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1

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

PubMed Central

A genomic island encoding the biosynthesis and secretion pathway of putative hybrid nonribosomal peptide-polyketide colibactin has been recently described in Escherichia coli. Colibactin acts as a cyclomodulin and blocks the eukaryotic cell cycle. The origin and prevalence of the colibactin island among enterobacteria are unknown. We therefore screened 1,565 isolates of different genera and species related to the Enterobacteriaceae by PCR for the presence of this DNA element. The island was detected not only in E. coli but also in Klebsiella pneumoniae, Enterobacter aerogenes, and Citrobacter koseri isolates. It was highly conserved among these species and was always associated with the yersiniabactin determinant. Structural variations between individual strains were only observed in an intergenic region containing variable numbers of tandem repeats. In E. coli, the colibactin island was usually restricted to isolates of phylogenetic group B2 and inserted at the asnW tRNA locus. Interestingly, in K. pneumoniae, E. aerogenes, C. koseri, and three E. coli strains of phylogenetic group B1, the functional colibactin determinant was associated with a genetic element similar to the integrative and conjugative elements ICEEc1 and ICEKp1 and to several enterobacterial plasmids. Different asn tRNA genes served as chromosomal insertion sites of the ICE-associated colibactin determinant: asnU in the three E. coli strains of ECOR group B1, and different asn tRNA loci in K. pneumoniae. The detection of the colibactin genes associated with an ICE-like element in several enterobacteria provides new insights into the spread of this gene cluster and its putative mode of transfer. Our results shed light on the mechanisms of genetic exchange between members of the family Enterobacteriaceae. PMID:19720753

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

2009-01-01

2

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, Michèle; Watrin, Claude; Nougayrède, Jean-Philippe; Olier, Maïwenn; Oswald, Eric

2014-07-15

3

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

PubMed Central

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

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

2013-01-01

4

COMPUTATIONAL PREDICTION AND CHARACTERIZATION OF GENOMIC ISLANDS  

E-print Network

COMPUTATIONAL PREDICTION AND CHARACTERIZATION OF GENOMIC ISLANDS: INSIGHTS INTO BACTERIAL islands: insights into bacterial pathogenicity Examining Committee: Chair: Dr. Paul C.H. Li Associate of British Columbia Date Defended/Approved: Thursday April 16, 2009 #12;iii ABSTRACT Genomic islands (GIs

Hammerton, James

5

Genomic islands in pathogenic and environmental microorganisms  

Microsoft Academic Search

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

Ulrich Dobrindt; Bianca Hochhut; Ute Hentschel; Jörg Hacker

2004-01-01

6

Genomic Islands of Uropathogenic Escherichia coli Contribute to Virulence  

Microsoft Academic Search

Uropathogenic Escherichia coli (UPEC) strain CFT073 contains 13 large genomic islands ranging in size from 32 kb to 123 kb. Eleven of these genomic islands were individually deleted from the genome, and nine isogenic mutants were tested for their ability to colonize the CBA\\/J mouse model of ascending urinary tract infection. Three genomic island mutants (PAI-aspV, PAI-metV, and PAI-asnT) were

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

2009-01-01

7

CpG island density and its correlations with genomic features in mammalian genomes  

Microsoft Academic Search

ABSTRACT: BACKGROUND: CpG islands, which are clusters of CpG dinucleotides in GC-rich regions, are considered gene markers and represent an important feature of mammalian genomes. Previous studies of CpG islands have largely been on specific loci or within one genome. To date, there seems to be no comparative analysis of CpG islands and their density at the DNA sequence level

Leng Han; Bing Su; Wen-Hsiung Li; Zhongming Zhao

2008-01-01

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 of Speciation in Anopheles gambiae  

E-print Network

to understanding how biological diversity is generated. Many researchers have used quantitative trait locus (QTL between species (e.g., [1­6]). Although QTL mapping experiments are a powerful method for mapping large of genomic differentiation between naturally hybridizing taxa make it possible to take advantage of the many

Nachman, Michael

10

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

PubMed

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

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

2014-07-01

11

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

Microsoft Academic Search

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

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

2005-01-01

12

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

13

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

PubMed Central

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

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

2012-01-01

14

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

PubMed Central

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

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

2006-01-01

15

A systematic method to identify genomic islands and its applications in analyzing the genomes of Corynebacterium glutamicum and Vibrio vulnificus CMCP6 chromosome I  

Microsoft Academic Search

Motivation: Some genomic islands contain horizontally transferred genes, which play critical roles in altering the genotypes and phenotypes of organisms, and horizontal gene transfer has been recognized as a universal event throughout bacterial evolution. A windowless method to display the dis- tribution of genomic GC content, the cumulative GC profile, is proposed to identify genomic islands in genomes whose complete

Ren Zhang; Chun-ting Zhang

2004-01-01

16

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

17

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

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

Non-methylated islands in fish genomes are GC-poor.  

PubMed

In the vertebrate genomes studied to date the 5' end of many genes are associated with distinctive sequences known as CpG islands. CpG islands have three properties: they are non-methylated; the dinucleotide CpG occurs at the frequency predicted by base composition; and they are GC-rich. Unexpectedly we have found that CpG islands in certain fish only have the first two properties; that is, their GC-content is not elevated compared to bulk genomic DNA. Based on this finding, we speculate that the GC-richness of CpG islands in vertebrates other than fish is a passive consequence of a higher mutation rate in regions of open chromatin under conditions where the nucleotide precursor pools are biased. PMID:2027755

Cross, S; Kovarik, P; Schmidtke, J; Bird, A

1991-04-11

20

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

Microsoft Academic Search

Background: We sought to assess whether the concept of relative entropy (information capacity), could aid our understanding of the process of horizontal gene transfer in microbes. We analyzed the differences in information capacity between prokaryotic chromosomes, genomic islands (GI), phages, and plasmids. Relative entropy was estimated using the Kullback-Leibler measure. Results: Relative entropy was highest in bacterial chromosomes and had

J. Bohlin; Passel van M. W. J

2012-01-01

21

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

22

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

23

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

24

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

Microsoft Academic Search

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

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

2005-01-01

25

Quality assessment of maize assembled genomic islands (MAGIs) and large-scale experimental verification of predicted genes  

Microsoft Academic Search

Recent sequencing efforts have targeted the gene-rich regions of the maize (Zea mays L.) genome. We report the release of an improved assembly of maize assembled genomic islands (MAGIs). The 114,173 resulting contigs have been subjected to computational and physical quality assessments. Comparisons to the sequences of maize bacterial artificial chromosomes suggest that at least 97% (160 of 165) of

Yan Fu; Scott J. Emrich; Ling Guo; Tsui-Jung Wen; Daniel A. Ashlock; Srinivas Aluru; Patrick S. Schnable

2005-01-01

26

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

PubMed

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

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

2012-02-15

27

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

Microsoft Academic Search

Background: Horizontal gene transfer (HGT) is considered a strong evolutionary force shaping the content of microbial genomes in a substantial manner. It is the difference in speed enabling the rapid adaptation to changing environmental demands that distinguishes HGT from gene genesis, duplications or mutations. For a precise characterization, algorithms are needed that identify transfer events with high reliability. Frequently, the

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

2006-01-01

28

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

29

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

PubMed

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

2013-06-01

30

Gene Islands Integrated into tRNAGly Genes Confer Genome Diversity on a Pseudomonas aeruginosa Clone  

PubMed Central

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

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

2002-01-01

31

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

32

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

PubMed

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

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

2014-01-01

33

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, Geneviève; Yáñez-Guerra, Luis Alfonso; Ramos-Aboites, Hilda E.; Pernodet, Jean-Luc; Anné, Jozef; van Wezel, Gilles P.; Barona-Gómez, Francisco

2013-01-01

34

AT-rich Islands in Genomic DNA as a Novel Target for AT-specific DNA-reactive Antitumor Drugs*S  

E-print Network

AT-rich Islands in Genomic DNA as a Novel Target for AT-specific DNA-reactive Antitumor Drugs­100% AT), herein referred to as "AT islands." Experimentally detected bizelesin lesions agree with these in silico predictions. Actual bizelesin adducts clustered within the model AT island naked DNA, whereas

Benham, Craig J.

35

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

Microsoft Academic Search

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

Jean-Baptiste Rioux; Nadège Philippe; Sandrine Pereira; David Pignol; Long-Fei Wu; Nicolas Ginet; Ramy K. Aziz

2010-01-01

36

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

37

Antimicrobial Resistance, Class 1 Integrons, and Genomic Island 1 in Salmonella Isolates from Vietnam  

PubMed Central

Background The objective was to investigate the phenotypic and genotypic resistance and the horizontal transfer of resistance determinants from Salmonella isolates from humans and animals in Vietnam. Methodology/Principal Findings The susceptibility of 297 epidemiologically unrelated non-typhoid Salmonella isolates was investigated by disk diffusion assay. The isolates were screened for the presence of class 1 integrons and Salmonella genomic island 1 by PCR. The potential for the transfer of resistance determinants was investigated by conjugation experiments. Resistance to gentamicin, kanamycin, chloramphenicol, streptomycin, trimethoprim, ampicillin, nalidixic acid, sulphonamides, and tetracycline was found in 13 to 50% of the isolates. Nine distinct integron types were detected in 28% of the isolates belonging to 11 Salmonella serovars including S. Tallahassee. Gene cassettes identified were aadA1, aadA2, aadA5, blaPSE-1, blaOXA-30, dfrA1, dfrA12, dfrA17, and sat, as well as open reading frames with unknown functions. Most integrons were located on conjugative plasmids, which can transfer their antimicrobial resistance determinants to Escherichia coli or Salmonella Enteritidis, or with Salmonella Genomic Island 1 or its variants. The resistance gene cluster in serovar Emek identified by PCR mapping and nucleotide sequencing contained SGI1-J3 which is integrated in SGI1 at another position than the majority of SGI1. This is the second report on the insertion of SGI1 at this position. High-level resistance to fluoroquinolones was found in 3 multiresistant S. Typhimurium isolates and was associated with mutations in the gyrA gene leading to the amino acid changes Ser83Phe and Asp87Asn. Conclusions Resistance was common among Vietnamese Salmonella isolates from different sources. Legislation to enforce a more prudent use of antibiotics in both human and veterinary medicine should be implemented by the authorities in Vietnam. PMID:20195474

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

2010-01-01

38

Evaluation of single CpG sites as proxies of CpG island methylation states at the genome scale  

PubMed Central

Methylation of a CpG island is a faithful marker of silencing of its associated gene. Different approaches report the methylation status of a CpG island based on the determination of one or a few CpG sites by assuming the homogeneity of methylation along the element. This strategy is frequently applied in both locus-specific and genome-wide studies, but often without a validation of the representativeness of the interrogated CpG site compared with the whole element. We have evaluated the predictive informativeness of the HpaII sites located in CpG islands using data from high-resolution methylome maps, which offer the possibility to assess the methylation homogeneity of each CpG island and to determine the reporter accuracy of single sites as surrogate markers. An excellent correlation was observed between the HpaII and CpG island methylation levels (r > 0.93). At the qualitative level, the predictive sensitivity of HpaII was >95% with >92% specificity for methylated CpG islands and >90% sensitivity with >95% specificity for unmethylated CpG islands. This analysis provides a global validation framework for strategies based on the use of the methylation-sensitive HpaII restriction enzyme. PMID:23066096

Barrera, Victor; Peinado, Miguel A.

2012-01-01

39

Evaluation of single CpG sites as proxies of CpG island methylation states at the genome scale.  

PubMed

Methylation of a CpG island is a faithful marker of silencing of its associated gene. Different approaches report the methylation status of a CpG island based on the determination of one or a few CpG sites by assuming the homogeneity of methylation along the element. This strategy is frequently applied in both locus-specific and genome-wide studies, but often without a validation of the representativeness of the interrogated CpG site compared with the whole element. We have evaluated the predictive informativeness of the HpaII sites located in CpG islands using data from high-resolution methylome maps, which offer the possibility to assess the methylation homogeneity of each CpG island and to determine the reporter accuracy of single sites as surrogate markers. An excellent correlation was observed between the HpaII and CpG island methylation levels (r > 0.93). At the qualitative level, the predictive sensitivity of HpaII was >95% with >92% specificity for methylated CpG islands and >90% sensitivity with >95% specificity for unmethylated CpG islands. This analysis provides a global validation framework for strategies based on the use of the methylation-sensitive HpaII restriction enzyme. PMID:23066096

Barrera, Víctor; Peinado, Miguel A

2012-12-01

40

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

41

Comparative analysis using K-mer and K-flank patterns provides evidence for CpG island sequence evolution in mammalian genomes.  

PubMed

CpG islands are GC-rich regions often located in the 5' end of genes and normally protected from cytosine methylation in mammals. The important role of CpG islands in gene transcription strongly suggests evolutionary conservation in the mammalian genome. However, as CpG dinucleotides are over-represented in CpG islands, comparative CpG island analysis using conventional sequence analysis techniques remains a major challenge in the epigenetics field. In this study, we conducted a comparative analysis of all CpG island sequences in 10 mammalian genomes. As sequence similarity methods and character composition techniques such as information theory are particularly difficult to conduct, we used exact patterns in CpG island sequences and single character discrepancies to identify differences in CpG island sequences. First, by calculating genome distance based on rank correlation tests, we show that k-mer and k-flank patterns around CpG sites can be used to correctly reconstruct the phylogeny of 10 mammalian genomes. Further, we used various machine learning algorithms to demonstrate that CpG islands sequences can be characterized using k-mers. In addition, by testing a human model on the nine different mammalian genomes, we provide the first evidence that k-mer signatures are consistent with evolutionary history. PMID:23519616

Chae, Heejoon; Park, Jinwoo; Lee, Seong-Whan; Nephew, Kenneth P; Kim, Sun

2013-05-01

42

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

43

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

PubMed

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

2008-05-27

44

Genome-wide Association Study of Anthropometric Traits in Kor?ula Island, Croatia  

PubMed Central

Aim To identify genetic variants underlying six anthropometric traits: body height, body weight, body mass index, brachial circumference, waist circumference, and hip circumference, using a genome-wide association study. Methods The study was carried out in the isolated population of the island of Kor?ula, Croatia, with 898 adult examinees who participated in the larger DNA-based genetic epidemiological study in 2007. Anthropometric measurements followed standard internationally accepted procedures. Examinees were genotyped using HumanHap 370CNV chip by Illumina, with a genome-wide scan containing 316?730 single nucleotide polymorphisms (SNP). Results A total of 11 SNPs were associated with the investigated traits at the level of P?genome-wide significance under the assumption of independent multiple testing, the consistency of association between the 2 variants and a set of anthropometric traits makes CRIM1 and ITGA1 highly interesting for further replication and functional follow-up. Increased linkage disequilibrium between the used markers in an isolated population makes the formal significance threshold overly stringent, and changed allele frequencies in isolate population may contribute to identifying variants that would not be easily identified in large outbred populations. PMID:19260139

Polasek, Ozren; Marusic, Ana; Rotim, Kresimir; Hayward, Caroline; Vitart, Veronique; Huffman, Jennifer; Campbell, Susan; Jankovic, Stipan; Boban, Mladen; Biloglav, Zrinka; Kolcic, Ivana; Krzelj, Vjekoslav; Terzic, Janos; Matec, Lana; Tometic, Gordan; Nonkovic, Dijana; Nincevic, Jasna; Pehlic, Marina; Zedelj, Jurica; Velagic, Vedran; Juricic, Danica; Kirac, Iva; Belak Kovacevic, Sanja; Wright, Alan F.; Campbell, Harry; Rudan, Igor

2009-01-01

45

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

PubMed Central

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

2012-01-01

46

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

PubMed

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

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

2014-11-01

47

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

PubMed Central

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

Pichon, Christophe; Felden, Brice

2005-01-01

48

Vibrio cholerae VttRA and VttRB Regulatory Influences Extend beyond the Type 3 Secretion System Genomic Island  

PubMed Central

A subset of non-O1/non-O139 serogroup strains of Vibrio cholerae cause disease using type 3 secretion system (T3SS)-mediated mechanisms. An ?50-kb genomic island carries genes encoding the T3SS structural apparatus, effector proteins, and two transmembrane transcriptional regulators, VttRA and VttRB, which are ToxR homologues. Previous experiments demonstrated that VttRA and VttRB are necessary for colonization in vivo and promote bile-dependent T3SS gene expression in vitro. To better understand the scope of genes that are potential targets of VttRA and VttRB regulation, we performed deep RNA sequencing using O39 serogroup strain AM-19226 and derivatives carrying deletions in vttRA and vttRB grown in bile. Comparison of the transcript profiles from ?vttRA and ?vttRB mutant strains to the isogenic parent strain confirmed that VttRA and VttRB regulate expression of some T3SS island genes and provided additional information about relative expression levels and operon organization. Interestingly, the data also suggested that additional genes, located outside the T3SS island and encoding functions involved in motility, chemotaxis, type 6 secretion, transcriptional regulation, and stress responses, may also by regulated by VttRA and VttRB. We verified transcript levels for selected genes by quantitative reverse transcription (RT)-PCR and then focused additional studies on motility and biofilm formation. The results suggest that VttRA and VttRB act as part of a complex transcriptional network that coordinates virulence gene expression with multiple cellular phenotypes. VttRA and VttRB therefore represent horizontally acquired transcriptional regulators with the ability to influence global gene expression in addition to modulating gene expression within the T3SS genomic island. PMID:23524608

Chaand, Mudit

2013-01-01

49

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

PubMed Central

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

Quesada, Jose M.; Soriano, Maria Isabel

2012-01-01

50

Systematic evaluation of genome-wide methylated DNA enrichment using a CpG island array  

Microsoft Academic Search

BACKGROUND: Recent progress in high-throughput technologies has greatly contributed to the development of DNA methylation profiling. Although there are several reports that describe methylome detection of whole genome bisulfite sequencing, the high cost and heavy demand on bioinformatics analysis prevents its extensive application. Thus, current strategies for the study of mammalian DNA methylomes is still based primarily on genome-wide methylated

Liu Yang; Kunlin Zhang; Wei Dai; Ximiao He; Qian Zhao; Jing Wang; Zhong Sheng Sun

2011-01-01

51

[The origin of polyploid genomes of bluegrasses Poa L. and gene flow between Northern Pacific and sub-Antarctic islands].  

PubMed

The involvement of present-day diploid bluegrass species in the formation of polyploid genomes was investigated using comparison of sequences of internal transcribed spacers ITS1 and ITS2, and the 5.8S rDNA sequence. It was demonstrated that highly polyploid New Zealand bluegrasses, P. cita (2n = 84; ca. 96 to 100), P. chathamica (2n = 112), and P. litorosa (2n = 263 to 266) formed separate highly supported clade together with tetraploids (2n = 28) P. intrusa, P. anceps, and P. trioides (Austrofestuca littoralis). Among the diploid species (2n = 14), the closest relatives of these species, as well as of the polyploid species of section Poa, are the genomes of Eurasian species P. remota, P. chaixcii (sect. Homalopoa), P densa (Bolbophorum), and P. sibirica (sect. Macropoa). Nuclear genomes of polyploid Stenopoa, Tichopoa, Oreinos, and Secundae are definitely related to the genome of Arctic species P. pseudabbreviata (sect. Abbreviatae). On the contrary, judging by the genes for nuclear 45S rRNA, genomes of diploid P. trivialis (sect. Pandemos), P. annua, and P. supina (sect. Ochlopoa both) are only remotely related to the genomes of highly polyploid species (distances p between them and other bluegrass species from different sections of subgenus Poa constitute 6-10% and 11-15%, respectively). The conclusion on the relationships between highly polyploid and diploid bluegrass species was tested using analysis of synapomorphic mutations in the 5.8S rRNA gene. It was demonstrated that genomes of Poa eminens (2n = 42) and P. schischkinii (2n = 70) (sect. Arctopoa both) were noticeably different in ITS regions from the genomes of the members of the type subgenus Poa. A comparison of the Arctopoa ITS regions showed that the differences between them constituted only 0.2%. At the same time, p distances between the Arctopoa ITS and those from the species belonging to other sections of the genus Poa varied from 5 to 14%. South American species P chonotica (sect. Andinae) (=Ncoraepoa chonotica) (2n = 42) was found to be related to Arctagrostis, Festucella, and Hookerochloa, being at the same time quite distant from the other species of the genus Poa. Polymorphic in chromosome number highly polyploid species of Northern Hemisphere, P. arctica (2n = 42 to 106), P. turneri (2n = 42, 63 to 64), and P. smirnovii (2n = 42, 70) (sect. Malacanthae) are relative to a large group of tetraploid (2n = 28) endemic bluegrass species from New Zealand and sub-Antarctic islands (P. novae-zelandiae and allied species). PMID:21434413

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

2010-12-01

52

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

PubMed Central

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

2010-01-01

53

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, Sebastien; Burrus, Vincent

2014-01-01

54

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

PubMed

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

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

2014-10-01

55

Draft Genome Sequence of the Filamentous Cyanobacterium Leptolyngbya sp. Strain Heron Island J, Exhibiting Chromatic Acclimation  

PubMed Central

Leptolyngbya sp. strain Heron Island is a cyanobacterium exhibiting chromatic acclimation. However, this strain has strong interactions with other bacteria, making it impossible to obtain axenic cultures for sequencing. A protocol involving an analysis of tetranucleotide frequencies, G+C content, and BLAST searches has been described for separating the cyanobacterial scaffolds from those of its cooccurring bacteria. PMID:24503993

Paul, Robin; Jinkerson, Robert E.; Buss, Kristina; Steel, Jason; Mohr, Remus; Hess, Wolfgang R.; Chen, Min

2014-01-01

56

Molecular analysis of secretion genes located on the syr-syp genomic island of Pseudomonas syringae pv. syringae strain B301D  

E-print Network

An RND (resistance-nodulation-cell division) transporter, called the PseC protein, was identified at the left border of the syr-syp genomic island of Pseudomonas syringae pv. syringae strain B301D. The PseC protein exhibited amino acid homology to a...

Kang, Hyojeung

2005-02-17

57

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

58

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

PubMed

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

Danish-Daniel, Muhd; Gan, Huan You; Gan, Han Ming; Saari, Nur Azna; Usup, Gires

2014-01-01

59

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

60

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

61

The evolution of mammalian genomic imprinting was accompanied by the acquisition of novel CpG islands.  

