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Sample records for colibactin genomic island

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

    PubMed Central

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

    2009-01-01

    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. PMID:19720753

  2. Escherichia coli?ClbS is a colibactin resistance protein.

    PubMed

    Bossuet-Greif, Nadège; Dubois, Damien; Petit, Claude; Tronnet, Sophie; Martin, Patricia; Bonnet, Richard; Oswald, Eric; Nougayrède, Jean-Philippe

    2016-03-01

    The genomic pks island codes for the biosynthetic machinery that produces colibactin, a peptide-polyketide metabolite. Colibactin is a genotoxin that contributes to the virulence of extra-intestinal pathogenic Escherichia coli and promotes colorectal cancer. In this work, we examined whether the pks-encoded clbS gene of unknown function could participate in the self-protection of E. coli-producing colibactin. A clbS mutant was not impaired in the ability to inflict DNA damage in HeLa cells, but the bacteria activated the SOS response and ceased to replicate. This autotoxicity phenotype was markedly enhanced in a clbS?uvrB double mutant inactivated for DNA repair by nucleotide excision but was suppressed in a clbS?clbA double mutant unable to produce colibactin. In addition, ectopic expression of clbS protected infected HeLa cells from colibactin. Thus, ClbS is a resistance protein blocking the genotoxicity of colibactin both in the procaryotic and the eucaryotic cells. PMID:26560421

  3. Gut Symbionts from Distinct Hosts Exhibit Genotoxic Activity via Divergent Colibactin Biosynthesis Pathways

    PubMed Central

    Vizcaino, Maria I.; Crawford, Jason M.

    2014-01-01

    Secondary metabolites produced by nonribosomal peptide synthetase (NRPS) or polyketide synthase (PKS) pathways are chemical mediators of microbial interactions in diverse environments. However, little is known about their distribution, evolution, and functional roles in bacterial symbionts associated with animals. A prominent example is colibactin, a largely unknown family of secondary metabolites produced by Escherichia coli via a hybrid NRPS-PKS biosynthetic pathway that inflicts DNA damage upon eukaryotic cells and contributes to colorectal cancer and tumor formation in the mammalian gut. Thus far, homologs of this pathway have only been found in closely related Enterobacteriaceae, while a divergent variant of this gene cluster was recently discovered in a marine alphaproteobacterial Pseudovibrio strain. Herein, we sequenced the genome of Frischella perrara PEB0191, a bacterial gut symbiont of honey bees and identified a homologous colibactin biosynthetic pathway related to those found in Enterobacteriaceae. We show that the colibactin genomic island (GI) has conserved gene synteny and biosynthetic module architecture across F. perrara, Enterobacteriaceae, and the Pseudovibrio strain. Comparative metabolomics analyses of F. perrara and E. coli further reveal that these two bacteria produce related colibactin pathway-dependent metabolites. Finally, we demonstrate that F. perrara, like E. coli, causes DNA damage in eukaryotic cells in vitro in a colibactin pathway-dependent manner. Together, these results support that divergent variants of the colibactin biosynthetic pathway are widely distributed among bacterial symbionts, producing related secondary metabolites and likely endowing its producer with functional capabilities important for diverse symbiotic associations. PMID:25527542

  4. Gut symbionts from distinct hosts exhibit genotoxic activity via divergent colibactin biosynthesis pathways.

    PubMed

    Engel, Philipp; Vizcaino, Maria I; Crawford, Jason M

    2015-02-01

    Secondary metabolites produced by nonribosomal peptide synthetase (NRPS) or polyketide synthase (PKS) pathways are chemical mediators of microbial interactions in diverse environments. However, little is known about their distribution, evolution, and functional roles in bacterial symbionts associated with animals. A prominent example is colibactin, a largely unknown family of secondary metabolites produced by Escherichia coli via a hybrid NRPS-PKS biosynthetic pathway that inflicts DNA damage upon eukaryotic cells and contributes to colorectal cancer and tumor formation in the mammalian gut. Thus far, homologs of this pathway have only been found in closely related Enterobacteriaceae, while a divergent variant of this gene cluster was recently discovered in a marine alphaproteobacterial Pseudovibrio strain. Herein, we sequenced the genome of Frischella perrara PEB0191, a bacterial gut symbiont of honey bees and identified a homologous colibactin biosynthetic pathway related to those found in Enterobacteriaceae. We show that the colibactin genomic island (GI) has conserved gene synteny and biosynthetic module architecture across F. perrara, Enterobacteriaceae, and the Pseudovibrio strain. Comparative metabolomics analyses of F. perrara and E. coli further reveal that these two bacteria produce related colibactin pathway-dependent metabolites. Finally, we demonstrate that F. perrara, like E. coli, causes DNA damage in eukaryotic cells in vitro in a colibactin pathway-dependent manner. Together, these results support that divergent variants of the colibactin biosynthetic pathway are widely distributed among bacterial symbionts, producing related secondary metabolites and likely endowing its producer with functional capabilities important for diverse symbiotic associations. PMID:25527542

  5. The Genotoxin Colibactin Is a Determinant of Virulence in Escherichia coli K1 Experimental Neonatal Systemic Infection.

    PubMed

    McCarthy, Alex J; Martin, Patricia; Cloup, Emilie; Stabler, Richard A; Oswald, Eric; Taylor, Peter W

    2015-09-01

    Escherichia coli strains expressing the K1 capsule are a major cause of sepsis and meningitis in human neonates. The development of these diseases is dependent on the expression of a range of virulence factors, many of which remain uncharacterized. Here, we show that all but 1 of 34 E. coli K1 neonatal isolates carried clbA and clbP, genes contained within the pks pathogenicity island and required for the synthesis of colibactin, a polyketide-peptide genotoxin that causes genomic instability in eukaryotic cells by induction of double-strand breaks in DNA. Inactivation of clbA and clbP in E. coli A192PP, a virulent strain of serotype O18:K1 that colonizes the gastrointestinal tract and translocates to the blood compartment with very high frequency in experimental infection of the neonatal rat, significantly reduced the capacity of A192PP to colonize the gut, engender double-strand breaks in DNA, and cause invasive, lethal disease. Mutation of clbA, which encodes a pleiotropic enzyme also involved in siderophore synthesis, impacted virulence to a greater extent than mutation of clbP, encoding an enzyme specific to colibactin synthesis. Restoration of colibactin gene function by complementation reestablished the fully virulent phenotype. We conclude that colibactin contributes to the capacity of E. coli K1 to colonize the neonatal gastrointestinal tract and to cause invasive disease in the susceptible neonate. PMID:26150540

  6. Critical Intermediates Reveal New Biosynthetic Events in the Enigmatic Colibactin Pathway.

    PubMed

    Li, Zhong-Rui; Li, Yongxin; Lai, Jennifer Y H; Tang, Jianqiang; Wang, Bin; Lu, Liang; Zhu, Guoqiang; Wu, Xiyang; Xu, Ying; Qian, Pei-Yuan

    2015-08-17

    Colibactin is a potent genotoxin that induces DNA double-strand breaks; it is produced by Escherichia coli strains harboring a pks+ island. However, the structure of this compound remains elusive. Here, using transformation-associated recombination (TAR) cloning to perform heterologous expression, we took advantage of the significantly increased yield of colibactin pathway-related compounds to determine and isolate a series of vital (pre)colibactin intermediates. The chemical structures of compounds 8, 10 and 11 were identified by NMR and MS(n) analyses. The new 1H-pyrrolo[3,4-c]pyridine-3,6(2H,5H)-dione- and thiazole-containing compound 10 provides new insights regarding the biosynthetic pathway to (pre)colibactin and establishes foundations for future investigation of the intriguing (pre)colibactin structures and its modes of action. PMID:26052818

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

    PubMed Central

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

    2013-01-01

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

  8. The colibactin warhead crosslinks DNA

    PubMed Central

    Vizcaino, Maria I.; Crawford, Jason M.

    2015-01-01

    Members of the human microbiota are increasingly being correlated to human health and disease states, but the majority of the underlying microbial metabolites that regulate host-microbe interactions remain largely unexplored. Select strains of E. coli present in the human colon have been linked to initiating inflammation-induced colorectal cancer through an unknown small molecule-mediated process. The responsible nonribosomal peptide-polyketide hybrid pathway encodes “colibactin,” a largely uncharacterized family of small molecules. Genotoxic small molecules from this pathway capable of initiating cancer formation have remained elusive due to their high instability. Guided by metabolomic analyses, here we employ a combination of NMR spectroscopy and bioinformatics-guided isotopic labeling studies to characterize the colibactin warhead, an unprecedented substituted spirobicyclic structure. The warhead crosslinks duplex DNA in vitro, providing direct experimental evidence for colibactin’s DNA-damaging activity. The data support unexpected models for both colibactin biosynthesis and its mode of action. PMID:25901819

  9. The colibactin warhead crosslinks DNA

    NASA Astrophysics Data System (ADS)

    Vizcaino, Maria I.; Crawford, Jason M.

    2015-05-01

    Members of the human microbiota are increasingly being correlated to human health and disease states, but the majority of the underlying microbial metabolites that regulate host-microbe interactions remain largely unexplored. Select strains of Escherichia coli present in the human colon have been linked to the initiation of inflammation-induced colorectal cancer through an unknown small-molecule-mediated process. The responsible non-ribosomal peptide-polyketide hybrid pathway encodes ‘colibactin’, which belongs to a largely uncharacterized family of small molecules. Genotoxic small molecules from this pathway that are capable of initiating cancer formation have remained elusive due to their high instability. Guided by metabolomic analyses, here we employ a combination of NMR spectroscopy and bioinformatics-guided isotopic labelling studies to characterize the colibactin warhead, an unprecedented substituted spirobicyclic structure. The warhead crosslinks duplex DNA in vitro, providing direct experimental evidence for colibactin's DNA-damaging activity. The data support unexpected models for both colibactin biosynthesis and its mode of action.

  10. In vivo evidence for a prodrug activation mechanism during colibactin maturation.

    PubMed

    Bian, Xiaoying; Fu, Jun; Plaza, Alberto; Herrmann, Jennifer; Pistorius, Dominik; Stewart, A Francis; Zhang, Youming; Müller, Rolf

    2013-07-01

    Releasing the cytopath: We have identified an N-myristoyl-D-asparagine (1) as the free N-terminal prodrug scaffold in cytopathogenic Escherichia coli strains expressing the colibactin gene cluster. Colibactin is released in vivo upon cleavage of precolibactin. We provide for the first time in vivo evidence of the prodrug-like release mechanism of colibactin. PMID:23744512

  11. IslandViewer update: Improved genomic island discovery and visualization.

    PubMed

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

    2013-07-01

    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

  12. n-Gram characterization of genomic islands in bacterial genomes.

    PubMed

    Pavlovi?-Lazeti?, Gordana M; Miti?, Nenad S; Beljanski, Milos V

    2009-03-01

    The paper presents a novel, n-gram-based method for analysis of bacterial genome segments known as genomic islands (GIs). Identification of GIs in bacterial genomes is an important task since many of them represent inserts that may contribute to bacterial evolution and pathogenesis. In order to characterize and distinguish GIs from rest of the genome, binary classification of islands based on n-gram frequency distribution have been performed. It consists of testing the agreement of islands n-gram frequency distributions with the complete genome and backbone sequence. In addition, a statistic based on the maximal order Markov model is used to identify significantly overrepresented and underrepresented n-grams in islands. The results may be used as a basis for Zipf-like analysis suggesting that some of the n-grams are overrepresented in a subset of islands and underrepresented in the backbone, or vice versa, thus complementing the binary classification. The method is applied to strain-specific regions in the Escherichia coli O157:H7 EDL933 genome (O-islands), resulting in two groups of O-islands with different n-gram characteristics. It refines a characterization based on other compositional features such as G+C content and codon usage, and may help in identification of GIs, and also in research and development of adequate drugs targeting virulence genes in them. PMID:19101056

  13. Island length distribution in genome sequencing.

    PubMed

    Percus, O E; Percus, J K

    1999-09-01

    We consider the general problem of constructing a physical map of a genome by welding islands of overlapping clones. Both distribution of clone length and non-uniform probability of overlap detection are taken into account, the latter restricted to the Markov case in which only the location of the end of the developing island is required. Exact results for the distribution of island length are obtained in the special cases of fixed clone length or rigid overlap criterion, and mean and variance for the general situation. Determination of ocean length distribution permits island number and contig number distributions to be found as well. PMID:10501922

  14. The Floating (Pathogenicity) Island: A Genomic Dessert.

    PubMed

    Novick, Richard P; Ram, Geeta

    2016-02-01

    Among the prokaryotic genomic islands (GIs) involved in horizontal gene transfer (HGT) are the classical pathogenicity islands, including the integrative and conjugative elements (ICEs), the gene-transfer agents (GTAs), and the staphylococcal pathogenicity islands (SaPIs), the primary focus of this review. While the ICEs and GTAs mediate HGT autonomously, the SaPIs are dependent on specific phages. The ICEs transfer primarily their own DNA, the GTAs exclusively transfer unlinked host DNA, and the SaPIs combine the capabilities of both. Thus the SaPIs derive their importance from the genes they carry (their genetic cargo) and the genes they move. They act not only as versatile high-frequency mobilizers but also as mediators of phage interference and consequently are major benefactors of their host bacteria. PMID:26744223

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

    PubMed

    Brotherton, Carolyn A; Balskus, Emily P

    2013-03-01

    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

  16. Genomic Island Identification Software v 1.0

    Energy Science and Technology Software Center (ESTSC)

    2014-08-25

    Genomic islands are key mobile DNA elements in bacterial evolution, that can distinguish pathogenic strains from each other, or distinguish pathogenic strains from non-pathogenic strains. Their detection in genomes is a challenging problem. We present 3 main software components that attack the island detection problem on two different bases: 1) the preference of islands to insert in chromosomal tRNA or tmRNA genes (islander.pl), and 2) islands’ sporadic occurrence among closely related strains. The latter principlemore » is employed in both an algorithm (learnedPhyloblocks.pl) and a visualization method (panGenome.pl). Component islander.pl finds islands based on their preference for a particular target gene type. We annotate each tRNA and tmRNA gene, find fragments of each such gene as candidates for the distal ends of islands, and filter candidates to remove false positives. Component learnedPhyloblocks.pl uses islands found by islander.pl and other methods as a training set to find new islands. Reference genomes are aligned using mugsy, then the “phylotypes” or patterns of occurrence in the reference set are determined for each position in the target genome, and those phylotypes most enriched in the training set of islands are followed to detect yet more islands. Component panGenome.pl produces a big-data visualization of the chromosomally-ordered “pan-genome”, that includes every gene of every reference genome (x-axis, pan-genome order; y-axis, reference genomes; color-coding, gene presence/absence etc.), islands appearing as dark patches.« less

  17. Genomic Island Identification Software v 1.0

    SciTech Connect

    2014-08-25

    Genomic islands are key mobile DNA elements in bacterial evolution, that can distinguish pathogenic strains from each other, or distinguish pathogenic strains from non-pathogenic strains. Their detection in genomes is a challenging problem. We present 3 main software components that attack the island detection problem on two different bases: 1) the preference of islands to insert in chromosomal tRNA or tmRNA genes (islander.pl), and 2) islands’ sporadic occurrence among closely related strains. The latter principle is employed in both an algorithm (learnedPhyloblocks.pl) and a visualization method (panGenome.pl). Component islander.pl finds islands based on their preference for a particular target gene type. We annotate each tRNA and tmRNA gene, find fragments of each such gene as candidates for the distal ends of islands, and filter candidates to remove false positives. Component learnedPhyloblocks.pl uses islands found by islander.pl and other methods as a training set to find new islands. Reference genomes are aligned using mugsy, then the “phylotypes” or patterns of occurrence in the reference set are determined for each position in the target genome, and those phylotypes most enriched in the training set of islands are followed to detect yet more islands. Component panGenome.pl produces a big-data visualization of the chromosomally-ordered “pan-genome”, that includes every gene of every reference genome (x-axis, pan-genome order; y-axis, reference genomes; color-coding, gene presence/absence etc.), islands appearing as dark patches.

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

    ERIC Educational Resources Information Center

    Clark, Mary Anne

    2009-01-01

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

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

    ERIC Educational Resources Information Center

    Clark, Mary Anne

    2009-01-01

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

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

    PubMed

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

    2015-07-01

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

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

    PubMed Central

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

    2015-01-01

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

  2. IslandViewer: an integrated interface for computational identification and visualization of genomic islands

    PubMed Central

    Langille, Morgan G. I.; Brinkman, Fiona S. L.

    2009-01-01

    Summary: Genomic islands (clusters of genes of probable horizontal origin; GIs) play a critical role in medically important adaptations of bacteria. Recently, several computational methods have been developed to predict GIs that utilize either sequence composition bias or comparative genomics approaches. IslandViewer is a web accessible application that provides the first user-friendly interface for obtaining precomputed GI predictions, or predictions from user-inputted sequence, using the most accurate methods for genomic island prediction: IslandPick, IslandPath-DIMOB and SIGI-HMM. The graphical interface allows easy viewing and downloading of island data in multiple formats, at both the chromosome and gene level, for method-specific, or overlapping, GI predictions. Availability: The IslandViewer web service is available at http://www.pathogenomics.sfu.ca/islandviewer and the source code is freely available under the GNU GPL license. Contact: brinkman@sfu.ca PMID:19151094

  3. Oral Tolerance Failure upon Neonatal Gut Colonization with Escherichia coli Producing the Genotoxin Colibactin

    PubMed Central

    Secher, Thomas; Payros, Delphine; Brehin, Camille; Boury, Michele; Watrin, Claude; Gillet, Marion; Bernard-Cadenat, Isabelle; Menard, Sandrine; Theodorou, Vassilia; Saoudi, Abdelhadi; Olier, Maiwenn

    2015-01-01

    The intestinal barrier controls the balance between tolerance and immunity to luminal antigens. When this finely tuned equilibrium is deregulated, inflammatory disorders can occur. There is a concomitant increase, in urban populations of developed countries, of immune-mediated diseases along with a shift in Escherichia coli population from the declining phylogenetic group A to the newly dominant group B2, including commensal strains producing a genotoxin called colibactin that massively colonized the gut of neonates. Here, we showed that mother-to-offspring early gut colonization by colibactin-producing E. coli impairs intestinal permeability and enhances the transepithelial passage of luminal antigen, leading to an increased immune activation. Functionally, this was accompanied by a dramatic increase in local and systemic immune responses against a fed antigen, decreased regulatory T cell population, tolerogenic dendritic cells, and enhanced mucosal delayed-type hypersensitivity response. Conversely, the abolition of colibactin expression by mutagenesis abrogates the alteration of oral tolerance induced by neonatal colonization by E. coli. In conclusion, the vertical colonization by E. coli producing the genotoxin colibactin enhances intestinal translocation and subsequently alters oral tolerance. Thus, early colonization by E. coli from the newly dominant phylogenetic group B2, which produces colibactin, may represent a risk factor for the development of immune-mediated diseases. PMID:25824839

  4. Oral tolerance failure upon neonatal gut colonization with Escherichia coli producing the genotoxin colibactin.

    PubMed

    Secher, Thomas; Payros, Delphine; Brehin, Camille; Boury, Michele; Watrin, Claude; Gillet, Marion; Bernard-Cadenat, Isabelle; Menard, Sandrine; Theodorou, Vassilia; Saoudi, Abdelhadi; Olier, Maiwenn; Oswald, Eric

    2015-06-01

    The intestinal barrier controls the balance between tolerance and immunity to luminal antigens. When this finely tuned equilibrium is deregulated, inflammatory disorders can occur. There is a concomitant increase, in urban populations of developed countries, of immune-mediated diseases along with a shift in Escherichia coli population from the declining phylogenetic group A to the newly dominant group B2, including commensal strains producing a genotoxin called colibactin that massively colonized the gut of neonates. Here, we showed that mother-to-offspring early gut colonization by colibactin-producing E. coli impairs intestinal permeability and enhances the transepithelial passage of luminal antigen, leading to an increased immune activation. Functionally, this was accompanied by a dramatic increase in local and systemic immune responses against a fed antigen, decreased regulatory T cell population, tolerogenic dendritic cells, and enhanced mucosal delayed-type hypersensitivity response. Conversely, the abolition of colibactin expression by mutagenesis abrogates the alteration of oral tolerance induced by neonatal colonization by E. coli. In conclusion, the vertical colonization by E. coli producing the genotoxin colibactin enhances intestinal translocation and subsequently alters oral tolerance. Thus, early colonization by E. coli from the newly dominant phylogenetic group B2, which produces colibactin, may represent a risk factor for the development of immune-mediated diseases. PMID:25824839

  5. Genomic islands of speciation in Anopheles gambiae.

    PubMed

    Turner, Thomas L; Hahn, Matthew W; Nuzhdin, Sergey V

    2005-09-01

    The African malaria mosquito, Anopheles gambiae sensu stricto (A. gambiae), provides a unique opportunity to study the evolution of reproductive isolation because it is divided into two sympatric, partially isolated subtaxa known as M form and S form. With the annotated genome of this species now available, high-throughput techniques can be applied to locate and characterize the genomic regions contributing to reproductive isolation. In order to quantify patterns of differentiation within A. gambiae, we hybridized population samples of genomic DNA from each form to Affymetrix GeneChip microarrays. We found that three regions, together encompassing less than 2.8 Mb, are the only locations where the M and S forms are significantly differentiated. Two of these regions are adjacent to centromeres, on Chromosomes 2L and X, and contain 50 and 12 predicted genes, respectively. Sequenced loci in these regions contain fixed differences between forms and no shared polymorphisms, while no fixed differences were found at nearby control loci. The third region, on Chromosome 2R, contains only five predicted genes; fixed differences in this region were also verified by direct sequencing. These "speciation islands" remain differentiated despite considerable gene flow, and are therefore expected to contain the genes responsible for reproductive isolation. Much effort has recently been applied to locating the genes and genetic changes responsible for reproductive isolation between species. Though much can be inferred about speciation by studying taxa that have diverged for millions of years, studying differentiation between taxa that are in the early stages of isolation will lead to a clearer view of the number and size of regions involved in the genetics of speciation. Despite appreciable levels of gene flow between the M and S forms of A. gambiae, we were able to isolate three small regions of differentiation where genes responsible for ecological and behavioral isolation are likely to be located. We expect reproductive isolation to be due to changes at a small number of loci, as these regions together contain only 67 predicted genes. Concentrating future mapping experiments on these regions should reveal the genes responsible for reproductive isolation between forms. PMID:16076241

  6. Genomic island 2 of Brucella melitensis is a major virulence determinant: functional analyses of genomic islands.

    PubMed

    Rajashekara, Gireesh; Covert, Jill; Petersen, Erik; Eskra, Linda; Splitter, Gary

    2008-09-01

    Brucella genomic islands (GIs) share similarities in their genomic organization to pathogenicity islands from other bacteria and are likely acquired by lateral gene transfer. Here, we report the identification of a GI that is important for the pathogenicity of Brucella melitensis. The deletion of GI-1, GI-5, or GI-6 did not affect bacterial growth in macrophages as well as their virulence in interferon regulatory factor 1-deficient (IRF-1(-/-)) mice, suggesting that these islands do not contribute to Brucella virulence. However, the deletion of GI-2 resulted in the attenuation of bacterial growth in macrophages and virulence in IRF-1(-/-) mice. The GI-2 mutant also displayed a rough lipopolysaccharide (LPS) phenotype indicated by acriflavin agglutination, suggesting that in vitro and in vivo attenuation is a result of LPS alteration. Further, systematic analysis of the entire GI-2 revealed two open reading frames (ORFs), BMEI0997 and I0998, that encode hypothetical sugar transferases and contribute to LPS alteration, as the deletion of either of these ORFs resulted in a rough phenotype similar to that of the GI-2 mutant. Complementation analyses indicated that in addition to I0997 and I0998, I0999 is required to restore the smooth LPS in the GI-2 mutant as well as its full in vitro and in vivo virulence. The I0999 sequence analysis suggested that it might function as a transporter to help facilitate the transport or linking of the O antigen to the LPS. Our study also indicated that the rough LPS resulting from the GI-2 deletion may affect pathogen-associated molecular pattern recognition by Toll-like receptors. PMID:18641138

  7. A computational approach for identifying pathogenicity islands in prokaryotic genomes

    PubMed Central

    Yoon, Sung Ho; Hur, Cheol-Goo; Kang, Ho-Young; Kim, Yeoun Hee; Oh, Tae Kwang; Kim, Jihyun F

    2005-01-01

    Background Pathogenicity islands (PAIs), distinct genomic segments of pathogens encoding virulence factors, represent a subgroup of genomic islands (GIs) that have been acquired by horizontal gene transfer event. Up to now, computational approaches for identifying PAIs have been focused on the detection of genomic regions which only differ from the rest of the genome in their base composition and codon usage. These approaches often lead to the identification of genomic islands, rather than PAIs. Results We present a computational method for detecting potential PAIs in complete prokaryotic genomes by combining sequence similarities and abnormalities in genomic composition. We first collected 207 GenBank accessions containing either part or all of the reported PAI loci. In sequenced genomes, strips of PAI-homologs were defined based on the proximity of the homologs of genes in the same PAI accession. An algorithm reminiscent of sequence-assembly procedure was then devised to merge overlapping or adjacent genomic strips into a large genomic region. Among the defined genomic regions, PAI-like regions were identified by the presence of homolog(s) of virulence genes. Also, GIs were postulated by calculating G+C content anomalies and codon usage bias. Of 148 prokaryotic genomes examined, 23 pathogenic and 6 non-pathogenic bacteria contained 77 candidate PAIs that partly or entirely overlap GIs. Conclusion Supporting the validity of our method, included in the list of candidate PAIs were thirty four PAIs previously identified from genome sequencing papers. Furthermore, in some instances, our method was able to detect entire PAIs for those only partial sequences are available. Our method was proven to be an efficient method for demarcating the potential PAIs in our study. Also, the function(s) and origin(s) of a candidate PAI can be inferred by investigating the PAI queries comprising it. Identification and analysis of potential PAIs in prokaryotic genomes will broaden our knowledge on the structure and properties of PAIs and the evolution of bacterial pathogenesis. PMID:16033657

  8. GI-POP: a combinational annotation and genomic island prediction pipeline for ongoing microbial genome projects.

    PubMed

    Lee, Chi-Ching; Chen, Yi-Ping Phoebe; Yao, Tzu-Jung; Ma, Cheng-Yu; Lo, Wei-Cheng; Lyu, Ping-Chiang; Tang, Chuan Yi

    2013-04-10

    Sequencing of microbial genomes is important because of microbial-carrying antibiotic and pathogenetic activities. However, even with the help of new assembling software, finishing a whole genome is a time-consuming task. In most bacteria, pathogenetic or antibiotic genes are carried in genomic islands. Therefore, a quick genomic island (GI) prediction method is useful for ongoing sequencing genomes. In this work, we built a Web server called GI-POP (http://gipop.life.nthu.edu.tw) which integrates a sequence assembling tool, a functional annotation pipeline, and a high-performance GI predicting module, in a support vector machine (SVM)-based method called genomic island genomic profile scanning (GI-GPS). The draft genomes of the ongoing genome projects in contigs or scaffolds can be submitted to our Web server, and it provides the functional annotation and highly probable GI-predicting results. GI-POP is a comprehensive annotation Web server designed for ongoing genome project analysis. Researchers can perform annotation and obtain pre-analytic information include possible GIs, coding/non-coding sequences and functional analysis from their draft genomes. This pre-analytic system can provide useful information for finishing a genome sequencing project. PMID:23318308

  9. On detection and assessment of statistical significance of Genomic Islands

    PubMed Central

    Chatterjee, Raghunath; Chaudhuri, Keya; Chaudhuri, Probal

    2008-01-01

    Background Many of the available methods for detecting Genomic Islands (GIs) in prokaryotic genomes use markers such as transposons, proximal tRNAs, flanking repeats etc., or they use other supervised techniques requiring training datasets. Most of these methods are primarily based on the biases in GC content or codon and amino acid usage of the islands. However, these methods either do not use any formal statistical test of significance or use statistical tests for which the critical values and the P-values are not adequately justified. We propose a method, which is unsupervised in nature and uses Monte-Carlo statistical tests based on randomly selected segments of a chromosome. Such tests are supported by precise statistical distribution theory, and consequently, the resulting P-values are quite reliable for making the decision. Results Our algorithm (named Design-Island, an acronym for Detection of Statistically Significant Genomic Island) runs in two phases. Some 'putative GIs' are identified in the first phase, and those are refined into smaller segments containing horizontally acquired genes in the refinement phase. This method is applied to Salmonella typhi CT18 genome leading to the discovery of several new pathogenicity, antibiotic resistance and metabolic islands that were missed by earlier methods. Many of these islands contain mobile genetic elements like phage-mediated genes, transposons, integrase and IS elements confirming their horizontal acquirement. Conclusion The proposed method is based on statistical tests supported by precise distribution theory and reliable P-values along with a technique for visualizing statistically significant islands. The performance of our method is better than many other well known methods in terms of their sensitivity and accuracy, and in terms of specificity, it is comparable to other methods. PMID:18380895

  10. Expression analysis of the colibactin gene cluster coding for a novel polyketide in Escherichia coli.

    PubMed

    Homburg, Stefan; Oswald, Eric; Hacker, Jörg; Dobrindt, Ulrich

    2007-10-01

    The recently described hybrid nonribosomal peptide-polyketide colibactin, found in various Escherichia coli strains, invokes a cytopathic effect in HeLa cells upon cocultivation with these bacteria. However, not much is known so far about the transcriptional organization of the colibactin genes (clb) or the regulation of their transcription. Here, the operon structure of the colibactin gene cluster of E. coli strain Nissle 1917 was investigated by means of reverse transcriptase (RT)-PCR and seven transcripts were found of which four are transcribed polycistronically. The polycistrons comprise the genes clbC to clbG, clbI to clbN, clbO to clbP, and clbR to clbA and span 6.3, 23.3, 3.9, and 0.9 kb, respectively. Furthermore, transcript levels for different cultivation conditions were determined by RT-PCR of the whole cluster as well as by luciferase reporter gene assays of the genes clbA, clbB, clbQ, and clbR. RT-PCR revealed an overall increased transcription in shaking cultures as well as of the genes clbA to clbH in general. Luciferase reporter gene fusions indicated an influence of the carbon source on clb gene expression. PMID:17714479

  11. Mobilization of Genomic Islands of Staphylococcus aureus by Temperate Bacteriophage

    PubMed Central

    Moon, Bo Youn; Park, Joo Youn; Robinson, D. Ashley; Thomas, Jonathan C.; Park, Yong Ho; Thornton, Justin A.; Seo, Keun Seok

    2016-01-01

    The virulence of Staphylococcus aureus, in both human and animal hosts, is largely influenced by the acquisition of mobile genetic elements (MGEs). Most S. aureus strains carry a variety of MGEs, including three genomic islands (νSaα, νSaβ, νSaγ) that are diverse in virulence gene content but conserved within strain lineages. Although the mobilization of pathogenicity islands, phages and plasmids has been well studied, the mobilization of genomic islands is poorly understood. We previously demonstrated the mobilization of νSaβ by the adjacent temperate bacteriophage ϕSaBov from strain RF122. In this study, we demonstrate that ϕSaBov mediates the mobilization of νSaα and νSaγ, which are located remotely from ϕSaBov, mostly to recipient strains belonging to ST151. Phage DNA sequence analysis revealed that chromosomal DNA excision events from RF122 were highly specific to MGEs, suggesting sequence-specific DNA excision and packaging events rather than generalized transduction by a temperate phage. Disruption of the int gene in ϕSaBov did not affect phage DNA excision, packaging, and integration events. However, disruption of the terL gene completely abolished phage DNA packing events, suggesting that the primary function of temperate phage in the transfer of genomic islands is to allow for phage DNA packaging by TerL and that transducing phage particles are the actual vehicle for transfer. These results extend our understanding of the important role of bacteriophage in the horizontal transfer and evolution of genomic islands in S. aureus. PMID:26953931

  12. Comparative Whole-Genome Hybridization Reveals Genomic Islands in Brucella Species†

    PubMed Central

    Rajashekara, Gireesh; Glasner, Jeremy D.; Glover, David A.; Splitter, Gary A.

    2004-01-01

    Brucella species are responsible for brucellosis, a worldwide zoonotic disease causing abortion in domestic animals and Malta fever in humans. Based on host preference, the genus is divided into six species. Brucella abortus, B. melitensis, and B. suis are pathogenic to humans, whereas B. ovis and B. neotomae are nonpathogenic to humans and B. canis human infections are rare. Limited genome diversity exists among Brucella species. Comparison of Brucella species whole genomes is, therefore, likely to identify factors responsible for differences in host preference and virulence restriction. To facilitate such studies, we used the complete genome sequence of B. melitensis 16M, the species highly pathogenic to humans, to construct a genomic microarray. Hybridization of labeled genomic DNA from Brucella species to this microarray revealed a total of 217 open reading frames (ORFs) altered in five Brucella species analyzed. These ORFs are often found in clusters (islands) in the 16M genome. Examination of the genomic context of these islands suggests that many are horizontally acquired. Deletions of genetic content identified in Brucella species are conserved in multiple strains of the same species, and genomic islands missing in a given species are often restricted to that particular species. These findings suggest that, whereas the loss or gain of genetic material may be related to the host range and virulence restriction of certain Brucella species for humans, independent mechanisms involving gene inactivation or altered expression of virulence determinants may also contribute to these differences. PMID:15262941

  13. Comparative analysis of essential genes in prokaryotic genomic islands

    PubMed Central

    Zhang, Xi; Peng, Chong; Zhang, Ge; Gao, Feng

    2015-01-01

    Essential genes are thought to encode proteins that carry out the basic functions to sustain a cellular life, and genomic islands (GIs) usually contain clusters of horizontally transferred genes. It has been assumed that essential genes are not likely to be located in GIs, but systematical analysis of essential genes in GIs has not been explored before. Here, we have analyzed the essential genes in 28 prokaryotes by statistical method and reached a conclusion that essential genes in GIs are significantly fewer than those outside GIs. The function of 362 essential genes found in GIs has been explored further by BLAST against the Virulence Factor Database (VFDB) and the phage/prophage sequence database of PHAge Search Tool (PHAST). Consequently, 64 and 60 eligible essential genes are found to share the sequence similarity with the virulence factors and phage/prophages-related genes, respectively. Meanwhile, we find several toxin-related proteins and repressors encoded by these essential genes in GIs. The comparative analysis of essential genes in genomic islands will not only shed new light on the development of the prediction algorithm of essential genes, but also give a clue to detect the functionality of essential genes in genomic islands. PMID:26223387

  14. Genomic islands predict functional adaptation in marine actinobacteria

    SciTech Connect

    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

    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

  15. Methyl-CpG island-associated genome signature tags

    DOEpatents

    Dunn, John J

    2014-05-20

    Disclosed is a method for analyzing the organismic complexity of a sample through analysis of the nucleic acid in the sample. In the disclosed method, through a series of steps, including digestion with a type II restriction enzyme, ligation of capture adapters and linkers and digestion with a type IIS restriction enzyme, genome signature tags are produced. The sequences of a statistically significant number of the signature tags are determined and the sequences are used to identify and quantify the organisms in the sample. Various embodiments of the invention described herein include methods for using single point genome signature tags to analyze the related families present in a sample, methods for analyzing sequences associated with hyper- and hypo-methylated CpG islands, methods for visualizing organismic complexity change in a sampling location over time and methods for generating the genome signature tag profile of a sample of fragmented DNA.

  16. Structural characteristics of genomic islands associated with GMP synthases as integration hotspot among sequenced microbial genomes.

    PubMed

    Song, Lei; Pan, Yuting; Chen, Sihong; Zhang, Xuehong

    2012-02-01

    tRNA, tmRNA and some small RNA genes are recognized as general integration hotspots of genomic islands (GIs). The GMP synthase gene (guaA) has been firstly identified as one insertion hotspot of foreign DNA fragments. Thirty four islands integrated into the guaA genes were identified in the 987 completely sequenced archaeal and bacterial genomes. These alien islands were widely distributed within the host strains belonging to Proteobacteria, Firmicutes and Actinobacteria. The analysis of structural characteristics of these GIs is important for further determination of the island mobility and transference into suitable hosts. The putative functional integrases encoded by guaA-associated islands were mainly composed of phage P4 integrases, and followed by phage PhiLC3 integrases. Interestingly, island-encoding AlpA is close to P4 integrase and is deduced to be the positive transcriptional regulatory factor of P4 integrase while the XRE protein is close to PhiLC3 integrase and may be the negative transcriptional regulatory factor of PhiLC3 integrase. An 8-bp consensus sequence (5'-GAGTGGGA-3') within the direct repeats of these GIs is the cutting site of the P4 integrases encoding by guaA-associated islands, in which the third nucleotide (G) is the key site. The large-scale investigation of the content of GMP synthase gene hotspots may be useful to find important functional islands within members of many key bacterial species and to transfer useful islands into more suitable hosts. PMID:22306813

  17. Islander: A database of precisely mapped genomic islands in tRNA and tmRNA genes

    SciTech Connect

    Hudson, Corey M.; Lau, Britney Y.; Williams, Kelly P.

    2014-11-05

    Genomic islands are mobile DNAs that are major agents of bacterial and archaeal evolution. Integration into prokaryotic chromosomes usually occurs site-specifically at tRNA or tmRNA gene (together, tDNA) targets, catalyzed by tyrosine integrases. This splits the target gene, yet sequences within the island restore the disrupted gene; the regenerated target and its displaced fragment precisely mark the endpoints of the island. We applied this principle to search for islands in genomic DNA sequences. Our algorithm identifies tDNAs, finds fragments of those tDNAs in the same replicon and removes unlikely candidate islands through a series of filters. A search for islands in 2168 whole prokaryotic genomes produced 3919 candidates. The website Islander (recently moved to http://bioinformatics.sandia.gov/islander/) presents these precisely mapped candidate islands, the gene content and the island sequence. The algorithm further insists that each island encode an integrase, and attachment site sequence identity is carefully noted; therefore, the database also serves in the study of integrase site-specificity and its evolution.

  18. Islander: A database of precisely mapped genomic islands in tRNA and tmRNA genes

    DOE PAGESBeta

    Hudson, Corey M.; Lau, Britney Y.; Williams, Kelly P.

    2014-11-05

    Genomic islands are mobile DNAs that are major agents of bacterial and archaeal evolution. Integration into prokaryotic chromosomes usually occurs site-specifically at tRNA or tmRNA gene (together, tDNA) targets, catalyzed by tyrosine integrases. This splits the target gene, yet sequences within the island restore the disrupted gene; the regenerated target and its displaced fragment precisely mark the endpoints of the island. We applied this principle to search for islands in genomic DNA sequences. Our algorithm identifies tDNAs, finds fragments of those tDNAs in the same replicon and removes unlikely candidate islands through a series of filters. A search for islandsmore » in 2168 whole prokaryotic genomes produced 3919 candidates. The website Islander (recently moved to http://bioinformatics.sandia.gov/islander/) presents these precisely mapped candidate islands, the gene content and the island sequence. The algorithm further insists that each island encode an integrase, and attachment site sequence identity is carefully noted; therefore, the database also serves in the study of integrase site-specificity and its evolution.« less

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

    PubMed Central

    2012-01-01

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

  20. Genomic Islands in the Pathogenic Filamentous Fungus Aspergillus fumigatus

    PubMed Central

    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

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

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

    PubMed Central

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

    2012-01-01

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

  2. Comparative metabolomics and structural characterizations illuminate colibactin pathway-dependent small molecules.

    PubMed

    Vizcaino, Maria I; Engel, Philipp; Trautman, Eric; Crawford, Jason M

    2014-07-01

    The gene cluster responsible for synthesis of the unknown molecule "colibactin" has been identified in mutualistic and pathogenic Escherichia coli. The pathway endows its producer with a long-term persistence phenotype in the human bowel, a probiotic activity used in the treatment of ulcerative colitis, and a carcinogenic activity under host inflammatory conditions. To date, functional small molecules from this pathway have not been reported. Here we implemented a comparative metabolomics and targeted structural network analyses approach to identify a catalog of small molecules dependent on the colibactin pathway from the meningitis isolate E. coli IHE3034 and the probiotic E. coli Nissle 1917. The structures of 10 pathway-dependent small molecules are proposed based on structural characterizations and network relationships. The network will provide a roadmap for the structural and functional elucidation of a variety of other small molecules encoded by the pathway. From the characterized small molecule set, in vitro bacterial growth inhibitory and mammalian CNS receptor antagonist activities are presented. PMID:24932672

  3. Identification and comparative analysis of a genomic island in Mycobacterium avium subsp. hominissuis.

    PubMed

    Lahiri, Annesha; Sanchini, Andrea; Semmler, Torsten; Schäfer, Hubert; Lewin, Astrid

    2014-11-01

    Mycobacterium avium subsp. hominissuis (MAH) is an environmental bacterium causing opportunistic infections. The objective of this study was to identify flexible genome regions in MAH isolated from different sources. By comparing five complete and draft MAH genomes we identified a genomic island conferring additional flexibility to the MAH genomes. The island was absent in one of the five strains and had sizes between 16.37 and 84.85kb in the four other strains. The genes present in the islands differed among strains and included phage- and plasmid-derived genes, integrase genes, hypothetical genes, and virulence-associated genes like mmpL or mce genes. PMID:25217830

  4. Islander: a database of integrative islands in prokaryotic genomes, the associated integrases and their DNA site specificities.

