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1

Genetic Structure and Distribution of the Colibactin Genomic Island among Members of the Family Enterobacteriaceae? †  

PubMed Central

A genomic island encoding the biosynthesis and secretion pathway of putative hybrid nonribosomal peptide-polyketide colibactin has been recently described in Escherichia coli. Colibactin acts as a cyclomodulin and blocks the eukaryotic cell cycle. The origin and prevalence of the colibactin island among enterobacteria are unknown. We therefore screened 1,565 isolates of different genera and species related to the Enterobacteriaceae by PCR for the presence of this DNA element. The island was detected not only in E. coli but also in Klebsiella pneumoniae, Enterobacter aerogenes, and Citrobacter koseri isolates. It was highly conserved among these species and was always associated with the yersiniabactin determinant. Structural variations between individual strains were only observed in an intergenic region containing variable numbers of tandem repeats. In E. coli, the colibactin island was usually restricted to isolates of phylogenetic group B2 and inserted at the asnW tRNA locus. Interestingly, in K. pneumoniae, E. aerogenes, C. koseri, and three E. coli strains of phylogenetic group B1, the functional colibactin determinant was associated with a genetic element similar to the integrative and conjugative elements ICEEc1 and ICEKp1 and to several enterobacterial plasmids. Different asn tRNA genes served as chromosomal insertion sites of the ICE-associated colibactin determinant: asnU in the three E. coli strains of ECOR group B1, and different asn tRNA loci in K. pneumoniae. The detection of the colibactin genes associated with an ICE-like element in several enterobacteria provides new insights into the spread of this gene cluster and its putative mode of transfer. Our results shed light on the mechanisms of genetic exchange between members of the family Enterobacteriaceae.

Putze, Johannes; Hennequin, Claire; Nougayrede, Jean-Philippe; Zhang, Wenlan; Homburg, Stefan; Karch, Helge; Bringer, Marie-Agnes; Fayolle, Corinne; Carniel, Elisabeth; Rabsch, Wolfgang; Oelschlaeger, Tobias A.; Oswald, Eric; Forestier, Christiane; Hacker, Jorg; Dobrindt, Ulrich

2009-01-01

2

Analysis of structure-function relationships in the colibactin-maturating enzyme ClbP.  

PubMed

pks genomic island of Escherichia coli is involved in the synthesis of the non-ribosomal peptide-type genotoxin colibactin, which has been suggesting as affecting the host immune response and having an impact on cancer development. The pks-encoded enzyme ClbP is an atypical peptidase that contributes to the synthesis of colibactin. In this work, we identified key features of ClbP. Bacterial fractionation and Western-blot analysis revealed the docking of ClbP to the bacterial inner membrane via a C-terminal domain harboring three predicted transmembrane helices. Whereas only one helix was necessary for the location in the inner membrane, the complete sequence of the C-terminal domain was necessary for ClbP bioactivity. In addition, the N-terminal sequence of ClbP allowed the SRP/Sec/YidC- and MreB-dependent translocation of the enzymatic domain in the periplasmic compartment, a feature also essential for ClbP bioactivity. Finally, the comparison of ClbP structure with that of the paralogs FmtA-like and AmpC revealed at an extremity of the catalytic groove a negative electrostatic potential surface characteristic of ClbP. Site-directed mutagenesis experiments identified in this zone two aspartic residues that were important for ClbP bioactivity. Overall, these results suggest a model for precolibactin activation by ClbP and pave a way for the design of inhibitors targeting colibactin production. PMID:23041299

Cougnoux, Antony; Gibold, Lucie; Robin, Frederic; Dubois, Damien; Pradel, Nathalie; Darfeuille-Michaud, Arlette; Dalmasso, Guillaume; Delmas, Julien; Bonnet, Richard

2012-10-02

3

Escherichia coli Producing Colibactin Triggers Premature and Transmissible Senescence in Mammalian Cells  

PubMed Central

Cellular senescence is an irreversible state of proliferation arrest evoked by a myriad of stresses including oncogene activation, telomere shortening/dysfunction and genotoxic insults. It has been associated with tumor activation, immune suppression and aging, owing to the secretion of proinflammatory mediators. The bacterial genotoxin colibactin, encoded by the pks genomic island is frequently harboured by Escherichia coli strains of the B2 phylogenetic group. Mammalian cells exposed to live pks+ bacteria exhibit DNA-double strand breaks (DSB) and undergo cell-cycle arrest and death. Here we show that cells that survive the acute bacterial infection with pks+ E. coli display hallmarks of cellular senescence: chronic DSB, prolonged cell-cycle arrest, enhanced senescence-associated ?-galactosidase (SA-?-Gal) activity, expansion of promyelocytic leukemia nuclear foci and senescence-associated heterochromatin foci. This was accompanied by reactive oxygen species production and pro-inflammatory cytokines, chemokines and proteases secretion. These mediators were able to trigger DSB and enhanced SA-?-Gal activity in bystander recipient cells treated with conditioned medium from senescent cells. Furthermore, these senescent cells promoted the growth of human tumor cells. In conclusion, the present data demonstrated that the E. coli genotoxin colibactin induces cellular senescence and subsequently propel bystander genotoxic and oncogenic effects.

Secher, Thomas; Samba-Louaka, Ascel; Oswald, Eric; Nougayrede, Jean-Philippe

2013-01-01

4

An Integrative Approach for Genomic Island Prediction in Prokaryotic Genomes  

Microsoft Academic Search

\\u000a A genomic island (GI) is a segment of genomic sequence that is horizontally transferred from other genomes. The detection of genomic islands\\u000a is extremely important to the medical research. Most of current computational approaches that use sequence composition to\\u000a predict genomic islands have the problem of low prediction accuracy. In this paper, we report, for the first time, that gene

Han Wang; John Fazekas; Matthew Booth; Qi Liu; Dongsheng Che

2011-01-01

5

IslandViewer update: Improved genomic island discovery and visualization.  

PubMed

IslandViewer (http://pathogenomics.sfu.ca/islandviewer) is a web-accessible application for the computational 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 because they disproportionately encode virulence factors and other adaptations of medical, environmental and industrial interest. Many computational tools exist for the prediction of GIs, but three of the most accurate methods are available in integrated form via IslandViewer: IslandPath-DIMOB, SIGI-HMM and IslandPick. IslandViewer GI predictions are precomputed for all complete microbial genomes from National Center for Biotechnology Information, with an option to upload other genomes and/or perform customized analyses using different settings. Here, we report recent changes to the IslandViewer framework that have vastly improved its efficiency in handling an increasing number of users, plus better facilitate custom genome analyses. Users may also now overlay additional annotations such as virulence factors, antibiotic resistance genes and pathogen-associated genes on top of current GI predictions. Comparisons of GIs between user-selected genomes are now facilitated through a highly requested side-by-side viewer. IslandViewer improvements aim to provide a more flexible interface, coupled with additional highly relevant annotation information, to aid analysis of GIs in diverse microbial species. PMID:23677610

Dhillon, Bhavjinder K; Chiu, Terry A; Laird, Matthew R; Langille, Morgan G I; Brinkman, Fiona S L

2013-05-15

6

Detection of genomic islands via segmental genome heterogeneity  

Microsoft Academic Search

While the recognition of genomic islands can be a powerful mechanism for identifying genes that distinguish related bacteria, few methods have been developed to identify them specifically. Rather, identification of islands often begins with cataloging individual genes likely to have been recently introduced into the genome; regions with many putative alien genes are then examined for other features suggestive of

Aaron J. Arvey; Rajeev K. Azad; Alpan Raval; Jeffrey G. Lawrence

2009-01-01

7

Detecting genomic islands using bioinformatics approaches  

Microsoft Academic Search

Bacterial genomes contain clusters of genes that are acquired by horizontal transfer, called genomic islands (GIs). GIs are frequently associated with microbial adaptations that are of medical and environmental interest, and they have had a substantial impact on bacterial evolution. Therefore, there is growing interest in efficiently identifying GIs in newly sequenced bacterial genomes. Several computational methods for detecting GIs

Morgan G. I. Langille; William W. L. Hsiao; Fiona S. L. Brinkman

2010-01-01

8

Evaluation of genomic island predictors using a comparative genomics approach  

Microsoft Academic Search

BACKGROUND: Genomic islands (GIs) are clusters of genes in prokaryotic genomes of probable horizontal origin. GIs are disproportionately associated with microbial adaptations of medical or environmental interest. Recently, multiple programs for automated detection of GIs have been developed that utilize sequence composition characteristics, such as G+C ratio and dinucleotide bias. To robustly evaluate the accuracy of such methods, we propose

Morgan G. I. Langille; William W. L. Hsiao; Fiona S. L. Brinkman

2008-01-01

9

SIGI: score-based identification of genomic islands  

Microsoft Academic Search

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.

Rainer Merkl

2004-01-01

10

A prodrug resistance mechanism is involved in colibactin biosynthesis and cytotoxicity.  

PubMed

Commensal Escherichia coli residing in the human gut produce colibactin, a small-molecule genotoxin of unknown structure that has been implicated in the development of colon cancer. Colibactin biosynthesis is hypothesized to involve a prodrug resistance strategy that entails initiation of biosynthesis via construction of an N-terminal prodrug scaffold and late-stage cleavage of this structural motif during product export. Here we describe the biochemical characterization of the prodrug synthesis, elongation, and cleavage enzymes from the colibactin biosynthetic pathway. We show that nonribosomal peptide synthetases ClbN and ClbB assemble and process an N-acyl-D-asparagine prodrug scaffold that serves as a substrate for the periplasmic D-amino peptidase ClbP. In addition to affording information about structural features of colibactin, this work reveals the biosynthetic logic underlying the prodrug resistance strategy and suggests that cytotoxicity requires amide bond cleavage. PMID:23406518

Brotherton, Carolyn A; Balskus, Emily P

2013-02-20

11

Detection of genomic islands via segmental genome heterogeneity  

PubMed Central

While the recognition of genomic islands can be a powerful mechanism for identifying genes that distinguish related bacteria, few methods have been developed to identify them specifically. Rather, identification of islands often begins with cataloging individual genes likely to have been recently introduced into the genome; regions with many putative alien genes are then examined for other features suggestive of recent acquisition of a large genomic region. When few phylogenetic relatives are available, the identification of alien genes relies on their atypical features relative to the bulk of the genes in the genome. The weakness of these ‘bottom–up’ approaches lies in the difficulty in identifying robustly those genes which are atypical, or phylogenetically restricted, due to recent foreign ancestry. Herein, we apply an alternative ‘top–down’ approach where bacterial genomes are recursively divided into progressively smaller regions, each with uniform composition. In this way, large chromosomal regions with atypical features are identified with high confidence due to the simultaneous analysis of multiple genes. This approach is based on a generalized divergence measure to quantify the compositional difference between segments in a hypothesis-testing framework. We tested the proposed genome island prediction algorithm on both artificial chimeric genomes and genuine bacterial genomes.

Arvey, Aaron J.; Azad, Rajeev K.; Raval, Alpan; Lawrence, Jeffrey G.

2009-01-01

12

Burkholderia pseudomallei genome plasticity associated with genomic island variation  

PubMed Central

Background Burkholderia pseudomallei is a soil-dwelling saprophyte and the cause of melioidosis. Horizontal gene transfer contributes to the genetic diversity of this pathogen and may be an important determinant of virulence potential. The genome contains genomic island (GI) regions that encode a broad array of functions. Although there is some evidence for the variable distribution of genomic islands in B. pseudomallei isolates, little is known about the extent of variation between related strains or their association with disease or environmental survival. Results Five islands from B. pseudomallei strain K96243 were chosen as representatives of different types of genomic islands present in this strain, and their presence investigated in other B. pseudomallei. In silico analysis of 10 B. pseudomallei genome sequences provided evidence for the variable presence of these regions, together with micro-evolutionary changes that generate GI diversity. The diversity of GIs in 186 isolates from NE Thailand (83 environmental and 103 clinical isolates) was investigated using multiplex PCR screening. The proportion of all isolates positive by PCR ranged from 12% for a prophage-like island (GI 9), to 76% for a metabolic island (GI 16). The presence of each of the five GIs did not differ between environmental and disease-associated isolates (p > 0.05 for all five islands). The cumulative number of GIs per isolate for the 186 isolates ranged from 0 to 5 (median 2, IQR 1 to 3). The distribution of cumulative GI number did not differ between environmental and disease-associated isolates (p = 0.27). The presence of GIs was defined for the three largest clones in this collection (each defined as a single sequence type, ST, by multilocus sequence typing); these were ST 70 (n = 15 isolates), ST 54 (n = 11), and ST 167 (n = 9). The rapid loss and/or acquisition of gene islands was observed within individual clones. Comparisons were drawn between isolates obtained from the environment and from patients with melioidosis in order to examine the role of genomic islands in virulence and clinical associations. There was no reproducible association between the individual or cumulative presence of five GIs and a range of clinical features in 103 patients with melioidosis. Conclusion Horizontal gene transfer of mobile genetic elements can rapidly alter the gene repertoire of B. pseudomallei. This study confirms the utility of a range of approaches in defining the presence and significance of genomic variation in natural populations of B. pseudomallei.

Tumapa, Sarinna; Holden, Matthew TG; Vesaratchavest, Mongkol; Wuthiekanun, Vanaporn; Limmathurotsakul, Direk; Chierakul, Wirongrong; Feil, Edward J; Currie, Bart J; Day, Nicholas PJ; Nierman, William C; Peacock, Sharon J

2008-01-01

13

Comparative Analysis of Mobilizable Genomic Islands  

PubMed Central

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.

Daccord, Aurelie; Ceccarelli, Daniela; Rodrigue, Sebastien

2013-01-01

14

Genome Island: A Virtual Science Environment in Second Life  

ERIC Educational Resources Information Center

|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…

Clark, Mary Anne

2009-01-01

15

Genomic Islands Analysis of Three Actinobacillus pleuropneumoniae Strains by Comparative Genomic Methods  

Microsoft Academic Search

A Genomic island (GI) often encodes an integrase gene that specifies the island's position in the host genome, which is part of a genome that has evidence of horizontal origins. GI can code for many functions, which can be involved in symbiosis or pathogenesis, and may help an organism's adaptation. Many sub- classes of GIs exist that are based on

Ren-Feng Li; Xiang-Qin Tian; Jin-Qing Jiang; Xue-Bin Li; San-Hu Wang

2011-01-01

16

Evolutionary forces shaping genomic islands of population differentiation in humans  

PubMed Central

Background Levels of differentiation among populations depend both on demographic and selective factors: genetic drift and local adaptation increase population differentiation, which is eroded by gene flow and balancing selection. We describe here the genomic distribution and the properties of genomic regions with unusually high and low levels of population differentiation in humans to assess the influence of selective and neutral processes on human genetic structure. Methods Individual SNPs of the Human Genome Diversity Panel (HGDP) showing significantly high or low levels of population differentiation were detected under a hierarchical-island model (HIM). A Hidden Markov Model allowed us to detect genomic regions or islands of high or low population differentiation. Results Under the HIM, only 1.5% of all SNPs are significant at the 1% level, but their genomic spatial distribution is significantly non-random. We find evidence that local adaptation shaped high-differentiation islands, as they are enriched for non-synonymous SNPs and overlap with previously identified candidate regions for positive selection. Moreover there is a negative relationship between the size of islands and recombination rate, which is stronger for islands overlapping with genes. Gene ontology analysis supports the role of diet as a major selective pressure in those highly differentiated islands. Low-differentiation islands are also enriched for non-synonymous SNPs, and contain an overly high proportion of genes belonging to the 'Oncogenesis' biological process. Conclusions Even though selection seems to be acting in shaping islands of high population differentiation, neutral demographic processes might have promoted the appearance of some genomic islands since i) as much as 20% of islands are in non-genic regions ii) these non-genic islands are on average two times shorter than genic islands, suggesting a more rapid erosion by recombination, and iii) most loci are strongly differentiated between Africans and non-Africans, a result consistent with known human demographic history.

2012-01-01

17

A quantitative account of genomic island acquisitions in prokaryotes  

PubMed Central

Background Microbial genomes do not merely evolve through the slow accumulation of mutations, but also, and often more dramatically, by taking up new DNA in a process called horizontal gene transfer. These innovation leaps in the acquisition of new traits can take place via the introgression of single genes, but also through the acquisition of large gene clusters, which are termed Genomic Islands. Since only a small proportion of all the DNA diversity has been sequenced, it can be hard to find the appropriate donors for acquired genes via sequence alignments from databases. In contrast, relative oligonucleotide frequencies represent a remarkably stable genomic signature in prokaryotes, which facilitates compositional comparisons as an alignment-free alternative for phylogenetic relatedness. In this project, we test whether Genomic Islands identified in individual bacterial genomes have a similar genomic signature, in terms of relative dinucleotide frequencies, and can therefore be expected to originate from a common donor species. Results When multiple Genomic Islands are present within a single genome, we find that up to 28% of these are compositionally very similar to each other, indicative of frequent recurring acquisitions from the same donor to the same acceptor. Conclusions This represents the first quantitative assessment of common directional transfer events in prokaryotic evolutionary history. We suggest that many of the resident Genomic Islands per prokaryotic genome originated from the same source, which may have implications with respect to their regulatory interactions, and for the elucidation of the common origins of these acquired gene clusters.

2011-01-01

18

Genomic Islands of Uropathogenic Escherichia coli Contribute to Virulence? †  

PubMed Central

Uropathogenic Escherichia coli (UPEC) strain CFT073 contains 13 large genomic islands ranging in size from 32 kb to 123 kb. Eleven of these genomic islands were individually deleted from the genome, and nine isogenic mutants were tested for their ability to colonize the CBA/J mouse model of ascending urinary tract infection. Three genomic island mutants (?PAI-aspV, ?PAI-metV, and ?PAI-asnT) were significantly outcompeted by wild-type CFT073 in the bladders and/or kidneys following transurethral cochallenge (P ? 0.0139). The PAI-metV mutant also showed significant attenuation in the ability to independently colonize the kidneys (P = 0.0011). Specific genes within these islands contributed to the observed phenotype, including a previously uncharacterized iron acquisition cluster, fbpABCD (c0294 to c0297 [c0294-97]), autotransporter, picU (c0350), and RTX family exoprotein, tosA (c0363) in the PAI-aspV island. The double deletion mutant with deletions in both copies of the fbp iron acquisition operon (?c0294-97 ?c2518-15) was significantly outcompeted by wild-type CFT073 in cochallenge. Strains with mutations in a type VI secretion system within the PAI-metV island did not show attenuation. The attenuation of the PAI-metV island was localized to genes c3405-10, encoding a putative phosphotransferase transport system, which is common to UPEC and avian pathogenic E. coli strains but absent from E. coli K-12. We have shown that, in addition to encoding virulence genes, genomic islands contribute to the overall fitness of UPEC strain CFT073 in vivo.

Lloyd, Amanda L.; Henderson, Tiffany A.; Vigil, Patrick D.; Mobley, Harry L. T.

2009-01-01

19

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

PubMed Central

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.

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

20

Genomic islands predict functional adaptation in marine actinobacteria  

SciTech Connect

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 functionally adaptive traits 2. In the case of environmental bacteria, these traits are largely inferred from bioinformatic or gene expression analyses 2, thus leaving few examples in which the functions of island genes have been experimentally characterized. Here we report the complete genome sequences of Salinispora tropica and S. arenicola, the first cultured, obligate marine Actinobacteria 3. These two species inhabit benthic marine environments and dedicate 8-10percent of their genomes to the biosynthesis of secondary metabolites. Despite a close phylogenetic relationship, 25 of 37 secondary metabolic pathways are species-specific and located within 21 genomic islands, thus providing new evidence linking secondary metabolism to ecological adaptation. Species-specific differences are also observed in CRISPR sequences, suggesting that variations in phage immunity provide fitness advantages that contribute to the cosmopolitan distribution of S. arenicola 4. The two Salinispora genomes have evolved by complex processes that include the duplication and acquisition of secondary metabolite genes, the products of which provide immediate opportunities for molecular diversification and ecological adaptation. Evidence that secondary metabolic pathways are exchanged by Horizontal Gene Transfer (HGT) yet are fixed among globally distributed populations 5 supports a functional role for their products and suggests that pathway acquisition represents a previously unrecognized force driving bacterial diversification

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

2009-04-01

21

Genomic islands from five strains of Burkholderia pseudomallei  

PubMed Central

Background Burkholderia pseudomallei is the etiologic agent of melioidosis, a significant cause of morbidity and mortality where this infection is endemic. Genomic differences among strains of B. pseudomallei are predicted to be one of the major causes of the diverse clinical manifestations observed among patients with melioidosis. The purpose of this study was to examine the role of genomic islands (GIs) as sources of genomic diversity in this species. Results We found that genomic islands (GIs) vary greatly among B. pseudomallei strains. We identified 71 distinct GIs from the genome sequences of five reference strains of B. pseudomallei: K96243, 1710b, 1106a, MSHR668, and MSHR305. The genomic positions of these GIs are not random, as many of them are associated with tRNA gene loci. In particular, the 3' end sequences of tRNA genes are predicted to be involved in the integration of GIs. We propose the term "tRNA-mediated site-specific recombination" (tRNA-SSR) for this mechanism. In addition, we provide a GI nomenclature that is based upon integration hotspots identified here or previously described. Conclusion Our data suggest that acquisition of GIs is one of the major sources of genomic diversity within B. pseudomallei and the molecular mechanisms that facilitate horizontally-acquired GIs are common across multiple strains of B. pseudomallei. The differential presence of the 71 GIs across multiple strains demonstrates the importance of these mobile elements for shaping the genetic composition of individual strains and populations within this bacterial species.

Tuanyok, Apichai; Leadem, Benjamin R; Auerbach, Raymond K; Beckstrom-Sternberg, Stephen M; Beckstrom-Sternberg, James S; Mayo, Mark; Wuthiekanun, Vanaporn; Brettin, Thomas S; Nierman, William C; Peacock, Sharon J; Currie, Bart J; Wagner, David M; Keim, Paul

2008-01-01

22

Genomic Islands in the Pathogenic Filamentous Fungus Aspergillus fumigatus  

PubMed Central

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”.

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.

2008-01-01

23

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

Microsoft Academic Search

Background  Bacterial virulence enhancement and drug resistance are major threats to public health worldwide. Interestingly, newly acquired\\u000a 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.\\u000a \\u000a \\u000a \\u000a \\u000a Results  Using a large-scale comparative genomic analysis of 1088 complete genomes from all available bacteria (1009)

Pengcheng Du; Yinxue Yang; Haiying Wang; Di Liu; George F Gao; Chen Chen

2011-01-01

24

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

PubMed Central

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.

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

2012-01-01

25

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

PubMed Central

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.

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

2011-01-01

26

A systematic method to identify genomic islands and its applications in analyzing the genomes of Corynebacterium glutamicum and Vibrio vulnificus CMCP6 chromosome I  

Microsoft Academic Search

Motivation: Some genomic islands contain horizontally transferred genes, which play critical roles in altering the genotypes and phenotypes of organisms, and horizontal gene transfer has been recognized as a universal event throughout bacterial evolution. A windowless method to display the dis- tribution of genomic GC content, the cumulative GC profile, is proposed to identify genomic islands in genomes whose complete

Ren Zhang; Chun-ting Zhang

2004-01-01

27

Genomic islands of divergence are not affected by geography of speciation in sunflowers.  

PubMed

Genomic studies of speciation often report the presence of highly differentiated genomic regions interspersed within a milieu of weakly diverged loci. The formation of these speciation islands is generally attributed to reduced inter-population gene flow near loci under divergent selection, but few studies have critically evaluated this hypothesis. Here, we report on transcriptome scans among four recently diverged pairs of sunflower (Helianthus) species that vary in the geographical context of speciation. We find that genetic divergence is lower in sympatric and parapatric comparisons, consistent with a role for gene flow in eroding neutral differences. However, genomic islands of divergence are numerous and small in all comparisons, and contrary to expectations, island number and size are not significantly affected by levels of interspecific gene flow. Rather, island formation is strongly associated with reduced recombination rates. Overall, our results indicate that the functional architecture of genomes plays a larger role in shaping genomic divergence than does the geography of speciation. PMID:23652015

Renaut, S; Grassa, C J; Yeaman, S; Moyers, B T; Lai, Z; Kane, N C; Bowers, J E; Burke, J M; Rieseberg, L H

2013-01-01

28

Stability, Entrapment and Variant Formation of Salmonella Genomic Island 1  

PubMed Central

Background The Salmonella genomic island 1 (SGI1) is a 42.4 kb integrative mobilizable element containing several antibiotic resistance determinants embedded in a complex integron segment In104. The numerous SGI1 variants identified so far, differ mainly in this segment and the explanations of their emergence were mostly based on comparative structure analyses. Here we provide experimental studies on the stability, entrapment and variant formation of this peculiar gene cluster originally found in S. Typhimurium. Methodology/Principal Findings Segregation and conjugation tests and various molecular techniques were used to detect the emerging SGI1 variants in Salmonella populations of 17 Salmonella enterica serovar Typhimurium DT104 isolates from Hungary. The SGI1s in these isolates proved to be fully competent in excision, conjugal transfer by the IncA/C helper plasmid R55, and integration into the E. coli chromosome. A trap vector has been constructed and successfully applied to capture the island on a plasmid. Monitoring of segregation of SGI1 indicated high stability of the island. SGI1-free segregants did not accumulate during long-term propagation, but several SGI1 variants could be obtained. Most of them appeared to be identical to SGI1-B and SGI1-C, but two new variants caused by deletions via a short-homology-dependent recombination process have also been detected. We have also noticed that the presence of the conjugation helper plasmid increased the formation of these deletion variants considerably. Conclusions/Significance Despite that excision of SGI1 from the chromosome was proven in SGI1+ Salmonella populations, its complete loss could not be observed. On the other hand, we demonstrated that several variants, among them two newly identified ones, arose with detectable frequencies in these populations in a short timescale and their formation was promoted by the helper plasmid. This reflects that IncA/C helper plasmids are not only involved in the horizontal spreading of SGI1, but may also contribute to its evolution.

Kiss, Janos; Nagy, Bela; Olasz, Ferenc

2012-01-01

29

CpG Islands Undermethylation in Human Genomic Regions under Selective Pressure  

PubMed Central

DNA methylation at CpG islands (CGIs) is one of the most intensively studied epigenetic mechanisms. It is fundamental for cellular differentiation and control of transcriptional potential. DNA methylation is involved also in several processes that are central to evolutionary biology, including phenotypic plasticity and evolvability. In this study, we explored the relationship between CpG islands methylation and signatures of selective pressure in Homo Sapiens, using a computational biology approach. By analyzing methylation data of 25 cell lines from the Encyclopedia of DNA Elements (ENCODE) Consortium, we compared the DNA methylation of CpG islands in genomic regions under selective pressure with the methylation of CpG islands in the remaining part of the genome. To define genomic regions under selective pressure, we used three different methods, each oriented to provide distinct information about selective events. Independently of the method and of the cell type used, we found evidences of undermethylation of CGIs in human genomic regions under selective pressure. Additionally, by analyzing SNP frequency in CpG islands, we demonstrated that CpG islands in regions under selective pressure show lower genetic variation. Our findings suggest that the CpG islands in regions under selective pressure seem to be somehow more “protected” from methylation when compared with other regions of the genome.

Cocozza, Sergio; Akhtar, Most. Mauluda; Miele, Gennaro; Monticelli, Antonella

2011-01-01

30

Defense Islands in Bacterial and Archaeal Genomes and Prediction of Novel Defense Systems ?†‡  

PubMed Central

The arms race between cellular life forms and viruses is a major driving force of evolution. A substantial fraction of bacterial and archaeal genomes is dedicated to antivirus defense. We analyzed the distribution of defense genes and typical mobilome components (such as viral and transposon genes) in bacterial and archaeal genomes and demonstrated statistically significant clustering of antivirus defense systems and mobile genes and elements in genomic islands. The defense islands are enriched in putative operons and contain numerous overrepresented gene families. A detailed sequence analysis of the proteins encoded by genes in these families shows that many of them are diverged variants of known defense system components, whereas others show features, such as characteristic operonic organization, that are suggestive of novel defense systems. Thus, genomic islands provide abundant material for the experimental study of bacterial and archaeal antivirus defense. Except for the CRISPR-Cas systems, different classes of defense systems, in particular toxin-antitoxin and restriction-modification systems, show nonrandom clustering in defense islands. It remains unclear to what extent these associations reflect functional cooperation between different defense systems and to what extent the islands are genomic “sinks” that accumulate diverse nonessential genes, particularly those acquired via horizontal gene transfer. The characteristics of defense islands resemble those of mobilome islands. Defense and mobilome genes are nonrandomly associated in islands, suggesting nonadaptive evolution of the islands via a preferential attachment-like mechanism underpinned by the addictive properties of defense systems such as toxins-antitoxins and an important role of horizontal mobility in the evolution of these islands.

Makarova, Kira S.; Wolf, Yuri I.; Snir, Sagi; Koonin, Eugene V.

2011-01-01

31

Orphan CpG Islands Identify Numerous Conserved Promoters in the Mammalian Genome  

Microsoft Academic Search

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

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

2010-01-01

32

Designing of a novel GA based on fuzzy system for prediction of CpG islands in the human genome  

Microsoft Academic Search

In this paper we proposed a novel genetic algorithm based on fuzzy system for identification CpG islands in human genome, called FGA-CGI (fuzzy GA-CpG Island). CpG islands play a fundamental role in genome analysis and annotation and contribute to increase the accuracy of promoter prediction. Recently, some approaches rely on large parameter space algorithms of predicting the CpG islands have

Li-Yeh Chuang; Yu-Jung Chen; Cheng-Hong Yang

2009-01-01

33

Intergenic, gene terminal, and intragenic CpG islands in the human genome  

PubMed Central

Background Recently, it has been discovered that the human genome contains many transcription start sites for non-coding RNA. Regulatory regions related to transcription of this non-coding RNAs are poorly studied. Some of these regulatory regions may be associated with CpG islands located far from transcription start-sites of any protein coding gene. The human genome contains many such CpG islands; however, until now their properties were not systematically studied. Results We studied CpG islands located in different regions of the human genome using methods of bioinformatics and comparative genomics. We have observed that CpG islands have a preference to overlap with exons, including exons located far from transcription start site, but usually extend well into introns. Synonymous substitution rate of CpG-containing codons becomes substantially reduced in regions where CpG islands overlap with protein-coding exons, even if they are located far downstream from transcription start site. CAGE tag analysis displayed frequent transcription start sites in all CpG islands, including those found far from transcription start sites of protein coding genes. Computational prediction and analysis of published ChIP-chip data revealed that CpG islands contain an increased number of sites recognized by Sp1 protein. CpG islands containing more CAGE tags usually also contain more Sp1 binding sites. This is especially relevant for CpG islands located in 3' gene regions. Various examples of transcription, confirmed by mRNAs or ESTs, but with no evidence of protein coding genes, were found in CAGE-enriched CpG islands located far from transcription start site of any known protein coding gene. Conclusions CpG islands located far from transcription start sites of protein coding genes have transcription initiation activity and display Sp1 binding properties. In exons, overlapping with these islands, the synonymous substitution rate of CpG containing codons is decreased. This suggests that these CpG islands are involved in transcription initiation, possibly of some non-coding RNAs.

2010-01-01

34

Genetic and Phenotypic Characterization of a Pseudomonas aeruginosa Population with High Frequency of Genomic Islands  

PubMed Central

Various genomic islands, PAPI-1, PAPI-2, PAGI-1, PAGI-2, PAGI-3, and PAGI-4, and the element pKLC102 have been characterized in different P. aeruginosa strains from diverse habitats and geographical locations. Chromosomal DNA macroarray of 100 P. aeruginosa strains isolated from 85 unrelated patients hospitalized in an intensive care unit was created to assess the occurrence of these genomic islands (GEIs). The macroarray was then hybridized with labeled probes derived from each genomic island. In addition, PFGE patterns with SpeI, frequency of virulence genes, and antimicrobial resistance patterns of the strains were studied. Our results showed that almost all P. aeruginosa strains presented up to eight virulence genes. By SpeI macrorestriction fragment analysis we were able to identify 49 restriction patterns; 35 patterns correspond to single strains and the remaining 14 to strains subgroup (a–n). Most of the strains showed variation in number or composition of GEIs and a specific antimicrobial pattern indicating that each strain was an unrelated isolate. In terms of the number of genomic islands per strain, 7 GEIs were found in 34% of the strains, 6 in 18%, 5 in 12%, 4 in 14%, 3 in 10%, 2 in 7%, and 1 in 4%; only one isolate did not present any GEI. The genomic islands PAPI-1 and PAPI-2 and the element pKLC102 were the most frequently detected. The analysis of the location of each GEI in the chromosome of two strains show that the islands PAGI-3, PAPI-1, PAPI-2 and pKLC102 are present in the insertion site previously reported, but that PAGI-2 and PAGI-4 are inserted in another chromosome place in a site not characterized yet. In conclusion our data show that P. aeruginosa strains exhibited an epidemic population structure with horizontal transfer of DNA resulting in a high frequency of GEIs.

Morales-Espinosa, Rosario; Soberon-Chavez, Gloria; Delgado-Sapien, Gabriela; Sandner-Miranda, Luisa; Mendez, Jose L.; Gonzalez-Valencia, Gerardo; Cravioto, Alejandro

2012-01-01

35

Long-Range Autocorrelations of CpG Islands in the Human Genome  

Microsoft Academic Search

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)

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

2012-01-01

36

Defining Genomic Islands and Uropathogen-Specific Genes in Uropathogenic Escherichia coli?  

PubMed Central

Uropathogenic Escherichia coli (UPEC) strains are responsible for the majority of uncomplicated urinary tract infections, which can present clinically as cystitis or pyelonephritis. UPEC strain CFT073, isolated from the blood of a patient with acute pyelonephritis, was most cytotoxic and most virulent in mice among our strain collection. Based on the genome sequence of CFT073, microarrays were utilized in comparative genomic hybridization (CGH) analysis of a panel of uropathogenic and fecal/commensal E. coli isolates. Genomic DNA from seven UPEC (three pyelonephritis and four cystitis) isolates and three fecal/commensal strains, including K-12 MG1655, was hybridized to the CFT073 microarray. The CFT073 genome contains 5,379 genes; CGH analysis revealed that 2,820 (52.4%) of these genes were common to all 11 E. coli strains, yet only 173 UPEC-specific genes were found by CGH to be present in all UPEC strains but in none of the fecal/commensal strains. When the sequences of three additional sequenced UPEC strains (UTI89, 536, and F11) and a commensal strain (HS) were added to the analysis, 131 genes present in all UPEC strains but in no fecal/commensal strains were identified. Seven previously unrecognized genomic islands (>30 kb) were delineated by CGH in addition to the three known pathogenicity islands. These genomic islands comprise 672 kb of the 5,231-kb (12.8%) genome, demonstrating the importance of horizontal transfer for UPEC and the mosaic structure of the genome. UPEC strains contain a greater number of iron acquisition systems than do fecal/commensal strains, which is reflective of the adaptation to the iron-limiting urinary tract environment. Each strain displayed distinct differences in the number and type of known virulence factors. The large number of hypothetical genes in the CFT073 genome, especially those shown to be UPEC specific, strongly suggests that many urovirulence factors remain uncharacterized.

Lloyd, Amanda L.; Rasko, David A.; Mobley, Harry L. T.

2007-01-01

37

Comparative genome sequencing identifies a prophage-associated genomic island linked to host adaptation of Lawsonia intracellularis infections.  

PubMed

Lawsonia intracellularis is an obligate intracellular bacterium and the causative agent of proliferative enteropathy (PE). The disease is endemic in pigs, emerging in horses and has also been reported in a variety of other animal species, including nonhuman primates. Comparing the whole genome sequences of a homologous porcine L. intracellularis isolate cultivated for 10 and 60 passages in vitro, we identified a 18-kb prophage-associated genomic island in the passage 10 (pathogenic variant) that was lost in the passage 60 (non-pathogenic variant). This chromosomal island comprises 15 genes downstream from the prophage DLP12 integrase gene. The prevalence of this genetic element was evaluated in 12 other L. intracellularis isolates and in 53 infected animals and was found to be conserved in all porcine isolates cultivated for up to 20 passages and was lost in isolates cultivated for more than 40 passages. Furthermore, the prophage region was also present in 26 fecal samples derived from pigs clinically affected with both acute and chronic forms of the disease. Nevertheless, equine L. intracellularis isolates evaluated did not harbor this genomic island regardless of the passage in vitro. Additionally, fecal samples from 21 clinically affected horses and four wild rabbits trapped in horse farms experiencing PE outbreaks did not show this prophage-associated island. Although the presence of this prophage-associated island was not essential for a virulent L. intracellularis phenotype, this genetic element was porcine isolate-specific and potentially contributed to the ecological specialization of this organism for the swine host. PMID:23826661

Vannucci, Fabio A; Kelley, Molly R; Gebhart, Connie J

2013-07-04

38

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

PubMed

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

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

2013-03-14

39

A quantitative account of genomic island acquisitions in prokaryotes  

Microsoft Academic Search

BACKGROUND: Microbial genomes do not merely evolve through the slow accumulation of mutations, but also, and often more dramatically, by taking up new DNA in a process called horizontal gene transfer. These innovation leaps in the acquisition of new traits can take place via the introgression of single genes, but also through the acquisition of large gene clusters, which are

T. E. Roos; Passel van M. W. J

2011-01-01

40

Genomic fingerprinting and serotyping of Salmonella from Galápagos iguanas demonstrates island differences in strain diversity.  

PubMed

Salmonella carriage patterns in wild and captive reptiles suggest that both geographical proximity and host ecological differences may determine bacterial diversity among reptile populations. In this study, we explore the relative importance of these factors on Salmonella diversity in free-living Galápagos iguanas. We isolated Salmonella enterica from marine iguanas (Amblyrhynchus cristatus) and land iguanas (Conolophus subcristatus and C. pallidus) living on two islands (Plaza Sur and Santa Fe). We evaluated Salmonella population patterns using genomic fingerprints, sequence typing and serotyping. Rep-PCR fingerprinting revealed significant grouping of isolates by iguana population. Island residence had the strongest effect on isolate similarity, but a smaller divergence among Salmonella isolates from different iguana ecotypes (land versus marine) was detected within each island. In contrast, sequence typing detected a marginal difference in isolate genotypes between islands. Sequence types corresponded strongly to serotype identity, with both islands hosting a unique serovar pool. Our findings suggest that both geographical location and host ecotype differences (either from within host strain selection or from differences in habitat use) contribute to Salmonella population patterns in the Galápagos Islands. PMID:23761248

Wheeler, Emily; Cann, Isaac K O; Mackie, Roderick I

2010-08-16

41

Antibiotic Resistance Genes and Salmonella Genomic Island 1 in Salmonella enterica Serovar Typhimurium Isolated in Italy  

PubMed Central

Fifty-four epidemiologically unrelated multidrug-resistant Salmonella enterica serovar Typhimurium isolates, collected between 1992 and 2000 in Italy, were analyzed for the presence of integrons. Strains were also tested for Salmonella genomic island 1 (SGI1), carrying antibiotic resistance genes in DT104 strains. A complete SGI1 was found in the majority of the DT104 strains. Two DT104 strains, showing resistance to streptomycin-spectinomycin and sulfonamides, carried a partially deleted SGI1 lacking the flost, tetR, and tetA genes, conferring chloramphenicol-florfenicol and tetracycline resistance, and the integron harboring the pse-1 gene cassette, conferring ampicillin resistance. The presence of SGI1 was also observed in serovar Typhimurium strains belonging to other phage types, suggesting either the potential mobility of this genomic island or changes in the phage-related phenotype of DT104 strains.

Carattoli, Alessandra; Filetici, Emma; Villa, Laura; Dionisi, Anna Maria; Ricci, Antonia; Luzzi, Ida

2002-01-01

42

Secondary Chromosomal Attachment Site and Tandem Integration of the Mobilizable Salmonella Genomic Island 1  

Microsoft Academic Search

BackgroundThe Salmonella genomic island 1 is an integrative mobilizable element (IME) originally identified in epidemic multidrug-resistant Salmonella enterica serovar Typhimurium (S. Typhimurium) DT104. SGI1 contains a complex integron, which confers various multidrug resistance phenotypes due to its genetic plasticity. Previous studies have shown that SGI1 integrates site-specifically into the S. enterica, Escherichia coli, or Proteus mirabilis chromosome at the 3?

Benoît Doublet; George R. Golding; Michael R. Mulvey; Axel Cloeckaert; Cecile Fairhead

2008-01-01

43

Regulation, Integrase-Dependent Excision, and Horizontal Transfer of Genomic Islands in Legionella pneumophila  

PubMed Central

Legionella pneumophila is a Gram-negative freshwater agent which multiplies in specialized nutrient-rich vacuoles of amoebae. When replicating in human alveolar macrophages, Legionella can cause Legionnaires' disease. Recently, we identified a new type of conjugation/type IVA secretion system (T4ASS) in L. pneumophila Corby (named trb-tra). Analogous versions of trb-tra are localized on the genomic islands Trb-1 and Trb-2. Both can exist as an episomal circular form, and Trb-1 can be transferred horizontally to other Legionella strains by conjugation. In our current work, we discovered the importance of a site-specific integrase (Int-1, lpc2818) for the excision and conjugation process of Trb-1. Furthermore, we identified the genes lvrRABC (lpc2813 to lpc2816) to be involved in the regulation of Trb-1 excision. In addition, we demonstrated for the first time that a Legionella genomic island (LGI) of L. pneumophila Corby (LpcGI-2) encodes a functional type IV secretion system. The island can be transferred horizontally by conjugation and is integrated site specifically into the genome of the transconjugants. LpcGI-2 generates three different episomal forms. The predominant episomal form, form A, is generated integrase dependently (Lpc1833) and transferred by conjugation in a pilT-dependent manner. Therefore, the genomic islands Trb-1 and LpcGI-2 should be classified as integrative and conjugative elements (ICEs). Coculture studies of L. pneumophila wild-type and mutant strains revealed that the int-1 and lvrRABC genes (located on Trb-1) as well as lpc1833 and pilT (located on LpcGI-2) do not influence the in vivo fitness of L. pneumophila in Acanthamoeba castellanii.

