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1

The genotoxin colibactin exacerbates lymphopenia and decreases survival rate in mice infected with septicemic Escherichia coli.  

PubMed

Sepsis is a life-threatening infection. Escherichia coli is the first known cause of bacteremia leading to sepsis. Lymphopenia was shown to predict bacteremia better than conventional markers of infection. The pks genomic island, which is harbored by extraintestinal pathogenic E. coli (ExPEC) and encodes the genotoxin colibactin, is epidemiologically associated with bacteremia. To investigate a possible relationship between colibactin and lymphopenia, we examined the effects of transient infection of lymphocytes with bacteria that were and those that were not producing the genotoxin. A mouse model of sepsis was used to compare the virulence of a clinical ExPEC isolate with its isogenic mutant impaired for the production of colibactin. We observed that colibactin induced double-strand breaks in the DNA of infected lymphocytes, leading to cell cycle arrest and to cell death by apoptosis. E. coli producing colibactin induced a more profound lymphopenia in septicemic mice, compared with the isogenic mutant unable to produce colibactin. In a sepsis model in which the mice were treated by rehydration and antibiotics, the production of colibactin by the bacteria was associated with a significantly lower survival rate. In conclusion, we demonstrate that production of colibactin by E. coli exacerbates lymphopenia associated with septicemia and could impair the chances to survive sepsis. PMID:24489107

Marcq, Ingrid; Martin, Patricia; Payros, Delphine; Cuevas-Ramos, Gabriel; Boury, Michčle; Watrin, Claude; Nougayrčde, Jean-Philippe; Olier, Maďwenn; Oswald, Eric

2014-07-15

2

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

PubMed Central

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

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

2014-01-01

3

Comparative Analysis of Mobilizable Genomic Islands  

PubMed Central

Mobilizable genomic islands (MGIs) are small genomic islands of less than 35 kbp containing an integrase gene and a sequence that resembles the origin of transfer (oriT) of an integrating conjugative element (ICE). MGIs have been shown to site-specifically integrate and excise from the chromosome of bacterial hosts and hijack the conjugative machinery of a coresident ICE to disseminate. To date, MGIs have been described in three strains belonging to three different Vibrio species. In this study, we report the discovery of 11 additional putative MGIs found in various species of Vibrio, Alteromonas, Pseudoalteromonas, and Methylophaga. We designed an MGI capture system that allowed us to relocate chromosomal MGIs onto a low-copy-number plasmid and facilitate their isolation and sequencing. Comparative genomics and phylogenetic analyses of these mobile genetic elements revealed their mosaic structure and their evolution through recombination and acquisition of exogenous DNA. MGIs were found to belong to a larger family of genomic islands (GIs) sharing a similar integrase gene and often integrated into the same integration site yet exhibiting a different mechanism of regulation of excision and mobilization. We found that MGIs can excise only when an ICE of the SXT/R391 family is coresident in the same cell, while GIs still excise regardless. PMID:23204461

Daccord, Aurélie; Ceccarelli, Daniela; Rodrigue, Sébastien

2013-01-01

4

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

PubMed

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

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

2007-10-01

5

Genomic islands of uropathogenic Escherichia coli contribute to virulence.  

PubMed

Uropathogenic Escherichia coli (UPEC) strain CFT073 contains 13 large genomic islands ranging in size from 32 kb to 123 kb. Eleven of these genomic islands were individually deleted from the genome, and nine isogenic mutants were tested for their ability to colonize the CBA/J mouse model of ascending urinary tract infection. Three genomic island mutants (Delta PAI-aspV, Delta PAI-metV, and Delta PAI-asnT) were significantly outcompeted by wild-type CFT073 in the bladders and/or kidneys following transurethral cochallenge (P islands contributed to the observed phenotype, including a previously uncharacterized iron acquisition cluster, fbpABCD (c0294 to c0297 [c0294-97]), autotransporter, picU (c0350), and RTX family exoprotein, tosA (c0363) in the PAI-aspV island. The double deletion mutant with deletions in both copies of the fbp iron acquisition operon (Deltac0294-97 Delta c2518-15) was significantly outcompeted by wild-type CFT073 in cochallenge. Strains with mutations in a type VI secretion system within the PAI-metV island did not show attenuation. The attenuation of the PAI-metV island was localized to genes c3405-10, encoding a putative phosphotransferase transport system, which is common to UPEC and avian pathogenic E. coli strains but absent from E. coli K-12. We have shown that, in addition to encoding virulence genes, genomic islands contribute to the overall fitness of UPEC strain CFT073 in vivo. PMID:19329634

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

2009-06-01

6

Mobilizable genomic islands: going mobile with oriT mimicry  

PubMed Central

Many bacterial chromosomes contain genomic islands, large DNA segments that became incorporated into the chromosome following their horizontal transmission. However, the mechanisms that mediate the lateral transfer of genomic islands are for the most part unknown. In this issue of Molecular Microbiology, Daccord et al describe a new type of transmissible genomic island that can be mobilized by co-resident integrating conjugative elements (ICEs). These ‘mobilizable genomic islands’ (MGIs) require many ICE-encoded factors for their transmission, including transcription activators to induce MGI excision, the relaxase to initiate transfer at the MGI oriT and the conjugation machinery to transport MGI DNA to recipient cells. However, MGIs encode their own integrases, which enable their recombination with the chromosome of a new host, as well as a variety of other genes that do not have functions related to mobility. The MGI oriT, which resembles the ICE oriT, can also serve as a site for initiation of ICE-mediated conjugative transfer of large regions of chromosomal DNA. Overall, these findings raise the possibility that mobilization of chromosomal DNA from cyptic oriTs within genomic islands or elsewhere on the chromosome could be more common place than has been previously appreciated. PMID:21038479

Waldor, Matthew K.

2010-01-01

7

A genomic island linked to ecotype divergence in Atlantic cod.  

PubMed

The genomic architecture underlying ecological divergence and ecological speciation with gene flow is still largely unknown for most organisms. One central question is whether divergence is genome-wide or localized in 'genomic mosaics' during early stages when gene flow is still pronounced. Empirical work has so far been limited, and the relative impacts of gene flow and natural selection on genomic patterns have not been fully explored. Here, we use ecotypes of Atlantic cod to investigate genomic patterns of diversity and population differentiation in a natural system characterized by high gene flow and large effective population sizes, properties which theoretically could restrict divergence in local genomic regions. We identify a genomic region of strong population differentiation, extending over approximately 20 cM, between pairs of migratory and stationary ecotypes examined at two different localities. Furthermore, the region is characterized by markedly reduced levels of genetic diversity in migratory ecotype samples. The results highlight the genomic region, or 'genomic island', as potentially associated with ecological divergence and suggest the involvement of a selective sweep. Finally, we also confirm earlier findings of localized genomic differentiation in three other linkage groups associated with divergence among eastern Atlantic populations. Thus, although the underlying mechanisms are still unknown, the results suggest that 'genomic mosaics' of differentiation may even be found under high levels of gene flow and that marine fishes may provide insightful model systems for studying and identifying initial targets of selection during ecological divergence. PMID:23611647

Hemmer-Hansen, Jakob; Nielsen, Einar E; Therkildsen, Nina O; Taylor, Martin I; Ogden, Rob; Geffen, Audrey J; Bekkevold, Dorte; Helyar, Sarah; Pampoulie, Christophe; Johansen, Torild; Carvalho, Gary R

2013-05-01

8

Patterns and architecture of genomic islands in marine bacteria  

PubMed Central

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

2012-01-01

9

Genomic islands predict functional adaptation in marine actinobacteria  

SciTech Connect

Linking functional traits to bacterial phylogeny remains a fundamental but elusive goal of microbial ecology 1. Without this information, it becomes impossible to resolve meaningful units of diversity and the mechanisms by which bacteria interact with each other and adapt to environmental change. Ecological adaptations among bacterial populations have been linked to genomic islands, strain-specific regions of DNA that house functionally adaptive traits 2. In the case of environmental bacteria, these traits are largely inferred from bioinformatic or gene expression analyses 2, thus leaving few examples in which the functions of island genes have been experimentally characterized. Here we report the complete genome sequences of Salinispora tropica and S. arenicola, the first cultured, obligate marine Actinobacteria 3. These two species inhabit benthic marine environments and dedicate 8-10percent of their genomes to the biosynthesis of secondary metabolites. Despite a close phylogenetic relationship, 25 of 37 secondary metabolic pathways are species-specific and located within 21 genomic islands, thus providing new evidence linking secondary metabolism to ecological adaptation. Species-specific differences are also observed in CRISPR sequences, suggesting that variations in phage immunity provide fitness advantages that contribute to the cosmopolitan distribution of S. arenicola 4. The two Salinispora genomes have evolved by complex processes that include the duplication and acquisition of secondary metabolite genes, the products of which provide immediate opportunities for molecular diversification and ecological adaptation. Evidence that secondary metabolic pathways are exchanged by Horizontal Gene Transfer (HGT) yet are fixed among globally distributed populations 5 supports a functional role for their products and suggests that pathway acquisition represents a previously unrecognized force driving bacterial diversification

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

2009-04-01

10

Methyl-CpG island-associated genome signature tags  

DOEpatents

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.

Dunn, John J

2014-05-20

11

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

PubMed Central

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

Wilson, James W; Nickerson, Cheryl A

2006-01-01

12

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

PubMed

Genomic islands are mobile DNAs that are major agents of bacterial and archaeal evolution. Integration into prokaryotic chromosomes usually occurs site-specifically at tRNA or tmRNA gene (together, tDNA) targets, catalyzed by tyrosine integrases. This splits the target gene, yet sequences within the island restore the disrupted gene; the regenerated target and its displaced fragment precisely mark the endpoints of the island. We applied this principle to search for islands in genomic DNA sequences. Our algorithm identifies tDNAs, finds fragments of those tDNAs in the same replicon and removes unlikely candidate islands through a series of filters. A search for islands in 2168 whole prokaryotic genomes produced 3919 candidates. The website Islander (recently moved to http://bioinformatics.sandia.gov/islander/) presents these precisely mapped candidate islands, the gene content and the island sequence. The algorithm further insists that each island encode an integrase, and attachment site sequence identity is carefully noted; therefore, the database also serves in the study of integrase site-specificity and its evolution. PMID:25378302

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

2015-01-28

13

Genomic islands: tools of bacterial horizontal gene transfer and evolution  

PubMed Central

Bacterial genomes evolve through mutations, rearrangements or horizontal gene transfer. Besides the core genes encoding essential metabolic functions, bacterial genomes also harbour a number of accessory genes acquired by horizontal gene transfer that might be beneficial under certain environmental conditions. The horizontal gene transfer contributes to the diversification and adaptation of microorganisms, thus having an impact on the genome plasticity. A significant part of the horizontal gene transfer is or has been facilitated by genomic islands (GEIs). GEIs are discrete DNA segments, some of which are mobile and others which are not, or are no longer mobile, which differ among closely related strains. A number of GEIs are capable of integration into the chromosome of the host, excision, and transfer to a new host by transformation, conjugation or transduction. GEIs play a crucial role in the evolution of a broad spectrum of bacteria as they are involved in the dissemination of variable genes, including antibiotic resistance and virulence genes leading to generation of hospital ‘superbugs’, as well as catabolic genes leading to formation of new metabolic pathways. Depending on the composition of gene modules, the same type of GEIs can promote survival of pathogenic as well as environmental bacteria. PMID:19178566

Juhas, Mario; van der Meer, Jan Roelof; Gaillard, Muriel; Harding, Rosalind M; Hood, Derek W; Crook, Derrick W

2009-01-01

14

Classification of genomic islands using decision trees and their ensemble algorithms  

Microsoft Academic Search

BACKGROUND: Genomic islands (GIs) are clusters of alien genes in some bacterial genomes, but not be seen in the genomes of other strains within the same genus. The detection of GIs is extremely important to the medical and environmental communities. Despite the discovery of the GI associated features, accurate detection of GIs is still far from satisfactory. RESULTS: In this

Dongsheng Che; Cory Hockenbury; Robert Marmelstein; Khaled Rasheed

2010-01-01

15

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

PubMed Central

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

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

2014-01-01

16

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

PubMed Central

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

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

2014-01-01

17

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

PubMed Central

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

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

2014-01-01

18

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

PubMed

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

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

2014-10-01

19

Genetic and phenotypic characterization of a Pseudomonas aeruginosa population with high frequency of genomic islands.  

PubMed

Various genomic islands, PAPI-1, PAPI-2, PAGI-1, PAGI-2, PAGI-3, and PAGI-4, and the element pKLC102 have been characterized in different P. aeruginosa strains from diverse habitats and geographical locations. Chromosomal DNA macroarray of 100 P. aeruginosa strains isolated from 85 unrelated patients hospitalized in an intensive care unit was created to assess the occurrence of these genomic islands (GEIs). The macroarray was then hybridized with labeled probes derived from each genomic island. In addition, PFGE patterns with SpeI, frequency of virulence genes, and antimicrobial resistance patterns of the strains were studied. Our results showed that almost all P. aeruginosa strains presented up to eight virulence genes. By SpeI macrorestriction fragment analysis we were able to identify 49 restriction patterns; 35 patterns correspond to single strains and the remaining 14 to strains subgroup (a-n). Most of the strains showed variation in number or composition of GEIs and a specific antimicrobial pattern indicating that each strain was an unrelated isolate. In terms of the number of genomic islands per strain, 7 GEIs were found in 34% of the strains, 6 in 18%, 5 in 12%, 4 in 14%, 3 in 10%, 2 in 7%, and 1 in 4%; only one isolate did not present any GEI. The genomic islands PAPI-1 and PAPI-2 and the element pKLC102 were the most frequently detected. The analysis of the location of each GEI in the chromosome of two strains show that the islands PAGI-3, PAPI-1, PAPI-2 and pKLC102 are present in the insertion site previously reported, but that PAGI-2 and PAGI-4 are inserted in another chromosome place in a site not characterized yet. In conclusion our data show that P. aeruginosa strains exhibited an epidemic population structure with horizontal transfer of DNA resulting in a high frequency of GEIs. PMID:22662157

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

2012-01-01

20

A Genomic Island of the Pathogen Leptospira interrogans Serovar Lai Can Excise from Its Chromosome? †  

PubMed Central

An examination of the two Leptospira interrogans genomes sequenced so far reveals few genetic differences, including an extra DNA region, 54 kb in length, in L. interrogans serovar Lai. This locus contains 103 predicted coding sequences that are absent from the genome of L. interrogans serovar Copenhageni, of which only 20% had significant BLASTP hits in GenBank. By analyzing the L. interrogans serovar Lai genome by pulsed-field gel electrophoresis, we also found that this 54-kb DNA fragment exists as a circular plasmid. This was confirmed by amplification of a DNA fragment corresponding to that of the predicted fragment if this region excised from the chromosome and its left and right ends joined together. In addition, cloning of the putative rep gene of this DNA region was responsible for autonomous replication in Leptospira spp., therefore generating a new Escherichia coli-Leptospira sp. shuttle vector. Taken together, our results show that this genomic island can excise from the chromosome and form a replicative plasmid. Analysis of the distribution of this genomic island revealed that highly related sequences exist in other L. interrogans virulent strains. This genomic island, containing a high proportion of novel genes, may have an important role in spreading genes, including virulence factors, among bacterial populations. PMID:17118975

Bourhy, Pascale; Salaün, Laurence; Lajus, Aurélie; Médigue, Claudine; Boursaux-Eude, Caroline; Picardeau, Mathieu

2007-01-01

21

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

PubMed Central

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

2014-01-01

22

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

PubMed

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

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

2013-01-01

23

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

Microsoft Academic Search

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

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

2007-01-01

24

Strain-specific genes of Helicobacter pylori: genome evolution driven by a novel type IV secretion system and genomic island transfer  

PubMed Central

The availability of multiple bacterial genome sequences has revealed a surprising extent of variability among strains of the same species. The human gastric pathogen Helicobacter pylori is known as one of the most genetically diverse species. We have compared the genome sequence of the duodenal ulcer strain P12 and six other H. pylori genomes to elucidate the genetic repertoire and genome evolution mechanisms of this species. In agreement with previous findings, we estimate that the core genome comprises about 1200 genes and that H. pylori possesses an open pan-genome. Strain-specific genes are preferentially located at potential genome rearrangement sites or in distinct plasticity zones, suggesting two different mechanisms of genome evolution. The P12 genome contains three plasticity zones, two of which encode type IV secretion systems and have typical features of genomic islands. We demonstrate for the first time that one of these islands is capable of self-excision and horizontal transfer by a conjugative process. We also show that excision is mediated by a protein of the XerD family of tyrosine recombinases. Thus, in addition to its natural transformation competence, conjugative transfer of genomic islands has to be considered as an important source of genetic diversity in H. pylori. PMID:20478826

Fischer, Wolfgang; Windhager, Lukas; Rohrer, Stefanie; Zeiller, Matthias; Karnholz, Arno; Hoffmann, Reinhard; Zimmer, Ralf; Haas, Rainer

2010-01-01

25

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

PubMed Central

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. PMID:16982006

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

2006-01-01

26

Regulation, integrase-dependent excision, and horizontal transfer of genomic islands in Legionella pneumophila.  

PubMed

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

Lautner, Monika; Schunder, Eva; Herrmann, Vroni; Heuner, Klaus

2013-04-01

27

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

PubMed Central

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

Lautner, Monika; Schunder, Eva; Herrmann, Vroni

2013-01-01

28

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

PubMed

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

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

2015-01-01

29

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

PubMed Central

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

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

2015-01-01

30

Microcin H47 System: An Escherichia coli Small Genomic Island with Novel Features  

PubMed Central

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

Azpiroz, María F.; Bascuas, Thais; Lavińa, Magela

2011-01-01

31

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

PubMed Central

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

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

2013-01-01

32

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

PubMed Central

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

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

2012-01-01

33

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

PubMed Central

Background A substantial amount of data has been accumulated supporting the important role of genomic islands (GEIs) - including pathogenicity islands (PAIs) - in bacterial genome plasticity and the evolution of bacterial pathogens. Their instability and the high level sequence similarity of different (partial) islands suggest an exchange of PAIs between strains of the same or even different bacterial species by horizontal gene transfer (HGT). Transfer events of archetypal large genomic islands of enterobacteria which often lack genes required for mobilisation or transfer have been rarely investigated so far. Results To study mobilisation of such large genomic regions in prototypic uropathogenic E. coli (UPEC) strain 536, PAI II536 was supplemented with the mobRP4 region, an origin of replication (oriVR6K), an origin of transfer (oriTRP4) and a chloramphenicol resistance selection marker. In the presence of helper plasmid RP4, conjugative transfer of the 107-kb PAI II536 construct occured from strain 536 into an E. coli K-12 recipient. In transconjugants, PAI II536 existed either as a cytoplasmic circular intermediate (CI) or integrated site-specifically into the recipient's chromosome at the leuX tRNA gene. This locus is the chromosomal integration site of PAI II536 in UPEC strain 536. From the E. coli K-12 recipient, the chromosomal PAI II536 construct as well as the CIs could be successfully remobilised and inserted into leuX in a PAI II536 deletion mutant of E. coli 536. Conclusions Our results corroborate that mobilisation and conjugal transfer may contribute to evolution of bacterial pathogens through horizontal transfer of large chromosomal regions such as PAIs. Stabilisation of these mobile genetic elements in the bacterial chromosome result from selective loss of mobilisation and transfer functions of genomic islands. PMID:21943043

2011-01-01

34

The clc Element of Pseudomonas sp. Strain B13, a Genomic Island with Various Catabolic Properties  

PubMed Central

Pseudomonas sp. strain B13 is a bacterium known to degrade chloroaromatic compounds. The properties to use 3- and 4-chlorocatechol are determined by a self-transferable DNA element, the clc element, which normally resides at two locations in the cell's chromosome. Here we report the complete nucleotide sequence of the clc element, demonstrating the unique catabolic properties while showing its relatedness to genomic islands and integrative and conjugative elements rather than to other known catabolic plasmids. As far as catabolic functions, the clc element harbored, in addition to the genes for chlorocatechol degradation, a complete functional operon for 2-aminophenol degradation and genes for a putative aromatic compound transport protein and for a multicomponent aromatic ring dioxygenase similar to anthranilate hydroxylase. The genes for catabolic functions were inducible under various conditions, suggesting a network of catabolic pathway induction. For about half of the open reading frames (ORFs) on the clc element, no clear functional prediction could be given, although some indications were found for functions that were similar to plasmid conjugation. The region in which these ORFs were situated displayed a high overall conservation of nucleotide sequence and gene order to genomic regions in other recently completed bacterial genomes or to other genomic islands. Most notably, except for two discrete regions, the clc element was almost 100% identical over the whole length to a chromosomal region in Burkholderia xenovorans LB400. This indicates the dynamic evolution of this type of element and the continued transition between elements with a more pathogenic character and those with catabolic properties. PMID:16484212

Gaillard, Muriel; Vallaeys, Tatiana; Vorhölter, Frank Jörg; Minoia, Marco; Werlen, Christoph; Sentchilo, Vladimir; Pühler, Alfred; van der Meer, Jan Roelof

2006-01-01

35

Homologues of insecticidal toxin complex genes within a genomic island in the marine bacterium Vibrio parahaemolyticus.  

PubMed

Three insecticidal toxin complex (tc)-like genes were identified in Vibrio parahaemolyticus 13-028/A3, which can cause acute hepatopancreatic necrosis disease in penaeid shrimp. The three genes are a tcdA-like gene (7710 bp), predicted to code for a 284-kDa protein; a tcdB-like gene (4272 bp), predicted to code for a 158-kDa protein; and a tccC3-like gene (2916 bp), predicted to encode a 107-kDa protein. All three predicted proteins contain conserved domains that are characteristic of their respective Tc proteins. By RT-PCR, all three tc-like genes were found to be expressed in this bacterium. Through genome walking and the use of PCR to join contigs surrounding these three genes, a genomic island (87 712 bp, named tc-GIvp) was found on chromosome II localized next to the tRNA Gly. The GC content of this island, which is not found in other Vibrio species, is 40%. The tc-GIvp is characterized to have 60 ORFs encoding regulatory or virulence factors. These include a type 6 secretion protein VgrG, EAL domain-containing proteins, fimbriae subunits and assembly proteins, invasin-like proteins, peptidoglycan-binding proteins, and Tc proteins. The tc-GIvp also contains 21 transposase genes, suggesting that it was acquired through horizontal transfer from other organisms. PMID:25272969

Tang, Kathy F J; Lightner, Donald V

2014-10-01

36

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

PubMed Central

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

Stevens, Patricia

2010-01-01

37

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

PubMed Central

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

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

2013-01-01

38

Identification of a Genomic Island Present in the Majority of Pathogenic Isolates of Pseudomonas aeruginosa  

PubMed Central

Pseudomonas aeruginosa, a ubiquitous gram-negative bacterium, is capable of colonizing a wide range of environmental niches and can also cause serious infections in humans. In order to understand the genetic makeup of pathogenic P. aeruginosa strains, a method of differential hybridization of arrayed libraries of cloned DNA fragments was developed. An M13 library of DNA from strain X24509, isolated from a patient with a urinary tract infection, was screened using a DNA probe from P. aeruginosa strain PAO1. The genome of PAO1 has been recently sequenced and can be used as a reference for comparisons of genetic organization in different strains. M13 clones that did not react with a DNA probe from PAO1 carried X24509-specific inserts. When a similar array hybridization analysis with DNA probes from different strains was used, a set of M13 clones which carried sequences present in the majority of human P. aeruginosa isolates from a wide range of clinical sources was identified. The inserts of these clones were used to identify cosmids encompassing a contiguous 48.9-kb region of the X24509 chromosome called PAGI-1 (for “P. aeruginosa genomic island 1”). PAGI-1 is incorporated in the X24509 chromosome at a locus that shows a deletion of a 6,729-bp region present in strain PAO1. Survey of the incidence of PAGI-1 revealed that this island is present in 85% of the strains from clinical sources. Approximately half of the PAGI-1-carrying strains show the same deletion as X24509, while the remaining strains contain both the PAGI-1 sequences and the 6,729-bp PAO1 segment. Sequence analysis of PAGI-1 revealed that it contains 51 predicted open reading frames. Several of these genes encoded products with predictable function based on their sequence similarities to known genes, including insertion sequences, determinants of regulatory proteins, a number of dehydrogenase gene homologs, and two for proteins of implicated in detoxification of reactive oxygen species. It is very likely that PAGI-1 was acquired by a large number of P. aeruginosa isolates through horizontal gene transfer. The selection for its maintenance may be the consequence of expression of any one of the genes of unknown function or the genes which allow P. aeruginosa to survive under the conditions that generate reactive oxygen species. Alternatively, one or both of the transcriptional regulators encoded in PAGI-1 may control the expression of genes in the P. aeruginosa chromosome, which provides a selective advantage for strains that have acquired this genomic island. PMID:11208781

Liang, Xiaoyou; Pham, Xuan-Quynh T.; Olson, Maynard V.; Lory, Stephen

2001-01-01

39

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

Microsoft Academic Search

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

A. Mark Osborn; Dietmar Böltner

2002-01-01

40

Cloning and sequencing of a genomic island found in the Brazilian purpuric fever clone of Haemophilus influenzae biogroup aegyptius.  

