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Sample records for colibactin genomic island

  1. 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

  2. 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

  3. 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, Michčle; Olier, Maďwenn; Nougayrčde, 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

  4. 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.

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

    PubMed Central

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

    2013-01-01

    Cellular senescence is an irreversible state of proliferation arrest evoked by a myriad of stresses including oncogene activation, telomere shortening/dysfunction and genotoxic insults. It has been associated with tumor activation, immune suppression and aging, owing to the secretion of proinflammatory mediators. The bacterial genotoxin colibactin, encoded by the pks genomic island is frequently harboured by Escherichia coli strains of the B2 phylogenetic group. Mammalian cells exposed to live pks+ bacteria exhibit DNA-double strand breaks (DSB) and undergo cell-cycle arrest and death. Here we show that cells that survive the acute bacterial infection with pks+ E. coli display hallmarks of cellular senescence: chronic DSB, prolonged cell-cycle arrest, enhanced senescence-associated ?-galactosidase (SA-?-Gal) activity, expansion of promyelocytic leukemia nuclear foci and senescence-associated heterochromatin foci. This was accompanied by reactive oxygen species production and pro-inflammatory cytokines, chemokines and proteases secretion. These mediators were able to trigger DSB and enhanced SA-?-Gal activity in bystander recipient cells treated with conditioned medium from senescent cells. Furthermore, these senescent cells promoted the growth of human tumor cells. In conclusion, the present data demonstrated that the E. coli genotoxin colibactin induces cellular senescence and subsequently propel bystander genotoxic and oncogenic effects. PMID:24116215

  6. 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

  7. The Microbes inside Us and the Race for Colibactin.

    PubMed

    Bode, Helge B

    2015-09-01

    Gut reaction: There is increasing evidence that the impact on human health and disease of the microbes living in and on us has been underestimated. Several of the small molecules produced by "our" bacteria are structurally highly complex and show unusual biosynthetic pathways or modes of action, as highlighted by the race to elucidate the structure and biosynthesis of colibactin, a genotoxic compound produced by human gut bacteria. PMID:26184782

  8. 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

  9. 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

  10. 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

  11. 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.

  12. 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…

  13. 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

  14. 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

  15. Sequence and functional analyses of Haemophilus spp. genomic islands

    PubMed Central

    Juhas, Mario; Power, Peter M; Harding, Rosalind M; Ferguson, David JP; Dimopoulou, Ioanna D; Elamin, Abdel RE; Mohd-Zain, Zaini; Hood, Derek W; Adegbola, Richard; Erwin, Alice; Smith, Arnold; Munson, Robert S; Harrison, Alistair; Mansfield, Lucielle; Bentley, Stephen; Crook, Derrick W

    2007-01-01

    Background A major part of horizontal gene transfer that contributes to the diversification and adaptation of bacteria is facilitated by genomic islands. The evolution of these islands is poorly understood. Some progress was made with the identification of a set of phylogenetically related genomic islands among the Proteobacteria, recognized from the investigation of the evolutionary origins of a Haemophilus influenzae antibiotic resistance island, namely ICEHin1056. More clarity comes from this comparative analysis of seven complete sequences of the ICEHin1056 genomic island subfamily. Results These genomic islands have core and accessory genes in approximately equal proportion, with none demonstrating recent acquisition from other islands. The number of variable sites within core genes is similar to that found in the host bacteria. Furthermore, the GC content of the core genes is similar to that of the host bacteria (38% to 40%). Most of the core gene content is formed by the syntenic type IV secretion system dependent conjugative module and replicative module. GC content and lack of variable sites indicate that the antibiotic resistance genes were acquired relatively recently. An analysis of conjugation efficiency and antibiotic susceptibility demonstrates that phenotypic expression of genomic island-borne genes differs between different hosts. Conclusion Genomic islands of the ICEHin1056 subfamily have a longstanding relationship with H. influenzae and H. parainfluenzae and are co-evolving as semi-autonomous genomes within the 'supragenomes' of their host species. They have promoted bacterial diversity and adaptation through becoming efficient vectors of antibiotic resistance by the recent acquisition of antibiotic resistance transposons. PMID:17996041

  16. 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

  17. Genomic Islands of Uropathogenic Escherichia coli Contribute to Virulence? †

    PubMed Central

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

    2009-01-01

    Uropathogenic Escherichia coli (UPEC) strain CFT073 contains 13 large genomic islands ranging in size from 32 kb to 123 kb. Eleven of these genomic islands were individually deleted from the genome, and nine isogenic mutants were tested for their ability to colonize the CBA/J mouse model of ascending urinary tract infection. Three genomic island mutants (?PAI-aspV, ?PAI-metV, and ?PAI-asnT) were significantly outcompeted by wild-type CFT073 in the bladders and/or kidneys following transurethral cochallenge (P ? 0.0139). The PAI-metV mutant also showed significant attenuation in the ability to independently colonize the kidneys (P = 0.0011). Specific genes within these islands contributed to the observed phenotype, including a previously uncharacterized iron acquisition cluster, fbpABCD (c0294 to c0297 [c0294-97]), autotransporter, picU (c0350), and RTX family exoprotein, tosA (c0363) in the PAI-aspV island. The double deletion mutant with deletions in both copies of the fbp iron acquisition operon (?c0294-97 ?c2518-15) was significantly outcompeted by wild-type CFT073 in cochallenge. Strains with mutations in a type VI secretion system within the PAI-metV island did not show attenuation. The attenuation of the PAI-metV island was localized to genes c3405-10, encoding a putative phosphotransferase transport system, which is common to UPEC and avian pathogenic E. coli strains but absent from E. coli K-12. We have shown that, in addition to encoding virulence genes, genomic islands contribute to the overall fitness of UPEC strain CFT073 in vivo. PMID:19329634

  18. 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

  19. Identification of phage-induced genomic islands in the 13 Streptococcus pyogenes strains using genome barcodes.

    PubMed

    Zhou, Chunbao; Wang, Jiaxin; Wang, Yao; Liang, Yanchun

    2014-01-01

    With the revolutionary invention of the high-throughput sequencing technique, the production of bacterial genomes is significantly sped up. The in silico characterisation of genomic islands (GIs) in the pathogenic bacterium becomes increasingly needed, due to the time consumption and the high cost of the experimental techniques. A GI can be computationally detected through the DNA composition. Barcode, a dimension reduction and visualisation technique of genomic DNA composition, was recently applied to detect different DNA compositions effectively. In this work, we proposed a Barcode-based technique to detect Phage-induced Genomic Islands (PGIs) in the 13 completely sequenced strains of Streptococcus pyogenes. Our experimental results showed that the detected PGIs are highly consistent with the known GIs, the novel PGIs are promising candidates for the clinical diagnosis of S. pyogenes. PMID:25946863

  20. 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

  1. 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

  2. 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.

  3. Comparative Metabolomics and Structural Characterizations Illuminate Colibactin Pathway-Dependent Small Molecules

    PubMed Central

    2015-01-01

    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

  4. A new experimental approach for studying bacterial genomic island evolution identifies island genes with bacterial host-specific expression patterns

    PubMed Central

    Wilson, James W; Nickerson, Cheryl A

    2006-01-01

    Background Genomic islands are regions of bacterial genomes that have been acquired by horizontal transfer and often contain blocks of genes that function together for specific processes. Recently, it has become clear that the impact of genomic islands on the evolution of different bacterial species is significant and represents a major force in establishing bacterial genomic variation. However, the study of genomic island evolution has been mostly performed at the sequence level using computer software or hybridization analysis to compare different bacterial genomic sequences. We describe here a novel experimental approach to study the evolution of species-specific bacterial genomic islands that identifies island genes that have evolved in such a way that they are differentially-expressed depending on the bacterial host background into which they are transferred. Results We demonstrate this approach by using a "test" genomic island that we have cloned from the Salmonella typhimurium genome (island 4305) and transferred to a range of Gram negative bacterial hosts of differing evolutionary relationships to S. typhimurium. Systematic analysis of the expression of the island genes in the different hosts compared to proper controls allowed identification of genes with genera-specific expression patterns. The data from the analysis can be arranged in a matrix to give an expression "array" of the island genes in the different bacterial backgrounds. A conserved 19-bp DNA site was found upstream of at least two of the differentially-expressed island genes. To our knowledge, this is the first systematic analysis of horizontally-transferred genomic island gene expression in a broad range of Gram negative hosts. We also present evidence in this study that the IS200 element found in island 4305 in S. typhimurium strain LT2 was inserted after the island had already been acquired by the S. typhimurium lineage and that this element is likely not involved in the integration or excision of island 4305. Conclusion The "clone-and-transfer" approach of evolutionary study identifies genes whose expression patterns indicate the existence of genera-specific regulatory mechanisms that influence the expression of horizontally-transferred DNA sections. The results provide key information that can be used to facilitate the identification of these regulatory mechanisms. PMID:16396675

  5. 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.

  6. 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

  7. 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

  8. 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

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

    PubMed Central

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

    2012-01-01

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

  10. 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

  11. 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

  12. 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

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

    PubMed Central

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

    2014-01-01

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

  14. Homologous recombination is involved in the diversity of replacement flexible genomic islands in aquatic prokaryotes

    PubMed Central

    López-Pérez, Mario; Martin-Cuadrado, Ana-Belen; Rodriguez-Valera, Francisco

    2014-01-01

    Different strains of the same prokaryotic species, even very similar ones, vary in large regions of their genomes. This flexible genome represents a huge reservoir of diversity that allows prokaryotes to exploit their environment efficiently. Most of the flexible genome is concentrated in genomic islands, some of which are present in all the strains and coding for similar functions but containing different genes. These replacement genomic islands are typically involved in exposed cellular structures, and their diversity has been connected to their recognition as targets by prokaryotic viruses (phages). We have compared genomes of closely related aquatic microbes from different origins and found examples of recent replacement of some of these flexible genomic islands. In all cases, that include Gram positive and negative bacteria and one archaeon, the replaced regions boundaries contain tell-tale peaks of increased, mostly synonymous, nucleotide substitutions. They tended to be sharper at the boundary closest to the origin of replication of the island. We will present the hypothesis that replacement flexible genomic islands are often exchanged by homologous recombination between different clonal frames. These recombination events are possibly selected due to the immediate reward provided by a change in the phage sensitivity spectrum. PMID:24904647

  15. 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

  16. 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

  17. 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

  18. 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

  19. 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

  20. 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

  1. 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...

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

    PubMed Central

    Zhao, Guangyuan; Shen, Wentao; Tuo, Decai; Li, Xiaoying

    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

  3. 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...

  4. 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

  5. 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

  6. 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; Andrčs, Jeremy; Cholley, Pierre-Etienne; Dillies, Marie-Agnčs; Jagla, Bernd; Koechler, Sandrine; Leva, Yann; Magdelenat, Ghislaine; Plewniak, Frédéric; Proux, Caroline; Coppée, Jean-Yves; Bertin, Philippe N.; Heipieper, Hermann J.; Arsčne-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 Carnoulčs 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 Carnoulčs (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

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

    PubMed

    Freel, Kelle C; Krueger, Martin C; Farasin, Julien; Brochier-Armanet, Céline; Barbe, Valérie; Andrčs, Jeremy; Cholley, Pierre-Etienne; Dillies, Marie-Agnčs; Jagla, Bernd; Koechler, Sandrine; Leva, Yann; Magdelenat, Ghislaine; Plewniak, Frédéric; Proux, Caroline; Coppée, Jean-Yves; Bertin, Philippe N; Heipieper, Hermann J; Arsčne-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 Carnoulčs 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 Carnoulčs (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

  8. 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

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

    PubMed Central

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

    2013-01-01

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

  10. 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

  11. Novel Type IV Secretion System Involved in Propagation of Genomic Islands?

    PubMed Central

    Juhas, Mario; Crook, Derrick W.; Dimopoulou, Ioanna D.; Lunter, Gerton; Harding, Rosalind M.; Ferguson, David J. P.; Hood, Derek W.

    2007-01-01

    Type IV secretion systems (T4SSs) mediate horizontal gene transfer, thus contributing to genome plasticity, evolution of infectious pathogens, and dissemination of antibiotic resistance and other virulence traits. A gene cluster of the Haemophilus influenzae genomic island ICEHin1056 has been identified as a T4SS involved in the propagation of genomic islands. This T4SS is novel and evolutionarily distant from the previously described systems. Mutation analysis showed that inactivation of key genes of this system resulted in a loss of phenotypic traits provided by a T4SS. Seven of 10 mutants with a mutation in this T4SS did not express the type IV secretion pilus. Correspondingly, disruption of the genes resulted in up to 100,000-fold reductions in conjugation frequencies compared to those of the parent strain. Moreover, the expression of this T4SS was found to be positively regulated by one of its components, the tfc24 gene. We concluded that this gene cluster represents a novel family of T4SSs involved in propagation of genomic islands. PMID:17122343

  12. 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

  13. 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

  14. 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

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

    PubMed Central

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

    2012-01-01

    Burkholderia pseudomallei, as a saprophytic bacterium that can cause a severe sepsis disease named melioidosis, has preserved several extra genes in its genome for survival. The sequenced genome of the organism showed high diversity contributed mainly from genomic islands (GIs). Comparative genome hybridization (CGH) of 3 clinical and 2 environmental isolates, using whole genome microarrays based on B. pseudomallei K96243 genes, revealed a difference in the presence of genomic islands between clinical and environmental isolates. The largest GI, GI8, of B. pseudomallei was observed as a 2 sub-GI named GIs8.1 and 8.2 with distinguishable %GC content and unequal presence in the genome. GIs8.1, 8.2 and 15 were found to be more common in clinical isolates. A new GI, GI16c, was detected on chromosome 2. Presences of GIs8.1, 8.2, 15 and 16c were evaluated in 70 environmental and 64 clinical isolates using PCR assays. A combination of GIs8.1 and 16c (positivity of either GI) was detected in 70% of clinical isolates and 11.4% of environmental isolates (P<0.001). Using BALB/c mice model, no significant difference of time to mortality was observed between K96243 isolate and three isolates without GIs under evaluation (P>0.05). Some virulence genes located in the absent GIs and the difference of GIs seems to contribute less to bacterial virulence. The PCR detection of 2 GIs could be used as a cost effective and rapid tool to detect potentially virulent isolates that were contaminated in soil. PMID:22675491

  16. 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

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

    PubMed

    Ronca, Sandra; Frossard, Aline; Guerrero, Leandro D; Makhalanyane, Thulani P; Aislabie, Jackie M; Cowan, Don A

    2015-01-01

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

  18. High-Density Transcriptional Initiation Signals Underline Genomic Islands in Bacteria

    PubMed Central

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

    2012-01-01

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

  19. 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

  20. 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

  1. Transcript profiling of the Pseudomonas aeruginosa genomic islands PAGI-2 and pKLC102.

    PubMed

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

    2008-06-01

    The phylogenetically ancient genomic islands of the abundant PAGI-2/pKLC102 family are prone to horizontal gene transfer amongst proteobacteria, and account for most genomic diversity in Pseudomonas aeruginosa. The mRNA expression levels of the sequenced PAGI-2 and pKLC102 islands were determined in P. aeruginosa clone C strains C and SG17M during exponential and stationary growth in Luria broth or Vogel-Bonner mineral medium. Of the 111 ORFs of PAGI-2, only one gene was significantly expressed at a level of more than 0.0001% of total RNA. The individual mRNA transcripts of the 103 pKLC102 ORFs, however, were present in the range of 0.001% to more than 1% in the bacterial RNA population, and amounted altogether to more than 10% of cellular RNA. Homologous genes were strongly transcribed from pKLC102, but not at all from PAGI-2 under the tested conditions. Thus PAGI-2, which was stably captured by its host chromosome, was transcriptionally silent, whereas the mRNA transcripts derived from the mobile and episomally replicating pKLC102 were constitutively more abundant in the cell than the mRNA pool transcribed from the core genome. PMID:18524914

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

    PubMed Central

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

    2012-01-01

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

  3. 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

  4. 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

  5. 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

  6. 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

  7. Diversity of the abundant pKLC102/PAGI-2 family of genomic islands in Pseudomonas aeruginosa.

    PubMed

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

    2007-03-01

    The known genomic islands of Pseudomonas aeruginosa clone C strains are integrated into tRNA(Lys) (pKLC102) or tRNA(Gly) (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

  8. 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

  9. Four genomic islands that mark post-1995 pandemic Vibrio parahaemolyticus isolates

    PubMed Central

    Hurley, Catherine C; Quirke, AnneMarie; Reen, F Jerry; Boyd, E Fidelma

    2006-01-01

    Background Vibrio parahaemolyticus is an aquatic, halophilic, Gram-negative bacterium, first discovered in 1950 in Japan during a food-poisoning outbreak. Infections resulting from consumption of V. parahaemolyticus have increased globally in the last 10 years leading to the bacterium's classification as a newly emerging pathogen. In 1996 the first appearance of a pandemic V. parahaemolyticus clone occurred, a new O3:K6 serotype strain that has now been identified worldwide as a major cause of seafood-borne gastroenteritis. Results We examined the sequenced genome of V. parahaemolyticus RIMD2210633, an O3:K6 serotype strain isolated in Japan in 1996, by bioinformatic analyses to uncover genomic islands (GIs) that may play a role in the emergence and pathogenesis of pandemic strains. We identified 7 regions ranging in size from 10 kb to 81 kb that had the characteristics of GIs such as aberrant base composition compared to the core genome, presence of phage-like integrases, flanked by direct repeats and the absence of these regions from closely related species. Molecular analysis of worldwide clinical isolates of V. parahaemolyticus recovered over the last 33 years demonstrated that a 24 kb region named V. parahaemolyticus island-1 (VPaI-1) encompassing ORFs VP0380 to VP0403 is only present in new O3:K6 and related strains recovered after 1995. We investigated the presence of 3 additional regions, VPaI-4 (VP2131 to VP2144), VPaI-5 (VP2900 to VP2910) and VPaI-6 (VPA1254 to VPA1270) by PCR assays and Southern blot analyses among the same set of V. parahaemolyticus isolates. These 3 VPaI regions also gave similar distribution patterns amongst the 41 strains examined. Conclusion The 4 VPaI regions examined may represent DNA acquired by the pandemic group of V. parahaemolyticus isolates that increased their fitness either in the aquatic environment or in their ability to infect humans. PMID:16672049

  10. Genome sequence of Bradyrhizobium sp. WSM1253; a microsymbiont of Ornithopus compressus from the Greek Island of Sifnos.