    PubMed

    Mantri, Yogita; Williams, Kelly P

    2004-01-01

    Prokaryotic chromosomes often contain islands, such as temperate phages or pathogenicity islands, delivered by site-specific integrases. Integration usually occurs within a tRNA or tmRNA gene, splitting the gene, yet sequences within the island restore the disrupted gene. The regenerated RNA gene and the displaced fragment of that gene thus mark the endpoints of the island. We applied this principle to search for islands in genomic DNA sequences. Our algorithm generates a list of tRNA and tmRNA genes, uses each as the query for a BLAST search of the starting DNA and removes unlikely hits through a series of filters. A search for islands in 106 whole bacterial genomes produced 143 candidates, with the search itself providing an estimate of three false candidates among these. Preliminary phylogenetic analysis of the associated integrases reduced this set to 89 cases of independently evolved site specificity, which showed strong bias for the tmRNA gene. The website Islander (http://www.indiana.edu/ approximately islander) presents the candidate islands in GenBank-style files and correlates integrase phylogeny with site specificity. PMID:14681358

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

    PubMed Central

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

    2006-01-01

    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 transferred pieces of DNA have a considerable length, comprise several genes and are called genomic islands (GIs) or more specifically pathogenicity or symbiotic islands. Results We have implemented the program SIGI-HMM that predicts GIs and the putative donor of each individual alien gene. It is based on the analysis of codon usage (CU) of each individual gene of a genome under study. CU of each gene is compared against a carefully selected set of CU tables representing microbial donors or highly expressed genes. Multiple tests are used to identify putatively alien genes, to predict putative donors and to mask putatively highly expressed genes. Thus, we determine the states and emission probabilities of an inhomogeneous hidden Markov model working on gene level. For the transition probabilities, we draw upon classical test theory with the intention of integrating a sensitivity controller in a consistent manner. SIGI-HMM was written in JAVA and is publicly available. It accepts as input any file created according to the EMBL-format. It generates output in the common GFF format readable for genome browsers. Benchmark tests showed that the output of SIGI-HMM is in agreement with known findings. Its predictions were both consistent with annotated GIs and with predictions generated by different methods. Conclusion SIGI-HMM is a sensitive tool for the identification of GIs in microbial genomes. It allows to interactively analyze genomes in detail and to generate or to test hypotheses about the origin of acquired genes. PMID:16542435

  6. Genome Sequences of Poaceae-Associated Gemycircularviruses from the Pacific Ocean Island of Tonga

    PubMed Central

    Male, Maketalena F.; Kami, Viliami; Kraberger, Simona

    2015-01-01

    We sampled and analyzed 43 Poaceae plants from the Pacific Ocean island of Tonga for the presence of circular DNA viruses. From these samples, we recovered three gemycircularvirus genomes, which share >99% identity, from Brachiaria deflexa (n = 2) and sugarcane (n = 1). These genomes share <61% genome-wide identity with other gemycircularvirus sequences in public databases. PMID:26472826

  7. Genome Sequences of Poaceae-Associated Gemycircularviruses from the Pacific Ocean Island of Tonga.

    PubMed

    Male, Maketalena F; Kami, Viliami; Kraberger, Simona; Varsani, Arvind

    2015-01-01

    We sampled and analyzed 43 Poaceae plants from the Pacific Ocean island of Tonga for the presence of circular DNA viruses. From these samples, we recovered three gemycircularvirus genomes, which share >99% identity, from Brachiaria deflexa (n = 2) and sugarcane (n = 1). These genomes share <61% genome-wide identity with other gemycircularvirus sequences in public databases. PMID:26472826

  8. Adaptive introgression between Anopheles sibling species eliminates a major genomic island but not reproductive isolation

    PubMed Central

    Clarkson, Chris S.; Weetman, David; Essandoh, John; Yawson, Alexander E.; Maslen, Gareth; Manske, Magnus; Field, Stuart G.; Webster, Mark; Antão, Tiago; MacInnis, Bronwyn; Kwiatkowski, Dominic; Donnelly, Martin J.

    2014-01-01

    Adaptive introgression can provide novel genetic variation to fuel rapid evolutionary responses, though it may be counterbalanced by potential for detrimental disruption of the recipient genomic background. We examine the extent and impact of recent introgression of a strongly selected insecticide-resistance mutation (Vgsc-1014F) located within one of two exceptionally large genomic islands of divergence separating the Anopheles gambiae species pair. Here we show that transfer of the Vgsc mutation results in homogenization of the entire genomic island region (~1.5% of the genome) between species. Despite this massive disruption, introgression is clearly adaptive with a dramatic rise in frequency of Vgsc-1014F and no discernable impact on subsequent reproductive isolation between species. Our results show (1) how resilience of genomes to massive introgression can permit rapid adaptive response to anthropogenic selection and (2) that even extreme prominence of genomic islands of divergence can be an unreliable indicator of importance in speciation. PMID:24963649

  9. Draft Genome of Rhodococcus rhodochrous TRN7, Isolated from the Coast of Trindade Island, Brazil

    PubMed Central

    Rodrigues, Edmo M.; Pylro, Victor S.; Dobbler, Priscila T.; Victoria, Filipe

    2016-01-01

    Here, we present a draft genome and annotation of Rhodococcus rhodochrous TRN7, isolated from Trindade Island, Brazil, which will provide genetic data to benefit the understanding of its metabolism. PMID:26941155

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

    PubMed Central

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

    2015-01-01

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

  11. Mitochondrial genomes suggest rapid evolution of dwarf California Channel Islands foxes (Urocyon littoralis).

    PubMed

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

    2015-01-01

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

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

    PubMed Central

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

    2015-01-01

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

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

    PubMed

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

    2015-01-01

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

  14. Genomic islands of speciation separate cichlid ecomorphs in an East African crater lake.

    PubMed

    Malinsky, Milan; Challis, Richard J; Tyers, Alexandra M; Schiffels, Stephan; Terai, Yohey; Ngatunga, Benjamin P; Miska, Eric A; Durbin, Richard; Genner, Martin J; Turner, George F

    2015-12-18

    The genomic causes and effects of divergent ecological selection during speciation are still poorly understood. Here we report the discovery and detailed characterization of early-stage adaptive divergence of two cichlid fish ecomorphs in a small (700 meters in diameter) isolated crater lake in Tanzania. The ecomorphs differ in depth preference, male breeding color, body shape, diet, and trophic morphology. With whole-genome sequences of 146 fish, we identified 98 clearly demarcated genomic "islands" of high differentiation and demonstrated the association of genotypes across these islands with divergent mate preferences. The islands contain candidate adaptive genes enriched for functions in sensory perception (including rhodopsin and other twilight-vision-associated genes), hormone signaling, and morphogenesis. Our study suggests mechanisms and genomic regions that may play a role in the closely related mega-radiation of Lake Malawi. PMID:26680190

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

    PubMed

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

    2014-02-10

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

  16. GI-SVM: A sensitive method for predicting genomic islands based on unannotated sequence of a single genome.

    PubMed

    Lu, Bingxin; Leong, Hon Wai

    2016-02-01

    Genomic islands (GIs) are clusters of functionally related genes acquired by lateral genetic transfer (LGT), and they are present in many bacterial genomes. GIs are extremely important for bacterial research, because they not only promote genome evolution but also contain genes that enhance adaption and enable antibiotic resistance. Many methods have been proposed to predict GI. But most of them rely on either annotations or comparisons with other closely related genomes. Hence these methods cannot be easily applied to new genomes. As the number of newly sequenced bacterial genomes rapidly increases, there is a need for methods to detect GI based solely on sequences of a single genome. In this paper, we propose a novel method, GI-SVM, to predict GIs given only the unannotated genome sequence. GI-SVM is based on one-class support vector machine (SVM), utilizing composition bias in terms of k-mer content. From our evaluations on three real genomes, GI-SVM can achieve higher recall compared with current methods, without much loss of precision. Besides, GI-SVM allows flexible parameter tuning to get optimal results for each genome. In short, GI-SVM provides a more sensitive method for researchers interested in a first-pass detection of GI in newly sequenced genomes. PMID:26907990

  17. Pre_GI: a global map of ontological links between horizontally transferred genomic islands in bacterial and archaeal genomes.

    PubMed

    Pierneef, Rian; Cronje, Louis; Bezuidt, Oliver; Reva, Oleg N

    2015-01-01

    The Predicted Genomic Islands database (Pre_GI) is a comprehensive repository of prokaryotic genomic islands (islands, GIs) freely accessible at http://pregi.bi.up.ac.za/index.php. Pre_GI, Version 2015, catalogues 26?744 islands identified in 2407 bacterial/archaeal chromosomes and plasmids. It provides an easy-to-use interface which allows users the ability to query against the database with a variety of fields, parameters and associations. Pre_GI is constructed to be a web-resource for the analysis of ontological roads between islands and cartographic analysis of the global fluxes of mobile genetic elements through bacterial and archaeal taxonomic borders. Comparison of newly identified islands against Pre_GI presents an alternative avenue to identify their ontology, origin and relative time of acquisition. Pre_GI aims to aid research on horizontal transfer events and materials through providing data and tools for holistic investigation of migration of genes through ecological niches and taxonomic boundaries. PMID:26200753

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

    PubMed Central

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

    2009-01-01

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

  19. A Novel Method to Predict Genomic Islands Based on Mean Shift Clustering Algorithm

    PubMed Central

    de Brito, Daniel M.; Maracaja-Coutinho, Vinicius; de Farias, Savio T.; Batista, Leonardo V.; do Rêgo, Thaís G.

    2016-01-01

    Genomic Islands (GIs) are regions of bacterial genomes that are acquired from other organisms by the phenomenon of horizontal transfer. These regions are often responsible for many important acquired adaptations of the bacteria, with great impact on their evolution and behavior. Nevertheless, these adaptations are usually associated with pathogenicity, antibiotic resistance, degradation and metabolism. Identification of such regions is of medical and industrial interest. For this reason, different approaches for genomic islands prediction have been proposed. However, none of them are capable of predicting precisely the complete repertory of GIs in a genome. The difficulties arise due to the changes in performance of different algorithms in the face of the variety of nucleotide distribution in different species. In this paper, we present a novel method to predict GIs that is built upon mean shift clustering algorithm. It does not require any information regarding the number of clusters, and the bandwidth parameter is automatically calculated based on a heuristic approach. The method was implemented in a new user-friendly tool named MSGIP—Mean Shift Genomic Island Predictor. Genomes of bacteria with GIs discussed in other papers were used to evaluate the proposed method. The application of this tool revealed the same GIs predicted by other methods and also different novel unpredicted islands. A detailed investigation of the different features related to typical GI elements inserted in these new regions confirmed its effectiveness. Stand-alone and user-friendly versions for this new methodology are available at http://msgip.integrativebioinformatics.me. PMID:26731657

  20. A Novel Method to Predict Genomic Islands Based on Mean Shift Clustering Algorithm.

    PubMed

    de Brito, Daniel M; Maracaja-Coutinho, Vinicius; de Farias, Savio T; Batista, Leonardo V; do Rêgo, Thaís G

    2016-01-01

    Genomic Islands (GIs) are regions of bacterial genomes that are acquired from other organisms by the phenomenon of horizontal transfer. These regions are often responsible for many important acquired adaptations of the bacteria, with great impact on their evolution and behavior. Nevertheless, these adaptations are usually associated with pathogenicity, antibiotic resistance, degradation and metabolism. Identification of such regions is of medical and industrial interest. For this reason, different approaches for genomic islands prediction have been proposed. However, none of them are capable of predicting precisely the complete repertory of GIs in a genome. The difficulties arise due to the changes in performance of different algorithms in the face of the variety of nucleotide distribution in different species. In this paper, we present a novel method to predict GIs that is built upon mean shift clustering algorithm. It does not require any information regarding the number of clusters, and the bandwidth parameter is automatically calculated based on a heuristic approach. The method was implemented in a new user-friendly tool named MSGIP-Mean Shift Genomic Island Predictor. Genomes of bacteria with GIs discussed in other papers were used to evaluate the proposed method. The application of this tool revealed the same GIs predicted by other methods and also different novel unpredicted islands. A detailed investigation of the different features related to typical GI elements inserted in these new regions confirmed its effectiveness. Stand-alone and user-friendly versions for this new methodology are available at http://msgip.integrativebioinformatics.me. PMID:26731657

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

    PubMed Central

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

    2008-01-01

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

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

    PubMed Central

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

    2015-01-01

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

  3. Contribution of the thermotolerance genomic island to increased thermal tolerance in Cronobacter strains.

    PubMed

    Orieskova, Maria; Kajsik, Michal; Szemes, Tomas; Holy, Ondrej; Forsythe, Stephen; Turna, Jan; Drahovska, Hana

    2016-03-01

    Cronobacter spp. are opportunistic pathogens associated with serious infections in neonates. Increased stress tolerance, including the thermotolerance of some Cronobacter strains, can promote their survival in production facilities and thus raise the possibility of contamination of dried infant formula which has been identified as a potential source of infection. Some Cronobacter strains contain a genomic island, which might be responsible for increased thermotolerance. By analysis of Cronobacter sequenced genomes this determinant was found to be present in only 49/73 Cronobacter sakazakii strains and in 9/14 Cronobacter malonaticus strains. The island was also found in 16/17 clinical isolates originating from two hospitals. Two configurations of the locus were detected; the first one with the size of 18 kbp containing the thrB-Q genes and a shorter version (6 kbp) harbouring only the thrBCD and thrOP genes. Strains containing the thermotolerance island survived significantly better at 58 °C comparing to a C. sakazakii isogenic mutant lacking the island and strains with the longer version of the island were 2-10 times more tolerant than those with the shortened sequence. The function of the genomic island was further confirmed by its cloning into a low-copy vector and transforming it into the isogenic mutant. Different levels of rpoS, encoding for stress-response sigma factor, expression were also associated with variability in strain thermotolerance. PMID:26748923

  4. Unusual Class 1 Integron Configuration Found in Salmonella Genomic Island 2 from Salmonella enterica Serovar Emek?

    PubMed Central

    Wilson, Neil L.; Hall, Ruth M.

    2010-01-01

    Salmonella genomic island 2 (SGI2) is an independently derived genomic island related to SGI1 with the integron in a different position. The integron in SGI2 was found to include an additional 2.1 kb derived from the tni module of Tn5058, Tn502, or Tn512 that was not detected previously. Independent evolution of the backbone was confirmed with 21 single base differences found in over 11.5 kb, representing 40% of the 27.4-kb SGI2 backbone. PMID:19884375

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

    PubMed

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

    2014-09-01

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

  6. Genomic Islands in Pathogenic Filamentous Fungus Aspergillus fumigatus

    Technology Transfer Automated Retrieval System (TEKTRAN)

    We present the genome sequences of a new clinical isolate, CEA10, of an important human pathogen, Aspergillus fumigatus, and two closely related, but rarely pathogenic species, Neosartorya fischeri NRRL181 and Aspergillus clavatus NRRL1. Comparative genomic analysis of CEA10 with the recently sequen...

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

    PubMed Central

    Morales-Espinosa, Rosario; Soberón-Chávez, Gloria; Delgado-Sapién, Gabriela; Sandner-Miranda, Luisa; Méndez, José L.; González-Valencia, Gerardo; Cravioto, Alejandro

    2012-01-01

    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. PMID:22662157

  8. A Hybrid Approach for CpG Island Detection in the Human Genome

    PubMed Central

    Yang, Cheng-Hong; Lin, Yu-Da; Chiang, Yi-Cheng; Chuang, Li-Yeh

    2016-01-01

    Background CpG islands have been demonstrated to influence local chromatin structures and simplify the regulation of gene activity. However, the accurate and rapid determination of CpG islands for whole DNA sequences remains experimentally and computationally challenging. Methodology/Principal Findings A novel procedure is proposed to detect CpG islands by combining clustering technology with the sliding-window method (PSO-based). Clustering technology is used to detect the locations of all possible CpG islands and process the data, thus effectively obviating the need for the extensive and unnecessary processing of DNA fragments, and thus improving the efficiency of sliding-window based particle swarm optimization (PSO) search. This proposed approach, named ClusterPSO, provides versatile and highly-sensitive detection of CpG islands in the human genome. In addition, the detection efficiency of ClusterPSO is compared with eight CpG island detection methods in the human genome. Comparison of the detection efficiency for the CpG islands in human genome, including sensitivity, specificity, accuracy, performance coefficient (PC), and correlation coefficient (CC), ClusterPSO revealed superior detection ability among all of the test methods. Moreover, the combination of clustering technology and PSO method can successfully overcome their respective drawbacks while maintaining their advantages. Thus, clustering technology could be hybridized with the optimization algorithm method to optimize CpG island detection. Conclusion/Significance The prediction accuracy of ClusterPSO was quite high, indicating the combination of CpGcluster and PSO has several advantages over CpGcluster and PSO alone. In addition, ClusterPSO significantly reduced implementation time. PMID:26727213

  9. An Atypical Orphan Carbohydrate-NRPS Genomic Island Encodes a Novel Lytic Transglycosylase

    PubMed Central

    Guo, Xun; Crawford, Jason M.

    2014-01-01

    SUMMARY Microbial genome sequencing platforms have produced a deluge of orphan biosynthetic pathways suspected of biosynthesizing new small molecules with pharmacological relevance. Genome synteny analysis provides an assessment of genomic island content, which is enriched in natural product gene clusters. Here we identified an atypical orphan carbohydrate-nonribosomal peptide synthetase (NRPS) genomic island in Photorhabdus luminescens using genome synteny analysis. Heterologous expression of the pathway led to the characterization of five new oligosaccharide metabolites with lysozyme inhibitory activities. The oligosaccharides harbor a 1,6-anhydro-β-D-N-acetyl-glucosamine (Glc-NAc) moiety, a rare structural feature for natural products. Gene deletion analysis and biochemical reconstruction of oligosaccharide production led to the discovery that a hypothetical protein in the pathway is a novel lytic transglycosylase responsible for bicyclic sugar formation. The example presented here supports a notion where targeting select genomic islands with a reduced reliance on known protein homologies could enhance the discovery of new metabolic chemistry and biology. PMID:25219963

  10. Defining genomic islands and uropathogen-specific genes in uropathogenic Escherichia coli.

    PubMed

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

    2007-05-01

    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. PMID:17351047

  11. Complete Genome Sequence of Papaya Ringspot Virus Isolated from Genetically Modified Papaya in Hainan Island, China.

    PubMed

    Zhao, Guangyuan; Yan, Pu; Shen, Wentao; Tuo, Decai; Li, Xiaoying; Zhou, Peng

    2015-01-01

    The complete genome sequence (10,326 nucleotides) of a papaya ringspot virus isolate infecting genetically modified papaya in Hainan Island of China was determined through reverse transcription (RT)-PCR. The virus shares 92% nucleotide sequence identity with the isolate that is unable to infect PRSV-resistant transgenic papaya. PMID:26358610

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

    PubMed Central

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

    2015-01-01

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

  13. Genomic evaluation, breed identification, and population structure of North American, English and Island Guernsey dairy cattle

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Genomic evaluations of dairy cattle in the United States have been available for Brown Swiss, Holsteins, and Jerseys since 2009 and for Ayrshires since 2013. As of February 2015, 2,281 Guernsey bulls and cows had genotypes from collaboration between the United States, Canada, England, and the island...

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

    PubMed

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

    2013-01-01

    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

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

    PubMed

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

    2013-01-01

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

  16. Adaptation in Toxic Environments: Arsenic Genomic Islands in the Bacterial Genus Thiomonas

    PubMed Central

    Freel, Kelle C.; Krueger, Martin C.; Farasin, Julien; Brochier-Armanet, Céline; Barbe, Valérie; Andrès, Jeremy; Cholley, Pierre-Etienne; Dillies, Marie-Agnès; Jagla, Bernd; Koechler, Sandrine; Leva, Yann; Magdelenat, Ghislaine; Plewniak, Frédéric; Proux, Caroline; Coppée, Jean-Yves; Bertin, Philippe N.; Heipieper, Hermann J.; Arsène-Ploetze, Florence

    2015-01-01

    Acid mine drainage (AMD) is a highly toxic environment for most living organisms due to the presence of many lethal elements including arsenic (As). Thiomonas (Tm.) bacteria are found ubiquitously in AMD and can withstand these extreme conditions, in part because they are able to oxidize arsenite. In order to further improve our knowledge concerning the adaptive capacities of these bacteria, we sequenced and assembled the genome of six isolates derived from the Carnoulès AMD, and compared them to the genomes of Tm. arsenitoxydans 3As (isolated from the same site) and Tm. intermedia K12 (isolated from a sewage pipe). A detailed analysis of the Tm. sp. CB2 genome revealed various rearrangements had occurred in comparison to what was observed in 3As and K12 and over 20 genomic islands (GEIs) were found in each of these three genomes. We performed a detailed comparison of the two arsenic-related islands found in CB2, carrying the genes required for arsenite oxidation and As resistance, with those found in K12, 3As, and five other Thiomonas strains also isolated from Carnoulès (CB1, CB3, CB6, ACO3 and ACO7). Our results suggest that these arsenic-related islands have evolved differentially in these closely related Thiomonas strains, leading to divergent capacities to survive in As rich environments. PMID:26422469

  17. Draft Genome Sequence of Halostagnicola sp. A56, an Extremely Halophilic Archaeon Isolated from the Andaman Islands.

    PubMed

    Kanekar, Sagar P; Saxena, Neha; Pore, Soham D; Arora, Preeti; Kanekar, P P; Dhakephalkar, P K

    2015-01-01

    The first draft genome of Halostagnicola sp. A56, isolated from the Andaman Islands is reported here. The A56 genome comprises 3,178,490 bp in 26 contigs with a G+C content of 60.8%. The genome annotation revealed that A56 could have potential applications for the production of polyhydroxyalkanoate or bioplastics. PMID:26564049

  18. Restriction landmark genomic scanning: analysis of CpG islands in genomes by 2D gel electrophoresis.

    PubMed

    Costello, Joseph F; Hong, Chibo; Plass, Christoph; Smiraglia, Dominic J

    2009-01-01

    Restriction landmark genomic scanning (RLGS) is a method that provides a quantitative genetic and epigenetic (cytosine methylation) assessment of thousands of CpG islands in a single gel without prior knowledge of gene sequence. The method is based on two-dimensional separation of radiolabeled genomic DNA into nearly 2,000 discrete fragments that have a high probability of containing gene sequences. Genomic DNA is digested with an infrequently cutting restriction enzyme, such as NotI or AscI, radiolabeled at the cleaved ends, digested with a second restriction enzyme, and then electrophoresed through a narrow, 60-cm-long agarose tube-shaped gel. The DNA in the tube gel is then digested by a third, more frequently cutting restriction enzyme and electrophoresed, in a direction perpendicular to the first separation, through a 5% nondenaturing polyacrylamide gel, and the gel is autoradiographed. Radiolabeled NotI or AscI sites are frequently used as "landmarks" because NotI or AscI cannot cleave methylated sites and since an estimated 89% and 83% of the recognition sites, respectively, are found within CpG islands. Using a methylation-sensitive enzyme, the technique has been termed RLGS-M. The resulting RLGS profile displays both the copy number and methylation status of the CpG islands. Integrated with high-resolution gene copy-number analyses, RLGS enables one to define genetic or epigenetic alteration in cells. These profiles are highly reproducible and are therefore amenable to inter- and intraindividual DNA sample comparisons. RLGS was the first of many technologies to allow large-scale DNA methylation analysis of CpG islands. PMID:18987812

  19. Identification and characterization of episomal forms of integrative genomic islands in the genus Francisella.

    PubMed

    Rydzewski, Kerstin; Tlapák, Hana; Niehaus, Indra P; Dabrowski, Piotr W; Grunow, Roland; Heuner, Klaus

    2015-12-01

    Recently, we identified a putative prophage on a genomic island (GI) within the genome sequence of Francisella hispaniensis isolate AS0-814 (Francisella tularensis subsp. novicida-like 3523) by the analysis of the CRISPR-Cas systems of Francisella. Various spacer DNAs within the CRISPR region of different F. tularensis subsp. novicida strains were found to be homologous to the putative prophage (Schunder et al., 2013, Int. J. Med. Microbiol. 303:51-60). Now we identified the GI (FhaGI-1) as a mobile element which is able to form a circular episomal structure. The circular episomal form of FhaGI-1 is generated by F. hispaniensis, and the excision of the island is an integrase-dependent and site-specific process. Furthermore, we could demonstrate that the excision of the island is also possible in other bacterial species (Escherichia coli). In addition, we could show that a genetically generated small variant of the island is also functional and, after its electroporation into strain F. tularensis subsp. holarctica LVS, the GI was stable and site-specifically integrated into the genome of the transformants. The integrase is sufficient for the integration and excision of the small variant into and from the DNA backbone, respectively. Thus, the element may be suitable to be used as a genetic tool in F. tularensis research. Furthermore, we identified the tRNA(Val) gene of Francisella as an integration site for GIs. Genomic island FphGI-1 was identified in Francisella philomiragia ATCC 25016. We were not able to detect the episomal form of this GI, probably due to a mutated attR site. However, we could demonstrate that integrative GIs are present in Francisella and that they may allow horizontal gene transfer between different Francisella species. PMID:26358917

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

    PubMed

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

    2015-02-01

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

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

    PubMed

    Papadopoulou, Anna; Knowles, L Lacey

    2015-06-01

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

  2. Genome characterization of Long Island tick rhabdovirus, a new virus identified in Amblyomma americanum ticks

    PubMed Central

    2014-01-01

    Background Ticks are implicated as hosts to a wide range of animal and human pathogens. The full range of microbes harbored by ticks has not yet been fully explored. Methods As part of a viral surveillance and discovery project in arthropods, we used unbiased high-throughput sequencing to examine viromes of ticks collected on Long Island, New York in 2013. Results We detected and sequenced the complete genome of a novel rhabdovirus originating from a pool of Amblyomma americanum ticks. This virus, which we provisionally name Long Island tick rhabdovirus, is distantly related to Moussa virus from Africa. Conclusions The Long Island tick rhabdovirus may represent a novel species within family Rhabdoviridae. PMID:24517260

  3. Position-Based Scanning for Comparative Genomics and Identification of Genetic Islands in Haemophilus influenzae Type b

    PubMed Central

    Bergman, Nicholas H.; Akerley, Brian J.

    2003-01-01

    Bacteria exhibit extensive genetic heterogeneity within species. In many cases, these differences account for virulence properties unique to specific strains. Several such loci have been discovered in the genome of the type b serotype of Haemophilus influenzae, a human pathogen able to cause meningitis, pneumonia, and septicemia. Here we report application of a PCR-based scanning procedure to compare the genome of a virulent type b (Hib) strain with that of the laboratory-passaged Rd KW20 strain for which a complete genome sequence is available. We have identified seven DNA segments or H. influenzae genetic islands (HiGIs) present in the type b genome and absent from the Rd genome. These segments vary in size and content and show signs of horizontal gene transfer in that their percent G+C content differs from that of the rest of the H. influenzae genome, they contain genes similar to those found on phages or other mobile elements, or they are flanked by DNA repeats. Several of these loci represent potential pathogenicity islands, because they contain genes likely to mediate interactions with the host. These newly identified genetic islands provide areas of investigation into both the evolution and pathogenesis of H. influenzae. In addition, the genome scanning approach developed to identify these islands provides a rapid means to compare the genomes of phenotypically diverse bacterial strains once the genome sequence of one representative strain has been determined. PMID:12595420

  4. PredictBias: a server for the identification of genomic and pathogenicity islands in prokaryotes.

    PubMed

    Pundhir, Sachin; Vijayvargiya, Hemant; Kumar, Anil

    2008-01-01

    Pathogenicity Islands (PAIs) are the sub-sets of Genomic Islands (GIs) that are acquired by horizontal gene transfer (HGT) and are generally shown to have a significant deviation in G+C, dinucleotide or codon frequency from core genome. Major approaches used for PAI identification are based on composition bias and/or similarity with known PAIs. These approaches either limit the search to GIs or to regions similar to previously annotated PAIs. PredictBias is a web application for the identification of genomic and pathogenicity islands in prokaryotes based on composition bias, presence of insertion elements, proximity with virulence-associated genes and absence in related non-pathogenic species. A profile database of virulence factors (VFPD) has been developed using 213 protein families associated to virulence retrieved from Pfam and PRINTS database. PredictBias performs a RPSBLAST search for regions with significant composition bias against VFPD. If a region encodes for at least one protein related to virulence then it is marked as potential PAI (biased-composition) otherwise as GI. Regions involved in virulence but having unsuspicious composition bias due to ancient HGT are identified by scanning genome segments (8 ORFs) with more than four significant hits to VFPD and are marked as potential PAI (unbiased-composition). The relative absence of potential PAIs in related non-pathogenic species can be investigated using 'compare genome feature' of PredictBias that further aids in validating the results and defining boundaries for PAIs. Performance measure analysis showed that the output of PredictBias is in agreement with the known findings. PredictBias is available at www.davvbiotech.res.in/PredictBias. PMID:19032158

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

    PubMed Central

    2014-01-01

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

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

    PubMed Central

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

    2011-01-01

    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. PMID:21738602

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

    PubMed

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

    2012-02-15

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

  8. Characterization of a Highly Conserved Island in the Otherwise Divergent Bordetella holmesii and Bordetella pertussis Genomes? §

    PubMed Central

    Diavatopoulos, D. A.; Cummings, C. A.; van der Heide, H. G. J.; van Gent, M.; Liew, S.; Relman, D. A.; Mooi, F. R.

    2006-01-01

    The recently discovered pathogen Bordetella holmesii has been isolated from the airways and blood of diseased humans. Genetic events contributing to the emergence of B. holmesii are not understood, and its phylogenetic position among the bordetellae remains unclear. To address these questions, B. holmesii strains were analyzed by comparative genomic hybridization (CGH) to a Bordetella pertussis microarray and by multilocus sequence typing. Both methods indicated substantial sequence divergence between B. pertussis and B. holmesii. However, CGH identified a putative pathogenicity island of 66 kb that is highly conserved between these species and contains several IS481 elements that may have been laterally transferred from B. pertussis to B. holmesii. This island contains, among other genes, a functional, iron-regulated locus encoding the biosynthesis, export, and uptake of the siderophore alcaligin. The acquisition of this genomic island by B. holmesii may have significantly contributed to its emergence as a human pathogen. Horizontal gene transfer between B. pertussis and B. holmesii may also explain the unusually high sequence identity of their 16S rRNA genes. PMID:17041054

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

    PubMed Central

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

    2013-01-01

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

  10. Newly introduced genomic prophage islands are critical determinants of in vivo competitiveness in the Liverpool Epidemic Strain of Pseudomonas aeruginosa.

    PubMed

    Winstanley, Craig; Langille, Morgan G I; Fothergill, Joanne L; Kukavica-Ibrulj, Irena; Paradis-Bleau, Catherine; Sanschagrin, François; Thomson, Nicholas R; Winsor, Geoff L; Quail, Michael A; Lennard, Nicola; Bignell, Alexandra; Clarke, Louise; Seeger, Kathy; Saunders, David; Harris, David; Parkhill, Julian; Hancock, Robert E W; Brinkman, Fiona S L; Levesque, Roger C

    2009-01-01

    Pseudomonas aeruginosa isolates have a highly conserved core genome representing up to 90% of the total genomic sequence with additional variable accessory genes, many of which are found in genomic islands or islets. The identification of the Liverpool Epidemic Strain (LES) in a children's cystic fibrosis (CF) unit in 1996 and its subsequent observation in several centers in the United Kingdom challenged the previous widespread assumption that CF patients acquire only unique strains of P. aeruginosa from the environment. To learn about the forces that shaped the development of this important epidemic strain, the genome of the earliest archived LES isolate, LESB58, was sequenced. The sequence revealed the presence of many large genomic islands, including five prophage clusters, one defective (pyocin) prophage cluster, and five non-phage islands. To determine the role of these clusters, an unbiased signature tagged mutagenesis study was performed, followed by selection in the chronic rat lung infection model. Forty-seven mutants were identified by sequencing, including mutants in several genes known to be involved in Pseudomonas infection. Furthermore, genes from four prophage clusters and one genomic island were identified and in direct competition studies with the parent isolate; four were demonstrated to strongly impact on competitiveness in the chronic rat lung infection model. This strongly indicates that enhanced in vivo competitiveness is a major driver for maintenance and diversifying selection of these genomic prophage genes. PMID:19047519

  11. Newly introduced genomic prophage islands are critical determinants of in vivo competitiveness in the Liverpool Epidemic Strain of Pseudomonas aeruginosa

    PubMed Central

    Winstanley, Craig; Langille, Morgan G.I.; Fothergill, Joanne L.; Kukavica-Ibrulj, Irena; Paradis-Bleau, Catherine; Sanschagrin, François; Thomson, Nicholas R.; Winsor, Geoff L.; Quail, Michael A.; Lennard, Nicola; Bignell, Alexandra; Clarke, Louise; Seeger, Kathy; Saunders, David; Harris, David; Parkhill, Julian; Hancock, Robert E.W.; Brinkman, Fiona S.L.; Levesque, Roger C.

    2009-01-01

    Pseudomonas aeruginosa isolates have a highly conserved core genome representing up to 90% of the total genomic sequence with additional variable accessory genes, many of which are found in genomic islands or islets. The identification of the Liverpool Epidemic Strain (LES) in a children’s cystic fibrosis (CF) unit in 1996 and its subsequent observation in several centers in the United Kingdom challenged the previous widespread assumption that CF patients acquire only unique strains of P. aeruginosa from the environment. To learn about the forces that shaped the development of this important epidemic strain, the genome of the earliest archived LES isolate, LESB58, was sequenced. The sequence revealed the presence of many large genomic islands, including five prophage clusters, one defective (pyocin) prophage cluster, and five non-phage islands. To determine the role of these clusters, an unbiased signature tagged mutagenesis study was performed, followed by selection in the chronic rat lung infection model. Forty-seven mutants were identified by sequencing, including mutants in several genes known to be involved in Pseudomonas infection. Furthermore, genes from four prophage clusters and one genomic island were identified and in direct competition studies with the parent isolate; four were demonstrated to strongly impact on competitiveness in the chronic rat lung infection model. This strongly indicates that enhanced in vivo competitiveness is a major driver for maintenance and diversifying selection of these genomic prophage genes. PMID:19047519

  12. Genomics in research and health care with Aboriginal and Torres Strait Islander peoples.

    PubMed

    McWhirter, Rebekah; Nicol, Dianne; Savulescu, Julian

    2015-01-01

    Genomics is increasingly becoming an integral component of health research and clinical care. The perceived difficulties associated with genetic research involving Aboriginal and Torres Strait Islander people mean that they have largely been excluded as research participants. This limits the applicability of research findings for Aboriginal and Torres Strait Islander patients. Emergent use of genomic technologies and personalised medicine therefore risk contributing to an increase in existing health disparities unless urgent action is taken. To allow the potential benefits of genomics to be more equitably distributed, and minimise potential harms, we recommend five actions: (1) ensure diversity of participants by implementing appropriate protocols at the study design stage; (2) target diseases that disproportionately affect disadvantaged groups; (3) prioritise capacity building to promote Indigenous leadership across research professions; (4) develop resources for consenting patients or participants from different cultural and linguistic backgrounds; and (5) integrate awareness of issues relating to Indigenous people into the governance structures, formal reviews, data collection protocols and analytical pipelines of health services and research projects. PMID:26507135

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

    PubMed

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

    2015-01-30

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

  14. Two novel Salmonella genomic island 1 variants in Proteus mirabilis isolates from swine farms in China.

    PubMed

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

    2015-07-01

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

  15. AbaR-Type Genomic Islands in Non-baumannii Acinetobacter Species Isolates from South Korea

    PubMed Central

    Kim, Dae Hun

    2015-01-01

    To investigate the presence and structure of AbaR-type genomic islands (GIs) in non-Acinetobacter baumannii isolates, a total of 155 non-baumannii Acinetobacter isolates from a South Korean hospital were analyzed. GIs were found in three Acinetobacter nosocomialis and two Acinetobacter seifertii isolates. Their structures were similar to those in A. baumannii isolates from Asian countries, including South Korea. The existence of AbaR-type GIs in non-baumannii Acinetobacter isolates is believed to be due to interspecies transfer of GI. PMID:26100696

  16. Molecular characteristics of Salmonella genomic island 1 in Proteus mirabilis isolates from poultry farms in China.

    PubMed

    Lei, Chang-Wei; Zhang, An-Yun; Liu, Bi-Hui; Wang, Hong-Ning; Guan, Zhong-Bin; Xu, Chang-Wen; Xia, Qing-Qing; Cheng, Han; Zhang, Dong-Dong

    2014-12-01

    Six out of the 64 studied Proteus mirabilis isolates from 11 poultry farms in China contained Salmonella genomic island 1 (SGI1). PCR mapping showed that the complete nucleotide sequences of SGI1s ranged from 33.2 to 42.5 kb. Three novel variants, SGI1-W, SGI1-X, and SGI1-Y, have been characterized. Resistance genes lnuF, dfrA25, and qnrB2 were identified in SGI1 for the first time. PMID:25267683

  17. Molecular Characteristics of Salmonella Genomic Island 1 in Proteus mirabilis Isolates from Poultry Farms in China

    PubMed Central

    Lei, Chang-Wei; Zhang, An-Yun; Liu, Bi-Hui; Guan, Zhong-Bin; Xu, Chang-Wen; Xia, Qing-Qing; Cheng, Han; Zhang, Dong-Dong

    2014-01-01

    Six out of the 64 studied Proteus mirabilis isolates from 11 poultry farms in China contained Salmonella genomic island 1 (SGI1). PCR mapping showed that the complete nucleotide sequences of SGI1s ranged from 33.2 to 42.5 kb. Three novel variants, SGI1-W, SGI1-X, and SGI1-Y, have been characterized. Resistance genes lnuF, dfrA25, and qnrB2 were identified in SGI1 for the first time. PMID:25267683

  18. 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

    2011-01-01

    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. PMID:21943043

  19. Genome-Wide CpG Island Profiling of Intraductal Papillary Mucinous Neoplasms of the Pancreas

    PubMed Central

    Hong, Seung-Mo; Omura, Noriyuki; Vincent, Audrey; Li, Ang; Knight, Spencer; Yu, Jun; Hruban, Ralph H.; Goggins, Michael

    2011-01-01

    Purpose Intraductal papillary mucinous neoplasms (IPMNs) are precursors to infiltrating pancreatic ductal adenocarcinomas. Widespread epigenetic alterations are characteristic of many cancers, yet few studies have systematically analyzed epigenetic alterations of neoplastic precursors. Our goal was to perform genome-wide CpG island methylation profiling to identify aberrantly methylated loci in IPMNs. Experimental Design We compared the CpG island methylation profiles of 6 IPMNs to normal primary pancreatic duct samples using methylation CpG island amplification (MCA) and Agilent CpG island microarray (MCAM) analysis. When selected 13 genes identified as differentially methylated by MCAM for methylation-specific PCR (MSP) analysis in an independent set of IPMNs and normal pancreas samples and performed expression analysis of selected genes. Results We identified 2,259 loci as differentially methylated in at least one of 6 IPMNs including 245 genes hypermethylated in IPMNs with high-grade dysplasia compared to normal pancreatic duct samples. Eleven of 13 genes evaluated by MSP were more commonly methylated in 61 IPMNs than in 43 normal pancreas samples. Several genes, (BNIP3, PTCHD2, SOX17, NXPH1, EBF3), were significantly more likely to be methylated in IPMNs with high-grade than with lower-grade dysplasia. One gene, Sox17, demonstrated loss of protein expression by immunohistochemistry in 22% (19 of 88) of IPMNs. The most specific marker, BNIP3, was not methylated in any IPMNs with low-grade dysplasia or in normal pancreas samples. Conclusions IPMNs undergo extensive aberrant CpG island hypermethylation. The detection of genes selectively methylated in high-grade IPMNs such as BNIP3 may have utility in the clinical evaluation of IPMNs. PMID:22173550

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

    PubMed Central

    Klockgether, Jens; Würdemann, Dieco; Reva, Oleg; Wiehlmann, Lutz; Tümmler, Burkhard

    2007-01-01

    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. PMID:17194795

  1. Identification of novel DNA fragments and partial sequence of a genomic island specific of Brucella pinnipedialis.

    PubMed

    Maquart, Marianne; Fardini, Yann; Zygmunt, Michel S; Cloeckaert, Axel

    2008-11-25

    Since the 1990s, Brucella strains have been isolated from a wide variety of marine mammals and were recently recognized as two different species, i.e. Brucella pinnipedialis for pinniped isolates and Brucella ceti for cetacean isolates. The aim of this study was to identify specific DNA fragments of marine mammal Brucella strains using a previously described infrequent restriction site-PCR (IRS-PCR) method but with three new couples of restriction enzymes applied on a larger panel of marine mammal Brucella isolates (n=74) and one human isolate from New Zealand likely from marine mammal origin. This study revealed five DNA fragments specific of Brucella strains isolated from marine mammals. Among them two new DNA fragments were specific of B. pinnipedialis but were not detected in hooded seal isolates. DNA fragment I identified in the previous IRS-PCR study and fragment VI of this study were located on a cloned and sequenced 6kb SacI fragment. Its nucleotide sequence revealed that it is likely part of a putative genomic island. Sequence analysis showed that it carries four ORFs coding for putative metabolic functions. Although hooded seal isolates are classified within B. pinnipedialis it was shown in this study that they do not carry this genomic island and this raises the question about their evolutionary history within B. pinnipedialis. PMID:18514443

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

    PubMed Central

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

    2015-01-01

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

  3. Characterization of genomic island 3 and genetic variability of Chilean field strains of Brucella abortus.

    PubMed

    Céspedes, Sandra; Salgado, Paulina; Valenzuela, Patricio; Vidal, Roberto; Oñate, Angel A

    2011-07-01

    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. PMID:21543580

  4. Characterization of Genomic Island 3 and Genetic Variability of Chilean Field Strains of Brucella abortus▿

    PubMed Central

    Céspedes, Sandra; Salgado, Paulina; Valenzuela, Patricio; Vidal, Roberto; Oñate, Angel A.