PubMed

A genomic island was identified in the Haemophilus influenzae biogroup aegyptius Brazilian purpuric fever (BPF) strain F3031. This island, which was also found in other BPF isolates, could not be detected in non-BPF biogroup aegyptius strains or in nontypeable or typeable H. influenzae strains, with the exception of a region present in the type b Eagan strain. This 34,378-bp island is inserted, in reference to H. influenzae Rd KW20, within a choline transport gene and contains a mosaic structure of Mu-like prophage genes, several hypothetical genes, and genes potentially encoding an Erwinia carotovora carotovoricin Er-like bacteriocin. The product of the tail fiber ORF in the bacteriocin-like region shows a hybrid structure where the C terminus is similar to an H. influenzae phage HP1 tail protein implicating this open reading frame in altering host specificity for a putative bacteriocin. Significant synteny is seen in the entire genomic island with genomic regions from Salmonella enterica subsp. enterica serovar Typhi CT18, Photorhabdus luminescens subsp. laumondii TT01, Chromobacterium violaceum, and to a lesser extent Haemophilus ducreyi 35000HP. In a previous work, we isolated several BPF-specific DNA fragments through a genome subtraction procedure, and we have found that a majority of these fragments map to this locus. In addition, several subtracted fragments generated from an independent laboratory by using different but related strains also map to this island. These findings underscore the importance of this BPF-specific chromosomal region in explaining some of the genomic differences between highly invasive BPF strains and non-BPF isolates of biogroup aegyptius. PMID:15784532

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

2005-04-01

41

Characterization of a genomic divergence island between black-and-yellow and gopher Sebastes rockfishes.  

PubMed

Islands of high genomic divergence that contain genes of evolutionary significance may form between diverging species. The gopher rockfish, Sebastes carnatus, and black-and-yellow rockfish, S. chrysomelas, are sympatrically distributed temperate marine species inhabiting rocky reefs and kelp forests on the west coast of the United States. Prior studies documented low levels of genetic divergence between the two species, except at a single microsatellite locus that displayed high divergence, Sra.7-2. To better characterize genome wide divergence, we scored 25 additional microsatellite loci. Mean neutral divergence between species (F(ST) = 0.01) changed little from prior estimates. Sra.7-2 continued to be an extreme divergence outlier. Five novel microsatellites within ± 15 kb of Sra.7-2 were characterized. High divergence, consistently low diversity in S. chrysomelas, and linkage disequilibrium were detected at these loci, suggesting the influence of recent selection. However, coalescent modelling of divergence at neutral and Sra.7-2 regions showed that initial divergence at Sra.7-2 was ancient, likely predating divergence at neutral regions. It is therefore unlikely that Sra.7-2 divergence represents solely recent ecological divergence within one species and may represent the action of recurrent selection. Introgressive gene flow (2N(E) m) was much higher (>1) at neutral than Sra.7-2 regions (<1) despite evidence that two S. carnatus individuals have recently mixed ancestry at the Sra.7-2 region. The Sra.7-2 genomic region is likely one of several regions containing genes involved in initiating and maintaining species integrity. Completion of the final stages of speciation appears to be a slow and ongoing process for these species. PMID:21557784

Buonaccorsi, Vincent P; Narum, Shawn R; Karkoska, Kristine A; Gregory, Steven; Deptola, Travis; Weimer, Alexander B

2011-06-01

42

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

PubMed Central

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

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

2013-01-01

43

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

PubMed Central

As populations diverge, genomic regions associated with adaptation display elevated differentiation. These genomic islands of adaptive divergence can inform conservation efforts in exploited species, by refining the delineation of management units, and providing genomic tools for more precise and effective population monitoring and the successful assignment of individuals and products. We explored heterogeneity in genomic divergence and its impact on the resolution of spatial population structure in exploited populations of Atlantic cod, Gadus morhua, using genome wide expressed sequence derived single nucleotide polymorphisms in 466 individuals sampled across the range. Outlier tests identified elevated divergence at 5.2% of SNPs, consistent with directional selection in one-third of linkage groups. Genomic regions of elevated divergence ranged in size from a single position to several cM. Structuring at neutral loci was associated with geographic features, whereas outlier SNPs revealed genetic discontinuities in both the eastern and western Atlantic. This fine-scale geographic differentiation enhanced assignment to region of origin, and through the identification of adaptive diversity, fundamentally changes how these populations should be conserved. This work demonstrates the utility of genome scans for adaptive divergence in the delineation of stock structure, the traceability of individuals and products, and ultimately a role for population genomics in fisheries conservation. PMID:23745137

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

2013-01-01

44

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

PubMed Central

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

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

2013-01-01

45

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

PubMed Central

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

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

2008-01-01

46

Infrequent occurrence of age-dependent changes in CpG island methylation as detected by restriction landmark genome scanning.  

PubMed

Hypermethylation of CpG islands, resulting in the inactivation of tumor suppressor genes, is an early event in the development of some malignancies. Recent studies suggest that this abnormal methylation may be a function of aging. The number of CpG islands that methylate with age is unknown. We used restriction landmark genome scanning (RLGS) to approximate the extent to which CpG islands change methylation status during aging. Comparison of more than 2000 loci in T lymphocytes isolated from newborn, middle age, and elderly people revealed that 29 loci ( approximately 1%) changed methylation status during aging, with 23 increasing methylation, and six decreasing. The same subset also changed methylation status with age in the esophagus, lung, and pancreas, but in variable directions. Virtual genome scanning identified one of these loci as a member of the forkhead family, recently implicated in aging, and another as an EST fragment. The methylation status of both correlated with level of expression. Confirming studies in multiple tissues from normal and DNMT1(+/-) mice demonstrated only one age dependent change in the methylation of more than 2000 loci, occurring in liver and kidney. These results indicate that the methylation status of the majority of CpG islands in both mice and humans is tightly controlled during aging, and that changes are infrequent and in humans confined to a specific subset of genes. PMID:12425956

Tra, John; Kondo, Tadashi; Lu, Qianjin; Kuick, Rork; Hanash, Samir; Richardson, Bruce

2002-09-01

47

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

Microsoft Academic Search

The selC tRNA gene is a common site for the insertion of pathogenicity islands in a variety of bacterial enteric pathogens. We demonstrate here that Escherichia coli that produces Shiga toxin 2d and does not harbor the locus of enterocyte effacement (LEE) contains, instead, a novel genomic island. In one representative strain (E. coli O91:H strain 4797\\/97), this island is

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

2001-01-01

48

Gene silencing triggers polycomb repressive complex 2 recruitment to CpG islands genome wide.  

PubMed

Polycomb group (PcG) proteins are required for normal differentiation and development and are frequently deregulated in cancer. PcG proteins are involved in gene silencing; however, their role in initiation and maintenance of transcriptional repression is not well defined. Here, we show that knockout of the Polycomb repressive complex 2 (PRC2) does not lead to significant gene expression changes in mouse embryonic stem cells (mESCs) and that it is dispensable for initiating silencing of target genes during differentiation. Transcriptional inhibition in mESCs is sufficient to induce genome-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 by default to nontranscribed CGI genes to maintain their silenced state and to protect cell identity. PMID:24999238

Riising, Eva Madi; Comet, Itys; Leblanc, Benjamin; Wu, Xudong; Johansen, Jens Vilstrup; Helin, Kristian

2014-08-01

49

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

PubMed Central

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

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

2010-01-01

50

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

PubMed

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

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

2013-11-01

51

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

PubMed Central

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

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

2002-01-01

52

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

PubMed Central

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

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

2008-01-01

53

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

PubMed Central

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

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

2014-01-01

54

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

PubMed Central

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

Luo, Peng; Rodrigue, Sébastien; Burrus, Vincent

2014-01-01

55

Pathogenicity islands: the tip of the iceberg  

Microsoft Academic Search

Pathogenicity islands represent distinct genetic elements encoding virulence factors of pathogenic bacteria. Pathogenicity islands belong to the class of genomic islands, which are common genetic elements sharing a set of unifying features. Genomic islands have been acquired by horizontal gene transfer. In recent years many different genomic islands have been discovered in a variety of pathogenic as well as non-pathogenic

Ute Hentschel; Jörg Hacker

2001-01-01

56

Genome-wide scan in Portuguese Island families identifies 5q31–5q35 as a susceptibility locus for schizophrenia and psychosis  

Microsoft Academic Search

Schizophrenia is a common psychiatric disorder with a complex genetic etiology. To understand the genetic basis of this syndrome in Portuguese Island populations, we performed a genome-wide scan of 29 families with schizophrenia, which identified a single region on 5q31–5q35 with strong linkage (NPL=3.09, P=0.0012 at D5S820). Empirical simulations set a genome-wide threshold of NPL=3.10 for significant linkage. Additional support

P Sklar; M T Pato; A Kirby; T L Petryshen; H Medeiros; C Carvalho; A Macedo; A Dourado; I Coelho; J Valente; M J Soares; C P Ferreira; M Lei; A Verner; T J Hudson; C P Morley; J L Kennedy; M H Azevedo; E Lander; M J Daly; C N Pato

2004-01-01

57

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

PubMed

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

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

2014-12-01

58

Establishment of a CpG island microarray for analyses of genome-wide DNA methylation in Chinese hamster ovary cells.  

PubMed

Optimizing productivity and growth rates of recombinant Chinese hamster ovary (CHO) cells requires insight into the regulation of cellular processes. In this regard, the elucidation of the epigenetic process of DNA methylation, known to influence transcription by a differential occurrence in CpG islands in promoter regions, is increasingly gaining importance. However, DNA methylation has not yet been investigated on a genomic scale in CHO cells and suitable tools have not existed until now. Based on the genomic and transcriptomic CHO data currently available, we developed a customized oligonucleotide microarray covering 19598 CpG islands (89 % of total bioinformatically identified CpG islands) in the CHO genome. We applied our CHO-specific CpG island microarray to investigate the effect of butyrate treatment on differential DNA methylation in CHO cultures in a time-dependent approach. Supplementation of butyrate is known to enhance cell specific productivities in CHO cells and leads to alterations of epigenetic silencing events. Gene ontology clusters regarding, e.g., chromatin modification or DNA repair, were significantly overrepresented 24 h after butyrate addition. Functional classifications furthermore indicated that several major signaling systems such as the Wnt/?-catenin pathway were affected by butyrate treatment. Our novel CHO-specific CpG island microarray will provide valuable information in future studies of cellular processes associated with productivity and product characteristics. PMID:24146078

Wippermann, Anna; Klausing, Sandra; Rupp, Oliver; Albaum, Stefan P; Büntemeyer, Heino; Noll, Thomas; Hoffrogge, Raimund

2014-01-01

59

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

PubMed Central

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

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

2014-01-01

60

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

PubMed Central

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

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

2014-01-01

61

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

PubMed Central

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

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

62

Gene-rich islands for fiber development in the cotton genome  

Technology Transfer Automated Retrieval System (TEKTRAN)

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

63

The Evolution of Mammalian Genomic Imprinting Was Accompanied by the Acquisition of Novel CpG Islands  

PubMed Central

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

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

2011-01-01

64

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

PubMed Central

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

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

2012-01-01

65

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

PubMed Central

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

Wang, Quan; Wang, Lei

2013-01-01

66

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

PubMed Central

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

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

2014-01-01

67

The pheV phenylalanine tRNA gene Klebsiella pneumoniae clinical isolates is an integration hotspot for possible niche-adaptation genomic islands.  

PubMed

Horizontally acquired genomic islands may allow bacteria to conquer and colonize previously uncharted niches. Four Klebsiella pneumoniae tRNA gene insertion hotspots (arg6, asn34, met56, and pheV) in 101 clinical isolates derived from blood, sputum, wound, bile or urine specimens were screened by long-range PCR for the presence or absence of integrated islands. The pheV phenylalanine tRNA gene was the most frequently occupied site and harbored at least three entirely distinct types of islands: (1) KpGI-1, a 3.7 kb island coding for four proteins, three of which showed high similarity to two hypothetical proteins and a Gcn5-related N-acetyltransferase in Salmonella enterica, (2) KpGI-2, a 6.4 kb island coding for five proteins including a truncated phage-like integrase, two helicase-related proteins, and a homolog of the functionally elusive Fic protein, and (3) KpGI-3, a 12.6 kb island which carried seven fimbriae-related genes, first identified in MGH78578. Consistent with the niche-adaptation hypothesis, KpGI-1-like islands which coded for the putative acetyltransferase were significantly over-represented in sputum isolates as compared to urine (P < 0.001), blood (P < 0.05) or bile (P < 0.05) derived isolates. Despite the unique nature of KpGI-2, likely homologs of orf5_KpGI-2 that coded for Fic were also found at undefined locations in six other clinical isolates, though none possessed the other KpGI-2 genes. We propose that the pheV-associated islands described in this study may contribute to fine tuning and adaptation of K. pneumoniae strains toward preferred infection and/or colonization pathways. PMID:19921332

Chen, Nan; Ou, Hong-Yu; van Aartsen, Jon Jurriaan; Jiang, XiaoFei; Li, Min; Yang, ZeHua; Wei, QuHao; Chen, XiaoYun; He, Xinyi; Deng, Zixin; Rajakumar, Kumar; Lu, Yuan

2010-03-01

68

A unique arabinose 5-phosphate isomerase found within a genomic island associated with the uropathogenicity of Escherichia coli CFT073.  

PubMed

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

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

2011-06-01

69

Genomic Island 2 Is an Unstable Genetic Element Contributing to Brucella Lipopolysaccharide Spontaneous Smooth-to-Rough Dissociation ? †  

PubMed Central

Brucella is a Gram-negative bacterium that causes a worldwide-distributed zoonosis. The genus includes smooth (S) and rough (R) species that differ in the presence or absence, respectively, of the O-polysaccharide of lipopolysaccharide. In S brucellae, the O-polysaccharide is a critical diagnostic antigen and a virulence determinant. However, S brucellae spontaneously dissociate into R forms, a problem in antigen and S vaccine production. Spontaneous R mutants of Brucella abortus, Brucella melitensis, and Brucella suis carried the chromosomal scar corresponding to genomic island 2 (GI-2) excision, an event causing the loss of the wboA and wboB O-polysaccharide genes, and the predicted excised circular intermediate was identified in B. abortus, B. melitensis, and B. suis cultures. Moreover, disruption of a putative phage integrase gene in B. abortus GI-2 caused a reduction in O-polysaccharide loss rates under conditions promoting S-R dissociation. However, spontaneous R mutants not carrying the GI-2 scar were also detected. These results demonstrate that the phage integrase-related GI-2 excision is a cause of S-R brucella dissociation and that other undescribed mechanisms must also be involved. In the R Brucella species, previous works have shown that Brucella ovis but not Brucella canis lacks GI-2, and a chromosomal scar identical to those in R mutants was observed. These results suggest that the phage integrase-promoted GI-2 excision played a role in B. ovis speciation and are consistent with other evidence, suggesting that this species and B. canis have emerged as two independent lineages. PMID:20952568

Mancilla, Marcos; López-Gońi, Ignacio; Moriyón, Ignacio; Zárraga, Ana María

2010-01-01

70

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

PubMed Central

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

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

2014-01-01

71

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

PubMed Central

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

2013-01-01

72

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

PubMed Central

Four different type IV secretion systems are variously represented in the genomes of different Helicobacter pylori strains. Two of these, encoded by tfs3 and tfs4 gene clusters are contained within self-transmissible genomic islands. Although chromosomal excision of tfs4 circular intermediates is reported to be dependent upon the function of a tfs4-encoded XerD tyrosine-like recombinase, other factors required for transfer to a recipient cell have not been demonstrated. Here, we characterize the functional activity of a putative tfs4-encoded VirD2-like relaxase protein. Tfs4 VirD2 was purified as a fusion to maltose-binding protein and demonstrated to bind and nick both supercoiled duplex DNA and oligonucleotides in vitro in a manner dependent upon the presence of Mg2+ but independently of any auxiliary proteins. Unusually, concentration-dependent nicking of duplex DNA appeared to require only transient protein-DNA interaction. Although phylogenetically distinct from established relaxase families, site-specific cleavage of oligonucleotides by Tfs4 VirD2 required the nick region sequence 5?-ATCCTG-3? common to transfer origins (oriT) recognized by MOBP conjugative relaxases. Cleavage resulted in covalent attachment of MBP-VirD2 to the 5?-cleaved end, consistent with conventional relaxase activity. Identification of an oriT-like sequence upstream of tfs4 virD2 and demonstration of VirD2 protein-protein interaction with a putative VirC1 relaxosome component indicate that transfer initiation of the tfs4 genomic island is analogous to mechanisms underlying mobilization of other integrated mobile elements, such as integrating conjugative elements, requiring site-specific targeting of relaxase activity to a cognate oriT sequence. PMID:23900838

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

2013-01-01

73

Genotoxic Klebsiella pneumoniae in Taiwan  

PubMed Central

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

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

2014-01-01

74

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

Microsoft Academic Search

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

Willem van Schaik; Janetta Top; David R. Riley; Jos Boekhorst; Joyce E. P. Vrijenhoek; Claudia M. E. Schapendonk; Antoni P. A. Hendrickx; Isaäc J. Nijman; Marc J. M. Bonten; Hervé Tettelin; Rob J. L. Willems

2010-01-01

75

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

PubMed Central

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

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

2015-01-01

76

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

E-print Network

methylation of CpG islands plays a crucial role in the regulation of gene expression. More than half of all, fibroblasts and leukocytes. We achieved an accuracy of up to 91% with an MCC of 0.8 using ten-fold cross and mostly results in silencing of downstream genes [2,3]. CpGs are significantly enriched in some parts

Zell, Andreas

77

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

PubMed Central

Since 2004, extended-spectrum cephalosporin (ESC)-resistant Salmonella enterica serovar Typhimurium (S. Typhimurium) isolates have been detected from cattle in the northern major island of Japan, Hokkaido. Resistance to ESCs was found to be mediated by CMY-2 type ?-lactamase among 22 epidemiologically unrelated isolates showing indistinguishable pulsed-field gel electrophoresis patterns. Southern blot analysis using I-CeuI-digested genomic DNA demonstrated that the CMY-2 ?-lactamase gene (blaCMY-2) was integrated in a 2.5-Mb chromosomal fragment. Genetic analysis of S. Typhimurium isolate L-3553 indicated that blaCMY-2 was located on a unique 125-kb genomic island, GI-VII-6, which consists of 140 open reading frames. Pairwise alignment of GI-VII-6 and Escherichia coli plasmid pAR060302 (size, 167 kb) revealed that a large proportion of GI-VII-6 (99%) shows a high sequence similarity (>99%) with pAR060302. GI-VII-6 contains 11 antimicrobial resistance genes including sul1, qacE?1, aadA2, and dfrA12 in the aadA2 region; sugE1 and blaCMY-2 in the blaCMY-2 region; and sul2, strA, strB, tet(A), and floR in the floR region. Two directly repeated IS26 copies were present at both ends of GI-VII-6. Junction regions of GI-VII-6 were flanked by an 8-bp direct repeat, indicating that GI-VII-6 was acquired by transposition involving IS26 transposase. PCR scanning revealed that the overall structure of GI-VII-6 was almost identical in the 22 isolates. Phylogenetic analysis suggested that S. Typhimurium isolates harboring GI-VII-6 belong to a different genomic lineage than other whole-genome-sequenced S. Typhimurium strains. These data indicate that a particular clone of S. Typhimurium harboring GI-VII-6 has spread among the cattle population in Hokkaido, Japan. PMID:21709089

Shahada, Francis; Sekizuka, Tsuyoshi; Kuroda, Makoto; Kusumoto, Masahiro; Ohishi, Daiki; Matsumoto, Atsuko; Okazaki, Hizuru; Tanaka, Kiyoshi; Uchida, Ikuo; Izumiya, Hidemasa; Watanabe, Haruo; Tamamura, Yukino; Iwata, Taketoshi; Akiba, Masato

2011-01-01

78

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

PubMed Central

Identification of widespread species collected from islands can be challenging due to the potential for local ecological and phenotypic divergence in isolated populations. We sought to determine how many species of the spruce budworm (Choristoneura fumiferana) complex reside in Cypress Hills, an isolated remnant coniferous forest in western Canada. We integrated data on behavior, ecology, morphology, mitochondrial DNA, and simple sequence repeats, comparing Cypress Hills populations to those from other regions of North America to determine which species they resembled most. We identified C. fumiferana, C. occidentalis, C. lambertiana, and hybrid forms in Cypress Hills. Adult flight phenology and pheromone attraction were identified as key life-history traits involved in maintaining the genomic integrity of species. Our study highlights the importance of extensive sampling of both specimens and a variety of characters for understanding species boundaries in biodiversity research. PMID:22393489

Lumley, Lisa M; Sperling, Felix AH

2011-01-01

79

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

PubMed

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

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

2014-05-28

80

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

PubMed Central

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

2012-01-01

81

The biphenyl- and 4-chlorobiphenyl-catabolic transposon Tn4371, a member of a new family of genomic islands related to IncP and Ti plasmids.  

PubMed

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

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

2003-08-01

82

Extensively drug-resistant pseudomonas aeruginosa isolates containing blaVIM-2 and elements of Salmonella genomic island 2: a new genetic resistance determinant in Northeast Ohio.  

PubMed

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

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

2014-10-01

83

Prokaryotic Genomes Eurkaryotic Genomes  

E-print Network

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

Qiu, Weigang

84

LOV-domain photoreceptor, encoded in a genomic island, attenuates the virulence of Pseudomonas syringae in light-exposed Arabidopsis leaves.  

PubMed

In Arabidopsis thaliana, light signals modulate the defences against bacteria. Here we show that light perceived by the LOV domain-regulated two-component system (Pst-Lov) of Pseudomonas syringae pv. tomato DC3000 (Pst DC3000) modulates virulence against A. thaliana. Bioinformatic analysis and the existence of an episomal circular intermediate indicate that the locus encoding Pst-Lov is present in an active genomic island acquired by horizontal transfer. Strains mutated at Pst-Lov showed enhanced growth on minimal medium and in leaves of A. thaliana exposed to light, but not in leaves incubated in darkness or buried in the soil. Pst-Lov repressed the expression of principal and alternative sigma factor genes and their downstream targets linked to bacterial growth, virulence and quorum sensing, in a strictly light-dependent manner. We propose that the function of Pst-Lov is to distinguish between soil (dark) and leaf (light) environments, attenuating the damage caused to host tissues while releasing growth out of the host. Therefore, in addition to its direct actions via photosynthesis and plant sensory receptors, light may affect plants indirectly via the sensory receptors of bacterial pathogens. PMID:23865633

Moriconi, Victoria; Sellaro, Romina; Ayub, Nicolás; Soto, Gabriela; Rugnone, Matías; Shah, Rashmi; Pathak, Gopal P; Gärtner, Wolfgang; Casal, Jorge J

2013-10-01

85

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

PubMed Central

Background The Type VI secretion apparatus is assembled by a conserved set of proteins encoded within a distinct locus. The putative effector proteins Hcp and VgrG are also encoded within these loci. We have identified numerous distinct Type VI secretion system (T6SS) loci in the genomes of several ecologically diverse Pantoea and Erwinia species and detected the presence of putative effector islands associated with the hcp and vgrG genes. Results Between two and four T6SS loci occur among the Pantoea and Erwinia species. While two of the loci (T6SS-1 and T6SS-2) are well conserved among the various strains, the third (T6SS-3) locus is not universally distributed. Additional orthologous loci are present in Pantoea sp. aB-valens and Erwinia billingiae Eb661. Comparative analysis of the T6SS-1 and T6SS-3 loci showed non-conserved islands associated with the vgrG and hcp, and vgrG genes, respectively. These regions had a G+C content far lower than the conserved portions of the loci. Many of the proteins encoded within the hcp and vgrG islands carry conserved domains, which suggests they may serve as effector proteins for the T6SS. A number of the proteins also show homology to the C-terminal extensions of evolved VgrG proteins. Conclusions Extensive diversity was observed in the number and content of the T6SS loci among the Pantoea and Erwinia species. Genomic islands could be observed within some of T6SS loci, which are associated with the hcp and vgrG proteins and carry putative effector domain proteins. We propose new hypotheses concerning a role for these islands in the acquisition of T6SS effectors and the development of novel evolved VgrG and Hcp proteins. PMID:22115407

2011-01-01

86

Genomic Island TnSmu2 of Streptococcus mutans Harbors a Nonribosomal Peptide Synthetase-Polyketide Synthase Gene Cluster Responsible for the Biosynthesis of Pigments Involved in Oxygen and H2O2 Tolerance ? †  

PubMed Central

The oral biofilm community consists of >800 microbial species, among which Streptococcus mutans is considered a primary pathogen for dental caries. The genomic island TnSmu2 of S. mutans comprises >2% of the genome. In this study, we demonstrate that TnSmu2 harbors a gene cluster encoding nonribosomal peptide synthetases (NRPS), polyketide synthases (PKS), and accessory proteins and regulators involved in nonribosomal peptide (NRP) and polyketide (PK) biosynthesis. Interestingly, the sequences of these genes and their genomic organizations and locations are highly divergent among different S. mutans strains, yet each TnSmu2 region encodes NRPS/PKS and accessory proteins. Mutagenesis of the structural genes and putative regulatory genes in strains UA159, UA140, and MT4653 resulted in colonies that were devoid of their yellow pigmentation (for strains UA140 and MT4653). In addition, these mutant strains also displayed retarded growth under aerobic conditions and in the presence of H2O2. High-performance liquid chromatography profiling of cell surface extracts identified unique peaks that were missing in the mutant strains, and partial characterization of the purified product from UA159 demonstrated that it is indeed a hybrid NRP/PK, as predicted. A genomic survey of 94 clinical S. mutans isolates suggests that the TnSmu2 gene cluster may be more prevalent than previously recognized. PMID:20639370

Wu, Chenggang; Cichewicz, Robert; Li, Yihong; Liu, Jinman; Roe, Bruce; Ferretti, Joseph; Merritt, Justin; Qi, Fengxia

2010-01-01

87

Island Biogeography  

NSDL National Science Digital Library

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

John Jungck (BioQUEST Curriculum Consortium; Biology)

2005-12-16

88

PIPS: Pathogenicity Island Prediction Software  

PubMed Central

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

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

2012-01-01

89

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

PubMed Central

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

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

2011-01-01

90

Galapagos Islands  

NASA Technical Reports Server (NTRS)

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

2002-01-01

91

Akpatok Island  

NASA Technical Reports Server (NTRS)

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

2002-01-01

92

Analysis of Human Peripheral Blood T Cells and Single-Cell-Derived T Cell Clones Uncovers Extensive Clonal CpG Island Methylation Heterogeneity throughout the Genome  

Microsoft Academic Search

Methylation of cytosine residues in CpG dinucleotides is generally associated with silencing of gene expression. DNA methylation, as a somatic event, has the potential of diversifying gene expression in individual cells of the same lineage. There is little quantitative data available concerning the extent of methylation heterogeneity in individual cells across the genome. T cells from the peripheral blood can

Xiaoxiang Zhu; Chun Deng; Rork Kuick; Raymond Yung; Barbara Lamb; James V. Neel; Bruce Richardson; Samir Hanash

1999-01-01

93

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

PubMed Central

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

Xu, Youqiang; Yao, Su; Li, Jinxia

2014-01-01

94

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

PubMed

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

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

2014-01-01

95

Identifying Pathogenicity Islands in Bacterial Pathogenomics Using Computational Approaches  

PubMed Central

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

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

2014-01-01

96

Island Hopping  

ERIC Educational Resources Information Center

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

Bennett, Gayle

2009-01-01

97

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

PubMed

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

2000-02-01

98

Island Panoramic  

USGS Multimedia Gallery

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

99

Island biology: looking towards the future.  