    PubMed

    Tiwari, Ravi; Howieson, John; Yates, Ron; Tian, Rui; Held, Britanny; Tapia, Roxanne; Han, Cliff; Seshadri, Rekha; Reddy, T B K; Huntemann, Marcel; Pati, Amrita; Woyke, Tanja; Markowitz, Victor; Ivanova, Natalia; Kyrpides, Nikos; Reeve, Wayne

    2015-01-01

    Bradyrhizobium sp. WSM1253 is a novel N2-fixing bacterium isolated from a root nodule of the herbaceous annual legume Ornithopus compressus that was growing on the Greek Island of Sifnos. WSM1253 emerged as a strain of interest in an Australian program that was selecting inoculant quality bradyrhizobial strains for inoculation of Mediterranean species of lupins (Lupinus angustifolius, L. princei, L. atlanticus, L. pilosus). In this report we describe, for the first time, the genome sequence information and annotation of this legume microsymbiont. The 8,719,808 bp genome has a G?+?C content of 63.09 % with 71 contigs arranged into two scaffolds. The assembled genome contains 8,432 protein-coding genes, 66 RNA genes and a single rRNA operon. This improved-high-quality draft rhizobial genome is one of 20 sequenced through a DOE Joint Genome Institute 2010 Community Sequencing Project. PMID:26629308

  11. 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

  12. 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

  13. 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

  14. Genome-wide Association Study of Biochemical Traits in Kor?ula Island, Croatia

    PubMed Central

    Zemunik, Tatijana; Boban, Mladen; Lauc, Gordan; Jankovi?, Stipan; Rotim, Krešimir; Vatavuk, Zoran; Ben?i?, Goran; ?ogaš, Zoran; Boraska, Vesna; Torlak, Vesela; Sušac, Jelena; Zobi?, Ivana; Rudan, Diana; Pulani?, Dražen; Modun, Darko; Mudni?, Ivana; Gunja?a, Grgo; Budimir, Danijela; Hayward, Caroline; Vitart, Veronique; Wright, Alan F.; Campbell, Harry; Rudan, Igor

    2009-01-01

    Aim To identify genetic variants underlying biochemical traits – total cholesterol, low-density lipoprotein (LDL) cholesterol, high-density lipoprotein (HDL) cholesterol, triglycerides, uric acid, albumin, and fibrinogen, in a genome-wide association study in an isolated population where rare variants of larger effect may be more easily identified. Methods The study included 944 adult inhabitants of the island of Kor?ula, as a part of a larger DNA-based genetic epidemiological study in 2007. Biochemical measurements were performed in a single laboratory with stringent internal and external quality control procedures. Examinees were genotyped using Human Hap370CNV chip by Illumina, with a genome-wide scan containing 346?027 single nucleotide polymorphisms (SNP). Results A total of 31 SNPs were associated with 7 investigated traits at the level of P?genome-wide significance under the assumption of independent multiple testing, replications of previous findings and consistency of association between the identified variants and more than one studied trait make such findings interesting for further functional follow-up studies. Changed allele frequencies in isolate population may contribute to identifying variants that would not be easily identified in much larger samples in outbred populations. PMID:19260141

  15. 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

  16. Relative entropy differences in bacterial chromosomes, plasmids, phages and genomic islands

    PubMed Central

    2012-01-01

    Background We sought to assess whether the concept of relative entropy (information capacity), could aid our understanding of the process of horizontal gene transfer in microbes. We analyzed the differences in information capacity between prokaryotic chromosomes, genomic islands (GI), phages, and plasmids. Relative entropy was estimated using the Kullback-Leibler measure. Results Relative entropy was highest in bacterial chromosomes and had the sequence chromosomes > GI > phage > plasmid. There was an association between relative entropy and AT content in chromosomes, phages, plasmids and GIs with the strongest association being in phages. Relative entropy was also found to be lower in the obligate intracellular Mycobacterium leprae than in the related M. tuberculosis when measured on a shared set of highly conserved genes. Conclusions We argue that relative entropy differences reflect how plasmids, phages and GIs interact with microbial host chromosomes and that all these biological entities are, or have been, subjected to different selective pressures. The rate at which amelioration of horizontally acquired DNA occurs within the chromosome is likely to account for the small differences between chromosomes and stably incorporated GIs compared to the transient or independent replicons such as phages and plasmids. PMID:22325062

  17. 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

  18. 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

  19. Gene islands integrated into tRNA(Gly) genes confer genome diversity on a Pseudomonas aeruginosa clone.

    PubMed

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

    2002-12-01

    Intraclonal genome diversity of Pseudomonas aeruginosa was studied in one of the most diverse mosaic regions of the P. aeruginosa chromosome. The ca. 110-kb large hypervariable region located near the lipH gene in two members of the predominant P. aeruginosa clone C, strain C and strain SG17M, was sequenced. In both strains the region consists of an individual strain-specific gene island of 111 (strain C) or 106 (SG17M) open reading frames (ORFs) and of a 7-kb stretch of clone C-specific sequence of 9 ORFs. The gene islands are integrated into conserved tRNA(Gly) genes and have a bipartite structure. The first part adjacent to the tRNA gene consists of strain-specific ORFs encoding metabolic functions and transporters, the majority of which have homologs of known function in other eubacteria, such as hemophores, cytochrome c biosynthesis, or mercury resistance. The second part is made up mostly of ORFs of yet-unknown function. Forty-seven of these ORFs are mutual homologs with a pairwise amino acid sequence identity of 35 to 88% and are arranged in the same order in the two gene islands. We hypothesize that this novel type of gene island derives from mobile elements which, upon integration, endow the recipient with strain-specific metabolic properties, thus possibly conferring on it a selective advantage in its specific habitat. PMID:12426355

  20. 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

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

    PubMed Central

    Quesada, Jose M.; Soriano, María Isabel

    2012-01-01

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

  2. 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

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

    PubMed Central

    Luo, Peng; Rodrigue, Sébastien; Burrus, Vincent

    2014-01-01

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

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

    PubMed Central

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

    2014-01-01

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

  5. 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

  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. 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

  8. 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

  9. 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...

  10. Genomic islands of divergence in hybridizing Heliconius butterflies identified by large-scale targeted sequencing

    PubMed Central

    Nadeau, Nicola J.; Whibley, Annabel; Jones, Robert T.; Davey, John W.; Dasmahapatra, Kanchon K.; Baxter, Simon W.; Quail, Michael A.; Joron, Mathieu; ffrench-Constant, Richard H.; Blaxter, Mark L.; Mallet, James; Jiggins, Chris D.

    2012-01-01

    Heliconius butterflies represent a recent radiation of species, in which wing pattern divergence has been implicated in speciation. Several loci that control wing pattern phenotypes have been mapped and two were identified through sequencing. These same gene regions play a role in adaptation across the whole Heliconius radiation. Previous studies of population genetic patterns at these regions have sequenced small amplicons. Here, we use targeted next-generation sequence capture to survey patterns of divergence across these entire regions in divergent geographical races and species of Heliconius. This technique was successful both within and between species for obtaining high coverage of almost all coding regions and sufficient coverage of non-coding regions to perform population genetic analyses. We find major peaks of elevated population differentiation between races across hybrid zones, which indicate regions under strong divergent selection. These ‘islands’ of divergence appear to be more extensive between closely related species, but there is less clear evidence for such islands between more distantly related species at two further points along the ‘speciation continuum’. We also sequence fosmid clones across these regions in different Heliconius melpomene races. We find no major structural rearrangements but many relatively large (greater than 1 kb) insertion/deletion events (including gain/loss of transposable elements) that are variable between races. PMID:22201164

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

    PubMed Central

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

    2011-01-01

    Pseudomonas syringae pv. phaseolicola is the causative agent of halo blight in the common bean, Phaseolus vulgaris. P. syringae pv. phaseolicola race 4 strain 1302A contains the avirulence gene avrPphB (syn. hopAR1), which resides on PPHGI-1, a 106 kb genomic island. Loss of PPHGI-1 from P. syringae pv. phaseolicola 1302A following exposure to the hypersensitive resistance response (HR) leads to the evolution of strains with altered virulence. Here we have used fluorescent protein reporter systems to gain insight into the mobility of PPHGI-1. Confocal imaging of dual-labelled P. syringae pv. phaseolicola 1302A strain, F532 (dsRFP in chromosome and eGFP in PPHGI-1), revealed loss of PPHGI-1::eGFP encoded fluorescence during plant infection and when grown in vitro on extracted leaf apoplastic fluids. Fluorescence-activated cell sorting (FACS) of fluorescent and non-fluorescent PPHGI-1::eGFP F532 populations showed that cells lost fluorescence not only when the GI was deleted, but also when it had excised and was present as a circular episome. In addition to reduced expression of eGFP, quantitative PCR on sub-populations separated by FACS showed that transcription of other genes on PPHGI-1 (avrPphB and xerC) was also greatly reduced in F532 cells harbouring the excised PPHGI-1::eGFP episome. Our results show how virulence determinants located on mobile pathogenicity islands may be hidden from detection by host surveillance systems through the suppression of gene expression in the episomal state. PMID:21483484

  12. 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

  13. 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 Ĺ 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 Ĺ 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.

  14. 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

  15. 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

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

    PubMed Central

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

    2010-01-01

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

  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. 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

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

    2014-11-01

    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

  19. 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

  20. 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

  1. 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

  2. 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

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

    PubMed Central

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

    2015-01-01

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

  4. 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

  5. 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

  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

    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

  7. 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

  8. 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

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

    PubMed Central

    2012-01-01

    Background Several strain-specific Klebsiella pneumoniae virulence determinants have been described, though these have almost exclusively been linked with hypervirulent liver abscess-associated strains. Through PCR interrogation of integration hotspots, chromosome walking, island-tagging and fosmid-based marker rescue we captured and sequenced KpGI-5, a novel genomic island integrated into the met56 tRNA gene of K. pneumoniae KR116, a bloodstream isolate from a patient with pneumonia and neutropenic sepsis. Results The 14.0 kb KpGI-5 island exhibited a genome-anomalous G?+?C content, possessed near-perfect 46 bp direct repeats, encoded a ?1-chaperone/usher fimbrial cluster (fim2) and harboured seven other predicted genes of unknown function. Transcriptional analysis demonstrated expression of three fim2 genes, and suggested that the fim2A-fim2K cluster comprised an operon. As fimbrial systems are frequently implicated in pathogenesis, we examined the role of fim2 by analysing KR2107, a streptomycin-resistant derivative of KR116, and three isogenic mutants (?fim, ?fim2 and ?fim?fim2) using biofilm assays, human cell adhesion assays and pair-wise competition-based murine models of intestinal colonization, lung infection and ascending urinary tract infection. Although no statistically significant role for fim2 was demonstrable, liver and kidney CFU counts for lung and urinary tract infection models, respectively, hinted at an ordered gradation of virulence: KR2107 (most virulent), KR2107?fim2, KR2107?fim and KR2107?fim?fim2 (least virulent). Thus, despite lack of statistical evidence there was a suggestion that fim and fim2 contribute additively to virulence in these murine infection models. However, further studies would be necessary to substantiate this hypothesis. Conclusion Although fim2 was present in 13% of Klebsiella spp. strains investigated, no obvious in vitro or in vivo role for the locus was identified, although there were subtle hints of involvement in urovirulence and bacterial dissemination from the respiratory tract. Based on our findings and on parallels with other fimbrial systems, we propose that fim2 has the potential to contribute beneficially to pathogenesis and/or environmental persistence of Klebsiella strains, at least under specific yet-to-be identified conditions. PMID:22520965

  10. Prokaryotic Genomes Eurkaryotic Genomes

    E-print Network

    Qiu, Weigang

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

  11. 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

  12. 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

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

    PubMed

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

    2002-09-01

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

  14. Synthesis of nickel-iron hydrogenase in Cupriavidus metallidurans is controlled by metal-dependent silencing and un-silencing of genomic islands.

    PubMed

    Herzberg, Martin; Schüttau, Marcel; Reimers, Matthias; Große, Cornelia; Hans-Günther-Schlegel; Nies, Dietrich H

    2015-04-01

    Cupriavidus metallidurans CH34 is able to grow autotrophically as a hydrogen-oxidizing bacterium and produces nickel-dependent hydrogenases, even under heterotrophic conditions. Loss of its two native plasmids resulted in inability of the resulting strain AE104 to synthesize the hydrogenases and to grow autotrophically in phosphate-poor, Tris-buffered mineral salts medium (TMM). Three of eleven previously identified catabolic genomic islands (CMGIs; Van Houdt et al., 2009), two of which harbor the genes for the membrane-bound (CMGI-2) and the soluble hydrogenase (CMGI-3), were silenced in strain AE104 when cultivated in phosphate-poor TMM, explaining its inability to produce hydrogenases. Production of the soluble hydrogenase from the aut region 1 of CMGI-3, and concomitant autotrophic growth, was recovered when the gene for the zinc importer ZupT was deleted in strain AE104. The transcriptome of the ?zupT mutant exhibited two up-regulated gene regions compared to its parent strain AE104. Expression of the genes in the aut region 1 increased independently of the presence of added zinc. A second gene region was expressed only under metal starvation conditions. This region encoded a TonB-dependent outer membrane protein, a putative metal chaperone plus paralogs of essential zinc-dependent proteins, indicating the presence of a zinc allocation pathway in C. metallidurans. Thus, expression of the genes for the soluble hydrogenase and the Calvin cycle enzymes on aut region 1 of CMGI-3 of C. metallidurans is under global control and needs efficient ZupT-dependent zinc allocation for a regulatory role, which might be discrimination of nickel. PMID:25720835

  15. 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

  16. 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

  17. Anatahan Island

    Atmospheric Science Data Center

    2013-04-19

    ... 18242). Anatahan Island is one of the Northern Mariana Islands in the western tropical Pacific. These islands are situated along the ... earthquake swarm that suggested the possibility of impending volcanic activity. The Micronesian Megapode is an endangered species of ...

  18. 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.

  19. 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

  20. 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

  1. 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

  2. Canary Islands

    Atmospheric Science Data Center

    2013-04-19

    article title:  The Canary Islands     View Larger Image A multi-angle view of the Canary Islands in a dust storm, February 29, 2000. At left is a true-color ... available at JPL February 29, 2000 - Canary Islands during a dust storm. project:  MISR ...

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

    PubMed Central

    Xu, Youqiang; Yao, Su; Li, Jinxia

    2014-01-01

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

  4. 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

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

    PubMed Central

    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

    2008-01-01

    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

  6. 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

  7. The complete sequence of a heterochromatic island from a higher eukaryote. The Cold Spring Harbor Laboratory, Washington University Genome Sequencing Center, and PE Biosystems Arabidopsis Sequencing Consortium.

    PubMed

    2000-02-01

    Heterochromatin, constitutively condensed chromosomal material, is widespread among eukaryotes but incompletely characterized at the nucleotide level. We have sequenced and analyzed 2.1 megabases (Mb) of Arabidopsis thaliana chromosome 4 that includes 0.5-0.7 Mb of isolated heterochromatin that resembles the chromosomal knobs described by Barbara McClintock in maize. This isolated region has a low density of expressed genes, low levels of recombination and a low incidence of genetrap insertion. Satellite repeats were absent, but tandem arrays of long repeats and many transposons were found. Methylation of these sequences was dependent on chromatin remodeling. Clustered repeats were associated with condensed chromosomal domains elsewhere. The complete sequence of a heterochromatic island provides an opportunity to study sequence determinants of chromosome condensation. PMID:10676819

  8. 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

  9. 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 ...

  10. Siberian Islands

    Atmospheric Science Data Center

    2013-04-16

    ... Distinguishing Clouds from Ice over the East Siberian Sea, Russia     View Larger Image ... clouds from snow and ice. The central portion of Russia's East Siberian Sea, including one of the New Siberian Islands, Novaya ...

  11. 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. ...

  12. 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.

  13. Island Cosmology

    E-print Network

    Sourish Dutta; Tanmay Vachaspati

    2009-04-29

    If the observed dark energy is a cosmological constant, the canonical state of the universe is de Sitter spacetime. In such a spacetime, quantum fluctuations that violate the null energy condition will create islands of matter that, if large enough, may resemble our observable universe. Phenomenological approaches to calculating density fluctuations yield a scale invariant spectrum with suitable amplitude. With time, the island of matter that is our observable universe, re-enters the cosmological constant sea.

  14. 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.

  15. 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

  16. Happy Island

    E-print Network

    Larry McLerran

    2011-05-20

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

  17. Assateague Island is Changing

    E-print Network

    Boynton, Walter R.

    and deposition of sand toward the island interior--allows the barrier island to migrate or rollover westward barrier island oceanbaymainland barrier island oceanbaymainland barrier island oceanbaymainland Bay Ocean "Barrier islands such as Assateague will be especially vulnerable to the effects of climate change and sea

  18. Hawaiian Islands

    NASA Technical Reports Server (NTRS)

    2002-01-01

    This Multiangle Imaging Spectro-Radiometer (MISR) image of five Hawaiian Islands was acquired by the instrument's vertical- viewing (nadir) camera on June 3, 2000. The image shows the islands of Oahu, Molokai, Lanai, Maui, and Kahoolawe. The prevailing Pacific trade winds bring higher levels of rainfall to the eastern slopes of the islands, leading to a greater abundance of vegetation on the windward coasts. The small change in observation angle across the nadir camera's field-of- view causes the right-hand portion of the image to be more affected by Sun glint, making the ocean surface appear brighter. Oahu is the westernmost of the islands seen in this image. Waikiki Beach and the city of Honolulu are located on the southern shore, to the west of Diamond Head caldera. MISR is one of several Earth-observing instruments on the Terra satellite, launched in December 1999. The Terra spacecraft, the flagship of a fleet of satellites dedicated to understanding our global environment, is part of NASA's Earth Sciences Enterprise, a long-term research program dedicated to understanding how human-induced and natural changes affect our world. Image courtesy NASA/GSFC/JPL, MISR Team

  19. 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.

  20. 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

  1. 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....

  2. 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....

