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
In Escherichia coli, the biosynthetic pathways of several small iron-scavenging molecules known as siderophores (enterobactin, salmochelins and yersiniabactin) and of a genotoxin (colibactin) are known to require a 4?-phosphopantetheinyl transferase (PPTase). Only two PPTases have been clearly identified: EntD and ClbA. The gene coding for EntD is part of the core genome of E. coli, whereas ClbA is encoded on the pks pathogenicity island which codes for colibactin. Interestingly, the pks island is physically associated with the high pathogenicity island (HPI) in a subset of highly virulent E. coli strains. The HPI carries the gene cluster required for yersiniabactin synthesis except for a gene coding its cognate PPTase. Here we investigated a potential interplay between the synthesis pathways leading to the production of siderophores and colibactin, through a functional interchangeability between EntD and ClbA. We demonstrated that ClbA could contribute to siderophores synthesis. Inactivation of both entD and clbA abolished the virulence of extra-intestinal pathogenic E. coli (ExPEC) in a mouse sepsis model, and the presence of either functional EntD or ClbA was required for the survival of ExPEC in vivo. This is the first report demonstrating a connection between multiple phosphopantetheinyl-requiring pathways leading to the biosynthesis of functionally distinct secondary metabolites in a given microorganism. Therefore, we hypothesize that the strict association of the pks island with HPI has been selected in highly virulent E. coli because ClbA is a promiscuous PPTase that can contribute to the synthesis of both the genotoxin and siderophores. The data highlight the complex regulatory interaction of various virulence features with different functions. The identification of key points of these networks is not only essential to the understanding of ExPEC virulence but also an attractive and promising target for the development of anti-virulence therapy strategies.
Martin, Patricia; Marcq, Ingrid; Magistro, Giuseppe; Penary, Marie; Garcie, Christophe; Payros, Delphine; Boury, Michele; Olier, Maiwenn; Nougayrede, Jean-Philippe; Audebert, Marc; Chalut, Christian; Schubert, Soren; Oswald, Eric
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
While the recognition of genomic islands can be a powerful mechanism for identifying genes that distinguish related bacteria, few methods have been developed to identify them specifically. Rather, identification of islands often begins with cataloging individual genes likely to have been recently introduced into the genome; regions with many putative alien genes are then examined for other features suggestive of
Aaron J. Arvey; Rajeev K. Azad; Alpan Raval; Jeffrey G. Lawrence
Genomic Islands (GIs) are genomic regions that are originally from other organisms, through a process known as Horizontal Gene Transfer (HGT). Detection of GIs plays a significant role in biomedical research since such align genomic regions usually contain important features, such as pathogenic genes. We have developed a use friendly graphic user interface, Genomic Island Suite of Tools (GIST), which is a platform for scientific users to predict GIs. This software package includes five commonly used tools, AlienHunter, IslandPath, Colombo SIGI-HMM, INDeGenIUS and Pai-Ida. It also includes an optimization program EGID that ensembles the result of existing tools for more accurate prediction. The tools in GIST can be used either separately or sequentially. GIST also includes a downloadable feature that facilitates collecting the input genomes automatically from the FTP server of the National Center for Biotechnology Information (NCBI). GIST was implemented in Java, and was compiled and executed on Linux/Unix operating systems. Availability The database is available for free at http://www5.esu.edu/cpsc/bioinfo/software/GIST
Hasan, Mohammad Shabbir; Liu, Qi; Wang, Han; Fazekas, John; Chen, Bernard; Che, Dongsheng
While the recognition of genomic islands can be a powerful mechanism for identifying genes that distinguish related bacteria, few methods have been developed to identify them specifically. Rather, identification of islands often begins with cataloging individual genes likely to have been recently introduced into the genome; regions with many putative alien genes are then examined for other features suggestive of recent acquisition of a large genomic region. When few phylogenetic relatives are available, the identification of alien genes relies on their atypical features relative to the bulk of the genes in the genome. The weakness of these ‘bottom–up’ approaches lies in the difficulty in identifying robustly those genes which are atypical, or phylogenetically restricted, due to recent foreign ancestry. Herein, we apply an alternative ‘top–down’ approach where bacterial genomes are recursively divided into progressively smaller regions, each with uniform composition. In this way, large chromosomal regions with atypical features are identified with high confidence due to the simultaneous analysis of multiple genes. This approach is based on a generalized divergence measure to quantify the compositional difference between segments in a hypothesis-testing framework. We tested the proposed genome island prediction algorithm on both artificial chimeric genomes and genuine bacterial genomes.
Arvey, Aaron J.; Azad, Rajeev K.; Raval, Alpan; Lawrence, Jeffrey G.
We performed statistical analyses of five conserved features of genomic islands of bacteria. Analyses were made based on 104 known genomic islands, which were identified by comparative methods. Four of these features include sequence size, abnormal G+C content, flanking tRNA gene, and embedded mobility gene, which are frequently investigated. One relatively new feature, G+C homogeneity, was also investigated. Among the 104 known genomic islands, 88.5% were found to fall in the typical length of 10-200 kb and 80.8% had G+C deviations with absolute values larger than 2%. For the 88 genomic islands whose hosts have been sequenced and annotated, 52.3% of them were found to have flanking tRNA genes and 64.7% had embedded mobility genes. For the homogeneity feature, 85% had an h homogeneity index less than 0.1, indicating that their G+C content is relatively uniform. Taking all the five features into account, 87.5% of 88 genomic islands had three of them. Only one genomic island had only one conserved feature and none of the genomic islands had zero features. These statistical results should help to understand the general structure of known genomic islands. We found that larger genomic islands tend to have relatively small G+C deviations relative to absolute values. For example, the absolute G+C deviations of 9 genomic islands longer than 100,000 bp were all less than 5%. This is a novel but reasonable result given that larger genomic islands should have greater restrictions in their G+C contents, in order to maintain the stable G+C content of the recipient genome. PMID:24668666
Guo, F-B; Xia, Z-K; Wei, W; Zhao, H-L
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
The African malaria mosquito, Anopheles gambiae sensu stricto (A. gambiae), provides a unique opportunity to study the evolution of reproductive isolation because it is divided into two sympatric, partially isolated subtaxa known as M form and S form. With the annotated genome of this species now available, high-throughput techniques can be applied to locate and characterize the genomic regions contributing to reproductive isolation. In order to quantify patterns of differentiation within A. gambiae, we hybridized population samples of genomic DNA from each form to Affymetrix GeneChip microarrays. We found that three regions, together encompassing less than 2.8 Mb, are the only locations where the M and S forms are significantly differentiated. Two of these regions are adjacent to centromeres, on Chromosomes 2L and X, and contain 50 and 12 predicted genes, respectively. Sequenced loci in these regions contain fixed differences between forms and no shared polymorphisms, while no fixed differences were found at nearby control loci. The third region, on Chromosome 2R, contains only five predicted genes; fixed differences in this region were also verified by direct sequencing. These “speciation islands” remain differentiated despite considerable gene flow, and are therefore expected to contain the genes responsible for reproductive isolation. Much effort has recently been applied to locating the genes and genetic changes responsible for reproductive isolation between species. Though much can be inferred about speciation by studying taxa that have diverged for millions of years, studying differentiation between taxa that are in the early stages of isolation will lead to a clearer view of the number and size of regions involved in the genetics of speciation. Despite appreciable levels of gene flow between the M and S forms of A. gambiae, we were able to isolate three small regions of differentiation where genes responsible for ecological and behavioral isolation are likely to be located. We expect reproductive isolation to be due to changes at a small number of loci, as these regions together contain only 67 predicted genes. Concentrating future mapping experiments on these regions should reveal the genes responsible for reproductive isolation between forms.
Genomic islands have been shown to harbor functional traits that differentiate ecologically distinct populations of environmental bacteria. A comparative analysis of the complete genome sequences of the marine Actinobacteria Salinispora tropica and Salinispora arenicola reveals that 75% of the species-specific genes are located in 21 genomic islands. These islands are enriched in genes associated with secondary metabolite biosynthesis providing evidence
Kevin Penn; Caroline Jenkins; Markus Nett; Daniel W Udwary; Erin A Gontang; Ryan P McGlinchey; Brian Foster; Alla Lapidus; Sheila Podell; Eric E Allen; Bradley S Moore; Paul R Jensen
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.
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 microsymbiont of the model legume Lotus japonicus, and monitored the transcriptional dynamics of the bacterium during symbiosis, microaerobiosis, and starvation. Global transcriptional profiling demonstrated that the clusters of genes within the symbiosis island (611 kb), a transmissible region distinct from other chromosomal regions, are collectively expressed during symbiosis, whereas genes outside the island are downregulated. This finding implies that the huge symbiosis island functions as clustered expression islands to support symbiotic nitrogen fixation. Interestingly, most transposase genes on the symbiosis island were highly upregulated in bacteroids, as were nif, fix, fdx, and rpoN. The genome region containing the fixNOPQ genes outside the symbiosis island was markedly upregulated as another expression island under both microaerobic and symbiotic conditions. The symbiosis profiling data suggested that there was activation of amino acid metabolism, as well as nif-fix gene expression. In contrast, genes for cell wall synthesis, cell division, DNA replication, and flagella were strongly repressed in differentiated bacteroids. A highly upregulated gene in bacteroids, mlr5932 (encoding 1-aminocyclopropane-1-carboxylate deaminase), was disrupted and was confirmed to be involved in nodulation enhancement, indicating that disruption of highly expressed genes is a useful strategy for exploring novel gene functions in symbiosis.
Uchiumi, Toshiki; Ohwada, Takuji; Itakura, Manabu; Mitsui, Hisayuki; Nukui, Noriyuki; Dawadi, Pramod; Kaneko, Takakazu; Tabata, Satoshi; Yokoyama, Tadashi; Tejima, Kouhei; Saeki, Kazuhiko; Omori, Hirofumi; Hayashi, Makoto; Maekawa, Takaki; Sriprang, Rutchadaporn; Murooka, Yoshikatsu; Tajima, Shigeyuki; Simomura, Kenshiro; Nomura, Mika; Suzuki, Akihiro; Shimoda, Yoshikazu; Sioya, Kouki; Abe, Mikiko; Minamisawa, Kiwamu
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 microsymbiont of the model legume Lotus japonicus, and monitored the transcriptional dynamics of the bacterium during symbiosis, microaerobiosis, and starvation. Global transcriptional profiling demonstrated that the clusters of genes within the symbiosis island (611 kb), a transmissible region distinct from other chromosomal regions, are collectively expressed during symbiosis, whereas genes outside the island are downregulated. This finding implies that the huge symbiosis island functions as clustered expression islands to support symbiotic nitrogen fixation. Interestingly, most transposase genes on the symbiosis island were highly upregulated in bacteroids, as were nif, fix, fdx, and rpoN. The genome region containing the fixNOPQ genes outside the symbiosis island was markedly upregulated as another expression island under both microaerobic and symbiotic conditions. The symbiosis profiling data suggested that there was activation of amino acid metabolism, as well as nif-fix gene expression. In contrast, genes for cell wall synthesis, cell division, DNA replication, and flagella were strongly repressed in differentiated bacteroids. A highly upregulated gene in bacteroids, mlr5932 (encoding 1-aminocyclopropane-1-carboxylate deaminase), was disrupted and was confirmed to be involved in nodulation enhancement, indicating that disruption of highly expressed genes is a useful strategy for exploring novel gene functions in symbiosis. PMID:15060047
Uchiumi, Toshiki; Ohwada, Takuji; Itakura, Manabu; Mitsui, Hisayuki; Nukui, Noriyuki; Dawadi, Pramod; Kaneko, Takakazu; Tabata, Satoshi; Yokoyama, Tadashi; Tejima, Kouhei; Saeki, Kazuhiko; Omori, Hirofumi; Hayashi, Makoto; Maekawa, Takaki; Sriprang, Rutchadaporn; Murooka, Yoshikatsu; Tajima, Shigeyuki; Simomura, Kenshiro; Nomura, Mika; Suzuki, Akihiro; Shimoda, Yoshikazu; Sioya, Kouki; Abe, Mikiko; Minamisawa, Kiwamu
Linking functional traits to bacterial phylogeny remains a fundamental but elusive goal of microbial ecology 1. Without this information, it becomes impossible to resolve meaningful units of diversity and the mechanisms by which bacteria interact with each other and adapt to environmental change. Ecological adaptations among bacterial populations have been linked to genomic islands, strain-specific regions of DNA that house functionally adaptive traits 2. In the case of environmental bacteria, these traits are largely inferred from bioinformatic or gene expression analyses 2, thus leaving few examples in which the functions of island genes have been experimentally characterized. Here we report the complete genome sequences of Salinispora tropica and S. arenicola, the first cultured, obligate marine Actinobacteria 3. These two species inhabit benthic marine environments and dedicate 8-10percent of their genomes to the biosynthesis of secondary metabolites. Despite a close phylogenetic relationship, 25 of 37 secondary metabolic pathways are species-specific and located within 21 genomic islands, thus providing new evidence linking secondary metabolism to ecological adaptation. Species-specific differences are also observed in CRISPR sequences, suggesting that variations in phage immunity provide fitness advantages that contribute to the cosmopolitan distribution of S. arenicola 4. The two Salinispora genomes have evolved by complex processes that include the duplication and acquisition of secondary metabolite genes, the products of which provide immediate opportunities for molecular diversification and ecological adaptation. Evidence that secondary metabolic pathways are exchanged by Horizontal Gene Transfer (HGT) yet are fixed among globally distributed populations 5 supports a functional role for their products and suggests that pathway acquisition represents a previously unrecognized force driving bacterial diversification
Penn, Kevin; Jenkins, Caroline; Nett, Markus; Udwary, Daniel; Gontang, Erin; McGlinchey, Ryan; Foster, Brian; Lapidus, Alla; Podell, Sheila; Allen, Eric; Moore, Bradley; Jensen, Paul
tRNA, tmRNA and some small RNA genes are recognized as general integration hotspots of genomic islands (GIs). The GMP synthase gene (guaA) has been firstly identified as one insertion hotspot of foreign DNA fragments. Thirty four islands integrated into the guaA genes were identified in the 987 completely sequenced archaeal and bacterial genomes. These alien islands were widely distributed within the host strains belonging to Proteobacteria, Firmicutes and Actinobacteria. The analysis of structural characteristics of these GIs is important for further determination of the island mobility and transference into suitable hosts. The putative functional integrases encoded by guaA-associated islands were mainly composed of phage P4 integrases, and followed by phage PhiLC3 integrases. Interestingly, island-encoding AlpA is close to P4 integrase and is deduced to be the positive transcriptional regulatory factor of P4 integrase while the XRE protein is close to PhiLC3 integrase and may be the negative transcriptional regulatory factor of PhiLC3 integrase. An 8-bp consensus sequence (5'-GAGTGGGA-3') within the direct repeats of these GIs is the cutting site of the P4 integrases encoding by guaA-associated islands, in which the third nucleotide (G) is the key site. The large-scale investigation of the content of GMP synthase gene hotspots may be useful to find important functional islands within members of many key bacterial species and to transfer useful islands into more suitable hosts. PMID:22306813
Song, Lei; Pan, Yuting; Chen, Sihong; Zhang, Xuehong
Background Different Cupriavidus metallidurans strains isolated from metal-contaminated and other anthropogenic environments were genotypically and phenotypically compared with C. metallidurans type strain CH34. The latter is well-studied for its resistance to a wide range of metals, which is carried for a substantial part by its two megaplasmids pMOL28 and pMOL30. Results Comparative genomic hybridization (CGH) indicated that the extensive arsenal of determinants involved in metal resistance was well conserved among the different C. metallidurans strains. Contrary, the mobile genetic elements identified in type strain CH34 were not present in all strains but clearly showed a pattern, although, not directly related to a particular biotope nor location (geographical). One group of strains carried almost all mobile genetic elements, while these were much less abundant in the second group. This occurrence was also reflected in their ability to degrade toluene and grow autotrophically on hydrogen gas and carbon dioxide, which are two traits linked to separate genomic islands of the Tn4371-family. In addition, the clear pattern of genomic islands distribution allowed to identify new putative genomic islands on chromosome 1 and 2 of C. metallidurans CH34. Conclusions Metal resistance determinants are shared by all C. metallidurans strains and their occurrence is apparently irrespective of the strain's isolation type and place. Cupriavidus metallidurans strains do display substantial differences in the diversity and size of their mobile gene pool, which may be extensive in some (including the type strain) while marginal in others.
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
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.
Hickey, William J.; Chen, Shicheng; Zhao, Jiangchao
Nicotine is an important chemical compound in nature that has been regarded as an environmental toxicant causing various preventable diseases. Several bacterial species are adapted to decompose this heterocyclic compound, including Pseudomonas and Arthrobacter. Pseudomonas putida S16 is a bacterium that degrades nicotine through the pyrrolidine pathway, similar to that present in animals. The corresponding late steps of the nicotine degradation pathway in P. putida S16 was first proposed and demonstrated to be from 2,5-dihydroxy-pyridine through the intermediates N-formylmaleamic acid, maleamic acid, maleic acid, and fumaric acid. Genomics of strain S16 revealed that genes located in the largest genome island play a major role in nicotine degradation and may originate from other strains, as suggested by the constructed phylogenetic tree and the results of comparative genomic analysis. The deletion of gene hpo showed that this gene is essential for nicotine degradation. This study defines the mechanism of nicotine degradation.
Tang, Hongzhi; Yao, Yuxiang; Wang, Lijuan; Yu, Hao; Ren, Yiling; Wu, Geng; Xu, Ping
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.
Waack, Stephan; Keller, Oliver; Asper, Roman; Brodag, Thomas; Damm, Carsten; Fricke, Wolfgang Florian; Surovcik, Katharina; Meinicke, Peter; Merkl, Rainer
Genomic studies of speciation often report the presence of highly differentiated genomic regions interspersed within a milieu of weakly diverged loci. The formation of these speciation islands is generally attributed to reduced inter-population gene flow near loci under divergent selection, but few studies have critically evaluated this hypothesis. Here, we report on transcriptome scans among four recently diverged pairs of sunflower (Helianthus) species that vary in the geographical context of speciation. We find that genetic divergence is lower in sympatric and parapatric comparisons, consistent with a role for gene flow in eroding neutral differences. However, genomic islands of divergence are numerous and small in all comparisons, and contrary to expectations, island number and size are not significantly affected by levels of interspecific gene flow. Rather, island formation is strongly associated with reduced recombination rates. Overall, our results indicate that the functional architecture of genomes plays a larger role in shaping genomic divergence than does the geography of speciation. PMID:23652015
Renaut, S; Grassa, C J; Yeaman, S; Moyers, B T; Lai, Z; Kane, N C; Bowers, J E; Burke, J M; Rieseberg, L H
Adaptive introgression can provide novel genetic variation to fuel rapid evolutionary responses, though it may be counterbalanced by potential for detrimental disruption of the recipient genomic background. We examine the extent and impact of recent introgression of a strongly selected insecticide-resistance mutation (Vgsc-1014F) located within one of two exceptionally large genomic islands of divergence separating the Anopheles gambiae species pair. Here we show that transfer of the Vgsc mutation results in homogenization of the entire genomic island region (~1.5% of the genome) between species. Despite this massive disruption, introgression is clearly adaptive with a dramatic rise in frequency of Vgsc-1014F and no discernable impact on subsequent reproductive isolation between species. Our results show (1) how resilience of genomes to massive introgression can permit rapid adaptive response to anthropogenic selection and (2) that even extreme prominence of genomic islands of divergence can be an unreliable indicator of importance in speciation.
