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Sample records for variable genomic islands

  1. Genomic island excisions in Bordetella petrii

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    Levillain Erwan

    2009-07-01

    Full Text Available Abstract Background Among the members of the genus Bordetella B. petrii is unique, since it is the only species isolated from the environment, while the pathogenic Bordetellae are obligately associated with host organisms. Another feature distinguishing B. petrii from the other sequenced Bordetellae is the presence of a large number of mobile genetic elements including several large genomic regions with typical characteristics of genomic islands collectively known as integrative and conjugative elements (ICEs. These elements mainly encode accessory metabolic factors enabling this bacterium to grow on a large repertoire of aromatic compounds. Results During in vitro culture of Bordetella petrii colony variants appear frequently. We show that this variability can be attributed to the presence of a large number of metastable mobile genetic elements on its chromosome. In fact, the genome sequence of B. petrii revealed the presence of at least seven large genomic islands mostly encoding accessory metabolic functions involved in the degradation of aromatic compounds and detoxification of heavy metals. Four of these islands (termed GI1 to GI3 and GI6 are highly related to ICEclc of Pseudomonas knackmussii sp. strain B13. Here we present first data about the molecular characterization of these islands. We defined the exact borders of each island and we show that during standard culture of the bacteria these islands get excised from the chromosome. For all but one of these islands (GI5 we could detect circular intermediates. For the clc-like elements GI1 to GI3 of B. petrii we provide evidence that tandem insertion of these islands which all encode highly related integrases and attachment sites may also lead to incorporation of genomic DNA which originally was not part of the island and to the formation of huge composite islands. By integration of a tetracycline resistance cassette into GI3 we found this island to be rather unstable and to be lost from

  2. Unsupervised statistical identification of genomic islands using ...

    Indian Academy of Sciences (India)

    Vibrio species. These investigations lead to observations that are of evolutionary ... Identification of genomic islands in prokaryotic genomes has received considerable attention in the literature due to .... For instance, selective pres- sures as a ...

  3. Genomic Variability of O Islands Encoding Tellurite Resistance in Enterohemorrhagic Escherichia coli O157:H7 Isolates

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

    2002-01-01

    Strains of Escherichia coli causing enterohemorrhagic colitis belonging to the O157:H7 lineage are reported to be highly related. Fifteen strains of E. coli O157:H7 and 1 strain of E. coli O46:H− (nonflagellated) were examined for the presence of potassium tellurite resistance (Ter). Ter genes comprising terABCDEF were shown previously to be part of a pathogenicity island also containing integrase, phage, and urease genes. PCR analysis, both conventional and light cycler based, demonstrated t...

  4. Genomic Variability of O Islands Encoding Tellurite Resistance in Enterohemorrhagic Escherichia coli O157:H7 Isolates

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

    2002-01-01

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

  5. Statistical analyses of conserved features of genomic islands in bacteria.

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    Guo, F-B; Xia, Z-K; Wei, W; Zhao, H-L

    2014-03-17

    We performed statistical analyses of five conserved features of genomic islands of bacteria. Analyses were made based on 104 known genomic islands, which were identified by comparative methods. Four of these features include sequence size, abnormal G+C content, flanking tRNA gene, and embedded mobility gene, which are frequently investigated. One relatively new feature, G+C homogeneity, was also investigated. Among the 104 known genomic islands, 88.5% were found to fall in the typical length of 10-200 kb and 80.8% had G+C deviations with absolute values larger than 2%. For the 88 genomic islands whose hosts have been sequenced and annotated, 52.3% of them were found to have flanking tRNA genes and 64.7% had embedded mobility genes. For the homogeneity feature, 85% had an h homogeneity index less than 0.1, indicating that their G+C content is relatively uniform. Taking all the five features into account, 87.5% of 88 genomic islands had three of them. Only one genomic island had only one conserved feature and none of the genomic islands had zero features. These statistical results should help to understand the general structure of known genomic islands. We found that larger genomic islands tend to have relatively small G+C deviations relative to absolute values. For example, the absolute G+C deviations of 9 genomic islands longer than 100,000 bp were all less than 5%. This is a novel but reasonable result given that larger genomic islands should have greater restrictions in their G+C contents, in order to maintain the stable G+C content of the recipient genome.

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

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    Clark, Mary Anne

    2009-01-01

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

  7. Evolutionary forces shaping genomic islands of population differentiation in humans

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    Hofer Tamara

    2012-03-01

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

  8. A quantitative account of genomic island acquisitions in prokaryotes

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    Roos Tom E

    2011-08-01

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

  9. Uropathogenic Escherichia coli pathogenicity islands and other ExPEC virulence genes may contribute to the genome variability of enteroinvasive E. coli.

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    da Silva, Laís Cristina; de Mello Santos, Ana Carolina; Silva, Rosa Maria

    2017-03-16

    Enteroinvasive Escherichia coli (EIEC) may be the causative agent of part of those million cases of diarrhea illness reported worldwide every year and attributable to Shigella. That is because both enteropathogens have many common characteristics that difficult their identification either by traditional microbiological methods or by molecular tools used in the clinical laboratory settings. While Shigella has been extensively studied, EIEC remains barely characterized at the molecular level. Recent EIEC important outbreaks, apparently generating more life-threatening cases, have prompted us to screen EIEC for virulence traits usually related to extraintestinal pathogenic E. coli (ExPEC). That could explain the appearance of EIEC strains presenting higher virulence potential. EIEC strains were distributed mainly in three phylogroups in a serogroup-dependent manner. Serogroups O124, O136, O144, and O152 were exclusively classified in phylogroup A; O143 in group E; and O28ac and O29 in group B1. Only two serogroups showed diverse phylogenetic origin as follows: O164 was assigned to groups A, B1, C, and B2 (one strain each), and O167 in groups E (five strains), and A (one strain) (Table 1). Eleven of 20 virulence genes (VGs) searched were detected, and the majority of the 19 different VGs combinations found were serogroup-specific. Uropathogenic E. coli (UPEC) PAI genetic markers were detected in all EIEC strains. PAIs I J96 and II CFT073 were the most frequent (92.1 and 80.4%, respectively). PAI IV 536 was restricted to some serogroups from phylogroups A, B1 and E. PAI I CFT073 was uniquely detected in phylogroups B2 and E. A total of 45 (88%) strains presented multiple PAI markers (two to four). PAIs I J96 and II CFT073 were found together in 80% of strains. EIEC is a DEC pathovar that presents VGs and pathogenicity island genetic markers typically associated with ExPEC, especially UPEC. These features are distributed in a phylogenetic and serogroup-dependent manner

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

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    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. Copyright © 2012 Elsevier B.V. All rights reserved.

  11. SIGI: score-based identification of genomic islands

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    Merkl Rainer

    2004-03-01

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

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

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    Chaudhuri Probal

    2008-04-01

    Full Text Available Abstract 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.

  13. Patterns and architecture of genomic islands in marine bacteria

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    Fernández-Gómez Beatriz

    2012-07-01

    Full Text Available Abstract 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 β-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.

  14. Temporal variability of mass transport across Canary Islands Channels

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    Marrero-Díaz, Ángeles; Rodríguez-Santana, Ángel; José Machín, Francisco; García-Weil, Luis; Sangrà, Pablo; Vélez-Belchí, Pedro; Fraile-Nuez, Eugenio

    2014-05-01

    The equatorward flowing Canary Current (CC) is the main feature of the circulation in the Canary Islands region. The CC flow perturbation by the Canary Islands originate the Canary Eddy Corridor which is the major pathway for long lived eddies in the subtropical North Atlantic (Sangrà et al., 2009, DSR). Therefore the variability of the CC passing through the Canary Archipelago will have both local and regional importance. Past studies on the CC variability trough the Canary Islands point out a clearly seasonal variability (Fraile-Nuez et al, 2010 (JGR); Hernández-Guerra et al, 2002 (DSR)). However those studies where focused on the eastern islands channels missing the variability through the western island channels which are the main source of long lived eddies. In order to fill this gap from November 2012 until September 2013 we conducted trimonthly surveys crossing the whole islands channels using opportunity ships (Naviera Armas Ferries). XBT and XCTD where launched along the cross channels transects. Additionally a closed box circling the Archipelago was performed on October 2013 as part of the cruise RAPROCAN-2013 (IEO) using also XBT and XCTD. Dynamical variables where derived inferring salinity from S(T,p) analytical relationships for the region updated with new XCTD data. High resolution, vertical sections of temperature, potential density, geostrophic velocity and transport where obtained. Our preliminary results suggest that the CC suffer a noticeable acceleration in those islands channels where eddy shedding is more frequent. They also indicate a clearly seasonal variability of the flows passing the islands channels. With this regard we observed significant differences on the obtained seasonal variability with respect the cited past studies on the eastern islands channel (Lanzarote / Fuerteventura - Africa coast). This work was co-funded by Canary Government (TRAMIC project: PROID20100092) and the European Union (FEDER).

  15. Proteus genomic island 1 (PGI1), a new resistance genomic island from two Proteus mirabilis French clinical isolates.

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    Siebor, Eliane; Neuwirth, Catherine

    2014-12-01

    To analyse the genetic environment of the antibiotic resistance genes in two clinical Proteus mirabilis isolates resistant to multiple antibiotics. PCR, gene walking and whole-genome sequencing were used to determine the sequence of the resistance regions, the surrounding genetic structure and the flanking chromosomal regions. A genomic island of 81.1 kb named Proteus genomic island 1 (PGI1) located at the 3'-end of trmE (formerly known as thdF) was characterized. The large MDR region of PGI1 (55.4 kb) included a class 1 integron (aadB and aadA2) and regions deriving from several transposons: Tn2 (blaTEM-135), Tn21, Tn6020-like transposon (aphA1b), a hybrid Tn502/Tn5053 transposon, Tn501, a hybrid Tn1696/Tn1721 transposon [tetA(A)] carrying a class 1 integron (aadA1) and Tn5393 (strA and strB). Several ISs were also present (IS4321, IS1R and IS26). The PGI1 backbone (25.7 kb) was identical to that identified in Salmonella Heidelberg SL476 and shared some identity with the Salmonella genomic island 1 (SGI1) backbone. An IS26-mediated recombination event caused the division of the MDR region into two parts separated by a large chromosomal DNA fragment of 197 kb, the right end of PGI1 and this chromosomal sequence being in inverse orientation. PGI1 is a new resistance genomic island from P. mirabilis belonging to the same island family as SGI1. The role of PGI1 in the spread of antimicrobial resistance genes among Enterobacteriaceae of medical importance needs to be evaluated. © The Author 2014. Published by Oxford University Press on behalf of the British Society for Antimicrobial Chemotherapy. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  16. Genomic islands predict functional adaptation in marine actinobacteria

    Energy Technology Data Exchange (ETDEWEB)

    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

  17. Methyl-CpG island-associated genome signature tags

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    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.

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

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    Surovcik Katharina

    2006-03-01

    Full Text Available Abstract Background Horizontal gene transfer (HGT is considered a strong evolutionary force shaping the content of microbial genomes in a substantial manner. It is the difference in speed enabling the rapid adaptation to changing environmental demands that distinguishes HGT from gene genesis, duplications or mutations. For a precise characterization, algorithms are needed that identify transfer events with high reliability. Frequently, the transferred pieces of DNA have a considerable length, comprise several genes and are called genomic islands (GIs or more specifically pathogenicity or symbiotic islands. Results We have implemented the program SIGI-HMM that predicts GIs and the putative donor of each individual alien gene. It is based on the analysis of codon usage (CU of each individual gene of a genome under study. CU of each gene is compared against a carefully selected set of CU tables representing microbial donors or highly expressed genes. Multiple tests are used to identify putatively alien genes, to predict putative donors and to mask putatively highly expressed genes. Thus, we determine the states and emission probabilities of an inhomogeneous hidden Markov model working on gene level. For the transition probabilities, we draw upon classical test theory with the intention of integrating a sensitivity controller in a consistent manner. SIGI-HMM was written in JAVA and is publicly available. It accepts as input any file created according to the EMBL-format. It generates output in the common GFF format readable for genome browsers. Benchmark tests showed that the output of SIGI-HMM is in agreement with known findings. Its predictions were both consistent with annotated GIs and with predictions generated by different methods. Conclusion SIGI-HMM is a sensitive tool for the identification of GIs in microbial genomes. It allows to interactively analyze genomes in detail and to generate or to test hypotheses about the origin of acquired

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

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

    2013-01-01

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

  20. Genetic Variability of Myxoma Virus Genomes

    OpenAIRE

    Braun, Christoph; Thürmer, Andrea; Daniel, Rolf; Schultz, Anne-Kathrin; Bulla, Ingo; Schirrmeier, Horst; Mayer, Dietmar; Neubert, Andreas; Czerny, Claus-Peter

    2017-01-01

    Myxomatosis is a recurrent problem on rabbit farms throughout Europe despite the success of vaccines. To identify gene variations of field and vaccine strains that may be responsible for changes in virulence, immunomodulation, and immunoprotection, the genomes of 6 myxoma virus (MYXV) strains were sequenced: German field isolates Munich-1, FLI-H, 2604, and 3207; vaccine strain MAV; and challenge strain ZA. The analyzed genomes ranged from 147.6 kb (strain MAV) to 161.8 kb (strain 3207). All s...

  1. CpG islands undermethylation in human genomic regions under selective pressure.

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    Sergio Cocozza

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

  2. Defense islands in bacterial and archaeal genomes and prediction of novel defense systems.

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

    2011-11-01

    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.

  3. Genetic variability of psychrotolerant Acidithiobacillus ferrivorans revealed by (meta)genomic analysis.

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    González, Carolina; Yanquepe, María; Cardenas, Juan Pablo; Valdes, Jorge; Quatrini, Raquel; Holmes, David S; Dopson, Mark

    2014-11-01

    Acidophilic microorganisms inhabit low pH environments such as acid mine drainage that is generated when sulfide minerals are exposed to air. The genome sequence of the psychrotolerant Acidithiobacillus ferrivorans SS3 was compared to a metagenome from a low temperature acidic stream dominated by an A. ferrivorans-like strain. Stretches of genomic DNA characterized by few matches to the metagenome, termed 'metagenomic islands', encoded genes associated with metal efflux and pH homeostasis. The metagenomic islands were enriched in mobile elements such as phage proteins, transposases, integrases and in one case, predicted to be flanked by truncated tRNAs. Cus gene clusters predicted to be involved in copper efflux and further Cus-like RND systems were predicted to be located in metagenomic islands and therefore, constitute part of the flexible gene complement of the species. Phylogenetic analysis of Cus clusters showed both lineage specificity within the Acidithiobacillus genus as well as niche specificity associated with an acidic environment. The metagenomic islands also contained a predicted copper efflux P-type ATPase system and a polyphosphate kinase potentially involved in polyphosphate mediated copper resistance. This study identifies genetic variability of low temperature acidophiles that likely reflects metal resistance selective pressures in the copper rich environment. Copyright © 2014 Institut Pasteur. Published by Elsevier Masson SAS. All rights reserved.

  4. The dnd operon for DNA phosphorothioation modification system in Escherichia coli is located in diverse genomic islands.

    Science.gov (United States)

    Ho, Wing Sze; Ou, Hong-Yu; Yeo, Chew Chieng; Thong, Kwai Lin

    2015-03-17

    Strains of Escherichia coli that are non-typeable by pulsed-field gel electrophoresis (PFGE) due to in-gel degradation can influence their molecular epidemiological data. The DNA degradation phenotype (Dnd(+)) is mediated by the dnd operon that encode enzymes catalyzing the phosphorothioation of DNA, rendering the modified DNA susceptible to oxidative cleavage during a PFGE run. In this study, a PCR assay was developed to detect the presence of the dnd operon in Dnd(+) E. coli strains and to improve their typeability. Investigations into the genetic environments of the dnd operon in various E. coli strains led to the discovery that the dnd operon is harboured in various diverse genomic islands. The dndBCDE genes (dnd operon) were detected in all Dnd(+) E. coli strains by PCR. The addition of thiourea improved the typeability of Dnd(+) E. coli strains to 100% using PFGE and the Dnd(+) phenotype can be observed in both clonal and genetically diverse E. coli strains. Genomic analysis of 101 dnd operons from genome sequences of Enterobacteriaceae revealed that the dnd operons of the same bacterial species were generally clustered together in the phylogenetic tree. Further analysis of dnd operons of 52 E. coli genomes together with their respective immediate genetic environments revealed a total of 7 types of genetic organizations, all of which were found to be associated with genomic islands designated dnd-encoding GIs. The dnd-encoding GIs displayed mosaic structure and the genomic context of the 7 islands (with 1 representative genome from each type of genetic organization) were also highly variable, suggesting multiple recombination events. This is also the first report where two dnd operons were found within a strain although the biological implication is unknown. Surprisingly, dnd operons were frequently found in pathogenic E. coli although their link with virulence has not been explored. Genomic islands likely play an important role in facilitating the horizontal

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    Lu, Bingxin; Leong, Hon Wai

    2016-02-01

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

  7. Genetic Variability of Myxoma Virus Genomes

    Science.gov (United States)

    Braun, Christoph; Thürmer, Andrea; Daniel, Rolf; Schultz, Anne-Kathrin; Bulla, Ingo; Schirrmeier, Horst; Mayer, Dietmar; Neubert, Andreas

    2016-01-01

    ABSTRACT Myxomatosis is a recurrent problem on rabbit farms throughout Europe despite the success of vaccines. To identify gene variations of field and vaccine strains that may be responsible for changes in virulence, immunomodulation, and immunoprotection, the genomes of 6 myxoma virus (MYXV) strains were sequenced: German field isolates Munich-1, FLI-H, 2604, and 3207; vaccine strain MAV; and challenge strain ZA. The analyzed genomes ranged from 147.6 kb (strain MAV) to 161.8 kb (strain 3207). All sequences were affected by several mutations, covering 24 to 93 open reading frames (ORFs) and resulted in amino acid substitutions, insertions, or deletions. Only strains Munich-1 and MAV revealed the deletion of 10 ORFs (M007L to M015L) and 11 ORFs (M007L to M008.1L and M149R to M008.1R), respectively. Major differences were observed in the 27 immunomodulatory proteins encoded by MYXV. Compared to the reference strain Lausanne, strains FLI-H, 2604, 3207, and ZA showed the highest amino acid identity (>98.4%). In strains Munich-1 and MAV, deletion of 5 and 10 ORFs, respectively, was observed, encoding immunomodulatory proteins with ankyrin repeats or members of the family of serine protease inhibitors. Furthermore, putative immunodominant surface proteins with homology to vaccinia virus (VACV) were investigated in the sequenced strains. Only strain MAV revealed above-average frequencies of amino acid substitutions and frameshift mutations. Finally, we performed recombination analysis and found signs of recombination in vaccine strain MAV. Phylogenetic analysis showed a close relationship of strain MAV and the MSW strain of Californian MYXV. However, in a challenge model, strain MAV provided full protection against lethal challenges with strain ZA. IMPORTANCE Myxoma virus (MYXV) is pathogenic for European rabbits and two North American species. Due to sophisticated strategies in immune evasion and oncolysis, MYXV is an important model virus for immunological and

  8. Highly variable rates of genome rearrangements between hemiascomycetous yeast lineages.

    Directory of Open Access Journals (Sweden)

    2006-03-01

    Full Text Available Hemiascomycete yeasts cover an evolutionary span comparable to that of the entire phylum of chordates. Since this group currently contains the largest number of complete genome sequences it presents unique opportunities to understand the evolution of genome organization in eukaryotes. We inferred rates of genome instability on all branches of a phylogenetic tree for 11 species and calculated species-specific rates of genome rearrangements. We characterized all inversion events that occurred within synteny blocks between six representatives of the different lineages. We show that the rates of macro- and microrearrangements of gene order are correlated within individual lineages but are highly variable across different lineages. The most unstable genomes correspond to the pathogenic yeasts Candida albicans and Candida glabrata. Chromosomal maps have been intensively shuffled by numerous interchromosomal rearrangements, even between species that have retained a very high physical fraction of their genomes within small synteny blocks. Despite this intensive reshuffling of gene positions, essential genes, which cluster in low recombination regions in the genome of Saccharomyces cerevisiae, tend to remain syntenic during evolution. This work reveals that the high plasticity of eukaryotic genomes results from rearrangement rates that vary between lineages but also at different evolutionary times of a given lineage.

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

    Directory of Open Access Journals (Sweden)

    Daniel M de Brito

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

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

    Science.gov (United States)

    Tokarz, Rafal; Sameroff, Stephen; Leon, Maria Sanchez; Jain, Komal; Lipkin, W Ian

    2014-02-11

    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. 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. 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. The Long Island tick rhabdovirus may represent a novel species within family Rhabdoviridae.

  11. First insights in the variability of Borrelia recurrentis genomes.

    Directory of Open Access Journals (Sweden)

    Durdica Marosevic

    2017-09-01

    Full Text Available Borrelia recurrentis is the causative agent of louse-borne relapsing fever, endemic to the Horn of Africa. New attention was raised in Europe, with the highest number of cases (n = 45 reported among migrants in 2015 in Germany and sporadically from other European countries. So far only one genome was sequenced, hindering the development of specific molecular diagnostic and typing tools. Here we report on modified culture conditions for B. recurrentis and the intraspecies genome variability of six isolates isolated and cultured in different years in order to explore the possibility to identify new targets for typing and examine the molecular epidemiology of the pathogen.Two historical isolates from Ethiopia and four isolates from migrants from Somalia (n = 3 and Ethiopia (n = 1 obtained in 2015 were cultured in MPK-medium supplemented with 50% foetal calf serum. Whole DNA was sequenced using Illumina MiSeq technology and analysed using the CLC Genomics Workbench and SPAdes de novo assembler. Compared to the reference B. recurrentis A1 29-38 SNPs were identified in the genome distributed on the chromosome and plasmids. In addition to that, plasmids of differing length, compared to the available reference genome were identified.The observed low genetic variability of B. recurrentis isolates is possibly due to the adaptation to a very conserved vector-host (louse-human cycle, or influenced by the fastidious nature of the pathogen and their resistance to in vitro growth. Nevertheless, isolates obtained in 2015 were bearing the same chromosomal SNPs and could be distinguished from the historical isolates by means of whole genome sequencing, but not hitherto used typing methods. This is the first study examining the molecular epidemiology of B. recurrentis and provides the necessary background for the development of better diagnostic tools.

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

    Directory of Open Access Journals (Sweden)

    James A Cahill

    Full Text Available 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.

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

    Directory of Open Access Journals (Sweden)

    Kelle C Freel

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

  14. LifeStyle-Specific-Islands (LiSSI): Integrated Bioinformatics Platform for Genomic Island Analysis

    DEFF Research Database (Denmark)

    Barbosa, Eudes; Rottger, Richard; Hauschild, Anne-Christin

    2017-01-01

    Distinct bacteria are able to cope with highly diverse lifestyles; for instance, they can be free living or host-associated. Thus, these organisms must possess a large and varied genomic arsenal to withstand different environmental conditions. To facilitate the identification of genomic features ...

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

    Science.gov (United States)

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

    2015-01-01

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

  16. Extensive Genome Rearrangements and Multiple Horizontal Gene Transfers in a Population of Pyrococcus Isolates from Vulcano Island, Italy▿ †

    Science.gov (United States)

    White, James R.; Escobar-Paramo, Patricia; Mongodin, Emmanuel F.; Nelson, Karen E.; DiRuggiero, Jocelyne

    2008-01-01

    The extent of chromosome rearrangements in Pyrococcus isolates from marine hydrothermal vents in Vulcano Island, Italy, was evaluated by high-throughput genomic methods. The results illustrate the dynamic nature of the genomes of the genus Pyrococcus and raise the possibility of a connection between rapidly changing environmental conditions and adaptive genomic properties. PMID:18723649

  17. Extensive genome rearrangements and multiple horizontal gene transfers in a population of pyrococcus isolates from Vulcano Island, Italy.

    Science.gov (United States)

    White, James R; Escobar-Paramo, Patricia; Mongodin, Emmanuel F; Nelson, Karen E; DiRuggiero, Jocelyne

    2008-10-01

    The extent of chromosome rearrangements in Pyrococcus isolates from marine hydrothermal vents in Vulcano Island, Italy, was evaluated by high-throughput genomic methods. The results illustrate the dynamic nature of the genomes of the genus Pyrococcus and raise the possibility of a connection between rapidly changing environmental conditions and adaptive genomic properties.

  18. Genomic islands of differentiation in two songbird species reveal candidate genes for hybrid female sterility.

    Science.gov (United States)

    Mořkovský, Libor; Janoušek, Václav; Reif, Jiří; Rídl, Jakub; Pačes, Jan; Choleva, Lukáš; Janko, Karel; Nachman, Michael W; Reifová, Radka

    2018-02-01

    Hybrid sterility is a common first step in the evolution of postzygotic reproductive isolation. According to Haldane's Rule, it affects predominantly the heterogametic sex. While the genetic basis of hybrid male sterility in organisms with heterogametic males has been studied for decades, the genetic basis of hybrid female sterility in organisms with heterogametic females has received much less attention. We investigated the genetic basis of reproductive isolation in two closely related avian species, the common nightingale (Luscinia megarhynchos) and the thrush nightingale (L. luscinia), that hybridize in a secondary contact zone and produce viable hybrid progeny. In accordance with Haldane's Rule, hybrid females are sterile, while hybrid males are fertile, allowing gene flow to occur between the species. Using transcriptomic data from multiple individuals of both nightingale species, we identified genomic islands of high differentiation (F ST ) and of high divergence (D xy ), and we analysed gene content and patterns of molecular evolution within these islands. Interestingly, we found that these islands were enriched for genes related to female meiosis and metabolism. The islands of high differentiation and divergence were also characterized by higher levels of linkage disequilibrium than the rest of the genome in both species indicating that they might be situated in genomic regions of low recombination. This study provides one of the first insights into genetic basis of hybrid female sterility in organisms with heterogametic females. © 2018 John Wiley & Sons Ltd.

  19. Study on the Mitochondrial Genome of Sea Island Cotton (Gossypium barbadense) by BAC Library Screening

    Institute of Scientific and Technical Information of China (English)

    SU Ai-guo; LI Shuang-shuang; LIU Guo-zheng; LEI Bin-bin; KANG Ding-ming; LI Zhao-hu; MA Zhi-ying; HUA Jin-ping

    2014-01-01

    The plant mitochondrial genome displays complex features, particularly in terms of cytoplasmic male sterility (CMS). Therefore, research on the cotton mitochondrial genome may provide important information for analyzing genome evolution and exploring the molecular mechanism of CMS. In this paper, we present a preliminary study on the mitochondrial genome of sea island cotton (Gossypium barbadense) based on positive clones from the bacterial artiifcial chromosome (BAC) library. Thirty-ifve primers designed with the conserved sequences of functional genes and exons of mitochondria were used to screen positive clones in the genome library of the sea island cotton variety called Pima 90-53. Ten BAC clones were obtained and veriifed for further study. A contig was obtained based on six overlapping clones and subsequently laid out primarily on the mitochondrial genome. One BAC clone, clone 6 harbored with the inserter of approximate 115 kb mtDNA sequence, in which more than 10 primers fragments could be ampliifed, was sequenced and assembled using the Solexa strategy. Fifteen mitochondrial functional genes were revealed in clone 6 by gene annotation. The characteristics of the syntenic gene/exon of the sequences and RNA editing were preliminarily predicted.

  20. Full genome sequences are key to disclose RHDV2 emergence in the Macaronesian islands.

    Science.gov (United States)

    Lopes, Ana M; Blanco-Aguiar, Jose; Martín-Alonso, Aaron; Leitão, Manuel; Foronda, Pilar; Mendes, Marco; Gonçalves, David; Abrantes, Joana; Esteves, Pedro J

    2018-02-01

    A recent publication by Carvalho et al. in "Virus Genes" (June 2017) reported the presence of the new variant of rabbit hemorrhagic disease virus (RHDV2) in the two larger islands of the archipelago of Madeira. Based on the capsid protein sequence, the authors suggested that the high sequence identity, along with the short time spanning between outbreaks, points to dissemination from Porto Santo to Madeira. By including information of the full RHDV2 genome of strains from Azores, Madeira, and the Canary Islands, we confirm the results obtained by Carvalho et al., but further show that several subtypes of RHDV2 circulate in these islands: non-recombinant RHDV2 in the Canary Islands, G1/RHDV2 in Azores, Porto Santo and Madeira, and NP/RHDV2 also in Madeira. Here we conclude that RHDV2 has been independently introduced in these archipelagos, and that in Madeira at least two independent introductions must have occurred. We provide additional information on the dynamics of RHDV2 in the Macaronesian archipelagos of Azores, Madeira, and the Canary Islands and highlight the importance of analyzing RHDV2 complete genome.

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

    Directory of Open Access Journals (Sweden)

    Castanos-Velez Esmeralda

    2006-09-01

    Full Text Available Abstract 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 distinct chromosomal islands with aberrant gene expression. Of these, 38 islands show a gain in expression and 43 a loss of expression. In total, 7.892 genes (25.3% of all human genes are located in aberrantly expressed islands. Many chromosomal regions that are linked to hereditary colorectal cancer show deregulated expression. Also, many known tumor genes localize to chromosomal islands of misregulated expression in CRC. Conclusion An extensive comparison with published CGH data suggests that chromosomal regions known for frequent deletions in colon cancer tend to show reduced expression. In contrast, regions that are often amplified in colorectal tumors exhibit heterogeneous expression patterns: even show a decrease of mRNA expression. Because for several islands of deregulated expression chromosomal aberrations have never been observed, we speculate that additional mechanisms (like abnormal states of regional chromatin also have a substantial impact on the formation of co-expression islands in colorectal carcinoma.

  2. Long-range autocorrelations of CpG islands in the human genome.

    Directory of Open Access Journals (Sweden)

    Benjamin Koester

    Full Text Available 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.

  3. Phylogenetic Relationships of the Fern Cyrtomium falcatum (Dryopteridaceae from Dokdo Island Based on Chloroplast Genome Sequencing

    Directory of Open Access Journals (Sweden)

    Gurusamy Raman

    2016-12-01

    Full Text Available Cyrtomium falcatum is a popular ornamental fern cultivated worldwide. Native to the Korean Peninsula, Japan, and Dokdo Island in the Sea of Japan, it is the only fern present on Dokdo Island. We isolated and characterized the chloroplast (cp genome of C. falcatum, and compared it with those of closely related species. The genes trnV-GAC and trnV-GAU were found to be present within the cp genome of C. falcatum, whereas trnP-GGG and rpl21 were lacking. Moreover, cp genomes of Cyrtomium devexiscapulae and Adiantum capillus-veneris lack trnP-GGG and rpl21, suggesting these are not conserved among angiosperm cp genomes. The deletion of trnR-UCG, trnR-CCG, and trnSeC in the cp genomes of C. falcatum and other eupolypod ferns indicates these genes are restricted to tree ferns, non-core leptosporangiates, and basal ferns. The C. falcatum cp genome also encoded ndhF and rps7, with GUG start codons that were only conserved in polypod ferns, and it shares two significant inversions with other ferns, including a minor inversion of the trnD-GUC region and an approximate 3 kb inversion of the trnG-trnT region. Phylogenetic analyses showed that Equisetum was found to be a sister clade to Psilotales-Ophioglossales with a 100% bootstrap (BS value. The sister relationship between Pteridaceae and eupolypods was also strongly supported by a 100% BS, but Bayesian molecular clock analyses suggested that C. falcatum diversified in the mid-Paleogene period (45.15 ± 4.93 million years ago and might have moved from Eurasia to Dokdo Island.

  4. Mechanisms driving variability in the ocean forcing of Pine Island Glacier.

    Science.gov (United States)

    Webber, Benjamin G M; Heywood, Karen J; Stevens, David P; Dutrieux, Pierre; Abrahamsen, E Povl; Jenkins, Adrian; Jacobs, Stanley S; Ha, Ho Kyung; Lee, Sang Hoon; Kim, Tae Wan

    2017-02-17

    Pine Island Glacier (PIG) terminates in a rapidly melting ice shelf, and ocean circulation and temperature are implicated in the retreat and growing contribution to sea level rise of PIG and nearby glaciers. However, the variability of the ocean forcing of PIG has been poorly constrained due to a lack of multi-year observations. Here we show, using a unique record close to the Pine Island Ice Shelf (PIIS), that there is considerable oceanic variability at seasonal and interannual timescales, including a pronounced cold period from October 2011 to May 2013. This variability can be largely explained by two processes: cumulative ocean surface heat fluxes and sea ice formation close to PIIS; and interannual reversals in ocean currents and associated heat transport within Pine Island Bay, driven by a combination of local and remote forcing. Local atmospheric forcing therefore plays an important role in driving oceanic variability close to PIIS.

  5. Genomic Islands: an overview of current software tools and future improvements

    Directory of Open Access Journals (Sweden)

    Soares Siomar de Castro

    2016-03-01

    Full Text Available Microbes are highly diverse and widely distributed organisms. They account for ~60% of Earth’s biomass and new predictions point for the existence of 1011 to 1012 species, which are constantly sharing genes through several different mechanisms. Genomic Islands (GI are critical in this context, as they are large regions acquired through horizontal gene transfer. Also, they present common features like genomic signature deviation, transposase genes, flanking tRNAs and insertion sequences. GIs carry large numbers of genes related to specific lifestyle and are commonly classified in Pathogenicity, Resistance, Metabolic or Symbiotic Islands. With the advent of the next-generation sequencing technologies and the deluge of genomic data, many software tools have been developed that aim to tackle the problem of GI prediction and they are all based on the prediction of GI common features. However, there is still room for the development of new software tools that implements new approaches, such as, machine learning and pangenomics based analyses. Finally, GIs will always hold a potential application in every newly invented genomic approach as they are directly responsible for much of the genomic plasticity of bacteria.

  6. Genomic Islands: an overview of current software tools and future improvements.

    Science.gov (United States)

    Soares, Siomar de Castro; Oliveira, Letícia de Castro; Jaiswal, Arun Kumar; Azevedo, Vasco

    2016-03-01

    Microbes are highly diverse and widely distributed organisms. They account for ~60% of Earth's biomass and new predictions point for the existence of 1011 to 1012 species, which are constantly sharing genes through several different mechanisms. Genomic Islands (GI) are critical in this context, as they are large regions acquired through horizontal gene transfer. Also, they present common features like genomic signature deviation, transposase genes, flanking tRNAs and insertion sequences. GIs carry large numbers of genes related to specific lifestyle and are commonly classified in Pathogenicity, Resistance, Metabolic or Symbiotic Islands. With the advent of the next-generation sequencing technologies and the deluge of genomic data, many software tools have been developed that aim to tackle the problem of GI prediction and they are all based on the prediction of GI common features. However, there is still room for the development of new software tools that implements new approaches, such as, machine learning and pangenomics based analyses. Finally, GIs will always hold a potential application in every newly invented genomic approach as they are directly responsible for much of the genomic plasticity of bacteria.

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

    OpenAIRE

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

    2007-01-01

    Abstract Background The genomes of Streptomyces coelicolor and Streptomyces lividans bear a considerable degree of synteny. While S. coelicolor is the model streptomycete for studying antibiotic synthesis and differentiation, S. lividans is almost exclusively considered as the preferred host, among actinomycetes, for cloning and expression of exogenous DNA. We used whole genome microarrays as a comparative genomics tool for identifying the subtle differences between these two chromosomes. Res...

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

    Science.gov (United States)

    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

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

    Science.gov (United States)

    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 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.

  10. Compositional searching of CpG islands in the human genome

    Science.gov (United States)

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

    2005-06-01

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

  11. Defense Islands in Bacterial and Archaeal Genomes and Prediction of Novel Defense Systems ▿†‡

    Science.gov (United States)

    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

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

    Directory of Open Access Journals (Sweden)

    Qianli Huang

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

  13. Island-Model Genomic Selection for Long-Term Genetic Improvement of Autogamous Crops.

    Science.gov (United States)

    Yabe, Shiori; Yamasaki, Masanori; Ebana, Kaworu; Hayashi, Takeshi; Iwata, Hiroyoshi

    2016-01-01

    Acceleration of genetic improvement of autogamous crops such as wheat and rice is necessary to increase cereal production in response to the global food crisis. Population and pedigree methods of breeding, which are based on inbred line selection, are used commonly in the genetic improvement of autogamous crops. These methods, however, produce a few novel combinations of genes in a breeding population. Recurrent selection promotes recombination among genes and produces novel combinations of genes in a breeding population, but it requires inaccurate single-plant evaluation for selection. Genomic selection (GS), which can predict genetic potential of individuals based on their marker genotype, might have high reliability of single-plant evaluation and might be effective in recurrent selection. To evaluate the efficiency of recurrent selection with GS, we conducted simulations using real marker genotype data of rice cultivars. Additionally, we introduced the concept of an "island model" inspired by evolutionary algorithms that might be useful to maintain genetic variation through the breeding process. We conducted GS simulations using real marker genotype data of rice cultivars to evaluate the efficiency of recurrent selection and the island model in an autogamous species. Results demonstrated the importance of producing novel combinations of genes through recurrent selection. An initial population derived from admixture of multiple bi-parental crosses showed larger genetic gains than a population derived from a single bi-parental cross in whole cycles, suggesting the importance of genetic variation in an initial population. The island-model GS better maintained genetic improvement in later generations than the other GS methods, suggesting that the island-model GS can utilize genetic variation in breeding and can retain alleles with small effects in the breeding population. The island-model GS will become a new breeding method that enhances the potential of genomic

  14. Island-Model Genomic Selection for Long-Term Genetic Improvement of Autogamous Crops.

    Directory of Open Access Journals (Sweden)

    Shiori Yabe

    Full Text Available Acceleration of genetic improvement of autogamous crops such as wheat and rice is necessary to increase cereal production in response to the global food crisis. Population and pedigree methods of breeding, which are based on inbred line selection, are used commonly in the genetic improvement of autogamous crops. These methods, however, produce a few novel combinations of genes in a breeding population. Recurrent selection promotes recombination among genes and produces novel combinations of genes in a breeding population, but it requires inaccurate single-plant evaluation for selection. Genomic selection (GS, which can predict genetic potential of individuals based on their marker genotype, might have high reliability of single-plant evaluation and might be effective in recurrent selection. To evaluate the efficiency of recurrent selection with GS, we conducted simulations using real marker genotype data of rice cultivars. Additionally, we introduced the concept of an "island model" inspired by evolutionary algorithms that might be useful to maintain genetic variation through the breeding process. We conducted GS simulations using real marker genotype data of rice cultivars to evaluate the efficiency of recurrent selection and the island model in an autogamous species. Results demonstrated the importance of producing novel combinations of genes through recurrent selection. An initial population derived from admixture of multiple bi-parental crosses showed larger genetic gains than a population derived from a single bi-parental cross in whole cycles, suggesting the importance of genetic variation in an initial population. The island-model GS better maintained genetic improvement in later generations than the other GS methods, suggesting that the island-model GS can utilize genetic variation in breeding and can retain alleles with small effects in the breeding population. The island-model GS will become a new breeding method that enhances the

  15. Complete Genome Sequences of Four Avian Paramyxoviruses of Serotype 10 Isolated from Rockhopper Penguins on the Falkland Islands

    OpenAIRE

    Goraichuk, Iryna V.; Dimitrov, Kiril M.; Sharma, Poonam; Miller, Patti J.; Swayne, David E.; Suarez, David L.; Afonso, Claudio L.

    2017-01-01

    ABSTRACT The first complete genome sequences of four avian paramyxovirus serotype 10 (APMV-10) isolates are described here. The viruses were isolated from rockhopper penguins on the Falkland Islands, sampled in 2007. All four genomes are 15,456 nucleotides in length, and phylogenetic analyses show them to be closely related.

  16. Complete Genome Sequences of Four Avian Paramyxoviruses of Serotype 10 Isolated from Rockhopper Penguins on the Falkland Islands

    Science.gov (United States)

    Goraichuk, Iryna V.; Dimitrov, Kiril M.; Sharma, Poonam; Miller, Patti J.; Swayne, David E.; Suarez, David L.

    2017-01-01

    ABSTRACT The first complete genome sequences of four avian paramyxovirus serotype 10 (APMV-10) isolates are described here. The viruses were isolated from rockhopper penguins on the Falkland Islands, sampled in 2007. All four genomes are 15,456 nucleotides in length, and phylogenetic analyses show them to be closely related. PMID:28572332

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

    Science.gov (United States)

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

    2007-01-01

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

  18. CpGislandEVO: A Database and Genome Browser for Comparative Evolutionary Genomics of CpG Islands

    Directory of Open Access Journals (Sweden)

    Guillermo Barturen

    2013-01-01

    Full Text Available Hypomethylated, CpG-rich DNA segments (CpG islands, CGIs are epigenome markers involved in key biological processes. Aberrant methylation is implicated in the appearance of several disorders as cancer, immunodeficiency, or centromere instability. Furthermore, methylation differences at promoter regions between human and chimpanzee strongly associate with genes involved in neurological/psychological disorders and cancers. Therefore, the evolutionary comparative analyses of CGIs can provide insights on the functional role of these epigenome markers in both health and disease. Given the lack of specific tools, we developed CpGislandEVO. Briefly, we first compile a database of statistically significant CGIs for the best assembled mammalian genome sequences available to date. Second, by means of a coupled browser front-end, we focus on the CGIs overlapping orthologous genes extracted from OrthoDB, thus ensuring the comparison between CGIs located on truly homologous genome segments. This allows comparing the main compositional features between homologous CGIs. Finally, to facilitate nucleotide comparisons, we lifted genome coordinates between assemblies from different species, which enables the analysis of sequence divergence by direct count of nucleotide substitutions and indels occurring between homologous CGIs. The resulting CpGislandEVO database, linking together CGIs and single-cytosine DNA methylation data from several mammalian species, is freely available at our website.

  19. Why close a bacterial genome? The plasmid of Alteromonas macleodii HOT1A3 is a vector for inter-specific transfer of a flexible genomic island

    Directory of Open Access Journals (Sweden)

    Eduard eFadeev

    2016-03-01

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

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

    Science.gov (United States)

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

    2014-12-01

    Six out of the 64 studied Proteus mirabilis isolates from 11 poultry farms in China contained Salmonella genomic island 1 (SGI1). PCR mapping showed that the complete nucleotide sequences of SGI1s ranged from 33.2 to 42.5 kb. Three novel variants, SGI1-W, SGI1-X, and SGI1-Y, have been characterized. Resistance genes lnuF, dfrA25, and qnrB2 were identified in SGI1 for the first time. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

  1. Tracing common origins of Genomic Islands in prokaryotes based on genome signature analyses.

    Science.gov (United States)

    van Passel, Mark Wj

    2011-09-01

    Horizontal gene transfer constitutes a powerful and innovative force in evolution, but often little is known about the actual origins of transferred genes. Sequence alignments are generally of limited use in tracking the original donor, since still only a small fraction of the total genetic diversity is thought to be uncovered. Alternatively, approaches based on similarities in the genome specific relative oligonucleotide frequencies do not require alignments. Even though the exact origins of horizontally transferred genes may still not be established using these compositional analyses, it does suggest that compositionally very similar regions are likely to have had a common origin. These analyses have shown that up to a third of large acquired gene clusters that reside in the same genome are compositionally very similar, indicative of a shared origin. This brings us closer to uncovering the original donors of horizontally transferred genes, and could help in elucidating possible regulatory interactions between previously unlinked sequences.

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

    Directory of Open Access Journals (Sweden)

    Hochhut Bianca

    2011-09-01

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

  3. Natural and Human-Induced Variability in Barrier-Island Response to Sea Level Rise

    Science.gov (United States)

    Miselis, Jennifer L.; Lorenzo-Trueba, Jorge

    2017-12-01

    Storm-driven sediment fluxes onto and behind barrier islands help coastal barrier systems keep pace with sea level rise (SLR). Understanding what controls cross-shore sediment flux magnitudes is critical for making accurate forecasts of barrier response to increased SLR rates. Here, using an existing morphodynamic model for barrier island evolution, observations are used to constrain model parameters and explore potential variability in future barrier behavior. Using modeled drowning outcomes as a proxy for vulnerability to SLR, 0%, 28%, and 100% of the barrier is vulnerable to SLR rates of 4, 7, and 10 mm/yr, respectively. When only overwash fluxes are increased in the model, drowning vulnerability increases for the same rates of SLR, suggesting that future increases in storminess may increase island vulnerability particularly where sediment resources are limited. Developed sites are more vulnerable to SLR, indicating that anthropogenic changes to overwash fluxes and estuary depths could profoundly affect future barrier response to SLR.

  4. Genetics of Genome-Wide Recombination Rate Evolution in Mice from an Isolated Island.

    Science.gov (United States)

    Wang, Richard J; Payseur, Bret A

    2017-08-01

    Recombination rate is a heritable quantitative trait that evolves despite the fundamentally conserved role that recombination plays in meiosis. Differences in recombination rate can alter the landscape of the genome and the genetic diversity of populations. Yet our understanding of the genetic basis of recombination rate evolution in nature remains limited. We used wild house mice ( Mus musculus domesticus ) from Gough Island (GI), which diverged recently from their mainland counterparts, to characterize the genetics of recombination rate evolution. We quantified genome-wide autosomal recombination rates by immunofluorescence cytology in spermatocytes from 240 F 2 males generated from intercrosses between GI-derived mice and the wild-derived inbred strain WSB/EiJ. We identified four quantitative trait loci (QTL) responsible for inter-F 2 variation in this trait, the strongest of which had effects that opposed the direction of the parental trait differences. Candidate genes and mutations for these QTL were identified by overlapping the detected intervals with whole-genome sequencing data and publicly available transcriptomic profiles from spermatocytes. Combined with existing studies, our findings suggest that genome-wide recombination rate divergence is not directional and its evolution within and between subspecies proceeds from distinct genetic loci. Copyright © 2017 by the Genetics Society of America.

  5. Description of genomic islands associated to the multidrug-resistant Pseudomonas aeruginosa clone ST277.

    Science.gov (United States)

    Silveira, Melise Chaves; Albano, Rodolpho Mattos; Asensi, Marise Dutra; Carvalho-Assef, Ana Paula D'Alincourt

    2016-08-01

    Multidrug-resistant Pseudomonas aeruginosa clone ST277 is disseminated in Brazil where it is mainly associated with the presence of metallo-β-lactamase SPM-1. Furthermore, it carries the class I integron In163 and a 16S rRNA methylase rmtD that confers aminoglycoside resistance. To analyze the genetic characteristics that might be responsible for the success of this endemic clone, genomes of four P. aeruginosa strains that were isolated in distinct years and in different Brazilian states were sequenced. The strains differed regarding the presence of the genes blaSPM-1 and rmtD. Genomic comparisons that included genomes of other clones that have spread worldwide from this species were also performed. These analyses revealed a 763,863bp region in the P. aeruginosa chromosome that concentrates acquired genetic structures comprising two new genomic islands (PAGI-13 and PAGI-14), a mobile element that could be used for ST277 fingerprinting and a recently reported Integrative and Conjugative Element (ICE) associated to blaSPM-1. The genetic elements rmtD and In163 are inserted in PAGI-13 while PAGI-14 has genes encoding proteins related to type III restriction system and phages. The data reported in this study provide a basis for a clearer understanding of the genetic content of clone ST277 and illustrate the mechanisms that are responsible for the success of these endemic clones. Copyright © 2016 Elsevier B.V. All rights reserved.

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

    DEFF Research Database (Denmark)

    Wipf, Juliette R K; Schwendener, Sybille; Nielsen, Jesper Boye

    2015-01-01

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

  7. Genome-wide CpG island methylation analysis implicates novel genes in the pathogenesis of renal cell carcinoma

    OpenAIRE

    Ricketts, Christopher J.; Morris, Mark R.; Gentle, Dean; Brown, Michael; Wake, Naomi; Woodward, Emma R.; Clarke, Noel; Latif, Farida; Maher, Eamonn R.

    2012-01-01

    In order to identify novel candidate tumor suppressor genes (TSGs) implicated in renal cell carcinoma (RCC), we performed genome-wide methylation profiling of RCC using the HumanMethylation27 BeadChips to assess methylation at >14,000 genes. Two hundred and twenty hypermethylated probes representing 205 loci/genes were identified in genomic CpG islands. A subset of TSGs investigated in detail exhibited frequent tumor methylation, promoter methylation associated transcriptional silencing an...

  8. Productivity and fishing pressure drive variability in fish parasite assemblages of the Line Islands, equatorial Pacific.

    Science.gov (United States)

    Wood, Chelsea L; Baum, Julia K; Reddy, Sheila M W; Trebilco, Rowan; Sandin, Stuart A; Zgliczynski, Brian J; Briggs, Amy A; Micheli, Fiorenza

    2015-05-01

    Variability in primary productivity and fishing pressure can shape the abundance, species composition, and diversity of marine life. Though parasites comprise nearly half of marine species, their responses to these important forces remain little explored. We quantified parasite assemblages at two spatial scales, across a gradient in productivity and fishing pressure that spans six coral islands of the Line Islands archipelago and within the largest Line Island, Kiritimati, which experiences a west-to-east gradient in fishing pressure and upwelling-driven productivity. In the across-islands data set, we found that increasing productivity was correlated with increased parasite abundance overall, but that the effects of productivity differed among parasite groups. Trophically transmitted parasites increased in abundance with increasing productivity, but directly transmitted parasites did not exhibit significant changes. This probably arises because productivity has stronger effects on the abundance of the planktonic crustaceans and herbivorous snails that serve as the intermediate hosts of trophically transmitted parasites than on the higher-trophic level fishes that are the sole hosts of directly transmitted parasites. We also found that specialist parasites increased in response to increasing productivity, while generalists did not, possibly because specialist parasites tend to be more strongly limited by host availability than are generalist parasites. After the effect of productivity was controlled for, fishing was correlated with decreases in the abundance of trophically transmitted parasites, while directly transmitted parasites appeared to track host density; we observed increases in the abundance of parasites using hosts that experienced fishing-driven compensatory increases in abundance. The within-island data set confirmed these patterns for the combined effects of productivity and fishing on parasite abundance, suggesting that our conclusions are robust

  9. Antibiotic resistance, integrons and Salmonella genomic island 1 among non-typhoidal Salmonella serovars in The Netherlands.

    NARCIS (Netherlands)

    Vo, An T T; Duijkeren, Engeline van; Fluit, Ad C; Wannet, Wim J B; Verbruggen, Anjo J; Maas, Henny M E; Gaastra, Wim

    2006-01-01

    The objective of this study was to investigate the antimicrobial resistance patterns, integron characteristics and gene cassettes as well as the presence of Salmonella genomic island 1 (SGI1) in non-typhoidal Salmonella (NTS) isolates from human and animal origin. Epidemiologically unrelated Dutch

  10. A genomic island provides Acidithiobacillus ferrooxidans ATCC 53993 additional copper resistance: a possible competitive advantage.

    Science.gov (United States)

    Orellana, Luis H; Jerez, Carlos A

    2011-11-01

    There is great interest in understanding how extremophilic biomining bacteria adapt to exceptionally high copper concentrations in their environment. Acidithiobacillus ferrooxidans ATCC 53993 genome possesses the same copper resistance determinants as strain ATCC 23270. However, the former strain contains in its genome a 160-kb genomic island (GI), which is absent in ATCC 23270. This GI contains, amongst other genes, several genes coding for an additional putative copper ATPase and a Cus system. A. ferrooxidans ATCC 53993 showed a much higher resistance to CuSO(4) (>100 mM) than that of strain ATCC 23270 (<25 mM). When a similar number of bacteria from each strain were mixed and allowed to grow in the absence of copper, their respective final numbers remained approximately equal. However, in the presence of copper, there was a clear overgrowth of strain ATCC 53993 compared to ATCC 23270. This behavior is most likely explained by the presence of the additional copper-resistance genes in the GI of strain ATCC 53993. As determined by qRT-PCR, it was demonstrated that these genes are upregulated when A. ferrooxidans ATCC 53993 is grown in the presence of copper and were shown to be functional when expressed in copper-sensitive Escherichia coli mutants. Thus, the reason for resistance to copper of two strains of the same acidophilic microorganism could be determined by slight differences in their genomes, which may not only lead to changes in their capacities to adapt to their environment, but may also help to select the more fit microorganisms for industrial biomining operations. © Springer-Verlag 2011

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

    OpenAIRE

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

    2007-01-01

    MobilomeFINDER (http://mml.sjtu.edu.cn/MobilomeFINDER) is an interactive online tool that facilitates bacterial genomic island or ‘mobile genome’ (mobilome) discovery; it integrates the ArrayOme and tRNAcc software packages. ArrayOme utilizes a microarray-derived comparative genomic hybridization input data set to generate ‘inferred contigs’ produced by merging adjacent genes classified as ‘present’. Collectively these ‘fragments’ represent a hypothetical ‘microarray-visualized genome (MVG)’....

  12. Postglacial Records of Southern Hemisphere Westerly Wind Variability From the New Zealand Subantarctic Auckland Islands

    Science.gov (United States)

    Moy, C. M.; Vandergoes, M.; Gilmer, G. J.; Nichols, J. E.; Dagg, B. J.; Wilson, G. S.; Browne, I. M.; Curtin, L. G.; Aebig, C.; McGlone, M.

    2015-12-01

    The strength and latitudinal position of the Southern Hemisphere westerly winds (SHWW) play a fundamental role in influencing mid latitude climate and carbon dioxide exchange between the Southern Ocean and the atmosphere. Despite their importance, our understanding of past changes in the SHWW is limited by few paleoclimate records from the modern wind maximum that are often not in agreement. The New Zealand subantarctic Auckland Islands are located within the core of the modern wind belt (50°S) where the ocean-atmospheric linkages between the Antarctic and middle latitudes are strong. In contrast to other subantarctic islands on the Campbell Plateau, the Auckland Islands have protected fjord sub-basins, deep lakes, and peatlands that are advantageous for the development of high-resolution paleoclimate records. We will present ongoing work towards the establishment of multi-proxy and multi-site reconstructions of past SHWW variability from the Auckland Islands. Modern process and paleoclimate results from two research cruises in 2014 and 2015 suggest that in lacustrine and fjord settings, the degree of water column mixing, the stable isotopic composition of n-alkanes and benthic foraminifera, the influx of terrestrial organic matter are good indicators of wind-induced mixing of the water column or precipitation-driven erosion within catchments. In ombrotrophic peatlands, hydrogen isotope ratios of specific organic molecules allow reconstructions of the hydrogen isotope ratios of precipitation, which is related to precipitation source area and the latitudinal position of the SHWW. Using macrofossil counts paired with abundances of leaf wax biomarkers, we are able to estimate the moisture balance at peatland coring sites. Early results indicate an overall strengthening of the SHWW at the Auckland Islands through the Holocene. We will discuss these results within the context of complimentary records developed from New Zealand and southern South America to ultimately

  13. Antimicrobial resistance, class 1 integrons, and genomic island 1 in Salmonella isolates from Vietnam.

    Directory of Open Access Journals (Sweden)

    An T T Vo

    Full Text Available BACKGROUND: The objective was to investigate the phenotypic and genotypic resistance and the horizontal transfer of resistance determinants from Salmonella isolates from humans and animals in Vietnam. METHODOLOGY/PRINCIPAL FINDINGS: The susceptibility of 297 epidemiologically unrelated non-typhoid Salmonella isolates was investigated by disk diffusion assay. The isolates were screened for the presence of class 1 integrons and Salmonella genomic island 1 by PCR. The potential for the transfer of resistance determinants was investigated by conjugation experiments. Resistance to gentamicin, kanamycin, chloramphenicol, streptomycin, trimethoprim, ampicillin, nalidixic acid, sulphonamides, and tetracycline was found in 13 to 50% of the isolates. Nine distinct integron types were detected in 28% of the isolates belonging to 11 Salmonella serovars including S. Tallahassee. Gene cassettes identified were aadA1, aadA2, aadA5, bla(PSE-1, bla(OXA-30, dfrA1, dfrA12, dfrA17, and sat, as well as open reading frames with unknown functions. Most integrons were located on conjugative plasmids, which can transfer their antimicrobial resistance determinants to Escherichia coli or Salmonella Enteritidis, or with Salmonella Genomic Island 1 or its variants. The resistance gene cluster in serovar Emek identified by PCR mapping and nucleotide sequencing contained SGI1-J3 which is integrated in SGI1 at another position than the majority of SGI1. This is the second report on the insertion of SGI1 at this position. High-level resistance to fluoroquinolones was found in 3 multiresistant S. Typhimurium isolates and was associated with mutations in the gyrA gene leading to the amino acid changes Ser83Phe and Asp87Asn. CONCLUSIONS: Resistance was common among Vietnamese Salmonella isolates from different sources. Legislation to enforce a more prudent use of antibiotics in both human and veterinary medicine should be implemented by the authorities in Vietnam.

  14. Complete chloroplast genome of Prunus yedoensis Matsum.(Rosaceae), wild and endemic flowering cherry on Jeju Island, Korea.

    Science.gov (United States)

    Cho, Myong-Suk; Hyun Cho, Chung; Yeon Kim, Su; Su Yoon, Hwan; Kim, Seung-Chul

    2016-09-01

    The complete chloroplast genome sequences of the wild flowering cherry, Prunus yedoensis Matsum., which is native and endemic to Jeju Island, Korea, is reported in this study. The genome size is 157 786 bp in length with 36.7% GC content, which is composed of LSC region of 85 908 bp, SSC region of 19 120 bp and two IR copies of 26 379 bp each. The cp genome contains 131 genes, including 86 coding genes, 8 rRNA genes and 37 tRNA genes. The maximum likelihood analysis was conducted to verify a phylogenetic position of the newly sequenced cp genome of P. yedoensis using 11 representatives of complete cp genome sequences within the family Rosaceae. The genus Prunus exhibited monophyly and the result of the phylogenetic relationship agreed with the previous phylogenetic analyses within Rosaceae.

  15. Soil structure interaction model and variability of parameters in seismic analysis of nuclear island connected building

    International Nuclear Information System (INIS)

    Subramanian, K.V.; Palekar, S.M.; Bavare, M.S.; Mapari, H.A.; Patel, S.C.; Pillai, C.S.

    2005-01-01

    This paper provides salient features of the Soil Structure Interaction analysis of Nuclear Island Connected Building (NICB). The dynamic analysis of NICB is performed on a full 3D model accounting for the probable variation in the stiffness of the founding medium. A range analyses was performed to establish the effect of variability of subgrade parameters on the results of seismic analyses of NICB. This paper presents details of various analyses with respect to the subgrade model, uncertainties in subgrade properties, results of seismic analyses and a study of effect of the variability of parameters on the results of these analyses. The results of this study indicate that the variability of soil parameters beyond a certain value of shear wave velocity does not influence the response and in fact the response marginally diminishes. (authors)

  16. RICE ice core: Black Carbon reflects climate variability at Roosevelt Island, West Antarctica

    Science.gov (United States)

    Ellis, Aja; Edwards, Ross; Bertler, Nancy; Winton, Holly; Goodwin, Ian; Neff, Peter; Tuohy, Andrea; Proemse, Bernadette; Hogan, Chad; Feiteng, Wang

    2015-04-01

    The Roosevelt Island Climate Evolution (RICE) project successfully drilled a deep ice core from Roosevelt Island during the 2011/2012 and 2012/2013 seasons. Located in the Ross Ice Shelf in West Antarctica, the site is an ideal location for investigating climate variability and the past stability of the Ross Ice Shelf. Black carbon (BC) aerosols are emitted by both biomass burning and fossil fuels, and BC particles emitted in the southern hemisphere are transported in the atmosphere and preserved in Antarctic ice. The past record of BC is expected to be sensitive to climate variability, as it is modulated by both emissions and transport. To investigate BC variability over the past 200 years, we developed a BC record from two overlapping ice cores (~1850-2012) and a high-resolution snow pit spanning 2010-2012 (cal. yr). Consistent results are found between the snow pit profiles and ice core records. Distinct decadal trends are found with respect to BC particle size, and the record indicates a steady rise in BC particle size over the last 100 years. Differences in emission sources and conditions may be a possible explanation for changes in BC size. These records also show a significant increase in BC concentration over the past decade with concentrations rising over 1.5 ppb (1.5*10^-9 ng/g), suggesting a fundamental shift in BC deposition to the site.

  17. Genome-wide association studies in an isolated founder population from the Pacific Island of Kosrae.

    Directory of Open Access Journals (Sweden)

    Jennifer K Lowe

    2009-02-01

    Full Text Available 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.