  3. 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…

  4. Tropical Islands Jan Verschelde

    E-print Network

    Verschelde, Jan

    Tropical Rain Forest 5 Linear Algebra Jan Verschelde (UIC) Tropical Islands 16 January 2014 5 / 26 #12Tropical Islands Jan Verschelde University of Illinois at Chicago Department of Mathematics Algebraic Geometry Seminar Jan Verschelde (UIC) Tropical Islands 16 January 2014 1 / 26 #12;Tropical Islands

  5. 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

  6. 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

  7. Extreme genomes

    PubMed Central

    DeLong, Edward F

    2000-01-01

    The complete genome sequence of Thermoplasma acidophilum, an acid- and heat-loving archaeon, has recently been reported. Comparative genomic analysis of this 'extremophile' is providing new insights into the metabolic machinery, ecology and evolution of thermophilic archaea. PMID:11178269

  8. Whole-genome plasticity among Mycobacterium avium subspecies: insights from comparative genomic hybridizations.

    PubMed

    Wu, Chia-wei; Glasner, Jeremy; Collins, Michael; Naser, Saleh; Talaat, Adel M

    2006-01-01

    Infection with Mycobacterium avium subsp. paratuberculosis causes Johne's disease in cattle and is also implicated in cases of Crohn's disease in humans. Another closely related strain, M. avium subsp. avium, is a health problem for immunocompromised patients. To understand the molecular pathogenesis of M. avium subspecies, we analyzed the genome contents of isolates collected from humans and domesticated or wildlife animals. Comparative genomic hybridizations indicated distinct lineages for each subspecies where the closest genomic relatedness existed between M. avium subsp. paratuberculosis isolates collected from human and clinical cow samples. Genomic islands (n = 24) comprising 846 kb were present in the reference M. avium subsp. avium strain but absent from 95% of M. avium subsp. paratuberculosis isolates. Additional analysis identified a group of 18 M. avium subsp. paratuberculosis-associated islands comprising 240 kb that were absent from most of the M. avium subsp. avium isolates. Sequence analysis of DNA regions flanking the genomic islands identified three large inversions in addition to several small inversions that could play a role in regulation of gene expression. Analysis of genes encoded in the genomic islands reveals factors that are probably important for various mechanisms of virulence. Overall, M. avium subsp. avium isolates displayed a higher level of genomic diversity than M. avium subsp. paratuberculosis isolates. Among M. avium subsp. paratuberculosis isolates, those from wildlife animals displayed the highest level of genomic rearrangements that were not observed in other isolates. The presented findings will affect the future design of diagnostics and vaccines for Johne's and Crohn's diseases and provide a model for genomic analysis of closely related bacteria. PMID:16385061

  9. Bouvet Island near Antarctica

    Atmospheric Science Data Center

    2013-04-16

    ... Lozier. Bouvet was convinced it was the northernmost tip of Antarctica but could not circumnavigate or land upon the island due to severe ... Bouvet Island location:  Antarctica Atlantic Ocean thumbnail:  ...

  10. 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)

  11. 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....

  12. 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.

  13. 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.

  14. 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....

  15. Island Biogeography Gillian Brooks

    E-print Network

    Jodice, Patrick

    Island Biogeography Gillian Brooks Foundations of Ecology Clemson University #12;Larger the area(c) + zlog(A) Is the relationship between species and area linear? Island Biogeography Theory ­ (1963 Foundation Present ­ Prof. of Entomology at Harvard University #12;Island Biogeography Theory (1963) E

  16. Comparative genomics of Helicobacter pylori

    PubMed Central

    Dong, Quan-Jiang; Wang, Qing; Xin, Ying-Nin; Li, Ni; Xuan, Shi-Ying

    2009-01-01

    Genomic sequences have been determined for a number of strains of Helicobacter pylori (H pylori) and related bacteria. With the development of microarray analysis and the wide use of subtractive hybridization techniques, comparative studies have been carried out with respect to the interstrain differences between H pylori and inter-species differences in the genome of related bacteria. It was found that the core genome of H pylori constitutes 1111 genes that are determinants of the species properties. A great pool of auxillary genes are mainly from the categories of cag pathogenicity islands, outer membrane proteins, restriction-modification system and hypothetical proteins of unknown function. Persistence of H pylori in the human stomach leads to the diversification of the genome. Comparative genomics suggest that a host jump has occurs from humans to felines. Candidate genes specific for the development of the gastric diseases were identified. With the aid of proteomics, population genetics and other molecular methods, future comparative genomic studies would dramatically promote our understanding of the evolution, pathogenesis and microbiology of H pylori. PMID:19705492

  17. 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

  18. 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

  19. 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

  20. 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...

  1. GENOMICS PROTEOMICS

    E-print Network

    Dever, Jennifer A.

    4/22/15 1 GENOMICS & PROTEOMICS I. Overview II. Con;g Assembly III.Genomics Projects IV.Gene expression and the Transcriptome V. Proteomics I. Overview-based database & research interface 2) Establish the loca;on of all genes and annotate

  2. 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

  3. 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

  4. 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

  5. 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

  6. 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...

  7. 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

  8. 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

  9. 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. ...

  10. Reykjavik, Island Praktikumsstelle: Museum, Kunstfestival

    E-print Network

    Nejdl, Wolfgang

    Reykjavik, Island Praktikumsstelle: Museum, Kunstfestival Praktikumszeitraum: Sommer 2005 Mein in Island lebenden, deutsch-schweizer Künstlers Dieter Roth motiviert, die den Kern des diesjährigen städtische Kultureinrichtung Islands als auch für das landesweit größte Kunstfestival tätig zu sein

  11. 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.

  12. 27 CFR 9.113 - North Fork of Long Island.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ...boundaries consist of all the land (and isolated islands including without limitation, Wicopesset Island, Robins Island, Fishers Island, Great Gull Island, Plum Island, and Shelter Island) in the Townships of Riverhead, Shelter Island, and...

  13. 27 CFR 9.113 - North Fork of Long Island.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ...boundaries consist of all the land (and isolated islands including without limitation, Wicopesset Island, Robins Island, Fishers Island, Great Gull Island, Plum Island, and Shelter Island) in the Townships of Riverhead, Shelter Island, and...

  14. 27 CFR 9.113 - North Fork of Long Island.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ...boundaries consist of all the land (and isolated islands including without limitation, Wicopesset Island, Robins Island, Fishers Island, Great Gull Island, Plum Island, and Shelter Island) in the Townships of Riverhead, Shelter Island, and...

  15. 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

  16. 75 FR 51098 - Protection Island and San Juan Islands National Wildlife Refuges, Jefferson, Island, San Juan...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-08-18

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

  17. 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…

  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. 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 ...

  20. 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.

  1. 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…

  2. Japan: Shikoku Island

    Atmospheric Science Data Center

    2013-04-16

    ... aircraft, and island stations in the waters surrounding Japan and Korea. They characterized meteorological conditions, measured the ... entire west end of Honshu Island, which crosses the upper half of the images, is covered with broken clouds. Away from the clouds, the ...

  3. 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.

  4. Genome databases

    SciTech Connect

    Courteau, J.

    1991-10-11

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

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

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

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

  6. 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.

  7. 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…

  8. 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

  9. 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

  10. 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.

  11. The Island Approach.

    ERIC Educational Resources Information Center

    Schroder, Peter C.

    1994-01-01

    Proposes the study of islands to develop a method of integrating sustainable development with sound resource management that can be extrapolated to more complex, highly populated continental coastal areas. (MDH)

  12. Pine Island Glacier

    Atmospheric Science Data Center

    2013-04-16

    ... 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 ...

  13. 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 Nińo 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 Nińo 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.

  14. Small islands adrift

    NASA Astrophysics Data System (ADS)

    Petherick, Anna

    2015-07-01

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

  15. 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)

  16. Pacific Islands Regional Office

    E-print Network

    kinds of dolphins and whales that live in the waters around the Hawaiian Islands, one species has become to harass, hunt, capture or kill, or attempt to do any of these activities to a marine mammal. Activities

  17. 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 `landmarksż along the chromosome and provide researchers information as to how close they may be to a gene or region of int...

  18. 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

  19. 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

  20. 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.

  1. Island species radiation and karyotypic stasis in Pachycladon allopolyploids

    PubMed Central

    2010-01-01

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

  2. 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

  3. CpG island chromatin is shaped by recruitment of ZF-CxxC proteins.

    PubMed

    Blackledge, Neil P; Thomson, John P; Skene, Peter J

    2013-11-01

    Most mammalian gene promoters are embedded within genomic regions called CpG islands, characterized by elevated levels of nonmethylated CpG dinucleotides. Here, we describe recent work demonstrating that CpG islands act as specific nucleation sites for the zinc finger CxxC domain-containing proteins CFP1 and KDM2A. Importantly, both CFP1 and KDM2A are associated with enzymatic activities that modulate specific histone lysine methylation marks. The action of these zinc finger CxxC domain proteins therefore imposes a defined chromatin architecture on CpG islands that distinguishes these important regulatory elements from the surrounding genome. The functional consequence of this CpG island-directed chromatin environment is discussed. PMID:24186071

  4. CpG Island Chromatin Is Shaped by Recruitment of ZF-CxxC Proteins

    PubMed Central

    Blackledge, Neil P.; Thomson, John P.; Skene, Peter J.

    2013-01-01

    Most mammalian gene promoters are embedded within genomic regions called CpG islands, characterized by elevated levels of nonmethylated CpG dinucleotides. Here, we describe recent work demonstrating that CpG islands act as specific nucleation sites for the zinc finger CxxC domain–containing proteins CFP1 and KDM2A. Importantly, both CFP1 and KDM2A are associated with enzymatic activities that modulate specific histone lysine methylation marks. The action of these zinc finger CxxC domain proteins therefore imposes a defined chromatin architecture on CpG islands that distinguishes these important regulatory elements from the surrounding genome. The functional consequence of this CpG island–directed chromatin environment is discussed. PMID:24186071

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

    PubMed

    Siezen, Roland J; van Hylckama Vlieg, Johan E T

    2011-08-30

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

  6. 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

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

  7. 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

  8. 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

  9. 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.

  10. Genomic Evolution of 11 Type Strains within Family Planctomycetaceae

    PubMed Central

    Zhou, Yizhuang; Yang, Linfeng; Liu, Tianxiang; Yang, Jinlong; Chen, Yanling; Su, Longxiang; Xu, Jin; Chen, Jing; Liu, Feng; Chen, Jiapeng; Dai, Wenkui; Ni, Peixiang; Fang, Chengxiang; Yang, Ruifu

    2014-01-01

    The species in family Planctomycetaceae are ideal groups for investigating the origin of eukaryotes. Their cells are divided by a lipidic intracytoplasmic membrane and they share a number of eukaryote-like molecular characteristics. However, their genomic structures, potential abilities, and evolutionary status are still unknown. In this study, we searched for common protein families and a core genome/pan genome based on 11 sequenced species in family Planctomycetaceae. Then, we constructed phylogenetic tree based on their 832 common protein families. We also annotated the 11 genomes using the Clusters of Orthologous Groups database. Moreover, we predicted and reconstructed their core/pan metabolic pathways using the KEGG (Kyoto Encyclopedia of Genes and Genomes) orthology system. Subsequently, we identified genomic islands (GIs) and structural variations (SVs) among the five complete genomes and we specifically investigated the integration of two Planctomycetaceae plasmids in all 11 genomes. The results indicate that Planctomycetaceae species share diverse genomic variations and unique genomic characteristics, as well as have huge potential for human applications. PMID:24489782

  11. 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

  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 From human genome to other

    E-print Network

    Linial, Michal

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

  15. 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.

  16. 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.

  17. 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.

  18. 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 ...

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

    PubMed Central

    Arsčne-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; Ličvremont, 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

  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. Public Health Genomics (PHG)

    Cancer.gov

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

  2. 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.

  3. Ian Cahatol Channel Islands

    E-print Network

    Shahabi, Cyrus

    High Cruz, Jessie West Adams Prep Jimmy Du Temple City High Michael Goulis Palos Verdes High Dana HandyStudents Ian Cahatol Channel Islands Chen, Catherine Palos Verdes High Hayward (Adam) Cox Ridgeview Fallbrook High Garrett Hara Mark Keppel High Hill, Timothy Daniel (Danny) Servite High Kenneth Holstad Long

  4. 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.

  5. 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...

  6. 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...

  7. 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,…

  8. Introduction Orcas Island

    E-print Network

    Brown, Sally

    (T. ordinoides), and Western Terrestrial (T. elegans) - and the Northern Alligator Lizard (Elgaria of the sharp-tailed snake before and had no idea a rare reptile species was found on the island. Blue (All locations are approximate) Outreach and Public Education In order to better educate the public

  9. 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...

  10. 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

  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. 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

  13. 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

  14. 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.

  15. 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.

  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. Personal Genomics, Personalized Medicine,

    E-print Network

    Napp, Nils

    /Science Translational Medicine panel discussion; MLA 2012 #12;Timeline: Human Genome Sequence HSLS, U.Pitt 1995 2014 2000 2003 2007 2007 2010 Human Genome Draft Sequence Complete Human Reference Genome Individual Human of a free living organism: Haemophilus Influenzae #12;Personal Genome Project HSLS, U.Pitt #12;Why get

  18. 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)

  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. 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

  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 (?ST = 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 (?ST = 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. 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. 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.

  4. 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; Sćther, Stein-Are; Sćtre, 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

  5. Linked selection and recombination rate variation drive the evolution of the genomic landscape of differentiation across the speciation continuum of Ficedula flycatchers

    PubMed Central

    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; Sćther, Stein-Are; Sćtre, Glenn-Peter; Török, Janos; Ellegren, Hans

    2015-01-01

    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

  6. 75 FR 61993 - Amendment of Class E Airspace; Kwajalein Island, Marshall Islands, RMI

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-10-07

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

  7. 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

  8. 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.

  9. 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

  10. 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

  11. 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

  12. 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

  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. 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

  15. Rice genomics: current status of genome sequencing.

    PubMed

    Matsumoto, T; Wu, J; Baba, T; Katayose, Y; Yamamoto, K; Sakata, K; Yano, M; Sasaki, T

    2001-01-01

    Since its establishment in 1991, the Rice Genome Research Program (RGP) has produced some basic tools for rice genome analysis, including a cDNA catalogue, a genetic linkage map and a yeast artificial chromosome (YAC)-based physical map. For the further development of rice genomics, RGP launched in 1998 an international collaborative project on rice genome sequencing. A P1-derived artificial chromosome (PAC)-based, sequence-ready physical map has been constructed using the PCR markers from cDNA sequences (expressed sequence tag [EST] markers). Selected PAC clones with 100-150 kb inserts from chromosomes 1 and 6 have been subjected to shotgun sequencing. The assembled genomic sequences, after predicting the gene-coding region, have been published both through a public database and through our website. As of January 2000, 1.9 Mb from 13 PAC clones were published. Future prospects for understanding rice genomic information at the nucleotide level are discussed. PMID:11387985

  16. 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 ...

  17. Thematic Review Conservation of Biodiversity on Islands

    E-print Network

    Thematic Review Conservation of Biodiversity on Islands: The contribution of the United Kingdom............................................................................................. 11 3. THE BIODIVERSITY OF ISLANDS INVOLVED WITH DI PROJECTS ........................................................................................... 49 6. THE DARWIN INITIATIVE'S CONTRIBUTION TO THE CBD'S ISLAND BIODIVERSITY PROGRAMME OF WORK

  18. 40 CFR 81.340 - Rhode Island.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 2011-07-01 2011-07-01 false Rhode Island. 81.340 Section 81.340 Protection of Environment...Attainment Status Designations § 81.340 Rhode Island. Rhode Island—TSP Designated area Does not meet primary...

  19. 40 CFR 81.340 - Rhode Island.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 2012-07-01 2012-07-01 false Rhode Island. 81.340 Section 81.340 Protection of Environment...Attainment Status Designations § 81.340 Rhode Island. Rhode Island—TSP Designated area Does not meet primary...

  20. 40 CFR 81.340 - Rhode Island.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 2013-07-01 2013-07-01 false Rhode Island. 81.340 Section 81.340 Protection of Environment...Attainment Status Designations § 81.340 Rhode Island. Rhode Island—TSP Designated area Does not meet primary...

  1. 40 CFR 81.356 - Virgin Islands.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 2014-07-01 2014-07-01 false Virgin Islands. 81.356 Section 81.356 Protection of Environment...Attainment Status Designations § 81.356 Virgin Islands. Virgin Islands—1971 Sulfur Dioxide NAAQS (Primary and...

  2. 40 CFR 81.340 - Rhode Island.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 2014-07-01 2014-07-01 false Rhode Island. 81.340 Section 81.340 Protection of Environment...Attainment Status Designations § 81.340 Rhode Island. Rhode Island—TSP Designated area Does not meet primary...

  3. 40 CFR 81.340 - Rhode Island.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 2010-07-01 2010-07-01 false Rhode Island. 81.340 Section 81.340 Protection of Environment...Attainment Status Designations § 81.340 Rhode Island. Rhode Island—TSP Designated area Does not meet primary...

  4. 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

  5. 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

  6. 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

  7. Urban heat island

    NASA Technical Reports Server (NTRS)

    Kim, Hongsuk H.

    1991-01-01

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

  8. Pine Island Glacier, Antarctica

    NASA Technical Reports Server (NTRS)

    2001-01-01

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

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

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

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

  9. Metabolic Syndrome in a Metapopulation of Croatian Island Isolates

    PubMed Central

    Kol?i?, Ivana; Vorko-Jovi?, Ariana; Salzer, Branka; Smoljanovi?, Mladen; Kern, Josipa; Vuleti?, 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

  10. Long Island Sound Report Card

    E-print Network

    Boynton, Walter R.

    Long Island Sound Report Card Grading the water quality and ecosystem health of the Urban Sea #12 EasternCentralEastern Narrows The east-west gradient of people and pollution Long Island Sound (100 meters). Both development and density of people increase from east to west along the Sound

  11. 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 ...

  12. 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...

  13. 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...

  14. 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

  15. 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

  16. 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

  17. 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 ...

  18. Not just another genome

    PubMed Central

    2011-01-01

    Sequence analysis of the Daphnia pulex genome holds some surprises that could not have been anticipated from what was learned so far from other arthropod genomes. It establishes Daphnia as an eco-genetical model organism par excellence. PMID:21294909

  19. 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.

