Sample records for colibactin genomic island

  1. Isolation of a Metabolite from the pks Island Provides Insights into Colibactin Biosynthesis and Activity.

    PubMed

    Brotherton, Carolyn A; Wilson, Matthew; Byrd, Gary; Balskus, Emily P

    2015-03-20

    Colibactin is a structurally uncharacterized, genotoxic natural product produced by commensal and pathogenic strains of E. coli that harbor the pks island. A new metabolite has been isolated from a pks(+) E. coli mutant missing an essential biosynthetic enzyme. The unusual azaspiro[2.4] bicyclic ring system of this molecule provides new insights into colibactin biosynthesis and suggests a mechanism through which colibactin and other pks-derived metabolites may exert genotoxicity. PMID:25753745

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

    PubMed Central

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

    2014-01-01

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

  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, Michèle; Olier, Maïwenn; Nougayrède, Jean-Philippe; Audebert, Marc; Chalut, Christian; Schubert, Sören; Oswald, Eric

    2013-01-01

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

  4. The colibactin warhead crosslinks DNA.

    PubMed

    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. PMID:25901819

  5. GIV: A Tool for Genomic Islands Visualization

    PubMed Central

    Che, Dongsheng; Wang, Han

    2013-01-01

    A Genomic Islands (GI) is a chunk of DNA sequence in a genome whose origin can be traced back to other organisms or viruses. The detection of GIs plays an indispensable role in biomedical research, due to the fact that GIs are highly related to special functionalities such as disease-causing GIs - pathogenicity islands. It is also very important to visualize genomic islands, as well as the supporting features corresponding to the genomic islands in the genome. We have developed a program, Genomic Island Visualization (GIV), which displays the locations of genomic islands in a genome, as well as the corresponding supportive feature information for GIs. GIV was implemented in C++, and was compiled and executed on Linux/Unix operating systems. Availability GIV is freely available for non-commercial use at http://www5.esu.edu/cpsc/bioinfo/software/GIV PMID:24250116

  6. Genomic islands in pathogenic and environmental microorganisms

    Microsoft Academic Search

    Ulrich Dobrindt; Bianca Hochhut; Ute Hentschel; Jörg Hacker

    2004-01-01

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

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

    PubMed

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

    2013-07-01

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

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

    PubMed

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

    2009-03-01

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

  9. Evaluation of genomic island predictors using a comparative genomics approach

    PubMed Central

    Langille, Morgan GI; Hsiao, William WL; Brinkman, Fiona SL

    2008-01-01

    Background Genomic islands (GIs) are clusters of genes in prokaryotic genomes of probable horizontal origin. GIs are disproportionately associated with microbial adaptations of medical or environmental interest. Recently, multiple programs for automated detection of GIs have been developed that utilize sequence composition characteristics, such as G+C ratio and dinucleotide bias. To robustly evaluate the accuracy of such methods, we propose that a dataset of GIs be constructed using criteria that are independent of sequence composition-based analysis approaches. Results We developed a comparative genomics approach (IslandPick) that identifies both very probable islands and non-island regions. The approach involves 1) flexible, automated selection of comparative genomes for each query genome, using a distance function that picks appropriate genomes for identification of GIs, 2) identification of regions unique to the query genome, compared with the chosen genomes (positive dataset) and 3) identification of regions conserved across all genomes (negative dataset). Using our constructed datasets, we investigated the accuracy of several sequence composition-based GI prediction tools. Conclusion Our results indicate that AlienHunter has the highest recall, but the lowest measured precision, while SIGI-HMM is the most precise method. SIGI-HMM and IslandPath/DIMOB have comparable overall highest accuracy. Our comparative genomics approach, IslandPick, was the most accurate, compared with a curated list of GIs, indicating that we have constructed suitable datasets. This represents the first evaluation, using diverse and, independent datasets that were not artificially constructed, of the accuracy of several sequence composition-based GI predictors. The caveats associated with this analysis and proposals for optimal island prediction are discussed. PMID:18680607

  10. 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

  11. GIST: Genomic island suite of tools for predicting genomic islands in genomic sequences

    PubMed Central

    Hasan, Mohammad Shabbir; Liu, Qi; Wang, Han; Fazekas, John; Chen, Bernard; Che, Dongsheng

    2012-01-01

    Genomic Islands (GIs) are genomic regions that are originally from other organisms, through a process known as Horizontal Gene Transfer (HGT). Detection of GIs plays a significant role in biomedical research since such align genomic regions usually contain important features, such as pathogenic genes. We have developed a use friendly graphic user interface, Genomic Island Suite of Tools (GIST), which is a platform for scientific users to predict GIs. This software package includes five commonly used tools, AlienHunter, IslandPath, Colombo SIGI-HMM, INDeGenIUS and Pai-Ida. It also includes an optimization program EGID that ensembles the result of existing tools for more accurate prediction. The tools in GIST can be used either separately or sequentially. GIST also includes a downloadable feature that facilitates collecting the input genomes automatically from the FTP server of the National Center for Biotechnology Information (NCBI). GIST was implemented in Java, and was compiled and executed on Linux/Unix operating systems. Availability The database is available for free at http://www5.esu.edu/cpsc/bioinfo/software/GIST PMID:22419842

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

    PubMed Central

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

    2009-01-01

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

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

    PubMed

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

    2007-10-01

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

  14. Genomic Islands in the Pathogenic Filamentous Fungus Aspergillus fumigatus

    E-print Network

    Cotty, Peter J.

    University School of Medicine, Washington DC, United States of America Abstract We present the genomeGenomic Islands in the Pathogenic Filamentous Fungus Aspergillus fumigatus Natalie D. Fedorova1 Institute, University of Dublin, Trinity College, Dublin, Ireland, 3 School of Medicine and Faculty of Life

  15. 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

  16. COMPUTATIONAL PREDICTION AND CHARACTERIZATION OF GENOMIC ISLANDS

    E-print Network

    Hammerton, James

    , antibiotic resistance, symbiotic interactions, and notable secondary metabolic capabilities. As the number; comparative genomics; evolution; bacteria; archaea; pathogenesis; phage #12;iv DEDICATION In memory of my

  17. EGID: an ensemble algorithm for improved genomic island detection in genomic sequences.

    PubMed

    Che, Dongsheng; Hasan, Mohammad Shabbir; Wang, Han; Fazekas, John; Huang, Jinling; Liu, Qi

    2011-01-01

    Genomic islands (GIs) are genomic regions that are originally transferred from other organisms. The detection of genomic islands in genomes can lead to many applications in industrial, medical and environmental contexts. Existing computational tools for GI detection suffer either low recall or low precision, thus leaving the room for improvement. In this paper, we report the development of our Ensemble algorithm for Genomic Island Detection (EGID). EGID utilizes the prediction results of existing computational tools, filters and generates consensus prediction results. Performance comparisons between our ensemble algorithm and existing programs have shown that our ensemble algorithm is better than any other program. EGID was implemented in Java, and was compiled and executed on Linux operating systems. EGID is freely available at http://www5.esu.edu/cpsc/bioinfo/software/EGID. PMID:22355228

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

    PubMed Central

    Chatterjee, Raghunath; Chaudhuri, Keya; Chaudhuri, Probal

    2008-01-01

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

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

    Microsoft Academic Search

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

    2009-01-01

    Genomic islands have been shown to harbor functional traits that differentiate ecologically distinct populations of environmental bacteria. A comparative analysis of the complete genome sequences of the marine Actinobacteria Salinispora tropica and Salinispora arenicola reveals that 75% of the species-specific genes are located in 21 genomic islands. These islands are enriched in genes associated with secondary metabolite biosynthesis providing evidence

  20. Patterns and architecture of genomic islands in marine bacteria

    PubMed Central

    2012-01-01

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

  1. Genomic islands from five strains of Burkholderia pseudomallei

    PubMed Central

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

    2008-01-01

    Background Burkholderia pseudomallei is the etiologic agent of melioidosis, a significant cause of morbidity and mortality where this infection is endemic. Genomic differences among strains of B. pseudomallei are predicted to be one of the major causes of the diverse clinical manifestations observed among patients with melioidosis. The purpose of this study was to examine the role of genomic islands (GIs) as sources of genomic diversity in this species. Results We found that genomic islands (GIs) vary greatly among B. pseudomallei strains. We identified 71 distinct GIs from the genome sequences of five reference strains of B. pseudomallei: K96243, 1710b, 1106a, MSHR668, and MSHR305. The genomic positions of these GIs are not random, as many of them are associated with tRNA gene loci. In particular, the 3' end sequences of tRNA genes are predicted to be involved in the integration of GIs. We propose the term "tRNA-mediated site-specific recombination" (tRNA-SSR) for this mechanism. In addition, we provide a GI nomenclature that is based upon integration hotspots identified here or previously described. Conclusion Our data suggest that acquisition of GIs is one of the major sources of genomic diversity within B. pseudomallei and the molecular mechanisms that facilitate horizontally-acquired GIs are common across multiple strains of B. pseudomallei. The differential presence of the 71 GIs across multiple strains demonstrates the importance of these mobile elements for shaping the genetic composition of individual strains and populations within this bacterial species. PMID:19038032

  2. 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

  3. Evidence of a Large Novel Gene Pool Associated with Prokaryotic Genomic Islands

    Microsoft Academic Search

    William W. L. Hsiao; Korine Ung; Dana Aeschliman; Jenny Bryan; Brett Brett Finlay; Fiona S. L. Brinkman

    2005-01-01

    Microbial genes that are ''novel'' (no detectable homologs in other species) have become of increasing interest as environmental sampling suggests that there are many more such novel genes in yet-to-be-cultured microorganisms. By analyzing known microbial genomic islands and prophages, we developed criteria for systematic identification of putative genomic islands (clusters of genes of probable horizontal origin in a prokaryotic genome)

  4. 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.

  5. Islander: a database of precisely mapped genomic islands in tRNA and tmRNA genes

    PubMed Central

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

    2015-01-01

    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. PMID:25378302

  6. Islander: a database of precisely mapped genomic islands in tRNA and tmRNA genes.

    PubMed

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

    2015-01-01

    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. PMID:25378302

  7. 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

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

    Microsoft Academic Search

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

    2011-01-01

    Background  Bacterial virulence enhancement and drug resistance are major threats to public health worldwide. Interestingly, newly acquired\\u000a genomic islands (GIs) from horizontal transfer between different bacteria strains were found in Vibrio cholerae, Streptococcus suis, and Mycobacterium tuberculosis, which caused outbreak of epidemic diseases in recently years.\\u000a \\u000a \\u000a \\u000a \\u000a Results  Using a large-scale comparative genomic analysis of 1088 complete genomes from all available bacteria (1009)

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

    PubMed Central

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

    2012-01-01

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

  10. Identification of genomic islands in six plant pathogens.

    PubMed

    Chen, Ling-Ling

    2006-06-01

    Genomic islands (GIs) play important roles in microbial evolution, which are acquired by horizontal gene transfer. In this paper, the GIs of six completely sequenced plant pathogens are identified using a windowless method based on Z curve representation of DNA sequences. Consequently, four, eight, four, one, two and four GIs are recognized with the length greater than 20-Kb in plant pathogens Agrobacterium tumefaciens str. C58, Rolstonia solanacearum GMI1000, Xanthomonas axonopodis pv. citri str. 306 (Xac), Xanthomonas campestris pv. campestris str. ATCC33913 (Xcc), Xylella fastidiosa 9a5c and Pseudomonas syringae pv. tomato str. DC3000, respectively. Most of these regions share a set of conserved features of GIs, including an abrupt change in GC content compared with that of the rest of the genome, the existence of integrase genes at the junction, the use of tRNA as the integration sites, the presence of genetic mobility genes, the difference of codon usage, codon preference and amino acid usage, etc. The identification of these GIs will benefit the research for the six important phytopathogens. PMID:16581205

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

    PubMed Central

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

    2014-01-01

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

  12. 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

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

    PubMed

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

    2014-04-01

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

    Microsoft Academic Search

    Yulia A Medvedeva; Marina V Fridman; Nina J Oparina; Dmitry B Malko; Ekaterina O Ermakova; Ivan V Kulakovskiy; Andreas Heinzel; Vsevolod J Makeev

    2010-01-01

    BACKGROUND: Recently, it has been discovered that the human genome contains many transcription start sites for non-coding RNA. Regulatory regions related to transcription of this non-coding RNAs are poorly studied. Some of these regulatory regions may be associated with CpG islands located far from transcription start-sites of any protein coding gene. The human genome contains many such CpG islands; however,

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

    PubMed Central

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

    2011-01-01

    The arms race between cellular life forms and viruses is a major driving force of evolution. A substantial fraction of bacterial and archaeal genomes is dedicated to antivirus defense. We analyzed the distribution of defense genes and typical mobilome components (such as viral and transposon genes) in bacterial and archaeal genomes and demonstrated statistically significant clustering of antivirus defense systems and mobile genes and elements in genomic islands. The defense islands are enriched in putative operons and contain numerous overrepresented gene families. A detailed sequence analysis of the proteins encoded by genes in these families shows that many of them are diverged variants of known defense system components, whereas others show features, such as characteristic operonic organization, that are suggestive of novel defense systems. Thus, genomic islands provide abundant material for the experimental study of bacterial and archaeal antivirus defense. Except for the CRISPR-Cas systems, different classes of defense systems, in particular toxin-antitoxin and restriction-modification systems, show nonrandom clustering in defense islands. It remains unclear to what extent these associations reflect functional cooperation between different defense systems and to what extent the islands are genomic “sinks” that accumulate diverse nonessential genes, particularly those acquired via horizontal gene transfer. The characteristics of defense islands resemble those of mobilome islands. Defense and mobilome genes are nonrandomly associated in islands, suggesting nonadaptive evolution of the islands via a preferential attachment-like mechanism underpinned by the addictive properties of defense systems such as toxins-antitoxins and an important role of horizontal mobility in the evolution of these islands. PMID:21908672

  17. ARTICLE doi:10.1038/nature10172 Genomic island variability facilitates

    E-print Network

    Sorek, Rotem

    ARTICLE doi:10.1038/nature10172 Genomic island variability facilitates Prochlorococcus­virus cyanobacteria are extremely abundant in the oceans, as are the viruses that infect them. How hosts and viruses of Prochlorococcus and their viruses. Here we present a genome analysis of 77 substrains selected for resistance

  18. 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

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

    PubMed

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

    2015-01-01

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

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

    Microsoft Academic Search

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

    2009-01-01

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

  1. Discovery of novel Vibrio cholerae VSP II genomic islands using comparative genomic analysis

    PubMed Central

    Taviani, Elisa; Grim, Christopher J.; Choi, Jinna; Chun, Jongsik; Haley, Bradd; Hasan, Nur A.; Huq, Anwar; Colwell, R.R.

    2010-01-01

    This report describes Vibrio Seventh Pandemic Island II (VSP-II) and three novel variants revealed by comparative genomics of 23Vibrio cholerae strains and their presence among a large and diverse collection of V. cholerae isolates. Three VSP-II variants were previously reported and our results demonstrate the presence of three novel VSP-II in clinical and environmental V. cholerae marked by major deletions and genetic rearrangements. A new VSP-II cluster was found in the seven pandemic V. cholerae O1 El Tor strain CIRS101, which is dominant (95%) among recent (2004-2007) seven pandemic V. cholerae O1 El Tor isolates from two endemic sites, but was not found in older strains from the same region. Two other variants were found in V. cholerae TMA21 and RC385, two environmental strains from coastal Brazil and the Chesapeake Bay, respectively, the latter being prevalent among environmental V. cholerae non-O1/non-O139 and V. mimicus. Results of this study indicate that the VSP-II island has undergone significant rearrangement through a complex evolutionary pathway in V. cholerae. Interestingly, one of the new VSP-II revealed the presence of “old” and “new” V. cholerae O1 El Tor pandemic clones circulating in some of the areas where cholera is endemic. PMID:20528940

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

    PubMed Central

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

    2009-01-01

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

  3. A role for migration-linked genes and genomic islands in divergence of a songbird.

    PubMed

    Ruegg, Kristen; Anderson, Eric C; Boone, Jason; Pouls, Jazz; Smith, Thomas B

    2014-10-01

    Next-generation sequencing has made it possible to begin asking questions about the process of divergence at the level of the genome. For example, recently, there has been a debate around the role of 'genomic islands of divergence' (i.e. blocks of outlier loci) in facilitating the process of speciation-with-gene-flow. The Swainson's thrush, Catharus ustulatus, is a migratory songbird with two genetically distinct subspecies that differ in a number of traits known to be involved in reproductive isolation in birds (plumage coloration, song and migratory behaviour), despite contemporary gene flow along a secondary contact zone. Here, we use RAD-PE sequencing to test emerging hypotheses about the process of divergence at the level of the genome and identify genes and gene regions involved in differentiation in this migratory songbird. Our analyses revealed distinct genomic islands on 15 of the 23 chromosomes and an accelerated rate of divergence on the Z chromosome, one of the avian sex chromosomes. Further, an analysis of loci linked to traits known to be involved in reproductive isolation in songbirds showed that genes linked to migration are significantly more differentiated than expected by chance, but that these genes lie primarily outside the genomic islands. Overall, our analysis supports the idea that genes linked to migration play an important role in divergence in migratory songbirds, but we find no compelling evidence that the observed genomic islands are facilitating adaptive divergence in migratory behaviour. PMID:24954641

  4. Genomic hypomethylation and CpG island hypermethylation in prostatic intraepithelial neoplasm

    Microsoft Academic Search

    Nam-Yun Cho; Jung Ho Kim; Kyung Chul Moon; Gyeong Hoon Kang

    2009-01-01

    Altered DNA methylation in cancer cells is characterized by focal CpG island hypermethylation and diffuse genomic hypomethylation.\\u000a Both types of aberrant methylation are frequently found in human prostate adenocarcinoma (PCa). Prostatic intraepithelial\\u000a neoplasm (PIN), a precursor lesion of PCa, has been demonstrated to contain CpG island hypermethylation, but little is known\\u000a about the role of DNA hypomethylation. We analyzed the

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

    PubMed Central

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

    2007-01-01

    Uropathogenic Escherichia coli (UPEC) strains are responsible for the majority of uncomplicated urinary tract infections, which can present clinically as cystitis or pyelonephritis. UPEC strain CFT073, isolated from the blood of a patient with acute pyelonephritis, was most cytotoxic and most virulent in mice among our strain collection. Based on the genome sequence of CFT073, microarrays were utilized in comparative genomic hybridization (CGH) analysis of a panel of uropathogenic and fecal/commensal E. coli isolates. Genomic DNA from seven UPEC (three pyelonephritis and four cystitis) isolates and three fecal/commensal strains, including K-12 MG1655, was hybridized to the CFT073 microarray. The CFT073 genome contains 5,379 genes; CGH analysis revealed that 2,820 (52.4%) of these genes were common to all 11 E. coli strains, yet only 173 UPEC-specific genes were found by CGH to be present in all UPEC strains but in none of the fecal/commensal strains. When the sequences of three additional sequenced UPEC strains (UTI89, 536, and F11) and a commensal strain (HS) were added to the analysis, 131 genes present in all UPEC strains but in no fecal/commensal strains were identified. Seven previously unrecognized genomic islands (>30 kb) were delineated by CGH in addition to the three known pathogenicity islands. These genomic islands comprise 672 kb of the 5,231-kb (12.8%) genome, demonstrating the importance of horizontal transfer for UPEC and the mosaic structure of the genome. UPEC strains contain a greater number of iron acquisition systems than do fecal/commensal strains, which is reflective of the adaptation to the iron-limiting urinary tract environment. Each strain displayed distinct differences in the number and type of known virulence factors. The large number of hypothetical genes in the CFT073 genome, especially those shown to be UPEC specific, strongly suggests that many urovirulence factors remain uncharacterized. PMID:17351047

  6. Salmonella enterica Serotype Typhimurium DT 104 Antibiotic Resistance Genomic Island I in Serotype Paratyphi B

    PubMed Central

    Meunier, Danièle; Boyd, David; Mulvey, Michael R.; Baucheron, Sylvie; Mammina, Caterina; Nastasi, Antonino; Chaslus-Dancla, Elisabeth

    2002-01-01

    We have identified Salmonella genomic island I (SGI1) in an isolate of Salmonella enterica serotype Paratyphi B. This antibiotic-resistance gene cluster, which confers multidrug resistance, has been previously identified in S. enterica serotype Typhimurium phage types DT 104 and DT 120 and in S. enterica serotype Agona. PMID:11971780

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

    PubMed Central

    2014-01-01

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

  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. 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

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

    PubMed Central

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

    2012-01-01

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

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

    PubMed Central

    2014-01-01

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

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

    PubMed Central

    Lautner, Monika; Schunder, Eva; Herrmann, Vroni

    2013-01-01

    Legionella pneumophila is a Gram-negative freshwater agent which multiplies in specialized nutrient-rich vacuoles of amoebae. When replicating in human alveolar macrophages, Legionella can cause Legionnaires' disease. Recently, we identified a new type of conjugation/type IVA secretion system (T4ASS) in L. pneumophila Corby (named trb-tra). Analogous versions of trb-tra are localized on the genomic islands Trb-1 and Trb-2. Both can exist as an episomal circular form, and Trb-1 can be transferred horizontally to other Legionella strains by conjugation. In our current work, we discovered the importance of a site-specific integrase (Int-1, lpc2818) for the excision and conjugation process of Trb-1. Furthermore, we identified the genes lvrRABC (lpc2813 to lpc2816) to be involved in the regulation of Trb-1 excision. In addition, we demonstrated for the first time that a Legionella genomic island (LGI) of L. pneumophila Corby (LpcGI-2) encodes a functional type IV secretion system. The island can be transferred horizontally by conjugation and is integrated site specifically into the genome of the transconjugants. LpcGI-2 generates three different episomal forms. The predominant episomal form, form A, is generated integrase dependently (Lpc1833) and transferred by conjugation in a pilT-dependent manner. Therefore, the genomic islands Trb-1 and LpcGI-2 should be classified as integrative and conjugative elements (ICEs). Coculture studies of L. pneumophila wild-type and mutant strains revealed that the int-1 and lvrRABC genes (located on Trb-1) as well as lpc1833 and pilT (located on LpcGI-2) do not influence the in vivo fitness of L. pneumophila in Acanthamoeba castellanii. PMID:23354744

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

    Microsoft Academic Search

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

    2005-01-01

    A genomic island was identified in the Haemophilus influenzae biogroup aegyptius Brazilian purpuric fever (BPF) strain F3031. This island, which was also found in other BPF isolates, could not be detected in non-BPF biogroup aegyptius strains or in nontypeable or typeable H. influenzae strains, with the exception of a region present in the type b Eagan strain. This 34,378-bp island

  15. 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

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

    PubMed Central

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

    2015-01-01

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

  17. Resolving the structural features of genomic islands: A machine learning approach

    PubMed Central

    Vernikos, Georgios S.; Parkhill, Julian

    2008-01-01

    Large inserts of horizontally acquired DNA that contain functionally related genes with limited phylogenetic distribution are often referred to as genomic islands (GIs), and structural definitions of these islands, based on common features, have been proposed. Although a large number of mobile elements fall well within the GI definition, there are several concerns about the structural consensus for GIs: The current GI definition was put forward 10 yr ago when only 12 complete bacterial genomes were available, a large number of GIs deviate from that definition, and in silico predictions assuming a full/partial GI structural model bias the sampling of the GI structural space toward “well-structured” GIs. In this study, the structural features of genomic regions are sampled by a hypothesis-free, bottom-up search, and these are exploited in a machine learning approach with the aim of explicitly quantifying and modeling the contribution of each feature to the GI structure. Performing a whole-genome-based comparative analysis between 37 strains of three different genera and 12 outgroup genomes, 668 genomic regions were sampled and used to train structural GI models. The data show that, overall, GIs from the three different genera fall into distinct, genus-specific structural families. However, decreasing the taxa resolution, by studying GI structures across different genus boundaries, provides models that converge on a fairly similar GI structure, further suggesting that GIs can be seen as a superfamily of mobile elements, with core and variable structural features, rather than a well-defined family. PMID:18071028

  18. Active chromatin domains are defined by acetylation islands revealed by genome-wide mapping.

    PubMed

    Roh, Tae-Young; Cuddapah, Suresh; Zhao, Keji

    2005-03-01

    The identity and developmental potential of a human cell is specified by its epigenome that is largely defined by patterns of chromatin modifications including histone acetylation. Here we report high-resolution genome-wide mapping of diacetylation of histone H3 at Lys 9 and Lys 14 in resting and activated human T cells by genome-wide mapping technique (GMAT). Our data show that high levels of the H3 acetylation are detected in gene-rich regions. The chromatin accessibility and gene expression of a genetic domain is correlated with hyperacetylation of promoters and other regulatory elements but not with generally elevated acetylation of the entire domain. Islands of acetylation are identified in the intergenic and transcribed regions. The locations of the 46,813 acetylation islands identified in this study are significantly correlated with conserved noncoding sequences (CNSs) and many of them are colocalized with known regulatory elements in T cells. TCR signaling induces 4045 new acetylation loci that may mediate the global chromatin remodeling and gene activation. We propose that the acetylation islands are epigenetic marks that allow prediction of functional regulatory elements. PMID:15706033

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

    PubMed

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

    2015-01-30

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

  20. 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

  1. Sequence Analysis of the Mobile Genome Island pKLC102 of Pseudomonas aeruginosa C

    PubMed Central

    Klockgether, Jens; Reva, Oleg; Larbig, Karen; Tümmler, Burkhard

    2004-01-01

    The Pseudomonas aeruginosa plasmid pKLC102 coexists as a plasmid and a genome island in clone C strains. Whereas the related plasmid pKLK106 reversibly recombines with P. aeruginosa clone K chromosomes at one of the two tRNALys genes, pKLC102 is incorporated into the tRNALys gene only close to the pilA locus. Targeting of the other tRNALys copy in the chromosome is blocked by a 23,395-bp mosaic of truncated PAO open reading frames, transposons, and pKLC102 homologs. Annotation and phylogenetic analysis of the large 103,532-bp pKLC102 sequence revealed that pKLC102 is a hybrid of plasmid and phage origin. The plasmid lineage conferred oriV and genes for replication, partitioning, and conjugation, including a pil cluster encoding type IV thin sex pili and an 8,524-bp chvB glucan synthetase gene that is known to be a major determinant for host tropism and virulence. The phage lineage conferred integrase, att, and a syntenic set of conserved hypothetical genes also observed in the tRNAGly-associated genome islands of P. aeruginosa clone C chromosomes. In subgroup C isolates from patients with cystic fibrosis, pKLC102 was irreversibly fixed into the chromosome by the insertion of the large 23,061-bp class I transposon TNCP23, which is a composite of plasmid, integron, and IS6100 elements. Intramolecular transposition of a copy of IS6100 led to chromosomal inversions and disruption of plasmid synteny. The case of pKLC102 in P. aeruginosa clone C documents the intraclonal evolution of a genome island from a mobile ancestor via a reversibly integrated state to irreversible incorporation and dissipation in the chromosome. PMID:14702321