  18. Seasonal variability of the diapycnal mixing in the Canary Islands channels

    Science.gov (United States)

    Rodríguez-Santana, Angel; Marrero-Díaz, Angeles; Machín, Francisco Jose; García-Weil, Luis; Sangrà, Pablo; Vélez-Belchí, Pedro; Fraile-Nuez, Eugenio; Estrada-Allis, Sheila

    2014-05-01

    Trimonthly surveys of XBT and XCTD (Expandable Bathytermograph and Conductivity-Temperature-Depth) crossing the whole Canary Islands channels were carried out (projects TRAMIC and PROMECA) from November 2012 until September 2013 using opportunity ships (Naviera Armas Ferries). With this data set and using salinity analytical relationships (Machín et al, 2010), vertical sections of temperature and potential density were obtained for each channel and season. In order to estimate the intensity of the diapycnal mixing in the first 500 m of the pycnocline, vertical sections of Thorpe length scale, Turner angle and gradient Richardson number (from the geostrophic vertical shear) were calculated for all the cases. The first results show how the diapycnal mixing due to the vertical shear instabilities is more intense close to the islands and in summer when the seasonal pycnocline is present. Mixing due to double diffusion processes (salt fingers) was found without sizable changes in the permanent pycnocline. Net turbulence diffusivities and diapycnal diffusive fluxes with their variability spatial and temporal will be estimate for each channel taking into account that processes of double diffusion and turbulence induced by vertical shear are present at the same time. Additionally the results obtained from hydrographic data from the cruise RAPROCAN-2013 (IEO) (October 2013) around Canary Islands will be used to compare them with the channels results. This work was co-funded by Canary Government (TRAMIC project: PROID20100092), European Union (FEDER) and Spanish Government (PROMECA: CTM2008-04057/MAR and CTM2009-06993-E/MAR)

  19. GaussianCpG: a Gaussian model for detection of CpG island in human genome sequences.

    Science.gov (United States)

    Yu, Ning; Guo, Xuan; Zelikovsky, Alexander; Pan, Yi

    2017-05-24

    As crucial markers in identifying biological elements and processes in mammalian genomes, CpG islands (CGI) play important roles in DNA methylation, gene regulation, epigenetic inheritance, gene mutation, chromosome inactivation and nuclesome retention. The generally accepted criteria of CGI rely on: (a) %G+C content is ≥ 50%, (b) the ratio of the observed CpG content and the expected CpG content is ≥ 0.6, and (c) the general length of CGI is greater than 200 nucleotides. Most existing computational methods for the prediction of CpG island are programmed on these rules. However, many experimentally verified CpG islands deviate from these artificial criteria. Experiments indicate that in many cases %G+C is human genome. We analyze the energy distribution over genomic primary structure for each CpG site and adopt the parameters from statistics of Human genome. The evaluation results show that the new model can predict CpG islands efficiently by balancing both sensitivity and specificity over known human CGI data sets. Compared with other models, GaussianCpG can achieve better performance in CGI detection. Our Gaussian model aims to simplify the complex interaction between nucleotides. The model is computed not by the linear statistical method but by the Gaussian energy distribution and accumulation. The parameters of Gaussian function are not arbitrarily designated but deliberately chosen by optimizing the biological statistics. By using the pseudopotential analysis on CpG islands, the novel model is validated on both the real and artificial data sets.

  20. Microdiversification of a Pelagic Polynucleobacter Species Is Mainly Driven by Acquisition of Genomic Islands from a Partially Interspecific Gene Pool

    Science.gov (United States)

    Schmidt, Johanna; Jezberová, Jitka; Koll, Ulrike; Hahn, Martin W.

    2016-01-01

    ABSTRACT Microdiversification of a planktonic freshwater bacterium was studied by comparing 37 Polynucleobacter asymbioticus strains obtained from three geographically separated sites in the Austrian Alps. Genome comparison of nine strains revealed a core genome of 1.8 Mb, representing 81% of the average genome size. Seventy-five percent of the remaining flexible genome is clustered in genomic islands (GIs). Twenty-four genomic positions could be identified where GIs are potentially located. These positions are occupied strain specifically from a set of 28 GI variants, classified according to similarities in their gene content. One variant, present in 62% of the isolates, encodes a pathway for the degradation of aromatic compounds, and another, found in 78% of the strains, contains an operon for nitrate assimilation. Both variants were shown in ecophysiological tests to be functional, thus providing the potential for microniche partitioning. In addition, detected interspecific horizontal exchange of GIs indicates a large gene pool accessible to Polynucleobacter species. In contrast to core genes, GIs are spread more successfully across spatially separated freshwater habitats. The mobility and functional diversity of GIs allow for rapid evolution, which may be a key aspect for the ubiquitous occurrence of Polynucleobacter bacteria. IMPORTANCE Assessing the ecological relevance of bacterial diversity is a key challenge for current microbial ecology. The polyphasic approach which was applied in this study, including targeted isolation of strains, genome analysis, and ecophysiological tests, is crucial for the linkage of genetic and ecological knowledge. Particularly great importance is attached to the high number of closely related strains which were investigated, represented by genome-wide average nucleotide identities (ANI) larger than 97%. The extent of functional diversification found on this narrow phylogenetic scale is compelling. Moreover, the transfer of

  1. Associations of dragonflies (Odonata) to habitat variables within the Maltese Islands: a spatio-temporal approach.

    Science.gov (United States)

    Balzan, Mario V

    2012-01-01

    Relatively little information is available on environmental associations and the conservation of Odonata in the Maltese Islands. Aquatic habitats are normally spatio-temporally restricted, often located within predominantly rural landscapes, and are thereby susceptible to farmland water management practices, which may create additional pressure on water resources. This study investigates how odonate assemblage structure and diversity are associated with habitat variables of local breeding habitats and the surrounding agricultural landscapes. Standardized survey methodology for adult Odonata involved periodical counts over selected water-bodies (valley systems, semi-natural ponds, constructed agricultural reservoirs). Habitat variables relating to the type of water body, the floristic and physiognomic characteristics of vegetation, and the composition of the surrounding landscape, were studied and analyzed through a multivariate approach. Overall, odonate diversity was associated with a range of factors across multiple spatial scales, and was found to vary with time. Lentic water-bodies are probably of high conservation value, given that larval stages were mainly associated with this habitat category, and that all species were recorded in the adult stage in this habitat type. Comparatively, lentic and lotic seminatural waterbodies were more diverse than agricultural reservoirs and brackish habitats. Overall, different odonate groups were associated with different vegetation life-forms and height categories. The presence of the great reed, Arundo donax L., an invasive alien species that forms dense stands along several water-bodies within the Islands, seems to influence the abundance and/or occurrence of a number of species. At the landscape scale, roads and other ecologically disturbed ground, surface water-bodies, and landscape diversity were associated with particular components of the odonate assemblages. Findings from this study have several implications for the

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

    Science.gov (United States)

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

    2011-04-01

    Salmonella carriage patterns in wild and captive reptiles suggest that both geographical proximity and host ecological differences may determine bacterial diversity among reptile populations. In this study, we explore the relative importance of these factors on Salmonella diversity in free-living Galápagos iguanas. We isolated Salmonella enterica from marine iguanas (Amblyrhynchus cristatus) and land iguanas (Conolophus subcristatus and C. pallidus) living on two islands (Plaza Sur and Santa Fe). We evaluated Salmonella population patterns using genomic fingerprints, sequence typing and serotyping. Rep-PCR fingerprinting revealed significant grouping of isolates by iguana population. Island residence had the strongest effect on isolate similarity, but a smaller divergence among Salmonella isolates from different iguana ecotypes (land versus marine) was detected within each island. In contrast, sequence typing detected a marginal difference in isolate genotypes between islands. Sequence types corresponded strongly to serotype identity, with both islands hosting a unique serovar pool. Our findings suggest that both geographical location and host ecotype differences (either from within host strain selection or from differences in habitat use) contribute to Salmonella population patterns in the Galápagos Islands. © 2010 Society for Applied Microbiology and Blackwell Publishing Ltd.

  3. The Pacific Rat Race to Easter Island: Tracking the Prehistoric Dispersal of Rattus exulans Using Ancient Mitochondrial Genomes

    Directory of Open Access Journals (Sweden)

    Katrina West

    2017-05-01

    Full Text Available The location of the immediate eastern Polynesian origin for the settlement of Easter Island (Rapa Nui, remains unclear with conflicting archeological and linguistic evidence. Previous genetic commensal research using the Pacific rat, Rattus exulans; a species transported by humans across Remote Oceania and throughout the Polynesian Triangle, has identified broad interaction spheres across the region. However, there has been limited success in distinguishing finer-scale movements between Remote Oceanic islands as the same mitochondrial control region haplotype has been identified in the majority of ancient rat specimens. To improve molecular resolution and identify a pattern of prehistoric dispersal to Easter Island, we sequenced complete mitochondrial genomes from ancient Pacific rat specimens obtained from early archeological contexts across West and East Polynesia. Ancient Polynesian rat haplotypes are closely related and reflect the widely supported scenario of a central East Polynesian homeland region from which eastern expansion occurred. An Easter Island and Tubuai (Austral Islands grouping of related haplotypes suggests that both islands were established by the same colonization wave, proposed to have originated in the central homeland region before dispersing through the south-eastern corridor of East Polynesia.

  4. The Escherichia coli argW-dsdCXA genetic island is highly variable, and E. coli K1 strains commonly possess two copies of dsdCXA.

    Science.gov (United States)

    Moritz, Rebecca L; Welch, Rodney A

    2006-11-01

    The genome sequences of Escherichia coli pathotypes reveal extensive genetic variability in the argW-dsdCXA island. Interestingly, the archetype E. coli K1 neonatal meningitis strain, strain RS218, has two copies of the dsdCXA genes for d-serine utilization at the argW and leuX islands. Because the human brain contains d-serine, an epidemiological study emphasizing K1 isolates surveyed the dsdCXA copy number and function. Forty of 41 (97.5%) independent E. coli K1 isolates could utilize d-serine. Southern blot hybridization revealed physical variability within the argW-dsdC region, even among 22 E. coli O18:K1:H7 isolates. In addition, 30 of 41 K1 strains, including 21 of 22 O18:K1:H7 isolates, had two dsdCXA loci. Mutational analysis indicated that each of the dsdA genes is functional in a rifampin-resistant mutant of RS218, mutant E44. The high percentage of K1 strains that can use d-serine is in striking contrast to our previous observation that only 4 of 74 (5%) isolates in the diarrheagenic E. coli (DEC) collection have this activity. The genome sequence of diarrheagenic E. coli isolates indicates that the csrRAKB genes for sucrose utilization are often substituted for dsdC and a portion of dsdX present at the argW-dsdCXA island of extraintestinal isolates. Among DEC isolates there is a reciprocal pattern of sucrose fermentation versus d-serine utilization. The ability to use d-serine is a trait strongly selected for among E. coli K1 strains, which have the ability to infect a wide range of extraintestinal sites. Conversely, diarrheagenic E. coli pathotypes appear to have substituted sucrose for d-serine as a potential nutrient.

  5. Life-cycle modification in open oceans accounts for genome variability in a cosmopolitan phytoplankton.

    Science.gov (United States)

    von Dassow, Peter; John, Uwe; Ogata, Hiroyuki; Probert, Ian; Bendif, El Mahdi; Kegel, Jessica U; Audic, Stéphane; Wincker, Patrick; Da Silva, Corinne; Claverie, Jean-Michel; Doney, Scott; Glover, David M; Flores, Daniella Mella; Herrera, Yeritza; Lescot, Magali; Garet-Delmas, Marie-José; de Vargas, Colomban

    2015-06-01

    Emiliania huxleyi is the most abundant calcifying plankton in modern oceans with substantial intraspecific genome variability and a biphasic life cycle involving sexual alternation between calcified 2N and flagellated 1N cells. We show that high genome content variability in Emiliania relates to erosion of 1N-specific genes and loss of the ability to form flagellated cells. Analysis of 185 E. huxleyi strains isolated from world oceans suggests that loss of flagella occurred independently in lineages inhabiting oligotrophic open oceans over short evolutionary timescales. This environmentally linked physiogenomic change suggests life cycling is not advantageous in very large/diluted populations experiencing low biotic pressure and low ecological variability. Gene loss did not appear to reflect pressure for genome streamlining in oligotrophic oceans as previously observed in picoplankton. Life-cycle modifications might be common in plankton and cause major functional variability to be hidden from traditional taxonomic or molecular markers.

  6. Dispositional and situational variables related to evacuation at Three Mile Island

    International Nuclear Information System (INIS)

    Miller, I.S.

    1981-01-01

    The purpose of this study was to explore some of the factors influential in local residents' evacuating or remaining in the Three Mile Island area during the nuclear power plant accident of March, 1979. Investigated variables included individuals' behavioral dispositions to attend or to avoid threatening stimuli as well as situational concerns related to demographic characteristics and subjective experience. Investigation of situational variables also probed respondents' concerns about accident-related fears. Two main relationships were investigated. The first hypothesized that positive relationships existed both between dispositional attention to threat and evacuation and between dispositional avoidance of threat and remaining. The second investigation task of the research explored evacuation-related situational variables in regard to individuals' awareness of potential danger at TMI. No support was found for the hypothesized relationships between evacuation and dispositions relative to threat. Situational variables significantly related to evacuation included: specific directives to evacuate the area; disruption of telephone service during the week of the accident; and household proximity to TMI

  7. Ancient, recurrent phage attacks and recombination shaped dynamic sequence-variable mosaics at the root of phytoplasma genome evolution.

    Science.gov (United States)

    Wei, Wei; Davis, Robert E; Jomantiene, Rasa; Zhao, Yan

    2008-08-19

    Mobile genetic elements have impacted biological evolution across all studied organisms, but evidence for a role in evolutionary emergence of an entire phylogenetic clade has not been forthcoming. We suggest that mobile element predation played a formative role in emergence of the phytoplasma clade. Phytoplasmas are cell wall-less bacteria that cause numerous diseases in plants. Phylogenetic analyses indicate that these transkingdom parasites descended from Gram-positive walled bacteria, but events giving rise to the first phytoplasma have remained unknown. Previously we discovered a unique feature of phytoplasmal genome architecture, genes clustered in sequence-variable mosaics (SVMs), and suggested that such structures formed through recurrent, targeted attacks by mobile elements. In the present study, we discovered that cryptic prophage remnants, originating from phages in the order Caudovirales, formed SVMs and comprised exceptionally large percentages of the chromosomes of 'Candidatus Phytoplasma asteris'-related strains OYM and AYWB, occupying nearly all major nonsyntenic sections, and accounting for most of the size difference between the two genomes. The clustered phage remnants formed genomic islands exhibiting distinct DNA physical signatures, such as dinucleotide relative abundance and codon position GC values. Phytoplasma strain-specific genes identified as phage morons were located in hypervariable regions within individual SVMs, indicating that prophage remnants played important roles in generating phytoplasma genetic diversity. Because no SVM-like structures could be identified in genomes of ancestral relatives including Acholeplasma spp., we hypothesize that ancient phage attacks leading to SVM formation occurred after divergence of phytoplasmas from acholeplasmas, triggering evolution of the phytoplasma clade.

  8. Seasonal and interannual variability of dissolved oxygen around the Balearic Islands from hydrographic data

    Science.gov (United States)

    Balbín, R.; López-Jurado, J. L.; Aparicio-González, A.; Serra, M.

    2014-10-01

    Oceanographic data obtained between 2001 and 2011 by the Spanish Institute of Oceanography (IEO, Spain) have been used to characterise the spatial distribution and the temporal variability of the dissolved oxygen around the Balearic Islands (Mediterranean Sea). The study area includes most of the Western Mediterranean Sea, from the Alboran Sea to Cape Creus, at the border between France and Spain. Dissolved oxygen (DO) at the water surface is found to be in a state of equilibrium exchange with the atmosphere. In the spring and summer a subsurface oxygen supersaturation is observed due to the biological activity, above the subsurface fluorescence maximum. Minimum observed values of dissolved oxygen are related to the Levantine Intermediate Waters (LIW). An unusual minimum of dissolved oxygen concentrations was also recorded in the Alboran Sea Oxygen Minimum Zone. The Western Mediterranean Deep Waters (WMDW) and the Western Intermediate Waters (WIW) show higher values of dissolved oxygen than the Levantine Intermediate Waters due to their more recent formation. Using these dissolved oxygen concentrations it is possible to show that the Western Intermediate Waters move southwards across the Ibiza Channel and the deep water circulates around the Balearic Islands. It has also been possible to characterise the seasonal evolution of the different water masses and their dissolved oxygen content in a station in the Algerian sub-basin.

  9. Exploring temporal and spatial variability of precipitation of Weizhou Island, South China Sea

    Directory of Open Access Journals (Sweden)

    Shulin Deng

    2017-02-01

    New hydrological insights: (1 Rainfall amounts had a non-homogeneous temporal distribution during periods of 1961–1990, 1981–2010 and 1961–2010 on Weizhou Island. (2 Large scale atmospheric circulation may be the major atmospheric driving force of precipitation changes. (3 Precipitation has a cyclical nature on Weizhou Island. (4 Precipitation pattern on Weizhou Island is also affected by oceanic climate. The results provide a scientific basis for water resource management on Weizhou Island.

  10. Emergence of Salmonella genomic island 1 (SGI1) among Proteus mirabilis clinical isolates in Dijon, France.

    Science.gov (United States)

    Siebor, Eliane; Neuwirth, Catherine

    2013-08-01

    Salmonella genomic island 1 (SGI1) is often encountered in antibiotic-resistant Salmonella enterica and exceptionally in Proteus mirabilis. We investigated the prevalence of SGI1-producing clinical isolates of P. mirabilis in our hospital (Dijon, France). A total of 57 strains of P. mirabilis resistant to amoxicillin and/or gentamicin and/or trimethoprim/sulfamethoxazole isolated from August 2011 to February 2012 as well as 9 extended-spectrum β-lactamase (ESBL)-producing P. mirabilis from our collection were tested for the presence of SGI1 by PCR. The complete SGI1 structure from positive isolates [backbone and multidrug resistance (MDR) region] was sequenced. SGI1 was detected in 7 isolates; 5 out of the 57 isolates collected during the study period (9%) and 2 out of the 9 ESBL-producing strains of our collection. The structures of the seven SGI1s were distinct. Three different backbones were identified: one identical to the SGI1 backbone from the epidemic Salmonella Typhimurium DT104, one with variations already described in SGI1-K from Salmonella Kentucky (deletion and insertion of IS1359 in the region spanning from S005 to S009) and one with a variation never detected before (deletion from S005 to S009). Six different MDR regions were identified: four simple variants containing resistance genes already described and two variants harbouring a very complex structure including regions derived from several transposons and IS26 elements with aphA1a never reported to date in SGI1. SGI1 variants are widely distributed among P. mirabilis clinical strains and might spread to other commensal Enterobacteriaceae. This would become a serious public health problem.

  11. Variable selection models for genomic selection using whole-genome sequence data and singular value decomposition.

    Science.gov (United States)

    Meuwissen, Theo H E; Indahl, Ulf G; Ødegård, Jørgen

    2017-12-27

    Non-linear Bayesian genomic prediction models such as BayesA/B/C/R involve iteration and mostly Markov chain Monte Carlo (MCMC) algorithms, which are computationally expensive, especially when whole-genome sequence (WGS) data are analyzed. Singular value decomposition (SVD) of the genotype matrix can facilitate genomic prediction in large datasets, and can be used to estimate marker effects and their prediction error variances (PEV) in a computationally efficient manner. Here, we developed, implemented, and evaluated a direct, non-iterative method for the estimation of marker effects for the BayesC genomic prediction model. The BayesC model assumes a priori that markers have normally distributed effects with probability [Formula: see text] and no effect with probability (1 - [Formula: see text]). Marker effects and their PEV are estimated by using SVD and the posterior probability of the marker having a non-zero effect is calculated. These posterior probabilities are used to obtain marker-specific effect variances, which are subsequently used to approximate BayesC estimates of marker effects in a linear model. A computer simulation study was conducted to compare alternative genomic prediction methods, where a single reference generation was used to estimate marker effects, which were subsequently used for 10 generations of forward prediction, for which accuracies were evaluated. SVD-based posterior probabilities of markers having non-zero effects were generally lower than MCMC-based posterior probabilities, but for some regions the opposite occurred, resulting in clear signals for QTL-rich regions. The accuracies of breeding values estimated using SVD- and MCMC-based BayesC analyses were similar across the 10 generations of forward prediction. For an intermediate number of generations (2 to 5) of forward prediction, accuracies obtained with the BayesC model tended to be slightly higher than accuracies obtained using the best linear unbiased prediction of SNP

  12. A toxin antitoxin system promotes the maintenance of the IncA/C-mobilizable Salmonella Genomic Island 1.

    Science.gov (United States)

    Huguet, Kevin T; Gonnet, Mathieu; Doublet, Benoît; Cloeckaert, Axel

    2016-08-31

    The multidrug resistance Salmonella Genomic Island 1 (SGI1) is an integrative mobilizable element identified in several enterobacterial pathogens. This chromosomal island requires a conjugative IncA/C plasmid to be excised as a circular extrachromosomal form and conjugally mobilized in trans. Preliminary observations suggest stable maintenance of SGI1 in the host chromosome but paradoxically also incompatibility between SGI1 and IncA/C plasmids. Here, using a Salmonella enterica serovar Agona clonal bacterial population as model, we demonstrate that a Toxin-Antitoxin (TA) system encoded by SGI1 plays a critical role in its stable host maintenance when an IncA/C plasmid is concomitantly present. This system, designated sgiAT for Salmonella genomic island 1 Antitoxin and Toxin respectively, thus seems to play a stabilizing role in a situation where SGI1 is susceptible to be lost through plasmid IncA/C-mediated excision. Moreover and for the first time, the incompatibility between SGI1 and IncA/C plasmids was experimentally confirmed.

  13. Transcription-associated mutational pressure in the Parvovirus B19 genome: Reactivated genomes contribute to the variability of viral populations.

    Science.gov (United States)

    Khrustalev, Vladislav Victorovich; Ermalovich, Marina Anatolyevna; Hübschen, Judith M; Khrustaleva, Tatyana Aleksandrovna

    2017-12-21

    In this study we used non-overlapping parts of the two long open reading frames coding for nonstructural (NS) and capsid (VP) proteins of all available sequences of the Parvovirus B19 subgenotype 1a genome and found out that the rates of A to G, C to T and A to T mutations are higher in the first long reading frame (NS) of the virus than in the second one (VP). This difference in mutational pressure directions for two parts of the same viral genome can be explained by the fact of transcription of just the first long reading frame during the lifelong latency in nonerythroid cells. Adenine deamination (producing A to G and A to T mutations) and cytosine deamination (producing C to T mutations) occur more frequently in transcriptional bubbles formed by DNA "plus" strand of the first open reading frame. These mutations can be inherited only in case of reactivation of the infectious virus due to the help of Adenovirus that allows latent Parvovirus B19 to start transcription of the second reading frame and then to replicate its genome by the rolling circle mechanism using the specific origin. Results of this study provide evidence that the genomes reactivated from latency make significant contributions to the variability of Parvovirus B19. Copyright © 2017 Elsevier Ltd. All rights reserved.

  14. Spatio-Temporal Variability of Urban Heat Island and Urban Mobility

    Science.gov (United States)

    Kar, B.; Omitaomu, O.

    2017-12-01

    A 2016 report by the U.S. Census stated that while the rural areas cover 97% of the U.S. landmass, these areas house only 19.7% of the nation's population. Given that the U.S. coastal counties are home to more than 50% of the U.S. population, these urban areas are clustered along the coast that is susceptible to sea level rise induced impacts. In light of increasing climate variability and extreme events, it is pertinent to understand the Urban Heat Island (UHI) effect that results from increasing population density and mobility in the urban areas, and that contributes to increased energy consumption and temperature as well as unmitigated flooding events. For example, in Illinois, warmer summers contribute to heavy precipitation that overwhelms the region's drainage capacity. This study focuses on understanding the spatio-temporal variability of the relationship between population density and mobility distribution, and creation of UHI due to temperature change in selected cities across the U.S. This knowledge will help us understand the role of UHI in energy-water nexus in urban areas, specifically, energy consumption.

  15. Complete Genome Analysis of Thermus parvatiensis and Comparative Genomics of Thermus spp. Provide Insights into Genetic Variability and Evolution of Natural Competence as Strategic Survival Attributes

    Directory of Open Access Journals (Sweden)

    Charu Tripathi

    2017-07-01

    Full Text Available Thermophilic environments represent an interesting niche. Among thermophiles, the genus Thermus is among the most studied genera. In this study, we have sequenced the genome of Thermus parvatiensis strain RL, a thermophile isolated from Himalayan hot water springs (temperature >96°C using PacBio RSII SMRT technique. The small genome (2.01 Mbp comprises a chromosome (1.87 Mbp and a plasmid (143 Kbp, designated in this study as pTP143. Annotation revealed a high number of repair genes, a squeezed genome but containing highly plastic plasmid with transposases, integrases, mobile elements and hypothetical proteins (44%. We performed a comparative genomic study of the group Thermus with an aim of analysing the phylogenetic relatedness as well as niche specific attributes prevalent among the group. We compared the reference genome RL with 16 Thermus genomes to assess their phylogenetic relationships based on 16S rRNA gene sequences, average nucleotide identity (ANI, conserved marker genes (31 and 400, pan genome and tetranucleotide frequency. The core genome of the analyzed genomes contained 1,177 core genes and many singleton genes were detected in individual genomes, reflecting a conserved core but adaptive pan repertoire. We demonstrated the presence of metagenomic islands (chromosome:5, plasmid:5 by recruiting raw metagenomic data (from the same niche against the genomic replicons of T. parvatiensis. We also dissected the CRISPR loci wide all genomes and found widespread presence of this system across Thermus genomes. Additionally, we performed a comparative analysis of competence loci wide Thermus genomes and found evidence for recent horizontal acquisition of the locus and continued dispersal among members reflecting that natural competence is a beneficial survival trait among Thermus members and its acquisition depicts unending evolution in order to accomplish optimal fitness.

  16. Episodic swell growth inferred from variable uplift of the Cape Verde hotspot islands

    Science.gov (United States)

    Ramalho, R.; Helffrich, G.; Cosca, M.; Vance, D.; Hoffmann, D.; Schmidt, D.N.

    2010-01-01

    On the Beagle voyage, Charles Darwin first noted the creation and subsidence of ocean islands, establishing in geology's infancy that island freeboard changes with time. Hotspot ocean islands have an obvious mechanism for freeboard change through the growth of the bathymetric anomaly, or swell, on which the islands rest. Models for swell development indicate that flexural, thermal or dynamic pressure contributions, as well as spreading of melt residue from the hotspot, can all contribute to island uplift. Here we test various models for swell development using the uplift histories for the islands of the Cape Verde hotspot, derived from isotopic dating of marine terraces and subaerial to submarine lava-flow morphologies. The island uplift histories, in conjunction with inter-island spacing, uplift rate and timing differences, rule out flexural, thermal or dynamic pressure contributions. We also find that uplift cannot be reconciled with models that advocate the spreading of melt residue in swell development unless swell growth is episodic. Instead, we infer from the uplift histories that two processes have acted to raise the islands during the past 6 Myr. During an initial phase, mantle processes acted to build the swell. Subsequently, magmatic intrusions at the island edifice caused 350 m of local uplift at the scale of individual islands. Finally, swell-wide uplift contributed a further 100 m of surface rise.

  17. Tracing variability in the iodine isotopes and species along surface water transect from the North Sea to the Canary Islands

    DEFF Research Database (Denmark)

    He, Peng; Aldahan, Ala; Hou, Xiaolin

    2016-01-01

    A complete transect of surface water samples from the North Sea to the Canary Islands was collected during a continuous period in 2010. The samples were analyzed for total 129I and 127I isotopes and their iodide and iodate species. The results indicate a large variability in the total 129I and its...

  18. An Integrative Genomic Island Affects the Adaptations of Piezophilic Hyperthermophilic Archaeon Pyrococcus yayanosii to High Temperature and High Hydrostatic Pressure

    Directory of Open Access Journals (Sweden)

    Zhen Li

    2016-11-01

    Full Text Available Deep-sea hydrothermal vent environments are characterized by high hydrostatic pressure and sharp temperature and chemical gradients. Horizontal gene transfer is thought to play an important role in the microbial adaptation to such an extreme environment. In this study, a 21.4-kb DNA fragment was identified as a genomic island, designated PYG1, in the genomic sequence of the piezophilic hyperthermophile Pyrococcus yayanosii. According to the sequence alignment and functional annotation, the genes in PYG1 could tentatively be divided into five modules, with functions related to mobility, DNA repair, metabolic processes and the toxin-antitoxin system. Integrase can mediate the site-specific integration and excision of PYG1 in the chromosome of P. yayanosii A1. Gene replacement of PYG1 with a SimR cassette was successful. The growth of the mutant strain ∆PYG1 was compared with its parent strain P. yayanosii A2 under various stress conditions, including different pH, salinity, temperature and hydrostatic pressure. The ∆PYG1 mutant strain showed reduced growth when grown at 100 °C, while the biomass of ∆PYG1 increased significantly when cultured at 80 MPa. Differential expression of the genes in module Ⅲ of PYG1 was observed under different temperature and pressure conditions. This study demonstrates the first example of an archaeal integrative genomic island that could affect the adaptation of the hyperthermophilic piezophile P. yayanosii to high temperature and high hydrostatic pressure.

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

    DEFF Research Database (Denmark)

    Iacolina, Laura; Scandura, Massimo; J. Goedbloed, Daniel

    2016-01-01

    The evolution of island populations in natural systems is driven by local adaptation and genetic drift. However, evolutionary pathways may be altered by humans in several ways. The wild boar (WB) (Sus scrofa) is an iconic game species occurring in several islands, where it has been strongly manag...

  20. The Salmonella genomic island 1 is specifically mobilized in trans by the IncA/C multidrug resistance plasmid family.

    Science.gov (United States)

    Douard, Gregory; Praud, Karine; Cloeckaert, Axel; Doublet, Benoît

    2010-12-20

    The Salmonella genomic island 1 (SGI1) is a Salmonella enterica-derived integrative mobilizable element (IME) containing various complex multiple resistance integrons identified in several S. enterica serovars and in Proteus mirabilis. Previous studies have shown that SGI1 transfers horizontally by in trans mobilization in the presence of the IncA/C conjugative helper plasmid pR55. Here, we report the ability of different prevalent multidrug resistance (MDR) plasmids including extended-spectrum β-lactamase (ESBL) gene-carrying plasmids to mobilize the multidrug resistance genomic island SGI1. Through conjugation experiments, none of the 24 conjugative plasmids tested of the IncFI, FII, HI2, I1, L/M, N, P incompatibility groups were able to mobilize SGI1 at a detectable level (transfer frequency IncA/C incompatibility group. Several conjugative IncA/C MDR plasmids as well as the sequenced IncA/C reference plasmid pRA1 of 143,963 bp were shown to mobilize in trans SGI1 from a S. enterica donor to the Escherichia coli recipient strain. Depending on the IncA/C plasmid used, the conjugative transfer of SGI1 occurred at frequencies ranging from 10(-3) to 10(-6) transconjugants per donor. Of particular concern, some large IncA/C MDR plasmids carrying the extended-spectrum cephalosporinase bla(CMY-2) gene were shown to mobilize in trans SGI1. The ability of the IncA/C MDR plasmid family to mobilize SGI1 could contribute to its spread by horizontal transfer among enteric pathogens. Moreover, the increasing prevalence of IncA/C plasmids in MDR S. enterica isolates worldwide has potential implications for the epidemic success of the antibiotic resistance genomic island SGI1 and its close derivatives.

  1. Identifying Rare Variation in Cases of Schizophrenia in the Isolated Population of the Faroe Islands using Whole-genome Sequencing

    DEFF Research Database (Denmark)

    Als, Thomas Damm; Lescai, Francesco; Dahl, Hans

    to map risk variants involved in complex traits. We aim at utilizing samples of cases and controls of the isolated population of the Faroe Islands to conduct whole-genome-sequence analysis in order to identify rare genetic variants associated with schizophrenia. We will search for rare genetic variants...... of developing SZ. However, these studies are designed to examining only “the common variant” proportion of the genomic landscape of SZ. Due to increased genetic drift during founding and potential bottlenecks, followed by population expansion, isolated populations may be particularly useful in identifying rare...... disease variants, that may appear at higher frequencies and/or within a more clearly distinct haplotype structure compared to outbred populations. Small isolated populations also typically show reduced phenotypic, genetic and environmental heterogeneity, thus making them advantageous in studies aiming...

  2. Seasonal and interannual variability in grey seal diets on Sable Island, eastern Scotian Shelf

    Directory of Open Access Journals (Sweden)

    W D Bowen

    2007-01-01

    Full Text Available We studied seasonal and interannual variability in the diet of grey seals (Halichoerus grypus using faecal samples collected from Sable Island, Nova Scotia between 1991 and 1998. More than 28,000 prey from at least 28 taxa were identified from 1,245 faecal samples collect mainly in spring, fall and winter. Sand lance (Ammodytes dubius dominated the diet in all seasons and years, but the importance of this and other species varied over time. There was also evidence of seasonal and interannual variation in the size of prey consumed both within and among species. We compared diet composition with estimates of prey numbers and biomass from annual researchtrawl surveys conducted in March and July. Species-specific numerical corrections were applied to otolith counts to account for the complete digestion of otoliths, and fish catchability correction factors applied to trawl survey catches to account for trawl selectivity. Based on an odds ratio index of prey selectivity, grey seals positively selected sand lance in both seasons. Other species were either relatively avoided or eaten roughly in proportion to their estimated abundance.

  3. Variability of Basal Melt Beneath the Pine Island Glacier Ice Shelf, West Antarctica

    Science.gov (United States)

    Bindschadler, Robert; Vaughan, David G.; Vornberger, Patricia

    2011-01-01

    Observations from satellite and airborne platforms are combined with model calculations to infer the nature and efficiency of basal melting of the Pine Island Glacier ice shelf, West Antarctica, by ocean waters. Satellite imagery shows surface features that suggest ice-shelf-wide changes to the ocean s influence on the ice shelf as the grounding line retreated. Longitudinal profiles of ice surface and bottom elevations are analyzed to reveal a spatially dependent pattern of basal melt with an annual melt flux of 40.5 Gt/a. One profile captures a persistent set of surface waves that correlates with quasi-annual variations of atmospheric forcing of Amundsen Sea circulation patterns, establishing a direct connection between atmospheric variability and sub-ice-shelf melting. Ice surface troughs are hydrostatically compensated by ice-bottom voids up to 150m deep. Voids form dynamically at the grounding line, triggered by enhanced melting when warmer-than-average water arrives. Subsequent enlargement of the voids is thermally inefficient (4% or less) compared with an overall melting efficiency beneath the ice shelf of 22%. Residual warm water is believed to cause three persistent polynyas at the ice-shelf front seen in Landsat imagery. Landsat thermal imagery confirms the occurrence of warm water at the same locations.

  4. 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.

    Directory of Open Access Journals (Sweden)

    Tsuyoshi Sekizuka

    Full Text Available 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.

  5. Mid- to late Holocene Indian Ocean Monsoon variability recorded in four speleothems from Socotra Island, Yemen

    Science.gov (United States)

    Van Rampelbergh, Maïté; Fleitmann, Dominik; Verheyden, Sophie; Cheng, Hai; Edwards, Lawrence; De Geest, Peter; De Vleeschouwer, David; Burns, Stephen J.; Matter, Albert; Claeys, Philippe; Keppens, Eddy

    2013-04-01

    Four stalagmites covering the last 7.0 ka were sampled on Socotra, an island in the northern Indian Ocean to investigate the evolution of the northeast Indian Ocean Monsoon (IOM) since the mid Holocene. On Socotra, rain is delivered at the start of the southwest IOM in May-June and at the start of the northeast IOM from September to December. The Haggeher Mountains act as a barrier forcing precipitation brought by the northeast winds to fall preferentially on the eastern side of the island, where the studied caves are located. δ18O and δ13C and Mg/Ca and Sr/Ca signals in the stalagmites reflect precipitation amounts brought by the northeast winds. For stalagmite STM6, this amount effect is amplified by kinetic effects during calcite deposition. Combined interpretation of the stalagmites' signals suggest a weakening of the northeast precipitation between 6.0 and 3.8 ka. After 3.8 ka precipitation intensities remain constant with two superimposed drier periods, between 0 and 0.6 ka and from 2.2 to 3.8 ka. No link can be established with Greenland ice cores and with the summer IOM variability. In contrast to the stable northeast rainy season suggested by the records in this study, speleothem records from western Socotra indicate a wettening of the southwest rainy season on Socotra after 4.4 ka. The local wettening of western Socotra could relate to a more southerly path (more over the Indian Ocean) taken by the southwest winds. Stalagmite STM5, sampled at the fringe between both rain areas displays intermediate δ18O values. After 6.2 ka, similar precipitation changes are seen between eastern Socotra and northern Oman indicating that both regions are affected similarly by the monsoon. Different palaeoclimatologic records from the Arabian Peninsula currently located outside the ITCZ migration pathway display an abrupt drying around 6 ka due to their disconnection from the southwest rain influence. Records that are nowadays still receiving rain by the southwest winds

  6. Intra-species Genomic and Physiological Variability Impact Stress Resistance in Strains of Probiotic Potential.

    Science.gov (United States)

    Arnold, Jason W; Simpson, Joshua B; Roach, Jeffrey; Kwintkiewicz, Jakub; Azcarate-Peril, M Andrea

    2018-01-01

    Large-scale microbiome studies have established that most of the diversity contained in the gastrointestinal tract is represented at the strain level; however, exhaustive genomic and physiological characterization of human isolates is still lacking. With increased use of probiotics as interventions for gastrointestinal disorders, genomic and functional characterization of novel microorganisms becomes essential. In this study, we explored the impact of strain-level genomic variability on bacterial physiology of two novel human Lactobacillus rhamnosus strains (AMC143 and AMC010) of probiotic potential in relation to stress resistance. The strains showed differences with known probiotic strains ( L. rhamnosus GG, Lc705, and HN001) at the genomic level, including nucleotide polymorphisms, mutations in non-coding regulatory regions, and rearrangements of genomic architecture. Transcriptomics analysis revealed that gene expression profiles differed between strains when exposed to simulated gastrointestinal stresses, suggesting the presence of unique regulatory systems in each strain. In vitro physiological assays to test resistance to conditions mimicking the gut environment (acid, alkali, and bile stress) showed that growth of L. rhamnosus AMC143 was inhibited upon exposure to alkaline pH, while AMC010 and control strain LGG were unaffected. AMC143 also showed a significant survival advantage compared to the other strains upon bile exposure. Reverse transcription qPCR targeting the bile salt hydrolase gene ( bsh ) revealed that AMC143 expressed bsh poorly (a consequence of a deletion in the bsh promoter and truncation of bsh gene in AMC143), while AMC010 had significantly higher expression levels than AMC143 or LGG. Insertional inactivation of the bsh gene in AMC010 suggested that bsh could be detrimental to bacterial survival during bile stress. Together, these findings show that coupling of classical microbiology with functional genomics methods for the

  7. Intra-species Genomic and Physiological Variability Impact Stress Resistance in Strains of Probiotic Potential

    Directory of Open Access Journals (Sweden)

    Jason W. Arnold

    2018-02-01

    Full Text Available Large-scale microbiome studies have established that most of the diversity contained in the gastrointestinal tract is represented at the strain level; however, exhaustive genomic and physiological characterization of human isolates is still lacking. With increased use of probiotics as interventions for gastrointestinal disorders, genomic and functional characterization of novel microorganisms becomes essential. In this study, we explored the impact of strain-level genomic variability on bacterial physiology of two novel human Lactobacillus rhamnosus strains (AMC143 and AMC010 of probiotic potential in relation to stress resistance. The strains showed differences with known probiotic strains (L. rhamnosus GG, Lc705, and HN001 at the genomic level, including nucleotide polymorphisms, mutations in non-coding regulatory regions, and rearrangements of genomic architecture. Transcriptomics analysis revealed that gene expression profiles differed between strains when exposed to simulated gastrointestinal stresses, suggesting the presence of unique regulatory systems in each strain. In vitro physiological assays to test resistance to conditions mimicking the gut environment (acid, alkali, and bile stress showed that growth of L. rhamnosus AMC143 was inhibited upon exposure to alkaline pH, while AMC010 and control strain LGG were unaffected. AMC143 also showed a significant survival advantage compared to the other strains upon bile exposure. Reverse transcription qPCR targeting the bile salt hydrolase gene (bsh revealed that AMC143 expressed bsh poorly (a consequence of a deletion in the bsh promoter and truncation of bsh gene in AMC143, while AMC010 had significantly higher expression levels than AMC143 or LGG. Insertional inactivation of the bsh gene in AMC010 suggested that bsh could be detrimental to bacterial survival during bile stress. Together, these findings show that coupling of classical microbiology with functional genomics methods for the

  8. Ecological fitness, genomic islands and bacterial pathogenicity: A Darwinian view of the evolution of microbes

    OpenAIRE

    Hacker, Jörg; Carniel, Elisabeth

    2001-01-01

    The compositions of bacterial genomes can be changed rapidly and dramatically through a variety of processes including horizontal gene transfer. This form of change is key to bacterial evolution, as it leads to ‘evolution in quantum leaps’. Horizontal gene transfer entails the incorporation of genetic elements transferred from another organism—perhaps in an earlier generation—directly into the genome, where they form ‘genomic islands’, i.e. blocks of DNA with signatures of mobile genetic elem...

  9. Genome-wide prediction of traits with different genetic architecture through efficient variable selection.

    Science.gov (United States)

    Wimmer, Valentin; Lehermeier, Christina; Albrecht, Theresa; Auinger, Hans-Jürgen; Wang, Yu; Schön, Chris-Carolin

    2013-10-01

    In genome-based prediction there is considerable uncertainty about the statistical model and method required to maximize prediction accuracy. For traits influenced by a small number of quantitative trait loci (QTL), predictions are expected to benefit from methods performing variable selection [e.g., BayesB or the least absolute shrinkage and selection operator (LASSO)] compared to methods distributing effects across the genome [ridge regression best linear unbiased prediction (RR-BLUP)]. We investigate the assumptions underlying successful variable selection by combining computer simulations with large-scale experimental data sets from rice (Oryza sativa L.), wheat (Triticum aestivum L.), and Arabidopsis thaliana (L.). We demonstrate that variable selection can be successful when the number of phenotyped individuals is much larger than the number of causal mutations contributing to the trait. We show that the sample size required for efficient variable selection increases dramatically with decreasing trait heritabilities and increasing extent of linkage disequilibrium (LD). We contrast and discuss contradictory results from simulation and experimental studies with respect to superiority of variable selection methods over RR-BLUP. Our results demonstrate that due to long-range LD, medium heritabilities, and small sample sizes, superiority of variable selection methods cannot be expected in plant breeding populations even for traits like FRIGIDA gene expression in Arabidopsis and flowering time in rice, assumed to be influenced by a few major QTL. We extend our conclusions to the analysis of whole-genome sequence data and infer upper bounds for the number of causal mutations which can be identified by LASSO. Our results have major impact on the choice of statistical method needed to make credible inferences about genetic architecture and prediction accuracy of complex traits.

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

    Science.gov (United States)

    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 pVCR94ΔX as a prototype, we have investigated the regulatory circuitry that governs IncA/C plasmids dissemination and found that the transcriptional activator complex AcaCD is essential for the expression of plasmid transfer genes. Using chromatin immunoprecipitation coupled with exonuclease digestion (ChIP-exo) and RNA sequencing (RNA-seq) approaches, we have identified the sequences recognized by AcaCD and characterized the AcaCD regulon. Data mining using the DNA motif recognized by AcaCD revealed potential AcaCD-binding sites upstream of genes involved in the intracellular mobility functions (recombination directionality factor and mobilization genes) in two widespread classes of genomic islands (GIs) phylogenetically unrelated to IncA/C plasmids. The first class, SGI1, confers and propagates multidrug resistance in Salmonella enterica and Proteus mirabilis, whereas MGIVmi1 in Vibrio mimicus belongs to a previously uncharacterized class of GIs. We have demonstrated that through expression of AcaCD, IncA/C plasmids specifically trigger the excision and mobilization of the GIs at high frequencies. This study provides new evidence of the considerable impact of IncA/C plasmids on bacterial genome plasticity through their own mobility and the mobilization of genomic islands.

  11. Comparative Genomics of Rhodococcus equi Virulence Plasmids Indicates Host-Driven Evolution of the vap Pathogenicity Island.

    Science.gov (United States)

    MacArthur, Iain; Anastasi, Elisa; Alvarez, Sonsiray; Scortti, Mariela; Vázquez-Boland, José A

    2017-05-01

    The conjugative virulence plasmid is a key component of the Rhodococcus equi accessory genome essential for pathogenesis. Three host-associated virulence plasmid types have been identified the equine pVAPA and porcine pVAPB circular variants, and the linear pVAPN found in bovine (ruminant) isolates. We recently characterized the R. equi pangenome (Anastasi E, et al. 2016. Pangenome and phylogenomic analysis of the pathogenic actinobacterium Rhodococcus equi. Genome Biol Evol. 8:3140-3148.) and we report here the comparative analysis of the virulence plasmid genomes. Plasmids within each host-associated type were highly similar despite their diverse origins. Variation was accounted for by scattered single nucleotide polymorphisms and short nucleotide indels, while larger indels-mostly in the plasticity region near the vap pathogencity island (PAI)-defined plasmid genomic subtypes. Only one of the plasmids analyzed, of pVAPN type, was exceptionally divergent due to accumulation of indels in the housekeeping backbone. Each host-associated plasmid type carried a unique PAI differing in vap gene complement, suggesting animal host-specific evolution of the vap multigene family. Complete conservation of the vap PAI was observed within each host-associated plasmid type. Both diversity of host-associated plasmid types and clonality of specific chromosomal-plasmid genomic type combinations were observed within the same R. equi phylogenomic subclade. Our data indicate that the overall strong conservation of the R. equi host-associated virulence plasmids is the combined result of host-driven selection, lateral transfer between strains, and geographical spread due to international livestock exchanges. © The Author(s) 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

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

    Directory of Open Access Journals (Sweden)

    Bonten Marc JM

    2010-04-01

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

  13. Time-space variability of satellite chlorophyll-α in the Easter Island Province, southeastern Pacific Ocean

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    Isabel Andrade

    2014-10-01

    Full Text Available The Easter Island Province (EIP encompasses Easter Island (EI and Salas y Gómez Island (SGI, which are located in the eastern boundary of the south Pacific subtropical gyre. This province is one of the most oligotrophic region in the world ocean with a high degree of endemism and distinguished by having the clearest waters in the world. Issues related to the biophysical coupling that sustains biological production in this region are still poorly understood. Satellite data compiled over a ten year period was used to characterize the spatial and temporal chlorophyll-α (Chl-α variability around the EIP and determine the relationship between Chl-α and several physical forcing. Results shows a clear Chl-α annual cycle around the EIP, with maximum concentration during the austral winter. Chl-α spatial distribution shows a strong zonal dipole over EI that divides the island into two zones: southeast and northwest. Due to its small size and low elevation of SGI, it does not generate a significant local effect in Chl-α concentration, but a Chl-α increase is observed southeast of this island (~2 km associated to a seamount. The mean geostrophic current in the EIP flows eastward, associated with the southeastern boundary of the subtropical gyre. However, recurrent mesoscale eddies traveling northwestward and produce large surface current variability with periods of high velocities in opposite direction. In the spring, wakes of high Chl-α concentration can be observed over EI, associated with the generation and detachment of submesoscale eddies from EI, which could have important biological implications during periods of low regional biological production.

  14. Variability of morphometric characteristics of the leaves of European white elm from the area of Great War Island

    Directory of Open Access Journals (Sweden)

    Devetaković Jovana

    2013-01-01

    Full Text Available The European White Elm (Ulmus effusa Willd. is indicated as a rare and endangered species in the growing stock of the Republic of Serbia. In the area of Great War Island, its natural populations were reduced to 56 registered trees, which occur in three spatially isolated subpopulations. On the basis of the research conducted on the level of variability of adaptible morphometric characteristics of leaves from 14 selected test trees of European White Elm, it can be concluded that the degree of interpopulation variability is satisfactory, which is a good basis for the conservation of the available gene pool.

  15. A map to a new treasure island: the human genome and the concept of common heritage.

    Science.gov (United States)

    Byk, C

    1998-06-01

    While the 1970's have been called the environmental years, the 1990's could be seen as the genome years. As the challenge to map and to sequence the human genome mobilized the scientific community, risks and benefits of information and uses that would derive from this project have also raised ethical issues at the international level. The particular interest of the 1997 UNESCO Declaration relies on the fact that it emphasizes both the scientific importance of genetics and the appropriate reinforcement of human rights in this area. It considers the human genome, at least symbolically, as the common heritage of humanity.

  16. Destabilization of IncA and IncC plasmids by SGI1 and SGI2 type Salmonella genomic islands.

    Science.gov (United States)

    Harmer, Christopher J; Hamidian, Mohammad; Ambrose, Stephanie J; Hall, Ruth M

    Both the Salmonella genomic islands (SGI) and the conjugative IncC plasmids are known to contribute substantially to the acquisition of resistance to multiple antibiotics, and plasmids in the A/C group are known to mobilize the Salmonella genomic island SGI1, which also carries multiple antibiotic resistance genes. Plasmid pRMH760 (IncC; A/C 2 ) was shown to mobilize SGI1 variants SGI1-I, SGI1-F, SGI1-K and SGI2 from Salmonella enterica to Escherichia coli where it was integrated at the preferred location, at the end of the trmE (thdF) gene. The plasmid was transferred at a similar frequency. However, we observed that co-transfer of the SGI and the plasmid was rarer. In E. coli to E. coli transfer, the frequency of transfer of the IncC plasmid pRMH760 was at least 1000-fold lower when the donor carried SGI1-I or SGI1-K, indicating that the SGI suppresses transfer of the plasmid. In addition, pRMH760 was rapidly lost from both E. coli and S. enterica strains that also carried SGI1-I, SGI1-F or SGI2. However, plasmid loss was not seen when the SGI1 variant was SGI1-K, which lacks two segments of the SGI1 backbone. The complete sequence of the SGI1-I and SGI1-F were determined and SGI1-K also carries two single base substitutions relative to SGI1-I. The IncA (A/C 1 ) plasmid RA1 was also shown to mobilize SGI2-A and though there are significant differences between the backbones of IncA and IncC plasmids, RA1 was also rapidly lost when SGI2-A was present in the same cell. We conclude that there are multiple interactions, both cooperative and antagonistic, between an IncA or IncC plasmid and the SGI1 and SGI2 family genomic islands. Copyright © 2016 Elsevier B.V. All rights reserved.

  17. Gene Silencing Triggers Polycomb Repressive Complex 2 Recruitment to CpG Islands Genome Wide

    DEFF Research Database (Denmark)

    Riising, Eva Madi; Vacher-Comet, Itys; Leblanc, Benjamin Olivier

    2014-01-01

    -wide ectopic PRC2 recruitment to endogenous PcG target genes found in other tissues. PRC2 binding analysis shows that it is restricted to nucleosome-free CpG islands (CGIs) of untranscribed genes. Our results show that it is the transcriptional state that governs PRC2 binding, and we propose that it binds...

  18. Multi-region and single-cell sequencing reveal variable genomic heterogeneity in rectal cancer.

    Science.gov (United States)

    Liu, Mingshan; Liu, Yang; Di, Jiabo; Su, Zhe; Yang, Hong; Jiang, Beihai; Wang, Zaozao; Zhuang, Meng; Bai, Fan; Su, Xiangqian

    2017-11-23

    Colorectal cancer is a heterogeneous group of malignancies with complex molecular subtypes. While colon cancer has been widely investigated, studies on rectal cancer are very limited. Here, we performed multi-region whole-exome sequencing and single-cell whole-genome sequencing to examine the genomic intratumor heterogeneity (ITH) of rectal tumors. We sequenced nine tumor regions and 88 single cells from two rectal cancer patients with tumors of the same molecular classification and characterized their mutation profiles and somatic copy number alterations (SCNAs) at the multi-region and the single-cell levels. A variable extent of genomic heterogeneity was observed between the two patients, and the degree of ITH increased when analyzed on the single-cell level. We found that major SCNAs were early events in cancer development and inherited steadily. Single-cell sequencing revealed mutations and SCNAs which were hidden in bulk sequencing. In summary, we studied the ITH of rectal cancer at regional and single-cell resolution and demonstrated that variable heterogeneity existed in two patients. The mutational scenarios and SCNA profiles of two patients with treatment naïve from the same molecular subtype are quite different. Our results suggest each tumor possesses its own architecture, which may result in different diagnosis, prognosis, and drug responses. Remarkable ITH exists in the two patients we have studied, providing a preliminary impression of ITH in rectal cancer.

  19. Streams in the urban heat island: spatial and temporal variability in temperature

    Science.gov (United States)

    Somers, Kayleigh A.; Bernhardt, Emily S.; Grace, James B.; Hassett, Brooke A.; Sudduth, Elizabeth B.; Wang, Siyi; Urban, Dean L.

    2013-01-01

    Streams draining urban heat islands tend to be hotter than rural and forested streams at baseflow because of warmer urban air and ground temperatures, paved surfaces, and decreased riparian canopy. Urban infrastructure efficiently routes runoff over hot impervious surfaces and through storm drains directly into streams and can lead to rapid, dramatic increases in temperature. Thermal regimes affect habitat quality and biogeochemical processes, and changes can be lethal if temperatures exceed upper tolerance limits of aquatic fauna. In summer 2009, we collected continuous (10-min interval) temperature data in 60 streams spanning a range of development intensity in the Piedmont of North Carolina, USA. The 5 most urbanized streams averaged 21.1°C at baseflow, compared to 19.5°C in the 5 most forested streams. Temperatures in urban streams rose as much as 4°C during a small regional storm, whereas the same storm led to extremely small to no changes in temperature in forested streams. Over a kilometer of stream length, baseflow temperature varied by as much as 10°C in an urban stream and as little as 2°C in a forested stream. We used structural equation modeling to explore how reach- and catchment-scale attributes interact to explain maximum temperatures and magnitudes of storm-flow temperature surges. The best predictive model of baseflow temperatures (R2  =  0.461) included moderately strong pathways directly (extent of development and road density) and indirectly, as mediated by reach-scale factors (canopy closure and stream width), from catchment-scale factors. The strongest influence on storm-flow temperature surges appeared to be % development in the catchment. Reach-scale factors, such as the extent of riparian forest and stream width, had little mitigating influence (R2  =  0.448). Stream temperature is an essential, but overlooked, aspect of the urban stream syndrome and is affected by reach-scale habitat variables, catchment-scale urbanization

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

    Science.gov (United States)

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

    2014-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Farzana Abubakar Yousuf

    2014-01-01

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

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

    Science.gov (United States)

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

    2013-04-01

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

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

    Directory of Open Access Journals (Sweden)

    Reuben B Vercoe

    2013-04-01

    Full Text Available 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.

  4. EuGI: a novel resource for studying genomic islands to facilitate horizontal gene transfer detection in eukaryotes.

    Science.gov (United States)

    Clasen, Frederick Johannes; Pierneef, Rian Ewald; Slippers, Bernard; Reva, Oleg

    2018-05-03

    Genomic islands (GIs) are inserts of foreign DNA that have potentially arisen through horizontal gene transfer (HGT). There are evidences that GIs can contribute significantly to the evolution of prokaryotes. The acquisition of GIs through HGT in eukaryotes has, however, been largely unexplored. In this study, the previously developed GI prediction tool, SeqWord Gene Island Sniffer (SWGIS), is modified to predict GIs in eukaryotic chromosomes. Artificial simulations are used to estimate ratios of predicting false positive and false negative GIs by inserting GIs into different test chromosomes and performing the SWGIS v2.0 algorithm. Using SWGIS v2.0, GIs are then identified in 36 fungal, 22 protozoan and 8 invertebrate genomes. SWGIS v2.0 predicts GIs in large eukaryotic chromosomes based on the atypical nucleotide composition of these regions. Averages for predicting false negative and false positive GIs were 20.1% and 11.01% respectively. A total of 10,550 GIs were identified in 66 eukaryotic species with 5299 of these GIs coding for at least one functional protein. The EuGI web-resource, freely accessible at http://eugi.bi.up.ac.za , was developed that allows browsing the database created from identified GIs and genes within GIs through an interactive and visual interface. SWGIS v2.0 along with the EuGI database, which houses GIs identified in 66 different eukaryotic species, and the EuGI web-resource, provide the first comprehensive resource for studying HGT in eukaryotes.

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

    Science.gov (United States)

    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

  6. Comparative Genomics and Identification of an Enterotoxin-Bearing Pathogenicity Island, SEPI-1/SECI-1, in Staphylococcus epidermidis Pathogenic Strains.

    Science.gov (United States)

    Argemi, Xavier; Nanoukon, Chimène; Affolabi, Dissou; Keller, Daniel; Hansmann, Yves; Riegel, Philippe; Baba-Moussa, Lamine; Prévost, Gilles

    2018-02-25

    Staphylococcus epidermidis is a leading cause of nosocomial infections, majorly resistant to beta-lactam antibiotics, and may transfer several mobile genetic elements among the members of its own species, as well as to Staphylococcus aureus ; however, a genetic exchange from S. aureus to S. epidermidis remains controversial. We recently identified two pathogenic clinical strains of S. epidermidis that produce a staphylococcal enterotoxin C3-like (SEC) similar to that by S. aureus pathogenicity islands. This study aimed to determine the genetic environment of the SEC-coding sequence and to identify the mobile genetic elements. Whole-genome sequencing and annotation of the S. epidermidis strains were performed using Illumina technology and a bioinformatics pipeline for assembly, which provided evidence that the SEC-coding sequences were located in a composite pathogenicity island that was previously described in the S. epidermidis strain FRI909, called SePI-1/SeCI-1, with 83.8-89.7% nucleotide similarity. Various other plasmids were identified, particularly p_3_95 and p_4_95, which carry antibiotic resistance genes ( hsrA and dfrG , respectively), and share homologies with SAP085A and pUSA04-2-SUR11, two plasmids described in S. aureus . Eventually, one complete prophage was identified, ΦSE90, sharing 30 out of 52 coding sequences with the Acinetobacter phage vB_AbaM_IME200. Thus, the SePI-1/SeCI-1 pathogenicity island was identified in two pathogenic strains of S. epidermidis that produced a SEC enterotoxin causing septic shock. These findings suggest the existence of in vivo genetic exchange from S. aureus to S. epidermidis .

  7. Comparative Genomics and Identification of an Enterotoxin-Bearing Pathogenicity Island, SEPI-1/SECI-1, in Staphylococcus epidermidis Pathogenic Strains

    Directory of Open Access Journals (Sweden)

    Xavier Argemi

    2018-02-01

    Full Text Available Staphylococcus epidermidis is a leading cause of nosocomial infections, majorly resistant to beta-lactam antibiotics, and may transfer several mobile genetic elements among the members of its own species, as well as to Staphylococcus aureus; however, a genetic exchange from S. aureus to S. epidermidis remains controversial. We recently identified two pathogenic clinical strains of S. epidermidis that produce a staphylococcal enterotoxin C3-like (SEC similar to that by S. aureus pathogenicity islands. This study aimed to determine the genetic environment of the SEC-coding sequence and to identify the mobile genetic elements. Whole-genome sequencing and annotation of the S. epidermidis strains were performed using Illumina technology and a bioinformatics pipeline for assembly, which provided evidence that the SEC-coding sequences were located in a composite pathogenicity island that was previously described in the S. epidermidis strain FRI909, called SePI-1/SeCI-1, with 83.8–89.7% nucleotide similarity. Various other plasmids were identified, particularly p_3_95 and p_4_95, which carry antibiotic resistance genes (hsrA and dfrG, respectively, and share homologies with SAP085A and pUSA04-2-SUR11, two plasmids described in S. aureus. Eventually, one complete prophage was identified, ΦSE90, sharing 30 out of 52 coding sequences with the Acinetobacter phage vB_AbaM_IME200. Thus, the SePI-1/SeCI-1 pathogenicity island was identified in two pathogenic strains of S. epidermidis that produced a SEC enterotoxin causing septic shock. These findings suggest the existence of in vivo genetic exchange from S. aureus to S. epidermidis.

  8. Karyotype Variability and Inter-Population Genomic Differences in Freshwater Ostracods (Crustacea Showing Geographical Parthenogenesis

    Directory of Open Access Journals (Sweden)

    Radka Symonová

    2018-03-01

    Full Text Available Transitions from sexual to asexual reproduction are often associated with polyploidy and increased chromosomal plasticity in asexuals. We investigated chromosomes in the freshwater ostracod species Eucypris virens (Jurine, 1820, where sexual, asexual and mixed populations can be found. Our initial karyotyping of multiple populations from Europe and North Africa, both sexual and asexual, revealed a striking variability in chromosome numbers. This would suggest that chromosomal changes are likely to be accelerated in asexuals because the constraints of meiosis are removed. Hence, we employed comparative genomic hybridization (CGH within and among sexual and asexual populations to get insights into E. virens genome arrangements. CGH disclosed substantial genomic imbalances among the populations analyzed, and three patterns of genome arrangement between these populations: 1. Only putative ribosomal DNA (rDNA-bearing regions were conserved in the two populations compared indicating a high sequence divergence between these populations. This pattern is comparable with our findings at the interspecies level of comparison; 2. Chromosomal regions were shared by both populations to a varying extent with a distinct copy number variation in pericentromeric and presumable rDNA-bearing regions. This indicates a different rate of evolution in repetitive sequences; 3. A mosaic pattern of distribution of genomic material that can be explained as non-reciprocal genetic introgression and evidence of a hybrid origin of these individuals. We show an overall increased chromosomal dynamics in E. virens that is complementary with available phylogenetic and population genetic data reporting highly differentiated diploid sexual and asexual lineages with a wide variety of genetic backgrounds.

  9. Genomic timetree and historical biogeography of Caribbean island ameiva lizards (Pholidoscelis: Teiidae)

    OpenAIRE

    Tucker, Derek B.; Hedges, Stephen Blair; Colli, Guarino R.; Pyron, Robert Alexander; Sites, Jack W.

    2017-01-01

    Abstract The phylogenetic relationships and biogeographic history of Caribbean island ameivas (Pholidoscelis) are not well?known because of incomplete sampling, conflicting datasets, and poor support for many clades. Here, we use phylogenomic and mitochondrial DNA datasets to reconstruct a well?supported phylogeny and assess historical colonization patterns in the group. We obtained sequence data from 316 nuclear loci and one mitochondrial marker for 16 of 19 extant species of the Caribbean e...