Clarkson, Chris S.; Weetman, David; Essandoh, John; Yawson, Alexander E.; Maslen, Gareth; Manske, Magnus; Field, Stuart G.; Webster, Mark; Antao, Tiago; MacInnis, Bronwyn; Kwiatkowski, Dominic; Donnelly, Martin J.
Adaptive introgression can provide novel genetic variation to fuel rapid evolutionary responses, though it may be counterbalanced by potential for detrimental disruption of the recipient genomic background. We examine the extent and impact of recent introgression of a strongly selected insecticide-resistance mutation (Vgsc-1014F) located within one of two exceptionally large genomic islands of divergence separating the Anopheles gambiae species pair. Here we show that transfer of the Vgsc mutation results in homogenization of the entire genomic island region (~1.5% of the genome) between species. Despite this massive disruption, introgression is clearly adaptive with a dramatic rise in frequency of Vgsc-1014F and no discernable impact on subsequent reproductive isolation between species. Our results show (1) how resilience of genomes to massive introgression can permit rapid adaptive response to anthropogenic selection and (2) that even extreme prominence of genomic islands of divergence can be an unreliable indicator of importance in speciation. PMID:24963649
Clarkson, Chris S; Weetman, David; Essandoh, John; Yawson, Alexander E; Maslen, Gareth; Manske, Magnus; Field, Stuart G; Webster, Mark; Antão, Tiago; MacInnis, Bronwyn; Kwiatkowski, Dominic; Donnelly, Martin J
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
A significant part of horizontal gene transfer is facilitated by genomic islands. Haemophilus influenzae genomic island ICEHin1056 is an archetype of a genomic island that accounts for pandemic spread of antibiotics resistance. ICEHin1056 has modular structure and harbors modules involved in type IV secretion and integration. Previous studies have shown that ICEHin1056 encodes a functional type IV secretion system; however, other modules have not been characterized yet. Here we show that the module on the 5? extremity of ICEHin1056 consists of 15 genes that are well conserved in a number of related genomic islands. Furthermore by disrupting six genes of the investigated module of ICEHin1056 by site-specific mutagenesis we demonstrate that in addition to type IV secretion system module, the investigated module is also important for the successful conjugal transfer of ICEHin1056 from donor to recipient cells.
Juhas, Mario; Dimopoulou, Ioanna; Robinson, Esther; Elamin, Abdel; Harding, Rosalind; Hood, Derek; Crook, Derrick
Different strains of the same prokaryotic species, even very similar ones, vary in large regions of their genomes. This flexible genome represents a huge reservoir of diversity that allows prokaryotes to exploit their environment efficiently. Most of the flexible genome is concentrated in genomic islands, some of which are present in all the strains and coding for similar functions but containing different genes. These replacement genomic islands are typically involved in exposed cellular structures, and their diversity has been connected to their recognition as targets by prokaryotic viruses (phages). We have compared genomes of closely related aquatic microbes from different origins and found examples of recent replacement of some of these flexible genomic islands. In all cases, that include Gram positive and negative bacteria and one archaeon, the replaced regions boundaries contain tell-tale peaks of increased, mostly synonymous, nucleotide substitutions. They tended to be sharper at the boundary closest to the origin of replication of the island. We will present the hypothesis that replacement flexible genomic islands are often exchanged by homologous recombination between different clonal frames. These recombination events are possibly selected due to the immediate reward provided by a change in the phage sensitivity spectrum.
Lopez-Perez, Mario; Martin-Cuadrado, Ana-Belen; Rodriguez-Valera, Francisco
DNA methylation at CpG islands (CGIs) is one of the most intensively studied epigenetic mechanisms. It is fundamental for cellular differentiation and control of transcriptional potential. DNA methylation is involved also in several processes that are central to evolutionary biology, including phenotypic plasticity and evolvability. In this study, we explored the relationship between CpG islands methylation and signatures of selective pressure in Homo Sapiens, using a computational biology approach. By analyzing methylation data of 25 cell lines from the Encyclopedia of DNA Elements (ENCODE) Consortium, we compared the DNA methylation of CpG islands in genomic regions under selective pressure with the methylation of CpG islands in the remaining part of the genome. To define genomic regions under selective pressure, we used three different methods, each oriented to provide distinct information about selective events. Independently of the method and of the cell type used, we found evidences of undermethylation of CGIs in human genomic regions under selective pressure. Additionally, by analyzing SNP frequency in CpG islands, we demonstrated that CpG islands in regions under selective pressure show lower genetic variation. Our findings suggest that the CpG islands in regions under selective pressure seem to be somehow more "protected" from methylation when compared with other regions of the genome. PMID:21829712
Cocozza, Sergio; Akhtar, Most Mauluda; Miele, Gennaro; Monticelli, Antonella
DNA methylation at CpG islands (CGIs) is one of the most intensively studied epigenetic mechanisms. It is fundamental for cellular differentiation and control of transcriptional potential. DNA methylation is involved also in several processes that are central to evolutionary biology, including phenotypic plasticity and evolvability. In this study, we explored the relationship between CpG islands methylation and signatures of selective pressure in Homo Sapiens, using a computational biology approach. By analyzing methylation data of 25 cell lines from the Encyclopedia of DNA Elements (ENCODE) Consortium, we compared the DNA methylation of CpG islands in genomic regions under selective pressure with the methylation of CpG islands in the remaining part of the genome. To define genomic regions under selective pressure, we used three different methods, each oriented to provide distinct information about selective events. Independently of the method and of the cell type used, we found evidences of undermethylation of CGIs in human genomic regions under selective pressure. Additionally, by analyzing SNP frequency in CpG islands, we demonstrated that CpG islands in regions under selective pressure show lower genetic variation. Our findings suggest that the CpG islands in regions under selective pressure seem to be somehow more “protected” from methylation when compared with other regions of the genome.
Cocozza, Sergio; Akhtar, Most. Mauluda; Miele, Gennaro; Monticelli, Antonella
CpG islands (CGIs) are vertebrate genomic landmarks that encompass the promoters of most genes and often lack DNA methylation. Querying their apparent importance, the number of CGIs is reported to vary widely in different species and many do not co-localise with annotated promoters. We set out to quantify the number of CGIs in mouse and human genomes using CXXC Affinity
Robert S. Illingworth; Ulrike Gruenewald-Schneider; Shaun Webb; Alastair R. W. Kerr; Keith D. James; Daniel J. Turner; Colin Smith; David J. Harrison; Robert Andrews; Adrian P. Bird
Lawsonia intracellularis is an obligate intracellular bacterium and the causative agent of proliferative enteropathy (PE). The disease is endemic in pigs, emerging in horses and has also been reported in a variety of other animal species, including nonhuman primates. Comparing the whole genome sequences of a homologous porcine L. intracellularis isolate cultivated for 10 and 60 passages in vitro, we identified a 18-kb prophage-associated genomic island in the passage 10 (pathogenic variant) that was lost in the passage 60 (non-pathogenic variant). This chromosomal island comprises 15 genes downstream from the prophage DLP12 integrase gene. The prevalence of this genetic element was evaluated in 12 other L. intracellularis isolates and in 53 infected animals and was found to be conserved in all porcine isolates cultivated for up to 20 passages and was lost in isolates cultivated for more than 40 passages. Furthermore, the prophage region was also present in 26 fecal samples derived from pigs clinically affected with both acute and chronic forms of the disease. Nevertheless, equine L. intracellularis isolates evaluated did not harbor this genomic island regardless of the passage in vitro. Additionally, fecal samples from 21 clinically affected horses and four wild rabbits trapped in horse farms experiencing PE outbreaks did not show this prophage-associated island. Although the presence of this prophage-associated island was not essential for a virulent L. intracellularis phenotype, this genetic element was porcine isolate-specific and potentially contributed to the ecological specialization of this organism for the swine host.
Genomic islands have been shown to harbor functional traits that differentiate ecologically distinct populations of environmental bacteria. A comparative analysis of the complete genome sequences of the marine Actinobacteria Salinispora tropica and S. arenicola reveals that 75% of the species-specific genes are located in 21 genomic islands. These islands are enriched in genes associated with secondary metabolite biosynthesis providing evidence that secondary metabolism is linked to functional adaptation. Secondary metabolism accounts for 8.8% and 10.9% of the genes in the S. tropica and S. arenicola genomes, respectively, and represents the major functional category of annotated genes that differentiates the two species. Genomic islands harbor all 25 of the species-specific biosynthetic pathways, the majority of which occur in S. arenicola and may contribute to the cosmopolitan distribution of this species. Genome evolution is dominated by gene duplication and acquisition, which in the case of secondary metabolism provide immediate opportunities for the production of new bioactive products. Evidence that secondary metabolic pathways are exchanged horizontally, coupled with prior evidence for fixation among globally distributed populations, supports a functional role and suggests that the acquisition of natural product biosynthetic gene clusters represents a previously unrecognized force driving bacterial diversification. Species-specific differences observed in CRISPR (clustered regularly interspaced short palindromic repeat) sequences suggest that S. arenicola may possess a higher level of phage immunity, while a highly duplicated family of polymorphic membrane proteins provides evidence of a new mechanism of marine adaptation in Gram-positive bacteria.
Penn, Kevin; Jenkins, Caroline; Nett, Markus; Udwary, Daniel W.; Gontang, Erin A.; McGlinchey, Ryan P.; Foster, Brian; Lapidus, Alla; Podell, Sheila; Allen, Eric E.; Moore, Bradley S.; Jensen, Paul R.
Genomic islands, large potentially mobile regions of bacterial chromosomes, are a major contributor to bacteria evolution. Here, we investigated the fitness cost and phenotypic differences between the bacterium Pseudomonas aeruginosa PAO1 and a derivative carrying one integrated copy of the clc element, a 103-kb genomic island [and integrative and conjugative element (ICE)] originating in Pseudomonas sp. strain B13 and a close relative of genomic islands found in clinical and environmental isolates of P. aeruginosa. By using a combination of whole genome transcriptome profiling, phenotypic arrays, competition experiments, and biofilm formation studies, only few differences became apparent, such as reduced biofilm growth and fourfold stationary phase repression of genes involved in acetoin metabolism in PAO1 containing the clc element. In contrast, PAO1 carrying the clc element acquired the capacity to grow on 3-chlorobenzoate and 2-aminophenol as sole carbon and energy substrates. No fitness loss >1% was detectable in competition experiments between PAO1 and PAO1 carrying the clc element. The genes from the clc element were not silent in PAO1, and excision was observed, although transfer of clc from PAO1 to other recipient bacteria was reduced by two orders of magnitude. Our results indicate that newly acquired mobile DNA not necessarily invoke an important fitness cost on their host. Absence of immediate detriment to the host may have contributed to the wide distribution of genomic islands like clc in bacterial genomes. PMID:18448680
Gaillard, Muriel; Pernet, Nataskha; Vogne, Christelle; Hagenbüchle, Otto; van der Meer, Jan Roelof
Genomic islands, large potentially mobile regions of bacterial chromosomes, are a major contributor to bacteria evolution. Here, we investigated the fitness cost and phenotypic differences between the bacterium Pseudomonas aeruginosa PAO1 and a derivative carrying one integrated copy of the clc element, a 103-kb genomic island [and integrative and conjugative element (ICE)] originating in Pseudomonas sp. strain B13 and a close relative of genomic islands found in clinical and environmental isolates of P. aeruginosa. By using a combination of whole genome transcriptome profiling, phenotypic arrays, competition experiments, and biofilm formation studies, only few differences became apparent, such as reduced biofilm growth and fourfold stationary phase repression of genes involved in acetoin metabolism in PAO1 containing the clc element. In contrast, PAO1 carrying the clc element acquired the capacity to grow on 3-chlorobenzoate and 2-aminophenol as sole carbon and energy substrates. No fitness loss >1% was detectable in competition experiments between PAO1 and PAO1 carrying the clc element. The genes from the clc element were not silent in PAO1, and excision was observed, although transfer of clc from PAO1 to other recipient bacteria was reduced by two orders of magnitude. Our results indicate that newly acquired mobile DNA not necessarily invoke an important fitness cost on their host. Absence of immediate detriment to the host may have contributed to the wide distribution of genomic islands like clc in bacterial genomes.
Gaillard, Muriel; Pernet, Nataskha; Vogne, Christelle; Hagenbuchle, Otto; van der Meer, Jan Roelof
Burkholderia glumae is the major causal agent of bacterial panicle blight of rice, a growing disease problem in global rice production. To better understand its genome-scale characteristics, the genome of the highly virulent B. glumae strain 336gr-1 isolated from Louisiana, USA was sequenced using the Illumina Genome Analyser II system. De novo assembled 336gr-1 contigs were aligned and compared with the previously sequenced genome of B. glumae strain BGR1, which was isolated from an infected rice plant in South Korea. Comparative analysis of the whole genomes of B. glumae 336gr-1 and B. glumae BGR1 revealed numerous unique genomic regions present only in one of the two strains. These unique regions contained accessory genes including mobile elements and phage-related genes, and some of the unique regions in B. glumae BGR1 corresponded to predicted genomic islands. In contrast, little variation was observed in known and potential virulence genes between the two genomes. The considerable amount of plasticity largely based on accessory genes and genome islands observed from the comparison of the genomes of these two strains of B. glumae may explain the versatility of this bacterial species in various environmental conditions and geographic locations. PMID:23563926
Francis, Felix; Kim, Joohyun; Ramaraj, Thiru; Farmer, Andrew; Rush, Milton C; Ham, Jong Hyun
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.
The metaphor of 'genomic islands of speciation' was first used to describe heterogeneous differentiation among loci between the genomes of closely related species. The biological model proposed to explain these differences was that the regions showing high levels of differentiation were resistant to gene flow between species, while the remainder of the genome was being homogenized by gene flow and consequently showed lower levels of differentiation. However, the conditions under which such differentiation can occur at multiple unlinked loci are restrictive; additionally, essentially, all previous analyses have been carried out using relative measures of divergence, which can be misleading when regions with different levels of recombination are compared. Here, we test the model of differential gene flow by asking whether absolute divergence is also higher in the previously identified 'islands'. Using five species pairs for which full sequence data are available, we find that absolute measures of divergence are not higher in genomic islands. Instead, in all cases examined, we find reduced diversity in these regions, a consequence of which is that relative measures of divergence are abnormally high. These data therefore do not support a model of differential gene flow among loci, although islands of relative divergence may represent loci involved in local adaptation. Simulations using the program IMa2 further suggest that inferences of any gene flow may be incorrect in many comparisons. We instead present an alternative explanation for heterogeneous patterns of differentiation, one in which postspeciation selection generates patterns consistent with multiple aspects of the data. PMID:24845075
Cruickshank, Tami E; Hahn, Matthew W
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.
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
Salmonella carriage patterns in wild and captive reptiles suggest that both geographical proximity and host ecological differences may determine bacterial diversity among reptile populations. In this study, we explore the relative importance of these factors on Salmonella diversity in free-living Galápagos iguanas. We isolated Salmonella enterica from marine iguanas (Amblyrhynchus cristatus) and land iguanas (Conolophus subcristatus and C. pallidus) living on two islands (Plaza Sur and Santa Fe). We evaluated Salmonella population patterns using genomic fingerprints, sequence typing and serotyping. Rep-PCR fingerprinting revealed significant grouping of isolates by iguana population. Island residence had the strongest effect on isolate similarity, but a smaller divergence among Salmonella isolates from different iguana ecotypes (land versus marine) was detected within each island. In contrast, sequence typing detected a marginal difference in isolate genotypes between islands. Sequence types corresponded strongly to serotype identity, with both islands hosting a unique serovar pool. Our findings suggest that both geographical location and host ecotype differences (either from within host strain selection or from differences in habitat use) contribute to Salmonella population patterns in the Galápagos Islands. PMID:23761248
Wheeler, Emily; Cann, Isaac K O; Mackie, Roderick I
In this paper, we use a statistical estimator developed in astrophysics to study the distribution and organization of features of the human genome. Using the human reference sequence we quantify the global distribution of CpG islands (CGI) in each chromosome and demonstrate that the organization of the CGI across a chromosome is non-random, exhibits surprisingly long range correlations (10 Mb) and varies significantly among chromosomes. These correlations of CGI summarize functional properties of the genome that are not captured when considering variation in any particular separate (and local) feature. The demonstration of the proposed methods to quantify the organization of CGI in the human genome forms the basis of future studies. The most illuminating of these will assess the potential impact on phenotypic variation of inter-individual variation in the organization of the functional features of the genome within and among chromosomes, and among individuals for particular chromosomes.
Koester, Benjamin; Rea, Thomas J.; Templeton, Alan R.; Szalay, Alexander S.; Sing, Charles F.
Legionella pneumophila is a Gram-negative freshwater agent which multiplies in specialized nutrient-rich vacuoles of amoebae. When replicating in human alveolar macrophages, Legionella can cause Legionnaires' disease. Recently, we identified a new type of conjugation/type IVA secretion system (T4ASS) in L. pneumophila Corby (named trb-tra). Analogous versions of trb-tra are localized on the genomic islands Trb-1 and Trb-2. Both can exist as an episomal circular form, and Trb-1 can be transferred horizontally to other Legionella strains by conjugation. In our current work, we discovered the importance of a site-specific integrase (Int-1, lpc2818) for the excision and conjugation process of Trb-1. Furthermore, we identified the genes lvrRABC (lpc2813 to lpc2816) to be involved in the regulation of Trb-1 excision. In addition, we demonstrated for the first time that a Legionella genomic island (LGI) of L. pneumophila Corby (LpcGI-2) encodes a functional type IV secretion system. The island can be transferred horizontally by conjugation and is integrated site specifically into the genome of the transconjugants. LpcGI-2 generates three different episomal forms. The predominant episomal form, form A, is generated integrase dependently (Lpc1833) and transferred by conjugation in a pilT-dependent manner. Therefore, the genomic islands Trb-1 and LpcGI-2 should be classified as integrative and conjugative elements (ICEs). Coculture studies of L. pneumophila wild-type and mutant strains revealed that the int-1 and lvrRABC genes (located on Trb-1) as well as lpc1833 and pilT (located on LpcGI-2) do not influence the in vivo fitness of L. pneumophila in Acanthamoeba castellanii. PMID:23354744
Lautner, Monika; Schunder, Eva; Herrmann, Vroni; Heuner, Klaus
CpG island–like sequences are commonly thought to provide the sole signals for designating constitutively unmethylated regions in the genome, thus generating open chromatin domains within a sea of global repression. Using a new database obtained from comprehensive microarray analysis, we show that unmethylated regions (UMRs) seem to be formed during early embryogenesis, not as a result of CpG-ness, but rather
Ravid Straussman; Deborah Nejman; Douglas Roberts; Israel Steinfeld; Barak Blum; Nissim Benvenisty; Itamar Simon; Zohar Yakhini; Howard Cedar
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.