PubMed

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

62

Identification of novel genes in genomic islands that contribute to Salmonella typhimurium replication in macrophages  

Microsoft Academic Search

macrophagecells.AmutantlibraryofstrainATCC14028basedongenedisruptionbyhomologous recombination was screened in order to identify genes that are required for wild-type-like intracellular replication. Randomly generated chromosomal fragments from the genome of S. typhimurium were cloned into a temperature-sensitive vector, and approximately 8000 individual mutant clones were obtained by insertional-duplication mutagenesis (IDM) upon selection at non- permissive temperature. Large-scale screening for replication defects in mouse macrophages, but not

Jochen Klumpp; Thilo M. Fuchs

2007-01-01

63

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

64

Fraser Island Lady Elliot Island  

E-print Network

BRISBANE Fraser Island Lady Elliot Island Lady Musgrave Island Wilson Island Heron Island Great Hinchinbrook Island Lizard Island Double Island Green Island Fitzroy Island North and South Stradbroke Islands

Wang, Yan

65

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?Å resolution structure of SDR-WM99c reveals it to be a new member of the classical short-chain dehydrogenase/reductase (SDR) superfamily. The enzyme contains a nucleotide-binding domain and, like many other SDRs, is tetrameric in form. The active site contains a catalytic tetrad (Asn117, Ser146, Tyr159 and Lys163) and water molecules occupying the presumed NADP cofactor-binding pocket. An adjacent cleft is capped by a relatively mobile helical subdomain, which is well positioned to control substrate access. PMID:25286932

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

2014-01-01

66

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

PubMed Central

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

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

2011-01-01

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

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

E-print Network

G Islands Clemens Wrzodek*, Finja Bu¨ chel, Georg Hinselmann, Johannes Eichner, Florian Mittag, Andreas Zell methylation of CpG islands plays a crucial role in the regulation of gene expression. More than half of all human promoters contain CpG islands with a tissue-specific methylation pattern in differentiated cells

Zell, Andreas

69

Antimicrobial Resistance and Virulence Determinants in European Salmonella Genomic Island 1-Positive Salmonella enterica Isolates from Different Origins ? †  

PubMed Central

Salmonella genomic island 1 (SGI1) contains a multidrug resistance region conferring the ampicillin-chloramphenicol-streptomycin-sulfamethoxazole-tetracycline resistance phenotype encoded by blaPSE-1, floR, aadA2, sul1, and tet(G). Its increasing spread via interbacterial transfer and the emergence of new variants are important public health concerns. We investigated the molecular properties of SGI1-carrying Salmonella enterica serovars selected from a European strain collection. A total of 38 strains belonging to S. enterica serovar Agona, S. enterica serovar Albany, S. enterica serovar Derby, S. enterica serovar Kentucky, S. enterica serovar Newport, S. enterica serovar Paratyphi B dT+, and S. enterica serovar Typhimurium, isolated between 2002 and 2006 in eight European countries from humans, animals, and food, were subjected to antimicrobial susceptibility testing, molecular typing methods (XbaI pulsed-field gel electrophoresis [PFGE], plasmid analysis, and multilocus variable-number tandem-repeat analysis [MLVA]), as well as detection of resistance and virulence determinants (PCR/sequencing and DNA microarray analysis). Typing experiments revealed wide heterogeneity inside the strain collection and even within serovars. PFGE analysis distinguished a total of 26 different patterns. In contrast, the characterization of the phenotypic and genotypic antimicrobial resistance revealed serovar-specific features. Apart from the classical SGI1 organization found in 61% of the strains, seven different variants were identified with antimicrobial resistance properties associated with SGI1-A (S. Derby), SGI1-C (S. Derby), SGI1-F (S. Albany), SGI1-L (S. Newport), SGI1-K (S. Kentucky), SGI1-M (S. Typhimurium), and, eventually, a novel variant similar to SGI1-C with additional gentamicin resistance encoded by aadB. Only minor serovar-specific differences among virulence patterns were detected. In conclusion, the SGI1 carriers exhibited pathogenetic backgrounds comparable to the ones published for susceptible isolates. However, because of their multidrug resistance, they may be more relevant in clinical settings. PMID:21705546

Beutlich, Janine; Jahn, Silke; Malorny, Burkhard; Hauser, Elisabeth; Huhn, Stephan; Schroeter, Andreas; Rodicio, Maria Rosario; Appel, Bernd; Threlfall, John; Mevius, Dik; Helmuth, Reiner; Guerra, Beatriz

2011-01-01

70

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

71

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

72

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

PubMed Central

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

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

2011-01-01

73

A selC-Associated Genomic Island of the Extraintestinal Avian Pathogenic Escherichia coli Strain BEN2908 Is Involved in Carbohydrate Uptake and Virulence  

PubMed Central

The complete nucleotide sequence and genetic organization of a new genomic island (AGI-3) isolated from the extraintestinal avian pathogenic Escherichia coli strain BEN2908 is reported. This 49,600-bp island is inserted at the selC locus and contains putative mobile genetic elements such as a phage-related integrase gene, transposase genes, and direct repeats. AGI-3 shows a mosaic structure of five modules. Some of these modules are present in other E. coli strains and in other pathogenic bacterial species. The gene cluster aec-35 to aec-37 of module 1 encodes proteins associated with carbohydrates assimilation such as a major facilitator superfamily transporter (Aec-36), a glycosidase (Aec-37), and a putative transcriptional regulator of the LacI family (Aec-35). The aec-35 to aec-37 cluster was found in 11.6% of the tested pathogenic and nonpathogenic E. coli strains. When present, the aec-35 to aec-37 cluster is strongly associated with the selC locus (97%). Deletion of the aec-35-aec-37 region affects the assimilation of seven carbohydrates, decreases the growth rate of the strain in minimal medium containing galacturonate or trehalose, and attenuates the virulence of E. coli BEN2908 for chickens. PMID:16428402

Chouikha, Iman; Germon, Pierre; Bree, Annie; Gilot, Philippe; Moulin-Schouleur, Maryvonne; Schouler, Catherine

2006-01-01

74

experimental verification of predicted genes Quality assessment of maize assembled genomic islands (MAGIs) and large-scale  

E-print Network

. Baker Center for Bioinformatics and Biological Statistics, §§Center for Plant Genomics, and Departments suggest that at least 97% (160 of 165) of MAGIs are correctly assembled. Because the rates at which- pothesize that these ``orphans'' evolved quickly during maize evolution and or domestication. assembly

Schnable, Patrick S.

75

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

Microsoft Academic Search

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

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

2010-01-01

76

Genome organization in Halobacterium halobium : A 70 kb island of more (AT) rich DNA in the chromosome  

Microsoft Academic Search

The more A+T rich fractionated component (FII DNA) of the Halobacterium halobium genome constitutes one third of the total DNA and upon isolation consists of covalently closed circular DNA (pHH1 and minor cccDNA) and nonsupercoiled sequences. We have investigated the physical organization of the non cccDNA in FII by a chromosome walk using one copy of the halobacterial insertion element

Felicitas Pfeifer; Mary Betlach

1985-01-01

77

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

78

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

PubMed Central

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

Le Hello, Simon; Weill, Francois-Xavier; Guibert, Veronique; Praud, Karine; Cloeckaert, Axel

2012-01-01

79

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

80

GenomeViz: visualizing microbial genomes  

PubMed Central

Background An increasing number of microbial genomes are being sequenced and deposited in public databases. In addition, several closely related strains are also being sequenced in order to understand the genetic basis of diversity and mechanisms that lead to the acquisition of new genetic traits. These exercises have necessitated the requirement for visualizing microbial genomes and performing genome comparisons on a finer scale. We have developed GenomeViz to enable rapid visualization and subsequent comparisons of several microbial genomes in an interactive environment. Results Here we describe a program that allows visualization of both qualitative and quantitative information from complete and partially sequenced microbial genomes. Using GenomeViz, data deriving from studies on genomic islands, gene/protein classifications, GC content, GC skew, whole genome alignments, microarrays and proteomics may be plotted. Several genomes can be visualized interactively at the same time from a comparative genomic perspective and publication quality circular genome plots can be created. Conclusions GenomeViz should allow researchers to perform visualization and comparative analysis of up to eight different microbial genomes simultaneously. PMID:15601465

Ghai, Rohit; Hain, Torsten; Chakraborty, Trinad

2004-01-01

81

A highly conserved gene island of three genes on chromosome 3B of hexaploid wheat: diverse gene function and genomic structure maintained in a tightly linked block  

Microsoft Academic Search

BACKGROUND: The complexity of the wheat genome has resulted from waves of retrotransposable element insertions. Gene deletions and disruptions generated by the fast replacement of repetitive elements in wheat have resulted in disruption of colinearity at a micro (sub-megabase) level among the cereals. In view of genomic changes that are possible within a given time span, conservation of genes between

James M Breen; Thomas Wicker; Xiuying Kong; Juncheng Zhang; Wujun Ma; Etienne Paux; Catherine Feuillet; Rudi Appels; Matthew Bellgard

2010-01-01

82

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

83

Engineering a Reduced Escherichia coli Genome  

Microsoft Academic Search

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

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

2002-01-01

84

Northerly Island Studio NORTHERLY ISLAND  

E-print Network

of the Chicago Loop, is a peninsula sur- rounded by Lake Michigan and Burnham Harbor. The four teams were groupedNortherly Island Studio NORTHERLY ISLAND URBAN DESIGN STUDIO College of Urban Planning and Public Affairs CUPPA FALL 2005 NORTHERLY ISLAND URBAN DESIGN STUDIO College of Urban Planning and Public Affairs

Illinois at Chicago, University of

85

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

PubMed Central

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

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

2008-01-01

86

Bahama Islands  

NASA Technical Reports Server (NTRS)

This beautiful photograph from space shows the contrast between islands, clouds, shallow water and deep water of the Bahamas (25.0N, 76.5E). The Bahama Islands of Nassau (the smaller island) and Eleuthera are at the edge of the Bahama Bank where the water is shallow revealing the bottom in pale blue detail contrasted to the dark depths of the Exuma Sound where the bottom is over a thousand feet deep.

1983-01-01

87

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

88

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.

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

2014-01-01

89

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

90

Siberian Islands  

... East Siberian Sea, including one of the New Siberian Islands, Novaya Sibir, are portrayed in these views from data acquired on May ... Ocean and is ice-covered most of the year. The New Siberian Islands are almost always covered by snow and ice, and tundra vegetation is ...

2013-04-16

91

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

92

Pathogenicity island mobility and gene content.  

SciTech Connect

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

Williams, Kelly Porter

2013-10-01

93

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.

94

Tropical Islands Jan Verschelde  

E-print Network

Tropical Islands Jan Verschelde University of Illinois at Chicago Department of Mathematics Algebraic Geometry Seminar Jan Verschelde (UIC) Tropical Islands 16 January 2014 1 / 26 #12;Tropical Islands Verschelde (UIC) Tropical Islands 16 January 2014 2 / 26 #12;Tropical Islands 1 Introduction Introduction

Verschelde, Jan

95

CpG island mapping by epigenome prediction.  

PubMed

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

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

2007-06-01

96

Alcatraz Island  

NSDL National Science Digital Library

âÂÂThe RockâÂÂ, the oft-used vernacular phrase used to describe Alcatraz, is perhaps one of the Bay AreaâÂÂs most dramatic landscapes, and certainly itâÂÂs 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 AmericaâÂÂs most hardened (and colorful) criminals. The National Park Service recently created this rather well-done online exhibit that allows users to view objects from AlcatrazâÂÂs 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 âÂÂBattle of Alcatrazâ and the cellhouse rules. The site also features a number of thematic slide shows, including one that addresses the occupation of the island by members of the American Indian Movement from 1969 to 1971.

2005-01-01

97

RESEARCH ARTICLE Long-Range Bidirectional Strand Asymmetries Originate at CpG Islands in the  

E-print Network

RESEARCH ARTICLE Long-Range Bidirectional Strand Asymmetries Originate at CpG Islands in the Human In the human genome, CpG islands (CGIs), which are GC- and CpG-rich sequences, are associated in the creation of CGIs. Introduction Even though CpG islands (CGIs) have been suggested more than decade ago

Arndt, Peter

98

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

99

Pseudomonas aeruginosa Genomic Structure and Diversity  

PubMed Central

The Pseudomonas aeruginosa genome (G?+?C content 65–67%, size 5.5–7?Mbp) is made up of a single circular chromosome and a variable number of plasmids. Sequencing of complete genomes or blocks of the accessory genome has revealed that the genome encodes a large repertoire of transporters, transcriptional regulators, and two-component regulatory systems which reflects its metabolic diversity to utilize a broad range of nutrients. The conserved core component of the genome is largely collinear among P. aeruginosa strains and exhibits an interclonal sequence diversity of 0.5–0.7%. Only a few loci of the core genome are subject to diversifying selection. Genome diversity is mainly caused by accessory DNA elements located in 79 regions of genome plasticity that are scattered around the genome and show an anomalous usage of mono- to tetradecanucleotides. Genomic islands of the pKLC102/PAGI-2 family that integrate into tRNALys or tRNAGly genes represent hotspots of inter- and intraclonal genomic diversity. The individual islands differ in their repertoire of metabolic genes that make a large contribution to the pangenome. In order to unravel intraclonal diversity of P. aeruginosa, the genomes of two members of the PA14 clonal complex from diverse habitats and geographic origin were compared. The genome sequences differed by less than 0.01% from each other. One hundred ninety-eight of the 231 single nucleotide substitutions (SNPs) were non-randomly distributed in the genome. Non-synonymous SNPs were mainly found in an integrated Pf1-like phage and in genes involved in transcriptional regulation, membrane and extracellular constituents, transport, and secretion. In summary, P. aeruginosa is endowed with a highly conserved core genome of low sequence diversity and a highly variable accessory genome that communicates with other pseudomonads and genera via horizontal gene transfer. PMID:21808635

Klockgether, Jens; Cramer, Nina; Wiehlmann, Lutz; Davenport, Colin F.; Tummler, Burkhard

2011-01-01

100

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

Federal Register 2010, 2011, 2012, 2013

...1265-0000-10137-S3] Protection Island and San Juan Islands National Wildlife Refuges, Jefferson, Island, San Juan, Skagit, and Whatcom Counties...assessment (EA) for Protection Island and San Juan Islands National Wildlife...

2010-08-18

101

Microevolution in island rodents  

Microsoft Academic Search

We perform a meta-analysis on morphological data from four island rodent populations exhibiting microevolution (>˜?100 years). Data consisting of incidences of skeletal variants, cranial, and external measurements are from house mice (Mus musculus) on one Welsh and one Scottish island, black rats (Rattus rattus) on two Galapagos islands, and deer mice (Peromyscus maniculatus) on three California Channel islands. We report

Oliver R. W. Pergams; Mary V. Ashley

2001-01-01

102

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

103

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

104

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

E-print Network

on Maui Nui and Hawai`i (the Big Island). Keywords--Dubautia, genome mosaic, Hawaiian silversword alliance. 2004). In most plants, the plastid genomes are maternally inher- ited, while the nuclear genome that a plant genome resulting from a hy- bridization event would have maternal chloroplast and mi- tochondrial

105

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

PubMed

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

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

2014-06-01

106

Bouvet Island near Antarctica  

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

2013-04-16

107

Canary Island Archipelago  

NASA Technical Reports Server (NTRS)

This nearly vertical view of the Canary Archipelago (28.5N, 16.5W) shows five of the seven islands: Grand Canary, Tenerife, Gomera, Hierro and La Palma. The largest island in view is Tenerife. Island cloud wakes evident in this photo are the result of southerly winds giving rise to cloud banks on the lee side especially on Tenerife which has the highest volcanic peaks. Island water wakes and internal waves are also evident but not as apparent.

1989-01-01

108

Island Fox Paradox  

NSDL National Science Digital Library

Channel Island foxes, long the top predator in their ecosystem, show little fear of humans. Wild foxes often accost visitors on San Nicolas, the island with the most abundant fox population in the island chain. Now, archaeologists have new evidence that suggests foxes were carried to the islands by indigenous people thousands of years ago, and that humans shaped the evolution of the entire species. Do species introduced by native people thousands of years ago deserve protection?

Sharon Levy (Freelancer;)

2010-05-03

109

Arctic ice islands  

SciTech Connect

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

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

1988-01-01

110

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

111

Diomede Islands, Bering Straight  

NASA Technical Reports Server (NTRS)

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

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

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

2008-01-01

112

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

Federal Register 2010, 2011, 2012, 2013

...Safety Zone; Catawba Island Club Wedding Event, Catawba Island Club, Catawba...require an assessment of potential costs and benefits under section 6(a...Safety Zone; Catawba Island Club Wedding Event, Catawba Island Club,...

2013-09-25

113

Microbial Lifestyle and Genome Signatures  

PubMed Central

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

Dutta, Chitra; Paul, Sandip

2012-01-01

114

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

115

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

116

Classification: Biological Sciences, Evolution Widespread genomic divergence during sympatric  

E-print Network

, IN 46556-0369, U.S.A. Tel: (574)- 631-4159, Fax: (574)-631-4159; e-mail: feder.2@nd.edu Key Words: Apple maggot fly, Rhagoletis pomonella, host races, genomic continents of speciation, genomic islands

Pfrender, Michael

117

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

118

Comparative genomics of Helicobacter pylori  

PubMed Central

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

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

2009-01-01

119

Genome synthesis and genomic functional cores  

E-print Network

Genome synthesis and genomic functional cores Alessandra Carbone Département d.fr #12;Plan 1. algorithms + statistics to analyse microbial genomes without using biological information 2. space of genomes : from phylogeny to environmental classification 3. essential metabolic

Radulescu, Ovidiu

120

Cardiovascular Genomics  

PubMed Central

Purpose This article provides an update on cardiovascular genomics using three clinically relevant exemplars, including myocardial infarction (MI) and coronary artery disease (CAD), stroke, and sudden cardiac death (SCD). Organizational Construct Recent advances in cardiovascular genomic research, testing, and clinical implications are presented. Methods Genomic nurse experts reviewed and summarized recent salient literature to provide updates on three selected cardiovascular genomic conditions. Findings Research is ongoing to discover comprehensive genetic markers contributing to many common forms of cardiovascular disease (CVD), including MI and stroke. However, genomic technologies are increasingly being used clinically, particularly in patients with long QT syndrome (LQTS) or hypertrophic cardiomyopathy (HCM) who are at risk for SCD. Conclusions Currently, there are no clinically recommended genetic tests for many common forms of CVD even though direct-to-consumer genetic tests are being marketed to healthcare providers and the general public. On the other hand, genetic testing for patients with certain single gene conditions, including channelopathies (e.g., LQTS) and cardiomyopathies (e.g., HCM), is recommended clinically. Clinical Relevance Nurses play a pivotal role in cardiogenetics and are actively engaged in direct clinical care of patients and families with a wide variety of heritable conditions. It is important for nurses to understand current development of cardiovascular genomics and be prepared to translate the new genomic knowledge into practice. PMID:23368089

Wung, Shu-Fen; Hickey, Kathleen T.; Taylor, Jacquelyn Y.; Gallek, Matthew J.

2013-01-01

121

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

122

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.; Romisch, Karin; Rogers, Alex D.

2004-01-01

123

123Genomics  

NSDL National Science Digital Library

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

124

Finite island model for organelle and nuclear genes in plants  

Microsoft Academic Search

Recurrence equations for genetic diversities and differentiation were developed for hermaphrodite plant species in an island model of population structure. This was made possible by the definitions of diversities at all hierarchical levels from gamete to total population and by the definition of migration rates specific to plants for both nuclear and cytoplasmic genomes. Mating system was also incorporated. Numerical

R J Petit; A Kremer; D B Wagner

1993-01-01

125

Review study on CG islands and CpG methylation  

E-print Network

) � Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome (2007 remodel chromatin such that the epigenetic silencing of genes takes place. � De-novo methylation is: � Count(CpG)/E[CpG] � In general, value of this ratio is >.65 for CpG islands. � EMSA

Rohs, Remo

126

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

127

Nucleomorph genomes.  

PubMed

Nucleomorphs are the remnant nuclei of algal endosymbionts in cryptophytes and chlorarachniophytes, two evolutionarily distinct unicellular eukaryotic lineages that acquired photosynthesis secondarily by the engulfment of red and green algae, respectively. At less than one million base pairs in size, nucleomorph genomes are the most highly reduced nuclear genomes known, with three small linear chromosomes and a gene density similar to that seen in prokaryotes. The independent origin of nucleomorphs in cryptophytes and chlorarachniophytes presents an interesting opportunity to study the reductive evolutionary forces that have led to their remarkable convergence upon similar genome architectures and coding capacities. In this article, we review the current state of knowledge with respect to the structure, function, origin, and evolution of nucleomorph genomes across the known diversity of cryptophyte and chlorarachniophyte algae. PMID:19686079

Moore, Christa E; Archibald, John M

2009-01-01

128

DIPLOMARBEIT Islands of Music  

E-print Network

musical genres. Mountains and hills on these islands represent sub-genres. The islands are situated perceptually very different genres are separated by deep sea. The pieces of music from the collection raw music data (e.g. MP3s) without any further information such as which genres the pieces of music

Rauber,Andreas

129

DIPLOMARBEIT Islands of Music  

E-print Network

musical genres. Mountains and hills on these islands represent sub-genres. The islands are situated perceptually very di#11;erent genres are separated by deep sea. The pieces of music from the collection raw music data (e.g. MP3s) without any further information such as which genres the pieces of music

Rauber,Andreas

130

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.

131

Tracing Lifestyle Adaptation in Prokaryotic Genomes  

PubMed Central

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

Altermann, Eric

2012-01-01

132

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

133

76 FR 2572 - Amendment of Class E Airspace; Kwajalein Island, Marshall Islands, RMI  

Federal Register 2010, 2011, 2012, 2013

...Class E Airspace; Kwajalein Island, Marshall Islands, RMI AGENCY: Federal Aviation...Class E airspace; Kwajalein Island, Marshall Islands, RMI (75 FR 61993). Specifically...airspace area for Kwajalein Island, Marshall Islands, RMI, as published in the...

2011-01-14

134

The Erythroblastic Island  

PubMed Central

Erythroblastic islands are specialized microenvironmental compartments within which definitive mammalian erythroblasts proliferate and differentiate. These islands consist of a central macrophage that extends cytoplasmic protrusions to a ring of surrounding erythroblasts. The interaction of cells within the erythroblastic island is essential for both early and late stages of erythroid maturation. It has been proposed that early in erythroid maturation the macrophages provide nutrients, proliferative and survival signals to the erythroblasts, and phagocytose extruded erythroblast nuclei at the conclusion of erythroid maturation. There is also accumulating evidence for the role of macrophages in promoting enucleation itself. The central macrophages are identified by their unique immunophenotypic signature. Their pronounced adhesive properties, ability for avid endocytosis, lack of respiratory bursts, and consequent release of toxic oxidative species, make them perfectly adapted to function as nurse cells. Both macrophages and erythroblasts display adhesive interactions that maintain island integrity, and elucidating these details is an area of intense interest and investigation. Such interactions enable regulatory feedback within islands via cross talk between cells and also trigger intracellular signaling pathways that regulate gene expression. An additional control mechanism for cellular growth within the erythroblastic islands is through the modulation of apoptosis via feedback loops between mature and immature erythroblasts and between macrophages and immature erythroblasts. The focus of this chapter is to outline the mechanisms by which erythroblastic islands aid erythropoiesis, review the historical data surrounding their discovery, and highlight important unanswered questions. PMID:18282516

Manwani, Deepa; Bieker, James J.