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

    Science.gov (United States)

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

    2011-01-01

    Contemporary genetic variation among Latin Americans human groups reflects population migrations shaped by complex historical, social and economic factors. Consequently, admixture patterns may vary by geographic regions ranging from countries to neighborhoods. We examined the geographic variation of admixture across the island of Puerto Rico and the degree to which it could be explained by historic and social events. We analyzed a census-based sample of 642 Puerto Rican individuals that were genotyped for 93 ancestry informative markers (AIMs) to estimate African, European and Native American ancestry. Socioeconomic status (SES) data and geographic location were obtained for each individual. There was significant geographic variation of ancestry across the island. In particular, African ancestry demonstrated a decreasing East to West gradient that was partially explained by historical factors linked to the colonial sugar plantation system. SES also demonstrated a parallel decreasing cline from East to West. However, at a local level, SES and African ancestry were negatively correlated. European ancestry was strongly negatively correlated with African ancestry and therefore showed patterns complementary to African ancestry. By contrast, Native American ancestry showed little variation across the island and across individuals and appears to have played little social role historically. The observed geographic distributions of SES and genetic variation relate to historical social events and mating patterns, and have substantial implications for the design of studies in the recently admixed Puerto Rican population. More generally, our results demonstrate the importance of incorporating social and geographic data with genetics when studying contemporary admixed populations. PMID:21304981

  11. Ultrahigh-dimensional variable selection method for whole-genome gene-gene interaction analysis

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    Ueki Masao

    2012-05-01

    Full Text Available Abstract Background Genome-wide gene-gene interaction analysis using single nucleotide polymorphisms (SNPs is an attractive way for identification of genetic components that confers susceptibility of human complex diseases. Individual hypothesis testing for SNP-SNP pairs as in common genome-wide association study (GWAS however involves difficulty in setting overall p-value due to complicated correlation structure, namely, the multiple testing problem that causes unacceptable false negative results. A large number of SNP-SNP pairs than sample size, so-called the large p small n problem, precludes simultaneous analysis using multiple regression. The method that overcomes above issues is thus needed. Results We adopt an up-to-date method for ultrahigh-dimensional variable selection termed the sure independence screening (SIS for appropriate handling of numerous number of SNP-SNP interactions by including them as predictor variables in logistic regression. We propose ranking strategy using promising dummy coding methods and following variable selection procedure in the SIS method suitably modified for gene-gene interaction analysis. We also implemented the procedures in a software program, EPISIS, using the cost-effective GPGPU (General-purpose computing on graphics processing units technology. EPISIS can complete exhaustive search for SNP-SNP interactions in standard GWAS dataset within several hours. The proposed method works successfully in simulation experiments and in application to real WTCCC (Wellcome Trust Case–control Consortium data. Conclusions Based on the machine-learning principle, the proposed method gives powerful and flexible genome-wide search for various patterns of gene-gene interaction.

  12. Comparative genomics of four closely related Clostridium perfringens bacteriophages reveals variable evolution among core genes with therapeutic potential

    Directory of Open Access Journals (Sweden)

    Siragusa Gregory R

    2011-06-01

    Full Text Available Abstract Background Because biotechnological uses of bacteriophage gene products as alternatives to conventional antibiotics will require a thorough understanding of their genomic context, we sequenced and analyzed the genomes of four closely related phages isolated from Clostridium perfringens, an important agricultural and human pathogen. Results Phage whole-genome tetra-nucleotide signatures and proteomic tree topologies correlated closely with host phylogeny. Comparisons of our phage genomes to 26 others revealed three shared COGs; of particular interest within this core genome was an endolysin (PF01520, an N-acetylmuramoyl-L-alanine amidase and a holin (PF04531. Comparative analyses of the evolutionary history and genomic context of these common phage proteins revealed two important results: 1 strongly significant host-specific sequence variation within the endolysin, and 2 a protein domain architecture apparently unique to our phage genomes in which the endolysin is located upstream of its associated holin. Endolysin sequences from our phages were one of two very distinct genotypes distinguished by variability within the putative enzymatically-active domain. The shared or core genome was comprised of genes with multiple sequence types belonging to five pfam families, and genes belonging to 12 pfam families, including the holin genes, which were nearly identical. Conclusions Significant genomic diversity exists even among closely-related bacteriophages. Holins and endolysins represent conserved functions across divergent phage genomes and, as we demonstrate here, endolysins can have significant variability and host-specificity even among closely-related genomes. Endolysins in our phage genomes may be subject to different selective pressures than the rest of the genome. These findings may have important implications for potential biotechnological applications of phage gene products.

  13. A genome-wide methylation study on obesity: differential variability and differential methylation.

    Science.gov (United States)

    Xu, Xiaojing; Su, Shaoyong; Barnes, Vernon A; De Miguel, Carmen; Pollock, Jennifer; Ownby, Dennis; Shi, Hidong; Zhu, Haidong; Snieder, Harold; Wang, Xiaoling

    2013-05-01

    Besides differential methylation, DNA methylation variation has recently been proposed and demonstrated to be a potential contributing factor to cancer risk. Here we aim to examine whether differential variability in methylation is also an important feature of obesity, a typical non-malignant common complex disease. We analyzed genome-wide methylation profiles of over 470,000 CpGs in peripheral blood samples from 48 obese and 48 lean African-American youth aged 14-20 y old. A substantial number of differentially variable CpG sites (DVCs), using statistics based on variances, as well as a substantial number of differentially methylated CpG sites (DMCs), using statistics based on means, were identified. Similar to the findings in cancers, DVCs generally exhibited an outlier structure and were more variable in cases than in controls. By randomly splitting the current sample into a discovery and validation set, we observed that both the DVCs and DMCs identified from the first set could independently predict obesity status in the second set. Furthermore, both the genes harboring DMCs and the genes harboring DVCs showed significant enrichment of genes identified by genome-wide association studies on obesity and related diseases, such as hypertension, dyslipidemia, type 2 diabetes and certain types of cancers, supporting their roles in the etiology and pathogenesis of obesity. We generalized the recent finding on methylation variability in cancer research to obesity and demonstrated that differential variability is also an important feature of obesity-related methylation changes. Future studies on the epigenetics of obesity will benefit from both statistics based on means and statistics based on variances.

  14. Adaptive divergence despite strong genetic drift: genomic analysis of the evolutionary mechanisms causing genetic differentiation in the island fox (Urocyon littoralis)

    Science.gov (United States)

    FUNK, W. CHRIS; LOVICH, ROBERT E.; HOHENLOHE, PAUL A.; HOFMAN, COURTNEY A.; MORRISON, SCOTT A.; SILLETT, T. SCOTT; GHALAMBOR, CAMERON K.; MALDONADO, JESUS E.; RICK, TORBEN C.; DAY, MITCH D.; POLATO, NICHOLAS R.; FITZPATRICK, SARAH W.; COONAN, TIMOTHY J.; CROOKS, KEVIN R.; DILLON, ADAM; GARCELON, DAVID K.; KING, JULIE L.; BOSER, CHRISTINA L.; GOULD, NICHOLAS; ANDELT, WILLIAM F.

    2016-01-01

    The evolutionary mechanisms generating the tremendous biodiversity of islands have long fascinated evolutionary biologists. Genetic drift and divergent selection are predicted to be strong on islands and both could drive population divergence and speciation. Alternatively, strong genetic drift may preclude adaptation. We conducted a genomic analysis to test the roles of genetic drift and divergent selection in causing genetic differentiation among populations of the island fox (Urocyon littoralis). This species consists of 6 subspecies, each of which occupies a different California Channel Island. Analysis of 5293 SNP loci generated using Restriction-site Associated DNA (RAD) sequencing found support for genetic drift as the dominant evolutionary mechanism driving population divergence among island fox populations. In particular, populations had exceptionally low genetic variation, small Ne (range = 2.1–89.7; median = 19.4), and significant genetic signatures of bottlenecks. Moreover, islands with the lowest genetic variation (and, by inference, the strongest historical genetic drift) were most genetically differentiated from mainland gray foxes, and vice versa, indicating genetic drift drives genome-wide divergence. Nonetheless, outlier tests identified 3.6–6.6% of loci as high FST outliers, suggesting that despite strong genetic drift, divergent selection contributes to population divergence. Patterns of similarity among populations based on high FST outliers mirrored patterns based on morphology, providing additional evidence that outliers reflect adaptive divergence. Extremely low genetic variation and small Ne in some island fox populations, particularly on San Nicolas Island, suggest that they may be vulnerable to fixation of deleterious alleles, decreased fitness, and reduced adaptive potential. PMID:26992010

  15. Adaptive divergence despite strong genetic drift: genomic analysis of the evolutionary mechanisms causing genetic differentiation in the island fox (Urocyon littoralis).

    Science.gov (United States)

    Funk, W Chris; Lovich, Robert E; Hohenlohe, Paul A; Hofman, Courtney A; Morrison, Scott A; Sillett, T Scott; Ghalambor, Cameron K; Maldonado, Jesus E; Rick, Torben C; Day, Mitch D; Polato, Nicholas R; Fitzpatrick, Sarah W; Coonan, Timothy J; Crooks, Kevin R; Dillon, Adam; Garcelon, David K; King, Julie L; Boser, Christina L; Gould, Nicholas; Andelt, William F

    2016-05-01

    The evolutionary mechanisms generating the tremendous biodiversity of islands have long fascinated evolutionary biologists. Genetic drift and divergent selection are predicted to be strong on islands and both could drive population divergence and speciation. Alternatively, strong genetic drift may preclude adaptation. We conducted a genomic analysis to test the roles of genetic drift and divergent selection in causing genetic differentiation among populations of the island fox (Urocyon littoralis). This species consists of six subspecies, each of which occupies a different California Channel Island. Analysis of 5293 SNP loci generated using Restriction-site Associated DNA (RAD) sequencing found support for genetic drift as the dominant evolutionary mechanism driving population divergence among island fox populations. In particular, populations had exceptionally low genetic variation, small Ne (range = 2.1-89.7; median = 19.4), and significant genetic signatures of bottlenecks. Moreover, islands with the lowest genetic variation (and, by inference, the strongest historical genetic drift) were most genetically differentiated from mainland grey foxes, and vice versa, indicating genetic drift drives genome-wide divergence. Nonetheless, outlier tests identified 3.6-6.6% of loci as high FST outliers, suggesting that despite strong genetic drift, divergent selection contributes to population divergence. Patterns of similarity among populations based on high FST outliers mirrored patterns based on morphology, providing additional evidence that outliers reflect adaptive divergence. Extremely low genetic variation and small Ne in some island fox populations, particularly on San Nicolas Island, suggest that they may be vulnerable to fixation of deleterious alleles, decreased fitness and reduced adaptive potential. © 2016 John Wiley & Sons Ltd.

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

    Science.gov (United States)

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

    2015-01-01

    Conjugative plasmids of the A/C incompatibility group (IncA/C) have become substantial players in the dissemination of multidrug resistance. These large conjugative plasmids are characterized by their broad host-range, extended spectrum of antimicrobials resistance, and prevalence in enteric bacteria recovered from both environmental and clinical settings. Until recently, relatively little was known about the basic biology of IncA/C plasmids, mostly because of the hindrance of multidrug resistance for molecular biology experiments. To circumvent this issue, we previously developed pVCR94ΔX, a convenient prototype that codes for a reduced set of antibiotic resistances. Using pVCR94ΔX, we then characterized the regulatory pathway governing IncA/C plasmid dissemination. We found that the expression of roughly 2 thirds of the genes encoded by this plasmid, including large operons involved in the conjugation process, depends on an FlhCD-like master activator called AcaCD. Beyond the mobility of IncA/C plasmids, AcaCD was also shown to play a key role in the mobilization of different classes of genomic islands (GIs) identified in various pathogenic bacteria. By doing so, IncA/C plasmids can have a considerable impact on bacterial genomes plasticity and evolution.

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

    Science.gov (United States)

    Lee, Seung-Tae; Wiemels, Joseph L

    2016-02-18

    The epigenetic landscape of cancer includes both focal hypermethylation and broader hypomethylation in a genome-wide manner. By means of a comprehensive genomic analysis on 6637 tissues of 21 tumor types, we here show that the degrees of overall methylation in CpG island (CGI) and demethylation in intergenic regions, defined as 'backbone', largely vary among different tumors. Depending on tumor type, both CGI methylation and backbone demethylation are often associated with clinical, epidemiological and biological features such as age, sex, smoking history, anatomic location, histological type and grade, stage, molecular subtype and biological pathways. We found connections between CGI methylation and hypermutability, microsatellite instability, IDH1 mutation, 19p gain and polycomb features, and backbone demethylation with chromosomal instability, NSD1 and TP53 mutations, 5q and 19p loss and long repressive domains. These broad epigenetic patterns add a new dimension to our understanding of tumor biology and its clinical implications. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

  18. Tracing variability in the iodine isotopes and species along surface water transect from the North Sea to the Canary Islands

    International Nuclear Information System (INIS)

    Peng He; Ala Aldahan; Uppsala University, Uppsala; Xiaolin Hou; Chinese Academy of Sciences, Xi'an; Possnert, Goran

    2016-01-01

    A complete transect of surface water samples from the North Sea to the Canary Islands was collected during a continuous period in 2010. The samples were analyzed for total 129 I and 127 I isotopes and their iodide and iodate species. The results indicate a large variability in the total 129 I and its species along the transect, whereas less change and variation are observed for the total 127 I and its species. Transport of 129 I from the western English Channel via Biscay Bay is the main source of 129 I in the northeastern Atlantic Ocean. (author)

  19. Genomic Variability of Citrus tristeza virus (CTV Isolates Introduced into Morocco

    Directory of Open Access Journals (Sweden)

    Bouabid Lbida

    2004-08-01

    Full Text Available Genomic variability of the coat protein gene of Citrus tristeza virus isolates obtained from old Meyer lemon introductions in Morocco and more recent budwood introductions from Spain were studied. The coat protein gene of the virus was amplified directly from infected tissue by immunocapture RT-PCR and analysed by single stranded conformation polymorphism (SSCP and sequencing. Each isolate consisted of several related genomic variants, typical of a quasi-species. Although SSCP analysis has only limited typing ability it could be used in an initial screening to discriminate between isolates of different origin and to analyse the genomic structure of each isolate. Sequence analysis showed that the isolates of Spanish origin were closely related to mild isolates characterised in Florida and in Portugal. The Meyer lemon isolate on the other hand was related to severe strains of Meyer lemon characterised in Florida some years ago and to other severe strains from Brasil. A knowledge of the coat protein gene sequence is useful to trace the origin of the isolates.

  20. Insertion sequences as variability generators in the Mycoplasma hyopneumoniae and M. synoviae genomes

    Directory of Open Access Journals (Sweden)

    Elgion Lúcio Silva Loreto

    2007-01-01

    Full Text Available We have analyzed the sequenced genomes of three strains of Mycoplasma hyopneumoniae and one strain of M. synoviae, and have found three and two different transposable element families, respectively in each species. In M. hyopneumoniae, the Insertion Sequences of the IS4 family is represented by ISMHp1, a putatively active element. The IS3 family is represented by several degenerated sequences. A third element called tMH was found, which shows some characteristics reminiscent of retrotransposons. In M. synoviae, three different possibly active IS4 elements are present (ISMHp1-like; ISMs1 and IS1634-like elements. The IS30 family is represented by the degenerated IS1630-like element. The IS1634-like element is shown to be involved in chromosomal rearrangements and horizontal gene transfer (HGT. The ISMHp1-like element is shown to relate to the HGT of a 25-kb region from M. gallisepticum to M. synoviae. The fractions of these genomes that correspond to mobile elements varied from 1.35 to 3.13% in M. hyopneumonia strains and was 2.08% in M. synoviae. Although these species possess reduced genomes, they maintain mobile elements, perhaps as a mechanism for genetic variability production.

  1. Variability among the Most Rapidly Evolving Plastid Genomic Regions is Lineage-Specific: Implications of Pairwise Genome Comparisons in Pyrus (Rosaceae) and Other Angiosperms for Marker Choice

    Science.gov (United States)

    Ter-Voskanyan, Hasmik; Allgaier, Martin; Borsch, Thomas

    2014-01-01

    Plastid genomes exhibit different levels of variability in their sequences, depending on the respective kinds of genomic regions. Genes are usually more conserved while noncoding introns and spacers evolve at a faster pace. While a set of about thirty maximum variable noncoding genomic regions has been suggested to provide universally promising phylogenetic markers throughout angiosperms, applications often require several regions to be sequenced for many individuals. Our project aims to illuminate evolutionary relationships and species-limits in the genus Pyrus (Rosaceae)—a typical case with very low genetic distances between taxa. In this study, we have sequenced the plastid genome of Pyrus spinosa and aligned it to the already available P. pyrifolia sequence. The overall p-distance of the two Pyrus genomes was 0.00145. The intergenic spacers between ndhC–trnV, trnR–atpA, ndhF–rpl32, psbM–trnD, and trnQ–rps16 were the most variable regions, also comprising the highest total numbers of substitutions, indels and inversions (potentially informative characters). Our comparative analysis of further plastid genome pairs with similar low p-distances from Oenothera (representing another rosid), Olea (asterids) and Cymbidium (monocots) showed in each case a different ranking of genomic regions in terms of variability and potentially informative characters. Only two intergenic spacers (ndhF–rpl32 and trnK–rps16) were consistently found among the 30 top-ranked regions. We have mapped the occurrence of substitutions and microstructural mutations in the four genome pairs. High AT content in specific sequence elements seems to foster frequent mutations. We conclude that the variability among the fastest evolving plastid genomic regions is lineage-specific and thus cannot be precisely predicted across angiosperms. The often lineage-specific occurrence of stem-loop elements in the sequences of introns and spacers also governs lineage-specific mutations

  2. Variability among the most rapidly evolving plastid genomic regions is lineage-specific: implications of pairwise genome comparisons in Pyrus (Rosaceae and other angiosperms for marker choice.

    Directory of Open Access Journals (Sweden)

    Nadja Korotkova

    Full Text Available Plastid genomes exhibit different levels of variability in their sequences, depending on the respective kinds of genomic regions. Genes are usually more conserved while noncoding introns and spacers evolve at a faster pace. While a set of about thirty maximum variable noncoding genomic regions has been suggested to provide universally promising phylogenetic markers throughout angiosperms, applications often require several regions to be sequenced for many individuals. Our project aims to illuminate evolutionary relationships and species-limits in the genus Pyrus (Rosaceae-a typical case with very low genetic distances between taxa. In this study, we have sequenced the plastid genome of Pyrus spinosa and aligned it to the already available P. pyrifolia sequence. The overall p-distance of the two Pyrus genomes was 0.00145. The intergenic spacers between ndhC-trnV, trnR-atpA, ndhF-rpl32, psbM-trnD, and trnQ-rps16 were the most variable regions, also comprising the highest total numbers of substitutions, indels and inversions (potentially informative characters. Our comparative analysis of further plastid genome pairs with similar low p-distances from Oenothera (representing another rosid, Olea (asterids and Cymbidium (monocots showed in each case a different ranking of genomic regions in terms of variability and potentially informative characters. Only two intergenic spacers (ndhF-rpl32 and trnK-rps16 were consistently found among the 30 top-ranked regions. We have mapped the occurrence of substitutions and microstructural mutations in the four genome pairs. High AT content in specific sequence elements seems to foster frequent mutations. We conclude that the variability among the fastest evolving plastid genomic regions is lineage-specific and thus cannot be precisely predicted across angiosperms. The often lineage-specific occurrence of stem-loop elements in the sequences of introns and spacers also governs lineage-specific mutations. Sequencing

  3. Genetic variability of Rickettsia spp. in Ixodes persulcatus ticks from continental and island areas of the Russian Far East.

    Science.gov (United States)

    Igolkina, Y; Bondarenko, E; Rar, V; Epikhina, T; Vysochina, N; Pukhovskaya, N; Tikunov, A; Ivanov, L; Golovljova, I; Ivanov, М; Tikunova, N

    2016-10-01

    Rickettsia spp. are intracellular Gram-negative bacteria transmitted by arthropods. Two potentially pathogenic rickettsiae, Candidatus Rickettsia tarasevichiae and Rickettsia helvetica, have been found in unfed adult Ixodes persulcatus ticks. The aim of this study was to assess the prevalence and genetic variability of Rickettsia spp. in I. persulcatus ticks collected from different locations in the Russian Far East. In total, 604 adult I. persulcatus ticks collected from four sites in the Khabarovsk Territory (continental area) and one site in Sakhalin Island were examined for the presence of Rickettsia spp. by real-time PCR. Nested PCR with species-specific primers and sequencing were used for genotyping of revealed rickettsiae. The overall prevalence of Rickettsia spp. in ticks collected in different sites varied from 67.9 to 90.7%. However, the proportion of different Rickettsia species observed in ticks from Sakhalin Island significantly differed from that in ticks from the Khabarovsk Territory. In Sakhalin Island, R. helvetica prevailed in examined ticks, while Candidatus R. tarasevichiae was predominant in the Khabarovsk Territory. For gltA and ompB gene fragments, the sequences obtained for Candidatus R. tarasevichiae from all studied sites were identical to each other and to the known sequences of this species. According to sequence analysis of gltA, оmpB and sca4 genes, R. helvetica isolates from Sakhalin Island and the Khabarovsk Territory were identical to each other, but they differed from R. helvetica from other regions and from those found in other tick species. For the first time, DNA of pathogenic Rickettsia heilongjiangensis was detected in I. persulcatus ticks in two sites from the Khabarovsk Territory. The gltA, ompA and оmpB gene sequences of R. heilongjiangensis were identical to or had solitary mismatches with the corresponding sequences of R. heilongjiangensis found in other tick species. Copyright © 2016 Elsevier GmbH. All rights

  4. Normalization of High Dimensional Genomics Data Where the Distribution of the Altered Variables Is Skewed

    Science.gov (United States)

    Landfors, Mattias; Philip, Philge; Rydén, Patrik; Stenberg, Per

    2011-01-01

    Genome-wide analysis of gene expression or protein binding patterns using different array or sequencing based technologies is now routinely performed to compare different populations, such as treatment and reference groups. It is often necessary to normalize the data obtained to remove technical variation introduced in the course of conducting experimental work, but standard normalization techniques are not capable of eliminating technical bias in cases where the distribution of the truly altered variables is skewed, i.e. when a large fraction of the variables are either positively or negatively affected by the treatment. However, several experiments are likely to generate such skewed distributions, including ChIP-chip experiments for the study of chromatin, gene expression experiments for the study of apoptosis, and SNP-studies of copy number variation in normal and tumour tissues. A preliminary study using spike-in array data established that the capacity of an experiment to identify altered variables and generate unbiased estimates of the fold change decreases as the fraction of altered variables and the skewness increases. We propose the following work-flow for analyzing high-dimensional experiments with regions of altered variables: (1) Pre-process raw data using one of the standard normalization techniques. (2) Investigate if the distribution of the altered variables is skewed. (3) If the distribution is not believed to be skewed, no additional normalization is needed. Otherwise, re-normalize the data using a novel HMM-assisted normalization procedure. (4) Perform downstream analysis. Here, ChIP-chip data and simulated data were used to evaluate the performance of the work-flow. It was found that skewed distributions can be detected by using the novel DSE-test (Detection of Skewed Experiments). Furthermore, applying the HMM-assisted normalization to experiments where the distribution of the truly altered variables is skewed results in considerably higher

  5. Complex analyses of inverted repeats in mitochondrial genomes revealed their importance and variability.

    Science.gov (United States)

    Cechová, Jana; Lýsek, Jirí; Bartas, Martin; Brázda, Václav

    2018-04-01

    The NCBI database contains mitochondrial DNA (mtDNA) genomes from numerous species. We investigated the presence and locations of inverted repeat sequences (IRs) in these mtDNA sequences, which are known to be important for regulating nuclear genomes. IRs were identified in mtDNA in all species. IR lengths and frequencies correlate with evolutionary age and the greatest variability was detected in subgroups of plants and fungi and the lowest variability in mammals. IR presence is non-random and evolutionary favoured. The frequency of IRs generally decreased with IR length, but not for IRs 24 or 30 bp long, which are 1.5 times more abundant. IRs are enriched in sequences from the replication origin, followed by D-loop, stem-loop and miscellaneous sequences, pointing to the importance of IRs in regulatory regions of mitochondrial DNA. Data were produced using Palindrome analyser, freely available on the web at http://bioinformatics.ibp.cz. vaclav@ibp.cz. Supplementary data are available at Bioinformatics online.

  6. Genetic analysis of glucosinolate variability in broccoli florets using genome-anchored single nucleotide polymorphisms.

    Science.gov (United States)

    Brown, Allan F; Yousef, Gad G; Reid, Robert W; Chebrolu, Kranthi K; Thomas, Aswathy; Krueger, Christopher; Jeffery, Elizabeth; Jackson, Eric; Juvik, John A

    2015-07-01

    The identification of genetic factors influencing the accumulation of individual glucosinolates in broccoli florets provides novel insight into the regulation of glucosinolate levels in Brassica vegetables and will accelerate the development of vegetables with glucosinolate profiles tailored to promote human health. Quantitative trait loci analysis of glucosinolate (GSL) variability was conducted with a B. oleracea (broccoli) mapping population, saturated with single nucleotide polymorphism markers from a high-density array designed for rapeseed (Brassica napus). In 4 years of analysis, 14 QTLs were associated with the accumulation of aliphatic, indolic, or aromatic GSLs in floret tissue. The accumulation of 3-carbon aliphatic GSLs (2-propenyl and 3-methylsulfinylpropyl) was primarily associated with a single QTL on C05, but common regulation of 4-carbon aliphatic GSLs was not observed. A single locus on C09, associated with up to 40 % of the phenotypic variability of 2-hydroxy-3-butenyl GSL over multiple years, was not associated with the variability of precursor compounds. Similarly, QTLs on C02, C04, and C09 were associated with 4-methylsulfinylbutyl GSL concentration over multiple years but were not significantly associated with downstream compounds. Genome-specific SNP markers were used to identify candidate genes that co-localized to marker intervals and previously sequenced Brassica oleracea BAC clones containing known GSL genes (GSL-ALK, GSL-PRO, and GSL-ELONG) were aligned to the genomic sequence, providing support that at least three of our 14 QTLs likely correspond to previously identified GSL loci. The results demonstrate that previously identified loci do not fully explain GSL variation in broccoli. The identification of additional genetic factors influencing the accumulation of GSL in broccoli florets provides novel insight into the regulation of GSL levels in Brassicaceae and will accelerate development of vegetables with modified or enhanced GSL

  7. The stealth episome: suppression of gene expression on the excised genomic island PPHGI-1 from Pseudomonas syringae pv. phaseolicola.

    Directory of Open Access Journals (Sweden)

    Scott A C Godfrey

    2011-03-01

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

  8. A note on sea level variability at Clipperton Island from GEOSAT and in-situ observations

    Science.gov (United States)

    Maul, George A.; Hansen, Donald V.; Bravo, Nicolas J.

    During the 1986-1989 Exact Repeat Mission (ERM) of GEOSAT, in-situ observations of sea level at Clipperton Island (10°N/109°W) and satellite-tracked free-drifting drogued buoys in the eastern tropical Pacific Ocean are concurrently available. A map of the standard deviations of GEOSAT sea surface heights (2.9 years) shows a variance maximum along ˜12°N from Central America, past Clipperton to ˜160°W. Sea floor pressure gauge observations from a shallow (10m depth) site on Clipperton Island and an ERM crossover point in deep water nearby show a correlation of r = 0.76 with a residual of ±6.7 cm RMS. Approximately 17% of the difference (GEOSAT minus sea level) is characterized by a 4 cm amplitude 0° phase annual harmonic, which is probably caused by unaccounted-for tropospheric water vapor affecting the altimeter and/or ERM orbit error removal. Wintertime anticyclonic mesoscale eddies advecting past Clipperton Island each year have GEOSAT sea surface height and in-situ sea level signals of more than 30 cm, some of which are documented by the satellite-tracked drifters. Meridional profiles of the annual harmonic of zonal geostrophic current from GEOSAT and from the drifters both show synchronous maxima in the North Equatorial Countercurrent and the North Equatorial Current. Other Clipperton sea level maxima seen during late spring of each year may involve anticyclonic vortices formed along Central America the previous winter.

  9. Biofilm function and variability in a hydrothermal ecosystem: insights from environmental genomes

    Science.gov (United States)

    Meyer-Dombard, D. R.; Raymond, J.; Shock, E. L.

    2007-12-01

    The ability to adapt to variable environmental conditions is key to survival for all organisms, but may be especially crucial to microorganisms in extreme environments such as hydrothermal systems. Streamer biofilm communities (SBCs) made up of thermophilic chemotrophic microorganisms are common in alkaline-chloride geothermal environments worldwide, but the in situ physiochemical growth parameters and requirements of SBCs are largely unknown [1]. Hot springs in Yellowstone National Park's alkaline geyser basins support SBC growth. However, despite the relative geochemical homogeneity of source pools and widespread ecosystem suitability in these regions (as indicated by energetic profiling [2]), SBCs are not ubiquitous in these ecosystems. The ability of hydrothermal systems to support the growth of SBCs, the relationship between these geochemically driven environments and the microbes that live there, and the function of individuals in these communities are aspects that are adressed here by applying environmental genomics. Analysis of 16S rRNA and total membrane lipid extracts have revealed that community composition of SBCs in "Bison Pool" varies as a function of changing environmental conditions along the outflow channel. In addition, a significant crenarchaeal component was discovered in the "Bison Pool" SBCs. In general, the SBC bacterial diversity triples while the archaeal component varies little (from 3 to 2 genera) in a 5-10°C gradient with distance from the source. While these SBCs are low in overall diversity, the majority of the taxa identified represent uncultured groups of Bacteria and Archaea. As a result, the community function of these taxa and their role in the formation of the biofilms is unknown. However, recent genomic analysis from environmental DNA affords insight into the roles of specific organisms within SBCs at "Bison Pool," and integration of these data with an extensive corresponding geochemical dataset may indicate shifting community

  10. Involvement of β-carbonic anhydrase (β-CA) genes in bacterial genomic islands and horizontal transfer to protists.

    Science.gov (United States)

    Zolfaghari Emameh, Reza; Barker, Harlan R; Hytönen, Vesa P; Parkkila, Seppo

    2018-05-25

    Genomic islands (GIs) are a type of mobile genetic element (MGE) that are present in bacterial chromosomes. They consist of a cluster of genes which produce proteins that contribute to a variety of functions, including, but not limited to, regulation of cell metabolism, anti-microbial resistance, pathogenicity, virulence, and resistance to heavy metals. The genes carried in MGEs can be used as a trait reservoir in times of adversity. Transfer of genes using MGEs, occurring outside of reproduction, is called horizontal gene transfer (HGT). Previous literature has shown that numerous HGT events have occurred through endosymbiosis between prokaryotes and eukaryotes.Beta carbonic anhydrase (β-CA) enzymes play a critical role in the biochemical pathways of many prokaryotes and eukaryotes. We have previously suggested horizontal transfer of β-CA genes from plasmids of some prokaryotic endosymbionts to their protozoan hosts. In this study, we set out to identify β-CA genes that might have transferred between prokaryotic and protist species through HGT in GIs. Therefore, we investigated prokaryotic chromosomes containing β-CA-encoding GIs and utilized multiple bioinformatics tools to reveal the distinct movements of β-CA genes among a wide variety of organisms. Our results identify the presence of β-CA genes in GIs of several medically and industrially relevant bacterial species, and phylogenetic analyses reveal multiple cases of likely horizontal transfer of β-CA genes from GIs of ancestral prokaryotes to protists. IMPORTANCE The evolutionary process is mediated by mobile genetic elements (MGEs), such as genomic islands (GIs). A gene or set of genes in the GIs are exchanged between and within various species through horizontal gene transfer (HGT). Based on the crucial role that GIs can play in bacterial survival and proliferation, they were introduced as the environmental- and pathogen-associated factors. Carbonic anhydrases (CAs) are involved in many critical

  11. Sequence-Based Characterization of Tn5801-Like Genomic Islands in Tetracycline-Resistant Staphylococcus pseudintermedius and Other Gram-positive Bacteria from Humans and Animals

    DEFF Research Database (Denmark)

    de Vries, Lisbeth Elvira; Hasman, Henrik; Jurado Rabadán, Sonia

    2016-01-01

    Antibiotic resistance in pathogens is often associated with mobile genetic elements, such as genomic islands (GI) including integrative and conjugative elements (ICEs). These can transfer resistance genes within and between bacteria from humans and/or animals. The aim of this study was to investi......Antibiotic resistance in pathogens is often associated with mobile genetic elements, such as genomic islands (GI) including integrative and conjugative elements (ICEs). These can transfer resistance genes within and between bacteria from humans and/or animals. The aim of this study......-like GIs appear to be relatively common in tetracycline-resistant S. pseudintermedius in Denmark. Almost identical Tn5801-like GIs were identified in different Gram-positive species of pet and human origin, suggesting that horizontal transfer of these elements has occurred between S. pseudintermedius...

  12. Environmental Literacy in Madeira Island (Portugal): The Influence of Demographic Variables

    Science.gov (United States)

    Spinola, Hélder

    2016-01-01

    Demographic factors are among those that influence environmental literacy and, particularly, environmentally responsible behaviours, either directly or due to an aggregation effect dependent on other types of variables. Present study evaluates a set of demographic variables as predictors for environmental literacy among 9th grade students from…

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

    Energy Technology Data Exchange (ETDEWEB)

    Shah, Bhumika S., E-mail: bhumika.shah@mq.edu.au; Tetu, Sasha G. [Macquarie University, Research Park Drive, Sydney, NSW 2109 (Australia); Harrop, Stephen J. [University of New South Wales, Sydney, NSW 2052 (Australia); Paulsen, Ian T.; Mabbutt, Bridget C. [Macquarie University, Research Park Drive, Sydney, NSW 2109 (Australia)

    2014-09-25

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

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

    International Nuclear Information System (INIS)

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

    2014-01-01

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

  15. The spatial variability of air temperature and nocturnal urban heat island intensity in the city of Brno, Czech Republic

    Directory of Open Access Journals (Sweden)

    Dobrovolný Petr

    2015-09-01

    Full Text Available This study seeks to quantify the effects of a number of factors on the nocturnal air temperature field in a medium-sized central European city located in complex terrain. The main data sources consist of mobile air temperature measurements and a geographical database. Temperature measurements were taken along several profiles through the city centre and were made under a clear sky with no advection. Altogether nine sets of detailed measurements, in all seasons, were assembled. Altitude, quantity of vegetation, density of buildings and the structure of the transportation (road system were considered as explanatory variables. The result is that the normalized difference vegetation index (NDVI and the density of buildings were the most important factors, each of them explaining a substantial part (more than 50% of overall air temperature variability. Mobile measurements with NDVI values as a covariate were used for interpolation of air temperature for the entire study area. The spatial variability of nocturnal air temperature and UHI intensity in Brno is the main output presented. Air temperatures interpolated from mobile measurements and NDVI values indicate that the mean urban heat island (UHI intensity in the early night in summer is at its highest (approximately 5 °C in the city centre and decreases towards the suburban areas.

  16. Malaria early warning tool: linking inter-annual climate and malaria variability in northern Guadalcanal, Solomon Islands.

    Science.gov (United States)

    Smith, Jason; Tahani, Lloyd; Bobogare, Albino; Bugoro, Hugo; Otto, Francis; Fafale, George; Hiriasa, David; Kazazic, Adna; Beard, Grant; Amjadali, Amanda; Jeanne, Isabelle

    2017-11-21

    Malaria control remains a significant challenge in the Solomon Islands. Despite progress made by local malaria control agencies over the past decade, case rates remain high in some areas of the country. Studies from around the world have confirmed important links between climate and malaria transmission. This study focuses on understanding the links between malaria and climate in Guadalcanal, Solomon Islands, with a view towards developing a climate-based monitoring and early warning for periods of enhanced malaria transmission. Climate records were sourced from the Solomon Islands meteorological service (SIMS) and historical malaria case records were sourced from the National Vector-Borne Disease Control Programme (NVBDCP). A declining trend in malaria cases over the last decade associated with improved malaria control was adjusted for. A stepwise regression was performed between climate variables and climate-associated malaria transmission (CMT) at different lag intervals to determine where significant relationships existed. The suitability of these results for use in a three-tiered categorical warning system was then assessed using a Mann-Whitney U test. Of the climate variables considered, only rainfall had a consistently significant relationship with malaria in North Guadalcanal. Optimal lag intervals were determined for prediction using R 2 skill scores. A highly significant negative correlation (R = - 0.86, R 2  = 0.74, p malaria transmission periods in January-June. Cross-validation emphasized the suitability of this relationship for forecasting purposes [Formula: see text]  as did Mann-Whitney U test results showing that rainfall below or above specific thresholds was significantly associated with above or below normal malaria transmission, respectively. This study demonstrated that rainfall provides the best predictor of malaria transmission in North Guadalcanal. This relationship is thought to be underpinned by the unique hydrological conditions

  17. The Variable Regions of Lactobacillus rhamnosus Genomes Reveal the Dynamic Evolution of Metabolic and Host-Adaptation Repertoires.

    Science.gov (United States)

    Ceapa, Corina; Davids, Mark; Ritari, Jarmo; Lambert, Jolanda; Wels, Michiel; Douillard, François P; Smokvina, Tamara; de Vos, Willem M; Knol, Jan; Kleerebezem, Michiel

    2016-07-02

    Lactobacillus rhamnosus is a diverse Gram-positive species with strains isolated from different ecological niches. Here, we report the genome sequence analysis of 40 diverse strains of L. rhamnosus and their genomic comparison, with a focus on the variable genome. Genomic comparison of 40 L. rhamnosus strains discriminated the conserved genes (core genome) and regions of plasticity involving frequent rearrangements and horizontal transfer (variome). The L. rhamnosus core genome encompasses 2,164 genes, out of 4,711 genes in total (the pan-genome). The accessory genome is dominated by genes encoding carbohydrate transport and metabolism, extracellular polysaccharides (EPS) biosynthesis, bacteriocin production, pili production, the cas system, and the associated clustered regularly interspaced short palindromic repeat (CRISPR) loci, and more than 100 transporter functions and mobile genetic elements like phages, plasmid genes, and transposons. A clade distribution based on amino acid differences between core (shared) proteins matched with the clade distribution obtained from the presence-absence of variable genes. The phylogenetic and variome tree overlap indicated that frequent events of gene acquisition and loss dominated the evolutionary segregation of the strains within this species, which is paralleled by evolutionary diversification of core gene functions. The CRISPR-Cas system could have contributed to this evolutionary segregation. Lactobacillus rhamnosus strains contain the genetic and metabolic machinery with strain-specific gene functions required to adapt to a large range of environments. A remarkable congruency of the evolutionary relatedness of the strains' core and variome functions, possibly favoring interspecies genetic exchanges, underlines the importance of gene-acquisition and loss within the L. rhamnosus strain diversification. © The Author(s) 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  18. Genetic variability in MCF-7 sublines: evidence of rapid genomic and RNA expression profile modifications

    International Nuclear Information System (INIS)

    Nugoli, Mélanie; Theillet, Charles; Chuchana, Paul; Vendrell, Julie; Orsetti, Béatrice; Ursule, Lisa; Nguyen, Catherine; Birnbaum, Daniel; Douzery, Emmanuel JP; Cohen, Pascale

    2003-01-01

    Both phenotypic and cytogenetic variability have been reported for clones of breast carcinoma cell lines but have not been comprehensively studied. Despite this, cell lines such as MCF-7 cells are extensively used as model systems. In this work we documented, using CGH and RNA expression profiles, the genetic variability at the genomic and RNA expression levels of MCF-7 cells of different origins. Eight MCF-7 sublines collected from different sources were studied as well as 3 subclones isolated from one of the sublines by limit dilution. MCF-7 sublines showed important differences in copy number alteration (CNA) profiles. Overall numbers of events ranged from 28 to 41. Involved chromosomal regions varied greatly from a subline to another. A total of 62 chromosomal regions were affected by either gains or losses in the 11 sublines studied. We performed a phylogenetic analysis of CGH profiles using maximum parsimony in order to reconstruct the putative filiation of the 11 MCF-7 sublines. The phylogenetic tree obtained showed that the MCF-7 clade was characterized by a restricted set of 8 CNAs and that the most divergent subline occupied the position closest to the common ancestor. Expression profiles of 8 MCF-7 sublines were analyzed along with those of 19 unrelated breast cancer cell lines using home made cDNA arrays comprising 720 genes. Hierarchical clustering analysis of the expression data showed that 7/8 MCF-7 sublines were grouped forming a cluster while the remaining subline clustered with unrelated breast cancer cell lines. These data thus showed that MCF-7 sublines differed at both the genomic and phenotypic levels. The analysis of CGH profiles of the parent subline and its three subclones supported the heteroclonal nature of MCF-7 cells. This strongly suggested that the genetic plasticity of MCF-7 cells was related to their intrinsic capacity to generate clonal heterogeneity. We propose that MCF-7, and possibly the breast tumor it was derived from, evolved

  19. Quantifying the influence of land-use and surface characteristics on spatial variability in the urban heat island

    Science.gov (United States)

    Hart, Melissa A.; Sailor, David J.

    2009-03-01

    The urban thermal environment varies not only from its rural surroundings but also within the urban area due to intra-urban differences in land-use and surface characteristics. Understanding the causes of this intra-urban variability is a first step in improving urban planning and development. Toward this end, a method for quantifying causes of spatial variability in the urban heat island has been developed. This paper presents the method as applied to a specific test case of Portland, Oregon. Vehicle temperature traverses were used to determine spatial differences in summertime ~2 m air temperature across the metropolitan area in the afternoon. A tree-structured regression model was used to quantify the land-use and surface characteristics that have the greatest influence on daytime UHI intensity. The most important urban characteristic separating warmer from cooler regions of the Portland metropolitan area was canopy cover. Roadway area density was also an important determinant of local UHI magnitudes. Specifically, the air above major arterial roads was found to be warmer on weekdays than weekends, possibly due to increased anthropogenic activity from the vehicle sector on weekdays. In general, warmer regions of the city were associated with industrial and commercial land-use. The downtown core, whilst warmer than the rural surroundings, was not the warmest part of the Portland metropolitan area. This is thought to be due in large part to local shading effects in the urban canyons.

  20. Mesophotic bioerosion: Variability and structural impact on U.S. Virgin Island deep reefs

    Science.gov (United States)

    Weinstein, David K.; Smith, Tyler B.; Klaus, James S.

    2014-10-01

    Mesophotic reef corals, found 30-150 m below sea level, build complex structures that provide habitats for diverse ecosystems. Whereas bioerosion is known to impact the development and persistence of shallow reef structures, little is known regarding the extent of mesophotic bioerosion or how it might affect deeper reef geomorphology and carbonate accretion. Originally pristine experimental coral substrates and collected coral rubble were both used to investigate the variation and significance of mesophotic coral reef bioerosion south of St. Thomas, U.S. Virgin Islands. Bioerosion rates were calculated from experimental coral substrates exposed as framework for 1 and 2 years at four structurally distinct mesophotic coral reef habitats (between 30 and 45 m) as well as at a mid-shelf patch reef (21 m) and a shallow fringing patch reef (9 m). The long-term effects of macroboring were assessed by examining coral rubble collected at all sites. Overall, differences in bioerosional processes were found between shallow and mesophotic reefs. Increases in bioerosion on experimental substrates (amount of weight lost) were related to both decreasing seawater depth and increasing biomass of bioeroding parrotfish. Significant differences in coral skeleton bioerosion rates were also found between the transitional mesophotic reef zone (30-35 m) and the upper mesophotic reef zone (35-50 m) after 2 years of exposure, ranging from - 19.6 to 3.7 g/year. Total coral rubble macroboring was greater at most deep sites compared to shallower sites. Bioerosional grazing was found to dominate initial substrate modification in reefs 30.7 m and shallower, but sponges are believed to act as the main time-averaged long-term substrate bioeroders in reefs between 35 and 50 m. Although initial substrate bioerosion rates of a uniform substrate were relatively homogeneous in the 35-50 m depth zone, comparison of site composition suggests that mesophotic bioerosion will vary depending on the amount

  1. Variability of HIV-1 genomes among children and adolescents from Sao Paulo, Brazil.

    Directory of Open Access Journals (Sweden)

    Sabri Saeed Sanabani

    Full Text Available BACKGROUND: Genetic variability is a major feature of the human immunodeficiency virus type 1 (HIV-1 and considered the key factor to frustrating efforts to halt the virus epidemic. In this study, we aimed to investigate the genetic variability of HIV-1 strains among children and adolescents born from 1992 to 2009 in the state of Sao Paulo, Brazil. METHODOLOGY: Plasma and peripheral blood mononuclear cells (PBMC were collected from 51 HIV-1-positive children and adolescents on ART followed between September 1992 and July 2009. After extraction, the genetic materials were used in a polymerase chain reaction (PCR to amplify the viral near full length genomes (NFLGs from 5 overlapped fragments. NFLGs and partial amplicons were directly sequenced and data were phylogenetically inferred. RESULTS: Of the 51 samples studied, the NFLGs and partial fragments of HIV-1 from 42 PBMCs and 25 plasma were successfully subtyped. Results based on proviral DNA revealed that 22 (52.4% patients were infected with subtype B, 16 (38.1% were infected with BF1 mosaic variants and 4 (9.5% were infected with sub-subtype F1. All the BF1 recombinants were unique and distinct from any previously identified unique or circulating recombinant forms in South America. Evidence of dual infections was detected in 3 patients coinfected with the same or distinct HIV-1 subtypes. Ten of the 31 (32.2% and 12 of the 21 (57.1% subjects with recovered proviral and plasma, respectively, protease sequences were infected with major mutants resistant to protease inhibitors. The V3 sequences of 14 patients with available sequences from PBMC/or plasma were predicted to be R5-tropic virus except for two patients who harbored an X4 strain. CONCLUSIONS: The high proportion of HIV-1 BF1 recombinant, coinfection rate and vertical transmission in Brazil merits urgent attention and effective measures to reduce the transmission of HIV among spouses and sex partners.

  2. Length and GC content variability of introns among teleostean genomes in the light of the metabolic rate hypothesis.

    Directory of Open Access Journals (Sweden)

    Ankita Chaurasia

    Full Text Available A comparative analysis of five teleostean genomes, namely zebrafish, medaka, three-spine stickleback, fugu and pufferfish was performed with the aim to highlight the nature of the forces driving both length and base composition of introns (i.e., bpi and GCi. An inter-genome approach using orthologous intronic sequences was carried out, analyzing independently both variables in pairwise comparisons. An average length shortening of introns was observed at increasing average GCi values. The result was not affected by masking transposable and repetitive elements harbored in the intronic sequences. The routine metabolic rate (mass specific temperature-corrected using the Boltzmann's factor was measured for each species. A significant correlation held between average differences of metabolic rate, length and GC content, while environmental temperature of fish habitat was not correlated with bpi and GCi. Analyzing the concomitant effect of both variables, i.e., bpi and GCi, at increasing genomic GC content, a decrease of bpi and an increase of GCi was observed for the significant majority of the intronic sequences (from ∼ 40% to ∼ 90%, in each pairwise comparison. The opposite event, concomitant increase of bpi and decrease of GCi, was counter selected (from <1% to ∼ 10%, in each pairwise comparison. The results further support the hypothesis that the metabolic rate plays a key role in shaping genome architecture and evolution of vertebrate genomes.

  3. Length and GC content variability of introns among teleostean genomes in the light of the metabolic rate hypothesis.

    Science.gov (United States)

    Chaurasia, Ankita; Tarallo, Andrea; Bernà, Luisa; Yagi, Mitsuharu; Agnisola, Claudio; D'Onofrio, Giuseppe

    2014-01-01

    A comparative analysis of five teleostean genomes, namely zebrafish, medaka, three-spine stickleback, fugu and pufferfish was performed with the aim to highlight the nature of the forces driving both length and base composition of introns (i.e., bpi and GCi). An inter-genome approach using orthologous intronic sequences was carried out, analyzing independently both variables in pairwise comparisons. An average length shortening of introns was observed at increasing average GCi values. The result was not affected by masking transposable and repetitive elements harbored in the intronic sequences. The routine metabolic rate (mass specific temperature-corrected using the Boltzmann's factor) was measured for each species. A significant correlation held between average differences of metabolic rate, length and GC content, while environmental temperature of fish habitat was not correlated with bpi and GCi. Analyzing the concomitant effect of both variables, i.e., bpi and GCi, at increasing genomic GC content, a decrease of bpi and an increase of GCi was observed for the significant majority of the intronic sequences (from ∼ 40% to ∼ 90%, in each pairwise comparison). The opposite event, concomitant increase of bpi and decrease of GCi, was counter selected (from hypothesis that the metabolic rate plays a key role in shaping genome architecture and evolution of vertebrate genomes.

  4. The ISLAnds Project. III. Variable Stars in Six Andromeda Dwarf Spheroidal Galaxies

    Science.gov (United States)

    Martínez-Vázquez, Clara E.; Monelli, Matteo; Bernard, Edouard J.; Gallart, Carme; Stetson, Peter B.; Skillman, Evan D.; Bono, Giuseppe; Cassisi, Santi; Fiorentino, Giuliana; McQuinn, Kristen B. W.; Cole, Andrew A.; McConnachie, Alan W.; Martin, Nicolas F.; Dolphin, Andrew E.; Boylan-Kolchin, Michael; Aparicio, Antonio; Hidalgo, Sebastian L.; Weisz, Daniel R.

    2017-12-01

    We present a census of variable stars in six M31 dwarf spheroidal satellites observed with the Hubble Space Telescope. We detect 870 RR Lyrae (RRL) stars in the fields of And I (296), II (251), III (111), XV (117), XVI (8), and XXVIII (87). We also detect a total of 15 Anomalous Cepheids, three eclipsing binaries, and seven field RRL stars compatible with being members of the M31 halo or the Giant Stellar Stream. We derive robust and homogeneous distances to the six galaxies using different methods based on the properties of the RRL stars. Working with the up-to-date set of Period-Wesenheit (I, B-I) relations published by Marconi et al., we obtain distance moduli of μ 0 = [24.49, 24.16, 24.36, 24.42, 23.70, 24.43] mag (respectively), with systematic uncertainties of 0.08 mag and statistical uncertainties <0.11 mag. We have considered an enlarged sample of 16 M31 satellites with published variability studies, and compared their pulsational observables (e.g., periods and amplitudes) with those of 15 Milky Way satellites for which similar data are available. The properties of the (strictly old) RRL in both satellite systems do not show any significant difference. In particular, we found a strikingly similar correlation between the mean period distribution of the fundamental RRL pulsators (RRab) and the mean metallicities of the galaxies. This indicates that the old RRL progenitors were similar at the early stage in the two environments, suggesting very similar characteristics for the earliest stages of evolution of both satellite systems. Based on observations made with the NASA/ESA Hubble Space Telescope, obtained at the Space Telescope Science Institute, which is operated by the Association of Universities for Research in Astronomy, Inc., under NASA contract NAS 5-26555. These observations are associated with programs 13028 and 13739.

  5. Temporal variability of atmospheric radon-222 concentration at Gosan Station, Jeju Island, Korea, during 2009-2013

    Energy Technology Data Exchange (ETDEWEB)

    Song, Jung Min; Kim, Won Hyung; Kang, Chang Hee [Dept. of Chemistry, Jeju National University, Jeju (Korea, Republic of); Lee, Hae Young; Lee, Chul Kyu [Korea Global Atmosphere Watch Center, Korea Meteorological Administration, ChungNam (Korea, Republic of); Chambers, S.; Williams, A. G. [Australian Nuclear Science and Technology Organisation, Kirrawee DC (Australia)

    2015-02-15

    Atmospheric radon-222 (radon) measurements were made from 2009 to 2013 at the Gosan station of Jeju Island, one of the cleanest regions in Korea, in order to characterize the temporal variability (on diurnal, seasonal, and annual scales) and analyze the influence of changing air mass transport pathways on observed radon concentrations. The mean hourly radon concentration over the whole period was 2441 ± 1037 mBq/m{sup 3}. The seasonal cycle of radon at the Gosan station was characterized by a fall maximum and summer minimum, consistent with a reduction in nonfrozen terrestrial fetch from fall to summer. In order, the seasonal mean radon concentrations were 2962 mBq/m{sup 3} (fall) >2907 mBq/m{sup 3} (winter) >2219 mBq/m{sup 3} (spring) >1756 mBq/m{sup 3} (summer). Based on a 5-year composite, the maximum mean monthly radon concentration in October (3100 mBq/m{sup 3}) was more than twice the July minimum (1471 mBq/m{sup 3}). Diurnal composite radon concentrations for the whole period increased throughout the night to a maximum of 2788 mBq/m{sup 3} at around 7 a.m., and then gradually decreased to a minimum of 2050 mBq/m{sup 3} at around 3 p.m. The winter diurnal cycle had a small amplitude due to the low variability in atmospheric mixing depth associated with recent air mass fetch over the Yellow Sea. The diurnal cycle in summer, however, exhibited a relatively large amplitude due to changes in atmospheric mixing depth associated with recent fetch over Jeju Island. Back trajectory analysis showed that high radon events were typically associated with long-term air mass fetch over continental Asia. Specifically, the average radon concentration of air masses originating from China was about 2.4 times higher than that of air masses originating from the North Pacific Ocean.

  6. Temporal variability of atmospheric radon-222 concentration at Gosan Station, Jeju Island, Korea, during 2009-2013

    International Nuclear Information System (INIS)

    Song, Jung Min; Kim, Won Hyung; Kang, Chang Hee; Lee, Hae Young; Lee, Chul Kyu; Chambers, S.; Williams, A. G.

    2015-01-01

    Atmospheric radon-222 (radon) measurements were made from 2009 to 2013 at the Gosan station of Jeju Island, one of the cleanest regions in Korea, in order to characterize the temporal variability (on diurnal, seasonal, and annual scales) and analyze the influence of changing air mass transport pathways on observed radon concentrations. The mean hourly radon concentration over the whole period was 2441 ± 1037 mBq/m"3. The seasonal cycle of radon at the Gosan station was characterized by a fall maximum and summer minimum, consistent with a reduction in nonfrozen terrestrial fetch from fall to summer. In order, the seasonal mean radon concentrations were 2962 mBq/m"3 (fall) >2907 mBq/m"3 (winter) >2219 mBq/m"3 (spring) >1756 mBq/m"3 (summer). Based on a 5-year composite, the maximum mean monthly radon concentration in October (3100 mBq/m"3) was more than twice the July minimum (1471 mBq/m"3). Diurnal composite radon concentrations for the whole period increased throughout the night to a maximum of 2788 mBq/m"3 at around 7 a.m., and then gradually decreased to a minimum of 2050 mBq/m"3 at around 3 p.m. The winter diurnal cycle had a small amplitude due to the low variability in atmospheric mixing depth associated with recent air mass fetch over the Yellow Sea. The diurnal cycle in summer, however, exhibited a relatively large amplitude due to changes in atmospheric mixing depth associated with recent fetch over Jeju Island. Back trajectory analysis showed that high radon events were typically associated with long-term air mass fetch over continental Asia. Specifically, the average radon concentration of air masses originating from China was about 2.4 times higher than that of air masses originating from the North Pacific Ocean

  7. The Arsenic Resistance-Associated Listeria Genomic Island LGI2 Exhibits Sequence and Integration Site Diversity and a Propensity for Three Listeria monocytogenes Clones with Enhanced Virulence.

    Science.gov (United States)

    Lee, Sangmi; Ward, Todd J; Jima, Dereje D; Parsons, Cameron; Kathariou, Sophia

    2017-11-01

    In the foodborne pathogen Listeria monocytogenes , arsenic resistance is encountered primarily in serotype 4b clones considered to have enhanced virulence and is associated with an arsenic resistance gene cluster within a 35-kb chromosomal region, Listeria genomic island 2 (LGI2). LGI2 was first identified in strain Scott A and includes genes putatively involved in arsenic and cadmium resistance, DNA integration, conjugation, and pathogenicity. However, the genomic localization and sequence content of LGI2 remain poorly characterized. Here we investigated 85 arsenic-resistant L. monocytogenes strains, mostly of serotype 4b. All but one of the 70 serotype 4b strains belonged to clonal complex 1 (CC1), CC2, and CC4, three major clones associated with enhanced virulence. PCR analysis suggested that 53 strains (62.4%) harbored an island highly similar to LGI2 of Scott A, frequently (42/53) in the same location as Scott A ( LMOf2365_2257 homolog). Random-primed PCR and whole-genome sequencing revealed seven novel insertion sites, mostly internal to chromosomal coding sequences, among strains harboring LGI2 outside the LMOf2365_2257 homolog. Interestingly, many CC1 strains harbored a noticeably diversified LGI2 (LGI2-1) in a unique location ( LMOf2365_0902 homolog) and with a novel additional gene. With few exceptions, the tested LGI2 genes were not detected in arsenic-resistant strains of serogroup 1/2, which instead often harbored a Tn 554 -associated arsenic resistance determinant not encountered in serotype 4b. These findings indicate that in L. monocytogenes , LGI2 has a propensity for certain serotype 4b clones, exhibits content diversity, and is highly promiscuous, suggesting an ability to mobilize various accessory genes into diverse chromosomal loci. IMPORTANCE Listeria monocytogenes is widely distributed in the environment and causes listeriosis, a foodborne disease with high mortality and morbidity. Arsenic and other heavy metals can powerfully shape the

  8. Genomes

    National Research Council Canada - National Science Library

    Brown, T. A. (Terence A.)

    2002-01-01

    ... of genome expression and replication processes, and transcriptomics and proteomics. This text is richly illustrated with clear, easy-to-follow, full color diagrams, which are downloadable from the book's website...

  9. To be so bold: boldness is repeatable and related to within individual behavioural variability in North Island robins.

    Science.gov (United States)

    He, Ruchuan; Pagani-Núñez, Emilio; Chevallier, Clément; Barnett, Craig R A

    2017-07-01

    Behavioural research traditionally focusses on the mean responses of a group of individuals rather than variation in behaviour around the mean or among individuals. However, examining the variation in behaviour among and within individuals may also yield important insights into the evolution and maintenance of behaviour. Repeatability is the most commonly used measure of variability among individuals in behavioural research. However, there are other forms of variation within populations that have received less attention. One such measure is intraindividual variation in behaviour (IIV), which is a short-term fluctuation of within-individual behaviour. Such variation in behaviour might be important during interactions because it could decrease the ability of conspecific and heterospecific individuals to predict the behaviour of the subject, thus increasing the cost of the interaction. In this experiment, we made repeated measures of the latency of North Island robins to attack a prey in a novel situation (a form of boldness) and examined (i) repeatability of boldness (the propensity to take a risk), (ii) IIV of boldness, and (iii) whether there was a significant relationship between these two traits (a behavioural syndrome). We found that boldness was highly repeatable, that there were high levels of IIV in boldness, and that there was a negative relationship between boldness and IIV in boldness. This suggests that despite high levels of repeatability for this behaviour, there were also still significant differences in IIV among different individuals within the population. Moreover, bolder individuals had significantly less IIV in their boldness, which suggests that they were forming routines (which reduces behavioural variability) compared to shyer individuals. Our results definitively demonstrate that IIV itself varies across individuals and is linked with key behavioural traits, and we argue for the importance of future studies aimed at understanding its causes

  10. South pacific climate variability and its impact on low-lying islands

    Directory of Open Access Journals (Sweden)

    1998-01-01

    Full Text Available VARIABILITE CLIMATIQUE DU SUD PACIFIQUE ET SES IMPACTS SUR LES ILES BASSES. L’environnement climatique du Pacifique sud est conditionné par “l’extrême océanité” de la région et l’interaction étroite entre l’atmosphère et l’océan qui conditionne la vie et l’ensemble des paramètres environnementaux des pays insulaires. Les deux principaux phénomènes climatiques qui affectent la région sont : ENSO ( El Niño - Southern Oscillation et le réchauffement global. Ces deux signaux climatiques, facteurs principaux de la variabilité climatique du Pacifique, font sentir leur action sur l’élévation du niveau moyen de l’océan qui, à terme, peut mettre en cause l’existence même de certains archipels, sur les modifications de la vie océanique et de son exploitation, sur la fréquence et l’intensité des cyclones, sur l’alternance des sécheresses et des périodes humides, sur la production agricole, et sur la santé des lagons et des formations récifales. VARIABILIDAD CLIMÁTICA EN EL PACÍFICO SUR Y SU IMPACTO EN ISLAS BAJAS. El medio ambiente climático de la región del Pacífico Sur se caracteriza por la interacción intensa del océano y la atmósfera, la cual impacta la vida y otros parámetros medioambientales de la región. Dos fenómenos principales están condicionando la variabilidad climática de la región: El Niño y la Oscilación del Sur (ENSO y el Calentamiento Global. Estos dos componentes del cambio climático están afectando la elevación del nivel del mar, la vida en el océano, la frecuencia e intensidad de los huracanes, la ocurrencia de sequías e inundaciones, la potencialidad agrícola, la salud de las regiones costeras incluyendo lagunas y arrecifes. The climatic environment of the South Pacific region is characterized by the intense ocean atmosphere interaction which impacts the life and other environmental parameters of the region. Two main phenomenons are conditioning the climate variability of

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

    Science.gov (United States)

    Putonti, Catherine; Nowicki, Bogdan; Shaffer, Michael; Fofanov, Yuriy; Nowicki, Stella

    2013-09-04

    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. 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. 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

  12. Integration of the blaNDM-1 carbapenemase gene into Proteus genomic island 1 (PGI1-PmPEL) in a Proteus mirabilis clinical isolate.