Lautner, Monika; Schunder, Eva; Herrmann, Vroni
The locus of enterocyte effacement (LEE) and genomic O island 122 (OI-122) are pathogenicity islands in verocytotoxin-producing Escherichia coli (VTEC) serotypes that are associated with outbreaks and serious disease. Composed of three modules, OI-122 may occur as \\
Paulina Konczy; Kim Ziebell; Mariola Mascarenhas; Aileen Choi; Corinne Michaud; Andrew M. Kropinski; Thomas S. Whittam; Mark Wickham; Brett Finlay; Mohamed A. Karmali
Burkholderia pseudomallei, as a saprophytic bacterium that can cause a severe sepsis disease named melioidosis, has preserved several extra genes in its genome for survival. The sequenced genome of the organism showed high diversity contributed mainly from genomic islands (GIs). Comparative genome hybridization (CGH) of 3 clinical and 2 environmental isolates, using whole genome microarrays based on B. pseudomallei K96243 genes, revealed a difference in the presence of genomic islands between clinical and environmental isolates. The largest GI, GI8, of B. pseudomallei was observed as a 2 sub-GI named GIs8.1 and 8.2 with distinguishable %GC content and unequal presence in the genome. GIs8.1, 8.2 and 15 were found to be more common in clinical isolates. A new GI, GI16c, was detected on chromosome 2. Presences of GIs8.1, 8.2, 15 and 16c were evaluated in 70 environmental and 64 clinical isolates using PCR assays. A combination of GIs8.1 and 16c (positivity of either GI) was detected in 70% of clinical isolates and 11.4% of environmental isolates (P<0.001). Using BALB/c mice model, no significant difference of time to mortality was observed between K96243 isolate and three isolates without GIs under evaluation (P>0.05). Some virulence genes located in the absent GIs and the difference of GIs seems to contribute less to bacterial virulence. The PCR detection of 2 GIs could be used as a cost effective and rapid tool to detect potentially virulent isolates that were contaminated in soil.
Bartpho, Thanatchaporn; Wongsurawat, Thidathip; Wongratanacheewin, Surasakdi; Talaat, Adel M.; Karoonuthaisiri, Nitsara; Sermswan, Rasana W.
We report on an entropic edge detector based on the local calculation of the Jensen-Shannon divergence with application to the search for CpG islands. CpG islands are pieces of the genome related to gene expression and cell differentiation, and thus to cancer formation. Searching for these CpG islands is a major task in genetics and bioinformatics. Some algorithms have been proposed in the literature, based on moving statistics in a sliding window, but its size may greatly influence the results. The local use of Jensen-Shannon divergence is a completely different strategy: the nucleotide composition inside the islands is different from that in their environment, so a statistical distance—the Jensen-Shannon divergence—between the composition of two adjacent windows may be used as a measure of their dissimilarity. Sliding this double window over the entire sequence allows us to segment it compositionally. The fusion of those segments into greater ones that satisfy certain identification criteria must be achieved in order to obtain the definitive results. We find that the local use of Jensen-Shannon divergence is very suitable in processing DNA sequences for searching for compositionally different structures such as CpG islands, as compared to other algorithms in literature.
Luque-Escamilla, Pedro Luis; Martínez-Aroza, José; Oliver, José L.; Gómez-Lopera, Juan Francisco; Román-Roldán, Ramón
Genomic islands (GIs), frequently associated with the pathogenicity of bacteria and having a substantial influence on bacterial evolution, are groups of “alien” elements which probably undergo special temporal–spatial regulation in the host genome. Are there particular hallmark transcriptional signals for these “exotic” regions? We here explore the potential transcriptional signals that underline the GIs beyond the conventional views on basic sequence composition, such as codon usage and GC property bias. It showed that there is a significant enrichment of the transcription start positions (TSPs) in the GI regions compared to the whole genome of Salmonella enterica and Escherichia coli. There was up to a four-fold increase for the 70% GIs, implying high-density TSPs profile can potentially differentiate the GI regions. Based on this feature, we developed a new sliding window method GIST, Genomic-island Identification by Signals of Transcription, to identify these regions. Subsequently, we compared the known GI-associated features of the GIs detected by GIST and by the existing method Islandviewer to those of the whole genome. Our method demonstrates high sensitivity in detecting GIs harboring genes with biased GI-like function, preferred subcellular localization, skewed GC property, shorter gene length and biased “non-optimal” codon usage. The special transcriptional signals discovered here may contribute to the coordinate expression regulation of foreign genes. Finally, by using GIST, we detected many interesting GIs in the 2011 German E. coli O104:H4 outbreak strain TY-2482, including the microcin H47 system and gene cluster ycgXEFZ-ymgABC that activates the production of biofilm matrix. The aforesaid findings highlight the power of GIST to predict GIs with distinct intrinsic features to the genome. The heterogeneity of cumulative TSPs profiles may not only be a better identity for “alien” regions, but also provide hints to the special evolutionary course and transcriptional regulation of GI regions.
Huang, Qianli; Cheng, Xuanjin; Cheung, Man Kit; Kiselev, Sergey S.; Ozoline, Olga N.; Kwan, Hoi Shan
Based on molecular information theory, 10 T7-like promoter models were built for the T7 group of phages and used to scan their host genomes and closely related genomes. 38 genomes were scanned and 12 clusters of tandem promoters were identified in nine enteropathogens. Comparative analysis of these tandem promoter-bearing regions reveals that they are similar to each other, forming prophage-like islands of 4–13 kb. Each island appears to contain two or three tandem T7-like promoters within a stretch of 150–620 bases, but there are no corresponding RNA polymerase (RNAP) genes. The promoters would transcribe two to five putative phage-related proteins, but none of these resemble known phage structural proteins. An integrase belonging to the Int family of site-specific recombinases is encoded upstream of the tandem promoters. A direct repeat of 17–24 bases was found on the ends of all 12 islands. Comparative analysis of the islands shows that these islands appear to have recombined with each other. These results suggest that the islands could encode a group of satellite phages. Activation and function of the islands may depend on transcription by a T7-like RNAP after infection by a T7-like phage or foreign DNA that encodes a T7-like RNAP.
Chen, Zehua; Schneider, Thomas D.
Background A substantial amount of data has been accumulated supporting the important role of genomic islands (GEIs) - including pathogenicity islands (PAIs) - in bacterial genome plasticity and the evolution of bacterial pathogens. Their instability and the high level sequence similarity of different (partial) islands suggest an exchange of PAIs between strains of the same or even different bacterial species by horizontal gene transfer (HGT). Transfer events of archetypal large genomic islands of enterobacteria which often lack genes required for mobilisation or transfer have been rarely investigated so far. Results To study mobilisation of such large genomic regions in prototypic uropathogenic E. coli (UPEC) strain 536, PAI II536 was supplemented with the mobRP4 region, an origin of replication (oriVR6K), an origin of transfer (oriTRP4) and a chloramphenicol resistance selection marker. In the presence of helper plasmid RP4, conjugative transfer of the 107-kb PAI II536 construct occured from strain 536 into an E. coli K-12 recipient. In transconjugants, PAI II536 existed either as a cytoplasmic circular intermediate (CI) or integrated site-specifically into the recipient's chromosome at the leuX tRNA gene. This locus is the chromosomal integration site of PAI II536 in UPEC strain 536. From the E. coli K-12 recipient, the chromosomal PAI II536 construct as well as the CIs could be successfully remobilised and inserted into leuX in a PAI II536 deletion mutant of E. coli 536. Conclusions Our results corroborate that mobilisation and conjugal transfer may contribute to evolution of bacterial pathogens through horizontal transfer of large chromosomal regions such as PAIs. Stabilisation of these mobile genetic elements in the bacterial chromosome result from selective loss of mobilisation and transfer functions of genomic islands.
Streptococcus suis is an important zoonotic pathogen that can cause meningitis and sepsis in both pigs and humans. Infections in humans have been sporadic worldwide but two severe outbreaks occurred in China in recent years, while infections in pigs are a major problem in the swine industry. Some S. suis strains are more pathogenic than others with 2 sequence types (ST), ST1 and ST7, being well recognized as highly pathogenic. We analyzed 31 isolates from 23 serotypes and 25 STs by NimbleGen tiling microarray using the genome of a high pathogenicity (HP) ST1 strain, GZ1, as reference and a new algorithm to detect gene content difference. The number of genes absent in a strain ranged from 49 to 225 with a total of 632 genes absent in at least one strain, while 1346 genes were found to be invariably present in all strains as the core genome of S. suis, accounting for 68% of the GZ1 genome. The majority of genes are located in chromosomal blocks with two or more contiguous genes. Sixty two blocks are absent in two or more strains and defined as regions of difference (RDs), among which 26 are putative genomic islands (GIs). Clustering and statistical analyses revealed that 8 RDs including 6 putative GIs and 21 genes within these RDs are significantly associated with HP. Three RDs encode known virulence related factors including the extracellular factor, the capsular polysaccharide and a SrtF pilus. The strains were divided into 5 groups based on population genetic analysis of multilocus sequence typing data and the distribution of the RDs among the groups revealed gain and loss of RDs in different groups. Our study elucidated the gene content diversity of S. suis and identified genes that potentially promote HP.
Wang, Yiting; Zhang, Ji; Jing, Huaiqi; Chen, Chen; Segura, Mariela; Gottschalk, Marcelo; Xu, Jianguo
Streptococcus suis is an important zoonotic pathogen that can cause meningitis and sepsis in both pigs and humans. Infections in humans have been sporadic worldwide but two severe outbreaks occurred in China in recent years, while infections in pigs are a major problem in the swine industry. Some S. suis strains are more pathogenic than others with 2 sequence types (ST), ST1 and ST7, being well recognized as highly pathogenic. We analyzed 31 isolates from 23 serotypes and 25 STs by NimbleGen tiling microarray using the genome of a high pathogenicity (HP) ST1 strain, GZ1, as reference and a new algorithm to detect gene content difference. The number of genes absent in a strain ranged from 49 to 225 with a total of 632 genes absent in at least one strain, while 1346 genes were found to be invariably present in all strains as the core genome of S. suis, accounting for 68% of the GZ1 genome. The majority of genes are located in chromosomal blocks with two or more contiguous genes. Sixty two blocks are absent in two or more strains and defined as regions of difference (RDs), among which 26 are putative genomic islands (GIs). Clustering and statistical analyses revealed that 8 RDs including 6 putative GIs and 21 genes within these RDs are significantly associated with HP. Three RDs encode known virulence related factors including the extracellular factor, the capsular polysaccharide and a SrtF pilus. The strains were divided into 5 groups based on population genetic analysis of multilocus sequence typing data and the distribution of the RDs among the groups revealed gain and loss of RDs in different groups. Our study elucidated the gene content diversity of S. suis and identified genes that potentially promote HP. PMID:21479213
Zheng, Xiao; Zheng, Han; Lan, Ruiting; Ye, Changyun; Wang, Yiting; Zhang, Ji; Jing, Huaiqi; Chen, Chen; Segura, Mariela; Gottschalk, Marcelo; Xu, Jianguo
A system of versatile insertion plasmids was constructed that permits efficient delivery of the target sites of an ultra-rare-cutting endonuclease and the recombinase FLP into preselected sites of the bacterial genome. With the help of this system, the pathogenicity island LEE of the Escherichia coli O157:H7 genome was excised and isolated in vitro, deleted in vivo, rescued as a plasmid,
GYORGY POSFAI; MICHAEL D. KOOB; HEATHER A. KIRKPATRICK; FREDERICK R. BLATTNER
A system of versatile insertion plasmids was constructed that permits efficient delivery of the target sites of an ultra-rare-cutting endonuclease and the recombinase FLP into preselected sites of the bacterial genome. With the help of this system, the pathogenicity island LEE of the Escherichia coli O157:H7 genome was excised and isolated in vitro, deleted in vivo, rescued as a plasmid, and transferred into another strain.
Posfai, G; Koob, M D; Kirkpatrick, H A; Blattner, F R
Our group has initiated experiments to epigenetically profile CpG island hypermethylation in genomic DNA from tissue specimens of head and neck squamous cell carcinoma (HNSCC) using a microarray of 12,288 CpG island clones. Our technique, known as a methylation-specific restriction enzyme (MSRE) analysis, is a variation of the differential methylation hybridization (DMH) technique, in that it is not an array comparison of two DNA samples using methylation-specific restriction enzymes. Instead, it is a comparison of a single DNA sample's response to a methylation-sensitive restriction enzyme (HpaII) and its corresponding methylation-insensitive isoschizomer (MspI). Estimation of the reproducibility of this microarray assay by intraclass correlation (ICC) demonstrated that in four replicate experiments for three tumor specimens, the ICC observed for a given tumor specimen ranged from 0.68 to 0.85 without filtering of data. Repeated assays achieved 87% concordance or greater for all tumors after filtering of array data by fluorescence intensity. We utilized hierarchical clustering on a population of 37 HNSCC samples to cluster tumor samples with similar DNA methylation profiles. Supervised learning techniques are now being utilized to allow us to identify associations between specific epigenetic signatures and clinical parameters. Such techniques will allow us to identify select groups of CpG island loci that could be used as epigenetic markers for both diagnosis and prognosis in HNSCC. PMID:16717445
Adrien, L R; Schlecht, N F; Kawachi, N; Smith, R V; Brandwein-Gensler, M; Massimi, A; Chen, S; Prystowsky, M B; Childs, G; Belbin, T J
In order to determine the occurrence of AbaR-type genomic island in multidrug resistant Acinetobacter baumannii (MDRAb) strains circulating in Argentina, Uruguay, and Chile, we studied 51 MDRAb isolates recovered from several hospitals over 30 years. AbaR-type genomic resistance islands were found in 36 MDRAb isolates since 1986 till now. MLST technique allowed us to identify the presence of four different Clonal Complexes (109, 104, 119, 113) among the positive AbaR-type island positive strains. This is the first description of AbaR-type islands in the CC104 and CC113 that are the most widespread Clonal Complexes in Argentina. In addition, PCR mapping exposed different arrays to those previously described, evidencing the plasticity of this island. Our results evidence a widespread distribution of the AbaR-type genomic islands along the time in the MDRAb population, including the epidemic global clone 1 (GC1) as well as different clonal complexes to those already described in the literature. PMID:23397241
Ramírez, María Soledad; Vilacoba, Elisabet; Stietz, María Silvina; Merkier, Andrea Karina; Jeric, Paola; Limansky, Adriana S; Márquez, Carolina; Bello, Helia; Catalano, Mariana; Centrón, Daniela
One of the capabilities developed by bacteria is the ability to gain large fragments of DNA from other bacteria or to lose portions of their own genomes. Among these exchangeable fragments are the genomic islands (GIs). Nine GIs have been identified in Brucella, and genomic island 3 (GI-3) is shared by two pathogenic species, B. melitensis and B. abortus. GI-3 encodes mostly unknown proteins. One of the aims of this study was to perform pulsed-field gel electrophoresis (PFGE) on field isolates of B. abortus from Chile to determine whether these isolates are clonally related. Furthermore, we focused on the characterization of GI-3, studying its organization and the genetic conservation of the GI-3 sequence using techniques such as tiling-path PCR (TP-PCR) and restriction fragment length polymorphism-PCR (RFLP-PCR). Our results, after PFGE was performed on 69 field isolates of B. abortus from Chile, showed that the strains were genetically homogeneous. To increase the power of genetic discrimination among these strains, we used multiple locus variable-number tandem-repeat (VNTR) analysis with 16 loci (MLVA-16). The results obtained by MLVA-16 showed that the strains of B. abortus were genetically heterogeneous and that most of them clustered according to their geographic origin. Of the genetic loci studied, panel 2B was the one describing the highest diversity in the analysis, as well as locus Bruce19 in panel 2A. In relation to the study of GI-3, our experimental analysis by TP-PCR identified and confirmed that GI-3 is present in all wild strains of B. abortus, demonstrating the high stability of gene cluster GI-3 in Chilean field strains.
Cespedes, Sandra; Salgado, Paulina; Valenzuela, Patricio; Vidal, Roberto; Onate, Angel A.
BackgroundMajority of CpG dinucleotides in mammalian genomes tend to undergo DNA methylation, but most CpG islands are resistant to such epigenetic modification. Understanding about mechanisms that may lead to the methylation resistance of CpG islands is still very poor.Methodology\\/Principal FindingsUsing the genome-scale in vivo DNA methylation data from human brain, we investigated the flanking sequence features of methylation-resistant CpG islands,
Shicai Fan; Fang Fang; Xuegong Zhang; Michael Q. Zhang; Jörg Hoheisel
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
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
A procedure is described to isolate DNA probes from the bovine genome that are enriched in sites for the so-called rare cutter restriction endonucleases. A collection of SacII (CvCGCGG)-Hin-dIII fragments from bovine sperm was established in the plasmid Bluescript. 180 clones were picked at random and analysed for the presence of inserts with sites for the following rare cutters: EagI, BsshII, NarI, MluI, NruI, NaeI: 70% of the clones contained at least 1 site and 5% contained four different such sites. 22.8% had multiple sites for one or more of the rare cutters tested. Sequence analysis for 16 clones confirmed the cloning of DNA with a G+C content and a proportion of CpG vs GpCs indicative of CpG islands. PMID:8498709
De Rubertis, F; Comincini, S; Leone, P; Rognoni, G; Ferretti, L
Abstract We sequenced the complete mitochondrial genome of the Tioman Island rock gecko, Cnemaspis limi, which is known as an endemic species to Malaysia. The complete mitogenome is 16,680?bp in size, consisting of 37 genes coding for 13 proteins, 22 transfer RNAs, two ribosomal RNAs and one control region. The A?+?T content of the overall base composition of H-strand is 53.09% (T: 23.20%, C: 32.48%, A: 29.89% and G: 14.43%). The major non-coding region (control region) is 1254?bp in length with the A?+?T content of 55.09% and four replicates of a 76-bp repeat within this region. PMID:23631365
Yan, Jie; Tian, Chao; Zhou, Jianli; Bauer, Aaron M; Lee Grismer, L; Zhou, Kaiya
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.
Vo, An T. T.; van Duijkeren, Engeline; Gaastra, Wim; Fluit, Ad C.
A genomic island was identified in the Haemophilus influenzae biogroup aegyptius Brazilian purpuric fever (BPF) strain F3031. This island, which was also found in other BPF isolates, could not be detected in non-BPF biogroup aegyptius strains or in nontypeable or typeable H. influenzae strains, with the exception of a region present in the type b Eagan strain. This 34,378-bp island is inserted, in reference to H. influenzae Rd KW20, within a choline transport gene and contains a mosaic structure of Mu-like prophage genes, several hypothetical genes, and genes potentially encoding an Erwinia carotovora carotovoricin Er-like bacteriocin. The product of the tail fiber ORF in the bacteriocin-like region shows a hybrid structure where the C terminus is similar to an H. influenzae phage HP1 tail protein implicating this open reading frame in altering host specificity for a putative bacteriocin. Significant synteny is seen in the entire genomic island with genomic regions from Salmonella enterica subsp. enterica serovar Typhi CT18, Photorhabdus luminescens subsp. laumondii TT01, Chromobacterium violaceum, and to a lesser extent Haemophilus ducreyi 35000HP. In a previous work, we isolated several BPF-specific DNA fragments through a genome subtraction procedure, and we have found that a majority of these fragments map to this locus. In addition, several subtracted fragments generated from an independent laboratory by using different but related strains also map to this island. These findings underscore the importance of this BPF-specific chromosomal region in explaining some of the genomic differences between highly invasive BPF strains and non-BPF isolates of biogroup aegyptius.