2011-01-01

135

Genome databases  

SciTech Connect

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

Courteau, J.

1991-10-11

136

THE RELATIONSHIP BETWEEN FINE SCALE DNA STRUCTURE, GC CONTENT, AND FUNCTIONAL ELEMENTS IN 1 % OF THE HUMAN GENOME  

Microsoft Academic Search

GC content has been shown to be an important aspect of human genomic function. Extending beyond the scope of GC content alone, there is a class of regions in the genome that have especially high GC content and are enriched for the CG dinucleotide-called CpG islands. CpG islands have been linked to biologica\\\\1y functional genomic elements. DNA structure also contributes

STEPHEN C. J. PARKER; ELLIOTT H. MARGULIES; THOMAS D. TULLIUS

137

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

138

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.

139

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.

140

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

141

Heat Island Effect  

MedlinePLUS

... is part of a community's energy, air quality, water, or sustainability effort. Activities to reduce heat islands range from voluntary initiatives, such as cool pavement demonstration projects, to policy actions, such as requiring cool roofs via building ...

142

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.

143

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.

Griffith, Christopher

144

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.

Gardiner, Lisa; Universe, Windows T.

145

Black Island telecommunications upgrade  

NSF Publications Database

Title : Black Island telecommunications upgrade Type : Antarctic EAM NSF Org: OD / OPP Date : July 22, 1993 File : opp93107 OFFICE OF POLAR PROGRAMS ENVIRONMENT SECTION 202/357-7766 MEMORANDUM Date: July 22, 1993 From: Acting Environmental Officer Subject: Environmental Action Memorandum (Black Island Telecommunications Facility Upgrade) To: Director, Office of Polar Programs Manager, Polar Operations Section Safety and Health Officer Electronics Engineer Facilities Engineering Projects ...

146

Galveston Island and erosion  

E-print Network

protection. The 1970's and 1980's have seen the building of two new beachfront condominiums on East Beach and extensive housing subdivisions on west Galveston Island. Homecr aft Land Development (an affiliate of U. S. Homes), Mitchell Development Inc... problems in the future. Erosion is an old, continuing phenomenon on Galveston Island but most people do not seem concerned about it until they are directly im- pacted. PREVIOUS STUDIES I1any early studies concerning erosion and shoreline protection...

Bolleter, Jim Mason

2012-06-07

147

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

148

Development of Pabelokan Island  

SciTech Connect

Pertamina and Iiapco has an expanding complex of offshore production platforms in the S.E. Sumatra contract area of the Java Sea. One of the requirements for this complex is a treatment facility for water to be used in secondary recovery operations. Because of the water quality required, the water treatment system is substantially larger than that normally used off shore. Instead of constructing one or more platforms for the treatment system, a small coral island named Pabelokan Island has been utilized for this purpose. Although the water treatment system is the primary reason for the base, other facilities were co-located to centralize electric power generation, living quarters and recreation facilities, and facilities for storage and maintenance of offshore equipment. Future plans for the island include a gas-liquids recovery system. This work describes the island facilities, and provides a case study in responsible planning and construction techniques in the development of a coral island for use as an offshore base. The experience gained should be useful in the planning of other coral islands for similar purpose.

Powell, D.R.

1982-01-01

149

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

150

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

151

Comparative genomics- A perspective  

E-print Network

The rapidly emerging field of comparative genomics has yielded dramatic results. Comparative genome analysis has become feasible with the availability of a number of completely sequenced genomes. Comparison of complete genomes between organisms allow for global views on genome evolution and the availability of many completely sequenced genomes increases the predictive power in deciphering the hidden information in genome design, function and evolution. Thus, comparison of human genes with genes from other genomes in a genomic landscape could help assign novel functions for un-annotated genes. Here, we discuss the recently used techniques for comparative genomics and their derived inferences in genome biology.

Selvarajan Sivashankari; Piramanayagam Shanmughavel

152

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

PubMed

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

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

2014-01-01

153

Thematic Review Conservation of Biodiversity on Islands  

E-print Network

Thematic Review Conservation of Biodiversity on Islands: The contribution of the United Kingdom ........................................................................ 1 1.2 OVERVIEW OF ISLANDS .................................................................................................... 3 1.5 THE CHARACTERISTICS OF ISLANDS

154

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

155

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

156

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

157

Silencing Genomes  

NSDL National Science Digital Library

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

158

Comparative Whole-Genome Mapping To Determine Staphylococcus aureus Genome Size, Virulence Motifs, and Clonality  

PubMed Central

Despite being a clonal pathogen, Staphylococcus aureus continues to acquire virulence and antibiotic-resistant genes located on mobile genetic elements such as genomic islands, prophages, pathogenicity islands, and the staphylococcal chromosomal cassette mec (SCCmec) by horizontal gene transfer from other staphylococci. The potential virulence of a S. aureus strain is often determined by comparing its pulsed-field gel electrophoresis (PFGE) or multilocus sequence typing profiles to that of known epidemic or virulent clones and by PCR of the toxin genes. Whole-genome mapping (formerly optical mapping), which is a high-resolution ordered restriction mapping of a bacterial genome, is a relatively new genomic tool that allows comparative analysis across entire bacterial genomes to identify regions of genomic similarities and dissimilarities, including small and large insertions and deletions. We explored whether whole-genome maps (WGMs) of methicillin-resistant S. aureus (MRSA) could be used to predict the presence of methicillin resistance, SCCmec type, and Panton-Valentine leukocidin (PVL)-producing genes on an S. aureus genome. We determined the WGMs of 47 diverse clinical isolates of S. aureus, including well-characterized reference MRSA strains, and annotated the signature restriction pattern in SCCmec types, arginine catabolic mobile element (ACME), and PVL-carrying prophage, PhiSa2 or PhiSa2-like regions on the genome. WGMs of these isolates accurately characterized them as MRSA or methicillin-sensitive S. aureus based on the presence or absence of the SCCmec motif, ACME and the unique signature pattern for the prophage insertion that harbored the PVL genes. Susceptibility to methicillin resistance and the presence of mecA, SCCmec types, and PVL genes were confirmed by PCR. A WGM clustering approach was further able to discriminate isolates within the same PFGE clonal group. These results showed that WGMs could be used not only to genotype S. aureus but also to identify genetic motifs in MRSA that may predict virulence. PMID:22915603

Pantrang, Madhulatha; Stahl, Buffy; Briska, Adam M.; Stemper, Mary E.; Wagner, Trevor K.; Zentz, Emily B.; Callister, Steven M.; Lovrich, Steven D.; Henkhaus, John K.; Dykes, Colin W.

2012-01-01

159

Habitat and environment of islands: primary and supplemental island sets  

USGS Publications Warehouse

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

Matalas, Nicholas C.; Grossling, Bernardo F.

2002-01-01

160

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

161

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

Federal Register 2010, 2011, 2012, 2013

...10137-1265-0000 S3] Protection Island and San Juan Islands National Wildlife Refuges, Jefferson, San Juan, Skagit, Island, and Whatcom Counties...assessment (EA) for Protection Island and San Juan Islands National Wildlife...

2011-04-08

162

Long Island Solar Farm  

SciTech Connect

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

Anders, R.

2013-05-01

163

Reassembling island ecosystems: the case of Lord Howe Island  

Microsoft Academic Search

Exotic species that invade remote islands, usually following human settlement, have had catastrophic effects on native biota. However, on islands it is increasingly feasible to eradicate key exotic species allowing extant native species to recover in situ or to return naturally. The practice of marooning threatened species on islands where the threat is absent, irrespective of whether the threatened species

I. Hutton; J. P. Parkes; A. R. E. Sinclair

2007-01-01

164

Controlling summer heat islands: Proceedings  

SciTech Connect

A workshop was held on the energy and pollution implications of summertime urban heat islands and the potential to control them. The presentations, papers, and discussions fell into four broad categories: (1) the potential to conserve energy, reduce atmospheric pollution, and slow global warming by reducing summer heat islands; (2) the use of computer models to understand and simulate the heat island phenomenon; (3) measurements of heat islands; and (4) the design and implementation of heat island mitigation strategies. On the afternoon of the second day of the workshop, the participants divided into three workgroups. Group 1 discussed research needs to better quantify the effect of heat island mitigation on energy use. Group 2 discussed future research on the characterization and modeling of heat islands. And Group 3 discussed the development of a manual that would present to policy makers our current knowledge of techniques to mitigate heat islands and thereby save energy. This Proceedings documents the presentations and outcome of the Workshop.

Garbesi, K.; Akbari, H.; Martien, P. (eds.)

1989-11-01

165

Computing Optimal Islands C. Bautista  

E-print Network

Computing Optimal Islands C. Bautista J.M. D´iaz-B´a~nez D. Lara§ P. P´erez-Lantero ¶ J. Urrutia I S is called an island of S, if I2 is the intersection of S and a convex set C. An island of S is monochromatic a monochromatic4 island of maximum cardinality. The previous best running time for this problem was O(n3 log n)5

Díaz-Báñez, José Miguel

166

Urban heat island  

Microsoft Academic Search

The phenomenon of an urban heat island was investigated by the use of Landsat\\/Thematic Mapper data sets collected over the metropolitan area of Washington, DC. By combining the derived spectral albedos and temperatures, surface energy composites of five surface categories were analysed. The results indicate that urban heating is attributable to a large excess in heat from the rapidly heating

H. H. Kim

1992-01-01

167

Three Mile Island  

Microsoft Academic Search

This bibliography is divided into the following categories: Accident Overviews, Sequence and Causes; International Commentary and Reaction; Emergency Preparedness and Disaster Planning; Health Effects; Radioactive Releases and the Environment; Accident Investigations\\/Commissions; Nuclear Industry: Safety, Occupational, and Financial Issues; Media and Communications; Cleanup; Sociopolitical Response and Commentary; Restart; Legal Ramifications; Federal Documents: President's Commission on the Accident at Three Mile Island;

M. S. Wood; S. M. Shultz

1988-01-01

168

URBAN EXTENTS Falkland Islands  

E-print Network

URBAN EXTENTS BRAZIL CHILE PARAGUAY URUGUAY GRUMPv1 Falkland Islands A t l a n t i c O c e a n P Tropical (CIAT). Global Rural-Urban Mapping Project (GRUMP), Population Density. Palisades, NY: CIESIN Equal Area Projection Urban Extent Administrative Units National Boundaries Note: National boundaries

Columbia University

169

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.

170

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...

2010-07-20

171

Kiritimati, Kiribati (Christmas Island)  

NASA Technical Reports Server (NTRS)

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

2002-01-01

172

Hawaii's Sugar Islands.  

ERIC Educational Resources Information Center

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

Hawaiian Sugar Planters' Association, Aiea, HI.

173

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.

174

The Falkland Island Fox  

Microsoft Academic Search

IN a review in the current number of NATURE of Mr. Renshaw's ``Some Mammalian Types,'' reference is made to the ``Antarctic wolf of the Falkland Islands exterminated by the sheep farmers in self defence.'' Might I be permitted to add a word on this subject in correction of an erroneous impression current among many naturalists with regard to this animal?

R. N. Rudmose-Brown

1906-01-01

175

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...

176

Adaptation and diversification on islands  

Microsoft Academic Search

Charles Darwin's travels on HMS Beagle taught him that islands are an important source of evidence for evolution. Because many islands are young and have relatively few species, evolutionary adaptation and species proliferation are obvious and easy to study. In addition, the geographical isolation of many islands has allowed evolution to take its own course, free of influence from other

Jonathan B. Losos; Robert E. Ricklefs

2009-01-01

177

Pediatrics in the Marshall Islands  

SciTech Connect

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

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

1984-01-01

178

Costly island for Arctic drilling  

SciTech Connect

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

Not Available

1983-12-01

179

OCEANIC ISLANDS: MODELS OF DIVERSITY  

E-print Network

OCEANIC ISLANDS: MODELS OF DIVERSITY Rosemary G. Gillespie University of California, Berkeley I. Introduction II. Characteristics of Biodiversity III. Island Dynamics IV. Species Loss V. The Future of Biodiversity on Oceanic Islands GLOSSARY adaptive radiation Evolution of ecological and phe- notypic diversity

Gillespie, Rosemary

180

Turk Islands DominicaDominica  

E-print Network

® Martinique Caracas Turk Islands Aruba S t. Kitts Trinidad Caracas Guadeloupe DominicaDominica Antigua Turk Islands Barbados Grenada Aruba Barbuda S t. Kitts Montserrat Anguilla S t. Croix Trinidad S S E R ANTILLE S GR E ATE R ANTILLE S 20° 5° at 15N = 535 km (863 mi) (750 nm) Virgin Islands Original

181

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.

182

Genome Sequence of the Polyhydroxybutyrate Producer Pseudomonas extremaustralis, a Highly Stress-Resistant Antarctic Bacterium  

PubMed Central

Pseudomonas extremaustralis 14-3b presents genes involved in the synthesis of different polyhydroxyalkanoates, in tolerance and degradation of pollutants, and in microaerobic metabolism. Several genomic islands were detected. Genetic machinery could contribute to the adaptability to stressful conditions. This is the first genome sequence reported from a Pseudomonas isolated from cold environments. PMID:22493195

Tribelli, Paula M.; Raiger Iustman, Laura J.; Catone, Mariela V.; Di Martino, Carla; Revale, Santiago; Méndez, Beatriz S.

2012-01-01

183

Multidecadal shoreline changes of atoll islands in the Marshall Islands  

NASA Astrophysics Data System (ADS)

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

Ford, M.

2012-12-01

184

Magnetic Island Induced Bootstrap Current on Island Dynamics in Tokamaks  

SciTech Connect

When a magnetic island is embedded in toroidally symmetric tokamaks, the toroidal symmetry in |B| is broken [K. C. Shaing, Phys. Rev. Lett. 87, 245003 (2001)] . Here, B is the magnetic field. This broken symmetry induces an additional bootstrap current density in the vicinity of the island. It is illustrated that this island induced bootstrap current density modifies the island evolution equation and imposes a lower limit on the absolute value of the tearing mode stability parameter |{Delta}{prime}| for the island to be unstable. This lower limit depends on the local poloidal plasma beta {beta}{sub p}, the ratio of the plasma pressure to the poloidal magnetic field pressure. If {beta}{sub p} is high enough, the magnetic island is stable. This mechanism provides an alternative route to stabilize the island.

Spong, Donald A [ORNL; Shaing, K. C. [University of Wisconsin

2006-02-01

185

Magnetic island induced bootstrap current on island dynamics in tokamaks  

SciTech Connect

When a magnetic island is embedded in toroidally symmetric tokamaks, the toroidal symmetry in |B| is broken [K. C. Shaing, Phys. Rev. Lett. 87, 245003 (2001)]. Here, B is the magnetic field. This broken symmetry induces an additional bootstrap current density in the vicinity of the island. It is illustrated that this island induced bootstrap current density modifies the island evolution equation and imposes a lower limit on the absolute value of the tearing mode stability parameter {delta}{sup '} for the island to be unstable. This lower limit depends on the local poloidal plasma beta {beta}{sub p}, the ratio of the plasma pressure to the poloidal magnetic field pressure. If {beta}{sub p} is high enough, the magnetic island is stable. This mechanism provides an alternative route to stabilize the island.

Shaing, K.C.; Spong, D.A. [Engineering Physics Department, University of Wisconsin, Madison, Wisconsin 53706 (United States); Fusion Energy Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831 (United States)

2006-02-15

186

Features of Methylation and Gene Expression in the Promoter-Associated CpG Islands Using Human Methylome Data  

PubMed Central

CpG islands are typically located in the 5? end of genes and considered as gene markers because they play important roles in gene regulation via epigenetic change. In this study, we compared the features of CpG islands identified by several major algorithms by setting the parameter cutoff values in order to obtain a similar number of CpG islands in a genome. This approach allows us to systematically compare the methylation and gene expression patterns in the identified CpG islands. We found that Takai and Jones' algorithm tends to identify longer CpG islands but with weaker CpG island features (e.g., lower GC content and lower ratio of the observed over expected CpGs) and higher methylation level. Conversely, the CpG clusters identified by Hackenberg et al.'s algorithm using stringent criteria are shorter and have stronger features and lower methylation level. In addition, we used the genome-wide base-resolution methylation profile in two cell lines to show that genes with a lower methylation level at the promoter-associated CpG islands tend to express in more tissues and have stronger expression. Our results validated that the DNA methylation of promoter-associated CpG islands suppresses gene expression at the genome level. PMID:22474411

Du, Xin; Han, Leng; Guo, An-Yuan; Zhao, Zhongming

2012-01-01

187

Evolution of bacterial genomes  

Microsoft Academic Search

This review examines evolution of bacterial genomes with an emphasis on RNA based life, the transition to functional DNA and small evolving genomes (possibly plasmids) that led to larger, functional bacterial genomes.

J. T. Trevors

1997-01-01

188

The platypus genome unraveled.  

PubMed

The genome of the platypus has been sequenced, assembled, and annotated by an international genomics team. Like the animal itself the platypus genome contains an amalgam of mammal, reptile, and bird-like features. PMID:18555772

O'Brien, Stephen J

2008-06-13

189

LOUISIANA BARRIER ISLAND EROSION STUDY.  

USGS Publications Warehouse

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

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

1987-01-01

190

Integrated Genomic Map from Uropathogenic Escherichia coli J96  

Microsoft Academic Search

Escherichia coli J96 is a uropathogen having both broad similarities to and striking differences from nonpathogenic, laboratory E. coli K-12. Strain J96 contains three large (>100-kb) unique genomic segments integrated on the chromosome; two are recognized as pathogenicity islands containing urovirulence genes. Additionally, the strain possesses a fourth smaller accessory segment of 28 kb and two deletions relative to strain

LYLA J. MELKERSON-WATSON; CHRISTOPHER K. RODE; LIXIN ZHANG; BETSY FOXMAN; CRAIG A. BLOCH

2000-01-01

191

Genomic selection requires genomic control of inbreeding  

PubMed Central

Background In the past, pedigree relationships were used to control and monitor inbreeding because genomic relationships among selection candidates were not available until recently. The aim of this study was to understand the consequences for genetic variability across the genome when genomic information is used to estimate breeding values and in managing the inbreeding generated in the course of selection on genome-enhanced estimated breeding values. Methods These consequences were measured by genetic gain, pedigree- and genome-based rates of inbreeding, and local inbreeding across the genome. Breeding schemes were compared by simulating truncation selection or optimum contribution selection with a restriction on pedigree- or genome-based inbreeding, and with selection using estimated breeding values based on genome- or pedigree-based BLUP. Trait information was recorded on full-sibs of the candidates. Results When the information used to estimate breeding values and to constrain rates of inbreeding were either both pedigree-based or both genome-based, rates of genomic inbreeding were close to the desired values and the identical-by-descent profiles were reasonably uniform across the genome. However, with a pedigree-based inbreeding constraint and genome-based estimated breeding values, genomic rates of inbreeding were much higher than expected. With pedigree-instead of genome-based estimated breeding values, the impact of the largest QTL on the breeding values was much smaller, resulting in a more uniform genome-wide identical-by-descent profile but genomic rates of inbreeding were still higher than expected based on pedigree relationships, because they measure the inbreeding at a neutral locus not linked to any QTL. Neutral loci did not exist here, where there were 100 QTL on each chromosome. With a pedigree-based inbreeding constraint and genome-based estimated breeding values, genomic rates of inbreeding substantially exceeded the value of its constraint. In contrast, with a genome-based inbreeding constraint and genome-based estimated breeding values, marker frequencies changed, but this change was limited by the inbreeding constraint at the marker position. Conclusions To control inbreeding, it is necessary to account for it on the same basis as what is used to estimate breeding values, i.e. pedigree-based inbreeding control with traditional pedigree-based BLUP estimated breeding values and genome-based inbreeding control with genome-based estimated breeding values. PMID:22898324

2012-01-01

192

SCS: Signal, Context, and Structure Features for Genome-Wide Human Promoter Recognition  

Microsoft Academic Search

This paper integrates the signal, context, and structure features for genome-wide human promoter recognition, which is important in improving genome annotation and analyzing transcriptional regulation without experimental supports of ESTs, cDNAs, or mRNAs. First, CpG islands are salient biological signals associated with approximately 50 percent of mammalian promoters. Second, the genomic context of promoters may have biological significance, which is

Jia Zeng; Xiao-Yu Zhao; Xiao-Qin Cao; Hong Yan

2010-01-01

193

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

194

Further evidence of an Amerindian contribution to the Polynesian gene pool on Easter Island.  

PubMed

Available evidence suggests a Polynesian origin of the Easter Island population. We recently found that some native Easter Islanders also carried some common American Indian (Amerindian) human leukocyte antigen (HLA) alleles, which probably were introduced before Europeans discovered the island in 1722. In this study, we report molecular genetic investigations of 21 other selected native Easter Islanders. Analysis of mitochondrial DNA and Y chromosome markers showed no traces of an Amerindian contribution. However, high-resolution genomic HLA typing showed that two individuals carried some other common Amerindian HLA alleles, different from those found in our previous investigations. The new data support our previous evidence of an Amerindian contribution to the gene pool on Easter Island. PMID:19493235

Thorsby, E; Flåm, S T; Woldseth, B; Dupuy, B M; Sanchez-Mazas, A; Fernandez-Vina, M A

2009-06-01

195

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.

196

Animal Island Data  

NSDL National Science Digital Library

In this interactive application students playing at the easiest level count the number of each type of animal at the zoo on an island and choose the correct number to complete the list. The middle level has the student clicking on the number of each animal as shown in the bar graph. The hardest level requires students to interpret the data displayed in the bar graph. A worksheet is included in PDF format to be used for student work.

2011-01-01

197

Charge Islands Through Tunneling  

NASA Technical Reports Server (NTRS)

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

Robinson, Daryl C.

2002-01-01

198

Kodiak Island, Alaska  

NASA Technical Reports Server (NTRS)

Running vertically between Alaska on the right and Russia on the left, the Bering Strait is mostly free of ice in this true-color MODIS image acquired from data captured on May 31, 2001. To the lower right of the image, a phytoplankton bloom appears to be occurring at the mouth of Norton Sound, and is coloring the darker water a bright bluish green. At the bottom center of the image is snow-covered St. Lawrence Island.

2002-01-01

199

PLANT GENOMICS The coffee genome provides insight  

E-print Network

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

Napp, Nils

200

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

201

Genomic species are ecological species as revealed by comparative genomics in Agrobacterium tumefaciens.  

