.

    2015-04-01

    The dynamics of a local community of competing species with weak immigration from a static regional pool is studied. Implementing the generalized competitive Lotka-Volterra model with demographic noise, a rich dynamics with four qualitatively distinct phases is unfolded. When the overall interspecies competition is weak, the island species recapitulate the mainland species. For higher values of the competition parameter, the system still admits an equilibrium community, but now some of the mainland species are absent on the island. Further increase in competition leads to an intermittent "disordered" phase, where the dynamics is controlled by invadable combinations of species and the turnover rate is governed by the migration. Finally, the strong competition phase is glasslike, dominated by uninvadable states and noise-induced transitions. Our model contains, as a special case, the celebrated neutral island theories of Wilson-MacArthur and Hubbell. Moreover, we show that slight deviations from perfect neutrality may lead to each of the phases, as the Hubbell point appears to be quadracritical.

  1. Small variable segments constitute a major type of diversity of bacterial genomes at the species level

    PubMed Central

    2010-01-01

    Background Analysis of large scale diversity in bacterial genomes has mainly focused on elements such as pathogenicity islands, or more generally, genomic islands. These comprise numerous genes and confer important phenotypes, which are present or absent depending on strains. We report that despite this widely accepted notion, most diversity at the species level is composed of much smaller DNA segments, 20 to 500 bp in size, which we call microdiversity. Results We performed a systematic analysis of the variable segments detected by multiple whole genome alignments at the DNA level on three species for which the greatest number of genomes have been sequenced: Escherichia coli, Staphylococcus aureus, and Streptococcus pyogenes. Among the numerous sites of variability, 62 to 73% were loci of microdiversity, many of which were located within genes. They contribute to phenotypic variations, as 3 to 6% of all genes harbor microdiversity, and 1 to 9% of total genes are located downstream from a microdiversity locus. Microdiversity loci are particularly abundant in genes encoding membrane proteins. In-depth analysis of the E. coli alignments shows that most of the diversity does not correspond to known mobile or repeated elements, and it is likely that they were generated by illegitimate recombination. An intriguing class of microdiversity includes small blocks of highly diverged sequences, whose origin is discussed. Conclusions This analysis uncovers the importance of this small-sized genome diversity, which we expect to be present in a wide range of bacteria, and possibly also in many eukaryotic genomes. PMID:20433696

  2. Complete genome sequence of the fish pathogen Flavobacterium branchiophilum.

    PubMed

    Touchon, Marie; Barbier, Paul; Bernardet, Jean-François; Loux, Valentin; Vacherie, Benoit; Barbe, Valérie; Rocha, Eduardo P C; Duchaud, Eric

    2011-11-01

    Members of the genus Flavobacterium occur in a variety of ecological niches and represent an interesting diversity of lifestyles. Flavobacterium branchiophilum is the main causative agent of bacterial gill disease, a severe condition affecting various cultured freshwater fish species worldwide, in particular salmonids in Canada and Japan. We report here the complete genome sequence of strain FL-15 isolated from a diseased sheatfish (Silurus glanis) in Hungary. The analysis of the F. branchiophilum genome revealed putative mechanisms of pathogenicity strikingly different from those of the other, closely related fish pathogen Flavobacterium psychrophilum, including the first cholera-like toxin in a non-Proteobacteria and a wealth of adhesins. The comparison with available genomes of other Flavobacterium species revealed a small genome size, large differences in chromosome organization, and fewer rRNA and tRNA genes, in line with its more fastidious growth. In addition, horizontal gene transfer shaped the evolution of F. branchiophilum, as evidenced by its virulence factors, genomic islands, and CRISPR (clustered regularly interspaced short palindromic repeats) systems. Further functional analysis should help in the understanding of host-pathogen interactions and in the development of rational diagnostic tools and control strategies in fish farms. PMID:21926215

  3. Genomic organization of the neurofibromatosis 1 gene (NF1)

    SciTech Connect

    Li, Y.; O`Connell, P.; Huntsman Breidenbach, H. [Univ. of Utah, Salt Lake City, UT (United States)] [and others] [Univ. of Utah, Salt Lake City, UT (United States); and others