McGillivary, Glen; Tomaras, Andrew P.; Rhodes, Eric R.; Actis, Luis A.
It has been argued that the limited genetic diversity and reduced allelic heterogeneity observed in isolated founder populations facilitates discovery of loci contributing to both Mendelian and complex disease. A strong founder effect, severe isolation, and substantial inbreeding have dramatically reduced genetic diversity in natives from the island of Kosrae, Federated States of Micronesia, who exhibit a high prevalence of obesity and other metabolic disorders. We hypothesized that genetic drift and possibly natural selection on Kosrae might have increased the frequency of previously rare genetic variants with relatively large effects, making these alleles readily detectable in genome-wide association analysis. However, mapping in large, inbred cohorts introduces analytic challenges, as extensive relatedness between subjects violates the assumptions of independence upon which traditional association test statistics are based. We performed genome-wide association analysis for 15 quantitative traits in 2,906 members of the Kosrae population, using novel approaches to manage the extreme relatedness in the sample. As positive controls, we observe association to known loci for plasma cholesterol, triglycerides, and C-reactive protein and to a compelling candidate loci for thyroid stimulating hormone and fasting plasma glucose. We show that our study is well powered to detect common alleles explaining ?5% phenotypic variance. However, no such large effects were observed with genome-wide significance, arguing that even in such a severely inbred population, common alleles typically have modest effects. Finally, we show that a majority of common variants discovered in Caucasians have indistinguishable effect sizes on Kosrae, despite the major differences in population genetics and environment.
Lowe, Jennifer K.; Maller, Julian B.; Pe'er, Itsik; Neale, Benjamin M.; Salit, Jacqueline; Kenny, Eimear E.; Shea, Jessica L.; Burkhardt, Ralph; Smith, J. Gustav; Ji, Weizhen; Noel, Martha; Foo, Jia Nee; Blundell, Maude L.; Skilling, Vita; Garcia, Laura; Sullivan, Marcia L.; Lee, Heather E.; Labek, Anna; Ferdowsian, Hope; Auerbach, Steven B.; Lifton, Richard P.; Newton-Cheh, Christopher; Breslow, Jan L.; Stoffel, Markus; Daly, Mark J.; Altshuler, David M.; Friedman, Jeffrey M.
CpG islands (CGIs) are CpG-rich regions compared to CpG-depleted bulk DNA of mammalian genomes and are generally regarded as the epigenetic regulatory regions in association with unmethylation, promoter activity and histone modifications. Accurate identification of CpG islands with epigenetic regulatory function in bulk genomes is of wide interest. Here, the common features of functional CGIs are identified using an average mutual information method to differentiate functional CGIs from the remaining CGIs. A new approach (CpG mutual information, CpG_MI) was further explored to identify functional CGIs based on the cumulative mutual information of physical distances between two neighboring CpGs. Compared to current approaches, CpG_MI achieved the highest prediction accuracy. This approach also identified new functional CGIs overlapping with gene promoter regions which were missed by other algorithms. Nearly all CGIs identified by CpG_MI overlapped with histone modification marks. CpG_MI could also be used to identify potential functional CGIs in other mammalian genomes, as the CpG dinucleotide contents and cumulative mutual information distributions are almost the same among six mammalian genomes in our analysis. It is a reliable quantitative tool for the identification of functional CGIs from bulk genomes and helps in understanding the relationships between genomic functional elements and epigenomic modifications.
Su, Jianzhong; Zhang, Yan; Lv, Jie; Liu, Hongbo; Tang, Xiaoyan; Wang, Fang; Qi, Yunfeng; Feng, Yujia; Li, Xia
Vibrio cholerae poses a threat to human health, and new epidemic variants have been reported so far. Seventh pandemic V. cholerae strains are characterized by highly related genomic sequences but can be discriminated by a large set of Genomic Islands, phages and Integrative Conjugative Elements. Classical serotyping and biotyping methods do not easily discriminate among new variants arising worldwide, therefore the establishment of new methods for their identification is required. We developed a multiplex PCR assay for the rapid detection of the major 7th pandemic variants of V. cholerae O1 and O139. Three specific genomic islands (GI-12, GI-14 and GI-15), two phages (Kappa and TLC), Vibrio Seventh Pandemic Island 2 (VSP-II), and the ICEs of the SXT/R391 family were selected as targets of our multiplex PCR based on a comparative genomic approach. The optimization and specificity of the multiplex PCR was assessed on 5 V. cholerae 7th pandemic reference strains, and other 34 V. cholerae strains from various epidemic events were analyzed to validate the reliability of our method. This assay had sufficient specificity to identify twelve different V. cholerae genetic profiles, and therefore has the potential to be used as a rapid screening method. PMID:22062086
Spagnoletti, Matteo; Ceccarelli, Daniela; Colombo, Mauro M
Putative integrative and conjugative elements (ICEs), i.e., genomic islands which could excise, self-transfer by conjugation, and integrate into the chromosome of the bacterial host strain, were previously identified by in silico analysis in the sequenced genomes of Streptococcus agalactiae (M. Brochet et al., J. Bacteriol. 190:6913–6917, 2008). We investigated here the mobility of the elements integrated into the 3? end of a tRNALys gene. Three of the four putative ICEs tested were found to excise but only one (ICE_515_tRNALys) was found to transfer by conjugation not only to S. agalactiae strains but also to a Streptococcus pyogenes strain. Transfer was observed even if recipient cell already carries a related resident ICE or a genomic island flanked by attL and attR recombination sites but devoid of conjugation or recombination genes (CIs-Mobilizable Element [CIME]). The incoming ICE preferentially integrates into the 3? end of the tRNALys gene (i.e., the attR site of the resident element), leading to a CIME-ICE structure. Transfer of the whole composite element CIME-ICE was obtained, showing that the CIME is mobilizable in cis by the ICE. Therefore, genomic islands carrying putative virulence genes but lacking the mobility gene can be mobilized by a related ICE after site-specific accretion.
Puymege, Aurore; Bertin, Stephane; Chuzeville, Sarah; Guedon, Gerard
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
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.
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
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.
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
Here we determined the role of various genomic islands in E. coli K1 interactions with phagocytic A. castellanii and nonphagocytic brain microvascular endothelial cells. The findings revealed that the genomic islands deletion mutants of RS218 related to toxins (peptide toxin, ?-hemolysin), adhesins (P fimbriae, F17-like fimbriae, nonfimbrial adhesins, Hek, and hemagglutinin), protein secretion system (T1SS for hemolysin), invasins (IbeA, CNF1), metabolism (D-serine catabolism, dihydroxyacetone, glycerol, and glyoxylate metabolism) showed reduced interactions with both A. castellanii and brain microvascular endothelial cells. Interestingly, the deletion of RS218-derived genomic island 21 containing adhesins (P fimbriae, F17-like fimbriae, nonfimbrial adhesins, Hek, and hemagglutinin), protein secretion system (T1SS for hemolysin), invasins (CNF1), metabolism (D-serine catabolism) abolished E. coli K1-mediated HBMEC cytotoxicity in a CNF1-independent manner. Therefore, the characterization of these genomic islands should reveal mechanisms of evolutionary gain for E. coli K1 pathogenicity.
Yousuf, Farzana Abubakar; Yousuf, Zuhair; Iqbal, Junaid; Siddiqui, Ruqaiyyah; Khan, Hafsa; Khan, Naveed Ahmed
Genes for magnetosome formation in magnetotactic bacteria are clustered in large genomic magnetosome islands (MAI). Spontaneous deletions and rearrangements were frequently observed within these regions upon metabolic stress. This instability was speculated to be due to RecA-dependent homologous recombination between the numerous sequence repeats present within the MAI. Here we show that a RecA-deficient strain of Magnetospirillum gryphiswaldense (IK-1) no longer exhibits genetic instability of magnetosome formation. Strain IK-1 displayed higher sensitivity to oxygen and UV irradiation. Furthermore, the lack of RecA abolished allelic exchange in the mutant. Cells of strain IK-1 displayed a slightly altered (i.e., more elongated) morphology, whereas the absence of RecA did not affect the ability to synthesize wild-type-like magnetosomes. Our data provide evidence that the observed genetic instability of magnetosome formation in the wild type is due predominantly to RecA-mediated recombination. In addition, increased genetic stability could make strain IK-1 a useful tool for the expression of genes and further genetic engineering, as well as for biotechnological production of bacterial magnetosomes. PMID:21821768
Kolinko, Isabel; Jogler, Christian; Katzmann, Emanuel; Schüler, Dirk
Genes for magnetosome formation in magnetotactic bacteria are clustered in large genomic magnetosome islands (MAI). Spontaneous deletions and rearrangements were frequently observed within these regions upon metabolic stress. This instability was speculated to be due to RecA-dependent homologous recombination between the numerous sequence repeats present within the MAI. Here we show that a RecA-deficient strain of Magnetospirillum gryphiswaldense (IK-1) no longer exhibits genetic instability of magnetosome formation. Strain IK-1 displayed higher sensitivity to oxygen and UV irradiation. Furthermore, the lack of RecA abolished allelic exchange in the mutant. Cells of strain IK-1 displayed a slightly altered (i.e., more elongated) morphology, whereas the absence of RecA did not affect the ability to synthesize wild-type-like magnetosomes. Our data provide evidence that the observed genetic instability of magnetosome formation in the wild type is due predominantly to RecA-mediated recombination. In addition, increased genetic stability could make strain IK-1 a useful tool for the expression of genes and further genetic engineering, as well as for biotechnological production of bacterial magnetosomes.
Kolinko, Isabel; Jogler, Christian; Katzmann, Emanuel; Schuler, Dirk
Background Promoter and 5? end methylation regulation of tumour suppressor genes is a common feature of many cancers. Such occurrences often lead to the silencing of these key genes and thus they may contribute to the development of cancer, including prostate cancer. Methodology/Principal Findings In order to identify methylation changes in prostate cancer, we performed a genome-wide analysis of DNA methylation using Agilent human CpG island arrays. Using computational and gene-specific validation approaches we have identified a large number of potential epigenetic biomarkers of prostate cancer. Further validation of candidate genes on a separate cohort of low and high grade prostate cancers by quantitative MethyLight analysis has allowed us to confirm DNA hypermethylation of HOXD3 and BMP7, two genes that may play a role in the development of high grade tumours. We also show that promoter hypermethylation is responsible for downregulated expression of these genes in the DU-145 PCa cell line. Conclusions/Significance This study identifies novel epigenetic biomarkers of prostate cancer and prostate cancer progression, and provides a global assessment of DNA methylation in prostate cancer.
Briollais, Laurent; Sadikovic, Bekim; Ozcelik, Hilmi; Sunderji, Alia; Venkateswaran, Vasundara; Pinthus, Jehonathan; Fleshner, Neil; van der Kwast, Theodorus; Bapat, Bharati
Background. Majority of CpG dinucleotides in mammalian genomes tend to undergo DNA methylation, but most CpG islands are resistant to such epigenetic modification. Understanding about mechanisms that may lead to the methylation resistance of CpG islands is still very poor. Methodology\\/Principal Findings. Using the genome-scale in vivo DNA methylation data from human brain, we investigated the flanking sequence features of
Shicai Fan; Fang Fang; Xuegong Zhang; Michael Q. Zhang
Aim To identify genetic variants underlying biochemical traits – total cholesterol, low-density lipoprotein (LDL) cholesterol, high-density lipoprotein (HDL) cholesterol, triglycerides, uric acid, albumin, and fibrinogen, in a genome-wide association study in an isolated population where rare variants of larger effect may be more easily identified. Methods The study included 944 adult inhabitants of the island of Kor?ula, as a part of a larger DNA-based genetic epidemiological study in 2007. Biochemical measurements were performed in a single laboratory with stringent internal and external quality control procedures. Examinees were genotyped using Human Hap370CNV chip by Illumina, with a genome-wide scan containing 346?027 single nucleotide polymorphisms (SNP). Results A total of 31 SNPs were associated with 7 investigated traits at the level of P?1.00?×?10?5. Nine of SNPs implicated the role of SLC2A9 in uric acid regulation (P?=?4.10?×?10?6-2.58?×?10?12), as previously found in other populations. All 22 remaining associations fell into the P?=?1.00?×?10?5-1.00?×?10?6 significance range. One of them replicated the association between cholesteryl ester transfer protein (CETP) and HDL, and 7 associations were more than 100 kilobases away from the closest known gene. Nearby SNPs, rs4767631 and rs10444502, in gene kinase suppressor of ras 2 (KSR2) on chromosome 12 were associated with LDL cholesterol levels, and rs10444502 in the same gene with total cholesterol levels. Similarly, rs2839619 in gene PBX/knotted 1 homeobox 1 (PKNOX1) on chromosome 21 was associated with total and LDL cholesterol levels. The remaining 9 findings implied possible associations between phosphatidylethanolamine N-methyltransferase (PEMT) gene and total cholesterol; USP46, RAP1GDS1, and ZCCHC16 genes and triglycerides; BCAT1 and SLC14A2 genes and albumin; and NR3C2, GRIK2, and PCSK2 genes and fibrinogen. Conclusion Although this study was underpowered for most of the reported associations to reach formal threshold of genome-wide significance under the assumption of independent multiple testing, replications of previous findings and consistency of association between the identified variants and more than one studied trait make such findings interesting for further functional follow-up studies. Changed allele frequencies in isolate population may contribute to identifying variants that would not be easily identified in much larger samples in outbred populations.
Zemunik, Tatijana; Boban, Mladen; Lauc, Gordan; Jankovic, Stipan; Rotim, Kresimir; Vatavuk, Zoran; Bencic, Goran; ?ogas, Zoran; Boraska, Vesna; Torlak, Vesela; Susac, Jelena; Zobic, Ivana; Rudan, Diana; Pulanic, Drazen; Modun, Darko; Mudnic, Ivana; Gunjaca, Grgo; Budimir, Danijela; Hayward, Caroline; Vitart, Veronique; Wright, Alan F.; Campbell, Harry; Rudan, Igor
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?10?5, with one SNP (rs7792939 in gene zinc finger protein 498, ZNF498) associated with body weight, hip circumference, and brachial circumference (P?=?3.59-5.73?×?10?6), and another one (rs157350 in gene delta-sarcoglycan, SGCD) with both brachial and hip circumference (P?=?3.70-6.08?×?10?6). Variants in CRIM1, a gene regulating delivery of bone morphogenetic proteins to the cell surface, and ITGA1, involved in the regulation of mesenchymal stem cell proliferation and cartilage production, were also associated with brachial circumference (P?=?7.82 and 9.68?×?10?6, respectively) and represent interesting functional candidates. Other associations involved those between genes SEZ6L2 and MAX and waist circumference, XTP6 and brachial circumference, and AMPA1/GRIA1 and height. Conclusion Although the study was underpowered for the reported associations to reach formal threshold of 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.
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
The selC tRNA gene is a common site for the insertion of pathogenicity islands in a variety of bacterial enteric pathogens. We demonstrate here that Escherichia coli that produces Shiga toxin 2d and does not harbor the locus of enterocyte effacement (LEE) contains, instead, a novel genomic island. In one representative strain (E. coli O91:H strain 4797\\/97), this island is
H. Schmidt; W.-L. Zhang; U. Hemmrich; S. Jelacic; W. Brunder; P. I. Tarr; U. Dobrindt; J. Hacker; H. Karch
Magnetotactic bacteria are able to swim navigating along geomagnetic field lines. They synthesize ferromagnetic nanocrystals that are embedded in cytoplasmic membrane invaginations forming magnetosomes. Regularly aligned in the cytoplasm along cytoskeleton filaments, the magnetosome chain effectively forms a compass needle bestowing on bacteria their magnetotactic behaviour. A large genomic island, conserved among magnetotactic bacteria, contains the genes potentially involved in magnetosome formation. One of the genes, mamK has been described as encoding a prokaryotic actin-like protein which when it polymerizes forms in the cytoplasm filamentous structures that provide the scaffold for magnetosome alignment. Here, we have identified a series of genes highly similar to the mam genes in the genome of Magnetospirillum magneticum AMB-1. The newly annotated genes are clustered in a genomic islet distinct and distant from the known magnetosome genomic island and most probably acquired by lateral gene transfer rather than duplication. We focused on a mamK-like gene whose product shares 54.5% identity with the actin-like MamK. Filament bundles of polymerized MamK-like protein were observed in vitro with electron microscopy and in vivo in E. coli cells expressing MamK-like-Venus fusions by fluorescence microscopy. In addition, we demonstrate that mamK-like is transcribed in AMB-1 wild-type and ?mamK mutant cells and that the actin-like filamentous structures observed in the ?mamK strain are probably MamK-like polymers. Thus MamK-like is a new member of the prokaryotic actin-like family. This is the first evidence of a functional mam gene encoded outside the magnetosome genomic island.
Pereira, Sandrine; Pignol, David; Wu, Long-Fei; Ginet, Nicolas
Magnetotactic bacteria are able to swim navigating along geomagnetic field lines. They synthesize ferromagnetic nanocrystals that are embedded in cytoplasmic membrane invaginations forming magnetosomes. Regularly aligned in the cytoplasm along cytoskeleton filaments, the magnetosome chain effectively forms a compass needle bestowing on bacteria their magnetotactic behaviour. A large genomic island, conserved among magnetotactic bacteria, contains the genes potentially involved in magnetosome formation. One of the genes, mamK has been described as encoding a prokaryotic actin-like protein which when it polymerizes forms in the cytoplasm filamentous structures that provide the scaffold for magnetosome alignment. Here, we have identified a series of genes highly similar to the mam genes in the genome of Magnetospirillum magneticum AMB-1. The newly annotated genes are clustered in a genomic islet distinct and distant from the known magnetosome genomic island and most probably acquired by lateral gene transfer rather than duplication. We focused on a mamK-like gene whose product shares 54.5% identity with the actin-like MamK. Filament bundles of polymerized MamK-like protein were observed in vitro with electron microscopy and in vivo in E. coli cells expressing MamK-like-Venus fusions by fluorescence microscopy. In addition, we demonstrate that mamK-like is transcribed in AMB-1 wild-type and DeltamamK mutant cells and that the actin-like filamentous structures observed in the DeltamamK strain are probably MamK-like polymers. Thus MamK-like is a new member of the prokaryotic actin-like family. This is the first evidence of a functional mam gene encoded outside the magnetosome genomic island. PMID:20161777
Rioux, Jean-Baptiste; Philippe, Nadège; Pereira, Sandrine; Pignol, David; Wu, Long-Fei; Ginet, Nicolas
Metastatic melanoma is a malignant cancer with generally poor prognosis, with no targeted chemotherapy. To identify epigenetic changes related to melanoma, we have determined genome-wide methylated CpG island distributions by next-generation sequencing. Melanoma chromosomes tend to be differentially methylated over short CpG island tracts. CpG islands in the upstream regulatory regions of many coding and noncoding RNA genes, including, for example, TERC, which encodes the telomerase RNA, exhibit extensive hypermethylation, whereas several repeated elements, such as LINE 2, and several LTR elements, are hypomethylated in advanced stage melanoma cell lines. By using CpG island demethylation profiles, and by integrating these data with RNA-seq data obtained from melanoma cells, we have identified a co-expression network of differentially methylated genes with significance for cancer related functions. Focused assays of melanoma patient tissue samples for CpG island methylation near the noncoding RNA gene SNORD-10 demonstrated high specificity. PMID:24129253
Li, Jian-Liang; Mazar, Joseph; Zhong, Cuncong; Faulkner, Geoffrey J; Govindarajan, Subramaniam S; Zhang, Zhan; Dinger, Marcel E; Meredith, Gavin; Adams, Christopher; Zhang, Shaojie; Mattick, John S; Ray, Animesh; Perera, Ranjan J
We investigate genes of lytic, Bacillus thuringiensis bacteriophage 0305?8-36 that are non-essential for laboratory propagation, but might have a function in the wild. We isolate deletion mutants to identify these genes. The non-permutation of the genome (218.948 Kb, with a 6.479 Kb terminal repeat and 247 identified orfs) simplifies isolation of deletion mutants. We find two islands of non-essential genes. The first island (3.01% of the genomic DNA) has an informatically identified DNA translocation operon. Deletion causes no detectable growth defect during propagation in a dilute agarose overlay. Identification of the DNA translocation operon begins with a DNA relaxase and continues with a translocase and membrane-binding anchor proteins. The relaxase is in a family, first identified here, with homologs in other bacteriophages. The second deleted island (3.71% of the genome) has genes for two metallo-protein chaperonins and two tRNAs. Deletion causes a significant growth defect. In addition, (1) we find by “in situ” (in-plaque) single-particle fluorescence microscopy that adsorption to the host occurs at the tip of the 486 nm long tail, (2) we develop a procedure of 0305?8-36 purification that does not cause tail contraction, and (3) we then find by electron microscopy that 0305?8-36 undergoes tail tip-tail tip dimerization that potentially blocks adsorption to host cells, presumably with effectiveness that increases as the bacteriophage particle concentration increases. These observations provide an explanation of the previous observation that 0305?8-36 does not lyse liquid cultures, even though 0305?8-36 is genomically lytic.