Lautner, Monika; Schunder, Eva; Herrmann, Vroni

2013-01-01

44

CpG_MI: a novel approach for identifying functional CpG islands in mammalian genomes  

Microsoft Academic Search

CpG islands (CGIs) are CpG-rich regions compared to CpG-depleted bulk DNA of mammalian genomes and are generally regarded as the epigenetic regu- latory regions in association with unmethylation, promoter activity and histone modifications. Accurate identification of CpG islands with epigenetic regulatory function in bulk genomes is of wide interest. Here, the common features of func- tional CGIs are identified using

Jianzhong Su; Yan Zhang; Jie Lv; Hongbo Liu; Xiaoyan Tang; Fang Wang; Yunfeng Qi; Yujia Feng; Xia Li

2010-01-01

45

Compositional searching of CpG islands in the human genome  

NASA Astrophysics Data System (ADS)

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 are pieces of the genome related to gene expression and cell differentiation, and thus to cancer formation. Searching for these CpG islands is a major task in genetics and bioinformatics. Some algorithms have been proposed in the literature, based on moving statistics in a sliding window, but its size may greatly influence the results. The local use of Jensen-Shannon divergence is a completely different strategy: the nucleotide composition inside the islands is different from that in their environment, so a statistical distance—the Jensen-Shannon divergence—between the composition of two adjacent windows may be used as a measure of their dissimilarity. Sliding this double window over the entire sequence allows us to segment it compositionally. The fusion of those segments into greater ones that satisfy certain identification criteria must be achieved in order to obtain the definitive results. We find that the local use of Jensen-Shannon divergence is very suitable in processing DNA sequences for searching for compositionally different structures such as CpG islands, as compared to other algorithms in literature.

Luque-Escamilla, Pedro Luis; Martínez-Aroza, José; Oliver, José L.; Gómez-Lopera, Juan Francisco; Román-Roldán, Ramón

2005-06-01

46

Genomic Islands as a Marker to Differentiate between Clinical and Environmental Burkholderia pseudomallei  

PubMed Central

Burkholderia pseudomallei, as a saprophytic bacterium that can cause a severe sepsis disease named melioidosis, has preserved several extra genes in its genome for survival. The sequenced genome of the organism showed high diversity contributed mainly from genomic islands (GIs). Comparative genome hybridization (CGH) of 3 clinical and 2 environmental isolates, using whole genome microarrays based on B. pseudomallei K96243 genes, revealed a difference in the presence of genomic islands between clinical and environmental isolates. The largest GI, GI8, of B. pseudomallei was observed as a 2 sub-GI named GIs8.1 and 8.2 with distinguishable %GC content and unequal presence in the genome. GIs8.1, 8.2 and 15 were found to be more common in clinical isolates. A new GI, GI16c, was detected on chromosome 2. Presences of GIs8.1, 8.2, 15 and 16c were evaluated in 70 environmental and 64 clinical isolates using PCR assays. A combination of GIs8.1 and 16c (positivity of either GI) was detected in 70% of clinical isolates and 11.4% of environmental isolates (P<0.001). Using BALB/c mice model, no significant difference of time to mortality was observed between K96243 isolate and three isolates without GIs under evaluation (P>0.05). Some virulence genes located in the absent GIs and the difference of GIs seems to contribute less to bacterial virulence. The PCR detection of 2 GIs could be used as a cost effective and rapid tool to detect potentially virulent isolates that were contaminated in soil.

Bartpho, Thanatchaporn; Wongsurawat, Thidathip; Wongratanacheewin, Surasakdi; Talaat, Adel M.; Karoonuthaisiri, Nitsara; Sermswan, Rasana W.

2012-01-01

47

Particle Swarm Optimization with Reinforcement Learning for the Prediction of CpG Islands in the Human Genome  

PubMed Central

Background Regions with abundant GC nucleotides, a high CpG number, and a length greater than 200 bp in a genome are often referred to as CpG islands. These islands are usually located in the 5? end of genes. Recently, several algorithms for the prediction of CpG islands have been proposed. Methodology/Principal Findings We propose here a new method called CPSORL to predict CpG islands, which consists of a complement particle swarm optimization algorithm combined with reinforcement learning to predict CpG islands more reliably. Several CpG island prediction tools equipped with the sliding window technique have been developed previously. However, the quality of the results seems to rely too much on the choices that are made for the window sizes, and thus these methods leave room for improvement. Conclusions/Significance Experimental results indicate that CPSORL provides results of a higher sensitivity and a higher correlation coefficient in all selected experimental contigs than the other methods it was compared to (CpGIS, CpGcluster, CpGProd and CpGPlot). A higher number of CpG islands were identified in chromosomes 21 and 22 of the human genome than with the other methods from the literature. CPSORL also achieved the highest coverage rate (3.4%). CPSORL is an application for identifying promoter and TSS regions associated with CpG islands in entire human genomic. When compared to CpGcluster, the islands predicted by CPSORL covered a larger region in the TSS (12.2%) and promoter (26.1%) region. If Alu sequences are considered, the islands predicted by CPSORL (Alu) covered a larger TSS (40.5%) and promoter (67.8%) region than CpGIS. Furthermore, CPSORL was used to verify that the average methylation density was 5.33% for CpG islands in the entire human genome.

Chuang, Li-Yeh; Huang, Hsiu-Chen; Lin, Ming-Cheng; Yang, Cheng-Hong

2011-01-01

48

Microcin H47 system: an Escherichia coli small genomic island with novel features.  

PubMed

Genomic islands are DNA regions containing variable genetic information related to secondary metabolism. Frequently, they have the ability to excise from and integrate into replicons through site-specific recombination. Thus, they are usually flanked by short direct repeats that act as attachment sites, and contain genes for an integrase and an excisionase which carry out the genetic exchange. These mobility events would be at the basis of the horizontal transfer of genomic islands among bacteria.Microcin H47 is a ribosomally-synthesized antibacterial peptide that belongs to the group of chromosome-encoded microcins. The 13 kb-genetic system responsible for its production resides in the chromosome of the Escherichia coli H47 strain and is flanked by extensive and imperfect direct repeats. In this work, both excision and integration of the microcin H47 system were experimentally detected. The analyses were mainly performed in E. coli K12 cells carrying the microcin system cloned in a multicopy plasmid. As expected of a site-specific recombination event, the genetic exchange also occurred in a context deficient for homologous recombination. The DNA sequence of the attachment sites resulting from excision were hybrid between the sequences of the direct repeats. Unexpectedly, different hybrid attachment sites appeared which resulted from recombination in four segments of identity between the direct repeats. Genes encoding the trans-acting proteins responsible for the site-specific recombination were shown to be absent in the microcin H47 system. Therefore, they should be provided by the remaining genetic context, not only in the H47 strain but also in E. coli K12 cells, where both excision and integration occurred. Moreover, a survey of the attachment sites in data banks revealed that they are widely spread among E. coli strains. It is concluded that the microcin system is a small island -H47 genomic island- that would employ a parasitic strategy for its mobility. PMID:22022554

Azpiroz, María F; Bascuas, Thais; Laviña, Magela

2011-10-11

49

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

PubMed

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

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

2011-12-14

50

High-density transcriptional initiation signals underline genomic islands in bacteria.  

PubMed

Genomic islands (GIs), frequently associated with the pathogenicity of bacteria and having a substantial influence on bacterial evolution, are groups of "alien" elements which probably undergo special temporal-spatial regulation in the host genome. Are there particular hallmark transcriptional signals for these "exotic" regions? We here explore the potential transcriptional signals that underline the GIs beyond the conventional views on basic sequence composition, such as codon usage and GC property bias. It showed that there is a significant enrichment of the transcription start positions (TSPs) in the GI regions compared to the whole genome of Salmonella enterica and Escherichia coli. There was up to a four-fold increase for the 70% GIs, implying high-density TSPs profile can potentially differentiate the GI regions. Based on this feature, we developed a new sliding window method GIST, Genomic-island Identification by Signals of Transcription, to identify these regions. Subsequently, we compared the known GI-associated features of the GIs detected by GIST and by the existing method Islandviewer to those of the whole genome. Our method demonstrates high sensitivity in detecting GIs harboring genes with biased GI-like function, preferred subcellular localization, skewed GC property, shorter gene length and biased "non-optimal" codon usage. The special transcriptional signals discovered here may contribute to the coordinate expression regulation of foreign genes. Finally, by using GIST, we detected many interesting GIs in the 2011 German E. coli O104:H4 outbreak strain TY-2482, including the microcin H47 system and gene cluster ycgXEFZ-ymgABC that activates the production of biofilm matrix. The aforesaid findings highlight the power of GIST to predict GIs with distinct intrinsic features to the genome. The heterogeneity of cumulative TSPs profiles may not only be a better identity for "alien" regions, but also provide hints to the special evolutionary course and transcriptional regulation of GI regions. PMID:22448273

Huang, Qianli; Cheng, Xuanjin; Cheung, Man Kit; Kiselev, Sergey S; Ozoline, Olga N; Kwan, Hoi Shan

2012-03-20

51

Quality assessment of maize assembled genomic islands (MAGIs) and large-scale experimental verification of predicted genes  

Microsoft Academic Search

Recent sequencing efforts have targeted the gene-rich regions of the maize (Zea mays L.) genome. We report the release of an improved assembly of maize assembled genomic islands (MAGIs). The 114,173 resulting contigs have been subjected to computational and physical quality assessments. Comparisons to the sequences of maize bacterial artificial chromosomes suggest that at least 97% (160 of 165) of

Yan Fu; Scott J. Emrich; Ling Guo; Tsui-Jung Wen; Daniel A. Ashlock; Srinivas Aluru; Patrick S. Schnable

2005-01-01

52

Gene Islands Integrated into tRNAGly Genes Confer Genome Diversity on a Pseudomonas aeruginosa Clone  

PubMed Central

Intraclonal genome diversity of Pseudomonas aeruginosa was studied in one of the most diverse mosaic regions of the P. aeruginosa chromosome. The ca. 110-kb large hypervariable region located near the lipH gene in two members of the predominant P. aeruginosa clone C, strain C and strain SG17M, was sequenced. In both strains the region consists of an individual strain-specific gene island of 111 (strain C) or 106 (SG17M) open reading frames (ORFs) and of a 7-kb stretch of clone C-specific sequence of 9 ORFs. The gene islands are integrated into conserved tRNAGly genes and have a bipartite structure. The first part adjacent to the tRNA gene consists of strain-specific ORFs encoding metabolic functions and transporters, the majority of which have homologs of known function in other eubacteria, such as hemophores, cytochrome c biosynthesis, or mercury resistance. The second part is made up mostly of ORFs of yet-unknown function. Forty-seven of these ORFs are mutual homologs with a pairwise amino acid sequence identity of 35 to 88% and are arranged in the same order in the two gene islands. We hypothesize that this novel type of gene island derives from mobile elements which, upon integration, endow the recipient with strain-specific metabolic properties, thus possibly conferring on it a selective advantage in its specific habitat.

Larbig, Karen D.; Christmann, Andreas; Johann, Andre; Klockgether, Jens; Hartsch, Thomas; Merkl, Rainer; Wiehlmann, Lutz; Fritz, Hans-Joachim; Tummler, Burkhard

2002-01-01

53

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

PubMed

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

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

2013-01-24

54

Score-based prediction of genomic islands in prokaryotic genomes using hidden Markov models  

Microsoft Academic Search

Background: Horizontal gene transfer (HGT) is considered a strong evolutionary force shaping the content of microbial genomes in a substantial manner. It is the difference in speed enabling the rapid adaptation to changing environmental demands that distinguishes HGT from gene genesis, duplications or mutations. For a precise characterization, algorithms are needed that identify transfer events with high reliability. Frequently, the

Stephan Waack; Oliver Keller; Roman Asper; Thomas Brodag; Carsten Damm; Wolfgang Florian Fricke; Katharina Surovcik; Peter Meinicke; Rainer Merkl

2006-01-01

55

Mobilisation and remobilisation of a large archetypal pathogenicity island of uropathogenic Escherichia coli in vitro support the role of conjugation for horizontal transfer of genomic islands  

PubMed Central

Background A substantial amount of data has been accumulated supporting the important role of genomic islands (GEIs) - including pathogenicity islands (PAIs) - in bacterial genome plasticity and the evolution of bacterial pathogens. Their instability and the high level sequence similarity of different (partial) islands suggest an exchange of PAIs between strains of the same or even different bacterial species by horizontal gene transfer (HGT). Transfer events of archetypal large genomic islands of enterobacteria which often lack genes required for mobilisation or transfer have been rarely investigated so far. Results To study mobilisation of such large genomic regions in prototypic uropathogenic E. coli (UPEC) strain 536, PAI II536 was supplemented with the mobRP4 region, an origin of replication (oriVR6K), an origin of transfer (oriTRP4) and a chloramphenicol resistance selection marker. In the presence of helper plasmid RP4, conjugative transfer of the 107-kb PAI II536 construct occured from strain 536 into an E. coli K-12 recipient. In transconjugants, PAI II536 existed either as a cytoplasmic circular intermediate (CI) or integrated site-specifically into the recipient's chromosome at the leuX tRNA gene. This locus is the chromosomal integration site of PAI II536 in UPEC strain 536. From the E. coli K-12 recipient, the chromosomal PAI II536 construct as well as the CIs could be successfully remobilised and inserted into leuX in a PAI II536 deletion mutant of E. coli 536. Conclusions Our results corroborate that mobilisation and conjugal transfer may contribute to evolution of bacterial pathogens through horizontal transfer of large chromosomal regions such as PAIs. Stabilisation of these mobile genetic elements in the bacterial chromosome result from selective loss of mobilisation and transfer functions of genomic islands.

2011-01-01

56

Linking the Epigenome to the Genome: Correlation of Different Features to DNA Methylation of CpG Islands  

PubMed Central

DNA methylation of CpG islands plays a crucial role in the regulation of gene expression. More than half of all human promoters contain CpG islands with a tissue-specific methylation pattern in differentiated cells. Still today, the whole process of how DNA methyltransferases determine which region should be methylated is not completely revealed. There are many hypotheses of which genomic features are correlated to the epigenome that have not yet been evaluated. Furthermore, many explorative approaches of measuring DNA methylation are limited to a subset of the genome and thus, cannot be employed, e.g., for genome-wide biomarker prediction methods. In this study, we evaluated the correlation of genetic, epigenetic and hypothesis-driven features to DNA methylation of CpG islands. To this end, various binary classifiers were trained and evaluated by cross-validation on a dataset comprising DNA methylation data for 190 CpG islands in HEPG2, HEK293, fibroblasts and leukocytes. We achieved an accuracy of up to 91% with an MCC of 0.8 using ten-fold cross-validation and ten repetitions. With these models, we extended the existing dataset to the whole genome and thus, predicted the methylation landscape for the given cell types. The method used for these predictions is also validated on another external whole-genome dataset. Our results reveal features correlated to DNA methylation and confirm or disprove various hypotheses of DNA methylation related features. This study confirms correlations between DNA methylation and histone modifications, DNA structure, DNA sequence, genomic attributes and CpG island properties. Furthermore, the method has been validated on a genome-wide dataset from the ENCODE consortium. The developed software, as well as the predicted datasets and a web-service to compare methylation states of CpG islands are available at http://www.cogsys.cs.uni-tuebingen.de/software/dna-methylation/.

Wrzodek, Clemens; Buchel, Finja; Hinselmann, Georg; Eichner, Johannes; Mittag, Florian; Zell, Andreas

2012-01-01

57

Diversity of the Abundant pKLC102/PAGI-2 Family of Genomic Islands in Pseudomonas aeruginosa? †  

PubMed Central

The known genomic islands of Pseudomonas aeruginosa clone C strains are integrated into tRNALys (pKLC102) or tRNAGly (PAGI-2 and PAGI-3) genes and differ from their core genomes by distinctive tetranucleotide usage patterns. pKLC102 and the related island PAPI-1 from P. aeruginosa PA14 were spontaneously mobilized from their host chromosomes at frequencies of 10% and 0.3%, making pKLC102 the most mobile genomic island known with a copy number of 30 episomal circular pKLC102 molecules per cell. The incidence of islands of the pKLC102/PAGI-2 type was investigated in 71 unrelated P. aeruginosa strains from diverse habitats and geographic origins. pKLC102- and PAGI-2-like islands were identified in 50 and 31 strains, respectively, and 15 and 10 subtypes were differentiated by hybridization on pKLC102 and PAGI-2 macroarrays. The diversity of PAGI-2-type islands was mainly caused by one large block of strain-specific genes, whereas the diversity of pKLC102-type islands was primarily generated by subtype-specific combination of gene cassettes. Chromosomal loss of PAGI-2 could be documented in sequential P. aeruginosa isolates from individuals with cystic fibrosis. PAGI-2 was present in most tested Cupriavidus metallidurans and Cupriavidus campinensis isolates from polluted environments, demonstrating the spread of PAGI-2 across habitats and species barriers. The pKLC102/PAGI-2 family is prevalent in numerous beta- and gammaproteobacteria and is characterized by high asymmetry of the cDNA strands. This evolutionarily ancient family of genomic islands retained its oligonucleotide signature during horizontal spread within and among taxa.

Klockgether, Jens; Wurdemann, Dieco; Reva, Oleg; Wiehlmann, Lutz; Tummler, Burkhard

2007-01-01

58

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

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,

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

1997-01-01

59

Genome-wide methylated CpG island profiles of melanoma cells reveal a melanoma coregulation network  

PubMed Central

Metastatic melanoma is a malignant cancer with generally poor prognosis, with no targeted chemotherapy. To identify epigenetic changes related to melanoma, we have determined genome-wide methylated CpG island distributions by next-generation sequencing. Melanoma chromosomes tend to be differentially methylated over short CpG island tracts. CpG islands in the upstream regulatory regions of many coding and noncoding RNA genes, including, for example, TERC, which encodes the telomerase RNA, exhibit extensive hypermethylation, whereas several repeated elements, such as LINE 2, and several LTR elements, are hypomethylated in advanced stage melanoma cell lines. By using CpG island demethylation profiles, and by integrating these data with RNA-seq data obtained from melanoma cells, we have identified a co-expression network of differentially methylated genes with significance for cancer related functions. Focused assays of melanoma patient tissue samples for CpG island methylation near the noncoding RNA gene SNORD-10 demonstrated high specificity.

Li, Jian-Liang; Mazar, Joseph; Zhong, Cuncong; Faulkner, Geoffrey J.; Govindarajan, Subramaniam S.; Zhang, Zhan; Dinger, Marcel E.; Meredith, Gavin; Adams, Christopher; Zhang, Shaojie; Mattick, John S.; Ray, Animesh; Perera, Ranjan J.

2013-01-01

60

Characterization of Genomic Island 3 and Genetic Variability of Chilean Field Strains of Brucella abortus?  

PubMed Central

One of the capabilities developed by bacteria is the ability to gain large fragments of DNA from other bacteria or to lose portions of their own genomes. Among these exchangeable fragments are the genomic islands (GIs). Nine GIs have been identified in Brucella, and genomic island 3 (GI-3) is shared by two pathogenic species, B. melitensis and B. abortus. GI-3 encodes mostly unknown proteins. One of the aims of this study was to perform pulsed-field gel electrophoresis (PFGE) on field isolates of B. abortus from Chile to determine whether these isolates are clonally related. Furthermore, we focused on the characterization of GI-3, studying its organization and the genetic conservation of the GI-3 sequence using techniques such as tiling-path PCR (TP-PCR) and restriction fragment length polymorphism-PCR (RFLP-PCR). Our results, after PFGE was performed on 69 field isolates of B. abortus from Chile, showed that the strains were genetically homogeneous. To increase the power of genetic discrimination among these strains, we used multiple locus variable-number tandem-repeat (VNTR) analysis with 16 loci (MLVA-16). The results obtained by MLVA-16 showed that the strains of B. abortus were genetically heterogeneous and that most of them clustered according to their geographic origin. Of the genetic loci studied, panel 2B was the one describing the highest diversity in the analysis, as well as locus Bruce19 in panel 2A. In relation to the study of GI-3, our experimental analysis by TP-PCR identified and confirmed that GI-3 is present in all wild strains of B. abortus, demonstrating the high stability of gene cluster GI-3 in Chilean field strains.

Cespedes, Sandra; Salgado, Paulina; Valenzuela, Patricio; Vidal, Roberto; Onate, Angel A.

2011-01-01

61

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

PubMed Central

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.

Stevens, Patricia

2010-01-01

62

Putative Zinc Finger Protein Binding Sites Are Over-Represented in the Boundaries of Methylation-Resistant CpG Islands in the Human Genome  

Microsoft Academic Search

BackgroundMajority of CpG dinucleotides in mammalian genomes tend to undergo DNA methylation, but most CpG islands are resistant to such epigenetic modification. Understanding about mechanisms that may lead to the methylation resistance of CpG islands is still very poor.Methodology\\/Principal FindingsUsing the genome-scale in vivo DNA methylation data from human brain, we investigated the flanking sequence features of methylation-resistant CpG islands,

Shicai Fan; Fang Fang; Xuegong Zhang; Michael Q. Zhang; Jörg Hoheisel

2007-01-01

63

When phage, plasmids, and transposons collide: genomic islands, and conjugative- and mobilizable-transposons as a mosaic continuum  

Microsoft Academic Search

Plasmids and bacteriophage represent the classical vectors for gene transfer within the horizontal gene pool. However, the more recent discovery of an increasing array of other mobile genetic elements (MGE) including genomic islands (GIs), conjugative transposons (CTns), and mobilizable transposons (MTns) which each integrate within the chromosome, offer an increasingly diverse assemblage contributing to bacterial adaptation and evolution. Molecular characterisation

A. Mark Osborn; Dietmar Böltner

2002-01-01

64

Cloning and Sequencing of a Genomic Island Found in the Brazilian Purpuric Fever Clone of Haemophilus influenzae Biogroup Aegyptius  

PubMed Central

A genomic island was identified in the Haemophilus influenzae biogroup aegyptius Brazilian purpuric fever (BPF) strain F3031. This island, which was also found in other BPF isolates, could not be detected in non-BPF biogroup aegyptius strains or in nontypeable or typeable H. influenzae strains, with the exception of a region present in the type b Eagan strain. This 34,378-bp island is inserted, in reference to H. influenzae Rd KW20, within a choline transport gene and contains a mosaic structure of Mu-like prophage genes, several hypothetical genes, and genes potentially encoding an Erwinia carotovora carotovoricin Er-like bacteriocin. The product of the tail fiber ORF in the bacteriocin-like region shows a hybrid structure where the C terminus is similar to an H. influenzae phage HP1 tail protein implicating this open reading frame in altering host specificity for a putative bacteriocin. Significant synteny is seen in the entire genomic island with genomic regions from Salmonella enterica subsp. enterica serovar Typhi CT18, Photorhabdus luminescens subsp. laumondii TT01, Chromobacterium violaceum, and to a lesser extent Haemophilus ducreyi 35000HP. In a previous work, we isolated several BPF-specific DNA fragments through a genome subtraction procedure, and we have found that a majority of these fragments map to this locus. In addition, several subtracted fragments generated from an independent laboratory by using different but related strains also map to this island. These findings underscore the importance of this BPF-specific chromosomal region in explaining some of the genomic differences between highly invasive BPF strains and non-BPF isolates of biogroup aegyptius.

McGillivary, Glen; Tomaras, Andrew P.; Rhodes, Eric R.; Actis, Luis A.

2005-01-01

65

Evaluation of single CpG sites as proxies of CpG island methylation states at the genome scale.  

PubMed

Methylation of a CpG island is a faithful marker of silencing of its associated gene. Different approaches report the methylation status of a CpG island based on the determination of one or a few CpG sites by assuming the homogeneity of methylation along the element. This strategy is frequently applied in both locus-specific and genome-wide studies, but often without a validation of the representativeness of the interrogated CpG site compared with the whole element. We have evaluated the predictive informativeness of the HpaII sites located in CpG islands using data from high-resolution methylome maps, which offer the possibility to assess the methylation homogeneity of each CpG island and to determine the reporter accuracy of single sites as surrogate markers. An excellent correlation was observed between the HpaII and CpG island methylation levels (r > 0.93). At the qualitative level, the predictive sensitivity of HpaII was >95% with >92% specificity for methylated CpG islands and >90% sensitivity with >95% specificity for unmethylated CpG islands. This analysis provides a global validation framework for strategies based on the use of the methylation-sensitive HpaII restriction enzyme. PMID:23066096

Barrera, Víctor; Peinado, Miguel A

2012-10-12

66

Evaluation of single CpG sites as proxies of CpG island methylation states at the genome scale  

PubMed Central

Methylation of a CpG island is a faithful marker of silencing of its associated gene. Different approaches report the methylation status of a CpG island based on the determination of one or a few CpG sites by assuming the homogeneity of methylation along the element. This strategy is frequently applied in both locus-specific and genome-wide studies, but often without a validation of the representativeness of the interrogated CpG site compared with the whole element. We have evaluated the predictive informativeness of the HpaII sites located in CpG islands using data from high-resolution methylome maps, which offer the possibility to assess the methylation homogeneity of each CpG island and to determine the reporter accuracy of single sites as surrogate markers. An excellent correlation was observed between the HpaII and CpG island methylation levels (r > 0.93). At the qualitative level, the predictive sensitivity of HpaII was >95% with >92% specificity for methylated CpG islands and >90% sensitivity with >95% specificity for unmethylated CpG islands. This analysis provides a global validation framework for strategies based on the use of the methylation-sensitive HpaII restriction enzyme.

Barrera, Victor; Peinado, Miguel A.

2012-01-01

67

Conjugative Transfer and cis-Mobilization of a Genomic Island by an Integrative and Conjugative Element of Streptococcus agalactiae  

PubMed Central

Putative integrative and conjugative elements (ICEs), i.e., genomic islands which could excise, self-transfer by conjugation, and integrate into the chromosome of the bacterial host strain, were previously identified by in silico analysis in the sequenced genomes of Streptococcus agalactiae (M. Brochet et al., J. Bacteriol. 190:6913–6917, 2008). We investigated here the mobility of the elements integrated into the 3? end of a tRNALys gene. Three of the four putative ICEs tested were found to excise but only one (ICE_515_tRNALys) was found to transfer by conjugation not only to S. agalactiae strains but also to a Streptococcus pyogenes strain. Transfer was observed even if recipient cell already carries a related resident ICE or a genomic island flanked by attL and attR recombination sites but devoid of conjugation or recombination genes (CIs-Mobilizable Element [CIME]). The incoming ICE preferentially integrates into the 3? end of the tRNALys gene (i.e., the attR site of the resident element), leading to a CIME-ICE structure. Transfer of the whole composite element CIME-ICE was obtained, showing that the CIME is mobilizable in cis by the ICE. Therefore, genomic islands carrying putative virulence genes but lacking the mobility gene can be mobilized by a related ICE after site-specific accretion.

Puymege, Aurore; Bertin, Stephane; Chuzeville, Sarah; Guedon, Gerard

2013-01-01

68

Rapid detection by multiplex PCR of Genomic Islands, prophages and Integrative Conjugative Elements in V. cholerae 7th pandemic variants.  

PubMed

Vibrio cholerae poses a threat to human health, and new epidemic variants have been reported so far. Seventh pandemic V. cholerae strains are characterized by highly related genomic sequences but can be discriminated by a large set of Genomic Islands, phages and Integrative Conjugative Elements. Classical serotyping and biotyping methods do not easily discriminate among new variants arising worldwide, therefore the establishment of new methods for their identification is required. We developed a multiplex PCR assay for the rapid detection of the major 7th pandemic variants of V. cholerae O1 and O139. Three specific genomic islands (GI-12, GI-14 and GI-15), two phages (Kappa and TLC), Vibrio Seventh Pandemic Island 2 (VSP-II), and the ICEs of the SXT/R391 family were selected as targets of our multiplex PCR based on a comparative genomic approach. The optimization and specificity of the multiplex PCR was assessed on 5 V. cholerae 7th pandemic reference strains, and other 34 V. cholerae strains from various epidemic events were analyzed to validate the reliability of our method. This assay had sufficient specificity to identify twelve different V. cholerae genetic profiles, and therefore has the potential to be used as a rapid screening method. PMID:22062086

Spagnoletti, Matteo; Ceccarelli, Daniela; Colombo, Mauro M

2011-10-28

69

Comparative analysis using K-mer and K-flank patterns provides evidence for CpG island sequence evolution in mammalian genomes  

PubMed Central

CpG islands are GC-rich regions often located in the 5? end of genes and normally protected from cytosine methylation in mammals. The important role of CpG islands in gene transcription strongly suggests evolutionary conservation in the mammalian genome. However, as CpG dinucleotides are over-represented in CpG islands, comparative CpG island analysis using conventional sequence analysis techniques remains a major challenge in the epigenetics field. In this study, we conducted a comparative analysis of all CpG island sequences in 10 mammalian genomes. As sequence similarity methods and character composition techniques such as information theory are particularly difficult to conduct, we used exact patterns in CpG island sequences and single character discrepancies to identify differences in CpG island sequences. First, by calculating genome distance based on rank correlation tests, we show that k-mer and k-flank patterns around CpG sites can be used to correctly reconstruct the phylogeny of 10 mammalian genomes. Further, we used various machine learning algorithms to demonstrate that CpG islands sequences can be characterized using k-mers. In addition, by testing a human model on the nine different mammalian genomes, we provide the first evidence that k-mer signatures are consistent with evolutionary history.

Chae, Heejoon; Park, Jinwoo; Lee, Seong-Whan; Nephew, Kenneth P.; Kim, Sun

2013-01-01

70

Genomic islands of divergence and their consequences for the resolution of spatial structure in an exploited marine fish  

PubMed Central

As populations diverge, genomic regions associated with adaptation display elevated differentiation. These genomic islands of adaptive divergence can inform conservation efforts in exploited species, by refining the delineation of management units, and providing genomic tools for more precise and effective population monitoring and the successful assignment of individuals and products. We explored heterogeneity in genomic divergence and its impact on the resolution of spatial population structure in exploited populations of Atlantic cod, Gadus morhua, using genome wide expressed sequence derived single nucleotide polymorphisms in 466 individuals sampled across the range. Outlier tests identified elevated divergence at 5.2% of SNPs, consistent with directional selection in one-third of linkage groups. Genomic regions of elevated divergence ranged in size from a single position to several cM. Structuring at neutral loci was associated with geographic features, whereas outlier SNPs revealed genetic discontinuities in both the eastern and western Atlantic. This fine-scale geographic differentiation enhanced assignment to region of origin, and through the identification of adaptive diversity, fundamentally changes how these populations should be conserved. This work demonstrates the utility of genome scans for adaptive divergence in the delineation of stock structure, the traceability of individuals and products, and ultimately a role for population genomics in fisheries conservation.

Bradbury, Ian R; Hubert, Sophie; Higgins, Brent; Bowman, Sharen; Borza, Tudor; Paterson, Ian G; Snelgrove, Paul V R; Morris, Corey J; Gregory, Robert S; Hardie, David; Hutchings, Jeffrey A; Ruzzante, Daniel E; Taggart, Christopher T; Bentzen, Paul

2013-01-01

71

Nitrogen fixation island and rhizosphere competence traits in the genome of root-associated Pseudomonas stutzeri A1501  

PubMed Central

The capacity to fix nitrogen is widely distributed in phyla of Bacteria and Archaea but has long been considered to be absent from the Pseudomonas genus. We report here the complete genome sequencing of nitrogen-fixing root-associated Pseudomonas stutzeri A1501. The genome consists of a single circular chromosome with 4,567,418 bp. Comparative genomics revealed that, among 4,146 protein-encoding genes, 1,977 have orthologs in each of the five other Pseudomonas representative species sequenced to date. The genome contains genes involved in broad utilization of carbon sources, nitrogen fixation, denitrification, degradation of aromatic compounds, biosynthesis of polyhydroxybutyrate, multiple pathways of protection against environmental stress, and other functions that presumably give A1501 an advantage in root colonization. Genetic information on synthesis, maturation, and functioning of nitrogenase is clustered in a 49-kb island, suggesting that this property was acquired by lateral gene transfer. New genes required for the nitrogen fixation process have been identified within the nif island. The genome sequence offers the genetic basis for further study of the evolution of the nitrogen fixation property and identification of rhizosphere competence traits required in the interaction with host plants; moreover, it opens up new perspectives for wider application of root-associated diazotrophs in sustainable agriculture.

Yan, Yongliang; Yang, Jian; Dou, Yuetan; Chen, Ming; Ping, Shuzhen; Peng, Junping; Lu, Wei; Zhang, Wei; Yao, Ziying; Li, Hongquan; Liu, Wei; He, Sheng; Geng, Lizhao; Zhang, Xiaobing; Yang, Fan; Yu, Haiying; Zhan, Yuhua; Li, Danhua; Lin, Zhanglin; Wang, Yiping; Elmerich, Claudine; Lin, Min; Jin, Qi

2008-01-01

72

Infectivity and complete nucleotide sequence of the genome of a genetically distinct strain of maize streak virus from Reunion Island  

Microsoft Academic Search

Summary A complete infectious genome of an isolate of maize streak subgroup 1 geminivirus from Reunion Island (MSV-R) was cloned and sequenced. Using anAgrobacterium tumefaciens Ti plasmid delivery system, the cloned 2.7 kb circular DNA was shown to be infectious in maize. The agroinfected virus could be transmitted byCicadulina mbila, the most common vector species of MSV in Reunion. Analysis

M. Peterschmitt; M. Granier; R. Frutos; B. Reynaud

1996-01-01

73

The Stealth Episome: Suppression of Gene Expression on the Excised Genomic Island PPHGI-1 from Pseudomonas syringae pv. phaseolicola  

Microsoft Academic Search

Pseudomonas syringae pv. phaseolicola is the causative agent of halo blight in the common bean, Phaseolus vulgaris. P. syringae pv. phaseolicola race 4 strain 1302A contains the avirulence gene avrPphB (syn. hopAR1), which resides on PPHGI-1, a 106 kb genomic island. Loss of PPHGI-1 from P. syringae pv. phaseolicola 1302A following exposure to the hypersensitive resistance response (HR) leads to

Scott A. C. Godfrey; Helen C. Lovell; John W. Mansfield; David S. Corry; Robert W. Jackson; Dawn L. Arnold

2011-01-01

74

Stochasticity and bistability in horizontal transfer control of a genomic island in Pseudomonas  

PubMed Central

Genomic islands (GEI) comprise a recently recognized large family of potentially mobile DNA elements and play an important role in the rapid differentiation and adaptation of bacteria. Most importantly, GEIs have been implicated in the acquisition of virulence factors, antibiotic resistances or toxic compound metabolism. Despite detailed information on coding capacities of GEIs, little is known about the regulatory decisions in individual cells controlling GEI transfer. Here, we show how self-transfer of ICEclc, a GEI in Pseudomonas knackmussii B13 is controlled by a series of stochastic processes, the result of which is that only a few percent of cells in a population will excise ICEclc and launch transfer. Stochastic processes have been implicated before in producing bistable phenotypic transitions, such as sporulation and competence development, but never before in horizontal gene transfer (HGT). Bistability is instigated during stationary phase at the level of expression of an activator protein InrR that lays encoded on ICEclc, and then faithfully propagated to a bistable expression of the IntB13 integrase, the enzyme responsible for excision and integration of the ICEclc. Our results demonstrate how GEI of a very widespread family are likely to control their transfer rates. Furthermore, they help to explain why HGT is typically confined to few members within a population of cells. The finding that, despite apparent stochasticity, HGT rates can be modulated by external environmental conditions provides an explanation as to why selective conditions can promote DNA exchange.

Minoia, Marco; Gaillard, Muriel; Reinhard, Friedrich; Stojanov, Milos; Sentchilo, Vladimir; van der Meer, Jan Roelof

2008-01-01

75

Frequent mutations within the genomic magnetosome island of Magnetospirillum gryphiswaldense are mediated by RecA.  

PubMed

Genes for magnetosome formation in magnetotactic bacteria are clustered in large genomic magnetosome islands (MAI). Spontaneous deletions and rearrangements were frequently observed within these regions upon metabolic stress. This instability was speculated to be due to RecA-dependent homologous recombination between the numerous sequence repeats present within the MAI. Here we show that a RecA-deficient strain of Magnetospirillum gryphiswaldense (IK-1) no longer exhibits genetic instability of magnetosome formation. Strain IK-1 displayed higher sensitivity to oxygen and UV irradiation. Furthermore, the lack of RecA abolished allelic exchange in the mutant. Cells of strain IK-1 displayed a slightly altered (i.e., more elongated) morphology, whereas the absence of RecA did not affect the ability to synthesize wild-type-like magnetosomes. Our data provide evidence that the observed genetic instability of magnetosome formation in the wild type is due predominantly to RecA-mediated recombination. In addition, increased genetic stability could make strain IK-1 a useful tool for the expression of genes and further genetic engineering, as well as for biotechnological production of bacterial magnetosomes. PMID:21821768

Kolinko, Isabel; Jogler, Christian; Katzmann, Emanuel; Schüler, Dirk

2011-08-05

76

Frequent Mutations within the Genomic Magnetosome Island of Magnetospirillum gryphiswaldense Are Mediated by RecA?†  

PubMed Central

Genes for magnetosome formation in magnetotactic bacteria are clustered in large genomic magnetosome islands (MAI). Spontaneous deletions and rearrangements were frequently observed within these regions upon metabolic stress. This instability was speculated to be due to RecA-dependent homologous recombination between the numerous sequence repeats present within the MAI. Here we show that a RecA-deficient strain of Magnetospirillum gryphiswaldense (IK-1) no longer exhibits genetic instability of magnetosome formation. Strain IK-1 displayed higher sensitivity to oxygen and UV irradiation. Furthermore, the lack of RecA abolished allelic exchange in the mutant. Cells of strain IK-1 displayed a slightly altered (i.e., more elongated) morphology, whereas the absence of RecA did not affect the ability to synthesize wild-type-like magnetosomes. Our data provide evidence that the observed genetic instability of magnetosome formation in the wild type is due predominantly to RecA-mediated recombination. In addition, increased genetic stability could make strain IK-1 a useful tool for the expression of genes and further genetic engineering, as well as for biotechnological production of bacterial magnetosomes.

Kolinko, Isabel; Jogler, Christian; Katzmann, Emanuel; Schuler, Dirk

2011-01-01

77

Putative Zinc Finger Protein Binding Sites Are Over-Represented in the Boundaries of Methylation-Resistant CpG Islands in the Human Genome  

Microsoft Academic Search

Background. Majority of CpG dinucleotides in mammalian genomes tend to undergo DNA methylation, but most CpG islands are resistant to such epigenetic modification. Understanding about mechanisms that may lead to the methylation resistance of CpG islands is still very poor. Methodology\\/Principal Findings. Using the genome-scale in vivo DNA methylation data from human brain, we investigated the flanking sequence features of

Shicai Fan; Fang Fang; Xuegong Zhang; Michael Q. Zhang

2007-01-01

78

Under-representation of intrinsic terminators across bacterial genomic islands: Rho as a principal regulator of xenogenic DNA expression.  

PubMed

Two transcription termination mechanisms - intrinsic and Rho-dependent - have evolved in bacteria. The Rho factor occurs in most bacterial lineages, and has been hypothesized to play a global regulatory role. Genome-wide studies using microarray, 2D-gel electrophoresis and ChIP-chip provided evidence that Rho serves to silence transcription from horizontally acquired genes and prophages in Escherichia coli K-12, implicating the factor to be a part of the "cellular immune mechanism" protecting against deleterious phages and aberrant gene expression from acquired xenogenic DNA. We have investigated this model by adopting an alternate in silico approach and have extended the study to other species. Our analysis shows that several genomic islands across diverse phyla have under-representation of intrinsic terminators, similar to that experimentally observed in E. coli K-12. This implies that Rho-dependent termination is the predominant process operational in these islands and that silencing of foreign DNA is a conserved function of Rho. From the present analysis, it is evident that horizontally acquired islands have lost intrinsic terminators to facilitate Rho-dependent termination. These results underscore the importance of Rho as a conserved, genome-wide sentinel that regulates potentially toxic xenogenic DNA. PMID:22890136

Mitra, Anirban; Nagaraja, Valakunja

2012-08-04

79

Genome-wide Association Study of Anthropometric Traits in Kor?ula Island, Croatia  

PubMed Central

Aim To identify genetic variants underlying six anthropometric traits: body height, body weight, body mass index, brachial circumference, waist circumference, and hip circumference, using a genome-wide association study. Methods The study was carried out in the isolated population of the island of Kor?ula, Croatia, with 898 adult examinees who participated in the larger DNA-based genetic epidemiological study in 2007. Anthropometric measurements followed standard internationally accepted procedures. Examinees were genotyped using HumanHap 370CNV chip by Illumina, with a genome-wide scan containing 316?730 single nucleotide polymorphisms (SNP). Results A total of 11 SNPs were associated with the investigated traits at the level of P?genome-wide significance under the assumption of independent multiple testing, the consistency of association between the 2 variants and a set of anthropometric traits makes CRIM1 and ITGA1 highly interesting for further replication and functional follow-up. Increased linkage disequilibrium between the used markers in an isolated population makes the formal significance threshold overly stringent, and changed allele frequencies in isolate population may contribute to identifying variants that would not be easily identified in large outbred populations.