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

    PubMed Central

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

    2011-01-01

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

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

    Microsoft Academic Search

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

    1997-01-01

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

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

    PubMed Central

    Stevens, Patricia

    2010-01-01

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

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

    Microsoft Academic Search

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

    2007-01-01

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

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

    PubMed

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

    2014-01-01

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

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

    PubMed Central

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

    2013-01-01

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

  8. Truncated tni Module Adjacent to the Complex Integron of Salmonella Genomic Island 1 in Salmonella enterica Serovar Virchow

    Microsoft Academic Search

    Benoît Doublet; Chishih Chu; Cheng-Hsun Chiu; Yi-Chin Fan; Axel Cloeckaert

    2009-01-01

    Salmonella genomic island 1 was identified for the first time in Salmonella enterica serovar Virchow isolated from humans in Taiwan. The complex class 1 integron conferring multidrug resistance was shown to be inserted within open reading frame (ORF) S023 and contains for the first time a partial transpositional module. The 5-bp target duplication flanking the complex integron suggests that its

  9. Prevalence of genomic island PAPI-1 in clinical isolates of Pseudomonas aeruginosa in Iran.

    PubMed

    Sadeghifard, Nourkhoda; Rasaei, Seyedeh Zahra; Ghafourian, Sobhan; Zolfaghary, Mohammad Reza; Ranjbar, Reza; Raftari, Mohammad; Mohebi, Reza; Maleki, Abbas; Rahbar, Mohammad

    2012-03-01

    Pseudomonas aeruginosa, a gram-negative rod-shaped bacterium, is an opportunistic pathogen, which causes various serious diseases in humans and animals. The aims of this study were to evaluate of the presence of genomic island PAPI-1 in Pseudomonas aeruginosa isolated from Reference Laboratory of Ilam, Milad Hospital and Emam Khomeini Hospital, Iran and to study the frequency of extended spectrum beta-lactamases (ESBLs) among isolates. Forty-eight clinical isolates of P. aeruginosa were obtained during April to September 2010, and were evaluated for ESBLs by screening and confirmatory disk diffusion methods and PAPI-1 by PCR. Fifteen of 48 P. aeruginosa isolates were positive for ESBLs and 17 isolates positive for PAPI-1. This was first study of the prevalence of PAPI-1 in clinical isolates of P. aeruginosa in Iran, showing that most of PAPI-1 positive strains had high levels of antibiotic resistance and produced ESBLs. PMID:23082593

  10. Orphan CpG Islands Identify Numerous Conserved Promoters in the Mammalian Genome

    PubMed Central

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

    2010-01-01

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

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

    PubMed Central

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

    2009-01-01

    It has been argued that the limited genetic diversity and reduced allelic heterogeneity observed in isolated founder populations facilitates discovery of loci contributing to both Mendelian and complex disease. A strong founder effect, severe isolation, and substantial inbreeding have dramatically reduced genetic diversity in natives from the island of Kosrae, Federated States of Micronesia, who exhibit a high prevalence of obesity and other metabolic disorders. We hypothesized that genetic drift and possibly natural selection on Kosrae might have increased the frequency of previously rare genetic variants with relatively large effects, making these alleles readily detectable in genome-wide association analysis. However, mapping in large, inbred cohorts introduces analytic challenges, as extensive relatedness between subjects violates the assumptions of independence upon which traditional association test statistics are based. We performed genome-wide association analysis for 15 quantitative traits in 2,906 members of the Kosrae population, using novel approaches to manage the extreme relatedness in the sample. As positive controls, we observe association to known loci for plasma cholesterol, triglycerides, and C-reactive protein and to a compelling candidate loci for thyroid stimulating hormone and fasting plasma glucose. We show that our study is well powered to detect common alleles explaining ?5% phenotypic variance. However, no such large effects were observed with genome-wide significance, arguing that even in such a severely inbred population, common alleles typically have modest effects. Finally, we show that a majority of common variants discovered in Caucasians have indistinguishable effect sizes on Kosrae, despite the major differences in population genetics and environment. PMID:19197348

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

    PubMed Central

    Puymège, Aurore; Bertin, Stéphane; Chuzeville, Sarah; Guédon, Gérard

    2013-01-01

    Putative integrative and conjugative elements (ICEs), i.e., genomic islands which could excise, self-transfer by conjugation, and integrate into the chromosome of the bacterial host strain, were previously identified by in silico analysis in the sequenced genomes of Streptococcus agalactiae (M. Brochet et al., J. Bacteriol. 190:6913–6917, 2008). We investigated here the mobility of the elements integrated into the 3? end of a tRNALys gene. Three of the four putative ICEs tested were found to excise but only one (ICE_515_tRNALys) was found to transfer by conjugation not only to S. agalactiae strains but also to a Streptococcus pyogenes strain. Transfer was observed even if recipient cell already carries a related resident ICE or a genomic island flanked by attL and attR recombination sites but devoid of conjugation or recombination genes (CIs-Mobilizable Element [CIME]). The incoming ICE preferentially integrates into the 3? end of the tRNALys gene (i.e., the attR site of the resident element), leading to a CIME-ICE structure. Transfer of the whole composite element CIME-ICE was obtained, showing that the CIME is mobilizable in cis by the ICE. Therefore, genomic islands carrying putative virulence genes but lacking the mobility gene can be mobilized by a related ICE after site-specific accretion. PMID:23275243

  13. A Distinct and Divergent Lineage of Genomic Island-Associated Type IV Secretion Systems in Legionella

    PubMed Central

    Wee, Bryan A.; Woolfit, Megan; Beatson, Scott A.; Petty, Nicola K.

    2013-01-01

    Legionella encodes multiple classes of Type IV Secretion Systems (T4SSs), including the Dot/Icm protein secretion system that is essential for intracellular multiplication in amoebal and human hosts. Other T4SSs not essential for virulence are thought to facilitate the acquisition of niche-specific adaptation genes including the numerous effector genes that are a hallmark of this genus. Previously, we identified two novel gene clusters in the draft genome of Legionella pneumophila strain 130b that encode homologues of a subtype of T4SS, the genomic island-associated T4SS (GI-T4SS), usually associated with integrative and conjugative elements (ICE). In this study, we performed genomic analyses of 14 homologous GI-T4SS clusters found in eight publicly available Legionella genomes and show that this cluster is unusually well conserved in a region of high plasticity. Phylogenetic analyses show that Legionella GI-T4SSs are substantially divergent from other members of this subtype of T4SS and represent a novel clade of GI-T4SSs only found in this genus. The GI-T4SS was found to be under purifying selection, suggesting it is functional and may play an important role in the evolution and adaptation of Legionella. Like other GI-T4SSs, the Legionella clusters are also associated with ICEs, but lack the typical integration and replication modules of related ICEs. The absence of complete replication and DNA pre-processing modules, together with the presence of Legionella-specific regulatory elements, suggest the Legionella GI-T4SS-associated ICE is unique and may employ novel mechanisms of regulation, maintenance and excision. The Legionella GI-T4SS cluster was found to be associated with several cargo genes, including numerous antibiotic resistance and virulence factors, which may confer a fitness benefit to the organism. The in-silico characterisation of this new T4SS furthers our understanding of the diversity of secretion systems involved in the frequent horizontal gene transfers that allow Legionella to adapt to and exploit diverse environmental niches. PMID:24358157

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

    PubMed

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

    2008-05-27

    The capacity to fix nitrogen is widely distributed in phyla of Bacteria and Archaea but has long been considered to be absent from the Pseudomonas genus. We report here the complete genome sequencing of nitrogen-fixing root-associated Pseudomonas stutzeri A1501. The genome consists of a single circular chromosome with 4,567,418 bp. Comparative genomics revealed that, among 4,146 protein-encoding genes, 1,977 have orthologs in each of the five other Pseudomonas representative species sequenced to date. The genome contains genes involved in broad utilization of carbon sources, nitrogen fixation, denitrification, degradation of aromatic compounds, biosynthesis of polyhydroxybutyrate, multiple pathways of protection against environmental stress, and other functions that presumably give A1501 an advantage in root colonization. Genetic information on synthesis, maturation, and functioning of nitrogenase is clustered in a 49-kb island, suggesting that this property was acquired by lateral gene transfer. New genes required for the nitrogen fixation process have been identified within the nif island. The genome sequence offers the genetic basis for further study of the evolution of the nitrogen fixation property and identification of rhizosphere competence traits required in the interaction with host plants; moreover, it opens up new perspectives for wider application of root-associated diazotrophs in sustainable agriculture. PMID:18495935

  15. An ovelSalmonella genomic island 1 and rare integron types in Salmonella Typhimurium isolates from horses in The Netherlands

    Microsoft Academic Search

    An T. T. Vo; Engeline van Duijkeren; Ad C. Fluit; Wim Gaastra

    2007-01-01

    Methods: Sixty-one Salmonella isolates were screened for the presence of class 1 integrons by PCR. The gene cassettes of integron-positive isolates were detected by PCR, restriction fragment length polymorphism typing, and sequencing. The potential for the transfer of resistance determinants was investigated by conjugation experiments. The presence of Salmonella genomic island 1 (SGI1) or its variants was studied by PCR

  16. Variant Salmonella Genomic Island 1 Antibiotic Resistance Gene Cluster in Salmonella enterica Serovar Albany

    PubMed Central

    Doublet, Benoît; Lailler, Renaud; Meunier, Danièle; Brisabois, Anne; Boyd, David; Mulvey, Michael R.; Chaslus-Dancla, Elisabeth

    2003-01-01

    Salmonella genomic island 1 (SGI1) contains an antibiotic resistance gene cluster and has been previously identified in multidrug-resistant Salmonella enterica serovars Typhimurium DT104, Agona, and Paratyphi B. We identified a variant SGI1 antibiotic-resistance gene cluster in a multidrug-resistant strain of S. enterica serovar Albany isolated from food fish from Thailand and imported to France. In this strain, the streptomycin resistance aadA2 gene cassette in one of the SGI1 integrons was replaced by a dfrA1 gene cassette, conferring resistance to trimethoprim and an open reading frame of unknown function. Thus, this serovar Albany strain represents the fourth S. enterica serovar in which SGI1 has been identified and the first SGI1 example where gene cassette replacement took place in one of its integron structures. The antibiotic resistance gene cluster of serovar Albany strain 7205.00 constitutes a new SGI1 variant; we propose a name of SGI1-F. PMID:12737743

  17. 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

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

    PubMed Central

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

    2010-01-01

    Magnetotactic bacteria are able to swim navigating along geomagnetic field lines. They synthesize ferromagnetic nanocrystals that are embedded in cytoplasmic membrane invaginations forming magnetosomes. Regularly aligned in the cytoplasm along cytoskeleton filaments, the magnetosome chain effectively forms a compass needle bestowing on bacteria their magnetotactic behaviour. A large genomic island, conserved among magnetotactic bacteria, contains the genes potentially involved in magnetosome formation. One of the genes, mamK has been described as encoding a prokaryotic actin-like protein which when it polymerizes forms in the cytoplasm filamentous structures that provide the scaffold for magnetosome alignment. Here, we have identified a series of genes highly similar to the mam genes in the genome of Magnetospirillum magneticum AMB-1. The newly annotated genes are clustered in a genomic islet distinct and distant from the known magnetosome genomic island and most probably acquired by lateral gene transfer rather than duplication. We focused on a mamK-like gene whose product shares 54.5% identity with the actin-like MamK. Filament bundles of polymerized MamK-like protein were observed in vitro with electron microscopy and in vivo in E. coli cells expressing MamK-like-Venus fusions by fluorescence microscopy. In addition, we demonstrate that mamK-like is transcribed in AMB-1 wild-type and ?mamK mutant cells and that the actin-like filamentous structures observed in the ?mamK strain are probably MamK-like polymers. Thus MamK-like is a new member of the prokaryotic actin-like family. This is the first evidence of a functional mam gene encoded outside the magnetosome genomic island. PMID:20161777

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

    PubMed Central

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

    2013-01-01

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

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

    Microsoft Academic Search

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

    2006-01-01

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

  1. A Genome-Wide Screen for Normally Methylated Human CpG Islands That Can Identify Novel Imprinted Genes

    PubMed Central

    Strichman-Almashanu, Liora Z.; Lee, Richard S.; Onyango, Patrick O.; Perlman, Elizabeth; Flam, Folke; Frieman, Matthew B.; Feinberg, Andrew P.

    2002-01-01

    DNA methylation is a covalent modification of the nucleotide cytosine that is stably inherited at the dinucleotide CpG by somatic cells, and 70% of CpG dinucleotides in the genome are methylated. The exception to this pattern of methylation are CpG islands, CpG-rich sequences that are protected from methylation, and generally are thought to be methylated only on the inactive X-chromosome and in tumors, as well as differentially methylated regions (DMRs) in the vicinity of imprinted genes. To identify chromosomal regions that might harbor imprinted genes, we devised a strategy for isolating a library of normally methylated CpG islands. Most of the methylated CpG islands represented high copy number dispersed repeats. However, 62 unique clones in the library were characterized, all of which were methylated and GC-rich, with a GC content >50%. Of these, 43 clones also showed a CpGobs/CpGexp >0.6, of which 30 were studied in detail. These unique methylated CpG islands mapped to 23 chromosomal regions, and 12 were differentially methylated regions in uniparental tissues of germline origin, i.e., hydatidiform moles (paternal origin) and complete ovarian teratomas (maternal origin), even though many apparently were methylated in somatic tissues. We term these sequences gDMRs, for germline differentially methylated regions. At least two gDMRs mapped near imprinted genes, HYMA1 and a novel homolog of Elongin A and Elongin A2, which we term Elongin A3. Surprisingly, 18 of the methylated CpG islands were methylated in germline tissues of both parental origins, representing a previously uncharacterized class of normally methylated CpG islands in the genome, and which we term similarly methylated regions (SMRs). These SMRs, in contrast to the gDMRs, were significantly associated with telomeric band locations (P?=?.0008), suggesting a potential role for SMRs in chromosome organization. At least 10 of the methylated CpG islands were on average 85% conserved between mouse and human. These sequences will provide a valuable resource in the search for novel imprinted genes, for defining the molecular substrates of the normal methylome, and for identifying novel targets for mammalian chromatin formation. [The sequence data described in this paper have been submitted to the GenBank data library under accession nos. AF484557–AF484583.] PMID:11932239

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

    PubMed

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

    2015-05-01

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

  3. Small RNA genes expressed from Staphylococcus aureus genomic and pathogenicity islands with specific expression among pathogenic strains

    PubMed Central

    Pichon, Christophe; Felden, Brice

    2005-01-01

    Small RNA (sRNA) genes are expressed in all organisms, primarily as regulators of translation and message stability. We have developed comparative genomic approaches to identify sRNAs that are expressed by Staphylococcus aureus, the most common cause of hospital-acquired infections. This study represents an in-depth analysis of the RNome of a Gram-positive bacterium. A set of sRNAs candidates were identified in silico within intergenic regions, and their expression levels were monitored by using microarrays and confirmed by Northern blot hybridizations. Two sRNAs were also detected directly from purification and RNA sequence determination. In total, at least 12 sRNAs are expressed from the S. aureus genome, five from the core genome and seven from pathogenicity islands that confer virulence and antibiotic resistance. Three sRNAs are present in multiple (two to five) copies. For the sRNAs that are conserved throughout the bacterial phylogeny, their secondary structures were inferred by phylogenetic comparative methods. In vitro binding assays indicate that one sRNA encoded within a pathogenicity island is a trans-encoded antisense RNA regulating the expression of target genes at the posttranscriptional level. Some of these RNAs show large variations of expression among pathogenic strains, suggesting that they are involved in the regulation of staphylococcal virulence. PMID:16183745

  4. Genomic analysis of a migratory divide reveals candidate genes for migration and implicates selective sweeps in generating islands of differentiation.

    PubMed

    Delmore, Kira E; Hübner, Sariel; Kane, Nolan C; Schuster, Richard; Andrew, Rose L; Câmara, Francisco; Guigó, Roderic; Irwin, Darren E

    2015-04-01

    Differential gene flow, reductions in diversity following linked selection and/or features of the genome can structure patterns of genomic differentiation during the process of speciation. Possible sources of reproductive isolation are well studied between coastal and inland subspecies groups of Swainson's thrushes, with differences in seasonal migratory behaviour likely playing a key role in reducing hybrid fitness. We assembled and annotated a draft reference genome for this species and generated whole-genome shotgun sequence data for populations adjacent to the hybrid zone between these groups. We documented substantial genomewide heterogeneity in relative estimates of genetic differentiation between the groups. Within population diversity was lower in areas of high relative differentiation, supporting a role for selective sweeps in generating this pattern. Absolute genetic differentiation was reduced in these areas, further suggesting that recurrent selective sweeps in the ancestral population and/or between divergent populations following secondary contact likely occurred. Relative genetic differentiation was also higher near centromeres and on the Z chromosome, suggesting that features of the genome also contribute to genomewide heterogeneity. Genes linked to migratory traits were concentrated in islands of differentiation, supporting previous suggestions that seasonal migration is under divergent selection between Swainson's thrushes. Differences in migratory behaviour likely play a central role in the speciation of many taxa; we developed the infrastructure here to permit future investigations into the role several candidate genes play in reducing gene flow between not only Swainson's thrushes but other species as well. PMID:25808860

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

    PubMed Central

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

    2013-01-01

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

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

    PubMed Central

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

    2012-01-01

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

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

    PubMed Central

    Doublet, Benoît; Golding, George R.; Mulvey, Michael R.; Cloeckaert, Axel

    2008-01-01

    Background The Salmonella genomic island 1 is an integrative mobilizable element (IME) originally identified in epidemic multidrug-resistant Salmonella enterica serovar Typhimurium (S. Typhimurium) DT104. SGI1 contains a complex integron, which confers various multidrug resistance phenotypes due to its genetic plasticity. Previous studies have shown that SGI1 integrates site-specifically into the S. enterica, Escherichia coli, or Proteus mirabilis chromosome at the 3? end of thdF gene (attB site). Methodology/Principal Findings Here, we report the transfer of SGI1 to a ?thdF mutant of S. Typhimurium LT2. In the absence of thdF, the frequency of transconjugant formation was reduced by around thirty times of magnitude. Through DNA sequencing SGI1 was shown to integrate specifically into a secondary attachment site (2nd attB), which is located in the intergenic region between the chromosomal sodB and purR genes. At this 2nd attB site, we found that a significant fraction of SGI1 transconjugants (43% of wild type and 100% of ?thdF mutant) contained tandem SGI1 arrays. Moreover, in wild type S. Typhimurium LT2 transconjugants, SGI1 integrated into both attachment sites, i.e., thdF and sodB-purR. The formation of SGI1 tandem arrays occurred in both specific attB sites. There was heterogeneity in the size of the SGI1 tandem arrays detected in single transconjugant colonies. Some arrays consisted as far as six SGI1s arranged in tandem. These tandem arrays were shown to persist during serial passages with or without antibiotic selection pressure. Conclusions/Significance The ability of integration into two distinct chromosomal sites and tandem array formation of SGI1 could contribute to its spread and persistence. The existence of a secondary attachment site in the Salmonella chromosome has potential implications for the mobility of SGI1, which may integrate in other attachment sites of other bacterial pathogens that do not possess the 1st or 2nd specific SGI1 attB sites of Salmonella. PMID:18446190

  8. 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

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

    PubMed

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

    2014-01-01

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

  10. The master activator of IncA/C conjugative plasmids stimulates genomic islands and multidrug resistance dissemination.

    PubMed

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

    2014-10-01

    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

  11. 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

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

    Microsoft Academic Search

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

    2007-01-01

    Summary The complete sequence (92 770 bp) of a genomic island (GI) named SLG from Streptomyces lividans 66, encoding a novel DNA S-modification system (dnd), was determined. Its overall G+C content was 67.8%, lower than those of three sequenced Streptomyces genomes. Among 85 predicted open reading frames (ORFs) in SLG, 22 ORFs showed little homology with previously known proteins. SLG

  13. A genomic island present along the bacterial chromosome of the Parachlamydiaceae UWE25, an obligate amoebal endosymbiont, encodes a potentially functional F-like conjugative DNA transfer system

    Microsoft Academic Search

    Gilbert Greub; François Collyn; Lionel Guy; Claude-Alain Roten

    2004-01-01

    BACKGROUND: The genome of Protochlamydia amoebophila UWE25, a Parachlamydia-related endosymbiont of free-living amoebae, was recently published, providing the opportunity to search for genomic islands (GIs). RESULTS: On the residual cumulative G+C content curve, a G+C-rich 19-kb region was observed. This sequence is part of a 100-kb chromosome region, containing 100 highly co-oriented ORFs, flanked by two 17-bp direct repeats. Two

  14. Comparative genomic analysis of eight Leptospira strains from Japan and the Philippines revealing the existence of four putative novel genomic islands/islets in L. interrogans serovar Lai strain 56601.

    PubMed

    Youn, Jung-Ho; Hayashida, Kyoko; Koizumi, Nobuo; Ohnishi, Makoto; Sugimoto, Chihiro

    2014-12-01

    Leptospirosis is one of the most widespread zoonotic diseases worldwide and can be considered an emerging health problem to both human and animal. Despite the importance of the disease, complete genome sequences are currently available for only three Leptospira interrogans strains: 56601, Fiocruz L1-130, and IPAV. Therefore, intra- and inter-species comparative genomic analyses of Leptospira are limited. Here, to advance current knowledge of the genomic differences within Leptospira species, next-generation sequencing technology was used to examine the genomes of eight L. interrogans strains belonging to six different serogroups isolated from humans and dogs in Japan and the Philippines. The genomic sequences were mapped to that of the reference strain, L. interrogans serovar Lai strain 56601. The results revealed the presence of four novel genomic islands/islets (GIs) in strain 56601. This study provides a deeper insight into the molecular basis and evolutionary perspective of the virulence of leptospires. PMID:25449997

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

    PubMed Central

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

    2014-01-01

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

  16. 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

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

    PubMed

    Danish-Daniel, Muhd; 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

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

    PubMed Central

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

    2013-01-01

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

  19. A genome-wide map of aberrantly expressed chromosomal islands in colorectal cancer

    Microsoft Academic Search

    Eike Staub; Jörn Gröne; Detlev Mennerich; Stefan Röpcke; Irina Klamann; Bernd Hinzmann; Esmeralda Castanos-Velez; Benno Mann; Christian Pilarsky; Thomas Brümmendorf; Birgit Weber; Heinz-Johannes Buhr; André Rosenthal

    2006-01-01

    BACKGROUND: Cancer development is accompanied by genetic phenomena like deletion and amplification of chromosome parts or alterations of chromatin structure. It is expected that these mechanisms have a strong effect on regional gene expression. RESULTS: We investigated genome-wide gene expression in colorectal carcinoma (CRC) and normal epithelial tissues from 25 patients using oligonucleotide arrays. This allowed us to identify 81

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

    PubMed

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

    2015-04-01

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

  1. 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

  2. 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

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

    PubMed Central

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

    2014-01-01

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

  4. Whole-genome analysis of Salmonella enterica serovar Typhimurium T000240 reveals the acquisition of a genomic island involved in multidrug resistance via IS1 derivatives on the chromosome.

    PubMed

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

    2011-02-01

    Salmonella enterica serovar Typhimurium is frequently associated with life-threatening systemic infections, and the recent global emergence of multidrug resistance in S. enterica isolates from agricultural and clinical settings has raised concerns. In this study, we determined the whole-genome sequence of fluoroquinolone-resistant S. enterica serovar Typhimurium T000240 strain (DT12) isolated from human gastroenteritis in 2000. Comparative genome analysis revealed that T000240 displays high sequence similarity to strain LT2, which was originally isolated in 1940, indicating that progeny of LT2 might be reemerging. T000240 possesses a unique 82-kb genomic island, designated as GI-DT12, which is composed of multidrug resistance determinants, including a Tn2670-like composite transposon (class 1 integron [intI1, bla(oxa-30), aadA1, qacE?1, and sul1], mercury resistance proteins, and chloramphenicol acetyltransferase), a Tn10-like tetracycline resistance protein (tetA), the aerobactin iron-acquisition siderophore system (lutA and lucABC), and an iron transporter (sitABCD). Since GI-DT12 is flanked by IS1 derivatives, IS1-mediated recombination likely played a role in the acquisition of this genomic island through horizontal gene transfer. The aminoglycoside-(3)-N-acetyltransferase (aac(3)) gene and a class 1 integron harboring the dfrA1 gene cassette responsible for gentamicin and trimethoprim resistance, respectively, were identified on plasmid pSTMDT12_L and appeared to have been acquired through homologous recombination with IS26. This study represents the first characterization of the unique genomic island GI-DT12 that appears to be associated with possible IS1-mediated recombination in S. enterica serovar Typhimurium. It is expected that future whole-genome studies will aid in the characterization of the horizontal gene transfer events for the emerging S. enterica serovar Typhimurium strains. PMID:21098248

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

    PubMed Central

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

    2011-01-01

    Salmonella enterica serovar Typhimurium is frequently associated with life-threatening systemic infections, and the recent global emergence of multidrug resistance in S. enterica isolates from agricultural and clinical settings has raised concerns. In this study, we determined the whole-genome sequence of fluoroquinolone-resistant S. enterica serovar Typhimurium T000240 strain (DT12) isolated from human gastroenteritis in 2000. Comparative genome analysis revealed that T000240 displays high sequence similarity to strain LT2, which was originally isolated in 1940, indicating that progeny of LT2 might be reemerging. T000240 possesses a unique 82-kb genomic island, designated as GI-DT12, which is composed of multidrug resistance determinants, including a Tn2670-like composite transposon (class 1 integron [intI1, blaoxa-30, aadA1, qacE?1, and sul1], mercury resistance proteins, and chloramphenicol acetyltransferase), a Tn10-like tetracycline resistance protein (tetA), the aerobactin iron-acquisition siderophore system (lutA and lucABC), and an iron transporter (sitABCD). Since GI-DT12 is flanked by IS1 derivatives, IS1-mediated recombination likely played a role in the acquisition of this genomic island through horizontal gene transfer. The aminoglycoside-(3)-N-acetyltransferase (aac(3)) gene and a class 1 integron harboring the dfrA1 gene cassette responsible for gentamicin and trimethoprim resistance, respectively, were identified on plasmid pSTMDT12_L and appeared to have been acquired through homologous recombination with IS26. This study represents the first characterization of the unique genomic island GI-DT12 that appears to be associated with possible IS1-mediated recombination in S. enterica serovar Typhimurium. It is expected that future whole-genome studies will aid in the characterization of the horizontal gene transfer events for the emerging S. enterica serovar Typhimurium strains. PMID:21098248

  6. A Unique Arabinose 5-Phosphate Isomerase Found within a Genomic Island Associated with the Uropathogenicity of Escherichia coli CFT073 ?