    Science.gov (United States)

    Girlich, Delphine; Dortet, Laurent; Poirel, Laurent; Nordmann, Patrice

    2015-01-01

    To decipher the mechanisms and their associated genetic determinants responsible for β-lactam resistance in a Proteus mirabilis clinical isolate. The entire genetic structure surrounding the β-lactam resistance genes was characterized by PCR, gene walking and DNA sequencing. Genes encoding the carbapenemase NDM-1 and the ESBL VEB-6 were located in a 38.5 kb MDR structure, which itself was inserted into a new variant of the Proteus genomic island 1 (PGI1). This new PGI1-PmPEL variant of 64.4 kb was chromosomally located, as an external circular form in the P. mirabilis isolate, suggesting potential mobility. This is the first known description of the bla(NDM-1) gene in a genomic island structure, which might further enhance the spread of the bla(NDM-1) carbapenemase gene among enteric pathogens. © The Author 2014. Published by Oxford University Press on behalf of the British Society for Antimicrobial Chemotherapy. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  13. Variability of morphometric caracteristics of one-year seedlings of different half-sib European White Elm (Ulmus effusa Wild. from the Great War Island

    Directory of Open Access Journals (Sweden)

    Devetaković, J.

    2013-12-01

    Full Text Available European White Elm is recognized as a rare and endangered species in the forest fund of the Republic of Serbia. During the past century massive drying of elms occurred and the indications of their extinction appeared, which consequently led to a reduction in genetic diversity and the danger of genetic drift. In the area of the Great War Island near Belgrade we found 56 trees of European White Elm that are spatially divided into three subpopulations. In order to assess the genetic potential of European White Elm in the Great War Island and to define adequate conservation measures variability of 14 selected test trees progeny was rated. Results shows that the satisfactory variability within the popoulation exists, which is a good basis for the conservation of genepool available.

  14. Comparative Genomics Reveals High Genomic Diversity in the Genus Photobacterium.

    Science.gov (United States)

    Machado, Henrique; Gram, Lone

    2017-01-01

    Vibrionaceae is a large marine bacterial family, which can constitute up to 50% of the prokaryotic population in marine waters. Photobacterium is the second largest genus in the family and we used comparative genomics on 35 strains representing 16 of the 28 species described so far, to understand the genomic diversity present in the Photobacterium genus. Such understanding is important for ecophysiology studies of the genus. We used whole genome sequences to evaluate phylogenetic relationships using several analyses (16S rRNA, MLSA, fur , amino-acid usage, ANI), which allowed us to identify two misidentified strains. Genome analyses also revealed occurrence of higher and lower GC content clades, correlating with phylogenetic clusters. Pan- and core-genome analysis revealed the conservation of 25% of the genome throughout the genus, with a large and open pan-genome. The major source of genomic diversity could be traced to the smaller chromosome and plasmids. Several of the physiological traits studied in the genus did not correlate with phylogenetic data. Since horizontal gene transfer (HGT) is often suggested as a source of genetic diversity and a potential driver of genomic evolution in bacterial species, we looked into evidence of such in Photobacterium genomes. Genomic islands were the source of genomic differences between strains of the same species. Also, we found transposase genes and CRISPR arrays that suggest multiple encounters with foreign DNA. Presence of genomic exchange traits was widespread and abundant in the genus, suggesting a role in genomic evolution. The high genetic variability and indications of genetic exchange make it difficult to elucidate genome evolutionary paths and raise the awareness of the roles of foreign DNA in the genomic evolution of environmental organisms.

  15. r2VIM: A new variable selection method for random forests in genome-wide association studies.

    Science.gov (United States)

    Szymczak, Silke; Holzinger, Emily; Dasgupta, Abhijit; Malley, James D; Molloy, Anne M; Mills, James L; Brody, Lawrence C; Stambolian, Dwight; Bailey-Wilson, Joan E

    2016-01-01

    Machine learning methods and in particular random forests (RFs) are a promising alternative to standard single SNP analyses in genome-wide association studies (GWAS). RFs provide variable importance measures (VIMs) to rank SNPs according to their predictive power. However, in contrast to the established genome-wide significance threshold, no clear criteria exist to determine how many SNPs should be selected for downstream analyses. We propose a new variable selection approach, recurrent relative variable importance measure (r2VIM). Importance values are calculated relative to an observed minimal importance score for several runs of RF and only SNPs with large relative VIMs in all of the runs are selected as important. Evaluations on simulated GWAS data show that the new method controls the number of false-positives under the null hypothesis. Under a simple alternative hypothesis with several independent main effects it is only slightly less powerful than logistic regression. In an experimental GWAS data set, the same strong signal is identified while the approach selects none of the SNPs in an underpowered GWAS. The novel variable selection method r2VIM is a promising extension to standard RF for objectively selecting relevant SNPs in GWAS while controlling the number of false-positive results.

  16. Dynamics of chromosome number and genome size variation in a cytogenetically variable sedge (Carex scoparia var. scoparia, Cyperaceae).

    Science.gov (United States)

    Chung, Kyong-Sook; Weber, Jaime A; Hipp, Andrew L

    2011-01-01

    High intraspecific cytogenetic variation in the sedge genus Carex (Cyperaceae) is hypothesized to be due to the "diffuse" or non-localized centromeres, which facilitate chromosome fission and fusion. If chromosome number changes are dominated by fission and fusion, then chromosome evolution will result primarily in changes in the potential for recombination among populations. Chromosome duplications, on the other hand, entail consequent opportunities for divergent evolution of paralogs. In this study, we evaluate whether genome size and chromosome number covary within species. We used flow cytometry to estimate genome sizes in Carex scoparia var. scoparia, sampling 99 plants (23 populations) in the Chicago region, and we used meiotic chromosome observations to document chromosome numbers and chromosome pairing relations. Chromosome numbers range from 2n = 62 to 2n = 68, and nuclear DNA 1C content from 0.342 to 0.361 pg DNA. Regressions of DNA content on chromosome number are nonsignificant for data analyzed by individual or population, and a regression model that excludes slope is favored over a model in which chromosome number predicts genome size. Chromosome rearrangements within cytogenetically variable Carex species are more likely a consequence of fission and fusion than of duplication and deletion. Moreover, neither genome size nor chromosome number is spatially autocorrelated, which suggests the potential for rapid chromosome evolution by fission and fusion at a relatively fine geographic scale (<350 km). These findings have important implications for ecological restoration and speciation within the largest angiosperm genus of the temperate zone.

  17. Single genome retrieval of context-dependent variability in mutation rates for human germline.

    Science.gov (United States)

    Sahakyan, Aleksandr B; Balasubramanian, Shankar

    2017-01-13

    Accurate knowledge of the core components of substitution rates is of vital importance to understand genome evolution and dynamics. By performing a single-genome and direct analysis of 39,894 retrotransposon remnants, we reveal sequence context-dependent germline nucleotide substitution rates for the human genome. The rates are characterised through rate constants in a time-domain, and are made available through a dedicated program (Trek) and a stand-alone database. Due to the nature of the method design and the imposed stringency criteria, we expect our rate constants to be good estimates for the rates of spontaneous mutations. Benefiting from such data, we study the short-range nucleotide (up to 7-mer) organisation and the germline basal substitution propensity (BSP) profile of the human genome; characterise novel, CpG-independent, substitution prone and resistant motifs; confirm a decreased tendency of moieties with low BSP to undergo somatic mutations in a number of cancer types; and, produce a Trek-based estimate of the overall mutation rate in human. The extended set of rate constants we report may enrich our resources and help advance our understanding of genome dynamics and evolution, with possible implications for the role of spontaneous mutations in the emergence of pathological genotypes and neutral evolution of proteomes.

  18. Calibration of multivariate scatter plots for exploratory analysis of relations within and between sets of variables in genomic research.

    Science.gov (United States)

    Graffelman, Jan; van Eeuwijk, Fred

    2005-12-01

    The scatter plot is a well known and easily applicable graphical tool to explore relationships between two quantitative variables. For the exploration of relations between multiple variables, generalisations of the scatter plot are useful. We present an overview of multivariate scatter plots focussing on the following situations. Firstly, we look at a scatter plot for portraying relations between quantitative variables within one data matrix. Secondly, we discuss a similar plot for the case of qualitative variables. Thirdly, we describe scatter plots for the relationships between two sets of variables where we focus on correlations. Finally, we treat plots of the relationships between multiple response and predictor variables, focussing on the matrix of regression coefficients. We will present both known and new results, where an important original contribution concerns a procedure for the inclusion of scales for the variables in multivariate scatter plots. We provide software for drawing such scales. We illustrate the construction and interpretation of the plots by means of examples on data collected in a genomic research program on taste in tomato.

  19. High-quality draft genome sequence of Ensifer meliloti Mlalz-1, a microsymbiont of Medicago laciniata (L.) miller collected in Lanzarote, Canary Islands, Spain.

    Science.gov (United States)

    Osman, Wan Adnawani Meor; van Berkum, Peter; León-Barrios, Milagros; Velázquez, Encarna; Elia, Patrick; Tian, Rui; Ardley, Julie; Gollagher, Margaret; Seshadri, Rekha; Reddy, T B K; Ivanova, Natalia; Woyke, Tanja; Pati, Amrita; Markowitz, Victor; Baeshen, Mohamed N; Baeshen, Naseebh Nabeeh; Kyrpides, Nikos; Reeve, Wayne

    2017-01-01

    10.1601/nm.1335 Mlalz-1 (INSDC = ATZD00000000) is an aerobic, motile, Gram-negative, non-spore-forming rod that was isolated from an effective nitrogen-fixing nodule of Medicago laciniata (L.) Miller from a soil sample collected near the town of Guatiza on the island of Lanzarote, the Canary Islands, Spain. This strain nodulates and forms an effective symbiosis with the highly specific host M. laciniata . This rhizobial genome was sequenced as part of the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) sequencing project. Here the features of 10.1601/nm.1335 Mlalz-1 are described, together with high-quality permanent draft genome sequence information and annotation. The 6,664,116 bp high-quality draft genome is arranged in 99 scaffolds of 100 contigs, containing 6314 protein-coding genes and 74 RNA-only encoding genes. Strain Mlalz-1 is closely related to 10.1601/nm.1335 10.1601/strainfinder?urlappend=%3Fid%3DIAM+12611 T , 10.1601/nm.1334 A 321 T and 10.1601/nm.17831 10.1601/strainfinder?urlappend=%3Fid%3DORS+1407 T , based on 16S rRNA gene sequences. gANI values of ≥98.1% support the classification of strain Mlalz-1 as 10.1601/nm.1335. Nodulation of M. laciniata requires a specific nodC allele, and the nodC gene of strain Mlalz-1 shares ≥98% sequence identity with nodC of M. laciniata -nodulating 10.1601/nm.1328 strains, but ≤93% with nodC of 10.1601/nm.1328 strains that nodulate other Medicago species. Strain Mlalz-1 is unique among sequenced 10.1601/nm.1335 strains in possessing genes encoding components of a T2SS and in having two versions of the adaptive acid tolerance response lpiA-acvB operon. In 10.1601/nm.1334 strain 10.1601/strainfinder?urlappend=%3Fid%3DWSM+419, lpiA is essential for enhancing survival in lethal acid conditions. The second copy of the lpiA-acvB operon of strain Mlalz-1 has highest sequence identity (> 96%) with that of 10.1601/nm.1334 strains, which suggests genetic

  20. Recombination events and variability among full-length genomes of co-circulating molluscum contagiosum virus subtypes 1 and 2.

    Science.gov (United States)

    López-Bueno, Alberto; Parras-Moltó, Marcos; López-Barrantes, Olivia; Belda, Sylvia; Alejo, Alí

    2017-05-01

    Molluscum contagiosum virus (MCV) is the sole member of the Molluscipoxvirus genus and causes a highly prevalent human disease of the skin characterized by the formation of a variable number of lesions that can persist for prolonged periods of time. Two major genotypes, subtype 1 and subtype 2, are recognized, although currently only a single complete genomic sequence corresponding to MCV subtype 1 is available. Using next-generation sequencing techniques, we report the complete genomic sequence of four new MCV isolates, including the first one derived from a subtype 2. Comparisons suggest a relatively distant evolutionary split between both MCV subtypes. Further, our data illustrate concurrent circulation of distinct viruses within a population and reveal the existence of recombination events among them. These results help identify a set of MCV genes with potentially relevant roles in molluscum contagiosum epidemiology and pathogenesis.

  1. Depauperate genetic variability detected in the American and European bison using genomic techniques

    DEFF Research Database (Denmark)

    Pertoldi, Cino; Tokarska, Magorzata; Wójcik, Jan M

    2009-01-01

    , likely reflecting drift overwhelming selection. We suggest that utilization of genome-wide screening technologies, followed by utilization of less expensive techniques (e.g. VeraCode and Fluidigm EP1), holds large potential for genetic monitoring of populations. Additionally, these techniques will allow...

  2. OI-57, a Genomic Island of Escherichia coli O157, Is Present in Other Seropathotypes of Shiga Toxin-Producing E. coli Associated with Severe Human Disease▿

    Science.gov (United States)

    Imamovic, Lejla; Tozzoli, Rosangela; Michelacci, Valeria; Minelli, Fabio; Marziano, Maria Luisa; Caprioli, Alfredo; Morabito, Stefano

    2010-01-01

    Strains of Shiga toxin-producing Escherichia coli (STEC) are a heterogeneous E. coli group that may cause severe disease in humans. STEC have been categorized into seropathotypes (SPTs) based on their phenotypic and molecular characteristics and the clinical features of the associated diseases. SPTs range from A to E, according to a decreasing rank of pathogenicity. To define the virulence gene asset (“virulome”) characterizing the highly pathogenic SPTs, we used microarray hybridization to compare the whole genomes of STEC belonging to SPTs B, C, and D with that of STEC O157 (SPT A). The presence of the open reading frames (ORFs) associated with SPTs A and B was subsequently investigated by PCR in a larger panel of STEC and in other E. coli strains. A genomic island termed OI-57 was present in SPTs A and B but not in the other SPTs. OI-57 harbors the putative virulence gene adfO, encoding a factor enhancing the adhesivity of STEC O157, and ckf, encoding a putative killing factor for the bacterial cell. PCR analyses showed that OI-57 was present in its entirety in the majority of the STEC genomes examined, indicating that it represents a stable acquisition of the positive clonal lineages. OI-57 was also present in a high proportion of the human enteropathogenic E. coli genomes assayed, suggesting that it could be involved in the attaching-and-effacing colonization of the intestinal mucosa. In conclusion, OI-57 appears to be part of the virulome of pathogenic STEC and further studies are needed to elucidate its role in the pathogenesis of STEC infections. PMID:20823207

  3. A novel program to design siRNAs simultaneously effective to highly variable virus genomes.

    Science.gov (United States)

    Lee, Hui Sun; Ahn, Jeonghyun; Jun, Eun Jung; Yang, Sanghwa; Joo, Chul Hyun; Kim, Yoo Kyum; Lee, Heuiran

    2009-07-10

    A major concern of antiviral therapy using small interfering RNAs (siRNAs) targeting RNA viral genome is high sequence diversity and mutation rate due to genetic instability. To overcome this problem, it is indispensable to design siRNAs targeting highly conserved regions. We thus designed CAPSID (Convenient Application Program for siRNA Design), a novel bioinformatics program to identify siRNAs targeting highly conserved regions within RNA viral genomes. From a set of input RNAs of diverse sequences, CAPSID rapidly searches conserved patterns and suggests highly potent siRNA candidates in a hierarchical manner. To validate the usefulness of this novel program, we investigated the antiviral potency of universal siRNA for various Human enterovirus B (HEB) serotypes. Assessment of antiviral efficacy using Hela cells, clearly demonstrates that HEB-specific siRNAs exhibit protective effects against all HEBs examined. These findings strongly indicate that CAPSID can be applied to select universal antiviral siRNAs against highly divergent viral genomes.

  4. Genetic variability, local selection and demographic history: genomic evidence of evolving towards allopatric speciation in Asian seabass.

    Science.gov (United States)

    Wang, Le; Wan, Zi Yi; Lim, Huan Sein; Yue, Gen Hua

    2016-08-01

    Genomewide analysis of genetic divergence is critically important in understanding the genetic processes of allopatric speciation. We sequenced RAD tags of 131 Asian seabass individuals of six populations from South-East Asia and Australia/Papua New Guinea. Using 32 433 SNPs, we examined the genetic diversity and patterns of population differentiation across all the populations. We found significant evidence of genetic heterogeneity between South-East Asian and Australian/Papua New Guinean populations. The Australian/Papua New Guinean populations showed a rather lower level of genetic diversity. FST and principal components analysis revealed striking divergence between South-East Asian and Australian/Papua New Guinean populations. Interestingly, no evidence of contemporary gene flow was observed. The demographic history was further tested based on the folded joint site frequency spectrum. The scenario of ancient migration with historical population size changes was suggested to be the best fit model to explain the genetic divergence of Asian seabass between South-East Asia and Australia/Papua New Guinea. This scenario also revealed that Australian/Papua New Guinean populations were founded by ancestors from South-East Asia during mid-Pleistocene and were completely isolated from the ancestral population after the last glacial retreat. We also detected footprints of local selection, which might be related to differential ecological adaptation. The ancient gene flow was examined and deemed likely insufficient to counteract the genetic differentiation caused by genetic drift. The observed genomic pattern of divergence conflicted with the 'genomic islands' scenario. Altogether, Asian seabass have likely been evolving towards allopatric speciation since the split from the ancestral population during mid-Pleistocene. © 2016 John Wiley & Sons Ltd.

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

    Science.gov (United States)

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

    2015-10-15

    The genomic island SGI1 and its variants, the important vehicles of multi-resistance in Salmonella strains, are integrative elements mobilized exclusively by the conjugative IncA/C plasmids. Integration and excision of the island are carried out by the SGI1-encoded site-specific recombinase Int and the recombination directionality factor Xis. Chromosomal integration ensures the stable maintenance and vertical transmission of SGI1, while excision is the initial step of horizontal transfer, followed by conjugation and integration into the recipient. We report here that SGI1 not only exploits the conjugal apparatus of the IncA/C plasmids but also utilizes the regulatory mechanisms of the conjugation system for the exact timing and activation of excision to ensure efficient horizontal transfer. This study demonstrates that the FlhDC-family activator AcaCD, which regulates the conjugation machinery of the IncA/C plasmids, serves as a signal of helper entry through binding to SGI1 xis promoter and activating SGI1 excision. Promoters of int and xis genes have been identified and the binding site of the activator has been located by footprinting and deletion analyses. We prove that expression of xis is activator-dependent while int is constitutively expressed, and this regulatory mechanism is presumably responsible for the efficient transfer and stable maintenance of SGI1. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

  6. Comparative Analysis Highlights Variable Genome Content of Wheat Rusts and Divergence of the Mating Loci

    Directory of Open Access Journals (Sweden)

    Christina A. Cuomo

    2017-02-01

    Full Text Available Three members of the Puccinia genus, Puccinia triticina (Pt, P. striiformis f.sp. tritici (Pst, and P. graminis f.sp. tritici (Pgt, cause the most common and often most significant foliar diseases of wheat. While similar in biology and life cycle, each species is uniquely adapted and specialized. The genomes of Pt and Pst were sequenced and compared to that of Pgt to identify common and distinguishing gene content, to determine gene variation among wheat rust pathogens, other rust fungi, and basidiomycetes, and to identify genes of significance for infection. Pt had the largest genome of the three, estimated at 135 Mb with expansion due to mobile elements and repeats encompassing 50.9% of contig bases; in comparison, repeats occupy 31.5% for Pst and 36.5% for Pgt. We find all three genomes are highly heterozygous, with Pst [5.97 single nucleotide polymorphisms (SNPs/kb] nearly twice the level detected in Pt (2.57 SNPs/kb and that previously reported for Pgt. Of 1358 predicted effectors in Pt, 784 were found expressed across diverse life cycle stages including the sexual stage. Comparison to related fungi highlighted the expansion of gene families involved in transcriptional regulation and nucleotide binding, protein modification, and carbohydrate degradation enzymes. Two allelic homeodomain pairs, HD1 and HD2, were identified in each dikaryotic Puccinia species along with three pheromone receptor (STE3 mating-type genes, two of which are likely representing allelic specificities. The HD proteins were active in a heterologous Ustilago maydis mating assay and host-induced gene silencing (HIGS of the HD and STE3 alleles reduced wheat host infection.

  7. Demethylation by 5-aza-2'-deoxycytidine in colorectal cancer cells targets genomic DNA whilst promoter CpG island methylation persists

    International Nuclear Information System (INIS)

    Mossman, David; Kim, Kyu-Tae; Scott, Rodney J

    2010-01-01

    DNA methylation and histone acetylation are epigenetic modifications that act as regulators of gene expression. Aberrant epigenetic gene silencing in tumours is a frequent event, yet the factors which dictate which genes are targeted for inactivation are unknown. DNA methylation and histone acetylation can be modified with the chemical agents 5-aza-2'-deoxycytidine (5-aza-dC) and Trichostatin A (TSA) respectively. The aim of this study was to analyse de-methylation and re-methylation and its affect on gene expression in colorectal cancer cell lines treated with 5-aza-dC alone and in combination with TSA. We also sought to identify methylation patterns associated with long term reactivation of previously silenced genes. Colorectal cancer cell lines were treated with 5-aza-dC, with and without TSA, to analyse global methylation decreases by High Performance Liquid Chromatography (HPLC). Re-methylation was observed with removal of drug treatments. Expression arrays identified silenced genes with differing patterns of expression after treatment, such as short term reactivation or long term reactivation. Sodium bisulfite sequencing was performed on the CpG island associated with these genes and expression was verified with real time PCR. Treatment with 5-aza-dC was found to affect genomic methylation and to a lesser extent gene specific methylation. Reactivated genes which remained expressed 10 days post 5-aza-dC treatment featured hypomethylated CpG sites adjacent to the transcription start site (TSS). In contrast, genes with uniformly hypermethylated CpG islands were only temporarily reactivated. These results imply that 5-aza-dC induces strong de-methylation of the genome and initiates reactivation of transcriptionally inactive genes, but this does not require gene associated CpG island de-methylation to occur. In addition, for three of our selected genes, hypomethylation at the TSS of an epigenetically silenced gene is associated with the long term reversion of

  8. Genome-wide analysis of differential transcriptional and epigenetic variability across human immune cell types

    DEFF Research Database (Denmark)

    Ecker, Simone; Chen, Lu; Pancaldi, Vera

    2017-01-01

    Background: A healthy immune system requires immune cells that adapt rapidly to environmental challenges. This phenotypic plasticity can be mediated by transcriptional and epigenetic variability. Results: We apply a novel analytical approach to measure and compare transcriptional and epigenetic v...

  9. Microdiversification of a Pelagic Polynucleobacter Species Is Mainly Driven by Acquisition of Genomic Islands from a Partially Interspecific Gene Pool

    Czech Academy of Sciences Publication Activity Database

    Hoetzinger, M.; Schmidt, J.; Jezberová, Jitka; Koll, U.; Hahn, M.W.

    2017-01-01

    Roč. 83, č. 3 (2017), č. článku e02266-16. ISSN 0099-2240 Institutional support: RVO:60077344 Keywords : Polynucleobacter * ecophysiology * environmental genomics * functional diversity Subject RIV: EE - Microbiology, Virology OBOR OECD: Microbiology Impact factor: 3.807, year: 2016

  10. Klebsiella pneumoniae asparagine tDNAs are integration hotspots for different genomic islands encoding microcin E492 production determinants and other putative virulence factors present in hypervirulent strains

    Directory of Open Access Journals (Sweden)

    Andrés Esteban Marcoleta

    2016-06-01

    Full Text Available Due to the developing of multi-resistant and invasive hypervirulent strains, Klebsiella pneumoniae has become one of the most urgent bacterial pathogen threats in the last years. Genomic comparison of a growing number of sequenced isolates has allowed the identification of putative virulence factors, proposed to be acquirable mainly through horizontal gene transfer. In particular, those related with synthesizing the antibacterial peptide microcin E492 (MccE492 and salmochelin siderophores were found to be highly prevalent among hypervirulent strains. The determinants for the production of both molecules were first reported as part of a 13-kbp segment of K. pneumoniae RYC492 chromosome, and were cloned and characterized in E. coli. However, the genomic context of this segment in K. pneumoniae remained uncharacterized.In this work we provided experimental and bioinformatics evidence indicating that the MccE492 cluster is part of a highly conserved 23-kbp genomic island (GI named GIE492, that was integrated in a specific asparagine-tRNA gene (asn-tDNA and was found in a high proportion of isolates from liver abscesses sampled around the world. This element resulted to be unstable and its excision frequency increased after treating bacteria with mytomicin C and upon the overexpression of the island-encoded integrase. Besides the MccE492 genetic cluster, it invariably included an integrase-coding gene, at least 7 protein-coding genes of unknown function, and a putative transfer origin that possibly allows this GI to be mobilized through conjugation. In addition, we analyzed the asn-tDNA loci of all the available K. pneumoniae assembled chromosomes to evaluate them as GI-integration sites. Remarkably, 73% of the strains harbored at least one GI integrated in one of the four asn-tDNA present in this species, confirming them as integration hotspots. Each of these tDNAs was occupied with different frequencies, although they were 100% identical. Also, we

  11. K19 capsular polysaccharide of Acinetobacter baumannii is produced via a Wzy polymerase encoded in a small genomic island rather than the KL19 capsule gene cluster.

    Science.gov (United States)

    Kenyon, Johanna J; Shneider, Mikhail M; Senchenkova, Sofya N; Shashkov, Alexander S; Siniagina, Maria N; Malanin, Sergey Y; Popova, Anastasiya V; Miroshnikov, Konstantin A; Hall, Ruth M; Knirel, Yuriy A

    2016-08-01

    Polymerization of the oligosaccharides (K units) of complex capsular polysaccharides (CPSs) requires a Wzy polymerase, which is usually encoded in the gene cluster that directs K unit synthesis. Here, a gene cluster at the Acinetobacter K locus (KL) that lacks a wzy gene, KL19, was found in Acinetobacter baumannii ST111 isolates 28 and RBH2 recovered from hospitals in the Russian Federation and Australia, respectively. However, these isolates produced long-chain capsule, and a wzy gene was found in a 6.1 kb genomic island (GI) located adjacent to the cpn60 gene. The GI also includes an acetyltransferase gene, atr25, which is interrupted by an insertion sequence (IS) in RBH2. The capsule structure from both strains was →3)-α-d-GalpNAc-(1→4)-α-d-GalpNAcA-(1→3)-β-d-QuipNAc4NAc-(1→, determined using NMR spectroscopy. Biosynthesis of the K unit was inferred to be initiated with QuiNAc4NAc, and hence the Wzy forms the β-(1→3) linkage between QuipNAc4NAc and GalpNAc. The GalpNAc residue is 6-O-acetylated in isolate 28 only, showing that atr25 is responsible for this acetylation. The same GI with or without an IS in atr25 was found in draft genomes of other KL19 isolates, as well as ones carrying a closely related CPS gene cluster, KL39, which differs from KL19 only in a gene for an acyltransferase in the QuiNAc4NR synthesis pathway. Isolates carrying a KL1 variant with the wzy and atr genes each interrupted by an ISAba125 also have this GI. To our knowledge, this study is the first report of genes involved in capsule biosynthesis normally found at the KL located elsewhere in A. baumannii genomes.

  12. Inference of haplotypic phase and missing genotypes in polyploid organisms and variable copy number genomic regions

    Directory of Open Access Journals (Sweden)

    Balding David J

    2008-12-01

    Full Text Available Abstract Background The power of haplotype-based methods for association studies, identification of regions under selection, and ancestral inference, is well-established for diploid organisms. For polyploids, however, the difficulty of determining phase has limited such approaches. Polyploidy is common in plants and is also observed in animals. Partial polyploidy is sometimes observed in humans (e.g. trisomy 21; Down's syndrome, and it arises more frequently in some human tissues. Local changes in ploidy, known as copy number variations (CNV, arise throughout the genome. Here we present a method, implemented in the software polyHap, for the inference of haplotype phase and missing observations from polyploid genotypes. PolyHap allows each individual to have a different ploidy, but ploidy cannot vary over the genomic region analysed. It employs a hidden Markov model (HMM and a sampling algorithm to infer haplotypes jointly in multiple individuals and to obtain a measure of uncertainty in its inferences. Results In the simulation study, we combine real haplotype data to create artificial diploid, triploid, and tetraploid genotypes, and use these to demonstrate that polyHap performs well, in terms of both switch error rate in recovering phase and imputation error rate for missing genotypes. To our knowledge, there is no comparable software for phasing a large, densely genotyped region of chromosome from triploids and tetraploids, while for diploids we found polyHap to be more accurate than fastPhase. We also compare the results of polyHap to SATlotyper on an experimentally haplotyped tetraploid dataset of 12 SNPs, and show that polyHap is more accurate. Conclusion With the availability of large SNP data in polyploids and CNV regions, we believe that polyHap, our proposed method for inferring haplotypic phase from genotype data, will be useful in enabling researchers analysing such data to exploit the power of haplotype-based analyses.

  13. A genome-wide methylation study on obesity Differential variability and differential methylation

    NARCIS (Netherlands)

    Xu, Xiaojing; Su, Shaoyong; Barnes, Vernon A.; De Miguel, Carmen; Pollock, Jennifer; Ownby, Dennis; Shi, Huidong; Zhu, Haidong; Snieder, Harold; Wang, Xiaoling

    2013-01-01

    Besides differential methylation, DNA methylation variation has recently been proposed and demonstrated to be a potential contributing factor to cancer risk. Here we aim to examine whether differential variability in methylation is also an important feature of obesity, a typical non-malignant common

  14. The influence of sea- and land-breeze circulations on the diurnal variability in precipitation over a tropical island

    Directory of Open Access Journals (Sweden)

    L. Zhu

    2017-11-01

    Full Text Available This study examines the diurnal variation in precipitation over Hainan Island in the South China Sea using gauge observations from 1951 to 2012 and Climate Prediction Center MORPHing technique (CMORPH satellite estimates from 2006 to 2015, as well as numerical simulations. The simulations are the first to use climatological mean initial and lateral boundary conditions to study the dynamic and thermodynamic processes (and the impacts of land–sea breeze circulations that control the rainfall distribution and climatology. Precipitation is most significant from April to October and exhibits a strong diurnal cycle resulting from land–sea breeze circulations. More than 60 % of the total annual precipitation over the island is attributable to the diurnal cycle with a significant monthly variability. The CMORPH and gauge datasets agree well, except that the CMORPH data underestimate precipitation and have a 1 h peak delay. The diurnal cycle of the rainfall and the related land–sea breeze circulations during May and June were well captured by convection-permitting numerical simulations with the Weather Research and Forecasting (WRF model, which were initiated from a 10-year average ERA-Interim reanalysis. The simulations have a slight overestimation of rainfall amounts and a 1 h delay in peak rainfall time. The diurnal cycle of precipitation is driven by the occurrence of moist convection around noontime owing to low-level convergence associated with the sea-breeze circulations. The precipitation intensifies rapidly thereafter and peaks in the afternoon with the collisions of sea-breeze fronts from different sides of the island. Cold pools of the convective storms contribute to the inland propagation of the sea breeze. Generally, precipitation dissipates quickly in the evening due to the cooling and stabilization of the lower troposphere and decrease of boundary layer moisture. Interestingly, the rather high island orography is not a

  15. A high HIV-1 strain variability in London, UK, revealed by full-genome analysis: Results from the ICONIC project

    Science.gov (United States)

    Frampton, Dan; Gallo Cassarino, Tiziano; Raffle, Jade; Hubb, Jonathan; Ferns, R. Bridget; Waters, Laura; Tong, C. Y. William; Kozlakidis, Zisis; Hayward, Andrew; Kellam, Paul; Pillay, Deenan; Clark, Duncan; Nastouli, Eleni; Leigh Brown, Andrew J.

    2018-01-01

    The initial analysis of genome sequences detected substantial hidden variability in the London HIV epidemic. Analysing full genome sequences, as opposed to only PR+RT, identified previously undetected recombinants. It provided a more reliable description of CRFs (that would be otherwise misclassified) and transmission clusters. PMID:29389981

  16. Variable Copy Number, Intra-Genomic Heterogeneities and Lateral Transfers of the 16S rRNA Gene in Pseudomonas

    Science.gov (United States)

    Bodilis, Josselin; Nsigue-Meilo, Sandrine; Besaury, Ludovic; Quillet, Laurent

    2012-01-01

    Even though the 16S rRNA gene is the most commonly used taxonomic marker in microbial ecology, its poor resolution is still not fully understood at the intra-genus level. In this work, the number of rRNA gene operons, intra-genomic heterogeneities and lateral transfers were investigated at a fine-scale resolution, throughout the Pseudomonas genus. In addition to nineteen sequenced Pseudomonas strains, we determined the 16S rRNA copy number in four other Pseudomonas strains by Southern hybridization and Pulsed-Field Gel Electrophoresis, and studied the intra-genomic heterogeneities by Denaturing Gradient Gel Electrophoresis and sequencing. Although the variable copy number (from four to seven) seems to be correlated with the evolutionary distance, some close strains in the P. fluorescens lineage showed a different number of 16S rRNA genes, whereas all the strains in the P. aeruginosa lineage displayed the same number of genes (four copies). Further study of the intra-genomic heterogeneities revealed that most of the Pseudomonas strains (15 out of 19 strains) had at least two different 16S rRNA alleles. A great difference (5 or 19 nucleotides, essentially grouped near the V1 hypervariable region) was observed only in two sequenced strains. In one of our strains studied (MFY30 strain), we found a difference of 12 nucleotides (grouped in the V3 hypervariable region) between copies of the 16S rRNA gene. Finally, occurrence of partial lateral transfers of the 16S rRNA gene was further investigated in 1803 full-length sequences of Pseudomonas available in the databases. Remarkably, we found that the two most variable regions (the V1 and V3 hypervariable regions) had probably been laterally transferred from another evolutionary distant Pseudomonas strain for at least 48.3 and 41.6% of the 16S rRNA sequences, respectively. In conclusion, we strongly recommend removing these regions of the 16S rRNA gene during the intra-genus diversity studies. PMID:22545126

  17. Barotropic wind-driven circulation patterns in a closed rectangular basin of variable depth influenced by a peninsula or an island

    Directory of Open Access Journals (Sweden)

    B. V. Chubarenko

    Full Text Available We study how a coastal obstruction (peninsula or coastal island affects the three-dimensional barotropic currents in an oblong rectangular basin with variable bathymetry across the basin width. The transverse depth profile is asymmetric and the peninsula or island lies in the middle of the long side of the rectangle. A semi-spectral model for the Boussinesq-approximated shallow water equations, developed in Haidvogel et al. and altered for semi-implicit numerical integration in time in Wang and Hutter, is used to find the steady barotropic state circulation pattern to external winds. The structural (qualitative rearrangements and quanti2tative features of the current pattern are studied under four principal wind directions and different lengths of the peninsula and its inclination relative to the shore. The essentially non-linear relationships of the water flux between the two sub-basins (formed by the obstructing peninsula and the corresponding cross-sectional area left open are found and analysed. It is further analysed whether the depth-integrated model, usually adopted by others, is meaningful when applied to the water exchange problems. The flow through the channel narrowing is quantitatively estimated and compared with the three-dimensional results. The dynamics of the vortex structure and the identification of the up-welling/down-welling zones around the obstruction are discussed in detail. The influence of the transformation of the peninsula into a coastal island on the global basin circulation is considered as are the currents in the channel. The geometric and physical reasons for the anisotropy of the current structure which prevail through all obtained solutions are also discussed.

    Key words: Oceanography: general (limnology; numerical modeling - Oceanography: physical (currents

  18. Barotropic wind-driven circulation patterns in a closed rectangular basin of variable depth influenced by a peninsula or an island

    Directory of Open Access Journals (Sweden)

    B. V. Chubarenko

    2000-06-01

    Full Text Available We study how a coastal obstruction (peninsula or coastal island affects the three-dimensional barotropic currents in an oblong rectangular basin with variable bathymetry across the basin width. The transverse depth profile is asymmetric and the peninsula or island lies in the middle of the long side of the rectangle. A semi-spectral model for the Boussinesq-approximated shallow water equations, developed in Haidvogel et al. and altered for semi-implicit numerical integration in time in Wang and Hutter, is used to find the steady barotropic state circulation pattern to external winds. The structural (qualitative rearrangements and quanti2tative features of the current pattern are studied under four principal wind directions and different lengths of the peninsula and its inclination relative to the shore. The essentially non-linear relationships of the water flux between the two sub-basins (formed by the obstructing peninsula and the corresponding cross-sectional area left open are found and analysed. It is further analysed whether the depth-integrated model, usually adopted by others, is meaningful when applied to the water exchange problems. The flow through the channel narrowing is quantitatively estimated and compared with the three-dimensional results. The dynamics of the vortex structure and the identification of the up-welling/down-welling zones around the obstruction are discussed in detail. The influence of the transformation of the peninsula into a coastal island on the global basin circulation is considered as are the currents in the channel. The geometric and physical reasons for the anisotropy of the current structure which prevail through all obtained solutions are also discussed.Key words: Oceanography: general (limnology; numerical modeling - Oceanography: physical (currents

  19. Consequences of Neglecting the Interannual Variability of the Solar Resource: A Case Study of Photovoltaic Power Among the Hawaiian Islands

    Energy Technology Data Exchange (ETDEWEB)

    Brancucci Martinez-Anido, Carlo [National Renewable Energy Laboratory (NREL), Golden, CO (United States); Bryce, Richard [National Renewable Energy Laboratory (NREL), Golden, CO (United States); Losada Carreno, Ignacio [National Renewable Energy Laboratory (NREL), Golden, CO (United States); Kumler, Andrew [National Renewable Energy Laboratory (NREL), Golden, CO (United States); Hodge, Brian S [National Renewable Energy Laboratory (NREL), Golden, CO (United States); Roberts, Billy J [National Renewable Energy Laboratory (NREL), Golden, CO (United States)

    2018-04-05

    The interannual variability of the solar irradiance and meteorological conditions are often ignored in favor of single-year data sets for modeling power generation and evaluating the economic value of photovoltaic (PV) power systems. Yet interannual variability significantly impacts the generation from one year to another of renewable power systems such as wind and PV. Consequently, the interannual variability of power generation corresponds to the interannual variability of capital returns on investment. The penetration of PV systems within the Hawaiian Electric Companies' portfolio has rapidly accelerated in recent years and is expected to continue to increase given the state's energy objectives laid out by the Hawaii Clean Energy Initiative. We use the National Solar Radiation Database (1998-2015) to characterize the interannual variability of the solar irradiance and meteorological conditions across the State of Hawaii. These data sets are passed to the National Renewable Energy Laboratory's System Advisory Model (SAM) to calculate an 18-year PV power generation data set to characterize the variability of PV power generation. We calculate the interannual coefficient of variability (COV) for annual average global horizontal irradiance (GHI) on the order of 2% and COV for annual capacity factor on the order of 3% across the Hawaiian archipelago. Regarding the interannual variability of seasonal trends, we calculate the COV for monthly average GHI values on the order of 5% and COV for monthly capacity factor on the order of 10%. We model residential-scale and utility-scale PV systems and calculate the economic returns of each system via the payback period and the net present value. We demonstrate that studies based on single-year data sets for economic evaluations reach conclusions that deviate from the true values realized by accounting for interannual variability.

  20. Complete mitochondrial genome sequences of Korean native horse from Jeju Island: uncovering the spatio-temporal dynamics.

    Science.gov (United States)

    Yoon, Sook Hee; Kim, Jaemin; Shin, Donghyun; Cho, Seoae; Kwak, Woori; Lee, Hak-Kyo; Park, Kyoung-Do; Kim, Heebal

    2017-04-01

    The Korean native horse (Jeju horse) is one of the most important animals in Korean historical, cultural, and economical viewpoints. In the early 1980s, the Jeju horse was close to extinction. The aim of this study is to explore the phylogenomics of Korean native horse focusing on spatio-temporal dynamics. We determined complete mitochondrial genome sequences for the first Korean native (n = 6) and additional Mongolian (n = 2) horses. Those sequences were analyzed together with 143 published ones using Bayesian coalescent approach as well as three different phylogenetic analysis methods, Bayesian inference, maximum likelihood, and neighbor-joining methods. The phylogenomic trees revealed that the Korean native horses had multiple origins and clustered together with some horses from four European and one Middle Eastern breeds. Our phylogenomic analyses also supported that there was no apparent association between breed or geographic location and the evolution of global horses. Time of the most recent common ancestor of the Korean native horse was approximately 13,200-63,200 years, which was much younger than 0.696 My of modern horses. Additionally, our results showed that all global horse lineages including Korean native horse existed prior to their domestication events occurred in about 6000-10,000 years ago. This is the first study on phylogenomics of the Korean native horse focusing on spatio-temporal dynamics. Our findings increase our understanding of the domestication history of the Korean native horses, and could provide useful information for horse conservation projects as well as for horse genomics, emergence, and the geographical distribution.

  1. Stratospheric ozone climatology and variability over a southern subtropical site: Reunion Island (21° S; 55° E

    Directory of Open Access Journals (Sweden)

    V. Sivakumar

    2007-11-01

    Full Text Available The study presents the climatological characteristics of stratospheric ozone observed over Reunion Island using in-situ (ozonesonde and SAOZ and satellite (UARS-HALOE, SAGE-II and TOMS measurements. It uses co-localised ozonesondes (from September 1992 to February 2005 and SAOZ measurements (from January 1993 to December 2004, SAGE-II data from October 1984 to February 1999 (~15 years, HALOE data from January 1991 to February 2005 (~15 years, and NIMBUS/TOMS data from January 1978 to December 2004 (27 years. The satellite measurements correspond to overpasses located nearby Reunion Island (21° S; 55° E. The height profiles of ozone concentration obtained from ozonesonde (0.5–29.5 km show less bias in comparison with the HALOE and SAGE-II measurements. Though, the satellite (HALOE and SAGE-II measurements underestimate the tropospheric ozone, they are in good agreement for the heights above 15 km. The bias between the measurements and the normalized ozone profile constructed from the ozonesonde and SAGE-II satellite measurement shows that the SAGE-II measurements are more accurate than the HALOE measurements in the lower stratosphere. The monthly variation of ozone concentration derived from ozonesonde and HALOE shows a nearly annual cycle with a maximum concentration during winter/spring and minimum concentration during summer/autumn months. The time evolution of total column ozone obtained from TOMS, SAOZ and the one computed from ozonesonde and SAGE-II, exhibits similar behaviour with analogous trends as above. The TOMS variation displays a higher value of total column ozone of about 3–5 DU (10% in comparison with the SAOZ and the integrated ozone from ozonesonde and SAGE-II.

  2. The prevalences of Salmonella Genomic Island 1 variants in human and animal Salmonella Typhimurium DT104 are distinguishable using a Bayesian approach.

    Directory of Open Access Journals (Sweden)

    Alison E Mather

    Full Text Available 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.

  3. Genome variability of foot-and-mouth disease virus during the short period of the 2010 epidemic in Japan.

    Science.gov (United States)

    Nishi, Tatsuya; Yamada, Manabu; Fukai, Katsuhiko; Shimada, Nobuaki; Morioka, Kazuki; Yoshida, Kazuo; Sakamoto, Kenichi; Kanno, Toru; Yamakawa, Makoto

    2017-02-01

    Foot-and-mouth disease virus (FMDV) is highly contagious and has a high mutation rate, leading to extensive genetic variation. To investigate how FMDV genetically evolves over a short period of an epidemic after initial introduction into an FMD-free area, whole L-fragment sequences of 104 FMDVs isolated from the 2010 epidemic in Japan, which continued for less than three months were determined and phylogenetically and comparatively analyzed. Phylogenetic analysis of whole L-fragment sequences showed that these isolates were classified into a single group, indicating that FMDV was introduced into Japan in the epidemic via a single introduction. Nucleotide sequences of 104 virus isolates showed more than 99.56% pairwise identity rates without any genetic deletion or insertion, although no sequences were completely identical with each other. These results indicate that genetic substitutions of FMDV occurred gradually and constantly during the epidemic and generation of an extensive mutant virus could have been prevented by rapid eradication strategy. From comparative analysis of variability of each FMDV protein coding region, VP4 and 2C regions showed the highest average identity rates and invariant rates, and were confirmed as highly conserved. In contrast, the protein coding regions VP2 and VP1 were confirmed to be highly variable regions with the lowest average identity rates and invariant rates, respectively. Our data demonstrate the importance of rapid eradication strategy in an FMD epidemic and provide valuable information on the genome variability of FMDV during the short period of an epidemic. Copyright © 2016 The Authors. Published by Elsevier B.V. All rights reserved.

  4. Heat Islands

    Science.gov (United States)

    EPA's Heat Island Effect Site provides information on heat islands, their impacts, mitigation strategies, related research, a directory of heat island reduction initiatives in U.S. communities, and EPA's Heat Island Reduction Program.

  5. Island biogeography

    DEFF Research Database (Denmark)

    Whittaker, Robert James; Fernández-Palacios, José María; Matthews, Thomas J.

    2017-01-01

    Islands provide classic model biological systems. We review how growing appreciation of geoenvironmental dynamics of marine islands has led to advances in island biogeographic theory accommodating both evolutionary and ecological phenomena. Recognition of distinct island geodynamics permits gener...

  6. Variable Number of Tandem Repeat Markers in the Genome Sequence of Mycosphaerella Fijiensis, the Causal Agent of Black Leaf Streak Disease of Banana (Musa spp.)

    Science.gov (United States)

    Mycosphaerella fijiensis, the causal agent of banana leaf streak disease (commonly known as black Sigatoka), is the most devastating pathogen attacking bananas (Musa spp). Recently the whole genome sequence of M. fijiensis became available. This sequence was screened for the presence of Variable Num...

  7. The influence of bed friction variability due to land cover on storm-driven barrier island morphodynamics

    Science.gov (United States)

    Passeri, Davina L.; Long, Joseph W.; Plant, Nathaniel G.; Bilskie, Matthew V.; Hagen, Scott C.

    2018-01-01

    Variations in bed friction due to land cover type have the potential to influence morphologic change during storm events; the importance of these variations can be studied through numerical simulation and experimentation at locations with sufficient observational data to initialize realistic scenarios, evaluate model accuracy and guide interpretations. Two-dimensional in the horizontal plane (2DH) morphodynamic (XBeach) simulations were conducted to assess morphodynamic sensitivity to spatially varying bed friction at Dauphin Island, AL using hurricanes Ivan (2004) and Katrina (2005) as experimental test cases. For each storm, three bed friction scenarios were simulated: (1) a constant Chezy coefficient across land and water, (2) a constant Chezy coefficient across land and depth-dependent Chezy coefficients across water, and (3) spatially varying Chezy coefficients across land based on land use/land cover (LULC) data and depth-dependent Chezy coefficients across water. Modeled post-storm bed elevations were compared qualitatively and quantitatively with post-storm lidar data. Results showed that implementing spatially varying bed friction influenced the ability of XBeach to accurately simulate morphologic change during both storms. Accounting for frictional effects due to large-scale variations in vegetation and development reduced cross-barrier sediment transport and captured overwash and breaching more accurately. Model output from the spatially varying friction scenarios was used to examine the need for an existing sediment transport limiter, the influence of pre-storm topography and the effects of water level gradients on storm-driven morphodynamics.

  8. Sequencing of mitochondrial genomes of nine Aspergillus and Penicillium species identifies mobile introns and accessory genes as main sources of genome size variability.

    Science.gov (United States)

    Joardar, Vinita; Abrams, Natalie F; Hostetler, Jessica; Paukstelis, Paul J; Pakala, Suchitra; Pakala, Suman B; Zafar, Nikhat; Abolude, Olukemi O; Payne, Gary; Andrianopoulos, Alex; Denning, David W; Nierman, William C

    2012-12-12

    The genera Aspergillus and Penicillium include some of the most beneficial as well as the most harmful fungal species such as the penicillin-producer Penicillium chrysogenum and the human pathogen Aspergillus fumigatus, respectively. Their mitochondrial genomic sequences may hold vital clues into the mechanisms of their evolution, population genetics, and biology, yet only a handful of these genomes have been fully sequenced and annotated. Here we report the complete sequence and annotation of the mitochondrial genomes of six Aspergillus and three Penicillium species: A. fumigatus, A. clavatus, A. oryzae, A. flavus, Neosartorya fischeri (A. fischerianus), A. terreus, P. chrysogenum, P. marneffei, and Talaromyces stipitatus (P. stipitatum). The accompanying comparative analysis of these and related publicly available mitochondrial genomes reveals wide variation in size (25-36 Kb) among these closely related fungi. The sources of genome expansion include group I introns and accessory genes encoding putative homing endonucleases, DNA and RNA polymerases (presumed to be of plasmid origin) and hypothetical proteins. The two smallest sequenced genomes (A. terreus and P. chrysogenum) do not contain introns in protein-coding genes, whereas the largest genome (T. stipitatus), contains a total of eleven introns. All of the sequenced genomes have a group I intron in the large ribosomal subunit RNA gene, suggesting that this intron is fixed in these species. Subsequent analysis of several A. fumigatus strains showed low intraspecies variation. This study also includes a phylogenetic analysis based on 14 concatenated core mitochondrial proteins. The phylogenetic tree has a different topology from published multilocus trees, highlighting the challenges still facing the Aspergillus systematics. The study expands the genomic resources available to fungal biologists by providing mitochondrial genomes with consistent annotations for future genetic, evolutionary and population

  9. Assessment of the intensity and spatial variability of urban heat islands over the Indian cities for Regional Climate Analysis

    Science.gov (United States)

    Sultana, S.; Satyanarayana, A. N. V.

    2016-12-01

    The Urban heat island (UHI) in general developed over cities, due to the drastic changes in land use and land cover (LULC), has profound impact on the atmospheric circulation patterns due to the changes in the energy transport mechanism which in turn affect the regional climate. In this study, an attempt has been made to quantify the intensity of UHI, and to identify the pockets of UHI over cities during last decade over fast developing cosmopolitan Indian cities such as New Delhi, Mumbai and Kolkata. For this purpose, Landsat TM and ETM+ images during winter period, in about 5 year intervals from 2002 to 2013, has been selected to retrieve the brightness temperatures and land use/cover, from which Land Surface Temperature (LST) has been estimated using Normalized Difference Vegetation Index (NDVI). Normalized Difference Build-up Index (NDBI) and Normalized Difference Bareness Index (NDBaI) are estimated to extract build-up areas and bare land from the satellite images to identify the UHI pockets over the study area. For this purpose image processing and GIS tools were employed. Results reveal a significant increase in the intensity of UHI and increase in its area of influence over all the three cities. An increase of 2 to 2.5 oC of UHI intensity over the study regions has been noticed. The range of increase in UHI intensity is found to be more over New Delhi compared to Mumbai and Kolkata which is more or less same. The number of hotspot pockets of UHI has also been increased as seen from the spatial distribution of LST, NDVI and NDBI. This result signifies the impact of rapid urbanization and infrastructural developments has a direct consequence in modulating the regional climate over the Indian cities.

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

    Directory of Open Access Journals (Sweden)

    De Maayer Pieter

    2011-11-01

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

  11. A 242-year seasonal-resolved speleothem record from Hainan Island: A window into variability of the precipitation δ18O in East Asia

    Science.gov (United States)

    Cai, Y.; An, Z.; Cheng, H.; Edwards, R. L.; Fung, I. Y.; Zhang, H.; Tan, L.; Bi, H.

    2016-12-01

    Hainan Island is located at the gateway of East Asian summer monsoon to the continent. The typical tropical monsoon climate at Hainan island is characterized by wet season during the summer and autumn and dry season during the winter and spring. Here, we present a seasonal resolved speleothem record spanning 242 years ( 50-292 AD) from Xianren Cave (E109°25`, N18°34`), which is situated in the Baoting County, Hainan Province. The monitoring inside the cave shows that the relative humidity kept saturated during the observed periods (one and half years) while the temperature varied seasonally following the temperature changes outside the cave, but with much smaller amplitude. Monthly observation of drip water inside the cave indicates that the isotope composition of drip water mainly responds to the changes in the precipitation isotope composition with less than two months' resident time. The visible annual lamination and distinct fluctuations of calcite Mg, Sr and Ba concentrations corroborate that the high-frequency oscillations of calcite δ18O largely capture the seasonal variation of the isotope composition of precipitation, although the temperature effect cannot be excluded. By setting the heaviest value of annual variation of calcite δ18O as the beginning of each annual cycle, we transferred the δ18O record of 11.2 cm in depth to a δ18O record of 242-year in age. The δ18O record of stalagmite XR-3 demonstrate clearly the annual, decadal and multi-decadal variations of amplitude from 2 to 4‰, in addition to the seasonal oscillation of amplitude varied from 1.5 to 2.5‰. The ensemble empirical mode decomposition results show that the dominant variability (54.6% of the total variance) is captured by the components at the timescale of 3-7 year, while the components on timescales of 22-24 -year, 80-year and 120-year capture 35.0%, 7.0% and 3.4% of the variance, respectively. We contribute the variability of speleothem δ18O at the timescale of 3-7 -year to

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

    Science.gov (United States)

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

    2015-11-01

    Phytophthora capsici is a virulent oomycete pathogen of many vegetable crops. Recently, it has been demonstrated that the recognition of the RXLR effector AVR3a1 of P. capsici (PcAVR3a1) triggers a hypersensitive response and plays a critical role in mediating non-host resistance. Here, we analyzed the occurrence of PcAVR3a1 in 57 isolates of P. capsici derived from globe squash, eggplant, tomato and bell pepper cocultivated in a small geographical area. The occurrence of PcAVR3a1 in environmental strains of P. capsici was confirmed by PCR in only 21 of these pathogen isolates. To understand the presence-absence pattern of PcAVR3a1 in environmental strains, the flanking region of this gene was sequenced. PcAVR3a1 was found within a genetic element that we named PcAVR3a1-GI (PcAVR3a1 genomic island). PcAVR3a1-GI was flanked by a 22-bp direct repeat, which is related to its site-specific recombination site. In addition to the PcAVR3a1 gene, PcAVR3a1-GI also encoded a phage integrase probably associated with the excision and integration of this mobile element. Exposure to plant induced the presence of an episomal circular intermediate of PcAVR3a1-GI, indicating that this mobile element is functional. Collectively, these findings provide evidence of PcAVR3a1 evolution via mobile elements in environmental strains of Phytophthora. © FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  13. Variability in patterns of macro-epiphytic leaf community of Posidonia oceanica in the Islands of Kuriate: Western coast of Tunisia

    Directory of Open Access Journals (Sweden)

    Ben Brahim Mounir

    2016-03-01

    Full Text Available Objective: To test the response of the epiphyte community structure and biomass of the Posidonia oceanica (P. oceanica leaves to natural disturbance. Methods: Sampling of P. oceanica was carried in winter and summer on three sites in Kuriate Islands (western coast of Tunisia subject to different environments disturbances. Shoots of P. oceanica were preserved in seawater-formalin (5% solution for macro-epiphytes species identification in the laboratory. The samples were examined for leaf surface per shoot and the coverage (expressed as a percentage of leaf surface of each morphological group, then carefully scraped with a razor blade. Epiphytes and scraped leaves were oven-dried at 60 °C for 48 h. Biomass was expressed as g dry weight/shoot. Results: The biomass and the percentage cover of macro-epiphytic leaves showed seasonal variation. The highest values of epiphytic leaves were detected in summer whereas the lowest values were registered during winter. ANOVA showed that Kuriate Islands functioned as a single ecosystem in terms assemblage of macro-epiphytic leaves since no significant variation was detected for biomass and percentage cover at the scale site. Our study showed that natural disturbance had no effect on the assemblage distribution and the biomass of macro-epiphyte on the leaves of P. oceanica between the scales of site, whereas variability at the smallest scale was detected. ANOVA showed that exposure to wind and current had no effect on the biomass of macro-epiphytes leaves. Conclusions: Biomass and assemblages of macro-epiphytic leaves of P. oceanica were high in summer and homogenous between all sites investigated. Natural disturbances such as exposure to wind have no effect on the distribution and the biomass of epiphytes on the shallow meadow.

  14. Variability of Atmospheric Radon-222 and Secondary Aerosol Components in Accordance with Air Mass Transport Pathways at Jeju Island, Korea, during 2011-2014

    International Nuclear Information System (INIS)

    Bu, Jun-Oh; Song, Jung-Min; Kim, Won-Hyung; Kang, Chang-Hee; Chambers, Scott D.; Williams, Alastair G.; Lee, Chulkyu

    2016-01-01

    Real-time monitoring of hourly atmospheric Radon-222 concentration and three daily monitoring of the secondary aerosol components of PM_1_0 were performed throughout 2011-2014 at Gosan station, Jeju Island, in order to characterize their background levels and temporal variation. The annual mean radon and PM_1_0 mass concentrations were 2326 ± 1198 mBq/m"3 and 37.1 ± 19.5 μg/m"3, respectively. Based on cluster analyses of air mass back trajectories, the frequencies of air masses originating from continental China, the Korean Peninsula, and North Pacific Ocean routes were 53, 28, and 19%, respectively. When the air masses were transported to Jeju Island from continental China, the concentrations of radon and secondary aerosol components (nss-SO_4"2"-, NO_3"-, NH_4"+) were relatively high: 2577 mBq/m"3 and 14.4 μg/m"3, respectively. In cases when the air masses have moved from the Korean Peninsula, the corresponding concentrations were 2247 mBq/m"3 and 11.4 μg/m"3, respectively. On the other hand, when the air masses came from the North Pacific Ocean, their radon and secondary aerosol concentrations decreased much further, 1372 mBq/m"3 and 10.5 μg/m"3, respectively. Consequently, the variability of atmospheric radon concentrations at Gosan station might be characterized by synoptic changes in air mass fetch as well as diurnal changes in atmospheric mixing depth.

  15. Variability of Atmospheric Radon-222 and Secondary Aerosol Components in Accordance with Air Mass Transport Pathways at Jeju Island, Korea, during 2011-2014

    Energy Technology Data Exchange (ETDEWEB)

    Bu, Jun-Oh; Song, Jung-Min; Kim, Won-Hyung; Kang, Chang-Hee [Jeju National University, Jeju (Korea, Republic of); Chambers, Scott D.; Williams, Alastair G. [Australian Nuclear Science and Technology Organisation, Kirrawee DC (Australia); Lee, Chulkyu [Korea Meteorological Administration, Seoul (Korea, Republic of)

    2016-06-15

    Real-time monitoring of hourly atmospheric Radon-222 concentration and three daily monitoring of the secondary aerosol components of PM{sub 10} were performed throughout 2011-2014 at Gosan station, Jeju Island, in order to characterize their background levels and temporal variation. The annual mean radon and PM{sub 10} mass concentrations were 2326 ± 1198 mBq/m{sup 3} and 37.1 ± 19.5 μg/m{sup 3}, respectively. Based on cluster analyses of air mass back trajectories, the frequencies of air masses originating from continental China, the Korean Peninsula, and North Pacific Ocean routes were 53, 28, and 19%, respectively. When the air masses were transported to Jeju Island from continental China, the concentrations of radon and secondary aerosol components (nss-SO{sub 4}{sup 2-}, NO{sub 3}{sup -}, NH{sub 4}{sup +}) were relatively high: 2577 mBq/m{sup 3} and 14.4 μg/m{sup 3}, respectively. In cases when the air masses have moved from the Korean Peninsula, the corresponding concentrations were 2247 mBq/m{sup 3} and 11.4 μg/m{sup 3}, respectively. On the other hand, when the air masses came from the North Pacific Ocean, their radon and secondary aerosol concentrations decreased much further, 1372 mBq/m{sup 3} and 10.5 μg/m{sup 3}, respectively. Consequently, the variability of atmospheric radon concentrations at Gosan station might be characterized by synoptic changes in air mass fetch as well as diurnal changes in atmospheric mixing depth.

  16. The value of small habitat islands for the conservation of genetic variability in a steppe grass species

    Science.gov (United States)

    Wódkiewicz, Maciej; Dembicz, Iwona; Moysiyenko, Ivan I.

    2016-10-01

    The habitat loss and fragmentation due to agricultural land-conversion affected the steppe throughout its range. In Ukraine, 95% of steppe was destroyed in the last two centuries. Remaining populations are confined to few refuges, like nature reserves, loess ravines, and kurgans (small burial mounds), the latter being often subject to destruction by archeological excavations. Stipa capillata L. is a typical grass species of Eurasian steppes and extrazonal dry grasslands, that was previously used as a model species in studies on steppe ecology. The aim of our research was to assess genetic diversity of S. capillata populations within different types of steppe refuges (loess ravines, biosphere reserve, kurgan) and to evaluate the value of the latter group for the preservation of genetic diversity in the study species. We assessed genetic diversity of 266 individuals from 15 populations (nine from kurgans, three from loess ravines and three from Askania-Nova Biosphere Reserve) with eight Universal Rice Primers (URPs). Studied populations showed high intra-population variability (I: 0.262-0.419, PPB: 52.08-82.64%). Populations from kurgans showed higher genetic differentiation (ΦST = 0.247) than those from loess ravines (ΦST = 0.120) and the biosphere reserve (ΦST = 0.142). Although the diversity metrics were to a small extent lower for populations from kurgans than from larger refugia we conclude that all studied populations of the species still preserve high genetic variability and are valuable for protection. To what extent this pattern holds true under continuous fragmentation in the future must be carefully monitored.

  17. Serratia marcescens harbouring SME-type class A carbapenemases in Canada and the presence of blaSME on a novel genomic island, SmarGI1-1.