  20. Genome synthesis and genomic functional cores

    E-print Network

    Radulescu, Ovidiu

    bacteria live in very good lab conditions there are genomes with more than 60% of genes with unknown, November 2002 Synthesis of a bacterial genome the chromosome will be inserted in a living cell (whose for a minimal set is not easy... Experiments : transposomal mutagenesis E.coli 620 genes / 3746 (Gerdes et al

  1. 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

  2. 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.

  3. 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.

  4. 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.

  5. 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 ...

  6. 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.

  7. International milk genomics consortium

    E-print Network

    Rocke, David M.

    Viewpoint International milk genomics consortium J. Bruce Germana, *, Floyd L. Schanbacherb , Bo Lo The first international symposium on Milk Genomics & Human Health brought scientists from around the world and across the milk research spectrum to the task of annotating the subsets of mammalian genomes responsible

  8. Genome BBiioollooggyy 2008, 99

    E-print Network

    Weng, Zhiping

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

  9. Advances in Whole Genome

    E-print Network

    Ciocan-Fontanine, Ionut

    Advances in Whole Genome Sequencing IMA Public Lecture: Tuesday, May 6, 2003, 7:30 p.m. Moos Tower sequenced genome, the virus Lambda at 50,000 nucleotides, was sequenced via the shotgun method by Sanger that this approach could not be applied to genomes over 100,000 nucleotides long, so a long period followed where

  10. GENOME OF CROCODILEPOX VIRUS

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  11. 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

  12. 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...

  13. 78 FR 58880 - Safety Zone; Catawba Island Club Wedding Event, Catawba Island Club, Catawba Island, OH

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-09-25

    ...Catawba Island Club, Catawba Island, OH ACTION: Temporary final rule...Lake Erie in the vicinity of Port Clinton, OH. This temporary safety zone is necessary...Lake Erie in the vicinity of Port Clinton, OH. The temporary safety zone is...

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

    E-print Network

    , in its caldera lake. VII. Overview and discussion I. W. B. Thornton1 *, S. Cook2 , J. S. Edwards3 , R. D by volcanic eruption in c. 1645, and Motmot, an emergent island in its caldera lake, was re-created in 1968 species-poor islands. The mid-level caldera plateau, as in 1932, was covered in fairly open forest

  15. 33 CFR 334.515 - Blount Island Command and Marine Corps Support Facility-Blount Island; Jacksonville, Florida...

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ...false Blount Island Command and Marine Corps Support Facility-Blount Island...515 Blount Island Command and Marine Corps Support Facility-Blount Island...identified as Blount Island Command and Marine Corps Support Facility-Blount...

  16. 33 CFR 334.515 - Blount Island Command and Marine Corps Support Facility-Blount Island; Jacksonville, Florida...

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ...false Blount Island Command and Marine Corps Support Facility-Blount Island...515 Blount Island Command and Marine Corps Support Facility-Blount Island...identified as Blount Island Command and Marine Corps Support Facility-Blount...

  17. Genome Sequence of the Human Pathogen Vibrio cholerae Amazonia

    PubMed Central

    Thompson, Cristiane C.; Marin, Michel A.; Dias, Graciela M.; Dutilh, Bas E.; Edwards, Robert A.; Iida, Tetsuya; Thompson, Fabiano L.; Vicente, Ana Carolina P.

    2011-01-01

    Vibrio cholerae O1 Amazonia is a pathogen that was isolated from cholera-like diarrhea cases in at least two countries, Brazil and Ghana. Based on multilocus sequence analysis, this lineage belongs to a distinct profile compared to strains from El Tor and classical biotypes. The genomic analysis revealed that it contains Vibrio pathogenicity island 2 and a set of genes related to pathogenesis and fitness, such as the type VI secretion system, present in choleragenic V. cholerae strains. PMID:21952545

  18. 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

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF ENERGY Federal Energy Regulatory Commission PSEG Long Island LLC, Long Island Electric Utility Servco LLC, Long Island Power Authority, Long Island Lighting Company; Notice of Petition for Declaratory Order Take notice that on August 1, 2013, pursuant to Rule...

  19. 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

  20. 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.

  1. 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

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

    PubMed Central

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

    2012-01-01

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

  3. 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

  4. Bacterial Genome Instability

    PubMed Central

    Darmon, Elise

    2014-01-01

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

  5. UCSC genome browser tutorial.

    PubMed

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

    2008-08-01

    The University of California Santa Cruz (UCSC) Genome Bioinformatics website consists of a suite of free, open-source, on-line tools that can be used to browse, analyze, and query genomic data. These tools are available to anyone who has an Internet browser and an interest in genomics. The website provides a quick and easy-to-use visual display of genomic data. It places annotation tracks beneath genome coordinate positions, allowing rapid visual correlation of different types of information. Many of the annotation tracks are submitted by scientists worldwide; the others are computed by the UCSC Genome Bioinformatics group from publicly available sequence data. It also allows users to upload and display their own experimental results or annotation sets by creating a custom track. The suite of tools, downloadable data files, and links to documentation and other information can be found at http://genome.ucsc.edu/. PMID:18514479

  6. 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.

  7. 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.

  8. YOU ARE CORDIALLY INVITED 2011 Long Island

    E-print Network

    Chen, Tsuhan

    YOU ARE CORDIALLY INVITED 2011 Long Island Leader's Forum Wednesday, March 9, 2011 The Long Island Leader's Forum is a valuable and long standing tradition for the horticulture industry on Long Island and success of the green industry on Long Island. Thanks to Fred Soviero, this year's Leader's Forum

  9. 77 FR 51473 - Safety Zone; Bostock 50th Anniversary Fireworks, Long Island Sound; Manursing Island, NY

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-08-24

    ...50th Anniversary Fireworks, Long Island Sound; Manursing Island, NY AGENCY: Coast...on the navigable waters of Long Island Sound in the vicinity of Manursing Island, NY...all vessels from a portion of Long Island Sound before, during, and immediately...

  10. AN EXAMINATION OF MOVEMENTS OF BOTTLENOSE DOLPHINS BETWEEN ISLANDS IN THE HAWAIIAN ISLAND CHAIN

    E-print Network

    Baird, Robin W.

    AN EXAMINATION OF MOVEMENTS OF BOTTLENOSE DOLPHINS BETWEEN ISLANDS IN THE HAWAIIAN ISLAND CHAIN Pivers Island Road, Beaufort, NC 28516 USA 3 4638 14th Street, Boulder, CO 80304 USA July 16, 2002 Report oceanic islands is extremely limited. We photo-identified bottlenose dolphins around the islands of Oahu

  11. Tree diversity on islands: assembly rules, passive sampling and the theory of island

    E-print Network

    ORIGINAL ARTICLE Tree diversity on islands: assembly rules, passive sampling and the theory in a temperate island archipelago. The theory of island biogeography (ToIB) predicts that island area affects species diversity by reducing immigration rates. The passive sampling hypothesis predicts that island area

  12. Enabling responsible public genomics.

    PubMed

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

    2010-01-01

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

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

    E-print Network

    Arianpour, Roozbeh

    2013-02-22

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

  14. 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)

  15. 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....

  16. Island Cosmology in the Landscape

    E-print Network

    Yun-Song Piao

    2008-06-11

    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 well in the observational bound. The results shown here indicate that the island emergently thermalized in the landscape can be consistent with our observable universe.

  17. No Company Is An Island 

    E-print Network

    Maddox, A.

    1989-01-01

    No company is an island. Utilities and their industrial customers are discovering that collaboration can breed opportunity while isolation can lead to ruin. Inter company relationships have changed over recent years and HL&P and its customers...

  18. Tsunami trapping near circular islands

    NASA Astrophysics Data System (ADS)

    Tinti, Stefano; Vannini, Cesare

    1995-09-01

    Trapping of long water waves that are induced by submarine earthquakes and that attack circular islands is studied by applying a theoretical model ( Tinti and Vannini, 1994) that is based on the linear shallow water approximation. The solution is computed as the superposition of the eigenmodes of the water basin. The tsunami trapping is seen in terms of the capability of the source to excite the “trapped” eigenmodes of the basin. The bottom depth dependence around the island is shown to be quite important in determining the trapping capability of the island: a depth profile that is downwardly concave as the distance from the island coasts increases is substantially more efficient in amplifying the incoming waves and in trapping their energy than a profile exhibiting an upward concavity.

  19. The PEDANT genome database

    PubMed Central

    Frishman, Dmitrij; Mokrejs, Martin; Kosykh, Denis; Kastenmüller, Gabi; Kolesov, Grigory; Zubrzycki, Igor; Gruber, Christian; Geier, Birgitta; Kaps, Andreas; Albermann, Kaj; Volz, Andreas; Wagner, Christian; Fellenberg, Matthias; Heumann, Klaus; Mewes, Hans-Werner

    2003-01-01

    The PEDANT genome database (http://pedant.gsf.de) provides exhaustive automatic analysis of genomic sequences by a large variety of established bioinformatics tools through a comprehensive Web-based user interface. One hundred and seventy seven completely sequenced and unfinished genomes have been processed so far, including large eukaryotic genomes (mouse, human) published recently. In this contribution, we describe the current status of the PEDANT database and novel analytical features added to the PEDANT server in 2002. Those include: (i) integration with the BioRS™ data retrieval system which allows fast text queries, (ii) pre-computed sequence clusters in each complete genome, (iii) a comprehensive set of tools for genome comparison, including genome comparison tables and protein function prediction based on genomic context, and (iv) computation and visualization of protein–protein interaction (PPI) networks based on experimental data. The availability of functional and structural predictions for 650 000 genomic proteins in well organized form makes PEDANT a useful resource for both functional and structural genomics. PMID:12519983

  20. Upolu Island, Western Samoa

    NASA Technical Reports Server (NTRS)

    2000-01-01

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

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

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

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

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

  1. Upolu Island, Western Samoa

    NASA Technical Reports Server (NTRS)

    2000-01-01

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

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

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

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

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

  2. 46 CFR 7.80 - Tybee Island, GA to St. Simons Island, GA.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... Tybee Island south of the entrance to Buck Hammock Creek. (b) A line drawn from the southernmost extremity of Little Tybee Island at Beach Hammock to the easternmost extremity of Wassaw Island. (c) A...

  3. 46 CFR 7.80 - Tybee Island, GA to St. Simons Island, GA.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... Tybee Island south of the entrance to Buck Hammock Creek. (b) A line drawn from the southernmost extremity of Little Tybee Island at Beach Hammock to the easternmost extremity of Wassaw Island. (c) A...

  4. 46 CFR 7.80 - Tybee Island, GA to St. Simons Island, GA.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... Tybee Island south of the entrance to Buck Hammock Creek. (b) A line drawn from the southernmost extremity of Little Tybee Island at Beach Hammock to the easternmost extremity of Wassaw Island. (c) A...

  5. 46 CFR 7.80 - Tybee Island, GA to St. Simons Island, GA.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... Tybee Island south of the entrance to Buck Hammock Creek. (b) A line drawn from the southernmost extremity of Little Tybee Island at Beach Hammock to the easternmost extremity of Wassaw Island. (c) A...

  6. 46 CFR 7.80 - Tybee Island, GA to St. Simons Island, GA.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... Tybee Island south of the entrance to Buck Hammock Creek. (b) A line drawn from the southernmost extremity of Little Tybee Island at Beach Hammock to the easternmost extremity of Wassaw Island. (c) A...

  7. 77 FR 34894 - Safety Zone; Bostock 50th Anniversary Fireworks, Long Island Sound; Manursing Island, NY

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-06-12

    ...Safety Zone; Bostock 50th Anniversary Fireworks, Long Island Sound; Manursing Island...vicinity of Manursing Island, NY for a fireworks display. This temporary safety zone...vessels from the hazards associated with fireworks displays. This rule is intended to...

  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, 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...

  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. 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...

  12. 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...

  13. 76 FR 19781 - Protection Island and San Juan Islands National Wildlife Refuges, Jefferson, San Juan, Skagit...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-04-08

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

  14. 78 FR 63860 - Amendment of Class D Airspace; Kwajalein Island, Marshall Islands, RMI

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-10-25

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

  15. Characterization and fine localization of two new genes in Xq28 using the genomic sequence/EST database screening approach

    SciTech Connect

    Faranda, S.; Frattini, A.; Zucchi, I.

    1996-06-15

    Two new genes were identified and mapped by searching the EST databases with genomic sequences obtained from putative CpG islands of the rodent-human hybrid X3000. Previous mapping of these CpG islands in the proximity of the host cell factor (HCFC1) and GdX genes automatically localized these two new genes to Xq28 in the interval between the L1 cell adhesion molecule (L1CAM) and the glucose-6-phosphate dehydrogenase (G6PD) loci. Both genes are relatively short, contain an ORF of 261 and 105 amino acids, respectively, and are ubiquitously expressed. Combining sequencing of selected CpG islands, derived from hybrids containing small portions of the human genome, with an EST database search is an easy method of identifying and mapping new genes to specific regions of the genome. 17 refs., 4 figs.

  16. Local genomic adaptation of coral reef-associated microbiomes to gradients of natural variability

    E-print Network

    Smith, Jennifer E.

    Local genomic adaptation of coral reef-associated microbiomes to gradients of natural variability-specific associations between macro- and microorganisms. On coral reefs, the benthic coverage of coral and algal from 22 coral reefs at 11 Line Islands in the central Pacific that together span a wide range

  17. Draft Genome Sequence of the Shellfish Larval Probiotic Bacillus pumilus RI06-95

    PubMed Central

    Hamblin, Meagan; Spinard, Edward; Gomez-Chiarri, Marta; Nelson, David R.

    2015-01-01

    Bacillus pumilus RI06-95 is a marine bacterium isolated in Narragansett, Rhode Island, which has shown probiotic activity against marine pathogens in larval shellfish. We report the genome of B. pumilus RI06-95, which provides insight into the microbe’s probiotic ability and may be used in future studies of the probiotic mechanism. PMID:26337873

  18. ORIGINAL ARTICLE A genome-wide analysis of 'Bounty' descendants implicates

    E-print Network

    Nyholt, Dale R.

    (*) Genomics Research Centre, Griffith Health Institute, Griffith University, Queensland 4222, Australia e-related genes suggests a disrupted sero- toninergic system that is perhaps specific to the Norfolk Island. Charlesworth Menzies Research Institute, University of Tasmania, Hobart, Tasmania 7000, Australia S. Macgregor

  19. Complete Genome Sequence of the Subsurface, Mesophilic Sulfate-Reducing Bacterium Desulfovibrio aespoeensis Aspo-2

    PubMed Central

    Bengtsson, Andreas; Edlund, Johanna; Rabe, Lisa; Hazen, Terry; Chakraborty, Romy; Goodwin, Lynne; Shapiro, Nicole

    2014-01-01

    Desulfovibrio aespoeensis Aspo-2, DSM 10631T, is a mesophilic, hydrogenotrophic sulfate-reducing bacterium sampled from a 600-m-deep subsurface aquifer in hard rock under the island of Äspö in southeastern Sweden. We report the genome sequence of this bacterium, which is a 3,629,109-bp chromosome; plasmids were not found. PMID:24874683

  20. Planning the Genome Institute's Future

    E-print Network

    Botstein, David

    floors of a house, resting on a foundation of the Human Genome Project, with "Genomics to Society" on top planning that society will realize the scientific and public health benefits of the Human Genome Project. It has been a genome community tradi- tion since before there was a Human Genome Project, and NHGRI

  1. State of cat genomics.

    PubMed

    O'Brien, Stephen J; Johnson, Warren; Driscoll, Carlos; Pontius, Joan; Pecon-Slattery, Jill; Menotti-Raymond, Marilyn

    2008-06-01

    Our knowledge of cat family biology was recently expanded to include a genomics perspective with the completion of a draft whole genome sequence of an Abyssinian cat. The utility of the new genome information has been demonstrated by applications ranging from disease gene discovery and comparative genomics to species conservation. Patterns of genomic organization among cats and inbred domestic cat breeds have illuminated our view of domestication, revealing linkage disequilibrium tracks consequent of breed formation, defining chromosome exchanges that punctuated major lineages of mammals and suggesting ancestral continental migration events that led to 37 modern species of Felidae. We review these recent advances here. As the genome resources develop, the cat is poised to make a major contribution to many areas in genetics and biology. PMID:18471926

  2. Genomics of sorghum.

    PubMed

    Paterson, Andrew H

    2008-01-01

    Sorghum (Sorghum bicolor (L.) Moench) is a subject of plant genomics research based on its importance as one of the world's leading cereal crops, a biofuels crop of high and growing importance, a progenitor of one of the world's most noxious weeds, and a botanical model for many tropical grasses with complex genomes. A rich history of genome analysis, culminating in the recent complete sequencing of the genome of a leading inbred, provides a foundation for invigorating progress toward relating sorghum genes to their functions. Further characterization of the genomes other than Saccharinae cereals may shed light on mechanisms, levels, and patterns of evolution of genome size and structure, laying the foundation for further study of sugarcane and other economically important members of the group. PMID:18483564

  3. Smith/Birnstiel mapping of genome rearrangements in Pseudomonas aeruginosa.

    PubMed

    Heuer, T; Bürger, C; Tümmler, B

    1998-04-01

    A novel application of the Smith/Birnstiel technique is presented for the analysis of intraspecies genomic diversity in small genomes. Rare-cutter total/N frequent-cutter partial restriction digestions are separated in N separate lanes by pulsed-field gel electrophoresis, blotted and hybridized with rare-cutter fragment ends as probes. The evaluation of the autoradiogram results in high-resolution restriction maps of 10-200 kbp regions. The technique was applied to the analysis of genome rearrangements in Pseudomonas aeruginosa strains. Comparison of the region encoding the tryptophan biosynthesis genes in the PAO and the IATS serotype 5 strains revealed that shared sequence characterized by almost identical restriction fingerprints was interrupted in the serotype 5 strain by small islands displaying strain-specific restriction site signatures. A multistep rearrangement in a hypervariable chromosome region downstream of the phn locus was detected in serial airway isolates from a patient with cystic fibrosis. PMID:9588793

  4. Complete genome sequence of Arcanobacterium haemolyticum type strain (11018T)

    PubMed Central

    Yasawong, Montri; Teshima, Hazuki; Lapidus, Alla; Nolan, Matt; Lucas, Susan; Glavina Del Rio, Tijana; Tice, Hope; Cheng, Jan-Fang; Bruce, David; Detter, Chris; Tapia, Roxanne; Han, Cliff; Goodwin, Lynne; Pitluck, Sam; Liolios, Konstantinos; Ivanova, Natalia; Mavromatis, Konstantinos; Mikhailova, Natalia; Pati, Amrita; Chen, Amy; Palaniappan, Krishna; Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D.; Rohde, Manfred; Sikorski, Johannes; Pukall, Rüdiger; Göker, Markus; Woyke, Tanja; Bristow, James; Eisen, Jonathan A.; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C.; Klenk, Hans-Peter

    2010-01-01

    Arcanobacterium haemolyticum (ex MacLean et al. 1946) Collins et al. 1983 is the type species of the genus Arcanobacterium, which belongs to the family Actinomycetaceae. The strain is of interest because it is an obligate parasite of the pharynx of humans and farm animal; occasionally, it causes pharyngeal or skin lesions. It is a Gram-positive, nonmotile and non-sporulating bacterium. The strain described in this study was isolated from infections amongst American soldiers of certain islands of the North and West Pacific. This is the first completed sequence of a member of the genus Arcanobacterium and the ninth type strain genome from the family Actinomycetaceae. The 1,986,154 bp long genome with its 1,821 protein-coding and 64 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project. PMID:21304742

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

    E-print Network

    , in its caldera lake. V. Colonization by ®gs (Ficus spp.), their dispersers and pollinators M. Shanahan1 activity in the early 1950s produced a series of temporary islands in the volcano's caldera lake. One

  6. Treeline Dynamics on Southern Vancouver Island, British Columbia

    E-print Network

    Smith, Dan

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

  7. phiGENOME: an integrative navigation throughout bacteriophage genomes.