Pathria, Saurav; Rolando, Mandy; Lieman, Karen; Hayes, Shirley; Hardies, Stephen; Serwer, Philip
More than 50% of mammalian genes are associated with CpG islands and thus they serve as a good gene marker. We have devised a simple method to scan large pieces of native or cloned genomic DNA for CpG islands. The method is based on the presence of multiple Hpa II and Hha I sites in CpG islands, at a frequency 30 times higher than in the rest of the genome. The steps include complete digestion of DNA with a rare-cutting restriction endonuclease (to produce large fragments with defined ends), partial digestion with Hpa II and Hha I, and subsequent Southern hybridization with an end probe. This identifies a CpG island as a cluster of sub-bands and, based on their electrophoretic mobility, one can immediately locate the island relative to the ends. For many vectors, universal probes flanking the cloning site are available, enabling the simultaneous analysis of a large number of samples. We demonstrated the usefulness of the method by analyzing known CpG islands in native genomic DNA and lambda, cosmid and P1 clones, and by isolating two novel transcribed islands from anonymous cosmid clones. Our method is quick, inexpensive, and can detect CpG islands with few or even no rare-cutter sites. PMID:9872453
Kato, R; Sasaki, H
Genes involved in magnetite biomineralization are clustered in the genome of the magnetotactic bacterium Magnetospirillum gryphiswaldense. We analyzed a 482-kb genomic fragment, in which we identified an approximately 130-kb region representing a putative genomic "magnetosome island" (MAI). In addition to all known magnetosome genes, the MAI contains genes putatively involved in magnetosome biomineralization and numerous genes with unknown functions, as well as pseudogenes, and it is particularly rich in insertion elements. Substantial sequence polymorphism of clones from different subcultures indicated that this region undergoes frequent rearrangements during serial subcultivation in the laboratory. Spontaneous mutants affected in magnetosome formation arise at a frequency of up to 10(-2) after prolonged storage of cells at 4 degrees C or exposure to oxidative stress. All nonmagnetic mutants exhibited extended and multiple deletions in the MAI and had lost either parts of or the entire mms and mam gene clusters encoding magnetosome proteins. The mutations were polymorphic with respect to the sites and extents of deletions, but all mutations were found to be associated with the loss of various copies of insertion elements, as revealed by Southern hybridization and PCR analysis. Insertions and deletions in the MAI were also found in different magnetosome-producing clones, indicating that parts of this region are not essential for the magnetic phenotype. Our data suggest that the genomic MAI undergoes frequent transposition events, which lead to subsequent deletion by homologous recombination under physiological stress conditions. This can be interpreted in terms of adaptation to physiological stress and might contribute to the genetic plasticity and mobilization of the magnetosome island. PMID:16237001
Ullrich, Susanne; Kube, Michael; Schübbe, Sabrina; Reinhardt, Richard; Schüler, Dirk
Genes involved in magnetite biomineralization are clustered in the genome of the magnetotactic bacterium Magnetospirillum gryphiswaldense. We analyzed a 482-kb genomic fragment, in which we identified an approximately 130-kb region representing a putative genomic “magnetosome island” (MAI). In addition to all known magnetosome genes, the MAI contains genes putatively involved in magnetosome biomineralization and numerous genes with unknown functions, as well as pseudogenes, and it is particularly rich in insertion elements. Substantial sequence polymorphism of clones from different subcultures indicated that this region undergoes frequent rearrangements during serial subcultivation in the laboratory. Spontaneous mutants affected in magnetosome formation arise at a frequency of up to 10?2 after prolonged storage of cells at 4°C or exposure to oxidative stress. All nonmagnetic mutants exhibited extended and multiple deletions in the MAI and had lost either parts of or the entire mms and mam gene clusters encoding magnetosome proteins. The mutations were polymorphic with respect to the sites and extents of deletions, but all mutations were found to be associated with the loss of various copies of insertion elements, as revealed by Southern hybridization and PCR analysis. Insertions and deletions in the MAI were also found in different magnetosome-producing clones, indicating that parts of this region are not essential for the magnetic phenotype. Our data suggest that the genomic MAI undergoes frequent transposition events, which lead to subsequent deletion by homologous recombination under physiological stress conditions. This can be interpreted in terms of adaptation to physiological stress and might contribute to the genetic plasticity and mobilization of the magnetosome island.
Ullrich, Susanne; Kube, Michael; Schubbe, Sabrina; Reinhardt, Richard; Schuler, Dirk
Neisseria meningitidis is an important human pathogen that is capable of killing within hours of infection. Its normal habitat is the nasopharynx of adult humans. Here we identify a genomic island (the prp gene cluster) in N. meningitidis that enables this species to utilize propionic acid as a supplementary carbon source during growth, particularly under nutrient poor growth conditions. The prp gene cluster encodes enzymes for a methylcitrate cycle. Novel aspects of the methylcitrate cycle in N. meningitidis include a propionate kinase which was purified and characterized, and a putative propionate transporter. This genomic island is absent from the close relative of N. meningitidis, the commensal Neisseria lactamica, which chiefly colonizes infants not adults. We reason that the possession of the prp genes provides a metabolic advantage to N. meningitidis in the adult oral cavity, which is rich in propionic acid-generating bacteria. Data from classical microbiological and sequence-based microbiome studies provide several lines of supporting evidence that N. meningitidis colonization is correlated with propionic acid generating bacteria, with a strong correlation between prp-containing Neisseria and propionic acid generating bacteria from the genus Porphyromonas, and that this may explain adolescent/adult colonization by N. meningitidis. PMID:24910087
Catenazzi, Maria Chiara E; Jones, Helen; Wallace, Iain; Clifton, Jacqueline; Chong, James P J; Jackson, Matthew A; Macdonald, Sandy; Edwards, James; Moir, James W B
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.
Quesada, Jose M.; Soriano, Maria Isabel
Genome wide methylation profiling of gliomas is likely to provide important clues to improving treatment outcomes. Restriction enzyme based approaches have been widely utilized for methylation profiling of cancer genomes and will continue to have importance in combination with higher density microarrays. With the availability of the human genome sequence and microarray probe sequences, these approaches can be readily characterized and optimized via in silico modeling. We adapted the previously described HpaII/MspI based Methylation Sensitive Restriction Enzyme (MSRE) assay for use with two-color Agilent 244K CpG island microarrays. In this assay, fragmented genomic DNA is digested in separate reactions with isoschizomeric HpaII (methylation-sensitive) and MspI (methylation-insensitive) restriction enzymes. Using in silico hybridization, we found that genomic fragmentation with BfaI was superior to MseI, providing a maximum effective coverage of 22,362 CpG islands in the human genome. In addition, we confirmed the presence of an internal control group of fragments lacking HpaII/MspI sites which enable separation of methylated and unmethylated fragments. We used this method on genomic DNA isolated from normal brain, U87MG cells, and a glioblastoma patient tumor sample and confirmed selected differentially methylated CpG islands using bisulfite sequencing. Along with additional validation points, we performed a receiver operating characteristics (ROC) analysis to determine the optimal threshold (p???0.001). Based on this threshold, we identified ?2,400 CpG islands common to all three samples and 145 CpG islands unique to glioblastoma. These data provide general guidance to individuals seeking to maximize effective coverage using restriction enzyme based methylation profiling approaches.
Tran, Anh; Escovedo, Cameron; Migdall-Wilson, Justine; Chou, Arthur P.; Chen, Weidong; Cloughesy, Timothy; Nelson, Stanley; Lai, Albert
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
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.
DNA methylation is an inheritable chemical modification of cytosine, and represents one of the most important epigenetic events. Computational prediction of the DNA methylation status can be employed to speed up the genome-wide methylation profiling, and to identify the key features that are correlated with various methylation patterns. Here, we develop CpGIMethPred, the support vector machine-based models to predict the methylation status of the CpG islands in the human genome under normal conditions. The features for prediction include those that have been previously demonstrated effective (CpG island specific attributes, DNA sequence composition patterns, DNA structure patterns, distribution patterns of conserved transcription factor binding sites and conserved elements, and histone methylation status) as well as those that have not been extensively explored but are likely to contribute additional information from a biological point of view (nucleosome positioning propensities, gene functions, and histone acetylation status). Statistical tests are performed to identify the features that are significantly correlated with the methylation status of the CpG islands, and principal component analysis is then performed to decorrelate the selected features. Data from the Human Epigenome Project (HEP) are used to train, validate and test the predictive models. Specifically, the models are trained and validated by using the DNA methylation data obtained in the CD4 lymphocytes, and are then tested for generalizability using the DNA methylation data obtained in the other 11 normal tissues and cell types. Our experiments have shown that (1) an eight-dimensional feature space that is selected via the principal component analysis and that combines all categories of information is effective for predicting the CpG island methylation status, (2) by incorporating the information regarding the nucleosome positioning, gene functions, and histone acetylation, the models can achieve higher specificity and accuracy than the existing models while maintaining a comparable sensitivity measure, (3) the histone modification (methylation and acetylation) information contributes significantly to the prediction, without which the performance of the models deteriorate, and, (4) the predictive models generalize well to different tissues and cell types. The developed program CpGIMethPred is freely available at http://users.ece.gatech.edu/~hzheng7/CGIMetPred.zip.
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; Fromme, Petra
Magnetosome biomineralization and magnetotaxis in magnetotactic bacteria are controlled by numerous, mostly unknown gene functions that are predominantly encoded by several operons located within the genomic magnetosome island (MAI). Genetic analysis of magnetotactic bacteria has remained difficult and requires the development of novel tools. We established a Cre-lox-based deletion method which allows the excision of large genomic fragments in Magnetospirillum gryphiswaldense. Two conjugative suicide plasmids harboring lox sites that flanked the target region were subsequently inserted into the chromosome by homologous recombination, requiring only one single-crossover event, respectively, and resulting in a double cointegrate. Excision of the targeted chromosomal segment that included the inserted plasmids and their resistance markers was induced by trans expression of Cre recombinase, which leaves behind a scar of only a single loxP site. The Cre helper plasmid was then cured from the deletant strain by relief of antibiotic selection. We have used this method for the deletion of 16.3-kb, 61-kb, and 67.3-kb fragments from the genomic MAI, either in a single round or in subsequent rounds of deletion, covering a region of approximately 87 kb that comprises the mamAB, mms6, and mamGFDC operons. As expected, all mutants were Mag? and some were Mot?; otherwise, they showed normal growth patterns, which indicates that the deleted region is not essential for viability in the laboratory. The method will facilitate future functional analysis of magnetosome genes and also can be utilized for large-scale genome engineering in magnetotactic bacteria.
Ullrich, Susanne; Schuler, Dirk
Magnetosome biomineralization and magnetotaxis in magnetotactic bacteria are controlled by numerous, mostly unknown gene functions that are predominantly encoded by several operons located within the genomic magnetosome island (MAI). Genetic analysis of magnetotactic bacteria has remained difficult and requires the development of novel tools. We established a Cre-lox-based deletion method which allows the excision of large genomic fragments in Magnetospirillum gryphiswaldense. Two conjugative suicide plasmids harboring lox sites that flanked the target region were subsequently inserted into the chromosome by homologous recombination, requiring only one single-crossover event, respectively, and resulting in a double cointegrate. Excision of the targeted chromosomal segment that included the inserted plasmids and their resistance markers was induced by trans expression of Cre recombinase, which leaves behind a scar of only a single loxP site. The Cre helper plasmid was then cured from the deletant strain by relief of antibiotic selection. We have used this method for the deletion of 16.3-kb, 61-kb, and 67.3-kb fragments from the genomic MAI, either in a single round or in subsequent rounds of deletion, covering a region of approximately 87 kb that comprises the mamAB, mms6, and mamGFDC operons. As expected, all mutants were Mag(-) and some were Mot(-); otherwise, they showed normal growth patterns, which indicates that the deleted region is not essential for viability in the laboratory. The method will facilitate future functional analysis of magnetosome genes and also can be utilized for large-scale genome engineering in magnetotactic bacteria. PMID:20173068
Ullrich, Susanne; Schüler, Dirk
A diazotrophic, acidophilic, iron-oxidizing bacterium, Leptospirillum ferrooxidans, known to be difficult to cultivate, was isolated from a fresh volcanic ash deposit on the island of Miyake, Japan. Here, we report the complete genome sequence of a cultured strain, C2-3. PMID:22815442
Fujimura, Reiko; Sato, Yoshinori; Nishizawa, Tomoyasu; Oshima, Kenshiro; Kim, Seok-Won; Hattori, Masahira; Kamijo, Takashi; Ohta, Hiroyuki
We present the draft genome sequences of two isolates of the Roseobacter lineage, 3SOLIMAR09 and 1FIGIMAR09, which were obtained from harbors of Mallorca Island, Spain, and are affiliated with the Sulfitobacter genus. Both isolates harbor the complete gene set for protocatechuate catabolism and incomplete pathways for several additional monoaromatic compounds.
Mas-Llado, Maria; Pina-Villalonga, Joana Maria; Brunet-Galmes, Isabel; Nogales, Balbina
A diazotrophic, acidophilic, iron-oxidizing bacterium, Leptospirillum ferrooxidans, known to be difficult to cultivate, was isolated from a fresh volcanic ash deposit on the island of Miyake, Japan. Here, we report the complete genome sequence of a cultured strain, C2-3.
Fujimura, Reiko; Sato, Yoshinori; Nishizawa, Tomoyasu; Oshima, Kenshiro; Kim, Seok-Won; Hattori, Masahira; Kamijo, Takashi
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.
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.
Despite the high endemicity of hepatitis A virus (HAV) in Indonesia, genetic information on those HAV strains is limited. Serum samples obtained from 76 individuals during outbreaks of hepatitis A in Jember (East Java) in 2006 and Tangerang (West Java) in 2007 and those from 82 patients with acute hepatitis in Solo (Central Java), Denpasar on Bali Island, Mataram on Lombok Island, and Makassar on Sulawesi Island in 2003 or 2007 were tested for the presence of HAV RNA by reverse transcription PCR with primers targeting the VP1-2B region (481 nucleotides, primer sequences at both ends excluded). Overall, 34 serum samples had detectable HAV RNA, including at least one viremic sample from each of the six regions. These 34 strains were 96.3-100 % identical to each other and formed a phylogenetic cluster within genotype IA. Six representative HAV isolates from each region shared 98.3-98.9 % identity over the entire genome and constituted a IA sublineage with a bootstrap value of 100 %, consisting of only Indonesian strains. HAV strains recovered from Japanese patients who were presumed to have contracted HAV infection while visiting Indonesia were closest to the Indonesian IA HAV strains obtained in the present study, with a high identity of 99.5-99.7 %, supporting the Indonesian origin of the imported strains. These results indicate that genetic analysis of HAV strains indigenous to HAV-endemic countries, including Indonesia, are useful for tracing infectious sources in imported cases of acute hepatitis A and for defining the epidemiological features of HAV infection in that country. PMID:24212885
Mulyanto; Wibawa, I Dewa Nyoman; Suparyatmo, Joseph Benedictus; Amirudin, Rifai; Ohnishi, Hiroshi; Takahashi, Masaharu; Nishizawa, Tsutomu; Okamoto, Hiroaki
There is strong evidence for both genetic and environmental risk factors comprising the aetiology of multiple sclerosis (MS). While much progress has been made in recent years in identifying common genetic variants using genome-wide association studies, alternative approaches have remained relatively neglected. The prevalence of MS in Orkney and Shetland is among the highest in the world. Previous studies have suggested that a higher degree of parental relatedness in these isolated communities may contribute to the high rates of MS, indicating that recessive effects have an important role in MS aetiology. The Northern Isles Multiple Sclerosis (NIMS) study investigated the potential role of genome-wide homozygosity in MS risk by genotyping 88 MS patients, 89 controls matched by age, sex and ancestry, and a further 89 controls matched for sex and ancestry, but passed the majority of lifetime risk of developing MS (>70 years of age). Three participants were removed on the basis of pedigree-genomic anomalies (n=263). Three measures of genome-wide homozygosity were generated for each individual, and association with MS was assessed using logistic regression models. No effect of genome-wide homozygosity was detected, indicating that inbreeding and consanguinity are not risk factors for MS in this population. PMID:21897447
McWhirter, Rebekah E; McQuillan, Ruth; Visser, Elizabeth; Counsell, Carl; Wilson, James F
There is strong evidence for both genetic and environmental risk factors comprising the aetiology of multiple sclerosis (MS). While much progress has been made in recent years in identifying common genetic variants using genome-wide association studies, alternative approaches have remained relatively neglected. The prevalence of MS in Orkney and Shetland is among the highest in the world. Previous studies have suggested that a higher degree of parental relatedness in these isolated communities may contribute to the high rates of MS, indicating that recessive effects have an important role in MS aetiology. The Northern Isles Multiple Sclerosis (NIMS) study investigated the potential role of genome-wide homozygosity in MS risk by genotyping 88 MS patients, 89 controls matched by age, sex and ancestry, and a further 89 controls matched for sex and ancestry, but passed the majority of lifetime risk of developing MS (>70 years of age). Three participants were removed on the basis of pedigree-genomic anomalies (n=263). Three measures of genome-wide homozygosity were generated for each individual, and association with MS was assessed using logistic regression models. No effect of genome-wide homozygosity was detected, indicating that inbreeding and consanguinity are not risk factors for MS in this population.