    1995-01-01

    Neurofibromatosis 1 maps to chromosome band 17q11.2, and the NF1 locus has been partially characterized. Even though the full-length NF1 cDNA has been sequenced, the complete genomic structure of the NF1 gene has not been elucidated. The 5{prime} end of NF1 is embedded in a CpG island containing a NotI restriction site, and the remainder of the gene lies in the adjacent 350-kb NotI fragment. In our efforts to develop a comprehensive screen for NF1 mutations, we have isolated genomic DNA clones that together harbor the entire NF1 cDNA sequence. We have identified all intron-exon boundaries of the coding region and established that it is composed of 59 exons. Furthermore, we have defined the 3{prime}-untranslated region (3{prime}-UTR) of the NF1 gene; it spans approximately 3.5 kb of genomic DNA sequence and is continuous with the stop codon. Oligonucleotide primer pairs synthesized from exon-flanking DNA sequences were used in the polymerase chain reaction with cloned, chromosome 17-specific genomic DNA as template to amplify NF1 exons 1 through 27b and the exon containing the 3{prime}-UTR separately. This information should be useful for implementing a comprehensive NF1 mutation screen using genomic DNA as template. 41 refs., 3 figs., 2 tabs.

  4. Evidence for Reductive Genome Evolution and Lateral Acquisition of Virulence Functions in Two Corynebacterium pseudotuberculosis Strains

    PubMed Central

    Silva, Artur; Ali, Amjad; Pinto, Anne C.; Santos, Anderson R.; Rocha, Aryanne A. M. C.; Lopes, Débora O.; Dorella, Fernanda A.; Pacheco, Luis G. C.; Costa, Marcília P.; Turk, Meritxell Z.; Seyffert, Núbia; Moraes, Pablo M. R. O.; Soares, Siomar C.; Almeida, Sintia S.; Castro, Thiago L. P.; Abreu, Vinicius A. C.; Trost, Eva; Baumbach, Jan; Tauch, Andreas; Schneider, Maria Paula C.; McCulloch, John; Cerdeira, Louise T.; Ramos, Rommel T. J.; Zerlotini, Adhemar; Dominitini, Anderson; Resende, Daniela M.; Coser, Elisângela M.; Oliveira, Luciana M.; Pedrosa, André L.; Vieira, Carlos U.; Guimarães, Cláudia T.; Bartholomeu, Daniela C.; Oliveira, Diana M.; Santos, Fabrício R.; Rabelo, Élida Mara; Lobo, Francisco P.; Franco, Glória R.; Costa, Ana Flávia; Castro, Ieso M.; Dias, Sílvia Regina Costa; Ferro, Jesus A.; Ortega, José Miguel; Paiva, Luciano V.; Goulart, Luiz R.; Almeida, Juliana Franco; Ferro, Maria Inês T.; Carneiro, Newton P.; Falcão, Paula R. K.; Grynberg, Priscila; Teixeira, Santuza M. R.; Brommonschenkel, Sérgio; Oliveira, Sérgio C.; Meyer, Roberto; Moore, Robert J.; Miyoshi, Anderson; Oliveira, Guilherme C.

    2011-01-01

    Background Corynebacterium pseudotuberculosis, a Gram-positive, facultative intracellular pathogen, is the etiologic agent of the disease known as caseous lymphadenitis (CL). CL mainly affects small ruminants, such as goats and sheep; it also causes infections in humans, though rarely. This species is distributed worldwide, but it has the most serious economic impact in Oceania, Africa and South America. Although C. pseudotuberculosis causes major health and productivity problems for livestock, little is known about the molecular basis of its pathogenicity. Methodology and Findings We characterized two C. pseudotuberculosis genomes (Cp1002, isolated from goats; and CpC231, isolated from sheep). Analysis of the predicted genomes showed high similarity in genomic architecture, gene content and genetic order. When C. pseudotuberculosis was compared with other Corynebacterium species, it became evident that this pathogenic species has lost numerous genes, resulting in one of the smallest genomes in the genus. Other differences that could be part of the adaptation to pathogenicity include a lower GC content, of about 52%, and a reduced gene repertoire. The C. pseudotuberculosis genome also includes seven putative pathogenicity islands, which contain several classical virulence factors, including genes for fimbrial subunits, adhesion factors, iron uptake and secreted toxins. Additionally, all of the virulence factors in the islands have characteristics that indicate horizontal transfer. Conclusions These particular genome characteristics of C. pseudotuberculosis, as well as its acquired virulence factors in pathogenicity islands, provide evidence of its lifestyle and of the pathogenicity pathways used by this pathogen in the infection process. All genomes cited in this study are available in the NCBI Genbank database (http://www.ncbi.nlm.nih.gov/genbank/) under accession numbers CP001809 and CP001829. PMID:21533164