    PubMed Central

    Mosberg, Joshua A.; Yep, Alejandra; Meredith, Timothy C.; Smith, Sara; Wang, Pan-Fen; Holler, Tod P.; Mobley, Harry L. T.; Woodard, Ronald W.

    2011-01-01

    Previous studies showed that deletion of genes c3405 to c3410 from PAI-metV, a genomic island from Escherichia coli CFT073, results in a strain that fails to compete with wild-type CFT073 after a transurethral cochallenge in mice and is deficient in the ability to independently colonize the mouse kidney. Our analysis of c3405 to c3410 suggests that these genes constitute an operon with a role in the internalization and utilization of an unknown carbohydrate. This operon is not found in E. coli K-12 but is present in a small number of pathogenic E. coli and Shigella boydii strains. One of the genes, c3406, encodes a protein with significant homology to the sugar isomerase domain of arabinose 5-phosphate isomerases but lacking the tandem cystathionine beta-synthase domains found in the other arabinose 5-phosphate isomerases of E. coli. We prepared recombinant c3406 protein, found it to possess arabinose 5-phosphate isomerase activity, and characterized this activity in detail. We also constructed a c3406 deletion mutant of E. coli CFT073 and demonstrated that this deletion mutant was still able to compete with wild-type CFT073 in a transurethral cochallenge in mice and could colonize the mouse kidney. These results demonstrate that the presence of c3406 is not essential for a pathogenic phenotype. PMID:21498648

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

    PubMed Central

    Krizova, Lenka; Dijkshoorn, Lenie; Nemec, Alexandr

    2011-01-01

    To assess the diversity of AbaR genomic resistance islands in Acinetobacter baumannii European clone I (MLST clonal complex 1), we investigated 26 multidrug-resistant strains of this major clone isolated from hospitals in 21 cities of 10 European countries between 1984 and 2005. Each strain harbored an AbaR structure integrated at the same position in the chromosomal ATPase gene. AbaR3, including four subtypes based on variations in class 1 integron cassettes, and AbaR10 were found in 15 and 2 strains, respectively, whereas a new, unique AbaR variant was discovered in each of the other 9 strains. These new variants, designated AbaR11 to AbaR19 (19.8 kb to 57.5 kb), seem to be truncated derivatives of AbaR3, likely resulting from the deletions of its internal parts mediated by either IS26 elements (AbaR12 to AbaR19) or homologous recombination (AbaR11). AbaR3 was detected in all 10 strains isolated in 1984 to 1991, while AbaR11 to AbaR19 were carried only by strains isolated since 1997. Our results and those from previous publications suggest that AbaR3 is the original form of AbaR in European clone I, which may have provided strains of the lineage with a selective advantage facilitating their spread in European hospitals in the 1980s or before. PMID:21537009

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

    PubMed

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

    2015-01-01

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

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

    PubMed Central

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

    2015-01-01

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

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

    E-print Network

    Zell, Andreas

    Linking the Epigenome to the Genome: Correlation of Different Features to DNA Methylation of Cp is not completely revealed. There are many hypotheses of which genomic features are correlated to the epigenome are limited to a subset of the genome and thus, cannot be employed, e.g., for genome-wide biomarker prediction

  11. 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

  12. 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

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

    Microsoft Academic Search

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

    1999-01-01

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

  14. Novel Insertion Sequence- and Transposon-Mediated Genetic Rearrangements in Genomic Island SGI1 of Salmonella enterica Serovar Kentucky?

    PubMed Central

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

    2008-01-01

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

  15. Salmonella Genomic Island 1 Multidrug Resistance Gene Clusters in Salmonella enterica Serovar Agona Isolated in Belgium in 1992 to 2002

    PubMed Central

    Doublet, Benoît; Butaye, Patrick; Imberechts, Hein; Boyd, David; Mulvey, Michael R.; Chaslus-Dancla, Elisabeth; Cloeckaert, Axel

    2004-01-01

    Salmonella genomic island 1 (SGI1) harbors a multidrug resistance (MDR) gene cluster which is a complex class 1 integron. Variant SGI1 MDR gene clusters conferring different MDR profiles have also been identified in several Salmonella enterica serovars and classified as SGI1-A to -F. A retrospective study was undertaken to characterize MDR regions from serovar Agona strains harboring SGI1 isolated from poultry in Belgium between 1992 and 2002. A total of 171 serovar Agona strains, displaying resistance to at least one antibiotic, were studied for the presence of SGI1. SGI1 was detected in 94 serovar Agona strains. The most prevalent variant was SGI1-A (85%), which harbors within the SGI1 complex class 1 integron a common region (CR1) containing orf513, a putative transposase gene, adjacent to the dfrA10 trimethoprim resistance gene. A new variant SGI1 named SGI1-G was identified in two strains. It consisted of the pse-1 gene cassette, as in SGI1-B, but with additional insertion of the orf513/dfrA10 region structure. Seven strains displaying the typical SGI1 MDR profile (Ap Cm Ff Sm Sp Su Tc) showed genetic variation at the 3? end of SGI1. These strains harbored the insertion of the CR1 containing orf513 as in SGI1-A, -D, and -G. However, downstream the right end of CR1, they presented different 7.4- to 8.5-kb deletions of the SGI1 3? end that extended to the chromosomal genes yieE and yieF. These results suggest a possible role of CR1 in deletion formation, as has been reported for some insertion sequences. Pulsed-field gel electrophoresis analysis showed that all the serovar Agona SGI1-carrying strains belonged to a single clone. Thus, SGI1 is largely encountered in serovar Agona strains isolated from poultry in Belgium, the most prevalent variant being SGI1-A. SGI1 MDR region undergoes recombinational events resulting in a diversity of MDR gene clusters. PMID:15215102

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

    PubMed Central

    2013-01-01

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

  17. Genotoxic Klebsiella pneumoniae in Taiwan

    PubMed Central

    Lai, Yi-Chyi; Lin, Ann-Chi; Chiang, Ming-Ko; Dai, Yu-Han; Hsu, Chih-Chieh; Lu, Min-Chi; Liau, Chun-Yi; Chen, Ying-Tsong

    2014-01-01

    Background Colibactin is a nonribosomal peptide-polyketide synthesized by multi-enzyme complexes encoded by the pks gene cluster. Colibactin-producing Escherichia coli have been demonstrated to induce host DNA damage and promote colorectal cancer (CRC) development. In Taiwan, the occurrence of pyogenic liver abscess (PLA) has been suggested to correlate with an increasing risk of CRC, and Klebsiella pneumoniae is the predominant PLA pathogen in Taiwan Methodology/Principal Findings At the asn tRNA loci of the newly sequenced K. pneumoniae 1084 genome, we identified a 208-kb genomic island, KPHPI208, of which a module identical to the E. coli pks colibactin gene cluster was recognized. KPHPI208 consists of eight modules, including the colibactin module and the modules predicted to be involved in integration, conjugation, yersiniabactin production, microcin production, and unknown functions. Transient infection of BALB/c normal liver cells with K. pneumoniae 1084 increased the phosphorylation of histone H2AX, indicating the induction of host DNA damage. Colibactin was required for the genotoxicity of K. pneumoniae 1084, as it was diminished by deletion of clbA gene and restored to the wild type level by trans-complementation with a clbA coding plasmid. Besides, BALB/c mice infected with K. pneumoniae 1084 exhibited enhanced DNA damage in the liver parenchymal cells when compared to the isogenic clbA deletion mutant. By PCR detection, the prevalence of pks-positive K. pneumoniae in Taiwan is 25.6%, which is higher than that reported in Europe (3.5%), and is significantly correlated with K1 type, which predominantly accounted for PLA in Taiwan. Conclusions Our knowledge regarding how bacteria contribute to carcinogenesis has just begun. The identification of genotoxic K. pneumoniae and its genetic components will facilitate future studies to elucidate the molecular basis underlying the link between K. pneumoniae, PLA, and CRC. PMID:24852749

  18. 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

  19. 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

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

    PubMed Central

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

    2011-01-01

    Twenty-two single-nucleotide polymorphisms (SNPs) in 10 gene regions previously identified in obesity and type 2 diabetes (T2D) genome-wide association studies (GWAS) were evaluated for association with metabolic traits in a sample from an island population of European descent. We performed a population-based study using 18 anthropometric and biochemical traits considered as continuous variables in a sample of 843 unrelated subjects (360 men and 483 women) aged 18–80 years old from the island of Hvar on the eastern Adriatic coast of Croatia. All eight GWAS SNPs in FTO were significantly associated with weight, body mass index, waist circumference and hip circumference; 20 of the 32 nominal P-values remained significant after permutation testing for multiple corrections. The strongest associations were found between the two TCF7L2 GWAS SNPs with fasting plasma glucose and HbA1c levels, all four P-values remained significant after permutation tests. Nominally significant associations were found between several SNPs and other metabolic traits; however, the significance did not hold after permutation tests. Although the sample size was modest, our study strongly replicated the association of FTO variants with obesity-related measures and TCF7L2 variants with T2D-related traits. The estimated effect sizes of these variants were larger or comparable to published studies. This is likely attributable to the homogenous genetic background of the relatively isolated study population. PMID:21150882

  1. 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

    2014-12-01

    Abstract The complete mitochondrial genome of the gnomefish Scombrops boops was determined by a PCR-based method. The total length of mitochondrial DNA (mtDNA) was 16,518?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

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

    PubMed

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

    2015-01-01

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

  3. 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

  4. 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

  5. Integrated analysis of genome-wide copy number alterations and gene expression in microsatellite stable, CpG island methylator phenotype-negative colon cancer.

    PubMed

    Loo, Lenora W M; Tiirikainen, Maarit; Cheng, Iona; Lum-Jones, Annette; Seifried, Ann; Church, James M; Gryfe, Robert; Weisenberger, Daniel J; Lindor, Noralane M; Gallinger, Steven; Haile, Robert W; Duggan, David J; Thibodeau, Stephen N; Casey, Graham; Le Marchand, Loïc

    2013-05-01

    Microsatellite stable (MSS), CpG island methylator phenotype (CIMP)-negative colorectal tumors, the most prevalent molecular subtype of colorectal cancer, are associated with extensive copy number alteration (CNA) events and aneuploidy. We report on the identification of characteristic recurrent CNA (with frequency >25%) events and associated gene expression profiles for a total of 40 paired tumor and adjacent normal colon tissues using genome-wide microarrays. We observed recurrent CNAs, namely gains at 1q, 7p, 7q, 8p12-11, 8q, 12p13, 13q, 20p, 20q, Xp, and Xq and losses at 1p36, 1p31, 1p21, 4p15-12, 4q12-35, 5q21-22, 6q26, 8p, 14q, 15q11-12, 17p, 18p, 18q, 21q21-22, and 22q. Within these genomic regions we identified 356 genes with significant differential expression (P < 0.0001 and ±1.5-fold change) in the tumor compared to adjacent normal tissue. Gene ontology and pathway analyses indicated that many of these genes were involved in functional mechanisms that regulate cell cycle, cell death, and metabolism. An amplicon present in >70% of the tumor samples at 20q11-20q13 contained several cancer-related genes (AHCY, POFUT1, RPN2, TH1L, and PRPF6) that were upregulated and demonstrated a significant linear correlation (P < 0.05) for gene dosage and gene expression. Copy number loss at 8p, a CNA associated with adenocarcinoma and poor prognosis, was observed in >50% of the tumor samples and demonstrated a significant linear correlation for gene dosage and gene expression for two potential tumor suppressor genes, MTUS1 (8p22) and PPP2CB (8p12). The results from our integration analysis illustrate the complex relationship between genomic alterations and gene expression in colon cancer. PMID:23341073

  6. The origin of polyploid genomes of bluegrasses Poa L. and Gene flow between northern pacific and subAntarctic Islands

    Microsoft Academic Search

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

    2010-01-01

    The involvement of present-day diploid bluegrass species in the formation of polyploid genomes was investigated using comparison\\u000a of sequences of internal transcribed spacers ITS1 and ITS2, and the 5.8S rRNA sequence. It was demonstrated that highly polyploid New Zealand bluegrasses, P. cita (2n = 84; ca. 96 to 100), P. chathamica (2n = 112), and P. litorosa (2n 263–266) formed

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

    Microsoft Academic Search

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

    2005-01-01

    The global dissemination of the multiply-antibiotic-resistant Salmonella enterica serovar Typhimurium DT104 clone with the resistance genes located in a class 1 integron, here designated In104, within genomic island SGI1 is a significant public health issue. Here, we have shown that SGI1 and variants of it carrying different combi- nations of resistance genes are found in several Salmonella enterica serovars. These

  8. The Prevalences of Salmonella Genomic Island 1 Variants in Human and Animal Salmonella Typhimurium DT104 Are Distinguishable Using a Bayesian Approach

    PubMed Central

    Mather, Alison E.; Denwood, Matthew J.; Haydon, Daniel T.; Matthews, Louise; Mellor, Dominic J.; Coia, John E.; Brown, Derek J.; Reid, Stuart W. J.

    2011-01-01

    Throughout the 1990 s, there was an epidemic of multidrug resistant Salmonella Typhimurium DT104 in both animals and humans in Scotland. The use of antimicrobials in agriculture is often cited as a major source of antimicrobial resistance in pathogenic bacteria of humans, suggesting that DT104 in animals and humans should demonstrate similar prevalences of resistance determinants. Until very recently, only the application of molecular methods would allow such a comparison and our understanding has been hindered by the fact that surveillance data are primarily phenotypic in nature. Here, using large scale surveillance datasets and a novel Bayesian approach, we infer and compare the prevalence of Salmonella Genomic Island 1 (SGI1), SGI1 variants, and resistance determinants independent of SGI1 in animal and human DT104 isolates from such phenotypic data. We demonstrate differences in the prevalences of SGI1, SGI1-B, SGI1-C, absence of SGI1, and tetracycline resistance determinants independent of SGI1 between these human and animal populations, a finding that challenges established tenets that DT104 in domestic animals and humans are from the same well-mixed microbial population. PMID:22125606

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

    PubMed Central

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

    2015-01-01

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

  10. A genomic island present along the bacterial chromosome of the Parachlamydiaceae UWE25, an obligate amoebal endosymbiont, encodes a potentially functional F-like conjugative DNA transfer system

    PubMed Central

    Greub, Gilbert; Collyn, François; Guy, Lionel; Roten, Claude-Alain

    2004-01-01

    Background The genome of Protochlamydia amoebophila UWE25, a Parachlamydia-related endosymbiont of free-living amoebae, was recently published, providing the opportunity to search for genomic islands (GIs). Results On the residual cumulative G+C content curve, a G+C-rich 19-kb region was observed. This sequence is part of a 100-kb chromosome region, containing 100 highly co-oriented ORFs, flanked by two 17-bp direct repeats. Two identical gly-tRNA genes in tandem are present at the proximal end of this genetic element. Several mobility genes encoding transposases and bacteriophage-related proteins are located within this chromosome region. Thus, this region largely fulfills the criteria of GIs. The G+C content analysis shows that several modules compose this GI. Surprisingly, one of them encodes all genes essential for F-like conjugative DNA transfer (traF, traG, traH, traN, traU, traW, and trbC), involved in sex pilus retraction and mating pair stabilization, strongly suggesting that, similarly to the other F-like operons, the parachlamydial tra unit is devoted to DNA transfer. A close relatedness of this tra unit to F-like tra operons involved in conjugative transfer is confirmed by phylogenetic analyses performed on concatenated genes and gene order conservation. These analyses and that of gly-tRNA distribution in 140 GIs suggest a proteobacterial origin of the parachlamydial tra unit. Conclusions A GI of the UWE25 chromosome encodes a potentially functional F-like DNA conjugative system. This is the first hint of a putative conjugative system in chlamydiae. Conjugation most probably occurs within free-living amoebae, that may contain hundreds of Parachlamydia bacteria tightly packed in vacuoles. Such a conjugative system might be involved in DNA transfer between internalized bacteria. Since this system is absent from the sequenced genomes of Chlamydiaceae, we hypothesize that it was acquired after the divergence between Parachlamydiaceae and Chlamydiaceae, when the Parachlamydia-related symbiont was an intracellular bacteria. It suggests that this heterologous DNA was acquired from a phylogenetically-distant bacteria sharing an amoebal vacuole. Since Parachlamydiaceae are emerging agents of pneumonia, this GI might be involved in pathogenicity. In future, conjugative systems might be developed as genetic tools for Chlamydiales. PMID:15615594

  11. 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

  12. Variant Salmonella Genomic Island 1 Antibiotic Resistance Gene Cluster Containing a Novel 3?-N-Aminoglycoside Acetyltransferase Gene Cassette, aac(3)-Id, in Salmonella enterica Serovar Newport

    PubMed Central

    Doublet, Benoît; Weill, François-Xavier; Fabre, Laetitia; Chaslus-Dancla, Elisabeth; Cloeckaert, Axel

    2004-01-01

    Salmonella genomic island 1 (SGI1) harbors an antibiotic resistance gene cluster and was previously identified in the multidrug-resistant Salmonella enterica serovars Typhimurium DT104, Agona, Paratyphi B, and Albany. This antibiotic resistance gene cluster is a complex class 1 integron and most often confers resistance to ampicillin (Ap), chloramphenicol (Cm)/florfenicol (Ff), streptomycin (Sm)/spectinomycin (Sp), sulfonamides (Su), and tetracycline (Tc) (ApCmFfSmSpSuTc profile). Recently, variant SGI1 antibiotic resistance gene clusters conferring different antibiotic resistance profiles have been identified in several S. enterica serovars and were classified as SGI1-A to -G. We identified a new variant SGI1 antibiotic resistance gene cluster in two multidrug-resistant S. enterica serovar Newport strains isolated from humans in France. In these strains, the Sm/Sp resistance gene cassette aadA2 inserted at the first attI1 site was replaced by two other aminoglycoside resistance gene cassettes. The first one contains a new resistance gene encoding an AAC(3)-I aminoglycoside 3-N-acetyltransferase that confers resistance to gentamicin (Gm) and sisomicin (Sc). This gene has been named aac(3)-Id. The second one harbors the Sm/Sp resistance gene aadA7. This gene cassette replacement in the SGI1 complex integron of serovar Newport strains constitutes a new variant SGI1 antibiotic resistance gene cluster named SGI1-H. The occurrence of SGI1 in different S. enterica serovars, now including serovar Newport, strengthens the hypothesis of horizontal transfer of SGI1. PMID:15388438

  13. 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

  14. CpG-island fragments from the HNRPA2B1/CBX3 genomic locus reduce silencing and enhance transgene expression from the hCMV promoter/enhancer in mammalian cells

    PubMed Central

    Williams, Steven; Mustoe, Tracey; Mulcahy, Tony; Griffiths, Mark; Simpson, David; Antoniou, Michael; Irvine, Alistair; Mountain, Andrew; Crombie, Robert

    2005-01-01

    Background The hCMV promoter is very commonly used for high level expression of transgenes in mammalian cells, but its utility is hindered by transcriptional silencing. Large genomic fragments incorporating the CpG island region of the HNRPA2B1 locus are resistant to transcriptional silencing. Results In this report we describe studies on the use of a novel series of vectors combining the HNRPA2B1 CpG island with the hCMV promoter for expression of transgenes in CHO-K1 cells. We show that the CpG island gives at least twenty-fold increases in the levels of EGFP and EPO observed in pools of transfectants, and that transgene expression levels remain high in such pools for more than 100 generations. These novel vectors also allow facile isolation of clonal CHO-K1 cell lines showing stable, high-level transgene expression. Conclusion Vectors incorporating the hnRPA2B1 CpG island give major benefits in transgene expression from the hCMV promoter, including substantial improvements in the level and stability of expression. The utility of these vectors for the improved production of recombinant proteins in CHO cells has been demonstrated. PMID:15935093

  15. Early Strains of Multidrug-Resistant Salmonella enterica Serovar Kentucky Sequence Type 198 from Southeast Asia Harbor Salmonella Genomic Island 1-J Variants with a Novel Insertion Sequence

    PubMed Central

    Le Hello, Simon; Weill, François-Xavier; Guibert, Véronique; Praud, Karine; Cloeckaert, Axel

    2012-01-01

    Salmonella genomic island 1 (SGI1) is a 43-kb integrative mobilizable element that harbors a great diversity of multidrug resistance gene clusters described in numerous Salmonella enterica serovars and also in Proteus mirabilis. The majority of SGI1 variants contain an In104-derivative complex class 1 integron inserted between resolvase gene res and open reading frame (ORF) S044 in SGI1. Recently, the international spread of ciprofloxacin-resistant S. enterica serovar Kentucky sequence type 198 (ST198) containing SGI1-K variants has been reported. A retrospective study was undertaken to characterize ST198 S. Kentucky strains isolated before the spread of the epidemic ST198-SGI1-K population in Africa and the Middle East. Here, we characterized 12 ST198 S. Kentucky strains isolated between 1969 and 1999, mainly from humans returning from Southeast Asia (n = 10 strains) or Israel (n = 1 strain) or from meat in Egypt (n = 1 strain). All these ST198 S. Kentucky strains did not belong to the XbaI pulsotype X1 associated with the African epidemic clone but to pulsotype X2. SGI1-J subgroup variants containing different complex integrons with a partial transposition module and inserted within ORF S023 of SGI1 were detected in six strains. The SGI1-J4 variant containing a partially deleted class 1 integron and thus showing a narrow resistance phenotype to sulfonamides was identified in two epidemiologically unrelated strains from Indonesia. The four remaining strains harbored a novel SGI1-J variant, named SGI1-J6, which contained aadA2, floR2, tetR(G)-tetA(G), and sul1 resistance genes within its complex integron. Moreover, in all these S. Kentucky isolates, a novel insertion sequence related to the IS630 family and named ISSen5 was found inserted upstream of the SGI1 complex integron in ORF S023. Thus, two subpopulations of S. Kentucky ST198 independently and exclusively acquired the SGI1 during the 1980s and 1990s. Unlike the ST198-X1 African epidemic subpopulation, the ST198-X2 subpopulation mainly from Asia harbors variants of the SGI1-J subgroup that are encountered mainly in the Far East, as previously described for S. enterica serovars Emek and Virchow. PMID:22802251

  16. Early strains of multidrug-resistant Salmonella enterica serovar Kentucky sequence type 198 from Southeast Asia harbor Salmonella genomic island 1-J variants with a novel insertion sequence.

    PubMed

    Le Hello, Simon; Weill, François-Xavier; Guibert, Véronique; Praud, Karine; Cloeckaert, Axel; Doublet, Benoît

    2012-10-01

    Salmonella genomic island 1 (SGI1) is a 43-kb integrative mobilizable element that harbors a great diversity of multidrug resistance gene clusters described in numerous Salmonella enterica serovars and also in Proteus mirabilis. The majority of SGI1 variants contain an In104-derivative complex class 1 integron inserted between resolvase gene res and open reading frame (ORF) S044 in SGI1. Recently, the international spread of ciprofloxacin-resistant S. enterica serovar Kentucky sequence type 198 (ST198) containing SGI1-K variants has been reported. A retrospective study was undertaken to characterize ST198 S. Kentucky strains isolated before the spread of the epidemic ST198-SGI1-K population in Africa and the Middle East. Here, we characterized 12 ST198 S. Kentucky strains isolated between 1969 and 1999, mainly from humans returning from Southeast Asia (n = 10 strains) or Israel (n = 1 strain) or from meat in Egypt (n = 1 strain). All these ST198 S. Kentucky strains did not belong to the XbaI pulsotype X1 associated with the African epidemic clone but to pulsotype X2. SGI1-J subgroup variants containing different complex integrons with a partial transposition module and inserted within ORF S023 of SGI1 were detected in six strains. The SGI1-J4 variant containing a partially deleted class 1 integron and thus showing a narrow resistance phenotype to sulfonamides was identified in two epidemiologically unrelated strains from Indonesia. The four remaining strains harbored a novel SGI1-J variant, named SGI1-J6, which contained aadA2, floR2, tetR(G)-tetA(G), and sul1 resistance genes within its complex integron. Moreover, in all these S. Kentucky isolates, a novel insertion sequence related to the IS630 family and named ISSen5 was found inserted upstream of the SGI1 complex integron in ORF S023. Thus, two subpopulations of S. Kentucky ST198 independently and exclusively acquired the SGI1 during the 1980s and 1990s. Unlike the ST198-X1 African epidemic subpopulation, the ST198-X2 subpopulation mainly from Asia harbors variants of the SGI1-J subgroup that are encountered mainly in the Far East, as previously described for S. enterica serovars Emek and Virchow. PMID:22802251

  17. Genome Bioinformatics

    NSDL National Science Digital Library

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

  18. Island Biogeography

    NSDL National Science Digital Library

    John Jungck (BioQUEST Curriculum Consortium; Biology)

    2005-12-16

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

  19. Orphan and gene related CpG Islands follow power-law-like distributions in several genomes: evidence of function-related and taxonomy-related modes of distribution.