    2011-01-01

    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. PMID:21543580

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

    PubMed

    Stevens, Patricia; van Elsas, Jan Dirk

    2010-10-01

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

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

    PubMed

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

    2014-01-01

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

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

    PubMed Central

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

    2013-01-01

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

  8. Why Close a Bacterial Genome? The Plasmid of Alteromonas Macleodii HOT1A3 is a Vector for Inter-Specific Transfer of a Flexible Genomic Island

    PubMed Central

    Fadeev, Eduard; De Pascale, Fabio; Vezzi, Alessandro; Hübner, Sariel; Aharonovich, Dikla; Sher, Daniel

    2016-01-01

    Genome sequencing is rapidly becoming a staple technique in environmental and clinical microbiology, yet computational challenges still remain, leading to many draft genomes which are typically fragmented into many contigs. We sequenced and completely assembled the genome of a marine heterotrophic bacterium, Alteromonas macleodii HOT1A3, and compared its full genome to several draft genomes obtained using different reference-based and de novo methods. In general, the de novo assemblies clearly outperformed the reference-based or hybrid ones, covering >99% of the genes and representing essentially all of the gene functions. However, only the fully closed genome (∼4.5 Mbp) allowed us to identify the presence of a large, 148 kbp plasmid, pAM1A3. While HOT1A3 belongs to A. macleodii, typically found in surface waters (“surface ecotype”), this plasmid consists of an almost complete flexible genomic island (fGI), containing many genes involved in metal resistance previously identified in the genomes of Alteromonas mediterranea (“deep ecotype”). Indeed, similar to A. mediterranea, A. macleodii HOT1A3 grows at concentrations of zinc, mercury, and copper that are inhibitory for other A. macleodii strains. The presence of a plasmid encoding almost an entire fGI suggests that wholesale genomic exchange between heterotrophic marine bacteria belonging to related but ecologically different populations is not uncommon. PMID:27014193

  9. Genomic diversity and differentiation of a managed island wild boar population.

    PubMed

    Iacolina, L; Scandura, M; Goedbloed, D J; Alexandri, P; Crooijmans, R P M A; Larson, G; Archibald, A; Apollonio, M; Schook, L B; Groenen, M A M; Megens, H-J

    2016-01-01

    The evolution of island populations in natural systems is driven by local adaptation and genetic drift. However, evolutionary pathways may be altered by humans in several ways. The wild boar (WB) (Sus scrofa) is an iconic game species occurring in several islands, where it has been strongly managed since prehistoric times. We examined genomic diversity at 49 803 single-nucleotide polymorphisms in 99 Sardinian WBs and compared them with 196 wild specimens from mainland Europe and 105 domestic pigs (DP; 11 breeds). High levels of genetic variation were observed in Sardinia (80.9% of the total number of polymorphisms), which can be only in part associated to recent genetic introgression. Both Principal Component Analysis and Bayesian clustering approach revealed that the Sardinian WB population is highly differentiated from the other European populations (FST=0.126-0.138), and from DP (FST=0.169). Such evidences were mostly unaffected by an uneven sample size, although clustering results in reference populations changed when the number of individuals was standardized. Runs of homozygosity (ROHs) pattern and distribution in Sardinian WB are consistent with a past expansion following a bottleneck (small ROHs) and recent population substructuring (highly homozygous individuals). The observed effect of a non-random selection of Sardinian individuals on diversity, FST and ROH estimates, stressed the importance of sampling design in the study of structured or introgressed populations. Our results support the heterogeneity and distinctiveness of the Sardinian population and prompt further investigations on its origins and conservation status. PMID:26243137

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

    PubMed Central

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

    2009-01-01

    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 obesity and other metabolic disorders. We hypothesized that genetic drift and possibly natural selection on Kosrae might have increased the frequency of previously rare genetic variants with relatively large effects, making these alleles readily detectable in genome-wide association analysis. However, mapping in large, inbred cohorts introduces analytic challenges, as extensive relatedness between subjects violates the assumptions of independence upon which traditional association test statistics are based. We performed genome-wide association analysis for 15 quantitative traits in 2,906 members of the Kosrae population, using novel approaches to manage the extreme relatedness in the sample. As positive controls, we observe association to known loci for plasma cholesterol, triglycerides, and C-reactive protein and to a compelling candidate loci for thyroid stimulating hormone and fasting plasma glucose. We show that our study is well powered to detect common alleles explaining ?5% phenotypic variance. However, no such large effects were observed with genome-wide significance, arguing that even in such a severely inbred population, common alleles typically have modest effects. Finally, we show that a majority of common variants discovered in Caucasians have indistinguishable effect sizes on Kosrae, despite the major differences in population genetics and environment. PMID:19197348

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

    PubMed Central

    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

    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. PMID:23745137

  12. Genomic diversity and differentiation of a managed island wild boar population

    PubMed Central

    Iacolina, L; Scandura, M; Goedbloed, D J; Alexandri, P; Crooijmans, R P M A; Larson, G; Archibald, A; Apollonio, M; Schook, L B; Groenen, M A M; Megens, H-J

    2016-01-01

    The evolution of island populations in natural systems is driven by local adaptation and genetic drift. However, evolutionary pathways may be altered by humans in several ways. The wild boar (WB) (Sus scrofa) is an iconic game species occurring in several islands, where it has been strongly managed since prehistoric times. We examined genomic diversity at 49 803 single-nucleotide polymorphisms in 99 Sardinian WBs and compared them with 196 wild specimens from mainland Europe and 105 domestic pigs (DP; 11 breeds). High levels of genetic variation were observed in Sardinia (80.9% of the total number of polymorphisms), which can be only in part associated to recent genetic introgression. Both Principal Component Analysis and Bayesian clustering approach revealed that the Sardinian WB population is highly differentiated from the other European populations (FST=0.126–0.138), and from DP (FST=0.169). Such evidences were mostly unaffected by an uneven sample size, although clustering results in reference populations changed when the number of individuals was standardized. Runs of homozygosity (ROHs) pattern and distribution in Sardinian WB are consistent with a past expansion following a bottleneck (small ROHs) and recent population substructuring (highly homozygous individuals). The observed effect of a non-random selection of Sardinian individuals on diversity, FST and ROH estimates, stressed the importance of sampling design in the study of structured or introgressed populations. Our results support the heterogeneity and distinctiveness of the Sardinian population and prompt further investigations on its origins and conservation status. PMID:26243137

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

    PubMed Central

    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

    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. PMID:18495935

  14. Isolation by environment in White-breasted Nuthatches (Sitta carolinensis) of the Madrean Archipelago sky islands: a landscape genomics approach.

    PubMed

    Manthey, Joseph D; Moyle, Robert G

    2015-07-01

    Understanding landscape processes driving patterns of population genetic differentiation and diversity has been a long-standing focus of ecology and evolutionary biology. Gene flow may be reduced by historical, ecological or geographic factors, resulting in patterns of isolation by distance (IBD) or isolation by environment (IBE). Although IBE has been found in many natural systems, most studies investigating patterns of IBD and IBE in nature have used anonymous neutral genetic markers, precluding inference of selection mechanisms or identification of genes potentially under selection. Using landscape genomics, the simultaneous study of genomic and ecological landscapes, we investigated the processes driving population genetic patterns of White-breasted Nuthatches (Sitta carolinensis) in sky islands (montane forest habitat islands) of the Madrean Archipelago. Using more than 4000 single nucleotide polymorphisms and multiple tests to investigate the relationship between genetic differentiation and geographic or ecological distance, we identified IBE, and a lack of IBD, among sky island populations of S. carolinensis. Using three tests to identify selection, we found 79 loci putatively under selection; of these, seven matched CDS regions in the Zebra Finch. The loci under selection were highly associated with climate extremes (maximum temperature of warmest month and minimum precipitation of driest month). These results provide evidence for IBE - disentangled from IBD - in sky island vertebrates and identify potential adaptive genetic variation. PMID:26037653

  15. Presence and characterization of a mosaic genomic island which distinguishes sorbitol-fermenting enterohemorrhagic Escherichia coli O157:H- from E. coli O157:H7.

    PubMed

    Janka, Andreas; Becker, Georg; Sonntag, Anne-Katharina; Bielaszewska, Martina; Dobrindt, Ulrich; Karch, Helge

    2005-08-01

    A mosaic genomic island comprising Shigella resistance locus (SRL) sequences flanked by segments of Escherichia coli O157:H7 strain EDL933 O islands 43, 81, and 82 was identified in sorbitol-fermenting (SF) enterohemorrhagic Escherichia coli (EHEC) O157:H(-) strain 493/89. This mosaic island is absent from strain EDL933. PCR targeting the SRL-related sequence is a useful tool to distinguish SF EHEC O157:H(-) from EHEC O157:H7. PMID:16085887

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

    PubMed Central

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

    2011-01-01

    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

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

    PubMed

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

    2014-11-01

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

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

    PubMed

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

    2015-05-19

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

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

    PubMed Central

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

    2015-01-01

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

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

    PubMed Central

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

    2010-01-01

    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. PMID:20161777

  1. Symbiosis Island Shuffling with Abundant Insertion Sequences in the Genomes of Extra-Slow-Growing Strains of Soybean Bradyrhizobia

    PubMed Central

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

    2015-01-01

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

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

    PubMed

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

    2015-06-15

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

  3. CpG islands of hepatitis B virus genome isolated from Chinese patients.

    PubMed

    Hou, Zhiwei; Huang, Jihua; Zhong, Chengyao; Li, Lianbing; Xie, Qingdong; Ma, Mingfu; Han, Tingting; Wang, Degang; Maldonado, Martin; Xu, Lan; Huang, Tianhua; Zhong, Ying

    2015-05-01

    There are differences in the distribution and length of HBV CpG islands and the viral mutations contribute greatly to the development of HBV-related diseases. However, little is known regarding the effects of such difference and mutations in HBV genotypes B and C sequences on the regulation of HBV gene expression and their clinical outcomes. To study the distribution, length and genetic trait of CpG islands in normal and mutant sequences of HBV genotypes B and C, 320 HBV isolates from Chinese patients were retrieved from GenBank. Programs CLUSTALX 1.83 and MethPrimer were employed to perform multiple sequence alignments and to predict CpG islands, respectively. 72.0% genotype B isolates contained three conventional CpG islands, and 76.1% genotype C only contained CpG islands II and III. 14.6% genotype B and 7.5% genotype C contained three novel CpG islands. In genotype B, lengths of conventional CpG islands between normal and mutant isolates exhibited substantial variations, but in genotype C, those were relatively stable. CpG island II could be "truncated" or "split". "Truncated" region mutations were associated with structural and functional abnormalities of HBV genes. Rate of "split" CpG island II in genotype B was much higher than that in genotype C. In the majority of isolates from HCC and HBV-ACLF, genotype C lacked CpG island I and novel islands. Distribution, length and genetic trait of CpG islands in HBV genotypes B and C might affect their methylation status, and further affect regulation of HBV gene expression, leading to different clinical outcomes. PMID:25688883

  4. A multiresistance megaplasmid pLG1 bearing a hylEfm genomic island in hospital Enterococcus faecium isolates.

    PubMed

    Laverde Gomez, Jenny A; van Schaik, Willem; Freitas, Ana R; Coque, Teresa M; Weaver, Keith E; Francia, Maria Victoria; Witte, Wolfgang; Werner, Guido

    2011-02-01

    Enterococcus faecium is considered to be a nosocomial pathogen with increasing medical importance. The putative virulence factor, hyl(Efm), encoding a putative hyaluronidase, is enriched among the hospital-associated polyclonal subpopulation of E. faecium.. The hyl(Efm) gene is described to be part of a genomic island and was recently identified to be plasmid-located. Here, we present a description of the structure, localization, and distribution of the putative pathogenicity factor hyl(Efm) and its putative island among 39 clinical isolates and elucidate the composition and host range of pLG1, a hyl(Efm) multiresistance plasmid of approximately 281.02kb. The hyl(Efm) gene was located within a 17,824-bp element highly similar to the putative genomic island (GI) structure that had been previously described. This genomic region was conserved among 39 hyl(Efm)-positive strains with variation in a specific region downstream of hyl(Efm) in 18 strains. The putative hyl(Efm) was located on large plasmids (150-350kb) in 37 strains. pLG1 could be horizontally transferred into four different E. faecium recipient strains (n=4) but not into E. faecalis (n=3). Sequencing of pLG1 resolved putative plasmid replication, conjugation, and maintenance determinants as well as a pilin gene cluster, carbon uptake and utilization genes, heavy metal and antibiotic resistance clusters. The hyl(Efm) transferable plasmid pLG1 bears additional putative pathogenicity factors and antibiotic resistance genes. These findings suggest horizontal gene transfer of virulence factors and antibiotic resistance gene clusters by a single genetic event (conjugative transfer) which might be triggered by heavy antibiotic use common in health care units where E. faecium is increasingly prevalent. PMID:20951641

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

    PubMed Central

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

    2013-01-01

    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

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

    PubMed

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

    2013-01-01

    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

  7. Genome-wide CpG island methylation and intergenic demethylation propensities vary among different tumor sites

    PubMed Central

    Lee, Seung-Tae; Wiemels, Joseph L.

    2016-01-01

    The epigenetic landscape of cancer includes both focal hypermethylation and broader hypomethylation in a genome-wide manner. By means of a comprehensive genomic analysis on 6637 tissues of 21 tumor types, we here show that the degrees of overall methylation in CpG island (CGI) and demethylation in intergenic regions, defined as ‘backbone’, largely vary among different tumors. Depending on tumor type, both CGI methylation and backbone demethylation are often associated with clinical, epidemiological and biological features such as age, sex, smoking history, anatomic location, histological type and grade, stage, molecular subtype and biological pathways. We found connections between CGI methylation and hypermutability, microsatellite instability, IDH1 mutation, 19p gain and polycomb features, and backbone demethylation with chromosomal instability, NSD1 and TP53 mutations, 5q and 19p loss and long repressive domains. These broad epigenetic patterns add a new dimension to our understanding of tumor biology and its clinical implications. PMID:26464434

  8. Genome-wide CpG island methylation and intergenic demethylation propensities vary among different tumor sites.

    PubMed

    Lee, Seung-Tae; Wiemels, Joseph L

    2016-02-18

    The epigenetic landscape of cancer includes both focal hypermethylation and broader hypomethylation in a genome-wide manner. By means of a comprehensive genomic analysis on 6637 tissues of 21 tumor types, we here show that the degrees of overall methylation in CpG island (CGI) and demethylation in intergenic regions, defined as 'backbone', largely vary among different tumors. Depending on tumor type, both CGI methylation and backbone demethylation are often associated with clinical, epidemiological and biological features such as age, sex, smoking history, anatomic location, histological type and grade, stage, molecular subtype and biological pathways. We found connections between CGI methylation and hypermutability, microsatellite instability, IDH1 mutation, 19p gain and polycomb features, and backbone demethylation with chromosomal instability, NSD1 and TP53 mutations, 5q and 19p loss and long repressive domains. These broad epigenetic patterns add a new dimension to our understanding of tumor biology and its clinical implications. PMID:26464434

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

    PubMed Central

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

    2014-01-01

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

  10. Stability of a Pseudomonas putida KT2440 bacteriophage-carried genomic island and its impact on rhizosphere fitness.

    PubMed

    Quesada, Jose M; Soriano, María Isabel; Espinosa-Urgel, Manuel

    2012-10-01

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

  11. A large genomic island allows Neisseria meningitidis to utilize propionic acid, with implications for colonization of the human nasopharynx

    PubMed Central

    Catenazzi, Maria Chiara E; Jones, Helen; Wallace, Iain; Clifton, Jacqueline; Chong, James P J; Jackson, Matthew A; Macdonald, Sandy; Edwards, James; Moir, James W B

    2014-01-01

    Neisseria meningitidis is an important human pathogen that is capable of killing within hours of infection. Its normal habitat is the nasopharynx of adult humans. Here we identify a genomic island (the prp gene cluster) in N. meningitidis that enables this species to utilize propionic acid as a supplementary carbon source during growth, particularly under nutrient poor growth conditions. The prp gene cluster encodes enzymes for a methylcitrate cycle. Novel aspects of the methylcitrate cycle in N. meningitidis include a propionate kinase which was purified and characterized, and a putative propionate transporter. This genomic island is absent from the close relative of N. meningitidis, the commensal Neisseria lactamica, which chiefly colonizes infants not adults. We reason that the possession of the prp genes provides a metabolic advantage to N. meningitidis in the adult oral cavity, which is rich in propionic acid-generating bacteria. Data from classical microbiological and sequence-based microbiome studies provide several lines of supporting evidence that N. meningitidis colonization is correlated with propionic acid generating bacteria, with a strong correlation between prp-containing Neisseria and propionic acid generating bacteria from the genus Porphyromonas, and that this may explain adolescent/adult colonization by N. meningitidis. PMID:24910087

  12. In Silico Enhanced Restriction Enzyme Based Methylation Analysis of the Human Glioblastoma Genome Using Agilent 244K CpG Island Microarrays.

    PubMed

    Tran, Anh; Escovedo, Cameron; Migdall-Wilson, Justine; Chou, Arthur P; Chen, Weidong; Cloughesy, Timothy; Nelson, Stanley; Lai, Albert

    2009-01-01

    Genome wide methylation profiling of gliomas is likely to provide important clues to improving treatment outcomes. Restriction enzyme based approaches have been widely utilized for methylation profiling of cancer genomes and will continue to have importance in combination with higher density microarrays. With the availability of the human genome sequence and microarray probe sequences, these approaches can be readily characterized and optimized via in silico modeling. We adapted the previously described HpaII/MspI based Methylation Sensitive Restriction Enzyme (MSRE) assay for use with two-color Agilent 244K CpG island microarrays. In this assay, fragmented genomic DNA is digested in separate reactions with isoschizomeric HpaII (methylation-sensitive) and MspI (methylation-insensitive) restriction enzymes. Using in silico hybridization, we found that genomic fragmentation with BfaI was superior to MseI, providing a maximum effective coverage of 22,362 CpG islands in the human genome. In addition, we confirmed the presence of an internal control group of fragments lacking HpaII/MspI sites which enable separation of methylated and unmethylated fragments. We used this method on genomic DNA isolated from normal brain, U87MG cells, and a glioblastoma patient tumor sample and confirmed selected differentially methylated CpG islands using bisulfite sequencing. Along with additional validation points, we performed a receiver operating characteristics (ROC) analysis to determine the optimal threshold (p islands common to all three samples and 145 CpG islands unique to glioblastoma. These data provide general guidance to individuals seeking to maximize effective coverage using restriction enzyme based methylation profiling approaches. PMID:20582289

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

    PubMed Central

    Luo, Peng; Rodrigue, Sébastien; Burrus, Vincent

    2014-01-01

    Dissemination of antibiotic resistance genes occurs mostly by conjugation, which mediates DNA transfer between cells in direct contact. Conjugative plasmids of the IncA/C incompatibility group have become a substantial threat due to their broad host-range, the extended spectrum of antimicrobial resistance they confer, their prevalence in enteric bacteria and their very efficient spread by conjugation. However, their biology remains largely unexplored. Using the IncA/C conjugative plasmid pVCR94ΔX as a prototype, we have investigated the regulatory circuitry that governs IncA/C plasmids dissemination and found that the transcriptional activator complex AcaCD is essential for the expression of plasmid transfer genes. Using chromatin immunoprecipitation coupled with exonuclease digestion (ChIP-exo) and RNA sequencing (RNA-seq) approaches, we have identified the sequences recognized by AcaCD and characterized the AcaCD regulon. Data mining using the DNA motif recognized by AcaCD revealed potential AcaCD-binding sites upstream of genes involved in the intracellular mobility functions (recombination directionality factor and mobilization genes) in two widespread classes of genomic islands (GIs) phylogenetically unrelated to IncA/C plasmids. The first class, SGI1, confers and propagates multidrug resistance in Salmonella enterica and Proteus mirabilis, whereas MGIVmi1 in Vibrio mimicus belongs to a previously uncharacterized class of GIs. We have demonstrated that through expression of AcaCD, IncA/C plasmids specifically trigger the excision and mobilization of the GIs at high frequencies. This study provides new evidence of the considerable impact of IncA/C plasmids on bacterial genome plasticity through their own mobility and the mobilization of genomic islands. PMID:25340549

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

    PubMed Central

    2010-01-01

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

  15. Draft Genome Sequences of Sarcina ventriculi Strains Isolated from Wild Japanese Macaques in Yakushima Island.

    PubMed

    Ushida, Kazunari; Tsuchida, Sayaka; Ogura, Yoshitoshi; Hayashi, Tetsuya; Sawada, Akiko; Hanya, Goro

    2016-01-01

    We report the draft genome sequences of Sarcina ventriculi strains 14 and 17, both isolated from feces of wild Yakushima macaques (Macaca fuscata yakui). These genomic sequences will be helpful for the phylogenetic consideration of the family Clostridiaceae and understanding of the contribution of intestinal microbiota to the survival of Yakushima macaques. PMID:26847899

  16. Draft Genome Sequences of Sarcina ventriculi Strains Isolated from Wild Japanese Macaques in Yakushima Island

    PubMed Central

    Tsuchida, Sayaka; Ogura, Yoshitoshi; Hayashi, Tetsuya; Sawada, Akiko; Hanya, Goro

    2016-01-01

    We report the draft genome sequences of Sarcina ventriculi strains 14 and 17, both isolated from feces of wild Yakushima macaques (Macaca fuscata yakui). These genomic sequences will be helpful for the phylogenetic consideration of the family Clostridiaceae and understanding of the contribution of intestinal microbiota to the survival of Yakushima macaques. PMID:26847899

  17. A genomic island defines subspecies-specific virulence features of the host-adapted pathogen Campylobacter fetus subsp. venerealis.

    PubMed

    Gorkiewicz, Gregor; Kienesberger, Sabine; Schober, Caroline; Scheicher, Sylvia R; Gülly, Christian; Zechner, Rudolf; Zechner, Ellen L

    2010-01-01

    The pathogen Campylobacter fetus comprises two subspecies, C. fetus subsp. fetus and C. fetus subsp. venerealis. Although these taxa are highly related on the genome level, they are adapted to distinct hosts and tissues. C. fetus subsp. fetus infects a diversity of hosts, including humans, and colonizes the gastrointestinal tract. In contrast, C. fetus subsp. venerealis is largely restricted to the bovine genital tract, causing epidemic abortion in these animals. In light of their close genetic relatedness, the specific niche preferences make the C. fetus subspecies an ideal model system to investigate the molecular basis of host adaptation. In this study, a subtractive-hybridization approach was applied to the genomes of the subspecies to identify different genes potentially underlying this specificity. The comparison revealed a genomic island uniquely present in C. fetus subsp. venerealis that harbors several genes indicative of horizontal transfer and that encodes the core components necessary for bacterial type IV secretion. Macromolecular transporters of this type deliver effector molecules to host cells, thereby contributing to virulence in various pathogens. Mutational inactivation of the putative secretion system confirmed its involvement in the pathogenicity of C. fetus subsp. venerealis. PMID:19897645

  18. A Genomic Island Defines Subspecies-Specific Virulence Features of the Host-Adapted Pathogen Campylobacter fetus subsp. venerealis▿ †

    PubMed Central

    Gorkiewicz, Gregor; Kienesberger, Sabine; Schober, Caroline; Scheicher, Sylvia R.; Gülly, Christian; Zechner, Rudolf; Zechner, Ellen L.

    2010-01-01

    The pathogen Campylobacter fetus comprises two subspecies, C. fetus subsp. fetus and C. fetus subsp. venerealis. Although these taxa are highly related on the genome level, they are adapted to distinct hosts and tissues. C. fetus subsp. fetus infects a diversity of hosts, including humans, and colonizes the gastrointestinal tract. In contrast, C. fetus subsp. venerealis is largely restricted to the bovine genital tract, causing epidemic abortion in these animals. In light of their close genetic relatedness, the specific niche preferences make the C. fetus subspecies an ideal model system to investigate the molecular basis of host adaptation. In this study, a subtractive-hybridization approach was applied to the genomes of the subspecies to identify different genes potentially underlying this specificity. The comparison revealed a genomic island uniquely present in C. fetus subsp. venerealis that harbors several genes indicative of horizontal transfer and that encodes the core components necessary for bacterial type IV secretion. Macromolecular transporters of this type deliver effector molecules to host cells, thereby contributing to virulence in various pathogens. Mutational inactivation of the putative secretion system confirmed its involvement in the pathogenicity of C. fetus subsp. venerealis. PMID:19897645

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

    PubMed Central

    2010-01-01

    Background CpG islands and nucleosome-free regions are both found in promoters. However, their association has never been studied. On the other hand, DNA methylation is absent in promoters but is enriched in gene bodies. Intragenic nucleosomes and their modifications have been recently associated with RNA splicing. Because the function of intragenic DNA methylation remains unclear, I explored the possibility of its involvement in splicing regulation. Results Here I show that CpG islands were associated not only with methylation-free promoters but also with nucleosome-free promoters. Nucleosome-free regions were observed only in promoters containing a CpG island. However, the DNA sequences of CpG islands predicted the opposite pattern, implying a limitation of sequence programs for the determination of nucleosome occupancy. In contrast to the methylation-and nucleosome-free states of CpG-island promoters, exons were densely methylated at CpGs and packaged into nucleosomes. Exon-enrichment of DNA methylation was specifically found in spliced exons and in exons with weak splice sites. The enrichment patterns were less pronounced in initial exons and in non-coding exons, potentially reflecting a lower need for their splicing. I also found that nucleosomes, DNA methylation, and H3K36me3 marked the exons of transcripts with low, medium, and high gene expression levels, respectively. Conclusions Human promoters containing a CpG island tend to remain nucleosome-free as well as methylation-free. In contrast, exons demonstrate a high degree of methylation and nucleosome occupancy. Exonic DNA methylation seems to function together with exonic nucleosomes and H3K36me3 for the proper splicing of transcripts with different expression levels. PMID:20602769

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

    PubMed Central

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

    2014-01-01

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

  1. Draft Genome Sequences of Two Isolates of the Roseobacter Group, Sulfitobacter sp. Strains 3SOLIMAR09 and 1FIGIMAR09, from Harbors of Mallorca Island (Mediterranean Sea)

    PubMed Central

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

    2014-01-01

    We present the draft genome sequences of two isolates of the Roseobacter lineage, 3SOLIMAR09 and 1FIGIMAR09, which were obtained from harbors of Mallorca Island, Spain, and are affiliated with the Sulfitobacter genus. Both isolates harbor the complete gene set for protocatechuate catabolism and incomplete pathways for several additional monoaromatic compounds. PMID:24855294

  2. Cytotoxic Chromosomal Targeting by CRISPR/Cas Systems Can Reshape Bacterial Genomes and Expel or Remodel Pathogenicity Islands

    PubMed Central

    Vercoe, Reuben B.; Chang, James T.; Dy, Ron L.; Taylor, Corinda; Gristwood, Tamzin; Clulow, James S.; Richter, Corinna; Przybilski, Rita; Pitman, Andrew R.; Fineran, Peter C.

    2013-01-01

    In prokaryotes, clustered regularly interspaced short palindromic repeats (CRISPRs) and their associated (Cas) proteins constitute a defence system against bacteriophages and plasmids. CRISPR/Cas systems acquire short spacer sequences from foreign genetic elements and incorporate these into their CRISPR arrays, generating a memory of past invaders. Defence is provided by short non-coding RNAs that guide Cas proteins to cleave complementary nucleic acids. While most spacers are acquired from phages and plasmids, there are examples of spacers that match genes elsewhere in the host bacterial chromosome. In Pectobacterium atrosepticum the type I-F CRISPR/Cas system has acquired a self-complementary spacer that perfectly matches a protospacer target in a horizontally acquired island (HAI2) involved in plant pathogenicity. Given the paucity of experimental data about CRISPR/Cas–mediated chromosomal targeting, we examined this process by developing a tightly controlled system. Chromosomal targeting was highly toxic via targeting of DNA and resulted in growth inhibition and cellular filamentation. The toxic phenotype was avoided by mutations in the cas operon, the CRISPR repeats, the protospacer target, and protospacer-adjacent motif (PAM) beside the target. Indeed, the natural self-targeting spacer was non-toxic due to a single nucleotide mutation adjacent to the target in the PAM sequence. Furthermore, we show that chromosomal targeting can result in large-scale genomic alterations, including the remodelling or deletion of entire pre-existing pathogenicity islands. These features can be engineered for the targeted deletion of large regions of bacterial chromosomes. In conclusion, in DNA–targeting CRISPR/Cas systems, chromosomal interference is deleterious by causing DNA damage and providing a strong selective pressure for genome alterations, which may have consequences for bacterial evolution and pathogenicity. PMID:23637624

  3. Cytotoxic chromosomal targeting by CRISPR/Cas systems can reshape bacterial genomes and expel or remodel pathogenicity islands.

    PubMed

    Vercoe, Reuben B; Chang, James T; Dy, Ron L; Taylor, Corinda; Gristwood, Tamzin; Clulow, James S; Richter, Corinna; Przybilski, Rita; Pitman, Andrew R; Fineran, Peter C

    2013-04-01

    In prokaryotes, clustered regularly interspaced short palindromic repeats (CRISPRs) and their associated (Cas) proteins constitute a defence system against bacteriophages and plasmids. CRISPR/Cas systems acquire short spacer sequences from foreign genetic elements and incorporate these into their CRISPR arrays, generating a memory of past invaders. Defence is provided by short non-coding RNAs that guide Cas proteins to cleave complementary nucleic acids. While most spacers are acquired from phages and plasmids, there are examples of spacers that match genes elsewhere in the host bacterial chromosome. In Pectobacterium atrosepticum the type I-F CRISPR/Cas system has acquired a self-complementary spacer that perfectly matches a protospacer target in a horizontally acquired island (HAI2) involved in plant pathogenicity. Given the paucity of experimental data about CRISPR/Cas-mediated chromosomal targeting, we examined this process by developing a tightly controlled system. Chromosomal targeting was highly toxic via targeting of DNA and resulted in growth inhibition and cellular filamentation. The toxic phenotype was avoided by mutations in the cas operon, the CRISPR repeats, the protospacer target, and protospacer-adjacent motif (PAM) beside the target. Indeed, the natural self-targeting spacer was non-toxic due to a single nucleotide mutation adjacent to the target in the PAM sequence. Furthermore, we show that chromosomal targeting can result in large-scale genomic alterations, including the remodelling or deletion of entire pre-existing pathogenicity islands. These features can be engineered for the targeted deletion of large regions of bacterial chromosomes. In conclusion, in DNA-targeting CRISPR/Cas systems, chromosomal interference is deleterious by causing DNA damage and providing a strong selective pressure for genome alterations, which may have consequences for bacterial evolution and pathogenicity. PMID:23637624

  4. History shaped the geographic distribution of genomic admixture on the island of Puerto Rico.

    PubMed

    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; Burchard, Esteban González; Martínez-Cruzado, Juan Carlos

    2011-01-01

    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. PMID:21304981

  5. High-quality permanent draft genome sequence of Bradyrhizobium sp. Tv2a.2, a microsymbiont of Tachigali versicolor discovered in Barro Colorado Island of Panama

    PubMed Central

    2015-01-01

    Bradyrhizobiumsp. Tv2a.2 is an aerobic, motile, Gram-negative, non-spore-forming rod that was isolated from an effective nitrogen-fixing root nodule of Tachigali versicolor collected in Barro Colorado Island of Panama. Here we describe the features of Bradyrhizobiumsp. Tv2a.2, together with high-quality permanent draft genome sequence information and annotation. The 8,496,279 bp high-quality draft genome is arranged in 87 scaffolds of 87 contigs, contains 8,109 protein-coding genes and 72 RNA-only encoding genes. This rhizobial genome was sequenced as part of the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) project. PMID:26203338

  6. High-quality permanent draft genome sequence of Bradyrhizobium sp. Tv2a.2, a microsymbiont of Tachigali versicolor discovered in Barro Colorado Island of Panama.

    PubMed

    Tian, Rui; Parker, Matthew; Seshadri, Rekha; Reddy, Tbk; Markowitz, Victor; Ivanova, Natalia; Pati, Amrita; Woyke, Tanja; Baeshen, Mohammed N; Baeshen, Nabih A; Kyrpides, Nikos; Reeve, Wayne

    2015-01-01

    Bradyrhizobiumsp. Tv2a.2 is an aerobic, motile, Gram-negative, non-spore-forming rod that was isolated from an effective nitrogen-fixing root nodule of Tachigali versicolor collected in Barro Colorado Island of Panama. Here we describe the features of Bradyrhizobiumsp. Tv2a.2, together with high-quality permanent draft genome sequence information and annotation. The 8,496,279 bp high-quality draft genome is arranged in 87 scaffolds of 87 contigs, contains 8,109 protein-coding genes and 72 RNA-only encoding genes. This rhizobial genome was sequenced as part of the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) project. PMID:26203338

  7. Unraveling the regulatory network of IncA/C plasmid mobilization: When genomic islands hijack conjugative elements

    PubMed Central

    Carraro, Nicolas; Matteau, Dominick; Burrus, Vincent; Rodrigue, Sébastien

    2015-01-01

    Conjugative plasmids of the A/C incompatibility group (IncA/C) have become substantial players in the dissemination of multidrug resistance. These large conjugative plasmids are characterized by their broad host-range, extended spectrum of antimicrobials resistance, and prevalence in enteric bacteria recovered from both environmental and clinical settings. Until recently, relatively little was known about the basic biology of IncA/C plasmids, mostly because of the hindrance of multidrug resistance for molecular biology experiments. To circumvent this issue, we previously developed pVCR94?X, a convenient prototype that codes for a reduced set of antibiotic resistances. Using pVCR94?X, we then characterized the regulatory pathway governing IncA/C plasmid dissemination. We found that the expression of roughly 2 thirds of the genes encoded by this plasmid, including large operons involved in the conjugation process, depends on an FlhCD-like master activator called AcaCD. Beyond the mobility of IncA/C plasmids, AcaCD was also shown to play a key role in the mobilization of different classes of genomic islands (GIs) identified in various pathogenic bacteria. By doing so, IncA/C plasmids can have a considerable impact on bacterial genomes plasticity and evolution. PMID:26442183

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  9. Genome-scale detection of hypermethylated CpG islands in circulating cell-free DNA of hepatocellular carcinoma patients.

    PubMed

    Wen, Lu; Li, Jingyi; Guo, Huahu; Liu, Xiaomeng; Zheng, Shengmin; Zhang, Dafang; Zhu, Weihua; Qu, Jianhui; Guo, Limin; Du, Dexiao; Jin, Xiao; Zhang, Yuhao; Gao, Yun; Shen, Jie; Ge, Hao; Tang, Fuchou; Huang, Yanyi; Peng, Jirun

    2015-11-01

    Despite advances in DNA methylome analyses of cells and tissues, current techniques for genome-scale profiling of DNA methylation in circulating cell-free DNA (ccfDNA) remain limited. Here we describe a methylated CpG tandems amplification and sequencing (MCTA-Seq) method that can detect thousands of hypermethylated CpG islands simultaneously in ccfDNA. This highly sensitive technique can work with genomic DNA as little as 7.5 pg, which is equivalent to 2.5 copies of the haploid genome. We have analyzed a cohort of tissue and plasma samples (n = 151) of hepatocellular carcinoma (HCC) patients and control subjects, identifying dozens of high-performance markers in blood for detecting small HCC (≤ 3 cm). Among these markers, 4 (RGS10, ST8SIA6, RUNX2 and VIM) are mostly specific for cancer detection, while the other 15, classified as a novel set, are already hypermethylated in the normal liver tissues. Two corresponding classifiers have been established, combination of which achieves a sensitivity of 94% with a specificity of 89% for the plasma samples from HCC patients (n = 36) and control subjects including cirrhosis patients (n = 17) and normal individuals (n = 38). Notably, all 15 alpha-fetoprotein-negative HCC patients were successfully identified. Comparison between matched plasma and tissue samples indicates that both the cancer and noncancerous tissues contribute to elevation of the methylation markers in plasma. MCTA-Seq will facilitate the development of ccfDNA methylation biomarkers and contribute to the improvement of cancer detection in a clinical setting. PMID:26516143

  10. Genome-scale detection of hypermethylated CpG islands in circulating cell-free DNA of hepatocellular carcinoma patients

    PubMed Central

    Wen, Lu; Li, Jingyi; Guo, Huahu; Liu, Xiaomeng; Zheng, Shengmin; Zhang, Dafang; Zhu, Weihua; Qu, Jianhui; Guo, Limin; Du, Dexiao; Jin, Xiao; Zhang, Yuhao; Gao, Yun; Shen, Jie; Ge, Hao; Tang, Fuchou; Huang, Yanyi; Peng, Jirun

    2015-01-01

    Despite advances in DNA methylome analyses of cells and tissues, current techniques for genome-scale profiling of DNA methylation in circulating cell-free DNA (ccfDNA) remain limited. Here we describe a methylated CpG tandems amplification and sequencing (MCTA-Seq) method that can detect thousands of hypermethylated CpG islands simultaneously in ccfDNA. This highly sensitive technique can work with genomic DNA as little as 7.5 pg, which is equivalent to 2.5 copies of the haploid genome. We have analyzed a cohort of tissue and plasma samples (n = 151) of hepatocellular carcinoma (HCC) patients and control subjects, identifying dozens of high-performance markers in blood for detecting small HCC (≤ 3 cm). Among these markers, 4 (RGS10, ST8SIA6, RUNX2 and VIM) are mostly specific for cancer detection, while the other 15, classified as a novel set, are already hypermethylated in the normal liver tissues. Two corresponding classifiers have been established, combination of which achieves a sensitivity of 94% with a specificity of 89% for the plasma samples from HCC patients (n = 36) and control subjects including cirrhosis patients (n = 17) and normal individuals (n = 38). Notably, all 15 alpha-fetoprotein-negative HCC patients were successfully identified. Comparison between matched plasma and tissue samples indicates that both the cancer and noncancerous tissues contribute to elevation of the methylation markers in plasma. MCTA-Seq will facilitate the development of ccfDNA methylation biomarkers and contribute to the improvement of cancer detection in a clinical setting. PMID:26516143

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

    PubMed

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

    2015-04-01

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

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

    PubMed Central

    Wang, Quan; Wang, Lei

    2013-01-01

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

  13. Genome-wide analysis of the salmonella Fis regulon and its regulatory mechanism on pathogenicity islands.

    PubMed

    Wang, Hui; Liu, Bin; Wang, Quan; Wang, Lei

    2013-01-01

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

  14. Emergence of Extensively Drug-Resistant Proteus mirabilis Harboring a Conjugative NDM-1 Plasmid and a Novel Salmonella Genomic Island 1 Variant, SGI1-Z.