PubMed

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

202

3. Markov chains and hidden Markov models This chapter will study a single sequence. We first use an example of CpG islands to  

E-print Network

an example of CpG islands to introduce the model of Markov chain. 3.1 Markov chains In human genome wherever. In these regions we see many more CpG dinucleotides than elsewhere. Such regions are called CpG islands. What sort of probabilistic model might we use for CpG islands? Since dinucleotides are important, we want a model in which

Xie, Jun

203

Personal Genomics, Personalized Medicine,  

E-print Network

Personal Genomics, Personalized Medicine, & YOU Carrie Iwema, PhD, MLS 21st May 2012 AAAS/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

Napp, Nils

204

Genome Medicine 2009, 11  

E-print Network

Genome Medicine 2009, 11::39 Research AA kkeerrnneell--bbaasseedd iinntteeggrraattiioonn ooff of fusing more than one source of genome-wide data, such as the genome, transcriptome, proteome support in which many genome-wide data sources are combined. Integration occurs within the patient domain

205

Culex genome is not just another genome for comparative genomics  

PubMed Central

Formal publication of the Culex genome sequence has closed the human disease vector triangle by meeting the Anopheles gambiae and Aedes aegypti genome sequences. Compared to these other mosquitoes, Culex quinquefasciatus possesses many specific hallmark characteristics, and may thus provide different angles for research which ultimately leads to a practical solution for controlling the ever increasing burden of insect-vector-borne diseases around the globe. We argue the special importance of the cosmopolitan species- Culex genome sequence by invoking many interesting questions and the possible of potential of the Culex genome to answer those. PMID:22463777

2012-01-01

206

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

207

Computing Optimal Islands C. Bautista  

E-print Network

Computing Optimal Islands C. Bautista J.M. D´iaz-B´a~nez D. Lara P. P´erez-Lantero § J. Urrutia¶ I S is called an island of S, if I is the intersection of S and a convex set C. In this paper we give an O(n3 )-time algorithm to find a monochromatic island of maximum cardinality. Our approach also optimizes other

Urrutia, Jorge

208

The Genetic Structure of Pacific Islanders  

PubMed Central

Human genetic diversity in the Pacific has not been adequately sampled, particularly in Melanesia. As a result, population relationships there have been open to debate. A genome scan of autosomal markers (687 microsatellites and 203 insertions/deletions) on 952 individuals from 41 Pacific populations now provides the basis for understanding the remarkable nature of Melanesian variation, and for a more accurate comparison of these Pacific populations with previously studied groups from other regions. It also shows how textured human population variation can be in particular circumstances. Genetic diversity within individual Pacific populations is shown to be very low, while differentiation among Melanesian groups is high. Melanesian differentiation varies not only between islands, but also by island size and topographical complexity. The greatest distinctions are among the isolated groups in large island interiors, which are also the most internally homogeneous. The pattern loosely tracks language distinctions. Papuan-speaking groups are the most differentiated, and Austronesian or Oceanic-speaking groups, which tend to live along the coastlines, are more intermixed. A small “Austronesian” genetic signature (always <20%) was detected in less than half the Melanesian groups that speak Austronesian languages, and is entirely lacking in Papuan-speaking groups. Although the Polynesians are also distinctive, they tend to cluster with Micronesians, Taiwan Aborigines, and East Asians, and not Melanesians. These findings contribute to a resolution to the debates over Polynesian origins and their past interactions with Melanesians. With regard to genetics, the earlier studies had heavily relied on the evidence from single locus mitochondrial DNA or Y chromosome variation. Neither of these provided an unequivocal signal of phylogenetic relations or population intermixture proportions in the Pacific. Our analysis indicates the ancestors of Polynesians moved through Melanesia relatively rapidly and only intermixed to a very modest degree with the indigenous populations there. PMID:18208337

Friedlaender, Jonathan S; Friedlaender, Françoise R; Reed, Floyd A; Kidd, Kenneth K; Kidd, Judith R; Chambers, Geoffrey K; Lea, Rodney A; Loo, Jun-Hun; Koki, George; Hodgson, Jason A; Merriwether, D. Andrew; Weber, James L

2008-01-01

209

WIND DATA REPORT Thompson Island  

E-print Network

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

Massachusetts at Amherst, University of

210

WIND DATA REPORT Thompson Island  

E-print Network

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

Massachusetts at Amherst, University of

211

WIND DATA REPORT Thompson Island  

E-print Network

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

Massachusetts at Amherst, University of

212

WIND DATA REPORT Thompson Island  

E-print Network

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

Massachusetts at Amherst, University of

213

Cognitive Constraints and Island Effects.  

PubMed

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

Hofmeister, Philip; Sag, Ivan A

2010-06-01

214

Cognitive Constraints and Island Effects  

PubMed Central

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

Hofmeister, Philip; Sag, Ivan A.

2012-01-01

215

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

216

Islands of the Arctic  

NASA Astrophysics Data System (ADS)

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

Dowdeswell, Julian; Hambrey, Michael

2002-11-01

217

From Genomes of Species  

NSDL National Science Digital Library

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

R. Brian Watts (CÃÂégep de la GaspÃÂésie et des ÃÂÃÂles, GaspÃÂé;)

2005-12-01

218

Three Mile Island assessments  

Microsoft Academic Search

This paper describes the accident which occurred at Three Mile Island Unit Two (TMI-2) near Middletown, Pennsylvania, including the radioactivity released, consequences of off-site releases, and subsequent cleanup activities. Population dose estimates are presented from exposure to ⁸⁸Kr, ¹³³Xe, \\/sup 133m\\/Xe, ¹³⁵Xe, \\/sup 135m\\/Xe, and ¹³¹I. Based on animal studies and careful calculations, the health effects group has determined that

Daniels

1983-01-01

219

Three Mile Island  

SciTech Connect

This bibliography is divided into the following categories: Accident Overviews, Sequence and Causes; International Commentary and Reaction; Emergency Preparedness and Disaster Planning; Health Effects; Radioactive Releases and the Environment; Accident Investigations/Commissions; Nuclear Industry: Safety, Occupational, and Financial Issues; Media and Communications; Cleanup; Sociopolitical Response and Commentary; Restart; Legal Ramifications; Federal Documents: President's Commission on the Accident at Three Mile Island; Federal Documents: Nuclear Regulatory Commission; Federal Documents: United States Department of Energy; Federal Documents: Miscellaneous Reports; Pennsylvania State Documents; Federal and State Hearings; and Popular Literature.

Wood, M.S.; Shultz, S.M.

1988-01-01

220

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

221

Island of Hawaii  

NASA Technical Reports Server (NTRS)

The three main volcanoes which make up the island of Hawaii (19.5N, 155.5W) include the older large shield volcanoes Mauna Loa, Mauna Kea and the more recent Kilauea. The rift zones of Mauna Loa and Mauna Kea are delineated by the black lava flows whereas the smaler Kilauea can be seen venting steam. This color image is one of a pair (see STS052-95-037) to compare the differences between color film and color infrared film.

1992-01-01

222

Islands in the landscape  

E-print Network

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

T. Clifton; Andrei Linde; Navin Sivanandam

2007-01-10

223

Genome Maps, a new generation genome browser.  

PubMed

Genome browsers have gained importance as more genomes and related genomic information become available. However, the increase of information brought about by new generation sequencing technologies is, at the same time, causing a subtle but continuous decrease in the efficiency of conventional genome browsers. Here, we present Genome Maps, a genome browser that implements an innovative model of data transfer and management. The program uses highly efficient technologies from the new HTML5 standard, such as scalable vector graphics, that optimize workloads at both server and client sides and ensure future scalability. Thus, data management and representation are entirely carried out by the browser, without the need of any Java Applet, Flash or other plug-in technology installation. Relevant biological data on genes, transcripts, exons, regulatory features, single-nucleotide polymorphisms, karyotype and so forth, are imported from web services and are available as tracks. In addition, several DAS servers are already included in Genome Maps. As a novelty, this web-based genome browser allows the local upload of huge genomic data files (e.g. VCF or BAM) that can be dynamically visualized in real time at the client side, thus facilitating the management of medical data affected by privacy restrictions. Finally, Genome Maps can easily be integrated in any web application by including only a few lines of code. Genome Maps is an open source collaborative initiative available in the GitHub repository (https://github.com/compbio-bigdata-viz/genome-maps). Genome Maps is available at: http://www.genomemaps.org. PMID:23748955

Medina, Ignacio; Salavert, Francisco; Sanchez, Rubén; de Maria, Alejandro; Alonso, Roberto; Escobar, Pablo; Bleda, Marta; Dopazo, Joaquín

2013-07-01

224

PRIBILOF ISLAND ALEUT COMMUNITY St. George Island / Traditional Council  

E-print Network

PRIBILOF ISLAND ALEUT COMMUNITY 01 St. George Island / Traditional Council P.O. BOX 940 ST. GEORGE Traditional Council is a federally recognized tribal government by the United States Government, and WHEREAS, the St. George Traditional Council is the governing body of the St. George Tribe, and WHEREAS

225

Incongruence of morphology and genetic markers in Hyles tithymali (Lepidoptera: Sphingidae) from the Canary Islands  

Microsoft Academic Search

Hyles t. tithymali on the Canary Islands has been observed to occur in two larval morphotypes, connected by intermediate forms along a geographical cline from east to west. In this study, it was tested whether this distribution of phenotypes reflects a genealogical division of the population. mtDNA sequence data (COI + II, tRNA-leu) and genomic fingerprints from intersimple sequence repeat

A. K. Hundsdoerfer; M. Wink

2006-01-01

226

Open Sea -Cayman IslandsOpen Sea -Cayman Islands 0 50 100 150 20025  

E-print Network

Open Sea - Cayman IslandsOpen Sea - Cayman Islands 0 50 100 150 20025 Kilometers Cayman Islands Exclusive Economic Zone - Cayman Islands Cayman Islands Cuba Jamaica Honduras #12;Coral Reefs - Grand CaymanCoral Reefs - Grand Cayman 0 1 2 3 4 50.5 Kilometers Cayman Islands National Biodiversity Action Plan www

Exeter, University of

227

DNA Microarray Analysis of Genome Dynamics in Yersinia pestis: Insights into Bacterial Genome Microevolution and Niche Adaptation  

PubMed Central

Genomics research provides an unprecedented opportunity for us to probe into the pathogenicity and evolution of the world's most deadly pathogenic bacterium, Yersinia pestis, in minute detail. In our present work, extensive microarray analysis in conjunction with PCR validation revealed that there are considerable genome dynamics, due to gene acquisition and loss, in natural populations of Y. pestis. We established a genomotyping system to group homologous isolates of Y. pestis, based on profiling or gene acquisition and loss in their genomes, and then drew an outline of parallel microevolution of the Y. pestis genome. The acquisition of a number of genomic islands and plasmids most likely induced Y. pestis to evolve rapidly from Yersinia pseudotuberculosis to a new, deadly pathogen. Horizontal gene acquisition also plays a key role in the dramatic evolutionary segregation of Y. pestis lineages (biovars and genomovars). In contrast to selective genome expansion by gene acquisition, genome reduction occurs in Y. pestis through the loss of DNA regions. We also theorized about the links between niche adaptation and genome microevolution. The transmission, colonization, and expansion of Y. pestis in the natural foci of endemic plague are parallel and directional and involve gradual adaptation to the complex of interactions between the environment, the hosts, and the pathogen itself. These adaptations are based on the natural selections against the accumulation of genetic changes within genome. Our data strongly support that the modern plague originated from Yunnan Province in China, due to the arising of biovar orientalis from biovar antiqua rather than mediaevalis. PMID:15262950

Zhou, Dongsheng; Han, Yanping; Song, Yajun; Tong, Zongzhong; Wang, Jin; Guo, Zhaobiao; Pei, Decui; Pang, Xin; Zhai, Junhui; Li, Min; Cui, Baizhong; Qi, Zhizhen; Jin, Lixia; Dai, Ruixia; Du, Zongmin; Bao, Jingyue; Zhang, Xiuqing; Yu, Jun; Wang, Jian; Huang, Peitang; Yang, Ruifu

2004-01-01

228

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

229

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.

230

The genomic landscape of species divergence in Ficedula flycatchers.  

PubMed

Unravelling the genomic landscape of divergence between lineages is key to understanding speciation. The naturally hybridizing collared flycatcher and pied flycatcher are important avian speciation models that show pre- as well as postzygotic isolation. We sequenced and assembled the 1.1-Gb flycatcher genome, physically mapped the assembly to chromosomes using a low-density linkage map and re-sequenced population samples of each species. Here we show that the genomic landscape of species differentiation is highly heterogeneous with approximately 50 'divergence islands' showing up to 50-fold higher sequence divergence than the genomic background. These non-randomly distributed islands, with between one and three regions of elevated divergence per chromosome irrespective of chromosome size, are characterized by reduced levels of nucleotide diversity, skewed allele-frequency spectra, elevated levels of linkage disequilibrium and reduced proportions of shared polymorphisms in both species, indicative of parallel episodes of selection. Proximity of divergence peaks to genomic regions resistant to sequence assembly, potentially including centromeres and telomeres, indicate that complex repeat structures may drive species divergence. A much higher background level of species divergence of the Z chromosome, and a lower proportion of shared polymorphisms, indicate that sex chromosomes and autosomes are at different stages of speciation. This study provides a roadmap to the emerging field of speciation genomics. PMID:23103876

Ellegren, Hans; Smeds, Linnéa; Burri, Reto; Olason, Pall I; Backström, Niclas; Kawakami, Takeshi; Künstner, Axel; Mäkinen, Hannu; Nadachowska-Brzyska, Krystyna; Qvarnström, Anna; Uebbing, Severin; Wolf, Jochen B W

2012-11-29

231

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

232

Diabetes in Asian and Pacific Islander Americans  

MedlinePLUS

... Islander Americans Diabetes in Asian and Pacific Islander Americans 4 Steps to Manage Your Diabetes for Life ... the disease. PDF Version (1,036 KB) * Asian Americans/Pacific Islanders and Diabetes (from the Office on ...

233

40 CFR 81.340 - Rhode Island.  

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

2014-07-01

234

40 CFR 81.356 - Virgin Islands.  

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

2014-07-01

235

Solar energy for Beaver Island  

Microsoft Academic Search

Beaver Island is the largest of a string of islands extending into Lake Michigan from Michigan's upper peninsula. About 12 miles long and 5 miles across at its widest point, it has been permanently inhabited for over 150 years. It presently has about 350 year-round residents, but the population swells to over 1500 in the summer. In the fall of

Heins

2009-01-01

236

Ellis Island: The Immigrants' Experience.  

ERIC Educational Resources Information Center

Presents a lesson where the students participate in a simulation of the process at Ellis Island in order to understand the feelings people underwent during immigration. Explains that the students choose and research a character, either fictional or a relative, and act out the experience of entering Ellis Island. (CMK)

Koman, Rita G.

1999-01-01

237

Rethinking Easter Island's ecological catastrophe  

Microsoft Academic Search

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

Terry L. Hunt

2007-01-01

238

Controlling summer heat islands: Proceedings  

Microsoft Academic Search

A workshop was held on the energy and pollution implications of summertime urban heat islands and the potential to control them. The presentations, papers, and discussions fell into four broad categories: (1) the potential to conserve energy, reduce atmospheric pollution, and slow global warming by reducing summer heat islands; (2) the use of computer models to understand and simulate the

K. Garbesi; H. Akbari; P. Martien

1989-01-01

239

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

240

Volcanic Island Appears Near Tonga  

NASA Astrophysics Data System (ADS)

A volcano known as Home Reef is now believed to be the source of a small island that appeared recently in Tonga, accordingto scientists from the Smithsonian Institution's Global Volcanism Program who had initially placed the location of the eruption and resulting island at nearby Metis Shoal. Mariners onboard the yacht Maiken

Zielinski, Sarah

2006-11-01

241

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

Microsoft Academic Search

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

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

1995-01-01

242

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

243

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

244

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.

245

What is a genome?  

PubMed

The field of genomics is expanding rapidly, yet the meanings of the word ‘genome’ have yet to be conceptualized in explicit, coherent and useful frameworks. We develop and apply an evolutionary conceptualization of the genome,which represents a logical extension of the evolutionary definition of a gene developed by George C.Williams. An evolutionary genome thus represents a set of genetic material, in a lineage, that due to common interests tends to favour the same or similar phenotypes.This conceptualization provides novel perspectives on genome functions, boundaries and evolution, which should help to guide theoretical and empirical genomics research. PMID:23967454

Stencel, A; Crespi, B

2013-07-01

246

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

PubMed Central

Clostridium perfringens is a Gram-positive, anaerobic spore-forming bacterium commonly found in soil, sediments, and the human gastrointestinal tract. C. perfringens is responsible for a wide spectrum of disease, including food poisoning, gas gangrene (clostridial myonecrosis), enteritis necroticans, and non-foodborne gastrointestinal infections. The complete genome sequences of Clostridium perfringens strain ATCC 13124, a gas gangrene isolate and the species type strain, and the enterotoxin-producing food poisoning strain SM101, were determined and compared with the published C. perfringens strain 13 genome. Comparison of the three genomes revealed considerable genomic diversity with >300 unique “genomic islands” identified, with the majority of these islands unusually clustered on one replichore. PCR-based analysis indicated that the large genomic islands are widely variable across a large collection of C. perfringens strains. These islands encode genes that correlate to differences in virulence and phenotypic characteristics of these strains. Significant differences between the strains include numerous novel mobile elements and genes encoding metabolic capabilities, strain-specific extracellular polysaccharide capsule, sporulation factors, toxins, and other secreted enzymes, providing substantial insight into this medically important bacterial pathogen. PMID:16825665

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

2006-01-01

247

Comprehensive analysis of CpG islands in human chromosomes 21 and 22  

NASA Astrophysics Data System (ADS)

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

Takai, Daiya; Jones, Peter A.

2002-03-01

248

Integrating sequence, evolution and functional genomics in regulatory genomics  

PubMed Central

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

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

2009-01-01

249

Pine Island Glacier, Antarctica  

NASA Technical Reports Server (NTRS)

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

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

2001-01-01

250

Muklu Island. [Muklu Island is an artificial island used as an offshore drilling platform  

SciTech Connect

Mukluk Island, emerging from 48 ft of water, is destined to become the largest and most expensive artificial island in the Alaska Beaufort Sea. The field is believed to contain geologic structures similar to those at Prudhoe Bay, Alaska's megagiant oil field to the southeast. After completion Mukluk will measure 350 ft above water. Five test wells will drill to determine the structures reserves.

Not Available

1983-10-01

251

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

252

Selecting Genomes for Reconstruction of Ancestral Genomes  

E-print Network

greedy algorithms for this problem are proposed and tested on computer simulation data as well,11], HIV [6], and the 1918 flu virus [15] have also been constructed. Parsimony, maximum likelihood, it is often impossible to sequence all the extant genomes that are evolved from the target ancestral genome

Zhang, Louxin

253

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

Microsoft Academic Search

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

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

2003-01-01

254

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).

255

Cancer: Genomics of metastasis  

Microsoft Academic Search

Cancer cells that invade other parts of the body do so by accumulating genomic aberrations. Analysis of the genomic differences between primary and metastatic tumours should aid the understanding of this process.

Joe Gray

2010-01-01

256

GENOMICS AND ENVIRONMENTAL RESEARCH  

EPA Science Inventory

The impact of recently developed and emerging genomics technologies on environmental sciences has significant implications for human and ecological risk assessment issues. The linkage of data generated from genomics, transcriptomics, proteomics, metabalomics, and ecology can be ...

257

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

258

Genome Sequencing Centers  

Cancer.gov

The Cancer Genome Atlas (TCGA) Genome Sequencing Centers (GSCs) perform large-scale DNA sequencing using the latest sequencing technologies. Supported by the National Human Genome Research Institute (NHGRI) large-scale sequencing program, the GSCs generate the enormous volume of data required by TCGA, while continually improving existing technologies and methods to expand the frontier of what can be achieved in cancer genome sequencing.

259

NotI subtraction and NotI-specific microarrays to detect copy number and methylation changes in whole genomes  

Microsoft Academic Search

Methylation, deletions, and amplifications of cancer genes constitute important mechanisms in carcinogenesis. For genome-wide analysis of these changes, we propose the use of NotI clone microarrays and genomic subtraction, because NotI recognition sites are closely associated with CpG islands and genes. We show here that the CODE (Cloning Of DEleted sequences) genomic subtraction procedure can be adapted to NotI flanking

Jingfeng Li; Alexei Protopopov; Fuli Wang; Vera Senchenko; Valentin Petushkov; Olga Vorontsova; Lev Petrenko; Veronika Zabarovska; Olga Muravenko; Eleonora Braga; Lev Kisselev; Michael I. Lerman; Vladimir Kashuba; George Klein; Ingemar Ernberg; Claes Wahlestedt; Eugene R. Zabarovsky

2002-01-01

260

INTRODUCTION TO GENOMIC MEDICINE  

E-print Network

Pharmacogenomics May 23 Susceptibility Genetics June 6 Cancer Genomics June 13 Genomics of Microbes and Microbiomes Implications of Genomics in Clinical Medicine February 7 Molecular Biology/Genetics Refresher - 1 February 14 Molecular Biology/Genetics Refresher - 2 February 21 The Genetic Basis of Disease February 28 Introduction

261

Genome Organization Analysis Tool  

E-print Network

point mutations of genes have been the basis of comparative sequence analyses, most often used as a tool for phylogenetic and evolutionary studies. However, point mutations are of limited utility when comparing either slowly evolving genes and genomes or rapidly evolving genes and genomes such as some pathogenic viral genomes. Even when the nucleotide sequences of

Aaron Kaluszka; Cynthia Gibas

262

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

263

Genome BBiioollooggyy 2008, 99  

E-print Network

Genome BBiioollooggyy 2008, 99::245 Minireview DDiiaattoomm ggeennoommeess ccoommee ooff aaggee The results of two published genome sequences from marine diatoms provide basic insights into how in the contemporary ocean. Published: 2 January 2009 Genome BBiioollooggyy 2008, 99::245 (doi:10.1186/gb-2008

264

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

PubMed

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

Mammen, L; Norton, S A

1997-10-01

265

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.

266

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.