    Science.gov (United States)

    Mataseje, L F; Boyd, D A; Delport, J; Hoang, L; Imperial, M; Lefebvre, B; Kuhn, M; Van Caeseele, P; Willey, B M; Mulvey, M R

    2014-07-01

    An increasing prevalence since 2010 of Serratia marcescens harbouring the Ambler class A carbapenemase SME prompted us to further characterize these isolates. Isolates harbouring bla(SME) were identified by PCR and sequencing. Phenotypic analysis for carbapenemase activity was carried out by a modified Hodge test and a modified Carba NP test. Antimicrobial susceptibilities were determined by Etest and Vitek 2. Typing was by PFGE of macrorestriction digests. Whole-genome sequencing of three isolates was carried out to characterize the genomic region harbouring the bla(SME)-type genes. All S. marcescens harbouring SME-type enzymes could be detected using a modified Carba NP test. Isolates harbouring bla(SME) were resistant to penicillins and carbapenems, but remained susceptible to third-generation cephalosporins, as well as fluoroquinolones and trimethoprim/sulfamethoxazole. Isolates exhibited diverse genetic backgrounds, though 57% of isolates were found in three clusters. Analysis of whole-genome sequence data from three isolates revealed that the bla(SME) gene occurred in a novel cryptic prophage genomic island, SmarGI1-1. There has been an increasing occurrence of S. marcescens harbouring bla(SME) in Canada since 2010. The bla(SME) gene was found on a genomic island, SmarGI1-1, that can be excised and circularized, which probably contributes to its dissemination amongst S. marcescens. © The Author 2014. Published by Oxford University Press on behalf of the British Society for Antimicrobial Chemotherapy. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  18. TIA: algorithms for development of identity-linked SNP islands for analysis by massively parallel DNA sequencing.

    Science.gov (United States)

    Farris, M Heath; Scott, Andrew R; Texter, Pamela A; Bartlett, Marta; Coleman, Patricia; Masters, David

    2018-04-11

    . It also allows the definition of sequence length and sequence variability of the target region as well as the less variable flanking regions for tailoring to MPS platforms. As shown in this study, TIA can be used to discover identity-linked SNP islands within the human genome, useful for differentiating individuals by targeted resequencing on MPS technologies.

  19. Comparative Analyses of Nonpathogenic, Opportunistic, and Totally Pathogenic Mycobacteria Reveal Genomic and Biochemical Variabilities and Highlight the Survival Attributes of Mycobacterium tuberculosis

    Science.gov (United States)

    Singh, Yadvir; Kohli, Sakshi; Ahmad, Javeed; Ehtesham, Nasreen Z.; Tyagi, Anil K.

    2014-01-01

    ABSTRACT Mycobacterial evolution involves various processes, such as genome reduction, gene cooption, and critical gene acquisition. Our comparative genome size analysis of 44 mycobacterial genomes revealed that the nonpathogenic (NP) genomes were bigger than those of opportunistic (OP) or totally pathogenic (TP) mycobacteria, with the TP genomes being smaller yet variable in size—their genomic plasticity reflected their ability to evolve and survive under various environmental conditions. From the 44 mycobacterial species, 13 species, representing TP, OP, and NP, were selected for genomic-relatedness analyses. Analysis of homologous protein-coding genes shared between Mycobacterium indicus pranii (NP), Mycobacterium intracellulare ATCC 13950 (OP), and Mycobacterium tuberculosis H37Rv (TP) revealed that 4,995 (i.e., ~95%) M. indicaus pranii proteins have homology with M. intracellulare, whereas the homologies among M. indicus pranii, M. intracellulare ATCC 13950, and M. tuberculosis H37Rv were significantly lower. A total of 4,153 (~79%) M. indicus pranii proteins and 4,093 (~79%) M. intracellulare ATCC 13950 proteins exhibited homology with the M. tuberculosis H37Rv proteome, while 3,301 (~82%) and 3,295 (~82%) M. tuberculosis H37Rv proteins showed homology with M. indicus pranii and M. intracellulare ATCC 13950 proteomes, respectively. Comparative metabolic pathway analyses of TP/OP/NP mycobacteria showed enzymatic plasticity between M. indicus pranii (NP) and M. intracellulare ATCC 13950 (OP), Mycobacterium avium 104 (OP), and M. tuberculosis H37Rv (TP). Mycobacterium tuberculosis seems to have acquired novel alternate pathways with possible roles in metabolism, host-pathogen interactions, virulence, and intracellular survival, and by implication some of these could be potential drug targets. PMID:25370496

  20. Seasonal variability in physicochemical characteristics of small water bodies across a High Arctic wetland, Polar Bear Pass, Bathurst Island, Nunavut, Canada

    Science.gov (United States)

    Abnizova, A.; Miller, E.; Shakil, S.; Young, K. L.

    2012-12-01

    Small water bodies (lakes, ponds) in permafrost environments make up roughly half of the total area of surface water, but their relevance to nutrient and carbon fluxes on a landscape scale still remains largely unknown. Small variations in pond water balance as a result of seasonal changes in precipitation, evaporation, or drainage processes have the potential to produce considerable changes in the carbon and nutrient budgets as small changes in the water level can have a major effect on volumes and surface areas of ponds. The aims of this study were (1) to identify the main characteristics in pond hydrology both seasonally and between years; (2) to identify factors controlling variation in measured physicochemical variables; and (3) to detect seasonal trends in the hydrological and chemical characteristics of ponds located in an extensive low-gradient High Arctic wetland. We conducted detailed limnological surveys of 50 wetland ponds located at Polar Bear Pass (PBP), Bathurst Island, Nunavut, Canada during 2007-2010. The results indicate large seasonal variability in physicochemical parameters that is associated with pond water budget changes, especially for ponds with steady water levels vs. dynamic ponds (fluctuating water levels). Principal component analysis (PCA) of the datasets indicated that major ion content, specifically calcium (Ca2+), was responsible for much of the variability among the ponds in both 2008 and 2009. Additionally in 2009 most of the variability was also due to specific conductivity in the summer and magnesium (Mg2+) in the fall. These trends are typically identified as a result of dilution or evapo-concentration processes in small water bodies. In 2007, a warm and dry year, pH and potassium (K+) were responsible for much of variation between ponds. This is attributed to high vegetation growth in ponds and a longer growing season. While no trend was identified in 2010 (PCA analysis), calculations of greenhouse gas (GHG) emissions from 50

  1. The variability of the large genomic segment of Tahyna orthobunyavirus and an all-atom exploration of its anti-viral drug resistance

    Czech Academy of Sciences Publication Activity Database

    Kilian, Patrik; Valdés, James J.; Lecina-Casas, D.; Chrudimský, T.; Růžek, Daniel

    2013-01-01

    Roč. 20, 2013-Dec (2013), s. 304-311 ISSN 1567-1348 R&D Projects: GA ČR GAP502/11/2116; GA MŠk(CZ) EE2.3.30.0032 Institutional support: RVO:60077344 Keywords : Tahyna virus * Orthobunyavirus * California complex * Genetic variability * Large genomic segment Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 3.264, year: 2013

  2. Genomic Variability of Haemophilus influenzae Isolated from Mexican Children Determined by Using Enterobacterial Repetitive Intergenic Consensus Sequences and PCR

    OpenAIRE

    Gomez-De-Leon, Patricia; Santos, Jose I.; Caballero, Javier; Gomez, Demostenes; Espinosa, Luz E.; Moreno, Isabel; Piñero, Daniel; Cravioto, Alejandro

    2000-01-01

    Genomic fingerprints from 92 capsulated and noncapsulated strains of Haemophilus influenzae from Mexican children with different diseases and healthy carriers were generated by PCR using the enterobacterial repetitive intergenic consensus (ERIC) sequences. A cluster analysis by the unweighted pair-group method with arithmetic averages based on the overall similarity as estimated from the characteristics of the genomic fingerprints, was conducted to group the strains. A total of 69 fingerprint...

  3. Genomes of Helicobacter pylori from native Peruvians suggest admixture of ancestral and modern lineages and reveal a western type cag-pathogenicity island

    Directory of Open Access Journals (Sweden)

    Rahman Syed

    2006-07-01

    Full Text Available Abstract Background Helicobacter pylori is presumed to be co-evolved with its human host and is a highly diverse gastric pathogen at genetic levels. Ancient origins of H. pylori in the New World are still debatable. It is not clear how different waves of human migrations in South America contributed to the evolution of strain diversity of H. pylori. The objective of our 'phylogeographic' study was to gain fresh insights into these issues through mapping genetic origins of H. pylori of native Peruvians (of Amerindian ancestry and their genomic comparison with isolates from Spain, and Japan. Results For this purpose, we attempted to dissect genetic identity of strains by fluorescent amplified fragment length polymorphism (FAFLP analysis, multilocus sequence typing (MLST of the 7 housekeeping genes (atpA, efp, ureI, ppa, mutY, trpC, yphC and the sequence analyses of the babB adhesin and oipA genes. The whole cag pathogenicity-island (cagPAI from these strains was analyzed using PCR and the geographic type of cagA phosphorylation motif EPIYA was determined by gene sequencing. We observed that while European genotype (hp-Europe predominates in native Peruvian strains, approximately 20% of these strains represent a sub-population with an Amerindian ancestry (hsp-Amerind. All of these strains however, irrespective of their ancestral affiliation harbored a complete, 'western' type cagPAI and the motifs surrounding it. This indicates a possible acquisition of cagPAI by the hsp-Amerind strains from the European strains, during decades of co-colonization. Conclusion Our observations suggest presence of ancestral H. pylori (hsp-Amerind in Peruvian Amerindians which possibly managed to survive and compete against the Spanish strains that arrived to the New World about 500 years ago. We suggest that this might have happened after native Peruvian H. pylori strains acquired cagPAI sequences, either by new acquisition in cag-negative strains or by recombination

  4. First report in Africa of two clinical isolates of Proteus mirabilis carrying Salmonella genomic island (SGI1) variants, SGI1-PmABB and SGI1-W.

    Science.gov (United States)

    Soliman, Ahmed M; Ahmed, Ashraf M; Shimamoto, Toshi; El-Domany, Ramadan A; Nariya, Hirofumi; Shimamoto, Tadashi

    2017-07-01

    Two Proteus mirabilis strains, designated PmTAN59 and PmKAF126, were isolated from two different Egyptian cities in 2014 and 2015, respectively. PmTAN59 was isolated from a sputum swab from a pneumonia patient in Tanta University Teaching Hospital. PmKAF126 was isolated from a patient with a diabetic foot infection in a hospital in the city of Kafr El-Sheikh. The two isolates were identified with bacterial small ribosomal RNA (16S rRNA) gene amplification and sequencing and tested for antimicrobial sensitivity with a Kirby-Bauer disk diffusion assay. The two strains were resistant to amoxicillin/clavulante, ampicillin, cefotaxime, cefoxitin, ceftriaxone, chloramphenicol, ciprofloxacin, colistin, gentamicin, kanamycin, nalidixic acid, spectinomycin, streptomycin, sulfamethoxazole/trimethoprime, and tetracycline, but sensitive to aztreonam, imipenem, and meropenem. Molecular characterization was used to map the entire backbone, including the multiple antibiotic resistance (MDR) region, of Salmonella genomic island 1 (SGI1). Both isolates carried a structure similar to SGI1, with two different MDR regions corresponding to SGI1-PmABB in PmTAN59 and SGI1-W in PmKAF126. SGI1-PmABB carried an integron of ~1.5kb with a two-gene cassette, aacCA5-aadA7, which confers resistance to gentamicin, streptomycin, and spectinomycin, whereas SGI1-W carried an integron of ~1.9kb containing aadA2-lnuF, which confers resistance to spectinomycin, streptomycin, and lincosamides. PmKAF126 carried the entire SGI1 sequence, however PmTAN59 carried a SGI1 structure with a deletion in the region from ORF S005 to ORF S009 and accompanied by insertion of IS1359 (1258bp). Furthermore, PmTAN59 carried class 2 integron of ~2.2kb containing dfrA1-sat2-aadA1. An ERIC-PCR analysis detected no clonal relationship between the two strains. Molecular screening for other antimicrobial resistance genes and a plasmid analysis indicated that PmTAN59 carried an IncFIB plasmid type. This strain also carried bla

  5. Variable Selection in Heterogeneous Datasets: A Truncated-rank Sparse Linear Mixed Model with Applications to Genome-wide Association Studies.

    Science.gov (United States)

    Wang, Haohan; Aragam, Bryon; Xing, Eric P

    2018-04-26

    A fundamental and important challenge in modern datasets of ever increasing dimensionality is variable selection, which has taken on renewed interest recently due to the growth of biological and medical datasets with complex, non-i.i.d. structures. Naïvely applying classical variable selection methods such as the Lasso to such datasets may lead to a large number of false discoveries. Motivated by genome-wide association studies in genetics, we study the problem of variable selection for datasets arising from multiple subpopulations, when this underlying population structure is unknown to the researcher. We propose a unified framework for sparse variable selection that adaptively corrects for population structure via a low-rank linear mixed model. Most importantly, the proposed method does not require prior knowledge of sample structure in the data and adaptively selects a covariance structure of the correct complexity. Through extensive experiments, we illustrate the effectiveness of this framework over existing methods. Further, we test our method on three different genomic datasets from plants, mice, and human, and discuss the knowledge we discover with our method. Copyright © 2018. Published by Elsevier Inc.

  6. Canary Islands

    Science.gov (United States)

    1992-01-01

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

  7. Genome variability in European and American bison detected using the BovineSNP50 BeadChip

    DEFF Research Database (Denmark)

    Pertoldi, C.; Wójcik, Jan M; Tokarska, Małgorzata

    2010-01-01

     The remaining wild populations of bison have all been through severe bottlenecks. The genomic consequences of these bottlenecks present an interesting area to study. Using a very large panel of SNPs developed in Bos taurus we have carried out a genome-wide screening on the European bison (Bison...... bonasus; EB) and on two subspecies of American bison: the plains bison (B. bison bison; PB) and the wood bison (B. bison athabascae; WB). One hundred bison samples were genotyped for 52,978 SNPs along with seven breeds of domestic bovine Bos taurus. Only 2,209 of the SNPs were polymorphic in the bison...

  8. An assessment of postcranial indices, ratios, and body mass versus eco-geographical variables of prehistoric Jomon, Yayoi agriculturalists, and Kumejima Islanders of Japan.

    Science.gov (United States)

    Seguchi, Noriko; Quintyn, Conrad B; Yonemoto, Shiori; Takamuku, Hirofumi

    2017-09-10

    We explore variations in body and limb proportions of the Jomon hunter-gatherers (14,000-2500 BP), the Yayoi agriculturalists (2500-1700 BP) of Japan, and the Kumejima Islanders of the Ryukyus (1600-1800 AD) with 11 geographically diverse skeletal postcranial samples from Africa, Europe, Asia, Australia, and North America using brachial-crural indices, femur head-breadth-to-femur length ratio, femur head-breadth-to-lower-limb-length ratio, and body mass as indicators of phenotypic climatic adaptation. Specifically, we test the hypothesis that variation in limb proportions seen in Jomon, Yayoi, and Kumejima is a complex interaction of genetic adaptation; development and allometric constraints; selection, gene flow and genetic drift with changing cultural factors (i.e., nutrition) and climate. The skeletal data (1127 individuals) were subjected to principle components analysis, Manly's permutation multiple regression tests, and Relethford-Blangero analysis. The results of Manly's tests indicate that body proportions and body mass are significantly correlated with latitude, and minimum and maximum temperatures while limb proportions were not significantly correlated with these climatic variables. Principal components plots separated "climatic zones:" tropical, temperate, and arctic populations. The indigenous Jomon showed cold-adapted body proportions and warm-adapted limb proportions. Kumejima showed cold-adapted body proportions and limbs. The Yayoi adhered to the Allen-Bergmann expectation of cold-adapted body and limb proportions. Relethford-Blangero analysis showed that Kumejima experienced gene flow indicated by high observed variances while Jomon experienced genetic drift indicated by low observed variances. The complex interaction of evolutionary forces and development/nutritional constraints are implicated in the mismatch of limb and body proportions. © 2017 Wiley Periodicals, Inc.

  9. Discovering human germ cell mutagens with whole genome sequencing: Insights from power calculations reveal the importance of controlling for between-family variability.

    Science.gov (United States)

    Webster, R J; Williams, A; Marchetti, F; Yauk, C L

    2018-07-01

    Mutations in germ cells pose potential genetic risks to offspring. However, de novo mutations are rare events that are spread across the genome and are difficult to detect. Thus, studies in this area have generally been under-powered, and no human germ cell mutagen has been identified. Whole Genome Sequencing (WGS) of human pedigrees has been proposed as an approach to overcome these technical and statistical challenges. WGS enables analysis of a much wider breadth of the genome than traditional approaches. Here, we performed power analyses to determine the feasibility of using WGS in human families to identify germ cell mutagens. Different statistical models were compared in the power analyses (ANOVA and multiple regression for one-child families, and mixed effect model sampling between two to four siblings per family). Assumptions were made based on parameters from the existing literature, such as the mutation-by-paternal age effect. We explored two scenarios: a constant effect due to an exposure that occurred in the past, and an accumulating effect where the exposure is continuing. Our analysis revealed the importance of modeling inter-family variability of the mutation-by-paternal age effect. Statistical power was improved by models accounting for the family-to-family variability. Our power analyses suggest that sufficient statistical power can be attained with 4-28 four-sibling families per treatment group, when the increase in mutations ranges from 40 to 10% respectively. Modeling family variability using mixed effect models provided a reduction in sample size compared to a multiple regression approach. Much larger sample sizes were required to detect an interaction effect between environmental exposures and paternal age. These findings inform study design and statistical modeling approaches to improve power and reduce sequencing costs for future studies in this area. Crown Copyright © 2018. Published by Elsevier B.V. All rights reserved.

  10. Detecting correlation between allele frequencies and environmental variables as a signature of selection. A fast computational approach for genome-wide studies

    DEFF Research Database (Denmark)

    Guillot, Gilles; Vitalis, Renaud; Rouzic, Arnaud le

    2014-01-01

    to disentangle the potential effect of environmental variables from the confounding effect of population history. For the routine analysis of genome-wide datasets, one also needs fast inference and model selection algorithms. We propose a method based on an explicit spatial model which is an instance of spatial...... for the most common types of genetic markers, obtained either at the individual or at the population level. Analyzing the simulated data produced under a geostatistical model then under an explicit model of selection, we show that the method is efficient. We also re-analyze a dataset relative to nineteen pine...

  11. Variable number of tandem repeat markers in the genome sequence of Mycosphaerella fijiensis, the causal agent of black leaf streak disease of banana (Musa spp).

    Science.gov (United States)

    Garcia, S A L; Van der Lee, T A J; Ferreira, C F; Te Lintel Hekkert, B; Zapater, M-F; Goodwin, S B; Guzmán, M; Kema, G H J; Souza, M T

    2010-11-09

    We searched the genome of Mycosphaerella fijiensis for molecular markers that would allow population genetics analysis of this plant pathogen. M. fijiensis, the causal agent of banana leaf streak disease, also known as black Sigatoka, is the most devastating pathogen attacking bananas (Musa spp). Recently, the entire genome sequence of M. fijiensis became available. We screened this database for VNTR markers. Forty-two primer pairs were selected for validation, based on repeat type and length and the number of repeat units. Five VNTR markers showing multiple alleles were validated with a reference set of isolates from different parts of the world and a population from a banana plantation in Costa Rica. Polymorphism information content values varied from 0.6414 to 0.7544 for the reference set and from 0.0400 and 0.7373 for the population set. Eighty percent of the polymorphism information content values were above 0.60, indicating that the markers are highly informative. These markers allowed robust scoring of agarose gels and proved to be useful for variability and population genetics studies. In conclusion, the strategy we developed to identify and validate VNTR markers is an efficient means to incorporate markers that can be used for fungicide resistance management and to develop breeding strategies to control banana black leaf streak disease. This is the first report of VNTR-minisatellites from the M. fijiensis genome sequence.

  12. Calibration of multivariate scatter plots for exploratory analysis of relations within and between sets of variables in genomic research

    NARCIS (Netherlands)

    Graffelman, J.; Eeuwijk, van F.A.

    2005-01-01

    The scatter plot is a well known and easily applicable graphical tool to explore relationships between two quantitative variables. For the exploration of relations between multiple variables, generalisations of the scatter plot are useful. We present an overview of multivariate scatter plots

  13. The spatial variability of nitrogen and phosphorus concentration in a sand aquifer influenced by onsite sewage treatment and disposal systems: a case study on St. George Island, Florida.

    Science.gov (United States)

    Corbet, D Reide; Dillon, Kevin; Burnett, William; Schaefer, Geoff

    2002-01-01

    Groundwater from a shallow freshwater lens on St. George Island, a barrier island located in the Panhandle of Florida, eventually discharges into Apalachicola Bay or the Gulf of Mexico. Nutrient concentrations in groundwaters were monitored downfield from three onsite sewage treatment and disposal systems (OSTDS) on the island. Estimates of natural groundwater nutrient concentrations were obtained from an adjacent uninhabited island. Silicate, which was significantly higher in the imported drinking water relative to the surficial aquifer on St. George Island (12.2+/-1.9 mg Si l(-1) and 2.9+/-0.2 mg Si l(-1), respectively), was used as a natural conservative tracer. Our observations showed that nitrogen concentrations were attenuated to a greater extent than that of phosphorus relative to the conservative tracer. At the current setback distance (23 m), both nitrogen and phosphate concentrations are still elevated above natural levels by as much as 2 and 7 times, respectively. Increasing the setback distance to 50 m and raising the drainfields 1 m above the ground surface could reduce nutrient levels to natural concentrations (1.1+/-0.1 mg N l(-1), 0.20+/-0.02 mg P l(-1)).

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

    Science.gov (United States)

    Lisa M. Lumley; Felix A.H. Sperling

    2011-01-01

    Identification of widespread species collected from islands can be challenging due to the potential for local ecological and phenotypic divergence in isolated populations. We sought to determine how many species of the spruce budworm (Choristoneura fumiferana) complex reside in Cypress Hills, an isolated remnant coniferous forest in western Canada....

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

    Science.gov (United States)

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

    2015-01-01

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

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

    Science.gov (United States)

    Ford, M.

    2012-12-01

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

  17. Statistical correction of the Winner's Curse explains replication variability in quantitative trait genome-wide association studies.

    Directory of Open Access Journals (Sweden)

    Cameron Palmer

    2017-07-01

    Full Text Available Genome-wide association studies (GWAS have identified hundreds of SNPs responsible for variation in human quantitative traits. However, genome-wide-significant associations often fail to replicate across independent cohorts, in apparent inconsistency with their apparent strong effects in discovery cohorts. This limited success of replication raises pervasive questions about the utility of the GWAS field. We identify all 332 studies of quantitative traits from the NHGRI-EBI GWAS Database with attempted replication. We find that the majority of studies provide insufficient data to evaluate replication rates. The remaining papers replicate significantly worse than expected (p < 10-14, even when adjusting for regression-to-the-mean of effect size between discovery- and replication-cohorts termed the Winner's Curse (p < 10-16. We show this is due in part to misreporting replication cohort-size as a maximum number, rather than per-locus one. In 39 studies accurately reporting per-locus cohort-size for attempted replication of 707 loci in samples with similar ancestry, replication rate matched expectation (predicted 458, observed 457, p = 0.94. In contrast, ancestry differences between replication and discovery (13 studies, 385 loci cause the most highly-powered decile of loci to replicate worse than expected, due to difference in linkage disequilibrium.

  18. Sociodemographic Factors Influencing Island Food Consumption in the Pacific Islander Health Study

    OpenAIRE

    Baumhofer, Nicole Kau'i

    2016-01-01

    This dissertation explores the relationships between island food consumption, sociodemographic variables, and cardiovascular risk using data from the Pacific Islander Health Study (PIHS). Chapter 1 explores the associations between self-reported level of island food consumption and key covariates. Island food consumption was modeled using Poisson regression and adjusted for demographic, socioeconomic, and cultural characteristics. Increased Pacific Island cultural affinity was the strongest p...

  19. Genomic Characterization of Variable Surface Antigens Reveals a Telomere Position Effect as a Prerequisite for RNA Interference-Mediated Silencing in Paramecium tetraurelia

    Science.gov (United States)

    Baranasic, Damir; Oppermann, Timo; Cheaib, Miriam; Cullum, John; Schmidt, Helmut

    2014-01-01

    ABSTRACT Antigenic or phenotypic variation is a widespread phenomenon of expression of variable surface protein coats on eukaryotic microbes. To clarify the mechanism behind mutually exclusive gene expression, we characterized the genetic properties of the surface antigen multigene family in the ciliate Paramecium tetraurelia and the epigenetic factors controlling expression and silencing. Genome analysis indicated that the multigene family consists of intrachromosomal and subtelomeric genes; both classes apparently derive from different gene duplication events: whole-genome and intrachromosomal duplication. Expression analysis provides evidence for telomere position effects, because only subtelomeric genes follow mutually exclusive transcription. Microarray analysis of cultures deficient in Rdr3, an RNA-dependent RNA polymerase, in comparison to serotype-pure wild-type cultures, shows cotranscription of a subset of subtelomeric genes, indicating that the telomere position effect is due to a selective occurrence of Rdr3-mediated silencing in subtelomeric regions. We present a model of surface antigen evolution by intrachromosomal gene duplication involving the maintenance of positive selection of structurally relevant regions. Further analysis of chromosome heterogeneity shows that alternative telomere addition regions clearly affect transcription of closely related genes. Consequently, chromosome fragmentation appears to be of crucial importance for surface antigen expression and evolution. Our data suggest that RNAi-mediated control of this genetic network by trans-acting RNAs allows rapid epigenetic adaptation by phenotypic variation in combination with long-term genetic adaptation by Darwinian evolution of antigen genes. PMID:25389173

  20. Full Genome Sequencing Reveals New Southern African Territories Genotypes Bringing Us Closer to Understanding True Variability of Foot-and-Mouth Disease Virus in Africa

    Science.gov (United States)

    Lasecka-Dykes, Lidia; Wright, Caroline F.; Di Nardo, Antonello; Logan, Grace; Mioulet, Valerie; Jackson, Terry; Tuthill, Tobias J.; Knowles, Nick J.; King, Donald P.

    2018-01-01

    Foot-and-mouth disease virus (FMDV) causes a highly contagious disease of cloven-hooved animals that poses a constant burden on farmers in endemic regions and threatens the livestock industries in disease-free countries. Despite the increased number of publicly available whole genome sequences, FMDV data are biased by the opportunistic nature of sampling. Since whole genomic sequences of Southern African Territories (SAT) are particularly underrepresented, this study sequenced 34 isolates from eastern and southern Africa. Phylogenetic analyses revealed two novel genotypes (that comprised 8/34 of these SAT isolates) which contained unusual 5′ untranslated and non-structural encoding regions. While recombination has occurred between these sequences, phylogeny violation analyses indicated that the high degree of sequence diversity for the novel SAT genotypes has not solely arisen from recombination events. Based on estimates of the timing of ancestral divergence, these data are interpreted as being representative of un-sampled FMDV isolates that have been subjected to geographical isolation within Africa by the effects of the Great African Rinderpest Pandemic (1887–1897), which caused a mass die-out of FMDV-susceptible hosts. These findings demonstrate that further sequencing of African FMDV isolates is likely to reveal more unusual genotypes and will allow for better understanding of natural variability and evolution of FMDV. PMID:29652800

  1. Cytomegalovirus sequence variability, amplicon length, and DNase-sensitive non-encapsidated genomes are obstacles to standardization and commutability of plasma viral load results.

    Science.gov (United States)

    Naegele, Klaudia; Lautenschlager, Irmeli; Gosert, Rainer; Loginov, Raisa; Bir, Katia; Helanterä, Ilkka; Schaub, Stefan; Khanna, Nina; Hirsch, Hans H

    2018-04-22

    Cytomegalovirus (CMV) management post-transplantation relies on quantification in blood, but inter-laboratory and inter-assay variability impairs commutability. An international multicenter study demonstrated that variability is mitigated by standardizing plasma volumes, automating DNA extraction and amplification, and calibration to the 1st-CMV-WHO-International-Standard as in the FDA-approved Roche-CAP/CTM-CMV. However, Roche-CAP/CTM-CMV showed under-quantification and false-negative results in a quality assurance program (UK-NEQAS-2014). To evaluate factors contributing to quantification variability of CMV viral load and to develop optimized CMV-UL54-QNAT. The UL54 target of the UK-NEQAS-2014 variant was sequenced and compared to 329 available CMV GenBank sequences. Four Basel-CMV-UL54-QNAT assays of 361 bp, 254 bp, 151 bp, and 95 bp amplicons were developed that only differed in reverse primer positions. The assays were validated using plasmid dilutions, UK-NEQAS-2014 sample, as well as 107 frozen and 69 prospectively collected plasma samples from transplant patients submitted for CMV QNAT, with and without DNase-digestion prior to nucleic acid extraction. Eight of 43 mutations were identified as relevant in the UK-NEQAS-2014 target. All Basel-CMV-UL54 QNATs quantified the UK-NEQAS-2014 but revealed 10-fold increasing CMV loads as amplicon size decreased. The inverse correlation of amplicon size and viral loads was confirmed using 1st-WHO-International-Standard and patient samples. DNase pre-treatment reduced plasma CMV loads by >90% indicating the presence of unprotected CMV genomic DNA. Sequence variability, amplicon length, and non-encapsidated genomes obstruct standardization and commutability of CMV loads needed to develop thresholds for clinical research and management. Besides regular sequence surveys, matrix and extraction standardization, we propose developing reference calibrators using 100 bp amplicons. Copyright © 2018 Elsevier B.V. All

  2. Positive selection in the chromosome 16 VKORC1 genomic region has contributed to the variability of anticoagulant response in humans.

    Directory of Open Access Journals (Sweden)

    Blandine Patillon

    Full Text Available VKORC1 (vitamin K epoxide reductase complex subunit 1, 16p11.2 is the main genetic determinant of human response to oral anticoagulants of antivitamin K type (AVK. This gene was recently suggested to be a putative target of positive selection in East Asian populations. In this study, we genotyped the HGDP-CEPH Panel for six VKORC1 SNPs and downloaded chromosome 16 genotypes from the HGDP-CEPH database in order to characterize the geographic distribution of footprints of positive selection within and around this locus. A unique VKORC1 haplotype carrying the promoter mutation associated with AVK sensitivity showed especially high frequencies in all the 17 HGDP-CEPH East Asian population samples. VKORC1 and 24 neighboring genes were found to lie in a 505 kb region of strong linkage disequilibrium in these populations. Patterns of allele frequency differentiation and haplotype structure suggest that this genomic region has been submitted to a near complete selective sweep in all East Asian populations and only in this geographic area. The most extreme scores of the different selection tests are found within a smaller 45 kb region that contains VKORC1 and three other genes (BCKDK, MYST1 (KAT8, and PRSS8 with different functions. Because of the strong linkage disequilibrium, it is not possible to determine if VKORC1 or one of the three other genes is the target of this strong positive selection that could explain present-day differences among human populations in AVK dose requirement. Our results show that the extended region surrounding a presumable single target of positive selection should be analyzed for genetic variation in a wide range of genetically diverse populations in order to account for other neighboring and confounding selective events and the hitchhiking effect.

  3. Marshall Islands

    OpenAIRE

    World Bank

    2015-01-01

    This note aims to build understanding of the existing disaster risk financing and insurance (DRFI) tools in use in The Marshall Islands and to identify gaps where potential engagement could further develop financial resilience. The likelihood that a hazardous event will have a significant impact on the Marshall Islands has risen with the increasing levels of population and assets in the urban ...

  4. Identifying Pathogenicity Islands in Bacterial Pathogenomics Using Computational Approaches

    Directory of Open Access Journals (Sweden)

    Dongsheng Che

    2014-01-01

    Full Text Available 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.

  5. The effects of island ontogeny on species diversity and phylogeny

    NARCIS (Netherlands)

    Valente, Luis M.; Etienne, Rampal S.; Phillimore, Albert B.

    2014-01-01

    A major goal of island biogeography is to understand how island communities are assembled over time. However, we know little about the influence of variable area and ecological opportunity on island biotas over geological time-scales. Islands have limited life spans, and it has been posited that

  6. Sperm variables as predictors of fertility in Black Castellana roosters; use in the selection of sperm donors for genome resource banking purposes

    Energy Technology Data Exchange (ETDEWEB)

    Santiago Moreno, J.; Lopez Sebastian, A.; Castano, C.; Coloma, M. A.; Gomez Brunet, A.; Toledano Diaz, A.; Prieto, M. T.; Campo, J. L.

    2009-07-01

    Semen was collected from 10 Black Castellana roosters and the classic sperm variables (ejaculate volume, sperm concentration and sperm motility) examined. In addition, the hypo-osmotic swelling test was used to investigate sperm cell membrane integrity, and acidic aniline blue staining used to screen for morphological abnormalities (including acrosome integrity) and to examine the condensation status of the chromatin. The latter was also examined by Gram staining. Large and small semen volumes were associated high and low sperm concentrations respectively (R2=0.04, P<0.05). The percentage of motile spermatozoa correlated strongly with the percentage of sperm cells showing an intact acrosome (R2=0.13, P<0.001) and with the percentage of morphologically normal spermatozoa (R2=0.04, P<0.05). The percentage of Gram positive spermatozoa was positively correlated with semen appearance (R2=0.12, P<0.05), sperm cell concentration (R2=0.13, P<0.05), and with the sperm motility variables studied (R2=0.14, P<0.05 for percentage mobility, and R2=0.12, P<0.05 for quality of movement). Only three of the 10 roosters, all with fertilisation potentials of 80-90%, were considered potential sperm donors for genome resource banking purposes. The remaining birds were all of low fertility (. 50%); in fact, some produced semen volumes too small to perform fertility tests. Semen volume and membrane integrity were found to be the best variables for predicting the fertilisation potential of rooster ejaculates. (Author) 37 refs.

  7. High-Affinity Methanotrophy Informed by Genome-Wide Analysis of Upland Soil Cluster Alpha (USCα) from Axel Heiberg Island, Canadian High Arctic

    Science.gov (United States)

    Rusley, C.; Onstott, T. C.; Lau, M.

    2017-12-01

    Methane (CH4) is a potent greenhouse gas whose proper budgeting is vital to climate predictions. Recent studies have identified upland Arctic mineral cryosols as consistent CH4 sinks, drawing CH4 from both the atmosphere and underlying anaerobic soil layers. Global atmospheric CH4 uptake is proposed to be mediated by high-affinity methanotrophs based on the detection of the marker gene pmoA (particulate methane monooxygenase beta subunit). However, a lack of pure cultures and scarcity of genomic information have hindered our understanding of their metabolic capabilities and versatility. Together with the missing genetic linkage between its pmoA and 16S ribosomal RNA (rRNA) gene, the factors that control the distribution and magnitude of high-affinity methanotrophy in the Arctic permafrost-affected region have remained elusive. Using 21 metagenomic datasets of surface soils obtained from long-term core incubation experiments,1 this bioinformatics study aimed to reconstruct the draft genome of the Upland Soil Cluster α-proteobacteria (USCα), the high-affinity methanotroph previously detected in the samples,2 and to determine its phylogeny and metabolic requirements. We obtained a genome bin containing the high-affinity form of the USCα-like pmoA gene. The 3.03 Mbp assembly is 91.6% complete with a unique set of single-copy marker genes. The 16S rRNA gene fragment of USCα belongs to the α-proteobacterial family Beijerinckiaceae. Genome annotation indicates possible formaldehyde oxidation via tetrahydromethanopterin-linked C1 transfer pathways, acetate utilization, carbon fixation via the Calvin-Benson-Bassham cycle, and glycogen production. Notably, the key enzymes for formaldehyde assimilation via the serine and ribulose monophosphate pathways are missing. The presence of genes encoding nitrate reductase and hemoglobin suggests adaptation to low O2 under water-logged conditions. Since USCα has versatile carbon metabolisms, it may not be an obligate methanotroph

  8. The KL24 gene cluster and a genomic island encoding a Wzy polymerase contribute genes needed for synthesis of the K24 capsular polysaccharide by the multiply antibiotic resistant Acinetobacter baumannii isolate RCH51.

    Science.gov (United States)

    Kenyon, Johanna J; Kasimova, Anastasiya A; Shneider, Mikhail M; Shashkov, Alexander S; Arbatsky, Nikolay P; Popova, Anastasiya V; Miroshnikov, Konstantin A; Hall, Ruth M; Knirel, Yuriy A

    2017-03-01

    The whole-genome sequence of the multiply antibiotic resistant Acinetobacter baumannii isolate RCH51 belonging to sequence type ST103 (Institut Pasteur scheme) revealed that the set of genes at the capsule locus, KL24, includes four genes predicted to direct the synthesis of 3-acetamido-3,6-dideoxy-d-galactose (d-Fuc3NAc), and this sugar was found in the capsular polysaccharide (CPS). One of these genes, fdtE, encodes a novel bifunctional protein with an N-terminal FdtA 3,4-ketoisomerase domain and a C-terminal acetyltransferase domain. KL24 lacks a gene encoding a Wzy polymerase to link the oligosaccharide K units to form the CPS found associated with isolate RCH51, and a wzy gene was found in a small genomic island (GI) near the cpn60 gene. This GI is in precisely the same location as another GI carrying wzy and atr genes recently found in several A. baumannii isolates, but it does not otherwise resemble it. The CPS isolated from RCH51, studied by sugar analysis and 1D and 2D 1H and 13C NMR spectroscopy, revealed that the K unit has a branched pentasaccharide structure made up of Gal, GalNAc and GlcNAc residues with d-Fuc3NAc as a side branch, and the K units are linked via a β-d-GlcpNAc-(1→3)-β-d-Galp linkage formed by the Wzy encoded by the GI. The functions of the glycosyltransferases encoded by KL24 were assigned to formation of specific bonds. A correspondence between the order of the genes in KL24 and other KL and the order of the linkages they form was noted, and this may be useful in future predictions of glycosyltransferase specificities.

  9. Millennial-scale precipitation variability over Easter Island (South Pacific) during MIS 3: inter-hemispheric teleconnections with North Atlantic abrupt cold events

    Science.gov (United States)

    Margalef, O.; Cacho, I.; Pla-Rabes, S.; Cañellas-Boltà, N.; Pueyo, J. J.; Sáez, A.; Pena, L. D.; Valero-Garcés, B. L.; Rull, V.; Giralt, S.

    2015-04-01

    Marine Isotope Stage 3 (MIS 3, 59.4-27.8 kyr BP) is characterized by the occurrence of rapid millennial-scale climate oscillations known as Dansgaard-Oeschger cycles (DO) and by abrupt cooling events in the North Atlantic known as Heinrich events. Although both the timing and dynamics of these events have been broadly explored in North Atlantic records, the response of the tropical and subtropical latitudes to these rapid climatic excursions, particularly in the Southern Hemisphere, still remains unclear. The Rano Aroi peat record (Easter Island, 27° S) provides a unique opportunity to understand atmospheric and oceanic changes in the South Pacific during these DO cycles because of its singular location, which is influenced by the South Pacific Anticyclone (SPA), the Southern Westerlies (SW), and the Intertropical Convergence Zone (ITCZ) linked to the South Pacific Convergence Zone (SPCZ). The Rano Aroi sequence records 6 major events of enhanced precipitation between 38 and 65 kyr BP. These events are compared with other hydrological records from the tropical and subtropical band supporting a coherent regional picture, with the dominance of humid conditions in Southern Hemisphere tropical band during Heinrich Stadials (HS) 5, 5a and 6 and other Stadials while dry conditions prevailed in the Northern tropics. This antiphased hydrological pattern between hemispheres has been attributed to ITCZ migration, which in turn might be associated with an eastward expansion of the SPCZ storm track, leading to an increased intensity of cyclogenic storms reaching Easter Island. Low Pacific Sea Surface Temperature (SST) gradients across the Equator were coincident with the here-defined Rano Aroi humid events and consistent with a reorganization of Southern Pacific atmospheric and oceanic circulation also at higher latitudes during Heinrich and Dansgaard-Oeschger stadials.

  10. Modeling the distribution of Norway rats (Rattus norvegicus on offshore islands in the Falkland Islands

    Directory of Open Access Journals (Sweden)

    Michael A. Tabak

    2015-01-01

    Full Text Available Non-native rats (Rattus spp. threaten native island species worldwide. Efforts to eradicate them from islands have increased in frequency and become more ambitious in recent years. However, the long-term success of some eradication efforts has been compromised by the ability of rats, particularly Norway rats (Rattus norvegicus which are good swimmers, to recolonize islands following eradications. In the Falkland Islands, an archipelago in the South Atlantic Ocean, the distance of 250 m between islands (once suggested as the minimum separation distance for an effective barrier to recolonization has shown to be insufficient. Norway rats are present on about half of the 503 islands in the Falklands. Bird diversity is lower on islands with rats and two vulnerable passerine species, Troglodytes cobbi (the only endemic Falkland Islands passerine and Cinclodes antarcticus, have greatly reduced abundances and/or are absent on islands with rats. We used logistic regression models to investigate the potential factors that may determine the presence of Norway rats on 158 islands in the Falkland Islands. Our models included island area, distance to the nearest rat-infested island, island location, and the history of island use by humans as driving variables. Models best supported by data included only distance to the nearest potential source of rats and island area, but the relative magnitude of the effect of distance and area on the presence of rats varied depending on whether islands were in the eastern or western sector of the archipelago. The human use of an island was not a significant parameter in any models. A very large fraction (72% of islands within 500 m of the nearest potential rat source had rats, but 97% of islands farther than 1,000 m away from potential rat sources were free of rats.

  11. Limitations of variable number of tandem repeat typing identified through whole genome sequencing of Mycobacterium avium subsp. paratuberculosis on a national and herd level.

    Science.gov (United States)

    Ahlstrom, Christina; Barkema, Herman W; Stevenson, Karen; Zadoks, Ruth N; Biek, Roman; Kao, Rowland; Trewby, Hannah; Haupstein, Deb; Kelton, David F; Fecteau, Gilles; Labrecque, Olivia; Keefe, Greg P; McKenna, Shawn L B; De Buck, Jeroen

    2015-03-08

    Mycobacterium avium subsp. paratuberculosis (MAP), the causative bacterium of Johne's disease in dairy cattle, is widespread in the Canadian dairy industry and has significant economic and animal welfare implications. An understanding of the population dynamics of MAP can be used to identify introduction events, improve control efforts and target transmission pathways, although this requires an adequate understanding of MAP diversity and distribution between herds and across the country. Whole genome sequencing (WGS) offers a detailed assessment of the SNP-level diversity and genetic relationship of isolates, whereas several molecular typing techniques used to investigate the molecular epidemiology of MAP, such as variable number of tandem repeat (VNTR) typing, target relatively unstable repetitive elements in the genome that may be too unpredictable to draw accurate conclusions. The objective of this study was to evaluate the diversity of bovine MAP isolates in Canadian dairy herds using WGS and then determine if VNTR typing can distinguish truly related and unrelated isolates. Phylogenetic analysis based on 3,039 SNPs identified through WGS of 124 MAP isolates identified eight genetically distinct subtypes in dairy herds from seven Canadian provinces, with the dominant type including over 80% of MAP isolates. VNTR typing of 527 MAP isolates identified 12 types, including "bison type" isolates, from seven different herds. At a national level, MAP isolates differed from each other by 1-2 to 239-240 SNPs, regardless of whether they belonged to the same or different VNTR types. A herd-level analysis of MAP isolates demonstrated that VNTR typing may both over-estimate and under-estimate the relatedness of MAP isolates found within a single herd. The presence of multiple MAP subtypes in Canada suggests multiple introductions into the country including what has now become one dominant type, an important finding for Johne's disease control. VNTR typing often failed to

  12. Pathogenicity island mobility and gene content.

    Energy Technology Data Exchange (ETDEWEB)

    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.

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

    Science.gov (United States)

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

    1998-01-01

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

  14. Bioavailability and Variability of Cd, Pb, Zn, and Cu Pollution in Soft Tissues and Shell of Saccostrea cucullata Collected from the Coast of Qeshm Island, Persian Gulf, Iran

    Directory of Open Access Journals (Sweden)

    Ali Kazemi

    2016-07-01

    Full Text Available Background: Marine pollution is a global environmental problem that its monitoring by ideal biomonitors is of great importance. Marine organisms, especially mussels, have the ability to accumulate metals from the environment; they can be considered as a biomonitoring agent. Methods: In this study, concentrations of heavy metals were measured in Saccostrea cucullata collected from seven sites on Qeshm Island's Coast. To achieve a digesting sample, each soft tissue was obtained and each of the shell homogeneous powders, 0.8 g and 1 g, respectively, were mixed with 10 mL HNO3 (69% and poured into a PTFE digestion vessel. The prepared samples were evaluated for Cd, Cu, and Zn by using a flame AAS Model 67OG and for Pb by using a graphite furnace AAS. Results: The distributions of metals between soft tissues and shells were compared in each sampling site. For seven sites, Cd, Zn, and Cu levels in soft tissues were higher than in the shells, but Pb level was higher in the shells than in the soft tissues. In addition, the results indicated the coefficient of variation (CV in the soft tissues was lower than the shells for Cd, and in the shells lower than the soft tissues for Pb, whereas the CV values were different in both the soft tissues and shells for Zn and Cu. Conclusion: The results of this study support using these materials in S. cucullata for biomonitoring. Shells are appropriate for monitoring Pb contamination, and the soft tissues are more apt for monitoring Cd, Zn, and Cu contamination.

  15. Evaluating aggregate effects of rare and common variants in the 1000 Genomes Project exon sequencing data using latent variable structural equation modeling.

    Science.gov (United States)

    Nock, Nl; Zhang, Lx

    2011-11-29

    Methods that can evaluate aggregate effects of rare and common variants are limited. Therefore, we applied a two-stage approach to evaluate aggregate gene effects in the 1000 Genomes Project data, which contain 24,487 single-nucleotide polymorphisms (SNPs) in 697 unrelated individuals from 7 populations. In stage 1, we identified potentially interesting genes (PIGs) as those having at least one SNP meeting Bonferroni correction using univariate, multiple regression models. In stage 2, we evaluate aggregate PIG effects on trait, Q1, by modeling each gene as a latent construct, which is defined by multiple common and rare variants, using the multivariate statistical framework of structural equation modeling (SEM). In stage 1, we found that PIGs varied markedly between a randomly selected replicate (replicate 137) and 100 other replicates, with the exception of FLT1. In stage 1, collapsing rare variants decreased false positives but increased false negatives. In stage 2, we developed a good-fitting SEM model that included all nine genes simulated to affect Q1 (FLT1, KDR, ARNT, ELAV4, FLT4, HIF1A, HIF3A, VEGFA, VEGFC) and found that FLT1 had the largest effect on Q1 (βstd = 0.33 ± 0.05). Using replicate 137 estimates as population values, we found that the mean relative bias in the parameters (loadings, paths, residuals) and their standard errors across 100 replicates was on average, less than 5%. Our latent variable SEM approach provides a viable framework for modeling aggregate effects of rare and common variants in multiple genes, but more elegant methods are needed in stage 1 to minimize type I and type II error.

  16. Winner's Curse Correction and Variable Thresholding Improve Performance of Polygenic Risk Modeling Based on Genome-Wide Association Study Summary-Level Data.

    Directory of Open Access Journals (Sweden)

    Jianxin Shi

    2016-12-01

    Full Text Available Recent heritability analyses have indicated that genome-wide association studies (GWAS have the potential to improve genetic risk prediction for complex diseases based on polygenic risk score (PRS, a simple modelling technique that can be implemented using summary-level data from the discovery samples. We herein propose modifications to improve the performance of PRS. We introduce threshold-dependent winner's-curse adjustments for marginal association coefficients that are used to weight the single-nucleotide polymorphisms (SNPs in PRS. Further, as a way to incorporate external functional/annotation knowledge that could identify subsets of SNPs highly enriched for associations, we propose variable thresholds for SNPs selection. We applied our methods to GWAS summary-level data of 14 complex diseases. Across all diseases, a simple winner's curse correction uniformly led to enhancement of performance of the models, whereas incorporation of functional SNPs was beneficial only for selected diseases. Compared to the standard PRS algorithm, the proposed methods in combination led to notable gain in efficiency (25-50% increase in the prediction R2 for 5 of 14 diseases. As an example, for GWAS of type 2 diabetes, winner's curse correction improved prediction R2 from 2.29% based on the standard PRS to 3.10% (P = 0.0017 and incorporating functional annotation data further improved R2 to 3.53% (P = 2×10-5. Our simulation studies illustrate why differential treatment of certain categories of functional SNPs, even when shown to be highly enriched for GWAS-heritability, does not lead to proportionate improvement in genetic risk-prediction because of non-uniform linkage disequilibrium structure.

  17. Identification and characterization of a highly variable region in mitochondrial genomes of fusarium species and analysis of power generation from microbial fuel cells

    Science.gov (United States)

    Hamzah, Haider Mousa

    In the microbial fuel cell (MFC) project, power generation from Shewanella oneidensis MR-1 was analyzed looking for a novel system for both energy generation and sustainability. The results suggest the possibility of generating electricity from different organic substances, which include agricultural and industrial by-products. Shewanella oneidensis MR-1 generates usable electrons at 30°C using both submerged and solid state cultures. In the MFC biocathode experiment, most of the CO2 generated at the anodic chamber was converted into bicarbonate due the activity of carbonic anhydrase (CA) of the Gluconobacter sp.33 strain. These findings demonstrate the possibility of generation of electricity while at the same time allowing the biomimetic sequestration of CO2 using bacterial CA. In the mitochondrial genomes project, the filamentous fungal species Fusarium oxysporum was used as a model. This species causes wilt of several important agricultural crops. A previous study revealed that a highly variable region (HVR) in the mitochondrial DNA (mtDNA) of three species of Fusarium contained a large, variable unidentified open reading frame (LV-uORF). Using specific primers for two regions of the LV-uORF, six strains were found to contain the ORF by PCR and database searches identified 18 other strains outside of the Fusarium oxysporum species complex. The LV-uORF was also identified in three isolates of the F. oxysporum species complex. Interestingly, several F. oxysporum isolates lack the LV-uORF and instead contain 13 ORFs in the HVR, nine of which are unidentified. The high GC content and codon usage of the LV-uORF indicate that it did not co-evolve with other mt genes and was horizontally acquired and was introduced to the Fusarium lineage prior to speciation. The nonsynonymous/synonymous (dN/dS) ratio of the LV-uORFs (0.43) suggests it is under purifying selection and the putative polypeptide is predicted to be located in the mitochondrial membrane. Growth assays

  18. Class renormalization: islands around islands

    International Nuclear Information System (INIS)

    Meiss, J.D.

    1986-01-01

    An orbit of 'class' is one that rotates about a periodic orbit of one lower class with definite frequency. This contrasts to the 'level' of a periodic orbit which is the number of elements in its continued fraction expansion. Level renormalization is conventionally used to study the structure of quasi-periodic orbits. The scaling structure of periodic orbits encircling other periodic orbits in area preserving maps is discussed here. Fixed points corresponding to the accumulation of p/q bifurcations are found and scaling exponents determined. Fixed points for q > 2 correspond to self-similar islands around islands. Frequencies of the island boundary circles at the fixed points are obtained. Importance of this scaling for the motion of particles in stochastic regions is emphasized. (author)

  19. Genetic variability and forensic efficiency of 39 microsatellite loci in the Li ethnic group from Hainan Island in the South China Sea.

    Science.gov (United States)

    Chen, Jing; Xie, Bingbing; Yang, Yaran; Yang, Meng; Liu, Chao; Lv, Yuexin; Chen, Chuguang; Liu, Xu; Fang, Xiangdong; Wu, Huijuan; Yan, Jiangwei

    2017-08-01

    Investigation of allele and genotype frequencies of microsatellite loci in various populations is an essential pre-requisite in forensic application. The present study obtained population genetic data and forensic parameters of 39 autosomal Short Tandem Repeats (STRs) loci from a Chinese Li ethnic group and estimated the genetic relationships between Li and other reference populations. Thirty-nine STR loci, which include D19S433, D5S818, D21S11, D18S51, D6S1043, D3S1358, D13S317, D7S820, D16S539, CSF1PO, Penta D, D2S441, vWA, D8S1179, TPOX, Penta E, TH01, D12S391, D2S1338, FGA, D6S477, D18S535, D19S253, D15S659, D11S2368, D20S470, D1S1656, D22-GATA198B05, D8S1132, D4S2366, D21S1270, D13S325, D9S925, D3S3045, D14S608, D10S1435, D7S3048, D17S1290 and D5S2500, were amplified in two multiplex DNA-STR fluorescence detection systems for 189 unrelated healthy individuals of the Chinese Li ethnic group. The allele frequency distribution and several parameters commonly used in forensic science were statistically analysed. A total of 378 alleles were observed with corresponding allelic frequencies ranging from 0.0026-0.5899. The power of discrimination and power of exclusion ranged from 0.7569-0.9672 and 0.2513-0.7355, respectively. The power of exclusion (PE) ranged from 0.2580-0.7943 for trio paternity cases and 0.1693-0.5940 for duo paternity cases. The polymorphism information content (PIC) ranged from 0.5001-0.8611. The cumulative match probability across these 39 loci was 2.4242 × 10 -38 . The results indicate that 39 STR loci are polymorphic among the Li ethnic group in Hainan Island in the South China Sea. This set of polymorphic STR loci provide highly polymorphic information and forensic efficiency for forensic individual identification and paternity testing, as well as basic population data for population genetics and anthropological research.

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

    Science.gov (United States)

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

    2015-06-01

    We identified a Streptococcus agalactiae metabolic region (fru2) coding for a Phosphoenolpyruvate:carbohydrate phosphoTransferase System (PTS) homologous to the Frz system of extraintestinal pathogenic Escherichia coli strains. The Frz system is involved in environmental sensing and regulation of the expression of adaptation and virulence genes in E. coli. The S. agalactiae fru2 region codes three subunits of a PTS transporter of the fructose-mannitol family, a transcriptional activator of PTSs of the MtlR family, an allulose-6 phosphate-3-epimerase, a transaldolase and a transketolase. We demonstrated that all these genes form an operon. The fru2 operon is present in a 17494-bp genomic island. We analyzed by multilocus sequence typing a population of 492 strains representative of the S. agalactiae population and we showed that the presence of the fru2 operon is linked to the phylogeny of S. agalactiae. The fru2 operon is always present within strains of clonal complexes CC 1, CC 7, CC 10, CC 283 and singletons ST 130 and ST 288, but never found in other CCs and STs. Our results indicate that the fru2 operon was acquired during the evolution of the S. agalactiae species from a common ancestor before the divergence of CC 1, CC 7, CC 10, CC 283, ST 130 and ST 288. As S. agalactiae strains of CC 1 and CC 10 are frequently isolated from adults with invasive disease, we hypothesize that the S. agalactiae Fru2 system senses the environment to allow the bacterium to adapt to new conditions encountered during the infection of adults. Copyright © 2015 Elsevier B.V. All rights reserved.

  1. insights from the genome of Melitaea cinxia

    OpenAIRE

    Ahola, Virpi; Wahlberg, Niklas; Frilander, Mikko J.

    2017-01-01

    The first lepidopteran genome (Bombyx mori) was published in 2004. Ten years later the genome of Melitaea cinxia came out as the third butterfly genome published, and the first eukaryotic genome sequenced in Finland. Owing to Ilkka Hanski, the M. cinxia system in the angstrom land Islands has become a famous model for metapopulation biology. More than 20 years of research on this system provides a strong ecological basis upon which a genetic framework could be built. Genetic knowledge is an e...

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

    Directory of Open Access Journals (Sweden)

    Rachel A Mann

    Full Text Available 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.

  3. Genome plasticity of Vibrio parahaemolyticus: microevolution of the 'pandemic group'

    Directory of Open Access Journals (Sweden)

    Liu Xiumei

    2008-11-01

    Full Text Available Abstract Background Outbreak of V. parahaemolyticus infections occurred since 1996 was linked to a proposed clonal complex, the pandemic group. The whole genome sequence provides an unprecedented opportunity for dissecting genome plasticity and phylogeny of the populations of V. parahaemolyticus. In the present work, a whole-genome cDNA microarray was constructed to compare the genomic contents of a collection of 174 strains of V. parahaemolyticus. Results Genes that present variably in the genome accounted for about 22% of the whole gene pool on the genome. The phylogenetic analysis of microarray data generated a minimum spanning tree that depicted the phylogenetic structure of the 174 strains. Strains were assigned into five complexes (C1 to C5, and those in each complex were related genetically and phylogenetically. C3 and C4 represented highly virulent clinical clones. C2 and C3 constituted two different clonal complexes 'old-O3:K6 clone' and 'pandemic clone', respectively. C3 included all the 39 pandemic strains tested (trh-, tdh+ and GS-PCR+, while C2 contained 12 pre-1996 'old' O3:K6 strains (trh+, tdh- and GS-PCR- tested herein. The pandemic clone (post-1996 'new' O3:K6 and its derivates O4:K68, O1:K25, O1:KUT and O6:K18 might be emerged from the old-O3:K6 clone, which was promoted by acquisition of toxRS/new sequence and genomic islands. A phylogenetic intermediate O3:K6 clade (trh-, tdh- and GS-PCR+ was identified between the pandemic and old-O3:K6 clones. Conclusion A comprehensive overview of genomic contents in a large collection of global isolates from the microarray-based comparative genomic hybridization data enabled us to construct a phylogenetic structure of V. parahaemolyticus and an evolutionary history of the pandemic group (clone of this pathogen.

  4. Intraclonal Genome Stability of the Metallo-β-lactamase SPM-1-producing Pseudomonas aeruginosa ST277, an Endemic Clone Disseminated in Brazilian Hospitals

    Directory of Open Access Journals (Sweden)

    Ana Paula Barbosa Nascimento

    2016-12-01

    Full Text Available Carbapenems represent the mainstay therapy for the treatment of serious P. aeruginosa infections. However, the emergence of carbapenem resistance has jeopardized the clinical use of this important class of compounds. The production of SPM-1 metallo-β-lactamase has been the most common mechanism of carbapenem resistance identified in P. aeruginosa isolated from Brazilian medical centres. Interestingly, a single SPM-1-producing P. aeruginosa clone belonging to the ST277 has been widely spread within the Brazilian territory. In the current study, we performed a next-generation sequencing of six SPM-1-producing P. aeruginosa ST277 isolates. The core genome contains 5 899 coding genes relative to the reference strain P. aeruginosa PAO1. A total of 26 genomic islands were detected in these isolates. We identified remarkable elements inside these genomic islands, such as copies of the blaSPM-1 gene conferring resistance to carbapenems and a type I-C CRISPR-Cas system, which is involved in protection of the chromosome against foreign DNA. In addition, we identified single nucleotide polymorphisms causing amino acid changes in antimicrobial resistance and virulence-related genes. Together, these factors could contribute to the marked resistance and persistence of the SPM-1-producing P. aeruginosa ST277 clone. A comparison of the SPM-1-producing P. aeruginosa ST277 genomes showed that their core genome has a high level nucleotide similarity and synteny conservation. The variability observed was mainly due to acquisition of genomic islands carrying several antibiotic resistance genes.

  5. Intraclonal Genome Stability of the Metallo-β-lactamase SPM-1-producing Pseudomonas aeruginosa ST277, an Endemic Clone Disseminated in Brazilian Hospitals.

    Science.gov (United States)

    Nascimento, Ana P B; Ortiz, Mauro F; Martins, Willames M B S; Morais, Guilherme L; Fehlberg, Lorena C C; Almeida, Luiz G P; Ciapina, Luciane P; Gales, Ana C; Vasconcelos, Ana T R

    2016-01-01

    Carbapenems represent the mainstay therapy for the treatment of serious P. aeruginosa infections. However, the emergence of carbapenem resistance has jeopardized the clinical use of this important class of compounds. The production of SPM-1 metallo-β-lactamase has been the most common mechanism of carbapenem resistance identified in P. aeruginosa isolated from Brazilian medical centers. Interestingly, a single SPM-1-producing P. aeruginosa clone belonging to the ST277 has been widely spread within the Brazilian territory. In the current study, we performed a next-generation sequencing of six SPM-1-producing P. aeruginosa ST277 isolates. The core genome contains 5899 coding genes relative to the reference strain P. aeruginos a PAO1. A total of 26 genomic islands were detected in these isolates. We identified remarkable elements inside these genomic islands, such as copies of the bla SPM-1 gene conferring resistance to carbapenems and a type I-C CRISPR-Cas system, which is involved in protection of the chromosome against foreign DNA. In addition, we identified single nucleotide polymorphisms causing amino acid changes in antimicrobial resistance and virulence-related genes. Together, these factors could contribute to the marked resistance and persistence of the SPM-1-producing P. aeruginosa ST277 clone. A comparison of the SPM-1-producing P. aeruginosa ST277 genomes showed that their core genome has a high level nucleotide similarity and synteny conservation. The variability observed was mainly due to acquisition of genomic islands carrying several antibiotic resistance genes.

  6. Pacific Islands Climate Change Virtual Library

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The Virtual Library provides access to web based climate variability and climate change information and tools relevant to the Pacific Islands including case studies,...

  7. Genomic Resources of Three Pulsatilla Species Reveal Evolutionary Hotspots, Species-Specific Sites and Variable Plastid Structure in the Family Ranunculaceae.