McWhirter, Rebekah E; McQuillan, Ruth; Visser, Elizabeth; Counsell, Carl; Wilson, James F
BackgroundPromoter and 5? end methylation regulation of tumour suppressor genes is a common feature of many cancers. Such occurrences often lead to the silencing of these key genes and thus they may contribute to the development of cancer, including prostate cancer.Methodology\\/Principal FindingsIn order to identify methylation changes in prostate cancer, we performed a genome-wide analysis of DNA methylation using Agilent
Ken Kron; Vaijayanti Pethe; Laurent Briollais; Bekim Sadikovic; Hilmi Ozcelik; Alia Sunderji; Vasundara Venkateswaran; Jehonathan Pinthus; Neil Fleshner; Theodorus van der Kwast; Bharati Bapat; Mikhail V. Blagosklonny
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 DNA enrichment combined with DNA microarray detection or sequencing. Methylated DNA enrichment is a key step in a microarray based genome-wide methylation profiling study, and even for future high-throughput sequencing based methylome analysis. Results In order to evaluate the sensitivity and accuracy of methylated DNA enrichment, we investigated and optimized a number of important parameters to improve the performance of several enrichment assays, including differential methylation hybridization (DMH), microarray-based methylation assessment of single samples (MMASS), and methylated DNA immunoprecipitation (MeDIP). With advantages and disadvantages unique to each approach, we found that assays based on methylation-sensitive enzyme digestion and those based on immunoprecipitation detected different methylated DNA fragments, indicating that they are complementary in their relative ability to detect methylation differences. Conclusions Our study provides the first comprehensive evaluation for widely used methodologies for methylated DNA enrichment, and could be helpful for developing a cost effective approach for DNA methylation profiling.
Fis, one of the most important nucleoid-associated proteins, functions as a global regulator of transcription in bacteria that has been comprehensively studied in Escherichia coli K12. Fis also influences the virulence of Salmonella enterica and pathogenic E. coli by regulating their virulence genes, however, the relevant mechanism is unclear. In this report, using combined RNA-seq and chromatin immunoprecipitation (ChIP)-seq technologies, we first identified 1646 Fis-regulated genes and 885 Fis-binding targets in the S. enterica serovar Typhimurium, and found a Fis regulon different from that in E. coli. Fis has been reported to contribute to the invasion ability of S. enterica. By using cell infection assays, we found it also enhances the intracellular replication ability of S. enterica within macrophage cell, which is of central importance for the pathogenesis of infections. Salmonella pathogenicity islands (SPI)-1 and SPI-2 are crucial for the invasion and survival of S. enterica in host cells. Using mutation and overexpression experiments, real-time PCR analysis, and electrophoretic mobility shift assays, we demonstrated that Fis regulates 63 of the 94 Salmonella pathogenicity island (SPI)-1 and SPI-2 genes, by three regulatory modes: i) binds to SPI regulators in the gene body or in upstream regions; ii) binds to SPI genes directly to mediate transcriptional activation of themselves and downstream genes; iii) binds to gene encoding OmpR which affects SPI gene expression by controlling SPI regulators SsrA and HilD. Our results provide new insights into the impact of Fis on SPI genes and the pathogenicity of S. enterica.
Wang, Quan; Wang, Lei
Fis, one of the most important nucleoid-associated proteins, functions as a global regulator of transcription in bacteria that has been comprehensively studied in Escherichia coli K12. Fis also influences the virulence of Salmonella enterica and pathogenic E. coli by regulating their virulence genes, however, the relevant mechanism is unclear. In this report, using combined RNA-seq and chromatin immunoprecipitation (ChIP)-seq technologies, we first identified 1646 Fis-regulated genes and 885 Fis-binding targets in the S. enterica serovar Typhimurium, and found a Fis regulon different from that in E. coli. Fis has been reported to contribute to the invasion ability of S. enterica. By using cell infection assays, we found it also enhances the intracellular replication ability of S. enterica within macrophage cell, which is of central importance for the pathogenesis of infections. Salmonella pathogenicity islands (SPI)-1 and SPI-2 are crucial for the invasion and survival of S. enterica in host cells. Using mutation and overexpression experiments, real-time PCR analysis, and electrophoretic mobility shift assays, we demonstrated that Fis regulates 63 of the 94 Salmonella pathogenicity island (SPI)-1 and SPI-2 genes, by three regulatory modes: i) binds to SPI regulators in the gene body or in upstream regions; ii) binds to SPI genes directly to mediate transcriptional activation of themselves and downstream genes; iii) binds to gene encoding OmpR which affects SPI gene expression by controlling SPI regulators SsrA and HilD. Our results provide new insights into the impact of Fis on SPI genes and the pathogenicity of S. enterica. PMID:23717649
Wang, Hui; Liu, Bin; Wang, Quan; Wang, Lei
Vibrio vulnificus is a ubiquitous inhabitant of the marine coastal environment, and an important pathogen of humans. We characterized a globally distributed sample of environmental isolates from a range of habitats and hosts and compared these with isolates recovered from cases of human infection. Multilocus sequence typing data using six housekeeping genes divided 63 of the 67 isolates into the two main lineages previously noted for this species, and this division was also confirmed using the 16S rRNA and open reading frame VV0401 markers. Lineage I was comprised exclusively of biotype 1 isolates, whereas lineage II contained biotype 1 and all biotype 2 isolates. Four isolates did not cluster within either lineage: two biotype 3 and two biotype 1 isolates. The proportion of isolates recovered from a clinical setting was noted to be higher in lineage I than in lineage II. Lineage I isolates were also associated with a 33-kb genomic island (region XII), one of three regions identified by genome comparisons as unique to the species. Region XII contained an arylsulfatase gene cluster, a sulfate reduction system, two chondroitinase genes, and an oligopeptide ABC transport system, all of which are absent from the majority of lineage II isolates. Arylsulfatases and the sulfate reduction system, along with performing a scavenging role, have been hypothesized to play a role in pathogenic processes in other bacteria. Our data suggest that lineage I may have a higher pathogenic potential and that region XII, along with other regions, may give isolates a selective advantage either in the human host or in the aquatic environment or both.
Cohen, Ana Luisa V.; Oliver, James D.; DePaola, Angelo; Feil, Edward J.; Fidelma Boyd, E.
Purpose Hypospadias is one of the most frequent genital malformations in the male newborn, and results from abnormal penile and urethral development. The etiology of hypospadias remains largely unknown despite intensive investigations. Fetal androgens have a crucial role in genital differentiation. Recent studies have suggested that molecular mechanisms that underlie the effects of androgens on the fetus may involve disruption of epigenetic programming of gene expression during development. We assessed whether epigenetic modification of DNA methylation is associated with hypospadias in a case-control study of 12 hypospadias and 8 control subjects. Materials and Methods Genome-wide DNA methylation profiling was performed on the study subjects using the Illumina Infinium® HumanMethylation450 Bead-Chip, which enables the direct investigation of methylation status of more than 485,000 individual CpG sites throughout the genome. The methylation level at each CpG site was compared between cases and controls using the t test and logistic regression. Results We identified 14 CpG sites that were associated with hypospadias with p <0.00001. These CpG sites were in or near the SCARB1, MYBPH, SORBS1, LAMA4, HOXD11, MYO1D, EGFL7, C10orf41, LMAN1L and SULF1 genes. Two CpG sites in SCARB1 and MYBPH genes remained statistically significant after correction for multiple testing (p = 2.61×10?09, pcorrected = 0.008; p = 3.06×10?08, pcorrected = 0.02, respectively). Conclusions To our knowledge this is the first study to investigate hypospadias using a unique and novel epigenetic approach. Our findings suggest DNA methylation patterns are useful in identifying new genes such as SCARB1 and MYBPH that may be involved in the etiology of hypospadias.
Choudhry, Shweta; Deshpande, Archana; Qiao, Liang; Beckman, Kenneth; Sen, Saunak; Baskin, Laurence S.
We devised software tools to systematically investig- ate the contents and contexts of bacterial tRNA and tmRNA genes, which are known insertion hotspots for genomic islands (GIs). The strategy, based on MAUVE-facilitated multigenome comparisons, was used to examine 87 Escherichia coli MG1655 tRNA and tmRNA genes and their orthologues in E.coli EDL933, E.coli CFT073 and Shigella flexneri Sf301. Our approach
Hong-Yu Ou; Ling-Ling Chen; James Lonnen; Roy R. Chaudhuri; Ali Bin Thani; Rebecca Smith; Natalie J. Garton; Jay Hinton; Mark Pallen; Michael R. Barer; Kumar Rajakumar
Enterococci are the third leading cause of hospital associated infections and have gained increased importance due to their fast adaptation to the clinical environment by acquisition of antibiotic resistance and pathogenicity traits. Enterococcus faecalis harbours a pathogenicity island (PAI) of 153 kb containing several virulence factors including the enterococcal surface protein (esp). Until now only internal fragments of the PAI or larger chromosomal regions containing it have been transfered. Here we demonstrate precise excision, circularization and horizontal transfer of the entire PAI element from the chromosome of E. faecalis strain UW3114. This PAI (ca. 200 kb) contained some deletions and insertions as compared to the PAI of the reference strain MMH594, transferred precisely and integrated site-specifically into the chromosome of E. faecalis (intergenic region) and Enterococcus faecium (tRNAlys). The internal PAI structure was maintained after transfer. We assessed phenotypic changes accompanying acquisition of the PAI and expression of some of its determinants. The esp gene is expressed on the surface of donor and both transconjugants. Biofilm formation and cytolytic activity were enhanced in E. faecalis transconjugants after acquisition of the PAI. No differences in pathogenicity of E. faecalis were detected using a mouse bacteraemia and a mouse peritonitis models (tail vein and intraperitoneal injection). A 66 kb conjugative pheromone-responsive plasmid encoding erm(B) (pLG2) that was transferred in parallel with the PAI was sequenced. pLG2 is a pheromone responsive plasmid that probably promotes the PAI horizontal transfer, encodes antibiotic resistance features and contains complete replication and conjugation modules of enterococcal origin in a mosaic-like composition. The E. faecalis PAI can undergo precise intra- and interspecies transfer probably with the help of conjugative elements like conjugative resistance plasmids, supporting the role of horizontal gene transfer and antibiotic selective pressure in the successful establishment of certain enterococci as nosocomial pathogens.
Laverde Gomez, Jenny A.; Hendrickx, Antoni P. A.; Willems, Rob J.; Top, Janetta; Sava, Irina; Huebner, Johannes; Witte, Wolfgang; Werner, Guido
Enterococci are the third leading cause of hospital associated infections and have gained increased importance due to their fast adaptation to the clinical environment by acquisition of antibiotic resistance and pathogenicity traits. Enterococcus faecalis harbours a pathogenicity island (PAI) of 153 kb containing several virulence factors including the enterococcal surface protein (esp). Until now only internal fragments of the PAI or larger chromosomal regions containing it have been transferred. Here we demonstrate precise excision, circularization and horizontal transfer of the entire PAI element from the chromosome of E. faecalis strain UW3114. This PAI (ca. 200 kb) contained some deletions and insertions as compared to the PAI of the reference strain MMH594, transferred precisely and integrated site-specifically into the chromosome of E. faecalis (intergenic region) and Enterococcus faecium (tRNAlys). The internal PAI structure was maintained after transfer. We assessed phenotypic changes accompanying acquisition of the PAI and expression of some of its determinants. The esp gene is expressed on the surface of donor and both transconjugants. Biofilm formation and cytolytic activity were enhanced in E. faecalis transconjugants after acquisition of the PAI. No differences in pathogenicity of E. faecalis were detected using a mouse bacteraemia and a mouse peritonitis models (tail vein and intraperitoneal injection). A 66 kb conjugative pheromone-responsive plasmid encoding erm(B) (pLG2) that was transferred in parallel with the PAI was sequenced. pLG2 is a pheromone responsive plasmid that probably promotes the PAI horizontal transfer, encodes antibiotic resistance features and contains complete replication and conjugation modules of enterococcal origin in a mosaic-like composition. The E. faecalis PAI can undergo precise intra- and interspecies transfer probably with the help of conjugative elements like conjugative resistance plasmids, supporting the role of horizontal gene transfer and antibiotic selective pressure in the successful establishment of certain enterococci as nosocomial pathogens. PMID:21559082
Laverde Gomez, Jenny A; Hendrickx, Antoni P A; Willems, Rob J; Top, Janetta; Sava, Irina; Huebner, Johannes; Witte, Wolfgang; Werner, Guido
Background The complexity of the wheat genome has resulted from waves of retrotransposable element insertions. Gene deletions and disruptions generated by the fast replacement of repetitive elements in wheat have resulted in disruption of colinearity at a micro (sub-megabase) level among the cereals. In view of genomic changes that are possible within a given time span, conservation of genes between species tends to imply an important functional or regional constraint that does not permit a change in genomic structure. The ctg1034 contig completed in this paper was initially studied because it was assigned to the Sr2 resistance locus region, but detailed mapping studies subsequently assigned it to the long arm of 3B and revealed its unusual features. Results BAC shotgun sequencing of the hexaploid wheat (Triticum aestivum cv. Chinese Spring) genome has been used to assemble a group of 15 wheat BACs from the chromosome 3B physical map FPC contig ctg1034 into a 783,553 bp genomic sequence. This ctg1034 sequence was annotated for biological features such as genes and transposable elements. A three-gene island was identified among >80% repetitive DNA sequence. Using bioinformatics analysis there were no observable similarity in their gene functions. The ctg1034 gene island also displayed complete conservation of gene order and orientation with syntenic gene islands found in publicly available genome sequences of Brachypodium distachyon, Oryza sativa, Sorghum bicolor and Zea mays, even though the intergenic space and introns were divergent. Conclusion We propose that ctg1034 is located within the heterochromatic C-band region of deletion bin 3BL7 based on the identification of heterochromatic tandem repeats and presence of significant matches to chromodomain-containing gypsy LTR retrotransposable elements. We also speculate that this location, among other highly repetitive sequences, may account for the relative stability in gene order and orientation within the gene island. Sequence data from this article have been deposited with the GenBank Data Libraries under accession no. GQ422824
Streptococcus mutans is the primary etiological agent of human dental caries and, at times, of infective endocarditis. Within the oral cavity, the pathogen is subjected to conditions of stress. A well-conserved protein complex named ClpP (caseinolytic protease) plays a vital role in adaptation under stress conditions. To gain a better understanding of the global role of the ClpP protease in cellular homeostasis, a transcriptome analysis was performed using a ?clpP mutant strain. The expression levels of more than 100 genes were up- or downregulated in the ?clpP mutant compared to the wild type. Notably, the expression of genes in several genomic islands, such as TnSmu1 and TnSmu2, was differentially modulated in the ?clpP mutant strain. ClpP deficiency also increased the expression of genes associated with a putative CRISPR locus. Furthermore, several stress-related genes and genes encoding bacteriocin-related peptides and many transcription factors were also found to be altered in the ?clpP mutant strain. A comparative analysis of the two-dimensional protein profile of the wild type and the ?clpP mutant strains showed altered protein profiles. Comparison of the transcriptome data with the proteomic data identified four common gene products, suggesting that the observed altered protein expression of these genes could be due to altered transcription. The results presented here indicate that ClpP-mediated proteolysis plays an important global role in the regulation of several important traits in this pathogen.
Chattoraj, Partho; Banerjee, Anirban; Biswas, Saswati; Biswas, Indranil
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.
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
One of the properties of bacteria is their capacity to acquire large fragments of genomic DNA from other bacteria or to loose important parts of their own genome. Such fragments include genomic islands (GIs); nine GIs are present in Brucella, including genomic island 3 (GI-3), present in B. abortus, B. melitensis and B. ovis. The GI-3 have 29 open reading frames (ORFs) most of them with unknown function. Within the GI-3, the ORFs BAB1_0267 encodes a hypothetical protein sharing a SH3 domain and BAB1_270 a zinc-dependent metallopeptidase. We have obtained deletion mutants for BAB1_0267 and BAB1_0270 ORFs present within GI-3, which have been named the ?0267 and ?0270, respectively; in both cases the mutation did not affect the growth of bacteria. Both mutants were evaluated with respect to their growth rates, their ability to invade and replicate in the non-professional and professional phagocytes, HeLa and J774.A1 cells, respectively. Their persistence in the spleens of mice was also evaluated. The mutants efficiently invaded HeLa and J774.A1 cells but both mutants showed a decreased intracellular survival in macrophages and HeLa cells 72 and 96h post-infection, respectively, and were non-detected in J774.A1 cells 120h post infection. With respect to in vivo persistence ?0267 was detected through the fourth week while ?0270 decreased at 7 days disappearing the second week. Our results indicated that deletion of BAB1_0267 and BAB1_270 are necessary to establish an optimal infectious process in B. abortus 2308, having more effect the deletion of ORF BAB1_0270. Therefore these ORFs, principally BAB1_0270 are important virulent of B. abortus. PMID:24928771
Ortiz-Román, Luisa; Riquelme-Neira, Roberto; RobertoVidal; Oñate, Angel
The LEE pathogenicity island has been acquired on multiple occasions within the different lineages of enteropathogenic and enterohemorrhagic Escherichia coli. In each lineage, LEE expression is regulated by complex networks of pathways, including core pathways shared by all lineages and lineage-specific pathways. Within the O157:H7 lineage of enterohemorrhagic E. coli, strain-to-strain variation in LEE expression has been observed, implying that expression patterns can diversify even within highly related subpopulations. Using comparative genomics of E. coli O157:H7 subpopulations, we have identified one source of strain-level variation affecting LEE expression. The variation occurs in prophage-dense regions of the genome that lie immediately adjacent to the late regions of the pch prophage carrying pchA, pchB, pchC, and a newly identified pch gene, pchX. Genomic segments extending from the holin S region to the pchA, pchB, pchC, and pchX genes of their respective prophage are highly conserved but are nonetheless embedded within adjacent genomic segments that are extraordinarily variable, termed pch adjacent genomic regions (pch AGR). Despite the remarkable degree of variation, the pattern of variation in pch AGR is highly correlated with the distribution of phylogenetic markers on the backbone of the genome. Quantitative analysis of transcription from the LEE1 promoter further revealed that variation in the pch AGR has substantial effects on absolute levels and patterns of LEE1 transcription. Variation in the pch AGR therefore serves as a mechanism to diversify LEE expression patterns, and the lineage-specific pattern of pch AGR variation could ultimately influence ecological or virulence characteristics of subpopulations within each lineage. PMID:19329643
Yang, Zhijie; Kim, Jaehyoung; Zhang, Chaomei; Zhang, Min; Nietfeldt, Joeseph; Southward, Carolyn M; Surette, Michael G; Kachman, Stephen D; Benson, Andrew K
The LEE pathogenicity island has been acquired on multiple occasions within the different lineages of enteropathogenic and enterohemorrhagic Escherichia coli. In each lineage, LEE expression is regulated by complex networks of pathways, including core pathways shared by all lineages and lineage-specific pathways. Within the O157:H7 lineage of enterohemorrhagic E. coli, strain-to-strain variation in LEE expression has been observed, implying that expression patterns can diversify even within highly related subpopulations. Using comparative genomics of E. coli O157:H7 subpopulations, we have identified one source of strain-level variation affecting LEE expression. The variation occurs in prophage-dense regions of the genome that lie immediately adjacent to the late regions of the pch prophage carrying pchA, pchB, pchC, and a newly identified pch gene, pchX. Genomic segments extending from the holin S region to the pchA, pchB, pchC, and pchX genes of their respective prophage are highly conserved but are nonetheless embedded within adjacent genomic segments that are extraordinarily variable, termed pch adjacent genomic regions (pch AGR). Despite the remarkable degree of variation, the pattern of variation in pch AGR is highly correlated with the distribution of phylogenetic markers on the backbone of the genome. Quantitative analysis of transcription from the LEE1 promoter further revealed that variation in the pch AGR has substantial effects on absolute levels and patterns of LEE1 transcription. Variation in the pch AGR therefore serves as a mechanism to diversify LEE expression patterns, and the lineage-specific pattern of pch AGR variation could ultimately influence ecological or virulence characteristics of subpopulations within each lineage.