Polasek, Ozren; Marusic, Ana; Rotim, Kresimir; Hayward, Caroline; Vitart, Veronique; Huffman, Jennifer; Campbell, Susan; Jankovic, Stipan; Boban, Mladen; Biloglav, Zrinka; Kolcic, Ivana; Krzelj, Vjekoslav; Terzic, Janos; Matec, Lana; Tometic, Gordan; Nonkovic, Dijana; Nincevic, Jasna; Pehlic, Marina; Zedelj, Jurica; Velagic, Vedran; Juricic, Danica; Kirac, Iva; Belak Kovacevic, Sanja; Wright, Alan F.; Campbell, Harry; Rudan, Igor

2009-01-01

80

Site-specific accretion of an integrative conjugative element together with a related genomic island leads to cis mobilization and gene capture.  

PubMed

Genomic islands, flanked by attachment sites, devoid of conjugation and recombination modules and related to the integrative and conjugative element (ICE) ICESt3, were previously found in Streptococcus thermophilus. Here, we show that ICESt3 transfers to a recipient harbouring a similar engineered genomic island, CIMEL?catR?, and integrates by site-specific recombination into its attachment sites, leading to their accretion. The resulting composite island can excise, showing that ICESt3 mobilizes CIMEL?catR?, in cis. ICESt3, CIMEL?catR?, and the whole composite element can transfer from the strain harbouring the composite structure. The ICESt3 transfer to a recipient bearing CIMEL?catR?, can also lead to retromobilization, i.e. its capture by the donor. This is the first demonstration of specific conjugative mobilization of a genomic island in cis and the first report of ICE-mediated retromobilization. CIMEL?catR?, would be the prototype of a novel class of non-autonomous mobile elements (CIMEs: CIs mobilizable elements), which hijack the recombination and conjugation machinery of related ICEs to excise, transfer and integrate. Few genome analyses have shown that CIMEs could be widespread and have revealed internal repeats that could result from accretions in numerous genomic islands, suggesting that accretion and cis mobilization have a key role in evolution of genomic islands. PMID:21722203

Bellanger, Xavier; Morel, Catherine; Gonot, Fabien; Puymege, Aurore; Decaris, Bernard; Guédon, Gérard

2011-07-04

81

A Second Actin-Like MamK Protein in Magnetospirillum magneticum AMB-1 Encoded Outside the Genomic Magnetosome Island  

PubMed Central

Magnetotactic bacteria are able to swim navigating along geomagnetic field lines. They synthesize ferromagnetic nanocrystals that are embedded in cytoplasmic membrane invaginations forming magnetosomes. Regularly aligned in the cytoplasm along cytoskeleton filaments, the magnetosome chain effectively forms a compass needle bestowing on bacteria their magnetotactic behaviour. A large genomic island, conserved among magnetotactic bacteria, contains the genes potentially involved in magnetosome formation. One of the genes, mamK has been described as encoding a prokaryotic actin-like protein which when it polymerizes forms in the cytoplasm filamentous structures that provide the scaffold for magnetosome alignment. Here, we have identified a series of genes highly similar to the mam genes in the genome of Magnetospirillum magneticum AMB-1. The newly annotated genes are clustered in a genomic islet distinct and distant from the known magnetosome genomic island and most probably acquired by lateral gene transfer rather than duplication. We focused on a mamK-like gene whose product shares 54.5% identity with the actin-like MamK. Filament bundles of polymerized MamK-like protein were observed in vitro with electron microscopy and in vivo in E. coli cells expressing MamK-like-Venus fusions by fluorescence microscopy. In addition, we demonstrate that mamK-like is transcribed in AMB-1 wild-type and ?mamK mutant cells and that the actin-like filamentous structures observed in the ?mamK strain are probably MamK-like polymers. Thus MamK-like is a new member of the prokaryotic actin-like family. This is the first evidence of a functional mam gene encoded outside the magnetosome genomic island.

Pereira, Sandrine; Pignol, David; Wu, Long-Fei; Ginet, Nicolas

2010-01-01

82

Genome-wide methylated CpG island profiles of melanoma cells reveal a melanoma coregulation network.  

PubMed

Metastatic melanoma is a malignant cancer with generally poor prognosis, with no targeted chemotherapy. To identify epigenetic changes related to melanoma, we have determined genome-wide methylated CpG island distributions by next-generation sequencing. Melanoma chromosomes tend to be differentially methylated over short CpG island tracts. CpG islands in the upstream regulatory regions of many coding and noncoding RNA genes, including, for example, TERC, which encodes the telomerase RNA, exhibit extensive hypermethylation, whereas several repeated elements, such as LINE 2, and several LTR elements, are hypomethylated in advanced stage melanoma cell lines. By using CpG island demethylation profiles, and by integrating these data with RNA-seq data obtained from melanoma cells, we have identified a co-expression network of differentially methylated genes with significance for cancer related functions. Focused assays of melanoma patient tissue samples for CpG island methylation near the noncoding RNA gene SNORD-10 demonstrated high specificity. PMID:24129253

Li, Jian-Liang; Mazar, Joseph; Zhong, Cuncong; Faulkner, Geoffrey J; Govindarajan, Subramaniam S; Zhang, Zhan; Dinger, Marcel E; Meredith, Gavin; Adams, Christopher; Zhang, Shaojie; Mattick, John S; Ray, Animesh; Perera, Ranjan J

2013-10-16

83

Insertion site and distribution of a genomic island conferring DNA phosphorothioation in the Mycobacterium abscessus complex.  

PubMed

Nearly half of US clinical isolates of the emerging pathogen Mycobacterium abscessus were reported to exhibit smeared DNA during PFGE. This DNA degradation (Dnd) phenotype results from DNA phosphorothioation, a sulfur modification found in other bacteria and conferred by dnd genes located on mobile elements. Putative dnd genes are located on a 19.6 kbp genomic island (GI) in the M. abscessus type strain ATCC 19977. We confirmed that ATCC 19977(T) is Dnd-positive by PFGE and we developed a PCR assay to predict Dnd phenotype. Dnd-positive strains generated an amplicon from dndC whereas Dnd-negative strains generated a bridge amplicon that spanned the GI insertion site, indicating they lacked the entire 'Dnd-GI'. Comparative analyses of sequences from the bridge amplicon with ATCC 19977(T) revealed the Dnd-GI is flanked by 22 bp repeats in M. abscessus sensu stricto and inserted downstream of a tRNA-Ala gene and between inverted repeats. Regions flanking the Dnd-GI were highly conserved within the M. abscessus complex. Bioinformatics studies suggest the Dnd-GI inserted independently into a strain of Mycobacterium massiliense and that other species of mycobacteria also have dnd genes, supporting reports that the Dnd phenotype is common among actinomycetes. Within the M. abscessus complex, Dnd-positive clinical isolates were primarily M. abscessus sensu stricto, and tandem repeat typing indicated these isolates were highly related, confirming previous PFGE studies and revealing a widespread family of strains with significance in human disease. PMID:24014661

Howard, Susan T; Newman, Kristopher L; McNulty, Steven; Brown-Elliott, Barbara A; Vasireddy, Ravikiran; Bridge, Linda; Wallace, Richard J

2013-09-06

84

Islands of non-essential genes, including a DNA translocation operon, in the genome of bacteriophage 0305?8-36.  

PubMed

We investigate genes of lytic, Bacillus thuringiensis bacteriophage 0305?8-36 that are non-essential for laboratory propagation, but might have a function in the wild. We isolate deletion mutants to identify these genes. The non-permutation of the genome (218.948 Kb, with a 6.479 Kb terminal repeat and 247 identified orfs) simplifies isolation of deletion mutants. We find two islands of non-essential genes. The first island (3.01% of the genomic DNA) has an informatically identified DNA translocation operon. Deletion causes no detectable growth defect during propagation in a dilute agarose overlay. Identification of the DNA translocation operon begins with a DNA relaxase and continues with a translocase and membrane-binding anchor proteins. The relaxase is in a family, first identified here, with homologs in other bacteriophages. The second deleted island (3.71% of the genome) has genes for two metallo-protein chaperonins and two tRNAs. Deletion causes a significant growth defect. In addition, (1) we find by "in situ" (in-plaque) single-particle fluorescence microscopy that adsorption to the host occurs at the tip of the 486 nm long tail, (2) we develop a procedure of 0305?8-36 purification that does not cause tail contraction, and (3) we then find by electron microscopy that 0305?8-36 undergoes tail tip-tail tip dimerization that potentially blocks adsorption to host cells, presumably with effectiveness that increases as the bacteriophage particle concentration increases. These observations provide an explanation of the previous observation that 0305?8-36 does not lyse liquid cultures, even though 0305?8-36 is genomically lytic. PMID:22666654

Pathria, Saurav; Rolando, Mandy; Lieman, Karen; Hayes, Shirley; Hardies, Stephen; Serwer, Philip

2012-01-01

85

A genome-wide search for alleles and haplotypes associated with autism and related pervasive developmental disorders on the Faroe Islands  

Microsoft Academic Search

The involvement of genetic factors in the etiology of autism has been clearly established. We undertook a genome-wide search for regions containing susceptibility genes for autism in 12 subjects with childhood autism and related pervasive developmental disorders (PDDs) and 44 controls from the relatively isolated population of the Faroe Islands. In total, 601 microsatellite markers distributed throughout the human genome

M B Lauritsen; T D Als; H A Dahl; T J Flint; A G Wang; M Vang; T A Kruse; H Ewald; O Mors

2006-01-01

86

Complete Genome Sequences of Five Chrysodeixis chalcites Nucleopolyhedrovirus Genotypes from a Canary Islands Isolate  

PubMed Central

The Chrysodeixis chalcites single nucleopolyhedrovirus (ChchSNPV) infects and kills C. chalcites larvae, an important pest of banana crops in the Canary Islands. Five genotypes present in the most prevalent and widespread isolate in the Canary Islands were sequenced, providing genetic data relevant to the genotypic and phenotypic diversity of this virus.

Bernal, Alexandra; Williams, Trevor; Munoz, Delia; Caballero, Primitivo

2013-01-01

87

Complete Genome Sequences of Five Chrysodeixis chalcites Nucleopolyhedrovirus Genotypes from a Canary Islands Isolate.  

PubMed

The Chrysodeixis chalcites single nucleopolyhedrovirus (ChchSNPV) infects and kills C. chalcites larvae, an important pest of banana crops in the Canary Islands. Five genotypes present in the most prevalent and widespread isolate in the Canary Islands were sequenced, providing genetic data relevant to the genotypic and phenotypic diversity of this virus. PMID:24158555

Bernal, Alexandra; Williams, Trevor; Muñoz, Delia; Caballero, Primitivo; Simón, Oihane

2013-10-24

88

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

PubMed Central

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.

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

2012-01-01

89

Magnetospirillum magneticum AMB-1 peroxiredoxins contribute to the aerotolerance and genetic stability of the genomic magnetosome island.  

PubMed

The magnetotactic bacterium Magnetospirillum magneticum AMB-1 can grow at variable oxygen concentrations, although the intracellular magnetic structures, magnetosomes, are only synthesized under microaerobic or anaerobic conditions. Three members of the peroxiredoxin family were identified in M. magneticum AMB-1. All purified recombinant proteins displayed thiol-dependent peroxidase activities. Allelic replacement mutagenesis revealed that, although the absence of the three peroxidase genes had no effect on either the growth or the formation of magnetosome under anaerobic conditions, the growth of mutants was compromised in an aerobic culture. Moreover, an accelerated loss in the genomic 'magnetosome island' (MAI) was observed in the null mutants cultured in the presence of oxygen. Taken together, these data suggest that the thiol-peroxidases identified act as key antioxidants in magnetotactic bacteria and, as a result, contribute to maintaining their capacity to synthesize magnetosome by shielding the genetic stability of the genomic MAI in adaptation to constant physiological change and stress. PMID:21535101

Ge, Xin; Wang, Kuan; Bo, Tao; Kou, Yanbo; Liu, Weifeng; Chen, Guanjun

2011-05-16

90

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

PubMed Central

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.

Quesada, Jose M.; Soriano, Maria Isabel

2012-01-01

91

The Burkholderia cepacia Epidemic Strain Marker Is Part of a Novel Genomic Island Encoding Both Virulence and Metabolism-Associated Genes in Burkholderia cenocepacia  

PubMed Central

The Burkholderia cepacia epidemic strain marker (BCESM) is a useful epidemiological marker for virulent B. cenocepacia strains that infect patients with cystic fibrosis. However, there was no evidence that the original marker, identified by random amplified polymorphic DNA fingerprinting, contributed to pathogenicity. Here we demonstrate that the BCESM is part of a novel genomic island encoding genes linked to both virulence and metabolism. The BCESM was present on a 31.7-kb low-GC-content island that encoded 35 predicted coding sequences (CDSs): an N-acyl homoserine lactone (AHL) synthase gene (cciI) and corresponding transcriptional regulator (cciR), representing the first time cell signaling genes have been found on a genomic island; fatty acid biosynthesis genes; an IS66 family transposase; transcriptional regulator CDSs; amino acid metabolism genes; and a group of hypothetical genes. Mutagenesis of the AHL synthase, amidase (amiI), and porin (opcI) genes on the island was carried out. Testing of the isogenic mutants in a rat model of chronic lung infection demonstrated that the amidase played a role in persistence, while the AHL synthase and porin were both involved in virulence. The island, designated the B. cenocepacia island (cci), is the first genomic island to be defined in the B. cepacia complex and its discovery validates the original epidemiological correlation of the BCESM with virulent CF strains. The features of the cci, which overlap both pathogenicity and metabolism, expand the concept of bacterial pathogenicity islands and illustrate the diversity of accessory functions that can be acquired by lateral gene transfer in bacteria.

Baldwin, Adam; Sokol, Pamela A.; Parkhill, Julian; Mahenthiralingam, Eshwar

2004-01-01

92

Genome-Wide Association Studies in an Isolated Founder Population from the Pacific Island of Kosrae  

Microsoft Academic Search

It has been argued that the limited genetic diversity and reduced allelic heterogeneity observed in isolated founder populations facilitates discovery of loci contributing to both Mendelian and complex disease. A strong founder effect, severe isolation, and substantial inbreeding have dramatically reduced genetic diversity in natives from the island of Kosrae, Federated States of Micronesia, who exhibit a high prevalence of

Jennifer K. Lowe; Julian B. Maller; Itsik Peer; Benjamin M. Neale; Jacqueline Salit; Eimear E. Kenny; Jessica L. Shea; Ralph Burkhardt; J. Gustav Smith; Weizhen Ji; Martha Noel; Jia Nee Foo; Maude L. Blundell; Vita Skilling; Laura Garcia; Marcia L. Sullivan; Heather E. Lee; Anna Labek; Hope Ferdowsian; Steven B. Auerbach; Richard P. Lifton; Christopher Newton-Cheh; Jan L. Breslow; Markus Stoffel; Mark J. Daly; David M. Altshuler; Jeffrey M. Friedman

2009-01-01

93

Complete Genome Sequence of Leptospirillum ferrooxidans Strain C2-3, Isolated from a Fresh Volcanic Ash Deposit on the Island of Miyake, Japan  

PubMed Central

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.

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

2012-01-01

94

Contrasting chromatin organization of CpG islands and exons in the human genome  

Microsoft Academic Search

Background  CpG islands and nucleosome-free regions are both found in promoters. However, their association has never been studied. On\\u000a the other hand, DNA methylation is absent in promoters but is enriched in gene bodies. Intragenic nucleosomes and their modifications\\u000a have been recently associated with RNA splicing. Because the function of intragenic DNA methylation remains unclear, I explored\\u000a the possibility of its

Jung Kyoon Choi

2010-01-01

95

An Aeromonas caviae Genomic Island Is Required for both O-Antigen Lipopolysaccharide Biosynthesis and Flagellin Glycosylation ?  

PubMed Central

Aeromonas caviae Sch3N possesses a small genomic island that is involved in both flagellin glycosylation and lipopolysaccharide (LPS) O-antigen biosynthesis. This island appears to have been laterally acquired as it is flanked by insertion element-like sequences and has a much lower G+C content than the average aeromonad G+C content. Most of the gene products encoded by the island are orthologues of proteins that have been shown to be involved in pseudaminic acid biosynthesis and flagellin glycosylation in both Campylobacter jejuni and Helicobacter pylori. Two of the genes, lst and lsg, are LPS specific as mutation of them results in the loss of only a band for the LPS O-antigen. Lsg encodes a putative Wzx flippase, and mutation of Lsg affects only LPS; this finding supports the notion that flagellin glycosylation occurs within the cell before the flagellins are exported and assembled and not at the surface once the sugar has been exported. The proteins encoded by flmA, flmB, neuA, flmD, and neuB are thought to make up a pseudaminic acid biosynthetic pathway, and mutation of any of these genes resulted in the loss of motility, flagellar expression, and a band for the LPS O-antigen. Furthermore, pseudaminic acid was shown to be present on both flagellin subunits that make up the polar flagellum filament, to be present in the LPS O-antigen of the A. caviae wild-type strain, and to be absent from the A. caviae flmD mutant strain.

Tabei, S. Mohammed B.; Hitchen, Paul G.; Day-Williams, Michaela J.; Merino, Susana; Vart, Richard; Pang, Poh-Choo; Horsburgh, Gavin J.; Viches, Silvia; Wilhelms, Markus; Tomas, Juan M.; Dell, Anne; Shaw, Jonathan G.

2009-01-01

96

History Shaped the Geographic Distribution of Genomic Admixture on the Island of Puerto Rico  

PubMed Central

Contemporary genetic variation among Latin Americans human groups reflects population migrations shaped by complex historical, social and economic factors. Consequently, admixture patterns may vary by geographic regions ranging from countries to neighborhoods. We examined the geographic variation of admixture across the island of Puerto Rico and the degree to which it could be explained by historic and social events. We analyzed a census-based sample of 642 Puerto Rican individuals that were genotyped for 93 ancestry informative markers (AIMs) to estimate African, European and Native American ancestry. Socioeconomic status (SES) data and geographic location were obtained for each individual. There was significant geographic variation of ancestry across the island. In particular, African ancestry demonstrated a decreasing East to West gradient that was partially explained by historical factors linked to the colonial sugar plantation system. SES also demonstrated a parallel decreasing cline from East to West. However, at a local level, SES and African ancestry were negatively correlated. European ancestry was strongly negatively correlated with African ancestry and therefore showed patterns complementary to African ancestry. By contrast, Native American ancestry showed little variation across the island and across individuals and appears to have played little social role historically. The observed geographic distributions of SES and genetic variation relate to historical social events and mating patterns, and have substantial implications for the design of studies in the recently admixed Puerto Rican population. More generally, our results demonstrate the importance of incorporating social and geographic data with genetics when studying contemporary admixed populations.

Via, Marc; Gignoux, Christopher R.; Roth, Lindsey A.; Fejerman, Laura; Galanter, Joshua; Choudhry, Shweta; Toro-Labrador, Gladys; Viera-Vera, Jorge; Oleksyk, Taras K.; Beckman, Kenneth; Ziv, Elad; Risch, Neil

2011-01-01

97

The evolution of mammalian genomic imprinting was accompanied by the acquisition of novel CpG islands.  

PubMed

Parent-of-origin-dependent expression of imprinted genes is mostly associated with allele-specific DNA methylation of the CpG islands (CGIs) called germ line differentially methylated regions (gDMRs). Although the essential role of gDMRs for genomic imprinting has been well established, little is known about how they evolved. In several imprinted loci, the CGIs forming gDMRs may have emerged with the insertion of a retrotransposon or retrogene. To examine the generality of the hypothesis that the CGIs forming gDMRs were novel CGIs recently acquired during mammalian evolution, we reviewed the time of novel CGI emergence for all the maternal gDMR loci using the novel data analyzed in this study combined with the data from previous reports. The comparative sequence analyses using mouse, human, dog, cow, elephant, tammar, opossum, platypus, and chicken genomic sequences were carried out for Peg13, Meg1/Grb10, Plagl1/Zac1, Gnas, and Slc38a4 imprinted loci to obtain comprehensive results. The combined data showed that emergence of novel CGIs occurred universally in the maternal gDMR loci at various time points during mammalian evolution. Furthermore, the analysis of Meg1/Grb10 locus provided evidence that gradual base pair-wise sequence change was involved in the accumulation of CpG sequence, suggesting the mechanism of novel CGI emergence is more complex than the suggestion that CpG sequences originated solely by insertion of CpG-rich transposable elements. We propose that acquisition of novel CGIs was a key genomic change for the evolution of imprinting and that it usually occurred in the maternal gDMR loci. PMID:22016334

Suzuki, Shunsuke; Shaw, Geoffrey; Kaneko-Ishino, Tomoko; Ishino, Fumitoshi; Renfree, Marilyn B

2011-10-19

98

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

PubMed Central

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.

Wang, Quan; Wang, Lei

2013-01-01

99

Emergence of a Virulent Clade of Vibrio vulnificus and Correlation with the Presence of a 33-Kilobase Genomic Island?  

PubMed Central

Vibrio vulnificus is a ubiquitous inhabitant of the marine coastal environment, and an important pathogen of humans. We characterized a globally distributed sample of environmental isolates from a range of habitats and hosts and compared these with isolates recovered from cases of human infection. Multilocus sequence typing data using six housekeeping genes divided 63 of the 67 isolates into the two main lineages previously noted for this species, and this division was also confirmed using the 16S rRNA and open reading frame VV0401 markers. Lineage I was comprised exclusively of biotype 1 isolates, whereas lineage II contained biotype 1 and all biotype 2 isolates. Four isolates did not cluster within either lineage: two biotype 3 and two biotype 1 isolates. The proportion of isolates recovered from a clinical setting was noted to be higher in lineage I than in lineage II. Lineage I isolates were also associated with a 33-kb genomic island (region XII), one of three regions identified by genome comparisons as unique to the species. Region XII contained an arylsulfatase gene cluster, a sulfate reduction system, two chondroitinase genes, and an oligopeptide ABC transport system, all of which are absent from the majority of lineage II isolates. Arylsulfatases and the sulfate reduction system, along with performing a scavenging role, have been hypothesized to play a role in pathogenic processes in other bacteria. Our data suggest that lineage I may have a higher pathogenic potential and that region XII, along with other regions, may give isolates a selective advantage either in the human host or in the aquatic environment or both.

Cohen, Ana Luisa V.; Oliver, James D.; DePaola, Angelo; Feil, Edward J.; Fidelma Boyd, E.

2007-01-01

100

Investigation into the role of five Salmonella enterica serovar Enteritidis genomic islands in colonization of the chicken reproductive tract and other organs following oral challenge.  

PubMed

Salmonella enterica serovar Enteritidis is a major cause of human gastrointestinal tract disease, infection being due in large part to the consumption of contaminated eggs. Recent genome sequencing of S. enterica serovars has identified genomic islands, the presence of which differs between serovars. Using defined mutants, we have investigated the contribution that five such loci play in the colonization of the avian reproductive tract, other organs and avian macrophages. All loci appear to play a small role in infection of liver and spleen, but not in colonization of the reproductive tract or macrophages. PMID:22889182

Coward, Chris; Sait, Leanne; Williams, Lisa; Humphrey, Tom J; Cogan, Tristan; Maskell, Duncan J

2012-09-12

101

Genome-wide DNA Methylation Profiling of CpG Islands in Hypospadias  

PubMed Central

Purpose Hypospadias is one of the most frequent genital malformations in the male newborn, and results from abnormal penile and urethral development. The etiology of hypospadias remains largely unknown despite intensive investigations. Fetal androgens have a crucial role in genital differentiation. Recent studies have suggested that molecular mechanisms that underlie the effects of androgens on the fetus may involve disruption of epigenetic programming of gene expression during development. We assessed whether epigenetic modification of DNA methylation is associated with hypospadias in a case-control study of 12 hypospadias and 8 control subjects. Materials and Methods Genome-wide DNA methylation profiling was performed on the study subjects using the Illumina Infinium® HumanMethylation450 Bead-Chip, which enables the direct investigation of methylation status of more than 485,000 individual CpG sites throughout the genome. The methylation level at each CpG site was compared between cases and controls using the t test and logistic regression. Results We identified 14 CpG sites that were associated with hypospadias with p <0.00001. These CpG sites were in or near the SCARB1, MYBPH, SORBS1, LAMA4, HOXD11, MYO1D, EGFL7, C10orf41, LMAN1L and SULF1 genes. Two CpG sites in SCARB1 and MYBPH genes remained statistically significant after correction for multiple testing (p = 2.61×10?09, pcorrected = 0.008; p = 3.06×10?08, pcorrected = 0.02, respectively). Conclusions To our knowledge this is the first study to investigate hypospadias using a unique and novel epigenetic approach. Our findings suggest DNA methylation patterns are useful in identifying new genes such as SCARB1 and MYBPH that may be involved in the etiology of hypospadias.

Choudhry, Shweta; Deshpande, Archana; Qiao, Liang; Beckman, Kenneth; Sen, Saunak; Baskin, Laurence S.

2013-01-01

102

SGI1-K, a Variant of the SGI1 Genomic Island Carrying a Mercury Resistance Region, in Salmonella enterica Serovar Kentucky  

Microsoft Academic Search

A multiple-antibiotic-resistant Salmonella enterica serovar Kentucky strain was found to contain SGI1-K, a variant form of the Salmonella genomic island 1 (SGI1) with an In4-type class 1 integron that contains only one cassette array, aacCA5-aadA7, and an adjacent mercury resistance module. Part of the 3-conserved segment (3-CS) of the integron, together with the inverted short segment from the right-hand end

Renee S. Levings; Sally R. Partridge; Steven P. Djordjevic; Ruth M. Hall

2007-01-01

103

Diversity and Evolution of AbaR Genomic Resistance Islands in Acinetobacter baumannii Strains of European Clone I?†  

PubMed Central

To assess the diversity of AbaR genomic resistance islands in Acinetobacter baumannii European clone I (MLST clonal complex 1), we investigated 26 multidrug-resistant strains of this major clone isolated from hospitals in 21 cities of 10 European countries between 1984 and 2005. Each strain harbored an AbaR structure integrated at the same position in the chromosomal ATPase gene. AbaR3, including four subtypes based on variations in class 1 integron cassettes, and AbaR10 were found in 15 and 2 strains, respectively, whereas a new, unique AbaR variant was discovered in each of the other 9 strains. These new variants, designated AbaR11 to AbaR19 (19.8 kb to 57.5 kb), seem to be truncated derivatives of AbaR3, likely resulting from the deletions of its internal parts mediated by either IS26 elements (AbaR12 to AbaR19) or homologous recombination (AbaR11). AbaR3 was detected in all 10 strains isolated in 1984 to 1991, while AbaR11 to AbaR19 were carried only by strains isolated since 1997. Our results and those from previous publications suggest that AbaR3 is the original form of AbaR in European clone I, which may have provided strains of the lineage with a selective advantage facilitating their spread in European hospitals in the 1980s or before.

Krizova, Lenka; Dijkshoorn, Lenie; Nemec, Alexandr

2011-01-01

104

Intra- and Interspecies Genomic Transfer of the Enterococcus faecalis Pathogenicity Island  

PubMed Central

Enterococci are the third leading cause of hospital associated infections and have gained increased importance due to their fast adaptation to the clinical environment by acquisition of antibiotic resistance and pathogenicity traits. Enterococcus faecalis harbours a pathogenicity island (PAI) of 153 kb containing several virulence factors including the enterococcal surface protein (esp). Until now only internal fragments of the PAI or larger chromosomal regions containing it have been transfered. Here we demonstrate precise excision, circularization and horizontal transfer of the entire PAI element from the chromosome of E. faecalis strain UW3114. This PAI (ca. 200 kb) contained some deletions and insertions as compared to the PAI of the reference strain MMH594, transferred precisely and integrated site-specifically into the chromosome of E. faecalis (intergenic region) and Enterococcus faecium (tRNAlys). The internal PAI structure was maintained after transfer. We assessed phenotypic changes accompanying acquisition of the PAI and expression of some of its determinants. The esp gene is expressed on the surface of donor and both transconjugants. Biofilm formation and cytolytic activity were enhanced in E. faecalis transconjugants after acquisition of the PAI. No differences in pathogenicity of E. faecalis were detected using a mouse bacteraemia and a mouse peritonitis models (tail vein and intraperitoneal injection). A 66 kb conjugative pheromone-responsive plasmid encoding erm(B) (pLG2) that was transferred in parallel with the PAI was sequenced. pLG2 is a pheromone responsive plasmid that probably promotes the PAI horizontal transfer, encodes antibiotic resistance features and contains complete replication and conjugation modules of enterococcal origin in a mosaic-like composition. The E. faecalis PAI can undergo precise intra- and interspecies transfer probably with the help of conjugative elements like conjugative resistance plasmids, supporting the role of horizontal gene transfer and antibiotic selective pressure in the successful establishment of certain enterococci as nosocomial pathogens.

Laverde Gomez, Jenny A.; Hendrickx, Antoni P. A.; Willems, Rob J.; Top, Janetta; Sava, Irina; Huebner, Johannes; Witte, Wolfgang; Werner, Guido

2011-01-01

105

Whole-Genome Analysis of Salmonella enterica Serovar Typhimurium T000240 Reveals the Acquisition of a Genomic Island Involved in Multidrug Resistance via IS1 Derivatives on the Chromosome ? †  

PubMed Central

Salmonella enterica serovar Typhimurium is frequently associated with life-threatening systemic infections, and the recent global emergence of multidrug resistance in S. enterica isolates from agricultural and clinical settings has raised concerns. In this study, we determined the whole-genome sequence of fluoroquinolone-resistant S. enterica serovar Typhimurium T000240 strain (DT12) isolated from human gastroenteritis in 2000. Comparative genome analysis revealed that T000240 displays high sequence similarity to strain LT2, which was originally isolated in 1940, indicating that progeny of LT2 might be reemerging. T000240 possesses a unique 82-kb genomic island, designated as GI-DT12, which is composed of multidrug resistance determinants, including a Tn2670-like composite transposon (class 1 integron [intI1, blaoxa-30, aadA1, qacE?1, and sul1], mercury resistance proteins, and chloramphenicol acetyltransferase), a Tn10-like tetracycline resistance protein (tetA), the aerobactin iron-acquisition siderophore system (lutA and lucABC), and an iron transporter (sitABCD). Since GI-DT12 is flanked by IS1 derivatives, IS1-mediated recombination likely played a role in the acquisition of this genomic island through horizontal gene transfer. The aminoglycoside-(3)-N-acetyltransferase (aac(3)) gene and a class 1 integron harboring the dfrA1 gene cassette responsible for gentamicin and trimethoprim resistance, respectively, were identified on plasmid pSTMDT12_L and appeared to have been acquired through homologous recombination with IS26. This study represents the first characterization of the unique genomic island GI-DT12 that appears to be associated with possible IS1-mediated recombination in S. enterica serovar Typhimurium. It is expected that future whole-genome studies will aid in the characterization of the horizontal gene transfer events for the emerging S. enterica serovar Typhimurium strains.

Izumiya, Hidemasa; Sekizuka, Tsuyoshi; Nakaya, Hideo; Taguchi, Masumi; Oguchi, Akio; Ichikawa, Natsuko; Nishiko, Rika; Yamazaki, Shuji; Fujita, Nobuyuki; Watanabe, Haruo; Ohnishi, Makoto; Kuroda, Makoto

2011-01-01

106

Genome scan of hybridizing sunflowers from Texas (Helianthus annuus and H. debilis) reveals asymmetric patterns of introgression and small islands of genomic differentiation  

Microsoft Academic Search

Although the sexual transfer of genetic material between species (i.e. introgression) has been documented in many groups of plants and animals, genome-wide patterns of introgression are poorly understood. Is most of the genome permeable to interspecific gene flow, or is introgression typically restricted to a handful of genomic regions? Here, we assess the genomic extent and direction of introgression between

M. S CASCITELLI; K. D. W HITNEY; R. A. R ANDELL; ATTHEW K ING; C. A. B UERKLE; L. H. R IESEBERG

2010-01-01

107

A Hypervariable 130Kilobase Genomic Region of Magnetospirillum gryphiswaldense Comprises a Magnetosome Island Which Undergoes Frequent Rearrangements during Stationary Growth  

Microsoft Academic Search

Genes involved in magnetite biomineralization are clustered in the genome of the magnetotactic bacterium Magnetospirillum gryphiswaldense. We analyzed a 482-kb genomic fragment, in which we identified an approx- imately 130-kb region representing a putative genomic \\

Susanne Ullrich; Michael Kube; Sabrina Schubbe; Richard Reinhardt; Dirk Schuler

2005-01-01

108

ClpP of Streptococcus mutans differentially regulates expression of genomic islands, mutacin production, and antibiotic tolerance.  

PubMed

Streptococcus mutans is the primary etiological agent of human dental caries and, at times, of infective endocarditis. Within the oral cavity, the pathogen is subjected to conditions of stress. A well-conserved protein complex named ClpP (caseinolytic protease) plays a vital role in adaptation under stress conditions. To gain a better understanding of the global role of the ClpP protease in cellular homeostasis, a transcriptome analysis was performed using a DeltaclpP mutant strain. The expression levels of more than 100 genes were up- or downregulated in the DeltaclpP mutant compared to the wild type. Notably, the expression of genes in several genomic islands, such as TnSmu1 and TnSmu2, was differentially modulated in the DeltaclpP mutant strain. ClpP deficiency also increased the expression of genes associated with a putative CRISPR locus. Furthermore, several stress-related genes and genes encoding bacteriocin-related peptides and many transcription factors were also found to be altered in the DeltaclpP mutant strain. A comparative analysis of the two-dimensional protein profile of the wild type and the DeltaclpP mutant strains showed altered protein profiles. Comparison of the transcriptome data with the proteomic data identified four common gene products, suggesting that the observed altered protein expression of these genes could be due to altered transcription. The results presented here indicate that ClpP-mediated proteolysis plays an important global role in the regulation of several important traits in this pathogen. PMID:20038588

Chattoraj, Partho; Banerjee, Anirban; Biswas, Saswati; Biswas, Indranil

2009-12-28

109

ClpP of Streptococcus mutans Differentially Regulates Expression of Genomic Islands, Mutacin Production, and Antibiotic Tolerance? †  

PubMed Central

Streptococcus mutans is the primary etiological agent of human dental caries and, at times, of infective endocarditis. Within the oral cavity, the pathogen is subjected to conditions of stress. A well-conserved protein complex named ClpP (caseinolytic protease) plays a vital role in adaptation under stress conditions. To gain a better understanding of the global role of the ClpP protease in cellular homeostasis, a transcriptome analysis was performed using a ?clpP mutant strain. The expression levels of more than 100 genes were up- or downregulated in the ?clpP mutant compared to the wild type. Notably, the expression of genes in several genomic islands, such as TnSmu1 and TnSmu2, was differentially modulated in the ?clpP mutant strain. ClpP deficiency also increased the expression of genes associated with a putative CRISPR locus. Furthermore, several stress-related genes and genes encoding bacteriocin-related peptides and many transcription factors were also found to be altered in the ?clpP mutant strain. A comparative analysis of the two-dimensional protein profile of the wild type and the ?clpP mutant strains showed altered protein profiles. Comparison of the transcriptome data with the proteomic data identified four common gene products, suggesting that the observed altered protein expression of these genes could be due to altered transcription. The results presented here indicate that ClpP-mediated proteolysis plays an important global role in the regulation of several important traits in this pathogen.

Chattoraj, Partho; Banerjee, Anirban; Biswas, Saswati; Biswas, Indranil

2010-01-01

110

Antimicrobial Resistance and Virulence Determinants in European Salmonella Genomic Island 1-Positive Salmonella enterica Isolates from Different Origins ? †  

PubMed Central

Salmonella genomic island 1 (SGI1) contains a multidrug resistance region conferring the ampicillin-chloramphenicol-streptomycin-sulfamethoxazole-tetracycline resistance phenotype encoded by blaPSE-1, floR, aadA2, sul1, and tet(G). Its increasing spread via interbacterial transfer and the emergence of new variants are important public health concerns. We investigated the molecular properties of SGI1-carrying Salmonella enterica serovars selected from a European strain collection. A total of 38 strains belonging to S. enterica serovar Agona, S. enterica serovar Albany, S. enterica serovar Derby, S. enterica serovar Kentucky, S. enterica serovar Newport, S. enterica serovar Paratyphi B dT+, and S. enterica serovar Typhimurium, isolated between 2002 and 2006 in eight European countries from humans, animals, and food, were subjected to antimicrobial susceptibility testing, molecular typing methods (XbaI pulsed-field gel electrophoresis [PFGE], plasmid analysis, and multilocus variable-number tandem-repeat analysis [MLVA]), as well as detection of resistance and virulence determinants (PCR/sequencing and DNA microarray analysis). Typing experiments revealed wide heterogeneity inside the strain collection and even within serovars. PFGE analysis distinguished a total of 26 different patterns. In contrast, the characterization of the phenotypic and genotypic antimicrobial resistance revealed serovar-specific features. Apart from the classical SGI1 organization found in 61% of the strains, seven different variants were identified with antimicrobial resistance properties associated with SGI1-A (S. Derby), SGI1-C (S. Derby), SGI1-F (S. Albany), SGI1-L (S. Newport), SGI1-K (S. Kentucky), SGI1-M (S. Typhimurium), and, eventually, a novel variant similar to SGI1-C with additional gentamicin resistance encoded by aadB. Only minor serovar-specific differences among virulence patterns were detected. In conclusion, the SGI1 carriers exhibited pathogenetic backgrounds comparable to the ones published for susceptible isolates. However, because of their multidrug resistance, they may be more relevant in clinical settings.

Beutlich, Janine; Jahn, Silke; Malorny, Burkhard; Hauser, Elisabeth; Huhn, Stephan; Schroeter, Andreas; Rodicio, Maria Rosario; Appel, Bernd; Threlfall, John; Mevius, Dik; Helmuth, Reiner; Guerra, Beatriz

2011-01-01

111

CpG Island microarray probe sequences derived from a physical library are representative of CpG Islands annotated on the human genome  

Microsoft Academic Search

An effective tool for the global analysis of both DNA methylation status and protein-chromatin interac- tions is a microarray constructed with sequences containing regulatory elements. One type of array sui- ted for this purpose takes advantage of the strong association between CpG Islands (CGIs) and gene regulatory regions. We have obtained 20 736 clones from a CGI Library and used

Lawrence E. Heisler; Dax Torti; Paul C. Boutros; Charles Chan; Neil Winegarden; Mark Takahashi; Patrick Yau; Tim H.-M. Huang; Peggy J. Farnham; Igor Jurisica; James R. Woodgett; Rod Bremner; Linda Z. Penn; Sandy D. Der

2005-01-01

112

The mouse surfeit locus contains a cluster of six genes associated with four CpG-rich islands in 32 kilobases of genomic DNA.  

PubMed Central

The clustered arrangement (no two adjacent genes are separated by more than 73 base pairs [bp] and two genes overlap by 133 bp at their 3' ends) of the four genes (Surf-1 to -4) identified so far in the mouse surfeit locus (T. Williams, J. Yon, C. Huxley, and M. Fried, Proc. Natl. Acad. Sci. USA 85:3527-3530, 1988) is the tightest gene clustering found in any mammalian genome to date and strongly suggests the possibility of cis-interaction and/or coregulation of gene expression. Thus, we are analyzing the surfeit genes in detail and are defining the extent of the cluster. Here we present the sequence of the entire Surf-4 gene and define the 3' and 5' extents of its mRNAs. The Surf-4 gene has heterogeneous transcriptional start sites, and its 5' end lies in a CpG-rich island. The gene specifies three mRNAs, with the two most abundant mRNAs differing in the locations of their 3' polyadenylation sites. Only the most abundant Surf-4 mRNA would overlap the 3' end of the Surf-2 gene by 133 bp. Two new genes (Surf-5 and Surf-6) have been identified in the surfeit gene cluster by Northern (RNA) blot analysis. The 5' end of Surf-6 lies within the CpG-rich island about 8 kilobases (kb) from the CpG-rich island containing the 5' end of Surf-3, and Surf-5 lies between Surf-3 and Surf-6. Thus, the cluster contains a unique arrangement of four CpG-rich islands within 32 kb associated with the 5' ends of the six surfeit genes. The neighboring CpG-rich islands have been located 500 and 100 kb distant on either side of the surfeit cluster, indicating that the end of the cluster of islands has been reached. Images

Huxley, C; Fried, M

1990-01-01

113

Analysis of a genomic island housing genes for DNA S-modification system in Streptomyces lividans 66 and its counterparts in other distantly related bacteria.  