PubMed

Oceanic islands are renowned for the profound scientific insights that their fascinating biotas have provided to biologists during the past two centuries. Research presented at Island Biology 2014-an international conference, held in Honolulu, Hawaii (7-11 July 2014), which attracted 253 presenters and 430 participants from at least 35 countries(1)-demonstrated that islands are reclaiming a leading role in ecology and evolution, especially for synthetic studies at the intersections of macroecology, evolution, community ecology and applied ecology. New dynamics in island biology are stimulated by four major developments. We are experiencing the emergence of a truly global and comprehensive island research community incorporating previously neglected islands and taxa. Macroecology and big-data analyses yield a wealth of global-scale synthetic studies and detailed multi-island comparisons, while other modern research approaches such as genomics, phylogenetic and functional ecology, and palaeoecology, are also dispersing to islands. And, increasingly tight collaborations between basic research and conservation management make islands places where new conservation solutions for the twenty-first century are being tested. Islands are home to a disproportionate share of the world's rare (and extinct) species, and there is an urgent need to develop increasingly collaborative and innovative research to address their conservation requirements. PMID:25339655

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

2014-10-01

100

Thermal Islands  

NSDL National Science Digital Library

In this problem-based learning unit, students learn about the causes and impacts of urban heat islands. Numerous studies have shown how concrete pavements and buildings retain heat in cities, making cities several degrees warmer than the surrounding countryside. Students investigate the role of cities in our climate, specifically how the urban heat island affects climate. Instructions to access NASA data are provided along with additional resources and activities. This module was developed for use in the Earth System Science Education Alliance (ESSEA) professional development courses for middle and high school teachers and is also available to teachers to adapt for general classroom use. See Related & Supplemental URLs for a demo course showing how this module is integrated into an ESSEA course for teachers.

101

Streamlined Island  

NASA Technical Reports Server (NTRS)

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

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

2003-01-01

102

Metagenomic islands of hyperhalophiles: the case of Salinibacter ruber  

PubMed Central

Background Saturated brines are extreme environments of low diversity. Salinibacter ruber is the only bacterium that inhabits this environment in significant numbers. In order to establish the extent of genetic diversity in natural populations of this microbe, the genomic sequence of reference strain DSM 13855 was compared to metagenomic fragments recovered from climax saltern crystallizers and obtained with 454 sequencing technology. This kind of analysis reveals the presence of metagenomic islands, i.e. highly variable regions among the different lineages in the population. Results Three regions of the sequenced isolate were scarcely represented in the metagenome thus appearing to vary among co-occurring S. ruber cells. These metagenomic islands showed evidence of extensive genomic corruption with atypically low GC content, low coding density, high numbers of pseudogenes and short hypothetical proteins. A detailed analysis of island gene content showed that the genes in metagenomic island 1 code for cell surface polysaccharides. The strain-specific genes of metagenomic island 2 were found to be involved in biosynthesis of cell wall polysaccharide components. Finally, metagenomic island 3 was rich in DNA related enzymes. Conclusion The genomic organisation of S. ruber variable genomic regions showed a number of convergences with genomic islands of marine microbes studied, being largely involved in variable cell surface traits. This variation at the level of cell envelopes in an environment devoid of grazing pressure probably reflects a global strategy of bacteria to escape phage predation. PMID:19951421

2009-01-01

103

The tad locus: postcards from the widespread colonization island  

Microsoft Academic Search

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

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

2007-01-01

104

Folly Island Tidal Lines  

USGS Multimedia Gallery

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

105

Folly Island Tidal Lines  

USGS Multimedia Gallery

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

106

Lengauer T: CpG island mapping by epigenome prediction  

E-print Network

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

Christoph Bock; Jörn Walter; Martina Paulsen; Thomas Lengauer

107

Alcatraz Island  

NSDL National Science Digital Library

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

2005-01-01

108

DNA methylation and the analysis of CpG Islands  

E-print Network

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

Czygrinow, Andrzej

109

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

Federal Register 2010, 2011, 2012, 2013, 2014

...RIN 1625-AA00 Safety Zone; Catawba Island Club Wedding Event, Catawba Island Club, Catawba Island, OH ACTION: Temporary final...165.T09-0840 Safety Zone; Catawba Island Club Wedding Event, Catawba Island Club, Catawba...

2013-09-25

110

Life of an Island  

NSDL National Science Digital Library

In this lesson covers the evolution of a volcanic island from origin to erosion. Students will be able to determine the relative ages of the Northwestern Hawaiian Islands, given their position in the archipelago and why these islands are so much smaller than the main islands of the Hawaiian chain. They will discover that volcanic islands form over a hot spot on the ocean floor and that islands form and erode in eight stages, so the relative age of an island or atoll can be determined based on its state of growth or erosion.

Museum, Bishop

111

Evidence for metaviromic islands in marine phages  

PubMed Central

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

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

2014-01-01

112

Hawaiian Island Archipelago  

NASA Technical Reports Server (NTRS)

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

1985-01-01

113

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

PubMed

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

Kunzmann, Martin H; Sieber, Stephan A

2012-11-01

114

Engineering a Reduced Escherichia coli Genome  

PubMed Central

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

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

2002-01-01

115

Pathogenicity Islands in Bacterial Pathogenesis  

PubMed Central

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

Schmidt, Herbert; Hensel, Michael

2004-01-01

116

The Francisella pathogenicity island.  

PubMed

The Francisella pathogenicity island (FPI) is a cluster of 16-19 genes, which is found duplicated in most of the Francisella genomes that have been sequenced. Although 16 FPI genes are highly conserved there are 2-3 putative genes that are absent or interrupted by stop codons in some strains. Francisella strains with experimentally induced mutations in FPI genes are highly attenuated in virulence and show defects in intramacrophage growth. There is experimental evidence indicating that the regulation of most FPI genes is affected by the presence of the virulence regulator MglA and by the concentration of iron in the growth medium. Although studies of mRNA expression show that essentially all FPI genes are transcribed, only a handful of FPI-encoded proteins have been detected by biochemical methods. The cumulative biochemical and genetic data to date have not yet been able to ascribe a biochemical function to any of the FPI-encoded proteins. However, bioinformatics analysis suggests that some of the FPI-encoded proteins are part of a type VI secretion system. PMID:17395722

Nano, Francis E; Schmerk, Crystal

2007-06-01

117

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

PubMed Central

It is well known that patterns of nucleotide composition vary within and among genomes, although the reasons why these variations exist are not completely understood. Between-genome compositional variation has been exploited to assign environmental shotgun sequences to their most likely originating genomes, whereas within-genome variation has been used to identify recently acquired genetic material such as pathogenicity islands. Recent sequence assignment techniques have achieved high levels of accuracy on artificial data sets, but the relative difficulty of distinguishing lineages with varying degrees of relatedness, and different types of genomic sequence, has not been examined in depth. We investigated the compositional differences in a set of 774 sequenced microbial genomes, finding rapid divergence among closely related genomes, but also convergence of compositional patterns among genomes with similar habitats. Support vector machines were then used to distinguish all pairs of genomes based on genome fragments 500 nucleotides in length. The nearly 300,000 accuracy scores obtained from these trials were used to construct general models of distinguishability versus taxonomic and compositional indices of genomic divergence. Unusual genome pairs were evident from their large residuals relative to the fitted model, and we identified several factors including genome reduction, putative lateral genetic transfer, and habitat convergence that influence the distinguishability of genomes. The positional, compositional, and functional context of a fragment within a genome has a strong influence on its likelihood of correct classification, but in a way that depends on the taxonomic and ecological similarity of the comparator genome. PMID:20333228

Perry, Scott C.; Beiko, Robert G.

2010-01-01

118

Overwash on Assateague Island  

USGS Multimedia Gallery

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

119

Pine Island Glacier  

Atmospheric Science Data Center

article title:  Pine Island Glacier, Antarctica     View Larger Image ... (MISR) images of the Pine Island Glacier in western Antarctica was acquired on December 12, 2000 during Terra orbit 5246. At left ...

2013-04-16

120

Galapagos Islands Flyby  

NSDL National Science Digital Library

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

Pape, Dave; Feldman, Gene

1994-03-13

121

Island of Timor, Indonesia  

NASA Technical Reports Server (NTRS)

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

1989-01-01

122

Overwash on Assateague Island  

USGS Multimedia Gallery

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

123

How Are Islands Formed?  

NSDL National Science Digital Library

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

2001-01-01

124

on Hurricane Island, Maine  

Microsoft Academic Search

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

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

125

Genome Research  

NSDL National Science Digital Library

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

1995-01-01

126

Apostle Islands National Lakeshore  

NSDL National Science Digital Library

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

127

Surface evolution of faceted islands  

NASA Astrophysics Data System (ADS)

Ge islands were grown on Si(0 0 1) by ultrahigh vacuum magnetron sputter epitaxy and their surface was investigated by scanning tunneling microscopy. The facets composing the island surface were identified and their area was measured as a function of island size. Three kinds of islands were observed: pyramids, dome shaped islands and large dislocated islands. A statistical analysis revealed that domes do not ripen in a self-similar way. The main facets composing the surface of dislocated islands were identified.

Rastelli, Armando; von Känel, Hans

2002-09-01

128

Island Biogeography and Landscape Ecology  

Microsoft Academic Search

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

Ioannis Vogiatzakis; Geoffrey H. Griffiths

129

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

Microsoft Academic Search

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

K. Shiota

2004-01-01

130

The Flores Island tsunamis  

Microsoft Academic Search

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

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

1993-01-01

131

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

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

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

132

Stewart Head from Folly Island  

USGS Multimedia Gallery

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

133

Whole-Genome Plasticity among Mycobacterium avium Subspecies: Insights from Comparative Genomic Hybridizations†  

PubMed Central

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

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

2006-01-01

134

Barnacles on Folly Island  

USGS Multimedia Gallery

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

135

Build an Island  

NSDL National Science Digital Library

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

136

Island Natural Science School.  

ERIC Educational Resources Information Center

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

Toronto Board of Education (Ontario).

137

Intervention in Solomon Islands  

Microsoft Academic Search

From the late 1990s Solomon Islands had been moving towards the status of a ‘failed state’. Corruption was widespread and there was considerable resentment expressed by Guadalcanal people towards immigrants from the neighbouring island of Malaita, because of the perceived economic gains made by the latter at the former's expense. Conflict over this issue led to the coup of 5

Derek McDougall

2004-01-01

138

Genome duplications (polyploidy) / ancientGenome duplications (polyploidy) / ancient genome duplications (genome duplications (paleopolyploidypaleopolyploidy))  

E-print Network

Genome duplications (polyploidy) / ancientGenome duplications (polyploidy) / ancient genome duplications (genome duplications (paleopolyploidypaleopolyploidy)) Mechanism? e.g. a diploid cell undergoes;Paramecium genome duplicationsParamecium genome duplications #12;Comparison of two scaffolds originating from

Utrecht, Universiteit

139

Genome duplications (polyploidy) / ancientGenome duplications (polyploidy) / ancient genome duplications (genome duplications (paleopolyploidypaleopolyploidy))  

E-print Network

Genome duplications (polyploidy) / ancientGenome duplications (polyploidy) / ancient genome duplications (genome duplications (paleopolyploidypaleopolyploidy)) e.g. a diploid cell undergoes failed genome duplicationsParamecium genome duplications #12;Comparison of two scaffolds originating from a

Utrecht, Universiteit

140

Complete Genome Sequence of Helicobacter cinaedi Strain PAGU611, Isolated in a Case of Human Bacteremia  

PubMed Central

We report the complete genome sequence of Helicobacter cinaedi strain PAGU611, isolated in a case of human bacteremia. The PAGU611 genome comprises a 2,078,348-bp chromosome and a 23,054-bp plasmid. The chromosome contains a unique genomic island, encoding a type VI secretion system and clustered regularly interspaced short palindromic repeat (CRISPR) loci. PMID:22740670

Goto, Takatsugu; Ogura, Yoshitoshi; Hirakawa, Hideki; Tomida, Junko; Morita, Yuji; Akaike, Takaaki; Hayashi, Tetsuya

2012-01-01

141

Color and genomic ancestry in Brazilians  

Microsoft Academic Search

This work was undertaken to ascertain to what degree the physical appearance of a Brazilian individual was predictive of genomic African ancestry. Using a panel of 10 population-specific alleles, we assigned to each person an African ancestry index (AAI). The procedure was able to tell apart, with no overlaps, 20 males from northern Portugal from 20 males from Sao TomeIsland

Flavia C. Parra; Roberto C. Amado; Jose R. Lambertucci; Jorge Rocha; Carlos M. Antunes; Sergio D. J. Pena

2003-01-01

142

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

PubMed

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

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

2006-07-01

143

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

Microsoft Academic Search

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

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

2011-01-01

144

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

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

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

145

Complete Genome Sequence and Comparative Genomics of Shigella flexneri Serotype 2a Strain 2457T  

Microsoft Academic Search

We determined the complete genome sequence of Shigella flexneri serotype 2a strain 2457T (4,599,354 bp). Shigella species cause >1 million deaths per year from dysentery and diarrhea and have a lifestyle that is markedly different from those of closely related bacteria, including Escherichia coli. The genome exhibits the backbone and island mosaic structure of E. coli pathogens, albeit with much

J. Wei; M. B. Goldberg; V. Burland; M. M. Venkatesan; W. Deng; G. Fournier; G. F. Mayhew; G. Plunkett; D. J. Rose; A. Darling; B. Mau; N. T. Perna; S. M. Payne; L. J. Runyen-Janecky; S. Zhou; D. C. Schwartz; F. R. Blattner

2003-01-01

146

Conservation Strategy for Sable Island  

E-print Network

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

Jones, Ian L.

147

The Island Institute  

NSDL National Science Digital Library

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

148

Easter Island Revisited  

NSDL National Science Digital Library

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

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

2007-09-21

149

Island Watershed Activity.  

ERIC Educational Resources Information Center

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

Benson, Rod

2003-01-01

150

Heat Island Effect  

MedlinePLUS

... temperatures also promote the formation of ground-level ozone. Compromised human health and comfort : Warmer days and ... island mitigation is part of a community's energy, air quality, water, or sustainability effort. Activities to reduce heat ...

151

Christmas Island birds returning  

NASA Astrophysics Data System (ADS)

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

152

Mapping Staten Island  

NSDL National Science Digital Library

Staten Island has been in the news recently due to the severity of the damage wrought by Hurricane Sandy. For those wishing to know more about the history of this venerable community, this website is a gem. Mapping Staten Island is part of an in situ exhibit at the Museum of the City of New York that looks at the geography and history of Staten Island. The exhibit examines the borough's historical transformation through maps, government documents, and newspapers. By clicking on the Explore the Maps section, visitors can use a graphic interface that overlays dozens of historic maps, including an 1845 land use map and a 1781 chart and harbor map of the area, on the contemporary geography of Staten Island. Also, visitors can use the scroll bar near the bottom of the page to look at the maps in a chronological fashion.

153

Photographs of Tinian Island  

NSDL National Science Digital Library

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

Christopher Griffith

154

Heat Island Effect  

NSDL National Science Digital Library

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

155

Island Inequality Map  

NSDL National Science Digital Library

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

Illuminations National Council of Teachers of Math

2009-01-15

156

Urban Heat Islands  

NSDL National Science Digital Library

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

Lisa Gardiner

157

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

Microsoft Academic Search

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

Kevin R. Crooks; Dirk Van Vuren

158

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

Technology Transfer Automated Retrieval System (TEKTRAN)

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

159

Genomics & Medicine Doug Brutlag  

E-print Network

Molecular Docking Gene Therapy #12;Genomics, Bioinformatics & Computational Biology Computational Biology - RNA Proteomics - Protein Understanding Metabolism Understanding Disease Inherited Diseases - OMIMComputational Biology BioinformaticsBioinformaticsGenomicsGenomics Structural GenomicsStructural Genomics Computational

Brutlag, Doug

160

Initiation of DNA replication at CpG islands in mammalian chromosomes.  

PubMed Central

CpG islands are G+C-rich regions approximately 1 kb long that are free of methylation and contain the promoters of many mammalian genes. Analysis of in vivo replication intermediates at three hamster genes and one human gene showed that the CpG island regions, but not their flanks, were present in very short nascent strands, suggesting that they are replication origins (ORIs). CpG island-like fragments were enriched in a population of short nascent strands from human erythroleukaemic cells, suggesting that islands constitute a significant fraction of endogenous ORIs. Correspondingly, bulk CpG islands were found to replicate coordinately early in S phase. Our results imply that CpG islands are initiation sites for both transcription and DNA replication, and may represent genomic footprints of replication initiation. PMID:9545253

Delgado, S; Gómez, M; Bird, A; Antequera, F

1998-01-01

161

Comparative genomic analysis of Lactobacillus rhamnosus GG reveals pili containing a human- mucus binding protein  

Microsoft Academic Search

To unravel the biological function of the widely used probiotic bacterium Lactobacillus rhamnosus GG, we compared its 3.0-Mbp genome sequence with the similarly sized genome of L. rhamnosus LC705, an adjunct starter culture exhibiting reduced binding to mucus. Both genomes demonstrated high sequence identity and synteny. However, for both strains, genomic islands, 5 in GG and 4 in LC705, punctuated

M. Kankainen; L. Paulin; S. Tynkkynen; I. von Ossowski; J. Reunanen; P. Partanen; R. Satokari; S. Vesterlund; A. P. A. Hendrickx; S. Lebeer; S. C. J. de Keersmaecker; J. Vanderleyden; T. Hamalainen; S. Laukkanen; N. Salovuori; J. Ritari; E. Alatalo; R. Korpela; T. Mattila-Sandholm; A. Lassig; K. Hatakka; K. T. Kinnunen; H. Karjalainen; M. Saxelin; K. Laakso; A. Surakka; A. Palva; T. Salusjarvi; P. Auvinen; W. M. de Vos

2009-01-01

162

Antarctic Genomics  

PubMed Central

With the development of genomic science and its battery of technologies, polar biology stands on the threshold of a revolution, one that will enable the investigation of important questions of unprecedented scope and with extraordinary depth and precision. The exotic organisms of polar ecosystems are ideal candidates for genomic analysis. Through such analyses, it will be possible to learn not only the novel features that enable polar organisms to survive, and indeed thrive, in their extreme environments, but also fundamental biological principles that are common to most, if not all, organisms. This article aims to review recent developments in Antarctic genomics and to demonstrate the global context of such studies. PMID:18629155

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

2004-01-01

163

Modeling Catastrophic Barrier Island Dynamics  

NASA Astrophysics Data System (ADS)

Barrier islands, thin strips of sand lying parallel to the mainland coastline, along the U.S. Atlantic and Gulf Coasts appear to have maintained their form for thousands of years in the face of rising sea level. The mechanisms that allow barrier islands to remain robust are transport of sediment from the ocean side of barriers to the top and backside during storms, termed island overwash, and the growth and alongshore propagation of tidal deltas near barrier island inlets. Dynamically these processes provide the necessary feedbacks to maintain a barrier island in an attractor that withstands rising sea level within a phase space of barrier island geometrical characteristics. Current barrier island configurations along the Atlantic and Gulf coasts exist among a wide range of storm climate and underlying geologic conditions and therefore the environment that forces overwash and tidal delta dynamics varies considerably. It has been suggested that barrier islands in certain locations such as those between Avon and Buxton (losing 76% of island width since 1852) and Chandeleur islands (losing 85% of its surface area since 2005) along the Atlantic and Gulf coasts, respectively, may be subject to a catastrophic shift in barrier island attractor states - more numerous inlets cutting barriers in some locations and the complete disappearance of barrier islands in other locations. In contrast to common models for barrier islands that neglect storm dynamics and often only consider cross-shore response, we use an alongshore extended model for barrier island dynamics including beach erosion, island overwash and inlet cutting during storms, and beach accretion, tidal delta growth and dune and vegetation growth between storms to explore the response of barrier islands to a wide range of environmental forcing. Results will be presented that show how barrier island attractor states are altered with variations in the rate of sea level rise, storminess, and underlying geology. We will also investigate the conditions necessary for a barrier island attractor similar to those found along the Atlantic and Gulf coasts to become unstable.

Whitley, J. W.; McNamara, D.

2012-12-01

164

Heron Island, Australia  

NASA Technical Reports Server (NTRS)

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

2002-01-01

165

Genomic Adaptation of the Lactobacillus casei Group  

PubMed Central

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

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

2013-01-01

166

Genomics Glossary  

NSDL National Science Digital Library

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

Chitty, Mary Glen.

167

Restoration of a tropical island: Cousine Island, Seychelles  

Microsoft Academic Search

Tropical island species and ecosystems are threatened worldwide as a result of increasing human pressure. Yet some of these\\u000a islands also lend themselves to restoration, as they are physically defined units that can be given focused attention, as\\u000a long as resources are available and clear conservation targets are set. Cousine Island, Seychelles, is a tropical island that\\u000a has received such

Michael J. Samways; Peter M. Hitchins; Orty Bourquin; Jock Henwood

2010-01-01

168

Archaeoastronomy of Easter Island  

NASA Astrophysics Data System (ADS)

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.

Edwards, Edmundo

169

Island species radiation and karyotypic stasis in Pachycladon allopolyploids  

PubMed Central

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

2010-01-01

170

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

PubMed Central

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 CTX? and RS1?. PMID:25359919

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

171

Computational prediction of methylation status in human genomic sequences  

Microsoft Academic Search

Epigenetic effects in mammals depend largely on heritable genomic methylation patterns. We describe a computational pattern recognition method that is used to predict the methylation landscape of human brain DNA. This method can be applied both to CpG islands and to non-CpG island regions. It computes the methylation propensity for an 800-bp region centered on a CpG dinucleotide based on

Rajdeep Das; Nevenka Dimitrova; Zhenyu Xuan; Robert A. Rollins; Fatemah Haghighi; John R. Edwards; Jingyue Ju; Timothy H. Bestor; Michael Q. Zhang

2006-01-01

172

Salt Marshes at Chincoteague Island  

USGS Multimedia Gallery

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

173

Mosquito Point at Chincoteague Island  

USGS Multimedia Gallery

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

174

The human genome: a multifractal analysis  

PubMed Central

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

2011-01-01

175

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

E-print Network

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

176

HEAT ISLAND REDUCTION STRATEGIES GUIDEBOOK  

EPA Science Inventory

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

177

CpG island mapping by epigenome prediction  

Microsoft Academic Search

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

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

2005-01-01

178

Siberian Expedition: Wrangel Island  

NSDL National Science Digital Library

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

179

Island Biogeography Gillian Brooks  

E-print Network

SpeciesArea Curve H.C. Watson (1859) Arrhenius(1921) S = cAz Gleason (1922) log(S) = log(c) + zlog(A) Is the relationship between species and area linear? Island Biogeography Theory ­ (1963 with increase in species richness? #12;Both immigration and extinction lines are curved. (?) Any assumptions

Jodice, Patrick

180

Atsena Otie Key Island  

USGS Multimedia Gallery

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

181

GREEN HOMES LONG ISLAND  

E-print Network

energy bill, reduce your carbon footprint... at little or no cost to you. #12;A Message From Supervisor energy-efficient and reduce our community's carbon footprint. Why do we call it Long Island Green Homes to yourevery day. By making basic improvements to yourevery day home, you can reduce your carbon footprint

Kammen, Daniel M.