    PubMed

    Qin, Shangshang; Qi, Hui; Zhang, Qijing; Zhao, Di; Liu, Zhen-Zhen; Tian, Hao; Xu, Lijuan; Xu, Hui; Zhou, Mengmeng; Feng, Xianju; Liu, Hong-Min

    2015-10-01

    Acquisition of blaNDM-1 in bacterial species, such as Proteus mirabilis that is intrinsically resistant to tetracycline, tigecycline and colistin, will make clinical treatment extremely difficult. Here, we characterized an NDM-1-producing clinical isolate of P. mirabilis (PM58) that displayed an extensively drug-resistant (XDR) phenotype, susceptible only to aztreonam. Molecular analysis revealed that PM58 harbored both a conjugative NDM-1 plasmid and a novel Salmonella genomic island 1 variant on chromosome. PMID:26195511

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

    SciTech Connect

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

    2014-09-25

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

  16. 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

    PubMed Central

    2010-01-01

    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 species tends to imply an important functional or regional constraint that does not permit a change in genomic structure. The ctg1034 contig completed in this paper was initially studied because it was assigned to the Sr2 resistance locus region, but detailed mapping studies subsequently assigned it to the long arm of 3B and revealed its unusual features. Results BAC shotgun sequencing of the hexaploid wheat (Triticum aestivum cv. Chinese Spring) genome has been used to assemble a group of 15 wheat BACs from the chromosome 3B physical map FPC contig ctg1034 into a 783,553 bp genomic sequence. This ctg1034 sequence was annotated for biological features such as genes and transposable elements. A three-gene island was identified among >80% repetitive DNA sequence. Using bioinformatics analysis there were no observable similarity in their gene functions. The ctg1034 gene island also displayed complete conservation of gene order and orientation with syntenic gene islands found in publicly available genome sequences of Brachypodium distachyon, Oryza sativa, Sorghum bicolor and Zea mays, even though the intergenic space and introns were divergent. Conclusion We propose that ctg1034 is located within the heterochromatic C-band region of deletion bin 3BL7 based on the identification of heterochromatic tandem repeats and presence of significant matches to chromodomain-containing gypsy LTR retrotransposable elements. We also speculate that this location, among other highly repetitive sequences, may account for the relative stability in gene order and orientation within the gene island. Sequence data from this article have been deposited with the GenBank Data Libraries under accession no. GQ422824 PMID:20507561

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

    PubMed Central

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

    2014-01-01

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

  18. Genomic islands 1 and 2 play key roles in the evolution of extensively drug-resistant ST235 isolates of Pseudomonas aeruginosa.

    PubMed

    Roy Chowdhury, Piklu; Scott, Martin; Worden, Paul; Huntington, Peter; Hudson, Bernard; Karagiannis, Thomas; Charles, Ian G; Djordjevic, Steven P

    2016-03-01

    Pseudomonas aeruginosa are noscomially acquired, opportunistic pathogens that pose a major threat to the health of burns patients and the immunocompromised. We sequenced the genomes of P. aeruginosa isolates RNS_PA1, RNS_PA46 and RNS_PAE05, which displayed resistance to almost all frontline antibiotics, including gentamicin, piperacillin, timentin, meropenem, ceftazidime and colistin. We provide evidence that the isolates are representatives of P. aeruginosa sequence type (ST) 235 and carry Tn6162 and Tn6163 in genomic islands 1 (GI1) and 2 (GI2), respectively. GI1 disrupts the endA gene at precisely the same chromosomal location as in P. aeruginosa strain VR-143/97, of unknown ST, creating an identical CA direct repeat. The class 1 integron associated with Tn6163 in GI2 carries a blaGES-5-aacA4-gcuE15-aphA15 cassette array conferring resistance to carbapenems and aminoglycosides. GI2 is flanked by a 12 nt direct repeat motif, abuts a tRNA-gly gene, and encodes proteins with putative roles in integration, conjugative transfer as well as integrative conjugative element-specific proteins. This suggests that GI2 may have evolved from a novel integrative conjugative element. Our data provide further support to the hypothesis that genomic islands play an important role in de novo evolution of multiple antibiotic resistance phenotypes in P. aeruginosa. PMID:26962050

  19. Identification and Characterization of a Novel Genomic Island Integrated at selC in Locus of Enterocyte Effacement-Negative, Shiga Toxin-Producing Escherichia coli

    PubMed Central

    Schmidt, H.; Zhang, W.-L.; Hemmrich, U.; Jelacic, S.; Brunder, W.; Tarr, P. I.; Dobrindt, U.; Hacker, J.; Karch, H.

    2001-01-01

    The selC tRNA gene is a common site for the insertion of pathogenicity islands in a variety of bacterial enteric pathogens. We demonstrate here that Escherichia coli that produces Shiga toxin 2d and does not harbor the locus of enterocyte effacement (LEE) contains, instead, a novel genomic island. In one representative strain (E. coli O91:H? strain 4797/97), this island is 33,014 bp long and, like LEE in E. coli O157:H7, is integrated 15 bp downstream of selC. This E. coli O91:H? island contains genes encoding a novel serine protease, termed EspI; an adherence-associated locus, similar to iha of E. coli O157:H7; an E. coli vitamin B12 receptor (BtuB); an AraC-type regulatory module; and four homologues of E. coli phosphotransferase proteins. The remaining sequence consists largely of complete and incomplete insertion sequences, prophage sequences, and an intact phage integrase gene that is located directly downstream of the chromosomal selC. Recombinant EspI demonstrates serine protease activity using pepsin A and human apolipoprotein A-I as substrates. We also detected Iha-reactive protein in outer membranes of a recombinant clone and 10 LEE-negative, Shiga toxin-producing E. coli (STEC) strains by immunoblot analysis. Using PCR analysis of various STEC, enteropathogenic E. coli, enterotoxigenic E. coli, enteroaggregative E. coli, uropathogenic E. coli, and enteroinvasive E. coli strains, we detected the iha homologue in 59 (62%) of 95 strains tested. In contrast, espI and btuB were present in only two (2%) and none of these strains, respectively. We conclude that the newly described island occurs exclusively in a subgroup of STEC strains that are eae negative and contain the variant stx2d gene. PMID:11598060

  20. Where does Neisseria acquire foreign DNA from: an examination of the source of genomic and pathogenic islands and the evolution of the Neisseria genus

    PubMed Central

    2013-01-01

    Background Pathogenicity islands (PAIs) or genomic islands (GEIs) are considered to be the result of a recent horizontal transfer. Detecting PAIs/GEIs as well as their putative source can provide insight into the organism’s pathogenicity within its host. Previously we introduced a tool called S-plot which provides a visual representation of the variation in compositional properties across and between genomic sequences. Utilizing S-plot and new functionality developed here, we examined 18 publicly available Neisseria genomes, including strains of both pathogenic and non-pathogenic species, in order to identify regions of unusual compositional properties (RUCPs) using both a sliding window as well as a gene-by-gene approach. Results Numerous GEIs and PAIs were identified including virulence genes previously found within the pathogenic Neisseria species. While some genes were conserved amongst all species, only pathogenic species, or an individual species, a number of genes were detected that are unique to an individual strain. While the majority of such genes have an origin unknown, a number of putative sources including pathogenic and capsule-containing bacteria were determined, indicative of gene exchange between Neisseria spp. and other bacteria within their microhabitat. Furthermore, we uncovered evidence that both N. meningitidis and N. gonorrhoeae have separately acquired DNA from their human host. Data suggests that all three Neisseria species have received horizontally transferred elements post-speciation. Conclusions Using this approach, we were able to not only find previously identified regions of virulence but also new regions which may be contributing to the virulence of the species. This comparative analysis provides a means for tracing the evolutionary history of the acquisition of foreign DNA within this genus. Looking specifically at the RUCPs present within the 18 genomes considered, a stronger similarity between N. meningitidis and N. lactamica is observed, suggesting that N. meningitidis arose before N. gonorrhoeae. PMID:24007216

  1. Whole-genome bisulfite sequencing maps from multiple human tissues reveal novel CpG islands associated with tissue-specific regulation.

    PubMed

    Mendizabal, Isabel; Yi, Soojin V

    2016-01-01

    CpG islands (CGIs) are one of the most widely studied regulatory features of the human genome, with critical roles in development and disease. Despite such significance and the original epigenetic definition, currently used CGI sets are typically predicted from DNA sequence characteristics. Although CGIs are deeply implicated in practical analyses of DNA methylation, recent studies have shown that such computational annotations suffer from inaccuracies. Here we used whole-genome bisulfite sequencing from 10 diverse human tissues to identify a comprehensive, experimentally obtained, single-base resolution CGI catalog. In addition to the unparalleled annotation precision, our method is free from potential bias due to arbitrary sequence features or probe affinity differences. In addition to clarifying substantial false positives in the widely used University of California Santa Cruz (UCSC) annotations, our study identifies numerous novel epigenetic loci. In particular, we reveal significant impact of transposable elements on the epigenetic regulatory landscape of the human genome and demonstrate ubiquitous presence of transcription initiation at CGIs, including alternative promoters in gene bodies and non-coding RNAs in intergenic regions. Moreover, coordinated DNA methylation and chromatin modifications mark tissue-specific enhancers at novel CGIs. Enrichment of specific transcription factor binding from ChIP-seq supports mechanistic roles of CGIs on the regulation of tissue-specific transcription. The new CGI catalog provides a comprehensive and integrated list of genomic hotspots of epigenetic regulation. PMID:26512062

  2. Whole-genome bisulfite sequencing maps from multiple human tissues reveal novel CpG islands associated with tissue-specific regulation

    PubMed Central

    Mendizabal, Isabel; Yi, Soojin V.

    2016-01-01

    CpG islands (CGIs) are one of the most widely studied regulatory features of the human genome, with critical roles in development and disease. Despite such significance and the original epigenetic definition, currently used CGI sets are typically predicted from DNA sequence characteristics. Although CGIs are deeply implicated in practical analyses of DNA methylation, recent studies have shown that such computational annotations suffer from inaccuracies. Here we used whole-genome bisulfite sequencing from 10 diverse human tissues to identify a comprehensive, experimentally obtained, single-base resolution CGI catalog. In addition to the unparalleled annotation precision, our method is free from potential bias due to arbitrary sequence features or probe affinity differences. In addition to clarifying substantial false positives in the widely used University of California Santa Cruz (UCSC) annotations, our study identifies numerous novel epigenetic loci. In particular, we reveal significant impact of transposable elements on the epigenetic regulatory landscape of the human genome and demonstrate ubiquitous presence of transcription initiation at CGIs, including alternative promoters in gene bodies and non-coding RNAs in intergenic regions. Moreover, coordinated DNA methylation and chromatin modifications mark tissue-specific enhancers at novel CGIs. Enrichment of specific transcription factor binding from ChIP-seq supports mechanistic roles of CGIs on the regulation of tissue-specific transcription. The new CGI catalog provides a comprehensive and integrated list of genomic hotspots of epigenetic regulation. PMID:26512062

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

    PubMed Central

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

    2012-01-01

    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. PMID:22923590

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

    PubMed

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

    2015-07-01

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

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

    PubMed

    Lumley, Lisa M; Sperling, Felix Ah

    2011-10-01

    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. PMID:22393489

  6. The master regulator of IncA/C plasmids is recognized by the Salmonella Genomic island SGI1 as a signal for excision and conjugal transfer

    PubMed Central

    Kiss, János; Papp, Péter Pál; Szabó, Mónika; Farkas, Tibor; Murányi, Gábor; Szakállas, Erik; Olasz, Ferenc

    2015-01-01

    The genomic island SGI1 and its variants, the important vehicles of multi-resistance in Salmonella strains, are integrative elements mobilized exclusively by the conjugative IncA/C plasmids. Integration and excision of the island are carried out by the SGI1-encoded site-specific recombinase Int and the recombination directionality factor Xis. Chromosomal integration ensures the stable maintenance and vertical transmission of SGI1, while excision is the initial step of horizontal transfer, followed by conjugation and integration into the recipient. We report here that SGI1 not only exploits the conjugal apparatus of the IncA/C plasmids but also utilizes the regulatory mechanisms of the conjugation system for the exact timing and activation of excision to ensure efficient horizontal transfer. This study demonstrates that the FlhDC-family activator AcaCD, which regulates the conjugation machinery of the IncA/C plasmids, serves as a signal of helper entry through binding to SGI1 xis promoter and activating SGI1 excision. Promoters of int and xis genes have been identified and the binding site of the activator has been located by footprinting and deletion analyses. We prove that expression of xis is activator-dependent while int is constitutively expressed, and this regulatory mechanism is presumably responsible for the efficient transfer and stable maintenance of SGI1. PMID:26209134

  7. A genomic island integrated into recA of Vibrio cholerae contains a divergent recA and provides multi-pathway protection from DNA damage.

    PubMed

    Rapa, Rita A; Islam, Atiqul; Monahan, Leigh G; Mutreja, Ankur; Thomson, Nicholas; Charles, Ian G; Stokes, Harold W; Labbate, Maurizio

    2015-04-01

    Lateral gene transfer (LGT) has been crucial in the evolution of the cholera pathogen, Vibrio cholerae. The two major virulence factors are present on two different mobile genetic elements, a bacteriophage containing the cholera toxin genes and a genomic island (GI) containing the intestinal adhesin genes. Non-toxigenic V.?cholerae in the aquatic environment are a major source of novel DNA that allows the pathogen to morph via LGT. In this study, we report a novel GI from a non-toxigenic V.?cholerae strain containing multiple genes involved in DNA repair including the recombination repair gene recA that is 23% divergent from the indigenous recA and genes involved in the translesion synthesis pathway. This is the first report of a GI containing the critical gene recA and the first report of a GI that targets insertion into a specific site within recA. We show that possession of the island in Escherichia coli is protective against DNA damage induced by UV-irradiation and DNA targeting antibiotics. This study highlights the importance of genetic elements such as GIs in the evolution of V.?cholerae and emphasizes the importance of environmental strains as a source of novel DNA that can influence the pathogenicity of toxigenic strains. PMID:24889424

  8. The master regulator of IncA/C plasmids is recognized by the Salmonella Genomic island SGI1 as a signal for excision and conjugal transfer.

    PubMed

    Kiss, János; Papp, Péter Pál; Szabó, Mónika; Farkas, Tibor; Murányi, Gábor; Szakállas, Erik; Olasz, Ferenc

    2015-10-15

    The genomic island SGI1 and its variants, the important vehicles of multi-resistance in Salmonella strains, are integrative elements mobilized exclusively by the conjugative IncA/C plasmids. Integration and excision of the island are carried out by the SGI1-encoded site-specific recombinase Int and the recombination directionality factor Xis. Chromosomal integration ensures the stable maintenance and vertical transmission of SGI1, while excision is the initial step of horizontal transfer, followed by conjugation and integration into the recipient. We report here that SGI1 not only exploits the conjugal apparatus of the IncA/C plasmids but also utilizes the regulatory mechanisms of the conjugation system for the exact timing and activation of excision to ensure efficient horizontal transfer. This study demonstrates that the FlhDC-family activator AcaCD, which regulates the conjugation machinery of the IncA/C plasmids, serves as a signal of helper entry through binding to SGI1 xis promoter and activating SGI1 excision. Promoters of int and xis genes have been identified and the binding site of the activator has been located by footprinting and deletion analyses. We prove that expression of xis is activator-dependent while int is constitutively expressed, and this regulatory mechanism is presumably responsible for the efficient transfer and stable maintenance of SGI1. PMID:26209134

  9. A genomic island integrated into recA of Vibrio cholerae contains a divergent recA and provides multi-pathway protection from DNA damage

    PubMed Central

    Rapa, Rita A; Islam, Atiqul; Monahan, Leigh G; Mutreja, Ankur; Thomson, Nicholas; Charles, Ian G; Stokes, Harold W; Labbate, Maurizio

    2015-01-01

    Lateral gene transfer (LGT) has been crucial in the evolution of the cholera pathogen, Vibrio cholerae. The two major virulence factors are present on two different mobile genetic elements, a bacteriophage containing the cholera toxin genes and a genomic island (GI) containing the intestinal adhesin genes. Non-toxigenic V. cholerae in the aquatic environment are a major source of novel DNA that allows the pathogen to morph via LGT. In this study, we report a novel GI from a non-toxigenic V. cholerae strain containing multiple genes involved in DNA repair including the recombination repair gene recA that is 23% divergent from the indigenous recA and genes involved in the translesion synthesis pathway. This is the first report of a GI containing the critical gene recA and the first report of a GI that targets insertion into a specific site within recA. We show that possession of the island in Escherichia coli is protective against DNA damage induced by UV-irradiation and DNA targeting antibiotics. This study highlights the importance of genetic elements such as GIs in the evolution of V. cholerae and emphasizes the importance of environmental strains as a source of novel DNA that can influence the pathogenicity of toxigenic strains. PMID:24889424

  10. The complete mitochondrial genome of the gnomefish Scombrops boops (Teleostei, Perciformes, Scombropidae) from the Pacific Ocean off the Japanese Islands.

    PubMed

    Tsunashima, Tadasuke; Itoi, Shiro; Abe, Koko; Takigawa, Tomoyuki; Inoue, Satoshi; Kozen, Takahiro; Ono, Naoto; Noguchi, Shunsuke; Nakai, Shizuko; Takai, Noriyuki; Huang, Ming-Chih; Sugita, Haruo

    2016-01-01

    The complete mitochondrial genome of the gnomefish Scombrops boops was determined by a PCR-based method. The total length of mitochondrial DNA (mtDNA) was 16,517?bp, including 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes and one control region. The mitochondrial gene arrangement of the gnomefish mtDNA was identical to those of typical teleosts. This is the first report of the complete mitochondrial genome of a member of the Scombropidae family and will be useful for the development of molecular tools for ecological research. PMID:25484172

  11. The Biphenyl- and 4-Chlorobiphenyl-Catabolic Transposon Tn4371, a Member of a New Family of Genomic Islands Related to IncP and Ti Plasmids

    PubMed Central

    Toussaint, Ariane; Merlin , Christophe; Monchy, Sébastien; Benotmane, M. Abderrafi; Leplae, Raphaël; Mergeay, Max; Springael, Dirk

    2003-01-01

    The nucleotide sequence of the biphenyl catabolic transposon Tn4371 has been completed and analyzed. It confirmed that the element has a mosaic structure made of several building blocks. In addition to previously identified genes coding for a tyrosine recombinase related to phage integrases and for biphenyl degradation enzymes very similar to those of Achromobacter georgiopolitanum KKS102, Tn4371 carries many plasmid-related genes involved in replication, partition, and other, as-yet-unknown, plasmid functions. One gene cluster contains most of the genes required to express a type IV secretion-mating pair formation apparatus coupled with a TraG ATPase, all of which are related to those found on IncP and Ti plasmids. Orthologues of all Tn4371 plasmid-related genes and of the tyrosine recombinase gene were found, with a very similar organization, in the chromosome of Ralstonia solanacearum and on the yet-to-be-determined genomic sequences of Erwinia chrysanthemi and Azotobacter vinelandii. In each of these chromosomal segments, conserved segments were separated by different groups of genes, which also differed from the Tn4371 bph genes. The conserved blocks of genes were also identified, in at least two copies, in the chromosome of Ralstonia metallidurans CH34. Tn4371 thus appears to represent a new family of potentially mobile genomic islands with a broad host range since they reside in a wide range of soil proteobacteria, including plant pathogens. PMID:12902278

  12. A Role for Tn6029 in the Evolution of the Complex Antibiotic Resistance Gene Loci in Genomic Island 3 in Enteroaggregative Hemorrhagic Escherichia coli O104:H4

    PubMed Central

    Chowdhury, Piklu Roy; Charles, Ian G.; Djordjevic, Steven P.

    2015-01-01

    In enteroaggregative hemorrhagic Escherichia coli (EAHEC) O104 the complex antibiotic resistance gene loci (CRL) found in the region of divergence 1 (RD1) within E. coli genomic island 3 (GI3) contains blaTEM-1, strAB, sul2, tet(A)A, and dfrA7 genes encoding resistance to ampicillin, streptomycin, sulfamethoxazole, tetracycline and trimethoprim respectively. The precise arrangement of antibiotic resistance genes and the role of mobile elements that drove the evolutionary events and created the CRL have not been investigated. We used a combination of bioinformatics and iterative BLASTn searches to determine the micro-evolutionary events that likely led to the formation of the CRL in GI3 using the closed genome sequences of EAHEC O104:H4 strains 2011C-3493 and 2009EL-2050 and high quality draft genomes of EAHEC E. coli O104:H4 isolates from sporadic cases not associated with the initial outbreak. Our analyses indicate that the CRL in GI3 evolved from a progenitor structure that contained an In2-derived class 1 integron in a Tn21/Tn1721 hybrid backbone. Within the hybrid backbone, a Tn6029-family transposon, identified here as Tn6029C abuts the sul1 gene in the 3´-Conserved Segment (-CS) of a class 1 integron generating a unique molecular signature that has only previously been observed in pASL01a, a small plasmid found in commensal E. coli in West Africa. From this common progenitor, independent IS26-mediated events created two novel transposons identified here as Tn6029D and Tn6222 in 2011C-3493 and 2009EL-2050 respectively. Analysis of RD1 within GI3 reveals IS26 has played a crucial role in the assembly of regions within the CRL. PMID:25675217

  13. A role for Tn6029 in the evolution of the complex antibiotic resistance gene loci in genomic island 3 in enteroaggregative hemorrhagic Escherichia coli O104:H4.

    PubMed

    Roy Chowdhury, Piklu; Charles, Ian G; Djordjevic, Steven P

    2015-01-01

    In enteroaggregative hemorrhagic Escherichia coli (EAHEC) O104 the complex antibiotic resistance gene loci (CRL) found in the region of divergence 1 (RD1) within E. coli genomic island 3 (GI3) contains blaTEM-1, strAB, sul2, tet(A)A, and dfrA7 genes encoding resistance to ampicillin, streptomycin, sulfamethoxazole, tetracycline and trimethoprim respectively. The precise arrangement of antibiotic resistance genes and the role of mobile elements that drove the evolutionary events and created the CRL have not been investigated. We used a combination of bioinformatics and iterative BLASTn searches to determine the micro-evolutionary events that likely led to the formation of the CRL in GI3 using the closed genome sequences of EAHEC O104:H4 strains 2011C-3493 and 2009EL-2050 and high quality draft genomes of EAHEC E. coli O104:H4 isolates from sporadic cases not associated with the initial outbreak. Our analyses indicate that the CRL in GI3 evolved from a progenitor structure that contained an In2-derived class 1 integron in a Tn21/Tn1721 hybrid backbone. Within the hybrid backbone, a Tn6029-family transposon, identified here as Tn6029C abuts the sul1 gene in the 3'-Conserved Segment (-CS) of a class 1 integron generating a unique molecular signature that has only previously been observed in pASL01a, a small plasmid found in commensal E. coli in West Africa. From this common progenitor, independent IS26-mediated events created two novel transposons identified here as Tn6029D and Tn6222 in 2011C-3493 and 2009EL-2050 respectively. Analysis of RD1 within GI3 reveals IS26 has played a crucial role in the assembly of regions within the CRL. PMID:25675217

  14. Extensively Drug-Resistant Pseudomonas aeruginosa Isolates Containing blaVIM-2 and Elements of Salmonella Genomic Island 2: a New Genetic Resistance Determinant in Northeast Ohio

    PubMed Central

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

    2014-01-01

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

  15. Extensive amplification of GI-VII-6, a multidrug resistance genomic island of Salmonella enterica serovar Typhimurium, increases resistance to extended-spectrum cephalosporins

    PubMed Central

    Lee, Ken-ichi; Kusumoto, Masahiro; Sekizuka, Tsuyoshi; Kuroda, Makoto; Uchida, Ikuo; Iwata, Taketoshi; Okamoto, Susumu; Yabe, Kimiko; Inaoka, Takashi; Akiba, Masato

    2015-01-01

    GI-VII-6 is a chromosomally integrated multidrug resistance genomic island harbored by a specific clone of Salmonella enterica serovar Typhimurium (S.Typhimurium). It contains a gene encoding CMY-2 β-lactamase (blaCMY−2), and therefore contributes to extended-spectrum cephalosporin resistance. To elucidate the significance of GI-VII-6 on adaptive evolution, spontaneous mutants of S. Typhimurium strain L-3553 were selected on plates containing cefotaxime (CTX). The concentrations of CTX were higher than its minimum inhibition concentration to the parent strain. The mutants appeared on the plates containing 12.5 and 25 mg/L CTX at a frequency of 10−6 and 10−8, respectively. No colonies were observed at higher CTX concentrations. The copy number of blaCMY−2 increased up to 85 per genome in the mutants, while the parent strain contains one copy of that in the chromosome. This elevation was accompanied by increased amount of transcription. The blaCMY−2 copy number in the mutants drastically decreased in the absence of antimicrobial selection pressure. Southern hybridization analysis and short-read mapping indicated that the entire 125 kb GI-VII-6 or parts of it were tandemly amplified. GI-VII-6 amplification occurred at its original position, although it also transposed to other locations in the genome in some mutants, including an endogenous plasmid in some of the mutants, leading to the amplification of GI-VII-6 at different loci. Insertion sequences were observed at the junction of the amplified regions in the mutants, suggesting their significant roles in the transposition and amplification. Plasmid copy number in the selected mutants was 1.4 to 4.4 times higher than that of the parent strain. These data suggest that transposition and amplification of the blaCMY−2-containing region, along with the copy number variation of the plasmid, contributed to the extensive amplification of blaCMY−2 and increased resistance to CTX. PMID:25713569

  16. 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

    2011-01-01

    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. PMID:22115407

  17. Genetic analysis of environmental strains of the plant pathogen Phytophthora capsici reveals heterogeneous repertoire of effectors and possible effector evolution via genomic island.

    PubMed

    Iribarren, María Josefina; Pascuan, Cecilia; Soto, Gabriela; Ayub, Nicolás Daniel

    2015-11-01

    Phytophthora capsici is a virulent oomycete pathogen of many vegetable crops. Recently, it has been demonstrated that the recognition of the RXLR effector AVR3a1 of P. capsici (PcAVR3a1) triggers a hypersensitive response and plays a critical role in mediating non-host resistance. Here, we analyzed the occurrence of PcAVR3a1 in 57 isolates of P. capsici derived from globe squash, eggplant, tomato and bell pepper cocultivated in a small geographical area. The occurrence of PcAVR3a1 in environmental strains of P. capsici was confirmed by PCR in only 21 of these pathogen isolates. To understand the presence-absence pattern of PcAVR3a1 in environmental strains, the flanking region of this gene was sequenced. PcAVR3a1 was found within a genetic element that we named PcAVR3a1-GI (PcAVR3a1 genomic island). PcAVR3a1-GI was flanked by a 22-bp direct repeat, which is related to its site-specific recombination site. In addition to the PcAVR3a1 gene, PcAVR3a1-GI also encoded a phage integrase probably associated with the excision and integration of this mobile element. Exposure to plant induced the presence of an episomal circular intermediate of PcAVR3a1-GI, indicating that this mobile element is functional. Collectively, these findings provide evidence of PcAVR3a1 evolution via mobile elements in environmental strains of Phytophthora. PMID:26443834

  18. 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

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

    2002-02-01

    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

  19. Characterization of a Resistance-Nodulation-Cell Division Transporter System Associated with the syr-syp Genomic Island of Pseudomonas syringae pv. syringae

    PubMed Central

    Kang, Hyojeung; Gross, Dennis C.

    2005-01-01

    A tripartite resistance-nodulation-cell division (RND) transporter system, called the PseABC efflux system, was identified at the left border of the syr-syp genomic island of Pseudomonas syringae pv. syringae strain B301D. The PseABC efflux system was located within a 5.7-kb operon that encodes an outer membrane protein (PseA), a periplasmic membrane fusion protein (PseB), and an RND-type cytoplasmic membrane protein (PseC). The PseABC efflux system exhibited amino acid homology to a putative RND efflux system of Ralstonia solanacearum, with identities of 48% for PseA, 51% for PseB, and 61% for PseC. A nonpolar mutation within the pseC gene was generated by nptII insertional mutagenesis. The resultant mutant strain showed a larger reduction in syringopeptin secretion (67%) than in syringomycin secretion (41%) compared to parental strain B301D (P < 0.05). A ?-glucuronidase assay with a pseA::uidA reporter construct indicated that the GacS/GacA two-component system controls expression of the pseA gene. Quantitative real-time reverse transcription-PCR was used to determine transcript levels of the syringomycin (syrB1) and syringopeptin (sypA) synthetase genes in strain B301D-HK4 (a pseC mutant). The expression of the sypA gene by mutant strain B301D-HK4 corresponded to approximately 13% of that by parental strain B301D, whereas the syrB1 gene expression by mutant strain B301D-HK4 was nearly 61% (P < 0.05). In addition, the virulence of mutant strain B301D-HK4 for immature cherry fruits was reduced by about 58% compared to parental strain B301D (P < 0.05). Although the resistance of mutant strain B301D-HK4 to any antibiotic used in this study was not reduced compared to parental strain B301D, a drug-supersensitive acrB mutant of Escherichia coli showed two- to fourfold-increased resistance to acriflavine, erythromycin, and tetracycline upon heterologous expression of the pseA, pseB, and pseC genes (pseABC efflux genes). The PseABC efflux system is the first RND transporter system described for P. syringae, and it has an important role in secretion of syringomycin and syringopeptin. PMID:16151087

  20. Canary Islands

    NASA Technical Reports Server (NTRS)

    1992-01-01

    This easterly looking view shows the seven major volcanic islands of the Canary Island chain (28.0N, 16.5W) and offers a unique view of the islands that have become a frequent vacation spot for Europeans. The northwest coastline of Africa, (Morocco and Western Sahara), is visible in the background. Frequently, these islands create an impact on local weather (cloud formations) and ocean currents (island wakes) as seen in this photo.

  1. Draft genome of Leisingera aquaemixtae CECT 8399T, a member of the Roseobacter clade isolated from a junction of fresh and ocean water in Jeju Island, South Korea

    PubMed Central

    Rodrigo-Torres, Lidia; Pujalte, María J.; Arahal, David R.

    2016-01-01

    We report the draft genome sequence and annotation of Leisingera aquaemixtae CECT 8399T (DDBJ/EMBL/GenBank accession number CYSR00000000) which comprises 4,614,060 bp, 4313 protein coding genes, 54 tRNA coding genes and 7 rRNA coding genes. General findings of the annotated genome, such as pigment indigoidine operon, phenylacetate oxidation genes or predictable number of replicons, are commented in comparison to other Leisingera species. Average Nucleotide Identity between available genomes of type strains of species of Leisingera and Phaeobacter genera has been calculated to evaluate its current classification. PMID:26981415

  2. The genome sequence of Sea-Island cotton (Gossypium barbadense) provides insights into the allopolyploidization and development of superior spinnable fibres

    PubMed Central

    Yuan, Daojun; Tang, Zhonghui; Wang, Maojun; Gao, Wenhui; Tu, Lili; Jin, Xin; Chen, Lingling; He, Yonghui; Zhang, Lin; Zhu, Longfu; Li, Yang; Liang, Qiqi; Lin, Zhongxu; Yang, Xiyan; Liu, Nian; Jin, Shuangxia; Lei, Yang; Ding, Yuanhao; Li, Guoliang; Ruan, Xiaoan; Ruan, Yijun; Zhang, Xianlong

    2015-01-01

    Gossypium hirsutum contributes the most production of cotton fibre, but G. barbadense is valued for its better comprehensive resistance and superior fibre properties. However, the allotetraploid genome of G. barbadense has not been comprehensively analysed. Here we present a high-quality assembly of the 2.57 gigabase genome of G. barbadense, including 80,876 protein-coding genes. The double-sized genome of the A (or At) (1.50 Gb) against D (or Dt) (853 Mb) primarily resulted from the expansion of Gypsy elements, including Peabody and Retrosat2 subclades in the Del clade, and the Athila subclade in the Athila/Tat clade. Substantial gene expansion and contraction were observed and rich homoeologous gene pairs with biased expression patterns were identified, suggesting abundant gene sub-functionalization occurred by allopolyploidization. More specifically, the CesA gene family has adapted differentially temporal expression patterns, suggesting an integrated regulatory mechanism of CesA genes from At and Dt subgenomes for the primary and secondary cellulose biosynthesis of cotton fibre in a “relay race”-like fashion. We anticipate that the G. barbadense genome sequence will advance our understanding the mechanism of genome polyploidization and underpin genome-wide comparison research in this genus. PMID:26634818

  3. The genome sequence of Sea-Island cotton (Gossypium barbadense) provides insights into the allopolyploidization and development of superior spinnable fibres.

    PubMed

    Yuan, Daojun; Tang, Zhonghui; Wang, Maojun; Gao, Wenhui; Tu, Lili; Jin, Xin; Chen, Lingling; He, Yonghui; Zhang, Lin; Zhu, Longfu; Li, Yang; Liang, Qiqi; Lin, Zhongxu; Yang, Xiyan; Liu, Nian; Jin, Shuangxia; Lei, Yang; Ding, Yuanhao; Li, Guoliang; Ruan, Xiaoan; Ruan, Yijun; Zhang, Xianlong

    2015-01-01

    Gossypium hirsutum contributes the most production of cotton fibre, but G. barbadense is valued for its better comprehensive resistance and superior fibre properties. However, the allotetraploid genome of G. barbadense has not been comprehensively analysed. Here we present a high-quality assembly of the 2.57 gigabase genome of G. barbadense, including 80,876 protein-coding genes. The double-sized genome of the A (or At) (1.50 Gb) against D (or Dt) (853?Mb) primarily resulted from the expansion of Gypsy elements, including Peabody and Retrosat2 subclades in the Del clade, and the Athila subclade in the Athila/Tat clade. Substantial gene expansion and contraction were observed and rich homoeologous gene pairs with biased expression patterns were identified, suggesting abundant gene sub-functionalization occurred by allopolyploidization. More specifically, the CesA gene family has adapted differentially temporal expression patterns, suggesting an integrated regulatory mechanism of CesA genes from At and Dt subgenomes for the primary and secondary cellulose biosynthesis of cotton fibre in a "relay race"-like fashion. We anticipate that the G. barbadense genome sequence will advance our understanding the mechanism of genome polyploidization and underpin genome-wide comparison research in this genus. PMID:26634818

  4. PIPS: Pathogenicity Island Prediction Software

    PubMed Central

    Soares, Siomar C.; Abreu, Vinícius A. C.; Ramos, Rommel T. J.; Cerdeira, Louise; Silva, Artur; Baumbach, Jan; Trost, Eva; Tauch, Andreas; Hirata, Raphael; Mattos-Guaraldi, Ana L.; Miyoshi, Anderson; Azevedo, Vasco

    2012-01-01

    The adaptability of pathogenic bacteria to hosts is influenced by the genomic plasticity of the bacteria, which can be increased by such mechanisms as horizontal gene transfer. Pathogenicity islands play a major role in this type of gene transfer because they are large, horizontally acquired regions that harbor clusters of virulence genes that mediate the adhesion, colonization, invasion, immune system evasion, and toxigenic properties of the acceptor organism. Currently, pathogenicity islands are mainly identified in silico based on various characteristic features: (1) deviations in codon usage, G+C content or dinucleotide frequency and (2) insertion sequences and/or tRNA genetic flanking regions together with transposase coding genes. Several computational techniques for identifying pathogenicity islands exist. However, most of these techniques are only directed at the detection of horizontally transferred genes and/or the absence of certain genomic regions of the pathogenic bacterium in closely related non-pathogenic species. Here, we present a novel software suite designed for the prediction of pathogenicity islands (pathogenicity island prediction software, or PIPS). In contrast to other existing tools, our approach is capable of utilizing multiple features for pathogenicity island detection in an integrative manner. We show that PIPS provides better accuracy than other available software packages. As an example, we used PIPS to study the veterinary pathogen Corynebacterium pseudotuberculosis, in which we identified seven putative pathogenicity islands. PMID:22355329

  5. The genomic island SGI1, containing the multiple antibiotic resistance region of Salmonella enterica serovar Typhimurium DT104 or variants of it, is widely distributed in other S. enterica serovars.

    PubMed

    Levings, Renee S; Lightfoot, Diane; Partridge, Sally R; Hall, Ruth M; Djordjevic, Steven P

    2005-07-01

    The global dissemination of the multiply-antibiotic-resistant Salmonella enterica serovar Typhimurium DT104 clone with the resistance genes located in a class 1 integron, here designated In104, within genomic island SGI1 is a significant public health issue. Here, we have shown that SGI1 and variants of it carrying different combinations of resistance genes are found in several Salmonella enterica serovars. These are serovars Cerro, Derby, Dusseldorf, Infantis, Kiambu, and Paratyphi B dT(+) isolated from human infections and serovar Emek from sewage effluent. Two new variants, SGI1-I and SGI1-J, both of which include the dfrA1-orfC cassette array, were identified. PMID:15968049

  6. The Genomic Island SGI1, Containing the Multiple Antibiotic Resistance Region of Salmonella enterica Serovar Typhimurium DT104 or Variants of It, Is Widely Distributed in Other S. enterica Serovars

    PubMed Central

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

    2005-01-01

    The global dissemination of the multiply-antibiotic-resistant Salmonella enterica serovar Typhimurium DT104 clone with the resistance genes located in a class 1 integron, here designated In104, within genomic island SGI1 is a significant public health issue. Here, we have shown that SGI1 and variants of it carrying different combinations of resistance genes are found in several Salmonella enterica serovars. These are serovars Cerro, Derby, Dusseldorf, Infantis, Kiambu, and Paratyphi B dT+ isolated from human infections and serovar Emek from sewage effluent. Two new variants, SGI1-I and SGI1-J, both of which include the dfrA1-orfC cassette array, were identified. PMID:15968049

  7. Galapagos Islands

    NASA Technical Reports Server (NTRS)

    2002-01-01

    This true-color image of the Galapagos Islands was acquired on March 12, 2002, by the Moderate-resolution Imaging Spectroradiometer (MODIS), flying aboard NASA's Terra satellite. The Galapagos Islands, which are part of Ecuador, sit in the Pacific Ocean about 1000 km (620 miles) west of South America. As the three craters on the largest island (Isabela Island) suggest, the archipelago was created by volcanic eruptions, which took place millions of years ago. Unlike most remote islands in the Pacific, the Galapagos have gone relatively untouched by humans over the past few millennia. As a result, many unique species have continued to thrive on the islands. Over 95 percent of the islands' reptile species and nearly three quarters of its land bird species cannot be found anywhere else in the world. Two of the more well known are the Galapagos giant tortoise and marine iguanas. The unhindered evolutionary development of the islands' species inspired Charles Darwin to begin The Origin of Species eight years after his visit there. To preserve the unique wildlife on the islands, the Ecuadorian government made the entire archipelago a national park in 1959. Each year roughly 60,000 tourists visit these islands to experience what Darwin did over a century and a half ago. Image courtesy Jacques Descloitres, MODIS Land Rapid Response Team at NASA GSFC

  8. Akpatok Island

    NASA Technical Reports Server (NTRS)

    2002-01-01

    Akpatok Island lies in Ungava Bay in northern Quebec, Canada. Accessible only by air, Akpatok Island rises out of the water as sheer cliffs that soar 500 to 800 feet (150 to 243 m) above the sea surface. The island is an important sanctuary for cliff-nesting seabirds. Numerous ice floes around the island attract walrus and whales, making Akpatok a traditional hunting ground for native Inuit people. This image was acquired by Landsat 7's Enhanced Thematic Mapper plus (ETM+) sensor on January 22, 2001. Image provided by the USGS EROS Data Center Satellite Systems Branch

  9. Island Hopping

    ERIC Educational Resources Information Center

    Bennett, Gayle

    2009-01-01

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

  10. Identifying Pathogenicity Islands in Bacterial Pathogenomics Using Computational Approaches

    PubMed Central

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

    2014-01-01

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

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

    PubMed

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

    2008-03-01

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

  12. Devon Island

    Atmospheric Science Data Center

    2013-04-17

    article title:  Mars Researchers Rendezvous on Remote Arctic Island   ... each summer since 1999, researchers from NASA's Haughton-Mars Project and the Mars Society reside at this "polar desert" location to study the geologic and ...

  13. Two types of genetic carrier, the IncP genomic island and the novel IncP-1? plasmid, for the aac(2')-IIa gene that confers kasugamycin resistance in Acidovorax avenae ssp. avenae.