PubMed

The complete sequence (92 770 bp) of a genomic island (GI) named SLG from Streptomyces lividans 66, encoding a novel DNA S-modification system (dnd), was determined. Its overall G+C content was 67.8%, lower than those of three sequenced Streptomyces genomes. Among 85 predicted open reading frames (ORFs) in SLG, 22 ORFs showed little homology with previously known proteins. SLG displays a mosaic structure composed of four modules, indicative of multiple recombination events in its formation. Spontaneous excision and circularization of SLG was observed, and the excision rate appeared to be induced at least fivefold by MNNG exposure. Using constructed mini-islands of SLG, we demonstrated that Slg01, a P4-like integrase, was sufficient to promote SLG integration, excision and circularization. Eleven counterpart dnd clusters, which also mapped to GIs in 10 chromosomes and a plasmid, were found in taxonomically unrelated bacterial species from various geographic niches. Additionally, c. 10% of actinomycetes were found to possess a dnd cluster in a survey involving 74 strains. Comparison of dnd clusters in the 12 bacteria strongly suggests that these dnd-bearing elements might have evolved from a common ancestor similar to plasmid-originated chromosome II of Pseudoalteromonas haloplanktis TAC125. PMID:17640271

He, Xinyi; Ou, Hong-Yu; Yu, Qing; Zhou, Xiufen; Wu, Jun; Liang, Jingdan; Zhang, Wei; Rajakumar, Kumar; Deng, Zixin

2007-07-19

114

Dynamics of the SetCD-Regulated Integration and Excision of Genomic Islands Mobilized by Integrating Conjugative Elements of the SXT/R391 Family  

PubMed Central

Mobilizable genomic islands (MGIs) are small genomic islands that are mobilizable by SXT/R391 integrating conjugative elements (ICEs) due to similar origins of transfer. Their site-specific integration and excision are catalyzed by the integrase that they encode, but their conjugative transfer entirely depends upon the conjugative machinery of SXT/R391 ICEs. In this study, we report the mechanisms that control the excision and integration processes of MGIs. We found that while the MGI-encoded integrase IntMGI is sufficient to promote MGI integration, efficient excision from the host chromosome requires the combined action of IntMGI and of a novel recombination directionality factor, RdfM. We determined that the genes encoding these proteins are activated by SetCD, the main transcriptional activators of SXT/R391 ICEs. Although they share the same regulators, we found that unlike rdfM, intMGI has a basal level of expression in the absence of SetCD. These findings explain how an MGI can integrate into the chromosome of a new host in the absence of a coresident ICE and shed new light on the cross talk that can occur between mobilizable and mobilizing elements that mobilize them, helping us to understand part of the rules that dictate horizontal transfer mechanisms.

Daccord, Aurelie; Mursell, Mathias; Poulin-Laprade, Dominic

2012-01-01

115

Isolation of a novel retinoic acid-responsive gene by selection of genomic fragments derived from CpG-island-enriched DNA.  

PubMed Central

One of the primary goals in transcription factor research is the elucidation of the genetic networks controlled by a factor or by members of a family of closely related factors. The pleiotropic effects of retinoic acid (PA) in the developing and adult animal are mediated by ligand-inducible transcription factors (RA receptors [RARs] and retinoid X receptors [RXRs]) that belong to the superfamily of nuclear receptors. Regulatory regions of PA effector genes contain RAR and RXR binding sites (RAR elements [RAREs] and RXR elements [RXREs]) that generally consist of direct or everted repeats of the core half-site motif, (A/G)G(G/T)TCA. In order to identify novel genes regulated by RA, we devised a selection strategy based on the premise that regulatory regions of a large number of housekeeping and tissue-specific genes are embodied within CpG island DNA. In this method, referred to as CpG-selected and amplified binding, fragments derived from the CpG island fraction of the murine genome are selected by a gel mobility shift assay using in vitro-transcribed and -translated RXR-RAR. Multiple rounds of selection coupled with amplification of the fragments by PCR enabled us to clone a population of CG-rich fragments of which approximately one-fifth contained consensus RAREs or RXREs. Twelve genomic fragments containing novel response elements are described, and the transcription unit associated with one of them, NN-84AG, was characterized in detail. The mouse NN-84AG transcript is upregulated by RA in F9 embryonal carcinoma cells and is homologous to an expressed sequence tag (EST41159) derived from a human infant brain cDNA library. Cloning of the murine NN8-4AG genomic sequence places the RXRE in the proximity of the transcription initiation sites of the gene. Although sequence analysis indicates that the EST41159 gene product is novel, a region of amino acid identity with sequences of a yeast polypeptide of, as yet, unknown function and the Drosophila trithorax protein suggests the presence of an evolutionarily and functionally conserved domain. Our study demonstrates that transcription factor binding sites and corresponding regulated genes can be identified by selecting fragments derived from the CpG island fraction of the genome.

Shago, M; Giguere, V

1996-01-01

116

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

PubMed Central

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.

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

2013-01-01

117

Dynamic analysis of a genomic island in Magnetospirillum sp. strain AMB-1 reveals how magnetosome synthesis developed  

Microsoft Academic Search

The entire structure of a 98kb genomic region that abounds in genes related to magnetosome synthesis was first described in the Magnetospirillum sp. strain AMB-1. The deletion of this 98kb genomic region and the circular form after excision from the chromosome was detected by PCR amplification. This strongly suggests that the region has undergone a lateral gene transfer. The region

Yorikane Fukuda; Yoshiko Okamura; Haruko Takeyama; Tadashi Matsunaga

2006-01-01

118

Life-history traits maintain the genomic integrity of sympatric species of the spruce budworm (Choristoneura fumiferana) group on an isolated forest island  

PubMed Central

Identification of widespread species collected from islands can be challenging due to the potential for local ecological and phenotypic divergence in isolated populations. We sought to determine how many species of the spruce budworm (Choristoneura fumiferana) complex reside in Cypress Hills, an isolated remnant coniferous forest in western Canada. We integrated data on behavior, ecology, morphology, mitochondrial DNA, and simple sequence repeats, comparing Cypress Hills populations to those from other regions of North America to determine which species they resembled most. We identified C. fumiferana, C. occidentalis, C. lambertiana, and hybrid forms in Cypress Hills. Adult flight phenology and pheromone attraction were identified as key life-history traits involved in maintaining the genomic integrity of species. Our study highlights the importance of extensive sampling of both specimens and a variety of characters for understanding species boundaries in biodiversity research.

Lumley, Lisa M; Sperling, Felix AH

2011-01-01

119

Characterization of Salmonella enterica Serovar Typhimurium Isolates Harboring a Chromosomally Encoded CMY-2 ?-Lactamase Gene Located on a Multidrug Resistance Genomic Island?†  

PubMed Central

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 (blaCMY-2) was integrated in a 2.5-Mb chromosomal fragment. Genetic analysis of S. Typhimurium isolate L-3553 indicated that blaCMY-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 blaCMY-2 in the blaCMY-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.

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

2011-01-01

120

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

Microsoft Academic Search

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

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

2008-01-01

121

Replication of genetic variants from genome-wide association studies with metabolic traits in an island population of the Adriatic coast of Croatia  

PubMed Central

Twenty-two single-nucleotide polymorphisms (SNPs) in 10 gene regions previously identified in obesity and type 2 diabetes (T2D) genome-wide association studies (GWAS) were evaluated for association with metabolic traits in a sample from an island population of European descent. We performed a population-based study using 18 anthropometric and biochemical traits considered as continuous variables in a sample of 843 unrelated subjects (360 men and 483 women) aged 18–80 years old from the island of Hvar on the eastern Adriatic coast of Croatia. All eight GWAS SNPs in FTO were significantly associated with weight, body mass index, waist circumference and hip circumference; 20 of the 32 nominal P-values remained significant after permutation testing for multiple corrections. The strongest associations were found between the two TCF7L2 GWAS SNPs with fasting plasma glucose and HbA1c levels, all four P-values remained significant after permutation tests. Nominally significant associations were found between several SNPs and other metabolic traits; however, the significance did not hold after permutation tests. Although the sample size was modest, our study strongly replicated the association of FTO variants with obesity-related measures and TCF7L2 variants with T2D-related traits. The estimated effect sizes of these variants were larger or comparable to published studies. This is likely attributable to the homogenous genetic background of the relatively isolated study population.

Karns, Rebekah; Zhang, Ge; Jeran, Nina; Havas-Augustin, Dubravka; Missoni, Sasa; Niu, Wen; Indugula, Subba Rao; Sun, Guangyun; Durakovic, Zijad; Narancic, Nina Smolej; Rudan, Pavao; Chakraborty, Ranajit; Deka, Ranjan

2011-01-01

122

Characterization of a novel chaperone/usher fimbrial operon present on KpGI-5, a methionine tRNA gene-associated genomic island in Klebsiella pneumoniae  

PubMed Central

Background Several strain-specific Klebsiella pneumoniae virulence determinants have been described, though these have almost exclusively been linked with hypervirulent liver abscess-associated strains. Through PCR interrogation of integration hotspots, chromosome walking, island-tagging and fosmid-based marker rescue we captured and sequenced KpGI-5, a novel genomic island integrated into the met56 tRNA gene of K. pneumoniae KR116, a bloodstream isolate from a patient with pneumonia and neutropenic sepsis. Results The 14.0 kb KpGI-5 island exhibited a genome-anomalous G?+?C content, possessed near-perfect 46 bp direct repeats, encoded a ?1-chaperone/usher fimbrial cluster (fim2) and harboured seven other predicted genes of unknown function. Transcriptional analysis demonstrated expression of three fim2 genes, and suggested that the fim2A-fim2K cluster comprised an operon. As fimbrial systems are frequently implicated in pathogenesis, we examined the role of fim2 by analysing KR2107, a streptomycin-resistant derivative of KR116, and three isogenic mutants (?fim, ?fim2 and ?fim?fim2) using biofilm assays, human cell adhesion assays and pair-wise competition-based murine models of intestinal colonization, lung infection and ascending urinary tract infection. Although no statistically significant role for fim2 was demonstrable, liver and kidney CFU counts for lung and urinary tract infection models, respectively, hinted at an ordered gradation of virulence: KR2107 (most virulent), KR2107?fim2, KR2107?fim and KR2107?fim?fim2 (least virulent). Thus, despite lack of statistical evidence there was a suggestion that fim and fim2 contribute additively to virulence in these murine infection models. However, further studies would be necessary to substantiate this hypothesis. Conclusion Although fim2 was present in 13% of Klebsiella spp. strains investigated, no obvious in vitro or in vivo role for the locus was identified, although there were subtle hints of involvement in urovirulence and bacterial dissemination from the respiratory tract. Based on our findings and on parallels with other fimbrial systems, we propose that fim2 has the potential to contribute beneficially to pathogenesis and/or environmental persistence of Klebsiella strains, at least under specific yet-to-be identified conditions.

2012-01-01

123

Genome-wide association of serum uric acid concentration: replication of sequence variants in an island population of the Adriatic coast of Croatia  

PubMed Central

Summary A genome-wide association study of serum uric acid levels was performed in a relatively isolated population of European descent from an island of the Adriatic coast of Croatia. The study sample included 532 unrelated and 768 related individuals from 235 pedigrees. Inflation due to relatedness was controlled by using genomic control. Genetic association was assessed with 2,241,249 SNPs in 1300 samples after adjusting for age and gender. Our study replicated four previously reported serum uric acid loci (SLC2A9, ABCG2, RREB1, and SLC22A12). The strongest association was found with a SNP in SLC2A9 (rs13129697, P=2.33×10?19), which exhibited significant gender-specific effects, 35.76?mol/L (P=2.11×10?19) in females and 19.58 ?mol/L (P=5.40×10?5) in males. Within this region of high linkage disequilibrium, we also detected a strong association with a non-synonymous SNP, rs16890979 (P=2.24×10?17), a putative causal variant for serum uric acid variation. In addition, we identified several novel loci suggestive of association with uric acid levels (SEMA5A, TMEM18, SLC28A2, and ODZ2), although the P-values (P<5×10?6) did not reach the threshold of genome-wide significance. Together, these findings provide further confirmation of previously reported uric acid-related genetic variants and highlight suggestive new loci for additional investigation.

Karns, Rebekah; Zhang, Ge; Sun, Guangyun; Indugula, Subba Rao; Cheng, Hong; Havas-Augustin, Dubravka; Novokmet, Natalija; Rudan, Dusko; Durakovic, Zijad; Missoni, Sasa; Chakraborty, Ranajit; Rudan, Pavao; Deka, Ranjan

2012-01-01

124

Genome organization in Halobacterium halobium : A 70 kb island of more (AT) rich DNA in the chromosome  

Microsoft Academic Search

The more A+T rich fractionated component (FII DNA) of the Halobacterium halobium genome constitutes one third of the total DNA and upon isolation consists of covalently closed circular DNA (pHH1 and minor cccDNA) and nonsupercoiled sequences. We have investigated the physical organization of the non cccDNA in FII by a chromosome walk using one copy of the halobacterial insertion element

Felicitas Pfeifer; Mary Betlach

1985-01-01

125

Genomic variability of O islands encoding tellurite resistance in enterohemorrhagic Escherichia coli O157:H7 isolates.  

PubMed

Strains of Escherichia coli causing enterohemorrhagic colitis belonging to the O157:H7 lineage are reported to be highly related. Fifteen strains of E. coli O157:H7 and 1 strain of E. coli O46:H(-) (nonflagellated) were examined for the presence of potassium tellurite resistance (Te(r)). Te(r) genes comprising terABCDEF were shown previously to be part of a pathogenicity island also containing integrase, phage, and urease genes. PCR analysis, both conventional and light cycler based, demonstrated that about one-half of the Te(r) E. coli O157:H7 strains (6 of 15), including the Sakai strain, which has been sequenced, carried a single copy of the Te(r) genes. Five of the strains, including EDL933, which has also been sequenced, contained two copies. Three other O157:H7 strains and the O46:H(-) strain did not contain the Te(r) genes. In strains containing two copies, the Te(r) genes were associated with the serW and serX tRNA genes. Five O157:H7 strains resembled the O157 Sakai strain whose sequence contained one copy, close to serX, whereas in one isolate the single copy was associated with serW. There was no correlation between Te(r) and the ability to produce Shiga toxin ST1 or ST2. The Te(r) MIC for most strains, containing either one or two copies, was 1,024 micro g/ml, although for a few the MIC was intermediate, 64 to 128 micro g/ml, which could be increased to 512 micro g/ml by pregrowth of strains in subinhibitory concentrations of potassium tellurite. Reverse transcriptase PCR analysis confirmed that in most strains Te(r) was constitutive but that in the rest it was inducible and involved induction of terB and terC genes. Only the terB, -C, -D, and -E genes are required for Te(r). The considerable degree of homology between the ter genes on IncH12 plasmid R478, which originated in Serratia marcescens, and pTE53, from an E. coli clinical isolate, suggests that the pathogenicity island was acquired from a plasmid. This work demonstrates diversity among E. coli O157:H7 isolates, at least as far as the presence of Te(r) genes is concerned. PMID:12169592

Taylor, Diane E; Rooker, Michelle; Keelan, Monika; Ng, Lai-King; Martin, Irene; Perna, Nicole T; Burland, N T Valerie; Blattner, Fredrick R

2002-09-01

126

Compromised DNA damage repair promotes genetic instability of the genomic magnetosome island in Magnetospirillum magneticum AMB-1.  

PubMed

Magnetotactic bacteria (MTB) are capable of synthesizing nano-sized, intracellular membrane-bound magnetosomes. To learn more about the genetic factors involved in magnetosome formation, transposon mutagenesis was carried out by conjugation using a hyperactive mariner transposon to obtain nonmagnetic mutants of Magnetospirillum magneticum AMB-1. A mutant with defect in uvrA gene encoding the DNA binding subunit of the UvrABC complex responsible for the process of nucleotide excision repair, was obtained. Growth, magnetosome formation and maintenance of magnetosome island (MAI) were further analyzed in the absence of UvrA. Interruption of uvrA led to decreased capacity to form magnetosome when cultured in the presence of oxygen. The deficiency in UvrA also resulted in an accelerated loss of the MAI under aerobic conditions indicating that the nucleotide excision repair system guards against the instability of the MAI. The incapacity of MTB to efficiently initiate recombination mediated by RecA rescued the instability of MAI observed in uvrA mutant. Elevated recombination activity resulting from the accumulation of unrepaired mutations may thus account for the instability of MAI in the absence of UvrA. PMID:22538470

Bo, Tao; Wang, Kuan; Ge, Xin; Chen, Guanjun; Liu, Weifeng

2012-04-27

127

Comparative genomics of the type VI secretion systems of Pantoea and Erwinia species reveals the presence of putative effector islands that may be translocated by the VgrG and Hcp proteins  

PubMed Central

Background The Type VI secretion apparatus is assembled by a conserved set of proteins encoded within a distinct locus. The putative effector proteins Hcp and VgrG are also encoded within these loci. We have identified numerous distinct Type VI secretion system (T6SS) loci in the genomes of several ecologically diverse Pantoea and Erwinia species and detected the presence of putative effector islands associated with the hcp and vgrG genes. Results Between two and four T6SS loci occur among the Pantoea and Erwinia species. While two of the loci (T6SS-1 and T6SS-2) are well conserved among the various strains, the third (T6SS-3) locus is not universally distributed. Additional orthologous loci are present in Pantoea sp. aB-valens and Erwinia billingiae Eb661. Comparative analysis of the T6SS-1 and T6SS-3 loci showed non-conserved islands associated with the vgrG and hcp, and vgrG genes, respectively. These regions had a G+C content far lower than the conserved portions of the loci. Many of the proteins encoded within the hcp and vgrG islands carry conserved domains, which suggests they may serve as effector proteins for the T6SS. A number of the proteins also show homology to the C-terminal extensions of evolved VgrG proteins. Conclusions Extensive diversity was observed in the number and content of the T6SS loci among the Pantoea and Erwinia species. Genomic islands could be observed within some of T6SS loci, which are associated with the hcp and vgrG proteins and carry putative effector domain proteins. We propose new hypotheses concerning a role for these islands in the acquisition of T6SS effectors and the development of novel evolved VgrG and Hcp proteins.

2011-01-01

128

The genome factor in region-specific DNA damage: the DNA-reactive drug U-78779 prefers mixed A/T-G/C sequences at the nucleotide level but is region-specific for long pure AT islands at the genomic level.  

PubMed

Bizelesin is the first anticancer drug capable of damaging specific regions of the genome with clusters of its binding sites T(A/T)(4)A. This study characterized the sequence- and region-specificity of a bizelesin analogue, U-78779, designed to interact with mixed A/T-G/C motifs. At the nucleotide level, U-78779 was found to prefer runs of A/Ts interspersed with 1 or 2 G/C pairs, although 25% of the identified sites corresponded to pure AT motifs similar to bizelesin sites. The in silico computational analysis showed that the preferred mixed A/T-G/C motifs distribute uniformly at the genomic level. In contrast, the secondary, pure AT motifs (A/T)(6)A were found densely clustered in the same long islands of AT-rich DNA that bizelesin targets. Mapping the sites and quantitating the frequencies of U-78779 adducts in model AT island and non-AT island naked DNAs demonstrated that clusters of pure AT motifs outcompete isolated mixed A/T-G/C sites in attracting drug binding. Regional preference of U-78779 for AT island domains was verified also in DNA from drug-treated cells. Thus, while the primary sequence preference gives rise to non-region-specific scattered lesions, the clustering of the minor pure AT binding motifs seems to determine region-specificity of U-78779 in the human genome. The closely correlated cytotoxic activities of U-78779 and bizelesin in several cell lines further imply that both drugs may share common cellular targets. This study underscores the significance of the genome factor in a drug's potential for region-specific DNA damage, by showing that it can take precedence over drug binding preferences at the nucleotide level. PMID:11814348

Herzig, Maryanne C S; Rodriguez, Karl A; Trevino, Alex V; Dziegielewski, Jaroslaw; Arnett, Brenda; Hurley, Laurence; Woynarowski, Jan M

2002-02-01

129

A highly conserved gene island of three genes on chromosome 3B of hexaploid wheat: diverse gene function and genomic structure maintained in a tightly linked block  

Microsoft Academic Search

BACKGROUND: The complexity of the wheat genome has resulted from waves of retrotransposable element insertions. Gene deletions and disruptions generated by the fast replacement of repetitive elements in wheat have resulted in disruption of colinearity at a micro (sub-megabase) level among the cereals. In view of genomic changes that are possible within a given time span, conservation of genes between

James M Breen; Thomas Wicker; Xiuying Kong; Juncheng Zhang; Wujun Ma; Etienne Paux; Catherine Feuillet; Rudi Appels; Matthew Bellgard

2010-01-01

130

Diagnosis and Prognostication of Ductal Adenocarcinomas of the Pancreas Based on Genome-Wide DNA Methylation Profiling by Bacterial Artificial Chromosome Array-Based Methylated CpG Island Amplification  

PubMed Central

To establish diagnostic criteria for ductal adenocarcinomas of the pancreas (PCs), bacterial artificial chromosome (BAC) array-based methylated CpG island amplification was performed using 139 tissue samples. Twelve BAC clones, for which DNA methylation status was able to discriminate cancerous tissue (T) from noncancerous pancreatic tissue in the learning cohort with a specificity of 100%, were identified. Using criteria that combined the 12 BAC clones, T-samples were diagnosed as cancers with 100% sensitivity and specificity in both the learning and validation cohorts. DNA methylation status on 11 of the BAC clones, which was able to discriminate patients showing early relapse from those with no relapse in the learning cohort with 100% specificity, was correlated with the recurrence-free and overall survival rates in the validation cohort and was an independent prognostic factor by multivariate analysis. Genome-wide DNA methylation profiling may provide optimal diagnostic markers and prognostic indicators for patients with PCs.

Gotoh, Masahiro; Arai, Eri; Wakai-Ushijima, Saori; Hiraoka, Nobuyoshi; Kosuge, Tomoo; Hosoda, Fumie; Shibata, Tatsuhiro; Kondo, Tadashi; Yokoi, Sana; Imoto, Issei; Inazawa, Johji; Kanai, Yae

2011-01-01

131

The Genome Sequence of the Tomato-Pathogenic Actinomycete Clavibacter michiganensis subsp. michiganensis NCPPB382 Reveals a Large Island Involved in Pathogenicity  

Microsoft Academic Search

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 GC content (72.6%). Annotation revealed 3,080 putative protein-encoding sequences; only 26 pseudogenes were detected. Two rrn operons, 45 tRNAs, and three

Karl-Heinz Gartemann; Birte Abt; Thomas Bekel; Annette Burger; Jutta Engemann; Monika Flugel; Lars Gaigalat; Alexander Goesmann; Ines Grafen; J. Kalinowski; O. Kaup; O. Kirchner; L. Krause; B. Linke; A. McHardy; F. Meyer; S. Pohle; C. Ruckert; S. Schneiker; E.-M. Zellermann; A. Puhler; R. Eichenlaub; O. Kaiser; D. Bartels

2008-01-01

132

The Genome Sequence of the Tomato-Pathogenic Actinomycete Clavibacter michiganensis subsp. michiganensis NCPPB382 Reveals a Large Island Involved in Pathogenicity? †  

PubMed Central

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.

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

2008-01-01

133

Happy Island  

NASA Astrophysics Data System (ADS)

I discuss the phase diagram for QCD in the baryon chemical potential and temperature plane. I argue that there is a new phase of matter different from the deconfined Quark Gluon Plasma: Quarkyonic Matter. Quarkyonic Matter is confined and exists at densities parametrically large compared to the QCD scale, when the number of quark colors, Nc is large. I motivate the possibility that Quarkyonic Matter is in an inhomogeneous phase, and is surrounded by lines of phase transitions, making a Happy Island in the ?B-T plane. I conjecture about the geography of Happy Island.

McLerran, Larry

2012-01-01

134

A genome-wide linkage scan identifies multiple chromosomal regions influencing serum lipid levels in the population on the Samoan islands.  

PubMed

Abnormal lipid levels are important risk factors for cardiovascular diseases. We conducted genome-wide variance component linkage analyses to search for loci influencing total cholesterol (TC), LDL, HDL and triglyceride in families residing in American Samoa and Samoa as well as in a combined sample from the two polities. We adjusted the traits for a number of environmental covariates, such as smoking, alcohol consumption, physical activity, and material lifestyle. We found suggestive univariate linkage with log of the odds (LOD) scores > 3 for LDL on 6p21-p12 (LOD 3.13) in Samoa and on 12q21-q23 (LOD 3.07) in American Samoa. Furthermore, in American Samoa on 12q21, we detected genome-wide linkage (LOD(eq) 3.38) to the bivariate trait TC-LDL. Telomeric of this region, on 12q24, we found suggestive bivariate linkage to TC-HDL (LOD(eq) 3.22) in the combined study sample. In addition, we detected suggestive univariate linkage (LOD 1.9-2.93) on chromosomes 4p-q, 6p, 7q, 9q, 11q, 12q 13q, 15q, 16p, 18q, 19p, 19q and Xq23 and suggestive bivariate linkage (LOD(eq) 2.05-2.62) on chromosomes 6p, 7q, 12p, 12q, and 19p-q. In conclusion, chromosome 6p and 12q may host promising susceptibility loci influencing lipid levels; however, the low degree of overlap between the three study samples strongly encourages further studies of the lipid-related traits. PMID:18594117

Aberg, Karolina; Dai, Feng; Sun, Guangyun; Keighley, Ember; Indugula, Subba Rao; Bausserman, Linda; Viali, Satupaitea; Tuitele, John; Deka, Ranjan; Weeks, Daniel E; McGarvey, Stephen T

2008-07-01

135

Complete Nucleotide Sequence of a 43-Kilobase Genomic Island Associated with the Multidrug Resistance Region of Salmonella enterica Serovar Typhimurium DT104 and Its Identification in Phage Type DT120 and Serovar Agona  

PubMed Central

This study describes the characterization of the recently described Salmonella genomic island 1 (SGI1) (D. A. Boyd, G. A. Peters, L.-K. Ng, and M. R. Mulvey, FEMS Microbiol. Lett. 189:285–291, 2000), which harbors the genes associated with the ACSSuT phenotype in a Canadian isolate of Salmonella enterica serovar Typhimurium DT104. A 43-kb region has been completely sequenced and found to contain 44 predicted open reading frames (ORFs) which comprised ?87% of the total sequence. Fifteen ORFs did not show any significant homology to known gene sequences. A number of ORFs show significant homology to plasmid-related genes, suggesting, at least in part, a plasmid origin for the SGI1, although some with homology to phage-related genes were identified. The SGI1 was identified in a number of multidrug-resistant DT120 and S. enterica serovar Agona strains with similar antibiotic-resistant phenotypes. The G+C content suggests a potential mosaic structure for the SGI1. Emergence of the SGI1 in serovar Agona strains is discussed.

Boyd, David; Peters, Geoffrey A.; Cloeckaert, Axel; Boumedine, Karim Sidi; Chaslus-Dancla, Elisabeth; Imberechts, Hein; Mulvey, Michael R.

2001-01-01

136

Lavender Islands  

Microsoft Academic Search

Lavender Islands: Portrait of the Whole Family is the first national strengths-based study of lesbian, gay, and bisexual (LGB) people in New Zealand. The 133-item survey was made available both by website and paper copy from April to July 2004. Multidisciplinary interest areas were developed by a community reference group, and included identity and self-definition, families of origin, relationships and

Mark Henrickson; Stephen Neville; Claire Jordan; Sara Donaghey

2007-01-01

137

Polymerase chain reaction-aided genomic sequencing of an X chromosome-linked CpG island: methylation patterns suggest clonal inheritance, CpG site autonomy, and an explanation of activity state stability.  

PubMed Central

The 5' region of the gene encoding human X chromosome-linked phosphoglycerate kinase 1 (PGK1) is a promoter-containing CpG island known to be methylated at 119 of 121 CpG dinucleotides in a 450-base-pair region on the inactive human X chromosome in the hamster-human cell line X8-6T2. Here we report the use of polymerase chain reaction-aided genomic sequencing to determine the complete methylation pattern of this region in clones derived from X8-6T2 cells after treatment with the methylation inhibitor 5-azacytidine. We find (i) a clone showing full expression of human phosphoglycerate kinase is fully unmethylated in this region; (ii) clones not expressing human phosphoglycerate kinase remain methylated at approximately 50% of CpG sites, with a pattern of interspersed methylated (M) and unmethylated (U) sites different for each clone; (iii) singles, defined as M-U-M or U-M-U, are common; and (iv) a few CpG sites are partially methylated. The data are interpreted according to a model of multiple, autonomous CpG sites, and estimates are made for two key parameters, maintenance efficiency (Em approximately 99.9% per site per generation) and de novo methylation efficiency (Ed approximately 5%). These parameter values and the hypothesis that several independent sites must be unmethylated for transcription can explain the stable maintenance of X chromosome inactivation. We also consider how the active region is kept free of methylation and suggest that transcription inhibits methylation by decreasing Em so that methylation cannot be maintained. Thus, multiple CpG sites, independent with respect to a dynamic methylation system, can stabilize two alternative states of methylation and transcription. Images

Pfeifer, G P; Steigerwald, S D; Hansen, R S; Gartler, S M; Riggs, A D

1990-01-01

138

Polymerase chain reaction-aided genomic sequencing of an X chromosome-linked CpG island: Methylation patterns suggest clonal inheritance, CpG site autonomy, and an explanation of activity state stability  

SciTech Connect

The 5{prime} region of the gene encoding human X chromosome-linked phosphoglycerate kinase 1 (PGK1) is a promoter-containing CpG island known to be methylated at 119 of 121 CpG dinucleotides in a 450-base-pair region on the inactive human X chromosome in the hamster-human cell line X8-6T2. Here the authors report the use of polymerase chain reaction-aided genomic sequencing to determine the complete methylation pattern of this region in clones derived form X8-6T2 cells after treatment with the methylation inhibitor 5-azacytidine. They fine (i) a clone showing full expression of human phosphoglycerate kinase is fully unmethylated in this region; (ii) clones not expressing human phosphoglycerate kinase remain methylated at {approximately}50% of CpG sites, with a pattern of interspersed methylated (M) and unmethylated (U) sites different for each clone; (iii) singles, defined as M-U-M or U-M-U, are common; and (iv) a few CpG sites are partially methylated. The data are interpreted according to a model of multiple, autonomous CpG sites, and estimates are made for two key parameters, maintenance efficiency and de novo methylation efficiency. They also consider how the active region is kept free of methylation and suggest that transcription inhibits methylation by decreasing E{sub m} so that methylation cannot be maintained. Thus, multiple CpG sites, independent with respect to a dynamic methylation system, can stabilize two alternative states of methylation and transcription.

Pfeifer, G.P.; Steigerwald, S.D.; Riggs, A.D. (Beckman Research Inst. of the City of Hope, Duarte, CA (United States)); Hansen, R.S.; Gartler, S.M. (Univ. of Washington, Seattle (United States))

1990-11-01

139

To Build an Island  

NSDL National Science Digital Library

This lesson plan will give students a basic overview of the geography of islands. They will learn where islands are located throughout the world and will study two very different island groups (the Philippines and the British Isles) to illustrate the diversity of islands of the world. Students will explore island flora and fauna, languages, and climates and cultures.

140

CpG Island Mapping by Epigenome Prediction  

Microsoft Academic Search

CpG islands were originally identified by epigenetic and functional properties, namely, absence of DNA methylation and frequent promoter association. However, this concept was quickly replaced by simple DNA sequence criteria, which allowed for genome-wide annotation of CpG islands in the absence of large-scale epigenetic datasets. Although widely used, the current CpG island criteria incur significant disadvantages: (1) reliance on arbitrary

Christoph Bock; Jörn Walter; Martina Paulsen; Thomas Lengauer

2007-01-01

141

Pathogenicity islands: a molecular toolbox for bacterial virulence  

Microsoft Academic Search

Summary Pathogenicity islands (PAIs) are distinct genetic ele- ments on the chromosomes of a large number of bacterial pathogens. PAIs encode various virulence factors and are normally absent from non-pathogenic strains of the same or closely related species. PAIs are considered to be a subclass of genomic islands that are acquired by horizontal gene transfer via transduction, conjugation and transformation,

Ohad Gal-Mor; B. Brett Finlay

2006-01-01

142

Metagenomic islands of hyperhalophiles: the case of Salinibacter ruber  

PubMed Central

Background Saturated brines are extreme environments of low diversity. Salinibacter ruber is the only bacterium that inhabits this environment in significant numbers. In order to establish the extent of genetic diversity in natural populations of this microbe, the genomic sequence of reference strain DSM 13855 was compared to metagenomic fragments recovered from climax saltern crystallizers and obtained with 454 sequencing technology. This kind of analysis reveals the presence of metagenomic islands, i.e. highly variable regions among the different lineages in the population. Results Three regions of the sequenced isolate were scarcely represented in the metagenome thus appearing to vary among co-occurring S. ruber cells. These metagenomic islands showed evidence of extensive genomic corruption with atypically low GC content, low coding density, high numbers of pseudogenes and short hypothetical proteins. A detailed analysis of island gene content showed that the genes in metagenomic island 1 code for cell surface polysaccharides. The strain-specific genes of metagenomic island 2 were found to be involved in biosynthesis of cell wall polysaccharide components. Finally, metagenomic island 3 was rich in DNA related enzymes. Conclusion The genomic organisation of S. ruber variable genomic regions showed a number of convergences with genomic islands of marine microbes studied, being largely involved in variable cell surface traits. This variation at the level of cell envelopes in an environment devoid of grazing pressure probably reflects a global strategy of bacteria to escape phage predation.

2009-01-01

143

Island Formation: Constructing a Coral Island  

ERIC Educational Resources Information Center

|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…

Austin, Heather; Edd, Amelia

2009-01-01

144

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.

2010-02-03

145

Microevolution in island rodents  

Microsoft Academic Search

We perform a meta-analysis on morphological data from four island rodent populations exhibiting microevolution (>˜?100 years). Data consisting of incidences of skeletal variants, cranial, and external measurements are from house mice (Mus musculus) on one Welsh and one Scottish island, black rats (Rattus rattus) on two Galapagos islands, and deer mice (Peromyscus maniculatus) on three California Channel islands. We report

Oliver R. W. Pergams; Mary V. Ashley

2001-01-01

146

Pathogenicity Islands in Bacterial Pathogenesis  

PubMed Central

In this review, we focus on a group of mobile genetic elements designated pathogenicity islands (PAI). These elements play a pivotal role in the virulence of bacterial pathogens of humans and are also essential for virulence in pathogens of animals and plants. Characteristic molecular features of PAI of important human pathogens and their role in pathogenesis are described. The availability of a large number of genome sequences of pathogenic bacteria and their benign relatives currently offers a unique opportunity for the identification of novel pathogen-specific genomic islands. However, this knowledge has to be complemented by improved model systems for the analysis of virulence functions of bacterial pathogens. PAI apparently have been acquired during the speciation of pathogens from their nonpathogenic or environmental ancestors. The acquisition of PAI not only is an ancient evolutionary event that led to the appearance of bacterial pathogens on a timescale of millions of years but also may represent a mechanism that contributes to the appearance of new pathogens within a human life span. The acquisition of knowledge about PAI, their structure, their mobility, and the pathogenicity factors they encode not only is helpful in gaining a better understanding of bacterial evolution and interactions of pathogens with eukaryotic host cells but also may have important practical implications such as providing delivery systems for vaccination, tools for cell biology, and tools for the development of new strategies for therapy of bacterial infections.

Schmidt, Herbert; Hensel, Michael

2004-01-01

147

Microevolution in island rodents  

Microsoft Academic Search

\\u000a We perform a meta-analysis on morphological data from four island rodent populations exhibiting microevolution (island, black rats (Rattus rattus) on two Galapagos islands, and deer mice (Peromyscus maniculatus) on three California Channel islands. We

Oliver R. W. Pergams; Mary V. Ashley

148

Island Fox Paradox  

NSDL National Science Digital Library

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?

Sharon Levy (Freelancer;)

2010-05-03

149

Arctic ice islands  

SciTech Connect

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.

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

1988-01-01

150

Disturbed island ecology  

Microsoft Academic Search

The natural occurrence of significant disturbances to the operation of insular ecosystems has tended to be downplayed in the development of island ecological theory. Despite the importance of events such as Hurricane Hugo, which in 1989 affected islands in the Caribbean, islands that are disturbed tend to be viewed as deviants from the `true path' described by equilibrium models. However,

Robert J. Whittaker

1995-01-01

151

Target analysis of ?-alkylidene-?-butyrolactones in uropathogenic E. coli.  

PubMed

?-Alkylidene-?-butyrolactones are quite common in nature and exhibit a broad spectrum of biological activities. We therefore synthesized a small library of xanthatine inspired ?-alkylidene-?-butyrolactones to screen non-pathogenic and uropathogenic E. coli strains by activity based protein profiling (ABPP). The identified targets are involved in cellular redox processes and give first insight into the preferred binding sites of this privileged motif. Furthermore the gene of one protein, c2450, which was only identified in uropathogenic E. coli belongs to a genomic island which encodes a hybrid polyketide/non-ribosomal peptide synthetase (PKS/NRPS). This system is responsible for the synthesis of colibactin, a natural product which causes DNA double strand breaks in eukaryotic cells leading to the activation of the DNA damage checkpoint pathway and subsequent cell cycle arrest. While the role of several proteins that are involved in the colibactin synthesis has been elucidated, the function of c2450 remains elusive. Investigation of the binding site showed that c2450 is modified at a cysteine residue which may be important for the catalytic activity. PMID:22990910

Kunzmann, Martin H; Sieber, Stephan A

2012-09-18

152

Apostle Islands National Lakeshore  

NSDL National Science Digital Library

Near the western end of Lake Superior lies a forested archipelago of twenty-two islands called the Apostles. The Apostle Islands National Lakeshore (est. 1970) is composed of 20 of the 22 islands as well as a 12 mile strip of shoreline on the mainland. This National Park Service site contains an Explore the Islands section to get to know the natural wonders and human history of the islands. It offers information about: the islands, including a list of flora; lighthouses and shipwrecks; eagles and bears; sea caves; old growth forests; Lake Superior, including a fish species list; and the formation of sandscapes. The history of farming, stone quarries, and fisheries on the islands are also covered.

153

The SPI-3 Pathogenicity Island of Salmonella enterica  

Microsoft Academic Search

Pathogenicity islands are chromosomal clusters of pathogen-specific virulence genes often found at tRNA loci. We have determined the molecular genetic structure of SPI-3, a 17-kb pathogenicity island located at the selC tRNA locus of Salmonella enterica serovar Typhimurium. The G1C content of SPI-3 (47.5%) differs from that of the Salmonella genome (52%), consistent with the notion that these sequences have

ANNE-BEATRICE BLANC-POTARD; FELIX SOLOMON; JAYSON KAYSER; EDUARDO A. GROISMAN

1999-01-01

154

Island Biogeography and Landscape Ecology  

Microsoft Academic Search

MacArthur and Wilson’s theory (1967) set out to identify and measure the variables involved in the colonisation of islands\\u000a by biota and their subsequent evolution or extinction. The key biogeographical variables identified by their theory were island\\u000a size and distance from the mainland. They suggested that an island’s biodiversity is proportionate to the island’s size (i.e.\\u000a the larger the island

Ioannis Vogiatzakis; Geoffrey H. Griffiths

155

Pseudomonas Genome Database: improved comparative analysis and population genomics capability for Pseudomonas genomes.  

PubMed

Pseudomonas is a metabolically-diverse genus of bacteria known for its flexibility and leading free living to pathogenic lifestyles in a wide range of hosts. The Pseudomonas Genome Database (http://www.pseudomonas.com) integrates completely-sequenced Pseudomonas genome sequences and their annotations with genome-scale, high-precision computational predictions and manually curated annotation updates. The latest release implements an ability to view sequence polymorphisms in P. aeruginosa PAO1 versus other reference strains, incomplete genomes and single gene sequences. This aids analysis of phenotypic variation between closely related isolates and strains, as well as wider population genomics and evolutionary studies. The wide range of tools for comparing Pseudomonas annotations and sequences now includes a strain-specific access point for viewing high precision computational predictions including updated, more accurate, protein subcellular localization and genomic island predictions. Views link to genome-scale experimental data as well as comparative genomics analyses that incorporate robust genera-geared methods for predicting and clustering orthologs. These analyses can be exploited for identifying putative essential and core Pseudomonas genes or identifying large-scale evolutionary events. The Pseudomonas Genome Database aims to provide a continually updated, high quality source of genome annotations, specifically tailored for Pseudomonas researchers, but using an approach that may be implemented for other genera-level research communities. PMID:20929876

Winsor, Geoffrey L; Lam, David K W; Fleming, Leanne; Lo, Raymond; Whiteside, Matthew D; Yu, Nancy Y; Hancock, Robert E W; Brinkman, Fiona S L

2010-10-06

156

Pseudomonas Genome Database: improved comparative analysis and population genomics capability for Pseudomonas genomes  

PubMed Central

Pseudomonas is a metabolically-diverse genus of bacteria known for its flexibility and leading free living to pathogenic lifestyles in a wide range of hosts. The Pseudomonas Genome Database (http://www.pseudomonas.com) integrates completely-sequenced Pseudomonas genome sequences and their annotations with genome-scale, high-precision computational predictions and manually curated annotation updates. The latest release implements an ability to view sequence polymorphisms in P. aeruginosa PAO1 versus other reference strains, incomplete genomes and single gene sequences. This aids analysis of phenotypic variation between closely related isolates and strains, as well as wider population genomics and evolutionary studies. The wide range of tools for comparing Pseudomonas annotations and sequences now includes a strain-specific access point for viewing high precision computational predictions including updated, more accurate, protein subcellular localization and genomic island predictions. Views link to genome-scale experimental data as well as comparative genomics analyses that incorporate robust genera-geared methods for predicting and clustering orthologs. These analyses can be exploited for identifying putative essential and core Pseudomonas genes or identifying large-scale evolutionary events. The Pseudomonas Genome Database aims to provide a continually updated, high quality source of genome annotations, specifically tailored for Pseudomonas researchers, but using an approach that may be implemented for other genera-level research communities.

Winsor, Geoffrey L.; Lam, David K. W.; Fleming, Leanne; Lo, Raymond; Whiteside, Matthew D.; Yu, Nancy Y.; Hancock, Robert E. W.; Brinkman, Fiona S. L.