182

Arts & Genomics  

NSDL National Science Digital Library

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

183

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

PubMed Central

Lactobacillus casei is remarkably adaptable to diverse habitats and widely used in the food industry. To reveal the genomic features that contribute to its broad ecological adaptability and examine the evolution of the species, the genome sequence of L. casei ATCC 334 is analyzed and compared with other sequenced lactobacilli. This analysis reveals that ATCC 334 contains a high number of coding sequences involved in carbohydrate utilization and transcriptional regulation, reflecting its requirement for dealing with diverse environmental conditions. A comparison of the genome sequences of ATCC 334 to L. casei BL23 reveals 12 and 19 genomic islands, respectively. For a broader assessment of the genetic variability within L. casei, gene content of 21 L. casei strains isolated from various habitats (cheeses, n = 7; plant materials, n = 8; and human sources, n = 6) was examined by comparative genome hybridization with an ATCC 334-based microarray. This analysis resulted in identification of 25 hypervariable regions. One of these regions contains an overrepresentation of genes involved in carbohydrate utilization and transcriptional regulation and was thus proposed as a lifestyle adaptation island. Differences in L. casei genome inventory reveal both gene gain and gene decay. Gene gain, via acquisition of genomic islands, likely confers a fitness benefit in specific habitats. Gene decay, that is, loss of unnecessary ancestral traits, is observed in the cheese isolates and likely results in enhanced fitness in the dairy niche. This study gives the first picture of the stable versus variable regions in L. casei and provides valuable insights into evolution, lifestyle adaptation, and metabolic diversity of L. casei. PMID:20333194

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

2009-01-01

184

Genome sequence and comparative genome analysis of Lactobacillus casei: insights into their niche-associated evolution.  

PubMed

Lactobacillus casei is remarkably adaptable to diverse habitats and widely used in the food industry. To reveal the genomic features that contribute to its broad ecological adaptability and examine the evolution of the species, the genome sequence of L. casei ATCC 334 is analyzed and compared with other sequenced lactobacilli. This analysis reveals that ATCC 334 contains a high number of coding sequences involved in carbohydrate utilization and transcriptional regulation, reflecting its requirement for dealing with diverse environmental conditions. A comparison of the genome sequences of ATCC 334 to L. casei BL23 reveals 12 and 19 genomic islands, respectively. For a broader assessment of the genetic variability within L. casei, gene content of 21 L. casei strains isolated from various habitats (cheeses, n = 7; plant materials, n = 8; and human sources, n = 6) was examined by comparative genome hybridization with an ATCC 334-based microarray. This analysis resulted in identification of 25 hypervariable regions. One of these regions contains an overrepresentation of genes involved in carbohydrate utilization and transcriptional regulation and was thus proposed as a lifestyle adaptation island. Differences in L. casei genome inventory reveal both gene gain and gene decay. Gene gain, via acquisition of genomic islands, likely confers a fitness benefit in specific habitats. Gene decay, that is, loss of unnecessary ancestral traits, is observed in the cheese isolates and likely results in enhanced fitness in the dairy niche. This study gives the first picture of the stable versus variable regions in L. casei and provides valuable insights into evolution, lifestyle adaptation, and metabolic diversity of L. casei. PMID:20333194

Cai, Hui; Thompson, Rebecca; Budinich, Mateo F; Broadbent, Jeff R; Steele, James L

2009-01-01

185

Genomics of Transposable Elements in the Triticeae  

Microsoft Academic Search

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

François Sabot; Alan H. Schulman

186

Genetic relationships of D-genome species based on two types of EST-SSR markers derived from G. arboreum and G. raimondii in Gossypium  

Microsoft Academic Search

The tetraploid cotton species, which includes two commercially important species, Gossypium hirsutum L. and Gossypium barbadense L., were synthesized by A and D compound genomes. There are two A-genome species and 13 D-genome species in Gossypium. The A-genome species are distributed throughout Africa and Asia, and the D-genome species occur primarily in Mexico, but also in Peru, the Galapagos Islands

W. Z. Guo; Z. Q. Sang; B. L. Zhou; T. Z. Zhang

2007-01-01

187

Physiological Genomics  

NSDL National Science Digital Library

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

1969-12-31

188

The Shell Island Dilemma  

NSDL National Science Digital Library

The objective of this inquiry simulation is to investigate the issues concerning the fate of the Shell Island Resort, which is in danger of being destroyed by a migrating inlet, and then debate the future of this and other oceanfront structures threatened by coastal erosion. As students engage in their investigation, they are asked to identify the social, political, and scientific issues with which different stakeholders must deal. They will place themselves into the role of one of the stakeholders. The site lists the stakeholders and provides several sources of information for each. After reviewing the resources, students will prepare a statement to decide what should be the next course of action regarding the Shell Island Resort. Students then will present statements in a debate to decide the future of the resort.

189

Pine Island Iceberg Formation  

NSDL National Science Digital Library

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

Perkins, Lori; Bindschadler, Bob; Diner, Dave

2002-01-10

190

Syntactic Islands in Uyghur  

E-print Network

...........................................................................................................................55 vi Abbreviations 1 1st person 2 2nd person 3 3rd person ABL ablative case ACC accusative case ATB Across the Board Movement AUX auxiliary CAUS causative CNPC Complex Noun Phrase Constraint CSC Coordinate Structure... the complex noun phrase constraint (CNPC), wh-islands, and the coordinate structure constraint (CSC) in Uyghur. With regard to the CNPC, I provide evidence that nominalized embedded clauses, non-nominal embedded clauses, and relative clauses (nominal...

Major, Travis

2014-05-31

191

Leyte Island, Philippines  

NASA Technical Reports Server (NTRS)

The effects of Tropical Storm Thelma in November 1991, three weeks prior to the taking of this photo can still be seen on Leyte, (10.5N, 125.0E). Flash floods and mud slides triggered by the heavy rainfall and aggravated by logging operations on the mountain slopes, added to the general destruction caused by the storm. Fresh water runoff (lens) into the ocean are still evident as numerous bright semi circles around the island perimeter.

1991-01-01

192

Dauphin Island Sea Lab  

NSDL National Science Digital Library

Dauphin Island Sea Lab is Alabama's marine education and research center. Lab also provides a public aquarium that focuses solely on the native eco-systems of the Mobile Bay estuary. Site provides information on graduate programs, undergraduate opportunities, faculty, facilities, and news and events. Explore the Education and Aquarium sections for teacher resources and information on workshops, student summer camps, and academic-year programs.

193

Southern Vancouver Island  

NSDL National Science Digital Library

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

194

Poetic Waves: Angel Island  

NSDL National Science Digital Library

While many visitors to San Francisco may be familiar with Alcatraz Island, they may be less familiar with the story of Angel Island, which is also located nearby. From 1910 to 1940, the island served as immigration station for newly arrived Asian American immigrants to the United States. While here, these people began to bond over their shared experiences, and also started to learn about the difficult time that they would face in this new land. This multimedia website pays tribute to their experiences through offering compelling information about this place through audio narration and music. As the title of the site suggests, visitors can read some of the poetry the immigrants carved into the barracks where they lived when they were being processed upon arrival. The website accurately suggests that âÂÂâ¦there is no direct connection between them except for the languages, the time period, and place.â Of course, visitors may wish to continue their visit to the site, by taking the online tour of the facility, which includes the hospital building, the pier, and the barracks.

2005-01-01

195

Complete Genome Sequence of a Pseudomonas putida Clinical Isolate, Strain H8234  

PubMed Central

We report the complete genome sequence of Pseudomonas putida strain H8234, which was isolated from a hospital patient presenting with bacteremia. This strain has a single chromosome (6,870,827 bp) that contains 6,305 open reading frames. The strain is not a pathogen but exhibits multidrug resistance associated with 40 genomic islands. PMID:23868128

Bernal, Patricia; Udaondo, Zulema; Segura, Ana; Ramos, Juan-Luis

2013-01-01

196

Comparing Genomes of Helicobacter pylori Strains from the High-Altitude Desert of Ladakh, India  

Microsoft Academic Search

The genomic diversity of Helicobacter pylori from the vast Indian subcontinent is largely unknown. We compared the genomes of 10 H. pylori strains from Ladakh, North India. Molecular analysis was carried out to identify rearrangements within and outside the cag pathogenicity island (cag PAI) and DNA sequence divergence in candidate genes. Analyses of virulence genes (such as the cag PAI

Farhana Kauser; M. Abid Hussain; Irshad Ahmed; Naheed Ahmad; Aejaz Habeeb; Aleem A. Khan; Niyaz Ahmed

2005-01-01

197

Citrus Genomics  

PubMed Central

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

Talon, Manuel; Gmitter Jr., Fred G.

2008-01-01

198

Cotton Genomics  

Microsoft Academic Search

Cotton has a very narrow gene pool resulting from its evolutionary history, domestication, and modern crop improvement practices.\\u000a As a nonfood crop subject to many pests and diseases, cotton was among the first beneficiaries of genetic engineering, broadening\\u000a its gene pool with genes from other organisms. Accelerating progress in cotton genomics promises to increase knowledge, and\\u000a utilization, of the intrinsic

A. H. Paterson

199

Ancient genomics.  

PubMed

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

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

2015-01-19

200

Ancient genomics  

PubMed Central

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

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

2015-01-01

201

Genomic Avenue to Avian Colisepticemia  

PubMed Central

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

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

2015-01-01

202

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

PubMed Central

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

2011-01-01

203

Reunion Island Volcano Erupts  

NASA Technical Reports Server (NTRS)

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

2002-01-01

204

Galveston Island and erosion  

E-print Network

. VITA 73 74 80 85 97 101 115 LIST OF TABLES Table Page 1. Ai rphoto Scale Determination with the Aid of a Base Map . . 16 2. Actual-vs-l4easured Photo Scale and Resulting Error 3. Tropical Cyclones Affecting the Texas Coast from 1952...-1983 17 64 4. Projected Sea-level Rise 72 5. Potential Sand Sources and Sinks for Galveston Island . . . . 80 Al. Vegetation-line Changes on West Beach from July 3, 1977 to September 22, 1983; Impact of Recent Storm Events AZ. Changes...

Bolleter, Jim Mason

2012-06-07

205

Urban heat island  

NASA Technical Reports Server (NTRS)

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

Kim, Hongsuk H.

1991-01-01

206

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

PubMed Central

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

Böhle, U R; Hilger, H H; Martin, W F

1996-01-01

207

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

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

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

208

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

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

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

209

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

E-print Network

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

Minnesota, University of

210

Dermaptera of Niue Island, and material from the Cook Islands  

Microsoft Academic Search

The dermapteran faunas of Niue Island and the Cook Islands are composed entirely of cosmopolitan species. Niue I. has two species, Chelisoches morio and Euborellia annulipes (the latter is a new record). The Cook Is have three species—the two found on Niue, and Marava arachidis, which is a new record.

Logan Hudson

1974-01-01

211

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

PubMed

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

Robins, William P; Mekalanos, John J

2014-01-01

212

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

PubMed Central

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

Mekalanos, John J.

2014-01-01

213

Genome Characterization Centers  

Cancer.gov

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

214

Natural Selection and Random Genetic Drift as Causes of Evolution on Islands  

Microsoft Academic Search

The evolutionary processes responsible for adaptation and speciation on islands differ in several ways from those on the mainland. Most attention has been given to the random genetic drift that arises when a population is founded from just a few colonizing genomes. Theoretical obstacles to `founder effect speciation' are discussed, together with recent proposals for avoiding them. It is argued

N. H. Barton

1996-01-01

215

Genomic Evolution of 11 Type Strains within Family Planctomycetaceae  

PubMed Central

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

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

2014-01-01

216

Thematic Review Conservation of Biodiversity on Islands  

E-print Network

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

217

Richmond's Urban Heat Island  

NSDL National Science Digital Library

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

Yow, Donald M.

218

Murre Colony on Prince Island  

USGS Multimedia Gallery

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

219

Tidal Pool on Folly Island  

USGS Multimedia Gallery

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

220

Salt Marshes at Chincoteague Island  

USGS Multimedia Gallery

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

221

The Theory of Island Biogeography  

E-print Network

The Theory of Island Biogeography Robert H. MacArthur and Edward O. Wilson The young biologists" dominated by the collection of data. In The Theory of Island Biogeography they set out to change that by devel- oping a general mathema- tical theory that would make sense of a key ecological problem

Landweber, Laura

222

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

PubMed Central

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

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

2010-01-01

223

Roentgenologic aspects of bone islands.  

PubMed

A review of radiographs of 143 Adult Health Study and 46 non-sample subjects made over a period of 23 years established sites, sizes, ages at detection, and prevalence of 209 bone islands in 189 subjects. Except for 18 new bone islands, all appeared during the period of observation. Twenty-six of them changed: of these, 21 enlarged, 4 became smaller, and 1 disappeared. There was no association with atomic bomb radiation dose. Bone islands were more frequent in the pelvis and femora but often occurred in the ribs. Five bone islands in adolescents enlarged proportionally to bone growth, suggesting that they often participate metabolically in the normal osseous system. Bone islands must be differentiated from osteoblastic metastases. PMID:870936

Onitsuka, H

1977-06-01

224

Okhotskia: International Sakhalin Island Project  

NSDL National Science Digital Library

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

2010-05-12

225

Okhotskia: International Sakhalin Island Project  

NSDL National Science Digital Library

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

226

The Human Genome From human genome to other  

E-print Network

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

Linial, Michal

227

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

PubMed Central

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

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

2011-01-01

228

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

Microsoft Academic Search

Rhizobia are symbiotic nitrogen-fixing soil bacteria that are associated with host legumes. The establishment of rhizobial symbiosis requires signal exchanges between partners in microaerobic environments that result in mutualism for the two partners. We developed a macroarray for Mesorhizobium loti MAFF303099, a microsym- biont of the model legume Lotus japonicus, and monitored the transcriptional dynamics of the bacterium during symbiosis,

Toshiki Uchiumi; Takuji Ohwada; Manabu Itakura; Hisayuki Mitsui; Noriyuki Nukui; Pramod Dawadi; Takakazu Kaneko; Satoshi Tabata; Tadashi Yokoyama; Kouhei Tejima; Kazuhiko Saeki; Hirofumi Omori; Makoto Hayashi; Takaki Maekawa; Rutchadaporn Sriprang; Yoshikatsu Murooka; Shigeyuki Tajima; Kenshiro Simomura; Mika Nomura; Akihiro Suzuki; Yoshikazu Shimoda; Kouki Sioya; Mikiko Abe; Kiwamu Minamisawa

2004-01-01

229

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

PubMed

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

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

2014-07-01

230

An Island-Based Approach for Differential Expression Analysis  

PubMed Central

High-throughput mRNA sequencing (also known as RNA-Seq) promises to be the technique of choice for studying transcriptome profiles. This technique provides the ability to develop precise methodologies for transcript and gene expression quantification, novel transcript and exon discovery, and splice variant detection. One of the limitations of current RNA-Seq methods is the dependency on annotated biological features (e.g. exons, transcripts, genes) to detect expression differences across samples. This forces the identification of expression levels and the detection of significant changes to known genomic regions. Any significant changes that occur in unannotated regions will not be captured. To overcome this limitation, we developed a novel segmentation approach, Island-Based (IB), for analyzing differential expression in RNA-Seq and targeted sequencing (exome capture) data without specific knowledge of an isoform. The IB segmentation determines individual islands of expression based on windowed read counts that can be compared across experimental conditions to determine differential island expression. In order to detect differentially expressed genes, the significance of islands (p-values) are combined using Fisher’s method. We tested and evaluated the performance of our approach by comparing it to the existing differentially expressed gene (DEG) methods: CuffDiff, DESeq, and edgeR using two benchmark MAQC RNA-Seq datasets. The IB algorithm outperforms all three methods in both datasets as illustrated by an increased auROC.

Eteleeb, Abdallah M.; Flight, Robert M.; Harrison, Benjamin J.; Petruska, Jeffrey C.

2014-01-01

231

Reconstructing Austronesian population history in Island Southeast Asia  

PubMed Central

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

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

2014-01-01

232

Comparative genomics and transcriptomics of Propionibacterium acnes.  

PubMed

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

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

2011-01-01

233

Investigation of islands in stellarator designs.  

NASA Astrophysics Data System (ADS)

Islands are a crucial issue in designing stellarators such as NCSX. The presence of islands is associated with radial magnetic fields and results in poor plasma confinement. It is important to identify what is the physical cause of the islands, and whether the islands may be controlled using boundary perturbations, provided by trim coils. Computationally, equilibria with islands are calculated using PIES, and island widths and resonant perturbations may be determined. Analytic expressions of island width are used to identify the causes of island formation. Perturbations to the plasma boundary can be used in an attempt to manipulate island formation. A numerical procedure is described, and the results of island optimization are presented. By manipulating the phase of zero beta islands, self-healing effects are examined.

Hudson, S. R.; Monticello, D. A.; Reiman, A. H.

2000-10-01

234

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

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

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

235

The Populus Genome and Comparative Genomics  

Microsoft Academic Search

\\u000a \\u000a Populus was the first tree genome, and one of the first plant genomes, to be sequenced. The sequencing project and subsequent annotation\\u000a was a collaborative, international effort, with the bulk of the sequencing carried out by the US Department of Energy Joint\\u000a Genome Institute. Due to the high degree of sequence coverage, the hybrid BAC library-whole genome shotgun approach employed,

Carl J. Douglas; Stephen P. DiFazio

236

Extreme chromosomal heterogeneity in a small-island population of Rumex acetosa.  

PubMed

Chromosome analyses of 227 mature plants of the dioecious species Rumex acetosa collected on the small island of Skomer have revealed an extremely high level of unique and polymorphic variation. The three common polymorphisms in this species--supernumerary segments on chromosomes 1 and 6, and B-chromosomes--are widespread on the island and the frequency of supernumerary segment 1 is higher than in all 37 mainland populations previously studied. Novel variants, unknown elsewhere, occur in each polymorphism. Fourteen different chromosome rearrangements are unique to the island, and eleven of these were detected in 67 plants from a small area which had undergone a population crash in 1977. It is argued that the genome of R. acetosa is undergoing rapid reorganisation on this small island which may be associated with an enforced shift towards inbreeding in this dioecious species. PMID:2732084

Parker, J S; Wilby, A S

1989-02-01

237

Global Collembola on Deception Island.  

PubMed

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

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

2012-01-01

238

Global Collembola on Deception Island  

PubMed Central

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

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

2012-01-01

239

Metabolic Syndrome in a Metapopulation of Croatian Island Isolates  

PubMed Central

Aim To investigate the prevalence and factors associated with the metabolic syndrome in 9 isolated populations on Adriatic islands, Croatia, and in the group of immigrants to these islands. Methods Random samples of 100 inhabitants from each village and 101 immigrants were collected during 2002 and 2003. Bivariate and multivariate methods were used in data analysis. Age, gender, village, diet, smoking habits, physical activity, education, occupational class, and personal genetic history (a pedigree-based estimate of the individual genome-wide heterozygosity level) were used as independent variables in logistic regression. Results A total of 343 (34%) examinees met criteria of the metabolic syndrome diagnosis, with significant differences in the prevalence among villages (P?=?0.002). Metabolic syndrome was most frequently detected on Mljet island (53%), where all examinees exhibited fasting plasma glucose over 6.1 mmol/L. Examinees with metabolic syndrome were significantly older than those without it (median age 60.0 vs 53.0; P<0.001). Women were more frequently diagnosed than men (39% vs 28%; P<0.001). The highest prevalence of the metabolic syndrome was found in the autochthonous group, whereas the lowest proportion was recorded in the admixed group (39% vs 21%, respectively, P?=?0.017). However, only age (odds ratio [OR], 1.06; 95% confidence intervals [CI], 1.03-1.08) and having a university degree (OR, 0.18; 95% CI 0.04-0.92) were significantly associated with metabolic syndrome in the regression model. Conclusion Metabolic syndrome was not associated with pedigree-based individual genome-wide heterozygosity estimate, after controlling for a number of confounding factors. More precise marker based genomic measures are needed to provide a clear answer whether metabolic syndrome development is influenced by the population genetic structure. PMID:16909456

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

2006-01-01

240

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

SciTech Connect

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

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

2011-01-01

241

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

E-print Network

. The genome is divided by 21.2-kb inverted repeats into two single-copy regions of 80 kb and contains only 99The Plant Cell, Vol. 14, 2659­2679, November 2002, www.plantcell.org © 2002 American Society of Plant Biologists GENOMICS ARTICLE The Chlamydomonas reinhardtii Plastid Chromosome: Islands of Genes

dePamphilis, Claude

242

Islands of Adventure Notes from the Office  

E-print Network

Theme Park at the Universal Studios Orlando Resort. Islands of Adventure is a wonderful world of fantasyHighlights · Islands of Adventure · Notes from the Office · Birthdays · Manners TheELIWeekly Islands of Adventure Theme Park Fun This Saturday, February 7th, the ELI is headed to Islands of Adventure

Pilyugin, Sergei S.

243

Islands of Adventure New ELI Offices  

E-print Network

Highlights Islands of Adventure New ELI Offices Notes from the Office Manners, Culture, & Grammar TheELIWeekly Islands of Adventure Theme Park Fun! Islands of Adventure is a theme park in Orlando: The cost of transportation is $20 for a seat on the bus. Islands of Adventure tickets cost $92. What

Pilyugin, Sergei S.

244

Personal Genomics, Personalized Medicine,  

E-print Network

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

Napp, Nils

245

Turbulence in Coastal Fronts near the Mouths of Block Island and Long Island Sounds  

E-print Network

Turbulence in Coastal Fronts near the Mouths of Block Island and Long Island Sounds Edward R near the mouths of Block Island Sound (BIS) and Long Island Sound (LIS). These measurements extend from; Finestructure; Mixing processes; Coastal; Autonomous underwater vehicle; USA, New York, Long Island Sound; USA

Goodman, Louis

246

Eukaryotic genome size databases  

PubMed Central

Three independent databases of eukaryotic genome size information have been launched or re-released in updated form since 2005: the Plant DNA C-values Database (), the Animal Genome Size Database () and the Fungal Genome Size Database (). In total, these databases provide freely accessible genome size data for >10 000 species of eukaryotes assembled from more than 50 years' worth of literature. Such data are of significant importance to the genomics and broader scientific community as fundamental features of genome structure, for genomics-based comparative biodiversity studies, and as direct estimators of the cost of complete sequencing programs. PMID:17090588

Gregory, T. Ryan; Nicol, James A.; Tamm, Heidi; Kullman, Bellis; Kullman, Kaur; Leitch, Ilia J.; Murray, Brian G.; Kapraun, Donald F.; Greilhuber, Johann; Bennett, Michael D.

2007-01-01

247

Wild Ponies on Assateague Island  

USGS Multimedia Gallery

Wild ponies on Assateague Island. Wild ponies have lived on Assateague since the 1600s, although how they were introduced to Assateague is still debated. There are now around 300 or so wild ponies in Maryland and Virginia....

248

Oil Spill Threatens Galapagos Islands  

NSDL National Science Digital Library

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

De Nie, Michael W.