    Science.gov (United States)

    Szczecińska, Monika; Sawicki, Jakub

    2015-09-15

    The European continent is presently colonized by nine species of the genus Pulsatilla, five of which are encountered only in mountainous regions of southwest and south-central Europe. The remaining four species inhabit lowlands in the north-central and eastern parts of the continent. Most plants of the genus Pulsatilla are rare and endangered, which is why most research efforts focused on their biology, ecology and hybridization. The objective of this study was to develop genomic resources, including complete plastid genomes and nuclear rRNA clusters, for three sympatric Pulsatilla species that are most commonly found in Central Europe. The results will supply valuable information about genetic variation, which can be used in the process of designing primers for population studies and conservation genetics research. The complete plastid genomes together with the nuclear rRNA cluster can serve as a useful tool in hybridization studies. Six complete plastid genomes and nuclear rRNA clusters were sequenced from three species of Pulsatilla using the Illumina sequencing technology. Four junctions between single copy regions and inverted repeats and junctions between the identified locally-collinear blocks (LCB) were confirmed by Sanger sequencing. Pulsatilla genomes of 120 unique genes had a total length of approximately 161-162 kb, and 21 were duplicated in the inverted repeats (IR) region. Comparative plastid genomes of newly-sequenced Pulsatilla and the previously-identified plastomes of Aconitum and Ranunculus species belonging to the family Ranunculaceae revealed several variations in the structure of the genome, but the gene content remained constant. The nuclear rRNA cluster (18S-ITS1-5.8S-ITS2-26S) of studied Pulsatilla species is 5795 bp long. Among five analyzed regions of the rRNA cluster, only Internal Transcribed Spacer 2 (ITS2) enabled the molecular delimitation of closely-related Pulsatilla patens and Pulsatilla vernalis. The determination of complete

  8. Molecules in the mud: Combining ancient DNA and lipid biomarkers to reconstruct vegetation response to climate variability during the Last Interglacial and the Holocene on Baffin Island, Arctic Canada

    Science.gov (United States)

    Crump, S. E.; Sepúlveda, J.; Bunce, M.; Miller, G. H.

    2017-12-01

    Modern ecological studies are revealing that the "greening" of the Arctic, resulting from a poleward shift in woody vegetation ranges, is already underway. The increasing abundance of shrubs in tundra ecosystems plays an important role in the global climate system through multiple positive feedbacks, yet uncertainty in future predictions of terrestrial vegetation means that climate models are likely not capturing these feedbacks accurately. Recently developed molecular techniques for reconstructing past vegetation and climate allow for a closer look at the paleo-record in order to improve our understanding of tundra community responses to climate variability; our current research focus is to apply these tools to both Last Interglacial and Holocene warm times. Here we present initial results from a small lake on southern Baffin Island spanning the last 7.2 ka. We reconstruct climate with both bulk geochemical and biomarker proxies, primarily using biogenic silica and branched glycerol dialkyl glycerol tetraethers (brGDGTs) as temperature indicators. We assess shifts in plant community using multivariate analysis of sedimentary ancient DNA (sedaDNA) metabarcoding data. This combination of approaches reveals that the vegetation community has responded sensitively to early Holocene warmth, Neoglacial cooling, and possibly modern anthropogenic warming. To our knowledge, this represents the first combination of a quantitative, biomarker-based climate reconstruction with a sedaDNA-based paleoecological reconstruction, and offers a glimpse at the potential of these molecular techniques used in tandem.

  9. CpG island mapping by epigenome prediction.

    Directory of Open Access Journals (Sweden)

    Christoph Bock

    2007-06-01

    Full Text Available 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

  10. CpG island mapping by epigenome prediction.

    Science.gov (United States)

    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

  11. Association Mapping and the Genomic Consequences of Selection in Sunflower

    Science.gov (United States)

    Mandel, Jennifer R.; Nambeesan, Savithri; Bowers, John E.; Marek, Laura F.; Ebert, Daniel; Rieseberg, Loren H.; Knapp, Steven J.; Burke, John M.

    2013-01-01

    The combination of large-scale population genomic analyses and trait-based mapping approaches has the potential to provide novel insights into the evolutionary history and genome organization of crop plants. Here, we describe the detailed genotypic and phenotypic analysis of a sunflower (Helianthus annuus L.) association mapping population that captures nearly 90% of the allelic diversity present within the cultivated sunflower germplasm collection. We used these data to characterize overall patterns of genomic diversity and to perform association analyses on plant architecture (i.e., branching) and flowering time, successfully identifying numerous associations underlying these agronomically and evolutionarily important traits. Overall, we found variable levels of linkage disequilibrium (LD) across the genome. In general, islands of elevated LD correspond to genomic regions underlying traits that are known to have been targeted by selection during the evolution of cultivated sunflower. In many cases, these regions also showed significantly elevated levels of differentiation between the two major sunflower breeding groups, consistent with the occurrence of divergence due to strong selection. One of these regions, which harbors a major branching locus, spans a surprisingly long genetic interval (ca. 25 cM), indicating the occurrence of an extended selective sweep in an otherwise recombinogenic interval. PMID:23555290

  12. Bacillus subtilis genome diversity.

    Science.gov (United States)

    Earl, Ashlee M; Losick, Richard; Kolter, Roberto

    2007-02-01

    Microarray-based comparative genomic hybridization (M-CGH) is a powerful method for rapidly identifying regions of genome diversity among closely related organisms. We used M-CGH to examine the genome diversity of 17 strains belonging to the nonpathogenic species Bacillus subtilis. Our M-CGH results indicate that there is considerable genetic heterogeneity among members of this species; nearly one-third of Bsu168-specific genes exhibited variability, as measured by the microarray hybridization intensities. The variable loci include those encoding proteins involved in antibiotic production, cell wall synthesis, sporulation, and germination. The diversity in these genes may reflect this organism's ability to survive in diverse natural settings.

  13. Variable number of tandem repeat markers in the genome sequence of Mycosphaerella fijiensis, the causal agent of black leaf streak disease of banana (Musa spp)

    NARCIS (Netherlands)

    Garcia, S.A.L.; Lee, van der T.A.J.; Ferreira, C.F.; Lintel Hekkert, te B.; Zapater, M.F.; Goodwin, S.B.; Guzmán, M.; Kema, G.H.J.; Souza, M.T.

    2010-01-01

    ABSTRACT. We searched the genome of Mycosphaerella fijiensis for molecular markers that would allow population genetics analysis of this plant pathogen. M. fijiensis, the causal agent of banana leaf streak disease, also known as black Sigatoka, is the most devastating pathogen attacking bananas

  14. Genome sequence of Salinisphaera shabanensis, a gammaproteobacterium from the harsh, variable environment of the brine-seawater interface of the Shaban Deep in the Red Sea.

    KAUST Repository

    Antunes, Andre

    2011-09-01

    We present the genome of Salinisphaera shabanensis, isolated from a brine-seawater interface and representing a new order within the Gammaproteobacteria. Its adaptations to physicochemical and nutrient availability fluctuations include six genes encoding heavy metal-translocating P-type ATPases and multiple genes involved in iron uptake, siderophore production, and poly-β-hydroxybutyrate synthesis.

  15. Genome sequence of Salinisphaera shabanensis, a gammaproteobacterium from the harsh, variable environment of the brine-seawater interface of the Shaban Deep in the Red Sea.

    KAUST Repository

    Antunes, Andre; Alam, Intikhab; Bajic, Vladimir B.; Stingl, Ulrich

    2011-01-01

    We present the genome of Salinisphaera shabanensis, isolated from a brine-seawater interface and representing a new order within the Gammaproteobacteria. Its adaptations to physicochemical and nutrient availability fluctuations include six genes encoding heavy metal-translocating P-type ATPases and multiple genes involved in iron uptake, siderophore production, and poly-β-hydroxybutyrate synthesis.

  16. Tenarife Island, Canary Island Archipelago, Atlantic Ocean

    Science.gov (United States)

    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.

  17. Genomic Resources of Three Pulsatilla Species Reveal Evolutionary Hotspots, Species-Specific Sites and Variable Plastid Structure in the Family Ranunculaceae

    Directory of Open Access Journals (Sweden)

    Monika Szczecińska

    2015-09-01

    Full Text Available Background: The European continent is presently colonized by nine species of the genus Pulsatilla, five of which are encountered only in mountainous regions of southwest and south-central Europe. The remaining four species inhabit lowlands in the north-central and eastern parts of the continent. Most plants of the genus Pulsatilla are rare and endangered, which is why most research efforts focused on their biology, ecology and hybridization. The objective of this study was to develop genomic resources, including complete plastid genomes and nuclear rRNA clusters, for three sympatric Pulsatilla species that are most commonly found in Central Europe. The results will supply valuable information about genetic variation, which can be used in the process of designing primers for population studies and conservation genetics research. The complete plastid genomes together with the nuclear rRNA cluster can serve as a useful tool in hybridization studies. Methodology/principal findings: Six complete plastid genomes and nuclear rRNA clusters were sequenced from three species of Pulsatilla using the Illumina sequencing technology. Four junctions between single copy regions and inverted repeats and junctions between the identified locally-collinear blocks (LCB were confirmed by Sanger sequencing. Pulsatilla genomes of 120 unique genes had a total length of approximately 161–162 kb, and 21 were duplicated in the inverted repeats (IR region. Comparative plastid genomes of newly-sequenced Pulsatilla and the previously-identified plastomes of Aconitum and Ranunculus species belonging to the family Ranunculaceae revealed several variations in the structure of the genome, but the gene content remained constant. The nuclear rRNA cluster (18S-ITS1-5.8S-ITS2-26S of studied Pulsatilla species is 5795 bp long. Among five analyzed regions of the rRNA cluster, only Internal Transcribed Spacer 2 (ITS2 enabled the molecular delimitation of closely-related Pulsatilla

  18. Unveiling the pan-genome of the SXT/R391 family of ICEs: molecular characterisation of new variable regions of SXT/R391-like ICEs detected in Pseudoalteromonas sp. and Vibrio scophthalmi.

    Science.gov (United States)

    Rodríguez-Blanco, Arturo; Lemos, Manuel L; Osorio, Carlos R

    2016-08-01

    Integrating conjugative elements (ICEs) of the SXT/R391 family have been identified in fish-isolated bacterial strains collected from marine aquaculture environments of the northwestern Iberian Peninsula. Here we analysed the variable regions of two ICEs, one preliminarily characterised in a previous study (ICEVscSpa3) and one newly identified (ICEPspSpa1). Bacterial strains harboring these ICEs were phylogenetically assigned to Vibrio scophthalmi and Pseudoalteromonas sp., thus constituting the first evidence of SXT/R391-like ICEs in the genus Pseudoalteromonas to date. Variable DNA regions, which confer element-specific properties to ICEs of this family, were characterised. Interestingly, the two ICEs contained 29 genes not found in variable DNA insertions of previously described ICEs. Most notably, variable gene content for ICEVscSpa3 showed similarity to genes potentially involved in housekeeping functions of replication, nucleotide metabolism and transcription. For these genes, closest homologues were found clustered in the genome of Pseudomonas psychrotolerans L19, suggesting a transfer as a block to ICEVscSpa3. Genes encoding antibiotic resistance, restriction modification systems and toxin/antitoxin systems were absent from hotspots of ICEVscSpa3. In contrast, the variable gene content of ICEPspSpa1 included genes involved in restriction/modification functions in two different hotspots and genes related to ICE maintenance. The present study unveils a relatively large number of novel genes in SXT/R391-ICEs, and demonstrates the major role of ICE elements as contributors to horizontal gene transfer.

  19. Partial pressure (or fugacity) of carbon dioxide, salinity and other variables collected from time series observations using Bubble type equilibrator for autonomous carbon dioxide (CO2) measurement, Carbon dioxide (CO2) gas analyzer and other instruments from HERON ISLAND, KANGAROO ISLAND and others in the Coral Sea, Great Australian Bight and Tasman Sea from 2009-10-09 to 2012-11-28 (NODC Accession 0100062)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — NCEI Accession 0100062 includes chemical, meteorological, physical and time series data collected from HERON ISLAND, KANGAROO ISLAND, MARIA ISLAND, MOORING_HERON...

  20. Dissolved inorganic carbon, total alkalinity, nitrate, phosphate, temperature and other variables collected from time series observations at Heron Island Reef Flat from 2010-06-01 to 2010-12-13 (NODC Accession 0127256)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This archival package contains carbonate chemistry and environmental parameters data that were collected from a 200-day time series monitoring on the Heron Island...

  1. Examples of storm impacts on barrier islands: Chapter 4

    Science.gov (United States)

    Plant, Nathaniel G.; Doran, Kara; Stockdon, Hilary F.

    2017-01-01

    This chapter focuses on the morphologic variability of barrier islands and on the differences in storm response. It describes different types of barrier island response to individual storms, as well as the integrated response of barrier islands to many storms. The chapter considers case study on the Chandeleur Island chain, where a decadal time series of island elevation measurements have documented a wide range of barrier island responses to storms and long-term processes that are representative of barrier island behaviour at many other locations. These islands are low elevation, extremely vulnerable to storms and exhibit a diversity of storm responses. Additionally, this location experiences a moderately high rate of relative sea-level rise, increasing its vulnerability to the combined impacts of storms and long-term erosional processes. Understanding how natural processes, including storm impacts and intervening recovery periods interact with man-made restoration processes is also broadly relevant to understand the natural and human response to future storms.

  2. The CpG island searcher: a new WWW resource.

    Science.gov (United States)

    Takai, Daiya; Jones, Peter A

    2003-01-01

    Clusters of CpG dinucleotides in GC rich regions of the genome called "CpG islands" frequently occur in the 5' ends of genes. Methylation of CpG islands plays a role in transcriptional silencing in higher organisms in certain situations. We have established a CpG-island-extraction algorithm, which we previously developed [Takai and Jones, 2002], on a web site which has a simple user interface to identify CpG islands from submitted sequences of up to 50kb. The web site determines the locations of CpG islands using parameters (lower limit of %GC, ObsCpG/ExpCpG, length) set by the user, to display the value of parameters on each CpG island, and provides a graphical map of CpG dinucleotide distribution and borders of CpG islands. A command-line version of the CpG islands searcher has also been developed for larger sequences. The CpG Island Searcher was applied to the latest sequence and mapping information of human chromosomes 20, 21 and 22, and a total of 2345 CpG islands were extracted and 534 (23%) of them contained first coding exons and 650 (28%) contained other exons. The CpG Island Searcher is available on the World Wide Web at http://www.cpgislands.com or http://www.uscnorris.com/cpgislands/cpg.cgi.

  3. Comparative genomics of Helicobacter pylori strains of China associated with different clinical outcome.

    Directory of Open Access Journals (Sweden)

    Yuanhai You

    Full Text Available In this study, a whole-genome CombiMatrix Custom oligonucleotide tiling microarray with 90,000 probes covering six sequenced Helicobacter pylori (H. pylori genomes was designed. This microarray was used to compare the genomic profiles of eight unsequenced strains isolated from patients with different gastroduodenal diseases in Heilongjiang province of China. Since significant genomic variation was found among these strains, an additional 76 H. pylori strains associated with different clinical outcomes were isolated from various provinces of China. These strains were tested by polymerase chain reaction to demonstrate this distinction. We identified several highly variable regions in strains associated with gastritis, gastric ulceration, and gastric cancer. These regions are associated with genes involved in the bacterial type I, type II, and type III R-M systems. They were also associated with the virB gene, which lies on the well-studied cag pathogenic island. While previous studies have reported on the diverse genetic characterization of this pathogenic island, in this study, we find that it is conserved in all strains tested by microarray. Moreover, a number of genes involved in the type IV secretion system, which is related to horizontal DNA transfer between H. pylori strains, were identified in the comparative analysis of the strain-specific genes. These findings may provide insight into new biomarkers for the prediction of gastric diseases.

  4. Secas Island Stable Isotope Data (delta 18O) for 1707 to 1984

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Secas Island Coral d18O, used to reconstruct seasonal and interannual variability in the Intertropical Convergence Zone. Site Location: Secas Island, Gulf of...

  5. Evolution of the rpoB-psbZ region in fern plastid genomes: notable structural rearrangements and highly variable intergenic spacers.

    Science.gov (United States)

    Gao, Lei; Zhou, Yuan; Wang, Zhi-Wei; Su, Ying-Juan; Wang, Ting

    2011-04-13

    The rpoB-psbZ (BZ) region of some fern plastid genomes (plastomes) has been noted to go through considerable genomic changes. Unraveling its evolutionary dynamics across all fern lineages will lead to clarify the fundamental process shaping fern plastome structure and organization. A total of 24 fern BZ sequences were investigated with taxon sampling covering all the extant fern orders. We found that: (i) a tree fern Plagiogyria japonica contained a novel gene order that can be generated from either the ancestral Angiopteris type or the derived Adiantum type via a single inversion; (ii) the trnY-trnE intergenic spacer (IGS) of the filmy fern Vandenboschia radicans was expanded 3-fold due to the tandem 27-bp repeats which showed strong sequence similarity with the anticodon domain of trnY; (iii) the trnY-trnE IGSs of two horsetail ferns Equisetum ramosissimum and E. arvense underwent an unprecedented 5-kb long expansion, more than a quarter of which was consisted of a single type of direct repeats also relevant to the trnY anticodon domain; and (iv) ycf66 has independently lost at least four times in ferns. Our results provided fresh insights into the evolutionary process of fern BZ regions. The intermediate BZ gene order was not detected, supporting that the Adiantum type was generated by two inversions occurring in pairs. The occurrence of Vandenboschia 27-bp repeats represents the first evidence of partial tRNA gene duplication in fern plastomes. Repeats potentially forming a stem-loop structure play major roles in the expansion of the trnY-trnE IGS.

  6. Evolution of the rpoB-psbZ region in fern plastid genomes: notable structural rearrangements and highly variable intergenic spacers

    Directory of Open Access Journals (Sweden)

    Su Ying-Juan

    2011-04-01

    Full Text Available Abstract Background The rpoB-psbZ (BZ region of some fern plastid genomes (plastomes has been noted to go through considerable genomic changes. Unraveling its evolutionary dynamics across all fern lineages will lead to clarify the fundamental process shaping fern plastome structure and organization. Results A total of 24 fern BZ sequences were investigated with taxon sampling covering all the extant fern orders. We found that: (i a tree fern Plagiogyria japonica contained a novel gene order that can be generated from either the ancestral Angiopteris type or the derived Adiantum type via a single inversion; (ii the trnY-trnE intergenic spacer (IGS of the filmy fern Vandenboschia radicans was expanded 3-fold due to the tandem 27-bp repeats which showed strong sequence similarity with the anticodon domain of trnY; (iii the trnY-trnE IGSs of two horsetail ferns Equisetum ramosissimum and E. arvense underwent an unprecedented 5-kb long expansion, more than a quarter of which was consisted of a single type of direct repeats also relevant to the trnY anticodon domain; and (iv ycf66 has independently lost at least four times in ferns. Conclusions Our results provided fresh insights into the evolutionary process of fern BZ regions. The intermediate BZ gene order was not detected, supporting that the Adiantum type was generated by two inversions occurring in pairs. The occurrence of Vandenboschia 27-bp repeats represents the first evidence of partial tRNA gene duplication in fern plastomes. Repeats potentially forming a stem-loop structure play major roles in the expansion of the trnY-trnE IGS.

  7. Researching Pacific island livelihoods:

    DEFF Research Database (Denmark)

    Egelund Christensen, Andreas; Mertz, Ole

    2010-01-01

    on contemporary theories of nissology and conceptual analytical frameworks for island research. Through a review of selected case-study-based island literature on changing livelihoods coming out of the South Pacific, we wish to illustrate and discuss advantages of finding common grounds for small island studies....... The focus is on two dimensions of island livelihood, migration and natural resource management, both of which are significant contributors in making island livelihoods and shaping Pacific seascapes. We argue that there is still a substantial lack of studies targeting small island dynamics that are empirical...

  8. Nucleotide variability of Ťahyňa virus (Bunyaviridae, Orthobunyavirus) small (S) and medium (M) genomic segments in field strains differing in biological properties

    Czech Academy of Sciences Publication Activity Database

    Kilian, P.; Růžek, Daniel; Danielová, V.; Hypša, Václav; Grubhoffer, Libor

    2010-01-01

    Roč. 149, č. 1 (2010), s. 119-123 ISSN 0168-1702 R&D Projects: GA MŠk(CZ) LC06009 Institutional research plan: CEZ:AV0Z60220518 Keywords : Tahyna virus * Bunyavirus * california group * genetic variability * virulence Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 2.905, year: 2010

  9. A Predominant Variable-Number Tandem-Repeat Cluster of Mycobacterium tuberculosis Isolates among Asylum Seekers in the Netherlands and Denmark, Deciphered by Whole-Genome Sequencing.

    NARCIS (Netherlands)

    Jajou, Rana; de Neeling, Albert; Rasmussen, Erik Michael; Norman, Anders; Mulder, Arnout; van Hunen, Rianne; de Vries, Gerard; Haddad, Walid; Anthony, Richard; Lillebaek, Troels; van der Hoek, Wim; van Soolingen, Dick

    In many countries,Mycobacterium tuberculosisisolates are routinely subjected to variable-number tandem-repeat (VNTR) typing to investigateM. tuberculosistransmission. Unexpectedly, cross-border clusters were identified among African refugees in the Netherlands and Denmark, although transmission in

  10. Os and S isotope studies of ultramafic rocks in the Duke Island Complex, Alaska: variable degrees of crustal contamination of magmas in an arc setting and implications for Ni-Cu-PGE sulfide mineralization

    Science.gov (United States)

    Stifter, Eric C.; Ripley, Edward M.; Li, Chusi

    2016-10-01

    The Duke Island Complex is one of the several "Ural-Alaskan" intrusions of Cretaceous age that occur along the coast of SE Alaska. Significant quantities of magmatic Ni-Cu-PGE sulfide mineralization are locally found in the complex, primarily within olivine clinopyroxenites. Sulfide mineralization is Ni-poor, consistent with petrologic evidence which indicates that sulfide saturation was reached after extensive olivine crystallization. Olivine clinopyroxenites were intruded by magmas that produced sulfide-poor, adcumulate dunites. As part of a study to investigate the potential for Ni-rich sulfide mineralization in association with the dunites, a Re-Os and S isotope study of the dunites, as well as sulfide mineralization in the olivine clinopyroxenites, was initiated. Importantly, recent drilling in the complex identified the presence of sulfidic and carbonaceous country rocks that may have been involved in the contamination of magmas and generation of sulfide mineralization. γOs (110 Ma) values of two sulfidic country rocks are 1022 and 2011. δ34S values of the country rocks range from -2.6 to -16.1 ‰. 187Os/188Os ratios of sulfide minerals in the mineralization hosted by olivine clinopyroxenites are variable and high, with γOs (110 Ma) values between 151 and 2059. Extensive interaction with Re-rich sedimentary country rocks is indicated. In contrast, γOs (110 Ma) values of the dunites are significantly lower, ranging between 2 and 16. 187Os/188Os ratios increase with decreasing Os concentration. This inverse relation is similar to that shown by ultramafic rocks from several arc settings, as well as altered abyssal dunites and peridotites. The relation may be indicative of magma derivation from a sub-arc mantle that had experienced metasomatism via slab-derived fluids. Alternatively, the relation may be indicative of minor contamination of magma by crustal rocks with low Os concentrations but high 187Os/188Os ratios. A third alternative is that the low Os

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

    OpenAIRE

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

    2014-01-01

    We present the draft genome sequence of Vibrio cholerae InDRE 3140 recovered in 2013 during a cholera outbreak in Mexico. The genome showed the Vibrio 7th pandemic islands VSP1 and VSP2, the pathogenic islands VPI-1 and VPI-2, the integrative and conjugative element SXT/R391 (ICE-SXT), and both prophages CTXφ and RS1φ.

  12. Diomede Islands, Bering Straight

    Science.gov (United States)

    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.

  13. Tales of island tails

    NARCIS (Netherlands)

    Groot, de Alma V.; Oost, Albert P.; Veeneklaas, Roos M.; Lammerts, Evert Jan; Duin, van Willem E.; Wesenbeeck, van Bregje K.

    2016-01-01

    The Frisian islands (Southern North Sea) have extensive island tails, i.e. the entire downdrift side of an island consisting of salt marshes, dunes, beaches and beach plains, and green beaches. Currently, large parts of these tails are ageing and losing dynamics, partly due to human influence.

  14. Rhode Island unemployment

    OpenAIRE

    Leonard Lardaro

    2010-01-01

    How can a state like Rhode Island have such a high unemployment rate? This question has been asked often over the past year, especially since at one point, Rhode Island found itself with the dubious distinction of having the highest unemployment rate in the United States. Following that extreme, Rhode Island seemed to settle into a niche where its rank was third nationally.

  15. Genomic Variability of Mycobacterium tuberculosis Strains of the Euro-American Lineage Based on Large Sequence Deletions and 15-Locus MIRU-VNTR Polymorphism

    Science.gov (United States)

    Rindi, Laura; Medici, Chiara; Bimbi, Nicola; Buzzigoli, Andrea; Lari, Nicoletta; Garzelli, Carlo

    2014-01-01

    A sample of 260 Mycobacterium tuberculosis strains assigned to the Euro-American family was studied to identify phylogenetically informative genomic regions of difference (RD). Mutually exclusive deletions of regions RD115, RD122, RD174, RD182, RD183, RD193, RD219, RD726 and RD761 were found in 202 strains; the RDRio deletion was detected exclusively among the RD174-deleted strains. Although certain deletions were found more frequently in certain spoligotype families (i.e., deletion RD115 in T and LAM, RD174 in LAM, RD182 in Haarlem, RD219 in T and RD726 in the “Cameroon” family), the RD-defined sublineages did not specifically match with spoligotype-defined families, thus arguing against the use of spoligotyping for establishing exact phylogenetic relationships between strains. Notably, when tested for katG463/gyrA95 polymorphism, all the RD-defined sublineages belonged to Principal Genotypic Group (PGG) 2, except sublineage RD219 exclusively belonging to PGG3; the 58 Euro-American strains with no deletion were of either PGG2 or 3. A representative sample of 197 isolates was then analyzed by standard 15-locus MIRU-VNTR typing, a suitable approach to independently assess genetic relationships among the strains. Analysis of the MIRU-VNTR typing results by using a minimum spanning tree (MST) and a classical dendrogram showed groupings that were largely concordant with those obtained by RD-based analysis. Isolates of a given RD profile show, in addition to closely related MIRU-VNTR profiles, related spoligotype profiles that can serve as a basis for better spoligotype-based classification. PMID:25197794

  16. Association analysis of genomic loci important for grain weight control in elite common wheat varieties cultivated with variable water and fertiliser supply.

    Directory of Open Access Journals (Sweden)

    Kunpu Zhang

    Full Text Available Grain weight, an essential yield component, is under strong genetic control and markedly influenced by the environment. Here, by genome-wide association analysis with a panel of 94 elite common wheat varieties, 37 loci were found significantly associated with thousand-grain weight (TGW in one or more environments differing in water and fertiliser levels. Five loci were stably associated with TGW under all 12 environments examined. Their elite alleles had positive effects on TGW. Four, two, three, and two loci were consistently associated with TGW in the irrigated and fertilised (IF, rainfed (RF, reduced nitrogen (RN, and reduced phosphorus (RP environments. The elite alleles of the IF-specific loci enhanced TGW under well-resourced conditions, whereas those of the RF-, RN-, or RP-specific loci conferred tolerance to the TGW decrease when irrigation, nitrogen, or phosphorus were reduced. Moreover, the elite alleles of the environment-independent and -specific loci often acted additively to enhance TGW. Four additional loci were found associated with TGW in specific locations, one of which was shown to contribute to the TGW difference between two experimental sites. Further analysis of 14 associated loci revealed that nine affected both grain length and width, whereas the remaining loci influenced either grain length or width, indicating that these loci control grain weight by regulating kernel size. Finally, the elite allele of Xpsp3152 frequently co-segregated with the larger grain haplotype of TaGW2-6A, suggesting probable genetic and functional linkages between Xpsp3152 and GW2 that are important for grain weight control in cereal plants. Our study provides new knowledge on TGW control in elite common wheat lines, which may aid the improvement of wheat grain weight trait in further research.

  17. Extreme genomes

    OpenAIRE

    DeLong, Edward F

    2000-01-01

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

  18. Grass genomes

    OpenAIRE

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

    1998-01-01

    For the most part, studies of grass genome structure have been limited to the generation of whole-genome genetic maps or the fine structure and sequence analysis of single genes or gene clusters. We have investigated large contiguous segments of the genomes of maize, sorghum, and rice, primarily focusing on intergenic spaces. Our data indicate that much (>50%) of the maize genome is composed of interspersed repetitive DNAs, primarily nested retrotransposons that in...

  19. Genome-resolved metaproteomic characterization of preterm infant gut microbiota development reveals species-specific metabolic shifts and variabilities during early life.

    Science.gov (United States)

    Xiong, Weili; Brown, Christopher T; Morowitz, Michael J; Banfield, Jillian F; Hettich, Robert L

    2017-07-10

    Establishment of the human gut microbiota begins at birth. This early-life microbiota development can impact host physiology during infancy and even across an entire life span. However, the functional stability and population structure of the gut microbiota during initial colonization remain poorly understood. Metaproteomics is an emerging technology for the large-scale characterization of metabolic functions in complex microbial communities (gut microbiota). We applied a metagenome-informed metaproteomic approach to study the temporal and inter-individual differences of metabolic functions during microbial colonization of preterm human infants' gut. By analyzing 30 individual fecal samples, we identified up to 12,568 protein groups for each of four infants, including both human and microbial proteins. With genome-resolved matched metagenomics, proteins were confidently identified at the species/strain level. The maximum percentage of the proteome detected for the abundant organisms was ~45%. A time-dependent increase in the relative abundance of microbial versus human proteins suggested increasing microbial colonization during the first few weeks of early life. We observed remarkable variations and temporal shifts in the relative protein abundances of each organism in these preterm gut communities. Given the dissimilarity of the communities, only 81 microbial EggNOG orthologous groups and 57 human proteins were observed across all samples. These conserved microbial proteins were involved in carbohydrate, energy, amino acid and nucleotide metabolism while conserved human proteins were related to immune response and mucosal maturation. We identified seven proteome clusters for the communities and showed infant gut proteome profiles were unstable across time and not individual-specific. Applying a gut-specific metabolic module (GMM) analysis, we found that gut communities varied primarily in the contribution of nutrient (carbohydrates, lipids, and amino acids

  20. Cancer genomics

    DEFF Research Database (Denmark)

    Norrild, Bodil; Guldberg, Per; Ralfkiær, Elisabeth Methner

    2007-01-01

    Almost all cells in the human body contain a complete copy of the genome with an estimated number of 25,000 genes. The sequences of these genes make up about three percent of the genome and comprise the inherited set of genetic information. The genome also contains information that determines whe...

  1. Paradise Islands? Island States and Environmental Performance

    Directory of Open Access Journals (Sweden)

    Sverker C. Jagers

    2016-03-01

    Full Text Available Island states have been shown to outperform continental states on a number of large-scale coordination-related outcomes, such as levels of democracy and institutional quality. The argument developed and tested in this article contends that the same kind of logic may apply to islands’ environmental performance, too. However, the empirical analysis shows mixed results. Among the 105 environmental outcomes that we analyzed, being an island only has a positive impact on 20 of them. For example, island states tend to outcompete continental states with respect to several indicators related to water quality but not in aspects related to biodiversity, protected areas, or environmental regulations. In addition, the causal factors previously suggested to make islands outperform continental states in terms of coordination have weak explanatory power in predicting islands’ environmental performance. We conclude the paper by discussing how these interesting findings can be further explored.

  2. DNA sequence explains seemingly disordered methylation levels in partially methylated domains of Mammalian genomes.

    Directory of Open Access Journals (Sweden)

    Dimos Gaidatzis

    2014-02-01

    Full Text Available For the most part metazoan genomes are highly methylated and harbor only small regions with low or absent methylation. In contrast, partially methylated domains (PMDs, recently discovered in a variety of cell lines and tissues, do not fit this paradigm as they show partial methylation for large portions (20%-40% of the genome. While in PMDs methylation levels are reduced on average, we found that at single CpG resolution, they show extensive variability along the genome outside of CpG islands and DNase I hypersensitive sites (DHS. Methylation levels range from 0% to 100% in a roughly uniform fashion with only little similarity between neighboring CpGs. A comparison of various PMD-containing methylomes showed that these seemingly disordered states of methylation are strongly conserved across cell types for virtually every PMD. Comparative sequence analysis suggests that DNA sequence is a major determinant of these methylation states. This is further substantiated by a purely sequence based model which can predict 31% (R(2 of the variation in methylation. The model revealed CpG density as the main driving feature promoting methylation, opposite to what has been shown for CpG islands, followed by various dinucleotides immediately flanking the CpG and a minor contribution from sequence preferences reflecting nucleosome positioning. Taken together we provide a reinterpretation for the nucleotide-specific methylation levels observed in PMDs, demonstrate their conservation across tissues and suggest that they are mainly determined by specific DNA sequence features.

  3. Genome sequencing and analysis of the first complete genome of Lactobacillus kunkeei strain MP2, an Apis mellifera gut isolate

    Directory of Open Access Journals (Sweden)

    Freddy Asenjo

    2016-04-01

    Full Text Available Background. The honey bee (Apis mellifera is the most important pollinator in agriculture worldwide. However, the number of honey bees has fallen significantly since 2006, becoming a huge ecological problem nowadays. The principal cause is CCD, or Colony Collapse Disorder, characterized by the seemingly spontaneous abandonment of hives by their workers. One of the characteristics of CCD in honey bees is the alteration of the bacterial communities in their gastrointestinal tract, mainly due to the decrease of Firmicutes populations, such as the Lactobacilli. At this time, the causes of these alterations remain unknown. We recently isolated a strain of Lactobacillus kunkeei (L. kunkeei strain MP2 from the gut of Chilean honey bees. L. kunkeei, is one of the most commonly isolated bacterium from the honey bee gut and is highly versatile in different ecological niches. In this study, we aimed to elucidate in detail, the L. kunkeei genetic background and perform a comparative genome analysis with other Lactobacillus species. Methods. L. kunkeei MP2 was originally isolated from the guts of Chilean A. mellifera individuals. Genome sequencing was done using Pacific Biosciences single-molecule real-time sequencing technology. De novo assembly was performed using Celera assembler. The genome was annotated using Prokka, and functional information was added using the EggNOG 3.1 database. In addition, genomic islands were predicted using IslandViewer, and pro-phage sequences using PHAST. Comparisons between L. kunkeei MP2 with other L. kunkeei, and Lactobacillus strains were done using Roary. Results. The complete genome of L. kunkeei MP2 comprises one circular chromosome of 1,614,522 nt. with a GC content of 36,9%. Pangenome analysis with 16 L. kunkeei strains, identified 113 unique genes, most of them related to phage insertions. A large and unique region of L. kunkeei MP2 genome contains several genes that encode for phage structural protein and

  4. Genomic insights into the uncultured genus 'Candidatus Magnetobacterium' in the phylum Nitrospirae.

    Science.gov (United States)

    Lin, Wei; Deng, Aihua; Wang, Zhang; Li, Ying; Wen, Tingyi; Wu, Long-Fei; Wu, Martin; Pan, Yongxin

    2014-12-01

    Magnetotactic bacteria (MTB) of the genus 'Candidatus Magnetobacterium' in phylum Nitrospirae are of great interest because of the formation of hundreds of bullet-shaped magnetite magnetosomes in multiple bundles of chains per cell. These bacteria are worldwide distributed in aquatic environments and have important roles in the biogeochemical cycles of iron and sulfur. However, except for a few short genomic fragments, no genome data are available for this ecologically important genus, and little is known about their metabolic capacity owing to the lack of pure cultures. Here we report the first draft genome sequence of 3.42 Mb from an uncultivated strain tentatively named 'Ca. Magnetobacterium casensis' isolated from Lake Miyun, China. The genome sequence indicates an autotrophic lifestyle using the Wood-Ljungdahl pathway for CO2 fixation, which has not been described in any previously known MTB or Nitrospirae organisms. Pathways involved in the denitrification, sulfur oxidation and sulfate reduction have been predicted, indicating its considerable capacity for adaptation to variable geochemical conditions and roles in local biogeochemical cycles. Moreover, we have identified a complete magnetosome gene island containing mam, mad and a set of novel genes (named as man genes) putatively responsible for the formation of bullet-shaped magnetite magnetosomes and the arrangement of multiple magnetosome chains. This first comprehensive genomic analysis sheds light on the physiology, ecology and biomineralization of the poorly understood 'Ca. Magnetobacterium' genus.

  5. Comparative Genomics Reveals High Genomic Diversity in the Genus Photobacterium

    DEFF Research Database (Denmark)

    Machado, Henrique; Gram, Lone

    2017-01-01

    was widespread and abundant in the genus, suggesting a role in genomic evolution. The high genetic variability and indications of genetic exchange make it difficult to elucidate genome evolutionary paths and raise the awareness of the roles of foreign DNA in the genomic evolution of environmental organisms.......Vibrionaceae is a large marine bacterial family, which can constitute up to 50% of the prokaryotic population in marine waters. Photobacterium is the second largest genus in the family and we used comparative genomics on 35 strains representing 16 of the 28 species described so far, to understand...... the genomic diversity present in the Photobacterium genus. Such understanding is important for ecophysiology studies of the genus. We used whole genome sequences to evaluate phylogenetic relationships using several analyses (16S rRNA, MLSA, fur, amino-acid usage, ANI), which allowed us to identify two...

  6. Holocene Evolution and Sediment Provenance of Horn Island, Mississippi, USA

    Science.gov (United States)

    Schulze, N.; Wallace, D. J.; Miner, M. D.

    2017-12-01

    As one of the most stable islands in the Mississippi-Alabama barrier island chain, Horn Island provides critical habitat, plays an important role in regulating estuarine conditions in the Mississippi Sound, and helps to attenuate wave energy and storm surge for the mainland. The provenance of sediments comprising Horn Island is largely unknown and has implications for mode of island genesis and evolution. The existing literature proposes that island chain formation was initiated by bar emergence from a subaqueous spit that grew laterally westward from Dauphin Island in the east. Decelerating sea level rise 4,000 to 5,000 years ago facilitated island formation. This proposed mode of formation is supported by a lone radiocarbon date from lagoonal sediments below Horn Island, suggesting the system formed after 4,615 ± 215 years BP. Rivers supplying suspended sediment include the Mississippi, Pascagoula, Mobile and Apalachicola, but the variable nature of their paths and sediment supply means that Horn Island has received differing amounts of sediment from these proximal rivers throughout the Holocene. To analyze the stratigraphy and sediment characteristics of Horn Island, we will utilize 24 vibracores (up to 6 meters in length) from offshore Horn Island that were obtained by the United States Geological Survey (USGS) and 9 onshore drill cores (up to 28 meters in length) from the Mississippi Department of Environmental Quality. High-resolution LiDAR data collected by the National Oceanic and Atmospheric Administration in 2010 will be used to describe modern geomorphic barrier environments. We will employ down-core x-ray diffraction and x-ray fluorescence analyses to identify mineralogical and chemical signatures that potentially correspond to unique signatures of the fluvial sources of proximal rivers. New radiocarbon ages will be used to constrain the timing of island formation and alterations in sediment supply. High-resolution shallow geophysical data will provide

  7. Tanzania - Mafia Island Airport

    Data.gov (United States)

    Millennium Challenge Corporation — The evaluation design and subsequent data gathering activities will address the following key research questions: a) Has the Mafia Island Airport Upgrade Project...

  8. Climate Change in the Pacific Islands

    Science.gov (United States)

    Hamnett, Michael P.

    Climate change have been a major concern among Pacific Islanders since the late 1990s. During that period, Time Magazine featured a cover story that read: Say Goodbye to the Marshall Islands, Kiribati, and Tuvalu from sea level rise. Since that time, the South Pacific Regional Environment Programme, UN and government agencies and academic researchers have been assessing the impacts of long-term climate change and seasonal to inter-annual climate variability on the Pacific Islands. The consensus is that long-term climate change will result in more extreme weather and tidal events including droughts, floods, tropical cyclones, coastal erosion, and salt water inundation. Extreme weather events already occur in the Pacific Islands and they are patterned. El Niño Southern Oscillation (ENSO) events impact rainfall, tropical cyclone and tidal patterns. In 2000, the first National Assessment of the Consequences of Climate Variability and Change concluded that long-term climate change will result in more El Niño events or a more El Niño like climate every year. The bad news is that will mean more natural disasters. The good news is that El Niño events can be predicted and people can prepare for them. The reallly bad news is that some Pacific Islands are already becoming uninhabitable because of erosion of land or the loss of fresh water from droughts and salt water intrusion. Many of the most vulnerable countries already overseas populations in New Zealand, the US, or larger Pacific Island countries. For some Pacific Islander abandoning their home countries will be their only option.

  9. Revised genomic consensus for the hypermethylated CpG island region of the human L1 transposon and integration sites of full length L1 elements from recombinant clones made using methylation-tolerant host strains

    DEFF Research Database (Denmark)

    Crowther, P J; Doherty, J P; Linsenmeyer, M E

    1991-01-01

    preferentially from L1 members which have accumulated mutations that have removed sites of methylation. We present a revised consensus from the 5' presumptive control region of these elements. This revised consensus contains a consensus RNA polymerase III promoter which would permit the synthesis of transcripts......Efficient recovery of clones from the 5' end of the human L1 dispersed repetitive elements necessitates the use of deletion mcr- host strains since this region contains a CpG island which is hypermethylated in vivo. Clones recovered with conventional mcr+ hosts seem to have been derived...... from the 5' end of full length L1 elements. Such potential transcripts are likely to exhibit a high degree of secondary structure. In addition, we have determined the flanking sequences for 6 full length L1 elements. The majority of full length L1 clones show no convincing evidence for target site...

  10. Intersectional gene flow between insular endemics of Ilex (Aquifoliaceae) on the Bonin Islands and the Ryukyu Islands.

    Science.gov (United States)

    Setoguchi, H; Watanabe, I

    2000-06-01

    Hybridization and introgression play important roles in plant evolution, and their occurrence on the oceanic islands provides good examples of plant speciation and diversification. Restriction fragment length polymorphisms (RFLPs) and trnL (UAA) 3'exon-trnF (GAA) intergenic spacer (IGS) sequences of chloroplast DNA (cpDNA), and the sequences of internal transcribed spacer (ITS) of nuclear ribosomal DNA were examined to investigate the occurrence of gene transfer in Ilex species on the Bonin Islands and the Ryukyu Islands in Japan. A gene phylogeny for the plastid genome is in agreement with the morphologically based taxonomy, whereas the nuclear genome phylogeny clusters putatively unrelated endemics both on the Bonin and the Ryukyu Islands. Intersectional hybridization and nuclear gene flow were independently observed in insular endemics of Ilex on both sets of islands without evidence of plastid introgression. Gene flow observed in these island systems can be explained by ecological features of insular endemics, i.e., limits of distribution range or sympatric distribution in a small land area.

  11. Genome Imprinting

    Indian Academy of Sciences (India)

    the cell nucleus (mitochondrial and chloroplast genomes), and. (3) traits governed ... tively good embryonic development but very poor development of membranes and ... Human homologies for the type of situation described above are naturally ..... imprint; (b) New modifications of the paternal genome in germ cells of each ...

  12. Baculovirus Genomics

    NARCIS (Netherlands)

    Oers, van M.M.; Vlak, J.M.

    2007-01-01

    Baculovirus genomes are covalently closed circles of double stranded-DNA varying in size between 80 and 180 kilobase-pair. The genomes of more than fourty-one baculoviruses have been sequenced to date. The majority of these (37) are pathogenic to lepidopteran hosts; three infect sawflies

  13. Genomic Testing

    Science.gov (United States)

    ... this database. Top of Page Evaluation of Genomic Applications in Practice and Prevention (EGAPP™) In 2004, the Centers for Disease Control and Prevention launched the EGAPP initiative to establish and test a ... and other applications of genomic technology that are in transition from ...

  14. Ancient genomes

    OpenAIRE

    Hoelzel, A Rus

    2005-01-01

    Ever since its invention, the polymerase chain reaction has been the method of choice for work with ancient DNA. In an application of modern genomic methods to material from the Pleistocene, a recent study has instead undertaken to clone and sequence a portion of the ancient genome of the cave bear.

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

    Science.gov (United States)

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

    2015-01-01

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

  16. Vancouver Island gas supply

    International Nuclear Information System (INIS)

    Des Brisay, C.

    2005-01-01

    Terasen Gas is pursuing alternatives for the supply of additional natural gas capacity to Vancouver Island. Its subsidiary, Terasen Gas (Vancouver Island) Inc. (TGVI), is responding to the need for delivery of increased gas supply and, is supporting plans for new gas-fired power generation on Vancouver Island. TGVI's proposal for new natural gas capacity involves a combination of compression and pipeline loops as well as the addition of a storage facility for liquefied natural gas (LNG) at Mt. Hayes to help manage price volatility. This presentation outlined the objectives and components of the resource planning process, including demand forecast scenarios and the preferred infrastructure options. tabs., figs

  17. Numerical modeling of atoll island hydrogeology.

    Science.gov (United States)

    Bailey, R T; Jenson, J W; Olsen, A E

    2009-01-01

    We implemented Ayers and Vachers' (1986) inclusive conceptual model for atoll island aquifers in a comprehensive numerical modeling study to evaluate the response of the fresh water lens to selected controlling climatic and geologic variables. Climatic factors include both constant and time-varying recharge rates, with particular attention paid to the effects of El Niño and the associated drought it brings to the western Pacific. Geologic factors include island width; hydraulic conductivity of the uppermost Holocene-age aquifer, which contains the fresh water lens; the depth to the contact with the underlying, and much more conductive, Pleistocene karst aquifer, which transmits tidal signals to the base of the lens; and the presence or absence of a semiconfining reef flat plate on the ocean side. Sensitivity analyses of steady-steady simulations show that lens thickness is most strongly sensitive to the depth to the Holocene-Pleistocene contact and to the hydraulic conductivity of the Holocene aquifer, respectively. Comparisons between modeling results and published observations of atoll island lens thicknesses suggest a hydraulic conductivity of approximately 50 m/d for leeward islands and approximately 400 m/d for windward islands. Results of transient simulations show that lens thickness fluctuations during average seasonal conditions and El Niño events are quite sensitive to island width, recharge rate, and hydraulic conductivity of the Holocene aquifer. In general, the depletion of the lens during drought conditions is most drastic for small, windward islands. Simulation results suggest that recovery from a 6-month drought requires about 1.5 years.

  18. Terrestrial radiation measurements in Marshall Islands

    International Nuclear Information System (INIS)

    Gudiksen, P.H.

    1978-01-01

    With the prospect of habitation in the near future, radiological surveys were undertaken of Enewetak and Bikini Atolls to provide a basis for determining whether or not the atolls can be safely reinhabited. The surveys included all of the forty islands within Enewetak Atoll, but only the two principal islands, Bikini and Eneu Islands, of Bikini Atoll. These atolls were former U.S. nuclear weapons test sites in the Pacific. Integral parts of the surveys were the measurements of the distributions of radioactivity in the soil and the resulting gamma ray exposure rates for external dose estimation. Numerous soil samples were collected from both atolls for analysis by Ge (Li) gamma spectrometry and by wet chemistry techniques. At Enewetak Atoll the gamma exposure rates were measured by TLDs and a helicopter-borne array of Nal detectors, while at Bikini Atoll portable Nal detectors, pressurized ion-chambers, and TLDs were utilized. The predominant species measured in the soil samples collected from both atolls were 90 Sr, 239,240 Pu, 137 Cs and 60 Co with the latter two nuclides being the primary contributors to the gamma-ray exposure rates. The geographical distribution of the exposure rates measured on both atolls, was highly variable ranging from less than 1 μR/h on islands that had not been impacted radiologically by the testing program, to over 100 μR/h near weapon detonation sites. Thus, within Enewetak Atoll, the highest soil activities and gamma-ray exposure rates were measured on the northern islands, where the weapons testing had been most intense. Bikini Island exhibited contamination levels that were considerably higher than those on Eneu Island. Generally, the highest activity levels were observed within the island interiors or in proximity to ground zero sites, and could usually be related to the surrounding vegetation density. The island of Yvonne, within Enewetak Atoll, is the most severely contaminated land area. Particles containing as much as several

  19. Island formation without attractive interaction

    NARCIS (Netherlands)

    Jansen, A.P.J.

    2008-01-01

    We show that adsorbates on surfaces can form islands even if there are no attractive interactions. Instead, strong repulsion between adsorbates at short distances can lead to islands, because such islands increase the entropy of the adsorbates that are not part of the islands. We suggest that this

  20. Complexity of nearshore strontium-to-calcium ratio variability in a core sample of the massive coral Siderastrea siderea obtained in Coral Bay, St. John, U.S. Virgin Islands

    Science.gov (United States)

    Reich, Christopher D.; Kuffner, Ilsa B.; Hickey, T. Don; Morrison, Jennifer M.; Flannery, Jennifer A.

    2013-01-01

    Strontium-to-calcium ratios (Sr/Ca) were measured on the skeletal matrix of a core sample from a colony of the massive coral Siderastrea siderea collected in Coral Bay, St. John, U.S. Virgin Islands. Strontium and calcium are incorporated into the coral skeleton during the precipitation of aragonite by the coral polyps and their ratio is highly temperature dependent. The robustness of this temperature dependence makes Sr/Ca a reliable proxy for sea surface temperature (SST). Details presented from the St. John S. siderea core indicate that terrestrial inputs of sediment and freshwater can disrupt the chemical balance and subsequently complicate the utility of Sr/Ca in reconstructing historical SST. An approximately 44-year-long record of Sr/Ca shows that an annual SST signal is recorded but with an increasing Sr/Ca trend from 1980 to present, which is likely the result of runoff from the mountainous terrain of St. John. The overwhelming influence of the terrestrial fingerprint on local seawater chemistry makes utilizing Sr/Ca as a SST proxy in nearshore environments very difficult.

  1. Coalescence of magnetic islands

    International Nuclear Information System (INIS)

    Pellat, R.

    1982-01-01

    The paper gives the analytical theory of the coalescence instability and of a new, one island, instability. These instabilities are expected to be relevant for the disruptions observed in Tokamak experiments and astrophysical plasmas

  2. Heat Island Compendium

    Science.gov (United States)

    Heat islands can be mitigated through measures like planting trees and vegetation, installing green roofs and cool roofs, and using cool pavements. The compendium describes all of these strategies and shows how communities around the country are being used

  3. Herbarium genomics

    DEFF Research Database (Denmark)

    Bakker, Freek T.; Lei, Di; Yu, Jiaying

    2016-01-01

    Herbarium genomics is proving promising as next-generation sequencing approaches are well suited to deal with the usually fragmented nature of archival DNA. We show that routine assembly of partial plastome sequences from herbarium specimens is feasible, from total DNA extracts and with specimens...... up to 146 years old. We use genome skimming and an automated assembly pipeline, Iterative Organelle Genome Assembly, that assembles paired-end reads into a series of candidate assemblies, the best one of which is selected based on likelihood estimation. We used 93 specimens from 12 different...... correlation between plastome coverage and nuclear genome size (C value) in our samples, but the range of C values included is limited. Finally, we conclude that routine plastome sequencing from herbarium specimens is feasible and cost-effective (compared with Sanger sequencing or plastome...

  4. Three Mile Island revisited

    International Nuclear Information System (INIS)

    MacLeod, G.K.

    1986-01-01

    The accident at Three Mile Island proved that the Pennsylvania Department of Health lacked the tools to deal with the serious health consequences that occurred during and after this emergency. Despite the relative safety of nuclear power generation, we must be better prepared for the health and medical consequences of serous radiation emergencies. The author reviews the Three Mile Island accident through the eyes of newspaper reporters

  5. Islands and Islandness in Rock Music Lyrics

    Directory of Open Access Journals (Sweden)

    Daniele Mezzana

    2012-05-01

    Full Text Available This paper presents a first exploration, qualitative in character, based on a review of 412 songs produced in the period 1960-2009, about islands in rock music as both social products and social tools potentially contributing to shaping ideas, emotions, will, and desires. An initial taxonomy of 24 themes clustered under five meta-themes of space, lifestyle, emotions, symbolism, and social-political relations is provided, together with some proposals for further research.

  6. MHC variability in heritage breeds of chickens.

    Science.gov (United States)

    Fulton, J E; Lund, A R; McCarron, A M; Pinegar, K N; Korver, D R; Classen, H L; Aggrey, S; Utterbach, C; Anthony, N B; Berres, M E

    2016-02-01

    The chicken Major Histocompatibility Complex (MHC) is very strongly associated with disease resistance and thus is a very important region of the chicken genome. Historically, MHC (B locus) has been identified by the use of serology with haplotype specific alloantisera. These antisera can be difficult to produce and frequently cross-react with multiple haplotypes and hence their application is generally limited to inbred and MHC-defined lines. As a consequence, very little information about MHC variability in heritage chicken breeds is available. DNA-based methods are now available for examining MHC variability in these previously uncharacterized populations. A high density SNP panel consisting of 101 SNP that span a 230,000 bp region of the chicken MHC was used to examine MHC variability in 17 heritage populations of chickens from five universities from Canada and the United States. The breeds included 6 heritage broiler lines, 3 Barred Plymouth Rock, 2 New Hampshire and one each of Rhode Island Red, Light Sussex, White Leghorn, Dark Brown Leghorn, and 2 synthetic lines. These heritage breeds contained from one to 11 haplotypes per line. A total of 52 unique MHC haplotypes were found with only 10 of them identical to serologically defined haplotypes. Furthermore, nine MHC recombinants with their respective parental haplotypes were identified. This survey confirms the value of these non-commercially utilized lines in maintaining genetic diversity. The identification of multiple MHC haplotypes and novel MHC recombinants indicates that diversity is being generated and maintained within these heritage populations. © 2016 Poultry Science Association Inc.

  7. Conjugative type IVb pilus recognizes lipopolysaccharide of recipient cells to initiate PAPI-1 pathogenicity island transfer in Pseudomonas aeruginosa

    Science.gov (United States)

    Pseudomonas aeruginosa pathogenicity island 1 (PAPI-1) is one of the largest genomic islands of this important opportunistic human pathogen. Previous studies have shown that PAPI-1 encodes several putative virulence factors, a major regulator of biofilm formation, and antibiotic-resistance traits, a...

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

    Science.gov (United States)

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

    2016-01-04

    The Pseudomonas Genome Database (http://www.pseudomonas.com) is well known for the application of community-based annotation approaches for producing a high-quality Pseudomonas aeruginosa PAO1 genome annotation, and facilitating whole-genome comparative analyses with other Pseudomonas strains. To aid analysis of potentially thousands of complete and draft genome assemblies, this database and analysis platform was upgraded to integrate curated genome annotations and isolate metadata with enhanced tools for larger scale comparative analysis and visualization. Manually curated gene annotations are supplemented with improved computational analyses that help identify putative drug targets and vaccine candidates or assist with evolutionary studies by identifying orthologs, pathogen-associated genes and genomic islands. The database schema has been updated to integrate isolate metadata that will facilitate more powerful analysis of genomes across datasets in the future. We continue to place an emphasis on providing high-quality updates to gene annotations through regular review of the scientific literature and using community-based approaches including a major new Pseudomonas community initiative for the assignment of high-quality gene ontology terms to genes. As we further expand from thousands of genomes, we plan to provide enhancements that will aid data visualization and analysis arising from whole-genome comparative studies including more pan-genome and population-based approaches. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

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

    Science.gov (United States)

    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.

  10. A dependence modelling study of extreme rainfall in Madeira Island

    Science.gov (United States)

    Gouveia-Reis, Délia; Guerreiro Lopes, Luiz; Mendonça, Sandra

    2016-08-01

    The dependence between variables plays a central role in multivariate extremes. In this paper, spatial dependence of Madeira Island's rainfall data is addressed within an extreme value copula approach through an analysis of maximum annual data. The impact of altitude, slope orientation, distance between rain gauge stations and distance from the stations to the sea are investigated for two different periods of time. The results obtained highlight the influence of the island's complex topography on the spatial distribution of extreme rainfall in Madeira Island.

  11. Heron Island, Australia

    Science.gov (United States)

    2002-01-01

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

  12. Cephalopod genomics

    DEFF Research Database (Denmark)

    Albertin, Caroline B.; Bonnaud, Laure; Brown, C. Titus

    2012-01-01

    The Cephalopod Sequencing Consortium (CephSeq Consortium) was established at a NESCent Catalysis Group Meeting, ``Paths to Cephalopod Genomics-Strategies, Choices, Organization,'' held in Durham, North Carolina, USA on May 24-27, 2012. Twenty-eight participants representing nine countries (Austria......, Australia, China, Denmark, France, Italy, Japan, Spain and the USA) met to address the pressing need for genome sequencing of cephalopod mollusks. This group, drawn from cephalopod biologists, neuroscientists, developmental and evolutionary biologists, materials scientists, bioinformaticians and researchers...... active in sequencing, assembling and annotating genomes, agreed on a set of cephalopod species of particular importance for initial sequencing and developed strategies and an organization (CephSeq Consortium) to promote this sequencing. The conclusions and recommendations of this meeting are described...

  13. The complete mitochondrial DNA genome of a greater horseshoe bat subspecies, Rhinolophus ferrumequinum quelpartis (Chiroptera: Rhinolophidae).

    Science.gov (United States)

    Yoon, Kwang Bae; Kim, Ji Young; Kim, Hye Ri; Cho, Jae Youl; Park, Yung Chul

    2013-02-01

    There are two subspecies of Rhinolophus ferrumequinum currently recognized in South Korea. The Korean greater horseshoe bat subspecies, Rhinolophus ferrumequinum quelpartis, is distributed only in Jeju Island. The complete mitochondrial genome of the island subspecies was determined and revealed 99.7% similarity to the mainland subspecies Rhinolophus ferrumequinum korai. If d-loop region is excluded, similarity of the two genomes was 99.9%.

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

    Science.gov (United States)

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

    2014-10-30

    We present the draft genome sequence of Vibrio cholerae InDRE 3140 recovered in 2013 during a cholera outbreak in Mexico. The genome showed the Vibrio 7th pandemic islands VSP1 and VSP2, the pathogenic islands VPI-1 and VPI-2, the integrative and conjugative element SXT/R391 (ICE-SXT), and both prophages CTXφ and RS1φ. Copyright © 2014 Díaz-Quiñonez et al.

  15. Genome Sequencing

    DEFF Research Database (Denmark)

    Sato, Shusei; Andersen, Stig Uggerhøj

    2014-01-01

    The current Lotus japonicus reference genome sequence is based on a hybrid assembly of Sanger TAC/BAC, Sanger shotgun and Illumina shotgun sequencing data generated from the Miyakojima-MG20 accession. It covers nearly all expressed L. japonicus genes and has been annotated mainly based on transcr......The current Lotus japonicus reference genome sequence is based on a hybrid assembly of Sanger TAC/BAC, Sanger shotgun and Illumina shotgun sequencing data generated from the Miyakojima-MG20 accession. It covers nearly all expressed L. japonicus genes and has been annotated mainly based...

  16. Genomic individuality and its biological implications.

    Science.gov (United States)

    Zhao, J

    1996-06-01

    It is a widely accepted fundamental concept that all somatic genomes of a human individual are identical to each other. The theoretical basis of this concept is that all of these somatic genomes are the descendants of the genome of a single fertilized cell as well as the simple replicated products of asexual reproduction, thus not forming any new recombined genomes. The question here is whether such a concept might only represent one side of somatic genome biology and, even worse, whether it has perhaps already led to a very prevalent misconception that within the organism body, there exists no variability among individual somatic genomes. A hypothesis, called genomic individuality, is proposed, simply saying that every individual somatic genome, perhaps with rare exceptions, has its own unique or individual 'genetic identity' or 'fingerprint', which is characterized by its distinctive sequences or patterns of deoxyribonucleic acid molecules, or both. Thus, no two somatic genomes can be identical to each other in every or all aspects, and consequently, there must be a great deal of genomic variation present within the body of any multicellular organism. The concept or hypothesis of genomic individuality would not only provide a more complete understanding of genome biology, but also suggest a new insight into the studies of the biology of cells and organisms.

  17. The Salmonella enterica Pan-genome

    DEFF Research Database (Denmark)

    Jacobsen, Annika; Hendriksen, Rene S.; Aarestrup, Frank Møller

    2011-01-01

    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......, 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...

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

    Directory of Open Access Journals (Sweden)

    David A Marques

    2016-02-01

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

  19. Small Island Visitor Attractions

    Directory of Open Access Journals (Sweden)

    Haven Allahar

    2015-03-01

    Full Text Available This article proposes a process framework for developing and managing visitor attractions (VA in small island developing states with Trinidad and Tobago, a two-island state in the Caribbean, as the case study. An extensive literature review was conducted, supported by field observations, individual depth interviews, and small and large focus group meetings. The process framework identified four sets of processes: national policy formulation and legislation; inventory, classification, evaluation, and ranking of VA; general operations management involving project management activities; and site specific activities of development, operations, and maintenance. The value of the framework lies in the fact that no similar framework applicable to small islands was covered in the literature and validation was obtained from a panel of experts and a cross section of tourism stakeholders in Tobago.