267

Long Island Solar Farm Project Overview  

E-print Network

and construct arrays ~ 2 years of output (88,000 MWh equivalent) Long Island Solar Farm #12;Other PollutantsLong Island Solar Farm #12;Project Overview The Long Island Solar Farm (LISF) is a 32-megawatt solar photovoltaic power plant built through a collaboration including BP Solar, the Long Island Power

Ohta, Shigemi

268

Genomic plasticity of the causative agent of melioidosis, Burkholderia pseudomallei  

PubMed Central

Burkholderia pseudomallei is a recognized biothreat agent and the causative agent of melioidosis. This Gram-negative bacterium exists as a soil saprophyte in melioidosis-endemic areas of the world and accounts for 20% of community-acquired septicaemias in northeastern Thailand where half of those affected die. Here we report the complete genome of B. pseudomallei, which is composed of two chromosomes of 4.07 megabase pairs and 3.17 megabase pairs, showing significant functional partitioning of genes between them. The large chromosome encodes many of the core functions associated with central metabolism and cell growth, whereas the small chromosome carries more accessory functions associated with adaptation and survival in different niches. Genomic comparisons with closely and more distantly related bacteria revealed a greater level of gene order conservation and a greater number of orthologous genes on the large chromosome, suggesting that the two replicons have distinct evolutionary origins. A striking feature of the genome was the presence of 16 genomic islands (GIs) that together made up 6.1% of the genome. Further analysis revealed these islands to be variably present in a collection of invasive and soil isolates but entirely absent from the clonally related organism B. mallei. We propose that variable horizontal gene acquisition by B. pseudomallei is an important feature of recent genetic evolution and that this has resulted in a genetically diverse pathogenic species. PMID:15377794

Holden, Matthew T. G.; Titball, Richard W.; Peacock, Sharon J.; Cerdeno-Tarraga, Ana M.; Atkins, Timothy; Crossman, Lisa C.; Pitt, Tyrone; Churcher, Carol; Mungall, Karen; Bentley, Stephen D.; Sebaihia, Mohammed; Thomson, Nicholas R.; Bason, Nathalie; Beacham, Ifor R.; Brooks, Karen; Brown, Katherine A.; Brown, Nat F.; Challis, Greg L.; Cherevach, Inna; Chillingworth, Tracy; Cronin, Ann; Crossett, Ben; Davis, Paul; DeShazer, David; Feltwell, Theresa; Fraser, Audrey; Hance, Zahra; Hauser, Heidi; Holroyd, Simon; Jagels, Kay; Keith, Karen E.; Maddison, Mark; Moule, Sharon; Price, Claire; Quail, Michael A.; Rabbinowitsch, Ester; Rutherford, Kim; Sanders, Mandy; Simmonds, Mark; Songsivilai, Sirirurg; Stevens, Kim; Tumapa, Sarinna; Vesaratchavest, Monkgol; Whitehead, Sally; Yeats, Corin; Barrell, Bart G.; Oyston, Petra C. F.; Parkhill, Julian

2004-01-01

269

Synthesizing knowledge of ocean islands  

NASA Astrophysics Data System (ADS)

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

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

2011-11-01

270

WIND DATA REPORT Thompson Island  

E-print Network

WIND DATA REPORT Thompson Island March 1, 2005 ­ May 31, 2005 Prepared for Massachusetts Technology Collaborative 75 North Drive Westborough, MA 01581 by Christopher N. Elkinton Anthony L. Rogers Anthony F. Ellis

Massachusetts at Amherst, University of

271

WIND DATA REPORT Thompson Island  

E-print Network

WIND DATA REPORT Thompson Island December 1, 2004 ­ February 28, 2005 Prepared for Massachusetts Anthony F. Ellis April 13, 2005 Renewable Energy Research Laboratory University of Massachusetts, Amherst

Massachusetts at Amherst, University of

272

WIND DATA REPORT Thompson Island  

E-print Network

WIND DATA REPORT Thompson Island March 1, 2003 ­ May 31, 2003 Prepared for Massachusetts Technology Collaborative 75 North Drive Westborough, MA 01581 by James F. Manwell Anthony F. Ellis Christopher N. Elkinton

Massachusetts at Amherst, University of

273

WIND DATA REPORT Thompson Island  

E-print Network

WIND DATA REPORT Thompson Island March 1, 2004 ­ May 31, 2004 Prepared for Massachusetts Technology Collaborative 75 North Drive Westborough, MA 01581 by James F. Manwell Anthony F. Ellis Christopher N. Elkinton

Massachusetts at Amherst, University of

274

No Company Is An Island  

E-print Network

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

Maddox, A.

275

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

276

Living in a changing environment: insights into host adaptation in Neisseria meningitidis from comparative genomics.  

PubMed

Neisseria meningitidis (the meningococcus) colonizes the human nasopharynx of about 10% of the human population. However, for reasons that are still mostly unknown meningococci occasionally enter the cerebrospinal fluid leading to often fatal bacterial meningitis especially in children and young adults. The genetic basis for the observed differences in the pathogenic potential of different strains has only partially been unravelled so far. With the advent of whole genome sequencing technologies, complete genome sequences from three pathogenic meningococcal strains have become available and allow for a comprehensive analysis of the genomic and genetic differences occurring within this species. In this review, the general properties of the meningococcal genomes so far sequenced is given with an emphasis on the chromosomal rearrangements that have occurred, and the genomic islands and prophages that have been identified. The concomitant development of microarray technology for comparative genome hybridization studies of a large set of different meningococcal isolates as well as strains from other Neisseria species has extended our understanding of meningococcal population genetics on a genome-wide scale thus bridging the gap between meningococcal epidemiology and genomics. Finally, we briefly discuss the potential impact of meningococcal life style on its genome architecture and how in turn this genomic make-up might lead to a virulent phenotype making N. meningitidis an accidental pathogen. The overall properties of the meningococcal genome are characterized by genomic variability and instability, resulting in increased functional flexibility within this species. PMID:17572149

Schoen, Christoph; Joseph, Biju; Claus, Heike; Vogel, Ulrich; Frosch, Matthias

2007-11-01

277

Chapter 14: Genome  

E-print Network

Annotation of other genomes NCBI may assemble a genome prior to annotation, add annotations to a genome assembled elsewhere, or simply process an annotated genome to produce RefSeqs and maps for display in Map Viewer (Chapter 20). The basic procedures used to annotate other eukaryotic genomes are essentially the same as those used to annotate the human genome. However, the overall process is adjusted to accommodate the different types of input data that are available for each organism. Genes can be annotated on any genome for which a significant number of mRNA, EST, or protein sequences are available. Other features, such as clones, STS markers, and SNPs, can also be annotated whenever the relevant data are available for an organism. For example, genes and other features are placed on the mouse Whole Genome Shotgun (WGS) assembly from the Mouse Genome Sequencing Consortium (MGSC) by skipping the assembly steps used in the human process but following the annotation steps with relatively minor adjustments. A variation of the human process is also used to assemble and annotate genomic contigs from finished mouse clone sequences (see the Map Viewer display of the mouse genome).

Paul Kitts

278

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

E-print Network

ORIGINAL ARTICLE Tree diversity on islands: assembly rules, passive sampling and the theory of island biogeography K. C. Burns1,2 *, Jenny Berg1 , Ada Bialynicka-Birula1 , Sabrina Kratchmer1 in a temperate island archipelago. The theory of island biogeography (ToIB) predicts that island area affects

279

Genomic sequencing in cancer.  

PubMed

Genomic sequencing has provided critical insights into the etiology of both simple and complex diseases. The enormous reductions in cost for whole genome sequencing have allowed this technology to gain increasing use. Whole genome analysis has impacted research of complex diseases including cancer by allowing the systematic analysis of entire genomes in a single experiment, thereby facilitating the discovery of somatic and germline mutations, and identification of the insertions, deletions, and structural rearrangements, including translocations and inversions, in novel disease genes. Whole-genome sequencing can be used to provide the most comprehensive characterization of the cancer genome, the complexity of which we are only beginning to understand. Hence in this review, we focus on whole-genome sequencing in cancer. PMID:23178448

Tuna, Musaffe; Amos, Christopher I

2013-11-01

280

URBAN HEAT ISLAND  

E-print Network

We are all familiar with the fact that cities are generally warmer than the surrounding, more rural areas. We see it referenced most nights in our television weather reports. It is especially significant on nights with clear skies and light winds which favor radiational cooling. This is most significant in the rural areas but in the city, the excess heat absorbed during the day and the local heat sources maintain higher nighttime readings. During the days or nights with strong winds and clouds the differences are minimized due to mixing and the advective cooling of the city by the winds. Because of this relative warmth, a city may be referred to as an urban heat island. The reason the city is warmer than the country comes down to a difference between the energy gains and losses of each region. There are a number of factors that contribute to the relative warmth of cities according to Ackerman: During the day in rural areas, the solar energy absorbed near the ground evaporates water from the vegetation and soil. Thus, while there is a net solar energy gain, this is compensated to some degree by evaporative cooling. In cities, where there is less vegetation, the buildings, streets and sidewalks absorb the

unknown authors

281

URBAN HEAT ISLAND  

E-print Network

We are all familiar with the fact that cities are generally warmer than the surrounding, more rural areas. We see it referenced most nights in our television weather reports. It is especially significant on nights with clear skies and light winds which favor radiational cooling. This is most significant in the rural areas but in the city, the excess heat absorbed during the day and the local heat sources maintain higher nighttime readings. During the days or nights with strong winds and clouds the differences are minimzed due to mixing and the advective cooling of the city by the winds. Because of this relative warmth, a city may be referred to as an urban heat island. The reason the city is warmer than the country comes down to a difference between the energy gains and losses of each region. There are a number of factors that contribute to the relative warmth of cities according to Ackerman: During the day in rural areas, the solar energy absorbed near the ground evaporates water from the vegetation and soil. Thus, while there is a net solar energy gain, this is compensated to some degree by evaporative cooling. In cities, where there is less vegetation, the buildings, streets and sidewalks absorb the

unknown authors

282

The Staphylococcus aureus Pathogenicity Island 1 Protein gp6 Functions as an Internal Scaffold during Capsid Size Determination  

Microsoft Academic Search

Staphylococcus aureus pathogenicity island 1 (SaPI1) is a mobile genetic element that carries genes for several superantigen toxins. SaPI1 is normally stably integrated into the host genome but can become mobilized by “helper” bacteriophage 80?, leading to the packaging of SaPI1 genomes into phage-like transducing particles that are composed of structural proteins supplied by the helper phage but having smaller

Altaira D. Dearborn; Michael S. Spilman; Priyadarshan K. Damle; Jenny R. Chang; Eric B. Monroe; Jamil S. Saad; Gail E. Christie; Terje Dokland

2011-01-01

283

CpG-discover: A machine learning approach for CpG islands identification from human DNA sequence  

Microsoft Academic Search

CpG islands (CGIs) play a fundamental role in genome analysis as genomic markers and tumor markers. Identification of potential CGIs has contributed not only to the prediction of promoters of most house-keeping genes and many tissue-specific genes but also to the understanding of the epigenetic causes of cancer. The most current methods for identifying CGIs suffered from various limitations and

Man Lan; Yu Xu; Lin Li; Fei Wang; Ying Zuo; Yuan Chen; Chew Lim Tan; Jian Su

2009-01-01

284

Urban heat islands in China  

Microsoft Academic Search

We used 1954–1983 surface temperature from 42 Chinese urban (average population 1.7*106) and rural (average population 1.5*105) station pairs to study the urban heat island effects. Despite the fact that the rural stations are not true rural stations, the magnitude of the heat islands was calculated to average 0.23 °C over the thirty-year period with a minimum value during the

Wei-Chyung Wang; Zhaomei Zengl; Thomas R. Karl

1990-01-01

285

Eugene Island Block 330 field  

Microsoft Academic Search

The Eugene Island Block 330 field ranks third in cumulative hydrocarbon production on the federal Outer Continental Shelf of the United States and at peak production was the largest O.C.S. oil-producing field. This giant field, located offshore Louisiana, covers parts of seven blocks in the Eugene Island area, South Addition. The field was discovered by the Pennzoil 1, OCS-G 2115

D. S. Holland; D. R. Lammlein; J. B. Leedy

1988-01-01

286

Magnetic island formation in tokamaks  

SciTech Connect

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

Yoshikawa, S.

1989-04-01

287

Enabling responsible public genomics.  

PubMed

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

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

2010-01-01

288

Number of CpG islands and genes in human and mouse  

SciTech Connect

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

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

1993-11-15

289

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

PubMed Central

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

2013-01-01

290

HeteroGenome: database of genome periodicity  

PubMed Central

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

291

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

NASA Astrophysics Data System (ADS)

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

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

2014-09-01

292

Complete genome sequence of the plant commensal Pseudomonas fluorescens Pf5  

Microsoft Academic Search

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

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

2005-01-01

293

First Full Genome Sequence of a Human Enterovirus A120, Isolated in Madagascar  

PubMed Central

We report the first complete genome sequence of an enterovirus isolate belonging to the human enterovirus A species of the Picornaviridae family and to type A120 (EV-A120). The EV-A120 isolate MAD-2741-11 was obtained from the stool of a healthy child living on Madagascar Island. The isolate genome was amplified by a reverse transcription-PCR method, and the consensus sequence was determined. PMID:24948760

Joffret, Marie-Line; Delpeyroux, Francis; Heraud, Jean-Michel

2014-01-01

294

Genome scans and elusive candidate genes: detecting the variation that matters for speciation.  

PubMed

Next-generation sequencing is providing us with vast amounts of genetic data, yet we are currently struggling in our attempts to make sense of them. In particular, it has proven difficult to link phenotypic divergence and speciation to genome level divergence. In the current issue of Molecular Ecology, Ruegg et al. () present new empirical results from two closely related bird taxa. They use a promising approach combining genome scan and candidate gene analysis. Their results suggest that we may have been looking in vain for candidate speciation genes by focusing only on genes found within genomic islands of divergence. This is because genes important in divergence and speciation may not be detected by genome scans and because features of the genomic architecture per se may have a large effect on the pattern of genome divergence. PMID:25263403

Saetre, Glenn-Peter

2014-10-01

295

Horse Genome Project  

NSDL National Science Digital Library

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

296

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

297

Reference Based Genome Compression  

E-print Network

DNA sequencing technology has advanced to a point where storage is becoming the central bottleneck in the acquisition and mining of more data. Large amounts of data are vital for genomics research, and generic compression tools, while viable, cannot offer the same savings as approaches tuned to inherent biological properties. We propose an algorithm to compress a target genome given a known reference genome. The proposed algorithm first generates a mapping from the reference to the target genome, and then compresses this mapping with an entropy coder. As an illustration of the performance: applying our algorithm to James Watson's genome with hg18 as a reference, we are able to reduce the 2991 megabyte (MB) genome down to 6.99 MB, while Gzip compresses it to 834.8 MB.

Chern, Bobbie; Manolakos, Alexandros; No, Albert; Venkat, Kartik; Weissman, Tsachy

2012-01-01

298

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

NASA Technical Reports Server (NTRS)

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

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

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

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

2001-01-01

299

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

NASA Technical Reports Server (NTRS)

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

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

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

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

2001-01-01

300

One million served: Rhode Island`s recycling facility  

SciTech Connect

Rhode Island`s landfill and adjacent materials recovery facility (MRF) in Johnston, both owned by the quasi-public Rhode Island Resource Recovery Corp. (RIRRC, Johnston), serve the entire state. The $12-million recycling facility was built in 1989 next to the state`s sole landfill, the Central Landfill, which accepts only in-state trash. The MRF is operated for RIRRC by New England CRInc. (Hampton, N.H.), a unit of Waste Management, Inc. (WMI, Oak Brook, Ill.). It handles a wide variety of materials, from the usual newspaper, cardboard, and mixed containers to new streams such as wood waste, scrap metal, aseptic packaging (milk and juice boxes), and even textiles. State municipalities are in the process of adding many of these new recyclable streams into their curbside collection programs, all of which feed the facility.

Malloy, M.G.

1997-11-01

301

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

302

Meeting Highlights: Genome Informatics  

PubMed Central

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

Ashurst, Jennifer

2003-01-01

303

Querying genomic databases  

SciTech Connect

A natural-language interface has been developed that retrieves genomic information by using a simple subset of English. The interface spares the biologist from the task of learning database-specific query languages and computer programming. Currently, the interface deals with the E. coli genome. It can, however, be readily extended and shows promise as a means of easy access to other sequenced genomic databases as well.

Baehr, A.; Hagstrom, R.; Joerg, D.; Overbeek, R.

1991-09-01

304

Propagation of Big Island eddies  

NASA Astrophysics Data System (ADS)

Using satellite altimetry data, we have observed a series of anticyclonic eddies as they form at the Big Island of Hawaii and have tracked them as they move away from the island. While similar eddies have been observed near the Hawaiian Islands in previous studies, the fate of the anticyclonic eddies has previously been unclear. The eddies that we observed initially propagated to the southwest but consistently changed propagation direction to the northwest later in their lifetimes. This was intriguing to us, as theoretically, the decay of isolated anticyclonic eddies on a ? plane should cause them to continually move toward the southwest. Such isolated eddy dynamics are unable to account for the observed change to northwestward eddy propagation, and the presence of the westward flowing North Equatorial Current turns out to be important to the Big Island eddy dynamics. The eddies are not passively advected by the North Equatorial Current; rather, the mean flow changes the propagation characteristics of the eddies. An existing theory that includes meridionally varying, purely zonal mean flow is shown to account for the observed propagation of the Big Island eddies if the zonal variation of the mean flow is considered.

Holland, Christina L.; Mitchum, Gary T.

2001-01-01

305

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.

306

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.

307

Between Two Fern Genomes  

PubMed Central

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

2014-01-01

308

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

PubMed Central

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

2011-01-01

309

Restriction Landmark Genomic Scanning (RLGS) spot identification by second generation virtual RLGS in multiple genomes with multiple enzyme combinations  

PubMed Central

Background Restriction landmark genomic scanning (RLGS) is one of the most successfully applied methods for the identification of aberrant CpG island hypermethylation in cancer, as well as the identification of tissue specific methylation of CpG islands. However, a limitation to the utility of this method has been the ability to assign specific genomic sequences to RLGS spots, a process commonly referred to as "RLGS spot cloning." Results We report the development of a virtual RLGS method (vRLGS) that allows for RLGS spot identification in any sequenced genome and with any enzyme combination. We report significant improvements in predicting DNA fragment migration patterns by incorporating sequence information into the migration models, and demonstrate a median Euclidian distance between actual and predicted spot migration of 0.18 centimeters for the most complex human RLGS pattern. We report the confirmed identification of 795 human and 530 mouse RLGS spots for the most commonly used enzyme combinations. We also developed a method to filter the virtual spots to reduce the number of extra spots seen on a virtual profile for both the mouse and human genomes. We demonstrate use of this filter to simplify spot cloning and to assist in the identification of spots exhibiting tissue-specific methylation. Conclusion The new vRLGS system reported here is highly robust for the identification of novel RLGS spots. The migration models developed are not specific to the genome being studied or the enzyme combination being used, making this tool broadly applicable. The identification of hundreds of mouse and human RLGS spot loci confirms the strong bias of RLGS studies to focus on CpG islands and provides a valuable resource to rapidly study their methylation. PMID:18053125

Smiraglia, Dominic J; Kazhiyur-Mannar, Ramakrishnan; Oakes, Christopher C; Wu, Yue-Zhong; Liang, Ping; Ansari, Tahmina; Su, Jian; Rush, Laura J; Smith, Laura T; Yu, Li; Liu, Chunhui; Dai, Zunyan; Chen, Shih-Shih; Wang, Shu-Huei; Costello, Joseph; Ioshikhes, Ilya; Dawson, David W; Hong, Jason S; Teitell, Michael A; Szafranek, Angela; Camoriano, Marta; Song, Fei; Elliott, Rosemary; Held, William; Trasler, Jacquetta M; Plass, Christoph; Wenger, Rephael

2007-01-01

310

HLA in anthropology: the enigma of Easter Island.  

PubMed

In this article, we first present four significant cases where human leukocyte antigen (HLA) studies have been useful for the reconstruction of human peopling history on the worldwide scale; i.e., the spread of modern humans from East Africa, the colonization of East Asia along two geographic routes, the co-evolution of genes and languages in Africa, and the peopling of Europe through a main northward migration. These examples show that natural selection did not erase the genetic signatures of our past migrations in the HLA genetic diversity patterns observed today. In the second part, we summarize our studies on Easter Island. Using genomic HLA typing, we could trace an introduction of HLA alleles of native American (Amerindian) origin to Easter Island before the Peruvian slave trades; i.e., before the 1860s, and provide suggestive evidence that they may have already been introduced in prehistoric time. Our results give further support to an initial Polynesian population of the island, but also reveal an early contribution by Amerindians. Together, our data illustrate the usefulness of typing for HLA alleles to complement genetic analyses in anthropological investigations. PMID:25095505

Sanchez-Mazas, Alicia; Thorsby, Erik

2013-01-01

311

phiGENOME: an integrative navigation throughout bacteriophage genomes.  

PubMed

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

Stano, Matej; Klucar, Lubos

2011-11-01

312

The American Experience: Coney Island  

NSDL National Science Digital Library

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

313

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.

314

Rotating Accelerator-Mode Islands  

E-print Network

The existence of rotating accelerator-mode islands (RAIs), performing quasiregular motion in rotational resonances of order $m>1$ of the standard map, is firmly established by an accurate numerical analysis of all the known data. It is found that many accelerator-mode islands for relatively small nonintegrability parameter $K$ are RAIs visiting resonances of different orders $m\\leq 3$. For sufficiently large $K$, one finds also ``pure'' RAIs visiting only resonances of the {\\em same} order, $m=2$ or $m=3$. RAIs, even quite small ones, are shown to exhibit sufficient stickiness to produce an anomalous chaotic transport. The RAIs are basically different in nature from accelerator-mode islands in resonances of the ``forced'' standard map which was extensively studied recently in the context of quantum accelerator modes.

Oded Barash; Itzhack Dana

2006-12-24

315

Rhode Island Critical Resource Atlas  

NSDL National Science Digital Library

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

316

The Big Island of Hawaii  

NASA Technical Reports Server (NTRS)

Boasting snow-covered mountain peaks and tropical forest, the Island of Hawaii, the largest of the Hawaiian Islands, is stunning at any altitude. This false-color composite (processed to simulate true color) image of Hawaii was constructed from data gathered between 1999 and 2001 by the Enhanced Thematic Mapper plus (ETM+) instrument, flying aboard the Landsat 7 satellite. The Landsat data were processed by the National Oceanographic and Atmospheric Administration (NOAA) to develop a landcover map. This map will be used as a baseline to chart changes in land use on the islands. Types of change include the construction of resorts along the coastal areas, and the conversion of sugar plantations to other crop types. Hawaii was created by a 'hotspot' beneath the ocean floor. Hotspots form in areas where superheated magma in the Earth's mantle breaks through the Earth's crust. Over the course of millions of years, the Pacific Tectonic Plate has slowly moved over this hotspot to form the entire Hawaiian Island archipelago. The black areas on the island (in this scene) that resemble a pair of sun-baked palm fronds are hardened lava flows formed by the active Mauna Loa Volcano. Just to the north of Mauna Loa is the dormant grayish Mauna Kea Volcano, which hasn't erupted in an estimated 3,500 years. A thin greyish plume of smoke is visible near the island's southeastern shore, rising from Kilauea-the most active volcano on Earth. Heavy rainfall and fertile volcanic soil have given rise to Hawaii's lush tropical forests, which appear as solid dark green areas in the image. The light green, patchy areas near the coasts are likely sugar cane plantations, pineapple farms, and human settlements. Courtesy of the NOAA Coastal Services Center Hawaii Land Cover Analysis project

2002-01-01

317

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.