    PubMed

    Tsiagkas, Giannis; Nikolaou, Christoforos; Almirantis, Yannis

    2014-12-01

    CpG Islands (CGIs) are compositionally defined short genomic stretches, which have been studied in the human, mouse, chicken and later in several other genomes. Initially, they were assigned the role of transcriptional regulation of protein-coding genes, especially the house-keeping ones, while more recently there is found evidence that they are involved in several other functions as well, which might include regulation of the expression of RNA genes, DNA replication etc. Here, an investigation of their distributional characteristics in a variety of genomes is undertaken for both whole CGI populations as well as for CGI subsets that lie away from known genes (gene-unrelated or "orphan" CGIs). In both cases power-law-like linearity in double logarithmic scale is found. An evolutionary model, initially put forward for the explanation of a similar pattern found in gene populations is implemented. It includes segmental duplication events and eliminations of most of the duplicated CGIs, while a moderate rate of non-duplicated CGI eliminations is also applied in some cases. Simulations reproduce all the main features of the observed inter-CGI chromosomal size distributions. Our results on power-law-like linearity found in orphan CGI populations suggest that the observed distributional pattern is independent of the analogous pattern that protein coding segments were reported to follow. The power-law-like patterns in the genomic distributions of CGIs described herein are found to be compatible with several other features of the composition, abundance or functional role of CGIs reported in the current literature across several genomes, on the basis of the proposed evolutionary model. PMID:25242375

  20. Christmas Island

    Microsoft Academic Search

    H. B. Guppy

    1888-01-01

    HAVING read with much interest the description of Christmas Island by Captain Aldrich and Mr. Lister, I have endeavoured to interpret some of the facts there given in the light of my own examination of similar islands in the Western Pacific. As pointed out by Captain Wharton, the complete casing of an island, 1200 feet in height, with coral rock

  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. 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

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

    PubMed Central

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

    2011-01-01

    To establish diagnostic criteria for ductal adenocarcinomas of the pancreas (PCs), bacterial artificial chromosome (BAC) array-based methylated CpG island amplification was performed using 139 tissue samples. Twelve BAC clones, for which DNA methylation status was able to discriminate cancerous tissue (T) from noncancerous pancreatic tissue in the learning cohort with a specificity of 100%, were identified. Using criteria that combined the 12 BAC clones, T-samples were diagnosed as cancers with 100% sensitivity and specificity in both the learning and validation cohorts. DNA methylation status on 11 of the BAC clones, which was able to discriminate patients showing early relapse from those with no relapse in the learning cohort with 100% specificity, was correlated with the recurrence-free and overall survival rates in the validation cohort and was an independent prognostic factor by multivariate analysis. Genome-wide DNA methylation profiling may provide optimal diagnostic markers and prognostic indicators for patients with PCs. PMID:21197409

  4. 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

  5. Earth Island

    NSDL National Science Digital Library

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

  6. Identifying Pathogenicity Islands in Bacterial Pathogenomics Using Computational Approaches

    PubMed Central

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

    2014-01-01

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

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

    Microsoft Academic Search

    K. Aberg; Feng Dai; Guangyun Sun; Ember Keighley; Subba Rao Indugula; Linda Bausserman; Satupaitea Viali; John Tuitele; Ranjan Deka; Stephen T. McGarvey

    2008-01-01

    Abnormal lipid levels are important risk factors for cardiovascular diseases. We conducted genome-wide variance component linkage analyses to search for loci influ- encing total cholesterol (TC), LDL, HDL and triglyceride in families residing in American Samoa and Samoa as well as in a combined sample from the two polities. We adjusted the traits for a number of environmental covariates, such

  8. 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

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

    PubMed

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

    2014-01-01

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

  10. Nihoa Island

    NSDL National Science Digital Library

    2007-08-09

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

  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. 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 ...

  13. 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

  14. The Yersinia high-pathogenicity island (HPI): evolutionary and functional aspects

    Microsoft Academic Search

    Sören Schubert; Alexander Rakin; Jürgen Heesemann

    2004-01-01

    The high-pathogenicity island (HPI) is a genomic island essential for the mouse-virulence phenotype in Yersinia and indispensable for pathogenicity of Yersinia and certain pathotypes of Escherichia coli. In contrast to most genomic islands, the HPI is a functional island widely disseminated among members of the family of Enterobacteriaceae. The HPI-encoded phage P4-like integrase together with excisionase and recombination sites make

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

    PubMed

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

    2015-04-01

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

  16. 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.

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

    PubMed Central

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

    2008-01-01

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

  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. Finding exonic islands in a sea of non-coding sequence: splicing related constraints on protein composition and evolution are common in intron-rich genomes

    PubMed Central

    Warnecke, Tobias; Parmley, Joanna L; Hurst, Laurence D

    2008-01-01

    Background In mammals, splice-regulatory domains impose marked trends on the relative abundance of certain amino acids near exon-intron boundaries. Is this a mammalian particularity or symptomatic of exonic splicing regulation across taxa? Are such trends more common in species that a priori have a harder time identifying exon ends, that is, those with pre-mRNA rich in intronic sequence? We address these questions surveying exon composition in a sample of phylogenetically diverse genomes. Results Biased amino acid usage near exon-intron boundaries is common throughout the metazoa but not restricted to the metazoa. There is extensive cross-species concordance as to which amino acids are affected, and reduced/elevated abundances are well predicted by knowledge of splice enhancers. Species expected to rely on exon definition for splicing, that is, those with a higher ratio of intronic to coding sequence, more introns per gene and longer introns, exhibit more amino acid skews. Notably, this includes the intron-rich basidiomycete Cryptococcus neoformans, which, unlike intron-poor ascomycetes (Schizosaccharomyces pombe, Saccharomyces cerevisiae), exhibits compositional biases reminiscent of the metazoa. Strikingly, 5 prime ends of nematode exons deviate radically from normality: amino acids strongly preferred near boundaries are strongly avoided in other species, and vice versa. This we suggest is a measure to avoid attracting trans-splicing machinery. Conclusion Constraints on amino acid composition near exon-intron boundaries are phylogenetically widespread and characteristic of species where exon localization should be problematic. That compositional biases accord with sequence preferences of splice-regulatory proteins and are absent in ascomycetes is consistent with selection on exonic splicing regulation. PMID:18257921

  20. 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.

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  2. CpG Island Mapping by Epigenome Prediction

    Microsoft Academic Search

    Christoph Bock; Jörn Walter; Martina Paulsen; Thomas Lengauer

    2007-01-01

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

  3. Pathogenicity islands: a molecular toolbox for bacterial virulence

    Microsoft Academic Search

    Ohad Gal-Mor; B. Brett Finlay

    2006-01-01

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

  4. Microbial Genomics

    NSDL National Science Digital Library

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

  5. To Build an Island

    NSDL National Science Digital Library

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

  6. Computational prediction of methylation status in human genomic sequences

    E-print Network

    G islands Although progress recently has been made toward whole- genome DNA methylation profiling by using of human brain DNA. This method can be applied both to CpG islands and to non-CpG island regions methylation patterns for all 22 human autosomes. DNA methylation epigenomics methylation prediction Cp

  7. CpG island mapping by epigenome prediction.

    PubMed

    Bock, Christoph; Walter, Jörn; Paulsen, Martina; Lengauer, Thomas

    2007-06-01

    CpG islands were originally identified by epigenetic and functional properties, namely, absence of DNA methylation and frequent promoter association. However, this concept was quickly replaced by simple DNA sequence criteria, which allowed for genome-wide annotation of CpG islands in the absence of large-scale epigenetic datasets. Although widely used, the current CpG island criteria incur significant disadvantages: (1) reliance on arbitrary threshold parameters that bear little biological justification, (2) failure to account for widespread heterogeneity among CpG islands, and (3) apparent lack of specificity when applied to the human genome. This study is driven by the idea that a quantitative score of "CpG island strength" that incorporates epigenetic and functional aspects can help resolve these issues. We construct an epigenome prediction pipeline that links the DNA sequence of CpG islands to their epigenetic states, including DNA methylation, histone modifications, and chromatin accessibility. By training support vector machines on epigenetic data for CpG islands on human Chromosomes 21 and 22, we identify informative DNA attributes that correlate with open versus compact chromatin structures. These DNA attributes are used to predict the epigenetic states of all CpG islands genome-wide. Combining predictions for multiple epigenetic features, we estimate the inherent CpG island strength for each CpG island in the human genome, i.e., its inherent tendency to exhibit an open and transcriptionally competent chromatin structure. We extensively validate our results on independent datasets, showing that the CpG island strength predictions are applicable and informative across different tissues and cell types, and we derive improved maps of predicted "bona fide" CpG islands. The mapping of CpG islands by epigenome prediction is conceptually superior to identifying CpG islands by widely used sequence criteria since it links CpG island detection to their characteristic epigenetic and functional states. And it is superior to purely experimental epigenome mapping for CpG island detection since it abstracts from specific properties that are limited to a single cell type or tissue. In addition, using computational epigenetics methods we could identify high correlation between the epigenome and characteristics of the DNA sequence, a finding which emphasizes the need for a better understanding of the mechanistic links between genome and epigenome. PMID:17559301

  8. 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....

  9. 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....

  10. Alcatraz Island

    NSDL National Science Digital Library

    2005-01-01

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

  11. DNA methylation and the analysis of CpG Islands

    E-print Network

    Czygrinow, Andrzej

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

  12. Tenarife Island, Canary Island Archipelago, Atlantic Ocean

    NASA Technical Reports Server (NTRS)

    1991-01-01

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

  13. 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…

  14. 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

  15. DNA clustering and genome complexity.

    PubMed

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

    2014-12-01

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

  16. Evidence for metaviromic islands in marine phages

    PubMed Central

    Mizuno, Carolina Megumi; Ghai, Rohit; Rodriguez-Valera, Francisco

    2014-01-01

    Metagenomic islands (MGIs) have been defined as genomic regions in prokaryotic genomes that under-recruit from metagenomes where most of the same genome recruits at close to 100% identity over most of its length. The presence of MGIs in prokaryotes has been associated to the diversity of concurrent lineages that vary at this level to disperse the predatory pressure of phages that, reciprocally, maintain high clonal diversity in the population and improve ecosystem performance. This was proposed as a Constant-Diversity (C-D) model. Here we have investigated the regions of phage genomes under-recruiting in a metavirome constructed with a sample from the same habitat where they were retrieved. Some of the genes found to under-recruit are involved in host recognition as would be expected from the C-D model. Furthermore, the recruitment of intragenic regions known to be involved in molecular recognition also had a significant under-recruitment compared to the rest of the gene. However, other genes apparently disconnected from the recognition process under-recruited often, specifically the terminases involved in packaging of the phage genome in the capsid and a few others. In addition, some highly related phage genomes (at nucleotide sequence level) had no metaviromic islands (MVIs). We speculate that the latter might be generalist phages with broad infection range that do not require clone specific lineages. PMID:24550898

  17. Engineering a Reduced Escherichia coli Genome

    PubMed Central

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

    2002-01-01

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

  18. Pathogenicity Islands in Bacterial Pathogenesis

    PubMed Central

    Schmidt, Herbert; Hensel, Michael

    2004-01-01

    In this review, we focus on a group of mobile genetic elements designated pathogenicity islands (PAI). These elements play a pivotal role in the virulence of bacterial pathogens of humans and are also essential for virulence in pathogens of animals and plants. Characteristic molecular features of PAI of important human pathogens and their role in pathogenesis are described. The availability of a large number of genome sequences of pathogenic bacteria and their benign relatives currently offers a unique opportunity for the identification of novel pathogen-specific genomic islands. However, this knowledge has to be complemented by improved model systems for the analysis of virulence functions of bacterial pathogens. PAI apparently have been acquired during the speciation of pathogens from their nonpathogenic or environmental ancestors. The acquisition of PAI not only is an ancient evolutionary event that led to the appearance of bacterial pathogens on a timescale of millions of years but also may represent a mechanism that contributes to the appearance of new pathogens within a human life span. The acquisition of knowledge about PAI, their structure, their mobility, and the pathogenicity factors they encode not only is helpful in gaining a better understanding of bacterial evolution and interactions of pathogens with eukaryotic host cells but also may have important practical implications such as providing delivery systems for vaccination, tools for cell biology, and tools for the development of new strategies for therapy of bacterial infections. PMID:14726454

  19. AnnotateGenomicRegions: a web application

    PubMed Central

    2014-01-01

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

  20. Galapagos Islands Flyby

    NSDL National Science Digital Library

    Dave Pape

    1994-03-13

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

  1. 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....

  2. Japan: Shikoku Island

    Atmospheric Science Data Center

    2013-04-16

    ... and island stations in the waters surrounding Japan and Korea. They characterized meteorological conditions, measured the atmospheric ... flew overhead. These MISR images, centered just north of Shikoku Island in southwest Japan, were acquired on April 13, 2001 ...

  3. 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:  ...

  4. 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.

  5. Island of Timor, Indonesia

    NASA Technical Reports Server (NTRS)

    1989-01-01

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

  6. 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.

  7. How Are Islands Formed?

    NSDL National Science Digital Library

    2001-01-01

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

  8. Barrier island configuration.

    PubMed

    Dolan, R; Hayden, B; Jones, C

    1979-04-27

    The 11 Virginia barrier islands are undergoing rapid changes in shore-line configuration. If this trend continues for another 100 years, two capelike features will develop. The process responsible for this island-chain pattern may be a standing edge wave trapped between Assateague Island and Cape Charles. PMID:17758013

  9. on Hurricane Island, Maine

    Microsoft Academic Search

    R. E. Leonard; P. W. Conkling; J. L. McMahon

    In 1981, a study was initiated to measure the effects of low-level trampling (100 to 200 tramples) on selected vegetation on Hurricane Island, Maine. Low levels of trampling are representative of general recreational use patterns on most Maine islands. The study was designed to compare percent survival of common island species when subjected to low-level trampling, to observe treadway formation,

  10. Diomede Islands, Bering Straight

    NASA Technical Reports Server (NTRS)

    2008-01-01

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

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

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

  11. 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....

  12. Apostle Islands National Lakeshore

    NSDL National Science Digital Library

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

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

    PubMed

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

    2014-06-01

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

  14. Genome Research

    NSDL National Science Digital Library

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

  15. The Salmonella enterica pan-genome.

    PubMed

    Jacobsen, Annika; Hendriksen, Rene S; Aaresturp, Frank M; Ussery, David W; Friis, Carsten

    2011-10-01

    Salmonella enterica is divided into four subspecies containing a large number of different serovars, several of which are important zoonotic pathogens and some show a high degree of host specificity or host preference. We compare 45 sequenced S. enterica genomes that are publicly available (22 complete and 23 draft genome sequences). Of these, 35 were found to be of sufficiently good quality to allow a detailed analysis, along with two Escherichia coli strains (K-12 substr. DH10B and the avian pathogenic E. coli (APEC O1) strain). All genomes were subjected to standardized gene finding, and the core and pan-genome of Salmonella were estimated to be around 2,800 and 10,000 gene families, respectively. The constructed pan-genomic dendrograms suggest that gene content is often, but not uniformly correlated to serotype. Any given Salmonella strain has a large stable core, whilst there is an abundance of accessory genes, including the Salmonella pathogenicity islands (SPIs), transposable elements, phages, and plasmid DNA. We visualize conservation in the genomes in relation to chromosomal location and DNA structural features and find that variation in gene content is localized in a selection of variable genomic regions or islands. These include the SPIs but also encompass phage insertion sites and transposable elements. The islands were typically well conserved in several, but not all, isolates--a difference which may have implications in, e.g., host specificity. PMID:21643699

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

    Microsoft Academic Search

    K. Shiota

    2004-01-01

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

  17. The Flores Island tsunamis

    Microsoft Academic Search

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

    1993-01-01

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

  18. Island biogeography Islands over-proportionally important in biogeography,

    E-print Network

    Kiehn, Michael

    continental islands; oceanic islands Alfred R. Wallace: 1823-1913 Studies of island biota are important. Wallace: In the absence of predation and competition, organisms on isolated landmasses may survive

  19. 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

  20. 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.

  1. ANTHROPOLOGY 343 PACIFIC ISLANDS ARCHAEOLOGY

    E-print Network

    ANTHROPOLOGY 343 PACIFIC ISLANDS ARCHAEOLOGY 2014, Fall Term William S. Ayres Department Archaeology, Ayres, Fall 2014 1 Anthropology 343 Pacific Islands Archaeology University of Oregon Fall islands are revealed through archaeological evidence. A review of basic archaeological concepts provides

  2. 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. ...

  3. On island arcs

    Microsoft Academic Search

    Patrick J. Coleman

    1975-01-01

    Older concepts of island arcs, prior to the 1960's, were dominated by the Indonesian model and described in terms of geosynclinal theory, but not altogether fruitfully. Platetectonics theory has given new insights into the genesis, mode of formation, behaviour and ultimate fate of island arcs. Subduction with descent of the lithospheric slab is the governing phenomenon. As the slab descends

  4. 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.

  5. VEGETATION OF HENDERSON ISLAND

    Microsoft Academic Search

    GUSTAV PAULAY; T. SPENCER

    On the basis of field surveys from the north and north-west beaches, the vegetation of Henderson Island can be classified into 11 vegetation communities: 2 in littoral environments with sandy substrates, 4 on rocky coasts and 5 associated with the limestone plateau. Apart from the cutting of 'miro' wood by Pitcairn islanders, the communities are remarkably undisturbed, with only 5

  6. 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 ...

  7. 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…

  8. Microbial lifestyle and genome signatures.

    PubMed

    Dutta, Chitra; Paul, Sandip

    2012-04-01

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

  9. 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

  10. 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

  11. Ten years of bacterial genome sequencing: comparative-genomics-based discoveries.

    PubMed

    Binnewies, Tim T; Motro, Yair; Hallin, Peter F; Lund, Ole; Dunn, David; La, Tom; Hampson, David J; Bellgard, Matthew; Wassenaar, Trudy M; Ussery, David W

    2006-07-01

    It has been more than 10 years since the first bacterial genome sequence was published. Hundreds of bacterial genome sequences are now available for comparative genomics, and searching a given protein against more than a thousand genomes will soon be possible. The subject of this review will address a relatively straightforward question: "What have we learned from this vast amount of new genomic data?" Perhaps one of the most important lessons has been that genetic diversity, at the level of large-scale variation amongst even genomes of the same species, is far greater than was thought. The classical textbook view of evolution relying on the relatively slow accumulation of mutational events at the level of individual bases scattered throughout the genome has changed. One of the most obvious conclusions from examining the sequences from several hundred bacterial genomes is the enormous amount of diversity--even in different genomes from the same bacterial species. This diversity is generated by a variety of mechanisms, including mobile genetic elements and bacteriophages. An examination of the 20 Escherichia coli genomes sequenced so far dramatically illustrates this, with the genome size ranging from 4.6 to 5.5 Mbp; much of the variation appears to be of phage origin. This review also addresses mobile genetic elements, including pathogenicity islands and the structure of transposable elements. There are at least 20 different methods available to compare bacterial genomes. Metagenomics offers the chance to study genomic sequences found in ecosystems, including genomes of species that are difficult to culture. It has become clear that a genome sequence represents more than just a collection of gene sequences for an organism and that information concerning the environment and growth conditions for the organism are important for interpretation of the genomic data. The newly proposed Minimal Information about a Genome Sequence standard has been developed to obtain this information. PMID:16773396

  12. Conservation Strategy for Sable Island

    E-print Network

    Jones, Ian L.

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

  13. The Island Institute

    NSDL National Science Digital Library

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

  14. Heat Island Effect

    NSDL National Science Digital Library

    For people living in and around cities, heat islands are of growing concern. This phenomenon describes urban and suburban temperatures that are 2 to 10 degrees F (1 to 6 degrees C) hotter than nearby rural areas. Elevated temperatures can impact communities by increasing peak energy demand, air conditioning costs, air pollution levels, and heat-related illness and mortality. The materials available here describe the basic causes of the heat island effect, and what can be done to mitigate some of the impacts. There is also an overview of the Urban Heat Island Pilot Project (UHIPP), an initiative being conducted in five cities in the U.S. to adopt and evaluate heat island reduction strategies and programs.

  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. Photographs of Tinian Island

    NSDL National Science Digital Library

    Christopher Griffith

    This collection of photographs depicts the 509th Composite Bomb Group on Tinian Island in the Pacific, the crews of the Enola Gay and Bock's Car, and actual atomic bombs that were used on Hiroshima and Nagasaki.

  17. Easter Island Revisited

    NSDL National Science Digital Library

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

    2007-09-21

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

  18. Perioperative Genomics

    PubMed Central

    Nagele, Peter

    2011-01-01

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

  19. Island Inequality Map

    NSDL National Science Digital Library

    Illuminations National Council of Teachers of Math

    2009-01-15

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

  20. Urban Heat Islands

    NSDL National Science Digital Library

    Lisa Gardiner

    In this activity, students learn about the urban heat island effect by investigating which areas of their schoolyard have higher temperatures - trees, grass, asphalt, and other materials. Based on their results, they hypothesize how concentrations of surfaces that absorb heat might affect the temperature in cities - the urban heat island effect. Then they analyze data about the history of Los Angeles heat waves and look for patterns in the Los Angeles climate data and explore patterns.

  1. Conservation of the Island Spotted Skunk and Island Fox in a Recovering Island Ecosystenl

    Microsoft Academic Search

    Kevin R. Crooks; Dirk Van Vuren

    We review available information on the ecolo­ gy of island spotted skunks (Spilogale gracilis amphiala) and island foxes (Urocyon littoralis santacruzae) on Santa Cruz Island, with a focus on recent research, and present new infonnation on distribution and abundance. Our objective is to evaluate the present and future status of skunks and foxes in the context of ongoing island recov­

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

    PubMed Central

    Liang, Chunguang; Dandekar, Thomas

    2006-01-01

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

  3. An Enterotoxin-Bearing Pathogenicity Island in Staphylococcus epidermidis?†

    PubMed Central

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

    2011-01-01

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

  4. 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...

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

    PubMed

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

    2007-05-01

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

  6. Aquaculture Genomics

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  7. 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

  8. Comparison of 61 sequenced Escherichia coli genomes.

    PubMed

    Lukjancenko, Oksana; Wassenaar, Trudy M; Ussery, David W

    2010-11-01

    Escherichia coli is an important component of the biosphere and is an ideal model for studies of processes involved in bacterial genome evolution. Sixty-one publically available E. coli and Shigella spp. sequenced genomes are compared, using basic methods to produce phylogenetic and proteomics trees, and to identify the pan- and core genomes of this set of sequenced strains. A hierarchical clustering of variable genes allowed clear separation of the strains into clusters, including known pathotypes; clinically relevant serotypes can also be resolved in this way. In contrast, when in silico MLST was performed, many of the various strains appear jumbled and less well resolved. The predicted pan-genome comprises 15,741 gene families, and only 993 (6%) of the families are represented in every genome, comprising the core genome. The variable or 'accessory' genes thus make up more than 90% of the pan-genome and about 80% of a typical genome; some of these variable genes tend to be co-localized on genomic islands. The diversity within the species E. coli, and the overlap in gene content between this and related species, suggests a continuum rather than sharp species borders in this group of Enterobacteriaceae. PMID:20623278

  9. Comparison of 61 Sequenced Escherichia coli Genomes

    PubMed Central

    Lukjancenko, Oksana; Wassenaar, Trudy M.

    2010-01-01

    Escherichia coli is an important component of the biosphere and is an ideal model for studies of processes involved in bacterial genome evolution. Sixty-one publically available E. coli and Shigella spp. sequenced genomes are compared, using basic methods to produce phylogenetic and proteomics trees, and to identify the pan- and core genomes of this set of sequenced strains. A hierarchical clustering of variable genes allowed clear separation of the strains into clusters, including known pathotypes; clinically relevant serotypes can also be resolved in this way. In contrast, when in silico MLST was performed, many of the various strains appear jumbled and less well resolved. The predicted pan-genome comprises 15,741 gene families, and only 993 (6%) of the families are represented in every genome, comprising the core genome. The variable or ‘accessory’ genes thus make up more than 90% of the pan-genome and about 80% of a typical genome; some of these variable genes tend to be co-localized on genomic islands. The diversity within the species E. coli, and the overlap in gene content between this and related species, suggests a continuum rather than sharp species borders in this group of Enterobacteriaceae. PMID:20623278

  10. Prediction of CpG-island function: CpG clustering vs. sliding-window methods

    PubMed Central

    2010-01-01

    Background Unmethylated stretches of CpG dinucleotides (CpG islands) are an outstanding property of mammal genomes. Conventionally, these regions are detected by sliding window approaches using %G + C, CpG observed/expected ratio and length thresholds as main parameters. Recently, clustering methods directly detect clusters of CpG dinucleotides as a statistical property of the genome sequence. Results We compare sliding-window to clustering (i.e. CpGcluster) predictions by applying new ways to detect putative functionality of CpG islands. Analyzing the co-localization with several genomic regions as a function of window size vs. statistical significance (p-value), CpGcluster shows a higher overlap with promoter regions and highly conserved elements, at the same time showing less overlap with Alu retrotransposons. The major difference in the prediction was found for short islands (CpG islets), often exclusively predicted by CpGcluster. Many of these islets seem to be functional, as they are unmethylated, highly conserved and/or located within the promoter region. Finally, we show that window-based islands can spuriously overlap several, differentially regulated promoters as well as different methylation domains, which might indicate a wrong merge of several CpG islands into a single, very long island. The shorter CpGcluster islands seem to be much more specific when concerning the overlap with alternative transcription start sites or the detection of homogenous methylation domains. Conclusions The main difference between sliding-window approaches and clustering methods is the length of the predicted islands. Short islands, often differentially methylated, are almost exclusively predicted by CpGcluster. This suggests that CpGcluster may be the algorithm of choice to explore the function of these short, but putatively functional CpG islands. PMID:20500903

  11. Archaeoastronomy of Easter Island

    NASA Astrophysics Data System (ADS)

    Edwards, Edmundo

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

  12. 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.

  13. Genomic acquisition of a capsular polysaccharide virulence cluster by non-pathogenic Burkholderia isolates

    E-print Network

    Sim, Bernice Meng Qi; Chantratita, Narisara; Ooi, Wen Fong; Nandi, Tannistha; Tewhey, Ryan; Wuthiekanun, Vanaporn; Thaipadungpanit, Janjira; Tumapa, Sarinna; Ariyaratne, Pramila; Sung, Wing-Kin; Sem, Xiao Hui; Chua, Hui Hoon; Ramnarayanan, Kalpana; Lin, Chi Ho; Liu, Yichun; Feil, Edward J; Glass, Mindy B; Tan, Gladys; Peacock, Sharon J; Tan, Patrick

    2010-08-27

    genomic islands, while 26 regions were novel. Variant B. thailandensis isolates exhibited isolated acquisition of a capsular polysaccharide biosynthesis gene cluster (B. pseudomallei-like capsular polysaccharide) closely resembling a similar cluster in B...