2011-01-01

157

Pseudomonas aeruginosa Genomic Structure and Diversity  

PubMed Central

The Pseudomonas aeruginosa genome (G?+?C content 65–67%, size 5.5–7?Mbp) is made up of a single circular chromosome and a variable number of plasmids. Sequencing of complete genomes or blocks of the accessory genome has revealed that the genome encodes a large repertoire of transporters, transcriptional regulators, and two-component regulatory systems which reflects its metabolic diversity to utilize a broad range of nutrients. The conserved core component of the genome is largely collinear among P. aeruginosa strains and exhibits an interclonal sequence diversity of 0.5–0.7%. Only a few loci of the core genome are subject to diversifying selection. Genome diversity is mainly caused by accessory DNA elements located in 79 regions of genome plasticity that are scattered around the genome and show an anomalous usage of mono- to tetradecanucleotides. Genomic islands of the pKLC102/PAGI-2 family that integrate into tRNALys or tRNAGly genes represent hotspots of inter- and intraclonal genomic diversity. The individual islands differ in their repertoire of metabolic genes that make a large contribution to the pangenome. In order to unravel intraclonal diversity of P. aeruginosa, the genomes of two members of the PA14 clonal complex from diverse habitats and geographic origin were compared. The genome sequences differed by less than 0.01% from each other. One hundred ninety-eight of the 231 single nucleotide substitutions (SNPs) were non-randomly distributed in the genome. Non-synonymous SNPs were mainly found in an integrated Pf1-like phage and in genes involved in transcriptional regulation, membrane and extracellular constituents, transport, and secretion. In summary, P. aeruginosa is endowed with a highly conserved core genome of low sequence diversity and a highly variable accessory genome that communicates with other pseudomonads and genera via horizontal gene transfer.

Klockgether, Jens; Cramer, Nina; Wiehlmann, Lutz; Davenport, Colin F.; Tummler, Burkhard

2011-01-01

158

Genome Sequences of Two Pathogenic Streptococcus agalactiae Isolates from the One-Humped Camel Camelus dromedarius.  

PubMed

Streptococcus agalactiae causes a range of clinical syndromes in camels (Camelus dromedarius). We report the genome sequences of two S. agalactiae isolates that induce abscesses in Kenyan camels. These genomes provide novel data on the composition of the S. agalactiae "pan genome" and reveal the presence of multiple genomic islands. PMID:23868134

Zubair, Saima; de Villiers, Etienne P; Younan, Mario; Andersson, Göran; Tettelin, Herve; Riley, David R; Jores, Joerg; Bongcam-Rudloff, Erik; Bishop, Richard P

2013-07-18

159

Genome Sequences of Two Pathogenic Streptococcus agalactiae Isolates from the One-Humped Camel Camelus dromedarius  

PubMed Central

Streptococcus agalactiae causes a range of clinical syndromes in camels (Camelus dromedarius). We report the genome sequences of two S. agalactiae isolates that induce abscesses in Kenyan camels. These genomes provide novel data on the composition of the S. agalactiae “pan genome” and reveal the presence of multiple genomic islands.

de Villiers, Etienne P.; Younan, Mario; Andersson, Goran; Tettelin, Herve; Riley, David R.; Jores, Joerg; Bongcam-Rudloff, Erik; Bishop, Richard P.

2013-01-01

160

Genome organization of epidemic Acinetobacter baumannii strains  

PubMed Central

Background Acinetobacter baumannii is an opportunistic pathogen responsible for hospital-acquired infections. A. baumannii epidemics described world-wide were caused by few genotypic clusters of strains. The occurrence of epidemics caused by multi-drug resistant strains assigned to novel genotypes have been reported over the last few years. Results In the present study, we compared whole genome sequences of three A. baumannii strains assigned to genotypes ST2, ST25 and ST78, representative of the most frequent genotypes responsible for epidemics in several Mediterranean hospitals, and four complete genome sequences of A. baumannii strains assigned to genotypes ST1, ST2 and ST77. Comparative genome analysis showed extensive synteny and identified 3068 coding regions which are conserved, at the same chromosomal position, in all A. baumannii genomes. Genome alignments also identified 63 DNA regions, ranging in size from 4 o 126 kb, all defined as genomic islands, which were present in some genomes, but were either missing or replaced by non-homologous DNA sequences in others. Some islands are involved in resistance to drugs and metals, others carry genes encoding surface proteins or enzymes involved in specific metabolic pathways, and others correspond to prophage-like elements. Accessory DNA regions encode 12 to 19% of the potential gene products of the analyzed strains. The analysis of a collection of epidemic A. baumannii strains showed that some islands were restricted to specific genotypes. Conclusion The definition of the genome components of A. baumannii provides a scaffold to rapidly evaluate the genomic organization of novel clinical A. baumannii isolates. Changes in island profiling will be useful in genomic epidemiology of A. baumannii population.

2011-01-01

161

Distinguishing Microbial Genome Fragments Based on Their Composition: Evolutionary and Comparative Genomic Perspectives  

PubMed Central

It is well known that patterns of nucleotide composition vary within and among genomes, although the reasons why these variations exist are not completely understood. Between-genome compositional variation has been exploited to assign environmental shotgun sequences to their most likely originating genomes, whereas within-genome variation has been used to identify recently acquired genetic material such as pathogenicity islands. Recent sequence assignment techniques have achieved high levels of accuracy on artificial data sets, but the relative difficulty of distinguishing lineages with varying degrees of relatedness, and different types of genomic sequence, has not been examined in depth. We investigated the compositional differences in a set of 774 sequenced microbial genomes, finding rapid divergence among closely related genomes, but also convergence of compositional patterns among genomes with similar habitats. Support vector machines were then used to distinguish all pairs of genomes based on genome fragments 500 nucleotides in length. The nearly 300,000 accuracy scores obtained from these trials were used to construct general models of distinguishability versus taxonomic and compositional indices of genomic divergence. Unusual genome pairs were evident from their large residuals relative to the fitted model, and we identified several factors including genome reduction, putative lateral genetic transfer, and habitat convergence that influence the distinguishability of genomes. The positional, compositional, and functional context of a fragment within a genome has a strong influence on its likelihood of correct classification, but in a way that depends on the taxonomic and ecological similarity of the comparator genome.

Perry, Scott C.; Beiko, Robert G.

2010-01-01

162

DNA methylation profiles of CpG islands for cellular differentiation and development in mammals  

Microsoft Academic Search

DNA methylation has been implicated in mammalian development. Transcription units contain CpG islands, but expression of CpG island associated genes in normal tissues was not believed to be controlled by DNA methylation. There are, however, numerous CpG islands containing tissue-dependent and differentially methylated regions (T-DMR), which are potential methylation sites in normal cells and tissues. Genomic scanning which focused on

K. Shiota

2004-01-01

163

Isolation of Estrogen-Responsive Genes with a CpG Island Library  

Microsoft Academic Search

In order to isolate novel estrogen-responsive genes, we utilized a CpG island library in which the regulatory regions of genes are enriched. CpG islands were screened for the ability to bind to a recombinant estrogen receptor protein with a genomic binding site (GBS) cloning method. Six CpG islands were selected, and they contained perfect, imperfect, and\\/or multiple half-palindromic estrogen-responsive elements

TORU WATANABE; SATOSHI INOUE; HISAHIKO HIROI; AKIRA ORIMO; HIROYUKI KAWASHIMA; MASAMI MURAMATSU

164

Basaltic island sand provenance  

SciTech Connect

The Hawaiian Islands are an ideal location to study basaltic sand provenance in that they are a series of progressively older basaltic shield volcanoes with arid to humid microclimates. Sixty-two sand samples were collected from beaches on the islands of Hawaii, Maui, Oahu and Kauai and petrographically analyzed. The major sand components are calcareous bioclasts, volcanic lithic fragments, and monomineralic grains of dense minerals and plagioclase. Proportions of these components vary from island to island, with bioclastic end members being more prevalent on older islands exhibiting well-developed fringing reef systems and volcanic end members more prevalent on younger, volcanically active islands. Climatic variations across the island of Hawaii are reflected in the percentage of weathered detritus, which is greater on the wetter, northern side of the island. The groundmass of glassy, basaltic lithics is predominantly black tachylite, with lesser brown sideromelane; microlitic and lathwork textures are more common than holohyaline vitric textures. Other common basaltic volcanic lithic fragments are holocrystalline aggregates of silt-sized pyroxene or olivine, opaque minerals and plagioclase. Sands derived from alkalic lavas are texturally and compositionally indistinguishable from sands derived from tholeiitic lavas. Although Hawaiian basaltic sands overlap in composition with magmatic arc-derived sands in terms of their relative QFL, QmPK and LmLvLs percentages, they are dissimilar in that they lack felsic components and are more enriched in lathwork volcanic lithic fragments, holocrystalline volcanic lithic fragments, and dense minerals.

Marsaglia, K.M. (Univ. of Texas, El Paso, TX (United States). Dept. of Geological Sciences)

1992-01-01

165

Island Natural Science School.  

ERIC Educational Resources Information Center

Prepared for students in grade six attending the Island Natural Science School, Toronto, Ontario, Canada, this booklet offers information and suggests activities in the areas of ecology, conservation, natural resources, and outdoor recreation. Introductory material describes island lore, its formation and significant features, followed by units of…

Toronto Board of Education (Ontario).

166

Marine and Island Ecology.  

ERIC Educational Resources Information Center

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…

Stephens, Lawrence J.; And Others

1988-01-01

167

Marine and Island Ecology.  

ERIC Educational Resources Information Center

|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…

Stephens, Lawrence J.; And Others

1988-01-01

168

Build an Island  

NSDL National Science Digital Library

This step by step presentation of the formation of a coral atoll includes eight frames, showing the volcanic island sinking as the fringing reef builds. Eventually the original island sinks well below the surface and only the reef remains as an atoll.

169

CpGPAP: CpG island predictor analysis platform  

PubMed Central

Background Genomic islands play an important role in medical, methylation and biological studies. To explore the region, we propose a CpG islands prediction analysis platform for genome sequence exploration (CpGPAP). Results CpGPAP is a web-based application that provides a user-friendly interface for predicting CpG islands in genome sequences or in user input sequences. The prediction algorithms supported in CpGPAP include complementary particle swarm optimization (CPSO), a complementary genetic algorithm (CGA) and other methods (CpGPlot, CpGProD and CpGIS) found in the literature. The CpGPAP platform is easy to use and has three main features (1) selection of the prediction algorithm; (2) graphic visualization of results; and (3) application of related tools and dataset downloads. These features allow the user to easily view CpG island results and download the relevant island data. CpGPAP is freely available at http://bio.kuas.edu.tw/CpGPAP/. Conclusions The platform's supported algorithms (CPSO and CGA) provide a higher sensitivity and a higher correlation coefficient when compared to CpGPlot, CpGProD, CpGIS, and CpGcluster over an entire chromosome.

2012-01-01

170

Finite island model for organelle and nuclear genes in plants  

Microsoft Academic Search

Recurrence equations for genetic diversities and differentiation were developed for hermaphrodite plant species in an island model of population structure. This was made possible by the definitions of diversities at all hierarchical levels from gamete to total population and by the definition of migration rates specific to plants for both nuclear and cytoplasmic genomes. Mating system was also incorporated. Numerical

R J Petit; A Kremer; D B Wagner

1993-01-01

171

Extreme genomes  

PubMed Central

The complete genome sequence of Thermoplasma acidophilum, an acid- and heat-loving archaeon, has recently been reported. Comparative genomic analysis of this 'extremophile' is providing new insights into the metabolic machinery, ecology and evolution of thermophilic archaea.

DeLong, Edward F

2000-01-01

172

Christmas Island birds returning  

NASA Astrophysics Data System (ADS)

Six months after their mass exodus, birds are beginning to return to Christmas Island. Roughly 17 million birds, almost the entire adult bird population, either perished or fled their mid-Pacific atoll home last autumn, leaving behind thousands of nestlings to starve (Eos, April 5, 1983, p. 131). It is believed that the strong El Niño altered the ecology of the surrounding waters and forced the birds to flee. Christmas Island is the world's largest coral atoll.“Ocean and atmosphere scientists are unsure of future directions for the El Niño conditions and cannot now predict what will happen to the birds in the coming months,” said Ralph W. Schreiber, curator of ornithology at the Natural History Museum of Los Angeles County in California. Heisthe ornithologist who discovered the disappearance. “The recovery of the bird populations depends on the food supply in the waters surrounding the island.” The island's birds feed exclusively on small fish and squid.

173

Coalescence of magnetic islands  

Microsoft Academic Search

The process of coalescence of magnetic islands is studied in an incompressible resistive MHD model. For intermediate values of resistivity, reconnection rate is independent of the resistivity, although the reconnection process is basically different from a Petschek-type model.

D. Biskamp; H. Welter

1980-01-01

174

Easter Island Revisited  

NSDL National Science Digital Library

Access to the article is free, however registration and sign-in are required. New information about Easter Island is helping to identify the cause of the massive deforestation that occurred prior to European arrival, but unanswered questions remain.

Jared Diamond (University of California at Los Angeles;Geography Department)

2007-09-21

175

Long Island Collection  

NSDL National Science Digital Library

The dedicated librarians at the Stony Brook University Library have created this most excellent research guide and digital archive that covers all things Long Island. On their homepage, visitors can use the Long Island Documents area to view recently acquired items from key figures in local (and national) history, such as George Clinton, James Jay, and Benjamin Tallmadge. Also on the site is the Books, Pamphlets, and Journals area. Here visitors can make their way through key documents, such as "Early Long Island: A Colonial Study" and "The Evolution of Long Island: A Story of Land and Sea." Also, the site pays tribute to a very exciting new acquisition: several letters from George Washington, donated by Dr. Henry Laufer, a history enthusiast. This site is a tremendously valuable resource and one that will serve as a model to other institutions seeking to do similar work.

2012-08-24

176

Island Inequality Map  

NSDL National Science Digital Library

The concepts of greater than, less than, and equal to are explored in this two-lesson unit. Students create piles of food on two islands, and their fish always swims toward the island with more food. The fish's mouth is open to represent the greater than and less than symbols. Students transition from the concrete representation of using piles of food and the fish to writing inequalities with numerals and symbols.

Math, Illuminations N.

2009-01-15

177

The Long Island Index  

Microsoft Academic Search

Using a multi-faceted approach that combines analysis of existing statistical data, original research, survey data, and comparative\\u000a case studies, the Long Island Index has helped to clarify the complex dynamics of the region and succeeded in reaching a wide audience including leaders who\\u000a shape regional policy. This chapter explores the nature of the target area, Long Island, defining the characteristics

Ann Golob

178

Development of Pabelokan Island  

SciTech Connect

Pertamina and Iiapco has an expanding complex of offshore production platforms in the S.E. Sumatra contract area of the Java Sea. One of the requirements for this complex is a treatment facility for water to be used in secondary recovery operations. Because of the water quality required, the water treatment system is substantially larger than that normally used off shore. Instead of constructing one or more platforms for the treatment system, a small coral island named Pabelokan Island has been utilized for this purpose. Although the water treatment system is the primary reason for the base, other facilities were co-located to centralize electric power generation, living quarters and recreation facilities, and facilities for storage and maintenance of offshore equipment. Future plans for the island include a gas-liquids recovery system. This work describes the island facilities, and provides a case study in responsible planning and construction techniques in the development of a coral island for use as an offshore base. The experience gained should be useful in the planning of other coral islands for similar purpose.

Powell, D.R.

1982-01-01

179

Microbial lifestyle and genome signatures.  

PubMed

Microbes are known for their unique ability to adapt to varying lifestyle and environment, even to the extreme or adverse ones. The genomic architecture of a microbe may bear the signatures not only of its phylogenetic position, but also of the kind of lifestyle to which it is adapted. The present review aims to provide an account of the specific genome signatures observed in microbes acclimatized to distinct lifestyles or ecological niches. Niche-specific signatures identified at different levels of microbial genome organization like base composition, GC-skew, purine-pyrimidine ratio, dinucleotide abundance, codon bias, oligonucleotide composition etc. have been discussed. Among the specific cases highlighted in the review are the phenomena of genome shrinkage in obligatory host-restricted microbes, genome expansion in strictly intra-amoebal pathogens, strand-specific codon usage in intracellular species, acquisition of genome islands in pathogenic or symbiotic organisms, discriminatory genomic traits of marine microbes with distinct trophic strategies, and conspicuous sequence features of certain extremophiles like those adapted to high temperature or high salinity. PMID:23024607

Dutta, Chitra; Paul, Sandip

2012-04-01

180

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

PubMed

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

Che, Shuai; Song, Lai; Song, Weizhi; Yang, Meng; Liu, Guiming; Lin, Xuezheng

2013-09-19

181

Site-Specific Mobilization of Vinyl Chloride Respiration Islands by a Mechanism Common in Dehalococcoides  

Microsoft Academic Search

Background  Vinyl chloride is a widespread groundwater pollutant and Group 1 carcinogen. A previous comparative genomic analysis revealed\\u000a that the vinyl chloride reductase operon, vcrABC, of Dehalococcoides sp. strain VS is embedded in a horizontally-acquired genomic island that integrated at the single-copy tmRNA gene, ssrA.\\u000a \\u000a \\u000a \\u000a \\u000a Results  We targeted conserved positions in available genomic islands to amplify and sequence four additional vcrABC -containing

Paul J McMurdie; Laura A Hug; Elizabeth A Edwards; Susan Holmes; Alfred M Spormann

2011-01-01

182

Bisulfite genomic sequencing of microdissected cells  

Microsoft Academic Search

Mapping of methylation patterns in CpG islands has become an important tool for understanding tissue- specific gene expression in both normal and patho- logical situations. However, the inherent cellular heterogeneity of any given tissues can affect the outcome and interpretation of molecular studies. In order to analyse genomic DNA methylation on a pure cell population from tissue sample, we have

Antoine Kerjean; Annick Vieillefond; Nicolas Thiounn; Mathilde Sibony; Marc Jeanpierre; Pierre Jouannet

2001-01-01

183

Dynamics of Pseudomonas aeruginosa genome evolution  

PubMed Central

One of the hallmarks of the Gram-negative bacterium Pseudomonas aeruginosa is its ability to thrive in diverse environments that includes humans with a variety of debilitating diseases or immune deficiencies. Here we report the complete sequence and comparative analysis of the genomes of two representative P. aeruginosa strains isolated from cystic fibrosis (CF) patients whose genetic disorder predisposes them to infections by this pathogen. The comparison of the genomes of the two CF strains with those of other P. aeruginosa presents a picture of a mosaic genome, consisting of a conserved core component, interrupted in each strain by combinations of specific blocks of genes. These strain-specific segments of the genome are found in limited chromosomal locations, referred to as regions of genomic plasticity. The ability of P. aeruginosa to shape its genomic composition to favor survival in the widest range of environmental reservoirs, with corresponding enhancement of its metabolic capacity is supported by the identification of a genomic island in one of the sequenced CF isolates, encoding enzymes capable of degrading terpenoids produced by trees. This work suggests that niche adaptation is a major evolutionary force influencing the composition of bacterial genomes. Unlike genome reduction seen in host-adapted bacterial pathogens, the genetic capacity of P. aeruginosa is determined by the ability of individual strains to acquire or discard genomic segments, giving rise to strains with customized genomic repertoires. Consequently, this organism can survive in a wide range of environmental reservoirs that can serve as sources of the infecting organisms.

Mathee, Kalai; Narasimhan, Giri; Valdes, Camilo; Qiu, Xiaoyun; Matewish, Jody M.; Koehrsen, Michael; Rokas, Antonis; Yandava, Chandri N.; Engels, Reinhard; Zeng, Erliang; Olavarietta, Raquel; Doud, Melissa; Smith, Roger S.; Montgomery, Philip; White, Jared R.; Godfrey, Paul A.; Kodira, Chinnappa; Birren, Bruce; Galagan, James E.; Lory, Stephen

2008-01-01

184

Perioperative Genomics  

PubMed Central

Since the completion of the Human Genome Project 10 years ago, the world has witnessed an incredible progress in human genetics and genomics.1 This progress was largely driven by the availability of better, faster and cheaper sequencing technology.2 While it took more than 10 years and more than 1 billion dollars to complete the Human Genome Project,3-5 an individual in the year 2011 can have his whole genome sequenced within a week for less than $30,000. With cheaper and faster sequencing came a wealth of novel discoveries which makes it timely to review how these newly found insights into the human genome are relevant for perioperative medicine. This review summarizes the basics of genetic inheritance, the human genome and modern sequencing methods, as well as genetic variation and how this knowledge may be applied to patient care and research in the perioperative setting.

Nagele, Peter

2011-01-01

185

Perioperative genomics.  

PubMed

Since the completion of the Human Genome Project 10 years ago, the world has witnessed an incredible progress in human genetics and genomics.(1) This progress was largely driven by the availability of better, faster and cheaper sequencing technology.(2) While it took more than 10 years and more than 1 billion dollars to complete the Human Genome Project,(3-5) an individual in the year 2011 can have his whole genome sequenced within a week for less than $30,000. With cheaper and faster sequencing came a wealth of novel discoveries which makes it timely to review how these newly found insights into the human genome are relevant for perioperative medicine. This article summarises the basics of genetic inheritance, the human genome and modern sequencing methods, as well as genetic variation and how this knowledge may be applied to patient care and research in the perioperative setting. PMID:22099920

Nagele, Peter

2011-12-01

186

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

Federal Register 2010, 2011, 2012, 2013

...Long Island Sound; Manursing Island, NY AGENCY: Coast Guard, DHS. ACTION: Final...Sound in the vicinity of Manursing Island, NY for a fireworks display. This temporary...Long Island Sound; Manursing Island, NY in the Federal Register (77 FR...

2012-08-24

187

78 FR 48668 - PSEG Long Island LLC, Long Island Electric Utility Servco LLC, Long Island Power Authority, Long...  

Federal Register 2010, 2011, 2012, 2013

...Utility Servco LLC, Long Island Power Authority, Long Island Lighting Company; Notice of Petition for Declaratory Order Take notice...Long Island Power Authority (Authority), and Long Island Lighting Company (LIPA); (the Authority and LIPA together,...

2013-08-09

188

Prophage Genomics  

PubMed Central

The majority of the bacterial genome sequences deposited in the National Center for Biotechnology Information database contain prophage sequences. Analysis of the prophages suggested that after being integrated into bacterial genomes, they undergo a complex decay process consisting of inactivating point mutations, genome rearrangements, modular exchanges, invasion by further mobile DNA elements, and massive DNA deletion. We review the technical difficulties in defining such altered prophage sequences in bacterial genomes and discuss theoretical frameworks for the phage-bacterium interaction at the genomic level. The published genome sequences from three groups of eubacteria (low- and high-G+C gram-positive bacteria and ?-proteobacteria) were screened for prophage sequences. The prophages from Streptococcus pyogenes served as test case for theoretical predictions of the role of prophages in the evolution of pathogenic bacteria. The genomes from further human, animal, and plant pathogens, as well as commensal and free-living bacteria, were included in the analysis to see whether the same principles of prophage genomics apply for bacteria living in different ecological niches and coming from distinct phylogenetical affinities. The effect of selection pressure on the host bacterium is apparently an important force shaping the prophage genomes in low-G+C gram-positive bacteria and ?-proteobacteria.

Canchaya, Carlos; Proux, Caroline; Fournous, Ghislain; Bruttin, Anne; Brussow, Harald

2003-01-01

189

Vegetation History of Laysan Island, Northwestern Hawaiian Islands  

Microsoft Academic Search

Paleoenvironmental investigations were undertaken on Laysan Island in the remote Northwestern Hawaiian Islands to investigate its flora before his- torical observations. Substantial impacts occurred to the island as a result of late nineteenth- and early twentieth-century guano mining, commercial feather col- lecting, and denudation of vegetation by feral rabbits. An account of Laysan's historically known vegetation is presented, followed by

John Stephen. Athens; James V. Ward; Dean W. Blinn

2007-01-01

190

Fanning Island Expedition, January 1970.  

National Technical Information Service (NTIS)

The interdisciplinary studies consisted of a sea phase, involving measurements in the South Equatorial Current and Undercurrent and measurement of the contribution of detritus from Fanning Island to the open sea; and an island phase, aimed at the physical...

K. E. Chave B. S. Gallagher F. I. Gonzalez D. C. Gordon G. Krasnick

1970-01-01

191

Personal genomics services: whose genomes?  

Microsoft Academic Search

New companies offering personal whole-genome information services over the internet are dynamic and highly visible players in the personal genomics field. For fees currently ranging from US$399 to US$2500 and a vial of saliva, individuals can now purchase online access to their individual genetic information regarding susceptibility to a range of chronic diseases and phenotypic traits based on a genome-wide

David Gurwitz; Yael Bregman-Eschet

2009-01-01

192

Geology of the Cook Islands  

Microsoft Academic Search

The geology of the 15 Cook Islands in the south-central Pacific is briefly described and their geological history outlined. All are the summit portions of extinct Tertiary volcanoes; six of the seven Northern Group islands are atolls, four of the Southern Group are makatea-type islands, and the others include a high mountainous volcanic island, a hilly near-atoll, an atoll, and

B. L. Wood

1967-01-01

193

PAPAYA GENOMICS  

Technology Transfer Automated Retrieval System (TEKTRAN)

Because of its relatively small genome (372Mb/1C) and ability to produce ripe fruit 9 to 12 months after planting, papaya (Carica papaya L.) can be a model for studying genes that affect fruit characters. We are developing papaya genomics to understand germplasm diversity, construct a high density g...

194

Grass genomes  

PubMed Central

For the most part, studies of grass genome structure have been limited to the generation of whole-genome genetic maps or the fine structure and sequence analysis of single genes or gene clusters. We have investigated large contiguous segments of the genomes of maize, sorghum, and rice, primarily focusing on intergenic spaces. Our data indicate that much (>50%) of the maize genome is composed of interspersed repetitive DNAs, primarily nested retrotransposons that insert between genes. These retroelements are less abundant in smaller genome plants, including rice and sorghum. Although 5- to 200-kb blocks of methylated, presumably heterochromatic, retrotransposons flank most maize genes, rice and sorghum genes are often adjacent. Similar genes are commonly found in the same relative chromosomal locations and orientations in each of these three species, although there are numerous exceptions to this collinearity (i.e., rearrangements) that can be detected at the levels of both the recombinational map and cloned DNA. Evolutionarily conserved sequences are largely confined to genes and their regulatory elements. Our results indicate that a knowledge of grass genome structure will be a useful tool for gene discovery and isolation, but the general rules and biological significance of grass genome organization remain to be determined. Moreover, the nature and frequency of exceptions to the general patterns of grass genome structure and collinearity are still largely unknown and will require extensive further investigation.

Bennetzen, Jeffrey L.; SanMiguel, Phillip; Chen, Mingsheng; Tikhonov, Alexander; Francki, Michael; Avramova, Zoya

1998-01-01

195

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 ...

196

Chapter 2 The Erythroblastic Island  

Microsoft Academic Search

Erythroblastic islands are specialized microenvironmental compartments within which definitive mammalian erythroblasts proliferate and differentiate. These islands consist of a central macrophage that extends cytoplasmic protrusions to a ring of surrounding erythroblasts. The interaction of cells within the erythroblastic island is essential for both early and late stages of erythroid maturation. It has been proposed that early in erythroid maturation the

Deepa Manwani; James J. Bieker

2008-01-01

197

Nurse Practitioner in Rhode Island.  

National Technical Information Service (NTIS)

A study of the future role of the nurse practitioner in Rhode Island is reported. The study was conducted by the Rhode Island Health Science Education Council under contract to the Rhode Island Department of Education, in response to a resolution of the 1...

1976-01-01

198

Three Mile Island revisited  

Microsoft Academic Search

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

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

1991-01-01

199

Three Mile Island  

Microsoft Academic Search

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;

M. S. Wood; S. M. Shultz

1988-01-01

200

Why the islands move.  

PubMed

Micronesian navigators routinely make voyages across large expanses of open ocean. To do this, a navigator must judge both the direction in which he is sailing and the distance he has travelled. The rising and setting points of the stars (and other cues) provide instantaneous information about direction, but distance can only be judged by integrating velocity-related information over time. Micronesian navigators judge distance in a way that seems odd. When they are out of sight of land, they imagine that the canoe is stationary and that the islands move back past them. For each voyage, they 'attend' to an island off to the side of the course which is out of sight over the horizon. As they sail, they imagine the island moving back along the horizon changing in bearing until it is imagined to be under the bearing it is known to have from the destination island. Then they know they are near their destination. There is good reason for using a frame of reference whose origin is defined by the boat. We show how it finesses a perceptual paradox--the rising and setting points of the stars do not exhibit motion parallax. PMID:6535986

Hutchins, E; Hinton, G E

1984-01-01

201

Hawaii's Sugar Islands.  

ERIC Educational Resources Information Center

|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,…

Hawaiian Sugar Planters' Association, Aiea, HI.

202

The Flores Island tsunamis  

NASA Astrophysics Data System (ADS)

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 December 16, television reports broadcast in Japan via satellite reported that 1000 people had been killed in Maumere and twothirds of the population of Babi Island had been swept away by the tsunamis.The current toll of the Flores earthquake is 2080 deaths and 2144 injuries, approximately 50% of which are attributed to the tsunamis. A tsunami survey plan was initiated within 3 days of the earthquake, and a cooperative international survey team was formed with four scientists from Indonesia, nine from Japan, three from the United States, one from the United Kingdom, and one from Korea.

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

203

Hawaii's Sugar Islands.  

ERIC Educational Resources Information Center

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,…

Hawaiian Sugar Planters' Association, Aiea, HI.

204

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.

205

Magnetic-island formation  

SciTech Connect

The response of a finite conductivity plasma to resonant magnetic perturbations is studied. The equations, which are derived for the time development of magnetic islands, help one interpret the singular currents which occur under the assumption of perfect plasma conductivity. The relation to the Rutherford regime of resistive instabilities is given.

Boozer, A.H.

1983-08-01

206

Man made floating island  

Microsoft Academic Search

An artificial island is described for use in energy production from ocean waves, comprising: a platform disposed atop the ocean surface; vertically disposed rigid posts extending beneath the platform short of the ocean floor; a stationary wave amplifier affixed to the posts, the wave amplifier of a conical shape with inclined sides for directing water upwardly from substantially any lateral

Martinak

1987-01-01

207

Earth Island Institute  

NSDL National Science Digital Library

Visitors to this homepage can learn about the Earth Island Institute and its mission, origins, and purpose. Materials include summaries of projects designed to promote conservation, preservation, and restoration of the Earth, a biography of the organization's founder, news articles, and information for people who wish to become involved in conservation or outreach efforts.

208

Rhode Island's Health 1979.  

National Technical Information Service (NTIS)

This is the fourth annual report on the health conditions and health expenditures of the people of Rhode Island and is the only such report to be issued by any State in the Nation. Topics covered include population trends, health status (natality, mortali...

1979-01-01

209

Islands and despots  

Microsoft Academic Search

This paper challenges a conventional wisdom: that when discussing political systems, small is democratic. And yet, can there be paradises without serpents? The presumed manageability of small island spaces promotes and nurtures dispositions for domination and control over nature and society. In such dark circumstances, authoritarian rule is a more natural fit than democracy. By adopting an inter-disciplinary perspective, this

Godfrey Baldacchino

2012-01-01

210

Antarctic Genomics  

PubMed Central

With the development of genomic science and its battery of technologies, polar biology stands on the threshold of a revolution, one that will enable the investigation of important questions of unprecedented scope and with extraordinary depth and precision. The exotic organisms of polar ecosystems are ideal candidates for genomic analysis. Through such analyses, it will be possible to learn not only the novel features that enable polar organisms to survive, and indeed thrive, in their extreme environments, but also fundamental biological principles that are common to most, if not all, organisms. This article aims to review recent developments in Antarctic genomics and to demonstrate the global context of such studies.

Clarke, Andrew; Cockell, Charles S.; Convey, Peter; Detrich III, H. William; Fraser, Keiron P. P.; Johnston, Ian A.; Methe, Barbara A.; Murray, Alison E.; Peck, Lloyd S.; Romisch, Karin; Rogers, Alex D.

2004-01-01

211

[Distribution and genetic organization of the pathogenicity island XII among the clinical strains of GBS].  

PubMed

Streptococcus agalactiae or group B streptococci (GBS) is the major cause of various diseases of the newborns and the adults. The genome of GBS contains from 14 to 15 mobile genetic elements (pathogenicity islands, PAI). It is well-known that many GBS virulence determinants are localized not in the core genome, but on the pathogenicity islands. The goal of this work was to determine the distribution and genetic organization of PAI XII containing virulence genes sspB1, scpB, lmb among the clinical strains of GBS. 74 clinical strains of GBS were analyzed using PCR with primers corresponding to the genes of the virulence factors located on PAI XII. The pathogenicity island XII was determined only in 22% of the clinical strains. The genetic organization of the island was different between strains. There was no correlation between the presence of PAI and the serotype of GBS. PMID:23785787

Kuleshevich, E V; Savicheva, A M; Arzhanova, O N; Suvorov, A N

2013-01-01

212

Genomics Glossary  

NSDL National Science Digital Library

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.

Chitty, Mary G.

213

Pine Island Iceberg Formation  

NSDL National Science Digital Library

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.

Perkins, Lori; Bindschadler, Bob; Diner, Dave

2002-01-10

214

Structural genomics  

Microsoft Academic Search

Structural genomics can be defined as structural biology on a large number of target proteins in parallel. This approach plays\\u000a an important role in modern structure-based drug design. Although a number of structural genomics initiatives have been initiated,\\u000a relatively few are associated with integral membrane proteins. This indicates the difficulties in expression, purification,\\u000a and crystallization of membrane proteins, which has

Kenneth Lundstrom

2006-01-01

215

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.

216

Animal Island Data  

NSDL National Science Digital Library

In this interactive application students playing at the easiest level count the number of each type of animal at the zoo on an island and choose the correct number to complete the list. The middle level has the student clicking on the number of each animal as shown in the bar graph. The hardest level requires students to interpret the data displayed in the bar graph. A worksheet is included in PDF format to be used for student work.

2011-01-01

217

Poetic Waves: Angel Island  

NSDL National Science Digital Library

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 ÂÂthere is no direct connection between them except for the languages, the time period, and place. 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.

2005-01-01

218

Islands of the Arctic  

NASA Astrophysics Data System (ADS)

Few environments on Earth are changing more dramatically than the Arctic. Sea ice retreat and thinning is unprecedented in the period of the satellite record. Surface air temperatures are the warmest in centuries. The biology of Arctic lakes is changing like never before in millennia. Everything is pointing to the meltdown predicted by climate model simulations for the next 100 years. At the same time, the Arctic remains one of the most pristine and beautiful places on Earth. For both those who know the Arctic and those who want to know it, this book is worth its modest price. There is much more to the Arctic than its islands, but there's little doubt that Greenland and the major northern archipelagos can serve as a great introduction to the environment and magnificence of the Arctic. The book uses the islands of the Arctic to give a good introduction to what the Arctic environment is all about. The first chapter sets the stage with an overview of the geography of the Arctic islands, and this is followed by chapters that cover many key aspects of the Arctic: the geology (origins), weather and climate, glaciers, ice sheets, sea ice, permafrost and other frozen ground issues, coasts, rivers, lakes, animals, people, and environmental impacts. The material is pitched at a level well suited for the interested layperson, but the book will also appeal to those who study the science of the Arctic.

Overpeck, Jonathan

2004-02-01

219

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

Microsoft Academic Search

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,

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

220

Genomic Adaptation of the Lactobacillus casei Group.  

PubMed

Lactobacillus casei, L. paracasei, and L. rhamnosus form a closely related taxonomic group (Lactobacillus casei group) within the facultatively heterofermentative lactobacilli. Here, we report the complete genome sequences of L. paracasei JCM 8130 and L. casei ATCC 393, and the draft genome sequence of L. paracasei COM0101, all of which were isolated from daily products. Furthermore, we re-annotated the genome of L. rhamnosus ATCC 53103 (also known as L. rhamnosus GG), which we have previously reported. We confirmed that ATCC 393 is distinct from other strains previously described as L. paracasei. The core genome of 10 completely sequenced strains of the L. casei group comprised 1,682 protein-coding genes. Although extensive genome-wide synteny was found among the L. casei group, the genomes of ATCC 53103, JCM 8130, and ATCC 393 contained genomic islands compared with L. paracasei ATCC 334. Several genomic islands, including carbohydrate utilization gene clusters, were found at the same loci in the chromosomes of the L. casei group. The spaCBA pilus gene cluster, which was first identified in GG, was also found in other strains of the L. casei group, but several L. paracasei strains including COM0101 contained truncated spaC gene. ATCC 53103 encoded a higher number of proteins involved in carbohydrate utilization compared with intestinal lactobacilli, and extracellular adhesion proteins, several of which are absent in other strains of the L. casei group. In addition to previously fully sequenced L. rhamnosus and L. paracasei strains, the complete genome sequences of L. casei will provide valuable insights into the evolution of the L. casei group. PMID:24116025

Toh, Hidehiro; Oshima, Kenshiro; Nakano, Akiyo; Takahata, Muneaki; Murakami, Masaru; Takaki, Takashi; Nishiyama, Hidetoshi; Igimi, Shizunobu; Hattori, Masahira; Morita, Hidetoshi

2013-10-08

221

Genomic Adaptation of the Lactobacillus casei Group  

PubMed Central

Lactobacillus casei, L. paracasei, and L. rhamnosus form a closely related taxonomic group (Lactobacillus casei group) within the facultatively heterofermentative lactobacilli. Here, we report the complete genome sequences of L. paracasei JCM 8130 and L. casei ATCC 393, and the draft genome sequence of L. paracasei COM0101, all of which were isolated from daily products. Furthermore, we re-annotated the genome of L. rhamnosus ATCC 53103 (also known as L. rhamnosus GG), which we have previously reported. We confirmed that ATCC 393 is distinct from other strains previously described as L. paracasei. The core genome of 10 completely sequenced strains of the L. casei group comprised 1,682 protein-coding genes. Although extensive genome-wide synteny was found among the L. casei group, the genomes of ATCC 53103, JCM 8130, and ATCC 393 contained genomic islands compared with L. paracasei ATCC 334. Several genomic islands, including carbohydrate utilization gene clusters, were found at the same loci in the chromosomes of the L. casei group. The spaCBA pilus gene cluster, which was first identified in GG, was also found in other strains of the L. casei group, but several L. paracasei strains including COM0101 contained truncated spaC gene. ATCC 53103 encoded a higher number of proteins involved in carbohydrate utilization compared with intestinal lactobacilli, and extracellular adhesion proteins, several of which are absent in other strains of the L. casei group. In addition to previously fully sequenced L. rhamnosus and L. paracasei strains, the complete genome sequences of L. casei will provide valuable insights into the evolution of the L. casei group.

Nakano, Akiyo; Takahata, Muneaki; Murakami, Masaru; Takaki, Takashi; Nishiyama, Hidetoshi; Igimi, Shizunobu; Hattori, Masahira; Morita, Hidetoshi

2013-01-01

222

Further evidence of an Amerindian contribution to the Polynesian gene pool on Easter Island.  

PubMed

Available evidence suggests a Polynesian origin of the Easter Island population. We recently found that some native Easter Islanders also carried some common American Indian (Amerindian) human leukocyte antigen (HLA) alleles, which probably were introduced before Europeans discovered the island in 1722. In this study, we report molecular genetic investigations of 21 other selected native Easter Islanders. Analysis of mitochondrial DNA and Y chromosome markers showed no traces of an Amerindian contribution. However, high-resolution genomic HLA typing showed that two individuals carried some other common Amerindian HLA alleles, different from those found in our previous investigations. The new data support our previous evidence of an Amerindian contribution to the gene pool on Easter Island. PMID:19493235

Thorsby, E; Flåm, S T; Woldseth, B; Dupuy, B M; Sanchez-Mazas, A; Fernandez-Vina, M A

2009-06-01

223

Characterization of the Genome Composition of Bartonella koehlerae by Microarray Comparative Genomic Hybridization Profiling†  

PubMed Central

Bartonella henselae is present in a wide range of wild and domestic feline hosts and causes cat-scratch disease and bacillary angiomatosis in humans. We have estimated here the gene content of Bartonella koehlerae, a novel species isolated from cats that was recently identified as an agent of human endocarditis. The investigation was accomplished by comparative genomic hybridization (CGH) to a microarray constructed from the sequenced 1.93-Mb genome of B. henselae. Control hybridizations of labeled DNA from the human pathogen Bartonella quintana with a reduced genome of 1.58 Mb were performed to evaluate the accuracy of the array for genes with known levels of sequence divergence. Genome size estimates of B. koehlerae by pulsed-field gel electrophoresis matched that calculated by the CGH, indicating a genome of 1.7 to 1.8 Mb with few unique genes. As in B. quintana, sequences in the prophage and the genomic islands were reported absent in B. koehlerae. In addition, sequence variability was recorded in the chromosome II-like region, where B. koehlerae showed an intermediate retention pattern of both coding and noncoding sequences. Although most of the genes missing in B. koehlerae are also absent from B. quintana, its phylogenetic placement near B. henselae suggests independent deletion events, indicating that host specificity is not solely attributed to genes in the genomic islands. Rather, the results underscore the instability of the genomic islands even within bacterial populations adapted to the same host-vector system, as in the case of B. henselae and B. koehlerae.

Lindroos, Hillevi L.; Mira, Alex; Repsilber, Dirk; Vinnere, Olga; Naslund, Kristina; Dehio, Michaela; Dehio, Christoph; Andersson, Siv G. E.