Goodwin, Mel

318

Microarray Comparative Genomic Hybridisation Analysis Incorporating Genomic Organisation, and Application to Enterobacterial Plant Pathogens  

PubMed Central

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

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

2009-01-01

319

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

PubMed

We report the first complete genome sequence of a beta-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; Carrère, 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

2008-09-01

320

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, Geraldine; Mangenot, Sophie; Glew, Michelle; Bontemps, Cyril; Capela, Delphine; Carrere, Sebastien; Cruveiller, Stephane; Dossat, Carole; Lajus, Aurelie; Marchetti, Marta; Poinsot, Verena; Rouy, Zoe; Servin, Bertrand; Saad, Maged; Schenowitz, Chantal; Barbe, Valerie; Batut, Jacques; Medigue, Claudine; Masson-Boivin, Catherine

2008-01-01

321

Pacific Islands The National Bycatch Report: Pacific Islands Region  

E-print Network

Reduction Success Stories Annual incidental take limits for two species of sea turtles (leatherback loggerhead and leatherback sea turtle bycatch. Circle hooks are also used by many participants in the Hawaii turtles) bycatch estimates were available for 2 fisheries and 23 species/groups in 2005. Pacific Islands

322

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

323

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

324

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.

325

Genomic taxonomy of vibrios  

Microsoft Academic Search

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

Cristiane C Thompson; Ana Vicente; Rangel C Souza; Ana Tereza R Vasconcelos; Tammi Vesth; Nelson Alves; David W Ussery; Tetsuya Iida; Fabiano L Thompson

2009-01-01

326

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

327

Species: Comparing Their Genome  

NSDL National Science Digital Library

The reprinted resource illustrates how mapping the genome of different species reveals that: all living things share parallel genes, the genome of other species can be used for human disease research, many diseases are caused by defective genes or proteins, and so far, the mouse offers the best insight into human disease.

Howard Hughes Medical Institute (Howard Hughes Medical Institute;)

2001-06-01

328

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

329

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

330

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

331

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

332

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 ...

333

Cancer and Asians/Pacific Islanders  

MedlinePLUS

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

334

Native Hawaiian & Other Pacific Islander Populations  

MedlinePLUS

... Other Pacific Islander individuals in the United States. States with the largest Native Hawaiian or Other Pacific Islander populations in 2011 were Hawaii (359,000) and California (329,000) . The Native ...

335

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.

336

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

337

The Complete Genome Sequence of Mycoplasma bovis Strain Hubei-1  

PubMed Central

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

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

2011-01-01

338

WEST SIDE OF WAKE ISLAND AIRFIELD TERMINAL, BUILDING 1502 LOOKING ...  

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

WEST SIDE OF WAKE ISLAND AIRFIELD TERMINAL, BUILDING 1502 LOOKING NORTHEAST AT SOUTHWEST CORNER SHOWING OVERHANGS (01/02/2008) - Wake Island Airfield, Terminal Building, West Side of Wake Avenue, Wake Island, Wake Island, UM

339

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 CORNER FROM ACROSS TARMAC (12/25/2007) - Wake Island Airfield, Terminal Building, West Side of Wake Avenue, Wake Island, Wake Island, UM

340

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

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

WAKE ISLAND AIRFIELD TERMINAL, BUILDING 1502 LOOKING NORTHWEST AT SOUTHEAST CORNER OF LOBBY OF BUILDING (12/29/2007) - Wake Island Airfield, Terminal Building, West Side of Wake Avenue, Wake Island, Wake Island, UM

341

WAKE ISLAND AIRFIELD TERMINAL, BUILDING 1502 LOOKING NORTHEAST AT WEST ...  

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

WAKE ISLAND AIRFIELD TERMINAL, BUILDING 1502 LOOKING NORTHEAST AT WEST SIDE SHOWING FLAG, GUN, ENGINES (12/29/2007) - Wake Island Airfield, Terminal Building, West Side of Wake Avenue, Wake Island, Wake Island, UM

342

WAKE ISLAND AIRFIELD TERMINAL, BUILDING 1502 LOOKING NORTHEAST AT SOUTHWEST ...  

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

WAKE ISLAND AIRFIELD TERMINAL, BUILDING 1502 LOOKING NORTHEAST AT SOUTHWEST CORNER FROM BEHIND CONTROL TOWER (12/28/2007) - Wake Island Airfield, Terminal Building, West Side of Wake Avenue, Wake Island, Wake Island, UM

343

SOUTHWEST CORNER OF WAKE ISLAND AIRFIELD TERMINAL, BUILDING 1502 LOOKING ...  

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

SOUTHWEST CORNER OF WAKE ISLAND AIRFIELD TERMINAL, BUILDING 1502 LOOKING EAST AT WEST FAÇADE WITH SCALE POLE (01/02/2008) - Wake Island Airfield, Terminal Building, West Side of Wake Avenue, Wake Island, Wake Island, UM

344

75 FR 77889 - Virgin Islands; Major Disaster and Related Determinations  

Federal Register 2010, 2011, 2012, 2013

...Territory of the U.S. Virgin Islands have been designated as adversely...this major disaster: The island of St. Croix for Public Assistance. All islands in the Territory of the U.S. Virgin Islands are eligible to...

2010-12-14

345

Flooding of regular islands by chaotic states  

E-print Network

We introduce a criterion for the existence of regular states in systems with a mixed phase space. If this condition is not fulfilled chaotic eigenstates substantially extend into a regular island. Wave packets started in the chaotic sea progressively flood the island. The extent of flooding by eigenstates and wave packets increases logarithmically with the size of the chaotic sea and the time, respectively. This new effect can be observed for island chains with just 10 islands.

A. Bäcker; R. Ketzmerick; A. G. Monastra

2004-09-14

346

Islands geologi frn Tertir till recent  

E-print Network

1 Islands geologi från Tertiär till recent #12;2 Islands geologi från Tertiär till recent Erik Sturkell Framsidan: Riftzonen på norra Island. En graben som går igenom Dalfjall som ligger inom Kraflas vulkansystem. Bilden är tagen från riksväg 1 norrut. © Erik Sturkell #12;3 Innehållsförteckning Island i

Ingólfsson, �lafur

347

Computing Maximal Islands C. Bautista-Santiago  

E-print Network

Computing Maximal Islands C. Bautista-Santiago J.M. D´iaz-B´a~nez D. Lara P. P´erez-Lantero § J, an island I(S, C) S is the inter- section of S and a convex region C. We study the problem of finding a maximal island according to cer- tain criterium. For instance, a largest monochromatic island I(S, C

Urrutia, Jorge

348

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

Code of Federal Regulations, 2010 CFR

...2010-10-01 false Folly Island, SC to Hilton Head Island, SC. 7.70 Section...Coast § 7.70 Folly Island, SC to Hilton Head Island, SC. (a) A line drawn...thence to the easternmost extremity of Hilton Head at latitude 32°13.2? N....

2010-10-01

349

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

Microsoft Academic Search

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

MARSHALL I. WEISLER

1995-01-01

350

How can endemic proboscideans help us understand the “island rule”? A case study of Mediterranean islands  

Microsoft Academic Search

Several hypotheses have been advanced to explain size-change processes in terrestrial vertebrates on islands and in island-like ecosystems. Extinct endemic insular proboscideans are especially appropriate subjects for investigating this issue, given the frequency with which proboscideans colonised islands, and the multiple patterns in size reduction experienced by endemic taxa on different islands, as well as on a single one. To

Maria Rita Palombo

2007-01-01

351

Two-fluid magnetic island dynamics in slab geometry. I. Isolated islands  

E-print Network

plasma confinement because heat and particles are able to travel radially from one side of an islandTwo-fluid magnetic island dynamics in slab geometry. I. Isolated islands Richard Fitzpatricka magnetic island propagating through a slab plasma with uniform but different ion and electron fluid

Fitzpatrick, Richard

352

Two-fluid magnetic island dynamics in slab geometry: I -Isolated islands  

E-print Network

. Such islands degrade plasma confinement because heat and particles are able to travel ra- dially from one sideTwo-fluid magnetic island dynamics in slab geometry: I - Isolated islands Richard Fitzpatrick magnetic island propagating through a slab plasma with uniform but different ion and electron fluid veloc

Fitzpatrick, Richard

353

33 CFR 80.720 - St. Simons Island, GA to Amelia Island, FL.  

Code of Federal Regulations, 2013 CFR

...2013-07-01 2013-07-01 false St. Simons Island, GA to Amelia Island, FL. 80.720 Section 80.720 Navigation...DEMARCATION LINES Seventh District § 80.720 St. Simons Island, GA to Amelia Island, FL. (a) A line drawn from St. Simons...

2013-07-01

354

33 CFR 80.720 - St. Simons Island, GA to Amelia Island, FL.  

Code of Federal Regulations, 2012 CFR

...2012-07-01 2012-07-01 false St. Simons Island, GA to Amelia Island, FL. 80.720 Section 80.720 Navigation...DEMARCATION LINES Seventh District § 80.720 St. Simons Island, GA to Amelia Island, FL. (a) A line drawn from St. Simons...

2012-07-01

355

33 CFR 80.720 - St. Simons Island, GA to Amelia Island, FL.  

Code of Federal Regulations, 2010 CFR

...2010-07-01 2010-07-01 false St. Simons Island, GA to Amelia Island, FL. 80.720 Section 80.720 Navigation...DEMARCATION LINES Seventh District § 80.720 St. Simons Island, GA to Amelia Island, FL. (a) A line drawn from St. Simons...

2010-07-01

356

33 CFR 80.720 - St. Simons Island, GA to Amelia Island, FL.  

Code of Federal Regulations, 2011 CFR

...2011-07-01 2011-07-01 false St. Simons Island, GA to Amelia Island, FL. 80.720 Section 80.720 Navigation...DEMARCATION LINES Seventh District § 80.720 St. Simons Island, GA to Amelia Island, FL. (a) A line drawn from St. Simons...

2011-07-01

357

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 Islands Rebekah Shirley , Christopher Jones, Daniel Kammen Energy and Resources Group, University xxxx Keywords: Carbon footprint Green house gas emissions Small Island Developing States Island regions

Kammen, Daniel M.

358

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

E-print Network

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

Pedlosky, Joseph

359

Genome Rearrangement: A Planning Approach  

E-print Network

Evolutionary trees of species can be reconstructed by pairwise comparison of their entire genomes. Such a comparison can be quantified by determining the number of events that change the order of genes in a genome. Earlier Erdem and Tillier formulated the pairwise comparison of entire genomes as the problem of planning rearrangement events that transform one genome to the other. We reformulate this problem as a planning problem to extend its applicability to genomes with multiple copies of genes and with unequal gene content, and illustrate its applicability and effectiveness on three real datasets: mitochondrial genomes of Metazoa, chloroplast genomes of Campanulaceae, chloroplast genomes of various land plants and green algae.

Tansel Uras; Esra Erdem

360

Unique DNA methylome profiles in CpG island methylator phenotype colon cancers  

PubMed Central

A subset of colorectal cancers was postulated to have the CpG island methylator phenotype (CIMP), a higher propensity for CpG island DNA methylation. The validity of CIMP, its molecular basis, and its prognostic value remain highly controversial. Using MBD-isolated genome sequencing, we mapped and compared genome-wide DNA methylation profiles of normal, non-CIMP, and CIMP colon specimens. Multidimensional scaling analysis revealed that each specimen could be clearly classified as normal, non-CIMP, and CIMP, thus signifying that these three groups have distinctly different global methylation patterns. We discovered 3780 sites in various genomic contexts that were hypermethylated in both non-CIMP and CIMP colon cancers when compared with normal colon. An additional 2026 sites were found to be hypermethylated in CIMP tumors only; and importantly, 80% of these sites were located in CpG islands. These data demonstrate on a genome-wide level that the additional hypermethylation seen in CIMP tumors occurs almost exclusively at CpG islands and support definitively that these tumors were appropriately named. When these sites were examined more closely, we found that 25% were adjacent to sites that were also hypermethylated in non-CIMP tumors. Thus, CIMP is also characterized by more extensive methylation of sites that are already prone to be hypermethylated in colon cancer. These observations indicate that CIMP tumors have specific defects in controlling both DNA methylation seeding and spreading and serve as an important first step in delineating molecular mechanisms that control these processes. PMID:21990380

Xu, Yaomin; Hu, Bo; Choi, Ae-Jin; Gopalan, Banu; Lee, Byron H.; Kalady, Matthew F.; Church, James M.; Ting, Angela H.

2012-01-01

361

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.

362

UV - VIRGIN ISLANDS NATIONAL PARK  

EPA Science Inventory

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

363

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...

364

The Virgin Islands robotic telescope  

NASA Astrophysics Data System (ADS)

The Etelman Observatory of the University of the Virgin Islands is the southernmost and easternmost optical observatory in the United States. The observatory is located at an elevation of 420 meters on the island of St. Thomas, US Virgin Islands. The site has exceptionally good seeing (frequently better than 1 arc-second), dark skies, and the ability to reach deep into the southern hemisphere and to plug the northern-hemisphere longitude gap between the US and Europe. Astronomers at the College of Charleston, South Carolina State University, and the University of the Virgin Islands have formed a consortium to refurbish the facility, conduct detailed site surveys, purchase a 0.5-meter telescope and instrumentation, and operate the facility robotically. The telescope, instrumentation, and dome have all been installed, and we are remotely obtaining commissioning observations. Our operations mode (manual, remote-controlled, or fully robotic) will simultaneously support our research, participation in multi-site campaigns, and the educational and outreach missions of our institutions. Further details are available at http://astro.uvi.edu/.

Neff, J. E.

2004-10-01

365

Chaos in easter island ecology.  

PubMed

This paper demonstrates that a recently proposed dynamical model for the ecology of Easter Island admits periodic and chaotic attractors, not previously reported. Such behavior may more realistically depict the population dynamics of general ecosystems and illustrates the power of simple models to produce the kind of complex behavior that is ubiquitous in such systems. PMID:21933513

Sprott, J C

2011-10-01

366

Sipuncula from Hainan Island (China)  

Microsoft Academic Search

Sipunculans from shallow depths ranging from 0 to 44 m, collected by two Chinese-German expeditions to Hainan Island (China) during the years 1990 and 1992, are recorded. Seventeen species in eight genera and five families are recognized from the total 271 individuals collected. An analysis of the sipunculan literature has shown that 10 of these species are new records for

S. Pagola-Carte; J. I. Saiz-Salinas

2000-01-01

367

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

368

The formation of island ecosystems  

Microsoft Academic Search

Island ecosystems are formed from the same generic building blocks as continental ecosystems. These can be reduced to five: (1) the terrestrial habitat (soil-parent material and topography), (2) the regional and local climate, (3) the regional biota with differential restrictions of accessibility, (4) the ecological roles assumed by the species including their potential for adaptation, and (5) the overriding dimensions

Dieter Mueller-Dombois

1992-01-01

369

Genomic imprinting: parental influence on the genome  

Microsoft Academic Search

Genomic imprinting affects several dozen mammalian genes and results in the expression of those genes from only one of the two parental chromosomes. This is brought about by epigenetic instructions — imprints — that are laid down in the parental germ cells. Imprinting is a particularly important genetic mechanism in mammals, and is thought to influence the transfer of nutrients

Wolf Reik; Jörn Walter

2001-01-01

370

Heat island development in Mexico City  

Microsoft Academic Search

The present paper describes the climatology of the near surface urban heat island of Mexico City, using hourly data from two recently installed automatic stations at a rural and an urban site. The results show that the nocturnal heat island was more frequent (75% of the time for the period examined) than daytime cases (25%). The maximum nocturnal heat island

Ernesto Jauregui

1997-01-01

371

Ecology of Great Salt Pond, Block Island  

EPA Science Inventory

Great Salt Pond is an island of estuarine water on Block Island, which sits in the middle of the Northwest Atlantic Continental Shelf. When the last continental glaciers retreated, they left a high spot on a terminal moraine. The rising sea from melting glaciers formed two island...

372

MARINE BOTTOM COMMUNITIES OF BLOCK ISLAND WATERS  

EPA Science Inventory

The sea has long been an integral part of Block Island's natural history, beginning when the rising sea surrounded the high spot on a Pleistocene terminal moraine that became Block Island. The southern New England continental shelf, which lies around Block Island, and the Great S...

373

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.

374

The island-mainland species turnover relationship.  

PubMed

Many oceanic islands are notable for their high endemism, suggesting that islands may promote unique assembly processes. However, mainland assemblages sometimes harbour comparable levels of endemism, suggesting that island biotas may not be as unique as is often assumed. Here, we test the uniqueness of island biotic assembly by comparing the rate of species turnover among islands and the mainland, after accounting for distance decay and environmental gradients. We modelled species turnover as a function of geographical and environmental distance for mainland (M-M) communities of Anolis lizards and Terrarana frogs, two clades that have diversified extensively on Caribbean islands and the mainland Neotropics. We compared mainland-island (M-I) and island-island (I-I) species turnover with predictions of the M-M model. If island assembly is not unique, then the M-M model should successfully predict M-I and I-I turnover, given geographical and environmental distance. We found that M-I turnover and, to a lesser extent, I-I turnover were significantly higher than predicted for both clades. Thus, in the first quantitative comparison of mainland-island species turnover, we confirm the long-held but untested assumption that island assemblages accumulate biodiversity differently than their mainland counterparts. PMID:22874754

Stuart, Yoel E; Losos, Jonathan B; Algar, Adam C

2012-10-01

375

Pacific Islands Monograph Series Style Guidelines  

E-print Network

1 Pacific Islands Monograph Series Style Guidelines Abbreviations and Acronyms Omit periods. Spell Tabai, the president; former President Clinton Capitalize Islanders when referring to people of the Pacific Islands Names of institutions, agreements, and the like are capitalized when the full title

376

Fur Seal Industry of the Pribilof Islands,  

E-print Network

Fur Seal Industry of the Pribilof Islands, 1786-1965 UNITED STATES DEPARTMENT OF THE INTERIOR FISH AND WILDLIFE SERVICE BUREAU OF COMMERCIAL FISHERIES Circular 275 #12;AVERAGE VALUE OF PRIBILOF ISLANDS Seal Industry of the Pribilof Islands, 1786-1965 By FRANCIS RILEY Circular 275 Washington, D.C. October

377

Big islands in dispersing billiardlike potentials.  

E-print Network

Big islands in dispersing billiard­like potentials. Vered Rom­Kedar The Department of Applied Abstract We derive a rigorous estimate of the size of islands (in both phase space and parameter space as a parameter ffl ! 0, islands of poly­ nomial size in ffl appear. This suggests that the loss of ergodicity via

378

40 CFR 81.432 - Virgin Islands.  

...2014-07-01 2014-07-01 false Virgin Islands. 81.432 Section 81.432 Protection...Important Value § 81.432 Virgin Islands. Area name Acreage Public Law establishing Federal land manager Virgin Islands NP 12,295 84-925...

2014-07-01

379

SUPERLATTICES OF ATOMS, MOLECULES AND ISLANDS  

E-print Network

SUPERLATTICES OF ATOMS, MOLECULES AND ISLANDS H. BRUNE Institut de Physique des Nanostructures quantum dots, and metallic islands, by means of self-assembly during atomic-beam growth on single crystal stabilize ordered superlattices, and vertical correlations of growth sequences of buried islands

Brune, Harald

380

Observation of energetic electrons within magnetic islands  

E-print Network

LETTERS Observation of energetic electrons within magnetic islands L.-J. CHEN1 *, A. BHATTACHARJEE1 suggests that volume- filling contracting magnetic islands formed during reconnection can produce a large electrons and magnetic islands during reconnection in the Earth's magnetosphere. The results indicate

Loss, Daniel

381

Ecology and Evolution: Islands of Change.  