  14. 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

  15. 123Genomics

    NSDL National Science Digital Library

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

  16. Your Genome

    NSDL National Science Digital Library

    2002-01-01

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

  17. Genomic adaptation of the Lactobacillus casei group.

    PubMed

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

    2013-01-01

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

  18. 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....

  19. 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....

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

    E-print Network

    dePamphilis, Claude

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

  1. Genomics Glossary

    NSDL National Science Digital Library

    Chitty, Mary Glen.

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

  2. Late Colonization of Easter Island

    Microsoft Academic Search

    Terry L. Hunt; Carl P. Lipo

    2006-01-01

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

  3. 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...

  4. Costly island for Arctic drilling

    SciTech Connect

    Not Available

    1983-12-01

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

  5. Siberian Expedition: Wrangel Island

    NSDL National Science Digital Library

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

  6. Island Ecology in Bermuda.

    ERIC Educational Resources Information Center

    Wulff, Barry L.; And Others

    1981-01-01

    Reports on an island ecology course offered by Eastern Connecticut State College providing opportunities for students to study the ecology and natural history of organisms found in a variety of subtropical habitats in Bermuda. Explains student selection criteria, trip preparation, evaluation criteria, daily programs, and habitats studied on the…

  7. Islands and despots

    Microsoft Academic Search

    Godfrey Baldacchino

    2012-01-01

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

  8. 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.

  9. Pine Island Bay

    Atmospheric Science Data Center

    2013-04-16

    ... of the sequence is due to a gap in image acquisition during Antarctic winter, when the glacier was in continuous darkness. Pine Island ... continent's fastest moving glacier. This area of the West Antarctic Ice Sheet is also believed to be the most susceptible to collapse. ...

  10. 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...

  11. CpG island mapping by epigenome prediction

    Microsoft Academic Search

    Christoph Bock; Jorn E Walter; Martina Paulsen; Thomas Lengauer

    2005-01-01

    epigenome,mapping,for CpG island detection,since it abstracts,from,specific properties,that are limited,to a single cell type or tissue. In addition, using computational epigenetics methods we could identify high correlation between the epigenome and characteristics of the DNA sequence, a finding which emphasizes the need for a better understanding of the mechanistic,links between,genome,and,epigenome. Citation: Bock C, Walter J, Paulsen M, Lengauer T (2007) CpG

  12. Integrated analysis of genome-wide DNA methylation and gene expression profiles in

    E-print Network

    Integrated analysis of genome-wide DNA methylation and gene expression profiles in molecular 15, 2013; Accepted July 2, 2013 ABSTRACT Aberrant DNA methylation of CpG islands, CpG island shores. To date, a systematic study on the effect of DNA methylation on gene expression using high resolution data

  13. The human genome: a multifractal analysis

    PubMed Central

    2011-01-01

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

  14. INDeGenIUS, a new method for high-throughput identification of specialized functional islands in completely sequenced organisms

    Microsoft Academic Search

    Sakshi Shrivastava; Ch. V. Siva Kumar Reddy; Sharmila S. Mande

    2010-01-01

    Genomic islands (GIs) are regions in the genome which are believed to have been acquired via horizontal gene transfer events\\u000a and are thus likely to be compositionally distinct from the rest of the genome. Majority of the genes located in a GI encode\\u000a a particular function. Depending on the genes they encode, GIs can be classified into various categories, such

  15. Novel Chikungunya Virus Variant in Travelers Returning from Indian Ocean Islands

    PubMed Central

    Parola, Philippe; de Lamballerie, Xavier; Jourdan, Jacques; Rovery, Clarisse; Vaillant, Véronique; Minodier, Philippe; Brouqui, Philippe; Flahault, Antoine; Charrel, Rémi N.

    2006-01-01

    Chikungunya virus (CHIKV) emerged in Indian Ocean islands in 2005 and is causing an ongoing outbreak that involves >260,000 patients, including travelers returning home from these islands. We investigated cases in 4 patients returning from Mayotte and Reunion Islands with CHIKV infection and a nurse infected in metropolitan France after direct contact with the blood of a traveler. Four patients had tenosynovitis and pain at wrist pressure, and 1 had life-threatening manifestations. Four CHIKV strains were isolated, including 1 from the patient with the autochthonous case. The complete genomic sequence identified a new CHIKV variant emerging from the East/central African evolutionary lineage. Aedes albopictus, the implicated vector of CHIKV in Indian Ocean islands, has dispersed worldwide in recent decades. High viral loads in patients returning from Indian Ocean islands to countries where Ae. albopictus is prevalent may be a source of epidemics. PMID:17176562

  16. The genus burkholderia: analysis of 56 genomic sequences.

    PubMed

    Ussery, D W; Kiil, K; Lagesen, K; Sicheritz-Pontén, T; Bohlin, J; Wassenaar, T M

    2009-01-01

    The genus Burkholderia consists of a number of very diverse species, both in terms of lifestyle (which varies from category B pathogens to apathogenic soil bacteria and plant colonizers) and their genetic contents. We have used 56 publicly available genomes to explore the genomic diversity within this genus, including genome sequences that are not completely finished, but are available from the NCBI database. Defining the pan- and core genomes of species results in insights in the conserved and variable fraction of genomes, and can verify (or question) historic, taxonomic groupings. We find only several hundred genes that are conserved across all Burkholderia genomes, whilst there are more than 40,000 gene families in the Burkholderia pan-genome. A BLAST matrix visualizes the fraction of conserved genes in pairwise comparisons. A BLAST atlas shows which genes are actually conserved in a number of genomes, located and visualized with reference to a chosen genome. Genomic islands are common in many Burkholderia genomes, and most of these can be readily visualized by DNA structural properties of the chromosome. Trees that are based on relatedness of gene family content yield different results depending on what genes are analyzed. Some of the differences can be explained by errors in incomplete genome sequences, but, as our data illustrate, the outcome of phylogenetic trees depends on the type of genes that are analyzed. PMID:19696499

  17. Pine Island Iceberg Formation

    NSDL National Science Digital Library

    Lori Perkins

    2002-01-10

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

  18. Arts & Genomics

    NSDL National Science Digital Library

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

  19. 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

  20. Southern Vancouver Island

    NSDL National Science Digital Library

    Landsat satellite images of Southern Vancouver Island are among the collection of the Canada Centre for Remote Sensing's Images of Canada series (reviewed in the June 7, 2000 Scout Report for Science and Engineering). Below the full-color .jpeg images are tables documenting the satellites and sensors used, date of acquisition, image resolution, area (km), and links to a reference map. Educational, hyperlinked text about the featured region and close-ups of important topographic features accompany the images.

  1. Integrated Analysis of Gene Expression, CpG Island Methylation, and Gene Copy Number in Breast Cancer Cells by Deep Sequencing

    Microsoft Academic Search

    Zhifu Sun; Yan W. Asmann; Krishna R. Kalari; Brian Bot; Jeanette E. Eckel-Passow; Tiffany R. Baker; Jennifer M. Carr; Irina Khrebtukova; Shujun Luo; Lu Zhang; Gary P. Schroth; Edith A. Perez; E. Aubrey Thompson

    2011-01-01

    We used deep sequencing technology to profile the transcriptome, gene copy number, and CpG island methylation status simultaneously in eight commonly used breast cell lines to develop a model for how these genomic features are integrated in estrogen receptor positive (ER+) and negative breast cancer. Total mRNA sequence, gene copy number, and genomic CpG island methylation were carried out using

  2. A Structural Split in the Human Genome

    Microsoft Academic Search

    Clara S. M. Tang; Richard J. Epstein; Guillaume Bourque

    2007-01-01

    BackgroundPromoter-associated CpG islands (PCIs) mediate methylation-dependent gene silencing, yet tend to co-locate to transcriptionally active genes. To address this paradox, we used data mining to assess the behavior of PCI-positive (PCI+) genes in the human genome.ResultsPCI+ genes exhibit a bimodal distribution: (1) a ‘housekeeping-like’ subset characterized by higher GC content and lower intron length\\/number, and (2) a ‘pseudogene paralog’ subset

  3. The plant geography of dredged-material islands along the Texas coast

    E-print Network

    Irish, Gary Joe

    1978-01-01

    Island. 12. Soil data ? Port Isabel Island. 65 67 13. Soil salinities of the supra-tidal zones of Bird Island and Jellyfish Island. 70 14. Island area and environmental data. 77 15. Multiple regressions of ordination positions on vegetated area... Drift Island Reed Island Gnat Island Tortuga Island Mangrove Island Crane Island Wind Tidal Flats Island Mesquite Island Port Mansfield Island Discontinued Island Jellyfish Island Bird Island Port Isabel Island Location Trinity Bay Trinity...

  4. Hybrid Origin and Genomic Mosaicism of Dubautia scabra (Hawaiian Silversword Alliance; Asteraceae, Madiinae)

    E-print Network

    Hybrid Origin and Genomic Mosaicism of Dubautia scabra (Hawaiian Silversword Alliance; Asteraceae incongruence is the placement of Dubautia scabra (DC.) D. D. Keck in the Hawaiian silversword alliance (HSA on Maui Nui and Hawai`i (the Big Island). Keywords--Dubautia, genome mosaic, Hawaiian silversword alliance

  5. Complete Genome Sequence of the Commensal Enterococcus faecalis 62, Isolated from a Healthy Norwegian Infant?

    PubMed Central

    Brede, Dag Anders; Snipen, Lars Gustav; Ussery, David Wayne; Nederbragt, Alexander J.; Nes, Ingolf F.

    2011-01-01

    The genome of Enterococcus faecalis 62, a commensal isolate from a healthy Norwegian infant, revealed multiple adaptive traits to the gastrointestinal tract (GIT) environment and the milk-containing diet of breast-fed infants. Adaptation to a commensal existence was emphasized by lactose and other carbohydrate metabolism genes within genomic islands, accompanied by the absence of virulence traits. PMID:21398545

  6. Complete genome sequence of the commensal Enterococcus faecalis 62, isolated from a healthy Norwegian infant.

    PubMed

    Brede, Dag Anders; Snipen, Lars Gustav; Ussery, David Wayne; Nederbragt, Alexander J; Nes, Ingolf F

    2011-05-01

    The genome of Enterococcus faecalis 62, a commensal isolate from a healthy Norwegian infant, revealed multiple adaptive traits to the gastrointestinal tract (GIT) environment and the milk-containing diet of breast-fed infants. Adaptation to a commensal existence was emphasized by lactose and other carbohydrate metabolism genes within genomic islands, accompanied by the absence of virulence traits. PMID:21398545

  7. Short communication Heritability and genome-wide linkage analysis of migraine in the genetic isolate of

    E-print Network

    Nyholt, Dale R.

    Short communication Heritability and genome-wide linkage analysis of migraine in the genetic Available online xxxx Keywords: Norfolk Island Migraine Genome Wide Linkage Analysis Association Chromosome 13 Chromosome 9 Migraine is a common neurovascular disorder with a complex envirogenomic aetiology

  8. Physiological Genomics

    NSDL National Science Digital Library

    1969-12-31

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

  9. Late colonization of Easter Island.

    PubMed

    Hunt, Terry L; Lipo, Carl P

    2006-03-17

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

  10. WIND DATA REPORT Thompson Island

    E-print Network

    Massachusetts at Amherst, University of

    WIND DATA REPORT Thompson Island September 1, 2003 ­ November 30, 2003 Prepared for Massachusetts...................................................................................................................... 9 Wind Speed Time Series............................................................................................................. 9 Wind Speed Distribution

  11. WIND DATA REPORT Thompson Island

    E-print Network

    Massachusetts at Amherst, University of

    WIND DATA REPORT Thompson Island March 1, 2003 ­ May 31, 2003 Prepared for Massachusetts Technology...................................................................................................................... 9 Wind Speed Time Series............................................................................................................. 9 Wind Speed Distributions

  12. WIND DATA REPORT Thompson Island

    E-print Network

    Massachusetts at Amherst, University of

    WIND DATA REPORT Thompson Island December 1, 2003 ­ February 29, 2004 Prepared for Massachusetts.................................................................................................................... 11 Wind Speed Time Series........................................................................................................... 11 Wind Speed Distribution

  13. WIND DATA REPORT Thompson Island

    E-print Network

    Massachusetts at Amherst, University of

    WIND DATA REPORT Thompson Island June 1, 2004 ­ August 31, 2004 Prepared for Massachusetts...................................................................................................................... 9 Wind Speed Time Series............................................................................................................. 9 Wind Speed Distribution

  14. WIND DATA REPORT Thompson Island

    E-print Network

    Massachusetts at Amherst, University of

    WIND DATA REPORT Thompson Island March 1, 2004 ­ May 31, 2004 Prepared for Massachusetts Technology...................................................................................................................... 9 Wind Speed Time Series............................................................................................................. 9 Wind Speed Distribution

  15. WIND DATA REPORT Thompson Island

    E-print Network

    Massachusetts at Amherst, University of

    WIND DATA REPORT Thompson Island June 1, 2003 ­ August 31, 2003 Prepared for Massachusetts...................................................................................................................... 9 Wind Speed Time Series............................................................................................................. 9 Wind Speed Distribution

  16. 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

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

    PubMed

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

    2015-02-01

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

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

    PubMed Central

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

    2015-01-01

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

  19. Islands of the Arctic

    NASA Astrophysics Data System (ADS)

    Dowdeswell, Julian; Hambrey, Michael

    2002-11-01

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

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

    PubMed Central

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

    2012-01-01

    Salmonella enterica serovar Typhimurium is one of the most prevalent serovars of Salmonella that causes human gastroenteritis. Here, we report the draft genome sequence of the S. Typhimurium multidrug-resistant strain ST1660/06. Comparative genomic analysis unveiled three strain-specific genomic islands that potentially confer the multidrug resistance and virulence of the strain. PMID:23105062

  1. Islands in the landscape

    E-print Network

    T. Clifton; Andrei Linde; Navin Sivanandam

    2007-01-10

    The string theory landscape consists of many metastable de Sitter vacua, populated by eternal inflation. Tunneling between these vacua gives rise to a dynamical system, which asymptotically settles down to an equilibrium state. We investigate the effects of sinks to anti-de Sitter space, and show how their existence can change probabilities in the landscape. Sinks can disturb the thermal occupation numbers that would otherwise exist in the landscape and may cause regions that were previously in thermal contact to be divided into separate, thermally isolated islands.

  2. Island colonization and evolution of the insular woody habit in Echium L. (Boraginaceae).

    PubMed Central

    Böhle, U R; Hilger, H H; Martin, W F

    1996-01-01

    Numerous island-inhabiting species of predominantly herbaceous angiosperm genera are woody shrubs or trees. Such "insular woodiness" is strongly manifested in the genus Echium, in which the continental species of circummediterranean distribution are herbaceous, whereas endemic species of islands along the Atlantic coast of north Africa are woody perennial shrubs. The history of 37 Echium species was traced with 70 kb of noncoding DNA determined from both chloroplast and nuclear genomes. In all, 239 polymorphic positions with 137 informative sites, in addition to 27 informative indels, were found. Island-dwelling Echium species are shown to descend from herbaceous continental ancestors via a single island colonization event that occurred < 20 million years ago. Founding colonization appears to have taken place on the Canary Islands, from which the Madeira and Cape Verde archipelagos were invaded. Colonization of island habitats correlates with a recent origin of perennial woodiness from herbaceous habit and was furthermore accompanied by intense speciation, which brought forth remarkable diversity of forms among contemporary island endemics. We argue that the origin of insular woodiness involved response to counter-selection of inbreeding depression in founding island colonies. Images Fig. 1 Fig. 3 PMID:8876207

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

    E-print Network

    Minnesota, University of

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

  4. Personal genomics services: whose genomes?

    PubMed Central

    Gurwitz, David; Bregman-Eschet, Yael

    2009-01-01

    New companies offering personal whole-genome information services over the internet are dynamic and highly visible players in the personal genomics field. For fees currently ranging from US$399 to US$2500 and a vial of saliva, individuals can now purchase online access to their individual genetic information regarding susceptibility to a range of chronic diseases and phenotypic traits based on a genome-wide SNP scan. Most of the companies offering such services are based in the United States, but their clients may come from nearly anywhere in the world. Although the scientific validity, clinical utility and potential future implications of such services are being hotly debated, several ethical and regulatory questions related to direct-to-consumer (DTC) marketing strategies of genetic tests have not yet received sufficient attention. For example, how can we minimize the risk of unauthorized third parties from submitting other people's DNA for testing? Another pressing question concerns the ownership of (genotypic and phenotypic) information, as well as the unclear legal status of customers regarding their own personal information. Current legislation in the US and Europe falls short of providing clear answers to these questions. Until the regulation of personal genomics services catches up with the technology, we call upon commercial providers to self-regulate and coordinate their activities to minimize potential risks to individual privacy. We also point out some specific steps, along the trustee model, that providers of DTC personal genomics services as well as regulators and policy makers could consider for addressing some of the concerns raised below. PMID:19259127

  5. Personal genomics services: whose genomes?

    PubMed

    Gurwitz, David; Bregman-Eschet, Yael

    2009-07-01

    New companies offering personal whole-genome information services over the internet are dynamic and highly visible players in the personal genomics field. For fees currently ranging from US$399 to US$2500 and a vial of saliva, individuals can now purchase online access to their individual genetic information regarding susceptibility to a range of chronic diseases and phenotypic traits based on a genome-wide SNP scan. Most of the companies offering such services are based in the United States, but their clients may come from nearly anywhere in the world. Although the scientific validity, clinical utility and potential future implications of such services are being hotly debated, several ethical and regulatory questions related to direct-to-consumer (DTC) marketing strategies of genetic tests have not yet received sufficient attention. For example, how can we minimize the risk of unauthorized third parties from submitting other people's DNA for testing? Another pressing question concerns the ownership of (genotypic and phenotypic) information, as well as the unclear legal status of customers regarding their own personal information. Current legislation in the US and Europe falls short of providing clear answers to these questions. Until the regulation of personal genomics services catches up with the technology, we call upon commercial providers to self-regulate and coordinate their activities to minimize potential risks to individual privacy. We also point out some specific steps, along the trustee model, that providers of DTC personal genomics services as well as regulators and policy makers could consider for addressing some of the concerns raised below. PMID:19259127

  6. Complete mitochondrial genome of the black giant squirrel Ratufa bicolor (Rodentia: Sciuridae).

    PubMed

    Kong, Lingming; Wang, Wenquan; Cong, Haiyan; Liu, Zexin; Li, Yuchun

    2014-01-01

    Abstract The complete mitochondrial genome of black giant squirrel (Ratufa bicolor) from Hainan Island was sequenced and characterized in detail. The 16,563?bp genome was composed of 13 protein-coding genes, 22 tRNAs, 2 rRNAs and 2 non-coding regions. The mitochondrial genome of R. bicolor presented in this report will be useful for species identification, conversation and clarifying the controversial taxonomic status of genus Ratufa. PMID:24397765

  7. Rain on small tropical islands

    NASA Astrophysics Data System (ADS)

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

    2011-04-01

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

  8. Genomic Avenue to Avian Colisepticemia

    PubMed Central

    Huja, Sagi; Oren, Yaara; Trost, Eva; Brzuszkiewicz, Elzbieta; Biran, Dvora; Blom, Jochen; Goesmann, Alexander; Gottschalk, Gerhard; Hacker, Jörg

    2015-01-01

    ABSTRACT Here we present an extensive genomic and genetic analysis of Escherichia coli strains of serotype O78 that represent the major cause of avian colisepticemia, an invasive infection caused by avian pathogenic Escherichia coli (APEC) strains. It is associated with high mortality and morbidity, resulting in significant economic consequences for the poultry industry. To understand the genetic basis of the virulence of avian septicemic E. coli, we sequenced the entire genome of a clinical isolate of serotype O78—O78:H19 ST88 isolate 789 (O78-9)—and compared it with three publicly available APEC O78 sequences and one complete genome of APEC serotype O1 strain. Although there was a large variability in genome content between the APEC strains, several genes were conserved, which are potentially critical for colisepticemia. Some of these genes are present in multiple copies per genome or code for gene products with overlapping function, signifying their importance. A systematic deletion of each of these virulence-related genes identified three systems that are conserved in all septicemic strains examined and are critical for serum survival, a prerequisite for septicemia. These are the plasmid-encoded protein, the defective ETT2 (E. coli type 3 secretion system 2) type 3 secretion system ETT2sepsis, and iron uptake systems. Strain O78-9 is the only APEC O78 strain that also carried the regulon coding for yersiniabactin, the iron binding system of the Yersinia high-pathogenicity island. Interestingly, this system is the only one that cannot be complemented by other iron uptake systems under iron limitation and in serum. PMID:25587010

  9. 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

  10. Silencing Genomes

    NSDL National Science Digital Library

    2007-06-12

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

  11. Citrus Genomics

    PubMed Central

    Talon, Manuel; Gmitter Jr., Fred G.

    2008-01-01

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

  12. Richmond's Urban Heat Island

    NSDL National Science Digital Library

    Donald M Yow

    Students will need to learn about urban heat islands before they will have all of the information necessary to complete this lab. Instructors may wish to accomplish this via lecture and/or assigned readings and discussion. You may wish to start with the following: Yow, D.M. 2007, "Urban Heat Islands: Observations, Impacts, and Adaptation," Geography Compass. Volume 2, October 2007, 1227-1251. Also, if your students have no prior experience with MS excel, guiding them through a quick tutorial is advisable. The first thing students will do in the exercise is report on some important causes of the UHI. Then, they will examine two real-world sites via photographs and Google Earth to discuss how each location's land use/land cover may affect local temperatures. Next, students will analyze data acquired at each site using MS excel. After that, students will be asked to think about potential impacts of the UHI. The exercise ends with a critical thinking exercise asking students to devise and evaluate strategies to communicate scientific knowledge to non-science professionals. Has minimal/no quantitative component Uses geophysics to solve problems in other fields

  13. Ancient genomics.

    PubMed

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

    2015-01-19

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

  14. 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

  15. Species-specific organization of CpG island promoters at mammalian homologous genes

    PubMed Central

    Cuadrado, Myriam; Sacristán, María; Antequera, Francisco

    2001-01-01

    An essential issue derived from the sequencing of the human and other genomes is the identification of gene regulatory elements. Using in vivo footprinting and expression analysis, here we show that mouse and human CpG island promoters at homologous genes have a completely different organization in terms of size and binding of transcription factors. Despite these species-specific differences, a unifying picture emerges from the precise confinement of protein–DNA interactions between the 5? boundary of the CpG islands and the transcription initiation site. This finding allows direct localization of promoters on genomic sequences and reveals a very high rate of variation and evolutionary divergence of mammalian regulatory regions. Our results also show that CpG island promoters associated with tissue-specific genes, such as the human ?-globin, are bound by ubiquitous factors that allow a constitutive low level of expression in many cell types. PMID:11454739

  16. 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...

  17. 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 ...

  18. An Island Effect in Japanese.

    ERIC Educational Resources Information Center

    Richards, Norvin

    2000-01-01

    Develops an argument for a pied-piping approach to the apparent absence of island effects in Japanese, along the lines of Nishigauchi (1986, 1990). Investigates the nature of pied-piping, developing a theory that accounts for the fact that wh-islands cannot be pied-piped. (Author/VWL)

  19. Island cosmology in the landscape

    Microsoft Academic Search

    Yun-Song Piao

    2008-01-01

    In the eternally inflationary background driven by the metastable vacua of the landscape, it is possible that some local quantum fluctuations with the null energy condition violation can be large enough to stride over the barriers among different vacua, so that create some islands full of radiation in new vacua, and then these emergently thermalized islands will enter into the

  20. Rethinking Easter Island's ecological catastrophe

    Microsoft Academic Search

    Terry L. Hunt

    2007-01-01

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

  1. 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...

  2. Filariasis in Palawan, Philippine Islands

    Microsoft Academic Search

    Benjamin D. Cabrera

    1964-01-01

    FILARIASIS in the Philippine Islands is endemic in certain areas of the Bicol Peninsula of Luzon, in the neighbouring islands of Samar and Leyte, and in Mindanao, where there are extensive plantations of abaca1. Here, the principal vector is Aedes poicilius, which breeds in the leaf axils especially of abaca and banana trees2. Baisas3 found that in some communities of

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

    PubMed Central

    Mekalanos, John J.

    2014-01-01

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

  4. Genomic science in understanding cholera outbreaks and evolution of Vibrio cholerae as a human pathogen.

    PubMed

    Robins, William P; Mekalanos, John J

    2014-01-01

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

  5. Okhotskia: International Sakhalin Island Project

    NSDL National Science Digital Library

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

  6. Okhotskia: International Sakhalin Island Project

    NSDL National Science Digital Library

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

  7. Momentum transport in magnetic islands

    NASA Astrophysics Data System (ADS)

    Waelbroeck, F. L.; Grasso, D.; Porcelli, F.; Tebaldi, C.

    2006-04-01

    We examine the transport of momentum across an island using the reduced magnetohydrodynamic (RMHD) model. We find that the Reynolds stress gives rise to a momentum source proportional to the resistivity. As a result of the frozen-in property the transport of momentum can be described by a one-dimensional equation, even for islands with finite aspect-ratio. We present numerical and analytic solutions of this transport equation and compare these solutions to numerical solutions of the full time- dependent RMHD equations. Of particular interest is the momentum transport in islands where the helical current density reverses sign. In such islands, the Reynolds stress also reverses sign, creating the possibility for localized zonal flow generation. The constant-psi approximation, however, fails in the presence of current reversal. We have developed new equilibrium solutions for thin islands that we plan to use to examine the transport of momentum in the presence of current reversal.

  8. 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

  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. Island tameness: living on islands reduces flight initiation distance

    PubMed Central

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

    2014-01-01

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

  11. 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.

  12. Reconstructing Austronesian population history in Island Southeast Asia

    PubMed Central

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

    2014-01-01

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

  13. 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

  14. 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

  15. 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.

  16. Pine Island Glacier, Antarctica

    NASA Technical Reports Server (NTRS)

    2001-01-01

    This ASTER image was acquired on December 12, 2000, and covers an area of 38 x 48 km. Pine Island Glacier has undergone a steady loss of elevation with retreat of the grounding line in recent decades. Now, space imagery has revealed a wide new crack that some scientists think will soon result in a calving event. Glaciologist Robert Bindschadler of NASA's Goddard Space Flight Center predicts this crack will result in the calving of a major iceberg, probably in less than 18 months. Discovery of the crack was possible due to multi-year image archives and high resolution imagery. This image is located at 74.1 degrees south latitude and 105.1 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.