    PubMed

    Yoshii, Atsushi; Omatsu, Tsutomu; Katayama, Yukie; Koyama, Satoshi; Mizutani, Tetsuya; Moriyama, Hiromitsu; Fukuhara, Toshiyuki

    2015-04-01

    A unique aminoglycoside antibiotic, kasugamycin (KSM), has been used to control many plant bacterial and fungal diseases in several countries. The emergence of KSM-resistant Acidovorax avenae ssp. avenae and Burkholderia glumae, which cause rice bacterial brown stripe and rice bacterial grain and seedling rot, respectively, is a serious threat for the effective control of these diseases. Previously, we have identified the aac(2')-IIa gene, encoding a KSM 2'-N-acetyltransferase, from both KSM-resistant pathogens. Although all KSM-resistant isolates from both species possess the aac(2')-IIa gene, only A.?avenae strain 83 showed higher resistance than other strains. In this research, kinetic analysis indicates that an amino acid substitution from serine to threonine at position 146 of AAC(2')-IIa in strain 83 is not involved in this increased resistance. Whole draft genome analysis of A.?avenae 83 shows that the aac(2')-IIa gene is carried by the novel IncP-1? plasmid pAAA83, whereas the genetic carrier of other strains, the IncP genomic island, is inserted into their chromosomes. The difference in the nucleotides of the promoter region of aac(2')-IIa between strain 83 and other strains indicates an additional transcription start site and results in the increased transcription of aac(2')-IIa in strain 83. Moreover, biological characterization of pAAA83 demonstrates that it can be transferred by conjugation and maintained in the host cells. These results demonstrate that acquisition of the aac(2')-IIa gene takes place in at least two ways and that the gene module, which includes aac(2')-IIa and the downstream gene, may be an important unit for the dissemination of antibiotic resistance. PMID:25131295

  14. Island of Okinawa, Japan

    NASA Technical Reports Server (NTRS)

    1982-01-01

    The island of Okinawa, (26.5N, 128.0E) largest of the Ryukyu Islands, Japan. The Ryukyu island group lies south of the main home islands of Japan in an arc towards the Chinese island Republic of Taiwan. As is typical throughout the Japanese home islands, intense urban development can be observed all over the island in this near vertical view.

  15. 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

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

    2001-01-01

    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. PMID:11544236

  16. Island biology: looking towards the future

    PubMed Central

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

    2014-01-01

    Oceanic islands are renowned for the profound scientific insights that their fascinating biotas have provided to biologists during the past two centuries. Research presented at Island Biology 2014—an international conference, held in Honolulu, Hawaii (7–11 July 2014), which attracted 253 presenters and 430 participants from at least 35 countries1—demonstrated that islands are reclaiming a leading role in ecology and evolution, especially for synthetic studies at the intersections of macroecology, evolution, community ecology and applied ecology. New dynamics in island biology are stimulated by four major developments. We are experiencing the emergence of a truly global and comprehensive island research community incorporating previously neglected islands and taxa. Macroecology and big-data analyses yield a wealth of global-scale synthetic studies and detailed multi-island comparisons, while other modern research approaches such as genomics, phylogenetic and functional ecology, and palaeoecology, are also dispersing to islands. And, increasingly tight collaborations between basic research and conservation management make islands places where new conservation solutions for the twenty-first century are being tested. Islands are home to a disproportionate share of the world's rare (and extinct) species, and there is an urgent need to develop increasingly collaborative and innovative research to address their conservation requirements. PMID:25339655

  17. Pathogenicity island mobility and gene content.

    SciTech Connect

    Williams, Kelly Porter

    2013-10-01

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

  18. Anatahan Island

    Atmospheric Science Data Center

    2013-04-19

    ... Snorkelers around this island are likely to encounter the fish Achilles Tang and the Moorish Idol (Acanthurus achilles and Zanclus ... Terra circles the Earth in the same orbit as Landsat 7, flying at an altitude of about 700 kilometers above the Earth's surface. ...

  19. Island Panoramic

    USGS Multimedia Gallery

    A panoramic view taken from an island in the Yellowstone River.  Upstream is to the right side of the picture while downstream is to the left.  The middle of the picture looks straight across to the descending right bank. ...

  20. An homolog of the Frz Phosphoenolpyruvate:carbohydrate phosphoTransferase System of extraintestinal pathogenic Escherichia coli is encoded on a genomic island in specific lineages of Streptococcus agalactiae.

    PubMed

    Patron, Kévin; Gilot, Philippe; Camiade, Emilie; Mereghetti, Laurent

    2015-06-01

    We identified a Streptococcus agalactiae metabolic region (fru2) coding for a Phosphoenolpyruvate:carbohydrate phosphoTransferase System (PTS) homologous to the Frz system of extraintestinal pathogenic Escherichia coli strains. The Frz system is involved in environmental sensing and regulation of the expression of adaptation and virulence genes in E. coli. The S. agalactiae fru2 region codes three subunits of a PTS transporter of the fructose-mannitol family, a transcriptional activator of PTSs of the MtlR family, an allulose-6 phosphate-3-epimerase, a transaldolase and a transketolase. We demonstrated that all these genes form an operon. The fru2 operon is present in a 17494-bp genomic island. We analyzed by multilocus sequence typing a population of 492 strains representative of the S. agalactiae population and we showed that the presence of the fru2 operon is linked to the phylogeny of S. agalactiae. The fru2 operon is always present within strains of clonal complexes CC 1, CC 7, CC 10, CC 283 and singletons ST 130 and ST 288, but never found in other CCs and STs. Our results indicate that the fru2 operon was acquired during the evolution of the S. agalactiae species from a common ancestor before the divergence of CC 1, CC 7, CC 10, CC 283, ST 130 and ST 288. As S. agalactiae strains of CC 1 and CC 10 are frequently isolated from adults with invasive disease, we hypothesize that the S. agalactiae Fru2 system senses the environment to allow the bacterium to adapt to new conditions encountered during the infection of adults. PMID:25733487

  1. Streamlined Island

    NASA Technical Reports Server (NTRS)

    2003-01-01

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

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

  2. GenomeD3Plot: a library for rich, interactive visualizations of genomic data in web applications

    PubMed Central

    Laird, Matthew R.; Langille, Morgan G.I.; Brinkman, Fiona S.L.

    2015-01-01

    Motivation: A simple static image of genomes and associated metadata is very limiting, as researchers expect rich, interactive tools similar to the web applications found in the post-Web 2.0 world. GenomeD3Plot is a light weight visualization library written in javascript using the D3 library. GenomeD3Plot provides a rich API to allow the rapid visualization of complex genomic data using a convenient standards based JSON configuration file. When integrated into existing web services GenomeD3Plot allows researchers to interact with data, dynamically alter the view, or even resize or reposition the visualization in their browser window. In addition GenomeD3Plot has built in functionality to export any resulting genome visualization in PNG or SVG format for easy inclusion in manuscripts or presentations. Results: GenomeD3Plot is being utilized in the recently released Islandviewer 3 (www.pathogenomics.sfu.ca/islandviewer/) to visualize predicted genomic islands with other genome annotation data. However, its features enable it to be more widely applicable for dynamic visualization of genomic data in general. Availability and implementation: GenomeD3Plot is licensed under the GNU-GPL v3 at https://github.com/brinkmanlab/GenomeD3Plot/. Contact: brinkman@sfu.ca PMID:26093150

  3. Folly Island Tidal Lines

    USGS Multimedia Gallery

    Lines of debris from tidal action on Folly Island. Folly Island, a preserve owned by the Maine Coast Heritage Trust, is about 7 acres. It is located in Bartlett Narrows, along the western coast of Mount Desert Island....

  4. Folly Island Tidal Lines

    USGS Multimedia Gallery

    Lines of debris from tidal action on Folly Island. Folly Island, a preserve owned by the Maine Coast Heritage Trust, is about 7 acres. It is located in Bartlett Narrows, along the western coast of Mount Desert Island....

  5. The Effect of Island-Island Interaction on Coarsening of Strained Islands

    NASA Astrophysics Data System (ADS)

    Liu, Feng

    2003-07-01

    We review recent studies on the effect of stress/strain-induced island-island interaction on coarsening of strained islands. For coarsening of strained 2D islands, there always exists a stable island size against coarsening. When coarsening proceeds via only mass transport between islands, the interaction broadens the island size distribution, leading to a power-law dependence of island size uniformity on island number density. When coarsening proceeds via island migration in addition to mass transport between islands, the interaction can effectively direct island motion through island edge diffusion, leading to self-assembly of a close-packing array of 2D islands with improved size uniformity. For coarsening of strained 3D islands, a stable island size against coarsening may only exist if a stress/strain induced island edge energy dominates over island surface energy. The island-island interaction then modifies the size of stable islands, driving it to increase exponentially with increasing film coverage.

  6. Island Formation: Constructing a Coral Island

    ERIC Educational Resources Information Center

    Austin, Heather; Edd, Amelia

    2009-01-01

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

  7. Island Formation: Constructing a Coral Island

    ERIC Educational Resources Information Center

    Austin, Heather; Edd, Amelia

    2009-01-01

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

  8. DNA clustering and genome complexity.

    PubMed

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

    2014-12-01

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

  9. Hawaiian Island Archipelago

    NASA Technical Reports Server (NTRS)

    1988-01-01

    In this view of the entire Hawaiian Island Archipelago (21.0N, 157.0W), the islands perturb the prevailing northeastewrly winds producing extensive cloud wakes in the lee of the islands. The atmospheric haze within the wake is a result of the near continuous eruptions of Kilauea volcano on the southeast coast of the big island of Hawaii.

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

    PubMed Central

    2011-01-01

    Background Vinyl chloride is a widespread groundwater pollutant and Group 1 carcinogen. A previous comparative genomic analysis revealed 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. Results We targeted conserved positions in available genomic islands to amplify and sequence four additional vcrABC -containing genomic islands from previously-unsequenced vinyl chloride respiring Dehalococcoides enrichments. We identified a total of 31 ssrA-specific genomic islands from Dehalococcoides genomic data, accounting for 47 reductive dehalogenase homologous genes and many other non-core genes. Sixteen of these genomic islands contain a syntenic module of integration-associated genes located adjacent to the predicted site of integration, and among these islands, eight contain vcrABC as genetic 'cargo'. These eight vcrABC -containing genomic islands are syntenic across their ~12 kbp length, but have two phylogenetically discordant segments that unambiguously differentiate the integration module from the vcrABC cargo. Using available Dehalococcoides phylogenomic data we estimate that these ssrA-specific genomic islands are at least as old as the Dehalococcoides group itself, which in turn is much older than human civilization. Conclusions The vcrABC -containing genomic islands are a recently-acquired subset of a diverse collection of ssrA-specific mobile elements that are a major contributor to strain-level diversity in Dehalococcoides, and may have been throughout its evolution. The high similarity between vcrABC sequences is quantitatively consistent with recent horizontal acquisition driven by ~100 years of industrial pollution with chlorinated ethenes. PMID:21635780

  11. Hawaiian Island Archipelago

    NASA Technical Reports Server (NTRS)

    1985-01-01

    The entire Hawaiian Island Archipelago (21.5N, 158.0W) is seen in this single view. The islands are a favorite international resort and tourist attraction drawing visitors from all over the world to enjoy the tropical climate, year round beaches and lush island flora. Being volcanic in origin, the islands' offer a rugged landscape and on the big island of Hawaii, there is still an occasional volcanic eruption of lava flows and steam vents.

  12. Engineering a Reduced Escherichia coli Genome

    PubMed Central

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

    2002-01-01

    Our goal is to construct an improved Escherichia coli to serve both as a better model organism and as a more useful technological tool for genome science. We developed techniques for precise genomic surgery and applied them to deleting the largest K-islands of E. coli, identified by comparative genomics as recent horizontal acquisitions to the genome. They are loaded with cryptic prophages, transposons, damaged genes, and genes of unknown function. Our method leaves no scars or markers behind and can be applied sequentially. Twelve K-islands were successfully deleted, resulting in an 8.1% reduced genome size, a 9.3% reduction of gene count, and elimination of 24 of the 44 transposable elements of E. coli. These are particularly detrimental because they can mutagenize the genome or transpose into clones being propagated for sequencing, as happened in 18 places of the draft human genome sequence. We found no change in the growth rate on minimal medium, confirming the nonessential nature of these islands. This demonstration of feasibility opens the way for constructing a maximally reduced strain, which will provide a clean background for functional genomics studies, a more efficient background for use in biotechnology applications, and a unique tool for studies of genome stability and evolution. [Sequence data described in this paper have been submitted to the DNA Data Bank of Japan, European Molecular Biology Laboratory, and GenBank databases under accession nos. AF402780, AF402779, and AF406953, respectively.] PMID:11932248

  13. AnnotateGenomicRegions: a web application

    PubMed Central

    2014-01-01

    Background Modern genomic technologies produce large amounts of data that can be mapped to specific regions in the genome. Among the first steps in interpreting the results is annotation of genomic regions with known features such as genes, promoters, CpG islands etc. Several tools have been published to perform this task. However, using these tools often requires a significant amount of bioinformatics skills and/or downloading and installing dedicated software. Results Here we present AnnotateGenomicRegions, a web application that accepts genomic regions as input and outputs a selection of overlapping and/or neighboring genome annotations. Supported organisms include human (hg18, hg19), mouse (mm8, mm9, mm10), zebrafish (danRer7), and Saccharomyces cerevisiae (sacCer2, sacCer3). AnnotateGenomicRegions is accessible online on a public server or can be installed locally. Some frequently used annotations and genomes are embedded in the application while custom annotations may be added by the user. Conclusions The increasing spread of genomic technologies generates the need for a simple-to-use annotation tool for genomic regions that can be used by biologists and bioinformaticians alike. AnnotateGenomicRegions meets this demand. AnnotateGenomicRegions is an open-source web application that can be installed on any personal computer or institute server. AnnotateGenomicRegions is available at: http://cru.genomics.iit.it/AnnotateGenomicRegions. PMID:24564446

  14. Pathogenicity Islands in Bacterial Pathogenesis

    PubMed Central

    Schmidt, Herbert; Hensel, Michael

    2004-01-01

    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. PMID:14726454

  15. ClbP Is a Prototype of a Peptidase Subgroup Involved in Biosynthesis of Nonribosomal Peptides*

    PubMed Central

    Dubois, Damien; Baron, Olivier; Cougnoux, Antony; Delmas, Julien; Pradel, Nathalie; Boury, Michèle; Bouchon, Bernadette; Bringer, Marie-Agnès; Nougayrède, Jean-Philippe; Oswald, Eric; Bonnet, Richard

    2011-01-01

    The pks genomic island of Escherichia coli encodes polyketide (PK) and nonribosomal peptide (NRP) synthases that allow assembly of a putative hybrid PK-NRP compound named colibactin that induces DNA double-strand breaks in eukaryotic cells. The pks-encoded machinery harbors an atypical essential protein, ClbP. ClbP crystal structure and mutagenesis experiments revealed a serine-active site and original structural features compatible with peptidase activity, which was detected by biochemical assays. Ten ClbP homologs were identified in silico in NRP genomic islands of closely and distantly related bacterial species. All tested ClbP homologs were able to complement a clbP-deficient E. coli mutant. ClbP is therefore a prototype of a new subfamily of extracytoplasmic peptidases probably involved in the maturation of NRP compounds. Such peptidases will be powerful tools for the manipulation of NRP biosynthetic pathways. PMID:21795676

  16. Barrier Island Hazard Mapping.

    ERIC Educational Resources Information Center

    Pilkey, Orrin H.; Neal, William J.

    1980-01-01

    Describes efforts to evaluate and map the susceptibility of barrier islands to damage from storms, erosion, rising sea levels and other natural phenomena. Presented are criteria for assessing the safety and hazard potential of island developments. (WB)

  17. Overwash on Assateague Island

    USGS Multimedia Gallery

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

  18. Falkland Islands, UK

    NASA Technical Reports Server (NTRS)

    1991-01-01

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

  19. Island of Timor, Indonesia

    NASA Technical Reports Server (NTRS)

    1989-01-01

    This almost totally cloud free, photo of the island of Timor, Indonesia (9.0S, 125.0E) illustrates the volcanic origin of the over 1500 islands of Indonesia. Close examination of the photo reveals several eroded volcanoes on the Island of Timor and several of the adjacent islands. The linear alignment of the volcanoes, as seen from space, indicates the edges of the tectonic plates of the Earth's crust where volcanic activity is most common.

  20. Arctic ice islands

    SciTech Connect

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

    1988-01-01

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

  1. Diomede Islands, Bering Straight

    NASA Technical Reports Server (NTRS)

    2008-01-01

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

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

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

  2. Bouvet Island near Antarctica

    Atmospheric Science Data Center

    2013-04-16

    ... island presents an obstacle to the westerly winds, and wake patterns in the cloud layers are visible downstream of the island's location. ... tip of Antarctica but could not circumnavigate or land upon the island due to severe weather. Steep cliffs surrounding most sides ...

  3. Overwash on Assateague Island

    USGS Multimedia Gallery

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

  4. Positive correlations between genomic %AT and genome size within strains of bacterial species.

    PubMed

    Bohlin, Jon; Sekse, Camilla; Skjerve, Eystein; Brynildsrud, Ola

    2014-06-01

    Genomic %AT has been found to correlate negatively with genome size in microbes. While microbes with large genomes are often GC rich and free living, AT-rich bacteria tend to be host associated with smaller genomes. With over 2000 fully sequenced and assembled microbial genomes available, we explored the relationship among genomic %AT, genome size, relative entropy (a measure associated with genetic drift) and fraction of genome islands (GIs) in microbial species with the genomes of more than 10 strains available. A negative correlation with genome size was found in six out of 12 phylogenetic groups and subphyla and a positive correlation in only two. At the species level, we found a trend of positive correlations between genomic %AT and genome size in eight out of 20 species, while only four showed a negative correlation. Estimated chromosomal fractions of GIs were found to correlate positively with genome size in the strains of 14 out of 18 species and genomic %AT in the strains of seven species (two correlated negatively). Although GIs explain most of the observed positive correlations between genomic %AT and size, Chlamydia trachomatis seem to be an exception; therefore, these findings needs to be further explored. PMID:24983532

  5. Great Ape Genomics

    PubMed Central

    Wall, Jeffrey D.

    2013-01-01

    The great ape families are the species most closely related to our own, comprising chimpanzees, bonobos, gorillas, and orangutans. They live exclusively in tropical rainforests in Central Africa and the islands of Southeast Asia. Due to their close evolutionary relationship with humans, great apes share many cognitive, physiological, and morphological similarities with humans. The members of the great ape family make obvious models to facilitate the further understanding about humans' biology and history. This review will discuss how the recent addition of genome-wide data from great apes has furthered humans' understanding of these species and humanity, especially in the realm of evolutionary genetics. PMID:24174434

  6. Widespread genomic divergence during sympatric speciation

    PubMed Central

    Michel, Andrew P.; Sim, Sheina; Powell, Thomas H. Q.; Taylor, Michael S.; Nosil, Patrik; Feder, Jeffrey L.

    2010-01-01

    Speciation with gene flow is expected to generate a heterogeneous pattern of genomic differentiation. The few genes under or physically linked to loci experiencing strong disruptive selection can diverge, whereas gene flow will homogenize the remainder of the genome, resulting in isolated “genomic islands of speciation.” We conducted an experimental test of this hypothesis in Rhagoletis pomonella, a model for sympatric ecological speciation. Contrary to expectations, we found widespread divergence throughout the Rhagoletis genome, with the majority of loci displaying host differences, latitudinal clines, associations with adult eclosion time, and within-generation responses to selection in a manipulative overwintering experiment. The latter two results, coupled with linkage disequilibrium analyses, provide experimental evidence that divergence was driven by selection on numerous independent genomic regions rather than by genome-wide genetic drift. “Continents” of multiple differentiated loci, rather than isolated islands of divergence, may characterize even the early stages of speciation. Our results also illustrate how these continents can exhibit variable topography, depending on selection strength, availability of preexisting genetic variation, linkage relationships, and genomic features that reduce recombination. For example, the divergence observed throughout the Rhagoletis genome was clearly accentuated in some regions, such as those harboring chromosomal inversions. These results highlight how the individual genes driving speciation can be embedded within an actively diverging genome. PMID:20457907

  7. Cancer Genomics

    PubMed Central

    Mardis, Elaine

    2015-01-01

    Modern cancer genomics has emerged from the combination of the Human Genome Reference, massively parallel sequencing, and the comparison of tumor to normal DNA sequences, revealing novel insights into the cancer genome and its amazing diversity. Recent developments in applying our knowledge of cancer genomics have focused on the utility of these data for clinical applications. The emergent results of this translation into the clinical setting already are changing the clinical care and monitoring of cancer patients.

  8. Microbial Lifestyle and Genome Signatures

    PubMed Central

    Dutta, Chitra; Paul, Sandip

    2012-01-01

    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

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

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

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

  10. Hydrologic data for Block Island, Rhode Island

    USGS Publications Warehouse

    Burns, Emily

    1993-01-01

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

  11. Stewart Head from Folly Island

    USGS Multimedia Gallery

    Stewart Head, as seen from Folly Island. Folly Island, a preserve owned by the Maine Coast Heritage Trust, is about 7 acres. It is located in Bartlett Narrows, along the western coast of Mount Desert Island. ...

  12. Island Natural Science School.

    ERIC Educational Resources Information Center

    Toronto Board of Education (Ontario).

    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…

  13. Barnacles on Folly Island

    USGS Multimedia Gallery

    Barnacles on a rock on Folly Island. Barnacles are crustaceans, related to lobsters and crabs, that often live in tidal zones. Once they become adults, they anchor themselves to a hard surface and filter feed. Folly Island, a preserve owned by the Maine Coast Heritage Trust, is about 7 acres. It is ...

  14. Islands in a Storm.

    ERIC Educational Resources Information Center

    Vail, Kathleen

    1995-01-01

    Smith Island in the Chesapeake Bay is actually a group of three islands: Ewell, Rhodes Point, and Tylerton. Dwindling enrollment jeopardizes the community's two schools that contain grades one through seven. The school board believes they can give the sixth and seventh graders at Ewell and Tylerton a better education on the mainland. (MLF)

  15. Basaltic island sand provenance

    SciTech Connect

    Marsaglia, K.M. . Dept. of Geological Sciences)

    1992-01-01

    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.

  16. Channel Islands rare plants

    USGS Publications Warehouse

    McEachern, K.

    1999-01-01

    Database contains information on 65 rare plant taxa on six islands from archive searches and field surveys, including population location, size and extent 1920-1999, population and habitat conditions, census data, phenological information, associated species. USGS-BRD, Channel Islands Field Station, Ventura, CA.

  17. Back to Treasure Island

    ERIC Educational Resources Information Center

    Shriki, Atara

    2011-01-01

    In this article, the author presents the Treasure Island problem and some inquiry activities derived from the problem. Trying to find where pirates buried a treasure leads to a surprising answer, multiple solutions, and a discussion of problem solving. The Treasure Island problem is an example of an inquiry activity that can be implemented in…

  18. Rhode Island Seafloor

    USGS Multimedia Gallery

    This photograph is of the seafloor on the Rhode Island coast and shows a skate on a fine-grained, likely silty or muddy seafloor. This photograph was collected to support research and management activities (e.g., wind farms and fisheries) along the Rhode Island inner continental shelf....

  19. Marine and Island Ecology.

    ERIC Educational Resources Information Center

    Stephens, Lawrence J.; And Others

    1988-01-01

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

  20. Perioperative Genomics

    PubMed Central

    Nagele, Peter

    2011-01-01

    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. PMID:22099920

  1. Prophage Genomics

    PubMed Central

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

    2003-01-01

    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. PMID:12794192

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

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

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

  3. Cognitive Constraints and Island Effects

    ERIC Educational Resources Information Center

    Hofmeister, Philip; Sag, Ivan A.

    2010-01-01

    Competence-based theories of island effects play a central role in generative grammar, yet the graded nature of many syntactic islands has never been properly accounted for. Categorical syntactic accounts of island effects have persisted in spite of a wealth of data suggesting that island effects are not categorical in nature and that…

  4. Cognitive Constraints and Island Effects

    ERIC Educational Resources Information Center

    Hofmeister, Philip; Sag, Ivan A.

    2010-01-01

    Competence-based theories of island effects play a central role in generative grammar, yet the graded nature of many syntactic islands has never been properly accounted for. Categorical syntactic accounts of island effects have persisted in spite of a wealth of data suggesting that island effects are not categorical in nature and that…

  5. SOYBEAN GENOMICS

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In recent years an understanding of the composition and organization of the soybean genome has developed. This has been the result of numerous advances in functional and structural genomics. This Soybean Monograph chapter offers a review of these advances and discusses specific literature supportin...

  6. Population Genomics of Infectious and Integrated Wolbachia pipientis Genomes in Drosophila ananassae

    PubMed Central

    Choi, Jae Young; Bubnell, Jaclyn E.; Aquadro, Charles F.

    2015-01-01

    Coevolution between Drosophila and its endosymbiont Wolbachia pipientis has many intriguing aspects. For example, Drosophila ananassae hosts two forms of W. pipientis genomes: One being the infectious bacterial genome and the other integrated into the host nuclear genome. Here, we characterize the infectious and integrated genomes of W. pipientis infecting D. ananassae (wAna), by genome sequencing 15 strains of D. ananassae that have either the infectious or integrated wAna genomes. Results indicate evolutionarily stable maternal transmission for the infectious wAna genome suggesting a relatively long-term coevolution with its host. In contrast, the integrated wAna genome showed pseudogene-like characteristics accumulating many variants that are predicted to have deleterious effects if present in an infectious bacterial genome. Phylogenomic analysis of sequence variation together with genotyping by polymerase chain reaction of large structural variations indicated several wAna variants among the eight infectious wAna genomes. In contrast, only a single wAna variant was found among the seven integrated wAna genomes examined in lines from Africa, south Asia, and south Pacific islands suggesting that the integration occurred once from a single infectious wAna genome and then spread geographically. Further analysis revealed that for all D. ananassae we examined with the integrated wAna genomes, the majority of the integrated wAna genomic regions is represented in at least two copies suggesting a double integration or single integration followed by an integrated genome duplication. The possible evolutionary mechanism underlying the widespread geographical presence of the duplicate integration of the wAna genome is an intriguing question remaining to be answered. PMID:26254486

  7. Population Genomics of Infectious and Integrated Wolbachia pipientis Genomes in Drosophila ananassae.

    PubMed

    Choi, Jae Young; Bubnell, Jaclyn E; Aquadro, Charles F

    2015-08-01

    Coevolution between Drosophila and its endosymbiont Wolbachia pipientis has many intriguing aspects. For example, Drosophila ananassae hosts two forms of W. pipientis genomes: One being the infectious bacterial genome and the other integrated into the host nuclear genome. Here, we characterize the infectious and integrated genomes of W. pipientis infecting D. ananassae (wAna), by genome sequencing 15 strains of D. ananassae that have either the infectious or integrated wAna genomes. Results indicate evolutionarily stable maternal transmission for the infectious wAna genome suggesting a relatively long-term coevolution with its host. In contrast, the integrated wAna genome showed pseudogene-like characteristics accumulating many variants that are predicted to have deleterious effects if present in an infectious bacterial genome. Phylogenomic analysis of sequence variation together with genotyping by polymerase chain reaction of large structural variations indicated several wAna variants among the eight infectious wAna genomes. In contrast, only a single wAna variant was found among the seven integrated wAna genomes examined in lines from Africa, south Asia, and south Pacific islands suggesting that the integration occurred once from a single infectious wAna genome and then spread geographically. Further analysis revealed that for all D. ananassae we examined with the integrated wAna genomes, the majority of the integrated wAna genomic regions is represented in at least two copies suggesting a double integration or single integration followed by an integrated genome duplication. The possible evolutionary mechanism underlying the widespread geographical presence of the duplicate integration of the wAna genome is an intriguing question remaining to be answered. PMID:26254486

  8. Small islands adrift

    NASA Astrophysics Data System (ADS)

    Petherick, Anna

    2015-07-01

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

  9. 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.

  10. Island Watershed Activity.

    ERIC Educational Resources Information Center

    Benson, Rod

    2003-01-01

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

  11. Belcher Islands, Canada

    NASA Technical Reports Server (NTRS)

    2008-01-01

    The Belcher Islands are an archipelago in Hudson Bay in Canada, belonging to the territory of Nunavit. The hamlet of Sanikiluaq is on the north coast of Flaherty Island. Over 1500 islands make up the archipelago. The folded sedimentary and volcanic rocks making up the islands are Proterozoic in age between 0.5 and 2.5 billion years old.

    The image mosaic was acquired 18 September 2006, covers an area of 45.7 x 113.3 km, and is located near 56.1 degrees north latitude, 79.4 degrees west longitude.

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

  12. Melville Island, Australia

    NASA Technical Reports Server (NTRS)

    1992-01-01

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

  13. Effects of island geometry in postdeposition island growth

    NASA Astrophysics Data System (ADS)

    Tataru, Oana; Family, Fereydoon; Amar, Jacques G.

    2000-11-01

    The results of kinetic Monte Carlo simulations of a realistic model of postdeposition island growth that takes into account the spatial extent of islands are presented. Simulations were carried out on one- and two-dimensional substrates for different values of the critical island size i and were compared with previous results for a point-island model. The use of a realistic island geometry results in enhanced island aggregation and coalescence. This leads to an increase in the average island size S as well as the exponent z describing the dependence of S on coverage. The shape of the island-size distribution for i=3 also changes dramatically due to the existence of ``magic'' islands.

  14. An Enterotoxin-Bearing Pathogenicity Island in Staphylococcus epidermidis.

    PubMed

    Madhusoodanan, Jyoti; Seo, Keun Seok; Remortel, Brian; Park, Joo Youn; Hwang, Sun Young; Fox, Lawrence K; Park, Yong Ho; Deobald, Claudia F; Wang, Dan; Liu, Song; Daugherty, Sean C; Gill, Ann Lindley; Bohach, Gregory A; Gill, Steven R

    2011-04-01

    Cocolonization of human mucosal surfaces causes frequent encounters between various staphylococcal species, creating opportunities for the horizontal acquisition of mobile genetic elements. The majority of Staphylococcus aureus toxins and virulence factors are encoded on S. aureus pathogenicity islands (SaPIs). Horizontal movement of SaPIs between S. aureus strains plays a role in the evolution of virulent clinical isolates. Although there have been reports of the production of toxic shock syndrome toxin 1 (TSST-1), enterotoxin, and other superantigens by coagulase-negative staphylococci, no associated pathogenicity islands have been found in the genome of Staphylococcus epidermidis, a generally less virulent relative of S. aureus. We show here the first evidence of a composite S. epidermidis pathogenicity island (SePI), the product of multiple insertions in the genome of a clinical isolate. The taxonomic placement of S. epidermidis strain FRI909 was confirmed by a number of biochemical tests and multilocus sequence typing. The genome sequence of this strain was analyzed for other unique gene clusters and their locations. This pathogenicity island encodes and expresses staphylococcal enterotoxin C3 (SEC3) and staphylococcal enterotoxin-like toxin L (SElL), as confirmed by quantitative reverse transcription-PCR (qRT-PCR) and immunoblotting. We present here an initial characterization of this novel pathogenicity island, and we establish that it is stable, expresses enterotoxins, and is not obviously transmissible by phage transduction. We also describe the genome sequence, excision, replication, and packaging of a novel bacteriophage in S. epidermidis FRI909, as well as attempts to mobilize the SePI element by this phage. PMID:21317317

  15. Antarctic Genomics

    PubMed Central

    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.; Römisch, Karin; Rogers, Alex D.

    2004-01-01

    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. PMID:18629155

  16. Tracing Lifestyle Adaptation in Prokaryotic Genomes

    PubMed Central

    Altermann, Eric

    2012-01-01

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

  17. A CPG ISLAND AT THE PROMOTER OF THE PDE8B GENE IS METHYLATED IN PLACENTA AND HYDATIDIFORM MOLES, BUT NOT IN CONTROL DNA

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Objective: We used a genome-wide CpG methylation screen, restriction landmark genome scanning (RLGS) to identify CpG islands that have altered methylation in complete hydatidiform moles (CHM), compared to control genomic DNA. Because CHM are diploid, but of uniparental parental inheritance and uniq...

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

    PubMed Central

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

    2015-01-01

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

  19. Heron Island, Australia

    NASA Technical Reports Server (NTRS)

    2002-01-01

    Heron Island is located at the sourthern end of Australia's 2,050 km-long Great Barrier Reef. Surrounded by coral reef and home to over 1000 species of fish, scuba divers and scientists alike are drawn to the island's resort and research station. The true-color image above was taken by Space Imaging's Ikonos satellite with a resolution of 4 meters per pixel-high enough to see individual boats tied up at the small marina. The narrow channel leading from the marina to the ocean was blasted and dredged decades ago, before the island became a national park. Since then the Australian government has implemented conservation measures, such as limiting the number of tourists and removing or recycling, instead of incinerating, all trash. One of the applications of remote sensing data from Ikonos is environmental monitoring, including studies of coral reef health. For more information about the island, read Heron Island. Image by Robert Simmon, based on data copyright Space Imaging

  20. Enhanced annotations and features for comparing thousands of Pseudomonas genomes in the Pseudomonas genome database

    PubMed Central

    Winsor, Geoffrey L.; Griffiths, Emma J.; Lo, Raymond; Dhillon, Bhavjinder K.; Shay, Julie A.; Brinkman, Fiona S. L.

    2016-01-01

    The Pseudomonas Genome Database (http://www.pseudomonas.com) is well known for the application of community-based annotation approaches for producing a high-quality Pseudomonas aeruginosa PAO1 genome annotation, and facilitating whole-genome comparative analyses with other Pseudomonas strains. To aid analysis of potentially thousands of complete and draft genome assemblies, this database and analysis platform was upgraded to integrate curated genome annotations and isolate metadata with enhanced tools for larger scale comparative analysis and visualization. Manually curated gene annotations are supplemented with improved computational analyses that help identify putative drug targets and vaccine candidates or assist with evolutionary studies by identifying orthologs, pathogen-associated genes and genomic islands. The database schema has been updated to integrate isolate metadata that will facilitate more powerful analysis of genomes across datasets in the future. We continue to place an emphasis on providing high-quality updates to gene annotations through regular review of the scientific literature and using community-based approaches including a major new Pseudomonas community initiative for the assignment of high-quality gene ontology terms to genes. As we further expand from thousands of genomes, we plan to provide enhancements that will aid data visualization and analysis arising from whole-genome comparative studies including more pan-genome and population-based approaches. PMID:26578582

  1. 11. VIEW NORTH, WOODLYNNE AVENUE ISLAND FROM 130 SOUTH ISLAND ...

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

    11. VIEW NORTH, WOODLYNNE AVENUE ISLAND FROM 130 SOUTH ISLAND - White Horse Pike Rond Point, Intersection of Crescent Boulevard (U.S. Route 130), White Horse Pike (U.S. Route 30), & Clay Avenue, Collingswood, Camden County, NJ

  2. Habitat and environment of islands: primary and supplemental island sets

    USGS Publications Warehouse

    Matalas, Nicholas C.; Grossling, Bernardo F.

    2002-01-01

    The original intent of the study was to develop a first-order synopsis of island hydrology with an integrated geologic basis on a global scale. As the study progressed, the aim was broadened to provide a framework for subsequent assessments on large regional or global scales of island resources and impacts on those resources that are derived from global changes. Fundamental to the study was the development of a comprehensive framework?a wide range of parameters that describe a set of 'saltwater' islands sufficiently large to Characterize the spatial distribution of the world?s islands; Account for all major archipelagos; Account for almost all oceanically isolated islands, and Account collectively for a very large proportion of the total area of the world?s islands whereby additional islands would only marginally contribute to the representativeness and accountability of the island set. The comprehensive framework, which is referred to as the ?Primary Island Set,? is built on 122 parameters that describe 1,000 islands. To complement the investigations based on the Primary Island Set, two supplemental island sets, Set A?Other Islands (not in the Primary Island Set) and Set B?Lagoonal Atolls, are included in the study. The Primary Island Set, together with the Supplemental Island Sets A and B, provides a framework that can be used in various scientific disciplines for their island-based studies on broad regional or global scales. The study uses an informal, coherent, geophysical organization of the islands that belong to the three island sets. The organization is in the form of a global island chain, which is a particular sequential ordering of the islands referred to as the 'Alisida.' The Alisida was developed through a trial-and-error procedure by seeking to strike a balance between 'minimizing the length of the global chain' and 'maximizing the chain?s geophysical coherence.' The fact that an objective function cannot be minimized and maximized simultaneously indicates that the Alisida is not unique. Global island chains other than the Alisida may better serve disciplines other than those of hydrology and geology.

  3. Genome Sequence of Bradyrhizobium tropiciagri Strain CNPSo 1112T, Isolated from a Root Nodule of Neonotonia wightii

    PubMed Central

    Delamuta, Jakeline Renata Marçon; Gomes, Douglas Fabiano; Ribeiro, Renan Augusto; Chueire, Ligia Maria Oliveira; Souza, Renata Carolini; Almeida, Luiz Gonzaga Paula; Vasconcelos, Ana Tereza Ribeiro

    2015-01-01

    CNPSo 1112T is a nitrogen-fixing symbiont of perennial soybean, a tropical legume forage. Its draft genome indicates a large genome with a circular chromosome and 9,554 coding sequences (CDSs). Operons of nodulation, nitrogen fixation, and uptake hydrogenase were present in the symbiotic island, and the genome encompasses several CDSs of stress tolerance. PMID:26679591

  4. Genome Sequence of Bradyrhizobium tropiciagri Strain CNPSo 1112T, Isolated from a Root Nodule of Neonotonia wightii.

    PubMed

    Delamuta, Jakeline Renata Marçon; Gomes, Douglas Fabiano; Ribeiro, Renan Augusto; Chueire, Ligia Maria Oliveira; Souza, Renata Carolini; Almeida, Luiz Gonzaga Paula; Vasconcelos, Ana Tereza Ribeiro; Hungria, Mariangela

    2015-01-01

    CNPSo 1112(T) is a nitrogen-fixing symbiont of perennial soybean, a tropical legume forage. Its draft genome indicates a large genome with a circular chromosome and 9,554 coding sequences (CDSs). Operons of nodulation, nitrogen fixation, and uptake hydrogenase were present in the symbiotic island, and the genome encompasses several CDSs of stress tolerance. PMID:26679591

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

    PubMed Central

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

    2005-01-01

    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. PMID:16109957

  6. Contextual view of Treasure Island from Yerba Buena Island, showing ...

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

    Contextual view of Treasure Island from Yerba Buena Island, showing Palace of Fine and Decorative Arts (Building 3), far right, Hall of Transportation (Building 2), middle, and The Administration Building (Building 1), far left, Port of Trade Winds is in foreground, camera facing northwest - Golden Gate International Exposition, Treasure Island, San Francisco, San Francisco County, CA

  7. Long Island Solar Farm

    SciTech Connect

    Anders, R.

    2013-05-01

    The Long Island Solar Farm (LISF) is a remarkable success story, whereby very different interest groups found a way to capitalize on unusual circumstances to develop a mutually beneficial source of renewable energy. The uniqueness of the circumstances that were necessary to develop the Long Island Solar Farm make it very difficult to replicate. The project is, however, an unparalleled resource for solar energy research, which will greatly inform large-scale PV solar development in the East. Lastly, the LISF is a superb model for the process by which the project developed and the innovation and leadership shown by the different players.

  8. Archaeoastronomy of Easter Island

    NASA Astrophysics Data System (ADS)

    Edwards, Edmundo

    Astronomer priests or "skywatchers" on Easter Island lived in stone towers that were used as observatories and built stone markers in the periphery that indicated the heliacal rising of certain stars that served to indicate the arrival of marine birds, turtles, the offshore fishing season, and times for planting and harvest. Petroglyphs related to such sites depict outriggers, fishhooks, pelagic fish, and turtles and supposedly represented a star map. In this chapter, we analyze a set of such skywatchers dwellings, and stone markers located upon the North coast of Easter Island that have astronomic orientations, its related petroglyphs, and the relations between these directions with their yearly activities and their ritual calendar.

  9. Island custom blocking technique

    SciTech Connect

    Carabetta, R.J. )

    1988-03-01

    The technique of Island blocking is being used more frequently since the advent of our new head and neck blocking techniques and the implementation of a newly devised lung protocol. The system presented affords the mould room personnel a quick and accurate means of island block fabrication without the constant remeasuring or subtle shifting to approximate correct placement. The cookie cutter is easily implemented into any department's existing block cutting techniques. The device is easily and inexpensively made either in a machine shop or acquired by contacting the author.

  10. Sakhalin Island terrain intelligence

    USGS Publications Warehouse

    U.S. Geological Survey Military Geology Branch

    1943-01-01

    This folio of maps and explanatory tables outlines the principal terrain features of Sakhalin Island. Each map and table is devoted to a specialized set of problems; together they cover the subjects of terrain appreciation, climate, rivers, water supply, construction materials, suitability for roads, suitability for airfields, fuels and other mineral resources, and geology. In most cases, the map of the island is divided into two parts: N. of latitude 50° N., Russian Sakhalin, and south of latitude 50° N., Japanese Sakhalin or Karafuto. These maps and data were compiled by the United States Geological Survey during the period from March to September, 1943.