ERIC Educational Resources Information Center

This book was designed for middle and junior high school science classes and focuses on island biogeography, ecology, and evolution. Sections include: (1) "Galapagos: Frame of Reference"; (2) "Ecology and Islands"; and (3) "Evolution." Nineteen standards-based activities use the Galapagos Islands as a running theme but are designed to help…

Benz, Richard

382

Island wakes in the Southern California Bight  

Microsoft Academic Search

Wind- and current-induced island wakes were investigated using a multiplatform approach of in situ, remote sensing, and numerical model simulations for the Southern California Bight (SCB). Island wind wakes are a result of sheltering from the wind, with weak wind mixing, strong heat storage, and consequent high sea surface temperature (SST). Wind wakes around Santa Catalina Island are most persistent

R. M. A. Caldeira; P. Marchesiello; N. P. Nezlin; P. M. DiGiacomo; J. C. McWilliams

2005-01-01

383

The Bahamas Bahamian Conservation Biology: Andros Island  

E-print Network

The Bahamas Bahamian Conservation Biology: Andros Island Summer Study Abroad TENTATIVE DATES: July_abroad@ncsu.edu http://studyabroad.ncsu.edu Explore the biodiversity of Andros, the largest island of the Bahamas from Ft. Lauderdale to Andros Island Note: Travel to Ft. Lauderdale and personal expenses

Langerhans, Brian

384

The Bahamas Bahamian Conservation Biology: Andros Island  

E-print Network

The Bahamas Bahamian Conservation Biology: Andros Island Summer Study Abroad DATES: May 31 - June_abroad@ncsu.edu http://studyabroad.ncsu.edu Explore the biodiversity of Andros, the largest island of the Bahamas: Travel to Andros Island and personal expenses are not included APPLY: Apply online at http

Langerhans, Brian

385

Genome sequence of adherent-invasive Escherichia coli and comparative genomic analysis with other E. coli pathotypes  

PubMed Central

Background Adherent and invasive Escherichia coli (AIEC) are commonly found in ileal lesions of Crohn's Disease (CD) patients, where they adhere to intestinal epithelial cells and invade into and survive in epithelial cells and macrophages, thereby gaining access to a typically restricted host niche. Colonization leads to strong inflammatory responses in the gut suggesting that AIEC could play a role in CD immunopathology. Despite extensive investigation, the genetic determinants accounting for the AIEC phenotype remain poorly defined. To address this, we present the complete genome sequence of an AIEC, revealing the genetic blueprint for this disease-associated E. coli pathotype. Results We sequenced the complete genome of E. coli NRG857c (O83:H1), a clinical isolate of AIEC from the ileum of a Crohn's Disease patient. Our sequence data confirmed a phylogenetic linkage between AIEC and extraintestinal pathogenic E. coli causing urinary tract infections and neonatal meningitis. The comparison of the NRG857c AIEC genome with other pathogenic and commensal E. coli allowed for the identification of unique genetic features of the AIEC pathotype, including 41 genomic islands, and unique genes that are found only in strains exhibiting the adherent and invasive phenotype. Conclusions Up to now, the virulence-like features associated with AIEC are detectable only phenotypically. AIEC genome sequence data will facilitate the identification of genetic determinants implicated in invasion and intracellular growth, as well as enable functional genomic studies of AIEC gene expression during health and disease. PMID:21108814

2010-01-01

386

Comparative Genomics of 12 Strains of Erwinia amylovora Identifies a Pan-Genome with a Large Conserved Core  

PubMed Central

The plant pathogen Erwinia amylovora can be divided into two host-specific groupings; strains infecting a broad range of hosts within the Rosaceae subfamily Spiraeoideae (e.g., Malus, Pyrus, Crataegus, Sorbus) and strains infecting Rubus (raspberries and blackberries). Comparative genomic analysis of 12 strains representing distinct populations (e.g., geographic, temporal, host origin) of E. amylovora was used to describe the pan-genome of this major pathogen. The pan-genome contains 5751 coding sequences and is highly conserved relative to other phytopathogenic bacteria comprising on average 89% conserved, core genes. The chromosomes of Spiraeoideae-infecting strains were highly homogeneous, while greater genetic diversity was observed between Spiraeoideae- and Rubus-infecting strains (and among individual Rubus-infecting strains), the majority of which was attributed to variable genomic islands. Based on genomic distance scores and phylogenetic analysis, the Rubus-infecting strain ATCC BAA-2158 was genetically more closely related to the Spiraeoideae-infecting strains of E. amylovora than it was to the other Rubus-infecting strains. Analysis of the accessory genomes of Spiraeoideae- and Rubus-infecting strains has identified putative host-specific determinants including variation in the effector protein HopX1Ea and a putative secondary metabolite pathway only present in Rubus-infecting strains. PMID:23409014

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

2013-01-01

387

Numerical Simulations of the Island-Induced Circulations over the Island of Hawaii during HaRP  

E-print Network

Numerical Simulations of the Island-Induced Circulations over the Island of Hawaii during HaRP YANG island-scale circulations over the island of Hawaii during the Hawaiian Rainband Project (HaRP, 11 July

Chen, Yi-Leng

388

Toward 959 nematode genomes  

PubMed Central

The sequencing of the complete genome of the nematode Caenorhabditis elegans was a landmark achievement and ushered in a new era of whole-organism, systems analyses of the biology of this powerful model organism. The success of the C. elegans genome sequencing project also inspired communities working on other organisms to approach genome sequencing of their species. The phylum Nematoda is rich and diverse and of interest to a wide range of research fields from basic biology through ecology and parasitic disease. For all these communities, it is now clear that access to genome scale data will be key to advancing understanding, and in the case of parasites, developing new ways to control or cure diseases. The advent of second-generation sequencing technologies, improvements in computing algorithms and infrastructure and growth in bioinformatics and genomics literacy is making the addition of genome sequencing to the research goals of any nematode research program a less daunting prospect. To inspire, promote and coordinate genomic sequencing across the diversity of the phylum, we have launched a community wiki and the 959 Nematode Genomes initiative (www.nematodegenomes.org/). Just as the deciphering of the developmental lineage of the 959 cells of the adult hermaphrodite C. elegans was the gateway to broad advances in biomedical science, we hope that a nematode phylogeny with (at least) 959 sequenced species will underpin further advances in understanding the origins of parasitism, the dynamics of genomic change and the adaptations that have made Nematoda one of the most successful animal phyla. PMID:24058822

Kumar, Sujai; Koutsovoulos, Georgios; Kaur, Gaganjot; Blaxter, Mark

2012-01-01

389

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

390

Comparative and Functional Genomics Comp Funct Genom 2003; 4: 239245.  

E-print Network

Comparative and Functional Genomics Comp Funct Genom 2003; 4: 239­245. Published online 1 April://www.botany.iastate.edu/mash/metnetex/metabolicnetex.html) is pub- licly available software in development for analysis of genome-wide RNA, protein and metabolite in the post-genome era is to understand how interactions among molecules in a cell determine its form

Wurtele, Eve Syrkin

391

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.

392

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 of genomic information that is being used to help researchers understand the gene content of organisms, how the expression of genes. In this introductory manuscript, I discuss select algae and how genomics is impacting

393

Genome-tools: a flexible package for genome sequence analysis.  

PubMed

Genome-tools is a Perl module, a set of programs, and a user interface that facilitates access to genome sequence information. The package is flexible, extensible, and designed to be accessible and useful to both nonprogrammers and programmers. Any relatively well-annotated genome available with standard GenBank genome files may be used with genome-tools. A simple Web-based front end permits searching any available genome with an intuitive interface. Flexible design choices also make it simple to handle revised versions of genome annotation files as they change. In addition, programmers can develop cross-genomic tools and analyses with minimal additional overhead by combining genome-tools modules with newly written modules. Genome-tools runs on any computer platform for which Perl is available, including Unix, Microsoft Windows, and Mac OS. By simplifying the access to large amounts of genomic data, genome-tools may be especially useful for molecular biologists looking at newly sequenced genomes, for which few informatics tools are available. The genome-tools Web interface is accessible at http://genome-tools.sourceforge.net, and the source code is available at http://sourceforge.net/projects/genome-tools. PMID:12503321

Lee, William; Chen, Swaine L

2002-12-01

394

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

395

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

E-print Network

of seed dispersing birds and mammals, and the Ficus fruit characters in¯uencing mode of colonization observed fruiting. Thirty-six vertebrate species occurring on Long Island are identi®ed as potential seed and fruit bats with generally smaller, red ®gs produced throughout the vertical structure of the forest

396

Human Genome Program  

SciTech Connect

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

Not Available

1993-01-01

397

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.

398

GenomeBiology.com  

NSDL National Science Digital Library

Genome Biology "serves the biological research community as an international forum, both in print and on the Web, for the dissemination, discussion and critical review of information about all areas of biology informed by genomic research." While a paid subscription is required to access all features on the Genome Biology Web site, non-subscribers will find a number of open-access resources as well. Offerings include research articles, conference reports, software downloads, lab protocols, and much more. This frequently updated and ever-evolving Web site will also publish and maintain databases at some point; users are encouraged to submit comments and suggestions.

1999-01-01

399

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

400

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.

401

Nanoindentation response of piezoelectric nano-islands  

NASA Astrophysics Data System (ADS)

Through three-dimensional finite element modeling, it is demonstrated that the nanoindentation response of piezoelectric nano-islands is strongly dependent on the shape of the nano-island and the depth of indentation. For indentations that are relatively deep (i.e., greater than 5% of the height of the islands), the substrate's elastic and plastic properties have a strong influence on the indentation response of piezoelectric nano-islands with substrate plasticity resulting in a significant reduction in the mechanical and electrical indentation stiffness. The predictions of the finite element models compare well with experiments on nano-islands of strontium-doped lead zirconate titanate.

Cheng, Guang; Sriram, Sharath; Bhaskaran, Madhu; Venkatesh, T. A.

2014-09-01

402

Shaded Relief Mosaic of Umnak Island, Aleutian Islands, Alaska  

NASA Technical Reports Server (NTRS)

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

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

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

2001-01-01

403

Generalized water-table map of Block Island, Rhode Island  

USGS Publications Warehouse

The map shows the altitude of water table surface above seal level in the glacial deposits that form Block Island. Because the sediments are only moderately permeable, the water table is close to the to the surface in most parts of the island, even in hilly areas. The map represents a generalized water-table configuration on the basis of data from many different sampling periods; because the data were collected at different times, they should not be used to determine a specific depth to water at a particular site. Water levels measured in 117 shallow wells (less than 35 feet deep) from June through September 1962 and from March through September 1988-90--periods when water levels were at about the same altitude above sea level--ranged from less than 1 to 24 feet below land surface and averaged about 6 feet below land surface.

Johnston, H.E.; Veeger, A.I.

1994-01-01

404

Comparative primate genomics: emerging patterns of genome content and dynamics  

PubMed Central

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

Rogers, Jeffrey; Gibbs, Richard A.

2014-01-01

405

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

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

2012-01-01

406

Hydrogeology and water resources of Block Island, Rhode Island  

USGS Publications Warehouse

Ground water is present on Block Island as a lens of freshwater that overlies saltwater. Yields of 2 to 5 gallons per minute are obtainable throughout the island, and yields of 25 gallons per minute are possible at many wells. Annual water use during 1990 is estimated to have been 53 million gallons, of which approximately 17 million gallons was delivered from a water company at Sands Pond. Demand by water company customers from May through October averages 74,000 gallons per day. The sustainable yield of Sands Pond during the drought years estimated to be only 45,000 gallons per day. Withdrawal of the remaining 29,000 gallons per day from Fresh Pond, proposed as an alternative source, would produce an estimated water-level decline of less than 1 foot. Block Island consists of a Pleistocene moraine deposit that includes meltwater deposits, till, sediment-flow deposits, and glacially transported blocks of Cretaceous strata and pre-Late Wisconsinan glacial deposits. The water table is a subdued reflection of the land-surface topography and flow is generally from the central, topographic highs toward the coast. Layers of low hydraulic- conductivity material impede vertical flow, creating steep vertical gradients. No evidence of widespread ground-water contamination was found during this study. Nitrate concentrations were below Federal Maximum Contaminant Levels at each of the 83 sites sampled. No evidence of dissolved organic constituents was found in groundwater at the 10 sites sampled, and ground-water samples collected near the landfill showed no evidence of contamination from landfill leachate. Dissolved-iron concentrations exceeded the Federal Secondary Maximum Contaminant Level in groundwater at 26 of 76 wells sampled. High iron concentrations were found predominantly in the eastern and northern parts of the island and are attributed to the presence of iron-bearing minerals and organic matter in the aquifer.

Veeger, A.I.; Johnston, H.E.

1994-01-01

407

The island rule: made to be broken?  

PubMed Central

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

Meiri, Shai; Cooper, Natalie; Purvis, Andy

2007-01-01

408

Pooled Genomic Indexing Miklos Csuros  

E-print Network

) & physical mapping (PGI) #12;Large genome sequencing · human ( ) · mouse and rat (1 yr) · cow, dog & Human Genome Sequencing Center Baylor College of Medicine #12;Pooled shotgun reads developed at Baylor College of Medicine Human Genome Sequencing Center 1. DNA from genomic clones are pooled together 2

Csürös, Miklós

409

The Center for integrative genomics  

E-print Network

The Center for integrative genomics Report 2005­2006 #12;Presentation Director's message 4 Scientific advisory committee 6 Organigram of the CIG 7 research The structure and function of genomes and their evolution alexandrereymond ­ Genome structure and expression 10 henrikKaessmann ­ Evolutionary genomics 12

Kaessmann, Henrik

410

Genomic definition of species  

SciTech Connect

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

Crkvenjakov, R.; Drmanac, R.

1991-07-01

411

Human papillomavirus genome variants  

PubMed Central

Amongst the human papillomaviruses (HPVs), the genus Alphapapillomavirus contains HPV types that are uniquely pathogenic. They can be classified into species and types based on genetic distances between viral genomes. Current circulating infectious HPVs constitute a set of viral genomes that have evolved with the rapid expansion of the human population. Viral variants were initially identified through restriction enzyme polymorphisms and more recently through sequence determination of viral fragments. Using partial sequence information, the history of variants, and the association of HPV variants with disease will be discussed with the main focus on the recent utilization of full genome sequence information for variant analyses. The use of multiple sequence alignments of complete viral genomes and phylogenetic analyses have begun to define variant lineages and sublineages using empirically defined differences of 1.0–10.0% and 0.5–1.0%, respectively. These studies provide the basis to define the genetics of HPV pathogenesis. PMID:23998342

Burk, Robert D.; Harari, Ariana; Chen, Zigui

2014-01-01

412

Researchers Compare Anthrax Genomes  

NSF Publications Database

... as a tool for the forensic analysis of microbes, scientists at The Institute for Genomic Research ... differences among nearly identical strains of microbes such as anthrax. Previous genetic marker ...

413

Lophotrochozoan mitochondrial genomes  

SciTech Connect

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

Valles, Yvonne; Boore, Jeffrey L.

2005-10-01

414

Barrier Island Failure During Hurricane Katrina  

NASA Astrophysics Data System (ADS)

Classical models of barrier-island response to storms predict that wave runup can periodically overtop an island and transport sand from its seaside to its bayside, forcing the island to migrate landward. While this process can destroy fixed human developments, the island survives with little net change in form or dimensions. In contrast, we find that Louisiana's Chandeleur Islands during Hurricane Katrina were not periodically overtopped by waves, but were continuously inundated by storm surge. When such inundation occurs locally on a barrier island, it can force the erosion of a narrow breach that connects sea and bay. However, little is known about the response of a barrier island when it is entirely submerged. Here, we show that the Chandeleur Islands approached complete failure, losing 84% of their surface area. Their Gulf of Mexico shorelines retreated landward an average of 268 m, the largest retreat ever reported for a storm. Sand was stripped from the islands, reducing their peak elevation from >6 m to <3 m and exposing them to further degradation and potential failure by future hurricanes of less intensity than Katrina. Further, the islands that survived Katrina were marsh remnants composed of mud and vegetation that relatively small waves diminished following the storm. The Chandeleur Islands are prone to failure because of their location on the Mississippi delta where small sand supply and large sea-level rise (induced locally by land subsidence) limit natural rebuilding of the islands following a storm. The response of the delta's barrier islands during Hurricane Katrina provides a warning of how the world's barrier islands might respond to storm-surge inundation should predictions of accelerated global sea level rise prove accurate.

Sallenger, A.; Howd, P.; Stockdon, H.; Wright, C. W.; Fauver, L.; Guy, K.

2006-12-01

415

Peach Structural Genomics  

Microsoft Academic Search

\\u000a Peach (Prunus persica) belongs to the Prunus genus and is a member of the Rosaceae family. It has been selected as a model species for genomics studies in virtue of several\\u000a features (Abbott et al., 2002): it has a short juvenile phase (2–3 years) if compared to many other tree species; it has a\\u000a small genome, just about twice the

Carlo Pozzi; Alberto Vecchietti

416

Molluscan Evolutionary Genomics  

SciTech Connect

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 life. This opens up opportunities as never before for evolutionary and organismal biologists to address questions of both processes and patterns of organismal change. We stand at the dawn of a new 'modern synthesis' period, paralleling that of the early 20th century when the fledgling field of genetics first identified the underlying basis for Darwin's theory. We must now unite the efforts of systematists, paleontologists, mathematicians, computer programmers, molecular biologists, developmental biologists, and others in the pursuit of discovering what genomics can teach us about the diversity of life. Genome-level sampling for mollusks to date has mostly been limited to mitochondrial genomes and it is likely that these will continue to provide the best targets for broad phylogenetic sampling in the near future. However, we are just beginning to see an inroad into complete nuclear genome sequencing, with several mollusks and other eutrochozoans having been selected for work about to begin. Here, we provide an overview of the state of molluscan mitochondrial genomics, highlight a few of the discoveries from this research, outline the promise of broadening this dataset, describe upcoming projects to sequence whole mollusk nuclear genomes, and challenge the community to prepare for making the best use of these data.

Simison, W. Brian; Boore, Jeffrey L.

2005-12-01

417

Population genomics of the endangered giant Gal?pagos 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

418

How the genome folds  

NASA Astrophysics Data System (ADS)

I describe Hi-C, a novel technology for probing the three-dimensional architecture of whole genomes by coupling proximity-based ligation with massively parallel sequencing. Working with collaborators at the Broad Institute and UMass Medical School, we used Hi-C to construct spatial proximity maps of the human genome at a resolution of 1Mb. These maps confirm the presence of chromosome territories and the spatial proximity of small, gene-rich chromosomes. We identified an additional level of genome organization that is characterized by the spatial segregation of open and closed chromatin to form two genome-wide compartments. At the megabase scale, the chromatin conformation is consistent with a fractal globule, a knot-free conformation that enables maximally dense packing while preserving the ability to easily fold and unfold any genomic locus. The fractal globule is distinct from the more commonly used globular equilibrium model. Our results demonstrate the power of Hi-C to map the dynamic conformations of whole genomes.

Lieberman Aiden, Erez

2012-02-01

419

Human Social Genomics  

PubMed Central

A growing literature in human social genomics has begun to analyze how everyday life circumstances influence human gene expression. Social-environmental conditions such as urbanity, low socioeconomic status, social isolation, social threat, and low or unstable social status have been found to associate with differential expression of hundreds of gene transcripts in leukocytes and diseased tissues such as metastatic cancers. In leukocytes, diverse types of social adversity evoke a common conserved transcriptional response to adversity (CTRA) characterized by increased expression of proinflammatory genes and decreased expression of genes involved in innate antiviral responses and antibody synthesis. Mechanistic analyses have mapped the neural “social signal transduction” pathways that stimulate CTRA gene expression in response to social threat and may contribute to social gradients in health. Research has also begun to analyze the functional genomics of optimal health and thriving. Two emerging opportunities now stand to revolutionize our understanding of the everyday life of the human genome: network genomics analyses examining how systems-level capabilities emerge from groups of individual socially sensitive genomes and near-real-time transcriptional biofeedback to empirically optimize individual well-being in the context of the unique genetic, geographic, historical, developmental, and social contexts that jointly shape the transcriptional realization of our innate human genomic potential for thriving. PMID:25166010

Cole, Steven W.

2014-01-01

420

An archaeal genomic signature  

NASA Technical Reports Server (NTRS)

Comparisons of complete genome sequences allow the most objective and comprehensive descriptions possible of a lineage's evolution. This communication uses the completed genomes from four major euryarchaeal taxa to define a genomic signature for the Euryarchaeota and, by extension, the Archaea as a whole. The signature is defined in terms of the set of protein-encoding genes found in at least two diverse members of the euryarchaeal taxa that function uniquely within the Archaea; most signature proteins have no recognizable bacterial or eukaryal homologs. By this definition, 351 clusters of signature proteins have been identified. Functions of most proteins in this signature set are currently unknown. At least 70% of the clusters that contain proteins from all the euryarchaeal genomes also have crenarchaeal homologs. This conservative set, which appears refractory to horizontal gene transfer to the Bacteria or the Eukarya, would seem to reflect the significant innovations that were unique and fundamental to the archaeal "design fabric." Genomic protein signature analysis methods may be extended to characterize the evolution of any phylogenetically defined lineage. The complete set of protein clusters for the archaeal genomic signature is presented as supplementary material (see the PNAS web site, www.pnas.org).

Graham, D. E.; Overbeek, R.; Olsen, G. J.; Woese, C. R.

2000-01-01

421

Barley Genomics: An Overview  

PubMed Central

Barley (Hordeum vulgare), first domesticated in the Near East, is a well-studied crop in terms of genetics, genomics, and breeding and qualifies as a model plant for Triticeae research. Recent advances made in barley genomics mainly include the following: (i) rapid accumulation of EST sequence data, (ii) growing number of studies on transcriptome, proteome, and metabolome, (iii) new modeling techniques, (iv) availability of genome-wide knockout collections as well as efficient transformation techniques, and (v) the recently started genome sequencing effort. These developments pave the way for a comprehensive functional analysis and understanding of gene expression networks linked to agronomically important traits. Here, we selectively review important technological developments in barley genomics and related fields and discuss the relevance for understanding genotype-phenotype relationships by using approaches such as genetical genomics and association studies. High-throughput genotyping platforms that have recently become available will allow the construction of high-density genetic maps that will further promote marker-assisted selection as well as physical map construction. Systems biology approaches will further enhance our knowledge and largely increase our abilities to design refined breeding strategies on the basis of detailed molecular physiological knowledge. PMID:18382615

Sreenivasulu, Nese; Graner, Andreas; Wobus, Ulrich

2008-01-01

422

Human social genomics.  

PubMed

A growing literature in human social genomics has begun to analyze how everyday life circumstances influence human gene expression. Social-environmental conditions such as urbanity, low socioeconomic status, social isolation, social threat, and low or unstable social status have been found to associate with differential expression of hundreds of gene transcripts in leukocytes and diseased tissues such as metastatic cancers. In leukocytes, diverse types of social adversity evoke a common conserved transcriptional response to adversity (CTRA) characterized by increased expression of proinflammatory genes and decreased expression of genes involved in innate antiviral responses and antibody synthesis. Mechanistic analyses have mapped the neural "social signal transduction" pathways that stimulate CTRA gene expression in response to social threat and may contribute to social gradients in health. Research has also begun to analyze the functional genomics of optimal health and thriving. Two emerging opportunities now stand to revolutionize our understanding of the everyday life of the human genome: network genomics analyses examining how systems-level capabilities emerge from groups of individual socially sensitive genomes and near-real-time transcriptional biofeedback to empirically optimize individual well-being in the context of the unique genetic, geographic, historical, developmental, and social contexts that jointly shape the transcriptional realization of our innate human genomic potential for thriving. PMID:25166010

Cole, Steven W

2014-08-01

423

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

424

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

425

Tambora Caldera, Sumbawa Island, Indonesia  

NASA Technical Reports Server (NTRS)

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

1988-01-01

426

The Roanoke Island Freedmen's Colony  

NSDL National Science Digital Library

During the Civil War, Roanoke Island, located between the coast of North Carolina and the Outer Banks, became a refuge for escaped slaves, called contrabands or freedmen. This site, created by University of Virginia professor Patricia C. Click presents an account of the history and selected documents and maps of the Roanoke Island Freedmens Colony, as the community was known. Documents include letters from Superintendent of the Colony, Horace James, a minister and abolitionist from Massachusetts, and letters from Freedmen themselves. The documents have been transcribed and are in .pdf format, so users should not expect to see scanned versions of 19th century originals. The projects section includes seven projects for high school and college students, using historical materials at the site, and from other related Web sites. Professor Click has written a book, Time Full of Trial: The Roanoke Island FreedmenâÂÂs Colony, 1862-1867, and the Preview section contains the table of contents and Chapter One. Links in the site refer to this book for more information; in the Maps section users are referred to its online ordering instructions for more information on the layout of the colony.

Click, Patricia C.

2001-01-01

427

Erythroblastic islands: niches for erythropoiesis.  