2005-01-01

224

Island induced bootstrap current on island dynamics in tokamaks  

NASA Astrophysics Data System (ADS)

When a magnetic island is imbedded in toroidally symmetric tokamaks, the toroidal symmetry in |B| is broken. Here, B is the magnetic field. This broken symmetry induces an additional bootstrap current density in the vicinity of the island. It is illustrated that this island induced bootstrap current density modifies the island evolution equation and imposes a lower limit on the absolute value of the tearing mode stability parameter | | for the island to be unstable. This lower limit depends on the local poloidal plasma beta, the ratio of the plasma pressure to the poloidal magnetic field pressure. If is high enough, the magnetic island is stable or, in other words, self-healing. The theory provides an explanation as to why an m = 2 island is not as commonly observed as m =3, 4, or 5 island in tokamaks. Here, m is the poloidal mode number. This mechanism also indicates an alternative route to stabilize the island in the long mean-free-path regime.

Land, I. S.

2005-10-01

225

Complete nucleotide sequence analysis of a Dengue-1 virus isolated on Easter Island, Chile.  

PubMed

Dengue-1 viruses responsible for the dengue fever outbreak in Easter Island in 2002 were isolated from acute-phase sera of dengue fever patients. In order to analyze the complete genome sequence, we designed primers to amplify contiguous segments across the entire sequence of the viral genome. RT-PCR products obtained were cloned, and complete nucleotide and deduced amino acid sequences were determined. This report constitutes the first complete genetic characterization of a DENV-1 isolate from Chile. Phylogenetic analysis shows that an Easter Island isolate is most closely related to Pacific DENV-1 genotype IV viruses. PMID:18815724

Cáceres, C; Yung, V; Araya, P; Tognarelli, J; Villagra, E; Vera, L; Fernández, J

2008-09-25

226

Genome databases  

SciTech Connect

Since the Genome Project began several years ago, a plethora of databases have been developed or are in the works. They range from the massive Genome Data Base at Johns Hopkins University, the central repository of all gene mapping information, to small databases focusing on single chromosomes or organisms. Some are publicly available, others are essentially private electronic lab notebooks. Still others limit access to a consortium of researchers working on, say, a single human chromosome. An increasing number incorporate sophisticated search and analytical software, while others operate as little more than data lists. In consultation with numerous experts in the field, a list has been compiled of some key genome-related databases. The list was not limited to map and sequence databases but also included the tools investigators use to interpret and elucidate genetic data, such as protein sequence and protein structure databases. Because a major goal of the Genome Project is to map and sequence the genomes of several experimental animals, including E. coli, yeast, fruit fly, nematode, and mouse, the available databases for those organisms are listed as well. The author also includes several databases that are still under development - including some ambitious efforts that go beyond data compilation to create what are being called electronic research communities, enabling many users, rather than just one or a few curators, to add or edit the data and tag it as raw or confirmed.

Courteau, J.

1991-10-11

227

Late colonization of Easter Island.  

PubMed

Easter Island (Rapa Nui) provides a model of human-induced environmental degradation. A reliable chronology is central to understanding the cultural, ecological, and demographic processes involved. Radiocarbon dates for the earliest stratigraphic layers at Anakena, Easter Island, and analysis of previous radiocarbon dates imply that the island was colonized late, about 1200 A.D. Substantial ecological impacts and major cultural investments in monumental architecture and statuary thus began soon after initial settlement. PMID:16527931

Hunt, Terry L; Lipo, Carl P

2006-03-09

228

Alternative energy technologies for the Caribbean islands  

Microsoft Academic Search

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

Pytlinski

1992-01-01

229

Polyfaceted Psychological Acculturation in Cook Islanders  

Microsoft Academic Search

Data on acculturation were collected from five groups of Cook Islanders who have been differentially exposed to traditional and Western (New Zealand) influences: Residents of a small, outer island; residents of the much larger capital island; Cook Islanders who have migrated to New Zealand, and others who were born in New Zealand; and non-Cook Island New Zealanders. Comparison of the

John Altrocchi; Laurel Altrocchi

1995-01-01

230

Listeria Genomics  

NASA Astrophysics Data System (ADS)

The opportunistic intracellular foodborne pathogen Listeria monocytogenes has become a paradigm for the study of host-pathogen interactions and bacterial adaptation to mammalian hosts. Analysis of L. monocytogenes infection has provided considerable insight into how bacteria invade cells, move intracellularly, and disseminate in tissues, as well as tools to address fundamental processes in cell biology. Moreover, the vast amount of knowledge that has been gathered through in-depth comparative genomic analyses and in vivo studies makes L. monocytogenes one of the most well-studied bacterial pathogens. This chapter provides an overview of progress in the exploration of genomic, transcriptomic, and proteomic data in Listeria spp. to understand genome evolution and diversity, as well as physiological aspects of metabolism used by bacteria when growing in diverse environments, in particular in infected hosts.

Cabanes, Didier; Sousa, Sandra; Cossart, Pascale

231

15. New York Connecting Railroad: Wards Island Viaduct. Wards Island, ...  

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

15. New York Connecting Railroad: Wards Island Viaduct. Wards Island, New York Co., NY. Sec. 4207, MP 7.65. - Northeast Railroad Corridor, Amtrak Route between New Jersey/New York & New York/Connecticut State Lines, New York, New York County, NY

232

Rain on small tropical islands  

NASA Astrophysics Data System (ADS)

A high-resolution rainfall climatology based on observations from the Tropical Rainfall Measuring Mission's Precipitation Radar (PR) instrument is used to evaluate the influence of small tropical islands on climatological rainfall. Islands with areas between one hundred and several thousand km2 are considered in both the Indo-Pacific Maritime Continent and Caribbean regions. Annual mean climatological (1997-2007) rainfall over each island is compared with that over the surrounding ocean region, and the difference is expressed as a percentage. In addition to total rainfall, rain frequency and intensity are also analyzed. Results are stratified into two 12 h halves of the diurnal cycle as well as eight 3 h periods, and also by a measure of each island's topographic relief. In both regions, there is a clear difference between larger islands (areas of a few hundred km2 or greater) and smaller ones. Both rain frequency and total rainfall are significantly enhanced over larger islands compared to the surrounding ocean. For smaller islands the enhancement is either negligibly small, statistically insignificant, or, in the case of Caribbean rain frequency, negative. The enhancement in total rainfall over larger islands is partly attributable to greater frequency and partly to greater intensity. A diurnal cycle in island enhancement is evident in frequency but not intensity, except over small Caribbean islands where the converse is true. For the larger islands, higher orography is associated with greater rainfall enhancements. The orographic effect is larger (percentagewise) in the Caribbean than in the Maritime Continent. Orographic precipitation enhancement manifests more strongly as increased frequency of precipitation rather than increased intensity and is present at night as well as during the day. The lack of a clear diurnal cycle in orographic enhancement suggests that much of the orographic rainfall enhancement is attributable to mechanically forced upslope flow rather than elevated surface heating.

Sobel, A. H.; Burleyson, C. D.; Yuter, S. E.

2011-04-01

233

Genomics of Transposable Elements in the Triticeae  

Microsoft Academic Search

Triticeae genomes are structured as blocks of relatively gene-dense “islands” surrounded by long expanses of repetitive DNA.\\u000a Most of the repetitive DNA is comprised of transposable elements; the greatest bulk of these are the Class I, or retrotransposons,\\u000a which transpose via an RNA intermediate. The remainder is Class II DNA transposons, which move by a “cut-and-paste” mechanism.\\u000a The LTR retrotransposons,

François Sabot; Alan H. Schulman

234

Genome Sequence and Comparative Genome Analysis of Lactobacillus casei: Insights into Their Niche-Associated Evolution  

PubMed Central

Lactobacillus casei is remarkably adaptable to diverse habitats and widely used in the food industry. To reveal the genomic features that contribute to its broad ecological adaptability and examine the evolution of the species, the genome sequence of L. casei ATCC 334 is analyzed and compared with other sequenced lactobacilli. This analysis reveals that ATCC 334 contains a high number of coding sequences involved in carbohydrate utilization and transcriptional regulation, reflecting its requirement for dealing with diverse environmental conditions. A comparison of the genome sequences of ATCC 334 to L. casei BL23 reveals 12 and 19 genomic islands, respectively. For a broader assessment of the genetic variability within L. casei, gene content of 21 L. casei strains isolated from various habitats (cheeses, n = 7; plant materials, n = 8; and human sources, n = 6) was examined by comparative genome hybridization with an ATCC 334-based microarray. This analysis resulted in identification of 25 hypervariable regions. One of these regions contains an overrepresentation of genes involved in carbohydrate utilization and transcriptional regulation and was thus proposed as a lifestyle adaptation island. Differences in L. casei genome inventory reveal both gene gain and gene decay. Gene gain, via acquisition of genomic islands, likely confers a fitness benefit in specific habitats. Gene decay, that is, loss of unnecessary ancestral traits, is observed in the cheese isolates and likely results in enhanced fitness in the dairy niche. This study gives the first picture of the stable versus variable regions in L. casei and provides valuable insights into evolution, lifestyle adaptation, and metabolic diversity of L. casei.

Cai, Hui; Thompson, Rebecca; Budinich, Mateo F.; Broadbent, Jeff R.

2009-01-01

235

GENOME MAPPING  

Technology Transfer Automated Retrieval System (TEKTRAN)

Genome maps can be thought of much like road maps except that, instead of traversing across land, they traverse across the chromosomes of an organism. Genetic markers serve as `landmarks¿ along the chromosome and provide researchers information as to how close they may be to a gene or region of int...

236

Invasive Rodent Eradication on Islands  

Microsoft Academic Search

Invasive mammals are the greatest threat to island biodiversity and invasive rodents are likely responsible for the greatest number of extinctions and ecosystem changes. Techniques for eradicating rodents from islands were developed over 2 decades ago. Since that time there has been a significant development and application of this conservation tool. We reviewed the literature on invasive rodent eradications to

GREGG HOWALD; C. JOSH DONLAN; JUAN PABLO GALVÁN; JAMES C. RUSSELL; JOHN PARKES; ARACELI SAMANIEGO; YIWEI WANG; DICK VEITCH; PIERO GENOVESI; MICHEL PASCAL; ALAN SAUNDERS; BERNIE TERSHY

2007-01-01

237

Roosevelt Island Tramway System Assessment.  

National Technical Information Service (NTIS)

The Roosevelt Island Tramway serves as an urban transit system in New York City. The system is based on conventional cable technology and connects a new urban community on Roosevelt Island in the East River to Manhattan. This system is the first urban tra...

C. P. Elms H. H. Hosenthien W. Bamberg W. Voss

1979-01-01

238

Newport Harbor Lighthouse Goat Island  

Microsoft Academic Search

The Newport Harbor Lighthouse may not be the best-known light in Newport Harbor, but its place in history is unchallenged as the first beacon to guide mariners into the bustling Newport of the early 1800s. The lighthouse stands on Goat Island, so named because early Newport residents pastured their goats there, and is known locally as Goat Island Lighthouse. This

Chet Smolski

1971-01-01

239

Erythroblastic islands: niches for erythropoiesis  

Microsoft Academic Search

Erythroblastic islands, the specialized niches in which erythroid precursors pro- liferate, differentiate, and enucleate, were first described 50 years ago by analysis of transmission electron micrographs of bone marrow. These hematopoietic sub- compartments are composed of erythro- blasts surrounding a central macrophage. A hiatus of several decades followed, during which the importance of erythro- blastic islands remained unrecognized as erythroid

Joel Anne Chasis; Narla Mohandas

2008-01-01

240

Genomics and the Evolution of Pathogenic Vibrio cholerae  

Microsoft Academic Search

In this chapter, the complete genome sequence of the human pathogen Vibrio cholerae is examined. We discuss, in particular,\\u000a the level of gene acquisition in the form of pathogenicity and genomic islands within the species, and the role of these elements\\u000a in the various lifestyles of the organism This chapter will highlight the significant role horizontal gene transfer plays\\u000a in

William S. Jermyn; Yvonne A. O’Shea; Anne Marie Quirke; E. Fidelma Boyd

241

Insular Organization of Gene Space in Grass Genomes  

PubMed Central

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.

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

2013-01-01

242

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.

2010-05-12

243

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.

244

Comparative whole-genome mapping to determine Staphylococcus aureus genome size, virulence motifs, and clonality.  

PubMed

Despite being a clonal pathogen, Staphylococcus aureus continues to acquire virulence and antibiotic-resistant genes located on mobile genetic elements such as genomic islands, prophages, pathogenicity islands, and the staphylococcal chromosomal cassette mec (SCCmec) by horizontal gene transfer from other staphylococci. The potential virulence of a S. aureus strain is often determined by comparing its pulsed-field gel electrophoresis (PFGE) or multilocus sequence typing profiles to that of known epidemic or virulent clones and by PCR of the toxin genes. Whole-genome mapping (formerly optical mapping), which is a high-resolution ordered restriction mapping of a bacterial genome, is a relatively new genomic tool that allows comparative analysis across entire bacterial genomes to identify regions of genomic similarities and dissimilarities, including small and large insertions and deletions. We explored whether whole-genome maps (WGMs) of methicillin-resistant S. aureus (MRSA) could be used to predict the presence of methicillin resistance, SCCmec type, and Panton-Valentine leukocidin (PVL)-producing genes on an S. aureus genome. We determined the WGMs of 47 diverse clinical isolates of S. aureus, including well-characterized reference MRSA strains, and annotated the signature restriction pattern in SCCmec types, arginine catabolic mobile element (ACME), and PVL-carrying prophage, PhiSa2 or PhiSa2-like regions on the genome. WGMs of these isolates accurately characterized them as MRSA or methicillin-sensitive S. aureus based on the presence or absence of the SCCmec motif, ACME and the unique signature pattern for the prophage insertion that harbored the PVL genes. Susceptibility to methicillin resistance and the presence of mecA, SCCmec types, and PVL genes were confirmed by PCR. A WGM clustering approach was further able to discriminate isolates within the same PFGE clonal group. These results showed that WGMs could be used not only to genotype S. aureus but also to identify genetic motifs in MRSA that may predict virulence. PMID:22915603

Shukla, Sanjay K; Pantrangi, Madhulatha; Stahl, Buffy; Briska, Adam M; Stemper, Mary E; Wagner, Trevor K; Zentz, Emily B; Callister, Steven M; Lovrich, Steven D; Henkhaus, John K; Dykes, Colin W

2012-08-22

245

Genome Sequence of the Shiga Toxin-Producing Escherichia coli Strain NCCP15657  

PubMed Central

Shiga toxin-producing Escherichia coli causes bloody diarrhea and hemolytic-uremic syndrome and serious outbreaks worldwide. Here, we report the draft genome sequence of E. coli NCCP15657 isolated from a patient. The genome has virulence genes, many in the locus of enterocyte effacement (LEE) island, encoding a metalloprotease, the Shiga toxin, and constituents of type III secretion.

Kim, Byung Kwon; Song, Geun Cheol; Hong, Gun Hyong; Seong, Won-Keun; Kim, Seon-Young; Jeong, Haeyoung; Kang, Sung Gyun; Kwon, Soon-Kyeong; Lee, Choong Hoon; Song, Ju Yeon; Yu, Dong Su; Park, Mi-Sun

2012-01-01

246

Inherent promoter bidirectionality facilitates maintenance of sequence integrity and transcription of parasitic DNA in mammalian genomes  

Microsoft Academic Search

BACKGROUND: Many mammalian genes are arranged in a bidirectional manner, sharing a common promoter and regulatory elements. This is especially true for promoters containing a CpG island, usually unmethylated and associated with an 'open' or accessible chromatin structure. In evolutionary terms, a primary function of genomic methylation is postulated to entail protection of the host genome from the disruption associated

Paul Kalitsis; Richard Saffery

2009-01-01

247

Plastid Genomes  

Microsoft Academic Search

Plastids possess their own genome, the plastome, and a specific machinery to decode its genetic information. The first evidence\\u000a for the presence of heritable material in plastids was reported at the beginning of the last century and was based on observations\\u000a of non-Mendelian inheritance of variegated leaf phenotypes. More than 50 years later, specific plastid-localized DNA was identified.\\u000a The first

R. M. Maier; C. Schmitz-Linneweber

248

Global Collembola on Deception Island  

PubMed Central

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.

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

2012-01-01

249

Inshore Fishes of Howland Island, Baker Island, Jarvis Island, Palmyra Atoll, and Kingman Reef. Atoll Research Bulletin No. 585.  

National Technical Information Service (NTIS)

A list is given of shore fishes known from Howland and Baker Islands, outliers of the Phoenix Islands group, and Jarvis Island, Palmyra Atoll, and Kingman Reef in the Line Islands group. The list was compiled from literature sources, museum collection dat...

B. Greene B. Zgliczynski B. C. Mundy C. Museberger E. Demartini R. Wass R. E. Schroeder

2010-01-01

250

Genomic analysis of ICEVchBan8: An atypical genetic element in Vibrio cholerae  

PubMed Central

Genomic islands (GIs) and integrative conjugative elements (ICEs) are major players in bacterial evolution since they encode genes involved in adaptive functions of medical or environmental importance. Here we performed the genomic analysis of ICEVchBan8, an unusual ICE found in the genome of a clinical non-toxigenic Vibrio cholerae O37 isolate. ICEVchBan8 shares most of its genetic structure with SXT/R391 ICEs. However, this ICE codes for a different integration/excision module is located at a different insertion site, and part of its genetic cargo shows homology to other pathogenicity islands of V. cholerae.

Taviani, Elisa; Spagnoletti, Matteo; Ceccarelli, Daniela; Haley, Bradd J.; Hasan, Nur A.; Chen, Arlene; Colombo, Mauro M.; Huq, Anwar; Colwell, Rita R.

2013-01-01

251

Paleomagnetic study of Deception Island, South Shetland Islands, Antarctica  

Microsoft Academic Search

A paleomagnetic study was carried out on recent volcanic rocks exposed on Deception Island (63.0°S, 60.6°W), Antarctica. Sampling comprised all stratigraphic units exposed on the island, which include basaltic, andesitic and trachytic lavas, basaltic dykes and pyroclastic flows. Following stepwise thermal and alternating field demagnetization procedures, consistent characteristic remanence directions were determined at 21 sites, using principal-component analysis. The overall

Andrés Baraldo; Augusto E. Rapalini; Harald Böhnel; Mabel Mena

2003-01-01

252

Draft Genome Sequence of Salmonella enterica Serovar Typhimurium ST1660/06, a Multidrug-Resistant Clinical Strain Isolated from a Diarrheic Patient  

PubMed Central

Salmonella enterica serovar Typhimurium is one of the most prevalent serovars of Salmonella that causes human gastroenteritis. Here, we report the draft genome sequence of the S. Typhimurium multidrug-resistant strain ST1660/06. Comparative genomic analysis unveiled three strain-specific genomic islands that potentially confer the multidrug resistance and virulence of the strain.

Li, Lei; Cheng, Chi Keung; Cheung, Man Kit; Law, Patrick Tik Wan; Ling, Julia Mei Lun; Kam, Kai Man; Cheung, William Man Wai

2012-01-01

253

Draft Genome Sequences of Helicobacter pylori Strains HPARG63 and HPARG8G, Cultured from Patients with Chronic Gastritis and Gastric Ulcer Disease  

PubMed Central

Helicobacter pylori colonizes the human gastric mucosa, leading to a spectrum of gastric diseases in susceptible populations. Here we announce the draft genome sequences of strains HPARG8G and HPARG63. The data for both genome sequences provide insights regarding the diversity in gene content and rearrangement of the genomic islands commonly harbored by H. pylori.

Armitano, Rita Ines; Zerbetto De Palma, Gerardo; Matteo, Mario Jose; Revale, Santiago; Romero, Soledad; Traglia, German Matias

2013-01-01

254

The Three Mile Island Disaster.  

ERIC Educational Resources Information Center

|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)|

Crosby, Emeral

1980-01-01

255

The Three Mile Island Disaster.  

ERIC Educational Resources Information Center

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)

Crosby, Emeral

1980-01-01

256

America's Islands (Revised April 1974).  

National Technical Information Service (NTIS)

Coastal islands of the United States have been surveyed and charted by the National Ocean Survey, formerly the Coast and Geodetic Survey, for well over a century. This important work is performed pursuant to hydrographic surveying, nautical charting and o...

1974-01-01

257

Synthesizing knowledge of ocean islands  

NASA Astrophysics Data System (ADS)

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.

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

2011-11-01

258

Magnetic island formation in tokamaks  

SciTech Connect

The size of a magnetic island created by a perturbing helical field in a tokamak is estimated. A helical equilibrium of a current- carrying plasma is found in a helical coordinate and the helically flowing current in the cylinder that borders the plasma is calculated. From that solution, it is concluded that the helical perturbation of /approximately/10/sup /minus/4/ of the total plasma current is sufficient to cause an island width of approximately 5% of the plasma radius. 6 refs.

Yoshikawa, S.

1989-04-01

259

Plant fossils from White Island  

Microsoft Academic Search

During the D.S.I.R. expedition to White Island in January 1947, plant fossils were discovered in bedded tuffaceous sands on the south side of the island, about 17 chains north-west of Ohauora Point. On this and other coastal headlands a formation of well bedded tuffaceous sands, locally including water-worn pebbles, is exposed from high-tide level to a height of at least

C. A. Fleming

1963-01-01

260

Functional relevance of CpG island length for regulation of gene expression.  

PubMed

CpG islands mark CpG-enriched regions in otherwise CpG-depleted vertebrate genomes. While the regulatory importance of CpG islands is widely accepted, it is little appreciated that CpG islands vary greatly in lengths. For example, CpG islands in the human genome vary ?30-fold in their lengths. Here we report findings suggesting that the lengths of CpG islands have functional consequences. Specifically, we show that promoters associated with long CpG islands (long-CGI promoters) are distinct from other promoters. First, long-CGI promoters are uniquely associated with genes with an intermediate level of gene expression breadths. Notably, intermediate expression breadths require the most complex mode of gene regulation, from the standpoint of information content. Second, long-CGI promoters encode more RNA polymerase II (Polr2a) binding sites than other promoters. Third, the actual binding patterns of Polr2a occur in a more tissue-specific manner in long-CGI promoters compared to other CGI promoters. Moreover, long-CGI promoters contain the largest numbers of experimentally characterized transcription start sites compared to other promoters, and the types of transcription start sites in them are biased toward tissue-specific patterns of gene expression. Finally, long-CGI promoters are preferentially associated with genes involved in development and regulation. Together, these findings indicate that functionally relevant variations of CpG islands exist. By investigating consequences of certain CpG island traits, we can gain additional insights into the mechanism and evolution of regulatory complexity of gene expression. PMID:21288871

Elango, Navin; Yi, Soojin V

2011-02-01

261

Functional Relevance of CpG Island Length for Regulation of Gene Expression  

PubMed Central

CpG islands mark CpG-enriched regions in otherwise CpG-depleted vertebrate genomes. While the regulatory importance of CpG islands is widely accepted, it is little appreciated that CpG islands vary greatly in lengths. For example, CpG islands in the human genome vary ?30-fold in their lengths. Here we report findings suggesting that the lengths of CpG islands have functional consequences. Specifically, we show that promoters associated with long CpG islands (long-CGI promoters) are distinct from other promoters. First, long-CGI promoters are uniquely associated with genes with an intermediate level of gene expression breadths. Notably, intermediate expression breadths require the most complex mode of gene regulation, from the standpoint of information content. Second, long-CGI promoters encode more RNA polymerase II (Polr2a) binding sites than other promoters. Third, the actual binding patterns of Polr2a occur in a more tissue-specific manner in long-CGI promoters compared to other CGI promoters. Moreover, long-CGI promoters contain the largest numbers of experimentally characterized transcription start sites compared to other promoters, and the types of transcription start sites in them are biased toward tissue-specific patterns of gene expression. Finally, long-CGI promoters are preferentially associated with genes involved in development and regulation. Together, these findings indicate that functionally relevant variations of CpG islands exist. By investigating consequences of certain CpG island traits, we can gain additional insights into the mechanism and evolution of regulatory complexity of gene expression.

Elango, Navin; Yi, Soojin V.

2011-01-01

262

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

PubMed Central

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.

2011-01-01

263

Genome Sequence of Yersinia pestis KIM†  

PubMed Central

We present the complete genome sequence of Yersinia pestis KIM, the etiologic agent of bubonic and pneumonic plague. The strain KIM, biovar Mediaevalis, is associated with the second pandemic, including the Black Death. The 4.6-Mb genome encodes 4,198 open reading frames (ORFs). The origin, terminus, and most genes encoding DNA replication proteins are similar to those of Escherichia coli K-12. The KIM genome sequence was compared with that of Y. pestis CO92, biovar Orientalis, revealing homologous sequences but a remarkable amount of genome rearrangement for strains so closely related. The differences appear to result from multiple inversions of genome segments at insertion sequences, in a manner consistent with present knowledge of replication and recombination. There are few differences attributable to horizontal transfer. The KIM and E. coli K-12 genome proteins were also compared, exposing surprising amounts of locally colinear “backbone,” or synteny, that is not discernible at the nucleotide level. Nearly 54% of KIM ORFs are significantly similar to K-12 proteins, with conserved housekeeping functions. However, a number of E. coli pathways and transport systems and at least one global regulator were not found, reflecting differences in lifestyle between them. In KIM-specific islands, new genes encode candidate pathogenicity proteins, including iron transport systems, putative adhesins, toxins, and fimbriae.

Deng, Wen; Burland, Valerie; Plunkett III, Guy; Boutin, Adam; Mayhew, George F.; Liss, Paul; Perna, Nicole T.; Rose, Debra J.; Mau, Bob; Zhou, Shiguo; Schwartz, David C.; Fetherston, Jaqueline D.; Lindler, Luther E.; Brubaker, Robert R.; Plano, Gregory V.; Straley, Susan C.; McDonough, Kathleen A.; Nilles, Matthew L.; Matson, Jyl S.; Blattner, Frederick R.; Perry, Robert D.

2002-01-01

264

JGI Fungal Genomics Program  

Microsoft Academic Search

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

Grigoriev; Igor V

2011-01-01

265

Genome Characterization Centers  

Cancer.gov

Genomics is a fast-moving field with novel technologies and platforms that help characterize the genome being made available to the research community on a continual basis. The Cancer Genome Atlas (TCGA) Genome Characterization Centers (GCCs) are responsible for characterizing all of the genomic changes found in the tumors studied as part of the TCGA program.

266

Metabolic Syndrome in a Metapopulation of Croatian Island Isolates  

PubMed Central

Aim To investigate the prevalence and factors associated with the metabolic syndrome in 9 isolated populations on Adriatic islands, Croatia, and in the group of immigrants to these islands. Methods Random samples of 100 inhabitants from each village and 101 immigrants were collected during 2002 and 2003. Bivariate and multivariate methods were used in data analysis. Age, gender, village, diet, smoking habits, physical activity, education, occupational class, and personal genetic history (a pedigree-based estimate of the individual genome-wide heterozygosity level) were used as independent variables in logistic regression. Results A total of 343 (34%) examinees met criteria of the metabolic syndrome diagnosis, with significant differences in the prevalence among villages (P?=?0.002). Metabolic syndrome was most frequently detected on Mljet island (53%), where all examinees exhibited fasting plasma glucose over 6.1 mmol/L. Examinees with metabolic syndrome were significantly older than those without it (median age 60.0 vs 53.0; P<0.001). Women were more frequently diagnosed than men (39% vs 28%; P<0.001). The highest prevalence of the metabolic syndrome was found in the autochthonous group, whereas the lowest proportion was recorded in the admixed group (39% vs 21%, respectively, P?=?0.017). However, only age (odds ratio [OR], 1.06; 95% confidence intervals [CI], 1.03-1.08) and having a university degree (OR, 0.18; 95% CI 0.04-0.92) were significantly associated with metabolic syndrome in the regression model. Conclusion Metabolic syndrome was not associated with pedigree-based individual genome-wide heterozygosity estimate, after controlling for a number of confounding factors. More precise marker based genomic measures are needed to provide a clear answer whether metabolic syndrome development is influenced by the population genetic structure.

Kolcic, Ivana; Vorko-Jovic, Ariana; Salzer, Branka; Smoljanovic, Mladen; Kern, Josipa; Vuletic, Silvije

2006-01-01

267

Developing and Applying a Transportation Model for Aquidneck Island, Rhode Island.  

National Technical Information Service (NTIS)

This research project focuses on Aquidneck Island in the State of Rhode Island. The research project has two primary objectives. First, the project builds the foundation for coordinated transportation and land use planning on Aquidneck Island using TransC...

F. Atash K. Woodward J. Boyce S. Eisenbeiser

2004-01-01

268

Bryophytes from Simeonof Island in the Shumagin Islands, southwestern Alaska  

USGS Publications Warehouse

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.

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

2004-01-01

269

Construction of an eco-island: A case study of Chongming Island, China  

Microsoft Academic Search

Chongming Island is the largest alluvial island in the world and is an ecologically sensitive area. It has been planned as a world famous eco-island for future development. Eco-island is a special concept of sustainable development for a small island. This paper explores the applicability of the eco-island concept with respect to six characteristics: integrated ecosystem structure and function, powerful

Baorong Huang; Zhiyun Ouyang; Hua Zheng; Huizhi Zhang; Xiaoke Wang

2008-01-01

270

Evolution of bacterial genomes.  

PubMed

This review examines evolution of bacterial genomes with an emphasis on RNA based life, the transition to functional DNA and small evolving genomes (possible plasmids) that led to larger, functional bacterial genomes. PMID:9111921

Trevors, J T

1997-03-01

271

Structure, Function, and Evolution of the Thiomonas spp. Genome  

PubMed Central

Bacteria of the Thiomonas genus are ubiquitous in extreme environments, such as arsenic-rich acid mine drainage (AMD). The genome of one of these strains, Thiomonas sp. 3As, was sequenced, annotated, and examined, revealing specific adaptations allowing this bacterium to survive and grow in its highly toxic environment. In order to explore genomic diversity as well as genetic evolution in Thiomonas spp., a comparative genomic hybridization (CGH) approach was used on eight different strains of the Thiomonas genus, including five strains of the same species. Our results suggest that the Thiomonas genome has evolved through the gain or loss of genomic islands and that this evolution is influenced by the specific environmental conditions in which the strains live.

Arsene-Ploetze, Florence; Koechler, Sandrine; Marchal, Marie; Coppee, Jean-Yves; Chandler, Michael; Bonnefoy, Violaine; Brochier-Armanet, Celine; Barakat, Mohamed; Barbe, Valerie; Battaglia-Brunet, Fabienne; Bruneel, Odile; Bryan, Christopher G.; Cleiss-Arnold, Jessica; Cruveiller, Stephane; Erhardt, Mathieu; Heinrich-Salmeron, Audrey; Hommais, Florence; Joulian, Catherine; Krin, Evelyne; Lieutaud, Aurelie; Lievremont, Didier; Michel, Caroline; Muller, Daniel; Ortet, Philippe; Proux, Caroline; Siguier, Patricia; Roche, David; Rouy, Zoe; Salvignol, Gregory; Slyemi, Djamila; Talla, Emmanuel; Weiss, Stephanie; Weissenbach, Jean; Medigue, Claudine; Bertin, Philippe N.

2010-01-01

272

Structure, function, and evolution of the Thiomonas spp. genome.  

PubMed

Bacteria of the Thiomonas genus are ubiquitous in extreme environments, such as arsenic-rich acid mine drainage (AMD). The genome of one of these strains, Thiomonas sp. 3As, was sequenced, annotated, and examined, revealing specific adaptations allowing this bacterium to survive and grow in its highly toxic environment. In order to explore genomic diversity as well as genetic evolution in Thiomonas spp., a comparative genomic hybridization (CGH) approach was used on eight different strains of the Thiomonas genus, including five strains of the same species. Our results suggest that the Thiomonas genome has evolved through the gain or loss of genomic islands and that this evolution is influenced by the specific environmental conditions in which the strains live. PMID:20195515

Arsène-Ploetze, Florence; Koechler, Sandrine; Marchal, Marie; Coppée, Jean-Yves; Chandler, Michael; Bonnefoy, Violaine; Brochier-Armanet, Céline; Barakat, Mohamed; Barbe, Valérie; Battaglia-Brunet, Fabienne; Bruneel, Odile; Bryan, Christopher G; Cleiss-Arnold, Jessica; Cruveiller, Stéphane; Erhardt, Mathieu; Heinrich-Salmeron, Audrey; Hommais, Florence; Joulian, Catherine; Krin, Evelyne; Lieutaud, Aurélie; Lièvremont, Didier; Michel, Caroline; Muller, Daniel; Ortet, Philippe; Proux, Caroline; Siguier, Patricia; Roche, David; Rouy, Zoé; Salvignol, Grégory; Slyemi, Djamila; Talla, Emmanuel; Weiss, Stéphanie; Weissenbach, Jean; Médigue, Claudine; Bertin, Philippe N

2010-02-26

273

Genomic species are ecological species as revealed by comparative genomics in Agrobacterium tumefaciens.  

PubMed

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

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

2011-07-27

274

One million served: Rhode Island`s recycling facility  

SciTech Connect

Rhode Island`s landfill and adjacent materials recovery facility (MRF) in Johnston, both owned by the quasi-public Rhode Island Resource Recovery Corp. (RIRRC, Johnston), serve the entire state. The $12-million recycling facility was built in 1989 next to the state`s sole landfill, the Central Landfill, which accepts only in-state trash. The MRF is operated for RIRRC by New England CRInc. (Hampton, N.H.), a unit of Waste Management, Inc. (WMI, Oak Brook, Ill.). It handles a wide variety of materials, from the usual newspaper, cardboard, and mixed containers to new streams such as wood waste, scrap metal, aseptic packaging (milk and juice boxes), and even textiles. State municipalities are in the process of adding many of these new recyclable streams into their curbside collection programs, all of which feed the facility.

Malloy, M.G.

1997-11-01

275

No evidence for biased co-transmission of speciation islands in Anopheles gambiae  

PubMed Central

Genome-scale scans have revealed highly heterogeneous levels of divergence between closely related taxa in many systems. Generally, a small number of regions show high differentiation, with the rest of the genome showing no or only low levels of divergence. These patterns have been interpreted as evidence for ongoing speciation-with-gene-flow, with introgression homogenizing the whole genome except loci involved in reproductive isolation. However, as the number of selected loci increases, the probability of introgression at unselected loci decreases unless there is a transmission ratio distortion causing an over-representation of specific combinations of alleles. Here we examine the transmission of three ‘speciation islands’ that contain fixed differences between the M and S forms of the mosquito, Anopheles gambiae. We made reciprocal crosses between M and S parents and genotyped over 2000 F2 individuals, developing a hierarchical likelihood model to identify specific genotypes that are under- or over-represented among the recombinant offspring. Though our overall results did not match the expected number of F2 genotypes, we found no biased co-transmission among M or S alleles in the three islands. Our likelihood model did identify transmission ratio distortion at two of the three islands, but this distortion was small (approx. 3%) and in opposite directions for the two islands. We discuss how our results impinge on hypotheses of current gene flow between M and S and ongoing speciation-with-gene-flow in this system.

Hahn, Matthew W.; White, Bradley J.; Muir, Christopher D.; Besansky, Nora J.

2012-01-01

276

GenomeViz: visualizing microbial genomes  

Microsoft Academic Search

Background: An increasing number of microbial genomes are being sequenced and deposited in public databases. In addition, several closely related strains are also being sequenced in order to understand the genetic basis of diversity and mechanisms that lead to the acquisition of new genetic traits. These exercises have necessitated the requirement for visualizing microbial genomes and performing genome comparisons on

Rohit Ghai; Torsten Hain; Trinad Chakraborty

2004-01-01

277

Genetic islands of Streptococcus agalactiae strains NEM316 and 2603VR and their presence in other Group B Streptococcal strains  

PubMed Central

Background Streptococcus agalactiae (Group B Streptococcus; GBS) is a major contributor to obstetric and neonatal bacterial sepsis. Serotype III strains cause the majority of late-onset sepsis and meningitis in babies, and thus appear to have an enhanced invasive capacity compared with the other serotypes that cause disease predominantly in immunocompromised pregnant women. We compared the serotype III and V whole genome sequences, strains NEM316 and 2603VR respectively, in an attempt to identify genetic attributes of strain NEM316 that might explain the propensity of strain NEM316 to cause late-onset disease in babies. Fourteen putative pathogenicity islands were described in the strain NEM316 whole genome sequence. Using PCR- and targeted microarray- strategies, the presence of these islands were assessed in a diverse strain collection including 18 colonizing isolates from healthy pregnant women, and 13 and 8 invasive isolates from infants with early- and late-onset sepsis, respectively. Results Side-by-side comparison of the strain NEM316 and strain 2603VR genomes revealed that they are extremely similar, with the only major difference being the capsulation loci and mobile genetic elements. PCR and Comparative Genome Hybridization (CGH) were used to define the presence of each island in 39 GBS isolates. Only islands I, VI, XII, and possibly X, met criteria of a true pathogenicity island, but no significant correlation was found between the presence of any of the fourteen islands and whether the strains were invasive or colonizing. Possible associations were seen between the presence of island VI and late-onset sepsis, and island X and early-onset sepsis, which warrant further investigation. Conclusion The NEM316 and 2603VR strains are remarkable in that their whole genome sequences are so similar, suggesting that the capsulation loci or other genetic differences, such as pathogenicity islands, are the main determinants of the propensity of serotype III strains to cause late-onset disease. This study supports the notion that GBS strain NEM316 has four putative pathogenicity islands, but none is absolutely necessary for disease causation, whether early- or late-onset sepsis. Mobile genetic elements are a common feature of GBS isolates, with each strain having its own peculiar burden of transposons, phages, integrases and integrated plasmids. The majority of these are unlikely to influence the disease capacity of an isolate. Serotype associated disease phenotypes may thus be solely related to differences in the capsulation loci.

Herbert, Mark A; Beveridge, Catriona JE; McCormick, David; Aten, Emmelien; Jones, Nicola; Snyder, Lori AS; Saunders, Nigel J

2005-01-01

278

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.

279

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.

280

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

PubMed Central

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.

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

2012-01-01

281

Genome Sequence of the Melanin-Producing Extremophile Aeromonas salmonicida subsp. pectinolytica Strain 34melT.  

PubMed

The genome of Aeromonas salmonicida subsp. pectinolytica strain 34mel(T), isolated from a heavily polluted river, contains several genomic islands and putative virulence genes. The identification of genes involved in resistance to different kinds of stress sheds light on the mechanisms used by this strain to thrive in an extreme environment. PMID:24029754

Pavan, M Elisa; Pavan, Esteban E; López, Nancy I; Levin, Laura; Pettinari, M Julia

2013-09-12

282

Genome Sequence of the Melanin-Producing Extremophile Aeromonas salmonicida subsp. pectinolytica Strain 34melT  

PubMed Central

The genome of Aeromonas salmonicida subsp. pectinolytica strain 34melT, isolated from a heavily polluted river, contains several genomic islands and putative virulence genes. The identification of genes involved in resistance to different kinds of stress sheds light on the mechanisms used by this strain to thrive in an extreme environment.

Pavan, M. Elisa; Pavan, Esteban E.; Lopez, Nancy I.; Levin, Laura

2013-01-01

283

Establishment of new mutations under divergence and genome hitchhiking  

PubMed Central

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.

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

2012-01-01

284

Genomics, genetic epidemiology, and genomic medicine.  

PubMed

Medical science is on the threshold of unparalleled progress as a result of the advent of genomics and related disciplines. Human genomics, the study of structure, function, and interactions of all genes in the human genome, promises to improve the diagnosis, treatment, and prevention of disease. This opportunity is the result of the recent completion of the Human Genome Project. It is anticipated that genomics will bring to physicians a powerful means to discover hereditary elements that interact with environmental factors leading to disease. However, the expected transformation toward genomics-based medicine will occur over decades. It will require efforts of many scientists and physicians to begin now to sort out the vast amounts of information in the human genome and translate it to meaningful applications in clinical practice. Meanwhile, practicing physicians and health professionals need to be trained in the principles, applications, and limitations of genomics and genomic medicine. Only then will we be in a position to benefit patients, which is the ultimate goal of accelerating scientific progress in medicine. In this inaugural article, we introduce and discuss concepts, facts, and methods of genomics and genetic epidemiology that will be drawn on in the forthcoming topics of the clinical genomics series. PMID:15822036

Lazaridis, Konstantinos N; Petersen, Gloria M

2005-04-01

285

Atoll reef-island formation and response to sea-level change: West Island, Cocos (Keeling) Islands  

Microsoft Academic Search

Reef islands around the margin of coral atolls generally comprise unconsolidated Holocene sands and gravels, overlying a reef flat or cemented conglomerate platform. Such islands have accreted within the last 3000–4000 years, since sea level has reached a level close to present and the reef flat and conglomerate platform have formed. Island morphology consists of an oceanward ridge, a less

C. D Woodroffe; R. F McLean; S. G Smithers; E. M Lawson

1999-01-01

286

Hawaiian Monk Seal on Laysan Island, 1983.  

National Technical Information Service (NTIS)

Data on population size, reproduction, and factors affecting survival were collected on the endangered Hawaiian monk seal, Monachus schauinslandi, on Laysan Island, Northwestern Hawaiian Islands, 23 April to 21 July 1983. Beach counts excluding weaned and...

D. J. Alcorn E. K. Buelna

1989-01-01

287

Cancer and Asians/Pacific Islanders  

MedlinePLUS

... but they are twice as likely to have stomach cancer. Although Asian/Pacific Islander women are 30% less ... are almost three times as likely to have stomach cancer. Both Asian/Pacific Islander men and women have ...