    PubMed

    Stano, Matej; Klucar, Lubos

    2011-11-01

    phiGENOME is a web-based genome browser generating dynamic and interactive graphical representation of phage genomes stored in the phiSITE, database of gene regulation in bacteriophages. phiGENOME is an integral part of the phiSITE web portal (http://www.phisite.org/phigenome) and it was optimised for visualisation of phage genomes with the emphasis on the gene regulatory elements. phiGENOME consists of three components: (i) genome map viewer built using Adobe Flash technology, providing dynamic and interactive graphical display of phage genomes; (ii) sequence browser based on precisely formatted HTML tags, providing detailed exploration of genome features on the sequence level and (iii) regulation illustrator, based on Scalable Vector Graphics (SVG) and designed for graphical representation of gene regulations. Bringing 542 complete genome sequences accompanied with their rich annotations and references, makes phiGENOME a unique information resource in the field of phage genomics. PMID:21824513

  8. Instability of Pathogenicity Islands in Uropathogenic Escherichia coli 536

    PubMed Central

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

    2004-01-01

    The uropathogenic Escherichia coli strain 536 carries at least five genetic elements on its chromosome that meet all criteria characteristic of pathogenicity islands (PAIs). One main feature of these distinct DNA regions is their instability. We applied the so-called island-probing approach and individually labeled all five PAIs of E. coli 536 with the counterselectable marker sacB to evaluate the frequency of PAI-negative colonies under the influence of different environmental conditions. Furthermore, we investigated the boundaries of these PAIs. According to our experiments, PAI II536 and PAI III536 were the most unstable islands followed by PAI I536 and PAI V536, whereas PAI IV536 was stable. In addition, we found that deletion of PAI II536 and PAI III536 was induced by several environmental stimuli. Whereas excision of PAI I536, PAI II536, and PAI V536 was based on site-specific recombination between short direct repeat sequences at their boundaries, PAI III536 was deleted either by site-specific recombination or by homologous recombination between two IS100-specific sequences. In all cases, deletion is thought to lead to the formation of nonreplicative circular intermediates. Such extrachromosomal derivatives of PAI II536 and PAI III536 were detected by a specific PCR assay. Our data indicate that the genome content of uropathogenic E. coli can be modulated by deletion of PAIs. PMID:15126470

  9. 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

  10. Between Two Fern Genomes

    PubMed Central

    2014-01-01

    Ferns are the only major lineage of vascular plants not represented by a sequenced nuclear genome. This lack of genome sequence information significantly impedes our ability to understand and reconstruct genome evolution not only in ferns, but across all land plants. Azolla and Ceratopteris are ideal and complementary candidates to be the first ferns to have their nuclear genomes sequenced. They differ dramatically in genome size, life history, and habit, and thus represent the immense diversity of extant ferns. Together, this pair of genomes will facilitate myriad large-scale comparative analyses across ferns and all land plants. Here we review the unique biological characteristics of ferns and describe a number of outstanding questions in plant biology that will benefit from the addition of ferns to the set of taxa with sequenced nuclear genomes. We explain why the fern clade is pivotal for understanding genome evolution across land plants, and we provide a rationale for how knowledge of fern genomes will enable progress in research beyond the ferns themselves. PMID:25324969

  11. Fungal Genomics Program

    SciTech Connect

    Grigoriev, Igor

    2012-03-12

    The JGI Fungal Genomics Program aims to scale up sequencing and analysis of fungal genomes to explore the diversity of fungi important for energy and the environment, and to promote functional studies on a system level. Combining new sequencing technologies and comparative genomics tools, JGI is now leading the world in fungal genome sequencing and analysis. Over 120 sequenced fungal genomes with analytical tools are available via MycoCosm (www.jgi.doe.gov/fungi), a web-portal for fungal biologists. Our model of interacting with user communities, unique among other sequencing centers, helps organize these communities, improves genome annotation and analysis work, and facilitates new larger-scale genomic projects. This resulted in 20 high-profile papers published in 2011 alone and contributing to the Genomics Encyclopedia of Fungi, which targets fungi related to plant health (symbionts, pathogens, and biocontrol agents) and biorefinery processes (cellulose degradation, sugar fermentation, industrial hosts). Our next grand challenges include larger scale exploration of fungal diversity (1000 fungal genomes), developing molecular tools for DOE-relevant model organisms, and analysis of complex systems and metagenomes.

  12. Evolutionary genomics of Entamoeba.

    PubMed

    Weedall, Gareth D; Hall, Neil

    2011-01-01

    Entamoeba histolytica is a human pathogen that causes amoebic dysentery and leads to significant morbidity and mortality worldwide. Understanding the genome and evolution of the parasite will help explain how, when and why it causes disease. Here we review current knowledge about the evolutionary genomics of Entamoeba: how differences between the genomes of different species may help explain different phenotypes, and how variation among E. histolytica parasites reveals patterns of population structure. The imminent expansion of the amount genome data will greatly improve our knowledge of the genus and of pathogenic species within it. PMID:21288488

  13. 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.

  14. Comparative genomics of 12 strains of Erwinia amylovora identifies a pan-genome with a large conserved core.

    PubMed

    Mann, Rachel A; Smits, Theo H M; Bühlmann, Andreas; Blom, Jochen; Goesmann, Alexander; Frey, Jürg E; Plummer, Kim M; Beer, Steven V; Luck, Joanne; Duffy, Brion; Rodoni, Brendan

    2013-01-01

    The plant pathogen Erwinia amylovora can be divided into two host-specific groupings; strains infecting a broad range of hosts within the Rosaceae subfamily Spiraeoideae (e.g., Malus, Pyrus, Crataegus, Sorbus) and strains infecting Rubus (raspberries and blackberries). Comparative genomic analysis of 12 strains representing distinct populations (e.g., geographic, temporal, host origin) of E. amylovora was used to describe the pan-genome of this major pathogen. The pan-genome contains 5751 coding sequences and is highly conserved relative to other phytopathogenic bacteria comprising on average 89% conserved, core genes. The chromosomes of Spiraeoideae-infecting strains were highly homogeneous, while greater genetic diversity was observed between Spiraeoideae- and Rubus-infecting strains (and among individual Rubus-infecting strains), the majority of which was attributed to variable genomic islands. Based on genomic distance scores and phylogenetic analysis, the Rubus-infecting strain ATCC BAA-2158 was genetically more closely related to the Spiraeoideae-infecting strains of E. amylovora than it was to the other Rubus-infecting strains. Analysis of the accessory genomes of Spiraeoideae- and Rubus-infecting strains has identified putative host-specific determinants including variation in the effector protein HopX1(Ea) and a putative secondary metabolite pathway only present in Rubus-infecting strains. PMID:23409014

  15. The Future of Microbial Genomics

    SciTech Connect

    Kyrpides, Nikos

    2010-06-02

    Nikos Kyrpides, head of the Genome Biology group at the DOE Joint Genome Institute discusses current challenges in the field of microbial genomics on June 2, 2010 at the "Sequencing, Finishing, Analysis in the Future" meeting in Santa Fe, NM

  16. Ginny Scholtes Genomics and Medicine

    E-print Network

    Brutlag, Doug

    Ginny Scholtes Genomics and Medicine Professor Douglas Brutlag December 2, 2010 How Hard Could It Be? The Integration of Personal Genomics into Medical Practice Personal genomics carries incredible potential to revolutionize the way

  17. Genome Statute and Legislation Database

    MedlinePLUS

    ... History Initiative Finding Reliable Health Information Online Genetic & Genomic Science and Research Genetic & Rare Diseases Information Center (GARD) Genetic Disorders, Genomics & Healthcare Genomic Medicine Online Health Resources For Health ...

  18. Resources | Office of Cancer Genomics

    Cancer.gov

    The Center for Cancer Genomics (CCG) was established to unify the National Cancer Institute's activities in cancer genomics, with the goal of advancing genomics research and translating findings into the clinic to improve the precise diagnosis and treatment of cancers.

  19. The Cancer Genome Atlas (TCGA)

    Cancer.gov

    The Cancer Genome Atlas (TCGA) is a comprehensive and coordinated effort to accelerate our understanding of the molecular basis of cancer through the application of genome analysis technologies, including large-scale genome sequencing.

  20. Genomic analysis of mouse tumorigenesis

    E-print Network

    Tam, Mandy Chi-Mun

    2006-01-01

    The availability of the human and mouse genome sequences has spurred a growing interest in analyzing mouse models of human cancer using genomic techniques. Comparative genomic studies on mouse and human tumors can be ...

  1. Genomes of surface isolates of Alteromonas macleodii: the life of a widespread marine opportunistic copiotroph

    PubMed Central

    López-Pérez, Mario; Gonzaga, Aitor; Martin-Cuadrado, Ana-Belen; Onyshchenko, Olga; Ghavidel, Akbar; Ghai, Rohit; Rodriguez-Valera, Francisco

    2012-01-01

    Alteromonas macleodii is a marine gammaproteobacterium with widespread distribution in temperate or tropical waters. We describe three genomes of isolates from surface waters around Europe (Atlantic, Mediterranean and Black Sea) and compare them with a previously described deep Mediterranean isolate (AltDE) that belongs to a widely divergent clade. The surface isolates are quite similar, the most divergent being the Black Sea (BS11) isolate. The genomes contain several genomic islands with different gene content. The recruitment of very similar genomic fragments from metagenomes in different locations indicates that the surface clade is globally abundant with little effect of geography, even the AltDE and the BS11 genomes recruiting from surface samples in open ocean locations. The finding of CRISPR protospacers of AltDE in a lysogenic phage in the Atlantic (English Channel) isolate illustrates a flow of genetic material among these clades and a remarkably wide distribution of this phage. PMID:23019517

  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. Genomics and Bioinformatics Doug Brutlag

    E-print Network

    Structural Genomics Systems Biology #12;Databases Machine Learning Robotics Statistics & Probability Artificial Intelligence Graph Theory Information Theory Algorithms Genomics, Bioinformatics & Computational Biology

  4. 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

  5. Photosymbiotic ascidians from Pari Island (Thousand Islands, Indonesia)

    PubMed Central

    Hirose, Euichi; Iskandar, Budhi Hascaryo; Wardiatno, Yusli

    2014-01-01

    Abstract 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

  6. FUNCTIONAL GENOMICS Mouse ENCODE

    E-print Network

    Petrov, Dmitri

    FUNCTIONAL GENOMICS Mouse ENCODE The authors outline the focus of the encyclopaedia of mouse DNA elements (Mouse ENCODE), which is already underway. The project will functionally annotate the mouse genome using the same experimental pipelines that were established for human ENCODE. Mouse ENCODE aims to add

  7. GENOME OF HORSEPOX VIRUS

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Here we present the genomic sequence of horsepox virus (HSPV) isolate MNR-76, an orthopoxvirus (OPV) isolated in 1976 from diseased Mongolian horses. The 212 kbp genome contained 7.5 kbp inverted terminal repeats (ITR) and lacked extensive terminal tandem repetition. HSPV contained 236 ORFs with sim...

  8. Genetics and Genomics

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Good progress is being made on genetics and genomics of sugar beet, however it is in process and the tools are now being generated and some results are being analyzed. The GABI BeetSeq project released a first draft of the sugar beet genome of KWS2320, a dihaploid (see http://bvseq.molgen.mpg.de/Gen...

  9. Genome Medicine 2009, 11

    E-print Network

    Genome Medicine 2009, 11::39 Research AA kkeerrnneell--bbaasseedd iinntteeggrraattiioonn ooff biology due to alternative splicing, post-translational modifications, as well as the influence. Published: 3 April 2009 Genome Medicine 2009, 11::39 (doi:10.1186/gm39) The electronic version

  10. | Office of Cancer Genomics

    Cancer.gov

    Dr. Louis Staudt, a member of the National Academy of Sciences, is a leading expert in lymphoma research within NCI’s intramural research program. He was recently named the Director of the Center for Cancer Genomics (CCG), the organization that encompasses the Office of Cancer Genomics. In this short interview, Dr. Staudt discusses the objectives, challenges, and future directions of the Center.

  11. Genomics for Weed Science

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Numerous genomic-based studies have provided insight to the physiological and evolutionary processes involved in developmental and environmental processes of model plants such as arabidopsis and rice. However, far fewer efforts have been attempted to use genomic resources to study physiological and ...

  12. 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

  13. 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

  14. 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

  15. 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

  16. 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

  17. 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

  18. 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

  19. 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

  20. 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

  1. 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

  2. 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

  3. 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

  4. 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

  5. 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

  6. 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

  7. 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

  8. Microbial Genomes Multiply

    NASA Technical Reports Server (NTRS)

    Doolittle, Russell F.

    2002-01-01

    The publication of the first complete sequence of a bacterial genome in 1995 was a signal event, underscored by the fact that the article has been cited more than 2,100 times during the intervening seven years. It was a marvelous technical achievement, made possible by automatic DNA-sequencing machines. The feat is the more impressive in that complete genome sequencing has now been adopted in many different laboratories around the world. Four years ago in these columns I examined the situation after a dozen microbial genomes had been completed. Now, with upwards of 60 microbial genome sequences determined and twice that many in progress, it seems reasonable to assess just what is being learned. Are new concepts emerging about how cells work? Have there been practical benefits in the fields of medicine and agriculture? Is it feasible to determine the genomic sequence of every bacterial species on Earth? The answers to these questions maybe Yes, Perhaps, and No, respectively.

  9. 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.

  10. 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

  11. 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

  12. 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

  13. 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...

  14. Bidding the CpG island goodbye

    PubMed Central

    2013-01-01

    Experiments on seven vertebrates suggest that identifying the locations of islands of non-methylated DNA provides more insights into evolutionarily-conserved epigenetic regulatory elements than studies of CpG islands. PMID:23467495

  15. 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.

  16. Mass Wasting in the Western Galapagos Islands 

    E-print Network

    Hall, Hillary

    2012-10-19

    Oceanic island volcanoes such as those in the Hawaiian, Canary and Galapagos Islands are known to become unstable, causing failures of the subaerial and submarine slopes of the volcanic edifices. These mass wasting events appear to be the primary...

  17. 33 CFR 334.1070 - San Francisco Bay between Treasure Island and Yerba Buena Island; naval restricted area.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... false San Francisco Bay between Treasure Island...Island; naval restricted area. 334.1070 Section...DANGER ZONE AND RESTRICTED AREA REGULATIONS § 334.1070 San Francisco Bay between Treasure Island...Island; naval restricted area. (a) The area....

  18. 33 CFR 110.6 - Portland Harbor, Portland, Maine (between Little Diamond Island and Great Diamond Island).

    Code of Federal Regulations, 2010 CFR

    2010-07-01

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

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

    Code of Federal Regulations, 2011 CFR

    2011-07-01

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

  20. 9 CFR 72.3 - Areas quarantined in the Virgin Islands of the United States, the Northern Mariana Islands, the...

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... Islands of the United States, the Northern Mariana Islands, the Commonwealth of Puerto Rico, and the... Mariana Islands, the Commonwealth of Puerto Rico, and the Island of Guam. The entire Territories of the... Commonwealth of Puerto Rico are quarantined....

  1. 9 CFR 72.3 - Areas quarantined in the Virgin Islands of the United States, the Northern Mariana Islands, the...

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... Islands of the United States, the Northern Mariana Islands, the Commonwealth of Puerto Rico, and the... Mariana Islands, the Commonwealth of Puerto Rico, and the Island of Guam. The entire Territories of the... Commonwealth of Puerto Rico are quarantined....

  2. 9 CFR 72.3 - Areas quarantined in the Virgin Islands of the United States, the Northern Mariana Islands, the...

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... Islands of the United States, the Northern Mariana Islands, the Commonwealth of Puerto Rico, and the... Mariana Islands, the Commonwealth of Puerto Rico, and the Island of Guam. The entire Territories of the... Commonwealth of Puerto Rico are quarantined....

  3. 9 CFR 72.3 - Areas quarantined in the Virgin Islands of the United States, the Northern Mariana Islands, the...

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... Islands of the United States, the Northern Mariana Islands, the Commonwealth of Puerto Rico, and the... Mariana Islands, the Commonwealth of Puerto Rico, and the Island of Guam. The entire Territories of the... Commonwealth of Puerto Rico are quarantined....

  4. 33 CFR 110.6 - Portland Harbor, Portland, Maine (between Little Diamond Island and Great Diamond Island).

    Code of Federal Regulations, 2012 CFR

    2012-07-01

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

  5. 33 CFR 110.6 - Portland Harbor, Portland, Maine (between Little Diamond Island and Great Diamond Island).

    Code of Federal Regulations, 2013 CFR

    2013-07-01

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

  6. 33 CFR 110.6 - Portland Harbor, Portland, Maine (between Little Diamond Island and Great Diamond Island).

    Code of Federal Regulations, 2014 CFR

    2014-07-01

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

  7. 33 CFR 334.1420 - Pacific Ocean off Orote Point, Apra Harbor, Island of Guam, Marianas Islands; small arms firing...