2001-01-01

249

Vanishing Island: Sea Level Rise  

NSDL National Science Digital Library

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

Halbert, Massy; Lyon, Jim; Yasutake, Mike; Lyon

250

Tsunami trapping near circular islands  

NASA Astrophysics Data System (ADS)

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

Tinti, Stefano; Vannini, Cesare

1995-09-01

251

Genomics and ornithology  

Microsoft Academic Search

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

Scott V. Edwards

2007-01-01

252

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

PubMed Central

Bacterial blight, caused by Pseudomonas savastanoi pv. glycinea (Psg), is a common disease of soybean. In an effort to compare a current field isolate with one isolated in the early 1960s, the genomes of two Psg strains, race 4 and B076, were sequenced using 454 pyrosequencing. The genomes of both Psg strains share more than 4,900 highly conserved genes, indicating very low genetic diversity between Psg genomes. Though conserved, genome rearrangements and recombination events occur commonly within the two Psg genomes. When compared to each other, 437 and 163 specific genes were identified in B076 and race 4, respectively. Most specific genes are plasmid-borne, indicating that acquisition and maintenance of plasmids may represent a major mechanism to change the genetic composition of the genome and even acquire new virulence factors. Type three secretion gene clusters of Psg strains are near identical with that of P. savastanoi pv. phaseolicola (Pph) strain 1448A and they shared 20 common effector genes. Furthermore, the coronatine biosynthetic cluster is present on a large plasmid in strain B076, but not in race 4. In silico subtractive hybridization-based comparative genomic analyses with nine sequenced phytopathogenic pseudomonads identified dozens of specific islands (SIs), and revealed that the genomes of Psg strains are more similar to those belonging to the same genomospecies such as Pph 1448A than to other phytopathogenic pseudomonads. The number of highly conserved genes (core genome) among them decreased dramatically when more genomes were included in the subtraction, suggesting the diversification of pseudomonads, and further indicating the genome heterogeneity among pseudomonads. However, the number of specific genes did not change significantly, suggesting these genes are indeed specific in Psg genomes. These results reinforce the idea of a species complex of P. syringae and support the reclassification of P. syringae into different species. PMID:21304594

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

2011-01-01

253

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

PubMed Central

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

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

2012-01-01

254

Habitat selection by South Island saddlebacks and Stewart Island robins reintroduced to Ulva Island  

E-print Network

Abstract: Determining whether animals select some habitats over others provides basic information about how animals meet their requirements for survival and reproduction. Habitat selection is therefore an important component of conservation research. Studies involving the release and establishment of threatened species on island refuges can be particularly insightful because breeding pairs should be able to select habitat of the highest quality within the range available. This study uses GIS technology to investigate the spatial distribution of breeding territories in relation to overall habitat availability of two threatened passerines, South Island saddlebacks (Philesturnus carunculatus carunculatus) and Stewart Island robins (Petroica australis rakiura) two years after their release onto predator-free Ulva Island. Both species established breeding territories around the periphery of the island in coastal forest fringe habitat and away from mature forest in the interior of the island. Compositional analysis suggested that both species prefer dense, fringe-type habitat with open ground cover and deep litter layers and avoid more mature forests, especially with moss cover. Thus habitat structure is likely to be more important for both species than plant-species composition. However, the possibility exists that the preference of coastal fringe habitat could represent an ‘ecological trap’, where habitat preference does not correspond to better quality habitat in terms of reproductive fitness. It will be useful to continue monitoring saddlebacks and robins to obtain data on survival and fecundity as the density of birds increases, and breeding

Kate E. Steffens; Philip J. Seddon; Renaud Mathieu; Ian G. Jamieson

255

Bryophytes from Simeonof Island in the Shumagin Islands, southwestern Alaska  

USGS Publications Warehouse

Simeonof Island is located south of the Alaska Peninsula in the hyperoceanic sector of the middle boreal subzone. We examined the bryoflora of Simeonof Island to determine species composition in an area where no previous collections had been reported. This field study was conducted in sites selected to represent the spectrum of environmental variation within Simeonof Island. Data were analyzed using published reports to compare bryophyte distribution patterns at three levels, the Northern Hemisphere, North America, and Alaska. A total of 271 bryophytes were identified: 202 mosses and 69 liverworts. The annotated list of species for Simeonof Island expands the known range for many species and fills distribution gaps within Hulte??n's Western Pacific Coast district. Maps and notes on the distribution of 14 significant distribution records are presented. Compared with bryophyte distribution in the Northern Hemisphere, the bryoflora of Simeonof Island primarily includes taxa of boreal (55%), temperate (20%), arctic (10%), and cosmopolitan (8%) distribution; 6% of the moss flora are western North America endemics. A description of the bryophytes present in the vegetation and habitat types is provided as is a quantitative analysis of the most frequently occurring bryophytes in crowberry heath.

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

2004-01-01

256

Genomic Encyclopedia of Fungi  

SciTech Connect

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.

Grigoriev, Igor

2012-08-10

257

JGI Fungal Genomics Program  

SciTech Connect

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

Grigoriev, Igor V.

2011-03-14

258

Treeline Dynamics on Southern Vancouver Island, British Columbia  

E-print Network

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

Smith, Dan

259

Bisulfite genomic sequencing of microdissected cells  

PubMed Central

Mapping of methylation patterns in CpG islands has become an important tool for understanding tissue-specific gene expression in both normal and pathological situations. However, the inherent cellular heterogeneity of any given tissues can affect the outcome and interpretation of molecular studies. In order to analyse genomic DNA methylation on a pure cell population from tissue sample, we have developed a simple technique of single-cell microdissection from cryostat sections which can be combined with bisulfite-mediated sequencing of 5-methylcytosine. We report here our results on the methylation status of the androgen receptor gene studied by bisulfite genomic sequencing on purified cells isolated from human testis. PMID:11691943

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

2001-01-01

260

Photosymbiotic ascidians from Pari Island (Thousand Islands, Indonesia)  

PubMed Central

Abstract Photosymbiotic ascidian fauna were surveyed in the subtidal zone off Pari Island in the Thousand Islands (Java Sea, Indonesia). Nine species were recorded: Didemnum molle, Trididemnum miniatum, Lissoclinum patella, L. punctatum, L. timorense, Diplosoma gumavirens, D. simile, D. simileguwa, and D. virens. All of these species have been previously recorded in the Ryukyu Archipelago, Japan. Diplosoma gumavirens and D. simileguwa were originally described from the Ryukyu Archipelago in 2009 and 2005, respectively, and all of the observed species are potentially widely distributed in Indo–West Pacific coral reefs. PMID:25061385

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

2014-01-01

261

Genomic evidence of geographically widespread effect of gene flow from polar bears into brown bears.  

PubMed

Polar bears are an arctic, marine adapted species that is closely related to brown bears. Genome analyses have shown that polar bears are distinct and genetically homogeneous in comparison to brown bears. However, these analyses have also revealed a remarkable episode of polar bear gene flow into the population of brown bears that colonized the Admiralty, Baranof, and Chichagof Islands (ABC Islands) of Alaska. Here, we present an analysis of data from a large panel of polar bear and brown bear genomes that includes brown bears from the ABC Islands, the Alaskan mainland and Europe. Our results provide clear evidence that gene flow between the two species had a geographically wide impact, with polar bear DNA found within the genomes of brown bears living both on the ABC Islands and in the Alaskan mainland. Intriguingly, while brown bear genomes contain up to 8.8% polar bear ancestry, polar bear genomes appear to be devoid of brown bear ancestry, suggesting the presence of a barrier to gene flow in that direction. This article is protected by copyright. All rights reserved. PMID:25490862

Cahill, James A; Stirling, Ian; Kistler, Logan; Salamzade, Rauf; Ersmark, Erik; Fulton, Tara L; Stiller, Mathias; Green, Richard E; Shapiro, Beth

2014-12-01

262

CG dinucleotide clustering is a species-specific property of the genome.  

PubMed

Cytosines at cytosine-guanine (CG) dinucleotides are the near-exclusive target of DNA methyltransferases in mammalian genomes. Spontaneous deamination of methylcytosine to thymine makes methylated cytosines unusually susceptible to mutation and consequent depletion. The loci where CG dinucleotides remain relatively enriched, presumably due to their unmethylated status during the germ cell cycle, have been referred to as CpG islands. Currently, CpG islands are solely defined by base compositional criteria, allowing annotation of any sequenced genome. Using a novel bioinformatic approach, we show that CG clusters can be identified as an inherent property of genomic sequence without imposing a base compositional a priori assumption. We also show that the CG clusters co-localize in the human genome with hypomethylated loci and annotated transcription start sites to a greater extent than annotations produced by prior CpG island definitions. Moreover, this new approach allows CG clusters to be identified in a species-specific manner, revealing a degree of orthologous conservation that is not revealed by current base compositional approaches. Finally, our approach is able to identify methylating genomes (such as Takifugu rubripes) that lack CG clustering entirely, in which it is inappropriate to annotate CpG islands or CG clusters. PMID:17932072

Glass, Jacob L; Thompson, Reid F; Khulan, Batbayar; Figueroa, Maria E; Olivier, Emmanuel N; Oakley, Erin J; Van Zant, Gary; Bouhassira, Eric E; Melnick, Ari; Golden, Aaron; Fazzari, Melissa J; Greally, John M

2007-01-01

263

Genome Instability in Lactobacillus rhamnosus GG  

PubMed Central

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

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

2013-01-01

264

Pacific Island Ecosystems Research Center  

NSDL National Science Digital Library

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

265

Atmospheric suspensions of Russky Island  

NASA Astrophysics Data System (ADS)

The paper presents the first in the history of observations the results of studying of atmospheric suspensions contained in snowpacks of Russian Island (Vladivostok) , including the territory of campus of the Far Eastern Federal University (seasons 2011/2012-2013/2014 years). The distribution of airborne particles of different sizes and different genesis in differ by anthropogenic load districts of the island is revealed: the Far Eastern Federal University campus , the bridge over the Eastern Bosphorus Strait and the village Kanal. It is shown that in connection with the increase of anthropogenic load on the Russian island , its ecological condition deteriorates due to the rise in the atmosphere fractions of nano-and micro-sized particles.

Golokhvast, Kirill S.; Nikiforov, P. A.; Chaika, V. V.

2014-11-01

266

Public Health Genomics (PHG)  

Cancer.gov

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

267

Islands, Reefs, and a Hotspot  

NSDL National Science Digital Library

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

Mel Goodwin

268

4. Photograph of a photograph in possession of Rock Island ...  

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

4. Photograph of a photograph in possession of Rock Island Arsenal Historical Office. NORTH ELEVATION IN UNALTERED CONDITION. DATED NOVEMBER 21, 1944. - Rock Island Arsenal, Building No. 109, Rodman Avenue & Fourth Street, Rock Island, Rock Island County, IL

269

3. Photograph of a photograph in possession of Rock Island ...  

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

3. Photograph of a photograph in possession of Rock Island Arsenal Historical Office. NORTH ELEVATION IN UNALTERED CONDITION. DATED NOVEMBER 21, 1944. - Rock Island Arsenal, Building No. 103, Rodman Avenue & First Street, Rock Island, Rock Island County, IL

270

10. Photograph of a photograph in possession of Rock Island ...  

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

10. Photograph of a photograph in possession of Rock Island Arsenal Historical Office. INTERIOR, LOOKING WEST. DATED OCTOBER 2, 1945. - Rock Island Arsenal, Building No. 138, Second Avenue between South Avenue & Ramsey Street, Rock Island, Rock Island County, IL

271

5. Photograph of a photograph in possession of Rock Island ...  

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

5. Photograph of a photograph in possession of Rock Island Arsenal Historical Office. WEST ELEVATION IN UNALTERED CONDITION. ORIGINALLY PUBLISHED 1898. - Rock Island Arsenal, Building No. 280, Sylvan Drive, Rock Island, Rock Island County, IL

272

11. Photograph of a photograph in possession of Rock Island ...  

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

11. Photograph of a photograph in possession of Rock Island Arsenal Historical Office. BASEMENT, SHOWING ORIGINAL OPEN INTERIOR PLAN. DATED APRIL 7, 1942. - Rock Island Arsenal, Building No. 56, North Avenue & East Avenue, Rock Island, Rock Island County, IL

273

7. Photograph of a photograph in possession of Rock Island ...  

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

7. Photograph of a photograph in possession of Rock Island Arsenal Historical Office. SOUTH AND EAST ELEVATIONS. DATED MARCH 19, 1945. - Rock Island Arsenal, Building No. 62, Rodman Avenue between First & Second Streets, Rock Island, Rock Island County, IL

274

5. Photograph of a photograph in possession of Rock Island ...  

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

5. Photograph of a photograph in possession of Rock Island Arsenal Historical Office. INTERIOR AFTER REMODELING INTO OFFICE SPACE. DATED FEBRUARY 13, 1943. - Rock Island Arsenal, Building No. 67, Rodman Avenue & Fourth Street, Rock Island, Rock Island County, IL

275

4. Photograph of a photograph in possession of Rock Island ...  

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

4. Photograph of a photograph in possession of Rock Island Arsenal Historical Office. NORTH AND WEST ELEVATIONS. DATED NOVEMBER 21, 1944. - Rock Island Arsenal, Building No. 108, Rodman Avenue between Third & Fourth Streets, Rock Island, Rock Island County, IL

276

9. Photograph of photograph in possession of Rock Island Arsenal ...  

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

9. Photograph of photograph in possession of Rock Island Arsenal Historical Office. WEST AND NORTH ELEVATIONS. ORIGINALLY PUBLISHED 1887. - Rock Island Arsenal, Building No. 90, East Avenue between North Avenue & King Drive, Rock Island, Rock Island County, IL

277

3. Photograph of a photograph in possession of Rock Island ...  

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

3. Photograph of a photograph in possession of Rock Island Arsenal Historical Office. SOUTH ELEVATION IN UNALTERED CONDITION. DATED MARCH 19, 1945. - Rock Island Arsenal, Building No. 61, Rodman Avenue & First Street, Rock Island, Rock Island County, IL

278

10. Photograph of a photograph in possession of Rock Island ...  

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

10. Photograph of a photograph in possession of Rock Island Arsenal Historical Office. SOUTH AND WEST ELEVATIONS IN UNALTERED CONDITION. DATED APRIL 18, 1941. - Rock Island Arsenal, Building No. 56, North Avenue & East Avenue, Rock Island, Rock Island County, IL

279

8. Photograph of a photograph in possession of Rock Island ...  

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

8. Photograph of a photograph in possession of Rock Island Arsenal Historical Office. SOUTH ELEVATON IN UNALTERED CONDITION. ORIGINALLY PUBLISHED 1898. - Rock Island Arsenal, Building No. 68, Rodman Avenue between Fourth Street & East Avenue, Rock Island, Rock Island County, IL

280

4. Photograph of a photograph in possession of Rock Island ...  

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

4. Photograph of a photograph in possession of Rock Island Arsenal Historical Office. LOOKING NORTH AFTER ADDITION OF CONICAL ROOF. ORIGINALLY PUBLISHED 1887. - Rock Island Arsenal, Building No. 53, North Avenue North of Midpoint, Rock Island, Rock Island County, IL

281

Island Bellwether: Climate Change and Energy Policy Strategy  

E-print Network

sustainable development planning to incorporate adaptation to climate change, sought greater scientifica) Island Bellwether: Climate Change and Energy Policy Strategy for Small Island Developing States #12;Island Bellwether: Climate Change and Energy Policy Strategy for Small Island Developing States

Delaware, University of

282

3. Light tower, view northwest, south side Ram Island ...  

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

3. Light tower, view northwest, south side - Ram Island Light Station, Ram Island, south of Ocean Point & just north of Fisherman Island, marking south side of Fisherman Island Passage, Ocean Point, Lincoln County, ME

283

WAKE ISLAND AIRFIELD TERMINAL, BUILDING 1502 LOOKING SOUTHEAST AT NORTHWEST ...  

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

WAKE ISLAND AIRFIELD TERMINAL, BUILDING 1502 LOOKING SOUTHEAST AT NORTHWEST FAÇADE AND BLAST WALL, DATE UNKNOWN - Wake Island Airfield, Terminal Building, West Side of Wake Avenue, Wake Island, Wake Island, UM

284

Evolutionary Genomics of the Nitrogen-Fixing Symbiotic Bacteria  

Microsoft Academic Search

Symbiotic bacteria, known as rhizobia, interact with the roots of leguminous plants and develop nitrogen-fixing nodules. In\\u000a this chapter, we will focus on the comparison of the complete genomes of Mesorhizobium loti, Sinorhizobium meliloti, Bradyrhizobium japonicum, Rhizobium leguminosarum, and Rhizobium etli. These bacteria contain the symbiosis genes in plasmids or chromosomal islands, perhaps as result of horizontal transfer.\\u000a The scattered

Víctor González; Luis Lozano; Santiago Castillo-Ramírez; Ismael Hernández González; Patricia Bustos; Rosa I. Santamaría; José L. Fernández; José L. Acosta; Guillermo Dávila

285

COMPARATIVE GENOMICS IN LEGUMES  

Technology Transfer Automated Retrieval System (TEKTRAN)

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

286

The human genome project  

SciTech Connect

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

Yager, T.D.; Zewert, T.E.; Hood, L.E. (California Institute of Technology, Pasadena, CA (United States))

1994-04-01

287

International milk genomics consortium  

E-print Network

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

Rocke, David M.

288

Genome BBiioollooggyy 2008, 99  

E-print Network

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

Weng, Zhiping

289

Profile: Native Hawaiians and Pacific Islanders  

MedlinePLUS

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

290

Mass Wasting in the Western Galapagos Islands  

E-print Network

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

Hall, Hillary

2012-10-19

291

LONG ISLAND SOUND STUDY CCMP, 1994  

EPA Science Inventory

The Comprehensive Conservation and Management Plan for Long Island Sound characterizes the priority problems affecting the Sound and identifies specific commitments and recommendations developed by the Long Island Sound Study (LISS) Management Conference. The CCMP provides a hist...

292

Obesity and Native Hawaiians/Pacific Islanders  

MedlinePLUS

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

293

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

PubMed Central

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

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

2014-01-01

294

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

PubMed

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

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

2014-01-01

295

Streamlined Islands in Ares Valles  

NASA Technical Reports Server (NTRS)

(Released 10 June 2002) The Science Although liquid water is not stable on the surface of Mars today, there is substantial geologic evidence that large quantities of water once flowed across the surface in the distant past. Streamlined islands, shown here, are one piece of evidence for this ancient water. The tremendous force of moving water, possibly from a catastrophic flood, carved these teardrop-shaped islands within a much larger channel called Ares Valles. The orientation of the islands can be used as an indicator of the direction the water flowed. The islands have a blunt end that is usually associated with an obstacle, commonly an impact crater. The crater is resistant to erosion and creates a geologic barrier around which the water must flow. As the water flows past the obstacle, its erosive power is directed outward, leaving the area in the lee of the obstacle relatively uneroded. However, some scientists have also argued that the area in the lee of the obstacle might be a depositional zone, where material is dropped out of the water as it briefly slows. The ridges observed on the high-standing terrain in the leeward parts of the islands may be benches carved into the rock that mark the height of the water at various times during the flood, or they might be indicative of layering in the leeward rock. As the water makes its way downstream, the interference of the water flow by the obstacle is reduced, and the water that was diverted around the obstacle rejoins itself at the narrow end of the island. Therefore, the direction of the water flow is parallel to the orientation of the island, and the narrow end of the island points downstream. In addition to the streamlined islands, the channel floor exhibits fluting that is also suggestive of flowing water. The flutes (also known as longitudinal grooves) are also parallel to the direction of flow, indicating that the water flow was turbulent and probably quite fast, which is consistent with the hypothesized catastrophic floods that came through Ares Valles. The Story In symbolism only, these guppy-shaped islands and current-like flutes of land beside them may conjure up a mental image of a flowing Martian river. This picture would only be half-right. Scientifically, no fish ever swam this channel, but these landforms do reveal that catastrophic floods of rushing water probably patterned the land in just this way. Geologists who study flood areas believe that a tremendous force of moving water probably carved both the islands and the small, parallel, 'current-like' ridges around them. The blunt end of the islands (the 'heads' of the 'fish') are probably ancient impact craters that posed obstacles to the water as it rushed down the channel in torrents. Because a crater is resistant to erosion, it creates a geologic barrier around which the water must flow. As the water makes its way downstream, the crater's interference with the water flow is reduced, so the water that was diverted around the obstacle rejoins at the narrow end of the island (the 'tail' of the 'fish'). Therefore, from this information, you can tell that the water flowed from the southeast to the northwest. As a rule of thumb for the future, you can say that the narrow end of the island points downstream. The result may be the island behind the crater, but geologists disagree about the exact process by which the island forms. Some scientists argue that the erosive power of the water is directed outward, leaving the area behind, or in the lee of, the obstacle relatively untouched. Other scientists argue that the water slows when it encounters the crater obstacle, and small particles of sand and 'dirt' drop out of the water and are deposited in the lee. There's another small associated uncertainty too. Look closely at the edges of the islands and notice how the land is terraced. These ledges might mark the height of the water at various times during the flood . . . or they might be an indication that layering occurred. It all depends on your hypothesis. Like the stream

2002-01-01

296

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

E-print Network

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

Luther, Douglas S.

297

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

E-print Network

created species­area curves from previously published lizard species richness and island area data. We islands. Keywords Lizards, spatial subsidies, small island effect, species­area curve, species richness species richness to deviate from species­area predictions, especially on small islands. Next, we examine

Wait, D. Alexander

298

Bathymetric constraints on the tectonic and volcanic evolution of Deception Island Volcano, South Shetland Islands  

E-print Network

basin situated behind the extinct South Shetland Islands arc. Deception Island has been well studied but its submerged flanks have not. A multibeam bathymetry survey was conducted around the island in 2005 Shetland island arc or of simple shear between the Scotia and Antarctic plates (Lawver et al. 1996, Barker

Wilcock, William

299

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

E-print Network

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

Kammen, Daniel M.

300

Genomes of marine cyanopodoviruses reveal multiple origins of diversity.  

PubMed

The marine cyanobacteria Prochlorococcus and Synechococcus are highly abundant in the global oceans, as are the cyanophage with which they co-evolve. While genomic analyses have been relatively extensive for cyanomyoviruses, only three cyanopodoviruses isolated on marine cyanobacteria have been sequenced. Here we present nine new cyanopodovirus genomes, and analyse them in the context of the broader group. The genomes range from 42.2 to 47.7 kb, with G+C contents consistent with those of their hosts. They share 12 core genes, and the pan-genome is not close to being fully sampled. The genomes contain three variable island regions, with the most hypervariable genes concentrated at one end of the genome. Concatenated core-gene phylogeny clusters all but one of the phage into three distinct groups (MPP-A and two discrete clades within MPP-B). The outlier, P-RSP2, has the smallest genome and lacks RNA polymerase, a hallmark of the Autographivirinae subfamily. The phage in group MPP-B contain photosynthesis and carbon metabolism associated genes, while group MPP-A and the outlier P-RSP2 do not, suggesting different constraints on their lytic cycles. Four of the phage encode integrases and three have a host integration signature. Metagenomic analyses reveal that cyanopodoviruses may be more abundant in the oceans than previously thought. PMID:23320838

Labrie, S J; Frois-Moniz, K; Osburne, M S; Kelly, L; Roggensack, S E; Sullivan, M B; Gearin, G; Zeng, Q; Fitzgerald, M; Henn, M R; Chisholm, S W

2013-05-01

301

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

Code of Federal Regulations, 2012 CFR

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

2012-07-01

302

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

Code of Federal Regulations, 2013 CFR

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

2013-07-01

303

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

Code of Federal Regulations, 2014 CFR

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

2014-07-01

304

JASON Project: Flying over the Channel Islands  

NSDL National Science Digital Library

By using Landsat-7-ETM+ data and USGS DEM Elevation data, we are able to take a virtual tour of the Channel Islands and the coast of California. For more information on the Channel Islands, please visit (http:--www.channel.islands.national-park.com).

Stuart Snodgrass

2003-01-09

305

Islands of Adventure Notes from the Office  

E-print Network

ELIWeekly Islands of Adventure Theme Park Fun! On Saturday, September 15th, we will be headed to Universal StudiosHighlights · Islands of Adventure · Notes from the Office · Birthdays · Manners The' Islands of Adventure. We will meet at the TRiP office in Reitz Union at 8:00am. We will return

Pilyugin, Sergei S.

306

ANNUAL FISH PASSAGE REPORT ROCK ISLAND DAM  

E-print Network

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

307

Island-finding ability of marine turtles  

E-print Network

, Lund University, Ecology Building, SE-223 62 Lund, Sweden 3 Dipartimento di Etologia, Ecologia grounds along the Brazilian coast to Ascension Island to nest, over 2200 km distant in the middle the fate of the early pilots flying to Ascension Island, a remote island in the middle of the Atlantic

Hays, Graeme

308

Past, Present, Future Erosion at Locke Island  

SciTech Connect

This report describes and documents the erosion that has occurred along the northeast side of Locke Island over the last 10 to 20 years. The principal cause of this erosion is the massive Locke Island landslide complex opposite the Columbia River along the White Bluffs, which constricts the flow of the river and deflects the river's thalweg southward against the island.

Bjornstad, Bruce N.

2006-08-08

309

Strategies for detecting genomic DNA methylation: a survey of US patents.  

PubMed

DNA methylation is one of the mechanisms for the epigenetic control of gene expression. Alterations in the methylation status of genomic DNA can result in the silencing of genes. Such control is of significance for a wide range of biological processes, ranging from cellular differentiation during development, genomic imprinting and X-chromosome inactivation to the maintenance of genome stability. The cytosine in the genomic DNA is converted to 5-methylcytosine. The hypermethylation of some CpG islands in genomic DNA could result in gene silencing and hypomethylation can lead to transcription and gene expression. There has been a great interest in developing molecular techniques to analyze genomic DNA methylation at the CpG islands. The discovery that DNA treatment with sodium bisulfite converts the cytosine to uracil while keeping the 5-methycytosine intact has opened the door to a number of strategies to investigate genomic DNA methylation both at regional and global levels. A survey of recently patented methods to analyze DNA methylation indicated a range of inventions from simple PCR to high throughput based technologies. The disease diagnosis was the prominent application of DNA methylation detection for most of these methods. Future inventions will likely concentrate on genome-scale DNA methylation discovery. PMID:20426762

Chaudhry, M Ahmad

2010-06-01

310

Birds are islands for parasites.  