  17. Commonalities and Differences among Symbiosis Islands of Three Mesorhizobium loti Strains

    PubMed Central

    Kasai-Maita, Hiroko; Hirakawa, Hideki; Nakamura, Yasukazu; Kaneko, Takakazu; Miki, Kumiko; Maruya, Jumpei; Okazaki, Shin; Tabata, Satoshi; Saeki, Kazuhiko; Sato, Shusei

    2013-01-01

    To shed light on the breadth of the host range of Mesorhizobium loti strain NZP2037, we determined the sequence of the NZP2037 symbiosis island and compared it with those of strain MAFF303099 and R7A islands. The determined 533 kb sequence of NZP2037 symbiosis island, on which 504 genes were predicted, implied its integration into a phenylalanine-tRNA gene and subsequent genome rearrangement. Comparative analysis revealed that the core regions of the three symbiosis islands consisted of 165 genes. We also identified several NZP2037-specific genes with putative functions in nodulation-related events, suggesting that these genes contribute to broaden the host range of NZP2037. PMID:23666538

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

    PubMed Central

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

    2011-01-01

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

  19. 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

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

    PubMed

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

    2015-04-01

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

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

    PubMed Central

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

    2015-01-01

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

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

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ...Mariana Islands, the Commonwealth of Puerto Rico, and the Island of Guam. 72...Mariana Islands, the Commonwealth of Puerto Rico, and the Island of Guam. ...Islands, and the Commonwealth of Puerto Rico are quarantined. [43 FR...

  3. Functional Relevance of CpG Island Length for Regulation of Gene Expression

    PubMed Central

    Elango, Navin; Yi, Soojin V.

    2011-01-01

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

  4. 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

  5. Genomic characterization of the Yersinia genus

    PubMed Central

    2010-01-01

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

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

    PubMed Central

    2011-01-01

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

  7. Constructing artificial islands in Canada's Beaufort Sea

    Microsoft Academic Search

    Dingle

    1982-01-01

    Since 1972, Esso has constructed 17 artificial islands in the Canadian Beaufort Sea in water shallower than 66 ft (20 m). The sandbag-retained island uses a berm of sandbags around the island, thus reducing the volume of fill required; an alternative construction is the sacrificial beach island characterized by long gradual beaches and used when fill is readily available. The

  8. Island Political Economy Geoff Bertram & Bernard Poirine

    E-print Network

    Paris-Sud XI, Université de

    323 Chapter 10 Island Political Economy Geoff Bertram & Bernard Poirine Introduction In this chapter we build on the observation that island economies, and especially small ones (population below one of development strategies. Common elements of "islandness" may serve to define island economies as a general

  9. West Nile virus in the British Virgin Islands.

    PubMed

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

    2014-06-01

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

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

    SciTech Connect

    Chauhan, Archana [ORNL; Layton, Alice [University of Tennessee, Knoxville (UTK); Williams, Daniel W [ORNL; Smart, Abby E. [University of Tennessee, Knoxville (UTK); Ripp, Steven Anthony [ORNL; Karpinets, Tatiana V [ORNL; Brown, Steven D [ORNL; Sayler, Gary Steven [ORNL

    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.

  11. Comparative Analysis of Mouse NotI Linking Clones with Mouse and Human Genomic Sequences and Transcripts

    Microsoft Academic Search

    Christoph PLASS; Jun KAWAI; Iveta KALCHEVA; Leslie DAVIS; Sachihiko WATANABE; Yoshihide HAYASHIZAKI; Verne CHAPMAN

    1995-01-01

    Notl cleavage sites are frequently associated with CpG islands that identify the 5' regulatory sites of functional genes in the genome. Therefore we analyzed a sample of 22 Notl linking clones prepared from mouse brain DNA, to determine whether these mouse Notl site associated clones could be used for comparative analysis of mouse and human genomes by cross-reaction with both

  12. Upolu Island, Western Samoa

    NASA Technical Reports Server (NTRS)

    2000-01-01

    Island nations in the South Pacific Ocean experience natural disasters associated with typhoons, and with their proximity to the Pacific Ocean's 'Ring of Fire.' This radar image shows 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

  13. Upolu Island, Western Samoa

    NASA Technical Reports Server (NTRS)

    2000-01-01

    Island nations in the South Pacific Ocean experience natural disasters associated with typhoons, and with their proximity to the Pacific Ocean's 'Ring of Fire.' This radar image shows 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

  14. PLANT GENOMICS The coffee genome provides insight

    E-print Network

    Napp, Nils

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

  15. GenomeViz: visualizing microbial genomes

    Microsoft Academic Search

    Rohit Ghai; Torsten Hain; Trinad Chakraborty

    2004-01-01

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

  16. The archaeoastronomy of Easter Island.

    NASA Astrophysics Data System (ADS)

    Liller, W.

    The orientations of the several hundred ancient stone monuments on Rapa Nui (Easter Island) have now been measured and analysed. The results indicate that approximately fifteen ceremonial platforms were carefully oriented solsticially or equinoctially.

  17. The archaeoastronomy of Easter Island

    Microsoft Academic Search

    W. Liller

    1991-01-01

    The orientations of the several hundred ancient stone monuments on Rapa Nui (Easter Island) have now been measured and analysed. The results indicate that approximately fifteen ceremonial platforms were carefully oriented solsticially or equinoctially.

  18. Oil Spill Threatens Galapagos Islands

    NSDL National Science Digital Library

    de Nie, Michael Willem.

    2001-01-01

    On January 16, the aging Ecuadorean tanker "Jessica" ran aground on San Cristobal Island, threatening the delicate ecosystem of the Galapagos Islands, famous as the location for much of Charles Darwin's key research. The Galapagos, 97 percent of which is a national park, is perhaps the last complete and preserved island archipelago. The captain of the ship has since accepted responsibility for misjudging his entry into the bay and running the ship aground, spilling approximately 160,000 gallons of oil. Efforts continue to refloat the ship and remove the 10,000 gallons left inside. Fortunately, favorable winds and currents have limited the amount of oil washing up on the Galapagos Islands, but the long-term effects remain to be seen.

  19. 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....

  20. Synthesizing knowledge of ocean islands

    NASA Astrophysics Data System (ADS)

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

    2011-11-01

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

  1. 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.

  2. Vanishing Island: Sea Level Rise

    NSDL National Science Digital Library

    Massy Halbert

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

  3. Magnetic island formation in tokamaks

    SciTech Connect

    Yoshikawa, S.

    1989-04-01

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

  4. Gene Flow–Dependent Genomic Divergence between Anopheles gambiae M and S Forms

    PubMed Central

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

    2012-01-01

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

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

    SciTech Connect

    Antequera, F.; Bird, A. (Univ. of Edinburgh (United Kingdom))

    1993-11-15

    Estimation of gene number in mammals is difficult due to the high proportion of noncoding DNA within the nucleus. In this study, the authors provide a direct measurement of the number of genes in human and mouse. They have taken advantage of the fact that many mammalian genes are associated with CpG islands whose distinctive properties allow their physical separation from bulk DNA. The results suggest that there are [approx]45,000 CpG islands per haploid genome in humans and 37,000 in the mouse. Sequence comparison confirms that about 20% of the human CpG islands are absent from the homologous mouse genes. Analysis of a selection of germ line followed by CpG loss through mutation. This process appears to be more rapid in rodents. Combining the number of CpG islands with the proportion of island-associated genes, the authors estimate that the total number of genes per haploid genome is [approx]80,000 in both organisms.

  6. The genome BLASTatlas-a GeneWiz extension for visualization of whole-genome homology.

    PubMed

    Hallin, Peter F; Binnewies, Tim T; Ussery, David W

    2008-05-01

    The development of fast and inexpensive methods for sequencing bacterial genomes has led to a wealth of data, often with many genomes being sequenced of the same species or closely related organisms. Thus, there is a need for visualization methods that will allow easy comparison of many sequenced genomes to a defined reference strain. The BLASTatlas is one such tool that is useful for mapping and visualizing whole genome homology of genes and proteins within a reference strain compared to other strains or species of one or more prokaryotic organisms. We provide examples of BLASTatlases, including the Clostridium tetani plasmid p88, where homologues for toxin genes can be easily visualized in other sequenced Clostridium genomes, and for a Clostridium botulinum genome, compared to 14 other Clostridium genomes. DNA structural information is also included in the atlas to visualize the DNA chromosomal context of regions. Additional information can be added to these plots, and as an example we have added circles showing the probability of the DNA helix opening up under superhelical tension. The tool is SOAP compliant and WSDL (web services description language) files are located on our website: (http://www.cbs.dtu.dk/ws/BLASTatlas), where programming examples are available in Perl. By providing an interoperable method to carry out whole genome visualization of homology, this service offers bioinformaticians as well as biologists an easy-to-adopt workflow that can be directly called from the programming language of the user, hence enabling automation of repeated tasks. This tool can be relevant in many pangenomic as well as in metagenomic studies, by giving a quick overview of clusters of insertion sites, genomic islands and overall homology between a reference sequence and a data set. PMID:18414733

  7. Discovery of MLL1 binding units, their localization to CpG Islands, and their potential function in mitotic chromatin

    PubMed Central

    2013-01-01

    Background Mixed Lineage Leukemia 1 (MLL1) is a mammalian ortholog of the Drosophila Trithorax. In Drosophila, Trithorax complexes transmit the memory of active genes to daughter cells through interactions with Trithorax Response Elements (TREs). However, despite their functional importance, nothing is known about sequence features that may act as TREs in mammalian genomic DNA. Results By analyzing results of reported DNA binding assays, we identified several CpG rich motifs as potential MLL1 binding units (defined as morphemes). We find that these morphemes are dispersed within a relatively large collection of human promoter sequences and appear densely packed near transcription start sites of protein-coding genes. Genome wide analyses localized frequent morpheme occurrences to CpG islands. In the human HOX loci, the morphemes are spread across CpG islands and in some cases tail into the surrounding shores and shelves of the islands. By analyzing results of chromatin immunoprecipitation assays, we found a connection between morpheme occurrences, CpG islands, and chromatin segments reported to be associated with MLL1. Furthermore, we found a correspondence of reported MLL1-driven “bookmarked” regions in chromatin to frequent occurrences of MLL1 morphemes in CpG islands. Conclusion Our results implicate the MLL1 morphemes in sequence-features that define the mammalian TREs and provide a novel function for CpG islands. Apparently, our findings offer the first evidence for existence of potential TREs in mammalian genomic DNA and the first evidence for a connection between CpG islands and gene-bookmarking by MLL1 to transmit the memory of highly active genes during mitosis. Our results further suggest a role for overlapping morphemes in producing closely packed and multiple MLL1 binding events in genomic DNA so that MLL1 molecules could interact and reside simultaneously on extended potential transcriptional maintenance elements in human chromosomes to transmit the memory of highly active genes during mitosis. PMID:24373511

  8. 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

    ...established to provide habitat for a diversity of birds...particular emphasis on nesting bald eagles and seabirds, as well...conserving wildlife and their habitats, CCPs identify wildlife-dependent...Island to enhance seabird nesting habitat and forest...

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

    PubMed Central

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

    2013-01-01

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

  10. Genome evolution in yeasts

    Microsoft Academic Search

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

    2004-01-01

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

  11. Genome Medicine 2009, 11

    E-print Network

    Genome Medicine 2009, 11::39 Research AA kkeerrnneell--bbaasseedd iinntteeggrraattiioonn ooff. Published: 3 April 2009 Genome Medicine 2009, 11::39 (doi:10.1186/gm39) The electronic version of fusing more than one source of genome-wide data, such as the genome, transcriptome, proteome

  12. 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

  13. 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)

  14. Volcanic hazard on Deception Island (South Shetland Islands, Antarctica)

    NASA Astrophysics Data System (ADS)

    Bartolini, S.; Geyer, A.; Martí, J.; Pedrazzi, D.; Aguirre-Díaz, G.

    2014-09-01

    Deception Island is the most active volcano in the South Shetland Islands and has been the scene of more than twenty identified eruptions over the past two centuries. In this contribution we present the first comprehensive long-term volcanic hazard assessment for this volcanic island. The research is based on the use of probabilistic methods and statistical techniques to estimate volcanic susceptibility, eruption recurrence and the most likely future eruptive scenarios. We perform a statistical analysis of the time series of past eruptions and the spatial extent of their products, including lava flows, fallout, pyroclastic density currents and lahars. The Bayesian event tree statistical method HASSET is applied to calculate eruption recurrence, while the QVAST tool is used in an analysis of past activity to calculate the possibility that new vents will open (volcanic susceptibility). On the basis of these calculations, we identify a number of significant scenarios using the GIS-based VORIS 2.0.1 and LAHARZ software and evaluate the potential extent of the main volcanic hazards to be expected on the island. This study represents a step forward in the evaluation of volcanic hazard on Deception Island and the results obtained are potentially useful for long-term emergency planning.

  15. From Genomes of Species

    NSDL National Science Digital Library

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

    2005-12-01

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

  16. Genome Analysis of the Meat Starter Culture Bacterium Staphylococcus carnosus TM300? †

    PubMed Central

    Rosenstein, Ralf; Nerz, Christiane; Biswas, Lalitha; Resch, Alexandra; Raddatz, Guenter; Schuster, Stephan C.; Götz, Friedrich

    2009-01-01

    The Staphylococcus carnosus genome has the highest GC content of all sequenced staphylococcal genomes, with 34.6%, and therefore represents a species that is set apart from S. aureus, S. epidermidis, S. saprophyticus, and S. haemolyticus. With only 2.56 Mbp, the genome belongs to a family of smaller staphylococcal genomes, and the ori and ter regions are asymmetrically arranged with the replichores I (1.05 Mbp) and II (1.5 Mbp). The events leading up to this asymmetry probably occurred not that long ago in evolution, as there was not enough time to approach the natural tendency of a physical balance. Unlike the genomes of pathogenic species, the TM300 genome does not contain mobile elements such as plasmids, insertion sequences, transposons, or STAR elements; also, the number of repeat sequences is markedly decreased, suggesting a comparatively high stability of the genome. While most S. aureus genomes contain several prophages and genomic islands, the TM300 genome contains only one prophage, ?TM300, and one genomic island, ?SCA1, which is characterized by a mosaic structure mainly composed of species-specific genes. Most of the metabolic core pathways are present in the genome. Some open reading frames are truncated, which reflects the nutrient-rich environment of the meat starter culture, making some functions dispensable. The genome is well equipped with all functions necessary for the starter culture, such as nitrate/nitrite reduction, various sugar degradation pathways, two catalases, and nine osmoprotection systems. The genome lacks most of the toxins typical of S. aureus as well as genes involved in biofilm formation, underscoring the nonpathogenic status. PMID:19060169

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

    NASA Technical Reports Server (NTRS)

    2001-01-01

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

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

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

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

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

    NASA Technical Reports Server (NTRS)

    2001-01-01

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

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

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

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

  19. 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

  20. 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

  1. 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

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

    Microsoft Academic Search

    Gireesh Rajashekara; Jeremy D. Glasner; David A. Glover; G. A. Splitter

    2004-01-01

    Brucella species are responsible for brucellosis, a worldwide zoonotic disease causing abortion in domestic animals and Malta fever in humans. Based on host preference, the genus is divided into six species. Brucella abortus, B. melitensis, and B. suis are pathogenic to humans, whereas B. ovis and B. neotomae are nonpathogenic to humans and B. canis human infections are rare. Limited

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

    Microsoft Academic Search

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

    2003-01-01

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

  4. 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

  5. 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.

  6. 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.

  7. Pacific Island Ecosystems Research Center

    NSDL National Science Digital Library

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

  8. Rhode Island Critical Resource Atlas

    NSDL National Science Digital Library

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

  9. The American Experience: Coney Island

    NSDL National Science Digital Library

    Long before Lawrence Ferlinghetti entitled his famous book of Beat poems A Coney Island of the Mind, the amusement park located on "a tiny spit of land at the foot of Brooklyn, NY" had come to represent a quintessential American desire for mechanized, manic fun. This companion site to the PBS airing this week of the American Experience provides a history of the amusement park, a substantial essay on the history of roller coasters, an enhanced transcript of the broadcast (available July 26), a gallery of Coney Island images, historical film clips of the park in action, a teacher's guide (which was not yet available when we visited), and an essay comparing Coney Island to the Internet. Watch out for that first hyperlink!

  10. Thermal island destabilization and the Greenwald limit

    NASA Astrophysics Data System (ADS)

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

    2015-02-01

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

  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. Islands, Reefs, and a Hotspot

    NSDL National Science Digital Library

    Mel Goodwin

    In this lesson students investigate the formation of the Hawaiian archipelago to see what geological processes produced the different physical forms seen among the Hawaiian Islands. Students will be able to describe eight stages in the formation of islands in the Hawaiian archipelago and will describe the movement of tectonic plates in the region including submarine volcanic eruptions, caldera formation, erosion, coral reef building, and atoll stages. They will also learn how a combination of hotspot activity and tectonic plate movement could produce the arrangement of seamounts observed in the Hawaiian archipelago.

  13. Differentiation of regions with atypical oligonucleotide composition in bacterial genomes

    PubMed Central

    Reva, Oleg N; Tümmler, Burkhard

    2005-01-01

    Background Complete sequencing of bacterial genomes has become a common technique of present day microbiology. Thereafter, data mining in the complete sequence is an essential step. New in silico methods are needed that rapidly identify the major features of genome organization and facilitate the prediction of the functional class of ORFs. We tested the usefulness of local oligonucleotide usage (OU) patterns to recognize and differentiate types of atypical oligonucleotide composition in DNA sequences of bacterial genomes. Results A total of 163 bacterial genomes of eubacteria and archaea published in the NCBI database were analyzed. Local OU patterns exhibit substantial intrachromosomal variation in bacteria. Loci with alternative OU patterns were parts of horizontally acquired gene islands or ancient regions such as genes for ribosomal proteins and RNAs. OU statistical parameters, such as local pattern deviation (D), pattern skew (PS) and OU variance (OUV) enabled the detection and visualization of gene islands of different functional classes. Conclusion A set of approaches has been designed for the statistical analysis of nucleotide sequences of bacterial genomes. These methods are useful for the visualization and differentiation of regions with atypical oligonucleotide composition prior to or accompanying gene annotation. PMID:16225667

  14. 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

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

    PubMed Central

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

    2009-01-01

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

  16. Cancer and Asians/Pacific Islanders

    MedlinePLUS

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

  17. Coastal mesoscale changes on Matagorda Island

    E-print Network

    Lariscy, Kevin William

    2001-01-01

    on the coastal geomorphology of Matagorda Island. Based on the statistical and morphometric analysis of the coastal landforms, the island was divided into three distinct sub-environments: an erosional eastern zone, a transitional mixed zone, and a depositional...

  18. Obesity and Native Hawaiians/Pacific Islanders

    MedlinePLUS

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

  19. Profile: Native Hawaiians and Pacific Islanders

    MedlinePLUS

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

  20. 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...

  1. 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

  2. Genome instability in Lactobacillus rhamnosus GG.

    PubMed

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

    2013-04-01

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

  3. 78 FR 63860 - Amendment of Class D Airspace; Kwajalein Island, Marshall Islands, RMI

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-10-25

    ...13-AWP-14] RIN 2120-AA66 Amendment of Class D Airspace; Kwajalein Island, Marshall Islands...action amends the Kwajalein Island Class D airspace description by amending the geographic...overlooked in the Kwajalein Island Class D airspace description. This action...

  4. Henderson Island prehistory: colonization and extinction on a remote Polynesian island

    Microsoft Academic Search

    MARSHALL I. WEISLER

    1995-01-01

    Situated at the extreme margin of the Indo-West Pacific biotic province, the four islands of the isolated Pitcairn Group hold interest for biogeographers and archaeologists alike. Human settlement may have been as early as the 8th century AD for the uplifted limestone island of Henderson, the most pristine island of its kind. An archaeological survey of the Pitcairn Islands is

  5. INSULAR AND MIGRANT SPECIES, LONGEVITY RECORDS, AND NEW SPECIES RECORDS ON GUANA ISLAND, BRITISH VIRGIN ISLANDS

    Microsoft Academic Search

    CLINT W. BOAL; FRED C. SIBLEY; TRACY S. ESTABROOK; JAMES LAZELL

    2006-01-01

    ABSTRACf.-We conducted mist netting each October from 1994 to 2004 on Guana Island, British Virgin Islands, and recorded bird sightings to develop a more complete inventory of the island's resident and migrant species. During our study, we recorded four new species for the British Virgin Islands: Magnolia Warbler (Dendroica magnolia; 1996), Golden-winged Warbler (Vennivora chrysoptera; 1997), Swainson's Thrush (Ca- tharus

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

    E-print Network

    Luther, Douglas S.

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

  7. 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

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

    PubMed

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

    2014-01-01

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

  9. 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.

  10. 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)....

  11. 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)....

  12. 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)....

  13. 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)....

  14. 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

  15. Geology and geochronology of the Line Island

    Microsoft Academic Search

    S. O. Schlanger; M. O. Garcia; B. H. Keating; J. J. Naughton; W. W. Sager; J. A. Haggerty; J. A. Philpotts; R. A. Duncan

    1984-01-01

    Geological and geophysical studies along the entire length of the Line Islands were undertaken in order to test the hot spot model for the origin of this major linear island chain. Volcanic rocks were recovered in 21 dredge hauls and fossiliferous sedimentary rocks were recovered in 19 dredge hauls. Volcanic rocks from the Line Islands are alkali basalts and hawaiites.

  16. Costing eradications of alien mammals from islands

    Microsoft Academic Search

    T. L. F. Martins; M. de L. Brooke; G. M. Hilton; S. Farnsworth; J. Gould; D. J. Pain

    2006-01-01

    The ability to estimate costs of alien species eradications is essential for a rigorous assessment of priorities for island restoration. Using a global data file from 41 islands, mostly gleaned from the 'grey' literature, we show that the cost of vertebrate eradications can be satisfactorily predicted if island area and species to be eradicated are known. About 72% of the

  17. Review on sustainable development of island microgrid

    Microsoft Academic Search

    Ping Ji; Xiao Xin Zhou; ShouYuan Wu

    2011-01-01

    In microgrid, distributed generators (DG) can be utilized effectively, and controlled intelligently and flexibly. By use of rich renewable energy sources (RES) on islands, island microgrids can be built to develop clean and pollution-free renewable energy power industry, which makes islands' natural balance of the regional energy industry achieved, the ‘renewable energy’ economy developed, the industrial structure optimized, and industrial

  18. Tiber Island in ancient and medieval Rome

    Microsoft Academic Search

    Margaret Angela Brucia

    1990-01-01

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

  19. 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.

  20. 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...

  1. 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...

  2. Concerns generated by islanding [electric power generation

    Microsoft Academic Search

    P. L. Villenueve

    2004-01-01

    The purpose of this article is to discuss islanding operation and to provide end-users with items to consider when determining distributed generation plant and equipment design requirements. Islanding is operating an electric generating plant without an external voltage and frequency reference. Operating in parallel is the opposite of islanding. This article attempts to describe the valid concerns that grid operators

  3. Bacterial contamination of goundwater in Jeju Island

    Microsoft Academic Search

    Y. Jo; J. Lee; S. Jun; R. Kim

    2009-01-01

    The aim of this study was to evaluate the contaminated groundwater with biological elements. The study area is located in Jeju Island, Korea. The island is formed with volcanic rock. To evaluate the chemical composition of the groundwater in the island, three rounds of water samplings were performed (August, October and November of 2007). Prior to water sampling for laboratory

  4. 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…

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

    Microsoft Academic Search

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

    2005-01-01

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

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

    Microsoft Academic Search

    CHEN Chuan-bo

    2005-01-01

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

  7. Review of islanding detection methods for distributed generation

    Microsoft Academic Search

    P. Mahat; Zhe Chen; B. Bak-Jensen

    2008-01-01

    This paper presents an overview of power system islanding and islanding detection techniques. Islanding detection techniques, for a distribution system with distributed generation (DG), can broadly be divided into remote and local techniques. A remote islanding detection technique is associated with islanding detection on the utility side, whereas a local technique is associated with islanding detection on the DG side.

  8. Genome Sequence of Gallaecimonas xiamenensis Type Strain 3-C-1

    PubMed Central

    Lai, Qiliang; Wang, Liping; Wang, Wanpeng

    2012-01-01

    Gallaecimonas xiamenensis 3-C-1T was isolated from a crude-oil-degrading consortium enriched from the surface seawater around Xiamen Island. Here, we present the draft genome of strain 3-C-1T, which contains 4,062,282 bp with a G+C content of 60.58% and contains 3,798 protein-coding genes and 65 tRNAs. PMID:23209203

  9. 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...

  10. 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…

  11. Coconut Island Visitor Information Packet

    E-print Network

    Holland, Kim N.

    Coconut Island Visitor Information Packet The Hawaii Institute of Marine Biology P.O. Box 1346.hawaii.edu/HIMB/welcome.html For dorm reservations and questions, contact housing managers at himbdorm@hawaii.edu (primary form a sponsor before proceeding with housing arrangements. For dorm reservations and questions, contact housing

  12. The flora of Antipodes Island

    Microsoft Academic Search

    E. J. Godley

    1989-01-01

    The history of botanical exploration of Antipodes Island begins in 1890 and is outlined up to 1985. The numbers of terrestrial species now known are algae (3), fungi (2), lichens (17), liverworts (37), mosses (21), lycopods (3), ferns (17), and flowering plants (52). Three of the latterare adventive (Poa annua, Stellaria media, Sonchus asper). The 20 species of indigenous monocotyledons

  13. 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...

  14. Birds are islands for parasites.

    PubMed

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

    2014-08-01

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

  15. Island Explorers Marine Science Program

    NSDL National Science Digital Library

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

  16. 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 ...

  17. Whole Genome Sequencing

    MedlinePLUS

    ... Most of the information you get from a genomic test tells you about your risk for disease, ... A health forecast: Understanding disease risk from whole genomic sequencing Weather forecasting tries to predict what the ...