288

Citizens' council protecting Sky Island wildlife corridor  

Treesearch

Pacific Northwest · Pacific Southwest ... Bookmark and Share. Title: Citizens' council protecting Sky Island wildlife corridor ... Connecting mountain islands and desert seas: biodiversity and management of the Madrean Archipelago II. Proc.

289

Recent Algal Stromatolites from the Canary Islands.  

National Technical Information Service (NTIS)

Algal stromatolites (oncolites) occur on the insular shelves of the Canary Islands in the eastern Atlantic. Specimens from an unnamed bank in these islands are made up predominantly of the encrusting nullipore, Goniolithon accretum; vary in size between 0...

R. L. McMaster J. T. Conover

1966-01-01

290

Coordinating Human Services Delivery in Rhode Island.  

National Technical Information Service (NTIS)

This report discusses some theoretical aspects of service delivery coordination in Rhode Island, examines coordination projects undertaken by other States, presents an overview of coordination efforts in Rhode Island, evaluates results of a special survey...

G. J. Beiser

1979-01-01

291

Bidding the CpG island goodbye  

PubMed Central

Experiments on seven vertebrates suggest that identifying the locations of islands of non-methylated DNA provides more insights into evolutionarily-conserved epigenetic regulatory elements than studies of CpG islands.

2013-01-01

292

Instability of Pathogenicity Islands in Uropathogenic Escherichia coli 536  

PubMed Central

The uropathogenic Escherichia coli strain 536 carries at least five genetic elements on its chromosome that meet all criteria characteristic of pathogenicity islands (PAIs). One main feature of these distinct DNA regions is their instability. We applied the so-called island-probing approach and individually labeled all five PAIs of E. coli 536 with the counterselectable marker sacB to evaluate the frequency of PAI-negative colonies under the influence of different environmental conditions. Furthermore, we investigated the boundaries of these PAIs. According to our experiments, PAI II536 and PAI III536 were the most unstable islands followed by PAI I536 and PAI V536, whereas PAI IV536 was stable. In addition, we found that deletion of PAI II536 and PAI III536 was induced by several environmental stimuli. Whereas excision of PAI I536, PAI II536, and PAI V536 was based on site-specific recombination between short direct repeat sequences at their boundaries, PAI III536 was deleted either by site-specific recombination or by homologous recombination between two IS100-specific sequences. In all cases, deletion is thought to lead to the formation of nonreplicative circular intermediates. Such extrachromosomal derivatives of PAI II536 and PAI III536 were detected by a specific PCR assay. Our data indicate that the genome content of uropathogenic E. coli can be modulated by deletion of PAIs.

Middendorf, Barbara; Hochhut, Bianca; Leipold, Kristina; Dobrindt, Ulrich; Blum-Oehler, Gabriele; Hacker, Jorg

2004-01-01

293

Genome evolution in yeasts  

Microsoft Academic Search

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

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

294

Exploring Other Genomes: Bacteria.  

ERIC Educational Resources Information Center

|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)|

Flannery, Maura C.

2001-01-01

295

How can endemic proboscideans help us understand the “island rule”? A case study of Mediterranean islands  

Microsoft Academic Search

Several hypotheses have been advanced to explain size-change processes in terrestrial vertebrates on islands and in island-like ecosystems. Extinct endemic insular proboscideans are especially appropriate subjects for investigating this issue, given the frequency with which proboscideans colonised islands, and the multiple patterns in size reduction experienced by endemic taxa on different islands, as well as on a single one. To

Maria Rita Palombo

2007-01-01

296

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

Federal Register 2010, 2011, 2012, 2013

...Long Island Sound; Manursing Island, NY AGENCY: Coast Guard, DHS. ACTION: Notice...Sound in the vicinity of Manursing Island, NY for a fireworks display. This temporary...Sound in the vicinity of Manursing Island, NY. The proposed safety zone is...

2012-06-12

297

33 CFR 80.720 - St. Simons Island, GA to Amelia Island, FL.  

Code of Federal Regulations, 2010 CFR

...2010-07-01 2010-07-01 false St. Simons Island, GA to Amelia Island, FL. 80.720 Section 80.720 Navigation and... Seventh District § 80.720 St. Simons Island, GA to Amelia Island, FL. (a) A line drawn from St. Simons Light...

2010-07-01

298

33 CFR 80.720 - St. Simons Island, GA to Amelia Island, FL.  

Code of Federal Regulations, 2010 CFR

...2009-07-01 2009-07-01 false St. Simons Island, GA to Amelia Island, FL. 80.720 Section 80.720 Navigation and... Seventh District § 80.720 St. Simons Island, GA to Amelia Island, FL. (a) A line drawn from St. Simons Light...

2009-07-01

299

Virtual Genome Scan: A Tool for Restriction Landmark-Based Scanning of the Human Genome  

PubMed Central

There is substantial interest in implementing technologies that allow comparisons of whole genomes of individuals and of tissues and cell populations. Restriction landmark genome scanning (RLGS) is a highly resolving gel-based technique in which several thousand fragments in genomic digests are visualized simultaneously and quantitatively analyzed. The widespread use of RLGS has been hampered by difficulty in deriving sequence information for displayed fragments and a lack of whole-genome sequence-based framework for interpreting RLGS patterns. We have developed informatics tools for comparisons of sample derived RLGS patterns with patterns predicted from the human genome sequence and displayed as Virtual Genome Scans (VGS). The tools developed allow sequence prediction of fragments in RLGS patterns obtained with different restriction enzyme combinations. The utility of VGS is demonstrated by the identification of restriction fragment length polymorphisms, and of amplifications, deletions, and methylation changes in tumor-derived CpG islands and the characterization of an amplified region in a breast tumor that spanned <230 kb on 17q23.

Rouillard, Jean-Marie; Erson, Ayse E.; Kuick, Rork; Asakawa, Jun-ichi; Wimmer, Katharina; Muleris, Martine; Petty, Elizabeth M.; Hanash, Samir

2001-01-01

300

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

Code of Federal Regulations, 2010 CFR

...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)....

2010-07-01

301

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

Code of Federal Regulations, 2010 CFR

...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)....

2009-07-01

302

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

Code of Federal Regulations, 2013 CFR

...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)....

2013-07-01

303

Tiber Island in ancient and medieval Rome  

Microsoft Academic Search

Whether formed from an alluvial deposit or from the erosion of a tufa ridge, Tiber Island existed at least as early as the eighth century BC. According to Roman tradition, however, the island was formed only in 509 BC, after the expulsion of the Tarquins. It is probable that this tradition arose from an early taboo placed on the island

Margaret Angela Brucia

1990-01-01

304

Ecology of Great Salt Pond, Block Island  

EPA Science Inventory

Great Salt Pond is an island of estuarine water on Block Island, which sits in the middle of the Northwest Atlantic Continental Shelf. When the last continental glaciers retreated, they left a high spot on a terminal moraine. The rising sea from melting glaciers formed two island...

305

27 CFR 9.170 - Long Island.  

Code of Federal Regulations, 2013 CFR

...section is âLong Island.â (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...

2013-04-01

306

Beneath the Waters of Cocos Island  

NSDL National Science Digital Library

Cocos Island, a remote volcanic summit in the middle of the Pacific Ocean, serves as a beacon for hungry predators, including thousands of hammerhead sharks that travel here each year in search of prey. This video segment from NOVA: "Island of Sharks" depicts some of the common predator-prey interactions that take place in the nutrient-rich waters surrounding the island.

Foundation, Wgbh E.

2009-07-27

307

The island-mainland species turnover relationship  

PubMed Central

Many oceanic islands are notable for their high endemism, suggesting that islands may promote unique assembly processes. However, mainland assemblages sometimes harbour comparable levels of endemism, suggesting that island biotas may not be as unique as is often assumed. Here, we test the uniqueness of island biotic assembly by comparing the rate of species turnover among islands and the mainland, after accounting for distance decay and environmental gradients. We modelled species turnover as a function of geographical and environmental distance for mainland (M–M) communities of Anolis lizards and Terrarana frogs, two clades that have diversified extensively on Caribbean islands and the mainland Neotropics. We compared mainland–island (M–I) and island–island (I–I) species turnover with predictions of the M–M model. If island assembly is not unique, then the M–M model should successfully predict M–I and I–I turnover, given geographical and environmental distance. We found that M–I turnover and, to a lesser extent, I–I turnover were significantly higher than predicted for both clades. Thus, in the first quantitative comparison of mainland–island species turnover, we confirm the long-held but untested assumption that island assemblages accumulate biodiversity differently than their mainland counterparts.

Stuart, Yoel E.; Losos, Jonathan B.; Algar, Adam C.

2012-01-01

308

Ecology and Evolution: Islands of Change.  

ERIC Educational Resources Information Center

This book was designed for middle and junior high school science classes and focuses on island biogeography, ecology, and evolution. Sections include: (1) "Galapagos: Frame of Reference"; (2) "Ecology and Islands"; and (3) "Evolution." Nineteen standards-based activities use the Galapagos Islands as a running theme but are designed to help…

Benz, Richard

309

Economic Impact of Block Island Race Week.  

National Technical Information Service (NTIS)

Block Island, an area of 11 square miles lies 15 miles off the Rhode Island Coast. Biennially since 1965, the Storm Trysail Club of New York has sponsored a week of yacht races at Block Island. The event, which takes place in the third week of June, comes...

J. F. Farrell

1973-01-01

310

Chasing land crabs on Christmas Island  

Microsoft Academic Search

Christmas Island, or 'Kiritimati', is the world's largest coral atoll. It is located in the Line Island group, some 3240 km (2015 miles) from Tarawa, Kiribati's main island. About 4810 people (2002 fig- ures) live scattered around the atoll, mainly in four villages on the eastern side. The atoll covers 575 square km (222 square miles), but land resources are

Mecki Kronen

2007-01-01

311

Water Island Study. Attachment 2. Development Options.  

National Technical Information Service (NTIS)

Attachment 2 of the Water Island Feasibility Study: Development Options, describes the potential uses of the undeveloped lands on Water Island to be examined. The most significant finding of this study for the Government of the Virgin Islands may be that ...

1980-01-01

312

The Foraminifera of the Pitcairn Islands  

Microsoft Academic Search

Foraminifera were recovered from 18 samples collected in the Pitcairn Islands, 12 from Henderson Island (including the best and most comprehensive collections) and three each from Oeno Atoll and Pitcairn Island itself. Although both algae and sediment samples were collected, the living Foraminifera came, almost exclusively, from phytal (attached or clinging) habitats. Foraminifera in the sediment samples are mainly thanatocoenoses.

JOHN E. WHITTAKER; RICHARD L. HODGKINSON

1995-01-01

313

Island wakes in the Southern California Bight  

Microsoft Academic Search

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

R. M. A. Caldeira; P. Marchesiello; N. P. Nezlin; P. M. DiGiacomo; J. C. McWilliams

2005-01-01

314

Ecology and Evolution: Islands of Change.  

ERIC Educational Resources Information Center

|This book was designed for middle and junior high school science classes and focuses on island biogeography, ecology, and evolution. Sections include: (1) "Galapagos: Frame of Reference"; (2) "Ecology and Islands"; and (3) "Evolution." Nineteen standards-based activities use the Galapagos Islands as a running theme but are designed to help…

Benz, Richard

315

Gravity Anomalies in the Galapagos Islands Area.  

National Technical Information Service (NTIS)

In a recent report Case et al, (1973) presented a free-air gravity map of the Galapagos Islands based on 32 gravity stations on the islands. They state that the Galapagos Islands are associated with an east-west trending 'residual negative anomaly' superi...

A. B. Watts J. R. Cochran

1973-01-01

316

The island-mainland species turnover relationship.  

PubMed

Many oceanic islands are notable for their high endemism, suggesting that islands may promote unique assembly processes. However, mainland assemblages sometimes harbour comparable levels of endemism, suggesting that island biotas may not be as unique as is often assumed. Here, we test the uniqueness of island biotic assembly by comparing the rate of species turnover among islands and the mainland, after accounting for distance decay and environmental gradients. We modelled species turnover as a function of geographical and environmental distance for mainland (M-M) communities of Anolis lizards and Terrarana frogs, two clades that have diversified extensively on Caribbean islands and the mainland Neotropics. We compared mainland-island (M-I) and island-island (I-I) species turnover with predictions of the M-M model. If island assembly is not unique, then the M-M model should successfully predict M-I and I-I turnover, given geographical and environmental distance. We found that M-I turnover and, to a lesser extent, I-I turnover were significantly higher than predicted for both clades. Thus, in the first quantitative comparison of mainland-island species turnover, we confirm the long-held but untested assumption that island assemblages accumulate biodiversity differently than their mainland counterparts. PMID:22874754

Stuart, Yoel E; Losos, Jonathan B; Algar, Adam C

2012-08-08

317

Past, Present, Future Erosion at Locke Island  

SciTech Connect

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.

Bjornstad, Bruce N.

2006-08-08

318

Island Explorers Marine Science Program  

NSDL National Science Digital Library

Describes science curriculum facilitated through hands-on marine science activities correlated with the California Science Framework. Curriculum focuses on major ocean concepts and Catalina Island. Program involves overnight field trip to Wrigley Institute. Teacher training component is in development. Two student activities focusing on garibaldi and kelp are available on the site.

319

The Three Mile Island crisis  

Microsoft Academic Search

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

P. S. Houts; P. D. Cleary; T. W. Hu

1988-01-01

320

Three Mile Island population registry  

Microsoft Academic Search

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

M. K. Goldhaber; G. K. Tokuhata; E. Digon; G. G. Caldwell; G. F. Stein; G. Lutz; D. Gur

2009-01-01

321

ITURUP AND SAKHALIN ISLAND STRAWBERRIES  

Technology Transfer Automated Retrieval System (TEKTRAN)

A plant collecting expedition to Iturup and Sakhalin Islands, Russian Federation, occurred between 21 July and 12 September 2003. Actinidia, Rubus, Ribes, and Vaccinium, as well as seven accessions of strawberries, Fragaria L., were collected. Among them, a wild strawberry, Fragaria iturupensis Stau...

322

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...

323

Impact of Three Mile Island  

Microsoft Academic Search

The decline of nuclear power began before the 1979 accident at Three Mile Island. The primary reason for deflation afflicting the nuclear industry is the oil price increase followed by other fuel price increases. These, along with the associated effects of conservation and increased energy productivity has led to reduced growth in electricity use and thus to reduced demand forecasts.

Gilinsky

1980-01-01

324

Magdalen Islands VAWT field test  

Microsoft Academic Search

In the spring of 1977, an experimental large vertical axis wind turbine (VAWT) was installed in the Magdalen Islands. The main objectives of the project are installation, operation and evaluation of the VAWT. The turbine has been operated at up to about 80 percent of design rpm. The information presented includes data from some of the 31 rpm tests which

P. South; A. Watts

1979-01-01

325

On a Crowded Desert Island.  

ERIC Educational Resources Information Center

Suggests reference sources most appropriate for a desert island. In addition to "Robinson Crusoe" (Daniel Defoe) and a reference guide to the literature of travel, the list includes basic books on reference work, guides to reference sources, journals, an almanac, encyclopedias, a guide to English usage, and a book of quotations. (14 references)…

Rothstein, Samuel

1989-01-01

326

Long Island Sound Resource Center  

NSDL National Science Digital Library

The Resource Center is a central clearinghouse for an ongoing web project to provide access to information and data related to the Long Island Sound. Visitors can learn about scientific research, access data, view interactive maps, search literature related to the Sound, browse a directory of organizations and information sources, or look for locations to access the Sound.

327

The Virgin Islands robotic telescope  

NASA Astrophysics Data System (ADS)

The Etelman Observatory of the University of the Virgin Islands is the southernmost and easternmost optical observatory in the United States. The observatory is located at an elevation of 420 meters on the island of St. Thomas, US Virgin Islands. The site has exceptionally good seeing (frequently better than 1 arc-second), dark skies, and the ability to reach deep into the southern hemisphere and to plug the northern-hemisphere longitude gap between the US and Europe. Astronomers at the College of Charleston, South Carolina State University, and the University of the Virgin Islands have formed a consortium to refurbish the facility, conduct detailed site surveys, purchase a 0.5-meter telescope and instrumentation, and operate the facility robotically. The telescope, instrumentation, and dome have all been installed, and we are remotely obtaining commissioning observations. Our operations mode (manual, remote-controlled, or fully robotic) will simultaneously support our research, participation in multi-site campaigns, and the educational and outreach missions of our institutions. Further details are available at http://astro.uvi.edu/.

Neff, J. E.

2004-10-01

328

Chaos in easter island ecology.  

PubMed

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

Sprott, J C

2011-10-01

329

Literacy in the Pacific Islands.  

ERIC Educational Resources Information Center

The post-colonial governments of the Pacific Islands are demanding universal literacy in European languages through the introduced social institutions of education, government, law, and economics. This shift from oral to literate societies is contributing significantly to the erosion of traditional languages and cultures. (Author/MT)

Topping, Donald M.

1987-01-01

330

Genomics and ornithology  

Microsoft Academic Search

Genomics is revolutionizing ornithology in the same ways it is reinvigorating other biological disciplines. In this review,\\u000a I will highlight applications of genomics and genomics technologies to the study of the ecology and evolution of birds, focusing\\u000a specifically on genome evolution, multilocus phylogeography, and gene expression in host–parasite interactions. Genomics is\\u000a providing unprecedented insight into the processes of genetic change

Scott V. Edwards

2007-01-01

331

Characteristics of the tomato nuclear genome as determined by sequencing undermethylated EcoR I digested fragments  

Microsoft Academic Search

A collection of 9,990 single-pass nuclear genomic sequences, corresponding to 5 Mb of tomato DNA, were obtained using methylation filtration (MF) strategy and reduced to 7,053 unique undermethylated genomic islands (UGIs) distributed as follows: (1) 59% non-coding sequences, (2) 28% coding sequences, (3) 12% transposons—96% of which are class I retroelements, and (4) 1% organellar sequences integrated into the nuclear genome

Y. Wang; R. S. van der Hoeven; R. Nielsen; L. A. Mueller; S. D. Tanksley

2005-01-01

332

NotI subtraction and NotI-specific microarrays to detect copy number and methylation changes in whole genomes  

Microsoft Academic Search

Methylation, deletions, and amplifications of cancer genes constitute important mechanisms in carcinogenesis. For genome-wide analysis of these changes, we propose the use of NotI clone microarrays and genomic subtraction, because NotI recognition sites are closely associated with CpG islands and genes. We show here that the CODE (Cloning Of DEleted sequences) genomic subtraction procedure can be adapted to NotI flanking

Jingfeng Li; Alexei Protopopov; Fuli Wang; Vera Senchenko; Valentin Petushkov; Olga Vorontsova; Lev Petrenko; Veronika Zabarovska; Olga Muravenko; Eleonora Braga; Lev Kisselev; Michael I. Lerman; Vladimir Kashuba; George Klein; Ingemar Ernberg; Claes Wahlestedt; Eugene R. Zabarovsky

2002-01-01

333

Nontypeable Haemophilus influenzae Genetic Islands Associated with Chronic Pulmonary Infection  

PubMed Central

Background Haemophilus influenzae (Hi) colonizes the human respiratory tract and is an important pathogen associated with chronic obstructive pulmonary disease (COPD). Bacterial factors that interact with the human host may be important in the pathogenesis of COPD. These factors, however, have not been well defined. The overall goal of this study was to identify bacterial genetic elements with increased prevalence among H. influenzae strains isolated from patients with COPD compared to those isolated from the pharynges of healthy individuals. Methodology/Principal Findings Four nontypeable H. influenzae (NTHi) strains, two isolated from the airways of patients with COPD and two from a healthy individual, were subjected to whole genome sequencing using 454 FLX Titanium technology. COPD strain-specific genetic islands greater than 500 bp in size were identified by in silico subtraction. Open reading frames residing within these islands include known Hi virulence genes such as lic2b, hgbA, iga, hmw1 and hmw2, as well as genes encoding urease and other enzymes involving metabolic pathways. The distributions of seven selected genetic islands were assessed among a panel of 421 NTHi strains of both disease and commensal origins using a Library-on-a-Slide high throughput dot blot DNA hybridization procedure. Four of the seven islands screened, containing genes that encode a methyltransferase, a dehydrogenase, a urease synthesis enzyme, and a set of unknown short ORFs, respectively, were more prevalent in COPD strains than in colonizing strains with prevalence ratios ranging from 1.21 to 2.85 (p?0.0002). Surprisingly, none of these sequences show increased prevalence among NTHi isolated from the airways of patients with cystic fibrosis. Conclusions/Significance Our data suggest that specific bacterial genes, many involved in metabolic functions, are associated with the ability of NTHi strains to survive in the lower airways of patients with COPD.

Zhang, Lixin; Xie, Jingping; Patel, Mayuri; Bakhtyar, Arsala; Ehrlich, Garth D.; Ahmed, Azad; Earl, Josh; Marrs, Carl F.; Clemans, Daniel; Murphy, Timothy F.; Gilsdorf, Janet R.

2012-01-01

334

78 FR 58880 - Safety Zone; Catawba Island Club Wedding Event, Catawba Island Club, Catawba Island, OH  

Federal Register 2010, 2011, 2012, 2013

...safety zone in the waters of Lake Erie in the vicinity of Port Clinton, OH...restrict vessels from a portion of Lake Erie during the fireworks event at Catawba Island...display will be taking place on Lake Erie in the vicinity of Port Clinton,...

2013-09-25

335

Comparative Analysis of the First Complete Enterococcus faecium Genome  

PubMed Central

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.

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

336

Genome Sequence Analyses of Pseudomonas savastanoi pv. glycinea and Subtractive Hybridization-Based Comparative Genomics with Nine Pseudomonads  

PubMed Central

Bacterial blight, caused by Pseudomonas savastanoi pv. glycinea (Psg), is a common disease of soybean. In an effort to compare a current field isolate with one isolated in the early 1960s, the genomes of two Psg strains, race 4 and B076, were sequenced using 454 pyrosequencing. The genomes of both Psg strains share more than 4,900 highly conserved genes, indicating very low genetic diversity between Psg genomes. Though conserved, genome rearrangements and recombination events occur commonly within the two Psg genomes. When compared to each other, 437 and 163 specific genes were identified in B076 and race 4, respectively. Most specific genes are plasmid-borne, indicating that acquisition and maintenance of plasmids may represent a major mechanism to change the genetic composition of the genome and even acquire new virulence factors. Type three secretion gene clusters of Psg strains are near identical with that of P. savastanoi pv. phaseolicola (Pph) strain 1448A and they shared 20 common effector genes. Furthermore, the coronatine biosynthetic cluster is present on a large plasmid in strain B076, but not in race 4. In silico subtractive hybridization-based comparative genomic analyses with nine sequenced phytopathogenic pseudomonads identified dozens of specific islands (SIs), and revealed that the genomes of Psg strains are more similar to those belonging to the same genomospecies such as Pph 1448A than to other phytopathogenic pseudomonads. The number of highly conserved genes (core genome) among them decreased dramatically when more genomes were included in the subtraction, suggesting the diversification of pseudomonads, and further indicating the genome heterogeneity among pseudomonads. However, the number of specific genes did not change significantly, suggesting these genes are indeed specific in Psg genomes. These results reinforce the idea of a species complex of P. syringae and support the reclassification of P. syringae into different species.

Qi, Mingsheng; Wang, Dongping; Bradley, Carl A.; Zhao, Youfu

2011-01-01

337

CpGIF: an algorithm for the identification of CpG islands  

PubMed Central

CpG islands (CGIs) play a fundamental role in genome analysis and annotation, and contribute to improving the accuracy of promoter prediction. Besides, CGIs in promoter regions are abnormally methylated in cancer cells and thus can be used as tumor markers. However, current methods for identifying CGIs suffer from various drawbacks. We present a new algorithm for detecting CGIs, called CpG Island Finder (CpGIF), which combines the best features in the most commonly used algorithms and avoids their disadvantages as much as possible. Five public tools for CpG island searching are used to compare with CpGIF for the assessment of accuracy and computational efficiency. The results reveal that CpGIF has higher performance coefficient and correlation coefficient than these previous methods, which indicates that CpGIF is able to provide high sensitivity and specificity at the same time. CpGIF is also faster than those methods with comparable prediction accuracy.

Sujuan, Ye; Asaithambi, Asai; Liu, Yunkai

2008-01-01

338

Beachrocks from the island of La Palma (Canary Islands, Spain)  

Microsoft Academic Search

Beachrocks on La Palma Island developed on platform-forming lavas of the Cumbre Vieja volcano. Some of these lavas are related to the 1585 (Puerto Naos), 1677 and 1971 (Echentive) eruptions. Radiocarbon dating of the Charco Verde beachrock gives a conventional age of 33?330±490 BP, while that at Playa Chica beach gives a calibrated age of 14?940±525 BP. The beachrocks, up

F. Calvet; M. C. Cabrera; J. C. Carracedo; J. Mangas; F. J. Pérez-Torrado; C. Recio; A. Travé

2003-01-01

339

Island-finding ability of marine turtles.  

PubMed Central

Green turtles (Chelonia mydas) swim from foraging grounds along the Brazilian coast to Ascension Island to nest, over 2200 km distant in the middle of the equatorial Atlantic. To test the hypothesis that turtles use wind-borne cues to locate Ascension Island we found turtles that had just completed nesting and then moved three individuals 50 km northwest (downwind) of the island and three individuals 50 km southeast (upwind). Their subsequent movements were tracked by satellite. Turtles released downwind returned to Ascension Island within 1, 2 and 4 days, respectively. By contrast, those released upwind had far more difficulty in relocating Ascension Island, two eventually returning after 10 and 27 days and the third heading back to Brazil after failing to find its way back to the island. These findings strongly support the hypothesis that wind-borne cues are used by turtles to locate Ascension Island.

Hays, Graeme C; Akesson, Susanne; Broderick, Annette C; Glen, Fiona; Godley, Brendan J; Papi, Floriano; Luschi, Paolo

2003-01-01

340

Magnetic island evolution in hot ion plasmas  

SciTech Connect

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.

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

341

The island rule: made to be broken?  

PubMed Central

The island rule is a hypothesis whereby small mammals evolve larger size on islands while large insular mammals dwarf. The rule is believed to emanate from small mammals growing larger to control more resources and enhance metabolic efficiency, while large mammals evolve smaller size to reduce resource requirements and increase reproductive output. We show that there is no evidence for the existence of the island rule when phylogenetic comparative methods are applied to a large, high-quality dataset. Rather, there are just a few clade-specific patterns: carnivores; heteromyid rodents; and artiodactyls typically evolve smaller size on islands whereas murid rodents usually grow larger. The island rule is probably an artefact of comparing distantly related groups showing clade-specific responses to insularity. Instead of a rule, size evolution on islands is likely to be governed by the biotic and abiotic characteristics of different islands, the biology of the species in question and contingency.

Meiri, Shai; Cooper, Natalie; Purvis, Andy

2007-01-01

342

Three Pathogenicity Islands of Vibrio cholerae Can Excise from the Chromosome and Form Circular Intermediates  

Microsoft Academic Search

Vibrio pathogenicity island-2 (VPI-2) is a 57-kb region integrated at a transfer RNA (tRNA)-serine locus that encompasses VC1758 to VC1809 on the V. cholerae N16961 genome and is present in pandemic isolates. VPI-2 encodes a P4-like integrase, a restriction modification system, a Mu phage-like region, and a sialic acid metabolism region, as well as neuraminidase (VC1784), which is a glycosylhydrolase

Ronan A. Murphy; E. Fidelma Boyd

2008-01-01

343

Genes expression analyses of sea-island cotton ( Gossypium barbadense L.) during fiber development  

Microsoft Academic Search

Sea-island cotton (Gossypium barbadense L.) is one of the most valuable cotton species due to its silkiness, luster, long staples, and high strength, but its fiber\\u000a development mechanism has not been surveyed comprehensively. We constructed a normalized fiber cDNA library (from ?2 to 25 dpa)\\u000a of G. barbadense cv. Pima 3-79 (the genetic standard line) by saturation hybridization with genomic DNA.

Li-Li Tu; Xian-Long Zhang; Shao-Guang Liang; Di-Qiu Liu; Long-Fu Zhu; Fan-Chang Zeng; Yi-Chun Nie; Xiao-Ping Guo; Feng-Lin Deng; Jia-Fu Tan; Li Xu

2007-01-01

344

Unique DNA methylome profiles in CpG island methylator phenotype colon cancers  

PubMed Central

A subset of colorectal cancers was postulated to have the CpG island methylator phenotype (CIMP), a higher propensity for CpG island DNA methylation. The validity of CIMP, its molecular basis, and its prognostic value remain highly controversial. Using MBD-isolated genome sequencing, we mapped and compared genome-wide DNA methylation profiles of normal, non-CIMP, and CIMP colon specimens. Multidimensional scaling analysis revealed that each specimen could be clearly classified as normal, non-CIMP, and CIMP, thus signifying that these three groups have distinctly different global methylation patterns. We discovered 3780 sites in various genomic contexts that were hypermethylated in both non-CIMP and CIMP colon cancers when compared with normal colon. An additional 2026 sites were found to be hypermethylated in CIMP tumors only; and importantly, 80% of these sites were located in CpG islands. These data demonstrate on a genome-wide level that the additional hypermethylation seen in CIMP tumors occurs almost exclusively at CpG islands and support definitively that these tumors were appropriately named. When these sites were examined more closely, we found that 25% were adjacent to sites that were also hypermethylated in non-CIMP tumors. Thus, CIMP is also characterized by more extensive methylation of sites that are already prone to be hypermethylated in colon cancer. These observations indicate that CIMP tumors have specific defects in controlling both DNA methylation seeding and spreading and serve as an important first step in delineating molecular mechanisms that control these processes.

Xu, Yaomin; Hu, Bo; Choi, Ae-Jin; Gopalan, Banu; Lee, Byron H.; Kalady, Matthew F.; Church, James M.; Ting, Angela H.

2012-01-01

345

Pine Island Glacier Calving (WMS)  

NSDL National Science Digital Library

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. This series of images from the MISR instrument on the Terra satellite not only shows the crack expanding and the iceberg breakoff, but the seaward moving glacial flow in the parts of the Pine Island Glacier upstream of the crack.

Perkins, Lori; Mitchell, Horace; Bindschadler, Bob; Diner, Dave

2005-03-09

346

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.

347

Tsunami Forecast for Galapagos Islands  

NASA Astrophysics Data System (ADS)

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.

Renteria, W.

2012-04-01

348

Stranded on a Desert Island  

NSDL National Science Digital Library

In this activity, learners are stranded on a tropical desert island. At an abandoned science lab on the island, they explore the properties of different materials to determine which are best to construct a shelter, boat, and path to aid in their survival. The properties investigated are: magnetism, conductivity, opacity, buoyancy, and elasticity. Learners practice research techniques, must work together, and need to design within constraints. This lesson plan includes definitions of key words, scenario sheet, lab sheets,and handouts. This activity is the third in a four part series of pre/post activities (Matter, Matter, What's the Matter?) created for an exhibit on material science, but can be used on its own.

Houston, Children'S M.

2009-01-01

349

Genome instability in Lactobacillus rhamnosus GG.  

PubMed

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

Sybesma, Wilbert; Molenaar, Douwe; van IJcken, Wilfred; Venema, Koen; Kort, Remco

2013-01-25

350

Genome Instability in Lactobacillus rhamnosus GG  

PubMed Central

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.

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

2013-01-01

351

Integrating sequence, evolution and functional genomics in regulatory genomics  

PubMed Central

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.

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

2009-01-01

352

Urban Heat Islands: Hotter Cities  

NSDL National Science Digital Library

The issue-focused, peer-reviewed article demonstrates how as cities add roads, buildings, industry, and people heat islands are created in urban areas. Some consequences include:human discomfort and sometimes human health risks, increase in energy use, leading to release of more greenhouse gases, air pollution and increased levels of urban ozone, and higher costs because of greater water and energy use.

Urban Heat Islands (University of Western Ontario;)

2004-11-01

353

An Island Made of Ice  

NASA Video Gallery

This time-lapse video shows the calving of an ice island from Greenland's Petermann Glacier and the drifting of the ice down the fjord and southward through Nares Strait. The images were captured between July 9 and September 13, 2012, by NASA's Terra and Aqua earth-observing satellites. This is the second time in three years that a city-sized hunk of ice has ripped off from the glacier. Credit: NASA's Earth Observatory > Related story > Download high-res video

gsfcvideo

2012-10-17

354

Flora of the Marquesas Islands  

NSDL National Science Digital Library

This Web site from the Smithsonian Institution's Department of Systematic Biology offers online access to taxonomic and geographical information on the vascular plants of the Marquesas Islands. An easy-to-use search tool retrieves plant checklists, which include species distribution and status information. Other features of this well-presented Web site include a searchable image gallery, curatorial information on collected specimens, a general account of the Marquesas, and some gorgeous panoramic photos. Look for additional features as the site develops.

355

Structural genomics: beyond the Human Genome Project  

Microsoft Academic Search

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

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

356

Phytophthora genomics: the plant destroyers' genome decoded  

Microsoft Academic Search

The year 2004 was an exciting one for the Phytophthora research community. The United States Department of Energy Joint Genome Institute (JGI) completed the draft genome sequence of two Phytophthora species, Phytophthora sojae and Phytophthora ramorum. In August of that year over 50 people gathered at JGI in Walnut Creek, California, for an annotation jamboree and searched for the secrets

Francine Govers; Mark Gijzen

2006-01-01

357

The Roanoke Island Freedmen's Colony  

NSDL National Science Digital Library

During the Civil War, Roanoke Island, located between the coast of North Carolina and the Outer Banks, became a refuge for escaped slaves, called contrabands or freedmen. This site, created by University of Virginia professor Patricia C. Click presents an account of the history and selected documents and maps of the Roanoke Island Freedmens Colony, as the community was known. Documents include letters from Superintendent of the Colony, Horace James, a minister and abolitionist from Massachusetts, and letters from Freedmen themselves. The documents have been transcribed and are in .pdf format, so users should not expect to see scanned versions of 19th century originals. The projects section includes seven projects for high school and college students, using historical materials at the site, and from other related Web sites. Professor Click has written a book, Time Full of Trial: The Roanoke Island FreedmenÂs Colony, 1862-1867, and the Preview section contains the table of contents and Chapter One. Links in the site refer to this book for more information; in the Maps section users are referred to its online ordering instructions for more information on the layout of the colony.

Click, Patricia C.

2001-01-01

358

Dense water formation around islands  

NASA Astrophysics Data System (ADS)

Basic constraints on the dense water formation rate and circulation resulting from cooling around an island are discussed. The domain under consideration consists of an island surrounded by a shelf, a continental slope, and a stratified ocean. Atmospheric cooling over the shelf forms a dense water that penetrates down the sloping bottom into the stratified basin. Strong azimuthal flows are generated over the sloping bottom as a result of thermal wind. Thermally direct and indirect mean overturning cells are also forced over the slope as a result of bands of convergent and divergent Reynolds stresses associated with the jets. The Coriolis force associated with the net mass flux into the downwelling region over the slope is balanced by these nonlinear terms, giving rise to a fundamentally different momentum budget than arises in semienclosed marginal seas subject to cooling. A similar momentum balance is found for cases with canyons and ridges around the island provided that the terms are considered in a coordinate system that follows the topography. Both eddy fluxes and the mean overturning cells are important for the radial heat flux, although the eddy fluxes typically dominate. The properties of the dense water formed over the shelf (temperature, diapycnal mass flux) are predicted well by application of baroclinic instability theory and simple heat and mass budgets. It is shown that each of these quantities depends only on a nondimensional number derived from environmental parameters such as the shelf depth, Coriolis parameter, offshore temperature field, and atmospheric forcing.

Spall, Michael A.

2013-05-01

359

Erythroblastic islands: niches for erythropoiesis  

PubMed Central

Erythroblastic islands, the specialized niches in which erythroid precursors proliferate, differentiate, and enucleate, were first described 50 years ago by analysis of transmission electron micrographs of bone marrow. These hematopoietic subcompartments are composed of erythroblasts surrounding a central macrophage. A hiatus of several decades followed, during which the importance of erythroblastic islands remained unrecognized as erythroid progenitors were shown to possess an autonomous differentiation program with a capacity to complete terminal differentiation in vitro in the presence of erythropoietin but without macrophages. However, as the extent of proliferation, differentiation, and enucleation efficiency documented in vivo could not be recapitulated in vitro, a resurgence of interest in erythroid niches has emerged. We now have an increased molecular understanding of processes operating within erythroid niches, including cell-cell and cell-extracellular matrix adhesion, positive and negative regulatory feedback, and central macrophage function. These features of erythroblast islands represent important contributors to normal erythroid development, as well as altered erythropoiesis found in such diverse diseases as anemia of inflammation and chronic disease, myelodysplasia, thalassemia, and malarial anemia. Coupling of historical, current, and future insights will be essential to understand the tightly regulated production of red cells both in steady state and stress erythropoiesis.

Mohandas, Narla

2008-01-01

360

Genome sequence of Idiomarina xiamenensis type strain 10-D-4.  

PubMed

Idiomarina xiamenensis strain 10-D-4(T) was isolated from an oil-degrading consortium enriched from surface seawater around the Xiamen island. Here, we present the draft genome of strain 10-D-4(T), which contains 2,899,282 bp with a G+C content of 49.48% and contains 2,673 protein-coding genes and 43 tRNA genes. PMID:23209204

Lai, Qiliang; Wang, Liping; Wang, Wanpeng; Shao, Zongze

2012-12-01

361

A species-generalized probabilistic model-based definition of CpG islands  

PubMed Central

The DNA of most vertebrates is depleted in CpG dinucleotides, the target for DNA methylation. The remaining CpGs tend to cluster in regions referred to as CpG islands (CGI). CGI have been useful as marking functionally relevant epigenetic loci for genome studies. For example, CGI are enriched in the promoters of vertebrate genes and thought to play an important role in regulation. Currently, CGI are defined algorithmically as an observed-to-expected ratio (O/E) of CpG greater than 0.6, G+C content greater than 0.5, and usually but not necessarily greater than a certain length. Here we find that the current definition leaves out important CpG clusters associated with epigenetic marks, relevant to development and disease, and does not apply at all to nonvertabrate genomes. We propose an alternative Hidden Markov model-based approach that solves these problems. We fit our model to genomes from 30 species, and the results support a new epigenomic view toward the development of DNA methylation in species diversity and evolution. The O/E of CpG in islands and nonislands segregated closely phylogenetically and showed substantial loss in both groups in animals of greater complexity, while maintaining a nearly constant difference in CpG O/E between islands and nonisland compartments. Lists of CGI for some species are available at http://www.rafalab.org.

Irizarry, Rafael A.; Wu, Hao; Feinberg, Andrew P.

2010-01-01

362

Researchers Compare Anthrax Genomes  

NSF Publications Database

... 703) 292-8440 mhenkart@nsf.gov Researchers Compare Anthrax Genomes In a pioneering use of genomics ... In the recent TIGR study, the scientists compared information gained from a previous investigation ...

363

Genomic Selection at CRV  

Microsoft Academic Search

CRV implemented genomic selection in 2006 and currently uses it in its breeding programs in the Netherlands\\/Flanders and New Zealand. Genomic predictions are combined with national breeding values and subsequently published.

A. P. W. de Roos; C. Schrooten; E. Mullaart; S. van der Beek; G. de Jong; W. Voskamp

364

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.

365

Automated Microfluidics for Genomics.  

National Technical Information Service (NTIS)

The Genomation Laboratory at the University of Washington is developing an automated fluid handling system called 'Acapella' to prepare microliter reactions for genomic analysis. The system prepares 5,000 samples in 8 hours for general-purpose chemistry a...

D. R. Meldrum W. H. Pence S. E. Moody D. L. Cunningham M. Holl

2001-01-01

366

Public Health Genomics (PHG)  

Cancer.gov

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

367

De novo methylation of the MyoD1 CpG island during the establishment of immortal cell lines.  

PubMed Central

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

Jones, P A; Wolkowicz, M J; Rideout, W M; Gonzales, F A; Marziasz, C M; Coetzee, G A; Tapscott, S J

1990-01-01

368

De novo methylation of the MyoD1 CpG island during the establishment of immortal cell lines.  

PubMed

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. PMID:2385586

Jones, P A; Wolkowicz, M J; Rideout, W M; Gonzales, F A; Marziasz, C M; Coetzee, G A; Tapscott, S J

1990-08-01

369

Public Health Assessment for Island Chemical Corporation/Virgin Island Chemical Corporation, Christiansted, St. Croix, U.S. Virgin Islands. CERCLIS No. VID980651095.  

National Technical Information Service (NTIS)

The Island Chemical/Virgin Island Chemical site is an inactive facility in the south central portion of St. Croix, U.S. Virgin Islands. Historical operations at the site resulted in contamination by various organic compounds, including chloroform, pyridin...