  11. Genotypic Characterization of Bradyrhizobium Strains Nodulating Endemic Woody Legumes of the Canary Islands by PCR-Restriction Fragment Length Polymorphism Analysis of Genes Encoding 16S rRNA (16S rDNA) and 16S-23S rDNA Intergenic Spacers, Repetitive Extragenic Palindromic PCR Genomic Fingerprinting, and Partial 16S rDNA Sequencing

    PubMed Central

    Vinuesa, Pablo; Rademaker, Jan L. W.; de Bruijn, Frans J.; Werner, Dietrich

    1998-01-01

    We present a phylogenetic analysis of nine strains of symbiotic nitrogen-fixing bacteria isolated from nodules of tagasaste (Chamaecytisus proliferus) and other endemic woody legumes of the Canary Islands, Spain. These and several reference strains were characterized genotypically at different levels of taxonomic resolution by computer-assisted analysis of 16S ribosomal DNA (rDNA) PCR-restriction fragment length polymorphisms (PCR-RFLPs), 16S-23S rDNA intergenic spacer (IGS) RFLPs, and repetitive extragenic palindromic PCR (rep-PCR) genomic fingerprints with BOX, ERIC, and REP primers. Cluster analysis of 16S rDNA restriction patterns with four tetrameric endonucleases grouped the Canarian isolates with the two reference strains, Bradyrhizobium japonicum USDA 110spc4 and Bradyrhizobium sp. strain (Centrosema) CIAT 3101, resolving three genotypes within these bradyrhizobia. In the analysis of IGS RFLPs with three enzymes, six groups were found, whereas rep-PCR fingerprinting revealed an even greater genotypic diversity, with only two of the Canarian strains having similar fingerprints. Furthermore, we show that IGS RFLPs and even very dissimilar rep-PCR fingerprints can be clustered into phylogenetically sound groupings by combining them with 16S rDNA RFLPs in computer-assisted cluster analysis of electrophoretic patterns. The DNA sequence analysis of a highly variable 264-bp segment of the 16S rRNA genes of these strains was found to be consistent with the fingerprint-based classification. Three different DNA sequences were obtained, one of which was not previously described, and all belonged to the B. japonicum/Rhodopseudomonas rDNA cluster. Nodulation assays revealed that none of the Canarian isolates nodulated Glycine max or Leucaena leucocephala, but all nodulated Acacia pendula, C. proliferus, Macroptilium atropurpureum, and Vigna unguiculata. PMID:9603820

  12. Salt Marshes at Chincoteague Island

    USGS Multimedia Gallery

    Salt marshes at Chincoteague Island. The salt marshes that make up Chincoteague Island are important habitat for migrating waterfowl. In addition, they serve an important role in protecting inland ecosystems and communities from oceanic storms....

  13. Mosquito Point at Chincoteague Island

    USGS Multimedia Gallery

    Salt marshes at Mosquito Point of Chincoteague Island. The salt marshes that make up Chincoteague Island are important habitat for migrating waterfowl. In addition, they serve an important role in protecting inland ecosystems and communities from oceanic storms....

  14. The human genome: a multifractal analysis

    PubMed Central

    2011-01-01

    Background Several studies have shown that genomes can be studied via a multifractal formalism. Recently, we used a multifractal approach to study the genetic information content of the Caenorhabditis elegans genome. Here we investigate the possibility that the human genome shows a similar behavior to that observed in the nematode. Results We report here multifractality in the human genome sequence. This behavior correlates strongly on the presence of Alu elements and to a lesser extent on CpG islands and (G+C) content. In contrast, no or low relationship was found for LINE, MIR, MER, LTRs elements and DNA regions poor in genetic information. Gene function, cluster of orthologous genes, metabolic pathways, and exons tended to increase their frequencies with ranges of multifractality and large gene families were located in genomic regions with varied multifractality. Additionally, a multifractal map and classification for human chromosomes are proposed. Conclusions Based on these findings, we propose a descriptive non-linear model for the structure of the human genome, with some biological implications. This model reveals 1) a multifractal regionalization where many regions coexist that are far from equilibrium and 2) this non-linear organization has significant molecular and medical genetic implications for understanding the role of Alu elements in genome stability and structure of the human genome. Given the role of Alu sequences in gene regulation, genetic diseases, human genetic diversity, adaptation and phylogenetic analyses, these quantifications are especially useful. PMID:21999602

  15. Genomics of Rapid Incipient Speciation in Sympatric Threespine Stickleback.

    PubMed

    Marques, David A; Lucek, Kay; Meier, Joana I; Mwaiko, Salome; Wagner, Catherine E; Excoffier, Laurent; Seehausen, Ole

    2016-02-01

    Ecological speciation is the process by which reproductively isolated populations emerge as a consequence of divergent natural or ecologically-mediated sexual selection. Most genomic studies of ecological speciation have investigated allopatric populations, making it difficult to infer reproductive isolation. The few studies on sympatric ecotypes have focused on advanced stages of the speciation process after thousands of generations of divergence. As a consequence, we still do not know what genomic signatures of the early onset of ecological speciation look like. Here, we examined genomic differentiation among migratory lake and resident stream ecotypes of threespine stickleback reproducing in sympatry in one stream, and in parapatry in another stream. Importantly, these ecotypes started diverging less than 150 years ago. We obtained 34,756 SNPs with restriction-site associated DNA sequencing and identified genomic islands of differentiation using a Hidden Markov Model approach. Consistent with incipient ecological speciation, we found significant genomic differentiation between ecotypes both in sympatry and parapatry. Of 19 islands of differentiation resisting gene flow in sympatry, all were also differentiated in parapatry and were thus likely driven by divergent selection among habitats. These islands clustered in quantitative trait loci controlling divergent traits among the ecotypes, many of them concentrated in one region with low to intermediate recombination. Our findings suggest that adaptive genomic differentiation at many genetic loci can arise and persist in sympatry at the very early stage of ecotype divergence, and that the genomic architecture of adaptation may facilitate this. PMID:26925837

  16. Genomics of Rapid Incipient Speciation in Sympatric Threespine Stickleback

    PubMed Central

    Marques, David A.; Lucek, Kay; Meier, Joana I.; Mwaiko, Salome; Wagner, Catherine E.; Excoffier, Laurent; Seehausen, Ole

    2016-01-01

    Ecological speciation is the process by which reproductively isolated populations emerge as a consequence of divergent natural or ecologically-mediated sexual selection. Most genomic studies of ecological speciation have investigated allopatric populations, making it difficult to infer reproductive isolation. The few studies on sympatric ecotypes have focused on advanced stages of the speciation process after thousands of generations of divergence. As a consequence, we still do not know what genomic signatures of the early onset of ecological speciation look like. Here, we examined genomic differentiation among migratory lake and resident stream ecotypes of threespine stickleback reproducing in sympatry in one stream, and in parapatry in another stream. Importantly, these ecotypes started diverging less than 150 years ago. We obtained 34,756 SNPs with restriction-site associated DNA sequencing and identified genomic islands of differentiation using a Hidden Markov Model approach. Consistent with incipient ecological speciation, we found significant genomic differentiation between ecotypes both in sympatry and parapatry. Of 19 islands of differentiation resisting gene flow in sympatry, all were also differentiated in parapatry and were thus likely driven by divergent selection among habitats. These islands clustered in quantitative trait loci controlling divergent traits among the ecotypes, many of them concentrated in one region with low to intermediate recombination. Our findings suggest that adaptive genomic differentiation at many genetic loci can arise and persist in sympatry at the very early stage of ecotype divergence, and that the genomic architecture of adaptation may facilitate this. PMID:26925837

  17. Imaging genomics

    PubMed Central

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

    2010-01-01

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

  18. Pathogenicity Island-Directed Transfer of Unlinked Chromosomal Virulence Genes

    PubMed Central

    Chen, John; Ram, Geeta; Penadés, José R.; Brown, Stuart; Novick, Richard P.

    2014-01-01

    Summary In recent decades, the notorious pathogen Staphylococcus aureus has become progressively more contagious, more virulent and more resistant to antibiotics. This implies a rather dynamic evolutionary capability, representing a remarkable level of genomic plasticity, most probably maintained by horizontal gene transfer. Here we report that the staphylococcal pathogenicity islands have a dual role in gene transfer: they not only mediate their own transfer, but they can independently direct the transfer of unlinked chromosomal segments containing virulence genes. While transfer of the island itself requires specific helper phages, transfer of unlinked chromosomal segments does not, so that potentially any pac-type phage will serve. These results reveal that SaPIs can increase the horizontal exchange of accessory genes associated with disease, and may shape pathogen genomes beyond the confines of their attachment sites. PMID:25498143

  19. HEAT ISLAND REDUCTION STRATEGIES GUIDEBOOK

    EPA Science Inventory

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

  20. HEAT ISLAND REDUCTION STRATEGIES GUIDEBOOK

    EPA Science Inventory

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

  1. Pediatrics in the Marshall Islands

    SciTech Connect

    Dungy, C.I.; Morgan, B.C.; Adams, W.H.

    1984-01-01

    The delivery of health care to children living on isolated island communities presents unique challenges to health professionals. An evolved method of providing longitudinal services to infants and children residing on islands of the Marshall Island chain - a central Pacific portion of the Micronesian archipelago - is presented. The difficulties associated with provision of comprehensive health care in a vast ocean area are discussed.

  2. Costly island for Arctic drilling

    SciTech Connect

    Not Available

    1983-12-01

    The largest artificial island in the frigid Beaufort Sea was recently completed. The $140-million teardrop-shaped island, the largest of 17 built in the Beaufort Sea, sits in 50-ft. of water, 20 miles northwest of the Prudhoe Bay oil fields on Alaska's North Slope. The problems encountered in constructing the island are discussed.

  3. Listeria Genomics

    NASA Astrophysics Data System (ADS)

    Cabanes, Didier; Sousa, Sandra; Cossart, Pascale

    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.

  4. Hawaii's Sugar Islands.

    ERIC Educational Resources Information Center

    Hawaiian Sugar Planters' Association, Aiea, HI.

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

  5. Kiritimati, Kiribati (Christmas Island)

    NASA Technical Reports Server (NTRS)

    2002-01-01

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

  6. Prince Edward Island.

    ERIC Educational Resources Information Center

    Timmons, Vianne

    2003-01-01

    This article profiles the educational system of Prince Edward Island and discusses initiatives for students who are at-risk. It describes programs and services for students who are at-risk, relevant educational legislation, areas of strength, challenges that need to be overcome, and areas of action. (Contains references.) (CR)

  7. Atsena Otie Key Island

    USGS Multimedia Gallery

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

  8. Block Island Seafloor

    USGS Multimedia Gallery

    This photograph is of the seafloor off the Block Island coast and shows a rock crab and several shrimp on a boulder that is covered with bryozoans. Shell fragments and other coarse grained sediment can be seen in the background (upper left corner). This photograph was collected to support research a...

  9. Plum Island Seafloor

    USGS Multimedia Gallery

    This photograph is of the seafloor off the Plum Island coast and shows spider crabs on seabed characterized by coarse sand, gravelly sediment and shell fragments. This photograph was collected as part of a collaborative seafloor mapping program between the USGS and the Connecticut Department of Envi...

  10. Multidecadal shoreline changes of atoll islands in the Marshall Islands

    NASA Astrophysics Data System (ADS)

    Ford, M.

    2012-12-01

    Atoll islands are considered highly vulnerable to the impacts of continued sea level rise. One of the most commonly predicted outcomes of continued sea level rise is widespread and chronic shoreline erosion. Despite the widespread implications of predicted erosion, the decadal scale changes of atoll island shorelines are poorly resolved. The Marshall Islands is one of only four countries where the majority of inhabited land is comprised of reef and atoll islands. Consisting of 29 atolls and 5 mid-ocean reef islands, the Marshall Islands are considered highly vulnerable to the impacts of sea level rise. A detailed analysis of shoreline change on over 300 islands on 10 atolls was undertaken using historic aerial photos (1945-1978) and modern high resolution satellite imagery (2004-2012). Results highlight the complex and dynamic nature of atoll islands, with significant shifts in shoreline position observed over the period of analysis. Results suggest shoreline accretion is the dominant mode of change on the islands studied, often associated with a net increase in vegetated island area. However, considerable inter- and intra-atoll variability exists with regards to shoreline stability. Findings are discussed with respect to island morphodynamics and potential hazard mitigation and planning responses within atoll settings.

  11. Magnetic Island Induced Bootstrap Current on Island Dynamics in Tokamaks

    SciTech Connect

    Spong, Donald A; Shaing, K. C.

    2006-02-01

    When a magnetic island is embedded in toroidally symmetric tokamaks, the toroidal symmetry in |B| is broken [K. C. Shaing, Phys. Rev. Lett. 87, 245003 (2001)] . 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 |{Delta}{prime}| for the island to be unstable. This lower limit depends on the local poloidal plasma beta {beta}{sub p}, the ratio of the plasma pressure to the poloidal magnetic field pressure. If {beta}{sub p} is high enough, the magnetic island is stable. This mechanism provides an alternative route to stabilize the island.

  12. Magnetic island induced bootstrap current on island dynamics in tokamaks

    SciTech Connect

    Shaing, K.C.; Spong, D.A.

    2006-02-15

    When a magnetic island is embedded in toroidally symmetric tokamaks, the toroidal symmetry in |B| is broken [K. C. Shaing, Phys. Rev. Lett. 87, 245003 (2001)]. 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 {delta}{sup '} for the island to be unstable. This lower limit depends on the local poloidal plasma beta {beta}{sub p}, the ratio of the plasma pressure to the poloidal magnetic field pressure. If {beta}{sub p} is high enough, the magnetic island is stable. This mechanism provides an alternative route to stabilize the island.

  13. Principal facts for gravity stations in the Rat Islands and Delarof Islands and Tanaga Island, Alaska

    USGS Publications Warehouse

    Healey, D.L.

    1975-01-01

    Gravity observations were made both east and west of the international dateline in the Aleutian Islands during 1970. A total of 280 gravity observations were made in the Rat Islands to the west and the Delarof Islands and Tanaga Island to the east. The principal facts and explanatory information for these data are included herein. These data have not been adjusted to the 1971 International Gravity Standardization Network datum.

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

    PubMed Central

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

    2009-01-01

    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. PMID:20333194

  15. Genome cartography: charting the apicomplexan genome

    PubMed Central

    Kissinger, Jessica C.; DeBarry, Jeremy

    2011-01-01

    Genes reside in particular genomic contexts that can be mapped at many levels. Historically, genetic maps were used primarily to locate genes. Recent technological advances in genome sequence determination have made the analysis and comparison of whole genomes possible and increasingly tractable. If we shift our focus from gene content (the inventory of genes contained within a genome), to genome composition and organization, what do we see? This review examines what has been learned about the evolution of the apicomplexan genome and the significance and impact of genomic location on our understanding of the eukaryotic genome and parasite biology. PMID:21764378

  16. 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...

  17. LOUISIANA BARRIER ISLAND EROSION STUDY.

    USGS Publications Warehouse

    Sallenger,, Asbury H., Jr.; Penland, Shea; Williams, S. Jeffress; Suter, John R.

    1987-01-01

    During 1986, the U. S. Geological Survey and the Louisiana Geological Survey began a five-year cooperative study focused on the processes which cause erosion of barrier islands. These processes must be understood in order to predict future erosion and to better manage our coastal resources. The study area includes the Louisiana barrier islands which serve to protect 41% of the nation's wetlands. These islands are eroding faster than any other barrier islands in the United States, in places greater than 20 m/yr. The study is divided into three parts: geological development of barrier islands, quantitative processes of barrier island erosion and applications of results. The study focuses on barrier islands in Louisiana although many of the results are applicable nationwide.

  18. Landscapes of Santa Rosa Island, Channel Islands National Park, California

    USGS Publications Warehouse

    Schumann, R. Randall; Minor, Scott A.; Muhs, Daniel R.; Pigati, Jeffery S.

    2014-01-01

    Santa Rosa Island (SRI) is the second-largest of the California Channel Islands. It is one of 4 east–west aligned islands forming the northern Channel Islands chain, and one of the 5 islands in Channel Islands National Park. The landforms, and collections of landforms called landscapes, of Santa Rosa Island have been created by tectonic uplift and faulting, rising and falling sea level, landslides, erosion and deposition, floods, and droughts. Landscape features, and areas delineating groups of related features on Santa Rosa Island, are mapped, classified, and described in this paper. Notable landscapes on the island include beaches, coastal plains formed on marine terraces, sand dunes, and sand sheets. In this study, the inland physiography has been classified into 4 areas based on relief and degree of fluvial dissection. Most of the larger streams on the island occupy broad valleys that have been filled with alluvium and later incised to form steep- to vertical-walled arroyos, or barrancas, leaving a relict floodplain above the present channel. A better understanding of the processes and mechanisms that created these landscapes enhances visitors’ enjoyment of their surroundings and contributes to improving land and resource management strategies in order to optimize and balance the multiple goals of conservation, preservation, restoration, and visitor experience.

  19. Permanent draft genome of 'Rhodopirellula islandica' strain K833.

    PubMed

    Kizina, Jana; Žure, Marina; Rhiel, Erhard; Munn, Colin Bernhard; Richter, Michael; Harder, Jens

    2015-12-01

    The planctomycete strain K833 was isolated from cold waters at the coast of Island and is tentatively named 'Rhodopirellula islandica'. It has a lower temperature range for growth than other genome-sequenced Rhodopirellula strains affiliating to Rhodopirellula baltica and 'Rhodopirellula europaea'. The permanent draft genome of strain K833 was obtained as part of a larger study on the biogeography of Rhodopirellula species in European marine waters. The genome consists of 55 contigs with a genome size of 7,433,200bp. With an average nucleotide identity of 81% to related genomes of R. baltica and 'R. europaea' and more than 4000 common genes, it will be a valuable source for the study of temperature adaptation of planctomycete genomes. PMID:26319626

  20. Genomic and comparative genomic analyses of Rickettsia heilongjiangensis provide insight into its evolution and pathogenesis.

    PubMed

    Duan, Changsong; Xiong, Xiaolu; Qi, Yong; Gong, Wenping; Jiao, Jun; Wen, Bohai

    2014-08-01

    Rickettsia heilongjiangensis, the causative agent of far eastern spotted fever, is an obligate intracellular gram-negative bacterium that belongs to the spotted fever group rickettsiae. To understand the evolution and pathogenesis of R. heilongjiangensis, we analyzed its genome and compared it with other rickettsial genomes available in GenBank. The R. heilongjiangensis chromosome contains 1333 genes, including 1297 protein coding genes and 36 RNA coding genes. The genome also contains 121 pseudogenes, 54 insertion sequences, and 39 tandem repeats. Sixteen genes encoding the major components of the type IV secretion systems were identified in the R. heilongjiangensis genome. In total, 37 β-barrel outer membrane proteins were predicted in the genome, eight of which have been previously confirmed to be outer membrane proteins. In addition, 266 potential virulence factor genes, seven partially deleted antibiotic resistance genes, and a genomic island were identified in the genome. The codon usage in the genome is compatible with its low GC content, and the amino acid usage shows apparent bias. A comparative genomic analysis showed that R. heilongjiangensis and R. japonica share one unique fragment that may be a target sequence for a diagnostic assay. The orthologs of 37 genes of R. heilongjiangensis were found in pathogenic R. rickettsii str. Sheila Smith but not in non-pathogenic R. rickettsii str. Iowa, which may explain why R. heilongjiangensis is pathogenic. Pan-genome analysis showed that R. heilongjiangensis and 42 other rickettsiae strains share 693 core genes with a pan-genome size of 4837 genes. The pan-genome-based phylogeny showed that R. heilongjiangensis was closely related to R. japonica. PMID:24924907

  1. Grand Island's good neighbors

    SciTech Connect

    Rabbe, D.L.

    1980-09-01

    Tornado-devasted Grand Island, Nebraska was spared the destruction of a 100 megawatt coal-fired power plant under construction. The town is a charter member of the Nebraska Municipal Power Pool, whose other members responded with help. Over 90 percent of the town was without power and most communications were severed. Power pool members restored vital water and sewer services and provided power for two weeks until lines and pumps were repaired. (DCK)

  2. Charge Islands Through Tunneling

    NASA Technical Reports Server (NTRS)

    Robinson, Daryl C.

    2002-01-01

    It has been recently reported that the electrical charge in a semiconductive carbon nanotube is not evenly distributed, but rather it is divided into charge "islands." This paper links the aforementioned phenomenon to tunneling and provides further insight into the higher rate of tunneling processes, which makes tunneling devices attractive. This paper also provides a basis for calculating the charge profile over the length of the tube so that nanoscale devices' conductive properties may be fully exploited.

  3. Draft Genome Sequence of the Commercial Biocontrol Strain Pantoea agglomerans P10c.

    PubMed

    Smits, Theo H M; Rezzonico, Fabio; Blom, Jochen; Goesmann, Alexander; Abelli, Azzurra; Kron Morelli, Roberto; Vanneste, Joël L; Duffy, Brion

    2015-01-01

    We report here the draft genome sequence of the biocontrol strain Pantoea agglomerans P10c, composed of a draft chromosome and two plasmids: the 559-kb large Pantoea plasmid 1 (pPag3) and a 182-kb plasmid (pPag1). A genomic island containing pantocin A biosynthesis genes was identified. PMID:26659685

  4. Draft Genome Sequence of the Commercial Biocontrol Strain Pantoea agglomerans P10c

    PubMed Central

    Rezzonico, Fabio; Blom, Jochen; Goesmann, Alexander; Abelli, Azzurra; Kron Morelli, Roberto; Vanneste, Joël L.; Duffy, Brion

    2015-01-01

    We report here the draft genome sequence of the biocontrol strain Pantoea agglomerans P10c, composed of a draft chromosome and two plasmids: the 559-kb large Pantoea plasmid 1 (pPag3) and a 182-kb plasmid (pPag1). A genomic island containing pantocin A biosynthesis genes was identified. PMID:26659685

  5. Personal genomics services: whose genomes?

    PubMed Central

    Gurwitz, David; Bregman-Eschet, Yael

    2009-01-01

    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 SNP scan. Most of the companies offering such services are based in the United States, but their clients may come from nearly anywhere in the world. Although the scientific validity, clinical utility and potential future implications of such services are being hotly debated, several ethical and regulatory questions related to direct-to-consumer (DTC) marketing strategies of genetic tests have not yet received sufficient attention. For example, how can we minimize the risk of unauthorized third parties from submitting other people's DNA for testing? Another pressing question concerns the ownership of (genotypic and phenotypic) information, as well as the unclear legal status of customers regarding their own personal information. Current legislation in the US and Europe falls short of providing clear answers to these questions. Until the regulation of personal genomics services catches up with the technology, we call upon commercial providers to self-regulate and coordinate their activities to minimize potential risks to individual privacy. We also point out some specific steps, along the trustee model, that providers of DTC personal genomics services as well as regulators and policy makers could consider for addressing some of the concerns raised below. PMID:19259127

  6. Personal genomics services: whose genomes?

    PubMed

    Gurwitz, David; Bregman-Eschet, Yael

    2009-07-01

    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 SNP scan. Most of the companies offering such services are based in the United States, but their clients may come from nearly anywhere in the world. Although the scientific validity, clinical utility and potential future implications of such services are being hotly debated, several ethical and regulatory questions related to direct-to-consumer (DTC) marketing strategies of genetic tests have not yet received sufficient attention. For example, how can we minimize the risk of unauthorized third parties from submitting other people's DNA for testing? Another pressing question concerns the ownership of (genotypic and phenotypic) information, as well as the unclear legal status of customers regarding their own personal information. Current legislation in the US and Europe falls short of providing clear answers to these questions. Until the regulation of personal genomics services catches up with the technology, we call upon commercial providers to self-regulate and coordinate their activities to minimize potential risks to individual privacy. We also point out some specific steps, along the trustee model, that providers of DTC personal genomics services as well as regulators and policy makers could consider for addressing some of the concerns raised below. PMID:19259127

  7. The Genome of the "Great Speciator" Provides Insights into Bird Diversification.

    PubMed

    Cornetti, Luca; Valente, Luis M; Dunning, Luke T; Quan, Xueping; Black, Richard A; Hébert, Olivier; Savolainen, Vincent

    2015-09-01

    Among birds, white-eyes (genus Zosterops) have diversified so extensively that Jared Diamond and Ernst Mayr referred to them as the "great speciator." The Zosterops lineage exhibits some of the fastest rates of species diversification among vertebrates, and its members are the most prolific passerine island colonizers. We present a high-quality genome assembly for the silvereye (Zosterops lateralis), a white-eye species consisting of several subspecies distributed across multiple islands. We investigate the genetic basis of rapid diversification in white-eyes by conducting genomic analyses at varying taxonomic levels. First, we compare the silvereye genome with those of birds from different families and searched for genomic features that may be unique to Zosterops. Second, we compare the genomes of different species of white-eyes from Lifou island (South Pacific), using whole genome resequencing and restriction site associated DNA. Third, we contrast the genomes of two subspecies of silvereye that differ in plumage color. In accordance with theory, we show that white-eyes have high rates of substitutions, gene duplication, and positive selection relative to other birds. Below genus level, we find that genomic differentiation accumulates rapidly and reveals contrasting demographic histories between sympatric species on Lifou, indicative of past interspecific interactions. Finally, we highlight genes possibly involved in color polymorphism between the subspecies of silvereye. By providing the first whole-genome sequence resources for white-eyes and by conducting analyses at different taxonomic levels, we provide genomic evidence underpinning this extraordinary bird radiation. PMID:26338191

  8. Islands of the Arctic

    NASA Astrophysics Data System (ADS)

    Overpeck, Jonathan

    2004-02-01

    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.

  9. Citrus Genomics

    PubMed Central

    Talon, Manuel; Gmitter Jr., Fred G.

    2008-01-01

    Citrus is one of the most widespread fruit crops globally, with great economic and health value. It is among the most difficult plants to improve through traditional breeding approaches. Currently, there is risk of devastation by diseases threatening to limit production and future availability to the human population. As technologies rapidly advance in genomic science, they are quickly adapted to address the biological challenges of the citrus plant system and the world's industries. The historical developments of linkage mapping, markers and breeding, EST projects, physical mapping, an international citrus genome sequencing project, and critical functional analysis are described. Despite the challenges of working with citrus, there has been substantial progress. Citrus researchers engaged in international collaborations provide optimism about future productivity and contributions to the benefit of citrus industries worldwide and to the human population who can rely on future widespread availability of this health-promoting and aesthetically pleasing fruit crop. PMID:18509486

  10. Ancient genomics

    PubMed Central

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

    2015-01-01

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

  11. Ancient genomics.

    PubMed

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

    2015-01-19

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

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

    PubMed Central

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

    2015-01-01

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

  13. 32 CFR 935.62 - Island Attorney.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 32 National Defense 6 2012-07-01 2012-07-01 false Island Attorney. 935.62 Section 935.62 National... WAKE ISLAND CODE Judiciary § 935.62 Island Attorney. There is an Island Attorney, appointed by the General Counsel as needed. The Island Attorney shall serve at the pleasure of the General Counsel....

  14. 32 CFR 935.62 - Island Attorney.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 32 National Defense 6 2014-07-01 2014-07-01 false Island Attorney. 935.62 Section 935.62 National... WAKE ISLAND CODE Judiciary § 935.62 Island Attorney. There is an Island Attorney, appointed by the General Counsel as needed. The Island Attorney shall serve at the pleasure of the General Counsel....

  15. 32 CFR 935.62 - Island Attorney.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 32 National Defense 6 2011-07-01 2011-07-01 false Island Attorney. 935.62 Section 935.62 National... WAKE ISLAND CODE Judiciary § 935.62 Island Attorney. There is an Island Attorney, appointed by the General Counsel as needed. The Island Attorney shall serve at the pleasure of the General Counsel....

  16. 32 CFR 935.62 - Island Attorney.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 32 National Defense 6 2013-07-01 2013-07-01 false Island Attorney. 935.62 Section 935.62 National... WAKE ISLAND CODE Judiciary § 935.62 Island Attorney. There is an Island Attorney, appointed by the General Counsel as needed. The Island Attorney shall serve at the pleasure of the General Counsel....

  17. 32 CFR 935.62 - Island Attorney.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 32 National Defense 6 2010-07-01 2010-07-01 false Island Attorney. 935.62 Section 935.62 National... WAKE ISLAND CODE Judiciary § 935.62 Island Attorney. There is an Island Attorney, appointed by the General Counsel as needed. The Island Attorney shall serve at the pleasure of the General Counsel....

  18. Pediatrics in the Marshall Islands.

    PubMed

    Dungy, C I; Morgan, B C; Adams, W H

    1984-01-01

    The delivery of health care to children living on isolated island communities presents unique challenges to health professionals. An evolved method of providing longitudinal services to infants and children residing on islands of the Marshall Island chain--a central Pacific portion of the Micronesian archipelago--is presented. The difficulties associated with provision of comprehensive health care in a vast ocean area are discussed. PMID:6418429

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

    PubMed Central

    2015-01-01

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

  20. Island biogeography of the Anthropocene.

    PubMed

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

    2014-09-25

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

  1. Cognitive Constraints and Island Effects

    PubMed Central

    Hofmeister, Philip; Sag, Ivan A.

    2012-01-01

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

  2. 78 FR 48668 - PSEG Long Island LLC, Long Island Electric Utility Servco LLC, Long Island Power Authority, Long...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-08-09

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

  3. 46 CFR 7.85 - St. Simons Island, GA to Little Talbot Island, FL.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 46 Shipping 1 2011-10-01 2011-10-01 false St. Simons Island, GA to Little Talbot Island, FL. 7.85... BOUNDARY LINES Atlantic Coast § 7.85 St. Simons Island, GA to Little Talbot Island, FL. (a) A line drawn... Island Light. (b) A line drawn from the southernmost extremity of Amelia Island to latitude 30°29.4?...

  4. 46 CFR 7.85 - St. Simons Island, GA to Little Talbot Island, FL.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 46 Shipping 1 2010-10-01 2010-10-01 false St. Simons Island, GA to Little Talbot Island, FL. 7.85... BOUNDARY LINES Atlantic Coast § 7.85 St. Simons Island, GA to Little Talbot Island, FL. (a) A line drawn... Island Light. (b) A line drawn from the southernmost extremity of Amelia Island to latitude 30°29.4?...

  5. 46 CFR 7.85 - St. Simons Island, GA to Little Talbot Island, FL.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 46 Shipping 1 2014-10-01 2014-10-01 false St. Simons Island, GA to Little Talbot Island, FL. 7.85... BOUNDARY LINES Atlantic Coast § 7.85 St. Simons Island, GA to Little Talbot Island, FL. (a) A line drawn... Island Light. (b) A line drawn from the southernmost extremity of Amelia Island to latitude 30°29.4?...

  6. 46 CFR 7.85 - St. Simons Island, GA to Little Talbot Island, FL.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 46 Shipping 1 2012-10-01 2012-10-01 false St. Simons Island, GA to Little Talbot Island, FL. 7.85... BOUNDARY LINES Atlantic Coast § 7.85 St. Simons Island, GA to Little Talbot Island, FL. (a) A line drawn... Island Light. (b) A line drawn from the southernmost extremity of Amelia Island to latitude 30°29.4?...

  7. 46 CFR 7.85 - St. Simons Island, GA to Little Talbot Island, FL.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 46 Shipping 1 2013-10-01 2013-10-01 false St. Simons Island, GA to Little Talbot Island, FL. 7.85... BOUNDARY LINES Atlantic Coast § 7.85 St. Simons Island, GA to Little Talbot Island, FL. (a) A line drawn... Island Light. (b) A line drawn from the southernmost extremity of Amelia Island to latitude 30°29.4?...

  8. Reunion Island Volcano Erupts

    NASA Technical Reports Server (NTRS)

    2002-01-01

    On January 16, 2002, lava that had begun flowing on January 5 from the Piton de la Fournaise volcano on the French island of Reunion abruptly decreased, marking the end of the volcano's most recent eruption. These false color MODIS images of Reunion, located off the southeastern coast of Madagascar in the Indian Ocean, were captured on the last day of the eruption (top) and two days later (bottom). The volcano itself is located on the southeast side of the island and is dark brown compared to the surrounding green vegetation. Beneath clouds (light blue) and smoke, MODIS detected the hot lava pouring down the volcano's flanks into the Indian Ocean. The heat, detected by MODIS at 2.1 um, has been colored red in the January 16 image, and is absent from the lower image, taken two days later on January 18, suggesting the lava had cooled considerably even in that short time. Earthquake activity on the northeast flank continued even after the eruption had stopped, but by January 21 had dropped to a sufficiently low enough level that the 24-hour surveillance by the local observatory was suspended. Reunion is essentially all volcano, with the northwest portion of the island built on the remains of an extinct volcano, and the southeast half built on the basaltic shield of 8,630-foot Piton de la Fournaise. A basaltic shield volcano is one with a broad, gentle slope built by the eruption of fluid basalt lava. Basalt lava flows easily across the ground remaining hot and fluid for long distances, and so they often result in enormous, low-angle cones. The Piton de la Fournaise is one of Earth's most active volcanoes, erupting over 150 times in the last few hundred years, and it has been the subject of NASA research because of its likeness to the volcanoes of Mars. Image courtesy Jacques Descloitres, MODIS Land Rapid Response Team at NASA GSFC

  9. Urban heat island

    NASA Technical Reports Server (NTRS)

    Kim, Hongsuk H.

    1991-01-01

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

  10. Pine Island Glacier, Antarctica

    NASA Technical Reports Server (NTRS)

    2001-01-01

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

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

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

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

  11. 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.

  12. Islands and Non-islands in Native and Heritage Korean.

    PubMed

    Kim, Boyoung; Goodall, Grant

    2016-01-01

    To a large extent, island phenomena are cross-linguistically invariable, but English and Korean present some striking differences in this domain. English has wh-movement and Korean does not, and while both languages show sensitivity to wh-islands, only English has island effects for adjunct clauses. Given this complex set of differences, one might expect Korean/English bilinguals, and especially heritage Korean speakers (i.e., early bilinguals whose L2 became their dominant language during childhood) to be different from native speakers, since heritage speakers have had more limited exposure to Korean, may have had incomplete acquisition and/or attrition, and may show significant transfer effects from the L2. Here we examine islands in heritage speakers of Korean in the U.S. Through a series of four formal acceptability experiments comparing these heritage speakers with native speakers residing in Korea, we show that the two groups are remarkably similar. Both show clear evidence for wh-islands and an equally clear lack of adjunct island effects. Given the very different linguistic environment that the heritage speakers have had since early childhood, this result lends support to the idea that island phenomena are largely immune to environmental influences and stem from deeper properties of the processor and/or grammar. Similarly, it casts some doubt on recent proposals that islands are learned from the input. PMID:26913017

  13. Islands and Non-islands in Native and Heritage Korean

    PubMed Central

    Kim, Boyoung; Goodall, Grant

    2016-01-01

    To a large extent, island phenomena are cross-linguistically invariable, but English and Korean present some striking differences in this domain. English has wh-movement and Korean does not, and while both languages show sensitivity to wh-islands, only English has island effects for adjunct clauses. Given this complex set of differences, one might expect Korean/English bilinguals, and especially heritage Korean speakers (i.e., early bilinguals whose L2 became their dominant language during childhood) to be different from native speakers, since heritage speakers have had more limited exposure to Korean, may have had incomplete acquisition and/or attrition, and may show significant transfer effects from the L2. Here we examine islands in heritage speakers of Korean in the U.S. Through a series of four formal acceptability experiments comparing these heritage speakers with native speakers residing in Korea, we show that the two groups are remarkably similar. Both show clear evidence for wh-islands and an equally clear lack of adjunct island effects. Given the very different linguistic environment that the heritage speakers have had since early childhood, this result lends support to the idea that island phenomena are largely immune to environmental influences and stem from deeper properties of the processor and/or grammar. Similarly, it casts some doubt on recent proposals that islands are learned from the input. PMID:26913017

  14. Keystone Island Flap: Effects of Islanding on Vascularity

    PubMed Central

    Nottle, Tim; Mills, John

    2016-01-01

    Background: Based on his clinical observations the “red dot sign” and hyperemic flare, Behan has advocated the superior vascularity of the island flap design for at least 2 decades. The aim of this study was to determine whether (1) surgical islanding of a flap alters the vascularity or blood supply of the flap and (2) these changes in blood supply explain Behan’s clinical observations of “red dot sign” and hyperemic flare. Methods: Patients undergoing local island fasciocutaneous flaps or anterolateral thigh fasciocutaneous free flaps were recruited for this trial from a single institution over a 10-month period (September 2013 to July 2014). Three adjacent specimens of skin and subcutaneous fat (control, non-island, and island) were harvested from each patient at various stages of their surgery for histological assessment. A pathologist reviewed randomized specimens for microvascular variables, including arteriole wall thickness, arteriole diameter, venule wall thickness, and venule diameter. Results: Thirteen patients (with 14 sets of specimen) were recruited for this study. When compared with the control state, both arteriole diameter and venule diameter in island flaps were significantly increased. Conclusions: These results validate Behan’s clinical observations of “red dot sign” and hyperemic flare. Further studies are required to directly compare island and non-island flap designs. PMID:27014546

  15. 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

  16. 19. New York Connecting Railroad: Randalls Island Viaduct. Randalls Island, ...

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

    19. New York Connecting Railroad: Randalls Island Viaduct. Randalls Island, New York Co., NY. Sec. 4207, MP 8.54. - Northeast Railroad Corridor, Amtrak Route between New Jersey/New York & New York/Connecticut State Lines, New York, New York County, NY

  17. Genome Sequence of Yersinia pestis KIM†

    PubMed Central

    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

    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. PMID:12142430

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

    PubMed Central

    Mekalanos, John J.

    2014-01-01

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

  19. Barcode Server: A Visualization-Based Genome Analysis System

    PubMed Central

    Mao, Fenglou; Olman, Victor; Wang, Yan; Xu, Ying

    2013-01-01

    We have previously developed a computational method for representing a genome as a barcode image, which makes various genomic features visually apparent. We have demonstrated that this visual capability has made some challenging genome analysis problems relatively easy to solve. We have applied this capability to a number of challenging problems, including (a) identification of horizontally transferred genes, (b) identification of genomic islands with special properties and (c) binning of metagenomic sequences, and achieved highly encouraging results. These application results inspired us to develop this barcode-based genome analysis server for public service, which supports the following capabilities: (a) calculation of the k-mer based barcode image for a provided DNA sequence; (b) detection of sequence fragments in a given genome with distinct barcodes from those of the majority of the genome, (c) clustering of provided DNA sequences into groups having similar barcodes; and (d) homology-based search using Blast against a genome database for any selected genomic regions deemed to have interesting barcodes. The barcode server provides a job management capability, allowing processing of a large number of analysis jobs for barcode-based comparative genome analyses. The barcode server is accessible at http://csbl1.bmb.uga.edu/Barcode. PMID:23457606

  20. Barcode server: a visualization-based genome analysis system.

    PubMed

    Mao, Fenglou; Olman, Victor; Wang, Yan; Xu, Ying

    2013-01-01

    We have previously developed a computational method for representing a genome as a barcode image, which makes various genomic features visually apparent. We have demonstrated that this visual capability has made some challenging genome analysis problems relatively easy to solve. We have applied this capability to a number of challenging problems, including (a) identification of horizontally transferred genes, (b) identification of genomic islands with special properties and (c) binning of metagenomic sequences, and achieved highly encouraging results. These application results inspired us to develop this barcode-based genome analysis server for public service, which supports the following capabilities: (a) calculation of the k-mer based barcode image for a provided DNA sequence; (b) detection of sequence fragments in a given genome with distinct barcodes from those of the majority of the genome, (c) clustering of provided DNA sequences into groups having similar barcodes; and (d) homology-based search using Blast against a genome database for any selected genomic regions deemed to have interesting barcodes. The barcode server provides a job management capability, allowing processing of a large number of analysis jobs for barcode-based comparative genome analyses. The barcode server is accessible at http://csbl1.bmb.uga.edu/Barcode. PMID:23457606

  1. Number of CpG islands and genes in human and mouse.

    PubMed Central

    Antequera, F; Bird, A

    1993-01-01

    Estimation of gene number in mammals is difficult due to the high proportion of noncoding DNA within the nucleus. In this study, we provide a direct measurement of the number of genes in human and mouse. We have taken advantage of the fact that many mammalian genes are associated with CpG islands whose distinctive properties allow their physical separation from bulk DNA. Our results suggest that there are approximately 45,000 CpG islands per haploid genome in humans and 37,000 in the mouse. Sequence comparison confirms that about 20% of the human CpG islands are absent from the homologous mouse genes. Analysis of a selection of genes suggests that both human and mouse are losing CpG islands over evolutionary time due to de novo methylation in the germ line followed by CpG loss through mutation. This process appears to be more rapid in rodents. Combining the number of CpG islands with the proportion of island-associated genes, we estimate that the total number of genes per haploid genome is approximately 80,000 in both organisms. Images Fig. 1 PMID:7505451

  2. Enjebi Island dose assessment

    SciTech Connect

    Robison, W.L.; Conrado, C.L.; Phillips, W.A.