  18. Comparative genomic workflow

    E-print Network

    Rajapakse, Jagath

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

  19. The cybernetic genome

    NASA Astrophysics Data System (ADS)

    Ben-Jacob, Eshel

    We propose a new picture of the genome as an adaptive cybernetic unit with self-awareness. We further propose that under colonial stress bacteria employ genetic communication which leads to the emergence of creative genomic web or “global brain”.

  20. Public Health Genomics (PHG)

    Cancer.gov

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

  1. Human Genome Center

    NSDL National Science Digital Library

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

  2. Structural genomics: beyond the Human Genome Project

    Microsoft Academic Search

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

    1999-01-01

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

  3. 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.

  4. 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.

  5. Comparative genome analysis and genome-guided physiological analysis of Roseobacter litoralis

    PubMed Central

    2011-01-01

    Background Roseobacter litoralis OCh149, the type species of the genus, and Roseobacter denitrificans OCh114 were the first described organisms of the Roseobacter clade, an ecologically important group of marine bacteria. Both species were isolated from seaweed and are able to perform aerobic anoxygenic photosynthesis. Results The genome of R. litoralis OCh149 contains one circular chromosome of 4,505,211 bp and three plasmids of 93,578 bp (pRLO149_94), 83,129 bp (pRLO149_83) and 63,532 bp (pRLO149_63). Of the 4537 genes predicted for R. litoralis, 1122 (24.7%) are not present in the genome of R. denitrificans. Many of the unique genes of R. litoralis are located in genomic islands and on plasmids. On pRLO149_83 several potential heavy metal resistance genes are encoded which are not present in the genome of R. denitrificans. The comparison of the heavy metal tolerance of the two organisms showed an increased zinc tolerance of R. litoralis. In contrast to R. denitrificans, the photosynthesis genes of R. litoralis are plasmid encoded. The activity of the photosynthetic apparatus was confirmed by respiration rate measurements, indicating a growth-phase dependent response to light. Comparative genomics with other members of the Roseobacter clade revealed several genomic regions that were only conserved in the two Roseobacter species. One of those regions encodes a variety of genes that might play a role in host association of the organisms. The catabolism of different carbon and nitrogen sources was predicted from the genome and combined with experimental data. In several cases, e.g. the degradation of some algal osmolytes and sugars, the genome-derived predictions of the metabolic pathways in R. litoralis differed from the phenotype. Conclusions The genomic differences between the two Roseobacter species are mainly due to lateral gene transfer and genomic rearrangements. Plasmid pRLO149_83 contains predominantly recently acquired genetic material whereas pRLO149_94 was probably translocated from the chromosome. Plasmid pRLO149_63 and one plasmid of R. denitrifcans (pTB2) seem to have a common ancestor and are important for cell envelope biosynthesis. Several new mechanisms of substrate degradation were indicated from the combination of experimental and genomic data. The photosynthetic activity of R. litoralis is probably regulated by nutrient availability. PMID:21693016

  6. 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 ...

  7. INTRODUCTION TO GENOMIC MEDICINE

    E-print Network

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

  8. LEGUME COMPARATIVE GENOMICS

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  9. Introduction into Plant Genomics

    Microsoft Academic Search

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

    2001-01-01

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

  10. 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

  11. The human genome project

    Microsoft Academic Search

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

    1994-01-01

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

  12. Genomic Structure and Phylogeny of the Plant Pathogen Ralstonia solanacearum Inferred from Gene Distribution Analysis? †

    PubMed Central

    Guidot, Alice; Prior, Philippe; Schoenfeld, Jens; Carrère, Sébastien; Genin, Stéphane; Boucher, Christian

    2007-01-01

    In the present study, we investigated the gene distribution among strains of the highly polymorphic plant pathogenic ?-proteobacterium Ralstonia solanacearum, paying particular attention to the status of known or candidate pathogenicity genes. Based on the use of comparative genomic hybridization on a pangenomic microarray for the GMI1000 reference strain, we have defined the conditions that allowed comparison of the repertoires of genes among a collection of 18 strains that are representative of the biodiversity of the R. solanacearum species. This identified a list of 2,690 core genes present in all tested strains. As a corollary, a list of 2,338 variable genes within the R. solanacearum species has been defined. The hierarchical clustering based on the distribution of variable genes is fully consistent with the phylotype classification that was previously defined from the nucleotide sequence analysis of four genes. The presence of numerous pathogenicity-related genes in the core genome indicates that R. solanacearum is an ancestral pathogen. The results establish the long coevolution of the two replicons that constitute the bacterial genome. We also demonstrate the clustering of variable genes in genomic islands. Most genomic islands are included in regions with an alternative codon usage, suggesting that they originate from acquisition of foreign genes through lateral gene transfers. Other genomic islands correspond to genes that have the same base composition as core genes, suggesting that they either might be ancestral genes lost by deletion in certain strains or might originate from horizontal gene transfers. PMID:17085551

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

    PubMed Central

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

    2011-01-01

    The virulence determinants of uropathogenic Escherichia coli have been studied extensively over the years, but relatively little is known about what differentiates isolates causing various types of urinary tract infections. In this study, we compared the genomic profiles of 45 strains from a range of different clinical backgrounds, i.e., urosepsis, pyelonephritis, cystitis, and asymptomatic bacteriuria (ABU), using comparative genomic hybridization analysis. A microarray based on 31 complete E. coli sequences was used. It emerged that there is little correlation between the genotypes of the strains and their disease categories but strong correlation between the genotype and the phylogenetic group association. Also, very few genetic differences may exist between isolates causing symptomatic and asymptomatic infections. Only relatively few genes that could potentially differentiate between the individual disease categories were identified. Among these were two genomic islands, namely, pathogenicity island (PAI)-CFT073-serU and PAI-CFT073-pheU, which were significantly more associated with the pyelonephritis and urosepsis isolates than with the ABU and cystitis isolates. These two islands harbor genes encoding virulence factors, such as P fimbriae (pyelonephritis-associated fimbriae) and an important immunomodulatory protein, TcpC. It seems that both urovirulence and growth fitness can be attributed to an assortment of genes rather than to a specific gene set. Taken together, urovirulence and fitness are the results of the interplay of a mixture of factors taken from a rich menu of genes. PMID:21421782

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

    PubMed Central

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

    2010-01-01

    The DNA of most vertebrates is depleted in CpG dinucleotides, the target for DNA methylation. The remaining CpGs tend to cluster in regions referred to as CpG islands (CGI). CGI have been useful as marking functionally relevant epigenetic loci for genome studies. For example, CGI are enriched in the promoters of vertebrate genes and thought to play an important role in regulation. Currently, CGI are defined algorithmically as an observed-to-expected ratio (O/E) of CpG greater than 0.6, G+C content greater than 0.5, and usually but not necessarily greater than a certain length. Here we find that the current definition leaves out important CpG clusters associated with epigenetic marks, relevant to development and disease, and does not apply at all to nonvertabrate genomes. We propose an alternative Hidden Markov model-based approach that solves these problems. We fit our model to genomes from 30 species, and the results support a new epigenomic view toward the development of DNA methylation in species diversity and evolution. The O/E of CpG in islands and nonislands segregated closely phylogenetically and showed substantial loss in both groups in animals of greater complexity, while maintaining a nearly constant difference in CpG O/E between islands and nonisland compartments. Lists of CGI for some species are available at http://www.rafalab.org. PMID:19777308

  15. Polar Bears International: Wrangel Island, Russia

    NSDL National Science Digital Library

    This site describes the ongoing research of the polar bears in the Russian High Arctic. Wrangel Island with neighboring small island, Herald Island, are the key reproductive areas for the Chukchi-Alaskan polar bear population. Marine areas and Wrangel and Herald islands provide optimum foraging habitats for polar bears, and polar bear densities in these marine habitats are high all year round. Approximately 350-500 pregnant female polar bears construct their maternity dens on Wrangel and Herald islands every fall, emerging with their cubs in spring. The research is described in terms of goals and objectives, structure, methods, equipment, staff, and implementations.

  16. Polar Bears International : Wrangel Island, Russia

    NSDL National Science Digital Library

    2007-12-12

    This site describes the ongoing research of the polar bears in the Russian High Arctic. Wrangel Island with neighboring small island, Herald Island, are the key reproductive areas for the Chukchi-Alaskan polar bear population. Marine areas and Wrangel and Herald islands provide optimum foraging habitats for polar bears, and polar bear densities in these marine habitats are high all year round. Approximately 350-500 pregnant female polar bears construct their maternity dens on Wrangel and Herald islands every fall, emerging with their cubs in spring. The research is described in terms of goals and objectives, structure, methods, equipment, staff, and implementations.

  17. Genomic analysis and temperature-dependent transcriptome profiles of the rhizosphere originating strain Pseudomonas aeruginosa M18

    PubMed Central

    2011-01-01

    Background Our previously published reports have described an effective biocontrol agent named Pseudomonas sp. M18 as its 16S rDNA sequence and several regulator genes share homologous sequences with those of P. aeruginosa, but there are several unusual phenotypic features. This study aims to explore its strain specific genomic features and gene expression patterns at different temperatures. Results The complete M18 genome is composed of a single chromosome of 6,327,754 base pairs containing 5684 open reading frames. Seven genomic islands, including two novel prophages and five specific non-phage islands were identified besides the conserved P. aeruginosa core genome. Each prophage contains a putative chitinase coding gene, and the prophage II contains a capB gene encoding a putative cold stress protein. The non-phage genomic islands contain genes responsible for pyoluteorin biosynthesis, environmental substance degradation and type I and III restriction-modification systems. Compared with other P. aeruginosa strains, the fewest number (3) of insertion sequences and the most number (3) of clustered regularly interspaced short palindromic repeats in M18 genome may contribute to the relative genome stability. Although the M18 genome is most closely related to that of P. aeruginosa strain LESB58, the strain M18 is more susceptible to several antimicrobial agents and easier to be erased in a mouse acute lung infection model than the strain LESB58. The whole M18 transcriptomic analysis indicated that 10.6% of the expressed genes are temperature-dependent, with 22 genes up-regulated at 28°C in three non-phage genomic islands and one prophage but none at 37°C. Conclusions The P. aeruginosa strain M18 has evolved its specific genomic structures and temperature dependent expression patterns to meet the requirement of its fitness and competitiveness under selective pressures imposed on the strain in rhizosphere niche. PMID:21884571

  18. 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.

  19. Shaded Relief Mosaic of Umnak Island, Aleutian Islands, Alaska

    NASA Technical Reports Server (NTRS)

    2001-01-01

    This image is a shaded relief mosaic of Umnak Island in Alaska's Aleutian Islands.

    It was created with Airsar data that was geocoded and combined into this mosaic as part of a NASA-funded Alaska Digital Elevation Model Project at the Alaska Synthetic Aperture Radar Facility (ASF) at the University of Alaska Geophysical Institute in Fairbanks, Alaska.

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

  20. The island rule: made to be broken?

    PubMed Central

    Meiri, Shai; Cooper, Natalie; Purvis, Andy

    2007-01-01

    The island rule is a hypothesis whereby small mammals evolve larger size on islands while large insular mammals dwarf. The rule is believed to emanate from small mammals growing larger to control more resources and enhance metabolic efficiency, while large mammals evolve smaller size to reduce resource requirements and increase reproductive output. We show that there is no evidence for the existence of the island rule when phylogenetic comparative methods are applied to a large, high-quality dataset. Rather, there are just a few clade-specific patterns: carnivores; heteromyid rodents; and artiodactyls typically evolve smaller size on islands whereas murid rodents usually grow larger. The island rule is probably an artefact of comparing distantly related groups showing clade-specific responses to insularity. Instead of a rule, size evolution on islands is likely to be governed by the biotic and abiotic characteristics of different islands, the biology of the species in question and contingency. PMID:17986433

  1. Magnetic island evolution in hot ion plasmas

    SciTech Connect

    Ishizawa, A.; Nakajima, N. [National Institute for Fusion Science, Toki 509-5292 (Japan); Waelbroeck, F. L.; Fitzpatrick, R.; Horton, W. [Institute for Fusion Studies, University of Texas at Austin, Austin, Texas 78712 (United States)

    2012-07-15

    Effects of finite ion temperature on magnetic island evolution are studied by means of numerical simulations of a reduced set of two-fluid equations which include ion as well as electron diamagnetism in slab geometry. The polarization current is found to be almost an order of magnitude larger in hot than in cold ion plasmas, due to the strong shear of ion velocity around the separatrix of the magnetic islands. As a function of the island width, the propagation speed decreases from the electron drift velocity (for islands thinner than the Larmor radius) to values close to the guiding-center velocity (for islands of order 10 times the Larmor radius). In the latter regime, the polarization current is destabilizing (i.e., it drives magnetic island growth). This is in contrast to cold ion plasmas, where the polarization current is generally found to have a healing effect on freely propagating magnetic island.

  2. Island-finding ability of marine turtles.

    PubMed Central

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

    2003-01-01

    Green turtles (Chelonia mydas) swim from foraging grounds along the Brazilian coast to Ascension Island to nest, over 2200 km distant in the middle of the equatorial Atlantic. To test the hypothesis that turtles use wind-borne cues to locate Ascension Island we found turtles that had just completed nesting and then moved three individuals 50 km northwest (downwind) of the island and three individuals 50 km southeast (upwind). Their subsequent movements were tracked by satellite. Turtles released downwind returned to Ascension Island within 1, 2 and 4 days, respectively. By contrast, those released upwind had far more difficulty in relocating Ascension Island, two eventually returning after 10 and 27 days and the third heading back to Brazil after failing to find its way back to the island. These findings strongly support the hypothesis that wind-borne cues are used by turtles to locate Ascension Island. PMID:12952621

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

    PubMed Central

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

    1990-01-01

    CpG dinucleotides are unevenly distributed in the vertebrate genome. Bulk DNA is depleted of CpGs and most of the cytosines in the dinucleotide in this fraction are methylated. On the other hand, CpG islands, which are often associated with genes, are unmethylated at testable sites in all normal tissues with the exception of genes on the inactive X chromosome. We used Hpa II/Msp I analysis and ligation-mediated polymerase chain reaction to examine the methylation of the MyoD1 CpG island in adult mouse tissues, early cultures of mouse embryo cells, and immortal fibroblastic cell lines. The island was almost devoid of methylation at CCGG sites in adult mouse tissues and in low-passage mouse embryo fibroblasts. In marked contrast, the island was methylated in 10T 1/2 cells and in six other immortal cell lines showing that methylation of this CpG island had occurred during escape from senescence. The island became even more methylated in chemically transformed derivatives of 10T 1/2 cells. Thus, CpG islands not methylated in normal tissues may become modified to an abnormally high degree during immortalization and transformation. Images PMID:2385586

  4. The Bluejay genome browser.

    PubMed

    Soh, Jung; Gordon, Paul M K; Sensen, Christoph W

    2012-03-01

    The Bluejay genome browser is a stand-alone visualization tool for the multi-scale viewing of annotated genomes and other genomic elements. Bluejay allows users to customize display features to suit their needs, and produces publication-quality graphics. Bluejay provides a multitude of ways to interrelate biological data at the genome scale. Users can load gene expression data into a genome display for expression visualization in context. Multiple genomes can be compared concurrently, including time series expression data, based on Gene Ontology labels. External, context-sensitive biological Web Services are linked to the displayed genomic elements ad hoc for in-depth genomic data analysis and interpretation. Users can mark multiple points of interest in a genome by creating waypoints, and exploit them for easy navigation of single or multiple genomes. Using this comprehensive visual environment, users can study a gene not just in relation to its genome, but also its transcriptome and evolutionary origins. Written in Java, Bluejay is platform-independent and is freely available from http://bluejay.ucalgary.ca. PMID:22389011

  5. Microbial genomic taxonomy

    PubMed Central

    2013-01-01

    A need for a genomic species definition is emerging from several independent studies worldwide. In this commentary paper, we discuss recent studies on the genomic taxonomy of diverse microbial groups and a unified species definition based on genomics. Accordingly, strains from the same microbial species share >95% Average Amino Acid Identity (AAI) and Average Nucleotide Identity (ANI), >95% identity based on multiple alignment genes, <10 in Karlin genomic signature, and?>?70% in silico Genome-to-Genome Hybridization similarity (GGDH). Species of the same genus will form monophyletic groups on the basis of 16S rRNA gene sequences, Multilocus Sequence Analysis (MLSA) and supertree analysis. In addition to the established requirements for species descriptions, we propose that new taxa descriptions should also include at least a draft genome sequence of the type strain in order to obtain a clear outlook on the genomic landscape of the novel microbe. The application of the new genomic species definition put forward here will allow researchers to use genome sequences to define simultaneously coherent phenotypic and genomic groups. PMID:24365132

  6. 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

  7. 25 CFR 241.2 - Annette Islands Reserve; definition; exclusive fishery; licenses.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ...Proclamation of April 28, 1916 (39 Stat. 1777), as the waters within three thousand feet from the shore lines at mean low tide of Annette Island, Ham Island, Walker Island, Lewis Island, Spire Island, Hemlock Island, and adjacent rocks and...

  8. 25 CFR 241.2 - Annette Islands Reserve; definition; exclusive fishery; licenses.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ...Proclamation of April 28, 1916 (39 Stat. 1777), as the waters within three thousand feet from the shore lines at mean low tide of Annette Island, Ham Island, Walker Island, Lewis Island, Spire Island, Hemlock Island, and adjacent rocks and...

  9. 25 CFR 241.2 - Annette Islands Reserve; definition; exclusive fishery; licenses.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ...Proclamation of April 28, 1916 (39 Stat. 1777), as the waters within three thousand feet from the shore lines at mean low tide of Annette Island, Ham Island, Walker Island, Lewis Island, Spire Island, Hemlock Island, and adjacent rocks and...

  10. 25 CFR 241.2 - Annette Islands Reserve; definition; exclusive fishery; licenses.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ...Proclamation of April 28, 1916 (39 Stat. 1777), as the waters within three thousand feet from the shore lines at mean low tide of Annette Island, Ham Island, Walker Island, Lewis Island, Spire Island, Hemlock Island, and adjacent rocks and...

  11. Okhotskia: International Kuril Island Project

    NSDL National Science Digital Library

    This website presents the International Kuril Island Project (IKIP), "an international collaboration of American, Russian, and Japanese scientists to survey the plants, insects, spiders, freshwater and terrestrial mollusks, freshwater fishes, amphibians, and reptiles of the Kuril Archipelago." The website was developed primarily "to provide easy access to project results and databases, both for participants and other interested scientists." Site visitors can link to the project proposal -- submitted by the University of Washington, Russian Academy of Sciences, and Hokkaido University -- to view text and images describing project Objectives, Rationale and Scope, Anticipated Future Research, and more. Links are also provided to project Results (including IKIP databases, publications, and presentations) and Island Info including sections on Vascular Plants, Stoneflies, Nesting Birds, and many more. Additionally, a very nicely organized photo gallery features maps and many beautiful photographs taken by project participants during collecting expeditions to the Kuril Archipelago.

  12. 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

  13. The Three Mile Island crisis

    SciTech Connect

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

    1988-01-01

    Since the March 1979 accident at the Three Mile Island (TMI) nuclear power plant, many studies have assessed its impacts. Compiled and summarized in this book are the results of five related surveys, all aimed at the scientific assessment of the psycho-socio-economic behavior of the residents around the TMI facility. These studies are based on a randomly selected, large sample of the population (with telephones) around TMI.

  14. Urban Heat Islands: Hotter Cities

    NSDL National Science Digital Library

    Urban Heat Islands (University of Western Ontario; )

    2004-11-01

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

  15. Climate Change in Small Islands

    NASA Astrophysics Data System (ADS)

    Tomé, Ricardo; Miranda, Pedro M. A.; Brito de Azevedo, Eduardo; Teixeira, Miguel A. C.

    2014-05-01

    Isolated islands are especially vulnerable to climate change. But their climate is generally not well reproduced in GCMs, due to their small size and complex topography. Here, results from a new generation of climate models, forced by scenarios RCP8.5 and RCP4.5 of greenhouse gases and atmospheric aerosol concentrations, established by the IPCC for its fifth report, are used to characterize the climate of the islands of Azores and Madeira, and its response to the ongoing global warming. The methodology developed here uses the new global model EC-Earth, data from ERA-Interim reanalysis and results from an extensive set of simulations with the WRF research model, using, for the first time, a dynamic approach for the regionalization of global fields at sufficiently fine resolutions, in which the effect of topographical complexity is explicitly represented. The results reviewed here suggest increases in temperature above 1C in the middle of the XXI century in Azores and Madeira, reaching values higher than 2.5C at the end of the century, accompanied by a reduction in the annual rainfall of around 10% in the Azores, which could reach 30% in Madeira. These changes are large enough to justify much broader impacts on island ecosystems and the human population. The results show the advantage of using the proposed methodology, in particular for an adequate representation of the precipitation regime in islands with complex topography, even suggesting the need for higher resolutions in future work. The WRF results are also compared against two different downscaling techniques using an air mass transformation model and a modified version of the upslope precipitation model of Smith and Barstad (2005).

  16. Flora of the Marquesas Islands

    NSDL National Science Digital Library

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

  17. How to Trace Island Freeboard

    Microsoft Academic Search

    Ricardo Alexandre dos Santos Ramalho

    \\u000a The vertical movements affecting island edifices have a direct effect on the evolutionary history of those edifices. During\\u000a the seamount stage, the height of the edifice relative to the ocean’s surface—a parameter that mostly depends on the volcanic\\u000a activity and the uplift\\/subsidence of the edifice—has a strong impact on the dominant eruptive style. This happens because\\u000a the height of the

  18. Slope protection for artificial island

    Microsoft Academic Search

    M. T. Czerniak; J. I. Collins; A. T. Shak

    1981-01-01

    The technology under development to protect artificial-island production platforms from Arctic sea and ice damage involves three major considerations: (1) sea conditions during the ice-free season, (2) ice conditions during winter, and (3) construction constraints imposed by material availability, transportation problems, and length of the construction season. So far, researchers have evaluated 15 different slope-protection systems on the basis of

  19. Tambora Caldera, Sumbawa Island, Indonesia

    NASA Technical Reports Server (NTRS)

    1988-01-01

    Tambora caldera on the island of Sumbawa, Indonesia (8.5S, 118.0E) is a large crater formed in 1815 when a huge volcanic eruption ejected millions of tons debris high into the atmosphere. The particulate matter was blown around the globe by winds, masking much of the Earth's surface from sunlight, lowering global temperatures. Snow fell in New England in June and freezes occurred in the summer of 1816 which became known as the year without a summer.

  20. Ribeiro's typology, genomes, and Spanish colonialism, as viewed from Gran Canaria and Colombia

    E-print Network

    introgression of genes through native women. In accordance to D. Ribeiro's typology for peoples subjected and emergent peoples. Recently, we coined the expression transplanted male genome for the event of substitution. The first inhabitants of these islands arrived around the middle of the second millennium BC, and an

  1. 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

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

    PubMed Central

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

    2015-01-01

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

  3. Comparative Genomics to Identify Genetic Variabilities Associated with Salmonella Typhimurium DT104

    E-print Network

    Chittka, Lars

    Europe and North America. This phage type displayed resistance to a panel of antibiotics and was isolated strains was the acquisition of the antibiotic resistance carrying Salmonella Genomic Island 1 (SGI1;3 Abstract Non-typhoidal Salmonella epidemics have a huge impact on animal and human health. During the 1980

  4. Processes of barrier island erosion

    SciTech Connect

    Sallenger, A.H. Jr. (Geological Survey, St. Petersburg, FL (USA)); Williams, S.J. (Geological Survey, Reston, VA (USA))

    1989-09-01

    During 1986, the US Geological Survey and the Louisiana Geological Survey began a 5-year study of the processes causing the extreme rates (up to 20 m/year) of erosion of Louisiana's barrier islands. These processes must be better understood in order to predict future erosion and to assess management and erosion mitigation plans. The study is divided into three parts: the geologic development of barrier islands, the critical processes leading to erosion, and applications of results. This paper provides an overview of the part of the study on critical processes. The process part includes modeling erosion of the barrier islands due to sea level rise, the net loss of sand offshore, gradients in longshore transport, and overwash. Evidence indicates that the low-lying barrier beaches on much of the Louisiana coast do not approach an equilibrium configuration. These beaches, which, in many places, are not protected by dunes, are overwashed even during moderate storms and apparently are not evolving to a configuration that limits overwash. As a result, even with stable sea level, the beaches will continue to overwash and migrate landward during storms. Commonly used methods of modeling beach response to rising sea level assume beaches approach an equilibrium configuration, hence applying these methods to coastal Louisiana is problematical.

  5. An update on chloroplast genomes

    Microsoft Academic Search

    V. Ravi; J. P. Khurana; A. K. Tyagi; P. Khurana

    2008-01-01

    Plant cells possess two more genomes besides the central nuclear genome: the mitochondrial genome and the chloroplast genome\\u000a (or plastome). Compared to the gigantic nuclear genome, these organelle genomes are tiny and are present in high copy number.\\u000a These genomes are less prone to recombination and, therefore, retain signatures of their age to a much better extent than\\u000a their nuclear

  6. Tsunami damage along the Andaman Islands coasts

    NASA Technical Reports Server (NTRS)

    2005-01-01

    Among the first places to be affected by the massive tidal wave that ripped across the Indian Ocean on December 26, 2004, were the Andaman Islands. Located approximately 850 kilometers north of the epicenter of the earthquake that triggered the tsunami, the islands were not only among the first land masses to be swept under the wave, they have also been rattled by a series of aftershocks. Administrated by the Indian government, about 300,000 people live on the remote island chain, including several indigenous tribes. As of January 3, over 6,000 were confirmed dead or missing in the Andaman Islands. This Moderate Resolution Imaging Spectroradiometer (MODIS) image shows the Andaman Islands on January 3, 2005. Compared to previous images of the islands, the beaches along the west side of the islands have been stripped bare, leaving a strip of bright tan land along the coast. The change is most notable on North Sentinel Island, home of the Sentinelese aboriginals, and on Interview Island, where the formerly green coastline has been replaced with an abnormally bright ring of bare sand. The large image reveals additional damage along all the islands of the Andaman chain.