PubMed

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

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

2014-08-01

311

HISTORIC WETLANDS OF PRUDENCE ISLAND  

EPA Science Inventory

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

312

Destination: Marshall Islands. Video Guide.  

ERIC Educational Resources Information Center

This video guide was developed by the Peace Corps' Office of World Wise Schools. Activities that the guide describes are for use in a 3- to 5-day unit on one of the nations of Oceania, the Republic of the Marshall Islands. The activities are designed to provide students with opportunities to: (1) compare and contrast Marshallese and U.S. culture;…

Legowski, Margaret

313

Long Island Sound Resource Center  

NSDL National Science Digital Library

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

314

On a Crowded Desert Island.  

ERIC Educational Resources Information Center

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

Rothstein, Samuel

1989-01-01

315

ANTHROPOLOGY 343 PACIFIC ISLANDS ARCHAEOLOGY  

E-print Network

process more than 50,000 years ago. The subsequent cultural patterns of adaptation to life on remote adaptations made by peoples moving into the Pacific and for clarifying their relationships to complex cultures and historic to contemporary island peoples, including issues of cultural resource management will be explored

316

Island Explorers Marine Science Program  

NSDL National Science Digital Library

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

317

Microbial genomic taxonomy  

PubMed Central

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

2013-01-01

318

GenomeBlast: a web tool for small genome comparison  

PubMed Central

Background Comparative genomics has become an essential approach for identifying homologous gene candidates and their functions, and for studying genome evolution. There are many tools available for genome comparisons. Unfortunately, most of them are not applicable for the identification of unique genes and the inference of phylogenetic relationships in a given set of genomes. Results GenomeBlast is a Web tool developed for comparative analysis of multiple small genomes. A new parameter called "coverage" was introduced and used along with sequence identity to evaluate global similarity between genes. With GenomeBlast, the following results can be obtained: (1) unique genes in each genome; (2) homologous gene candidates among compared genomes; (3) 2D plots of homologous gene candidates along the all pairwise genome comparisons; and (4) a table of gene presence/absence information and a genome phylogeny. We demonstrated the functions in GenomeBlast with an example of multiple herpesviral genome analysis and illustrated how GenomeBlast is useful for small genome comparison. Conclusion We developed a Web tool for comparative analysis of small genomes, which allows the user not only to identify unique genes and homologous gene candidates among multiple genomes, but also to view their graphical distributions on genomes, and to reconstruct genome phylogeny. GenomeBlast runs on a Linux server with 4 CPUs and 4 GB memory. The online version of GenomeBlast is available to public by using a Web browser with the URL . PMID:17217510

Lu, Guoqing; Jiang, Liying; Helikar, Resa MK; Rowley, Thaine W; Zhang, Luwen; Chen, Xianfeng; Moriyama, Etsuko N

2006-01-01

319

Polar Bears International: Wrangel Island, Russia  

NSDL National Science Digital Library

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

320

Polar Bears International : Wrangel Island, Russia  

NSDL National Science Digital Library

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

2007-12-12

321

Barrier island bistability induced by biophysical interactions  

NASA Astrophysics Data System (ADS)

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

Durán Vinent, Orencio; Moore, Laura J.

2015-02-01

322

Alternative energy technologies for the Caribbean islands  

SciTech Connect

All islands in the Caribbean except Puerto Rico can be classified as developing islands. Of these islands, all except Trinidad and Tobago are oil importers. Uncertainties concerning uninterrupted oil supply and increasing oil prices causes economic, social and political instability and jeopardizes further development of these islands. The paper discusses the energy situation of the Caribbean islands and presents alternative energy options. Several alternative energy projects financed by local, federal and international organizations are presented. Present and future uses of alternative energy technologies are described in different islands. Barrier which handicap developing and implementing alternative energy sources in the Caribbean are discussed. The potential and possible applications of alternative energy technologies such as: solar-thermal energy, photovoltaics, wind energy, ocean thermal energy conversion (OTEC), ocean currents and tides energy, biomass, peat energy, municipal solid wastes, bioconversion, hydropower, geothermal energy, nuclear energy and energy conservation are discussed in detail as means to alleviate the energy situation in the Caribbean islands.

Pytlinski, J.T. (Univ. of Puerto Rico, San Juan (Puerto Rico))

1992-01-01

323

Island-finding ability of marine turtles.  

PubMed Central

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

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

2003-01-01

324

HeteroGenome: database of genome periodicity.  

PubMed

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

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

2014-01-01

325

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

E-print Network

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

Smith, Jennifer E.

326

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

PubMed Central

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

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

2014-01-01

327

Fuzzy Genome Sequence Assembly for Single and Environmental Genomes  

E-print Network

Fuzzy Genome Sequence Assembly for Single and Environmental Genomes Sara Nasser, Adrienne Breland for multiple genome sequence assembly of cultured genomes (single organism) and environmental genomes (multiple DNA is the building block of all life on this planet, from single cell micro- scopic bacteria to more

Nicolescu, Monica

328

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

Code of Federal Regulations, 2011 CFR

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

2011-04-01

329

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

Code of Federal Regulations, 2012 CFR

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

2012-04-01

330

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

Code of Federal Regulations, 2013 CFR

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

2013-04-01

331

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

Code of Federal Regulations, 2010 CFR

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

2010-04-01

332

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

Code of Federal Regulations, 2014 CFR

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

2014-04-01

333

DNA methylation study of fetus genome through a genome-wide analysis  

PubMed Central

Background DNA methylation is a crucial epigenetic modification of the genome which is involved in embryonic development, transcription, chromatin structure, X chromosome inactivation, genomic imprinting and chromosome stability. Consistent with these important roles, DNA methylation has been demonstrated to be required for vertebrate early embryogenesis and essential for regulating temporal and spatial expression of genes controlling cell fate and differentiation. Further studies have shown that abnormal DNA methylation is associated with human diseases including the embryonic development diseases. We attempt to study the DNA methylation status of CpG islands in fetus related to fetus growth and development. Methods GeneChip® Human Tiling 2.0R Array set is used for analysis of methylated DNA in a whole-genome wide in 8 pairs amniotic fluid and maternal blood DNA samples. Results We found 1 fetus hypermethylation DNA markers and 4 fetus hypomethylation DNA markers though a Genome-wide analysis. These DNA markers all found to be associated with the critical genes for fetus growth and development (SH2D3C gene, EML3 gene, TRIM71 gene, HOXA3 gene and HOXA5 gene). Conclusions These genes can be used as a biomarker for association studying of embryonic development, pathological pregnancy and so on. The present study has provided new and fundamental insights into the roles that DNA methylation has in embryonic development and in the pathological pregnancy. PMID:24731722

2014-01-01

334

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

PubMed Central

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. PMID:19038058

Han, Haihong; Wong, Hin-chung; Kan, Biao; Guo, Zhaobiao; Zeng, Xiaotao; Yin, Shengjun; Liu, Xiumei; Yang, Ruifu; Zhou, Dongsheng

2008-01-01

335

Pine Island Glacier Calving (WMS)  

NSDL National Science Digital Library

The Pine Island Glacier is the largest discharger of ice in Antarctica and the continents fastest moving glacier. Even so, when a large crack formed across the glacier in mid 2000, it was surprising how fast the crack expanded, 15 meters per day, and how soon the resulting iceberg broke off, mid-November, 2001. This iceberg, called B-21, is 42 kilometers by 17 kilometers and contains seven years of glacier outflow released to the sea in a single event. This series of images from the MISR instrument on the Terra satellite not only shows the crack expanding and the iceberg breakoff, but the seaward moving glacial flow in the parts of the Pine Island Glacier upstream of the crack.

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

2005-03-09

336

Okhotskia: International Kuril Island Project  

NSDL National Science Digital Library

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

337

Genomics of Sorghum  

PubMed Central

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

Paterson, Andrew H.

2008-01-01

338

Genome sequence of the ?-rhizobium Cupriavidus taiwanensis and comparative genomics of rhizobia  

PubMed Central

We report the first complete genome sequence of a ?-proteobacterial nitrogen-fixing symbiont of legumes, Cupriavidus taiwanensis LMG19424. The genome consists of two chromosomes of size 3.42 Mb and 2.50 Mb, and a large symbiotic plasmid of 0.56 Mb. The C. taiwanensis genome displays an unexpected high similarity with the genome of the saprophytic bacterium C. eutrophus H16, despite being 0.94 Mb smaller. Both organisms harbor two chromosomes with large regions of synteny interspersed by specific regions. In contrast, the two species host highly divergent plasmids, with the consequence that C. taiwanensis is symbiotically proficient and less metabolically versatile. Altogether, specific regions in C. taiwanensis compared with C. eutrophus cover 1.02 Mb and are enriched in genes associated with symbiosis or virulence in other bacteria. C. taiwanensis reveals characteristics of a minimal rhizobium, including the most compact (35-kb) symbiotic island (nod and nif) identified so far in any rhizobium. The atypical phylogenetic position of C. taiwanensis allowed insightful comparative genomics of all available rhizobium genomes. We did not find any gene that was both common and specific to all rhizobia, thus suggesting that a unique shared genetic strategy does not support symbiosis of rhizobia with legumes. Instead, phylodistribution analysis of more than 200 Sinorhizobium meliloti known symbiotic genes indicated large and complex variations of their occurrence in rhizobia and non-rhizobia. This led us to devise an in silico method to extract genes preferentially associated with rhizobia. We discuss how the novel genes we have identified may contribute to symbiotic adaptation. PMID:18490699

Amadou, Claire; Pascal, Géraldine; Mangenot, Sophie; Glew, Michelle; Bontemps, Cyril; Capela, Delphine; Carrčre, Sébastien; Cruveiller, Stéphane; Dossat, Carole; Lajus, Aurélie; Marchetti, Marta; Poinsot, Véréna; Rouy, Zoé; Servin, Bertrand; Saad, Maged; Schenowitz, Chantal; Barbe, Valérie; Batut, Jacques; Médigue, Claudine; Masson-Boivin, Catherine

2008-01-01

339

Urban Heat Islands: Hotter Cities  

NSDL National Science Digital Library

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

Urban Heat Islands (University of Western Ontario;)

2004-11-01

340

Climate Change in Small Islands  

NASA Astrophysics Data System (ADS)

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

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

2014-05-01

341

Flora of the Marquesas Islands  

NSDL National Science Digital Library

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

342

[Novel bidirectional promoter from human genome].  

PubMed

In human and other mammalian genomes a number of closely linked gene pairs transcribed in opposite directions are found. According to bioinformatic analysis up to 10% of human genes are arranged in this way. In present work the fragment of human genome was cloned that separates genes localized at 2p13.1 and oriented "head-to-head", coding for hypothetical proteins with unknown functions--CCDC (Coiled Coil Domain Containing) 142 and TTC (TetraTricopeptide repeat Containing) 31. Intergenic CCDC142-TTC31 region overlaps with CpG-island and contains a number of potential binding sites for transcription factors. This fragment functions as bidirectional promoter in the system ofluciferase reporter gene expression upon transfection of human embryonic kidney (HEK293) cells. The vectors containing genes of two fluorescent proteins--green (EGFP) and red (DsRed2) in opposite orientations separated by the fragment of CCDC142-TTC31 intergenic region were constructed. In HEK293 cells transfected with these vectors simultaneous expression of two fluorescent proteins is observed. Truncated versions of intergenic region were obtained and their promoter activity measured. Minimal promoter fragment contains elements Inr, BRE, DPE characteristic for TATA-less promoters. Thus, from the human genome the novel bidirectional promoter was cloned that can be used for simultaneous constitutive expression of two genes in human cells. PMID:21790010

Orekhova, A S; Sverdlova, P S; Spirin, P V; Leonova, O G; Popenko, V I; Prasolov, V S; Rubtsov, P M

2011-01-01

343

Meeting highlights: genome informatics.  

PubMed

We bring you the highlights of the second Joint Cold Spring Harbor Laboratory and Wellcome Trust 'Genome Informatics' Conference, organized by Ewan Birney, Suzanna Lewis and Lincoln Stein. There were sessions on in silico data discovery, comparative genomics, annotation pipelines, functional genomics and integrative biology. The conference included a keynote address by Sydney Brenner, who was awarded the 2002 Nobel Prize in Physiology or Medicine (jointly with John Sulston and H. Robert Horvitz) a month later. PMID:18629014

Wixon, Jo; Ashurst, Jennifer

2003-01-01

344

The Genomic Data Mine  

Microsoft Academic Search

The genomic data mine represents a fundamental shift from genetics to genomics, essentially from the study of one gene at\\u000a a time to the study of entire genetic metabolic networks and whole genomes. Experimental laboratory data are deposited into\\u000a large public repositories and a wealth of computational data mining algorithms and tools are applied to mine the data. The\\u000a integration

Lorraine Tanabe

345

Planning the Genome Institute's Future  

E-print Network

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

Botstein, David

346

Fungal Genomics Program  

SciTech Connect

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

Grigoriev, Igor

2012-03-12

347

Genome@home  

NSDL National Science Digital Library

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

348

The Geee! in Genome  

NSDL National Science Digital Library

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

349

Between two fern genomes.  

PubMed

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

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

2014-01-01

350

Tsunami damage along the Andaman Islands coasts  

NASA Technical Reports Server (NTRS)

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

2005-01-01

351

Extensive linkage disequilibrium and parallel adaptive divergence across threespine stickleback genomes  

PubMed Central

Population genomic studies are beginning to provide a more comprehensive view of dynamic genome-scale processes in evolution. Patterns of genomic architecture, such as genomic islands of increased divergence, may be important for adaptive population differentiation and speciation. We used next-generation sequencing data to examine the patterns of local and long-distance linkage disequilibrium (LD) across oceanic and freshwater populations of threespine stickleback, a useful model for studies of evolution and speciation. We looked for associations between LD and signatures of divergent selection, and assessed the role of recombination rate variation in generating LD patterns. As predicted under the traditional biogeographic model of unidirectional gene flow from ancestral oceanic to derived freshwater stickleback populations, we found extensive local and long-distance LD in fresh water. Surprisingly, oceanic populations showed similar patterns of elevated LD, notably between large genomic regions previously implicated in adaptation to fresh water. These results support an alternative biogeographic model for the stickleback radiation, one of a metapopulation with appreciable bi-directional gene flow combined with strong divergent selection between oceanic and freshwater populations. As predicted by theory, these processes can maintain LD within and among genomic islands of divergence. These findings suggest that the genomic architecture in oceanic stickleback populations may provide a mechanism for the rapid re-assembly and evolution of multi-locus genotypes in newly colonized freshwater habitats, and may help explain genetic mapping of parallel phenotypic variation to similar loci across independent freshwater populations. PMID:22201169

Hohenlohe, Paul A.; Bassham, Susan; Currey, Mark; Cresko, William A.

2012-01-01

352

Circulation around a thin zonal island  

NASA Astrophysics Data System (ADS)

Laboratory and numerical experiments are used to study flow of a uniform-density fluid on the [beta]-plane around a thin zonally elongated island (or ridge segment in the abyss). This orientation is chosen specifically to highlight the roles of the zonal boundary layer dynamics in controlling the circulation around the island. There are examples of deep ocean topography that fall into this category which make the work directly applicable to oceanic flows. Linear theory for the transport around the island and the flow structure is based on a modification of the Island Rule (Pedlosky et al. 1997; Pratt & Pedlosky 1999). The linear solution gives a north south symmetric flow around the island with novel features, including stagnation points which divide the zonal boundary layers into eastward and westward flowing zones, and a western boundary layer of vanishing length, and zonal jets. Laboratory experiments agree with the linear theory for small degrees of nonlinearity, as measured by the ratio of the inertial to Munk boundary layer scales. With increasing nonlinearity the north south symmetry is broken. The southern stagnation point (for anticyclonic forcing) moves to the eastern tip of the island. The flow rounding the eastern tip from the northern side of the island now separates from the island. Time-dependence emerges and recirculation cells develop on the northern side of the island. Mean transport around the island is relatively unaffected by nonlinearity and given to within 20% by the modified Island Rule. Numerical solutions of the shallow water equations are in close agreement with the laboratory results. The transition from zonal to meridional island orientation occurs for island inclinations from zonal greater than about 20°.

Wells, J. R.; Helfrich, K. R.

2001-06-01

353

Brief Guide to Genomics: DNA, Genes and Genomes  

MedlinePLUS

... Human Genome Project A Brief Guide to Genomics DNA, Genes and Genomes Deoxyribonucleic acid (DNA) is the ... and lead to a disease such as cancer. DNA Sequencing Sequencing simply means determining the exact order ...

354

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

PubMed Central

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

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

2013-01-01

355

Genetic research and aboriginal and Torres Strait Islander Australians.  

PubMed

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

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

2012-12-01

356

Complete genome sequence of Mesorhizobium australicum type strain (WSM2073T)  

PubMed Central

Mesorhizobium australicum strain WSM2073T was isolated from root nodules on the pasture legume Biserrula pelecinus growing in Australia in 2000. This aerobic, motile, gram negative, non-spore-forming rod is poorly effective in N2 fixation on B. pelecinus and has gained the ability to nodulate B. pelecinus following in situ lateral transfer of a symbiosis island from the original inoculant strain for this legume, Mesorhizobium ciceri bv. biserrulae WSM1271. We describe that the genome size of M. australicum strain WSM2073T is 6,200,534 bp encoding 6,013 protein-coding genes and 67 RNA-only encoding genes. This genome does not contain any plasmids but has a 455.7 kb genomic island from Mesorhizobium ciceri bv. biserrulae WSM1271 that has been integrated into a phenylalanine-tRNA gene. PMID:24976896

Nandasena, Kemanthi; Yates, Ron; Tiwari, Ravi; O’Hara, Graham; Ninawi, Mohamed; Gu, Wei; Goodwin, Lynne; Detter, Chris; Tapia, Roxanne; Han, Cliff; Copeland, Alex; Liolios, Konstantinos; Chen, Amy; Markowitz, Victor; Pati, Amrita; Mavromatis, Konstantinos; Woyke, Tanja; Kyrpides, Nikos; Ivanova, Natalia; Howieson, John

2013-01-01

357

Genomic analysis of mouse tumorigenesis  

E-print Network

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

Tam, Mandy Chi-Mun

2006-01-01

358

FUNCTIONAL GENOMICS Program of Study  

E-print Network

FUNCTIONAL GENOMICS Program of Study Research Areas Students Applying Correspondence Graduate Genomics. Students receive training in the biological, physical and computational sciences through of primary institutional affiliation. The Functional Genomics program is administered through the Graduate

Thomas, Andrew

359

The Future of Microbial Genomics  

SciTech Connect

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

Kyrpides, Nikos [Genome Biology group at the DOE Joint Genome Institute

2010-06-02

360

The Cancer Genome Atlas (TCGA)  

Cancer.gov

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

361

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

PubMed Central

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

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

2012-01-01

362

Molluscan fauna of Gueishan Island, Taiwan.  

PubMed

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

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

2013-01-01

363

A signature for turbulence driven magnetic islands  

SciTech Connect

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

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

2014-09-15

364

75 FR 28643 - Pine Island, Matlacha Pass, Island Bay, and Caloosahatchee National Wildlife Refuges, Lee and...  

Federal Register 2010, 2011, 2012, 2013, 2014

...DEPARTMENT OF THE INTERIOR Fish and Wildlife Service [FWS-R4-R-2010-N051...Pine Island, Matlacha Pass, Island Bay, and Caloosahatchee National Wildlife Refuges, Lee and Charlotte Counties, FL AGENCY: Fish and...

2010-05-21

365

46 CFR 7.70 - Folly Island, SC to Hilton Head Island, SC.  

Code of Federal Regulations, 2013 CFR

...19.2? W. across St. Helena Sound to the abandoned lighthouse tower on Hunting Island charted in approximate position latitude...26.5? W. (d) A line drawn from the abandoned lighthouse on Hunting Island in approximate position latitude...

2013-10-01

366

46 CFR 7.70 - Folly Island, SC to Hilton Head Island, SC.  

Code of Federal Regulations, 2012 CFR

...19.2? W. across St. Helena Sound to the abandoned lighthouse tower on Hunting Island charted in approximate position latitude...26.5? W. (d) A line drawn from the abandoned lighthouse on Hunting Island in approximate position latitude...

2012-10-01

367

33 CFR 80.712 - Morris Island, SC to Hilton Head Island, SC.  

Code of Federal Regulations, 2012 CFR

...easternmost tip of Folley Island to the abandoned lighthouse tower on the northside of Lighthouse Inlet; thence west to the shoreline of Morris...across St. Helena Sound to the abandoned lighthouse tower on Hunting Island. (e) A...

2012-07-01

368

46 CFR 7.70 - Folly Island, SC to Hilton Head Island, SC.  

Code of Federal Regulations, 2014 CFR

...19.2? W. across St. Helena Sound to the abandoned lighthouse tower on Hunting Island charted in approximate position latitude...26.5? W. (d) A line drawn from the abandoned lighthouse on Hunting Island in approximate position latitude...

2014-10-01

369

Mobile genetic elements in the genome of the beneficial rhizobacterium Pseudomonas fluorescens Pf-5  

PubMed Central

Background Pseudomonas fluorescens Pf-5 is a plant-associated bacterium that inhabits the rhizosphere of a wide variety of plant species and and produces secondary metabolites suppressive of fungal and oomycete plant pathogens. The Pf-5 genome is rich in features consistent with its commensal lifestyle, and its sequence has revealed attributes associated with the strain's ability to compete and survive in the dynamic and microbiologically complex rhizosphere habitat. In this study, we analyzed mobile genetic elements of the Pf-5 genome in an effort to identify determinants that might contribute to Pf-5's ability to adapt to changing environmental conditions and/or colonize new ecological niches. Results Sequence analyses revealed that the genome of Pf-5 is devoid of transposons and IS elements and that mobile genetic elements (MGEs) are represented by prophages and genomic islands that collectively span over 260 kb. The prophages include an F-pyocin-like prophage 01, a chimeric prophage 03, a lambdoid prophage 06, and decaying prophages 02, 04 and 05 with reduced size and/or complexity. The genomic islands are represented by a 115-kb integrative conjugative element (ICE) PFGI-1, which shares plasmid replication, recombination, and conjugative transfer genes with those from ICEs found in other Pseudomonas spp., and PFGI-2, which resembles a portion of pathogenicity islands in the genomes of the plant pathogens Pseudomonas syringae and P. viridiflava. Almost all of the MGEs in the Pf-5 genome are associated with phage-like integrase genes and are integrated into tRNA genes. Conclusion Comparative analyses reveal that MGEs found in Pf-5 are subject to extensive recombination and have evolved in part via exchange of genetic material with other Pseudomonas spp. having commensal or pathogenic relationships with plants and animals. Although prophages and genomic islands from Pf-5 exhibit similarity to MGEs found in other Pseudomonas spp., they also carry a number of putative niche-specific genes that could affect the survival of P. fluorescens Pf-5 in natural habitats. Most notable are a ~35-kb segment of "cargo" genes in genomic island PFGI-1 and bacteriocin genes associated with prophages 1 and 4. PMID:19144133

2009-01-01

370

The Beetles of the Virgin Islands  

NSDL National Science Digital Library

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

371

Unlocking the bovine genome  

Technology Transfer Automated Retrieval System (TEKTRAN)

The draft genome sequence of cattle (Bos taurus) has now been analyzed by the Bovine Genome Sequencing and Analysis Consortium and the Bovine HapMap Consortium, which together represent an extensive collaboration involving more than 300 scientists from 25 different countries. ...

372

Human genome I  

SciTech Connect

An international conference, Human Genome I, was held Oct. 2-4, 1989 in San Diego, Calif. Selected speakers discussed: Current Status of the Genome Project; Technique Innovations; Interesting regions; Applications; and Organization - Different Views of Current and Future Science and Procedures. Posters, consisting of 119 presentations, were displayed during the sessions. 119 were indexed for inclusion to the Energy Data Base.

Not Available

1989-01-01

373

Molluscan Evolutionary Genomics  

Microsoft Academic Search

In the last 20 years there have been dramatic advances in techniques of high-throughput DNA sequencing, most recently accelerated by the Human Genome Project, a program that has determined the three billion base pair code on which we are based. Now this tremendous capability is being directed at other genome targets that are being sampled across the broad range of

W. Brian Simison; Jeffrey L. Boore

2005-01-01

374

Plant Functional Genomics  

NSDL National Science Digital Library

Nucleotide sequencing of the Arabidopsis genome is nearing completion, sequencing of the rice genome has begun, and large amounts of expressed sequence tag information are being obtained for many other plants. There are many opportunities to use this wealth of sequence information to accelerate progress toward a comprehensive understanding of the genetic mechanisms that control plant growth and development and responses to the environment.