  5. Computational Finishing of Large Sequence Contigs Reveals Interspersed Nested Repeats and Gene Islands in the rf1-associated Region of Maize

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The architecture of grass genomes varies on multiple levels. Large long terminal repeat (LTR) retrotransposon clusters occupy significant portions of the intergenic regions, and islands of protein-encoding genes are interspersed among the repeat clusters. Hence, advanced assembly techniques are requ...

  6. Palaeo-islands as refugia and sources of genetic diversity within volcanic archipelagos: the case of the widespread endemic Canarina canariensis (Campanulaceae).

    PubMed

    Mairal, M; Sanmartín, I; Aldasoro, J J; Culshaw, V; Manolopoulou, I; Alarcón, M

    2015-08-01

    Geographical isolation by oceanic barriers and climatic stability has been postulated as some of the main factors driving diversification within volcanic archipelagos. However, few studies have focused on the effect that catastrophic volcanic events have had on patterns of within-island differentiation in geological time. This study employed data from the chloroplast (cpDNA haplotypes) and the nuclear (AFLPs) genomes to examine the patterns of genetic variation in Canarina canariensis, an iconic plant species associated with the endemic laurel forest of the Canary Islands. We found a strong geographical population structure, with a first divergence around 0.8 Ma that has Tenerife as its central axis and divides Canarian populations into eastern and western clades. Genetic diversity was greatest in the geologically stable 'palaeo-islands' of Anaga, Teno and Roque del Conde; these areas were also inferred as the ancestral location of migrant alleles towards other disturbed areas within Tenerife or the nearby islands using a Bayesian approach to phylogeographical clustering. Oceanic barriers, in contrast, appear to have played a lesser role in structuring genetic variation, with intra-island levels of genetic diversity larger than those between-islands. We argue that volcanic eruptions and landslides after the merging of the palaeo-islands 3.5 Ma played key roles in generating genetic boundaries within Tenerife, with the palaeo-islands acting as refugia against extinction, and as cradles and sources of genetic diversity to other areas within the archipelago. PMID:26096229

  7. Nature: The Mouse Genome

    NSDL National Science Digital Library

    2003-01-01

    This Web site from the journal Nature offers a one-stop online resource for information on the mouse genome -- "the experimental key to the human genome." Visitors have free access to all content from the journal's special mouse genome issue. Web features include an interactive timeline detailing the history of the mouse in genetics, related news articles and commentary, Web links, and more. Scientific papers and letters to Nature are also available for those who would like to delve into the subject at depth. Additionally, the site provides a selection of classic research papers free to registered users until March 5, 2003.

  8. DNA interactive genome

    NSDL National Science Digital Library

    Dolan DNA Learning Center. Cold Spring Harbor Laboratory

    2005-01-01

    This site offers three interactive modules that explore the human genetic landscape and the methods used to map and sequence the entire human genome. The modules include a tour of the 23 pairs of chromosomes, genome mining to extract data about genes, and the Human Genome Project itself. Each module is subdivided into additional parts. These parts include videos, tutorials, and computer simulations. For instance, in one simulation visitors are to arrange a scrambled segment of DNA by clicking and dragging the fragments into the correct order. Copyright 2005 Eisenhower National Clearinghouse

  9. Human Genome Program

    SciTech Connect

    Not Available

    1993-01-01

    The DOE Human Genome program has grown tremendously, as shown by the marked increase in the number of genome-funded projects since the last workshop held in 1991. The abstracts in this book describe the genome research of DOE-funded grantees and contractors and invited guests, and all projects are represented at the workshop by posters. The 3-day meeting includes plenary sessions on ethical, legal, and social issues pertaining to the availability of genetic data; sequencing techniques, informatics support; and chromosome and cDNA mapping and sequencing.