    1987-07-01

    We have updeated the radiological dose assessment for Enjebi Island at Enewetak Atoll using data derived from analysis of food crops grown on Enjebi. This is a much more precise assessment of potential doses to people resettling Enjebi Island than the 1980 assessment in which there were no data available from food crops on Enjebi. Details of the methods and data used to evaluate each exposure pathway are presented. The terrestrial food chain is the most significant potential exposure pathway and /sup 137/Cs is the radionuclide responsible for most of the estimated dose over the next 50 y. The doses are calculated assuming a resettlement date of 1990. The average wholebody maximum annual estimated dose equivalent derived using our diet model is 166 mremy;the effective dose equivalent is 169 mremy. The estimated 30-, 50-, and 70-y integral whole-body dose equivalents are 3.5 rem, 5.1 rem, and 6.2 rem, respectively. Bone-marrow dose equivalents are only slightly higher than the whole-body estimates in each case. The bone-surface cells (endosteal cells) receive the highest dose, but they are a less sensitive cell population and are less sensitive to fatal cancer induction than whole body and bone marrow. The effective dose equivalents for 30, 50, and 70 y are 3.6 rem, 5.3 rem, and 6.6 rem, respectively. 79 refs., 17 figs., 24 tabs

  3. Opportunity at 'Cook Islands'

    NASA Technical Reports Server (NTRS)

    2009-01-01

    NASA's Mars Exploration Rover Opportunity used its navigation camera to take the images combined into this full-circle view of the rover's surroundings during the 1,825th Martian day, or sol, of Opportunity's surface mission (March 12, 2009). North is at the top.

    The rover had driven half a meter (1.5 feet) earlier on Sol 1825 to fine-tune its location for placing its robotic arm onto an exposed patch of outcrop including a target area informally called 'Cook Islands.' On the preceding sol, Opportunity turned around to drive frontwards and then drove 4.5 meters (15 feet) toward this outcrop. The tracks from the SOl 1824 drive are visible near the center of this view at about the 11 o'clock position. For scale, the distance between the parallel wheel tracks is about 1 meter (about 40 inches). Opportunity had previously been driving backward as a strategy to redistribute lubrication in a wheel drawing more electrical current than usual.

    The outcrop exposure that includes 'Cook Islands' is visible just below the center of the image.

    The terrain in this portion of Mars' Meridiani Planum region includes dark-toned sand ripples and lighter-toned bedrock.

    This view is presented as a cylindrical projection with geometric seam correction.

  4. Murre Colony on Prince Island

    USGS Multimedia Gallery

    A breeding colony of California common murres (Uria aalge californica) on Prince Island off San Miguel Island off Southern California. Ecologists Josh Adams and Jonathan Felis of the USGS Western Ecological Research Center shot this and other high-resolution digital telephotos from a research vessel...

  5. Salt Marshes at Chincoteague Island

    USGS Multimedia Gallery

    Salt marshes at Chincoteague Island. The salt marshes that make up Chincoteague Island are important habitat for migrating waterfowl. In addition, they serve an important role in protecting inland ecosystems and communities from oceanic storms. Mosquito point can be seen in the background where the ...

  6. Tidal Pool on Folly Island

    USGS Multimedia Gallery

    A tidal pool on Folly Island. Tidal pools are small pools of water that are left when the tide recedes. Because these pools have water more or less permanently, distinct ecosystems can develop separate from the surrounding beach. Folly Island, a preserve owned by the Maine Coast Heritage Trust, is a...

  7. Genomes on ice.

    PubMed

    Parkhill, Julian

    2016-03-01

    This month's Genome Watch discusses the analysis of a Helicobacter pylori genome from the preserved Copper-Age mummy known as the Iceman and how ancient genomes shed light on the history of bacterial pathogens. PMID:26853114

  8. Whole Genome Sequencing

    MedlinePLUS

    ... you want to learn. Search form Search Whole Genome Sequencing You are here Home Testing & Services Testing ... the full story, click here . What is whole genome sequencing? Whole genome sequencing is the mapping out ...

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

    PubMed Central

    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.

    2010-01-01

    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

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

    PubMed Central

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

    2011-01-01

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

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

    PubMed

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

    2014-02-22

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

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

    PubMed Central

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

    2014-01-01

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

  13. 75 FR 51098 - Protection Island and San Juan Islands National Wildlife Refuges, Jefferson, Island, San Juan...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-08-18

    ... Fish and Wildlife Service Protection Island and San Juan Islands National Wildlife Refuges, Jefferson... Wildlife Refuges (NWRs, Refuges) for public review and comment. The Draft CCP/WSP/EA describes our...) 457-9778. U.S. Mail: Kevin Ryan, Project Leader, Washington Maritime National Wildlife Refuge...

  14. Internal parasites of possums (Trichosurus vulpecula) from Kawau Island, Chatham Island and Stewart Island.

    PubMed

    Stankiewicz, M; Heath, D D; Cowan, P E

    1997-12-01

    As part of a search for pathogens that might be useful agents for biological control of possums, the three largest offshore islands of New Zealand that still have possums were surveyed to determine the pathogens present in these isolated populations. Brushtail possums from Kawau Island (n = 158), Chatham Island (n = 214) and Stewart Island (n = 194) were examined for internal parasites. Possums from Kawau Island were infected with Eimeria spp. (16.7%), Bertiella trichosuri (5.2%) and Purustrongyloides trichosuri (15.5%). No Paraustrostrongylus trichosuri or Trichostrongylus spp. were found. Possums from Chatham Island were infected with Eimeria spp. (10.9%). Bertiella trichosuri (3.6%), T colubriformis (6.6%), T retortaeformis (1%) and T. vitrinus (0.5%). No Parastrongyloides or Paraustrostrongylus spp. were found. Possums from Stewart Island were infected only with Eimeria spp. (4.6%). Because of their paucity of some parasites, the opportunity exists to use these offshore islands to study the introduction and spread of a parasite into a possum population, and what technology would be required to bring it to hyperendemicity. PMID:16031999

  15. 2. Light tower, view west towards Squirrel Island, south and ...

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

    2. Light tower, view west towards Squirrel Island, south and east sides - Ram Island Light Station, Ram Island, south of Ocean Point & just north of Fisherman Island, marking south side of Fisherman Island Passage, Ocean Point, Lincoln County, ME

  16. Comprehensive analysis of CpG islands in human chromosomes 21 and 22

    NASA Astrophysics Data System (ADS)

    Takai, Daiya; Jones, Peter A.

    2002-03-01

    CpG islands are useful markers for genes in organisms containing 5-methylcytosine in their genomes. In addition, CpG islands located in the promoter regions of genes can play important roles in gene silencing during processes such as X-chromosome inactivation, imprinting, and silencing of intragenomic parasites. The generally accepted definition of what constitutes a CpG island was proposed in 1987 by Gardiner-Garden and Frommer [Gardiner-Garden, M. & Frommer, M. (1987) J. Mol. Biol. 196, 261-282] as being a 200-bp stretch of DNA with a C+G content of 50% and an observed CpG/expected CpG in excess of 0.6. Any definition of a CpG island is somewhat arbitrary, and this one, which was derived before the sequencing of mammalian genomes, will include many sequences that are not necessarily associated with controlling regions of genes but rather are associated with intragenomic parasites. We have therefore used the complete genomic sequences of human chromosomes 21 and 22 to examine the properties of CpG islands in different sequence classes by using a search algorithm that we have developed. Regions of DNA of greater than 500 bp with a G+C equal to or greater than 55% and observed CpG/expected CpG of 0.65 were more likely to be associated with the 5' regions of genes and this definition excluded most Alu-repetitive elements. We also used genome sequences to show strong CpG suppression in the human genome and slight suppression in Drosophila melanogaster and Saccharomyces cerevisiae. This finding is compatible with the recent detection of 5-methylcytosine in Drosophila, and might suggest that S. cerevisiae has, or once had, CpG methylation.

  17. Reconstructing Austronesian population history in Island Southeast Asia

    PubMed Central

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

    2014-01-01

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

  18. Sympatric speciation in palms on an oceanic island.

    PubMed

    Savolainen, Vincent; Anstett, Marie-Charlotte; Lexer, Christian; Hutton, Ian; Clarkson, James J; Norup, Maria V; Powell, Martyn P; Springate, David; Salamin, Nicolas; Baker, William J

    2006-05-11

    The origin of species diversity has challenged biologists for over two centuries. Allopatric speciation, the divergence of species resulting from geographical isolation, is well documented. However, sympatric speciation, divergence without geographical isolation, is highly controversial. Claims of sympatric speciation must demonstrate species sympatry, sister relationships, reproductive isolation, and that an earlier allopatric phase is highly unlikely. Here we provide clear support for sympatric speciation in a case study of two species of palm (Arecaceae) on an oceanic island. A large dated phylogenetic tree shows that the two species of Howea, endemic to the remote Lord Howe Island, are sister taxa and diverged from each other well after the island was formed 6.9 million years ago. During fieldwork, we found a substantial disjunction in flowering time that is correlated with soil preference. In addition, a genome scan indicates that few genetic loci are more divergent between the two species than expected under neutrality, a finding consistent with models of sympatric speciation involving disruptive/divergent selection. This case study of sympatric speciation in plants provides an opportunity for refining theoretical models on the origin of species, and new impetus for exploring putative plant and animal examples on oceanic islands. PMID:16467788

  19. Reconstructing Austronesian population history in Island Southeast Asia.

    PubMed

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

    2014-01-01

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

  20. The clustering of CpG islands may constitute an important determinant of the 3D organization of interphase chromosomes

    PubMed Central

    Gushchanskaya, Ekaterina S; Artemov, Artem V; Ulyanov, Sergey V; Logacheva, Maria D; Penin, Aleksey A; Kotova, Elena S; Akopov, Sergey B; Nikolaev, Lev G; Iarovaia, Olga V; Sverdlov, Eugene D; Gavrilov, Alexey A; Razin, Sergey V

    2014-01-01

    We used the 4C-Seq technique to characterize the genome-wide patterns of spatial contacts of several CpG islands located on chromosome 14 in cultured chicken lymphoid and erythroid cells. We observed a clear tendency for the spatial clustering of CpG islands present on the same and different chromosomes, regardless of the presence or absence of promoters within these CpG islands. Accordingly, we observed preferential spatial contacts between Sp1 binding motifs and other GC-rich genomic elements, including the DNA sequence motifs capable of forming G-quadruplexes. However, an anchor placed in a gene/CpG island-poor area formed spatial contacts with other gene/CpG island-poor areas on chromosome 14 and other chromosomes. These results corroborate the two-compartment model of the spatial organization of interphase chromosomes and suggest that the clustering of CpG islands constitutes an important determinant of the 3D organization of the eukaryotic genome in the cell nucleus. Using the ChIP-Seq technique, we mapped the genome-wide CTCF deposition sites in the chicken lymphoid and erythroid cells that were used for the 4C analysis. We observed a good correlation between the density of CTCF deposition sites and the level of 4C signals for the anchors located in CpG islands but not for an anchor located in a gene desert. It is thus possible that CTCF contributes to the clustering of CpG islands observed in our experiments. PMID:24736527

  1. Genomic characterization of the Yersinia genus

    PubMed Central

    2010-01-01

    Background New DNA sequencing technologies have enabled detailed comparative genomic analyses of entire genera of bacterial pathogens. Prior to this study, three species of the enterobacterial genus Yersinia that cause invasive human diseases (Yersinia pestis, Yersinia pseudotuberculosis, and Yersinia enterocolitica) had been sequenced. However, there were no genomic data on the Yersinia species with more limited virulence potential, frequently found in soil and water environments. Results We used high-throughput sequencing-by-synthesis instruments to obtain 25- to 42-fold average redundancy, whole-genome shotgun data from the type strains of eight species: Y. aldovae, Y. bercovieri, Y. frederiksenii, Y. kristensenii, Y. intermedia, Y. mollaretii, Y. rohdei, and Y. ruckeri. The deepest branching species in the genus, Y. ruckeri, causative agent of red mouth disease in fish, has the smallest genome (3.7 Mb), although it shares the same core set of approximately 2,500 genes as the other members of the species, whose genomes range in size from 4.3 to 4.8 Mb. Yersinia genomes had a similar global partition of protein functions, as measured by the distribution of Cluster of Orthologous Groups families. Genome to genome variation in islands with genes encoding functions such as ureases, hydrogeneases and B-12 cofactor metabolite reactions may reflect adaptations to colonizing specific host habitats. Conclusions Rapid high-quality draft sequencing was used successfully to compare pathogenic and non-pathogenic members of the Yersinia genus. This work underscores the importance of the acquisition of horizontally transferred genes in the evolution of Y. pestis and points to virulence determinants that have been gained and lost on multiple occasions in the history of the genus. PMID:20047673

  2. Comparative Genomics and Transcriptomics of Propionibacterium acnes

    PubMed Central

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

    2011-01-01

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

  3. Ensembl Genomes 2016: more genomes, more complexity.

    PubMed

    Kersey, Paul Julian; Allen, James E; Armean, Irina; Boddu, Sanjay; Bolt, Bruce J; Carvalho-Silva, Denise; Christensen, Mikkel; Davis, Paul; Falin, Lee J; Grabmueller, Christoph; Humphrey, Jay; Kerhornou, Arnaud; Khobova, Julia; Aranganathan, Naveen K; Langridge, Nicholas; Lowy, Ernesto; McDowall, Mark D; Maheswari, Uma; Nuhn, Michael; Ong, Chuang Kee; Overduin, Bert; Paulini, Michael; Pedro, Helder; Perry, Emily; Spudich, Giulietta; Tapanari, Electra; Walts, Brandon; Williams, Gareth; Tello-Ruiz, Marcela; Stein, Joshua; Wei, Sharon; Ware, Doreen; Bolser, Daniel M; Howe, Kevin L; Kulesha, Eugene; Lawson, Daniel; Maslen, Gareth; Staines, Daniel M

    2016-01-01

    Ensembl Genomes (http://www.ensemblgenomes.org) is an integrating resource for genome-scale data from non-vertebrate species, complementing the resources for vertebrate genomics developed in the context of the Ensembl project (http://www.ensembl.org). Together, the two resources provide a consistent set of programmatic and interactive interfaces to a rich range of data including reference sequence, gene models, transcriptional data, genetic variation and comparative analysis. This paper provides an update to the previous publications about the resource, with a focus on recent developments. These include the development of new analyses and views to represent polyploid genomes (of which bread wheat is the primary exemplar); and the continued up-scaling of the resource, which now includes over 23 000 bacterial genomes, 400 fungal genomes and 100 protist genomes, in addition to 55 genomes from invertebrate metazoa and 39 genomes from plants. This dramatic increase in the number of included genomes is one part of a broader effort to automate the integration of archival data (genome sequence, but also associated RNA sequence data and variant calls) within the context of reference genomes and make it available through the Ensembl user interfaces. PMID:26578574

  4. Ensembl genomes 2016: more genomes, more complexity

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Ensembl Genomes (http://www.ensemblgenomes.org) is an integrating resource for genome-scale data from non-vertebrate species, complementing the resources for vertebrate genomics developed in the context of the Ensembl project (http://www.ensembl.org). Together, the two resources provide a consistent...

  5. Ensembl Genomes 2016: more genomes, more complexity

    PubMed Central

    Kersey, Paul Julian; Allen, James E.; Armean, Irina; Boddu, Sanjay; Bolt, Bruce J.; Carvalho-Silva, Denise; Christensen, Mikkel; Davis, Paul; Falin, Lee J.; Grabmueller, Christoph; Humphrey, Jay; Kerhornou, Arnaud; Khobova, Julia; Aranganathan, Naveen K.; Langridge, Nicholas; Lowy, Ernesto; McDowall, Mark D.; Maheswari, Uma; Nuhn, Michael; Ong, Chuang Kee; Overduin, Bert; Paulini, Michael; Pedro, Helder; Perry, Emily; Spudich, Giulietta; Tapanari, Electra; Walts, Brandon; Williams, Gareth; Tello–Ruiz, Marcela; Stein, Joshua; Wei, Sharon; Ware, Doreen; Bolser, Daniel M.; Howe, Kevin L.; Kulesha, Eugene; Lawson, Daniel; Maslen, Gareth; Staines, Daniel M.

    2016-01-01

    Ensembl Genomes (http://www.ensemblgenomes.org) is an integrating resource for genome-scale data from non-vertebrate species, complementing the resources for vertebrate genomics developed in the context of the Ensembl project (http://www.ensembl.org). Together, the two resources provide a consistent set of programmatic and interactive interfaces to a rich range of data including reference sequence, gene models, transcriptional data, genetic variation and comparative analysis. This paper provides an update to the previous publications about the resource, with a focus on recent developments. These include the development of new analyses and views to represent polyploid genomes (of which bread wheat is the primary exemplar); and the continued up-scaling of the resource, which now includes over 23 000 bacterial genomes, 400 fungal genomes and 100 protist genomes, in addition to 55 genomes from invertebrate metazoa and 39 genomes from plants. This dramatic increase in the number of included genomes is one part of a broader effort to automate the integration of archival data (genome sequence, but also associated RNA sequence data and variant calls) within the context of reference genomes and make it available through the Ensembl user interfaces. PMID:26578574

  6. Marte Valles Crater 'Island'

    NASA Technical Reports Server (NTRS)

    2004-01-01

    10 April 2004 Marte Valles is an outflow channel system that straddles 180oW longitude between the region south of Cerberus and far northwestern Amazonis. The floor of the Marte valleys have enigmatic platy flow features that some argue are formed by lava, others suggest they are remnants of mud flows. This Mars Global Surveyor (MGS) Mars Orbiter Camera (MOC) image shows an island created in the middle of the main Marte Valles channel as fluid---whether lava or mud---flowed past two older meteor impact craters. The craters are located near 21.5oN, 175.3oW. The image covers an area about 3 km (1.9 mi) across. Sunlight illuminates the scene from the lower left.

  7. Anatahan Volcano, Mariana Islands

    NASA Technical Reports Server (NTRS)

    2008-01-01

    In the early hours of February 7, ASTER captured this nighttime thermal infrared image of an eruption of Anatahan Volcano in the central Mariana Islands. The summit of the volcano is bright indicating there is a very hot area there. Streaming to the west is an ash plume, visible by the red color indicating the presence of silicate-rich particles. Dark grey areas are clouds that appear colder than the ocean. Anatahan is a stratovolcano that started erupting in May 2003, forming a new crater.

    The image covers an area of 56.3 x 41.8 km, and is located 16 degrees north latitude and 145.6 degrees east longitude.

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

  8. SRTM Anaglyph: Fiji Islands

    NASA Technical Reports Server (NTRS)

    2000-01-01

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

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

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

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

  9. Global Collembola on Deception Island.

    PubMed

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

    2012-01-01

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

  10. Global Collembola on Deception Island

    PubMed Central

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

    2012-01-01

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

  11. Funding Opportunity: Genomic Data Centers

    Cancer.gov

    Funding Opportunity CCG, Funding Opportunity Center for Cancer Genomics, CCG, Center for Cancer Genomics, CCG RFA, Center for cancer genomics rfa, genomic data analysis network, genomic data analysis network centers,

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

    PubMed Central

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

    2015-01-01

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

  13. Establishment of new mutations under divergence and genome hitchhiking

    PubMed Central

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

    2012-01-01

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

  14. The Cambrian of Bennett Island (New Siberian Islands)

    NASA Astrophysics Data System (ADS)

    Danukalova, M. K.; Kuzmichev, A. B.; Korovnikov, I. V.

    2014-07-01

    The paper presents new data on the Cambrian stratigraphy of Bennett Island, one of the least explored East Arctic islands. The section, about 500 m of total thickness, comprises four lithological units that store a record of the deposition history: (1) clastic sediments including storm sandstones; (2) shallow-marine mudstone; (3) lagoonal variegated mudstone and limestone; (4) black shale. It is suggested to classify the units as formations with their proper names. The section spans all epoches of the Cambrian stratigraphy constrained by trilobite fossils. In the Cambrian, territory of the island belonged to Siberia rather than to some exotic terrane, judging by abundant endemic Siberian trilobite species in the Bennett section. This inference is supported by synchronicity in recorded deposition events of Bennett Island and northeastern Siberia (Kharaulakh Mountains). The Cambrian sediments of the two areas were deposited in different parts of a single shallow sea which extended as far as Taimyr.

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

    PubMed Central

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

    2013-01-01

    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. PMID:24029754

  16. Draft Genome Sequence of the Polycyclic Aromatic Hydrocarbon-Degrading, Genetically Engineered Bioluminescent Bioreporter Pseudomonas fluorescens HK44

    SciTech Connect

    Chauhan, Archana; Layton, Alice; Williams, Daniel W; Smart, Abby E.; Ripp, Steven Anthony; Karpinets, Tatiana V; Brown, Steven D; Sayler, Gary Steven

    2011-01-01

    Pseudomonas fluorescens strain HK44 (DSM 6700) is a genetically engineered lux-based bioluminescent bioreporter. Here we report the draft genome sequence of strain HK44. Annotation of {approx}6.1 Mb sequence indicates that 30% of the traits are unique and distributed over 5 genomic islands, a prophage and two plasmids.

  17. Facial scarification and tattooing on Santa Catalina Island (Solomon Islands).

    PubMed

    Mammen, L; Norton, S A

    1997-10-01

    Ritual scarification is the culturally sanctioned process of incising the skin to achieve patterned scars. Scarification was practiced widely by traditional societies, but the encroachment of Western cultural expectations has made the practice increasingly uncommon. Ritual tattooing has a meaningful place in many traditional societies. Ritual scarification and tattooing are still found on Santa Catalina Island, an isolated member of the Solomon Islands in the south-west Pacific. PMID:9347234

  18. Enabling functional genomics with genome engineering

    PubMed Central

    Hilton, Isaac B.; Gersbach, Charles A.

    2015-01-01

    Advances in genome engineering technologies have made the precise control over genome sequence and regulation possible across a variety of disciplines. These tools can expand our understanding of fundamental biological processes and create new opportunities for therapeutic designs. The rapid evolution of these methods has also catalyzed a new era of genomics that includes multiple approaches to functionally characterize and manipulate the regulation of genomic information. Here, we review the recent advances of the most widely adopted genome engineering platforms and their application to functional genomics. This includes engineered zinc finger proteins, TALEs/TALENs, and the CRISPR/Cas9 system as nucleases for genome editing, transcription factors for epigenome editing, and other emerging applications. We also present current and potential future applications of these tools, as well as their current limitations and areas for future advances. PMID:26430154

  19. Enabling functional genomics with genome engineering.

    PubMed

    Hilton, Isaac B; Gersbach, Charles A

    2015-10-01

    Advances in genome engineering technologies have made the precise control over genome sequence and regulation possible across a variety of disciplines. These tools can expand our understanding of fundamental biological processes and create new opportunities for therapeutic designs. The rapid evolution of these methods has also catalyzed a new era of genomics that includes multiple approaches to functionally characterize and manipulate the regulation of genomic information. Here, we review the recent advances of the most widely adopted genome engineering platforms and their application to functional genomics. This includes engineered zinc finger proteins, TALEs/TALENs, and the CRISPR/Cas9 system as nucleases for genome editing, transcription factors for epigenome editing, and other emerging applications. We also present current and potential future applications of these tools, as well as their current limitations and areas for future advances. PMID:26430154

  20. Metabolic Syndrome in a Metapopulation of Croatian Island Isolates

    PubMed Central

    Kolčić, Ivana; Vorko-Jović, Ariana; Salzer, Branka; Smoljanović, Mladen; Kern, Josipa; Vuletić, Silvije

    2006-01-01

    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. PMID:16909456

  1. Skewed genomic variability in strains of the toxigenic bacterial pathogen, Clostridium perfringens

    PubMed Central

    Myers, Garry S.A.; Rasko, David A.; Cheung, Jackie K.; Ravel, Jacques; Seshadri, Rekha; DeBoy, Robert T.; Ren, Qinghu; Varga, John; Awad, Milena M.; Brinkac, Lauren M.; Daugherty, Sean C.; Haft, Daniel H.; Dodson, Robert J.; Madupu, Ramana; Nelson, William C.; Rosovitz, M.J.; Sullivan, Steven A.; Khouri, Hoda; Dimitrov, George I.; Watkins, Kisha L.; Mulligan, Stephanie; Benton, Jonathan; Radune, Diana; Fisher, Derek J.; Atkins, Helen S.; Hiscox, Tom; Jost, B. Helen; Billington, Stephen J.; Songer, J. Glenn; McClane, Bruce A.; Titball, Richard W.; Rood, Julian I.; Melville, Stephen B.; Paulsen, Ian T.

    2006-01-01

    Clostridium perfringens is a Gram-positive, anaerobic spore-forming bacterium commonly found in soil, sediments, and the human gastrointestinal tract. C. perfringens is responsible for a wide spectrum of disease, including food poisoning, gas gangrene (clostridial myonecrosis), enteritis necroticans, and non-foodborne gastrointestinal infections. The complete genome sequences of Clostridium perfringens strain ATCC 13124, a gas gangrene isolate and the species type strain, and the enterotoxin-producing food poisoning strain SM101, were determined and compared with the published C. perfringens strain 13 genome. Comparison of the three genomes revealed considerable genomic diversity with >300 unique “genomic islands” identified, with the majority of these islands unusually clustered on one replichore. PCR-based analysis indicated that the large genomic islands are widely variable across a large collection of C. perfringens strains. These islands encode genes that correlate to differences in virulence and phenotypic characteristics of these strains. Significant differences between the strains include numerous novel mobile elements and genes encoding metabolic capabilities, strain-specific extracellular polysaccharide capsule, sporulation factors, toxins, and other secreted enzymes, providing substantial insight into this medically important bacterial pathogen. PMID:16825665

  2. Profile: Native Hawaiians and Pacific Islanders

    MedlinePLUS

    ... Practices Native Hawaiian/Other Pacific Islander Asthma Cancer Chronic Liver Disease Diabetes Heart Disease HIV/AIDS Infant Heath & Mortality ... Islanders and Cancer Native Hawaiians/Pacific Islanders and Chronic Liver Disease Native Hawaiians/Pacific Islanders and Diabetes Native Hawaiians/ ...

  3. Natural hazards on the island of Hawaii

    USGS Publications Warehouse

    Peterson, D.W.; Mullineaux, D.R.

    1977-01-01

    The island of Hawaii and the other islands of the Hawaiian chain are products of volcanic eruptions. Lava flows from hundreds of thousands of eruptions through countless centuries have built the Hawaiian Islands. Some volcanoes on the island of Hawaii have been very active during historic time, and similar activity is expected to continue throughout the foreseeable future.

  4. 21 CFR 808.89 - Rhode Island.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 21 Food and Drugs 8 2013-04-01 2013-04-01 false Rhode Island. 808.89 Section 808.89 Food and Drugs... and Local Exemptions § 808.89 Rhode Island. The following Rhode Island medical device requirements are... from preemption under section 521(b) of the act: Rhode Island General Laws, Section 5-49-2.1,...

  5. 21 CFR 808.89 - Rhode Island.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 21 Food and Drugs 8 2012-04-01 2012-04-01 false Rhode Island. 808.89 Section 808.89 Food and Drugs... and Local Exemptions § 808.89 Rhode Island. The following Rhode Island medical device requirements are... from preemption under section 521(b) of the act: Rhode Island General Laws, Section 5-49-2.1,...

  6. 27 CFR 9.170 - Long Island.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 27 Alcohol, Tobacco Products and Firearms 1 2013-04-01 2013-04-01 false Long Island. 9.170 Section... Island. (a) Name. The name of the viticultural area described in this section is “Long Island.” (b) Approved maps. The appropriate maps for determining the boundary of the Long Island viticultural area...

  7. 27 CFR 9.170 - Long Island.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 27 Alcohol, Tobacco Products and Firearms 1 2014-04-01 2014-04-01 false Long Island. 9.170 Section... Island. (a) Name. The name of the viticultural area described in this section is “Long Island.” (b) Approved maps. The appropriate maps for determining the boundary of the Long Island viticultural area...

  8. 27 CFR 9.170 - Long Island.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 27 Alcohol, Tobacco Products and Firearms 1 2011-04-01 2011-04-01 false Long Island. 9.170 Section... Island. (a) Name. The name of the viticultural area described in this section is “Long Island.” (b) Approved maps. The appropriate maps for determining the boundary of the Long Island viticultural area...

  9. 27 CFR 9.170 - Long Island.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 27 Alcohol, Tobacco Products and Firearms 1 2010-04-01 2010-04-01 false Long Island. 9.170 Section... Island. (a) Name. The name of the viticultural area described in this section is “Long Island.” (b) Approved maps. The appropriate maps for determining the boundary of the Long Island viticultural area...

  10. 21 CFR 808.89 - Rhode Island.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 21 Food and Drugs 8 2011-04-01 2011-04-01 false Rhode Island. 808.89 Section 808.89 Food and Drugs... and Local Exemptions § 808.89 Rhode Island. The following Rhode Island medical device requirements are... from preemption under section 521(b) of the act: Rhode Island General Laws, Section 5-49-2.1,...

  11. 21 CFR 808.89 - Rhode Island.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 21 Food and Drugs 8 2014-04-01 2014-04-01 false Rhode Island. 808.89 Section 808.89 Food and Drugs... and Local Exemptions § 808.89 Rhode Island. The following Rhode Island medical device requirements are... from preemption under section 521(b) of the act: Rhode Island General Laws, Section 5-49-2.1,...

  12. 21 CFR 808.89 - Rhode Island.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 21 Food and Drugs 8 2010-04-01 2010-04-01 false Rhode Island. 808.89 Section 808.89 Food and Drugs... and Local Exemptions § 808.89 Rhode Island. The following Rhode Island medical device requirements are... from preemption under section 521(b) of the act: Rhode Island General Laws, Section 5-49-2.1,...

  13. 27 CFR 9.170 - Long Island.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 27 Alcohol, Tobacco Products and Firearms 1 2012-04-01 2012-04-01 false Long Island. 9.170 Section... Island. (a) Name. The name of the viticultural area described in this section is “Long Island.” (b) Approved maps. The appropriate maps for determining the boundary of the Long Island viticultural area...

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

    PubMed Central

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

    2013-01-01

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

  15. DNA microarray analysis of genome dynamics in Yersinia pestis: insights into bacterial genome microevolution and niche adaptation.

    PubMed

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

    2004-08-01

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

  16. Exploring Other Genomes: Bacteria.

    ERIC Educational Resources Information Center

    Flannery, Maura C.

    2001-01-01

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

  17. The genome BLASTatlas-a GeneWiz extension for visualization of whole-genome homology.

    PubMed

    Hallin, Peter F; Binnewies, Tim T; Ussery, David W

    2008-05-01

    The development of fast and inexpensive methods for sequencing bacterial genomes has led to a wealth of data, often with many genomes being sequenced of the same species or closely related organisms. Thus, there is a need for visualization methods that will allow easy comparison of many sequenced genomes to a defined reference strain. The BLASTatlas is one such tool that is useful for mapping and visualizing whole genome homology of genes and proteins within a reference strain compared to other strains or species of one or more prokaryotic organisms. We provide examples of BLASTatlases, including the Clostridium tetani plasmid p88, where homologues for toxin genes can be easily visualized in other sequenced Clostridium genomes, and for a Clostridium botulinum genome, compared to 14 other Clostridium genomes. DNA structural information is also included in the atlas to visualize the DNA chromosomal context of regions. Additional information can be added to these plots, and as an example we have added circles showing the probability of the DNA helix opening up under superhelical tension. The tool is SOAP compliant and WSDL (web services description language) files are located on our website: (http://www.cbs.dtu.dk/ws/BLASTatlas), where programming examples are available in Perl. By providing an interoperable method to carry out whole genome visualization of homology, this service offers bioinformaticians as well as biologists an easy-to-adopt workflow that can be directly called from the programming language of the user, hence enabling automation of repeated tasks. This tool can be relevant in many pangenomic as well as in metagenomic studies, by giving a quick overview of clusters of insertion sites, genomic islands and overall homology between a reference sequence and a data set. PMID:18414733

  18. Island cosmology in the landscape

    NASA Astrophysics Data System (ADS)

    Piao, Yun-Song

    2008-11-01

    In the eternally inflationary background driven by the metastable vacua of the landscape, it is possible that some local quantum fluctuations with the null energy condition violation can be large enough to stride over the barriers among different vacua, so that create some islands full of radiation in new vacua, and then these emergently thermalized islands will enter into the evolution of standard big bang cosmology. In this paper, we calculate the spectrum of curvature perturbation generated during the emergence of island. We find that generally the spectrum obtained is nearly scale invariant, which can be well related to that of slow roll inflation by a simple duality. This in some sense suggests a degeneracy between their scalar spectra. In addition, we also simply estimate the non-Gaussianity of perturbation, which is naturally large, yet, can lie in the observational bound well. The results shown here indicate that the island emergently thermalized in the landscape can be consistent with our observable universe.

  19. Synthesizing knowledge of ocean islands

    NASA Astrophysics Data System (ADS)

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

    2011-11-01

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

  20. The Three Mile Island Disaster.

    ERIC Educational Resources Information Center

    Crosby, Emeral

    1980-01-01

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

  1. Wild Ponies on Assateague Island

    USGS Multimedia Gallery

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

  2. Magnetic island formation in tokamaks

    SciTech Connect

    Yoshikawa, S.

    1989-04-01

    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.

  3. Linked selection and recombination rate variation drive the evolution of the genomic landscape of differentiation across the speciation continuum of Ficedula flycatchers.

    PubMed

    Burri, Reto; Nater, Alexander; Kawakami, Takeshi; Mugal, Carina F; Olason, Pall I; Smeds, Linnea; Suh, Alexander; Dutoit, Ludovic; Bureš, Stanislav; Garamszegi, Laszlo Z; Hogner, Silje; Moreno, Juan; Qvarnström, Anna; Ruži?, Milan; Sæther, Stein-Are; Sætre, Glenn-Peter; Török, Janos; Ellegren, Hans

    2015-11-01

    Speciation is a continuous process during which genetic changes gradually accumulate in the genomes of diverging species. Recent studies have documented highly heterogeneous differentiation landscapes, with distinct regions of elevated differentiation ("differentiation islands") widespread across genomes. However, it remains unclear which processes drive the evolution of differentiation islands; how the differentiation landscape evolves as speciation advances; and ultimately, how differentiation islands are related to speciation. Here, we addressed these questions based on population genetic analyses of 200 resequenced genomes from 10 populations of four Ficedula flycatcher sister species. We show that a heterogeneous differentiation landscape starts emerging among populations within species, and differentiation islands evolve recurrently in the very same genomic regions among independent lineages. Contrary to expectations from models that interpret differentiation islands as genomic regions involved in reproductive isolation that are shielded from gene flow, patterns of sequence divergence (dxy and relative node depth) do not support a major role of gene flow in the evolution of the differentiation landscape in these species. Instead, as predicted by models of linked selection, genome-wide variation in diversity and differentiation can be explained by variation in recombination rate and the density of targets for selection. We thus conclude that the heterogeneous landscape of differentiation in Ficedula flycatchers evolves mainly as the result of background selection and selective sweeps in genomic regions of low recombination. Our results emphasize the necessity of incorporating linked selection as a null model to identify genome regions involved in adaptation and speciation. PMID:26355005

  4. Genome Maps, a new generation genome browser.

    PubMed

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

    2013-07-01

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

  5. Genome Maps, a new generation genome browser

    PubMed Central

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

    2013-01-01

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

  6. 33 CFR 80.717 - Tybee Island, GA to St. Simons Island, GA.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

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

  7. 33 CFR 80.717 - Tybee Island, GA to St. Simons Island, GA.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

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

  8. 33 CFR 80.717 - Tybee Island, GA to St. Simons Island, GA.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

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

  9. 33 CFR 80.717 - Tybee Island, GA to St. Simons Island, GA.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

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

  10. 33 CFR 80.717 - Tybee Island, GA to St. Simons Island, GA.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

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

  11. Discovery of MLL1 binding units, their localization to CpG Islands, and their potential function in mitotic chromatin

    PubMed Central

    2013-01-01

    Background Mixed Lineage Leukemia 1 (MLL1) is a mammalian ortholog of the Drosophila Trithorax. In Drosophila, Trithorax complexes transmit the memory of active genes to daughter cells through interactions with Trithorax Response Elements (TREs). However, despite their functional importance, nothing is known about sequence features that may act as TREs in mammalian genomic DNA. Results By analyzing results of reported DNA binding assays, we identified several CpG rich motifs as potential MLL1 binding units (defined as morphemes). We find that these morphemes are dispersed within a relatively large collection of human promoter sequences and appear densely packed near transcription start sites of protein-coding genes. Genome wide analyses localized frequent morpheme occurrences to CpG islands. In the human HOX loci, the morphemes are spread across CpG islands and in some cases tail into the surrounding shores and shelves of the islands. By analyzing results of chromatin immunoprecipitation assays, we found a connection between morpheme occurrences, CpG islands, and chromatin segments reported to be associated with MLL1. Furthermore, we found a correspondence of reported MLL1-driven “bookmarked” regions in chromatin to frequent occurrences of MLL1 morphemes in CpG islands. Conclusion Our results implicate the MLL1 morphemes in sequence-features that define the mammalian TREs and provide a novel function for CpG islands. Apparently, our findings offer the first evidence for existence of potential TREs in mammalian genomic DNA and the first evidence for a connection between CpG islands and gene-bookmarking by MLL1 to transmit the memory of highly active genes during mitosis. Our results further suggest a role for overlapping morphemes in producing closely packed and multiple MLL1 binding events in genomic DNA so that MLL1 molecules could interact and reside simultaneously on extended potential transcriptional maintenance elements in human chromosomes to transmit the memory of highly active genes during mitosis. PMID:24373511

  12. JGI Fungal Genomics Program

    SciTech Connect

    Grigoriev, Igor V.

    2011-03-14

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

  13. Genomic Encyclopedia of Fungi

    SciTech Connect

    Grigoriev, Igor

    2012-08-10

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

  14. Pangenome Analysis of Burkholderia pseudomallei: Genome Evolution Preserves Gene Order despite High Recombination Rates

    PubMed Central

    Spring-Pearson, Senanu M.; Stone, Joshua K.; Doyle, Adina; Allender, Christopher J.; Okinaka, Richard T.; Mayo, Mark; Broomall, Stacey M.; Hill, Jessica M.; Karavis, Mark A.; Hubbard, Kyle S.; Insalaco, Joseph M.; McNew, Lauren A.; Rosenzweig, C. Nicole; Gibbons, Henry S.; Currie, Bart J.; Wagner, David M.; Keim, Paul; Tuanyok, Apichai

    2015-01-01

    The pangenomic diversity in Burkholderia pseudomallei is high, with approximately 5.8% of the genome consisting of genomic islands. Genomic islands are known hotspots for recombination driven primarily by site-specific recombination associated with tRNAs. However, recombination rates in other portions of the genome are also high, a feature we expected to disrupt gene order. We analyzed the pangenome of 37 isolates of B. pseudomallei and demonstrate that the pangenome is ‘open’, with approximately 136 new genes identified with each new genome sequenced, and that the global core genome consists of 4568±16 homologs. Genes associated with metabolism were statistically overrepresented in the core genome, and genes associated with mobile elements, disease, and motility were primarily associated with accessory portions of the pangenome. The frequency distribution of genes present in between 1 and 37 of the genomes analyzed matches well with a model of genome evolution in which 96% of the genome has very low recombination rates but 4% of the genome recombines readily. Using homologous genes among pairs of genomes, we found that gene order was highly conserved among strains, despite the high recombination rates previously observed. High rates of gene transfer and recombination are incompatible with retaining gene order unless these processes are either highly localized to specific sites within the genome, or are characterized by symmetrical gene gain and loss. Our results demonstrate that both processes occur: localized recombination introduces many new genes at relatively few sites, and recombination throughout the genome generates the novel multi-locus sequence types previously observed while preserving gene order. PMID:26484663

  15. Nuclear compartments, genome folding, and enhancer-promoter communication.

    PubMed

    Ulianov, Sergey V; Gavrilov, Alexey A; Razin, Sergey V

    2015-01-01

    The eukaryotic genome has an extremely complex spatial organization. The physical distances between regulatory elements of the genome, such as enhancers, promoters, insulators, and CpG-islands, do not necessarily reflect genomic distances. Some remote regulatory elements appear to interact physically with target promoters in the 3D nuclear space. These spatial contacts are thought to play a crucial role in the regulation of transcription. Recent studies performed using 3C (chromosome conformation capture)-based methods, FISH (fluorescence in situ hybridization) coupled with confocal microscopy, and other experimental approaches have revealed that the spatial interactions of distant genomic elements within a folded chromosome are specific and functionally relevant. Additionally, the spatial organization of the eukaryotic genome is linked to the functional compartmentalization of the cell nucleus. In this review, we discuss the current state of research on the functional architecture of the eukaryotic genome. Special emphasis is given to the role of the spatial organization of the genome in establishing communication between enhancers and promoters. The driving forces of the juxtaposition of remote genomic elements are also considered. PMID:25708464

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

    USGS Publications Warehouse

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

    2004-01-01

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

  17. Plant genomics: an overview.

    PubMed

    Campos-de Quiroz, Hugo

    2002-01-01

    Recent technological advancements have substantially expanded our ability to analyze and understand plant genomes and to reduce the gap existing between genotype and phenotype. The fast evolving field of genomics allows scientists to analyze thousand of genes in parallel, to understand the genetic architecture of plant genomes and also to isolate the genes responsible for mutations. Furthermore, whole genomes can now be sequenced. This review addresses these issues and also discusses ways to extract biological meaning from DNA data. Although genomic issuesare addressed from a plant perspective, this review provides insights into the genomic analyses of other organisms. PMID:12462991

  18. Complete Genome Sequence of the Soybean Symbiont Bradyrhizobium japonicum Strain USDA6T.

    PubMed

    Kaneko, Takakazu; Maita, Hiroko; Hirakawa, Hideki; Uchiike, Nobukazu; Minamisawa, Kiwamu; Watanabe, Akiko; Sato, Shusei

    2011-01-01

    The complete nucleotide sequence of the genome of the soybean symbiont Bradyrhizobium japonicum strain USDA6T was determined. The genome of USDA6T is a single circular chromosome of 9,207,384 bp. The genome size is similar to that of the genome of another soybean symbiont, B. japonicum USDA110 (9,105,828 bp). Comparison of the whole-genome sequences of USDA6T and USDA110 showed colinearity of major regions in the two genomes, although a large inversion exists between them. A significantly high level of sequence conservation was detected in three regions on each genome. The gene constitution and nucleotide sequence features in these three regions indicate that they may have been derived from a symbiosis island. An ancestral, large symbiosis island, approximately 860 kb in total size, appears to have been split into these three regions by unknown large-scale genome rearrangements. The two integration events responsible for this appear to have taken place independently, but through comparable mechanisms, in both genomes. PMID:24710291

  19. One million served: Rhode Island`s recycling facility

    SciTech Connect

    Malloy, M.G.