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... Pacific Ocean off Orote Point, Apra Harbor, Island of Guam, Marianas Islands; small arms firing range. 334.1420 Section... Pacific Ocean off Orote Point, Apra Harbor, Island of Guam, Marianas Islands; small arms firing...

  8. 33 CFR 334.1070 - San Francisco Bay between Treasure Island and Yerba Buena Island; naval restricted area.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ...2014-07-01 false San Francisco Bay between Treasure Island and Yerba Buena Island; naval restricted area. 334.1070 Section...334.1070 San Francisco Bay between Treasure Island and Yerba Buena Island; naval restricted...

  9. 33 CFR 334.1420 - Pacific Ocean off Orote Point, Apra Harbor, Island of Guam, Marianas Islands; small arms firing...

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... Pacific Ocean off Orote Point, Apra Harbor, Island of Guam, Marianas Islands; small arms firing range. 334.1420 Section... Pacific Ocean off Orote Point, Apra Harbor, Island of Guam, Marianas Islands; small arms firing...

  10. 33 CFR 334.1070 - San Francisco Bay between Treasure Island and Yerba Buena Island; naval restricted area.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ...2013-07-01 false San Francisco Bay between Treasure Island and Yerba Buena Island; naval restricted area. 334.1070 Section...334.1070 San Francisco Bay between Treasure Island and Yerba Buena Island; naval restricted...

  11. 33 CFR 334.1070 - San Francisco Bay between Treasure Island and Yerba Buena Island; naval restricted area.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ...2012-07-01 false San Francisco Bay between Treasure Island and Yerba Buena Island; naval restricted area. 334.1070 Section...334.1070 San Francisco Bay between Treasure Island and Yerba Buena Island; naval restricted...

  12. 33 CFR 334.1420 - Pacific Ocean off Orote Point, Apra Harbor, Island of Guam, Marianas Islands; small arms firing...

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... Pacific Ocean off Orote Point, Apra Harbor, Island of Guam, Marianas Islands; small arms firing range. 334.1420 Section... Pacific Ocean off Orote Point, Apra Harbor, Island of Guam, Marianas Islands; small arms firing...

  13. 33 CFR 334.1420 - Pacific Ocean off Orote Point, Apra Harbor, Island of Guam, Marianas Islands; small arms firing...

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... Pacific Ocean off Orote Point, Apra Harbor, Island of Guam, Marianas Islands; small arms firing range. 334.1420 Section... Pacific Ocean off Orote Point, Apra Harbor, Island of Guam, Marianas Islands; small arms firing...

  14. 33 CFR 334.1420 - Pacific Ocean off Orote Point, Apra Harbor, Island of Guam, Marianas Islands; small arms firing...

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... Pacific Ocean off Orote Point, Apra Harbor, Island of Guam, Marianas Islands; small arms firing range. 334.1420 Section... Pacific Ocean off Orote Point, Apra Harbor, Island of Guam, Marianas Islands; small arms firing...

  15. 33 CFR 334.1070 - San Francisco Bay between Treasure Island and Yerba Buena Island; naval restricted area.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ...2011-07-01 false San Francisco Bay between Treasure Island and Yerba Buena Island; naval restricted area. 334.1070 Section...334.1070 San Francisco Bay between Treasure Island and Yerba Buena Island; naval restricted...

  16. Small island biogeography in the Gulf of California: lizards, the subsidized island

    E-print Network

    Wait, D. Alexander

    Small island biogeography in the Gulf of California: lizards, the subsidized island biogeography the subsidized island biogeography (SIB) hypothesis, which predicts that spatial subsidies may cause insular. Methods To evaluate the SIB hypothesis, we first identified subsidized and unsubsidized islands based

  17. 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.

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

    E-print Network

    Qiu, Bo

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

  19. Two-fluid magnetic island dynamics in slab geometry: Determination of the island phase velocity

    E-print Network

    Fitzpatrick, Richard

    Two-fluid magnetic island dynamics in slab geometry: Determination of the island phase velocity R geometry: Determination of the island phase velocity R. Fitzpatrick, P. G. Watson, and F. L. Waelbroeck the phase-velocity of a comparatively wide, isolated, magnetic island, formed as a result of a nonlinear

  20. The Skirted Island: The Effect of Topography on the Flow Around Planetary Scale Islands

    E-print Network

    Pedlosky, Joseph

    The Skirted Island: The Effect of Topography on the Flow Around Planetary Scale Islands by Joseph ^ Corresponding author: e-mail, jpedlosky@whoi.edu #12;2 ABSTRACT The flow around planetary scale islands is examined when the island possesses a topographic skirt representing a steep continental shelf. The model

  1. 46 CFR 7.85 - St. Simons Island, GA to Little Talbot Island, FL.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ...2014-10-01 2014-10-01 false St. Simons Island, GA to Little Talbot Island, FL. 7.85 Section 7.85 Shipping ...LINES Atlantic Coast § 7.85 St. Simons Island, GA to Little Talbot Island, FL. (a) A line...

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

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ...2013-10-01 2013-10-01 false St. Simons Island, GA to Little Talbot Island, FL. 7.85 Section 7.85 Shipping ...LINES Atlantic Coast § 7.85 St. Simons Island, GA to Little Talbot Island, FL. (a) A line...

  3. 50 CFR Appendix E to Part 622 - Caribbean Island/Island Group Management Areas

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 2014-10-01 2014-10-01 false Caribbean Island/Island Group Management Areas E Appendix E to Part 622...622, App. E Appendix E to Part 622—Caribbean Island/Island Group Management Areas Table 1 of...

  4. The Status of Island Scrub Oak (Quercus pacifica) on Catalina Island, California1

    E-print Network

    The Status of Island Scrub Oak (Quercus pacifica) on Catalina Island, California1 Denise A. Knapp2 The island scrub oak is characterized by a shrubby (to 2 meters) or arborescent (to 5 meters or taller) growth form. It is the dominant species of the scrub oak chaparral community on Catalina Island, which

  5. 50 CFR Appendix E to Part 622 - Caribbean Island/Island Group Management Areas

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 2013-10-01 2013-10-01 false Caribbean Island/Island Group Management Areas E Appendix E to Part 622...622, App. E Appendix E to Part 622—Caribbean Island/Island Group Management Areas Table 1 of...

  6. 33 CFR 80.717 - Tybee Island, GA to St. Simons Island, GA.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 2013-07-01 2013-07-01 false Tybee Island, GA to St. Simons Island, GA. 80.717 Section 80.717 Navigation...DEMARCATION LINES Seventh District § 80.717 Tybee Island, GA to St. Simons Island, GA. (a) A...

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

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ...2010-10-01 2010-10-01 false St. Simons Island, GA to Little Talbot Island, FL. 7.85 Section 7.85 Shipping ...LINES Atlantic Coast § 7.85 St. Simons Island, GA to Little Talbot Island, FL. (a) A line...

  8. 33 CFR 80.717 - Tybee Island, GA to St. Simons Island, GA.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 2011-07-01 2011-07-01 false Tybee Island, GA to St. Simons Island, GA. 80.717 Section 80.717 Navigation...DEMARCATION LINES Seventh District § 80.717 Tybee Island, GA to St. Simons Island, GA. (a) A...

  9. 33 CFR 80.717 - Tybee Island, GA to St. Simons Island, GA.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 2010-07-01 2010-07-01 false Tybee Island, GA to St. Simons Island, GA. 80.717 Section 80.717 Navigation...DEMARCATION LINES Seventh District § 80.717 Tybee Island, GA to St. Simons Island, GA. (a) A...

  10. 46 CFR 7.85 - St. Simons Island, GA to Little Talbot Island, FL.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ...2011-10-01 2011-10-01 false St. Simons Island, GA to Little Talbot Island, FL. 7.85 Section 7.85 Shipping ...LINES Atlantic Coast § 7.85 St. Simons Island, GA to Little Talbot Island, FL. (a) A line...

  11. 33 CFR 80.717 - Tybee Island, GA to St. Simons Island, GA.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 2014-07-01 2014-07-01 false Tybee Island, GA to St. Simons Island, GA. 80.717 Section 80.717 Navigation...DEMARCATION LINES Seventh District § 80.717 Tybee Island, GA to St. Simons Island, GA. (a) A...

  12. 46 CFR 7.85 - St. Simons Island, GA to Little Talbot Island, FL.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ...2012-10-01 2012-10-01 false St. Simons Island, GA to Little Talbot Island, FL. 7.85 Section 7.85 Shipping ...LINES Atlantic Coast § 7.85 St. Simons Island, GA to Little Talbot Island, FL. (a) A line...

  13. 33 CFR 80.717 - Tybee Island, GA to St. Simons Island, GA.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 2012-07-01 2012-07-01 false Tybee Island, GA to St. Simons Island, GA. 80.717 Section 80.717 Navigation...DEMARCATION LINES Seventh District § 80.717 Tybee Island, GA to St. Simons Island, GA. (a) A...

  14. A household carbon footprint calculator for islands: Case study of the United States Virgin Islands

    E-print Network

    Kammen, Daniel M.

    Survey A household carbon footprint calculator for islands: Case study of the United States Virgin xxxx Keywords: Carbon footprint Green house gas emissions Small Island Developing States Island regions the carbon footprint of typical households within the US Virgin Islands. We find the average carbon footprint

  15. Fuzzy Genome Sequence Assembly for Single and Environmental Genomes

    E-print Network

    Nicolescu, Monica

    and to the first genome sequence as- sembly, Bacteriophage X174 [38]. In 1990 the Human Genome Project in 2003, two years before its projected date. #12;2 Sara Nasser, et al In 1993 The Institute for Genome advancements in technology that lead the to complete sequencing of the Human Genome and the H. influenzae

  16. COMPUTATIONAL GENOMICS: MAPPING, COMPARISON, AND ANNOTATION OF GENOMES

    E-print Network

    address key issues in the different stages of genome research: planning of a genome sequencing project areas: (1) In relation to the early stages of a genome project, we address physical mapping, and we structure and sequence analysis of orthologous human and mouse genomic regions, and develop ROSETTA

  17. Eukaryotic Genomics Data from the DOE Joint Genome Institute (JGI)

    DOE Data Explorer

    From the JGI webportal users can choose Eukaryotic genomes from a photo list, access the JGI FTP directories to download data files, use the Tree of Life navigation tool, or choose a genome and go directly to a website specific to that one genome. The individual sites include direct access to download sequence files, BLAST, search, view and navigate the genomic annotations.

  18. Center for Cancer Genomics | Office of Cancer Genomics

    Cancer.gov

    The Center for Cancer Genomics (CCG) was established to unify the National Cancer Institute's activities in cancer genomics, with the goal of advancing genomics research and translating findings into the clinic to improve the precise diagnosis and treatment of cancers. In addition to promoting genomic sequencing approach

  19. Unraveling the 3D genome: genomics tools for multiscale exploration

    E-print Network

    Straight, Aaron

    Unraveling the 3D genome: genomics tools for multiscale exploration Viviana I. Risca and William J genome and the roles it may play in regulating transcription. Here we review core methods and new tools-scale chromosomal domains, and discuss the emerging pic- ture of the 3D genome that these tools have revealed. Blind

  20. Update on Genomic Studies of Algae Paths toward Algal Genomics

    E-print Network

    Update on Genomic Studies of Algae Paths toward Algal Genomics Arthur R. Grossman* The Carnegie the expression of genes. In this introductory manuscript, I discuss select algae and how genomics is impacting our understanding of these organisms. Four algae for which near-full genome information has become

  1. 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.

  2. Virgin Islands Water Resources Research Institute Annual Technical Report

    E-print Network

    Island, St. John, St. Thomas and St. Croix. The islands are principally of volcanic origin and relyVirgin Islands Water Resources Research Institute Annual Technical Report FY 2009 Virgin Islands Islands are a Territory of the United States. The Territory consists of four principal islands - Water

  3. Comparative primate genomics: emerging patterns of genome content and dynamics

    PubMed Central

    Rogers, Jeffrey; Gibbs, Richard A.

    2014-01-01

    Preface Advances in genome sequencing technologies have created new opportunities for comparative primate genomics. Genome assemblies have been published for several primates, with analyses of several others underway. Whole genome assemblies for the great apes provide remarkable new information about the evolutionary origins of the human genome and the processes involved. Genomic data for macaques and other nonhuman primates provide valuable insight into genetic similarities and differences among species used as models for disease-related research. This review summarizes current knowledge regarding primate genome content and dynamics and offers a series of goals for the near future. PMID:24709753

  4. Annual Fish Passage Report -Rock Island Dam

    E-print Network

    Annual Fish Passage Report - Rock Island Dam Columbia River, Washington, 1965 By Paul D. Zimmer L. McKeman, Director Annual Fish Passage Report - Rock Island Dam Columbia River, Washington, 1965;#12;Annual Fish Passage Report - Rock Island Dam Columbia River, Washington, 1965 By PAUL D. ZIMMER, Fishery

  5. ANNUAL FISH PASSAGE REPORT ROCK ISLAND DAM

    E-print Network

    ANNUAL FISH PASSAGE REPORT ROCK ISLAND DAM COLUMBIA RIVER, WASHINGTON 1960 . SPECIAL SCIENTIFIC ISLAND DAM COLUMBIA RIVER, WASHINGTON, 1960 by Paul D. Zimmer and Clifton C. Davidson United States Fish This annual report of fishway operations at Rock Island Dam in 1960 is dedicated to the memory of co

  6. ANNUAL FISH PASSAGE REPORT ROCK ISLAND DAM

    E-print Network

    ANNUAL FISH PASSAGE REPORT ROCK ISLAND DAM COLUMBIA RIVER, WASHINGTON, 1959 :y .iiJA/i-3ri ^' WUUUi. ANNUAL FISH PASSAGE REPORT - ROCK ISLAND DAM COLUMBIA RIVER, WASHINGTON, 1959 by Paul D. Zimmer, Clifton and observations 10 Summary 13 #12;#12;ANNUAL FISH PASSAGE REPORT - ROCK ISLAND DAM COLUMBIA RIVER, WASHINGTON

  7. ANNUAL FISH PASSAGE REPORT ROCK ISLAND DAM

    E-print Network

    42) ANNUAL FISH PASSAGE REPORT ROCK ISLAND DAM COLUMBIA RIVER, WASHINGTON 1961 Marine Biological. McKeman, Director ANNUAL FISH PASSAGE REPORT - ROCK ISLAND DAM COLUMBIA RIVER, WASHINGTON, 1961--Fisheries No. 421 Washington, D. C. April 1962 #12;Rock Island Dam, Columbia River, Washington ii #12;CONTENTS

  8. Early Hominin Biogeography in Island Southeast Asia

    E-print Network

    Stanier, Charlie

    becoming extinct during the period in which Homo sapiens colonized the region. In 1859, Alfred RussellARTICLE Early Hominin Biogeography in Island Southeast Asia ROY LARICK AND RUSSELL L. CIOCHON. Cutting between island landmasses, Wallace's Line separates Sunda and the Eastern Island Arc (the Arc

  9. 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…

  10. 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...

  11. 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...

  12. 40 CFR 81.356 - Virgin Islands.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 2011-07-01 2011-07-01 false Virgin Islands. 81.356 Section 81.356 Protection of Environment...Attainment Status Designations § 81.356 Virgin Islands. Virgin Islands—SO2 Designated area Does not meet primary...

  13. 40 CFR 81.356 - Virgin Islands.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 2013-07-01 2013-07-01 false Virgin Islands. 81.356 Section 81.356 Protection of Environment...Attainment Status Designations § 81.356 Virgin Islands. Virgin Islands—SO2 Designated area Does not meet primary...

  14. Island-finding ability of marine turtles

    E-print Network

    Hays, Graeme

    Island-finding ability of marine turtles Graeme C. Hays1* , Susanne AĘ kesson2 , Annette C grounds along the Brazilian coast to Ascension Island to nest, over 2200 km distant in the middle of the equatorial Atlantic. To test the hypothesis that turtles use wind-borne cues to locate Ascension Island we

  15. 27 CFR 9.170 - Long Island.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ...2012-04-01 2012-04-01 false Long Island. 9.170 Section 9.170 Alcohol...Viticultural Areas § 9.170 Long Island. (a) Name. The name of the viticultural...area described in this section is “Long Island.” (b) Approved maps. The...

  16. 27 CFR 9.170 - Long Island.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ...2013-04-01 2013-04-01 false Long Island. 9.170 Section 9.170 Alcohol...Viticultural Areas § 9.170 Long Island. (a) Name. The name of the viticultural...area described in this section is “Long Island.” (b) Approved maps. The...

  17. 40 CFR 81.356 - Virgin Islands.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 2012-07-01 2012-07-01 false Virgin Islands. 81.356 Section 81.356 Protection of Environment...Attainment Status Designations § 81.356 Virgin Islands. Virgin Islands—SO2 Designated area Does not meet primary...

  18. 27 CFR 9.170 - Long Island.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ...2010-04-01 2010-04-01 false Long Island. 9.170 Section 9.170 Alcohol...Viticultural Areas § 9.170 Long Island. (a) Name. The name of the viticultural...area described in this section is “Long Island.” (b) Approved maps. The...

  19. Island Biogeography of Populations: An Introduced Species

    E-print Network

    Losos, Jonathan B.

    Island Biogeography of Populations: An Introduced Species Transforms Survival Patterns Thomas W of the underlying basis for the theoretical structure of island biogeography, have received little direct study. We determined a key population trait--survival--in the Bahamian lizard Anolis sagrei on islands

  20. 27 CFR 9.170 - Long Island.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ...2014-04-01 2014-04-01 false Long Island. 9.170 Section 9.170 Alcohol...Viticultural Areas § 9.170 Long Island. (a) Name. The name of the viticultural...area described in this section is “Long Island.” (b) Approved maps. The...

  1. SEDIMENT MANAGEMENT OPTIONS FOR GALVESTON ISLAND, TEXAS

    E-print Network

    US Army Corps of Engineers

    1 SEDIMENT MANAGEMENT OPTIONS FOR GALVESTON ISLAND, TEXAS ASHLEY E. FREY1 , ANDREW MORANG1 , DAVID.C.Thomas@usace.army.mil Abstract: Galveston Island is a major tourist and commercial center on the Gulf of Mexico at the mouth while the beach west of the Seawall has severely eroded. In order to protect the island and ensure

  2. 27 CFR 9.170 - Long Island.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ...2011-04-01 2011-04-01 false Long Island. 9.170 Section 9.170 Alcohol...Viticultural Areas § 9.170 Long Island. (a) Name. The name of the viticultural...area described in this section is “Long Island.” (b) Approved maps. The...