Yang, Zhijie; Kim, Jaehyoung; Zhang, Chaomei; Zhang, Min; Nietfeldt, Joeseph; Southward, Carolyn M.; Surette, Michael G.; Kachman, Stephen D.; Benson, Andrew K.
The role of CpG island methylation in normal development and cell differentiation is of keen interest, but remains poorly understood. We performed comprehensive DNA methylation profiling of promoter regions in normal peripheral blood by methylated CpG island amplification in combination with microarrays. This technique allowed us to simultaneously determine the methylation status of 6,177 genes, 92% of which include dense
Lanlan Shen; Yutaka Kondo; Yi Guo; Jiexin Zhang; Li Zhang; Saira Ahmed; Jingmin Shu; Xinli Chen; Robert A Waterland; Jean-Pierre J Issa
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
Yongliang Yan; Jian Yang; Yuetan Dou; Ming Chen; Shuzhen Ping; Junping Peng; Wei Lu; Wei Zhang; Ziying Yao; Hongquan Li; Wei Liu; Sheng He; Lizhao Geng; Xiaobing Zhang; Fan Yang; Haiying Yu; Yuhua Zhan; Danhua Li; Zhanglin Lin; Yiping Wang; Claudine Elmerich; Min Lin; Qi Jin
Four different type IV secretion systems are variously represented in the genomes of different Helicobacter pylori strains. Two of these, encoded by tfs3 and tfs4 gene clusters are contained within self-transmissible genomic islands. Although chromosomal excision of tfs4 circular intermediates is reported to be dependent upon the function of a tfs4-encoded XerD tyrosine-like recombinase, other factors required for transfer to a recipient cell have not been demonstrated. Here, we characterize the functional activity of a putative tfs4-encoded VirD2-like relaxase protein. Tfs4 VirD2 was purified as a fusion to maltose-binding protein and demonstrated to bind and nick both supercoiled duplex DNA and oligonucleotides in vitro in a manner dependent upon the presence of Mg(2+) but independently of any auxiliary proteins. Unusually, concentration-dependent nicking of duplex DNA appeared to require only transient protein-DNA interaction. Although phylogenetically distinct from established relaxase families, site-specific cleavage of oligonucleotides by Tfs4 VirD2 required the nick region sequence 5'-ATCCTG-3' common to transfer origins (oriT) recognized by MOBP conjugative relaxases. Cleavage resulted in covalent attachment of MBP-VirD2 to the 5'-cleaved end, consistent with conventional relaxase activity. Identification of an oriT-like sequence upstream of tfs4 virD2 and demonstration of VirD2 protein-protein interaction with a putative VirC1 relaxosome component indicate that transfer initiation of the tfs4 genomic island is analogous to mechanisms underlying mobilization of other integrated mobile elements, such as integrating conjugative elements, requiring site-specific targeting of relaxase activity to a cognate oriT sequence. PMID:23900838
Grove, Jane I; Alandiyjany, Maher N; Delahay, Robin M
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.
Lai, Yi-Chyi; Lin, Ann-Chi; Chiang, Ming-Ko; Dai, Yu-Han; Hsu, Chih-Chieh; Lu, Min-Chi; Liau, Chun-Yi; Chen, Ying-Tsong
Background Several strain-specific Klebsiella pneumoniae virulence determinants have been described, though these have almost exclusively been linked with hypervirulent liver abscess-associated strains. Through PCR interrogation of integration hotspots, chromosome walking, island-tagging and fosmid-based marker rescue we captured and sequenced KpGI-5, a novel genomic island integrated into the met56 tRNA gene of K. pneumoniae KR116, a bloodstream isolate from a patient with pneumonia and neutropenic sepsis. Results The 14.0 kb KpGI-5 island exhibited a genome-anomalous G?+?C content, possessed near-perfect 46 bp direct repeats, encoded a ?1-chaperone/usher fimbrial cluster (fim2) and harboured seven other predicted genes of unknown function. Transcriptional analysis demonstrated expression of three fim2 genes, and suggested that the fim2A-fim2K cluster comprised an operon. As fimbrial systems are frequently implicated in pathogenesis, we examined the role of fim2 by analysing KR2107, a streptomycin-resistant derivative of KR116, and three isogenic mutants (?fim, ?fim2 and ?fim?fim2) using biofilm assays, human cell adhesion assays and pair-wise competition-based murine models of intestinal colonization, lung infection and ascending urinary tract infection. Although no statistically significant role for fim2 was demonstrable, liver and kidney CFU counts for lung and urinary tract infection models, respectively, hinted at an ordered gradation of virulence: KR2107 (most virulent), KR2107?fim2, KR2107?fim and KR2107?fim?fim2 (least virulent). Thus, despite lack of statistical evidence there was a suggestion that fim and fim2 contribute additively to virulence in these murine infection models. However, further studies would be necessary to substantiate this hypothesis. Conclusion Although fim2 was present in 13% of Klebsiella spp. strains investigated, no obvious in vitro or in vivo role for the locus was identified, although there were subtle hints of involvement in urovirulence and bacterial dissemination from the respiratory tract. Based on our findings and on parallels with other fimbrial systems, we propose that fim2 has the potential to contribute beneficially to pathogenesis and/or environmental persistence of Klebsiella strains, at least under specific yet-to-be identified conditions.
Environmental genomic surveys have increasingly demon- strated the remarkable diversity of natural microbial commu- nities and have had a significant impact on our understanding of microbial ecology and evolution (10, 34). For example, data sets of environmental microbial sequences and fine-scale pop- ulation studies revealed the high level of genetic diversity be- tween strains or ribotypes in natural populations, as
James R. White; Patricia Escobar-Paramo; Emmanuel F. Mongodin; Karen E. Nelson; Jocelyne DiRuggiero
The Island Information web site provides numerous facts and figures about the earth's islands. Island data is organized into the following categories: island superlatives, principal world islands and groups, 100 largest islands of the world, largest islands by continent, largest islands of selected countries, 35 largest islands of the United States, largest islands of selected U.S. states, 38 largest islands of Canada, largest islands of Canadian provinces, largest lake islands of the world, most populous islands of the world, most populous island countries, islands divided by international borders, tallest islands of the world, former and alternative names of islands, and island misinformation. All of the information within the web site is displayed in easy-to-read charts.
Microsatellite stable (MSS), CpG island methylator phenotype (CIMP)-negative colorectal tumors, the most prevalent molecular subtype of colorectal cancer, are associated with extensive copy number alteration (CNA) events and aneuploidy. We report on the identification of characteristic recurrent CNA (with frequency >25%) events and associated gene expression profiles for a total of 40 paired tumor and adjacent normal colon tissues using genome-wide microarrays. We observed recurrent CNAs, namely gains at 1q, 7p, 7q, 8p12-11, 8q, 12p13, 13q, 20p, 20q, Xp, and Xq and losses at 1p36, 1p31, 1p21, 4p15-12, 4q12-35, 5q21-22, 6q26, 8p, 14q, 15q11-12, 17p, 18p, 18q, 21q21-22, and 22q. Within these genomic regions we identified 356 genes with significant differential expression (P < 0.0001 and ±1.5-fold change) in the tumor compared to adjacent normal tissue. Gene ontology and pathway analyses indicated that many of these genes were involved in functional mechanisms that regulate cell cycle, cell death, and metabolism. An amplicon present in >70% of the tumor samples at 20q11-20q13 contained several cancer-related genes (AHCY, POFUT1, RPN2, TH1L, and PRPF6) that were upregulated and demonstrated a significant linear correlation (P < 0.05) for gene dosage and gene expression. Copy number loss at 8p, a CNA associated with adenocarcinoma and poor prognosis, was observed in >50% of the tumor samples and demonstrated a significant linear correlation for gene dosage and gene expression for two potential tumor suppressor genes, MTUS1 (8p22) and PPP2CB (8p12). The results from our integration analysis illustrate the complex relationship between genomic alterations and gene expression in colon cancer. PMID:23341073
Loo, Lenora W M; Tiirikainen, Maarit; Cheng, Iona; Lum-Jones, Annette; Seifried, Ann; Church, James M; Gryfe, Robert; Weisenberger, Daniel J; Lindor, Noralane M; Gallinger, Steven; Haile, Robert W; Duggan, David J; Thibodeau, Stephen N; Casey, Graham; Le Marchand, Loïc
Summary A genome-wide association study of serum uric acid levels was performed in a relatively isolated population of European descent from an island of the Adriatic coast of Croatia. The study sample included 532 unrelated and 768 related individuals from 235 pedigrees. Inflation due to relatedness was controlled by using genomic control. Genetic association was assessed with 2,241,249 SNPs in 1300 samples after adjusting for age and gender. Our study replicated four previously reported serum uric acid loci (SLC2A9, ABCG2, RREB1, and SLC22A12). The strongest association was found with a SNP in SLC2A9 (rs13129697, P=2.33×10?19), which exhibited significant gender-specific effects, 35.76?mol/L (P=2.11×10?19) in females and 19.58 ?mol/L (P=5.40×10?5) in males. Within this region of high linkage disequilibrium, we also detected a strong association with a non-synonymous SNP, rs16890979 (P=2.24×10?17), a putative causal variant for serum uric acid variation. In addition, we identified several novel loci suggestive of association with uric acid levels (SEMA5A, TMEM18, SLC28A2, and ODZ2), although the P-values (P<5×10?6) did not reach the threshold of genome-wide significance. Together, these findings provide further confirmation of previously reported uric acid-related genetic variants and highlight suggestive new loci for additional investigation.
Karns, Rebekah; Zhang, Ge; Sun, Guangyun; Indugula, Subba Rao; Cheng, Hong; Havas-Augustin, Dubravka; Novokmet, Natalija; Rudan, Dusko; Durakovic, Zijad; Missoni, Sasa; Chakraborty, Ranajit; Rudan, Pavao; Deka, Ranjan
Strains of Escherichia coli causing enterohemorrhagic colitis belonging to the O157:H7 lineage are reported to be highly related. Fifteen strains of E. coli O157:H7 and 1 strain of E. coli O46:H? (nonflagellated) were examined for the presence of potassium tellurite resistance (Ter). Ter genes comprising terABCDEF were shown previously to be part of a pathogenicity island also containing integrase, phage, and urease genes. PCR analysis, both conventional and light cycler based, demonstrated that about one-half of the Ter E. coli O157:H7 strains (6 of 15), including the Sakai strain, which has been sequenced, carried a single copy of the Ter genes. Five of the strains, including EDL933, which has also been sequenced, contained two copies. Three other O157:H7 strains and the O46:H? strain did not contain the Ter genes. In strains containing two copies, the Ter genes were associated with the serW and serX tRNA genes. Five O157:H7 strains resembled the O157 Sakai strain whose sequence contained one copy, close to serX, whereas in one isolate the single copy was associated with serW. There was no correlation between Ter and the ability to produce Shiga toxin ST1 or ST2. The Ter MIC for most strains, containing either one or two copies, was 1,024 ?g/ml, although for a few the MIC was intermediate, 64 to 128 ?g/ml, which could be increased to 512 ?g/ml by pregrowth of strains in subinhibitory concentrations of potassium tellurite. Reverse transcriptase PCR analysis confirmed that in most strains Ter was constitutive but that in the rest it was inducible and involved induction of terB and terC genes. Only the terB, -C, -D, and -E genes are required for Ter. The considerable degree of homology between the ter genes on IncH12 plasmid R478, which originated in Serratia marcescens, and pTE53, from an E. coli clinical isolate, suggests that the pathogenicity island was acquired from a plasmid. This work demonstrates diversity among E. coli O157:H7 isolates, at least as far as the presence of Ter genes is concerned.
Taylor, Diane E.; Rooker, Michelle; Keelan, Monika; Ng, Lai-King; Martin, Irene; Perna, Nicole T.; Burland, N. T. Valerie; Blattner, Fredrick R.
Streptomyces lividans ZX1 has become a preferred host for DNA cloning in Streptomyces species over its progenitor, the wild-type strain 66 (stock number 1326 from the John Innes Center collection), especially when stable DNA is crucial for in vitro electrophoresis, because DNA from strain 66 contains a novel modification that makes it sensitive to oxidative double-strand cleavage during electrophoresis. Detailed analysis of this modification-deficient mutant (ZX1) revealed that it has several additional phenotypic traits associated with a chromosomal deletion of ca. 90 kb, which was cloned and mapped by using a cosmid library. Comparative sequence analysis of two clones containing the left and right deletion ends originating from strain 66 and one clone with the deletion and fused sequence cloned from strain ZX1 revealed a perfect 15-bp direct repeat, which may have mediated deletion and fusion to yield strain ZX1 by site-specific recombination. Analysis of AseI linking clones in the deleted region in relation to the published AseI map of strain ZX1 yielded a complete AseI map for the S. lividans 66 genome, on which the relative positions of a cloned phage phiHAU3 resistance (phiHAU3r) gene and the dnd gene cluster were precisely localized. Comparison of S. lividans ZX1 and its progenitor 66, as well as the sequenced genome of its close relative, Streptomyces coelicolor M145, reveals that the ca. 90-kb deletion in strain ZX1 may have originated from an insertion from an unknown source. PMID:15574907
Zhou, Xiufen; He, Xinyi; Li, Aiying; Lei, Fang; Kieser, Tobias; Deng, Zixin
Streptomyces lividans ZX1 has become a preferred host for DNA cloning in Streptomyces species over its progenitor, the wild-type strain 66 (stock number 1326 from the John Innes Center collection), especially when stable DNA is crucial for in vitro electrophoresis, because DNA from strain 66 contains a novel modification that makes it sensitive to oxidative double-strand cleavage during electrophoresis. Detailed analysis of this modification-deficient mutant (ZX1) revealed that it has several additional phenotypic traits associated with a chromosomal deletion of ca. 90 kb, which was cloned and mapped by using a cosmid library. Comparative sequence analysis of two clones containing the left and right deletion ends originating from strain 66 and one clone with the deletion and fused sequence cloned from strain ZX1 revealed a perfect 15-bp direct repeat, which may have mediated deletion and fusion to yield strain ZX1 by site-specific recombination. Analysis of AseI linking clones in the deleted region in relation to the published AseI map of strain ZX1 yielded a complete AseI map for the S. lividans 66 genome, on which the relative positions of a cloned phage ?HAU3 resistance (?HAU3r) gene and the dnd gene cluster were precisely localized. Comparison of S. lividans ZX1 and its progenitor 66, as well as the sequenced genome of its close relative, Streptomyces coelicolor M145, reveals that the ca. 90-kb deletion in strain ZX1 may have originated from an insertion from an unknown source.
Zhou, Xiufen; He, Xinyi; Li, Aiying; Lei, Fang; Kieser, Tobias; Deng, Zixin
A multiple-antibiotic-resistant Salmonella enterica serovar Kentucky strain was found to contain SGI1-K, a variant form of the Salmonella genomic island 1 (SGI1) with an In4-type class 1 integron that contains only one cassette array, aacCA5-aadA7, and an adjacent mercury resistance module. Part of the 3?-conserved segment (3?-CS) of the integron, together with the inverted short segment from the right-hand end of the integron transposition module normally found between the 3?-CS and IS6100 in In4 family integrons, has been removed by an IS6100-mediated deletion. IRt, the right-hand inverted repeat found at the outer end of the integron, abuts a mercury resistance region instead of the usual SGI1 backbone segment. The mer module is a hybrid of those found in Tn501 and Tn21. This mer region and a further uncharacterized segment of at least 10 kb appear to have been incorporated between IRt and the SGI1 backbone. These findings demonstrate that the multidrug resistance region in SGI1 can incorporate new DNA segments in the same way as multiple antibiotic resistance regions in plasmids.
Levings, Renee S.; Partridge, Sally R.; Djordjevic, Steven P.; Hall, Ruth M.
The CpG island methylator phenotype (CIMP) is an epigenetic phenomenon and plays an important role in tumourigenesis in various cancers. The identification of aberrant DNA methylation can be exploited for early diagnosis and risk assessment of patients. We identified a CIMP in myelodysplastic syndrome (MDS). Genes were screened for hypermethylation and transcription downregulation through genome-wide DNA methylation profiling and gene expression microarrays. Methylation-specific, real-time, and bisulfite-sequencing polymerase chain reaction were performed to validate selected genes. The hypermethylation of genes as a diagnostic tool for the detection of MDS was evaluated. Kaplan-Meier survival analysis and Cox regression were performed. A draft of an MDS CIMP was established and revised to 6 genes after validation in 20 patients and 20 controls. Further large-scale analysis showed that the majority of 211 MDS patients were hypermethylated in 6 genes. The area under the curve of CIMP was 0·9768 (95% confidence interval 0·9609-0·9928). A combination of 5 or more of the methylated genes showed a specificity of 95% and sensitivity of 91% for the diagnosis of MDS. We found CIMP positivity to be a significantly unfavourable prognostic factor for MDS. These results indicate that the newly established CIMP may improve diagnostic accuracy and prognosis assessment in MDS. PMID:24601943
Zhao, Xiaoli; Yang, Feng; Li, Shuang; Liu, Meixia; Ying, Shaoxu; Jia, Xiaodong; Wang, Xiaoqin
Background The Type VI secretion apparatus is assembled by a conserved set of proteins encoded within a distinct locus. The putative effector proteins Hcp and VgrG are also encoded within these loci. We have identified numerous distinct Type VI secretion system (T6SS) loci in the genomes of several ecologically diverse Pantoea and Erwinia species and detected the presence of putative effector islands associated with the hcp and vgrG genes. Results Between two and four T6SS loci occur among the Pantoea and Erwinia species. While two of the loci (T6SS-1 and T6SS-2) are well conserved among the various strains, the third (T6SS-3) locus is not universally distributed. Additional orthologous loci are present in Pantoea sp. aB-valens and Erwinia billingiae Eb661. Comparative analysis of the T6SS-1 and T6SS-3 loci showed non-conserved islands associated with the vgrG and hcp, and vgrG genes, respectively. These regions had a G+C content far lower than the conserved portions of the loci. Many of the proteins encoded within the hcp and vgrG islands carry conserved domains, which suggests they may serve as effector proteins for the T6SS. A number of the proteins also show homology to the C-terminal extensions of evolved VgrG proteins. Conclusions Extensive diversity was observed in the number and content of the T6SS loci among the Pantoea and Erwinia species. Genomic islands could be observed within some of T6SS loci, which are associated with the hcp and vgrG proteins and carry putative effector domain proteins. We propose new hypotheses concerning a role for these islands in the acquisition of T6SS effectors and the development of novel evolved VgrG and Hcp proteins.