    1997-11-01

    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.

  20. Brief Guide to Genomics: DNA, Genes and Genomes

    MedlinePLUS

    ... A Brief Guide to Genomics DNA, Genes and Genomes Deoxyribonucleic acid (DNA) is the chemical compound that ... a deletion of thousands of bases. The Human Genome Project The Human Genome Project, which was led ...

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

    PubMed Central

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

    2009-01-01

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

  2. Terrestrial bird population trends on Aguiguan (Goat Island), Mariana Islands

    USGS Publications Warehouse

    Amidon, Fred; Camp, Richard J.; Marshall, Ann P.; Pratt, Thane K.; Williams, Laura; Radley, Paul; Cruz, Justine B.

    2014-01-01

    The island of Aguiguan is part of the Mariana archipelago and currently supports populations of four endemic species, including one endemic genus, Cleptornis. Bird population trends since 1982 were recently assessed on the neighbouring islands of Saipan, Tinian, and Rota indicating declines in some native species. Point-transect surveys were conducted in 2008 by the U.S. Fish and Wildlife Service to assess population densities and trends on Aguiguan. Densities for six of the nine native birds—White-throated Ground-dove Gallicolumba xanthonura, Collared Kingfisher Todiramphus chloris, Rufous Fantail Rhipidura rufifrons, Golden White-eye Cleptornis marchei, Bridled White-eye Zosterops conspicillatus and Micronesian Starling Aplonis opaca—and the non-native bird—Island Collared-dove Streptopelia bitorquata—were significantly greater in 2008 than in 1982. No differences in densities were detected among the surveys for Mariana Fruit-dove Ptilinopus roseicapilla, and Micronesian MyzomelaMyzomela rubratra. Three federally and locally listed endangered birds—Nightingale Reed-warbler Acrocephalus luscinius, Mariana Swiftlet Collocalia bartschi, and Micronesian Megapode Megapodius laperous)—were either not detected during the point-transect counts, the surveys were not appropriate for the species, or the numbers of birds detected were too small to estimate densities. The factors behind the increasing trends for some species are unknown but may be related to increased forest cover on the island since 1982. With declining trends for some native species on neighbouring islands, the increasing and stable trends on Aguiguan is good news for forest bird populations in the region, as Aguiguan populations can help support conservation efforts on other islands in the archipelago.

  3. Genomic plasticity of the causative agent of melioidosis, Burkholderia pseudomallei

    PubMed Central

    Holden, Matthew T. G.; Titball, Richard W.; Peacock, Sharon J.; Cerdeño-Tárraga, Ana M.; Atkins, Timothy; Crossman, Lisa C.; Pitt, Tyrone; Churcher, Carol; Mungall, Karen; Bentley, Stephen D.; Sebaihia, Mohammed; Thomson, Nicholas R.; Bason, Nathalie; Beacham, Ifor R.; Brooks, Karen; Brown, Katherine A.; Brown, Nat F.; Challis, Greg L.; Cherevach, Inna; Chillingworth, Tracy; Cronin, Ann; Crossett, Ben; Davis, Paul; DeShazer, David; Feltwell, Theresa; Fraser, Audrey; Hance, Zahra; Hauser, Heidi; Holroyd, Simon; Jagels, Kay; Keith, Karen E.; Maddison, Mark; Moule, Sharon; Price, Claire; Quail, Michael A.; Rabbinowitsch, Ester; Rutherford, Kim; Sanders, Mandy; Simmonds, Mark; Songsivilai, Sirirurg; Stevens, Kim; Tumapa, Sarinna; Vesaratchavest, Monkgol; Whitehead, Sally; Yeats, Corin; Barrell, Bart G.; Oyston, Petra C. F.; Parkhill, Julian

    2004-01-01

    Burkholderia pseudomallei is a recognized biothreat agent and the causative agent of melioidosis. This Gram-negative bacterium exists as a soil saprophyte in melioidosis-endemic areas of the world and accounts for 20% of community-acquired septicaemias in northeastern Thailand where half of those affected die. Here we report the complete genome of B. pseudomallei, which is composed of two chromosomes of 4.07 megabase pairs and 3.17 megabase pairs, showing significant functional partitioning of genes between them. The large chromosome encodes many of the core functions associated with central metabolism and cell growth, whereas the small chromosome carries more accessory functions associated with adaptation and survival in different niches. Genomic comparisons with closely and more distantly related bacteria revealed a greater level of gene order conservation and a greater number of orthologous genes on the large chromosome, suggesting that the two replicons have distinct evolutionary origins. A striking feature of the genome was the presence of 16 genomic islands (GIs) that together made up 6.1% of the genome. Further analysis revealed these islands to be variably present in a collection of invasive and soil isolates but entirely absent from the clonally related organism B. mallei. We propose that variable horizontal gene acquisition by B. pseudomallei is an important feature of recent genetic evolution and that this has resulted in a genetically diverse pathogenic species. PMID:15377794

  4. Genomic evidence of geographically widespread effect of gene flow from polar bears into brown bears

    PubMed Central

    Cahill, James A; Stirling, Ian; Kistler, Logan; Salamzade, Rauf; Ersmark, Erik; Fulton, Tara L; Stiller, Mathias; Green, Richard E; Shapiro, Beth

    2015-01-01

    Polar bears are an arctic, marine adapted species that is closely related to brown bears. Genome analyses have shown that polar bears are distinct and genetically homogeneous in comparison to brown bears. However, these analyses have also revealed a remarkable episode of polar bear gene flow into the population of brown bears that colonized the Admiralty, Baranof and Chichagof islands (ABC islands) of Alaska. Here, we present an analysis of data from a large panel of polar bear and brown bear genomes that includes brown bears from the ABC islands, the Alaskan mainland and Europe. Our results provide clear evidence that gene flow between the two species had a geographically wide impact, with polar bear DNA found within the genomes of brown bears living both on the ABC islands and in the Alaskan mainland. Intriguingly, while brown bear genomes contain up to 8.8% polar bear ancestry, polar bear genomes appear to be devoid of brown bear ancestry, suggesting the presence of a barrier to gene flow in that direction. PMID:25490862

  5. Genomic evidence of geographically widespread effect of gene flow from polar bears into brown bears.

    PubMed

    Cahill, James A; Stirling, Ian; Kistler, Logan; Salamzade, Rauf; Ersmark, Erik; Fulton, Tara L; Stiller, Mathias; Green, Richard E; Shapiro, Beth

    2015-03-01

    Polar bears are an arctic, marine adapted species that is closely related to brown bears. Genome analyses have shown that polar bears are distinct and genetically homogeneous in comparison to brown bears. However, these analyses have also revealed a remarkable episode of polar bear gene flow into the population of brown bears that colonized the Admiralty, Baranof and Chichagof islands (ABC islands) of Alaska. Here, we present an analysis of data from a large panel of polar bear and brown bear genomes that includes brown bears from the ABC islands, the Alaskan mainland and Europe. Our results provide clear evidence that gene flow between the two species had a geographically wide impact, with polar bear DNA found within the genomes of brown bears living both on the ABC islands and in the Alaskan mainland. Intriguingly, while brown bear genomes contain up to 8.8% polar bear ancestry, polar bear genomes appear to be devoid of brown bear ancestry, suggesting the presence of a barrier to gene flow in that direction. PMID:25490862

  6. Photosymbiotic ascidians from Pari Island (Thousand Islands, Indonesia).

    PubMed

    Hirose, Euichi; Iskandar, Budhi Hascaryo; Wardiatno, Yusli

    2014-01-01

    Photosymbiotic ascidian fauna were surveyed in the subtidal zone off Pari Island in the Thousand Islands (Java Sea, Indonesia). Nine species were recorded: Didemnum molle, Trididemnum miniatum, Lissoclinum patella, L. punctatum, L. timorense, Diplosoma gumavirens, D. simile, D. simileguwa, and D. virens. All of these species have been previously recorded in the Ryukyu Archipelago, Japan. Diplosoma gumavirens and D. simileguwa were originally described from the Ryukyu Archipelago in 2009 and 2005, respectively, and all of the observed species are potentially widely distributed in Indo-West Pacific coral reefs. PMID:25061385

  7. Genome instability in Lactobacillus rhamnosus GG.

    PubMed

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

    2013-04-01

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

  8. Genome Instability in Lactobacillus rhamnosus GG

    PubMed Central

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

    2013-01-01

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

  9. GENOMICS AND ENVIRONMENTAL RESEARCH

    EPA Science Inventory

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

  10. Cancer Genomics Overview

    Cancer.gov

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

  11. Harvesting rice's dispensable genome.

    PubMed

    Wing, Rod A

    2015-01-01

    A rapid and cost-effective approach has been developed to harvest and map the dispensable genome, that is, population-level natural sequence variation within a species that is not present in static genome assemblies. PMID:26429765

  12. Thermal island destabilization and the Greenwald limit

    SciTech Connect

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

    2015-02-15

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

  13. Is heterostyly rare on oceanic islands?

    PubMed Central

    Watanabe, Kenta; Sugawara, Takashi

    2015-01-01

    Heterostyly has been considered rare or absent on oceanic islands. However, there has been no comprehensive review on this issue. Is heterostyly truly rare on oceanic islands? What makes heterostyly rare on such islands? To answer these questions, we review the reproductive studies on heterostyly on oceanic islands, with special emphasis on the heterostylous genus Psychotria in the Pacific Ocean as a model system. Overall, not many reproductive studies have been performed on heterostylous species on oceanic islands. In Hawaiian Psychotria, all 11 species are thought to have evolved dioecy from distyly. In the West Pacific, three species on the oceanic Bonin and Lanyu Islands are distylous (Psychotria homalosperma, P. boninensis and P. cephalophora), whereas three species on the continental Ryukyu Islands show various breeding systems, such as distyly (P. serpens), dioecy (P. rubra) and monoecy (P. manillensis). On some other Pacific oceanic islands, possibilities of monomorphy have been reported. For many Psychotria species, breeding systems are unknown, although recent studies indicate that heterostylous species may occur on some oceanic islands. A shift from heterostyly to other sexual systems may occur on some oceanic islands. This tendency may also contribute to the rarity of heterostyly, in addition to the difficulty in colonization/autochthonous evolution of heterostylous species on oceanic islands. Further investigation of reproductive systems of Psychotria on oceanic islands using robust phylogenetic frameworks would provide new insights into plant reproduction on oceanic islands. PMID:26199401

  14. Thermal island destabilization and the Greenwald limit

    NASA Astrophysics Data System (ADS)

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

    2015-02-01

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

  15. Dust Storm Hits Canary Islands

    NASA Technical Reports Server (NTRS)

    2002-01-01

    A thick pall of sand and dust blew out from the Sahara Desert over the Atlantic Ocean yesterday (January 6, 2002), engulfing the Canary Islands in what has become one of the worst sand storms ever recorded there. In this scene, notice how the dust appears particularly thick in the downwind wake of Tenerife, the largest of the Canary Islands. Perhaps the turbulence generated by the air currents flowing past the island's volcanic peaks is churning the dust back up into the atmosphere, rather than allowing it to settle toward the surface. This true-color image was captured by the Moderate-resolution Imaging Spectroradiometer (MODIS), flying aboard NASA's Terra satellite, on January 7, 2002. Image courtesy Jacques Descloitres, MODIS Land Rapid Response Team at NASA GSFC

  16. Atmospheric suspensions of Russky Island

    NASA Astrophysics Data System (ADS)

    Golokhvast, Kirill S.; Nikiforov, P. A.; Chaika, V. V.

    2014-11-01

    The paper presents the first in the history of observations the results of studying of atmospheric suspensions contained in snowpacks of Russian Island (Vladivostok) , including the territory of campus of the Far Eastern Federal University (seasons 2011/2012-2013/2014 years). The distribution of airborne particles of different sizes and different genesis in differ by anthropogenic load districts of the island is revealed: the Far Eastern Federal University campus , the bridge over the Eastern Bosphorus Strait and the village Kanal. It is shown that in connection with the increase of anthropogenic load on the Russian island , its ecological condition deteriorates due to the rise in the atmosphere fractions of nano-and micro-sized particles.

  17. Developmentally programmed 3' CpG island methylation confers tissue- and cell-type-specific transcriptional activation

    Technology Transfer Automated Retrieval System (TEKTRAN)

    During development, a small but significant number of CpG islands (CGIs) becomes methylated. The timing of developmentally programmed CGI methylation and associated mechanisms of transcriptional regulation during cellular differentiation, however, remain poorly characterized. Here we used genome-wid...

  18. Exploiting the genome

    SciTech Connect

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

    1998-09-11

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

  19. Genome Sequencing Centers

    Cancer.gov

    The Cancer Genome Atlas (TCGA) Genome Sequencing Centers (GSCs) perform large-scale DNA sequencing using the latest sequencing technologies. Supported by the National Human Genome Research Institute (NHGRI) large-scale sequencing program, the GSCs generate the enormous volume of data required by TCGA, while continually improving existing technologies and methods to expand the frontier of what can be achieved in cancer genome sequencing.

  20. Genome Data Analysis Centers

    Cancer.gov

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

  1. The Big Island of Hawaii

    NASA Technical Reports Server (NTRS)

    2002-01-01

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

    12. Photograph of a photograph in possession of Rock Island Arsenal Historical Office. COMMANDING OFFICER'S OFFICE, FIRST FLOOR. DATED 1898. - Rock Island Arsenal, Building No. 360, Gillespie Avenue between Rodman Avenue & North Avenue, Rock Island, Rock Island County, IL

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

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

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

  17. WAKE ISLAND AIRFIELD TERMINAL, BUILDING 1502 LOOKING EAST WITH PHOTO ...

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

    WAKE ISLAND AIRFIELD TERMINAL, BUILDING 1502 LOOKING EAST WITH PHOTO SCALE CENTERED ON BUILDING (12/30/2008) - Wake Island Airfield, Terminal Building, West Side of Wake Avenue, Wake Island, Wake Island, UM

  18. 3. Light tower, view northwest, south side Ram Island ...

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

    3. Light tower, view northwest, south side - Ram Island Light Station, Ram Island, south of Ocean Point & just north of Fisherman Island, marking south side of Fisherman Island Passage, Ocean Point, Lincoln County, ME

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

    NASA Astrophysics Data System (ADS)

    Amar, Jacques; Hubartt, Bradley

    2015-03-01

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

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

    PubMed

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

    2012-12-01

    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

  1. LEGUME COMPARATIVE GENOMICS

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  2. 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 ...

  3. Office of Cancer Genomics |

    Cancer.gov

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

  4. Streamlined Islands in Ares Valles

    NASA Technical Reports Server (NTRS)

    2002-01-01

    (Released 10 June 2002) The Science Although liquid water is not stable on the surface of Mars today, there is substantial geologic evidence that large quantities of water once flowed across the surface in the distant past. Streamlined islands, shown here, are one piece of evidence for this ancient water. The tremendous force of moving water, possibly from a catastrophic flood, carved these teardrop-shaped islands within a much larger channel called Ares Valles. The orientation of the islands can be used as an indicator of the direction the water flowed. The islands have a blunt end that is usually associated with an obstacle, commonly an impact crater. The crater is resistant to erosion and creates a geologic barrier around which the water must flow. As the water flows past the obstacle, its erosive power is directed outward, leaving the area in the lee of the obstacle relatively uneroded. However, some scientists have also argued that the area in the lee of the obstacle might be a depositional zone, where material is dropped out of the water as it briefly slows. The ridges observed on the high-standing terrain in the leeward parts of the islands may be benches carved into the rock that mark the height of the water at various times during the flood, or they might be indicative of layering in the leeward rock. As the water makes its way downstream, the interference of the water flow by the obstacle is reduced, and the water that was diverted around the obstacle rejoins itself at the narrow end of the island. Therefore, the direction of the water flow is parallel to the orientation of the island, and the narrow end of the island points downstream. In addition to the streamlined islands, the channel floor exhibits fluting that is also suggestive of flowing water. The flutes (also known as longitudinal grooves) are also parallel to the direction of flow, indicating that the water flow was turbulent and probably quite fast, which is consistent with the hypothesized catastrophic floods that came through Ares Valles. The Story In symbolism only, these guppy-shaped islands and current-like flutes of land beside them may conjure up a mental image of a flowing Martian river. This picture would only be half-right. Scientifically, no fish ever swam this channel, but these landforms do reveal that catastrophic floods of rushing water probably patterned the land in just this way. Geologists who study flood areas believe that a tremendous force of moving water probably carved both the islands and the small, parallel, 'current-like' ridges around them. The blunt end of the islands (the 'heads' of the 'fish') are probably ancient impact craters that posed obstacles to the water as it rushed down the channel in torrents. Because a crater is resistant to erosion, it creates a geologic barrier around which the water must flow. As the water makes its way downstream, the crater's interference with the water flow is reduced, so the water that was diverted around the obstacle rejoins at the narrow end of the island (the 'tail' of the 'fish'). Therefore, from this information, you can tell that the water flowed from the southeast to the northwest. As a rule of thumb for the future, you can say that the narrow end of the island points downstream. The result may be the island behind the crater, but geologists disagree about the exact process by which the island forms. Some scientists argue that the erosive power of the water is directed outward, leaving the area behind, or in the lee of, the obstacle relatively untouched. Other scientists argue that the water slows when it encounters the crater obstacle, and small particles of sand and 'dirt' drop out of the water and are deposited in the lee. There's another small associated uncertainty too. Look closely at the edges of the islands and notice how the land is terraced. These ledges might mark the height of the water at various times during the flood . . . or they might be an indication that layering occurred. It all depends on your hypothesis. Like the streamlined islands, the current-like flutes are parallel to the direction of flow, indicating that the water flow was turbulent and probably quite fast, which is consistent with the hypothesis that catastrophic floods broke forth in this region, known as Ares Vallis. Ares Vallis is the region where Pathfinder landed to help understand the possible history of water on Mars. Geologists want to understand not only if there was a catastrophic flood, but why it happened. Both orbiters and landers can add to the information on hand, but some Earth examples might provide clues as well. On our planet, some glacial valleys have had major catastrophic floods that were caused by the sudden outburst and drainage of glacial lakes. The Channeled Scabland in Washington state is great Earthly example of a place where the sudden failure of a glacier ice dam spewed out water, leaving a system of large, dry channels with flutes similar to the ones seen in this image. Did something similar happen to cause this outburst on Mars? Hopefully, future studies of THEMIS and other images will help us understand the answer.

  5. The Genome of the “Great Speciator” Provides Insights into Bird Diversification

    PubMed Central

    Cornetti, Luca; Valente, Luis M.; Dunning, Luke T.; Quan, Xueping; Black, Richard A.; Hébert, Olivier; Savolainen, Vincent

    2015-01-01

    Among birds, white-eyes (genus Zosterops) have diversified so extensively that Jared Diamond and Ernst Mayr referred to them as the “great speciator.” The Zosterops lineage exhibits some of the fastest rates of species diversification among vertebrates, and its members are the most prolific passerine island colonizers. We present a high-quality genome assembly for the silvereye (Zosterops lateralis), a white-eye species consisting of several subspecies distributed across multiple islands. We investigate the genetic basis of rapid diversification in white-eyes by conducting genomic analyses at varying taxonomic levels. First, we compare the silvereye genome with those of birds from different families and searched for genomic features that may be unique to Zosterops. Second, we compare the genomes of different species of white-eyes from Lifou island (South Pacific), using whole genome resequencing and restriction site associated DNA. Third, we contrast the genomes of two subspecies of silvereye that differ in plumage color. In accordance with theory, we show that white-eyes have high rates of substitutions, gene duplication, and positive selection relative to other birds. Below genus level, we find that genomic differentiation accumulates rapidly and reveals contrasting demographic histories between sympatric species on Lifou, indicative of past interspecific interactions. Finally, we highlight genes possibly involved in color polymorphism between the subspecies of silvereye. By providing the first whole-genome sequence resources for white-eyes and by conducting analyses at different taxonomic levels, we provide genomic evidence underpinning this extraordinary bird radiation. PMID:26338191

  6. LONG ISLAND SOUND STUDY CCMP, 1994

    EPA Science Inventory

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

  7. Obesity and Native Hawaiians/Pacific Islanders

    MedlinePLUS

    ... Population Profiles > Native Hawaiian/Other Pacific Islander > Obesity Obesity and Native Hawaiians/Pacific Islanders Native Hawaiians/Pacific ... data available at this time. HEALTH IMPACT OF OBESITY More than 80 percent of people with type ...

  8. Biodiversity on island chains: Neutral model simulations

    NASA Astrophysics Data System (ADS)

    Warren, Patrick B.

    2010-11-01

    A neutral ecology model is simulated on an island chain, in which neighboring islands can exchange individuals but only the first island is able to receive immigrants from a metacommunity. It is found by several measures that ? -diversity decreases along the chain. Subtle changes in taxon abundance distributions can be detected when islands in the chain are compared to diversity-matched single islands. The island chain is found to have unexpectedly rich dynamics. Significant ? -diversity correlations are found between islands in the chain, which are absent between diversity-matched single islands. The results potentially apply to human microbial biodiversity and biogeography and suggest that measurements of interindividual and intraindividual ? -diversity may give insights into microbial community assembly mechanisms.

  9. Immunizations and Asians and Pacific Islanders

    MedlinePLUS

    ... and Data > Minority Population Profiles > Asian American > Immunizations Immunizations and Asians and Pacific Islanders Asian/Pacific Islander ... 35 months reached the Healthy People goal for immunizations for hepatitis B, MMR (measles-mumps-rubella), polio ...

  10. Cancer and Asians/Pacific Islanders

    MedlinePLUS

    ... they are 60 percent more likely to have stomach cancer. Although Asian/Pacific Islander women are 30 percent ... are almost three times as likely to have stomach cancer. Both Asian/Pacific Islander men and women have ...

  11. Energy Transition Initiative: Island Energy Snapshot - U.S. Virgin Islands (Fact Sheet)

    SciTech Connect

    Not Available

    2015-03-01

    This profile provides a snapshot of the energy landscape of the U.S. Virgin Islands (USVI) - St. Thomas, St. John, and St. Croix. The Virgin Islands archipelago makes up the northern portion of the Lesser Antilles and the western island group of the Leeward Islands, forming the border between the Atlantic Ocean and the Caribbean Sea.

  12. 33 CFR 80.720 - St. Simons Island, GA to Amelia Island, FL.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 33 Navigation and Navigable Waters 1 2013-07-01 2013-07-01 false St. Simons Island, GA to Amelia Island, FL. 80.720 Section 80.720 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY INTERNATIONAL NAVIGATION RULES COLREGS DEMARCATION LINES Seventh District § 80.720 St. Simons Island, GA to Amelia Island, FL. (a) A...

  13. 33 CFR 80.720 - St. Simons Island, GA to Amelia Island, FL.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 33 Navigation and Navigable Waters 1 2012-07-01 2012-07-01 false St. Simons Island, GA to Amelia Island, FL. 80.720 Section 80.720 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY INTERNATIONAL NAVIGATION RULES COLREGS DEMARCATION LINES Seventh District § 80.720 St. Simons Island, GA to Amelia Island, FL. (a) A...

  14. 76 FR 2572 - Amendment of Class E Airspace; Kwajalein Island, Marshall Islands, RMI

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-01-14

    ... part 71 by amending Class E airspace; Kwajalein Island, Marshall Islands, RMI (75 FR 61993... Kwajalein Island, Marshall Islands, RMI, as published in the Federal ] Register on October 7, 2010, FR Doc. 2010-25220, (75 FR 61933) on page 61994, column 1, is corrected as follows: Sec. 71.1 Paragraph...

  15. Symbolic meanings of island in dreams.

    PubMed

    Takao, H

    1998-02-01

    Six dreams reported from neurotic patients in the therapy of Jungian analysis are presented to illustrate the symbolic meanings of islands in dreams. The island in dreams symbolizes (i) the entrance point into Jungian analysis, (ii) a complex in which a dreamer has got involved and (iii) the beginning of the newly organized ego consciousness. The multiple meanings of islands are suggested to originate from several levels of the unconscious from which the identical symbol of island comes from. PMID:9682934

  16. Pearl and Hermes Reef, Hawaiian Island Chain

    NASA Technical Reports Server (NTRS)

    1992-01-01

    Pearl and Hermes Reef (28.0N, 176.0W) in the Hawaiian Island Chain, are seen with several small sandy islands, forming an atoll that caps a seamount on the long chain that extends some 1,500 miles northwestward from the more familiar Hawaiian Islands proper. Pearl and Hermes Reef lies about 100 miles southeast of Midway island. A reticulate network of coral patch reefs separates the lagoon into more or less isolated pools.

  17. Streamlined Islands in Ares Valles

    NASA Technical Reports Server (NTRS)

    2002-01-01

    (Released 10 June 2002) The Science Although liquid water is not stable on the surface of Mars today, there is substantial geologic evidence that large quantities of water once flowed across the surface in the distant past. Streamlined islands, shown here, are one piece of evidence for this ancient water. The tremendous force of moving water, possibly from a catastrophic flood, carved these teardrop-shaped islands within a much larger channel called Ares Valles. The orientation of the islands can be used as an indicator of the direction the water flowed. The islands have a blunt end that is usually associated with an obstacle, commonly an impact crater. The crater is resistant to erosion and creates a geologic barrier around which the water must flow. As the water flows past the obstacle, its erosive power is directed outward, leaving the area in the lee of the obstacle relatively uneroded. However, some scientists have also argued that the area in the lee of the obstacle might be a depositional zone, where material is dropped out of the water as it briefly slows. The ridges observed on the high-standing terrain in the leeward parts of the islands may be benches carved into the rock that mark the height of the water at various times during the flood, or they might be indicative of layering in the leeward rock. As the water makes its way downstream, the interference of the water flow by the obstacle is reduced, and the water that was diverted around the obstacle rejoins itself at the narrow end of the island. Therefore, the direction of the water flow is parallel to the orientation of the island, and the narrow end of the island points downstream. In addition to the streamlined islands, the channel floor exhibits fluting that is also suggestive of flowing water. The flutes (also known as longitudinal grooves) are also parallel to the direction of flow, indicating that the water flow was turbulent and probably quite fast, which is consistent with the hypothesized catastrophic floods that came through Ares Valles. The Story In symbolism only, these guppy-shaped islands and current-like flutes of land beside them may conjure up a mental image of a flowing Martian river. This picture would only be half-right. Scientifically, no fish ever swam this channel, but these landforms do reveal that catastrophic floods of rushing water probably patterned the land in just this way. Geologists who study flood areas believe that a tremendous force of moving water probably carved both the islands and the small, parallel, 'current-like' ridges around them. The blunt end of the islands (the 'heads' of the 'fish') are probably ancient impact craters that posed obstacles to the water as it rushed down the channel in torrents. Because a crater is resistant to erosion, it creates a geologic barrier around which the water must flow. As the water makes its way downstream, the crater's interference with the water flow is reduced, so the water that was diverted around the obstacle rejoins at the narrow end of the island (the 'tail' of the 'fish'). Therefore, from this information, you can tell that the water flowed from the southeast to the northwest. As a rule of thumb for the future, you can say that the narrow end of the island points downstream. The result may be the island behind the crater, but geologists disagree about the exact process by which the island forms. Some scientists argue that the erosive power of the water is directed outward, leaving the area behind, or in the lee of, the obstacle relatively untouched. Other scientists argue that the water slows when it encounters the crater obstacle, and small particles of sand and 'dirt' drop out of the water and are deposited in the lee. There's another small associated uncertainty too. Look closely at the edges of the islands and notice how the land is terraced. These ledges might mark the height of the water at various times during the flood . . . or they might be an indication that layering occurred. It all depends on your hypothesis. Like the stream

  18. Genomes of marine cyanopodoviruses reveal multiple origins of diversity.

    PubMed

    Labrie, S J; Frois-Moniz, K; Osburne, M S; Kelly, L; Roggensack, S E; Sullivan, M B; Gearin, G; Zeng, Q; Fitzgerald, M; Henn, M R; Chisholm, S W

    2013-05-01

    The marine cyanobacteria Prochlorococcus and Synechococcus are highly abundant in the global oceans, as are the cyanophage with which they co-evolve. While genomic analyses have been relatively extensive for cyanomyoviruses, only three cyanopodoviruses isolated on marine cyanobacteria have been sequenced. Here we present nine new cyanopodovirus genomes, and analyse them in the context of the broader group. The genomes range from 42.2 to 47.7 kb, with G+C contents consistent with those of their hosts. They share 12 core genes, and the pan-genome is not close to being fully sampled. The genomes contain three variable island regions, with the most hypervariable genes concentrated at one end of the genome. Concatenated core-gene phylogeny clusters all but one of the phage into three distinct groups (MPP-A and two discrete clades within MPP-B). The outlier, P-RSP2, has the smallest genome and lacks RNA polymerase, a hallmark of the Autographivirinae subfamily. The phage in group MPP-B contain photosynthesis and carbon metabolism associated genes, while group MPP-A and the outlier P-RSP2 do not, suggesting different constraints on their lytic cycles. Four of the phage encode integrases and three have a host integration signature. Metagenomic analyses reveal that cyanopodoviruses may be more abundant in the oceans than previously thought. PMID:23320838

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

    PubMed

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

    2014-01-01

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

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

    PubMed Central

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

    2014-01-01

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

  1. Genetic structure of the Common Eider in the western Aleutian Islands prior to fox eradication

    USGS Publications Warehouse

    Sonsthagen, Sarah A.; Talbot, Sandra L.; Wilson, Robert E.; Petersen, Margaret R.; Williams, Jeffrey C.; Byrd, G. Vernon; McCracken, Kevin G.

    2013-01-01

    Since the late 18th century bird populations residing in the Aleutian Archipelago have been greatly reduced by introduced arctic foxes (Alopex lagopus). We analyzed data from microsatellite, nuclear intron, and mitochondrial (mtDNA) loci to examine the spatial genetic structure, demography, and gene flow among four Aleutian Island populations of the Common Eider (Somateria mollissima) much reduced by introduced foxes. In mtDNA, we found high levels of genetic structure within and between island groups (ΦST = 0.643), but we found no population subdivision in microsatellites or nuclear introns. Differences in genetic structure between the mitochondrial and nuclear genomes are consistent with the Common Eider's breeding and winter biology, as females are highly philopatric and males disperse. Nevertheless, significant differences between islands in the mtDNA of males and marginal significance (P =0.07) in the Z-linked locus Smo 1 suggest that males may also have some level of fidelity to island groups. Severe reduction of populations by the fox, coupled with females' high philopatry, may have left the genetic signature of a bottleneck effect, resulting in the high levels of genetic differentiation observed in mtDNA (ΦST = 0.460–0.807) between islands only 440 km apart. Reestablishment of the Common Eider following the fox's eradication was likely through recruitment from within the islands and bolstered by dispersal from neighboring islands, as suggested by the lack of genetic structure and asymmetry in gene flow between Attu and the other Near Islands.

  2. A genome blogger manifesto

    PubMed Central

    2012-01-01

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

  3. Chromium and Genomic Stability

    PubMed Central

    Wise, Sandra S.; Wise, John Pierce

    2014-01-01

    Many metals serve as micronutrients which protect against genomic instability. Chromium is most abundant in its trivalent and hexavalent forms. Trivalent chromium has historically been considered an essential element, though recent data indicate that while it can have pharmacological effects and value, it is not essential. There are no data indicating that trivalent chromium promotes genomic stability and, instead may promote genomic instability. Hexavalent chromium is widely accepted as highly toxic and carcinogenic with no nutritional value. Recent data indicate that it causes genomic instability and also has no role in promoting genomic stability. PMID:22192535

  4. The genomic landscape underlying phenotypic integrity in the face of gene flow in crows.

    PubMed

    Poelstra, J W; Vijay, N; Bossu, C M; Lantz, H; Ryll, B; Müller, I; Baglione, V; Unneberg, P; Wikelski, M; Grabherr, M G; Wolf, J B W

    2014-06-20

    The importance, extent, and mode of interspecific gene flow for the evolution of species has long been debated. Characterization of genomic differentiation in a classic example of hybridization between all-black carrion crows and gray-coated hooded crows identified genome-wide introgression extending far beyond the morphological hybrid zone. Gene expression divergence was concentrated in pigmentation genes expressed in gray versus black feather follicles. Only a small number of narrow genomic islands exhibited resistance to gene flow. One prominent genomic region (<2 megabases) harbored 81 of all 82 fixed differences (of 8.4 million single-nucleotide polymorphisms in total) linking genes involved in pigmentation and in visual perception-a genomic signal reflecting color-mediated prezygotic isolation. Thus, localized genomic selection can cause marked heterogeneity in introgression landscapes while maintaining phenotypic divergence. PMID:24948738

  5. 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...

  6. Past, Present, Future Erosion at Locke Island

    SciTech Connect

    Bjornstad, Bruce N.

    2006-08-08

    This report describes and documents the erosion that has occurred along the northeast side of Locke Island over the last 10 to 20 years. The principal cause of this erosion is the massive Locke Island landslide complex opposite the Columbia River along the White Bluffs, which constricts the flow of the river and deflects the river's thalweg southward against the island.

  7. Ecology and Evolution: Islands of Change.

    ERIC Educational Resources Information Center

    Benz, Richard

    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…

  8. 40 CFR 81.432 - Virgin Islands.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 40 Protection of Environment 17 2010-07-01 2010-07-01 false Virgin Islands. 81.432 Section 81.432... Visibility Is an Important Value § 81.432 Virgin Islands. Area name Acreage Public Law establishing Federal land manager Virgin Islands NP 12,295 84-925 USDI-NPS...

  9. 40 CFR 81.432 - Virgin Islands.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 40 Protection of Environment 18 2013-07-01 2013-07-01 false Virgin Islands. 81.432 Section 81.432... Visibility Is an Important Value § 81.432 Virgin Islands. Area name Acreage Public Law establishing Federal land manager Virgin Islands NP 12,295 84-925 USDI-NPS...

  10. 40 CFR 81.432 - Virgin Islands.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 40 Protection of Environment 18 2012-07-01 2012-07-01 false Virgin Islands. 81.432 Section 81.432... Visibility Is an Important Value § 81.432 Virgin Islands. Area name Acreage Public Law establishing Federal land manager Virgin Islands NP 12,295 84-925 USDI-NPS...

  11. 40 CFR 81.432 - Virgin Islands.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 40 Protection of Environment 18 2014-07-01 2014-07-01 false Virgin Islands. 81.432 Section 81.432... Visibility Is an Important Value § 81.432 Virgin Islands. Area name Acreage Public Law establishing Federal land manager Virgin Islands NP 12,295 84-925 USDI-NPS...

  12. 40 CFR 81.432 - Virgin Islands.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 40 Protection of Environment 17 2011-07-01 2011-07-01 false Virgin Islands. 81.432 Section 81.432... Visibility Is an Important Value § 81.432 Virgin Islands. Area name Acreage Public Law establishing Federal land manager Virgin Islands NP 12,295 84-925 USDI-NPS...

  13. 27 CFR 9.68 - Merritt Island.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 27 Alcohol, Tobacco Products and Firearms 1 2013-04-01 2013-04-01 false Merritt Island. 9.68... Merritt Island. (a) Name. The name of the viticultural area described in this section is “Merritt Island.” (b) Approved maps. The appropriate maps for determining the boundaries of the Merritt...

  14. 27 CFR 9.68 - Merritt Island.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 27 Alcohol, Tobacco Products and Firearms 1 2011-04-01 2011-04-01 false Merritt Island. 9.68... Merritt Island. (a) Name. The name of the viticultural area described in this section is “Merritt Island.” (b) Approved maps. The appropriate maps for determining the boundaries of the Merritt...

  15. 40 CFR 81.340 - Rhode Island.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 40 Protection of Environment 17 2011-07-01 2011-07-01 false Rhode Island. 81.340 Section 81.340... AREAS FOR AIR QUALITY PLANNING PURPOSES Section 107 Attainment Status Designations § 81.340 Rhode Island. Rhode Island—TSP Designated area Does not meet primary standards Does not meet secondary...

  16. 27 CFR 9.68 - Merritt Island.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 27 Alcohol, Tobacco Products and Firearms 1 2014-04-01 2014-04-01 false Merritt Island. 9.68... Merritt Island. (a) Name. The name of the viticultural area described in this section is “Merritt Island.” (b) Approved maps. The appropriate maps for determining the boundaries of the Merritt...

  17. 27 CFR 9.68 - Merritt Island.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 27 Alcohol, Tobacco Products and Firearms 1 2012-04-01 2012-04-01 false Merritt Island. 9.68... Merritt Island. (a) Name. The name of the viticultural area described in this section is “Merritt Island.” (b) Approved maps. The appropriate maps for determining the boundaries of the Merritt...

  18. MARINE BOTTOM COMMUNITIES OF BLOCK ISLAND WATERS

    EPA Science Inventory

    The sea has long been an integral part of Block Island's natural history, beginning when the rising sea surrounded the high spot on a Pleistocene terminal moraine that became Block Island. The southern New England continental shelf, which lies around Block Island, and the Great S...

  19. Microbial genomic taxonomy

    PubMed Central

    2013-01-01

    A need for a genomic species definition is emerging from several independent studies worldwide. In this commentary paper, we discuss recent studies on the genomic taxonomy of diverse microbial groups and a unified species definition based on genomics. Accordingly, strains from the same microbial species share >95% Average Amino Acid Identity (AAI) and Average Nucleotide Identity (ANI), >95% identity based on multiple alignment genes, <10 in Karlin genomic signature, and?>?70% in silico Genome-to-Genome Hybridization similarity (GGDH). Species of the same genus will form monophyletic groups on the basis of 16S rRNA gene sequences, Multilocus Sequence Analysis (MLSA) and supertree analysis. In addition to the established requirements for species descriptions, we propose that new taxa descriptions should also include at least a draft genome sequence of the type strain in order to obtain a clear outlook on the genomic landscape of the novel microbe. The application of the new genomic species definition put forward here will allow researchers to use genome sequences to define simultaneously coherent phenotypic and genomic groups. PMID:24365132

  20. Evolution: The Island of Misfit Mammoths.

    PubMed

    Roca, Alfred L

    2015-06-29

    The genomes of two woolly mammoths have been sequenced. One of the last survivors had reduced genetic diversity. Although divergent in their mitochondrial genomes, the mammoths had similar nuclear genomes, a finding germane to elephant conservation. PMID:26126277