  3. 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.

  4. he volcanic Hawaiian Islands are the most

    E-print Network

    Baird, Robin W.

    RESEARCH t he volcanic Hawaiian Islands are the most isolated archipelago in the world. They sit spinner dolphins in the main Hawaiian Islands one of the more well-studied populations of dolphins the west coast of Hawai`i ­ `the big island'. Within just a few kilometres of shore the bottom drops

  5. 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

  6. Hymenoptera Genome Database: integrating genome annotations in HymenopteraMine.

    PubMed

    Elsik, Christine G; Tayal, Aditi; Diesh, Colin M; Unni, Deepak R; Emery, Marianne L; Nguyen, Hung N; Hagen, Darren E

    2016-01-01

    We report an update of the Hymenoptera Genome Database (HGD) (http://HymenopteraGenome.org), a model organism database for insect species of the order Hymenoptera (ants, bees and wasps). HGD maintains genomic data for 9 bee species, 10 ant species and 1 wasp, including the versions of genome and annotation data sets published by the genome sequencing consortiums and those provided by NCBI. A new data-mining warehouse, HymenopteraMine, based on the InterMine data warehousing system, integrates the genome data with data from external sources and facilitates cross-species analyses based on orthology. New genome browsers and annotation tools based on JBrowse/WebApollo provide easy genome navigation, and viewing of high throughput sequence data sets and can be used for collaborative genome annotation. All of the genomes and annotation data sets are combined into a single BLAST server that allows users to select and combine sequence data sets to search. PMID:26578564

  7. Hymenoptera Genome Database: integrating genome annotations in HymenopteraMine

    PubMed Central

    Elsik, Christine G.; Tayal, Aditi; Diesh, Colin M.; Unni, Deepak R.; Emery, Marianne L.; Nguyen, Hung N.; Hagen, Darren E.

    2016-01-01

    We report an update of the Hymenoptera Genome Database (HGD) (http://HymenopteraGenome.org), a model organism database for insect species of the order Hymenoptera (ants, bees and wasps). HGD maintains genomic data for 9 bee species, 10 ant species and 1 wasp, including the versions of genome and annotation data sets published by the genome sequencing consortiums and those provided by NCBI. A new data-mining warehouse, HymenopteraMine, based on the InterMine data warehousing system, integrates the genome data with data from external sources and facilitates cross-species analyses based on orthology. New genome browsers and annotation tools based on JBrowse/WebApollo provide easy genome navigation, and viewing of high throughput sequence data sets and can be used for collaborative genome annotation. All of the genomes and annotation data sets are combined into a single BLAST server that allows users to select and combine sequence data sets to search. PMID:26578564

  8. Draft Genome Sequences of Corynebacterium kroppenstedtii CNM633/14 and CNM632/14, Multidrug-Resistant and Antibiotic-Sensitive Isolates from Nodules of Granulomatous Mastitis Patients

    PubMed Central

    Soriano, Francisco; Ariza-Miguel, Jaime; Marrodan-Ciordia, Teresa; Acedo, Alberto; Hernandez, Marta; Tauch, Andreas

    2015-01-01

    Corynebacterium kroppenstedtii has been associated with infections of the female breast. Genome sequencing of two strains revealed a specific genomic island in the multidrug-resistant isolate CNM633/14 with similarity to the R plasmid pJA144188 of Corynebacterium resistens DSM 45100, being indicative of the horizontal transfer of antibiotic resistance genes to C. kroppenstedtii. PMID:25999560

  9. The Genome Channel and Genome Annotation Consortium

    SciTech Connect

    Uberbacher, E.; Mural, R.; Shah, M.

    1997-09-01

    Human and model organism sequencing projects will soon be producing data at a rate which will require new methods and infrastructure for users to be able to effectively view and understand the data. A multi-institutional project was recently funded to provide large-scale analytical processing capabilities and the authors present the results of several pilot efforts related to this project. The goals of the project are as follows: provide an environment where annotation can be constructed based on multiple interoperable analysis tools and significant available computing power; provide an environment where characterization of long genomic sequence regions can be facilitated and analysis can maintained and updated over time; provide an interactive graphical environment where predictions, features and evidence from many tools can be combined by users into high-quality annotation and visualized by the community; provide high-throughput automated analysis methods which can be configured by genome centers for their use in constructing annotation and facilitating data submission; provide high-quality annotation to large genomic sequence regions which would otherwise go unannotated; and provide the community with the best sequence level view of genomes possible. The components of this system are a number of services, a broker that oversees the distribution and management of tasks and a data warehouse, with services implemented using distributed object technology. Multiple gene prediction is accomplished using several gene finding tools including the GRAIL-EST system and gene annotation from databases such as Genbank is also captured. The data warehouse supporting the Genome Channel view is updated daily by automated Internet agents and event triggers which facilitate analysis procedures.

  10. Genome engineering reveals large dispensable regions in Bacillus subtilis.

    PubMed

    Westers, Helga; Dorenbos, Ronald; van Dijl, Jan Maarten; Kabel, Jorrit; Flanagan, Tony; Devine, Kevin M; Jude, Florence; Seror, Simone J; Beekman, Aaron C; Darmon, Elise; Eschevins, Caroline; de Jong, Anne; Bron, Sierd; Kuipers, Oscar P; Albertini, Alessandra M; Antelmann, Haike; Hecker, Michael; Zamboni, Nicola; Sauer, Uwe; Bruand, Claude; Ehrlich, Dusko S; Alonso, Juan C; Salas, Margarita; Quax, Wim J

    2003-12-01

    Bacterial genomes contain 250 to 500 essential genes, as suggested by single gene disruptions and theoretical considerations. If this view is correct, the remaining nonessential genes of an organism, such as Bacillus subtilis, have been acquired during evolution in its perpetually changing ecological niches. Notably, approximately 47% of the approximately 4,100 genes of B. subtilis belong to paralogous gene families in which several members have overlapping functions. Thus, essential gene functions will outnumber essential genes. To answer the question to what extent the most recently acquired DNA contributes to the life of B. subtilis under standard laboratory growth conditions, we initiated a "reconstruction" of the B. subtilis genome by removing prophages and AT-rich islands. Stepwise deletion of two prophages (SPbeta, PBSX), three prophage-like regions, and the largest operon of B. subtilis (pks) resulted in a genome reduction of 7.7% and elimination of 332 genes. The resulting strain was phenotypically characterized by metabolic flux analysis, proteomics, and specific assays for protein secretion, competence development, sporulation, and cell motility. We show that genome engineering is a feasible strategy for functional analysis of large gene clusters, and that removal of dispensable genomic regions may pave the way toward an optimized Bacillus cell factory. PMID:12949151

  11. Experimental assessment of the accuracy of genomic selection in sugarcane.

    PubMed

    Gouy, M; Rousselle, Y; Bastianelli, D; Lecomte, P; Bonnal, L; Roques, D; Efile, J-C; Rocher, S; Daugrois, J; Toubi, L; Nabeneza, S; Hervouet, C; Telismart, H; Denis, M; Thong-Chane, A; Glaszmann, J C; Hoarau, J-Y; Nibouche, S; Costet, L

    2013-10-01

    Sugarcane cultivars are interspecific hybrids with an aneuploid, highly heterozygous polyploid genome. The complexity of the sugarcane genome is the main obstacle to the use of marker-assisted selection in sugarcane breeding. Given the promising results of recent studies of plant genomic selection, we explored the feasibility of genomic selection in this complex polyploid crop. Genetic values were predicted in two independent panels, each composed of 167 accessions representing sugarcane genetic diversity worldwide. Accessions were genotyped with 1,499 DArT markers. One panel was phenotyped in Reunion Island and the other in Guadeloupe. Ten traits concerning sugar and bagasse contents, digestibility and composition of the bagasse, plant morphology, and disease resistance were used. We used four statistical predictive models: bayesian LASSO, ridge regression, reproducing kernel Hilbert space, and partial least square regression. The accuracy of the predictions was assessed through the correlation between observed and predicted genetic values by cross validation within each panel and between the two panels. We observed equivalent accuracy among the four predictive models for a given trait, and marked differences were observed among traits. Depending on the trait concerned, within-panel cross validation yielded median correlations ranging from 0.29 to 0.62 in the Reunion Island panel and from 0.11 to 0.5 in the Guadeloupe panel. Cross validation between panels yielded correlations ranging from 0.13 for smut resistance to 0.55 for brix. This level of correlations is promising for future implementations. Our results provide the first validation of genomic selection in sugarcane. PMID:23907359

  12. Genome Sequencing and Cancer

    PubMed Central

    Mardis, Elaine R.

    2012-01-01

    New technologies for DNA sequencing, coupled with advanced analytical approaches, are now providing unprecedented speed and precision in decoding human genomes. This combination of technology and analysis, when applied to the study of cancer genomes, is revealing specific and novel information about the fundamental genetic mechanisms that underlie cancer’s development and progression. This review outlines the history of the past several years of development in this realm, and discusses the current and future applications that will further elucidate cancer’s genomic causes. PMID:22534183

  13. Human Genome Project

    SciTech Connect

    Block, S.; Cornwall, J.; Dally, W.; Dyson, F.; Fortson, N.; Joyce, G.; Kimble, H. J.; Lewis, N.; Max, C.; Prince, T.; Schwitters, R.; Weinberger, P.; Woodin, W. H.

    1998-01-04

    The study reviews Department of Energy supported aspects of the United States Human Genome Project, the joint National Institutes of Health/Department of Energy program to characterize all human genetic material, to discover the set of human genes, and to render them accessible for further biological study. The study concentrates on issues of technology, quality assurance/control, and informatics relevant to current effort on the genome project and needs beyond it. Recommendations are presented on areas of the genome program that are of particular interest to and supported by the Department of Energy.

  14. Human Genome Program

    SciTech Connect

    Not Available

    1993-01-01

    The DOE Human Genome program has grown tremendously, as shown by the marked increase in the number of genome-funded projects since the last workshop held in 1991. The abstracts in this book describe the genome research of DOE-funded grantees and contractors and invited guests, and all projects are represented at the workshop by posters. The 3-day meeting includes plenary sessions on ethical, legal, and social issues pertaining to the availability of genetic data; sequencing techniques, informatics support; and chromosome and cDNA mapping and sequencing.

  15. HISTORIC WETLANDS OF PRUDENCE ISLAND

    EPA Science Inventory

    Ten wetland sites around Narragansett Bay, Rhode Island have been selected for a multidisciplinary study. These wetland sites are being studied to develop indicators of "wetland health." The study includes assessing the ecological conditions of the wetlands in the past, and the c...

  16. On a Crowded Desert Island.

    ERIC Educational Resources Information Center

    Rothstein, Samuel

    1989-01-01

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

  17. Birds are islands for parasites

    PubMed Central

    Koop, Jennifer A. H.; DeMatteo, Karen E.; Parker, Patricia G.; Whiteman, Noah K.

    2014-01-01

    Understanding the mechanisms driving the extraordinary diversification of parasites is a major challenge in evolutionary biology. Co-speciation, one proposed mechanism that could contribute to this diversity is hypothesized to result from allopatric co-divergence of host–parasite populations. We found that island populations of the Galápagos hawk (Buteo galapagoensis) and a parasitic feather louse species (Degeeriella regalis) exhibit patterns of co-divergence across variable temporal and spatial scales. Hawks and lice showed nearly identical population genetic structure across the Galápagos Islands. Hawk population genetic structure is explained by isolation by distance among islands. Louse population structure is best explained by hawk population structure, rather than isolation by distance per se, suggesting that lice tightly track the recent population histories of their hosts. Among hawk individuals, louse populations were also highly structured, suggesting that hosts serve as islands for parasites from an evolutionary perspective. Altogether, we found that host and parasite populations may have responded in the same manner to geographical isolation across spatial scales. Allopatric co-divergence is likely one important mechanism driving the diversification of parasites. PMID:25099959

  18. UV - VIRGIN ISLANDS NATIONAL PARK

    EPA Science Inventory

    Brewer 144 is located in Virgin Islands NP, measuring ultraviolet solar radiation. Irradiance and column ozone are derived from this data. Ultraviolet solar radiation is measured with a Brewer Mark IV, single-monochrometer, spectrophotometer manufactured by SCI-TEC Instruments, I...

  19. The Manitoulin Island Space Program.

    ERIC Educational Resources Information Center

    Shaffer, Dianna

    1991-01-01

    Describes a space education program in rural Manitoulin Island, Ontario. Reports that gifted and talented students examined space exploration, built models, met with astronauts, and designed multimedia presentations. Explains that the students also hosted a one-day conference on space for students, teachers, and parents and later visited…

  20. Evidence for Reductive Genome Evolution and Lateral Acquisition of Virulence Functions in Two Corynebacterium pseudotuberculosis Strains

    PubMed Central

    Silva, Artur; Ali, Amjad; Pinto, Anne C.; Santos, Anderson R.; Rocha, Aryanne A. M. C.; Lopes, Débora O.; Dorella, Fernanda A.; Pacheco, Luis G. C.; Costa, Marcília P.; Turk, Meritxell Z.; Seyffert, Núbia; Moraes, Pablo M. R. O.; Soares, Siomar C.; Almeida, Sintia S.; Castro, Thiago L. P.; Abreu, Vinicius A. C.; Trost, Eva; Baumbach, Jan; Tauch, Andreas; Schneider, Maria Paula C.; McCulloch, John; Cerdeira, Louise T.; Ramos, Rommel T. J.; Zerlotini, Adhemar; Dominitini, Anderson; Resende, Daniela M.; Coser, Elisângela M.; Oliveira, Luciana M.; Pedrosa, André L.; Vieira, Carlos U.; Guimarăes, Cláudia T.; Bartholomeu, Daniela C.; Oliveira, Diana M.; Santos, Fabrício R.; Rabelo, Élida Mara; Lobo, Francisco P.; Franco, Glória R.; Costa, Ana Flávia; Castro, Ieso M.; Dias, Sílvia Regina Costa; Ferro, Jesus A.; Ortega, José Miguel; Paiva, Luciano V.; Goulart, Luiz R.; Almeida, Juliana Franco; Ferro, Maria Inęs T.; Carneiro, Newton P.; Falcăo, Paula R. K.; Grynberg, Priscila; Teixeira, Santuza M. R.; Brommonschenkel, Sérgio; Oliveira, Sérgio C.; Meyer, Roberto; Moore, Robert J.; Miyoshi, Anderson; Oliveira, Guilherme C.

    2011-01-01

    Background Corynebacterium pseudotuberculosis, a Gram-positive, facultative intracellular pathogen, is the etiologic agent of the disease known as caseous lymphadenitis (CL). CL mainly affects small ruminants, such as goats and sheep; it also causes infections in humans, though rarely. This species is distributed worldwide, but it has the most serious economic impact in Oceania, Africa and South America. Although C. pseudotuberculosis causes major health and productivity problems for livestock, little is known about the molecular basis of its pathogenicity. Methodology and Findings We characterized two C. pseudotuberculosis genomes (Cp1002, isolated from goats; and CpC231, isolated from sheep). Analysis of the predicted genomes showed high similarity in genomic architecture, gene content and genetic order. When C. pseudotuberculosis was compared with other Corynebacterium species, it became evident that this pathogenic species has lost numerous genes, resulting in one of the smallest genomes in the genus. Other differences that could be part of the adaptation to pathogenicity include a lower GC content, of about 52%, and a reduced gene repertoire. The C. pseudotuberculosis genome also includes seven putative pathogenicity islands, which contain several classical virulence factors, including genes for fimbrial subunits, adhesion factors, iron uptake and secreted toxins. Additionally, all of the virulence factors in the islands have characteristics that indicate horizontal transfer. Conclusions These particular genome characteristics of C. pseudotuberculosis, as well as its acquired virulence factors in pathogenicity islands, provide evidence of its lifestyle and of the pathogenicity pathways used by this pathogen in the infection process. All genomes cited in this study are available in the NCBI Genbank database (http://www.ncbi.nlm.nih.gov/genbank/) under accession numbers CP001809 and CP001829. PMID:21533164

  1. The evolution of animal genomes.

    PubMed

    Dunn, Casey W; Ryan, Joseph F

    2015-12-01

    Genome sequences are now available for hundreds of species sampled across the animal phylogeny, bringing key features of animal genome evolution into sharper focus. The field of animal evolutionary genomics has focused on identifying and classifying the diversity genomic features, reconstructing the history of evolutionary changes in animal genomes, and testing hypotheses about the evolutionary relationships of animals. The grand challenges moving forward are to connect evolutionary changes in genomes with particular evolutionary changes in phenotypes, and to determine which changes are driven by selection. This will require far greater genome sampling both across and within species, extensive phenotype data, a well resolved animal phylogeny, and advances in comparative methods. PMID:26363125

  2. Global features of the Alcanivorax borkumensis SK2 genome.

    PubMed

    Reva, Oleg N; Hallin, Peter F; Willenbrock, Hanni; Sicheritz-Ponten, Thomas; Tümmler, Burkhard; Ussery, David W

    2008-03-01

    The global feature of the completely sequenced Alcanivorax borkumensis SK2 type strain chromosome is its symmetry and homogeneity. The origin and terminus of replication are located opposite to each other in the chromosome and are discerned with high signal to noise ratios by maximal oligonucleotide usage biases on the leading and lagging strand. Genomic DNA structure is rather uniform throughout the chromosome with respect to intrinsic curvature, position preference or base stacking energy. The orthologs and paralogs of A. borkumensis genes with the highest sequence homology were found in most cases among gamma-Proteobacteria, with Acinetobacter and P. aeruginosa as closest relatives. A. borkumensis shares a similar oligonucleotide usage and promoter structure with the Pseudomonadales. A comparatively low number of only 18 genome islands with atypical oligonucleotide usage was detected in the A. borkumensis chromosome. The gene clusters that confer the assimilation of aliphatic hydrocarbons, are localized in two genome islands which were probably acquired from an ancestor of the Yersinia lineage, whereas the alk genes of Pseudomonas putida still exhibit the typical Alcanivorax oligonucleotide signature indicating a complex evolution of this major hydrocarbonoclastic trait. PMID:18081853