  20. A Genome-Wide Landscape of Retrocopies in Primate Genomes.

    Science.gov (United States)

    Navarro, Fábio C P; Galante, Pedro A F

    2015-07-29

    Gene duplication is a key factor contributing to phenotype diversity across and within species. Although the availability of complete genomes has led to the extensive study of genomic duplications, the dynamics and variability of gene duplications mediated by retrotransposition are not well understood. Here, we predict mRNA retrotransposition and use comparative genomics to investigate their origin and variability across primates. Analyzing seven anthropoid primate genomes, we found a similar number of mRNA retrotranspositions (∼7,500 retrocopies) in Catarrhini (Old Word Monkeys, including humans), but a surprising large number of retrocopies (∼10,000) in Platyrrhini (New World Monkeys), which may be a by-product of higher long interspersed nuclear element 1 activity in these genomes. By inferring retrocopy orthology, we dated most of the primate retrocopy origins, and estimated a decrease in the fixation rate in recent primate history, implying a smaller number of species-specific retrocopies. Moreover, using RNA-Seq data, we identified approximately 3,600 expressed retrocopies. As expected, most of these retrocopies are located near or within known genes, present tissue-specific and even species-specific expression patterns, and no expression correlation to their parental genes. Taken together, our results provide further evidence that mRNA retrotransposition is an active mechanism in primate evolution and suggest that retrocopies may not only introduce great genetic variability between lineages but also create a large reservoir of potentially functional new genomic loci in primate genomes. © The Author(s) 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  1. Whole-Genome Sequencing and Comparative Analysis of Mycobacterium brisbanense Reveals a Possible Soil Origin and Capability in Fertiliser Synthesis.

    Directory of Open Access Journals (Sweden)

    Wei Yee Wee

    Full Text Available Mycobacterium brisbanense is a member of Mycobacterium fortuitum third biovariant complex, which includes rapidly growing Mycobacterium spp. that normally inhabit soil, dust and water, and can sometimes cause respiratory tract infections in humans. We present the first whole-genome analysis of M. brisbanense UM_WWY which was isolated from a 70-year-old Malaysian patient. Molecular phylogenetic analyses confirmed the identification of this strain as M. brisbanense and showed that it has an unusually large genome compared with related mycobacteria. The large genome size of M. brisbanense UM_WWY (~7.7Mbp is consistent with further findings that this strain has a highly variable genome structure that contains many putative horizontally transferred genomic islands and prophage. Comparative analysis showed that M. brisbanense UM_WWY is the only Mycobacterium species that possesses a complete set of genes encoding enzymes involved in the urea cycle, suggesting that this soil bacterium is able to synthesize urea for use as plant fertilizers. It is likely that M. brisbanense UM_WWY is adapted to live in soil as its primary habitat since the genome contains many genes associated with nitrogen metabolism. Nevertheless, a large number of predicted virulence genes were identified in M. brisbanense UM_WWY that are mostly shared with well-studied mycobacterial pathogens such as Mycobacterium tuberculosis and Mycobacterium abscessus. These findings are consistent with the role of M. brisbanense as an opportunistic pathogen of humans. The whole-genome study of UM_WWY has provided the basis for future work of M. brisbanense.

  2. Whole-Genome Sequencing and Comparative Analysis of Mycobacterium brisbanense Reveals a Possible Soil Origin and Capability in Fertiliser Synthesis.

    Science.gov (United States)

    Wee, Wei Yee; Tan, Tze King; Jakubovics, Nicholas S; Choo, Siew Woh

    2016-01-01

    Mycobacterium brisbanense is a member of Mycobacterium fortuitum third biovariant complex, which includes rapidly growing Mycobacterium spp. that normally inhabit soil, dust and water, and can sometimes cause respiratory tract infections in humans. We present the first whole-genome analysis of M. brisbanense UM_WWY which was isolated from a 70-year-old Malaysian patient. Molecular phylogenetic analyses confirmed the identification of this strain as M. brisbanense and showed that it has an unusually large genome compared with related mycobacteria. The large genome size of M. brisbanense UM_WWY (~7.7Mbp) is consistent with further findings that this strain has a highly variable genome structure that contains many putative horizontally transferred genomic islands and prophage. Comparative analysis showed that M. brisbanense UM_WWY is the only Mycobacterium species that possesses a complete set of genes encoding enzymes involved in the urea cycle, suggesting that this soil bacterium is able to synthesize urea for use as plant fertilizers. It is likely that M. brisbanense UM_WWY is adapted to live in soil as its primary habitat since the genome contains many genes associated with nitrogen metabolism. Nevertheless, a large number of predicted virulence genes were identified in M. brisbanense UM_WWY that are mostly shared with well-studied mycobacterial pathogens such as Mycobacterium tuberculosis and Mycobacterium abscessus. These findings are consistent with the role of M. brisbanense as an opportunistic pathogen of humans. The whole-genome study of UM_WWY has provided the basis for future work of M. brisbanense.

  3. Island of Luzon, Philippines

    Science.gov (United States)

    1990-01-01

    In this north to south view of the Island of Luzon, Philippines (13.0N, 120.0E), the prominent Cordillera Central mountain range where gold, copper and silver are mined. The several large rivers that drain this region normally carry a heavy silt load to the sea but the absence of sediment plumes in this view is evidence of hot dry weather and lack of recent rains. Manila, the capital city is just visible at the south end of the island.

  4. Chatham Islands Climate Change

    International Nuclear Information System (INIS)

    Mullan, B.; Salinger, J.; Thompson, C.; Ramsay, D.; Wild, M.

    2005-06-01

    This brief report provides guidance on climate change specific to the Chatham Islands, to complement the information recently produced for local government by the Ministry for the Environment in 'Climate Change Effects and Impacts Assessment: A guidance manual for Local Government in New Zealand' and 'Coastal Hazards and Climate Change: A guidance manual for Local Government in New Zealand'. These previous reports contain a lot of generic information on climate change, and how to assess associated risks, that is relevant to the Chatham Islands Council.

  5. Island in the Air

    DEFF Research Database (Denmark)

    Simonsen, Dorthe Gert

    2017-01-01

    In this article, I explore the formation of airspace in Britain from 1910 to 1913. The technology of flight challenged the “flat discourse” of nationalized geography, drawing up instead a volumetric space in the sky as airplanes flew from the Continent to England. The drive to control aerial...... extension of the Island Kingdom, extrapolating its coastal borders into the sky. However, even as Parliament passed the Aerial Navigation Act in 1913, this legal construction of an island in the air could not endure the agency of airplanes. The formation of airspace, I argue, is a history particularly well...

  6. Archaeoastronomy of Easter Island

    Science.gov (United States)

    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.

  7. Long Island Solar Farm

    Energy Technology Data Exchange (ETDEWEB)

    Anders, R.

    2013-05-01

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

  8. A comparison of controls on freshwater lens morphology of small carbonate and siliciclastic islands: examples from barrier islands in Florida, USA

    Science.gov (United States)

    Schneider, James C.; Kruse, Sarah E.

    2003-12-01

    The freshwater lens on small islands may easily be overexploited or polluted due to dense development combined with improper management. On small carbonate islands complexities in fresh groundwater distribution are most commonly driven by geologic heterogeneities and their attendant impact on permeability and effective recharge patterns. Siliciclastic islands (composed primarily of quartz sand and other silica-based minerals) have been less well studied, and fewer common patterns of lens development have emerged. On some siliciclastic islands correlations between geology and lens geometries are weak; on these islands the freshwater lens geometry may be largely determined by how vegetation and terrain elevation affect recharge. Other factors such as unequal sea level on opposite sides of an island and transient variability (natural island migration and climate variability) may also be locally significant. Two barrier islands in the northeast Gulf of Mexico fall into this category of siliciclastic islands. Relationships between lens morphology, geology, vegetation, terrain, and sea level and transient effects are documented on St George Island and Dog Island, FL. Patterns of fresh groundwater occurrence are deduced with electrical and electromagnetic geophysical methods. Although isolated cores show geologic layering that could potentially control freshwater lens development, ground penetrating radar and seismic surveys show no evidence of semi-continuous subhorizontal layering. Inferred lens thickness and geometry suggests that site geology plays a relatively minor role as a cause of complexity in lens formation. Lens geometry does appear to be related to terrain and vegetation variability, and further complicated by the continuous reforming of these islands by coastal processes and human development.

  9. Comparative Genomics

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 11; Issue 8. Comparative Genomics - A Powerful New Tool in Biology. Anand K Bachhawat. General Article Volume 11 Issue 8 August 2006 pp 22-40. Fulltext. Click here to view fulltext PDF. Permanent link:

  10. Islanded operation of distribution networks

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2005-07-01

    This report summarises the results of a study assessing the benefits and risks to distribution network of generator islanding and examining the technical, commercial and regulatory changes required to facilitate the operation of islanding. The background to the study is traced, and details are given of a literature review, the technical criteria for operating sections of the network in islanding mode, and the impact of islanding on trading. Case studies and a detailed implementation plan, data acquisition, and commercial incentives are discussed.

  11. Islanded operation of distribution networks

    International Nuclear Information System (INIS)

    2005-01-01

    This report summarises the results of a study assessing the benefits and risks to distribution network of generator islanding and examining the technical, commercial and regulatory changes required to facilitate the operation of islanding. The background to the study is traced, and details are given of a literature review, the technical criteria for operating sections of the network in islanding mode, and the impact of islanding on trading. Case studies and a detailed implementation plan, data acquisition, and commercial incentives are discussed

  12. Pediatrics in the Marshall Islands

    International Nuclear Information System (INIS)

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

    1984-01-01

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

  13. The Island Smart Energy System and Market

    DEFF Research Database (Denmark)

    Ma, Zheng; Billanes, Joy Dalmacio; Jørgensen, Bo Nørregaard

    2017-01-01

    developing island smart energy systems with the integration of renewable energy resources can increase the energy supply and address the global island energy issues. The island smart energy system operates either in a single-island or in multi-islands. However the island characteristics and influ...

  14. Genomes in turmoil: quantification of genome dynamics in prokaryote supergenomes.

    Science.gov (United States)

    Puigbò, Pere; Lobkovsky, Alexander E; Kristensen, David M; Wolf, Yuri I; Koonin, Eugene V

    2014-08-21

    Genomes of bacteria and archaea (collectively, prokaryotes) appear to exist in incessant flux, expanding via horizontal gene transfer and gene duplication, and contracting via gene loss. However, the actual rates of genome dynamics and relative contributions of different types of event across the diversity of prokaryotes are largely unknown, as are the sizes of microbial supergenomes, i.e. pools of genes that are accessible to the given microbial species. We performed a comprehensive analysis of the genome dynamics in 35 groups (34 bacterial and one archaeal) of closely related microbial genomes using a phylogenetic birth-and-death maximum likelihood model to quantify the rates of gene family gain and loss, as well as expansion and reduction. The results show that loss of gene families dominates the evolution of prokaryotes, occurring at approximately three times the rate of gain. The rates of gene family expansion and reduction are typically seven and twenty times less than the gain and loss rates, respectively. Thus, the prevailing mode of evolution in bacteria and archaea is genome contraction, which is partially compensated by the gain of new gene families via horizontal gene transfer. However, the rates of gene family gain, loss, expansion and reduction vary within wide ranges, with the most stable genomes showing rates about 25 times lower than the most dynamic genomes. For many groups, the supergenome estimated from the fraction of repetitive gene family gains includes about tenfold more gene families than the typical genome in the group although some groups appear to have vast, 'open' supergenomes. Reconstruction of evolution for groups of closely related bacteria and archaea reveals an extremely rapid and highly variable flux of genes in evolving microbial genomes, demonstrates that extensive gene loss and horizontal gene transfer leading to innovation are the two dominant evolutionary processes, and yields robust estimates of the supergenome size.

  15. Solomon Islands Botany

    NARCIS (Netherlands)

    Steenis, van C.G.G.J.

    1969-01-01

    A discussion of the Results of the Royal Society Expedition to the British Solomon Islands Protectorate, 1965. Organized by E.J.H. Corner. Phil. Trans. R. Soc. B 255 (1969) 185-631, 196 fig. University Printing House, Shaftesbury Road, Cambridge. Obtainable through booksellers or direct to the Royal

  16. Pacific Island Pharmacovigilance

    DEFF Research Database (Denmark)

    McEwen, John; Vestergaard, Lasse S.; Sanburg, Amanda L C

    2016-01-01

    Many Pacific Island countries (PICs) are recipients of funding support from the Global Fund to Fight AIDS, Tuberculosis and Malaria (Global Fund). However, most of these countries cannot be expected to meet Global Fund and World Health Organization (WHO) minimum requirements for a functioning...

  17. Magnetic-island formation

    International Nuclear Information System (INIS)

    Boozer, A.H.

    1983-08-01

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

  18. Bone island and leprosy

    Energy Technology Data Exchange (ETDEWEB)

    Carpintero, P.; Garcia-Frasquet, A. [Department of Orthopaedic Surgery, Cordoba University, Medical School, Reina Sofia University Hospital, Cordoba (Spain); Tarradas, E. [Department of Imaging, Cordoba University, Medical School, Cordoba (Spain); Logrono, C. [Department of Dermatology, Reina Sofia University Hospital, Cordoba (Spain); Carrascal, A. [Department of Radiology, Infanta Elena Hospital, Huelva (Spain); Carreto, A. [Department of Radiology, Reina Sofia University Hospital, Cordoba (Spain)

    1998-06-01

    Objective. To determine the incidence of bone islands in leprosy patients. Design. X-rays of feet and hands of patients with Hansen`s disease (leprosy) were reviewed retrospectively. A second group of related age- and sex-matched patients who did not have Hansen`s disease was used for control purposes. Controls had undergone hand or foot X-rays during diagnosis of other pathologies. The patients with Hansen`s disease were compared with the control group, and were also analyzed as subgroups with different types of leprosy. The results were subjected to statistical analysis. Patients. Ninety patients with Hansen`s disease were randomly selected for this study. Patients who had had ulcers on hands or feet were excluded from the study. Results and conclusions. Bone islands were demonstrated in 20 patients with Hansen`s disease; no bone islands were observed in the controls. This was statistically significant (P<0.01). Bone islands were only seen in patients with lepromatous leprosy and borderline types but were not demonstrated in patients with tuberculoid leprosy. There was also a statistically significant relationship for a disease duration of 15 years or more. The cause of this raised incidence of enostosis in leprosy patients is not clear, but there may be a genetic predisposition in patients with leprosy, or it may be a side effect of leprosy, especially the lepromatous form. (orig.) With 4 figs., 2 tabs., 9 refs.

  19. Bone island and leprosy

    International Nuclear Information System (INIS)

    Carpintero, P.; Garcia-Frasquet, A.; Tarradas, E.; Logrono, C.; Carrascal, A.; Carreto, A.

    1998-01-01

    Objective. To determine the incidence of bone islands in leprosy patients. Design. X-rays of feet and hands of patients with Hansen's disease (leprosy) were reviewed retrospectively. A second group of related age- and sex-matched patients who did not have Hansen's disease was used for control purposes. Controls had undergone hand or foot X-rays during diagnosis of other pathologies. The patients with Hansen's disease were compared with the control group, and were also analyzed as subgroups with different types of leprosy. The results were subjected to statistical analysis. Patients. Ninety patients with Hansen's disease were randomly selected for this study. Patients who had had ulcers on hands or feet were excluded from the study. Results and conclusions. Bone islands were demonstrated in 20 patients with Hansen's disease; no bone islands were observed in the controls. This was statistically significant (P<0.01). Bone islands were only seen in patients with lepromatous leprosy and borderline types but were not demonstrated in patients with tuberculoid leprosy. There was also a statistically significant relationship for a disease duration of 15 years or more. The cause of this raised incidence of enostosis in leprosy patients is not clear, but there may be a genetic predisposition in patients with leprosy, or it may be a side effect of leprosy, especially the lepromatous form. (orig.)

  20. Whole genome DNA methylation: beyond genes silencing

    OpenAIRE

    Tirado-Magallanes, Roberto; Rebbani, Khadija; Lim, Ricky; Pradhan, Sriharsa; Benoukraf, Touati

    2016-01-01

    The combination of DNA bisulfite treatment with high-throughput sequencing technologies has enabled investigation of genome-wide DNA methylation at near base pair level resolution, far beyond that of the kilobase-long canonical CpG islands that initially revealed the biological relevance of this covalent DNA modification. The latest high-resolution studies have revealed a role for very punctual DNA methylation in chromatin plasticity, gene regulation and splicing. Here, we aim to outline the ...

  1. Data on genome analysis of Bacillus velezensis LS69.

    Science.gov (United States)

    Liu, Guoqiang; Kong, Yingying; Fan, Yajing; Geng, Ce; Peng, Donghai; Sun, Ming

    2017-08-01

    The data presented in this article are related to the published entitled "Whole-genome sequencing of Bacillus velezensis LS69, a strain with a broad inhibitory spectrum against pathogenic bacteria" (Liu et al., 2017) [1]. Genome analysis revealed B. velezensis LS69 has a good potential for biocontrol and plant growth promotion. This article provides an extended analysis of the genetic islands, core genes and amylolysin loci of B. velezensis LS69.

  2. Data on genome analysis of Bacillus velezensis LS69

    OpenAIRE

    Liu, Guoqiang; Kong, Yingying; Fan, Yajing; Geng, Ce; Peng, Donghai; Sun, Ming

    2017-01-01

    The data presented in this article are related to the published entitled “Whole-genome sequencing of Bacillus velezensis LS69, a strain with a broad inhibitory spectrum against pathogenic bacteria” (Liu et al., 2017) [1]. Genome analysis revealed B. velezensis LS69 has a good potential for biocontrol and plant growth promotion. This article provides an extended analysis of the genetic islands, core genes and amylolysin loci of B. velezensis LS69.

  3. Data on genome analysis of Bacillus velezensis LS69

    Directory of Open Access Journals (Sweden)

    Guoqiang Liu

    2017-08-01

    Full Text Available The data presented in this article are related to the published entitled “Whole-genome sequencing of Bacillus velezensis LS69, a strain with a broad inhibitory spectrum against pathogenic bacteria” (Liu et al., 2017 [1]. Genome analysis revealed B. velezensis LS69 has a good potential for biocontrol and plant growth promotion. This article provides an extended analysis of the genetic islands, core genes and amylolysin loci of B. velezensis LS69.

  4. Reassignment of Drosophila willistoni Genome Scaffolds to Chromosome II Arms

    OpenAIRE

    Garcia, Carolina; Delprat, Alejandra; Ruiz, Alfredo; Valente, Vera L. S.

    2015-01-01

    Drosophila willistoni is a geographically widespread Neotropical species. The genome of strain Gd-H4-1 from Guadeloupe Island (Caribbean) was sequenced in 2007 as part of the 12 Drosophila Genomes Project. The assembled scaffolds were joined based on conserved linkage and assigned to polytene chromosomes based on a handful of genetic and physical markers. This paucity of markers was particularly striking in the metacentric chromosome II, comprised two similarly sized arms, IIL and IIR, tradit...

  5. Personal genomics services: whose genomes?

    Science.gov (United States)

    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.

  6. Variability Bugs:

    DEFF Research Database (Denmark)

    Melo, Jean

    . Although many researchers suggest that preprocessor-based variability amplifies maintenance problems, there is little to no hard evidence on how actually variability affects programs and programmers. Specifically, how does variability affect programmers during maintenance tasks (bug finding in particular......)? How much harder is it to debug a program as variability increases? How do developers debug programs with variability? In what ways does variability affect bugs? In this Ph.D. thesis, I set off to address such issues through different perspectives using empirical research (based on controlled...... experiments) in order to understand quantitatively and qualitatively the impact of variability on programmers at bug finding and on buggy programs. From the program (and bug) perspective, the results show that variability is ubiquitous. There appears to be no specific nature of variability bugs that could...

  7. Recombination rate variation in mice from an isolated island.

    Science.gov (United States)

    Wang, Richard J; Gray, Melissa M; Parmenter, Michelle D; Broman, Karl W; Payseur, Bret A

    2017-01-01

    Recombination rate is a heritable trait that varies among individuals. Despite the major impact of recombination rate on patterns of genetic diversity and the efficacy of selection, natural variation in this phenotype remains poorly characterized. We present a comparison of genetic maps, sampling 1212 meioses, from a unique population of wild house mice (Mus musculus domesticus) that recently colonized remote Gough Island. Crosses to a mainland reference strain (WSB/EiJ) reveal pervasive variation in recombination rate among Gough Island mice, including subchromosomal intervals spanning up to 28% of the genome. In spite of this high level of polymorphism, the genomewide recombination rate does not significantly vary. In general, we find that recombination rate varies more when measured in smaller genomic intervals. Using the current standard genetic map of the laboratory mouse to polarize intervals with divergent recombination rates, we infer that the majority of evolutionary change occurred in one of the two tested lines of Gough Island mice. Our results confirm that natural populations harbour a high level of recombination rate polymorphism and highlight the disparities in recombination rate evolution across genomic scales. © 2016 John Wiley & Sons Ltd.

  8. Visualization for genomics: the Microbial Genome Viewer.

    NARCIS (Netherlands)

    Kerkhoven, R.; Enckevort, F.H.J. van; Boekhorst, J.; Molenaar, D; Siezen, R.J.

    2004-01-01

    SUMMARY: A Web-based visualization tool, the Microbial Genome Viewer, is presented that allows the user to combine complex genomic data in a highly interactive way. This Web tool enables the interactive generation of chromosome wheels and linear genome maps from genome annotation data stored in a

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

    Science.gov (United States)

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

    2009-06-01

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

  10. Impacts of fishing and environmental factors driving changes on littoral fish assemblages in a subtropical oceanic island

    Science.gov (United States)

    Sangil, Carlos; Martín-García, Laura; Hernández, José Carlos; Concepción, Laura; Fernández, Raúl; Clemente, Sabrina

    2013-08-01

    The structure of demersal fish assemblages of commercial interest was studied at 51 sites on La Palma Island (Canary Islands, northeastern Atlantic). On this island, demersal fish populations are limited and independent from other islands. As deep water separates the islands and the shallow sublittoral platforms are not continuous, adult inter-island migrations are not possible except between the islands of Lanzarote and Fuerteventura. Otherwise, each island functions as a closed system, and the status of an island fish assemblage depends on local environmental conditions and activities performed in situ by the islanders. These circumstances provide a unique opportunity to test the intrainsular variability of fish assemblages. With this background, environmental parameters, fishing pressure and distance to the MPA were considered to identify the main factors explaining the spatial variation of fish assemblages off La Palma Island. Twenty-six fish species were recorded, but 60% of the total fish biomass was represented by only five species (Sparisoma cretense, Pomadasys incisus, Canthidermis sufflamen, Diplodus cervinus cervinus and Bodianus scrofa). However, the structure of assemblages was heterogeneous in response to different variables and showed substantial spatial variation. The assemblages were strongly modified by the presence of upright seaweed cover, fishing activities, and certain environmental variables. Differences were more pronounced in species that occupied the higher trophic levels. The most disturbed assemblages were those located in areas with lower upright seaweed cover and with higher fishing pressure, whereas the best-preserved assemblages corresponded to sites with controlled fishing activities, located within the MPA.

  11. Growth of Co on Cu(111), Subsurface growth of trilayer Co islands

    DEFF Research Database (Denmark)

    Pedersen, M.Ø.; Bönicke, I.A.; Lægsgaard, E.

    1997-01-01

    The growth of cobalt on Cu(lll) has been studied using a variable-temperature scanning tunneling microscope (STM). Al a deposition temperature of 150 K, one observes the growth of three-layer Co islands with one subsurface layer. The Co islands are surrounded by a brim of Cu. The distinction...

  12. Complete Genome Sequence of Bacillus subtilis subsp. subtilis Strain ∆6

    NARCIS (Netherlands)

    Reuß, Daniel R; Thürmer, Andrea; Daniel, Rolf; Quax, Wim J; Stülke, Jörg

    2016-01-01

    Bacillus subtilis ∆6 is a genome-reduced strain that was cured from six prophages and AT-rich islands. This strain is of great interest for biotechnological applications. Here, we announce the full-genome sequence of this strain. Interestingly, the conjugative element ICEBs1 has most likely

  13. Determining coding CpG islands by identifying regions significant for pattern statistics on Markov chains.

    Science.gov (United States)

    Singer, Meromit; Engström, Alexander; Schönhuth, Alexander; Pachter, Lior

    2011-09-23

    Recent experimental and computational work confirms that CpGs can be unmethylated inside coding exons, thereby showing that codons may be subjected to both genomic and epigenomic constraint. It is therefore of interest to identify coding CpG islands (CCGIs) that are regions inside exons enriched for CpGs. The difficulty in identifying such islands is that coding exons exhibit sequence biases determined by codon usage and constraints that must be taken into account. We present a method for finding CCGIs that showcases a novel approach we have developed for identifying regions of interest that are significant (with respect to a Markov chain) for the counts of any pattern. Our method begins with the exact computation of tail probabilities for the number of CpGs in all regions contained in coding exons, and then applies a greedy algorithm for selecting islands from among the regions. We show that the greedy algorithm provably optimizes a biologically motivated criterion for selecting islands while controlling the false discovery rate. We applied this approach to the human genome (hg18) and annotated CpG islands in coding exons. The statistical criterion we apply to evaluating islands reduces the number of false positives in existing annotations, while our approach to defining islands reveals significant numbers of undiscovered CCGIs in coding exons. Many of these appear to be examples of functional epigenetic specialization in coding exons.

  14. Island solution; Inselloesung

    Energy Technology Data Exchange (ETDEWEB)

    Bah, Isaac

    2013-06-15

    On the Azores island Graciosa the Berlin-based company Younicos has installed a new electricity system with advanced storage technology, which will make the islanders independent from fossil fuels. With an energy mix of wind power, photovoltaics and biomass the dependence on fossil fuels should be terminated. In the center of the flagship project specifically developed hybrid batteries are used (combination of sodium-sulfur- and lithium-ion batteries) with 2.7 MW of power and a storage capacity of ten megawatts hours. [German] Auf der Azoren-Insel Graciosa installiert das Berliner Unternehmen Younicos ein neues Stromsystem mit modernster Speichertechnologie, das die Bewohner unabhaengig von fossilen Energietraegern machen soll. Mit einem Energiemix aus Windkraft, Photovoltaik und Biomasse soll die Abhaengigkeit von fossilen Brennstoffen beendet werden. Im Zentrum des Vorzeigeprojekts stehen speziell fuer den Inseleinsatz entwickelte Hybridbatterien (Kombination aus Natrium-Schwefel- und Lithium-Ionen-Akkus) mit 2,7 Megawatt Leistung und eine Speicherkapazitaet von zehn Megawattestunden.

  15. Urban heat island 1

    DEFF Research Database (Denmark)

    Bühler, Oliver; Jensen, Marina Bergen; Petersen, Karen Sejr

    2010-01-01

    Urban Heat Island beskriver det forhold, at temperaturen i byområder er højere end temperaturen i tilgrænsede landområder. Årsagen hertil ligger i den urbane arealanvendelse, hvor en mindre andel af arealerne er dækket af vegetation, og en større andel består af forseglede arealer.......Urban Heat Island beskriver det forhold, at temperaturen i byområder er højere end temperaturen i tilgrænsede landområder. Årsagen hertil ligger i den urbane arealanvendelse, hvor en mindre andel af arealerne er dækket af vegetation, og en større andel består af forseglede arealer....

  16. VRprofile: gene-cluster-detection-based profiling of virulence and antibiotic resistance traits encoded within genome sequences of pathogenic bacteria.

    Science.gov (United States)

    Li, Jun; Tai, Cui; Deng, Zixin; Zhong, Weihong; He, Yongqun; Ou, Hong-Yu

    2017-01-10

    VRprofile is a Web server that facilitates rapid investigation of virulence and antibiotic resistance genes, as well as extends these trait transfer-related genetic contexts, in newly sequenced pathogenic bacterial genomes. The used backend database MobilomeDB was firstly built on sets of known gene cluster loci of bacterial type III/IV/VI/VII secretion systems and mobile genetic elements, including integrative and conjugative elements, prophages, class I integrons, IS elements and pathogenicity/antibiotic resistance islands. VRprofile is thus able to co-localize the homologs of these conserved gene clusters using HMMer or BLASTp searches. With the integration of the homologous gene cluster search module with a sequence composition module, VRprofile has exhibited better performance for island-like region predictions than the other widely used methods. In addition, VRprofile also provides an integrated Web interface for aligning and visualizing identified gene clusters with MobilomeDB-archived gene clusters, or a variety set of bacterial genomes. VRprofile might contribute to meet the increasing demands of re-annotations of bacterial variable regions, and aid in the real-time definitions of disease-relevant gene clusters in pathogenic bacteria of interest. VRprofile is freely available at http://bioinfo-mml.sjtu.edu.cn/VRprofile. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  17. Phylogeography and genetic structure of endemic Acmispon argophyllus and A. dendroideus (Fabaceae) across the California Channel Islands.

    Science.gov (United States)

    Wallace, Lisa E; Wheeler, Gregory L; McGlaughlin, Mitchell E; Bresowar, Gerald; Helenurm, Kaius

    2017-05-01

    Taxa inhabiting the California Channel Islands exhibit variation in their degree of isolation, but few studies have considered patterns across the entire archipelago. We studied phylogeography of insular Acmispon argophyllus and A. dendroideus to determine whether infraspecific taxa are genetically divergent and to elucidate patterns of diversification across these islands. DNA sequences were collected from nuclear (ADH) and plastid genomes ( rpL16 , ndhA , psbD-trnT ) from >450 samples on the Channel Islands and California. We estimated population genetic diversity and structure, phylogenetic patterns among populations, and migration rates, and tested for population growth. Populations of northern island A. argophyllus var. niveus are genetically distinct from conspecific populations on southern islands. On the southern islands, A. argophyllus var. argenteus populations on Santa Catalina are phylogenetically distinct from populations of var. argenteus and var. adsurgens on the other southern islands. For A. dendroideus , we found the varieties to be monophyletic. Populations of A. dendroideus var. traskiae on San Clemente are genetically differentiated from other conspecific populations, whereas populations on the northern islands and Santa Catalina show varying degrees of gene flow. Evidence of population growth was found in both species. Oceanic barriers between islands have had a strong influence on population genetic structure in both Acmispon species, although the species have differing phylogeographic patterns. This study provides a contrasting pattern of dispersal on a near island system that does not follow a strict stepping-stone model, commonly found on isolated island systems. © 2017 Botanical Society of America.

  18. Non-CpG island promoter hypomethylation and miR-149 regulate the expression of SRPX2 in colorectal cancer

    DEFF Research Database (Denmark)

    Oster, Bodil; Linnet, Lene; Christensen, Lise Lotte

    2012-01-01

    Gene silencing by DNA hypermethylation of CpG islands is a well-characterized phenomenon in cancer. The effect of hypomethylation in particular of non-CpG island genes is much less well described. By genome-wide screening, we identified 105 genes in microsatellite stable (MSS) colorectal adenocar......Gene silencing by DNA hypermethylation of CpG islands is a well-characterized phenomenon in cancer. The effect of hypomethylation in particular of non-CpG island genes is much less well described. By genome-wide screening, we identified 105 genes in microsatellite stable (MSS) colorectal...... of non-CpG island-associated promoters deregulate gene expression nearly as frequent as do CpG-island hypermethylation. The hypomethylation of SRPX2 is focal and not part of a large block. Furthermore, it often translates to an increased expression level, which may be modulated by miR-149....

  19. Charge Islands Through Tunneling

    Science.gov (United States)

    Robinson, Daryl C.

    2002-01-01

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

  20. Islands in the Ocean

    Directory of Open Access Journals (Sweden)

    Elena Bagina

    2017-12-01

    Full Text Available Today’s China is an outpost of modern western architecture. All famous architects and firms build here. Having lost their historical context, the objects of traditional Chinese architecture become islands in the ocean of new development. Their destiny is controversial. Architectural masterpieces are perceived in a superficial manner not only by tourists, but also by local people. The link of times that used to be cherished in Chinese culture is being broken today.

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

    Science.gov (United States)

    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/. © The Author 2015. Published by Oxford University Press on behalf of Kazusa DNA Research Institute.

  2. Applying landscape genomic tools to forest management and restoration of Hawaiian koa (Acacia koa) in a changing environment.

    Science.gov (United States)

    Gugger, Paul F; Liang, Christina T; Sork, Victoria L; Hodgskiss, Paul; Wright, Jessica W

    2018-02-01

    Identifying and quantifying the importance of environmental variables in structuring population genetic variation can help inform management decisions for conservation, restoration, or reforestation purposes, in both current and future environmental conditions. Landscape genomics offers a powerful approach for understanding the environmental factors that currently associate with genetic variation, and given those associations, where populations may be most vulnerable under future environmental change. Here, we applied genotyping by sequencing to generate over 11,000 single nucleotide polymorphisms from 311 trees and then used nonlinear, multivariate environmental association methods to examine spatial genetic structure and its association with environmental variation in an ecologically and economically important tree species endemic to Hawaii, Acacia koa . Admixture and principal components analyses showed that trees from different islands are genetically distinct in general, with the exception of some genotypes that match other islands, likely as the result of recent translocations. Gradient forest and generalized dissimilarity models both revealed a strong association between genetic structure and mean annual rainfall. Utilizing a model for projected future climate on the island of Hawaii, we show that predicted changes in rainfall patterns may result in genetic offset, such that trees no longer may be genetically matched to their environment. These findings indicate that knowledge of current and future rainfall gradients can provide valuable information for the conservation of existing populations and also help refine seed transfer guidelines for reforestation or replanting of koa throughout the state.

  3. Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae : Implications for the microbial "pan-genome"

    NARCIS (Netherlands)

    Tettelin, H; Masignani, [No Value; Cieslewicz, MJ; Donati, C; Medini, D; Ward, NL; Angiuoli, SV; Crabtree, J; Jones, AL; Durkin, AS; DeBoy, RT; Davidsen, TM; Mora, M; Scarselli, M; Ros, IMY; Peterson, JD; Hauser, CR; Sundaram, JP; Nelson, WC; Madupu, R; Brinkac, LM; Dodson, RJ; Rosovitz, MJ; Sullivan, SA; Daugherty, SC; Haft, DH; Selengut, J; Gwinn, ML; Zhou, LW; Zafar, N; Khouri, H; Radune, D; Dimitrov, G; Watkins, K; O'Connor, KJB; Smith, S; Utterback, TR; White, O; Rubens, CE; Grandi, G; Madoff, LC; Kasper, DL; Telford, JL; Wessels, MR; Rappuoli, R; Fraser, CM

    2005-01-01

    The development of efficient and inexpensive genome sequencing methods has revolutionized the study of human bacterial pathogens and improved vaccine design. Unfortunately, the sequence of a single genome does not reflect how genetic variability drives pathogenesis within a bacterial species and

  4. Ancient genomics

    DEFF Research Database (Denmark)

    Der Sarkissian, Clio; Allentoft, Morten Erik; Avila Arcos, Maria del Carmen

    2015-01-01

    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...

  5. Marine genomics

    DEFF Research Database (Denmark)

    Oliveira Ribeiro, Ângela Maria; Foote, Andrew David; Kupczok, Anne

    2017-01-01

    Marine ecosystems occupy 71% of the surface of our planet, yet we know little about their diversity. Although the inventory of species is continually increasing, as registered by the Census of Marine Life program, only about 10% of the estimated two million marine species are known. This lag......-throughput sequencing approaches have been helping to improve our knowledge of marine biodiversity, from the rich microbial biota that forms the base of the tree of life to a wealth of plant and animal species. In this review, we present an overview of the applications of genomics to the study of marine life, from...

  6. Using a Bayesian network to predict barrier island geomorphologic characteristics

    Science.gov (United States)

    Gutierrez, Ben; Plant, Nathaniel G.; Thieler, E. Robert; Turecek, Aaron

    2015-01-01

    Quantifying geomorphic variability of coastal environments is important for understanding and describing the vulnerability of coastal topography, infrastructure, and ecosystems to future storms and sea level rise. Here we use a Bayesian network (BN) to test the importance of multiple interactions between barrier island geomorphic variables. This approach models complex interactions and handles uncertainty, which is intrinsic to future sea level rise, storminess, or anthropogenic processes (e.g., beach nourishment and other forms of coastal management). The BN was developed and tested at Assateague Island, Maryland/Virginia, USA, a barrier island with sufficient geomorphic and temporal variability to evaluate our approach. We tested the ability to predict dune height, beach width, and beach height variables using inputs that included longer-term, larger-scale, or external variables (historical shoreline change rates, distances to inlets, barrier width, mean barrier elevation, and anthropogenic modification). Data sets from three different years spanning nearly a decade sampled substantial temporal variability and serve as a proxy for analysis of future conditions. We show that distinct geomorphic conditions are associated with different long-term shoreline change rates and that the most skillful predictions of dune height, beach width, and beach height depend on including multiple input variables simultaneously. The predictive relationships are robust to variations in the amount of input data and to variations in model complexity. The resulting model can be used to evaluate scenarios related to coastal management plans and/or future scenarios where shoreline change rates may differ from those observed historically.

  7. MARICULTURE ON CROATIAN ISLANDS

    Directory of Open Access Journals (Sweden)

    Gordana Šarušić

    2000-09-01

    Full Text Available The first attempts of intensive mariculture in Croatia commenced at the very beginning of 1980’s. The mid-eighties brought an expansion of mariculture production, which has been continuously increasing. A few different marine organisms are intensively cultured - both fish and shellfish. Among them commercially most important and highly valued species are sea bass Dicentrarchus labrax and sea bream Sparus aurata. Mussel Mytilus galloprovincialis and oyster Ostrea edulis are the most important shellfish. Fish species such as dentex Dentex dentex, red sea bream Pagrus major and sheepshead bream Puntazzo puntazzo are reared too, but in a rather small quantities. Only recently the rearing, on-growing- of bluefin tuna Thunnus thynnus started in Croatia. The juveniles (70% are reared in a Croatian hatcheries, and 30% has to be imported mainly from Italy and France, due to a higher demand for this kind of culture among the small growers. Croatian part of Adriatic sea possesses a number of geomorfologicaly suitable sites and meteorological conditions which determined the choice - type - of intensive culture. All fish species are reared in a floating cages. The choice of cages i. e. semi off-shore or floating frames, size, rearing volume and design depend on the investors personal preference. The annual turnouf of a market size bass was about 600t and 300t bream in 1996., by 10 island farms which is 70% of total production in Croatia. Including other cultured fish species last year production was up to 1000t, and it™s being estimated to be about 1300t in the following year. The shellfish production on the islands is usually individual attempt of farmers, producing minor quantities mostly in polyculture. This production has bigger potential but it’s limited owing to the EU quality control regulations which do not allow the export, and by domestic market which has drastically decreased due to the collapse of tourism during the recent war. Almost 80

  8. Ecological biogeography of southern ocean islands: species-area relationships, human impacts, and conservation

    NARCIS (Netherlands)

    Chown, S.L.; Gremmen, N.J.M.; Gaston, K.J.

    1998-01-01

    Previous studies have concluded that southern ocean islands are anomalous because past glacial extent and current temperature apparently explain most variance in their species richness. Here, the relationships between physical variables and species richness of vascular plants, insects, land and

  9. Benefits to poorly studied taxa of conservation of bird and mammal diversity on islands.

    Science.gov (United States)

    Aslan, Clare; Holmes, Nick; Tershy, Bernie; Spatz, Dena; Croll, Donald A

    2015-02-01

    Protected area delineation and conservation action are urgently needed on marine islands, but the potential biodiversity benefits of these activities can be difficult to assess due to lack of species diversity information for lesser known taxa. We used linear mixed effects modeling and simple spatial analyses to investigate whether conservation activities based on the diversity of well-known insular taxa (birds and mammals) are likely to also capture the diversity of lesser known taxa (reptiles, amphibians, vascular land plants, ants, land snails, butterflies, and tenebrionid beetles). We assembled total, threatened, and endemic diversity data for both well-known and lesser known taxa and combined these with physical island biogeography characteristics for 1190 islands from 109 archipelagos. Among physical island biogeography factors, island area was the best indicator of diversity of both well-known and little-known taxa. Among taxonomic factors, total mammal species richness was the best indicator of total diversity of lesser known taxa, and the combination of threatened mammal and threatened bird diversity was the best indicator of lesser known endemic richness. The results of other intertaxon diversity comparisons were highly variable, however. Based on our results, we suggest that protecting islands above a certain minimum threshold area may be the most efficient use of conservation resources. For example, using our island database, if the threshold were set at 10 km(2) and the smallest 10% of islands greater than this threshold were protected, 119 islands would be protected. The islands would range in size from 10 to 29 km(2) and would include 268 lesser known species endemic to a single island, along with 11 bird and mammal species endemic to a single island. Our results suggest that for islands of equivalent size, prioritization based on total or threatened bird and mammal diversity may also capture opportunities to protect lesser known species endemic to

  10. Self-sustained magnetic islands

    Energy Technology Data Exchange (ETDEWEB)

    Chatenet, J H; Luciani, J F [Ecole Polytechnique, 91 - Palaiseau (France); Garbet, X [Association Euratom-CEA, Centre d` Etudes de Cadarache, 13 - Saint-Paul-lez-Durance (France). Dept. de Recherches sur la Fusion Controlee

    1996-06-01

    Numerical simulations of a single magnetic island evolution are presented in the regime where the island width is smaller than an ion Larmor radius. It is shown that the island rotation is controlled by particle diffusion due to collisions or a background of microturbulence. As expected from the theory of a stationary island, there exist cases where linearly stable magnetic perturbation are nonlinearly self-sustained. This situation corresponds to large poloidal beta and temperature gradient. The drive is due to diamagnetic frequency effects. However, this situation is not generic, and islands can also decay. It is found that a magnetic island is self-sustained for a negative off-diagonal diffusion coefficient. This case occurs in a tokamak if the inward particle pinch is due to the temperature gradient. (author). 30 refs.

  11. Self-sustained magnetic islands

    International Nuclear Information System (INIS)

    Chatenet, J.H.; Luciani, J.F.; Garbet, X.

    1996-06-01

    Numerical simulations of a single magnetic island evolution are presented in the regime where the island width is smaller than an ion Larmor radius. It is shown that the island rotation is controlled by particle diffusion due to collisions or a background of microturbulence. As expected from the theory of a stationary island, there exist cases where linearly stable magnetic perturbation are nonlinearly self-sustained. This situation corresponds to large poloidal beta and temperature gradient. The drive is due to diamagnetic frequency effects. However, this situation is not generic, and islands can also decay. It is found that a magnetic island is self-sustained for a negative off-diagonal diffusion coefficient. This case occurs in a tokamak if the inward particle pinch is due to the temperature gradient. (author)

  12. Pulsating variables

    International Nuclear Information System (INIS)

    1989-01-01

    The study of stellar pulsations is a major route to the understanding of stellar structure and evolution. At the South African Astronomical Observatory (SAAO) the following stellar pulsation studies were undertaken: rapidly oscillating Ap stars; solar-like oscillations in stars; 8-Scuti type variability in a classical Am star; Beta Cephei variables; a pulsating white dwarf and its companion; RR Lyrae variables and galactic Cepheids. 4 figs

  13. Demographic Ageing on Croatian Islands

    Directory of Open Access Journals (Sweden)

    Ivo Nejašmić

    2013-08-01

    Full Text Available This paper analyses the changes in the population structure of the Croatian islands by age, warns of the degree of ageing, provides spatial differentiation of this process and presents perspective of ageing at the level of settlement. Typing of population ageing is based on scores and has seven types. The total island population in 2011 belongs to the type 5 – very old population. Almost a half of the settlements (out of 303 have been affected by the highest levels of ageing (types 6 and 7. It was found that a quarter of island settlements will become “dead villages” in a foreseeable future; most of them are on small islands but also in the interior of larger islands. These are villages decaying in every respect, in which the way of life, as we know it, veins and goes out. The present ageing villagers are their last residents in most cases. Eve¬rything suggests that demographic recovery of the islands is not possible with the forces in situ. It is important to strike a balance between the needs and opportunities in order to successfully organize life on the islands, both small and large ones, and the fact is that there is a continuing disparity, which is especially profound in small islands. A sensitive and selective approach is needed to overcome the unfavourable demographic trends. Therefore it is necessary to respect the particularities of indi¬vidual islands and island groups in devising development strategy. Solutions to the problems must come of the local and wider community in synergy with relevant professional and scientific institutions. However, if the solutions are not found or measures do not give results, if the islands are left to desorganisation and senilisation, a part of the islands will become a wasteland. With regard to the value of this area whose wealth are people in the first place, this would be an intolerable civilization decline.

  14. Distribution of cesium-137 in tree crop products collected from residence islands impacted by the U.S. nuclear test program in the northern Marshall Islands

    International Nuclear Information System (INIS)

    Peters, S.K.G.; Kehl, S.R.; Martinelli, R.E.; Tamblin, M.W.; Hamilton, T.F.

    2013-01-01

    The Marshall Islands Program at the Lawrence Livermore National Laboratory has completed a series of radiological surveys at Bikini, Rongelap, Utroek, and Enewetak Atolls in the Marshall Islands designed to take a representative sample of food supplies with emphasis on determining 137 Cs activity concentrations in common food plants. Coconuts (Cocos nucifera L.) are the most common and abundant food plant, and provided a common sample type to characterize the level and variability of activity concentrations of 137 Cs in plant foods collected from different islands and atolls. Other dominant food types included Pandanus (Pandanus spp.) and breadfruit (Actocarpus spp.). In general, the activity concentration of 137 Cs in food plants was found to decrease significantly between the main residence islands on Bikini, Rongelap, Utrōk, and Enewetak Atolls. The mean activity concentration of 137 Cs measured in drinking coconut meat and juice was 0.72 (95 % CI 0.68-0.77) and 0.34 (95 % CI 0.30-0.38) Bq g -1 , respectively, on Bikini Island; 0.019 (95 % CI 0.017-0.021) and 0.027 (95 % CI 0.023-0.031) Bq g -1 , respectively, on Rongelap Island; 0.010 (95 % CI 0.007-0.013) and 0.007 (95 % CI 0.004-0.009) Bq g -1 , respectively, on Utroek Island; and 0.002 (95 % CI 0.0013-0.0024) and 0.002 (95 % CI 0.001-0.0025) Bq g -1 , respectively, on Enewetak Island. High levels of variability are reported across all islands. These results will be used to improve the accuracy and reliability of predictive dose assessments, help characterize levels of uncertainty and variability in activity concentrations of fallout radionuclides in plant foods, and allow atoll communities to make informed decisions about resettlement and possible options for cleanup and rehabilitation of islands and atolls. (author)

  15. Renewable energy islands in Europe

    Energy Technology Data Exchange (ETDEWEB)

    Oestergaard, Iben [ed.

    1998-12-31

    This publication includes a compiled presentation of various aspects concerning the possible transformation of some European islands into renewable energy communities and these projects were presented by a selection of pioneer islands at the first European Seminar on Renewable Energy Islands, held on the Danish island of Samsoee, 29-30 June 1998. This issue has increased in importance with the presentation of the ambitious EU-White Paper: `Energy for the future: Renewable Sources of Energy` which was adopted in 1998. One of the key elements of the strategy for an accelerated implementation of renewable energy is to transform 100 localities within Europe into communities which are to be 100% self-sufficient with renewable energy before 2010. In line with this strategy, the Danish Government appointed the island of Samsoe towards the end of 1997 to be the first `official` Danish, renewable energy island. This is to serve as a demonstration project for other local communities, both in Denmark as well as in the rest Europe. Gothland, Madeira, Canary Islands, Cape Verde, Arki, Crete, Minorca and Orkney Islands were represented. Environmental advantages of wind, solar and wave power for distant island communities were indicated. Serious savings would be achieved by limitation of fossil fuel import and utilization of local resources. (EG)

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

    Directory of Open Access Journals (Sweden)

    Fenglou Mao

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

  17. Genomic evolution of 11 type strains within family Planctomycetaceae.

    Directory of Open Access Journals (Sweden)

    Min Guo

    Full Text Available 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.

  18. Genome Sequences of Marine Shrimp Exopalaemon carinicauda Holthuis Provide Insights into Genome Size Evolution of Caridea.

    Science.gov (United States)

    Yuan, Jianbo; Gao, Yi; Zhang, Xiaojun; Wei, Jiankai; Liu, Chengzhang; Li, Fuhua; Xiang, Jianhai

    2017-07-05

    Crustacea, particularly Decapoda, contains many economically important species, such as shrimps and crabs. Crustaceans exhibit enormous (nearly 500-fold) variability in genome size. However, limited genome resources are available for investigating these species. Exopalaemon carinicauda Holthuis, an economical caridean shrimp, is a potential ideal experimental animal for research on crustaceans. In this study, we performed low-coverage sequencing and de novo assembly of the E. carinicauda genome. The assembly covers more than 95% of coding regions. E. carinicauda possesses a large complex genome (5.73 Gb), with size twice higher than those of many decapod shrimps. As such, comparative genomic analyses were implied to investigate factors affecting genome size evolution of decapods. However, clues associated with genome duplication were not identified, and few horizontally transferred sequences were detected. Ultimately, the burst of transposable elements, especially retrotransposons, was determined as the major factor influencing genome expansion. A total of 2 Gb repeats were identified, and RTE-BovB, Jockey, Gypsy, and DIRS were the four major retrotransposons that significantly expanded. Both recent (Jockey and Gypsy) and ancestral (DIRS) originated retrotransposons responsible for the genome evolution. The E. carinicauda genome also exhibited potential for the genomic and experimental research of shrimps.

  19. Comparative genomics of a Helicobacter pylori isolate from a Chinese Yunnan Naxi ethnic aborigine suggests high genetic divergence and phage insertion.

    Directory of Open Access Journals (Sweden)

    Yuanhai You

    Full Text Available Helicobacter pylori is a common pathogen correlated with several severe digestive diseases. It has been reported that isolates associated with different geographic areas, different diseases and different individuals might have variable genomic features. Here, we describe draft genomic sequences of H. pylori strains YN4-84 and YN1-91 isolated from patients with gastritis from the Naxi and Han populations of Yunnan, China, respectively. The draft sequences were compared to 45 other publically available genomes, and a total of 1059 core genes were identified. Genes involved in restriction modification systems, type four secretion system three (TFS3 and type four secretion system four (TFS4, were identified as highly divergent. Both YN4-84 and YN1-91 harbor intact cag pathogenicity island (cagPAI and have EPIYA-A/B/D type at the carboxyl terminal of cagA. The vacA gene type is s1m2i1. Another major finding was a 32.5-kb prophage integrated in the YN4-84 genome. The prophage shares most of its genes (30/33 with Helicobacter pylori prophage KHP30. Moreover, a 1,886 bp transposable sequence (IS605 was found in the prophage. Our results imply that the Naxi ethnic minority isolate YN4-84 and Han isolate YN1-91 belong to the hspEAsia subgroup and have diverse genome structure. The genome has been extensively modified in several regions involved in horizontal DNA transfer. The important roles played by phages in the ecology and microevolution of H. pylori were further emphasized. The current data will provide valuable information regarding the H. pylori genome based on historic human migrations and population structure.

  20. Organizations as Designed Islands

    Directory of Open Access Journals (Sweden)

    Pasquale Gagliardi

    2009-05-01

    Full Text Available The literature and practice of organizational design are mostly based on simplistic conceptions which ignore recent theoretical developments in organizational studies. Conceiving of organizations as ‘designed islands’, it is argued, can contribute to a more solid theoretical foundation to organization theory, viewed as normative science. Relying on the work of Peter Sloterdijk, who describes the forms of life in space in terms of spheres, the heuristic power of the island metaphor is explored. What can be learnt from the art of isolating in order to construct lived organizational environments is then discussed, and the paradoxical relationship between connection and isolation is highlighted.

  1. Three Mile Island

    International Nuclear Information System (INIS)

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

    1988-01-01

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

  2. Weather In Some Islands

    Institute of Scientific and Technical Information of China (English)

    王良华

    2007-01-01

    There are four seasons in a year. When spring comes, the weather is mild(温和的). Summer comes after spring. Summer is the hottest season of the year. Autumn follows summer. It is the best season of the year. Winter is the coldest season of the year. Some islands(岛) have their own particular(特别的) seasons because their weather is very much affected(影响) by the oceans(海洋) around them. In Britain, winter is not very cold and summer is not very hot.

  3. Cognitive Variability

    Science.gov (United States)

    Siegler, Robert S.

    2007-01-01

    Children's thinking is highly variable at every level of analysis, from neural and associative levels to the level of strategies, theories, and other aspects of high-level cognition. This variability exists within people as well as between them; individual children often rely on different strategies or representations on closely related problems…

  4. Islands and non-islands in native and heritage Korean

    Directory of Open Access Journals (Sweden)

    Boyoung eKim

    2016-02-01

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

  5. Holocene closure of Lib Pond, Marshall Islands.

    Directory of Open Access Journals (Sweden)

    Conor L Myhrvold

    Full Text Available Well-preserved sediment from closed water bodies of atolls such as Lib Pond are rare opportunities to reconstruct the past regional climate, which pieced together across a latitude and longitude range identify the range of movement patterns of wider scale climate phenomena such as the Intertropical Convergence Zone (ITCZ and El Niño Southern Oscillation (ENSO. We conducted the first physico-chemical survey of Lib Pond, a shallow, closed-water saline lake located on remote and difficult to access Lib Island in the Marshall Islands at 8° 18' 48.99″ N, 167 22' 51.90″ E in the Pacific Ocean, in July 2009. We performed a bathymetric survey, recorded salinity, dissolved oxygen, pH, and temperature profiles, monitored the tidal variability, and conducted a vegetation survey surrounding the lake. From bathymetric data we calculated the lake volume, which we used to estimate the lake's salt budget, and ultimately the residence time of water in the lake basin. We took a series of sediment cores from the lake, cores which indicate Lib Island's changing environment and climate. Radiocarbon measurements determined sediment age, and reveal significant mixing over the last 2 ka of deposition. We conclude that prior to 3 ka, Lib Island was an atoll with a central lagoon connected to the open ocean, which was then closed off from the open ocean to form the brackish system that exists today. We predict that the sediment accumulation in Lib Pond evident today will continue. As seawater is inhibited from exchanging with fresh water, Lib Pond will become a shallower lake with increasingly fresh water.

  6. Holocene closure of Lib Pond, Marshall Islands.

    Science.gov (United States)

    Myhrvold, Conor L; Janny, Fran; Nelson, Daniel; Ladd, S Nemiah; Atwood, Alyssa; Sachs, Julian P

    2014-01-01

    Well-preserved sediment from closed water bodies of atolls such as Lib Pond are rare opportunities to reconstruct the past regional climate, which pieced together across a latitude and longitude range identify the range of movement patterns of wider scale climate phenomena such as the Intertropical Convergence Zone (ITCZ) and El Niño Southern Oscillation (ENSO). We conducted the first physico-chemical survey of Lib Pond, a shallow, closed-water saline lake located on remote and difficult to access Lib Island in the Marshall Islands at 8° 18' 48.99″ N, 167 22' 51.90″ E in the Pacific Ocean, in July 2009. We performed a bathymetric survey, recorded salinity, dissolved oxygen, pH, and temperature profiles, monitored the tidal variability, and conducted a vegetation survey surrounding the lake. From bathymetric data we calculated the lake volume, which we used to estimate the lake's salt budget, and ultimately the residence time of water in the lake basin. We took a series of sediment cores from the lake, cores which indicate Lib Island's changing environment and climate. Radiocarbon measurements determined sediment age, and reveal significant mixing over the last 2 ka of deposition. We conclude that prior to 3 ka, Lib Island was an atoll with a central lagoon connected to the open ocean, which was then closed off from the open ocean to form the brackish system that exists today. We predict that the sediment accumulation in Lib Pond evident today will continue. As seawater is inhibited from exchanging with fresh water, Lib Pond will become a shallower lake with increasingly fresh water.

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

    Science.gov (United States)

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

    2016-01-04

    Ensembl Genomes (http://www.ensemblgenomes.org) is an integrating resource for genome-scale data from non-vertebrate species, complementing the resources for vertebrate genomics developed in the context of the Ensembl project (http://www.ensembl.org). Together, the two resources provide a consistent set of programmatic and interactive interfaces to a rich range of data including reference sequence, gene models, transcriptional data, genetic variation and comparative analysis. This paper provides an update to the previous publications about the resource, with a focus on recent developments. These include the development of new analyses and views to represent polyploid genomes (of which bread wheat is the primary exemplar); and the continued up-scaling of the resource, which now includes over 23 000 bacterial genomes, 400 fungal genomes and 100 protist genomes, in addition to 55 genomes from invertebrate metazoa and 39 genomes from plants. This dramatic increase in the number of included genomes is one part of a broader effort to automate the integration of archival data (genome sequence, but also associated RNA sequence data and variant calls) within the context of reference genomes and make it available through the Ensembl user interfaces. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

  8. Rodent malaria parasites : genome organization & comparative genomics

    NARCIS (Netherlands)

    Kooij, Taco W.A.

    2006-01-01

    The aim of the studies described in this thesis was to investigate the genome organization of rodent malaria parasites (RMPs) and compare the organization and gene content of the genomes of RMPs and the human malaria parasite P. falciparum. The release of the complete genome sequence of P.

  9. Speciation on oceanic islands: rapid adaptive divergence vs. cryptic speciation in a Guadalupe Island songbird (Aves: Junco.

    Directory of Open Access Journals (Sweden)

    Pau Aleixandre

    Full Text Available The evolutionary divergence of island populations, and in particular the tempo and relative importance of neutral and selective factors, is of central interest to the study of speciation. The rate of phenotypic evolution upon island colonization can vary greatly among taxa, and cases of convergent evolution can further confound the inference of correct evolutionary histories. Given the potential lability of phenotypic characters, molecular dating of insular lineages analyzed in a phylogenetic framework provides a critical tool to test hypotheses of phenotypic divergence since colonization. The Guadalupe junco is the only insular form of the polymorphic dark-eyed junco (Junco hyemalis, and shares eye and plumage color with continental morphs, yet presents an enlarged bill and reduced body size. Here we use variation in mtDNA sequence, morphological traits and song variables to test whether the Guadalupe junco evolved rapidly following a recent colonization by a mainland form of the dark-eyed junco, or instead represents a well-differentiated "cryptic" lineage adapted to the insular environment through long-term isolation, with plumage coloration a result of evolutionary convergence. We found high mtDNA divergence of the island lineage with respect to both continental J. hyemalis and J. phaeonotus, representing a history of isolation of about 600,000 years. The island lineage was also significantly differentiated in morphological and male song variables. Moreover, and contrary to predictions regarding diversity loss on small oceanic islands, we document relatively high levels of both haplotypic and song-unit diversity on Guadalupe Island despite long-term isolation in a very small geographic area. In contrast to prevailing taxonomy, the Guadalupe junco is an old, well-differentiated evolutionary lineage, whose similarity to mainland juncos in plumage and eye color is due to evolutionary convergence. Our findings confirm the role of remote islands

  10. Speciation on oceanic islands: rapid adaptive divergence vs. cryptic speciation in a Guadalupe Island songbird (Aves: Junco).

    Science.gov (United States)

    Aleixandre, Pau; Hernández Montoya, Julio; Milá, Borja

    2013-01-01

    The evolutionary divergence of island populations, and in particular the tempo and relative importance of neutral and selective factors, is of central interest to the study of speciation. The rate of phenotypic evolution upon island colonization can vary greatly among taxa, and cases of convergent evolution can further confound the inference of correct evolutionary histories. Given the potential lability of phenotypic characters, molecular dating of insular lineages analyzed in a phylogenetic framework provides a critical tool to test hypotheses of phenotypic divergence since colonization. The Guadalupe junco is the only insular form of the polymorphic dark-eyed junco (Junco hyemalis), and shares eye and plumage color with continental morphs, yet presents an enlarged bill and reduced body size. Here we use variation in mtDNA sequence, morphological traits and song variables to test whether the Guadalupe junco evolved rapidly following a recent colonization by a mainland form of the dark-eyed junco, or instead represents a well-differentiated "cryptic" lineage adapted to the insular environment through long-term isolation, with plumage coloration a result of evolutionary convergence. We found high mtDNA divergence of the island lineage with respect to both continental J. hyemalis and J. phaeonotus, representing a history of isolation of about 600,000 years. The island lineage was also significantly differentiated in morphological and male song variables. Moreover, and contrary to predictions regarding diversity loss on small oceanic islands, we document relatively high levels of both haplotypic and song-unit diversity on Guadalupe Island despite long-term isolation in a very small geographic area. In contrast to prevailing taxonomy, the Guadalupe junco is an old, well-differentiated evolutionary lineage, whose similarity to mainland juncos in plumage and eye color is due to evolutionary convergence. Our findings confirm the role of remote islands in driving

  11. HBV genotypic variability in Cuba.

    Directory of Open Access Journals (Sweden)

    Carmen L Loureiro

    Full Text Available The genetic diversity of HBV in human population is often a reflection of its genetic admixture. The aim of this study was to explore the genotypic diversity of HBV in Cuba. The S genomic region of Cuban HBV isolates was sequenced and for selected isolates the complete genome or precore-core sequence was analyzed. The most frequent genotype was A (167/250, 67%, mainly A2 (149, 60% but also A1 and one A4. A total of 77 isolates were classified as genotype D (31%, with co-circulation of several subgenotypes (56 D4, 2 D1, 5 D2, 7 D3/6 and 7 D7. Three isolates belonged to genotype E, two to H and one to B3. Complete genome sequence analysis of selected isolates confirmed the phylogenetic analysis performed with the S region. Mutations or polymorphisms in precore region were more common among genotype D compared to genotype A isolates. The HBV genotypic distribution in this Caribbean island correlates with the Y lineage genetic background of the population, where a European and African origin prevails. HBV genotypes E, B3 and H isolates might represent more recent introductions.

  12. HBV Genotypic Variability in Cuba

    Science.gov (United States)

    Loureiro, Carmen L.; Aguilar, Julio C.; Aguiar, Jorge; Muzio, Verena; Pentón, Eduardo; Garcia, Daymir; Guillen, Gerardo; Pujol, Flor H.