PubMed

Erythroblastic islands, the specialized niches in which erythroid precursors proliferate, differentiate, and enucleate, were first described 50 years ago by analysis of transmission electron micrographs of bone marrow. These hematopoietic subcompartments are composed of erythroblasts surrounding a central macrophage. A hiatus of several decades followed, during which the importance of erythroblastic islands remained unrecognized as erythroid progenitors were shown to possess an autonomous differentiation program with a capacity to complete terminal differentiation in vitro in the presence of erythropoietin but without macrophages. However, as the extent of proliferation, differentiation, and enucleation efficiency documented in vivo could not be recapitulated in vitro, a resurgence of interest in erythroid niches has emerged. We now have an increased molecular understanding of processes operating within erythroid niches, including cell-cell and cell-extracellular matrix adhesion, positive and negative regulatory feedback, and central macrophage function. These features of erythroblast islands represent important contributors to normal erythroid development, as well as altered erythropoiesis found in such diverse diseases as anemia of inflammation and chronic disease, myelodysplasia, thalassemia, and malarial anemia. Coupling of historical, current, and future insights will be essential to understand the tightly regulated production of red cells both in steady state and stress erythropoiesis. PMID:18650462

Chasis, Joel Anne; Mohandas, Narla

2008-08-01

428

Processes of barrier island erosion  

SciTech Connect

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

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

1989-09-01

429

Floating Cities, Islands and States  

E-print Network

Many small countries are in need of additional territory. They build landfills and expensive artificial islands. The ocean covers 71 per cent of the Earth surface. Those countries (or persons of wealth) starting the early colonization of the ocean may obtain advantages through additional territory or creating their own independent state. An old idea is building a big ship. The best solution to this problem, however, is the provision of floating cities, islands, and states. The author idea is to use for floating cities, islands, and states a cheap floating platform created from a natural ice field taken from the Arctic or Antarctic oceans. These cheap platforms protected by air-film (bottom and sides) and a conventional insulating cover (top) and having a cooling system can exist for an unlimited time. They can be increased in number or size at any time, float in warm oceans, travel to different continents and countries, serve as artificial airports, harbors and other marine improvements, as well as floating cities and industrial bases for virtually any use. Author researches and computes parameters of these ice floating platforms, other methods of building such floating territory, compares them and shows that the offered method is the most cheap and efficient means of ocean colonization.

Alexander Bolonkin

2008-04-04

430

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

PubMed

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

Emerson, Brent C; Faria, Christiana M A

2014-11-01

431

ProGenExpress: Visualization of quantitative data on prokaryotic genomes  

PubMed Central

Background The integration of genomic information with quantitative experimental data is a key component of systems biology. An increasing number of microbial genomes are being sequenced, leading to an increasing amount of data from post-genomics technologies. The genomes of prokaryotes contain many structures of interest, such as operons, pathogenicity islands and prophage sequences, whose behaviour is of interest during infection and disease. There is a need for simple and novel tools to display and analyse data from these integrated datasets, and we have developed ProGenExpress as a tool for visualising arbitrarily complex numerical data in the context of prokaryotic genomes. Results Here we describe ProGenExpress, an R package that allows researchers to easily and quickly visualize quantitative measurements, such as those produced by microarray experiments, in the context of the genome organization of sequenced prokaryotes. Data from microarrays, proteomics or other whole-genome technologies can be accurately displayed on the genome. ProGenExpress can also search for novel regions of interest that consist of groups of adjacent genes that show similar patterns across the experimental data set. We demonstrate ProGenExpress with microarray data from a time-course experiment involving Salmonella typhimurium. Conclusion ProGenExpress can be used to visualize quantitative data from complex experiments in the context of the genome of sequenced prokaryotes, and to find novel regions of interest. PMID:15829007

Watson, Michael

2005-01-01

432

Miocene structure of Mustang Island, Mustang Island East Addition and part of Matagorda Island, Outer Continental Shelf areas, Gulf of Mexico  

E-print Network

MIOCENE STRUCTURE OF MUSTANG ISLAND, MUSTANG ISLAND EAST ADDITION AND PART OF MATAGORDA ISLAND, OUTER CONTINENTAL SHELF AREAS, GULF OF MEXICO A Thesis by ROBERT KASANDE Submitted to the Office of Graduate Studies of Texas AdtM University... in partial fulfillment of the requirements for the degree of MASTER OF SCIENCE December 1995 Major Subject: Geophysics MIOCENE STRUCTURE OF MUSTANG ISLAND, MUSTANG ISLAND EAST ADDITION AND PART OF MATAGORDA ISLAND, OUTER CONTINENTAL SHELF AREAS, GULF...

Kasande, Robert

2012-06-07

433

SOLiD sequencing of four Vibrio vulnificus genomes enables comparative genomic analysis and identification of candidate clade-specific virulence genes  

PubMed Central

Background Vibrio vulnificus is the leading cause of reported death from consumption of seafood in the United States. Despite several decades of research on molecular pathogenesis, much remains to be learned about the mechanisms of virulence of this opportunistic bacterial pathogen. The two complete and annotated genomic DNA sequences of V. vulnificus belong to strains of clade 2, which is the predominant clade among clinical strains. Clade 2 strains generally possess higher virulence potential in animal models of disease compared with clade 1, which predominates among environmental strains. SOLiD sequencing of four V. vulnificus strains representing different clades (1 and 2) and biotypes (1 and 2) was used for comparative genomic analysis. Results Greater than 4,100,000 bases were sequenced of each strain, yielding approximately 100-fold coverage for each of the four genomes. Although the read lengths of SOLiD genomic sequencing were only 35 nt, we were able to make significant conclusions about the unique and shared sequences among the genomes, including identification of single nucleotide polymorphisms. Comparative analysis of the newly sequenced genomes to the existing reference genomes enabled the identification of 3,459 core V. vulnificus genes shared among all six strains and 80 clade 2-specific genes. We identified 523,161 SNPs among the six genomes. Conclusions We were able to glean much information about the genomic content of each strain using next generation sequencing. Flp pili, GGDEF proteins, and genomic island XII were identified as possible virulence factors because of their presence in virulent sequenced strains. Genomic comparisons also point toward the involvement of sialic acid catabolism in pathogenesis. PMID:20863407

2010-01-01

434

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, Debora O.; Dorella, Fernanda A.; Pacheco, Luis G. C.; Costa, Marcilia P.; Turk, Meritxell Z.; Seyffert, Nubia; 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, Elisangela M.; Oliveira, Luciana M.; Pedrosa, Andre L.; Vieira, Carlos U.; Guimaraes, Claudia T.; Bartholomeu, Daniela C.; Oliveira, Diana M.; Santos, Fabricio R.; Rabelo, Elida Mara; Lobo, Francisco P.; Franco, Gloria R.; Costa, Ana Flavia; Castro, Ieso M.; Dias, Silvia Regina Costa; Ferro, Jesus A.; Ortega, Jose Miguel; Paiva, Luciano V.; Goulart, Luiz R.; Almeida, Juliana Franco; Ferro, Maria Ines T.; Carneiro, Newton P.; Falcao, Paula R. K.; Grynberg, Priscila; Teixeira, Santuza M. R.; Brommonschenkel, Sergio; Oliveira, Sergio C.; Meyer, Roberto; Moore, Robert J.; Miyoshi, Anderson; Oliveira, Guilherme C.

2011-01-01

435

A signature for turbulence driven magnetic islands  

NASA Astrophysics Data System (ADS)

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.; Poyé, A.; Benkadda, S.; Yagi, M.; Garbet, X.; Sen, A.

2014-09-01

436

Genomic Targets in Saliva  

PubMed Central

Saliva, the most accessible and noninvasive biofluid of our body, harbors a wide spectrum of biological analytes informative for clinical diagnostic applications. While proteomic constituents are a logical first choice as salivary diagnostic analytes, genomic targets have emerged as highly informative and discriminatory. This awareness, coupled with the ability to harness genomic information by high-throughput technology platforms such as genome-wide microarrays, ideally positions salivary genomic targets for exploring the value of saliva for detection of specific disease states and augmenting the diagnostic and discriminatory value of the saliva proteome for clinical applications. Buccal cells and saliva have been used as sources of genomic DNA for a variety of clinical and forensic applications. For discovery of disease targets in saliva, the recent realization that there is a transcriptome in saliva presented an additional target for oral diagnostics. All healthy subjects evaluated have approximately 3,000 different mRNA molecules in their saliva. Almost 200 of these salivary mRNAs are present in all subjects. Exploration of the clinical utility of the salivary transcriptome in oral cancer subjects shows that four salivary mRNAs (OAZ, SAT, IL8, and IL1b) collectively have a discriminatory power of 91% sensitivity and specificity for oral cancer detection. Data are also now in place to validate the presence of unique diagnostic panels of salivary mRNAs in subjects with Sjöogren's disease. PMID:17435127

ZIMMERMANN, BERNHARD G.; PARK, NOH JIN; WONG, DAVID T.

2010-01-01

437

Genome position specific priors for genomic prediction  

PubMed Central

Background The accuracy of genomic prediction is highly dependent on the size of the reference population. For small populations, including information from other populations could improve this accuracy. The usual strategy is to pool data from different populations; however, this has not proven as successful as hoped for with distantly related breeds. BayesRS is a novel approach to share information across populations for genomic predictions. The approach allows information to be captured even where the phase of SNP alleles and casuative mutation alleles are reversed across populations, or the actual casuative mutation is different between the populations but affects the same gene. Proportions of a four-distribution mixture for SNP effects in segments of fixed size along the genome are derived from one population and set as location specific prior proportions of distributions of SNP effects for the target population. The model was tested using dairy cattle populations of different breeds: 540 Australian Jersey bulls, 2297 Australian Holstein bulls and 5214 Nordic Holstein bulls. The traits studied were protein-, fat- and milk yield. Genotypic data was Illumina 777K SNPs, real or imputed. Results Results showed an increase in accuracy of up to 3.5% for the Jersey population when using BayesRS with a prior derived from Australian Holstein compared to a model without location specific priors. The increase in accuracy was however lower than was achieved when reference populations were combined to estimate SNP effects, except in the case of fat yield. The small size of the Jersey validation set meant that these improvements in accuracy were not significant using a Hotelling-Williams t-test at the 5% level. An increase in accuracy of 1-2% for all traits was observed in the Australian Holstein population when using a prior derived from the Nordic Holstein population compared to using no prior information. These improvements were significant (P<0.05) using the Hotelling Williams t-test for protein- and fat yield. Conclusion For some traits the method might be advantageous compared to pooling of reference data for distantly related populations, but further investigation is needed to confirm the results. For closely related populations the method does not perform better than pooling reference data. However, it does give an increased accuracy compared to analysis based on only one reference population, without an increased computational burden. The approach described here provides a general setup for inclusion of location specific priors: the approach could be used to include biological information in genomic predictions. PMID:23050763

2012-01-01

438

Genome assortment, not serogroup, defines Vibrio cholerae pandemic strains  

SciTech Connect

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

Brettin, Thomas S [Los Alamos National Laboratory; Bruce, David C [Los Alamos National Laboratory; Challacombe, Jean F [Los Alamos National Laboratory; Detter, John C [Los Alamos National Laboratory; Han, Cliff S [Los Alamos National Laboratory; Munik, A C [Los Alamos National Laboratory; Chertkov, Olga [Los Alamos National Laboratory; Meincke, Linda [Los Alamos National Laboratory; Saunders, Elizabeth [Los Alamos National Laboratory; Choi, Seon Y [SEOUL NATL. UNIV.; Haley, Bradd J [U. MARYLAND; Taviani, Elisa [U. MARYLAND; Jeon, Yoon - Seong [INTL. VACCINE INST. SEOUL; Kim, Dong Wook [INTL. VACCINE INST. SEOUL; Lee, Jae - Hak [SEOUL NATL. UNIV.; Walters, Ronald A [PNNL; Hug, Anwar [NATL. INST. CHOLERIC ENTERIC DIS.; Colwell, Rita R [U. MARYLAND

2009-01-01

439

The urban heat island of Milan  

Microsoft Academic Search

Summary  Heat island contribution to the 148 year temperature series of Milan is evaluated by comparing Milan urban series with Milan\\u000a airport series and with other European and North Hemispheric series. The heat island trend is then compared with the growth\\u000a of the city radius and finally two relations between the city radius and the efffects of the heat island are

P. Bacci; M. Maugeri

1992-01-01

440

A photographic guide to some vascular plants of Kiska Island, Aleutian Islands, Alaska  

E-print Network

National Wildlife Refuge, is the second largest island in the Rat Island group of the western Aleutian disturbance, and the introduction of non-native Arctic foxes (introduced 1825, eradicated 1987) and Norway

Jones, Ian L.

441

Solar and Atmospheric Radiation Data for Broughton Island, eastern Baffin Island, Canada, 1971-73.  

National Technical Information Service (NTIS)

The three years partial record of radiation for Broughton Island reported here tends to support the thesis already demonstrated elsewhere for other climatological parameters that conditions on the eastern coast of Baffin Island and, implicitly, in Davis S...

J. D. Jacobs

1974-01-01

442

Genomics of cellulolytic bacteria.  

PubMed

The heterogeneous plant biomass is efficiently decomposed by the interplay of a great number of different enzymes. The enzyme systems in cellulolytic bacteria have been investigated by sequencing and bioinformatic analysis of genomes from plant biomass degrading microorganisms with valuable insights into the variety of the involved enzymes. This broadened our understanding of the biochemical mechanisms of plant polymer degradation and made the enzymes applicable for modern biotechnology. A list of the truly cellulolytic bacteria described and the available genomic information was examined for proteins with cellulolytic and hemicellulolytic capability. The importance of the isolation, characterization and genomic sequencing of cellulolytic microorganisms and their usage for sustainable energy production from biomass and other residues, is emphasized. PMID:25104562

Koeck, Daniela E; Pechtl, Alexander; Zverlov, Vladimir V; Schwarz, Wolfgang H

2014-10-01

443

Genomics, health, and society.  

PubMed

On June 27, 2001, the World Health Organization conducted hearings in Geneva for a Special Report on Genomics & Health. Initially intended as a document to address the ethical, legal, and social implications of the gathering genomics resolution (ELSI), the terms of reference of the report were significantly modified to give primary emphasis to a scientific and technological assessment of the implications of genomics for human health. The Citizens' Health Initiative, one of two NGOs invited to make submissions at these consultations, suggested that no less important than the scientific and technical assessment was a perspective which gave due attention to the social context and political economy of scientific/technological development and its deployment. The article below touches upon neglected health priorities of poor countries, intellectual property rights and patents, risk management, insurance and discrimination, and predictive (prenatal) testing, reproductive choice, and eugenics. PMID:17208760

Chan, Chee Khoon

2002-01-01

444

Genomics for Weed Science  

PubMed Central

Numerous genomic-based studies have provided insight to the physiological and evolutionary processes involved in developmental and environmental processes of model plants such as arabidopsis and rice. However, far fewer efforts have been attempted to use genomic resources to study physiological and evolutionary processes of weedy plants. Genomics-based tools such as extensive EST databases and microarrays have been developed for a limited number of weedy species, although application of information and resources developed for model plants and crops are possible and have been exploited. These tools have just begun to provide insights into the response of these weeds to herbivore and pathogen attack, survival of extreme environmental conditions, and interaction with crops. The potential of these tools to illuminate mechanisms controlling the traits that allow weeds to invade novel habitats, survive extreme environments, and that make weeds difficult to eradicate have potential for both improving crops and developing novel methods to control weeds. PMID:20808523

Horvath, David

2010-01-01

445

Functional genomics of trypanosomatids.  

PubMed

The decoding of the Tritryp reference genomes nearly 7 years ago provided a first peek into the biology of pathogenic trypanosomatids and a blueprint that has paved the way for genome-wide studies. Although 60-70% of the predicted protein coding genes in Trypanosoma brucei, Trypanosoma cruzi and Leishmania major remain unannotated, the functional genomics landscape is rapidly changing. Facilitated by the advent of next-generation sequencing technologies, improved structural and functional annotation and genes and their products are emerging. Information is also growing for the interactions between cellular components as transcriptomes, regulatory networks and metabolomes are characterized, ushering in a new era of systems biology. Simultaneously, the launch of comparative sequencing of multiple strains of kinetoplastids will finally lead to the investigation of a vast, yet to be explored, evolutionary and pathogenomic space. PMID:22132795

Choi, J; El-Sayed, N M

2012-01-01

446

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

447

The geomorphology of the Chandeleur Island Wetlands  

SciTech Connect

The Chandeleur Islands represent the largest and oldest transgressive barrier island arc in the northern Gulf of Mexico. Generated by the transgressive submergence of the St. Bernard delta complex, the Chandeleur Islands form the protective geologic framework for one of the richest areas of salt marsh and seagrass flats in Louisiana. The Chandeleur barrier island arc is 60 km long and consists of five individual islands backed by a linear, multiple bar system enclosing a shallow basin floored by extensive seagrass flats. The northern part of the Chandeleur chain is the highest in relief, elevation, width, and habitat diversity. Nonstorm morphology is predominantly a combination of continuous dunes and dune terraces. Numerous washover channels and large washover fans extend into the backbarrier environment. Further south, the island width decreases and washover flats and terraces dominate the shoreline morphology In the southernmost section, the island arc is fragmented into a series of small islands and shoals separated by tidal inlets. Between 1984 and 1989, aerial videotape, aerial photographic, and bathymetric surveys were used to map and monitor the geomorphic changes occurring along the shoreline and in backbarrier areas. The aerial videotape mapping surveys focused on the impacts of hurricanes Danny, Elena, and Juan on the geomorphology of the islands. Videotape imagery was acquired in July 1984 and in July (prestorm), August (post-Danny), September (post-Elena), and November (post-Juan) 1985. A coastal geomorphic classification was developed to map the spatial and temporal landscape changes between surveys.

Debusschere, K.; Penland, S.; Westphal, K. (Louisiana Geological Survey, Baton Rouge (USA)); Handley, L. (Fish and Wildlife Service, Slidell, LA (USA)); Michot, T. (Fish and Wildlife Service, Baton Rouge, LA (USA)); Reed, D.; Seal, R.

1990-09-01

448

Vegetation of eastern Unalaska Island, Aleutian Islands, Alaska  

USGS Publications Warehouse

Plant communities of Unalaska Island in the eastern Aleutian Islands of western Alaska, and their relationship to environmental variables, were studied using a combined Braun-Blanquet and multivariate approach. Seventy relevés represented the range of structural and compositional variation in the matrix of vegetation and landform zonation. Eleven major community types were distinguished within six physiognomic–ecological groups: I. Dry coastal meadows: Honckenya peploides beach meadow, Leymus mollis dune meadow. II. Mesic meadows: Athyrium filix-femina – Aconitum maximum meadow, Athyrium filix-femina – Calamagrostis nutkaensis meadow, Erigeron peregrinus – Thelypteris quelpaertensis meadow. III. Wet snowbed meadow: Carex nigricans snowbed meadow. IV. Heath: Linnaea borealis – Empetrum nigrum heath, Phyllodoce aleutica heath, Vaccinium uliginosum – Thamnolia vermicularis fellfield. V. Mire: Carex pluriflora – Plantago macrocarpa mire. VI. Deciduous shrub thicket: Salix barclayi – Athyrium filix-femina thicket. These were interpreted as a complex gradient primarily influenced by soil moisture, elevation, and pH. Phytogeographical and syntaxonomical analysis of the plant communities indicated that the dry coastal meadows, most of the heaths, and the mire vegetation belonged, respectively, to the widespread classes Honckenyo–Elymetea, Loiseleurio–Vaccinietea, and Scheuchzerio–Caricetea, characterized by their circumpolar and widespread species. Amphi-Beringian species were likely diagnostic of amphi-Beringian syntaxa, many of these yet to be described.

Talbot, Stephen S.; Schofield, Wilfred B.; Talbot, Sandra L.; Daniëls, Fred J. A.

2010-01-01

449

Crustal Thickness Beneath Ocean Islands  

NASA Astrophysics Data System (ADS)

We measured the thickness of the Earth's crust beneath about two dozen of the GDSN or GEOSCOPE stations located on ocean islands by stacking moveout-corrected high-quality P-to-S receiver functions (RFs). The RFs were filtered in the 0.05-0.5 Hz frequency bands to compress strong noises that are common for ocean island stations. Given the small (less than 2 s) time separation between the direct P and the P-to-S converted phase from the Moho, the PSmS phase, which has a negative polarity and can be clearly observed at almost all the stations, is used for the stacking. Preliminary resulting thickness at each of the stations is as follows: AFI (12.4 km), AIS (13.6), ASCN (9.6), BBSR (9.9), BORG (9.4), CRZF (6.6), GUMO (8.0), HNR (8.0), HOPE (19.0), KIP (13.0), MSEY (10.7), MSVF (15.1), NOUC (15.1), PAF (8.9), POHA (17.0), PPT (12.3), PTCN (10.4), RAR (12.8), RER (13.8), RPN (9.3), SEY (14.9), SHEL (17.5), TBT (14.1), XMAS (11.8). Crustal thickness at some of the stations has been measured previously, and our results are in general agreement with those measurements. Possible age-dependence of the resulting thickness and geological implications in the understanding of plume-lithosphere interactions and formation of ocean islands will be presented.

Gao, S. S.; Liu, K. H.; Cullers, R. L.

2005-12-01

450

Northwest Sumatra and Offshore Islands Field Survey after the December  

E-print Network

Northwest Sumatra and Offshore Islands Field Survey after the December 2004 Indian Ocean Tsunami on the west coast of northern and central Sumatra and offshore islands 3­4 months after the 26 December 2004 Islands, and included 22 sites in Aceh province in Sumatra and on Simeulue Island, Nias Island, the Banyak

451

REGULAR ARTICLES Islands of accelerator modes and homoclinic tangles  

E-print Network

REGULAR ARTICLES Islands of accelerator modes and homoclinic tangles Vered Rom Islands are divided according to their phase space structure--resonant islands and tangle islands modes of the standard map and of the web map are necessarily of the tangle island category

452

Computational genomics : mapping, comparison, and annotation of genomes  

E-print Network

The field of genomics provides many challenges to computer scientists and mathematicians. The area of computational genomics has been expanding recently, and the timely application of computer science in this field is ...

Batzoglou, Serafim

2000-01-01

453

Resequencing rice genomes: an emerging new era of rice genomics.  

PubMed

Rice is a model system for crop genomics studies. Much of the early work on rice genomics focused on analyzing genome-wide genetic variation to further understand rice gene functions in agronomic traits and to generate data and resources for rice research. The advent of next-generation high-throughput DNA sequencing technologies and the completion of high-quality reference genome sequences have enabled the development of sequencing-based genotyping and genome-wide association studies (GWAS) that have significantly advanced rice genetics research. This has led to the emergence of a new era of rice genomics aimed at bridging the knowledge gap between genotype and phenotype in rice. These technologies have also led to pyramid breeding through genomics-assisted select