  7. HeteroGenome: database of genome periodicity

    PubMed Central

    Chaley, Maria; Kutyrkin, Vladimir; Tulbasheva, Gayane; Teplukhina, Elena; Nazipova, Nafisa

    2014-01-01

    We present the first release of the HeteroGenome database collecting latent periodicity regions in genomes. Tandem repeats and highly divergent tandem repeats along with the regions of a new type of periodicity, known as profile periodicity, have been collected for the genomes of Saccharomyces cerevisiae, Arabidopsis thaliana, Caenorhabditis elegans and Drosophila melanogaster. We obtained data with the aid of a spectral-statistical approach to search for reliable latent periodicity regions (with periods up to 2000?bp) in DNA sequences. The original two-level mode of data presentation (a broad view of the region of latent periodicity and a second level indicating conservative fragments of its structure) was further developed to enable us to obtain the estimate, without redundancy, that latent periodicity regions make up ?10% of the analyzed genomes. Analysis of the quantitative and qualitative content of located periodicity regions on all chromosomes of the analyzed organisms revealed dominant characteristic types of periodicity in the genomes. The pattern of density distribution of latent periodicity regions on chromosome unambiguously characterizes each chromosome in genome. Database URL: http://www.jcbi.ru/lp_baze/ PMID:24857969

  8. Plant Genomes Central: Integrated Resources for Plant Genomics

    E-print Network

    Levin, Judith G.

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

  9. Examination of Genome Homogeneity in Prokaryotes Using Genomic Signatures

    PubMed Central

    Bohlin, Jon; Skjerve, Eystein

    2009-01-01

    Background DNA word frequencies, normalized for genomic AT content, are remarkably stable within prokaryotic genomes and are therefore said to reflect a “genomic signature.” The genomic signatures can be used to phylogenetically classify organisms from arbitrary sampled DNA. Genomic signatures can also be used to search for horizontally transferred DNA or DNA regions subjected to special selection forces. Thus, the stability of the genomic signature can be used as a measure of genomic homogeneity. The factors associated with the stability of the genomic signatures are not known, and this motivated us to investigate further. We analyzed the intra-genomic variance of genomic signatures based on AT content normalization (0th order Markov model) as well as genomic signatures normalized by smaller DNA words (1st and 2nd order Markov models) for 636 sequenced prokaryotic genomes. Regression models were fitted, with intra-genomic signature variance as the response variable, to a set of factors representing genomic properties such as genomic AT content, genome size, habitat, phylum, oxygen requirement, optimal growth temperature and oligonucleotide usage variance (OUV, a measure of oligonucleotide usage bias), measured as the variance between genomic tetranucleotide frequencies and Markov chain approximated tetranucleotide frequencies, as predictors. Principal Findings Regression analysis revealed that OUV was the most important factor (p<0.001) determining intra-genomic homogeneity as measured using genomic signatures. This means that the less random the oligonucleotide usage is in the sense of higher OUV, the more homogeneous the genome is in terms of the genomic signature. The other factors influencing variance in the genomic signature (p<0.001) were genomic AT content, phylum and oxygen requirement. Conclusions Genomic homogeneity in prokaryotes is intimately linked to genomic GC content, oligonucleotide usage bias (OUV) and aerobiosis, while oligonucleotide usage bias (OUV) is associated with genomic GC content, aerobiosis and habitat. PMID:19956556

  10. Microarray comparative genomic hybridisation analysis incorporating genomic organisation, and application to enterobacterial plant pathogens.

    PubMed

    Pritchard, Leighton; Liu, Hui; Booth, Clare; Douglas, Emma; François, Patrice; Schrenzel, Jacques; Hedley, Peter E; Birch, Paul R J; Toth, Ian K

    2009-08-01

    Microarray comparative genomic hybridisation (aCGH) provides an estimate of the relative abundance of genomic DNA (gDNA) taken from comparator and reference organisms by hybridisation to a microarray containing probes that represent sequences from the reference organism. The experimental method is used in a number of biological applications, including the detection of human chromosomal aberrations, and in comparative genomic analysis of bacterial strains, but optimisation of the analysis is desirable in each problem domain.We present a method for analysis of bacterial aCGH data that encodes spatial information from the reference genome in a hidden Markov model. This technique is the first such method to be validated in comparisons of sequenced bacteria that diverge at the strain and at the genus level: Pectobacterium atrosepticum SCRI1043 (Pba1043) and Dickeya dadantii 3937 (Dda3937); and Lactococcus lactis subsp. lactis IL1403 and L. lactis subsp. cremoris MG1363. In all cases our method is found to outperform common and widely used aCGH analysis methods that do not incorporate spatial information. This analysis is applied to comparisons between commercially important plant pathogenic soft-rotting enterobacteria (SRE) Pba1043, P. atrosepticum SCRI1039, P. carotovorum 193, and Dda3937.Our analysis indicates that it should not be assumed that hybridisation strength is a reliable proxy for sequence identity in aCGH experiments, and robustly extends the applicability of aCGH to bacterial comparisons at the genus level. Our results in the SRE further provide evidence for a dynamic, plastic 'accessory' genome, revealing major genomic islands encoding gene products that provide insight into, and may play a direct role in determining, variation amongst the SRE in terms of their environmental survival, host range and aetiology, such as phytotoxin synthesis, multidrug resistance, and nitrogen fixation. PMID:19696881

  11. The complete genome sequence of Mycoplasma bovis strain Hubei-1.

    PubMed

    Li, Yuan; Zheng, Huajun; Liu, Yang; Jiang, Yanwei; Xin, Jiuqing; Chen, Wei; Song, Zhiqiang

    2011-01-01

    Infection by Mycoplasma bovis (M. bovis) can induce diseases, such as pneumonia and otitis media in young calves and mastitis and arthritis in older animals. Here, we report the finished and annotated genome sequence of M. bovis strain Hubei-1, a strain isolated in 2008 that caused calf pneumonia on a Chinese farm. The genome of M. bovis strain Hubei-1 contains a single circular chromosome of 953,114 bp with a 29.37% GC content. We identified 803 open reading frames (ORFs) that occupy 89.5% of the genome. While 34 ORFs were Hubei-1 specific, 662 ORFs had orthologs in the M. bovis type strain PG45 genome. Genome analysis validated lateral gene transfer between M. bovis and the Mycoplasma mycoides subspecies mycoides, while phylogenetic analysis found that the closest M. bovis neighbor is Mycoplasma agalactiae. Glycerol may be the main carbon and energy source of M. bovis, and most of the biosynthesis pathways were incomplete. We report that 47 lipoproteins, 12 extracellular proteins and 18 transmembrane proteins are phase-variable and may help M. bovis escape the immune response. Besides lipoproteins and phase-variable proteins, genomic analysis found two possible pathogenicity islands, which consist of four genes and 11 genes each, and several other virulence factors including hemolysin, lipoate protein ligase, dihydrolipoamide dehydrogenase, extracellular cysteine protease and 5'-nucleotidase. PMID:21731639

  12. The Complete Genome Sequence of Mycoplasma bovis Strain Hubei-1

    PubMed Central

    Li, Yuan; Zheng, Huajun; Liu, Yang; Jiang, Yanwei; Xin, Jiuqing; Chen, Wei; Song, Zhiqiang

    2011-01-01

    Infection by Mycoplasma bovis (M. bovis) can induce diseases, such as pneumonia and otitis media in young calves and mastitis and arthritis in older animals. Here, we report the finished and annotated genome sequence of M. bovis strain Hubei-1, a strain isolated in 2008 that caused calf pneumonia on a Chinese farm. The genome of M. bovis strain Hubei-1 contains a single circular chromosome of 953,114 bp with a 29.37% GC content. We identified 803 open reading frames (ORFs) that occupy 89.5% of the genome. While 34 ORFs were Hubei-1 specific, 662 ORFs had orthologs in the M. bovis type strain PG45 genome. Genome analysis validated lateral gene transfer between M. bovis and the Mycoplasma mycoides subspecies mycoides, while phylogenetic analysis found that the closest M. bovis neighbor is Mycoplasma agalactiae. Glycerol may be the main carbon and energy source of M. bovis, and most of the biosynthesis pathways were incomplete. We report that 47 lipoproteins, 12 extracellular proteins and 18 transmembrane proteins are phase-variable and may help M. bovis escape the immune response. Besides lipoproteins and phase-variable proteins, genomic analysis found two possible pathogenicity islands, which consist of four genes and 11 genes each, and several other virulence factors including hemolysin, lipoate protein ligase, dihydrolipoamide dehydrogenase, extracellular cysteine protease and 5?-nucleotidase. PMID:21731639

  13. Genetic research and aboriginal and Torres Strait Islander Australians.

    PubMed

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

    2012-12-01

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

  14. The genome of the versatile nitrogen fixer Azorhizobium caulinodans ORS571

    PubMed Central

    Lee, Kyung-Bum; De Backer, Philippe; Aono, Toshihiro; Liu, Chi-Te; Suzuki, Shino; Suzuki, Tadahiro; Kaneko, Takakazu; Yamada, Manabu; Tabata, Satoshi; Kupfer, Doris M; Najar, Fares Z; Wiley, Graham B; Roe, Bruce; Binnewies, Tim T; Ussery, David W; D'Haeze, Wim; Den Herder, Jeroen; Gevers, Dirk; Vereecke, Danny; Holsters, Marcelle; Oyaizu, Hiroshi

    2008-01-01

    Background Biological nitrogen fixation is a prokaryotic process that plays an essential role in the global nitrogen cycle. Azorhizobium caulinodans ORS571 has the dual capacity to fix nitrogen both as free-living organism and in a symbiotic interaction with Sesbania rostrata. The host is a fast-growing, submergence-tolerant tropical legume on which A. caulinodans can efficiently induce nodule formation on the root system and on adventitious rootlets located on the stem. Results The 5.37-Mb genome consists of a single circular chromosome with an overall average GC of 67% and numerous islands with varying GC contents. Most nodulation functions as well as a putative type-IV secretion system are found in a distinct symbiosis region. The genome contains a plethora of regulatory and transporter genes and many functions possibly involved in contacting a host. It potentially encodes 4717 proteins of which 96.3% have homologs and 3.7% are unique for A. caulinodans. Phylogenetic analyses show that the diazotroph Xanthobacter autotrophicus is the closest relative among the sequenced genomes, but the synteny between both genomes is very poor. Conclusion The genome analysis reveals that A. caulinodans is a diazotroph that acquired the capacity to nodulate most probably through horizontal gene transfer of a complex symbiosis island. The genome contains numerous genes that reflect a strong adaptive and metabolic potential. These combined features and the availability of the annotated genome make A. caulinodans an attractive organism to explore symbiotic biological nitrogen fixation beyond leguminous plants. PMID:18522759

  15. A signature for turbulence driven magnetic islands

    SciTech Connect

    Agullo, O.; Muraglia, M.; Benkadda, S. [Aix-Marseille Université, CNRS, PIIM, UMR 7345 Marseille (France); France-Japan Magnetic Fusion Laboratory, LIA 336 CNRS, Marseille (France); Poyé, A. [Univ. Bordeaux, CNRS, CEA, CELIA (Centre Lasers Intenses et Applications), UMR 5107, F-33405 Talence (France); Yagi, M. [Plasma Theory and Simulation Gr., JAEA, Rokkasho (Japan); Garbet, X. [IRFM, CEA, St-Paul-Lez-Durance 13108 (France); Sen, A. [Institute for Plasma Research, Bhat, Gandhinagar 382428 (India)

    2014-09-15

    We investigate the properties of magnetic islands arising from tearing instabilities that are driven by an interchange turbulence. We find that such islands possess a specific signature that permits an identification of their origin. We demonstrate that the persistence of a small scale turbulence maintains a mean pressure profile, whose characteristics makes it possible to discriminate between turbulence driven islands from those arising due to an unfavourable plasma current density gradient. We also find that the island poloidal turnover time, in the steady state, is independent of the levels of the interchange and tearing energy sources. Finally, we show that a mixing length approach is adequate to make theoretical predictions concerning island flattening in the island rotation frame.

  16. Molluscan fauna of Gueishan Island, Taiwan.

    PubMed

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

    2013-01-01

    This dataset records the occurrence and inventory of molluscan fauna on Gueishan Island, the only active volcanic island in Taiwan, based on the literature survey and field investigation conducted between 2011 and 2012. The literature review involved seven studies published from 1934 to 2003, which collectively reported 112 species from 61 genera and 37 families of Mollusca on Gueishan Island. Through our field investigation, we identified 34 species from 28 genera and 23 families. Fourteen of these species were new records on Gueishan Island: Liolophura japonica, Lottia luchuana, Nerita costata, Nerita rumphii, Diplommatina suganikeiensis, Littoraria undulata, Solenomphala taiwanensis, Assiminea sp., Siphonaria laciniosa, Laevapex nipponica, Carychium hachijoensis, Succinea erythrophana, Zaptyx crassilamellata, and Allopeas pyrgula. In Total, there are 126 species from 71 genera and 45 families of Mollusca on Gueishan Island. These data have been published through GBIF [http://taibif.org.tw/ipt/resource.do?r=gueishan_island] and integrated into the Taiwan Malacofauna Database (http://shell.sinica.edu.tw/). PMID:23717182

  17. Horse Genome Project

    NSDL National Science Digital Library

    What's in a horse? As it turns out, what's in a horse is quite important, and the Horse Genome Project at the University of Kentucky is currently defining the genome of this animal. The Project is a cooperative international effort which involves some 100 scientists working in 20 countries. On the left-hand side of the page, visitors can make their way through five sections, including "The People", "The Horses", "Genomics 101", and "Applications of Genome Study". "The Horses" area is a good place to start, as it gives an overview of the animals being used in the project. In "Genomics 101", interested parties will find an overview of some basic terms used in the field, such as gene, allele, and mutation. The "Applications of Genome Study" area focuses in on how their work will be used to benefit the health and welfare of horses.

  18. The tiniest tiny genomes.

    PubMed

    Moran, Nancy A; Bennett, Gordon M

    2014-01-01

    Starting in 2006, surprisingly tiny genomes have been discovered from numerous bacterial symbionts of insect hosts. Despite their size, each retains some genes that enable provisioning of limiting nutrients or other capabilities required by hosts. Genome sequence analyses show that genome reduction is an ongoing process, resulting in a continuum of sizes, with the smallest genome currently known at 112 kilobases. Genome reduction is typical in host-restricted symbionts and pathogens, but the tiniest genomes are restricted to symbionts required by hosts and restricted to specialized host cells, resulting from long coevolution with hosts. Genes are lost in all functional categories, but core genes for central informational processes, including genes encoding ribosomal proteins, are mostly retained, whereas genes underlying production of cell envelope components are especially depleted. Thus, these entities retain cell-like properties but are heavily dependent on coadaptation of hosts, which continuously evolve to support the symbionts upon which they depend. PMID:24995872

  19. 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

  20. Understanding the Human Genome

    Microsoft Academic Search

    Douglas L. Brutlag

    1994-01-01

    Introduction to Molecular Medicine (pp. 153168). New York NY: Scientific American Inc.Understanding the Human GenomeDouglas L. Brutlag, Ph.D.There are many compelling reasons to determine the complete genetic information of thehuman organism. The genome contains the history of human evolution and specifies themechanism of human development; all humanity's physical capabilities and deficienciesare encoded in the genome. It is no wonder that

  1. Cancer Genomics Overview

    Cancer.gov

    Cancer Genomics Overview Cancer is a group of diseases caused by changes in a person's genome that allow a tumor to form. These changes can be inherited from one's parents, caused by environmental factors, or occur during natural processes such as cell division. The field of cancer genomics studies these changes. Once the cancer-causing changes are identified, scientists may be able to develop drugs to target these changes, resulting in a better understanding of cancer as well as improved treatments.

  2. Mass wasting in the Western Galapagos Islands

    NASA Astrophysics Data System (ADS)

    Hall, H.; Sager, W. W.

    2009-12-01

    Oceanic island volcanoes such as those comprising the Hawaiian, Canary and Galapagos Islands are known to become unstable with the passage of time, resulting in failures of the subaerial and submarine portion of the volcanic edifices. These mass wasting events appear to be the primary source of destruction and loss of volume of many oceanic islands, but our knowledge of mass wasting in seamount and island chains is still rudimentary. To better understand mass wasting in the western Galapagos Islands, multi-beam bathymetry, backscatter and sidescan sonar data were used to examine topography characteristic of mass wasting. Observations show that mass wasting plays an important role in the morphological development of Galapagos volcanoes. While volcanic activity continues to modify the submarine terrain, the data show that several types of mass wasting can be found in this archipelago. The steep upper slopes of the north and west flanks of Fernandina Island and the north and southwest flanks of Isabela Island are characterized by slump sheets. The lower slopes on the north and west flank of Fernandina and the southwest tip of Isabela Island are characterized by debris flows. The northwest tip of Isabela Island is characterized by chaotic slumping and detached blocks originating from the sector collapse of Volcan Ecuador. Unlike the giant landslides documented by GLORIA imagery around the Hawaiian Islands, the western Galapagos Islands appear to be characterized by small slumps and debris flows. Nevertheless, this study indicates that submarine mass wasting is widespread in the western Galapagos Islands and is an important component of erosion of these volcanic edifices.

  3. The Beetles of the Virgin Islands

    NSDL National Science Digital Library

    Provided in collaboration by researchers at Montana State and Ohio State universities, this database of the Beetles of the Virgin Islands contains records for over 34,000 specimens of 489 beetle species. The database also offers mapping capabilities for identifying beetle collection locations. Query by Island, Family, or Specimen to find details for each species -- including scientific name, number of specimens in the database, islands where this species has been collected, and collecting methods.

  4. Genome-wide patterns of natural variation reveal strong selective sweeps and ongoing genomic conflict in Drosophila mauritiana

    PubMed Central

    Nolte, Viola; Pandey, Ram Vinay; Kofler, Robert; Schlötterer, Christian

    2013-01-01

    Although it is well understood that selection shapes the polymorphism pattern in Drosophila, signatures of classic selective sweeps are scarce. Here, we focus on Drosophila mauritiana, an island endemic, which is closely related to Drosophila melanogaster. Based on a new, annotated genome sequence, we characterized the genome-wide polymorphism by sequencing pooled individuals (Pool-seq). We show that the interplay between selection and recombination results in a genome-wide polymorphism pattern characteristic for D. mauritiana. Two large genomic regions (>500 kb) showed the signature of almost complete selective sweeps. We propose that the absence of population structure and limited geographic distribution could explain why such pronounced sweep patterns are restricted to D. mauritiana. Further evidence for strong adaptive evolution was detected for several nucleoporin genes, some of which were not previously identified as genes involved in genomic conflict. Since this adaptive evolution is continuing after the split of D. mauritiana and Drosophila simulans, we conclude that genomic conflict is not restricted to short episodes, but rather an ongoing process in Drosophila. PMID:23051690

  5. 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

  6. Between two fern genomes.

    PubMed

    Sessa, Emily B; Banks, Jo Ann; Barker, Michael S; Der, Joshua P; Duffy, Aaron M; Graham, Sean W; Hasebe, Mitsuyasu; Langdale, Jane; Li, Fay-Wei; Marchant, D Blaine; Pryer, Kathleen M; Rothfels, Carl J; Roux, Stanley J; Salmi, Mari L; Sigel, Erin M; Soltis, Douglas E; Soltis, Pamela S; Stevenson, Dennis W; Wolf, Paul G

    2014-01-01

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

  7. [Landscape and ecological genomics].

    PubMed

    2013-10-01

    Landscape genomics is the modern version of landscape genetics, a discipline that arose approximately 10 years ago as a combination of population genetics, landscape ecology, and spatial statistics. It studies the effects of environmental variables on gene flow and other microevolutionary processes that determine genetic connectivity and variations in populations. In contrast to population genetics, it operates at the level of individual specimens rather than at the level of population samples. Another important difference between landscape genetics and genomics and population genetics is that, in the former, the analysis of gene flow and local adaptations takes quantitative account of landforms and features of the matrix, i.e., hostile spaces that separate species habitats. Landscape genomics is a part of population ecogenomics, which, along with community genomics, is a major part of ecological genomics. One of the principal purposes of landscape genomics is the identification and differentiation of various genome-wide and locus-specific effects. The approaches and computation tools developed for combined analysis of genomic and landscape variables make it possible to detect adaptation-related genome fragments, which facilitates the planning of conservation efforts and the prediction of species' fate in response to expected changes in the environment. PMID:25508669

  8. [Landscape and ecological genomics].

    PubMed

    Tetushkin, E Ia

    2013-10-01

    Landscape genomics is the modern version of landscape genetics, a discipline that arose approximately 10 years ago as a combination of population genetics, landscape ecology, and spatial statistics. It studies the effects of environmental variables on gene flow and other microevolutionary processes that determine genetic connectivity and variations in populations. In contrast to population genetics, it operates at the level of individual specimens rather than at the level of population samples. Another important difference between landscape genetics and genomics and population genetics is that, in the former, the analysis of gene flow and local adaptations takes quantitative account of landforms and features of the matrix, i.e., hostile spaces that separate species habitats. Landscape genomics is a part of population ecogenomics, which, along with community genomics, is a major part of ecological genomics. One of the principal purposes of landscape genomics is the identification and differentiation of various genome-wide and locus-specific effects. The approaches and computation tools developed for combined analysis of genomic and landscape variables make it possible to detect adaptation-related genome fragments, which facilitates the planning of conservation efforts and the prediction of species' fate in response to expected changes in the environment. PMID:25474890

  9. 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.

  10. The Geee! in Genome

    NSDL National Science Digital Library

    It's too late to catch the Geee! in Genome exhibit at the Canadian Museum of Nature, but virtual visitors can still check out the exhibit's excellent Web companion. The Web site, which is also available in French, is loaded with cool, interactive features on the everyday side of genomics. The Geee! in Genome Web site also contains a set of downloadable lesson plans and activities for grades 5 through 12. Together with the online features, these lesson plans offer a fun and engaging way to learn about genomics in the classroom.

  11. 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

  12. Human Genome Resources

    NSDL National Science Digital Library

    In an effort to track the progress of and provide access to the work of the Human Genome Project (see the October 14, 1998 Scout Report for Science & Engineering), the National Center for Biotechnology Information (NCBI) of the National Library of Medicine (NLM) has expanded their Web resource. An international research program "designed to construct detailed genetic and physical maps of the human genome." The Human Genome Resources page provides a wealth of relevant resources, from background information on the project, to specific sequences for each human chromosome (click on the desired chromosome), to Genome Maps of other organisms.

  13. Genome@home

    NSDL National Science Digital Library

    With Genome@home, a project at Stanford University, computer owners can become de facto researchers in virtual genome protein design. By downloading and running the Genome@home protein sequence design client, users lend their idle computer time to run calculations for use with such projects as designing new medical drugs, understanding protein evolution, and determining the function of newly sequenced genes. The program can run during other applications without affecting computer performance. The Genome@home Web site also provides a mountain of scientific background information and other resources for understanding the overall project and learning what's been accomplished so far.

  14. Structural & FunctionalStructural & Functional GenomicsGenomics

    E-print Network

    Boguski, Mark S.

    NCBINCBI Structural & FunctionalStructural & Functional GenomicsGenomics:: The Information Information National Library of Medicine National Institutes of Health Bethesda, Maryland Current Topics in Genome Analysis, 4 November 1997 #12;NCBINCBI Growth of Biomedical Information (1)Growth of Biomedical

  15. The evolution of birdsong on islands

    PubMed Central

    Morinay, Jennifer; Cardoso, Gonçalo C; Doutrelant, Claire; Covas, Rita

    2013-01-01

    Islands are simplified, isolated ecosystems, providing an ideal set-up to study evolution. Among several traits that are expected to change on islands, an interesting but poorly understood example concerns signals used in animal communication. Islands are typified by reduced species diversity, increased population density, and reduced mate competition, all of which could affect communication signals. We used birdsong to investigate whether there are systematic changes in communication signals on islands, by undertaking a broad comparison based on pairs of closely related island-mainland species across the globe. We studied song traits related to complexity (number of different syllables, frequency bandwidth), to vocal performance (syllable delivery rate, song duration), and also three particular song elements (rattles, buzzes, and trills) generally implicated in aggressive communication. We also investigated whether song complexity was related to the number of similar sympatric species. We found that island species were less likely to produce broadband and likely aggressive song elements (rattles and buzzes). By contrast, various aspects of song complexity and performance did not differ between island and mainland species. Species with fewer same-family sympatric species used wider frequency bandwidths, as predicted by the character release hypothesis, both on continents and on islands. Our study supports the hypothesis of a reduction in aggressive behavior on islands and suggests that discrimination against closely related species is an important factor influencing birdsong evolution. PMID:24455143

  16. WIND DATA REPORT Deer Island Parking Lot

    E-print Network

    Massachusetts at Amherst, University of

    WIND DATA REPORT Deer Island Parking Lot May 1, 2003 ­ July 15, 2003 Prepared for Massachusetts...................................................................................................................... 7 Wind Speed Time Series............................................................................................................. 7 Wind Speed Distributions

  17. WIND DATA REPORT Deer Island Outfall

    E-print Network

    Massachusetts at Amherst, University of

    WIND DATA REPORT Deer Island Outfall August 18, 2003 ­ December 4, 2003 Prepared for Massachusetts...................................................................................................................... 7 Wind Speed Time Series............................................................................................................. 7 Wind Speed Distributions

  18. Nauru Island Effect Detection Data Set

    DOE Data Explorer

    Long, Chuck

    During Nauru99 it was noted that the island was producing small clouds that advected over the ARM site. The Nauru Island Effect Study was run for 1.5 years and the methodology developed to detect the occurrence. Nauru ACRF downwelling SW, wind direction, and air temperature data are used, along with downwelling SW data from Licor radiometers located on the southern end of the island near the airport landing strip. A statistical analysis and comparison of data from the two locations is used to detect the likely occurrence of an island influence on the Nauru ACRF site data

  19. Climate change: Effects on reef island resources

    SciTech Connect

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

    1988-06-27

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

  20. Dendrochronology of strain-relaxed islands.

    PubMed

    Merdzhanova, T; Kiravittaya, S; Rastelli, A; Stoffel, M; Denker, U; Schmidt, O G

    2006-06-01

    We report on the observation and study of tree-ring structures below dislocated SiGe islands (superdomes) grown on Si(001) substrates. Analogous to the study of tree rings (dendrochronology), these footprints enable us to gain unambiguous information on the growth and evolution of superdomes and their neighboring islands. The temperature dependence of the critical volume for dislocation introduction is measured and related to the composition of the islands. We show clearly that island coalescence is the dominant pathway towards dislocation nucleation at low temperatures, while at higher temperatures anomalous coarsening is effective and leads to the formation of a depletion region around superdomes. PMID:16803325