Chris Somerville (Carnegie Institution of Washington;Department of Plant Biology); Shauna Somerville (Carnegie Institution of Washington;Department of Plant Biology)

1999-07-16

375

China: Public Health Genomics  

Microsoft Academic Search

China is a multicultural country that has arisen from its 56 ethnicities, with a diverse population of over 1.3 billion people and an imbalanced economic development. The health care system in China is tending to be overall funded through urban and rural health insurance plans. Although China has invested in the basic research of genome science, public health genomics-related programs

S. Zheng; M. Song; L. Wu; S. Yang; J. Shen; X. Lu; J. Du; W. Wang

2010-01-01

376

Single-cell genomics  

Microsoft Academic Search

Methods for genomic analysis at single-cell resolution enable new understanding of complex biological phenomena. Single-cell techniques, ranging from flow cytometry and microfluidics to PCR and sequencing, are used to understand the cellular composition of complex tissues, find new microbial species and perform genome-wide haplotyping.

Tomer Kalisky; Stephen R Quake

2011-01-01

377

Single-cell genomics  

Microsoft Academic Search

Efforts to describe and functionally categorize the amazing diversity of microbial life have long been hampered by our inability to cultivate most microorganisms in the laboratory. Recent technological advances in whole-genome amplification and cell sorting now permit insights into previously uncharacterized microorganisms, without prior cultivation. This month's Genome Watch reviews a selection of the initial attempts to exploit these important

Alan Walker; Julian Parkhill

2008-01-01

378

Automated Microbial Genome Annotation  

SciTech Connect

Miriam Land of the DOE Joint Genome Institute at Oak Ridge National Laboratory gives a talk on the current state and future challenges of moving toward automated microbial genome annotation at the "Sequencing, Finishing, Analysis in the Future" meeting in Santa Fe, NM

Land, Miriam [DOE Joint Genome Institute at Oak Ridge National Laboratory

2009-05-29

379

Genomics of Disease  

Technology Transfer Automated Retrieval System (TEKTRAN)

This edited book represents the 23rd symposium in the Stadler Genetics Symposia series, and the general theme of this conference was "The Genomics of Disease." The 24 national and international speakers were invited to discuss their world-class research into the advances that genomics has made on c...

380

Honey Bee Genome  

NSDL National Science Digital Library

Human genome sequencing center at Baylor College of medicine has completed the honey bee genome (2006). It is available for download by chromosome. It can also be searched using NCBI megablast. Other links include the Nature press release and PDFs of several other related articles.

0002-11-30

381

SGD: Saccharomyces Genome Database  

Microsoft Academic Search

The Saccharomyces Genome Database (SGD) provides Internet access to the complete Saccharomyces cerevisiae genomic s equence, i ts g enes a nd t heir products, the p henotypes of i ts m utants, a nd t he literature supporting these data. The amount of information and t he n umber o f features p rovided b y SGD have i

J. Michael Cherry; Caroline Adler; Catherine A. Ball; Stephen A. Chervitz; Selina S. Dwight; Erich T. Hester; Yankai Jia; Gail Juvik; Taiyun Roe; Mark Schroeder; Shuai Weng; David Botstein

1998-01-01

382

Nauru Island Effect Detection Data Set  

DOE Data Explorer

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

Long, Chuck

383

Nauru Island Effect Detection Data Set  

SciTech Connect

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

Long, Chuck

2010-07-15

384

Climate change: Effects on reef island resources  

SciTech Connect

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

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

1988-06-27

385

WIND DATA REPORT Deer Island Parking Lot  

E-print Network

............................................................................................................................ 1 Table of Figures............................................................................................................. 4 SECTION 4 - Significant Meteorological Events........................................................................................................................ 16 TABLE OF FIGURES Figure 1 - Site location at Deer Island Parking Lot site................

Massachusetts at Amherst, University of

386

WIND DATA REPORT Deer Island Outfall  

E-print Network

............................................................................................................................ 1 Table of Figures............................................................................................................. 4 SECTION 4 - Significant Meteorological Events........................................................................................................................ 16 TABLE OF FIGURES Figure 1 - Site location at Deer Island Outfall site. ......................

Massachusetts at Amherst, University of

387

Dendrochronology of strain-relaxed islands.  

PubMed

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

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

2006-06-01

388

Dendrochronology of Strain-Relaxed Islands  

SciTech Connect

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

Merdzhanova, T.; Kiravittaya, S.; Rastelli, A.; Stoffel, M.; Denker, U.; Schmidt, O.G. [Max-Planck-Institut fuer Festkoerperforschung, Heisenbergstrasse 1, D-70569 Stuttgart (Germany)

2006-06-09

389

Microbial Genomes Multiply  

NASA Technical Reports Server (NTRS)

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

Doolittle, Russell F.

2002-01-01

390

Genomics in Education  

NSDL National Science Digital Library

Created by Professor Sarah C.R. Elgin at Washington University, the Genome Sequencing Video Tour is "aimed at increasing the scientific literacy of biology students in the technology of genomic sequence." Here, visitors can watch the entire tour, which include segments featuring an exploration of current genomic research in a pathogenic bacteria and an animated explanation of the chemistry of cycle sequencing. The site also includes several key resources that have been developed in collaboration with Washington University biology students. Visitors will find four different bioinformatics lab demonstrations here including "Investigating Eukaryotic Genome: Cloning and Sequencing a Fragment of Yeast DNA". Also, science teachers shouldn't miss the research-based course "Research Explorations in Genomics" available here, and they should also be sure to check out the information about their Summer Research Fellows program, which gives high school teachers the opportunity to learn about new research projects in a faculty member's lab.

Elgin, Sarah C. R.

391

Genomic Instability and Cancer  

PubMed Central

Genomic instability is a characteristic of most cancer cells. It is an increased tendency of genome alteration during cell division. Cancer frequently results from damage to multiple genes controlling cell division and tumor suppressors. It is known that genomic integrity is closely monitored by several surveillance mechanisms, DNA damage checkpoint, DNA repair machinery and mitotic checkpoint. A defect in the regulation of any of these mechanisms often results in genomic instability, which predisposes the cell to malignant transformation. Posttranslational modifications of the histone tails are closely associated with regulation of the cell cycle as well as chromatin structure. Nevertheless, DNA methylation status is also related to genomic integrity. We attempt to summarize recent developments in this field and discuss the debate of driving force of tumor initiation and progression.

Yao, Yixin; Dai, Wei

2014-01-01

392

CDC: Public Health Genomics  

NSDL National Science Digital Library

Created in 1997, the Office of Public Health Genomics (OPHG) was established "to integrate genomics into public health research, policy, and programs, which could improve interventions designed to prevent and control the country's leading chronic, infectious, environmental, and occupational diseases." Visitors to the site should start by looking over their "Focus Areas", which include "Genomics and Health", "Family Health History", and "Genetic Testing". The "Genomics and Health" area is a great place to begin looking through the site, as it contains materials that explain the relationship between genetic history and family health. Here visitors will find activities that explain and illuminate environmental health, hereditary blood disorders, and pediatric genetics. Also, the site includes a "For Health Professionals" area which is perfect for current public health practitioners and those teaching about these subjects. Rounding out the site is their "Genomics and Health Impact" blog, which is definitely worth a look.

393

Active Transposition in Genomes  

PubMed Central

Transposons are DNA sequences capable of moving in genomes. Early evidence showed their accumulation in many species and suggested their continued activity in at least isolated organisms. In the past decade, with the development of various genomic technologies, it has become abundantly clear that ongoing activity is the rule rather than the exception. Active transposons of various classes are observed throughout plants and animals, including humans. They continue to create new insertions, have an enormous variety of structural and functional impact on genes and genomes, and play important roles in genome evolution. Transposon activities have been identified and measured by employing various strategies. Here, we summarize evidence of current transposon activity in various plant and animal genomes. PMID:23145912

Huang, Cheng Ran Lisa; Burns, Kathleen H.; Boeke, Jef D.

2013-01-01

394

The UCSC Genome Browser  

PubMed Central

The University of California Santa Cruz (UCSC) Genome Browser is a popular Web-based tool for quickly displaying a requested portion of a genome at any scale, accompanied by a series of aligned annotation “tracks.” The annotations generated by the UCSC Genome Bioinformatics Group and external collaborators include gene predictions, mRNA and expressed sequence tag alignments, simple nucleotide polymorphisms, expression and regulatory data, phenotype and variation data, and pairwise and multiple-species comparative genomics data. All information relevant to a region is presented in one window, facilitating biological analysis and interpretation. The database tables underlying the Genome Browser tracks can be viewed, downloaded, and manipulated using another Web-based application, the UCSC Table Browser. Users can upload personal datasets in a wide variety of formats as custom annotation tracks in both browsers for research or educational purposes. PMID:21975940

Karolchik, Donna; Hinrichs, Angie S.; Kent, W. James

2011-01-01

395

Saving the ‘disappearing islands’: Climate change governance, Pacific island states and cosmopolitan dispositions  

Microsoft Academic Search

The ‘disappearing islands’ is a distinct idea that emerged out of the Intergovernmental Panel on Climate Change report to describe the vulnerability of small island states in the Pacific to sea-level rise as a result of climate change. In this article I deploy the ‘disappearing islands’ to map the complex politics of climate change governance. Through various governmental rationalities the

F. R. Cameron

2011-01-01

396

76 FR 27253 - Safety Zone; Catawba Island Club Fireworks, Catawba Island Club, Port Clinton, OH  

Federal Register 2010, 2011, 2012, 2013, 2014

...USCG-2011-0216] RIN 1625-AA00 Safety Zone; Catawba Island Club Fireworks, Catawba Island Club, Port Clinton, OH AGENCY: Coast Guard, DHS...from portions of Lake Erie for the Catawba Island Club Memorial Day Fireworks. This temporary safety...

2011-05-11

397

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

Code of Federal Regulations, 2013 CFR

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

2013-07-01

398

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

Code of Federal Regulations, 2011 CFR

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

2011-07-01

399

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

Code of Federal Regulations, 2010 CFR

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

2010-07-01

400

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

Code of Federal Regulations, 2012 CFR

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

2012-07-01

401

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

Code of Federal Regulations, 2014 CFR

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

2014-07-01

402

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

Federal Register 2010, 2011, 2012, 2013, 2014

...10-AWP-14] RIN 2120-AA66 Amendment of Class E Airspace; Kwajalein Island, Marshall Islands...System from the legal description of the Class E airspace areas for Kwajalein Island, Bucholz...corrects the legal descriptions for the Class E airspace areas in the vicinity of the...

2010-10-07

403

Dinosaurs and the island rule: The dwarfed dinosaurs from Haeg Island Michael J. Benton a,  

E-print Network

Dinosaurs and the island rule: The dwarfed dinosaurs from Haeg Island Michael J. Benton a, , Zoltan 2009 Accepted 21 January 2010 Available online 28 January 2010 Keywords: Dinosaurs Cretaceous, in 1914, to suggest that the latest Cretaceous dinosaurs from Haeg, Romania were an island fauna, based

Benton, Michael

404

Resource utilization by two insular endemic mammalian carnivores, the island fox and island spotted skunk  

Microsoft Academic Search

We compared resource utilization of two insular endemic mammalian carnivores, the island spotted skunk and island fox, along niche dimensions of space, food, and time on Santa Cruz Island. We predicted that resource use by foxes and skunks would differ along one or more niche dimensions, and that both species would have broader niches or higher densities compared with mainland

Kevin R. Crooks; Dirk Van Vuren

1995-01-01

405

Hematology and Serum Chemistry of the Island Spotted Skunk on Santa Cruz Island  

Microsoft Academic Search

We determined serum biochemis- try and hematologic values for island spotted skunks (Spilogale gracilis amphiala) on Santa Cruz Island (California, USA). Samples were collected from island spotted skunks chemically restrained with ketamine hydrochloride and acepromazine in August 1999 (dry season) and from skunks manually restrained in August 2000 (dry season) and January 2001 (wet sea- son). One parameter, glucose, significantly

Kevin R. Crooks; D. K. Garcelon; Cheryl A. Scott; Jeffery T. Wilcox; Steven F. Timm; Dirk H. Van

2003-01-01

406

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

Microsoft Academic Search

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

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

407

183BEETLES OF BLOCK ISLAND BEETLES OF BLOCK ISLAND: RARE SPECIES  

E-print Network

183BEETLES OF BLOCK ISLAND BEETLES OF BLOCK ISLAND: RARE SPECIES THAT ONCE OCCURRED ON THE MAINLAND of the Rhode Is- land beetle fauna. In addition to the federally listed American Burying Beetle (Nicrophorus americanus), the Island is also home to the only population of the Clay Banks Tiger Beetle (Cicindela

Sikes, Derek S.

408

Evaluating alternative rodenticides for island conservation: roof rat eradication from the San Jorge Islands, Mexico  

Microsoft Academic Search

Introduced commensal rats (Rattus spp.) are a major contributor to the extinction and endangerment of island plants and animals. The use of the toxin brodifacoum to completely eradicate rats from islands is a powerful conservation tool. However, brodifacoum is toxic to animals other than rats and on some islands its use may not be feasible without prohibitively expensive mitigation. As

C. Josh Donlan; Gregg R. Howald; Bernie R. Tershy; Donald A. Croll

2003-01-01

409

Population genomics of the endangered giant Galápagos tortoise  

PubMed Central

Background The giant Galápagos tortoise, Chelonoidis nigra, is a large-sized terrestrial chelonian of high patrimonial interest. The species recently colonized a small continental archipelago, the Galápagos Islands, where it has been facing novel environmental conditions and limited resource availability. To explore the genomic consequences of this ecological shift, we analyze the transcriptomic variability of five individuals of C. nigra, and compare it to similar data obtained from several continental species of turtles. Results Having clarified the timing of divergence in the Chelonoidis genus, we report in C. nigra a very low level of genetic polymorphism, signatures of a weakened efficacy of purifying selection, and an elevated mutation load in coding and regulatory sequences. These results are consistent with the hypothesis of an extremely low long-term effective population size in this insular species. Functional evolutionary analyses reveal a reduced diversity of immunity genes in C. nigra, in line with the hypothesis of attenuated pathogen diversity in islands, and an increased selective pressure on genes involved in response to stress, potentially related to the climatic instability of its environment and its elongated lifespan. Finally, we detect no population structure or homozygosity excess in our five-individual sample. Conclusions These results enlighten the molecular evolution of an endangered taxon in a stressful environment and point to island endemic species as a promising model for the study of the deleterious effects on genome evolution of a reduced long-term population size. PMID:24342523

2013-01-01

410

Classical treatment of island cosmology  

SciTech Connect

Computing the perturbation spectrum in the recently proposed Island Cosmology remains an open problem. In this paper we present a classical computation of the perturbations generated in this scenario by assuming that the NEC-violating field behaves as a classical phantom field. Using an exactly solvable potential, we show that the model generates a scale-invariant spectrum of scalar perturbations, as well as a scale-invariant spectrum of gravitational waves. The scalar perturbations can have sufficient amplitude to seed cosmological structure, while the gravitational waves have a vastly diminished amplitude.

Dutta, Sourish [CERCA, Department of Physics, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106-7079 (United States)

2006-03-15

411

Island of Hawaii, Hawaiian Archipelago  

NASA Technical Reports Server (NTRS)

This single photo covers almost all of the big island of Hawaii (19.5N, 155.5E) in the Hawaiian Archipelago. The active Kilauea Volcano and lava flow is under clouds and hardly visible at the lower right edge but the Mauna Loa volcano crater and its older lava flow is at the bottom center. The Kona Coast, that produces the only coffee grown in the United States, is to the left. Mauna Kea is the extinct volcano and lava flow in the right center.

1983-01-01

412

Atmospheric Vortices near Guadalupe Island  

NASA Technical Reports Server (NTRS)

These MISR images from June 11, 2000 (Terra orbit 2569) demonstrate a turbulent atmospheric flow pattern known as the von Karman vortex street. This phenomenon is named after aerodynamicist Theodore von Karman, who theoretically derived the conditions under which it occurs. The alternating double row of vortices can form in the wake of an obstacle, in this instance the eastern Pacific island of Guadalupe. The rugged terrain of this volcanic Mexican island reaches a maximum elevation of 1.3 kilometers. The island is about 35 kilometers long and is located 260 kilometers west of Baja California.

The vortex pattern is made visible by the marine stratocumulus clouds around Guadalupe Island. The upper image is a color view obtained by MISR's vertical-viewing (nadir) camera. North is toward the left. The orientation of the vortex street indicates that the wind direction is from lower left to upper right (northwest to southeast). The areas within the vortex centers tend to be clear because the rotating motions induce a vertical wind component that can break up the cloud deck.

The lower view is a stereo picture generated from data acquired by MISR's fore- and aft-viewing 70-degree cameras. A 3-D effect is obtained by viewing the image with red/blue glasses and placing the red filter over your left eye. Note how the downwelling atmospheric motion (change in elevation from high to low) is accompanied by a clearing in the center of the first vortex. As the vortices propagate downstream, their rotational velocities weaken. As a consequence, the induced vertical motion and cloud-clearing effect weakens as well.

Theodore von Karman was a Professor of Aeronautics at Caltech and Director of Caltech's Guggenheim Aeronautical Laboratory from 1930-1949. He was one of the principal founders of the Jet Propulsion Laboratory.

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

2000-01-01

413

Evolution of Genome Architecture  

PubMed Central

Charles Darwin believed that all traits of organisms have been honed to near perfection by natural selection. The empirical basis underlying Darwin’s conclusions consisted of numerous observations made by him and other naturalists on the exquisite adaptations of animals and plants to their natural habitats and on the impressive results of artificial selection. Darwin fully appreciated the importance of heredity but was unaware of the nature and, in fact, the very existence of genomes. A century and a half after the publication of the “Origin”, we have the opportunity to draw conclusions from the comparisons of hundreds of genome sequences from all walks of life. These comparisons suggest that the dominant mode of genome evolution is quite different from that of the phenotypic evolution. The genomes of vertebrates, those purported paragons of biological perfection, turned out to be veritable junkyards of selfish genetic elements where only a small fraction of the genetic material is dedicated to encoding biologically relevant information. In sharp contrast, genomes of microbes and viruses are incomparably more compact, with most of the genetic material assigned to distinct biological functions. However, even in these genomes, the specific genome organization (gene order) is poorly conserved. The results of comparative genomics lead to the conclusion that the genome architecture is not a straightforward result of continuous adaptation but rather is determined by the balance between the selection pressure, that is itself dependent on the effective population size and mutation rate, the level of recombination, and the activity of selfish elements. Although genes and, in many cases, multigene regions of genomes possess elaborate architectures that ensure regulation of expression, these arrangements are evolutionarily volatile and typically change substantially even on short evolutionary scales when gene sequences diverge minimally. Thus, the observed genome archtiectures are, mostly, products of neutral processes or epiphenomena of more general selective processes, such as selection for genome streamlining in successful lineages with large populations. Selection for specific gene arrangements (elements of genome architecture) seems only to modulate the results of these processes. PMID:18929678

Koonin, Eugene V.

2012-01-01

414

PLANT GENOMICS The coffee genome provides insight  

E-print Network

, the genome includes several species-specific gene family expansions, among them N-methyltransferases (NMTs to the Rubiaceae family, which is part of the Euasterid I clade and the fourth largest family of angiosperms 25,574 protein-coding genes (4) (table S6), 92 microRNA precursors, and 2573 organellar-to-nuclear

Napp, Nils

415

Radiating on oceanic islands: patterns and processes of speciation in the land snail genus Theba (Risso 1826).  

PubMed

Island radiations have played a major role in shaping our current understanding of allopatric, sympatric and parapatric speciation. However, the fact that species divergence correlates with island size emphasizes the importance of geographic isolation (allopatry) in speciation. Based on molecular and morphological data, we investigated the diversification of the land snail genus Theba on the two Canary Islands of Lanzarote and Fuerteventura. Due to the geological history of both islands, this study system provides ideal conditions to investigate the interplay of biogeography, dispersal ability and differentiation in generating species diversity. Our analyses demonstrated extensive cryptic diversification of Theba on these islands, probably driven mainly by non-adaptive allopatric differentiation and secondary gene flow. In a few cases, we observed a complete absence of gene flow among sympatrically distributed forms suggesting an advanced stage of speciation. On the Jandía peninsula genome scans suggested genotype-environment associations and potentially adaptive diversification of two closely related Theba species to different ecological environments. We found support for the idea that genetic differentiation was enhanced by divergent selection in different environments. The diversification of Theba on both islands is therefore best explained by a mixture of non-adaptive and adaptive speciation, promoted by ecological and geomorphological factors. PMID:22493687

Greve, Carola; Gimnich, France; Hutterer, Rainer; Misof, Bernhard; Haase, Martin

2012-01-01

416

Radiating on Oceanic Islands: Patterns and Processes of Speciation in the Land Snail Genus Theba (Risso 1826)  

PubMed Central

Island radiations have played a major role in shaping our current understanding of allopatric, sympatric and parapatric speciation. However, the fact that species divergence correlates with island size emphasizes the importance of geographic isolation (allopatry) in speciation. Based on molecular and morphological data, we investigated the diversification of the land snail genus Theba on the two Canary Islands of Lanzarote and Fuerteventura. Due to the geological history of both islands, this study system provides ideal conditions to investigate the interplay of biogeography, dispersal ability and differentiation in generating species diversity. Our analyses demonstrated extensive cryptic diversification of Theba on these islands, probably driven mainly by non-adaptive allopatric differentiation and secondary gene flow. In a few cases, we observed a complete absence of gene flow among sympatrically distributed forms suggesting an advanced stage of speciation. On the Jandía peninsula genome scans suggested genotype-environment associations and potentially adaptive diversification of two closely related Theba species to different ecological environments. We found support for the idea that genetic differentiation was enhanced by divergent selection in different environments. The diversification of Theba on both islands is therefore best explained by a mixture of non-adaptive and adaptive speciation, promoted by ecological and geomorphological factors. PMID:22493687

Greve, Carola; Gimnich, France; Hutterer, Rainer; Misof, Bernhard; Haase, Martin

2012-01-01

417

Update on Genomic Studies of Algae Paths toward Algal Genomics  

E-print Network

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

418

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

DOE Data Explorer

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

419

Comparative and Functional Genomics Comp Funct Genom 2003; 4: 3136.  

E-print Network

Comparative and Functional Genomics Comp Funct Genom 2003; 4: 31­36. Published online in Wiley and mitochondria contain genomes John F. Allen* Plant Biochemistry, Center for Chemistry and Chemical Engineering that the nucleotide sequences of mitochondrial and chloroplast genomes would provide the answer has proved unfounded

Allen, John F.

420

Genome Analysis The MaSuRCA genome Assembler  

E-print Network

1 Genome Analysis The MaSuRCA genome Assembler Aleksey Zimin1,* , Guillaume Marçais1 , Daniela Puiu of the genome by short reads at a very low cost, which has prompted development of new assembly methods genome. We show that MaSuRCA performs on par or better than Allpaths-LG and sig- nificantly better than

Yorke, James

421

Institute for Plant Genomics and Biotechnology GENOMICS AND BIOTECHNOLOGY  

E-print Network

Institute for Plant Genomics and Biotechnology GENOMICS AND BIOTECHNOLOGY A multidisciplinary organization, the Institute for Plant Genomics and Biotechnology is a composed of faculty members representing projects at the Institute for Plant Genomics and Biotechnology include the development of transgenic plants

422

Dark matter in archaeal genomes: a rich source of novel mobile elements, defense systems and secretory complexes.  

PubMed

Microbial genomes encompass a sizable fraction of poorly characterized, narrowly spread fast-evolving genes. Using sensitive methods for sequences comparison and protein structure prediction, we performed a detailed comparative analysis of clusters of such genes, which we denote "dark matter islands", in archaeal genomes. The dark matter islands comprise up to 20% of archaeal genomes and show remarkable heterogeneity and diversity. Nevertheless, three classes of entities are common in these genomic loci: (a) integrated viral genomes and other mobile elements; (b) defense systems, and (c) secretory and other membrane-associated systems. The dark matter islands in the genome of thermophiles and mesophiles show similar general trends of gene content, but thermophiles are substantially enriched in predicted membrane proteins whereas mesophiles have a greater proportion of recognizable mobile elements. Based on this analysis, we predict the existence of several novel groups of viruses and mobile elements, previously unnoticed variants of CRISPR-Cas immune systems, and new secretory systems that might be involved in stress response, intermicrobial conflicts and biogenesis of novel, uncharacterized membrane structures. PMID:25113822

Makarova, Kira S; Wolf, Yuri I; Forterre, Patrick; Prangishvili, David; Krupovic, Mart; Koonin, Eugene V

2014-09-01

423

CRCHD SPN Project: Pacific Islander Cancer Control Network  

Cancer.gov

CRCHD SPN Project: Pacific Islander Cancer Control Network  Back to CRCHD Completed Research SPN Project Listing Pacific Islander Cancer Control Network Pacific Islander Cancer Control Network INVESTIGATOR: Allan Hubbell, M.D. INSTITUTION: Pacific

424

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

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

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

425

50 CFR 216.85 - Walrus and Otter Islands.  

Code of Federal Regulations, 2013 CFR

... 2013-10-01 false Walrus and Otter Islands. 216.85 Section 216...Administration § 216.85 Walrus and Otter Islands. By Executive Order 1044, dated February 27, 1909, Walrus and Otter Islands were set aside as bird...