    2015-01-01

    The genetic diversity of HBV in human population is often a reflection of its genetic admixture. The aim of this study was to explore the genotypic diversity of HBV in Cuba. The S genomic region of Cuban HBV isolates was sequenced and for selected isolates the complete genome or precore-core sequence was analyzed. The most frequent genotype was A (167/250, 67%), mainly A2 (149, 60%) but also A1 and one A4. A total of 77 isolates were classified as genotype D (31%), with co-circulation of several subgenotypes (56 D4, 2 D1, 5 D2, 7 D3/6 and 7 D7). Three isolates belonged to genotype E, two to H and one to B3. Complete genome sequence analysis of selected isolates confirmed the phylogenetic analysis performed with the S region. Mutations or polymorphisms in precore region were more common among genotype D compared to genotype A isolates. The HBV genotypic distribution in this Caribbean island correlates with the Y lineage genetic background of the population, where a European and African origin prevails. HBV genotypes E, B3 and H isolates might represent more recent introductions. PMID:25742179

  13. Enjebi Island dose assessment

    International Nuclear Information System (INIS)

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

    1987-07-01

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

  14. An Island Called Cuba

    Directory of Open Access Journals (Sweden)

    Jean Stubbs

    2011-06-01

    Full Text Available Review of: An Island Called Home: Returning to Jewish Cuba. Ruth Behar, photographs by Humberto Mayol. New Brunswick NJ: Rutgers University Press, 2007. xiii + 297 pp. (Cloth US$ 29.95 Fidel Castro: My Life: A Spoken Autobiography. Fidel Castro & Ignacio Ramonet. New York: Scribner/Simon & Schuster, 2008. vii + 724 pp. (Paper US$ 22.00, e-book US$ 14.99 Cuba: What Everyone Needs to Know. Julia E. Sweig. New York: Oxford University Press, 2009. xiv + 279 pp. (Paper US$ 16.95 [First paragraph] These three ostensibly very different books tell a compelling story of each author’s approach, as much as the subject matter itself. Fidel Castro: My Life: A Spoken Autobiography is based on a series of long interviews granted by the then-president of Cuba, Fidel Castro, to Spanish-Franco journalist Ignacio Ramonet. Cuba: What Everyone Needs to Know, by U.S. political analyst Julia Sweig, is one of a set country series, and, like Ramonet’s, presented in question/answer format. An Island Called Home: Returning to Jewish Cuba, with a narrative by Cuban-American anthropologist Ruth Behar and photographs by Cuban photographer Humberto Mayol, is a retrospective/introspective account of the Jewish presence in Cuba. While from Ramonet and Sweig we learn much about the revolutionary project, Behar and Mayol convey the lived experience of the small Jewish community against that backdrop.

  15. Partial pressure (or fugacity) of carbon dioxide, salinity and other variables collected from Surface underway observations using Barometric pressure sensor, Carbon dioxide (CO2) gas analyzer and other instruments from NOAA Ship KA'IMIMOANA in the Hawaiian Islands Humpback Whale National Marine Sanctuary, North Pacific Ocean and South Pacific Ocean from 2008-02-02 to 2008-11-16 (NODC Accession 0081043)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — NCEI Accession 0081043 includes Surface underway, chemical, meteorological and physical data collected from NOAA Ship KA'IMIMOANA in the Hawaiian Islands Humpback...

  16. Partial pressure (or fugacity) of carbon dioxide, salinity and other variables collected from Surface underway observations using Barometric pressure sensor, Carbon dioxide (CO2) gas analyzer and other instruments from NOAA Ship DAVID STARR JORDAN in the Channel Islands National Marine Sanctuary, Cordell Bank National Marine Sanctuary and others from 2007-07-25 to 2007-10-28 (NCEI Accession 0144352)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — NCEI Accession 0144352 includes Surface underway data collected from NOAA Ship DAVID STARR JORDAN in the Channel Islands National Marine Sanctuary, Cordell Bank...

  17. Monitoring developments in island waters

    International Nuclear Information System (INIS)

    Crellin, L.V.

    1995-01-01

    The environmental effects of islands in the Irish Sea of the offshore oil and gas industry are discussed in this paper, in particular on sand and gravel resources. This information is considered by the Department of Trade and Industry when granting prospecting, exploration and production licenses. Consultation between industry and islanders forms part of the license granting process. (UK)

  18. Islands for nuclear power stations

    International Nuclear Information System (INIS)

    Usher, E.F.F.W.; Fraser, A.P.

    1981-01-01

    The safety principles, design criteria and types of artificial island for an offshore nuclear power station are discussed with particular reference to siting adjacent to an industrial island. The paper concludes that the engineering problems are soluble and that offshore nuclear power stations will eventually be built but that much fundamental work is still required. (author)

  19. Funding Opportunity: Genomic Data Centers

    Science.gov (United States)

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

  20. Islanded operation of distributed networks

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2005-07-01

    This report summarises the findings of a study to investigate the regulatory, commercial and technical risks and benefits associated with the operation of distributed generation to power an islanded section of distributed network. A review of published literature was carried out, and UK generators were identified who could operate as part of an island network under the existing technical, regulatory, and safety framework. Agreement on case studies for consideration with distributed network operators (DNOs) is discussed as well as the quantification of the risks, benefits and costs of islanding, and the production of a case implementation plan for each case study. Technical issues associated with operating sections of network in islanded mode are described, and impacts of islanding on trading and settlement, and technical and commercial modelling are explored.

  1. A roadmap for island biology

    DEFF Research Database (Denmark)

    Patino, Jairo; Whittaker, Robert J.; Borges, Paulo A.V.

    2017-01-01

    Aims: The 50th anniversary of the publication of the seminal book, The Theory of Island Biogeography, by Robert H. MacArthur and Edward O. Wilson, is a timely moment to review and identify key research foci that could advance island biology. Here, we take a collaborative horizon-scanning approach...... to identify 50 fundamental questions for the continued development of the field. Location: Worldwide. Methods: We adapted a well-established methodology of horizon scanning to identify priority research questions in island biology, and initiated it during the Island Biology 2016 conference held in the Azores......); global change (5); conservation and management policies (5); and invasive alien species (4). Main conclusions: Collectively, this cross-disciplinary set of topics covering the 50 fundamental questions has the potential to stimulate and guide future research in island biology. By covering fields ranging...

  2. Islanded operation of distributed networks

    International Nuclear Information System (INIS)

    2005-01-01

    This report summarises the findings of a study to investigate the regulatory, commercial and technical risks and benefits associated with the operation of distributed generation to power an islanded section of distributed network. A review of published literature was carried out, and UK generators were identified who could operate as part of an island network under the existing technical, regulatory, and safety framework. Agreement on case studies for consideration with distributed network operators (DNOs) is discussed as well as the quantification of the risks, benefits and costs of islanding, and the production of a case implementation plan for each case study. Technical issues associated with operating sections of network in islanded mode are described, and impacts of islanding on trading and settlement, and technical and commercial modelling are explored

  3. The genome draft of coconut (Cocos nucifera).

    Science.gov (United States)

    Xiao, Yong; Xu, Pengwei; Fan, Haikuo; Baudouin, Luc; Xia, Wei; Bocs, Stéphanie; Xu, Junyang; Li, Qiong; Guo, Anping; Zhou, Lixia; Li, Jing; Wu, Yi; Ma, Zilong; Armero, Alix; Issali, Auguste Emmanuel; Liu, Na; Peng, Ming; Yang, Yaodong

    2017-11-01

    Coconut palm (Cocos nucifera,2n = 32), a member of genus Cocos and family Arecaceae (Palmaceae), is an important tropical fruit and oil crop. Currently, coconut palm is cultivated in 93 countries, including Central and South America, East and West Africa, Southeast Asia and the Pacific Islands, with a total growth area of more than 12 million hectares [1]. Coconut palm is generally classified into 2 main categories: "Tall" (flowering 8-10 years after planting) and "Dwarf" (flowering 4-6 years after planting), based on morphological characteristics and breeding habits. This Palmae species has a long growth period before reproductive years, which hinders conventional breeding progress. In spite of initial successes, improvements made by conventional breeding have been very slow. In the present study, we obtained de novo sequences of the Cocos nucifera genome: a major genomic resource that could be used to facilitate molecular breeding in Cocos nucifera and accelerate the breeding process in this important crop. A total of 419.67 gigabases (Gb) of raw reads were generated by the Illumina HiSeq 2000 platform using a series of paired-end and mate-pair libraries, covering the predicted Cocos nucifera genome length (2.42 Gb, variety "Hainan Tall") to an estimated ×173.32 read depth. A total scaffold length of 2.20 Gb was generated (N50 = 418 Kb), representing 90.91% of the genome. The coconut genome was predicted to harbor 28 039 protein-coding genes, which is less than in Phoenix dactylifera (PDK30: 28 889), Phoenix dactylifera (DPV01: 41 660), and Elaeis guineensis (EG5: 34 802). BUSCO evaluation demonstrated that the obtained scaffold sequences covered 90.8% of the coconut genome and that the genome annotation was 74.1% complete. Genome annotation results revealed that 72.75% of the coconut genome consisted of transposable elements, of which long-terminal repeat retrotransposons elements (LTRs) accounted for the largest proportion (92.23%). Comparative analysis of the

  4. Reconstructed Marine Fisheries Catches at a Remote Island Group: Pitcairn Islands (1950–2014

    Directory of Open Access Journals (Sweden)

    Amy R. Coghlan

    2017-09-01

    Full Text Available The remote Pitcairn Island Group in the South Pacific was designated one of the world's largest marine reserves in 2016, encompassing some of the few remaining near-pristine areas within EEZ boundaries. Pitcairn's domestic fisheries are small-scale, and consist mainly of subsistence (non-commercial and limited artisanal (commercial catches. There is no locally-based industrial (large-scale commercial fishery and the level of foreign industrial activity in recent times has been minimal, due in part to the low biomass of commercially valuable species, along with economic constraints of the EEZ's geographic isolation. Using a catch reconstruction method we estimated the total domestic marine catches for the Pitcairn Islands from 1950 to 2014. We show that overall the Pitcairn Islands' small-scale fisheries catches were almost 2.5 times higher than the data reported by the Food and Agriculture Organization (FAO of the United Nations on behalf of the Pitcairn Islands, however, this primarily reflects discrepancies prior to the 1980s. Overall, catches for the subsistence and artisanal sectors started with around 12 t·year−1 in 1950, but declined to 4 t·year−1 by 2014. Domestic reconstructed subsistence catch levels were entirely driven by changes in the human population on the island, with reconstructed artisanal catches only occurring in recent years (2000 onwards. Industrial fishing is entirely executed by foreign vessels, this catch is considerably variable throughout the years and ceases entirely in 2006. The implementation of one of the world's largest marine reserves surrounding the offshore waters of Pitcairn Island has been specifically designed not to affect the rates of subsistence and artisanal fishing conducted by the resident population. Although there is no industrial fishing in the Pitcairn EEZ at present, climate change is predicted to influence the routes of migrating commercially-targeted species, potentially altering fishing

  5. Modeling the conversion of hydroacoustic to seismic energy at island and continental margins: preliminary analysis of Ascension Island data

    International Nuclear Information System (INIS)

    Harben, P.; Rodgers, A.

    1999-01-01

    the T-phase amplitudes. For this paper we will focus on validating the finite difference method for modeling T-phases in the ocean and land environments and on modeling T-phases observed by the May 1999 Ascension Island Experiment. A network of broadband seismometers on Ascension Island recorded a large number of offshore airgun shots. The shots occurred at all azimuths around the island and at ranges from 1-45 km. Measurements of signal amplitude and duration will be made to understand the variability of T-phase behavior on Ascension Island. The sensitivity to topographic slope and island structure will also be investigated

  6. Exploring Other Genomes: Bacteria.

    Science.gov (United States)

    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)

  7. Island in an island – The suggestions for transportation improvement plan for Haidian Island, Haikou, Hainan

    Directory of Open Access Journals (Sweden)

    Sia Rosalind Juo Ling

    2017-01-01

    Full Text Available Haidian Island, which situated at the Northern part of Haikou City of Hainan Province, is an island within a city. Haidian Island is unique in term of it's development which centered around an university, the Hainan University, besides some others important landmarks, such as Haikou city hospital, Baishamen municipal park, Golf Driving Range etc. All commercials, residential, recreational activities etc are planned to serve Hainan University in particular. The study, taking ‘Haidian Island Area Development Control Plan’ as case study, would like to look into the importance of transportation and traffic planning. The study used observation, site investigation and traffic study methods to gather data needed. Firstly the study analyzed the current state of transportation system for Haidian Island in accordance to the Island Development Control plan and Haikou master plan and identified the problems. Then, the study made some recommendations for these problems. The study highlighted the important of non-motorized, cycling and walking as the main transportation system for an education-based island and as supportive to domestic tourism activities found. The transportation planning suggested by the study took ‘green and low-carbon’ approaches considered the role of University as the core activity in the island.

  8. Energy Self-Sufficient Island

    International Nuclear Information System (INIS)

    Bratic, S.; Krajacic, G.; Duic, N.; Cotar, A.; Jardas, D.

    2011-01-01

    In order to analyze energy self-sufficient island, example of a smaller island, connected to the power system of a bigger island with an undersea cable, was taken. Mounting substation 10/0,4 is situated on the island and for the moment it provides enough electricity using the medium voltage line. It is assumed that the island is situated on the north part of the Adriatic Sea. The most important problem that occurs on the island is the population drop that occurs for a significant number of years, therefore, life standard needs to be improved, and economic development needs to be encouraged immediately. Local authorities to stimulate sustainable development on the island through different projects, to breath in a new life to the island, open new jobs and attract new people to come live there. Because of the planned development and increase of the population, energy projects, planned as a support to sustainable development, and later achievement of the energy self-sufficiency, is described in this paper. Therefore, Rewisland methodology appliance is described taking into the account three possible scenarios of energy development. Each scenario is calculated until year 2030. Also, what is taken into the account is 100% usage of renewable sources of energy in 2030. Scenario PTV, PP, EE - This scenario includes installation of solar photovoltaic modules and solar thermal collectors on the buildings roofs, as well as well as implementation of energy efficiency on the island (replacement of the street light bulbs with LED lightning, replacement of the old windows and doors on the houses, as well as the installation of the thermal insulation). Scenario PV island - This scenario, similarly to the previous one, includes installation of solar photovoltaic modules and solar thermal collectors an the residential buildings, as well as the 2 MW photovoltaic power plant and ''Green Hotel'', a building that satisfies all of its energy needs completely from renewable energy sources

  9. Three Mile Island accident

    International Nuclear Information System (INIS)

    Barre, B.; Olivier, E.; Roux, J.P.; Pelle, P.

    2010-01-01

    Deluded by equivocal instrumentation signals, operators at TMI-2 (Three Mile Island - unit 2) misunderstood what was going on in the reactor and for 2 hours were taking inadequate decisions that turned a reactor incident into a major nuclear event that led to the melting of about one third of the core. The TMI accident had worldwide impacts in the domain of nuclear safety. The main consequences in France were: 1) the introduction of the major accident approach and the reinforcement of crisis management; 2) the improvement of the reactor design, particularly that of the pressurizer valves; 3) the implementation of safety probabilistic studies; 4) a better taking into account of the feedback experience in reactor operations; and 5) a better taking into account of the humane factor in reactor safety. (A.C.)

  10. Three Mile Island update

    International Nuclear Information System (INIS)

    Snyder, B.J.

    1984-01-01

    Almost six years after the accident at Three Mile Island-2, cleanup operations are proceeding and the financial condition of the owners has improved. The author reviews some of the cleanup activities and notes the milestones ahead before reaching the September, 1988 target date for completion. A decision to decommission or refurbish will follow the completion of fuel removal activities in 1987. The cleanup has produced considerable data and useful information. In particular, the experience of large-scale decontamination and radioactive waste processing, along with information on fission product transport, is relevant for maintenance and safe operation of other plants. Both macro- and microscopic examination of the core could help in developing safer reactors in the future. 3 figures, 1 table

  11. PWR: nuclear islands

    International Nuclear Information System (INIS)

    1989-01-01

    Framatome and its partners have produced this glossary of technical terms that can be used in writing English language documents relating to power plants (nuclear islands, individual components, nuclear services, etc.) with the hope of improving the quality of the documents intended for their clients, suppliers and partners and for others. This glossary will be particularly useful to the translators and authors of technical proposals, design documents, manufacturing documents, construction and operating documents concerning Pressurized Water Reactors written in English or French. It can also be useful as a reference document for students, researchers, journalists, etc., having to write on this subject. We would like to thank all those individuals working at the Ministere de la Recherche et de la Technologie, Electricite de France, Jeumont Schneider and Framatome who have contributed to this glossary. We would also appreciate any comments or sugestions intended to improve subsequent editions of this glossary [fr

  12. Mauritius - a Sustainable Island

    DEFF Research Database (Denmark)

    Larsen, Anders

    2010-01-01

    production is determined to be the way forward. A step in this direction is to devolve upon citizens the ability and motivation to produce electricity via small-scale distributed generation (SSDG), i.e. wind, photovoltaic and hydro installations below 50 kW. Given that SSDG is more expensive per installed......The Government of Mauritius has a long-term vision of transforming Mauritius into a sustainable Island. One important element towards the achievement of this vision is to increase the country's renewable energy usage and thereby reducing dependence on fossil fuels. Democratisation of energy...... capacity than the existing much larger power plants, subsidies are needed so as to provide incentives to small independent power producers (SIPP), households and firms to invest in SSDG.The paper presents the context, the theoretical considerations and the proposed incentive schemes to enable electricity...

  13. SRTM Anaglyph: Fiji Islands

    Science.gov (United States)

    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

  14. Genome analysis of E. coli isolated from Crohn's disease patients.

    Science.gov (United States)

    Rakitina, Daria V; Manolov, Alexander I; Kanygina, Alexandra V; Garushyants, Sofya K; Baikova, Julia P; Alexeev, Dmitry G; Ladygina, Valentina G; Kostryukova, Elena S; Larin, Andrei K; Semashko, Tatiana A; Karpova, Irina Y; Babenko, Vladislav V; Ismagilova, Ruzilya K; Malanin, Sergei Y; Gelfand, Mikhail S; Ilina, Elena N; Gorodnichev, Roman B; Lisitsyna, Eugenia S; Aleshkin, Gennady I; Scherbakov, Petr L; Khalif, Igor L; Shapina, Marina V; Maev, Igor V; Andreev, Dmitry N; Govorun, Vadim M

    2017-07-19

    Escherichia coli (E. coli) has been increasingly implicated in the pathogenesis of Crohn's disease (CD). The phylogeny of E. coli isolated from Crohn's disease patients (CDEC) was controversial, and while genotyping results suggested heterogeneity, the sequenced strains of E. coli from CD patients were closely related. We performed the shotgun genome sequencing of 28 E. coli isolates from ten CD patients and compared genomes from these isolates with already published genomes of CD strains and other pathogenic and non-pathogenic strains. CDEC was shown to belong to A, B1, B2 and D phylogenetic groups. The plasmid and several operons from the reference CD-associated E. coli strain LF82 were demonstrated to be more often present in CDEC genomes belonging to different phylogenetic groups than in genomes of commensal strains. The operons include carbon-source induced invasion GimA island, prophage I, iron uptake operons I and II, capsular assembly pathogenetic island IV and propanediol and galactitol utilization operons. Our findings suggest that CDEC are phylogenetically diverse. However, some strains isolated from independent sources possess highly similar chromosome or plasmids. Though no CD-specific genes or functional domains were present in all CD-associated strains, some genes and operons are more often found in the genomes of CDEC than in commensal E. coli. They are principally linked to gut colonization and utilization of propanediol and other sugar alcohols.

  15. Genome-wide methylation analysis identifies a core set of hypermethylated genes in CIMP-H colorectal cancer.

    Science.gov (United States)

    McInnes, Tyler; Zou, Donghui; Rao, Dasari S; Munro, Francesca M; Phillips, Vicky L; McCall, John L; Black, Michael A; Reeve, Anthony E; Guilford, Parry J

    2017-03-28

    Aberrant DNA methylation profiles are a characteristic of all known cancer types, epitomized by the CpG island methylator phenotype (CIMP) in colorectal cancer (CRC). Hypermethylation has been observed at CpG islands throughout the genome, but it is unclear which factors determine whether an individual island becomes methylated in cancer. DNA methylation in CRC was analysed using the Illumina HumanMethylation450K array. Differentially methylated loci were identified using Significance Analysis of Microarrays (SAM) and the Wilcoxon Signed Rank (WSR) test. Unsupervised hierarchical clustering was used to identify methylation subtypes in CRC. In this study we characterized the DNA methylation profiles of 94 CRC tissues and their matched normal counterparts. Consistent with previous studies, unsupervized hierarchical clustering of genome-wide methylation data identified three subtypes within the tumour samples, designated CIMP-H, CIMP-L and CIMP-N, that showed high, low and very low methylation levels, respectively. Differential methylation between normal and tumour samples was analysed at the individual CpG level, and at the gene level. The distribution of hypermethylation in CIMP-N tumours showed high inter-tumour variability and appeared to be highly stochastic in nature, whereas CIMP-H tumours exhibited consistent hypermethylation at a subset of genes, in addition to a highly variable background of hypermethylated genes. EYA4, TFPI2 and TLX1 were hypermethylated in more than 90% of all tumours examined. One-hundred thirty-two genes were hypermethylated in 100% of CIMP-H tumours studied and these were highly enriched for functions relating to skeletal system development (Bonferroni adjusted p value =2.88E-15), segment specification (adjusted p value =9.62E-11), embryonic development (adjusted p value =1.52E-04), mesoderm development (adjusted p value =1.14E-20), and ectoderm development (adjusted p value =7.94E-16). Our genome-wide characterization of DNA

  16. Genomics With Cloud Computing

    OpenAIRE

    Sukhamrit Kaur; Sandeep Kaur

    2015-01-01

    Abstract Genomics is study of genome which provides large amount of data for which large storage and computation power is needed. These issues are solved by cloud computing that provides various cloud platforms for genomics. These platforms provides many services to user like easy access to data easy sharing and transfer providing storage in hundreds of terabytes more computational power. Some cloud platforms are Google genomics DNAnexus and Globus genomics. Various features of cloud computin...

  17. Observations of infragravity motions for reef fringed islands and atolls

    Science.gov (United States)

    Becker, J. M.; Merrifield, M. A.; Ford, M.

    2012-12-01

    The frequency of flooding events that affect low lying islands and atolls in the Pacific is expected to increase under current sea level rise projections. Infragravity (IG) motions, with periods ranging from approximately 25 to 400 seconds, are an important component of wave driven flooding events for reef fringed islands and atolls. The IG variability during wave events is analyzed and interpreted dynamically from pressure and current observations at four cross-reef transects in the North Pacific Ocean that include sites in the Republic of the Marshall Islands and Guam. The IG motions are shown to depend upon the spectral properties of the incident wave forcing and reef flat characteristics that include reef flat length (ranging from 100m to 450m at the four sites) and total water level due to setup and tides. A small inundation event at one of the sites is shown to occur due to large shoreline infragravity energy.

  18. Genome Maps, a new generation genome browser.

    Science.gov (United States)

    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.

  19. Island biogeography of marine organisms

    Science.gov (United States)

    Pinheiro, Hudson T.; Bernardi, Giacomo; Simon, Thiony; Joyeux, Jean-Christophe; Macieira, Raphael M.; Gasparini, João Luiz; Rocha, Claudia; Rocha, Luiz A.

    2017-09-01

    Studies on the distribution and evolution of organisms on oceanic islands have advanced towards a dynamic perspective, where terrestrial endemicity results from island geographical aspects and geological history intertwined with sea-level fluctuations. Diversification on these islands may follow neutral models, decreasing over time as niches are filled, or disequilibrium states and progression rules, where richness and endemism rise with the age of the archipelago owing to the splitting of ancestral lineages (cladogenesis). However, marine organisms have received comparatively little scientific attention. Therefore, island and seamount evolutionary processes in the aquatic environment remain unclear. Here we analyse the evolutionary history of reef fishes that are endemic to a volcanic ridge of seamounts and islands to understand their relations to island evolution and sea-level fluctuations. We also test how this evolutionary history fits island biogeography theory. We found that most endemic species have evolved recently (Pleistocene epoch), during a period of recurrent sea-level changes and intermittent connectivity caused by repeated aerial exposure of seamounts, a finding that is consistent with an ephemeral ecological speciation process. Similar to findings for terrestrial biodiversity, our data suggest that the marine speciation rate on islands is negatively correlated with immigration rate. However, because marine species disperse better than terrestrial species, most niches are filled by immigration: speciation increases with the random accumulation of species with low dispersal ability, with few opportunities for in situ cladogenesis and adaptive radiation. Moreover, we confirm that sea-level fluctuations and seamount location play a critical role in marine evolution, mainly by intermittently providing stepping stones for island colonization.

  20. Bamboo Diversity in Sumba Island

    Directory of Open Access Journals (Sweden)

    KARSONO

    2005-04-01

    Full Text Available Bamboo is one of the economic plant which grow widely in the villages and have been used by the local people in the villages. Indonesia has about 10% of the world bamboo, 50% among them was endemic to Indonesia. According Widjaja (2001 Lesser Sunda Island which consists of Lombok, Sumbawa, Flores, Timor, Sumba and other small island eastern of Flores has 14 bamboo species, however, the information from the Sumba Island was lacking because of lacking data from this area except one species which was proposed by S. Soenarko in 1977 where the type specimens was collected by Iboet 443 in 1925. To fullfill data from the Sumba Island, an exploration to this area has been conducted on July 2003. The observation was done in West Sumba and East Sumba District, especially in two natioal parks at both districts. According to this inventory study in the Sumba Island, there were 10 bamboo species in Sumba Island, 1 species among them (Dinochloa sp. was a new species which has not been collected before, whereas the other species (Dinochloa kostermansiana has a new addition record from this area. The bamboo species in Sumba Island were Bambusa blumeana, Bambusa vulgaris, Dendocalamus asper, Dinochloa kostermansiana, Dinochloa sp., Gigantochloa atter, Nastus reholtumianus, Phyllostachys aurea, Schisotachyum brachycladum and Schizostachyum lima. From 10 recorded species, the genera Dinochloa and Nastus grow wild in the forest, whereas another species grow widly or cultivated in the garden. Furthermore, the genus Dinochloa was the only genus grow climbing. The endemic species found in Sumba Island was Nastus reholttumianus, whereas Dinochloa kostermansiana was also found in Flores Island.

  1. Genomic Approaches in Marine Biodiversity and Aquaculture

    Directory of Open Access Journals (Sweden)

    Jorge A Huete-Pérez

    2013-01-01

    Full Text Available Recent advances in genomic and post-genomic technologies have now established the new standard in medical and biotechnological research. The introduction of next-generation sequencing, NGS,has resulted in the generation of thousands of genomes from all domains of life, including the genomes of complex uncultured microbial communities revealed through metagenomics. Although the application of genomics to marine biodiversity remains poorly developed overall, some noteworthy progress has been made in recent years. The genomes of various model marine organisms have been published and a few more are underway. In addition, the recent large-scale analysis of marine microbes, along with transcriptomic and proteomic approaches to the study of teleost fishes, mollusks and crustaceans, to mention a few, has provided a better understanding of phenotypic variability and functional genomics. The past few years have also seen advances in applications relevant to marine aquaculture and fisheries. In this review we introduce several examples of recent discoveries and progress made towards engendering genomic resources aimed at enhancing our understanding of marine biodiversity and promoting the development of aquaculture. Finally, we discuss the need for auspicious science policies to address challenges confronting smaller nations in the appropriate oversight of this growing domain as they strive to guarantee food security and conservation of their natural resources.

  2. Genome-wide interval mapping using SNPs identifies new QTL for growth, body composition and several physiological variables in an F2 intercross between fat and lean chicken lines.

    Science.gov (United States)

    Demeure, Olivier; Duclos, Michel J; Bacciu, Nicola; Le Mignon, Guillaume; Filangi, Olivier; Pitel, Frédérique; Boland, Anne; Lagarrigue, Sandrine; Cogburn, Larry A; Simon, Jean; Le Roy, Pascale; Le Bihan-Duval, Elisabeth

    2013-09-30

    For decades, genetic improvement based on measuring growth and body composition traits has been successfully applied in the production of meat-type chickens. However, this conventional approach is hindered by antagonistic genetic correlations between some traits and the high cost of measuring body composition traits. Marker-assisted selection should overcome these problems by selecting loci that have effects on either one trait only or on more than one trait but with a favorable genetic correlation. In the present study, identification of such loci was done by genotyping an F2 intercross between fat and lean lines divergently selected for abdominal fatness genotyped with a medium-density genetic map (120 microsatellites and 1302 single nucleotide polymorphisms). Genome scan linkage analyses were performed for growth (body weight at 1, 3, 5, and 7 weeks, and shank length and diameter at 9 weeks), body composition at 9 weeks (abdominal fat weight and percentage, breast muscle weight and percentage, and thigh weight and percentage), and for several physiological measurements at 7 weeks in the fasting state, i.e. body temperature and plasma levels of IGF-I, NEFA and glucose. Interval mapping analyses were performed with the QTLMap software, including single-trait analyses with single and multiple QTL on the same chromosome. Sixty-seven QTL were detected, most of which had never been described before. Of these 67 QTL, 47 were detected by single-QTL analyses and 20 by multiple-QTL analyses, which underlines the importance of using different statistical models. Close analysis of the genes located in the defined intervals identified several relevant functional candidates, such as ACACA for abdominal fatness, GHSR and GAS1 for breast muscle weight, DCRX and ASPSCR1 for plasma glucose content, and ChEBP for shank diameter. The medium-density genetic map enabled us to genotype new regions of the chicken genome (including micro-chromosomes) that influenced the traits

  3. Reliving Island Life: Staging Stories of the Blasket Islands

    Directory of Open Access Journals (Sweden)

    Daithí Kearney

    2017-10-01

    Full Text Available The Blasket Islands are located off the south-west coast of Ireland. No longer inhabited, the Great Blasket Island and its distinctive culture have been documented by a variety of writers and are celebrated today in an interpretative centre on the mainland and in performances by Siamsa Tíre, The National Folk Theatre of Ireland. “Siamsa” developed from local initiatives in North Kerry during the early 1960s and is located today in Tralee, Co. Kerry. It aims to present Irish folklore and folk culture through the medium of theatre involving music, song, dance and mime but invariably no dialogue. In this paper, I focus on the production Oiléan, based loosely on the stories of the Blasket Islanders, which was initially devised as part of the fiftieth anniversary commemoration of the departure of the last inhabitants of the islands in 2003.

  4. Complex variables

    CERN Document Server

    Fisher, Stephen D

    1999-01-01

    The most important topics in the theory and application of complex variables receive a thorough, coherent treatment in this introductory text. Intended for undergraduates or graduate students in science, mathematics, and engineering, this volume features hundreds of solved examples, exercises, and applications designed to foster a complete understanding of complex variables as well as an appreciation of their mathematical beauty and elegance. Prerequisites are minimal; a three-semester course in calculus will suffice to prepare students for discussions of these topics: the complex plane, basic

  5. Equilibrium theory of island biogeography: A review

    Science.gov (United States)

    Angela D. Yu; Simon A. Lei

    2001-01-01

    The topography, climatic pattern, location, and origin of islands generate unique patterns of species distribution. The equilibrium theory of island biogeography creates a general framework in which the study of taxon distribution and broad island trends may be conducted. Critical components of the equilibrium theory include the species-area relationship, island-...

  6. Oak restoration trials: Santa Catalina Island

    Science.gov (United States)

    Lisa Stratton

    2002-01-01

    Two restoration trials involving four oak species have been implemented as part of a larger restoration program for Catalina Island. In 1997 the Catalina Island Conservancy began an active program of restoration after 50 years of ranching and farming activities on the island. The restoration program includes removing feral goats and pigs island-wide and converting 80...

  7. Whole-Genome-Sequencing characterization of bloodstream infection-causing hypervirulent Klebsiella pneumoniae of capsular serotype K2 and ST374.

    Science.gov (United States)

    Wang, Xiaoli; Xie, Yingzhou; Li, Gang; Liu, Jialin; Li, Xiaobin; Tian, Lijun; Sun, Jingyong; Ou, Hong-Yu; Qu, Hongping

    2018-01-01

    Hypervirulent K. pneumoniae variants (hvKP) have been increasingly reported worldwide, causing metastasis of severe infections such as liver abscesses and bacteremia. The capsular serotype K2 hvKP strains show diverse multi-locus sequence types (MLSTs), but with limited genetics and virulence information. In this study, we report a hypermucoviscous K. pneumoniae strain, RJF293, isolated from a human bloodstream sample in a Chinese hospital. It caused a metastatic infection and fatal septic shock in a critical patient. The microbiological features and genetic background were investigated with multiple approaches. The Strain RJF293 was determined to be multilocis sequence type (ST) 374 and serotype K2, displayed a median lethal dose (LD50) of 1.5 × 10 2 CFU in BALB/c mice and was as virulent as the ST23 K1 serotype hvKP strain NTUH-K2044 in a mouse lethality assay. Whole genome sequencing revealed that the RJF293 genome codes for 32 putative virulence factors and exhibits a unique presence/absence pattern in comparison to the other 105 completely sequenced K. pneumoniae genomes. Whole genome SNP-based phylogenetic analysis revealed that strain RJF293 formed a single clade, distant from those containing either ST66 or ST86 hvKP. Compared to the other sequenced hvKP chromosomes, RJF293 contains several strain-variable regions, including one prophage, one ICEKp1 family integrative and conjugative element and six large genomic islands. The sequencing of the first complete genome of an ST374 K2 hvKP clinical strain should reinforce our understanding of the epidemiology and virulence mechanisms of this bloodstream infection-causing hvKP with clinical significance.

  8. Variable stars

    International Nuclear Information System (INIS)

    Feast, M.W.; Wenzel, W.; Fernie, J.D.; Percy, J.R.; Smak, J.; Gascoigne, S.C.B.; Grindley, J.E.; Lovell, B.; Sawyer Hogg, H.B.; Baker, N.; Fitch, W.S.; Rosino, L.; Gursky, H.

    1976-01-01

    A critical review of variable stars is presented. A fairly complete summary of major developments and discoveries during the period 1973-1975 is given. The broad developments and new trends are outlined. Essential problems for future research are identified. (B.R.H. )

  9. JGI Fungal Genomics Program

    Energy Technology Data Exchange (ETDEWEB)

    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

  10. Genomic Encyclopedia of Fungi

    Energy Technology Data Exchange (ETDEWEB)

    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.

  11. Whole-genome sequencing of veterinary pathogens

    DEFF Research Database (Denmark)

    Ronco, Troels

    -electrophoresis and single-locus sequencing has been widely used to characterize such types of veterinary pathogens. However, DNA sequencing techniques have become fast and cost effective in recent years and whole-genome sequencing data provide a much higher discriminative power and reproducibility than any...... genetic background. This indicates that dairy cows can be natural carriers of S. aureus subtypes that in certain cases lead to CM. A group of isolates that mostly belonged to ST151 carried three pathogenicity islands that were primarily found in this group. The prevalence of resistance genes was generally...

  12. The Three Mile Island Disaster.

    Science.gov (United States)

    Crosby, Emeral

    1980-01-01

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

  13. Ship impact against protection islands

    DEFF Research Database (Denmark)

    Pedersen, Preben Terndrup

    1997-01-01

    The five most exposed piers and the anchor blocks on the East Bridge shall be protected by aritificial islands. Extensive analytical and experimental investitations were carried out to verify the efficiency of how these protection works....

  14. Three Mile Island Accident Data

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Three Mile Island Accident Data consists of mostly upper air and wind observations immediately following the nuclear meltdown occurring on March 28, 1979, near...

  15. Archaeology of Bet Dwarka Island

    Digital Repository Service at National Institute of Oceanography (India)

    Sundaresh; Gaur, A.S.

    Explorations along the shore and in the intertidal zone at Bet Dwarka island, Gujarat, India were carried out by the Marine Archaeology Centre of National Institute of Oceanography (NIO), Goa, India between 1981-1994. Artefacts of both...

  16. Autumn monitoring of resident avifauna on Guana Island, British Virgin Islands

    Science.gov (United States)

    Boal, Clint W.; Wunderle, Joseph M.; Arendt, Wayne J.

    2013-01-01

    Although the Caribbean region is considered a biodiversity hotspot and a priority for ecological conservation efforts, little information exists on population trends of West Indian landbirds. We combined avian survey data collected from three studies spanning a 16-year period on a small island with a minimal human presence in the British Virgin Islands. Although abundances varied among surveys, the same species were detected with rare exceptions. Despite stability in species composition, the resident landbirds were variable in their individual detectabilities. Survey detections relatively mirrored net captures for some species, but are quite different for others. We suspect that this is likely due to differences in detectability due to species-specific behaviors mediated by environmental conditions, such as rainfall, during the month or months prior to our surveys. It is difficult to assess the influence of timing or amount of precipitation on bird detections rates among our surveys due to a lack of consistent collection of location-specific weather data in the British Virgin Islands. Our study suggests monitoring efforts conducted in concert with collection of site-specific climate data would facilitate improved interpretation of survey data and a better understanding of avian species response to climate mediated changes.

  17. Genomic evidence of geographically widespread effect of gene flow from polar bears into brown bears

    OpenAIRE

    Cahill, James A; Stirling, Ian; Kistler, Logan; Salamzade, Rauf; Ersmark, Erik; Fulton, Tara L; Stiller, Mathias; Green, Richard E; Shapiro, Beth

    2015-01-01

    © 2014 The Authors. Molecular Ecology Published by John Wiley & Sons Ltd. Polar bears are an arctic, marine adapted species that is closely related to brown bears. Genome analyses have shown that polar bears are distinct and genetically homogeneous in comparison to brown bears. However, these analyses have also revealed a remarkable episode of polar bear gene flow into the population of brown bears that colonized the Admiralty, Baranof and Chichagof islands (ABC islands) of Alaska. Here, we...

  18. Surface display of a massively variable lipoprotein by a Legionella diversity-generating retroelement.

    Science.gov (United States)

    Arambula, Diego; Wong, Wenge; Medhekar, Bob A; Guo, Huatao; Gingery, Mari; Czornyj, Elizabeth; Liu, Minghsun; Dey, Sanghamitra; Ghosh, Partho; Miller, Jeff F

    2013-05-14

    Diversity-generating retroelements (DGRs) are a unique family of retroelements that confer selective advantages to their hosts by facilitating localized DNA sequence evolution through a specialized error-prone reverse transcription process. We characterized a DGR in Legionella pneumophila, an opportunistic human pathogen that causes Legionnaires disease. The L. pneumophila DGR is found within a horizontally acquired genomic island, and it can theoretically generate 10(26) unique nucleotide sequences in its target gene, legionella determinent target A (ldtA), creating a repertoire of 10(19) distinct proteins. Expression of the L. pneumophila DGR resulted in transfer of DNA sequence information from a template repeat to a variable repeat (VR) accompanied by adenine-specific mutagenesis of progeny VRs at the 3'end of ldtA. ldtA encodes a twin-arginine translocated lipoprotein that is anchored in the outer leaflet of the outer membrane, with its C-terminal variable region surface exposed. Related DGRs were identified in L. pneumophila clinical isolates that encode unique target proteins with homologous VRs, demonstrating the adaptability of DGR components. This work characterizes a DGR that diversifies a bacterial protein and confirms the hypothesis that DGR-mediated mutagenic homing occurs through a conserved mechanism. Comparative bioinformatics predicts that surface display of massively variable proteins is a defining feature of a subset of bacterial DGRs.

  19. Tracing common origins of Genomic Islands in prokaryotes based on genome signature analyses

    NARCIS (Netherlands)

    Passel, van M.W.J.

    2011-01-01

    Horizontal gene transfer constitutes a powerful and innovative force in evolution, but often little is known about the actual origins of transferred genes. Sequence alignments are generally of limited use in tracking the original donor, since still only a small fraction of the total genetic

  20. Magnetic island formation in tokamaks

    International Nuclear Information System (INIS)

    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

  1. Island biodiversity conservation needs palaeoecology

    DEFF Research Database (Denmark)

    Nogué, Sandra; de Nascimento, Lea; Froyd, Cynthia A.

    2017-01-01

    to human activities. Consequently, even the most degraded islands are a focus for restoration, eradication, and monitoring programmes to protect the remaining endemic and/or relict populations. Here, we build a framework that incorporates an assessment of the degree of change from multiple baseline...... and the introduction of non-native species. We provide exemplification of how such approaches can provide valuable information for biodiversity conservation managers of island ecosystems....

  2. [Nested species subsets of amphibians and reptiles in Thousand Island Lake].

    Science.gov (United States)

    Wang, Xi; Wang, Yan-Ping; Ding, Ping

    2012-10-01

    Habitat fragmentation is a main cause for the loss of biological diversity. Combining line-transect methods to survey the amphibians and reptiles on 23 islands on Thousand Island Lake in Zhejiang province, along with survey data on nearby plant species and habitat variables collected by GIS, we used the"BINMATNEST (binary matrix nestedness temperature calculator)" software and the Spearman rank correlation to examine whether amphibians and reptiles followed nested subsets and their influencing factors. The results showed that amphibians and reptiles were significantly nested, and that the island area and habitat type were significantly associated with their nested ranks. Therefore, to effectively protect amphibians and reptiles in the Thousand Islands Lake area we should pay prior attention to islands with larger areas and more habitat types.

  3. Genomics With Cloud Computing

    Directory of Open Access Journals (Sweden)

    Sukhamrit Kaur

    2015-04-01

    Full Text Available Abstract Genomics is study of genome which provides large amount of data for which large storage and computation power is needed. These issues are solved by cloud computing that provides various cloud platforms for genomics. These platforms provides many services to user like easy access to data easy sharing and transfer providing storage in hundreds of terabytes more computational power. Some cloud platforms are Google genomics DNAnexus and Globus genomics. Various features of cloud computing to genomics are like easy access and sharing of data security of data less cost to pay for resources but still there are some demerits like large time needed to transfer data less network bandwidth.

  4. Detection of recurrent transmission of 17q12 microdeletion by array comparative genomic hybridization in a fetus with prenatally diagnosed hydronephrosis, hydroureter, and multicystic kidney, and variable clinical spectrum in the family.

    Science.gov (United States)

    Chen, Chih-Ping; Chang, Shuenn-Dyh; Wang, Tzu-Hao; Wang, Liang-Kai; Tsai, Jeng-Daw; Liu, Yu-Peng; Chern, Schu-Rern; Wu, Peih-Shan; Su, Jun-Wei; Chen, Yu-Ting; Wang, Wayseen

    2013-12-01

    This study was aimed at detection of recurrent transmission of the 17q12 microdeletion in a fetus with congenital anomalies of the kidney and urinary tract. A 35-year-old woman was referred to the hospital at 20 weeks' gestation because of hydronephrosis in the fetus. The mother was normal and healthy. Her second child was a girl who had bilateral dysplastic kidneys that required hemodialysis, and died at the age of 5 years. During this pregnancy, the woman underwent amniocentesis at 18 weeks' gestation because of advanced maternal age. Cytogenetic analysis revealed a karyotype of 46,XY. Prenatal ultrasound showed left hydronephrosis with a tortuous ureter, right hydronephrosis, and increased echogenicity of the kidneys. Fetal magnetic resonance imaging showed right dilated renal calyces, left hydronephrosis, hydroureter, and multicystic kidney. The pregnancy was subsequently terminated. Array comparative genomic hybridization (aCGH) and fluorescence in situ hybridization were applied for genetic analysis using umbilical cord, maternal blood, and cultured amniocytes. aCGH analysis on umbilical cord detected a 1.75-Mb deletion at 17q12 including haploinsufficiency of LHX1 and HNF1B. aCGH analysis on maternal blood detected a 1.54-Mb deletion at 17q12 including haploinsufficiency of LHX1 and HNF1B. Metaphase fluorescence in situ hybridization analysis on cultured amniocytes and maternal blood lymphocytes using 17q12-specific bacterial artificial chromosome probe showed 17q12 microdeletion in the fetus and the mother. Prenatal diagnosis of recurrent renal and urinary tract abnormalities in the fetus should include a differential diagnosis of familial 17q12 microdeletion. Copyright © 2013. Published by Elsevier B.V.

  5. Community genomics among stratified microbial assemblages in the ocean's interior

    DEFF Research Database (Denmark)

    DeLong, Edward F; Preston, Christina M; Mincer, Tracy

    2006-01-01

    Microbial life predominates in the ocean, yet little is known about its genomic variability, especially along the depth continuum. We report here genomic analyses of planktonic microbial communities in the North Pacific Subtropical Gyre, from the ocean's surface to near-sea floor depths. Sequence......, and host-viral interactions. Comparative genomic analyses of stratified microbial communities have the potential to provide significant insight into higher-order community organization and dynamics....

  6. Three Mile Island

    International Nuclear Information System (INIS)

    2015-01-01

    This document addresses the Three Mile Island accident which resulted in a core partial fusion. It recalls that other reactors of this plant are still being operated. The operation of this PWR is briefly described, and the main events and phases of the accident are briefly presented (failure of the secondary circuit supply pump, failure of a pressurizer component and wrong information about it, mistaken reaction in the control room, core partial fusion due to insufficient cooling means). It shows that the accident occurred because of a combination of technical failures and human mistakes. This situation has put operator education and organisation into question again. The main actors and their mistakes, weaknesses and responsibilities are indicated: Metropolitan Edison (the operator), the NRC (the US nuclear safety authority). Some key figures are recalled, as well as the context of construction of the plant. Impacts and consequences are reviewed: implementation of new standards, population concern. The document outlines that radioactive exposures due to the accident were minor

  7. Arctic Islands LNG

    Energy Technology Data Exchange (ETDEWEB)

    Hindle, W.

    1977-01-01

    Trans-Canada Pipe Lines Ltd. made a feasibility study of transporting LNG from the High Arctic Islands to a St. Lawrence River Terminal by means of a specially designed and built 125,000 cu m or 165,000 cu m icebreaking LNG tanker. Studies were made of the climatology and of ice conditions, using available statistical data as well as direct surveys in 1974, 1975, and 1976. For on-schedule and unimpeded (unescorted) passage of the LNG carriers at all times of the year, special navigation and communications systems can be made available. Available icebreaking experience, charting for the proposed tanker routes, and tide tables for the Canadian Arctic were surveyed. Preliminary design of a proposed Arctic LNG icebreaker tanker, including containment system, reliquefaction of boiloff, speed, power, number of trips for 345 day/yr operation, and liquefaction and regasification facilities are discussed. The use of a minimum of three Arctic Class 10 ships would enable delivery of volumes of natural gas averaging 11.3 million cu m/day over a period of a year to Canadian markets. The concept appears to be technically feasible with existing basic technology.

  8. Nearshore sediment thickness, Fire Island, New York

    Science.gov (United States)

    Locker, Stanley D.; Miselis, Jennifer L.; Buster, Noreen A.; Hapke, Cheryl J.; Wadman, Heidi M.; McNinch, Jesse E.; Forde, Arnell S.; Stalk, Chelsea A.

    2017-04-03

    Investigations of coastal change at Fire Island, New York (N.Y.), sought to characterize sediment budgets and determine geologic framework controls on coastal processes. Nearshore sediment thickness is critical for assessing coastal system sediment availability, but it is largely unquantified due to the difficulty of conducting geological or geophysical surveys across the nearshore. This study used an amphibious vessel to acquire chirp subbottom profiles. These profiles were used to characterize nearshore geology and provide an assessment of nearshore sediment volume. Two resulting sediment-thickness maps are provided: total Holocene sediment thickness and the thickness of the active shoreface. The Holocene sediment section represents deposition above the maximum flooding surface that is related to the most recent marine transgression. The active shoreface section is the uppermost Holocene sediment, which is interpreted to represent the portion of the shoreface thought to contribute to present and future coastal behavior. The sediment distribution patterns correspond to previously defined zones of erosion, accretion, and stability along the island, demonstrating the importance of sediment availability in the coastal response to storms and seasonal variability. The eastern zone has a thin nearshore sediment thickness, except for an ebb-tidal deposit at the wilderness breach caused by Hurricane Sandy. Thicker sediment is found along a central zone that includes shoreface-attached sand ridges, which is consistent with a stable or accretional coastline in this area. The thickest overall Holocene section is found in the western zone of the study, where a thicker lower section of Holocene sediment appears related to the westward migration of Fire Island Inlet over several hundred years.

  9. Evolution of linear chromosomes and multipartite genomes in yeast mitochondria

    Science.gov (United States)

    Valach, Matus; Farkas, Zoltan; Fricova, Dominika; Kovac, Jakub; Brejova, Brona; Vinar, Tomas; Pfeiffer, Ilona; Kucsera, Judit; Tomaska, Lubomir; Lang, B. Franz; Nosek, Jozef

    2011-01-01

    Mitochondrial genome diversity in closely related species provides an excellent platform for investigation of chromosome architecture and its evolution by means of comparative genomics. In this study, we determined the complete mitochondrial DNA sequences of eight Candida species and analyzed their molecular architectures. Our survey revealed a puzzling variability of genome architecture, including circular- and linear-mapping and multipartite linear forms. We propose that the arrangement of large inverted repeats identified in these genomes plays a crucial role in alterations of their molecular architectures. In specific arrangements, the inverted repeats appear to function as resolution elements, allowing genome conversion among different topologies, eventually leading to genome fragmentation into multiple linear DNA molecules. We suggest that molecular transactions generating linear mitochondrial DNA molecules with defined telomeric structures may parallel the evolutionary emergence of linear chromosomes and multipartite genomes in general and may provide clues for the origin of telomeres and pathways implicated in their maintenance. PMID:21266473

  10. Migration Dilemmas of Islanders: Commuting Leading to Migration or Remaining at Home

    Directory of Open Access Journals (Sweden)

    Ivan Lajić

    2001-09-01

    Full Text Available The paper presents and discusses the results of an empirical survey carried out in April 2000 on the islands Prvić, Zlarin and Krapanj in the Šibenik coastal area. These islands are part of a group of islands marked by the highest rates of depopulation, in which even recently daily commuting was one of the most expressed forms of mechanical population development. Daily commuting is seen as an initial state leading to permanent migration, i.e. to out-migration. Potential migrants become familiar with the social, economic, cultural and other traits of their future destination area, which makes it easier for them to leave their places of origin. Thus, for the purposes of the research, the survey selected a population of daily commuters, mainly young people of working age who usually constitute the segment of the population most Iikely to migrate. The survey used both a questionnaire and interviews. Respondents belonged to two relevant groups of the island population: employees commuting each day to work and pupils commuting daily to school. Even though the sample included practically the entire island population with the given migrational and socio-demographic characteristics, the total number of respondents was still too small for the application of standard methods of statistical analysis. In order to gain better insight into the pre-migrational situation on the islands, a few adult islander commuters were added to the group of commuting employees. The goal of the research was to gain an understanding of commuting phenomena in the island micro-society, especially of the migration dilemmas of young islanders. The most frequent variables in the survey were: island/settlement, gender and school. Commuting between the island and mainland is the dominant form of spatial mobility among islanders and constitutes an essential part of their daily life. The most frequent reasons for commuting among islanders are school attendance, going to work, going

  11. Eastern Caribbean Circulation and Island Mass Effect on St. Croix, US Virgin Islands: A Mechanism for Relatively Consistent Recruitment Patterns

    Science.gov (United States)

    Chérubin, Laurent Marcel; Garavelli, Lysel

    2016-01-01

    The northeastern Caribbean Sea is under the seasonal influence of the Trade Winds but also of the Orinoco/Amazon freshwater plume. The latter is responsible for intensification of the Caribbean Current in general and of its eddy activity in the northern part of the Caribbean Sea. More importantly, we show in this study that the front of the freshwater plume drives a northward flow that impinges directly on the island of St. Croix in the United States Virgin Islands. The angle of incidence of the incoming flow controls the nature of the wake on both sides and ends of the island, which changes from cyclonic to anticylonic wake flow, with either attached or shed eddies. Using an off-line bio-physical model, we simulated the dispersal and recruitment of an abundant Caribbean coral reef fish, the bluehead wrasse (Thalassoma bifasciatum) in the context of the wake flow variability around St. Croix. Our results revealed the role played by the consistent seasonal forcing of the wake flow on the recruitment patterns around the island at the interannual scale. The interannual variability of the timing of arrival and northward penetration of the plume instead controls the nature of the wake, hence the regional spatial recruitment patterns. PMID:26942575

  12. Eastern Caribbean Circulation and Island Mass Effect on St. Croix, US Virgin Islands: A Mechanism for Relatively Consistent Recruitment Patterns.

    Directory of Open Access Journals (Sweden)

    Laurent Marcel Chérubin

    Full Text Available The northeastern Caribbean Sea is under the seasonal influence of the Trade Winds but also of the Orinoco/Amazon freshwater plume. The latter is responsible for intensification of the Caribbean Current in general and of its eddy activity in the northern part of the Caribbean Sea. More importantly, we show in this study that the front of the freshwater plume drives a northward flow that impinges directly on the island of St. Croix in the United States Virgin Islands. The angle of incidence of the incoming flow controls the nature of the wake on both sides and ends of the island, which changes from cyclonic to anticylonic wake flow, with either attached or shed eddies. Using an off-line bio-physical model, we simulated the dispersal and recruitment of an abundant Caribbean coral reef fish, the bluehead wrasse (Thalassoma bifasciatum in the context of the wake flow variability around St. Croix. Our results revealed the role played by the consistent seasonal forcing of the wake flow on the recruitment patterns around the island at the interannual scale. The interannual variability of the timing of arrival and northward penetration of the plume instead controls the nature of the wake, hence the regional spatial recruitment patterns.

  13. Comparative Genome Analysis and Genome Evolution

    NARCIS (Netherlands)

    Snel, Berend

    2002-01-01

    This thesis described a collection of bioinformatic analyses on complete genome sequence data. We have studied the evolution of gene content and find that vertical inheritance dominates over horizontal gene trasnfer, even to the extent that we can use the gene content to make genome phylogenies.

  14. Permanent Draft Genome of Strain ESFC-1: Ecological Genomics of a Newly Discovered Lineage of Filamentous Diazotrophic Cyanobacteria

    Science.gov (United States)

    Everroad, R. Craig; Stuart, Rhona K.; Bebout, Brad M.; Detweiler, Angela M.; Lee, Jackson Zan; Woebken, Dagmar; Bebout, Leslie E.; Pett-Ridge, Jennifer

    2016-01-01

    The nonheterocystous filamentous cyanobacterium, strain ESFC-1, is a recently described member of the order Oscillatoriales within the Cyanobacteria. ESFC-1 has been shown to be a major diazotroph in the intertidal microbial mat system at Elkhorn Slough, CA, USA. Based on phylogenetic analyses of the 16S RNA gene, ESFC-1 appears to belong to a unique, genus-level divergence; the draft genome sequence of this strain has now been determined. Here we report features of this genome as they relate to the ecological functions and capabilities of strain ESFC-1. The 5,632,035 bp genome sequence encodes 4914 protein-coding genes and 92 RNA genes. One striking feature of this cyanobacterium is the apparent lack of either uptake or bi-directional hydrogenases typically expected within a diazotroph. Additionally, a large genomic island is found that contains numerous low GC-content genes and genes related to extracellular polysaccharide production and cell wall synthesis and maintenance.

  15. Genomic Data Commons launches

    Science.gov (United States)

    The Genomic Data Commons (GDC), a unified data system that promotes sharing of genomic and clinical data between researchers, launched today with a visit from Vice President Joe Biden to the operations center at the University of Chicago.

  16. Rat Genome Database (RGD)

    Data.gov (United States)

    U.S. Department of Health & Human Services — The Rat Genome Database (RGD) is a collaborative effort between leading research institutions involved in rat genetic and genomic research to collect, consolidate,...

  17. Complete Genome Sequence of the Soybean Symbiont Bradyrhizobium japonicum Strain USDA6T

    Directory of Open Access Journals (Sweden)

    Nobukazu Uchiike

    2011-10-01

    Full Text Available The complete nucleotide sequence of the genome of the soybean symbiont Bradyrhizobium japonicum strain USDA6T was determined. The genome of USDA6T is a single circular chromosome of 9,207,384 bp. The genome size is similar to that of the genome of another soybean symbiont, B. japonicum USDA110 (9,105,828 bp. Comparison of the whole-genome sequences of USDA6T and USDA110 showed colinearity of major regions in the two genomes, although a large inversion exists between them. A significantly high level of sequence conservation was detected in three regions on each genome. The gene constitution and nucleotide sequence features in these three regions indicate that they may have been derived from a symbiosis island. An ancestral, large symbiosis island, approximately 860 kb in total size, appears to have been split into these three regions by unknown large-scale genome rearrangements. The two integration events responsible for this appear to have taken place independently, but through comparable mechanisms, in both genomes.

  18. Foundation Investigation for Ground Based Radar Project-Kwajalein Island, Marshall Islands

    Science.gov (United States)

    1990-04-01

    iL_ COPY MISCELLANEOUS PAPER GL-90-5 i iFOUNDATION INVESTIGATION FOR GROUND BASED RADAR PROJECT--KWAJALEIN ISLAND, MARSHALL ISLANDS by Donald E...C!assification) Foundatioa Investigation for Ground Based Radar Project -- Kwajalein Island, Marshall Islands 12. PERSONAL AUTHOR(S) Yule, Donald E...investigation for the Ground Based Radar Project -- Kwajalein Island, Marshall Islands , are presented.- eophysical tests comprised of surface refrac- tion

  19. Visualization for genomics: the Microbial Genome Viewer.

    Science.gov (United States)

    Kerkhoven, Robert; van Enckevort, Frank H J; Boekhorst, Jos; Molenaar, Douwe; Siezen, Roland J

    2004-07-22

    A Web-based visualization tool, the Microbial Genome Viewer, is presented that allows the user to combine complex genomic data in a highly interactive way. This Web tool enables the interactive generation of chromosome wheels and linear genome maps from genome annotation data stored in a MySQL database. The generated images are in scalable vector graphics (SVG) format, which is suitable for creating high-quality scalable images and dynamic Web representations. Gene-related data such as transcriptome and time-course microarray experiments can be superimposed on the maps for visual inspection. The Microbial Genome Viewer 1.0 is freely available at http://www.cmbi.kun.nl/MGV

  20. Network constrained wind integration on Vancouver Island

    International Nuclear Information System (INIS)

    Maddaloni, Jesse D.; Rowe, Andrew M.; Kooten, G. Cornelis van

    2008-01-01

    The aim of this study is to determine the costs and carbon emissions associated with operating a hydro-dominated electricity generation system (Vancouver Island, Canada) with varying degrees of wind penetration. The focus is to match the wind resource, system demand and abilities of extant generating facilities on a temporal basis, resulting in an operating schedule that minimizes system cost over a given period. This is performed by taking the perspective of a social planner who desires to find the lowest-cost mix of new and existing generation facilities. Unlike other studies, this analysis considers variable efficiency for thermal and hydro-generators, resulting in a fuel cost that varies with respect to generator part load. Since this study and others have shown that wind power may induce a large variance on existing dispatchable generators, forcing more frequent operation at reduced part load, inclusion of increased fuel cost at part load is important when investigating wind integration as it can significantly reduce the economic benefits of utilizing low-cost wind. Results indicate that the introduction of wind power may reduce system operating costs, but this depends heavily on whether the capital cost of the wind farm is considered. For the Vancouver Island mix with its large hydro-component, operating cost was reduced by a maximum of 15% at a wind penetration of 50%, with a negligible reduction in operating cost when the wind farm capital cost was included

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

    Science.gov (United States)

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

    2004-01-01

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

  2. Genomic prediction using subsampling

    OpenAIRE

    Xavier, Alencar; Xu, Shizhong; Muir, William; Rainey, Katy Martin

    2017-01-01

    Background Genome-wide assisted selection is a critical tool for the?genetic improvement of plants and animals. Whole-genome regression models in Bayesian framework represent the main family of prediction methods. Fitting such models with a large number of observations involves a prohibitive computational burden. We propose the use of subsampling bootstrap Markov chain in genomic prediction. Such method consists of fitting whole-genome regression models by subsampling observations in each rou...

  3. Whole Genome Epidemiological Typing of Salmonella

    DEFF Research Database (Denmark)

    Leekitcharoenphon, Pimlapas

    available Salmonella enterica genomes (accessed in April 2011). A consensus tree based on variation of the core genes gives better resolution than 16S rRNA and MLST that rarely provide separation between closely related strains. The performance of the pan-genome tree which is based on the presence....../absence of all genes across genomes, is similar to the consensus tree but with higher branching confidence value. The core genes can be divided into two categories: a few highly variable genes and a larger set of conserved core genes, with low variance. These core genes are useful for investigating molecular...... evolution and remain useful as candidate genes for bacterial genome typing-even if they cannot be expected to differentiate highly clonal isolates e.g. outbreak cases of Salmonella [I]. To achieve successful ‘real-time’ monitoring and identification of outbreaks, rapid and reliable sub-typing is essential...

  4. From genomic variation to personalized medicine

    DEFF Research Database (Denmark)

    Wesolowska, Agata; Schmiegelow, Kjeld

    Genomic variation is the basis of interindividual differences in observable traits and disease susceptibility. Genetic studies are the driving force of personalized medicine, as many of the differences in treatment efficacy can be attributed to our genomic background. The rapid development...... a considerable amount of the phenotype variability, hence the major difficulty of interpretation lies in the complexity of molecular interactions. This PhD thesis describes the state-of-art of the functional human variation research (Chapter 1) and introduces childhood acute lymphoblastic leukaemia (ALL...... the thesis and includes some final remarks on the perspectives of genomic variation research and personalized medicine. In summary, this thesis demonstrates the feasibility of integrative analyses of genomic v