  3. Fission and fusion in island taxa--serendipity, or something to be expected?

    PubMed

    Emerson, Brent C; Faria, Christiana M A

    2014-11-01

    A well-used metaphor for oceanic islands is that they act as 'natural laboratories' for the study of evolution. But how can islands or archipelagos be considered analogues of laboratories for understanding the evolutionary process itself? It is not necessarily the case that just because two or more related species occur on an island or archipelago, somehow, this can help us understand more about their evolutionary history. But in some cases, it can. In this issue of Molecular Ecology, Garrick et al. () use population-level sampling within closely related taxa of Galapagos giant tortoises to reveal a complex demographic history of the species Chelonoidis becki - a species endemic to Isabela Island, and geographically restricted to Wolf Volcano. Using microsatellite genotyping and mitochondrial DNA sequencing, they provide a strong case for C. becki being derived from C. darwini from the neighbouring island of Santiago. But the interest here is that colonization did not happen only once. Garrick et al. () reveal C. becki to be the product of a double colonization event, and their data reveal these two founding lineages to be now fusing back into one. Their results are compelling and add to a limited literature describing the evolutionary consequences of double colonization events. Here, we look at the broader implications of the findings of Garrick et al. () and suggest genomic admixture among multiple founding populations may be a characteristic feature within insular taxa. PMID:25330853

  4. Genome-wide SNP analysis explains coral diversity and recovery in the Ryukyu Archipelago.

    PubMed

    Shinzato, Chuya; Mungpakdee, Sutada; Arakaki, Nana; Satoh, Noriyuki

    2015-01-01

    Following a global coral bleaching event in 1998, Acropora corals surrounding most of Okinawa island (OI) were devastated, although they are now gradually recovering. In contrast, the Kerama Islands (KIs) only 30?km west of OI, have continuously hosted a great variety of healthy corals. Taking advantage of the decoded Acropora digitifera genome and using genome-wide SNP analyses, we clarified Acropora population structure in the southern Ryukyu Archipelago (sRA). Despite small genetic distances, we identified distinct clusters corresponding to specific island groups, suggesting infrequent long-distance dispersal within the sRA. Although the KIs were believed to supply coral larvae to OI, admixture analyses showed that such dispersal is much more limited than previously realized, indicating independent recovery of OI coral populations and the necessity of local conservation efforts for each region. We detected strong historical migration from the Yaeyama Islands (YIs) to OI, and suggest that the YIs are the original source of OI corals. In addition, migration edges to the KIs suggest that they are a historical sink population in the sRA, resulting in high diversity. This population genomics study provides the highest resolution data to date regarding coral population structure and history. PMID:26656261

  5. Genome-wide SNP analysis explains coral diversity and recovery in the Ryukyu Archipelago

    PubMed Central

    Shinzato, Chuya; Mungpakdee, Sutada; Arakaki, Nana; Satoh, Noriyuki

    2015-01-01

    Following a global coral bleaching event in 1998, Acropora corals surrounding most of Okinawa island (OI) were devastated, although they are now gradually recovering. In contrast, the Kerama Islands (KIs) only 30?km west of OI, have continuously hosted a great variety of healthy corals. Taking advantage of the decoded Acropora digitifera genome and using genome-wide SNP analyses, we clarified Acropora population structure in the southern Ryukyu Archipelago (sRA). Despite small genetic distances, we identified distinct clusters corresponding to specific island groups, suggesting infrequent long-distance dispersal within the sRA. Although the KIs were believed to supply coral larvae to OI, admixture analyses showed that such dispersal is much more limited than previously realized, indicating independent recovery of OI coral populations and the necessity of local conservation efforts for each region. We detected strong historical migration from the Yaeyama Islands (YIs) to OI, and suggest that the YIs are the original source of OI corals. In addition, migration edges to the KIs suggest that they are a historical sink population in the sRA, resulting in high diversity. This population genomics study provides the highest resolution data to date regarding coral population structure and history. PMID:26656261

  6. Origins and diversity of a cosmopolitan fern genus on an island archipelago.

    PubMed

    Wolf, Paul G; Rowe, Carol A; Der, Joshua P; Schilling, Martin P; Visger, Clayton J; Thomson, John A

    2015-01-01

    Isolated oceanic islands are characterized by patterns of biological diversity different from that on nearby continental mainlands. Isolation can provide the opportunity for evolutionary divergence, but also set the stage for hybridization between related taxa arriving from different sources. Ferns disperse by haploid spores, which are produced in large numbers and can travel long distances in air currents, enabling these plants to become established on most oceanic islands. Here, we examine the origins and patterns of diversity of the cosmopolitan fern genus Pteridium (Dennstaedtiaceae; bracken) on the Galapagos Islands. We use nucleotide sequences from two plastid genes, and two nuclear gene markers, to examine phylogeography of Pteridium on the Galapagos Islands. We incorporate data from a previous study to provide a worldwide context. We also sampled new specimens from South and Central America. We used flow cytometry to estimate genome size of some accessions. We found that both plastid and nuclear haplotypes fall into two distinct clades, consistent with a two-diploid-species taxonomy of P. aquilinum and P. esculentum. As predicted, the allotetraploid P. caudatum possesses nuclear haplotypes from both diploid species. Samples from the Galapagos include P. esculentum subsp. arachnoideum, P. caudatum and possible hybrids between them. Multiple Pteridium taxa were also observed growing together at some sites. We find evidence for multiple origins of Pteridium on the Galapagos Islands and multiple origins of tetraploid P. caudatum throughout its range in Central and South America. We also posit that P. caudatum may include recent diploid hybrids, backcrosses to P. esculentum, as well as allotetraploid plants. The Galapagos Islands are positioned close to the equator where they can receive dispersing propagules from both hemispheres. This may partly explain the high levels of diversity found for this cosmopolitan fern on these islands. PMID:26487677

  7. Origins and diversity of a cosmopolitan fern genus on an island archipelago

    PubMed Central

    Wolf, Paul G.; Rowe, Carol A.; Der, Joshua P.; Schilling, Martin P.; Visger, Clayton J.; Thomson, John A.

    2015-01-01

    Isolated oceanic islands are characterized by patterns of biological diversity different from that on nearby continental mainlands. Isolation can provide the opportunity for evolutionary divergence, but also set the stage for hybridization between related taxa arriving from different sources. Ferns disperse by haploid spores, which are produced in large numbers and can travel long distances in air currents, enabling these plants to become established on most oceanic islands. Here, we examine the origins and patterns of diversity of the cosmopolitan fern genus Pteridium (Dennstaedtiaceae; bracken) on the Galapagos Islands. We use nucleotide sequences from two plastid genes, and two nuclear gene markers, to examine phylogeography of Pteridium on the Galapagos Islands. We incorporate data from a previous study to provide a worldwide context. We also sampled new specimens from South and Central America. We used flow cytometry to estimate genome size of some accessions. We found that both plastid and nuclear haplotypes fall into two distinct clades, consistent with a two-diploid-species taxonomy of P. aquilinum and P. esculentum. As predicted, the allotetraploid P. caudatum possesses nuclear haplotypes from both diploid species. Samples from the Galapagos include P. esculentum subsp. arachnoideum, P. caudatum and possible hybrids between them. Multiple Pteridium taxa were also observed growing together at some sites. We find evidence for multiple origins of Pteridium on the Galapagos Islands and multiple origins of tetraploid P. caudatum throughout its range in Central and South America. We also posit that P. caudatum may include recent diploid hybrids, backcrosses to P. esculentum, as well as allotetraploid plants. The Galapagos Islands are positioned close to the equator where they can receive dispersing propagules from both hemispheres. This may partly explain the high levels of diversity found for this cosmopolitan fern on these islands. PMID:26487677

  8. Whole-Genome Pyrosequencing of an Epidemic Multidrug-Resistant Acinetobacter baumannii Strain Belonging to the European Clone II Group ? †

    PubMed Central

    Iacono, Michele; Villa, Laura; Fortini, Daniela; Bordoni, Roberta; Imperi, Francesco; Bonnal, Raoul J. P.; Sicheritz-Ponten, Thomas; De Bellis, Gianluca; Visca, Paolo; Cassone, Antonio; Carattoli, Alessandra

    2008-01-01

    The whole-genome sequence of an epidemic, multidrug-resistant Acinetobacter baumannii strain (strain ACICU) belonging to the European clone II group and carrying the plasmid-mediated blaOXA-58 carbapenem resistance gene was determined. The A. baumannii ACICU genome was compared with the genomes of A. baumannii ATCC 17978 and Acinetobacter baylyi ADP1, with the aim of identifying novel genes related to virulence and drug resistance. A. baumannii ACICU has a single chromosome of 3,904,116 bp (which is predicted to contain 3,758 genes) and two plasmids, pACICU1 and pACICU2, of 28,279 and 64,366 bp, respectively. Genome comparison showed 86.4% synteny with A. baumannii ATCC 17978 and 14.8% synteny with A. baylyi ADP1. A conspicuous number of transporters belonging to different superfamilies was predicted for A. baumannii ACICU. The relative number of transporters was much higher in ACICU than in ATCC 17978 and ADP1 (76.2, 57.2, and 62.5 transporters per Mb of genome, respectively). An antibiotic resistance island, AbaR2, was identified in ACICU and had plausibly evolved by reductive evolution from the AbaR1 island previously described in multiresistant strain A. baumannii AYE. Moreover, 36 putative alien islands (pAs) were detected in the ACICU genome; 24 of these had previously been described in the ATCC 17978 genome, 4 are proposed here for the first time and are present in both ATCC 17978 and ACICU, and 8 are unique to the ACICU genome. Fifteen of the pAs in the ACICU genome encode genes related to drug resistance, including membrane transporters and ex novo acquired resistance genes. These findings provide novel insight into the genetic basis of A. baumannii resistance. PMID:18411315

  9. Epidemiology & Genomics Research Program

    Cancer.gov

    The Epidemiology and Genomics Research Program, in the National Cancer Institute's Division of Cancer Control and Population Sciences, funds research in human populations to understand the determinants of cancer occurrence and outcomes.

  10. | Office of Cancer Genomics

    Cancer.gov

    This past July, I started a journey into the fields of communications and cancer research when I joined the Office of Cancer Genomics (OCG) as a fellow in the National Cancer Institute (NCI) Health Communications Internship Program (HCIP).

  11. GENOME RESPONSES TO ALLOPOLYPLOIDIZATION

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The timing and rate of genome variation induced by allopolyploidization in cereals was analyzed in the intergeneric wheat/rye hybrid triticale (X Triticosecale Wittmack) using amplified fragment length polymorphism (AFLP) analyses. The results showed that allopolyploidization induced considerable s...

  12. The genomics of Colletotrichum

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Colletotrichum are devastating fungal pathogens of major crop plants worldwide. This book chapter provides an overview of the genomics and transcriptomics of Colletotrichum. Included is an overview of the agricultural relevance of the genus Colletotrichum, the taxonomic position, information about ...

  13. Lophotrochozoan mitochondrial genomes

    SciTech Connect

    Valles, Yvonne; Boore, Jeffrey L.

    2005-10-01

    Progress in both molecular techniques and phylogeneticmethods has challenged many of the interpretations of traditionaltaxonomy. One example is in the recognition of the animal superphylumLophotrochozoa (annelids, mollusks, echiurans, platyhelminthes,brachiopods, and other phyla), although the relationships within thisgroup and the inclusion of some phyla remain uncertain. While much ofthis progress in phylogenetic reconstruction has been based on comparingsingle gene sequences, we are beginning to see the potential of comparinglarge-scale features of genomes, such as the relative order of genes.Even though tremendous progress is being made on the sequencedetermination of whole nuclear genomes, the dataset of choice forgenome-level characters for many animals across a broad taxonomic rangeremains mitochondrial genomes. We review here what is known aboutmitochondrial genomes of the lophotrochozoans and discuss the promisethat this dataset will enable insight into theirrelationships.

  14. Mouse genome database 2016

    PubMed Central

    Bult, Carol J.; Eppig, Janan T.; Blake, Judith A.; Kadin, James A.; Richardson, Joel E.

    2016-01-01

    The Mouse Genome Database (MGD; http://www.informatics.jax.org) is the primary community model organism database for the laboratory mouse and serves as the source for key biological reference data related to mouse genes, gene functions, phenotypes and disease models with a strong emphasis on the relationship of these data to human biology and disease. As the cost of genome-scale sequencing continues to decrease and new technologies for genome editing become widely adopted, the laboratory mouse is more important than ever as a model system for understanding the biological significance of human genetic variation and for advancing the basic research needed to support the emergence of genome-guided precision medicine. Recent enhancements to MGD include new graphical summaries of biological annotations for mouse genes, support for mobile access to the database, tools to support the annotation and analysis of sets of genes, and expanded support for comparative biology through the expansion of homology data. PMID:26578600

  15. | Office of Cancer Genomics

    Cancer.gov

    Ringing in the New Year is always a time for reflection. With several individual projects stirring in the Office and a new Center for Cancer Genomics recently inaugurated, 2011 was a prodigious year for OCG.

  16. Platyzoan mitochondrial genomes.

    PubMed

    Wey-Fabrizius, Alexandra R; Podsiadlowski, Lars; Herlyn, Holger; Hankeln, Thomas

    2013-11-01

    Platyzoa is a putative lophotrochozoan (spiralian) subtaxon within the protostome clade of Metazoa, comprising a range of biologically diverse, mostly small worm-shaped animals. The monophyly of Platyzoa, the relationships between the putative subgroups Platyhelminthes, Gastrotricha and Gnathifera (the latter comprising at least Gnathostomulida, "Rotifera" and Acanthocephala) as well as some aspects of the internal phylogenies of these subgroups are highly debated. Here we review how complete mitochondrial (mt) genome data contribute to these debates. We highlight special features of the mt genomes and discuss problems in mtDNA phylogenies of the clade. Mitochondrial genome data seem to be insufficient to resolve the position of the platyzoan clade within the Spiralia but can help to address internal phylogenetic questions. The present review includes a tabular survey of all published platyzoan mt genomes. PMID:23274056

  17. Genomic definition of species

    SciTech Connect

    Crkvenjakov, R.; Drmanac, R.

    1991-07-01

    The subject of this paper is the definition of species based on the assumption that genome is the fundamental level for the origin and maintenance of biological diversity. For this view to be logically consistent it is necessary to assume the existence and operation of the new law which we call genome law. For this reason the genome law is included in the explanation of species phenomenon presented here even if its precise formulation and elaboration are left for the future. The intellectual underpinnings of this definition can be traced to Goldschmidt. We wish to explore some philosophical aspects of the definition of species in terms of the genome. The point of proposing the definition on these grounds is that any real advance in evolutionary theory has to be correct in both its philosophy and its science.

  18. Genomics and vaccine development

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Genomic-based approaches are driving fundamental changes in our understanding of microbiology. Comparative analysis of microbial strain is providing new insights into pathogen evolution, virulence mechanisms, and host range specificity. Most importantly, gene discovery and genetic variations can now...

  19. Barrier island bistability induced by biophysical interactions

    NASA Astrophysics Data System (ADS)

    Durán Vinent, Orencio; Moore, Laura J.

    2015-02-01

    Barrier islands represent about 10% of the world’s coastline, sustain rich ecosystems, host valuable infrastructure and protect mainland coasts from storms. Future climate-change-induced increases in the intensity and frequency of major hurricanes and accelerations in sea-level rise will have a significant impact on barrier islands--leading to increased coastal hazards and flooding--yet our understanding of island response to external drivers remains limited. Here, we find that island response is intrinsically bistable and controlled by previously unrecognized dynamics: the competing, and quantifiable, effects of storm erosion, sea-level rise, and the aeolian and biological processes that enable and drive dune recovery. When the biophysical processes driving dune recovery dominate, islands tend to be high in elevation and vulnerability to storms is minimized. Alternatively, when the effects of storm erosion dominate, islands may become trapped in a perpetual state of low elevation and maximum vulnerability to storms, even under mild storm conditions. When sea-level rise dominates, islands become unstable and face possible disintegration. This quantification of barrier island dynamics is supported by data from the Virginia Barrier Islands, USA and provides a broader context for considering island response to climate change and the likelihood of potentially abrupt transitions in island state.

  20. Genome assortment, not serogroup, defines Vibrio cholerae pandemic strains

    SciTech Connect

    Brettin, Thomas S; Bruce, David C; Challacombe, Jean F; Detter, John C; Han, Cliff S; Munik, A C; Chertkov, Olga; Meincke, Linda; Saunders, Elizabeth; Choi, Seon Y; Haley, Bradd J; Taviani, Elisa; Jeon, Yoon - Seong; Kim, Dong Wook; Lee, Jae - Hak; Walters, Ronald A; Hug, Anwar; Colwell, Rita R

    2009-01-01

    Vibrio cholerae, the causative agent of cholera, is a bacterium autochthonous to the aquatic environment, and a serious public health threat. V. cholerae serogroup O1 is responsible for the previous two cholera pandemics, in which classical and El Tor biotypes were dominant in the 6th and the current 7th pandemics, respectively. Cholera researchers continually face newly emerging and re-emerging pathogenic clones carrying combinations of new serogroups as well as of phenotypic and genotypic properties. These genotype and phenotype changes have hampered control of the disease. Here we compare the complete genome sequences of 23 strains of V. cholerae isolated from a variety of sources and geographical locations over the past 98 years in an effort to elucidate the evolutionary mechanisms governing genetic diversity and genesis of new pathogenic clones. The genome-based phylogeny revealed 12 distinct V. cholerae phyletic lineages, of which one, designated the V. cholerae core genome (CG), comprises both O1 classical and EI Tor biotypes. All 7th pandemic clones share nearly identical gene content, i.e., the same genome backbone. The transition from 6th to 7th pandemic strains is defined here as a 'shift' between pathogenic clones belonging to the same O1 serogroup, but from significantly different phyletic lineages within the CG clade. In contrast, transition among clones during the present 7th pandemic period can be characterized as a 'drift' between clones, differentiated mainly by varying composition of laterally transferred genomic islands, resulting in emergence of variants, exemplified by V.cholerae serogroup O139 and V.cholerae O1 El Tor hybrid clones that produce cholera toxin of classical biotype. Based on the comprehensive comparative genomics presented in this study it is concluded that V. cholerae undergoes extensive genetic recombination via lateral gene transfer, and, therefore, genome assortment, not serogroup, should be used to define pathogenic V. cholerae clones.