2013-10-01

426

50 CFR 216.85 - Walrus and Otter Islands.  

Code of Federal Regulations, 2011 CFR

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

2011-10-01

427

50 CFR 216.85 - Walrus and Otter Islands.  

Code of Federal Regulations, 2010 CFR

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

2010-10-01

428

50 CFR 216.85 - Walrus and Otter Islands.  

Code of Federal Regulations, 2012 CFR

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

2012-10-01

429

Recovery Act Invests $116,000 at Apostle Islands  

USGS Multimedia Gallery

Secretary Salazar checks out the island's photovoltaic solar panels. Solar panels are the sole source of electricity for the islands and are used to run the interior of the lighthouse on Michigan Island....

2009-08-10

430

CRCHD SPN Publications: Pacific Islander Cancer Control Network (PICCN)  

Cancer.gov

CRCHD SPN Publications: Pacific Islander Cancer Control Network (PICCN)  Back to CRCHD Completed Research SPN Publications Pacific Islander Cancer Control Network (PICCN) Pacific Islander Cancer Control Network (PICCN) Principal Investigator:

431

Genome evolution in yeasts.  

PubMed

Identifying the mechanisms of eukaryotic genome evolution by comparative genomics is often complicated by the multiplicity of events that have taken place throughout the history of individual lineages, leaving only distorted and superimposed traces in the genome of each living organism. The hemiascomycete yeasts, with their compact genomes, similar lifestyle and distinct sexual and physiological properties, provide a unique opportunity to explore such mechanisms. We present here the complete, assembled genome sequences of four yeast species, selected to represent a broad evolutionary range within a single eukaryotic phylum, that after analysis proved to be molecularly as diverse as the entire phylum of chordates. A total of approximately 24,200 novel genes were identified, the translation products of which were classified together with Saccharomyces cerevisiae proteins into about 4,700 families, forming the basis for interspecific comparisons. Analysis of chromosome maps and genome redundancies reveal that the different yeast lineages have evolved through a marked interplay between several distinct molecular mechanisms, including tandem gene repeat formation, segmental duplication, a massive genome duplication and extensive gene loss. PMID:15229592

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

2004-07-01

432

NCBI Viral Genomes Resource.  

PubMed

Recent technological innovations have ignited an explosion in virus genome sequencing that promises to fundamentally alter our understanding of viral biology and profoundly impact public health policy. Yet, any potential benefits from the billowing cloud of next generation sequence data hinge upon well implemented reference resources that facilitate the identification of sequences, aid in the assembly of sequence reads and provide reference annotation sources. The NCBI Viral Genomes Resource is a reference resource designed to bring order to this sequence shockwave and improve usability of viral sequence data. The resource can be accessed at http://www.ncbi.nlm.nih.gov/genome/viruses/ and catalogs all publicly available virus genome sequences and curates reference genome sequences. As the number of genome sequences has grown, so too have the difficulties in annotating and maintaining reference sequences. The rapid expansion of the viral sequence universe has forced a recalibration of the data model to better provide extant sequence representation and enhanced reference sequence products to serve the needs of the various viral communities. This, in turn, has placed increased emphasis on leveraging the knowledge of individual scientific communities to identify important viral sequences and develop well annotated reference virus genome sets. PMID:25428358

Brister, J Rodney; Ako-Adjei, Danso; Bao, Yiming; Blinkova, Olga

2015-01-28

433

PAIDB v2.0: exploration and analysis of pathogenicity and resistance islands.  

PubMed

Pathogenicity is a complex multifactorial process confounded by the concerted activity of genetic regions associated with virulence and/or resistance determinants. Pathogenicity islands (PAIs) and resistance islands (REIs) are key to the evolution of pathogens and appear to play complimentary roles in the process of bacterial infection. While PAIs promote disease development, REIs give a fitness advantage to the host against multiple antimicrobial agents. The Pathogenicity Island Database (PAIDB, http://www.paidb.re.kr) has been the only database dedicated to providing comprehensive information on all reported PAIs and candidate PAIs in prokaryotic genomes. In this study, we present PAIDB v2.0, whose functionality is extended to incorporate REIs. PAIDB v2.0 contains 223 types of PAIs with 1331 accessions, and 88 types of REIs with 108 accessions. With an improved detection scheme, 2673 prokaryotic genomes were analyzed to locate candidate PAIs and REIs. With additional quantitative and qualitative advancements in database content and detection accuracy, PAIDB will continue to facilitate pathogenomic studies of both pathogenic and non-pathogenic organisms. PMID:25336619

Yoon, Sung Ho; Park, Young-Kyu; Kim, Jihyun F

2014-10-21

434

Rangiferine brucellosis on Baffin Island.  

PubMed

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

Ferguson, M A

1997-07-01

435

Genomic taxonomy of vibrios  

PubMed Central

Background Vibrio taxonomy has been based on a polyphasic approach. In this study, we retrieve useful taxonomic information (i.e. data that can be used to distinguish different taxonomic levels, such as species and genera) from 32 genome sequences of different vibrio species. We use a variety of tools to explore the taxonomic relationship between the sequenced genomes, including Multilocus Sequence Analysis (MLSA), supertrees, Average Amino Acid Identity (AAI), genomic signatures, and Genome BLAST atlases. Our aim is to analyse the usefulness of these tools for species identification in vibrios. Results We have generated four new genome sequences of three Vibrio species, i.e., V. alginolyticus 40B, V. harveyi-like 1DA3, and V. mimicus strains VM573 and VM603, and present a broad analyses of these genomes along with other sequenced Vibrio species. The genome atlas and pangenome plots provide a tantalizing image of the genomic differences that occur between closely related sister species, e.g. V. cholerae and V. mimicus. The vibrio pangenome contains around 26504 genes. The V. cholerae core genome and pangenome consist of 1520 and 6923 genes, respectively. Pangenomes might allow different strains of V. cholerae to occupy different niches. MLSA and supertree analyses resulted in a similar phylogenetic picture, with a clear distinction of four groups (Vibrio core group, V. cholerae-V. mimicus, Aliivibrio spp., and Photobacterium spp.). A Vibrio species is defined as a group of strains that share > 95% DNA identity in MLSA and supertree analysis, > 96% AAI, ? 10 genome signature dissimilarity, and > 61% proteome identity. Strains of the same species and species of the same genus will form monophyletic groups on the basis of MLSA and supertree. Conclusion The combination of different analytical and bioinformatics tools will enable the most accurate species identification through genomic computational analysis. This endeavour will culminate in the birth of the online genomic taxonomy whereby researchers and end-users of taxonomy will be able to identify their isolates through a web-based server. This novel approach to microbial systematics will result in a tremendous advance concerning biodiversity discovery, description, and understanding. PMID:19860885

Thompson, Cristiane C; Vicente, Ana Carolina P; Souza, Rangel C; Vasconcelos, Ana Tereza R; Vesth, Tammi; Alves, Nelson; Ussery, David W; Iida, Tetsuya; Thompson, Fabiano L

2009-01-01

436

The Genomic Revolution  

NSDL National Science Digital Library

This Web site, created to complement the museum's The Genomic Revolution exhibition, examines the mapping of the genome and its implications. It includes overviews of our genetic identity, our genome, choosing our genes, changing our genes, reshaping our world through genetics, and the many uses of DNA evidence. There is information about the museum's Institute for Comparative Genetics, ongoing research projects, and conferences on genetics. A timeline has highlights from the field of genetics, beginning with the 1859 publication of Darwin's The Origin of Species.

437

Traditional medicine and genomics  

PubMed Central

‘Omics’ developments in the form of genomics, proteomics and metabolomics have increased the impetus of traditional medicine research. Studies exploring the genomic, proteomic and metabolomic basis of human constitutional types based on Ayurveda and other systems of oriental medicine are becoming popular. Such studies remain important to developing better understanding of human variations and individual differences. Countries like India, Korea, China and Japan are investing in research on evidence-based traditional medicines and scientific validation of fundamental principles. This review provides an account of studies addressing relationships between traditional medicine and genomics. PMID:21829298

Joshi, Kalpana; Ghodke, Yogita; Shintre, Pooja

2010-01-01

438

Genomic insights into tuberculosis.  

PubMed

Prevalent since pre-history, human tuberculosis - caused by the pathogen Mycobacterium tuberculosis - remains a major source of death worldwide. Moreover, increasing drug resistance poses the threat of disease resurgence. However, the expanding application of genomic techniques is providing new avenues for combating this old foe. Whole-genome sequencing, comparative genomics and systems biology are generating new insights into the origins and ongoing evolution of M. tuberculosis, as well as the molecular basis for its pathogenicity. These have important implications for our perspective of the disease, development of new drugs and vaccines, and treatment of patients using existing therapeutics. PMID:24662221

Galagan, James E

2014-05-01

439

Small variable segments constitute a major type of diversity of bacterial genomes at the species level  

PubMed Central

Background Analysis of large scale diversity in bacterial genomes has mainly focused on elements such as pathogenicity islands, or more generally, genomic islands. These comprise numerous genes and confer important phenotypes, which are present or absent depending on strains. We report that despite this widely accepted notion, most diversity at the species level is composed of much smaller DNA segments, 20 to 500 bp in size, which we call microdiversity. Results We performed a systematic analysis of the variable segments detected by multiple whole genome alignments at the DNA level on three species for which the greatest number of genomes have been sequenced: Escherichia coli, Staphylococcus aureus, and Streptococcus pyogenes. Among the numerous sites of variability, 62 to 73% were loci of microdiversity, many of which were located within genes. They contribute to phenotypic variations, as 3 to 6% of all genes harbor microdiversity, and 1 to 9% of total genes are located downstream from a microdiversity locus. Microdiversity loci are particularly abundant in genes encoding membrane proteins. In-depth analysis of the E. coli alignments shows that most of the diversity does not correspond to known mobile or repeated elements, and it is likely that they were generated by illegitimate recombination. An intriguing class of microdiversity includes small blocks of highly diverged sequences, whose origin is discussed. Conclusions This analysis uncovers the importance of this small-sized genome diversity, which we expect to be present in a wide range of bacteria, and possibly also in many eukaryotic genomes. PMID:20433696

2010-01-01

440

Complete Genome Sequence of the Fish Pathogen Flavobacterium branchiophilum?†  

PubMed Central

Members of the genus Flavobacterium occur in a variety of ecological niches and represent an interesting diversity of lifestyles. Flavobacterium branchiophilum is the main causative agent of bacterial gill disease, a severe condition affecting various cultured freshwater fish species worldwide, in particular salmonids in Canada and Japan. We report here the complete genome sequence of strain FL-15 isolated from a diseased sheatfish (Silurus glanis) in Hungary. The analysis of the F. branchiophilum genome revealed putative mechanisms of pathogenicity strikingly different from those of the other, closely related fish pathogen Flavobacterium psychrophilum, including the first cholera-like toxin in a non-Proteobacteria and a wealth of adhesins. The comparison with available genomes of other Flavobacterium species revealed a small genome size, large differences in chromosome organization, and fewer rRNA and tRNA genes, in line with its more fastidious growth. In addition, horizontal gene transfer shaped the evolution of F. branchiophilum, as evidenced by its virulence factors, genomic islands, and CRISPR (clustered regularly interspaced short palindromic repeats) systems. Further functional analysis should help in the understanding of host-pathogen interactions and in the development of rational diagnostic tools and control strategies in fish farms. PMID:21926215

Touchon, Marie; Barbier, Paul; Bernardet, Jean-François; Loux, Valentin; Vacherie, Benoit; Barbe, Valérie; Rocha, Eduardo P. C.; Duchaud, Eric

2011-01-01

441

Association Mapping and the Genomic Consequences of Selection in Sunflower  

PubMed Central

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

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

442

DICKINSON BAY ISLANDS RESTORATION PROJECT MX964016  

EPA Science Inventory

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

443

Geology Fieldnotes: Padre Island National Seashore, Texas  

NSDL National Science Digital Library

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

444

Aleutian Island prehistory: Living in insular extremes  

Microsoft Academic Search

Peoples of the Aleutian Islands lived under a number of stressful environmental constraints, including extreme isolation, volcanic eruptions, seismic activity (including tsunamis), frequent storms, rough seas, gale?force winds, frequent fog and precipitation, and an exclusive marine diet. Nevertheless, the Aleutian Islands supported a large maritime population during late prehistoric times. Cultural adaptations to these conditions included the use of relatively

Allen P. McCartney; Douglas W. Veltre

1999-01-01

445

LONG ISLAND SOUND STUDY 2002 CCMP IR  

EPA Science Inventory

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

446

Sedimentary system of Long Island Sound  

SciTech Connect

Long Island Sound displays many of the characteristics of estuaries in simple form and is in many ways typical of estuaries on glaciated terraim that surround and North Atlantic. This article reviews previous research on the geology and related oceanography of Long Island Sound.

Gordon, R.B.

1980-12-01

447

40 CFR 81.356 - Virgin Islands.  

Code of Federal Regulations, 2011 CFR

... DESIGNATION OF AREAS FOR AIR QUALITY PLANNING PURPOSES Section...noted. Virgin Islands—Ozone (1-Hour Standard)2 Designated...noted. 2 The 1-hour ozone standard is revoked effective...AQCR X Virgin Islands—Ozone (8-Hour Standard)...

2011-07-01

448

40 CFR 81.340 - Rhode Island.  

Code of Federal Regulations, 2012 CFR

... DESIGNATION OF AREAS FOR AIR QUALITY PLANNING PURPOSES Section...otherwise noted. Rhode Island—Ozone (1-Hour Standard)2 Designated...noted. 2 The 1-hour ozone standard is revoked effective...otherwise noted. Rhode Island—Ozone (8-Hour Standard)...

2012-07-01

449

40 CFR 81.340 - Rhode Island.  

Code of Federal Regulations, 2011 CFR

... DESIGNATION OF AREAS FOR AIR QUALITY PLANNING PURPOSES Section...otherwise noted. Rhode Island—Ozone (1-Hour Standard)2 Designated...noted. 2 The 1-hour ozone standard is revoked effective...AQCR 120 X Rhode Island—Ozone (8-Hour Standard)...

2011-07-01

450

40 CFR 81.340 - Rhode Island.  

Code of Federal Regulations, 2010 CFR

... DESIGNATION OF AREAS FOR AIR QUALITY PLANNING PURPOSES Section...otherwise noted. Rhode Island—Ozone (1-Hour Standard)2 Designated...noted. 2 The 1-hour ozone standard is revoked effective...AQCR 120 X Rhode Island—Ozone (8-Hour Standard)...

2010-07-01

451

Bone island (enostosis): current concept — a review  

Microsoft Academic Search

An enostosis or bone island represents a focus of mature compact (cortical) bone within the cancellous bone (spongiosa). Thought by some to be a tumor-like condition and by others a hamartoma, this benign lesion is probably congenital or developmental in origin and reflects failure of resorption during endochondral ossification. A bone island can be virtually diagnosed based on its characteristic

Adam Greenspan

1995-01-01

452

Tin diselenide quantum-sized island films  

SciTech Connect

Island films based on the intermediate phases forming in Ge-Se and Sn-Se systems are prepared by the incongruent evaporation of film structures of a Sn{sub 1-x}Se{sub x} composition. The surface morphology of these structures is studied by atomic force microscopy (AFM). The effect of growth conditions on the size distribution of islands is established.

Kushkhov, A. R., E-mail: askerk@misis.ru [National University of Science and Technology 'MISIS,' (Russian Federation); Gaev, D. S., E-mail: dahir@mail.ru [Kabardino-Balkarian State University (Russian Federation); Rabinovich, O. I., E-mail: olegr@misis.ru [National University of Science and Technology 'MISIS,' (Russian Federation); Stolyarov, A. G. [Kabardino-Balkarian State University (Russian Federation)

2012-03-15

453

Helminths parasitising endemic geckoes from Canary Islands  

Microsoft Academic Search

Parasitological studies on geckoes in Europe are scarce but there are even fewer in the Canary Islands. A complete survey of the helminth communities of Tarentola boettgeri boettgeri, T. b. hierrensis, T. gornerensis, T. delalandii\\u000aand T. angustirnentalis (Sauria, Lacertidae) in the Canary Islands, Spain, was recently carried out. Larval cestodes constitute a significant part of the helminth community parasitising

V. Roca; J. E. Martin; E. Carbonell

1999-01-01

454

Mantle reservoirs and ocean island basalts  

Microsoft Academic Search

The mantle part of the continental lithosphere possesses in part Sr and Nd isotopic compositions similar to those of ocean island basalts. Here we investigate circumstances under which this mantle material may become detached from continental lithosphere, incorporated into the convective flow and thereby providing a source for some ocean island basalts.

Dan McKenzie; R. K. O'Nions

1983-01-01

455

The Coleoptera of the Seychelles islands  

E-print Network

, stored in a retrieval system or transmitted in any form by any means, electronic, mechanical of Endomychidae found in the Seychelles Islands. Key to the Endomychidae of the Seychelles Islands 1. Antennae 5-segmented and stout Trochoideus desjardinsi Antennae 9- or 10-segmented 2 2. Antennae 9-segmented; elytra

Mathis, Wayne N.

456

The Pacific Island Health Care Project  

PubMed Central

Introduction/Background: US Associated/Affiliated Pacific Islands (USAPI) include three freely associated states: Marshall Islands, Federated States of Micronesia, Palau, and three Territories: American Samoa, Guam, and Commonwealth of the Northern Mariana Islands. Objective: The Pacific Island Health Care Project (PIHCP) provides humanitarian medical referral/consultation/care to >500,000 indigenous people of these remote islands. Methods: In the mid-1990s, we developed a simple store-and-forward program to link the USAPI with Tripler Army Medical Center. This application allowed image attachment to email consultations. Results: More than 8000 Pacific Islanders have benefited from the program. Three thousand Pacific Islanders prior to telemedicine (1990–1997) and since store-and-forward telemedicine (1997-present), the PIHCP has helped an additional 5000. Records post dynamically and are stored in an archival database. Conclusion: The PIHCP is the longest running telemedicine program in the world delivering humanitarian medical care. It has bridged the Developing World of the remote Pacific Islands with advanced medical and surgical care available at a major US military teaching hospital. (The opinions expressed here are those of the author and not that of the Army, Department of Defense, or the US Government.) PMID:25353012

Person, Donald Ames

2014-01-01

457

Karst aquifers on small islands--the island of Olib, Croatia.  

PubMed

Water supply is a major problem in the Adriatic islands, especially during the summer tourism season, and represents a limiting factor to the islands' further economic development. Much attention has been given to water supply solutions, primarily in terms of attempting to use the existing island water. Unfortunately, few islands have favourable hydrological conditions to accumulate significant quantities of surface water or groundwater. In the period from 2001 to 2004, investigations were conducted on many islands to define their own freshwater or partially brackish water resources since desalinisation technology could resolve a significant part of the water supply demand on small and distant islands. Due to the specificity and complexity of research in karst areas, the study was conducted in phases and included the geological and hydrogeological reconnaissance of the island, aimed at locating possible areas on the island where the necessary quantities of groundwater of adequate quality could be captured; a detailed hydrogeological mapping of the specified areas, geophysical investigation and test drilling; and, over several days, test pumping of the most promising borehole. One of the islands investigated was the island of Olib. The conducted surveys indicated that it is possible to pump about 3.5 L/s of groundwater from the karst aquifer of the island of Olib, which fully complies with the sanitary quality of drinking water. PMID:22048924

Vlahovi?, Tatjana; Munda, Boris

2012-10-01

458

Barrier island vulnerability to breaching: a case study on Dauphin Island, Alabama  

USGS Publications Warehouse

Breaching of barrier islands can adversely impact society by severing infrastructure, destroying private properties, and altering water quality in back bays and estuaries. This study provides a scheme that assesses the relative vulnerability of a barrier island to breach during storms. Dauphin Island, Alabama was selected for this study because it has a well documented history of island breaches and extensive geological and geomorphic data. To assess the vulnerability of the island, we defined several variables contributing to the risk of breaching: island geology, breaching history, and island topography and geomorphology. These variables were combined to form a breaching index (BI) value for cross island computational bins, each bin every 50 m in the alongshore direction. Results suggest the eastern section of Dauphin Island has the lowest risk of breaching with the remaining portion of the island having a moderate to high risk of breaching. Two reaches in the western section of the island were found to be particularly vulnerable due primarily to their minimal cross-sectional dimensions.

Hansen, Mark; Sallenger, Asbury H.

2007-01-01

459

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

PubMed Central

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

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

2011-01-01

460

Epigenomics: beyond CpG islands  

Microsoft Academic Search

Epigenomic studies aim to define the location and nature of the genomic sequences that are epigenetically modified. Much progress has been made towards whole-genome epigenetic profiling using molecular techniques, but the analysis of such large and complex data sets is far from trivial given the correlated nature of sequence and functional characteristics within the genome. We describe the statistical solutions

Melissa J. Fazzari; John M. Greally

2004-01-01

461

Birds of Bylot Island and Adjacent Baffin Island,  

E-print Network

each summer since 1989, revealed an avifauna composed of 63 species, of which 35 were breeding. Thirteen species are new records for the region, including one for the Northwest Territories (black-headed gull Larus ridibundus) and two for the Canadian Arctic Archipelago (killdeer Charadrius vociferus; mew gull Larus canus). Two species, Canada goose (Branta canadensis) and red knot (Calidris canutus), were also confirmed as breeders for the first time in the region. A summary of these avifaunal observations, along with a review of previous observations made in the region, allows changes in population size and status of individual species to be identified. These records combined with those from earlier studies give a total of 74 species for the Bylot Island region, 45 confirmed as breeders. This makes the avian community in the area one of the most diverse known north of 70?N latitude in the Canadian Arctic Archipelago.

Denis Lepage; David N. Nettleship; Austin Reed

1997-01-01

462

Effects of magnetic islands on drift wave instability  

NASA Astrophysics Data System (ADS)

Magnetic islands have been implemented in the gyrokinetic toroidal code to study the effects of the islands on microturbulence. The pressure profile flattening is verified in the simulation with the islands. Simulations of ion temperature gradient instability find that different toroidal modes are linearly coupled together and that toroidal spectra become broader when the island width increases. The real frequencies and growth rates of different toroidal modes approach each other with the averaged value independent of the island width. The linear mode structures are enhanced at the island separatrices and weakened at the island centers, consistent with the flattening of the pressure profile inside the islands.

Jiang, P.; Lin, Z.; Holod, I.; Xiao, C.

2014-12-01

463

Phylogeography of Cape Verde Island skinks (Mabuya).  

PubMed

The Cape Verde Islands are of volcanic origin with most having appeared between the early Miocene and mid-Pleistocene. They contain six known species of Mabuya skinks. Phylogeographical relationships within and among the relatively widespread taxa M. stangeri, M. spinalis and M. delalandii were inferred, based on approximately 1 kbp of the cytochrome b gene (mitochondrial DNA). Reciprocal monophyly of M. spinalis and M. stangeri was established, which may have arisen from an early Pliocene/late Miocene cladogenetic event. Considerable between-island sequence divergence was detected among M. spinalis, which appears to have colonized the older islands (Sal and Boavista) first. Much lower sequence divergence was found in M. delalandii, indicating a more recent range expansion. Here, evidence points to colonization of the younger islands of Brava and Fogo soon after appearance. There are similarities between some of the described patterns and those seen in lizards from the Canary Islands. PMID:11412378

Brown, R P; Suarez, N M; Smith, A; Pestano, J

2001-06-01

464

Genomic Stability of Aggregatibacter actinomycetemcomitans during Persistent Oral Infection in Human  

PubMed Central

The genome of periodontal pathogen Aggregatibacter actinomycetemcomitans exhibits substantial variations in gene content among unrelated strains primarily due to the presence or absence of genomic islands. This study examined the genomic stability of A. actinomycetemcomitans during its persistent infection in the same host. Four pairs of A. actinomycetemcomitans strains, each pair isolated from an individual over time (0–10 years), were examined for their gains/losses of genes by whole genome sequencing, comparative genomic hybridization by microarray and PCR analysis. Possible effects due to genomic changes were further assessed by comparative transcriptome analysis using microarrays. The results showed that each pair of strains was clonally identical based on phylogenetic analysis of 150 core genes. A novel 24.1-Kb plasmid found in strain S23A was apparently lost in the sibling strain I23C. A 353-bp inversion affecting two essential genes of the serotype-specific gene cluster was found in the serotype antigen-nonexpressing strain I23C, while the same gene cluster was intact in the serotype-expressing sibling strain S23A. A 2,293-bp deletion affecting a gene encoding oxaloacetate decarboxylase and its neighbor region was found in strain SCC2302 but not in the sibling strain AAS4a. However, no evidence of gains or losses of genomic islands was found in the paired strains. Transcriptome profiles showed little or no difference in the paired strains. In conclusion, the genome of A. actinomycetemcomitans appears to be relatively stable during short-term infection. Several types of genomic changes were observed in the paired strains of A. actinomycetemcomitans recovered from the same subjects, including a mutation in serotype-specific gene cluster that may allow the bacteria to evade host immune response. PMID:23824402

Sun, Ruoxing; Kittichotirat, Weerayuth; Wang, Justin; Jan, Minnie; Chen, Weizhen; Asikainen, Sirkka; Bumgarner, Roger; Chen, Casey