  10. GenomeBiology.com

    NSDL National Science Digital Library

    Genome Biology "serves the biological research community as an international forum, both in print and on the Web, for the dissemination, discussion and critical review of information about all areas of biology informed by genomic research." While a paid subscription is required to access all features on the Genome Biology Web site, non-subscribers will find a number of open-access resources as well. Offerings include research articles, conference reports, software downloads, lab protocols, and much more. This frequently updated and ever-evolving Web site will also publish and maintain databases at some point; users are encouraged to submit comments and suggestions.

  11. Human Genome Project

    SciTech Connect

    Block, S.; Cornwall, J.; Dally, W.; Dyson, F.; Fortson, N.; Joyce, G.; Kimble, H. J.; Lewis, N.; Max, C.; Prince, T.; Schwitters, R.; Weinberger, P.; Woodin, W. H.

    1998-01-04

    The study reviews Department of Energy supported aspects of the United States Human Genome Project, the joint National Institutes of Health/Department of Energy program to characterize all human genetic material, to discover the set of human genes, and to render them accessible for further biological study. The study concentrates on issues of technology, quality assurance/control, and informatics relevant to current effort on the genome project and needs beyond it. Recommendations are presented on areas of the genome program that are of particular interest to and supported by the Department of Energy.

  12. The Center for integrative genomics

    E-print Network

    Kaessmann, Henrik

    The Center for integrative genomics Report 2005­2006 #12;Presentation Director's message 4 Scientific advisory committee 6 Organigram of the CIG 7 research The structure and function of genomes and their evolution alexandrereymond ­ Genome structure and expression 10 henrikKaessmann ­ Evolutionary genomics 12

  13. 5. Photograph of a photograph in possession of Rock Island ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    5. Photograph of a photograph in possession of Rock Island Arsenal Historical Office. WEST AND SOUTH ELEVATIONS, BEFORE REMOVAL OF CHIMNEY, FINIALS, GINGERBREAD, AND VARIEGATED SLATE ROOFING. DATED C. 1876. - Rock Island Arsenal, Building No. 321, Rodman Avenue & Rock Island Avenue, Rock Island, Rock Island County, IL

  14. Molluscan fauna of Gueishan Island, Taiwan.

    PubMed

    Huang, Chih-Wei; Hsiung, Ta-Wei; Lin, Si-Min; Wu, Wen-Lung

    2013-01-01

    This dataset records the occurrence and inventory of molluscan fauna on Gueishan Island, the only active volcanic island in Taiwan, based on the literature survey and field investigation conducted between 2011 and 2012. The literature review involved seven studies published from 1934 to 2003, which collectively reported 112 species from 61 genera and 37 families of Mollusca on Gueishan Island. Through our field investigation, we identified 34 species from 28 genera and 23 families. Fourteen of these species were new records on Gueishan Island: Liolophura japonica, Lottia luchuana, Nerita costata, Nerita rumphii, Diplommatina suganikeiensis, Littoraria undulata, Solenomphala taiwanensis, Assiminea sp., Siphonaria laciniosa, Laevapex nipponica, Carychium hachijoensis, Succinea erythrophana, Zaptyx crassilamellata, and Allopeas pyrgula. In Total, there are 126 species from 71 genera and 45 families of Mollusca on Gueishan Island. These data have been published through GBIF [http://taibif.org.tw/ipt/resource.do?r=gueishan_island] and integrated into the Taiwan Malacofauna Database (http://shell.sinica.edu.tw/). PMID:23717182

  15. Adaptive Decision Modeling in Wisconsin River Islands

    NASA Astrophysics Data System (ADS)

    Gyawali, R.; Greb, S. R.; Watkins, D. W., Jr.; Block, P.

    2014-12-01

    River islands in Wisconsin are of high ecological significance. Understanding of climate change impacts and appropriate management alternatives in these islands are of great interest to all stakeholders, including the State of Wisconsin and Bureau of Land Management (BLM) who have jurisdiction of these islands in WI. We use historical areal imagery to describe island dynamics and river morphometry, such as changes in island shape and size. Relationships of related changes are explored with concurrent changes in river flow regimes. In an effort to integrate climate change uncertainties into decision making, we demonstrate an application of a multistage adaptive decision making framework to Wisconsin River islands, with a particular emphasis on flood management and planning. The framework is comprised of hydro-climatic ensemble projections generated from CMIP5 climate model outputs and multiple hydrologic models, including statistical and physically based approaches.