1998-01-01

370

The island wind buoyancy connection  

NASA Astrophysics Data System (ADS)

A variety of recent studies have suggested that the meridional overturning circulation (MOC) is at least partially controlled by the Southern Ocean (SO) winds. The paradoxical implication is that a link exists between the global surface buoyancy flux to the ocean (which is needed for the density transformation between surface and deep water) and the SO winds. Although the dependency of buoyancy forcing on local wind is obvious, the global forcings are usually viewed independently with regard to their role as drivers of the global ocean circulation. The present idealized study is focused on understanding this wind buoyancy connection. In order to isolate and investigate the effect of SO winds on the overturning we have neglected other important key processes such as SO eddies.We present the wind buoyancy connection in the framework of a single gigantic island that lies between latitude bands free of continents (such as the land mass of the Americas). The unique geometry of a gigantic island on a sphere allows for a clear and insightful examination of the wind buoyancy connection. This is because it enables us to obtain analytical solutions and it circumvents the need to calculate the torque exerted on zonal sills adjacent to the island tips (e.g. the Bering Strait). The torque calculation is notoriously difficult and is avoided here by the clockwise integration, which goes twice through the western boundary of the island (in opposite directions) eliminating any unknown pressure torques.The link between SO winds and global buoyancy forcing is explored qualitatively, using salinity and temperature mixed dynamical-box models and a temperature slab model, and semiquantitatively, employing a reduced gravity model which includes parametrized thermodynamics. Our main finding is that, in all of these cases the island geometry implies that the stratification (and, hence, the air sea heat flux) can always adjust itself to allow the overturning forced by the wind. We find that, in the mixed dynamical-box models, the salinity and temperature differences between the boxes are inversely proportional to the MOC. In spite of the resulting smaller north south temperature difference, the meridional heat transport is enhanced.

de Boer, Agatha M.; Nof, Doron

2005-10-01

371

GenomeComp: a visualization tool for microbial genome comparison.  

PubMed

We have developed a software tool, GenomeComp, for summarizing, parsing and visualizing the genome sequences comparison results derived from voluminous BLAST textual output. With GenomeComp, the variation between genomes can be easily highlighted, such as repeat regions, insertions, deletions and rearrangements of genomic segments. This software provides a new visualizing tool for microbe comparative genomics. PMID:12842490

Yang, Jian; Wang, Jinhua; Yao, Zhi-Jian; Jin, Qi; Shen, Yan; Chen, Runsheng

2003-09-01

372

Mitochondrial genomes of two luminous beetles, Rhagophthalmus lufengensis and R. ohbai (Arthropoda, Insecta, Coleoptera)  

Microsoft Academic Search

We determined the mitochondrial DNA (mtDNA) sequences of two luminous beetles (Arthropoda, Insecta, Coleoptera), Rhagophthalmus lufengensis from Yunnan, China and Rhagophthalmus ohbai from Yaeyama Island, Japan. We identified all the 37 mtDNA genes of R. lufengensis (15,982 bp) and the 34 genes of R. ohbai (15,704 bp). R. lufengensis and R. ohbai genomes have higher A + T contents than other coleopteran genomes

Xueyan Li; Katsunori Ogoh; Nobuyoshi Ohba; Xingcai Liang; Yoshihiro Ohmiya

2007-01-01

373

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

Microsoft Academic Search

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

CHEN Chuan-bo

2005-01-01

374

Highly efficient PCR assay to discriminate allelic DNA methylation status using whole genome amplification  

Microsoft Academic Search

Background  We previously developed a simple method termed HpaII-McrBC PCR (HM-PCR) to discriminate allelic methylation status of the genomic sites of interest, and successfully applied it to\\u000a a comprehensive analysis of CpG islands (CGIs) on human chromosome 21q. However, HM-PCR requires 200 ng of genomic DNA to\\u000a examine one target site, thereby precluding its application to such samples that are limited

Yoichi Yamada; Takashi Ito

2011-01-01

375

Comparative Genomics of Escherichia coli Strains Causing Urinary Tract Infections ? †  

PubMed Central

The virulence determinants of uropathogenic Escherichia coli have been studied extensively over the years, but relatively little is known about what differentiates isolates causing various types of urinary tract infections. In this study, we compared the genomic profiles of 45 strains from a range of different clinical backgrounds, i.e., urosepsis, pyelonephritis, cystitis, and asymptomatic bacteriuria (ABU), using comparative genomic hybridization analysis. A microarray based on 31 complete E. coli sequences was used. It emerged that there is little correlation between the genotypes of the strains and their disease categories but strong correlation between the genotype and the phylogenetic group association. Also, very few genetic differences may exist between isolates causing symptomatic and asymptomatic infections. Only relatively few genes that could potentially differentiate between the individual disease categories were identified. Among these were two genomic islands, namely, pathogenicity island (PAI)-CFT073-serU and PAI-CFT073-pheU, which were significantly more associated with the pyelonephritis and urosepsis isolates than with the ABU and cystitis isolates. These two islands harbor genes encoding virulence factors, such as P fimbriae (pyelonephritis-associated fimbriae) and an important immunomodulatory protein, TcpC. It seems that both urovirulence and growth fitness can be attributed to an assortment of genes rather than to a specific gene set. Taken together, urovirulence and fitness are the results of the interplay of a mixture of factors taken from a rich menu of genes.

Vejborg, Rebecca Munk; Hancock, Viktoria; Schembri, Mark A.; Klemm, Per

2011-01-01

376

Comparative Apicomplexan genomics  

Microsoft Academic Search

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

Arnab Pain; Lisa Crossman; Julian Parkhill

2005-01-01

377

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...

378

COMPARATIVE GENOMICS IN LEGUMES  

Technology Transfer Automated Retrieval System (TEKTRAN)

The legume plant family will soon include three sequenced genomes. The majority of the gene-containing portions of the model legumes Medicago truncatula and Lotus japonicus have been sequenced in clone-by-clone projects, and the sequencing of the soybean genome is underway in a whole-genome shotgun ...

379

Genomics meets HIV1  

Microsoft Academic Search

Genomics is now a core element in the effort to develop a vaccine against HIV-1. Thanks to unprecedented progress in high-throughput genotyping and sequencing, in knowledge about genetic variation in humans, and in evolutionary genomics, it is finally possible to systematically search the genome for common genetic variants that influence the human response to HIV-1. The identification of such variants

David B. Goldstein; Amalio Telenti

2006-01-01

380

Interaction between magnetic island and electrostatic turbulence  

NASA Astrophysics Data System (ADS)

The interaction between electrostatic turbulence and a magnetic island is investigated numerically. The physical model used is a 2-D version of the Hasegawa-Wakatani equations extended to include a curvature term and to account for the presence of a magnetic island. This is the simplest model of electrostatic turbulence that takes into account the effect of magnetic shear. The magnetic curvature makes the model linearly unstable to interchange instability. As a first approximation, it is assumed that the island growth is not affected by the surrounding turbulence since the latter evolves on a much faster time scale. Thus, the model is electrostatic and the island can be treated as a fixed object. The equations are solved numerically in a slab box by using a finite difference, fully implicit code that uses PETSc libraries. The interchange turbulence with and without the magnetic island is compared. In particular, the response of the turbulence to different magnetic island widths and collisionality values is examined.

Militello, Fulvio; Fitzpatrick, Richard; Waelbroeck, Francois

2006-10-01

381

Molluscan fauna of Gueishan Island, Taiwan.  

PubMed

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

Huang, Chih-Wei; Hsiung, Ta-Wei; Lin, Si-Min; Wu, Wen-Lung

2013-01-24

382

Swimming from island to island: healing practice in Tonga.  

PubMed

The health care system of the Pacific island nation of Tonga serves as an example of enduring medical pluralism which incorporates traditional and Western medical practice and accommodates contemporary political and social change. Biomedicine is represented by the hospital and the community health centers; traditional medicine is practiced in homes by healers. Both types of therapies are popularly utilized for different ailments or for the same problem at different points in the illness. Contemporary healing is described and is also analyzed as an expression of social change occurring in Tonga as a result of a political movement toward democracy. PMID:10626277

McGrath, B B

1999-12-01

383

Solar and Atmospheric Radiation Data for Broughton Island, eastern Baffin Island, Canada, 1971-73.  

National Technical Information Service (NTIS)

The three years partial record of radiation for Broughton Island reported here tends to support the thesis already demonstrated elsewhere for other climatological parameters that conditions on the eastern coast of Baffin Island and, implicitly, in Davis S...

J. D. Jacobs

1974-01-01

384

A genome blogger manifesto  

PubMed Central

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.

2012-01-01

385

A genome blogger manifesto.  

PubMed

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

Corpas, Manuel

2012-10-26

386

Social identity in the modern United States Virgin Islands  

Microsoft Academic Search

The United States Virgin Islands (USVI) is a complex society with multiple diverse ethnic groups: Black Virgin Islanders, Eastern Caribbean islanders, Puerto Ricans, Spanish Dominicans, French Islanders, Americans (Continentals), Arabs and Asians. These ethnic differences as well as United States cultural imperialism have stymied any uniform Virgin Islands identity. Even though various ethnic groups share fundamental social characteristics, they nonetheless

Lomarsh Roopnarine

2010-01-01

387

Reading the geography of Sri Lankan island-ness: colonial repetitions, postcolonial possibilities  

Microsoft Academic Search

This article focuses on the cultural dimensions of Sri Lanka's island geography. In particular it argues the importance of regarding the geography of Sri Lankan island-ness as a representational and imaginative trope repetitively and textually inscribed over time. I trace the contours of a topological enclosure that seem so matter-of-fact, natural and characteristic of the Sri Lankan island-state. Inviolability and

Tariq Jazeel

2009-01-01

388

The geomorphology of the Chandeleur Island Wetlands  

SciTech Connect

The Chandeleur Islands represent the largest and oldest transgressive barrier island arc in the northern Gulf of Mexico. Generated by the transgressive submergence of the St. Bernard delta complex, the Chandeleur Islands form the protective geologic framework for one of the richest areas of salt marsh and seagrass flats in Louisiana. The Chandeleur barrier island arc is 60 km long and consists of five individual islands backed by a linear, multiple bar system enclosing a shallow basin floored by extensive seagrass flats. The northern part of the Chandeleur chain is the highest in relief, elevation, width, and habitat diversity. Nonstorm morphology is predominantly a combination of continuous dunes and dune terraces. Numerous washover channels and large washover fans extend into the backbarrier environment. Further south, the island width decreases and washover flats and terraces dominate the shoreline morphology In the southernmost section, the island arc is fragmented into a series of small islands and shoals separated by tidal inlets. Between 1984 and 1989, aerial videotape, aerial photographic, and bathymetric surveys were used to map and monitor the geomorphic changes occurring along the shoreline and in backbarrier areas. The aerial videotape mapping surveys focused on the impacts of hurricanes Danny, Elena, and Juan on the geomorphology of the islands. Videotape imagery was acquired in July 1984 and in July (prestorm), August (post-Danny), September (post-Elena), and November (post-Juan) 1985. A coastal geomorphic classification was developed to map the spatial and temporal landscape changes between surveys.

Debusschere, K.; Penland, S.; Westphal, K. (Louisiana Geological Survey, Baton Rouge (USA)); Handley, L. (Fish and Wildlife Service, Slidell, LA (USA)); Michot, T. (Fish and Wildlife Service, Baton Rouge, LA (USA)); Reed, D.; Seal, R.

1990-09-01

389

Climate change: Effects on reef island resources  

SciTech Connect

The salinity, depth, quantity, and reliability of fresh groundwater resources on coral reef islands and coastlines are environmentally important parameters. Groundwater influences or controls the terrestrial flora, salinity, and nutrient levels in the near-shore benthic environment, the rate and nature of sediment diagenesis, and the density of human habitation. Data from a number of Indo-Pacific reef islands suggest that freshwater inventory is a function of rainfall and island dimensions. A numerical model (SUTRA) has been used to simulate the responses of atoll island groundwater to changes in recharge (precipitation), sea level, and loss of island area due to flooding. The model has been calibrated for Enjebi Island, Enewetak Atoll, where a moderately permeable, water-table aquifer overlies a high-permeability formation. Total freshwater inventory is a monotonic but nonlinear function of recharge. If recharge and island area are constant, rising sea level increases the inventory of fresh water by increasing the useful volume of the aquifer above the high-permeability zone. Flooding of land area reduces the total freshwater inventory approximately in proportion to the loss of recharge area. The most significant results of the model simulation, however, are the findings that the inventory of low-salinity water (and by extrapolation, potable water) is disproportionately sensitive to changes in recharge, island dimensions, or recharge. Island freshwater resources may therefore be unexpectedly vulnerable to climate change.

Oberdorfer, J.A.; Buddemeier, R.W.

1988-06-27

390

Effect of sheared flow on magnetic islands  

SciTech Connect

The effect of sheared flow on a magnetic island is examined. In contrast to the density and temperature gradients which are flattened for sufficiently wide islands, it is found that the velocity gradient persists inside the separatrix whenever the constant-{psi} approximation is satisfied. It follows that velocity shear has a negligible effect on island amplitude in that approximation. The effect of the violation of the constant-{psi} approximation is explored by using the Kelvin-Stuart family of islands, and it is found that flattening is modest even when the separatrix encloses virtually all the current.

Waelbroeck, F. L.; Fitzpatrick, R.; Grasso, Daniela [Institute for Fusion Studies, University of Texas, Austin, Texas 78712 (United States); Burning Plasma Research Group, Department of Energetics, Politecnico di Torino and CNISM, C.so Duca degli Abruzzi 24, 10129 Turin (Italy)

2007-02-15

391

Enabling responsible public genomics.  

PubMed

As scientific understandings of genetics advance, researchers require increasingly rich datasets that combine genomic data from large numbers of individuals with medical and other personal information. Linking individuals' genetic data and personal information precludes anonymity and produces medically significant information--a result not contemplated by the established legal and ethical conventions governing human genomic research. To pursue the next generation of human genomic research and commerce in a responsible fashion, scientists, lawyers, and regulators must address substantial new issues, including researchers' duties with respect to clinically significant data, the challenges to privacy presented by genomic data, the boundary between genomic research and commerce, and the practice of medicine. This Article presents a new model for understanding and addressing these new challenges--a "public genomics" premised on the idea that ethically, legally, and socially responsible genomics research requires openness, not privacy, as its organizing principle. Responsible public genomics combines the data contributed by informed and fully consenting information altruists and the research potential of rich datasets in a genomic commons that is freely and globally available. This Article examines the risks and benefits of this public genomics model in the context of an ambitious genetic research project currently under way--the Personal Genome Project. This Article also (i) demonstrates that large-scale genomic projects are desirable, (ii) evaluates the risks and challenges presented by public genomics research, and (iii) determines that the current legal and regulatory regimes restrict beneficial and responsible scientific inquiry while failing to adequately protect participants. The Article concludes by proposing a modified normative and legal framework that embraces and enables a future of responsible public genomics. PMID:21243847

Conley, John M; Doerr, Adam K; Vorhaus, Daniel B

2010-01-01

392

Crustal Thickness Beneath Ocean Islands  

NASA Astrophysics Data System (ADS)

We measured the thickness of the Earth's crust beneath about two dozen of the GDSN or GEOSCOPE stations located on ocean islands by stacking moveout-corrected high-quality P-to-S receiver functions (RFs). The RFs were filtered in the 0.05-0.5 Hz frequency bands to compress strong noises that are common for ocean island stations. Given the small (less than 2 s) time separation between the direct P and the P-to-S converted phase from the Moho, the PSmS phase, which has a negative polarity and can be clearly observed at almost all the stations, is used for the stacking. Preliminary resulting thickness at each of the stations is as follows: AFI (12.4 km), AIS (13.6), ASCN (9.6), BBSR (9.9), BORG (9.4), CRZF (6.6), GUMO (8.0), HNR (8.0), HOPE (19.0), KIP (13.0), MSEY (10.7), MSVF (15.1), NOUC (15.1), PAF (8.9), POHA (17.0), PPT (12.3), PTCN (10.4), RAR (12.8), RER (13.8), RPN (9.3), SEY (14.9), SHEL (17.5), TBT (14.1), XMAS (11.8). Crustal thickness at some of the stations has been measured previously, and our results are in general agreement with those measurements. Possible age-dependence of the resulting thickness and geological implications in the understanding of plume-lithosphere interactions and formation of ocean islands will be presented.

Gao, S. S.; Liu, K. H.; Cullers, R. L.

2005-12-01

393

Energizing the Island Community: A Review of Policy Standpoints for Renewable Energy in Small Islands  

Microsoft Academic Search

This paper examines public policy towards energy production in small islands. It provides an overview of social and economic obstacles and opportunities affecting the supply of energy. On the whole, small islands tend to have better sources of renewable energy and fewer sources of fossil fuels. Islands tend to rely heavily on imported fossil fuels to generate electricity. Energy production

E. Kathy Stuart

394

Operation Ward's Island, A Guide to the Trees and Other Features of Ward's Island.  

ERIC Educational Resources Information Center

|This guide for teachers, students, and adults illustrates how it is possible to use Ward's Island as an outdoor laboratory. It contains a guide to 30 kinds of trees on the island, along with clearly drawn maps and illustrations. The guide helps the user to locate these trees along two nature trails. A section called "Ward's Island Roundup"…

New York City Board of Education, Brooklyn, NY. Bureau of Curriculum Development.

395

RCN: SEAPRE: Seabird Islands and Introduced Predators: Impacts of Presence and Eradication on Island Function  

Microsoft Academic Search

INTELLECTUAL MERIT: Seabird islands (islands with large populations of seabirds) are crucial to the survival of native animals and plants due to the large subsidies provided by nutrient inputs of marine origin. Seabird predators have devastated seabird populations and drastically altered vegetation processes and ecosystem function all over the world. These predators are now being eradicated on hundreds of islands,

Christa Mulder; Wendy Anderson; Don Croll; Josh Donlan; Julie Ellis; Stephen Kress; Bernie Tershy; Alexander Wait; Peter Bellingham; Robbie McDonald; José Miguel Fariña; Dave Towns; Eric Vidal; David Wardle; Chris Wilcox

396

The Late Holocene Stratigraphy of an Inlet-Dominated Barrier Island, Pea Island, North Carolina  

Microsoft Academic Search

Sedimentological, foraminiferal, geochemical, and geophysical data sets as well as aerial photographs have been used to investigate the natural processes (inlet dynamics, ocean\\/estuarine washover, and sea-level change) responsible for the late Holocene units preserved in the barrier island subsurface at Pea Island National Wildlife Refuge. Historic nautical charts indicate that three inlets characterized Pea Island between early European exploration (1590)

C. G. Smith; D. Ames; D. R. Corbett; S. Culver; D. Mallinson; S. R. Riggs; D. Vance

2002-01-01

397

33 CFR 80.717 - Tybee Island, GA to St. Simons Island, GA.  

Code of Federal Regulations, 2013 CFR

...drawn from the south-westernmost point on Sapelo Island to Wolf Island. (h) A north-south line (longitude 81°17.1ⲠW.) drawn from the south-easternmost point of Wolf Island to the northeasternmost point on Little St. Simons...

2013-07-01

398

Dinosaurs and the island rule: The dwarfed dinosaurs from Ha?eg Island  

Microsoft Academic Search

Islands are fascinating natural laboratories of evolution. One much debated theme among evolutionary ecologists is whether there is an ‘island rule’, the observation that large animals tend to become smaller and small animals larger. Franz Nopcsa was the first, in 1914, to suggest that the latest Cretaceous dinosaurs from Ha?eg, Romania were an island fauna, based on its low diversity

Michael J. Benton; Zoltan Csiki; Dan Grigorescu; Ragna Redelstorff; P. Martin Sander; Koen Stein; David B. Weishampel

2010-01-01

399

Collapse of Easter IslandLessons for Sustainability of Small Islands  

Microsoft Academic Search

The collapse of Easter Island is one of the world's major archeological and anthropological mysteries. Small islands are closed systems, and they represent a microcosm of the planet Earth, which is also a closed system on a planetary scale. Observing and comprehending interconnected economic, social and ecological changes taking place in small islands is relatively straightforward. This article contends that

Palanisamy Nagarajan

2006-01-01

400

The effects of island diffusion and breakup in island growth during ion-beam assisted deposition  

Microsoft Academic Search

In ion-beam assisted deposition (IBAD) island growth is in clear contrast with growth obtained without a bombardment. In this contribution we study the effects of island mobility and island breakup in IBAD by computer simulations. It is shown that during the initial stage of growth a scaling description similar to irreversible growth applies. However, eventually growth attains a quasi-stationary state

M. Rusanen; I. Koponen; J. Heinonen; J. Sillanpää

1999-01-01

401

Spiders from Some Pacific Islands, Part IV The Cook Islands and Niue  

Microsoft Academic Search

THE COOK ISLANDS are a group of small islands in the region of th e central South Pacific bounded by 8°_23° S. and 156°-16r W. They are di visible into two groups, th e northern Cooks which are small ato lls, and the southern Cooks which, wi th one exception , are volcanic islands. Th e sout hern Cooks are

B. J. MARPLES

402

Operation Ward's Island, A Guide to the Trees and Other Features of Ward's Island.  

ERIC Educational Resources Information Center

This guide for teachers, students, and adults illustrates how it is possible to use Ward's Island as an outdoor laboratory. It contains a guide to 30 kinds of trees on the island, along with clearly drawn maps and illustrations. The guide helps the user to locate these trees along two nature trails. A section called "Ward's Island Roundup" briefly…

New York City Board of Education, Brooklyn, NY. Bureau of Curriculum Development.

403

An island approach to industrial ecology: towards sustainability in the island context  

Microsoft Academic Search

Many fields of study have employed geophysical islands in experimental design with a great deal of success. An island is a closed and bounded system in many respects and presents a manageable unit of study. The island microcosm has been the basis for significant advances in areas such as evolutionary biology, ecosystem ecology and physical anthropology. The same properties that

P. J. Deschenes; Marian Chertow

2004-01-01

404

Imagery and Imaginary of Islander Identity: Older People and Migration in Irish Small-Island Communities  

ERIC Educational Resources Information Center

|This article examines the imagery and imaginaries of islander identity and makes an original contribution to the fields of gerontology and nissology. Drawing on data collected through in-depth interviews with 19 older residents of two small-island communities located off the island of Ireland, we address the central roles played by older people…

Burholt, Vanessa; Scharf, Thomas; Walsh, Kieran

2013-01-01

405

Magnesian halotrichite from White Island  

Microsoft Academic Search

A magnesian halotrichite [(Fe0.63Mg0.37).Al2(SO4)4.22H2O] from a fumarole deposit on the active andesitic volcano of White Island, New Zealand, occurs as the major component in the mixture halotrichite—H2S04-H20—alunogen, with accessory gypsum, alunite, anhydrite, quartz, cristo-balite, and tridymite. Optical, physical, and chemical data are given for the halotrichite. K :Na ratios in the alunite (85K:15Na) and in the solution (28K:72Na) show equilibrium

A. D. Cody; T. R. Grammer

1979-01-01

406

Genetic research and aboriginal and Torres Strait Islander Australians.  

PubMed

While human genetic research promises to deliver a range of health benefits to the population, genetic research that takes place in Indigenous communities has proven controversial. Indigenous peoples have raised concerns, including a lack of benefit to their communities, a diversion of attention and resources from non-genetic causes of health disparities and racism in health care, a reinforcement of "victim-blaming" approaches to health inequalities, and possible misuse of blood and tissue samples. Drawing on the international literature, this article reviews the ethical issues relevant to genetic research in Indigenous populations and considers how some of these have been negotiated in a genomic research project currently under way in a remote Aboriginal community. We consider how the different levels of Indigenous research governance operating in Australia impacted on the research project and discuss whether specific guidelines for the conduct of genetic research in Aboriginal and Torres Strait Islander communities are warranted. PMID:23188401

Kowal, Emma; Pearson, Glenn; Peacock, Chris S; Jamieson, Sarra E; Blackwell, Jenefer M

2012-10-12

407

Genome Sequence of Sphingomonas sp. Strain PAMC 26605, Isolated from Arctic Lichen (Ochrolechia sp.)  

PubMed Central

The endosymbiotic bacterium Sphingomonas sp. strain PAMC 26605 was isolated from Arctic lichens (Ochrolechia sp.) on the Svalbard Islands. Here we report the draft genome sequence of this strain, which could provide further insights into the symbiotic mechanism of lichens in extreme environments.

Shin, Seung Chul; Ahn, Do Hwan; Lee, Jong Kyu; Kim, Su Jin; Hong, Soon Gyu; Kim, Eun Hye

2012-01-01

408

Whole-genome shotgun sequencing of the sulfur-oxidizing chemoautotroph Tetrathiobacter kashmirensis.  

PubMed

The chemolithoautotrophic betaproteobacterium Tetrathiobacter kashmirensis belongs to the family Alcaligenaceae and is phylogenetically closely related to pathogens such as Taylorella and Bordetella species. While a complete inorganic sulfur oxidation gene cluster, soxCDYZAXWB, is present in its genome, pathogenicity islands or genes associated with virulence, disease, cellular invasion, and/or intracellular resistance are completely absent. PMID:21914874

Ghosh, Wriddhiman; George, Ashish; Agarwal, Atima; Raj, Praveen; Alam, Masrure; Pyne, Prosenjit; Das Gupta, Sujoy Kumar

2011-10-01

409

Whole-Genome Shotgun Sequencing of the Sulfur-Oxidizing Chemoautotroph Tetrathiobacter kashmirensis  

PubMed Central

The chemolithoautotrophic betaproteobacterium Tetrathiobacter kashmirensis belongs to the family Alcaligenaceae and is phylogenetically closely related to pathogens such as Taylorella and Bordetella species. While a complete inorganic sulfur oxidation gene cluster, soxCDYZAXWB, is present in its genome, pathogenicity islands or genes associated with virulence, disease, cellular invasion, and/or intracellular resistance are completely absent.

Ghosh, Wriddhiman; George, Ashish; Agarwal, Atima; Raj, Praveen; Alam, Masrure; Pyne, Prosenjit; Das Gupta, Sujoy Kumar

2011-01-01

410

Draft Genome Sequence of Pediococcus lolii NGRI 0510QT Isolated from Ryegrass Silage  

PubMed Central

Pediococcus lolii NGRI 0510QT was isolated from ryegrass silage produced on Ishigaki Island, Okinawa Prefecture, Japan. Here we present a draft genome sequence for this strain, consisting of 103 contigs for a total of 2,047,078 bp, 2,154 predicted coding sequences, and a G+C content of 42.1%.

Mori, Kazuki; Tashiro, Kosuke; Fujino, Yasuhiro; Nagayoshi, Yuko; Hayashi, Yoshiharu; Kuhara, Satoru; Ohshima, Toshihisa

2013-01-01

411

Draft Genome Sequence of Pediococcus lolii NGRI 0510Q(T) Isolated from Ryegrass Silage.  

PubMed

Pediococcus lolii NGRI 0510Q(T) was isolated from ryegrass silage produced on Ishigaki Island, Okinawa Prefecture, Japan. Here we present a draft genome sequence for this strain, consisting of 103 contigs for a total of 2,047,078 bp, 2,154 predicted coding sequences, and a G+C content of 42.1%. PMID:23405350

Doi, Katsumi; Mori, Kazuki; Tashiro, Kosuke; Fujino, Yasuhiro; Nagayoshi, Yuko; Hayashi, Yoshiharu; Kuhara, Satoru; Ohshima, Toshihisa

2013-02-07

412

Photocopy of photograph (original located at Mare Island Archives). Original ...  

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

Photocopy of photograph (original located at Mare Island Archives). Original photographer unknown. Isometric drawing, "early plan for Mare Island", 1870. - Mare Island Naval Shipyard, East of Nave Drive, Vallejo, Solano County, CA

413

50 CFR 216.85 - Walrus and Otter Islands.  

Code of Federal Regulations, 2012 CFR

... 2012-10-01 false Walrus and Otter Islands. 216.85 Section 216...Administration § 216.85 Walrus and Otter Islands. By Executive Order 1044, dated February 27, 1909, Walrus and Otter Islands were set aside as bird...

2012-10-01

414

50 CFR 216.85 - Walrus and Otter Islands.  

Code of Federal Regulations, 2010 CFR

... 2009-10-01 false Walrus and Otter Islands. 216.85 Section 216...Administration § 216.85 Walrus and Otter Islands. By Executive Order 1044, dated February 27, 1909, Walrus and Otter Islands were set aside as bird...

2009-10-01

415

50 CFR 216.85 - Walrus and Otter Islands.  

Code of Federal Regulations, 2011 CFR

... 2011-10-01 false Walrus and Otter Islands. 216.85 Section 216...Administration § 216.85 Walrus and Otter Islands. By Executive Order 1044, dated February 27, 1909, Walrus and Otter Islands were set aside as bird...

2011-10-01

416

50 CFR 216.85 - Walrus and Otter Islands.  

Code of Federal Regulations, 2010 CFR

... 2010-10-01 false Walrus and Otter Islands. 216.85 Section 216...Administration § 216.85 Walrus and Otter Islands. By Executive Order 1044, dated February 27, 1909, Walrus and Otter Islands were set aside as bird...

2010-10-01

417

Terrestrial Vertebrate Monitoring, Channel Islands National Park, 1993 Annual Report.  

National Technical Information Service (NTIS)

Terrestrial vertebrate monitoring was begun at Channel Islands National Park during the spring of 1993. Previously developed monitoring protocols for island fox, island deer mice, pacific slender salamanders, and several species of lizard were implemented...

C. A. Schwemm

1995-01-01

418

Perspective overview of Brunot's Island Bridge, looking ENE from west ...  

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

Perspective overview of Brunot's Island Bridge, looking ENE from west bank of Ohio River. - Ohio Connecting Railway, Brunot's Island Bridge, Spanning Ohio River at Brunot's Island, Pittsburgh, Allegheny County, PA

419

7 CFR 503.4 - Conformity with Plum Island regulations.  

Code of Federal Regulations, 2010 CFR

...2010-01-01 false Conformity with Plum Island regulations. 503.4 Section 503...DEPARTMENT OF AGRICULTURE CONDUCT ON PLUM ISLAND ANIMAL DISEASE CENTER § 503.4 Conformity with Plum Island regulations. Persons in and on...

2010-01-01

420

7 CFR 503.4 - Conformity with Plum Island regulations.  

Code of Federal Regulations, 2010 CFR

...2009-01-01 false Conformity with Plum Island regulations. 503.4 Section 503...DEPARTMENT OF AGRICULTURE CONDUCT ON PLUM ISLAND ANIMAL DISEASE CENTER § 503.4 Conformity with Plum Island regulations. Persons in and on...

2009-01-01

421

30 CFR 939.700 - Rhode Island Federal program.  

Code of Federal Regulations, 2010 CFR

... 3 2009-07-01 2009-07-01 false Rhode Island Federal program. 939.700 Section 939...OF SURFACE MINING OPERATIONS WITHIN EACH STATE RHODE ISLAND § 939.700 Rhode Island Federal program. (a) This part...

2009-07-01

422

30 CFR 939.700 - Rhode Island Federal program.  

Code of Federal Regulations, 2010 CFR

... 3 2010-07-01 2010-07-01 false Rhode Island Federal program. 939.700 Section 939...OF SURFACE MINING OPERATIONS WITHIN EACH STATE RHODE ISLAND § 939.700 Rhode Island Federal program. (a) This part...

2010-07-01

423

75 FR 17178 - Rhode Island Disaster #RI-00006  

Federal Register 2010, 2011, 2012, 2013

...Disaster Declaration 12098 and 12099] Rhode Island Disaster RI-00006 AGENCY...declaration of a major disaster for the State of Rhode Island (FEMA-1894-DR), dated 03...Counties (Economic Injury Loans Only): Rhode Island: Bristol. Connecticut: New...

2010-04-05

424

6. Keeper's house, southeast parlor, looking northwest Pumpkin Island ...  

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

6. Keeper's house, southeast parlor, looking northwest - Pumpkin Island Light Station, Pumpkin Island, at northern end of Eggemoggin Beach, off northwest end of Little Deer Island, Eggemoggin, Hancock County, ME

425

33 CFR 80.738 - Puerto Rico and Virgin Islands.  

Code of Federal Regulations, 2013 CFR

...2013-07-01 2013-07-01 false Puerto Rico and Virgin Islands. 80.738 Section...NAVIGATION RULES COLREGS DEMARCATION LINES Puerto Rico and Virgin Islands § 80.738 Puerto Rico and Virgin Islands. (a) Except...

2013-07-01

426

16. Photocopy of illustration from Rattray, Jeannette Edwards, Gardiner's Island, ...  

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

16. Photocopy of illustration from Rattray, Jeannette Edwards, Gardiner's Island, East Hampton, 1958; Photograph by Morton Pennypacker of painting MANOR HOUSE, GARDINER'S ISLAND, 1639 - Gardiner's Island Windmill, Napeague, Suffolk County, NY

427

Rangiferine brucellosis on Baffin Island.  

PubMed

The standard tube agglutination test (STAT) and the complement fixation test (CFT) were used to assess the seroprevalence of antibodies to Brucella spp. in caribou (Rangifer tarandus) from three populations on Baffin Island, Canada. During late winter from 1983 to 1986, sera from 17 of 40 North Baffin (43%), 11 of 33 Northeast Baffin (33%) and 12 of 82 South Baffin (15%) adult caribou had antibodies in the STAT at 1:50 or the CFT at 1:5. Seroprevalence increased as caribou matured with one (4%) of 25 calves, four (13%) of 31 yearlings, and 40 (26%) of 155 adult caribou being positive. However, seroprevalence did not differ with sex in any age class. Positive antibody titers were higher in adult females sampled in May, 3 to 4 wk before parturition, than in adult females sampled in late March and April. The strength of positive titers did not differ with the time of sampling among adult males. Pathologic signs of brucellosis were found in three (13%) of 23 caribou that were assumed to have active infections (caribou with CFT titers > 1:160). Brucella suis biovar 4 was isolated from 24 (60%) of 40 caribou from which lesions were submitted. Between 1986 and 1990, the annual incidence of reported human (Homo sapiens) cases averaged 3.4 (34:100,000) on Baffin Island. PMID:9249700

Ferguson, M A

1997-07-01

428

[Tuberculosis epidemiology in Mayotte Island].  

PubMed

Mayotte is a French territory island, part of the Comoros Archipelago in the Indian Ocean with 200,000 inhabitants. The tuberculosis control program started in 1976, although available epidemiological data remains incomplete. We conducted a retrospective hospital-based survey in 202 outpatients and hospital medical records from the Hospital Centre of the main city to contribute to the epidemiological evaluation of tuberculosis patterns. The tuberculosis frequency remains unchanged since 2000. It affects a young population partly coming from the other neighbouring Comoro Islands (69%) with illegal immigrate status (53% in 2004). The systematic diagnostic screening efficiency of the condition appears marginal. Pulmonary involvement is the most frequent clinical manifestation (78%), although severe extrapulmonary manifestations are not exceptional. Co-infection with HIV and multi resistance to antituberculosis agents are not frequent. Up to 60% of cases have been proven to be bacteriologically linked. The notification rate remains critically low with an estimate of 39% of notifications to the local sanitary authorities in charge of secondary cases screening. The case coverage seems limited both by low socio-economical status and poor health facility accessibility The loss of follow up is dramatically high, 41% on the overall period, and up to 51% in 2004. Our results make mandatory the reinforcement of a tuberculosis survey and control involvement within the context of this French territory. Screening, care and follow up are to be implemented particularly for vulnerable and precarious groups and for patients. PMID:18956814

Woessner, J; Receveur, M C; Malvy, D; Taytard, A

2008-10-01

429

Records of plant viruses for the Pacific Islands  

Microsoft Academic Search

This paper lists the known distribution of 57 plant viruses and viroids in the 22 Pacific Island countries covered by the\\u000a Secretariat of the Pacific Community (American Samoa, Cook Islands, FSM (Micronesia), Fiji, French Polynesia, Guam, Kiribati,\\u000a Marshall Islands, Nauru, New Caledonia, Niue, Northern Mariana Islands, Palau, Papua New Guinea, Pitcairn Islands, Solomon\\u000a Islands, Tokelau, Tonga, Tuvalu, Vanuatu, Wallis and

Michael N. Pearson; Michel Grisoni

2002-01-01

430

Assessing selected natural and anthropogenic impacts on freshwater lens morphology on small barrier Islands: Dog Island and St. George Island, Florida, USA  

Microsoft Academic Search

The freshwater lens morphologies of the barrier islands Dog Island and St. George Island on the panhandle coast of Florida (FL), USA, are controlled to varying degrees by both natural and anthropogenic factors. Variable-density groundwater flow models confirm that spatial variability of recharge values can account for the observed lens asymmetry on these islands. The depth to the base of

James C. Schneider; Sarah E. Kruse

2006-01-01

431

Global features of the Pseudomonas putida KT2440 genome sequence.  

PubMed

The compositional bias of the G+C, di- and tetranucleotide contents in the 6 181 862 bp Pseudomonas putida KT2440 genome was analysed in sliding windows of 4000 bp in steps of 1000 bp. The genome has a low GC skew (mean 0.066) between the leading and lagging strand. The values of GC contents (mean 61.6%) and of dinucleotide relative abundance exhibit skewed Gaussian distributions. The variance of tetranucleotide frequencies, which increases linearly with increasing GC content, shows two overlapping Gaussian distributions of genome sections with low (minor fraction) or high variance (major fraction). Eighty per cent of the chromosome shares similar GC contents and oligonucleotide bias, but 105 islands of 4000 bp or more show atypical GC contents and/or oligonucleotide signature. Almost all islands provide added value to the metabolic proficiency of P. putida as a saprophytic omnivore. Major features are the uptake and degradation of organic chemicals, ion transport and the synthesis and secretion of secondary metabolites. Other islands endow P. putida with determinants of resistance and defenceor with constituents and appendages of the cell wall. A total of 29 islands carry the signature of mobile elements such as phage, transposons, insertion sequence (IS) elements and group II introns, indicating recent acquisition by horizontal gene transfer. The largest gene carries the most unusual sequence that encodes a multirepeat threonine-rich surface adhesion protein. Among the housekeeping genes, only genes of the translational apparatus were located in segments with an atypical signature, suggesting that the synthesis of ribosomal proteins is uncoupled from the rapidly changing translational demands of the cell by the separate utilization of tRNA pools. PMID:12534464

Weinel, Christian; Nelson, Karen E; Tümmler, Burkhard

2002-12-01

432

Geology Fieldnotes: Padre Island National Seashore, Texas  

NSDL National Science Digital Library

This chain of barrier islands off the coast of Texas supports an abundance of wildlife, and is composed of a variety of environments, such as dunes, grasslands, and tidal flats. This National Park Service (NPS) site offers a brief profile of islands, as well as photos, maps, and links to visitor information and additional resources.

433

Long Island Geographic Information System (LI GIS)  

Cancer.gov

The Geographic Information System for Breast Cancer Studies on Long Island (LI GIS) is a unique research tool combining an extensive collection of data and other geospatial resources. The LI GIS is designed primarily to study potential relationships between environmental exposures and breast cancer in Nassau and Suffolk counties (Long Island), NY; however, its application can be extended to the study of other diseases.

434

LONG ISLAND SOUND STUDY 2002 CCMP IR  

EPA Science Inventory

The Long Island Sound Study Implementation Review (IR) summarizes the progress and challenges ahead for the for the Long Island Sound Study (LISS) through examination of it activities in relation to the CCMP. The LISS CCMP identified six major areas requiring management action: 1...

435

DICKINSON BAY ISLANDS RESTORATION PROJECT MX964016  

EPA Science Inventory

The restoration of three islands in Dickinson Bay will be accomplished by transporting clean clay to the designated sites. The islands will then be sculpted to the prescribed slopes and elevations. Vegetation will be transplanted along slopes and in the intertidal zones of each...

436

Aboriginal and Islander Education: Perspectives and Change.  

ERIC Educational Resources Information Center

|The seminar in this report focused on perspectives, recent developments, directions for improvement, and community involvement with regard to the education of Aboriginal and Torres Strait Islander children in Australia. The seminar underscored that there is considerable interest in Aboriginal and Islander education with attention centered on…

Taylor, Sandra C., Ed.; Baldauf, Richard B., Jr., Ed.

437

Andrew shortens lifetime of Louisiana Barrier Islands  

NASA Astrophysics Data System (ADS)

Because the Isles Dernieres, a series of four barrier islands off the coast of Louisiana, have one of the most rapidly eroding shorelines in the world, geologists at the U.S. Geological Survey and the Louisiana Geological Survey have been monitoring erosion activity over the last several years, said Jeff Williams of the USGS in Reston, Va. Hurricane Andrew, which struck the state on August 26, caused severe erosional damage to these islands that has shortened their lifetimes.Before Andrew struck, geologists projected that Raccoon Island would disappear below sea level by the year 2001 and that Whiskey Island would disappear by 2016. Now, due to the severe erosion from Hurricane Andrew, the scientists claim that the islands may disappear before the turn of the century, and the other islands in the Dernieres chain are expected to follow suit within 2 decades. Raccoon, Whiskey, Trinity, and East islands make up the Isles Dernieres, which existed as one island, known as the Isle Derniere, before an 1856 hurricane and subsequent erosion.

Bush, Susan

438

The Long Island Breast Cancer Study Project  

Microsoft Academic Search

In the early 1990s, breast cancer advocates petitioned the United States Congress to investigate the high rates of breast cancer on Long Island in the state of New York. The resulting law led to the Long Island Breast Cancer Study Project (LIBCSP) — more than ten research projects designed to study the possible causes of this increased incidence of cancer.

Deborah M. Winn

2005-01-01

439

Rhode Island Election Tickets: A Survey  

Microsoft Academic Search

Rhode Island was the first English colony in America to issue printed election ballots, with the first issued in the mid-1740s. This survey of Rhode Island election tickets, while not exhaustive, is representative of the use of tickets in elections spanning a period of over 150 years and documents state and local politics, political factions and election results from the

Russell J. DeSimone; Daniel C. Schofield

2007-01-01

440

IceBridge Flight Over Baffin Island  

NASA Website

Canada's Baffin Island. This island, the largest one in Canada, is home to an ice formation known as the Penny Ice Cap. This mission was a repeat of airborne surveys by the ATM and radar teams flown in 1995, 2000 and 2005, and added new ...