  16. Green Island Union Free School District and Green Island Teachers Association

    Microsoft Academic Search

    Donna C. Trautwein

    2010-01-01

    Proceeding Between Green Island Union Free School District And Green Island Teachers Association. PERB Case No. M 2009 ? 069. Report and Recommendations of Fact Finder, June 23, 2010 Donna Trautwein, Ph.D., Fact Finder.

  17. Whole-genome pyrosequencing of an epidemic multidrug-resistant Acinetobacter baumannii strain belonging to the European clone II group.

    PubMed

    Iacono, Michele; Villa, Laura; Fortini, Daniela; Bordoni, Roberta; Imperi, Francesco; Bonnal, Raoul J P; Sicheritz-Ponten, Thomas; De Bellis, Gianluca; Visca, Paolo; Cassone, Antonio; Carattoli, Alessandra

    2008-07-01

    The whole-genome sequence of an epidemic, multidrug-resistant Acinetobacter baumannii strain (strain ACICU) belonging to the European clone II group and carrying the plasmid-mediated bla(OXA)(-)(58) carbapenem resistance gene was determined. The A. baumannii ACICU genome was compared with the genomes of A. baumannii ATCC 17978 and Acinetobacter baylyi ADP1, with the aim of identifying novel genes related to virulence and drug resistance. A. baumannii ACICU has a single chromosome of 3,904,116 bp (which is predicted to contain 3,758 genes) and two plasmids, pACICU1 and pACICU2, of 28,279 and 64,366 bp, respectively. Genome comparison showed 86.4% synteny with A. baumannii ATCC 17978 and 14.8% synteny with A. baylyi ADP1. A conspicuous number of transporters belonging to different superfamilies was predicted for A. baumannii ACICU. The relative number of transporters was much higher in ACICU than in ATCC 17978 and ADP1 (76.2, 57.2, and 62.5 transporters per Mb of genome, respectively). An antibiotic resistance island, AbaR2, was identified in ACICU and had plausibly evolved by reductive evolution from the AbaR1 island previously described in multiresistant strain A. baumannii AYE. Moreover, 36 putative alien islands (pAs) were detected in the ACICU genome; 24 of these had previously been described in the ATCC 17978 genome, 4 are proposed here for the first time and are present in both ATCC 17978 and ACICU, and 8 are unique to the ACICU genome. Fifteen of the pAs in the ACICU genome encode genes related to drug resistance, including membrane transporters and ex novo acquired resistance genes. These findings provide novel insight into the genetic basis of A. baumannii resistance. PMID:18411315

  18. Parallel Island Model for Attribute Reduction

    Microsoft Academic Search

    Mohammad M. Rahman; Dominik ´ Slezak; Jakub Wroblewski

    2005-01-01

    \\u000a We develop a framework for parallel computation of the optimal rough set decision reducts from data. We adapt the island model\\u000a for evolutionary computing. The idea is to optimize reducts within separate populations (islands) and enable the best reducts-chromosomes\\u000a to migrate among islands. Experiments show that the proposed method speeds up calculations and also provides often better\\u000a quality of results,

  19. Invasive aliens on tropical East Asian islands

    Microsoft Academic Search

    Richard T. Corlett

    2010-01-01

    Tropical East Asia (TEA) has numerous islands, both continental and oceanic. This study uses information on invasive aliens\\u000a in terrestrial habitats on these islands to test the generality of the continental-oceanic contrast in invasibility, assess\\u000a the conservation impacts of invasive species, and suggest ways to mitigate these. The continental islands of Hong Kong and\\u000a Singapore are worst-case scenarios for continental

  20. Wheat and Barley Genome Sequencing

    Microsoft Academic Search

    Kellye Eversole; Andreas Graner; Nils Stein

    A high quality reference genome sequence is a prerequisite resource for accessing any gene, driving genomics-based approaches\\u000a to systems biology, and for efficient exploitation of natural and induced genetic diversity of an organism. Wheat and barley\\u000a possess genomes of a size that was long presumed to be not amenable for whole genome sequencing. So far, only limited genomic\\u000a sequencing of