Background In industrial fermentation processes, the rate of milk acidification by Streptococcus thermophilus is of major technological importance. The cell-envelope proteinase PrtS was previously shown to be a key determinant of the milk acidification activity in this species. The PrtS enzyme is tightly anchored to the cell wall via a mechanism involving the typical sortase A (SrtA) and initiates the breakdown of milk casein into small oligopeptides. The presence or absence of PrtS divides the S. thermophilus strains into two phenotypic groups i.e. the slow and the fast acidifying strains. The aim of this study was to improve the milk acidification rate of slow S. thermophilus strains, and hence optimise the fermentation process of dairy products. Results In the present work, we developed for the first time a strategy based on natural transformation to confer the rapid acidification phenotype to slow acidifying starter strains of S. thermophilus. First, we established by gene disruption that (i) prtS, encoding the cell-envelope proteinase, is a key factor responsible for rapid milk acidification in fast acidifying strains, and that (ii) srtA, encoding sortase A, is not absolutely required to express the PrtS activity. Second, a 15-kb PCR product encompassing the prtS genomic island was transfered by natural transformation using the competence-inducing peptide in three distinct prtS-defective genetic backgrounds having or not a truncated sortase A gene. We showed that in all cases the milk acidification rate of transformants was significantly increased, reaching a level similar to that of wild-type fast acidifying strains. Furthermore, it appeared that the prtS-encoded activity does not depend on the prtS copy number or on its chromosomal integration locus. Conclusion We have successfully used natural competence to transfer the prtS locus encoding the cell-envelope proteinase in three slow acidifying strains of S. thermophilus, allowing their conversion into fast acidifying derivatives. The efficient protocol developed in this article will provide the dairy industry with novel and optimised S. thermophilus starter strains.
This easterly looking view shows the seven major volcanic islands of the Canary Island chain (28.0N, 16.5W) and offers a unique view of the islands that have become a frequent vacation spot for Europeans. The northwest coastline of Africa, (Morocco and Western Sahara), is visible in the background. Frequently, these islands create an impact on local weather (cloud formations) and ocean currents (island wakes) as seen in this photo.
This no-frills UC-Santa Cruz Genome Bioinformatics Web site contains searchable "working drafts of the human genome and the mouse genome," which each represent "immense collaborative efforts" within the biomedical research community. Those who are active in genome research may find this Web site useful, especially for the multi-faceted genome browser that "provides a rapid and reliable display of any requested portion of genomes at any scale, together with dozens of aligned annotation tracks (known genes, predicted genes, ESTs, mRNAs, CpG islands, assembly gaps and coverage, chromosomal bands, mouse homologies, and more)." Users may also access Blat alignments, a table browser (provides tabular representation of the data as an alternative to the graphical display of the genome browser), downloadable versions of the data set, and more. The site also contains a helpful FAQ page and a News section that alerts the user to corrected errors, new features, etc. The extensive list of links leads to dozens of other genome databases, browsers, and related tools.
This excel workbook demonstrates the principles of the MacArthur-Wilson theory of Island Biogeography. It allows the user to define the mainland species pool, area of the island, and distance of the island from the mainland. Graphical output included species richness equilibrium at varying island size and distance. The workbook also allows the user to calculate a species-area function for data entered into the data input page. Several datasets on island area and species richness are included for various types of islands and species. Variables and formulas are defined in the accompanying tutorial.
John Jungck (BioQUEST Curriculum Consortium;Biology); Jennifer Spangenberg (Beloit College;)
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
This true-color image of the Galapagos Islands was acquired on March 12, 2002, by the Moderate-resolution Imaging Spectroradiometer (MODIS), flying aboard NASA's Terra satellite. The Galapagos Islands, which are part of Ecuador, sit in the Pacific Ocean about 1000 km (620 miles) west of South America. As the three craters on the largest island (Isabela Island) suggest, the archipelago was created by volcanic eruptions, which took place millions of years ago. Unlike most remote islands in the Pacific, the Galapagos have gone relatively untouched by humans over the past few millennia. As a result, many unique species have continued to thrive on the islands. Over 95 percent of the islands' reptile species and nearly three quarters of its land bird species cannot be found anywhere else in the world. Two of the more well known are the Galapagos giant tortoise and marine iguanas. The unhindered evolutionary development of the islands' species inspired Charles Darwin to begin The Origin of Species eight years after his visit there. To preserve the unique wildlife on the islands, the Ecuadorian government made the entire archipelago a national park in 1959. Each year roughly 60,000 tourists visit these islands to experience what Darwin did over a century and a half ago. Image courtesy Jacques Descloitres, MODIS Land Rapid Response Team at NASA GSFC
The adaptability of pathogenic bacteria to hosts is influenced by the genomic plasticity of the bacteria, which can be increased by such mechanisms as horizontal gene transfer. Pathogenicity islands play a major role in this type of gene transfer because they are large, horizontally acquired regions that harbor clusters of virulence genes that mediate the adhesion, colonization, invasion, immune system evasion, and toxigenic properties of the acceptor organism. Currently, pathogenicity islands are mainly identified in silico based on various characteristic features: (1) deviations in codon usage, G+C content or dinucleotide frequency and (2) insertion sequences and/or tRNA genetic flanking regions together with transposase coding genes. Several computational techniques for identifying pathogenicity islands exist. However, most of these techniques are only directed at the detection of horizontally transferred genes and/or the absence of certain genomic regions of the pathogenic bacterium in closely related non-pathogenic species. Here, we present a novel software suite designed for the prediction of pathogenicity islands (pathogenicity island prediction software, or PIPS). In contrast to other existing tools, our approach is capable of utilizing multiple features for pathogenicity island detection in an integrative manner. We show that PIPS provides better accuracy than other available software packages. As an example, we used PIPS to study the veterinary pathogen Corynebacterium pseudotuberculosis, in which we identified seven putative pathogenicity islands.
Soares, Siomar C.; Abreu, Vinicius A. C.; Ramos, Rommel T. J.; Cerdeira, Louise; Silva, Artur; Baumbach, Jan; Trost, Eva; Tauch, Andreas; Hirata, Raphael; Mattos-Guaraldi, Ana L.; Miyoshi, Anderson; Azevedo, Vasco
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
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.
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
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
Of the estimated 45 000 CpG islands in the human genome, the overwhelming majority are found at the 5? ends of genes and their identification and cloning are proving very useful for finding and isolating genes. Recent work has shed light on the chromosomal distribution and origin of CpG islands. It has been shown unequivocally that CpG islands are concentrated
Sally H Cross; Adrian P Bird
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…
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.
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
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; Flügel, Monika; Gaigalat, Lars; Goesmann, Alexander; Gräfen, Ines; Kalinowski, Jörn; Kaup, Olaf; Kirchner, Oliver; Krause, Lutz; Linke, Burkhard; McHardy, Alice; Meyer, Folker; Pohle, Sandra; Rückert, Christian; Schneiker, Susanne; Zellermann, Eva-Maria; Pühler, Alfred; Eichenlaub, Rudolf; Kaiser, Olaf; Bartels, Daniela
This video segment adapted from the NOW-RAMP 2002 Expedition documents a research expedition to Nihoa Island. It showcases Nihoa's unique birds and plants, the threat posed by invading grasshoppers, and restoration efforts.
Foundation, Wgbh E.
The distribution of EDL 933 O island 122 (OI-122) was investigated in 70 strains of Verocytotoxin-producing Escherichia coli (VTEC) of multiple serotypes that were classified into five “seropathotypes” (A through E) based on the reported occurrence of serotypes in human disease, in outbreaks, and/or in the hemolytic-uremic syndrome (HUS). Seropathotype A comprised 10 serotype O157:H7 and 3 serotype O157:NM strains. Seropathotype B (associated with outbreaks and HUS but less commonly than serotype O157:H7) comprised three strains each of serotypes O26:H11, O103:H2, O111:NM, O121:H19, and O145:NM. Seropathotype C comprised four strains each of serotypes O91:H21 and O113:H21 and eight strains of other serotypes that have been associated with sporadic HUS but not typically with outbreaks. Seropathotype D comprised 14 strains of serotypes that have been associated with diarrhea but not with outbreaks or HUS, and seropathotype E comprised animal VTEC strains of serotypes not implicated in human disease. All strains were tested for four EDL 933 OI-122 virulence genes (Z4321, Z4326, Z4332, and Z4333) by PCR. Negative PCRs were confirmed by Southern hybridization. Overall, 28 (40%) strains contained OI-122 (positive for all four virulence genes), 27 (38.6%) contained an “incomplete” OI-122 (positive for one to three genes), and 15 (21.4%) strains did not contain OI-122. The seropathotype distribution of complete OI-122 was as follows: 100% for seropathotype A, 60% for B, 36% for C, 15% for D, and 0% for E. The differences in the frequency of OI-122 between seropathotypes A, B, and C (associated with HUS) and seropathotypes D and E (not associated with HUS) and between seropathotypes A and B (associated with epidemic disease) and seropathotypes C, D, and E (not associated with epidemic disease) were highly significant (P < 0.0001).
Karmali, Mohamed A.; Mascarenhas, Mariola; Shen, Songhai; Ziebell, Kim; Johnson, Shelley; Reid-Smith, Richard; Isaac-Renton, Judith; Clark, Clifford; Rahn, Kris; Kaper, James B.
The distribution of EDL 933 O island 122 (OI-122) was investigated in 70 strains of Verocytotoxin-producing Escherichia coli (VTEC) of multiple serotypes that were classified into five "seropathotypes" (A through E) based on the reported occurrence of serotypes in human disease, in outbreaks, and/or in the hemolytic-uremic syndrome (HUS). Seropathotype A comprised 10 serotype O157:H7 and 3 serotype O157:NM strains. Seropathotype B (associated with outbreaks and HUS but less commonly than serotype O157:H7) comprised three strains each of serotypes O26:H11, O103:H2, O111:NM, O121:H19, and O145:NM. Seropathotype C comprised four strains each of serotypes O91:H21 and O113:H21 and eight strains of other serotypes that have been associated with sporadic HUS but not typically with outbreaks. Seropathotype D comprised 14 strains of serotypes that have been associated with diarrhea but not with outbreaks or HUS, and seropathotype E comprised animal VTEC strains of serotypes not implicated in human disease. All strains were tested for four EDL 933 OI-122 virulence genes (Z4321, Z4326, Z4332, and Z4333) by PCR. Negative PCRs were confirmed by Southern hybridization. Overall, 28 (40%) strains contained OI-122 (positive for all four virulence genes), 27 (38.6%) contained an "incomplete" OI-122 (positive for one to three genes), and 15 (21.4%) strains did not contain OI-122. The seropathotype distribution of complete OI-122 was as follows: 100% for seropathotype A, 60% for B, 36% for C, 15% for D, and 0% for E. The differences in the frequency of OI-122 between seropathotypes A, B, and C (associated with HUS) and seropathotypes D and E (not associated with HUS) and between seropathotypes A and B (associated with epidemic disease) and seropathotypes C, D, and E (not associated with epidemic disease) were highly significant (P < 0.0001). PMID:14605120
Karmali, Mohamed A; Mascarenhas, Mariola; Shen, Songhai; Ziebell, Kim; Johnson, Shelley; Reid-Smith, Richard; Isaac-Renton, Judith; Clark, Clifford; Rahn, Kris; Kaper, James B
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
Evidence for a Second Genomic Island Conferring Multidrug Resistance in a Clonal Group of Strains of Salmonella enterica Serovar Typhimurium and its Monophasic Variant Circulating in Italy, Denmark, and the United Kingdom?
During the 2000s, a new clonal group with resistances to ampicillin, streptomycin, sulfonamides, and tetracycline (ASSuT) emerged in Italy among strains of Salmonella enterica serovar Typhimurium and its monophasic variant, Salmonella enterica subspecies enterica serovar 4,,12:i:?. The PulseNet Europe database allowed us to identify ASSuT strains of both S. Typhimurium and its monophasic variant, isolated in Denmark and the United Kingdom, with the same or very closely related pulsed-field gel electrophoresis (PFGE) patterns as the Italian strains, suggesting that the ASSuT clonal group is circulating in different European countries. With the aim of analyzing the molecular basis of antibiotic resistance, resistance genes were identified and their localization was investigated in 66 ASSuT strains and, as controls, in 11 strains with different resistance patterns and PFGE profiles, belonging both to S. Typhimurium and to its monophasic variant, isolated from humans in Italy, Denmark, and the United Kingdom. All the ASSuT strains were positive for the following resistance genes: blaTEM-1, strA-strB, sul2, and tet(B). A localization experiment demonstrated that the ASSuT resistance genes are chromosomally located. This study confirms that a multidrug-resistant clonal group, ASSuT, of S. Typhimurium and its monophasic variant has emerged and is circulating in Italy, Denmark, and the United Kingdom. Moreover, the results of this work demonstrate that the multidrug resistance in this clonal group of Salmonella strains is conferred by a new genomic island.
Lucarelli, Claudia; Dionisi, Anna Maria; Torpdahl, Mia; Villa, Laura; Graziani, Caterina; Hopkins, Katie; Threlfall, John; Caprioli, Alfredo; Luzzi, Ida
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.
MGS MOC Release No. MOC2-514, 15 October 2003This Mars Global Surveyor (MGS) Mars Orbiter Camera (MOC) picture shows a streamlined island in Marte Vallis, a large outflow channel system that crosses the 180oW meridian between the Elysium and Amazonis regions of Mars. The flow patterns on the floor of Marte Vallis might be the remains of lava flows or mud flows. Marte is the Spanish word for Mars. Most of the largest valleys on the red planet are named for 'Mars' in various languages. This island is located near 21.8oN, 175.3oW. The picture covers an area 3 km (1.9 mi) wide and is illuminated by sunlight from the lower left.
This lesson plan will give students a basic overview of the geography of islands. They will learn where islands are located throughout the world and will study two very different island groups (the Philippines and the British Isles) to illustrate the diversity of islands of the world. Students will explore island flora and fauna, languages, and climates and cultures.
We introduce Markov models for segmentation of symbolic sequences, extending a segmentation procedure based on the Jensen-Shannon divergence that has been introduced earlier. Higher-order Markov models are more sensitive to the details of local patterns and in application to genome analysis, this makes it possible to segment a sequence at positions that are biologically meaningful. We show the advantage of higher-order Markov-model-based segmentation procedures in detecting compositional inhomogeneity in chimeric DNA sequences constructed from genomes of diverse species, and in application to the E. coli K12 genome, boundaries of genomic islands, cryptic prophages, and horizontally acquired regions are accurately identified.
Thakur, Vivek; Azad, Rajeev K.; Ramaswamy, Ram
Ã¢ÂÂThe RockÃ¢ÂÂ, the oft-used vernacular phrase used to describe Alcatraz, is perhaps one of the Bay AreaÃ¢ÂÂs most dramatic landscapes, and certainly itÃ¢ÂÂs 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 AmericaÃ¢ÂÂs most hardened (and colorful) criminals. The National Park Service recently created this rather well-done online exhibit that allows users to view objects from AlcatrazÃ¢ÂÂs 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 Ã¢ÂÂBattle of AlcatrazÃ¢ÂÂ 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.
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
Dominic J Smiraglia; Ramakrishnan Kazhiyur-Mannar; Christopher C Oakes; Yue-Zhong Wu; Ping Liang; Tahmina Ansari; Jian Su; Laura J Rush; Laura T Smith; Li Yu; Chunhui Liu; Zunyan Dai; Shih-Shih Chen; Shu-Huei Wang; Joseph Costello; Ilya Ioshikhes; David W Dawson; Jason S Hong; Michael A Teitell; Angela Szafranek; Marta Camoriano; Fei Song; Rosemary Elliott; William Held; Jacquetta M Trasler; Christoph Plass; Rephael Wenger
The process of coral island formation is often difficult for middle school students to comprehend. Coral island formation is a dynamic process, and students should have the opportunity to experience this process in a synergistic context. The authors provide instructional guidelines for constructing a coral island. Students play an interactive role…
Austin, Heather; Edd, Amelia
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
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.
Complete Genome Sequences of Eight Helicobacter pylori Strains with Different Virulence Factor Genotypes and Methylation Profiles, Isolated from Patients with Diverse Gastrointestinal Diseases on Okinawa Island, Japan, Determined Using PacBio Single-Molecule Real-Time Technology.
We report the complete genome sequences of eight Helicobacter pylori strains isolated from patients with gastrointestinal diseases in Okinawa, Japan. Whole-genome sequencing and DNA methylation detection were performed using the PacBio platform. De novo assembly determined a single, complete contig for each strain. Furthermore, methylation analysis identified virulence factor genotype-dependent motifs. PMID:24744331
Satou, Kazuhito; Shiroma, Akino; Teruya, Kuniko; Shimoji, Makiko; Nakano, Kazuma; Juan, Ayaka; Tamotsu, Hinako; Terabayashi, Yasunobu; Aoyama, Misako; Teruya, Morimi; Suzuki, Rumiko; Matsuda, Miyuki; Sekine, Akihiro; Kinjo, Nagisa; Kinjo, Fukunori; Yamaoka, Yoshio; Hirano, Takashi
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
Genomic Analysis of a Pathogenicity Island in Uropathogenic Escherichia coli CFT073: Distribution of Homologous Sequences among Isolates from Patients with Pyelonephritis, Cystitis, and Catheter Associated Bacteriuria and from Fecal Samples
Urinary tract infection is the most frequently diagnosed kidney and urologic disease and Escherichia coli is by far the most common etiologic agent. Uropathogenic strains have been shown to contain blocks of DNA termed pathogenicity islands (PAIs) which contribute to their virulence. We have defined one of these regions of DNA within the chromosome of a highly virulent E. coli
DEBRA M. GUYER; JYH-SHYANG KAO; HARRY L. T. MOBLEY
Background Modern genomic technologies produce large amounts of data that can be mapped to specific regions in the genome. Among the first steps in interpreting the results is annotation of genomic regions with known features such as genes, promoters, CpG islands etc. Several tools have been published to perform this task. However, using these tools often requires a significant amount of bioinformatics skills and/or downloading and installing dedicated software. Results Here we present AnnotateGenomicRegions, a web application that accepts genomic regions as input and outputs a selection of overlapping and/or neighboring genome annotations. Supported organisms include human (hg18, hg19), mouse (mm8, mm9, mm10), zebrafish (danRer7), and Saccharomyces cerevisiae (sacCer2, sacCer3). AnnotateGenomicRegions is accessible online on a public server or can be installed locally. Some frequently used annotations and genomes are embedded in the application while custom annotations may be added by the user. Conclusions The increasing spread of genomic technologies generates the need for a simple-to-use annotation tool for genomic regions that can be used by biologists and bioinformaticians alike. AnnotateGenomicRegions meets this demand. AnnotateGenomicRegions is an open-source web application that can be installed on any personal computer or institute server. AnnotateGenomicRegions is available at: http://cru.genomics.iit.it/AnnotateGenomicRegions.
Describes efforts to evaluate and map the susceptibility of barrier islands to damage from storms, erosion, rising sea levels and other natural phenomena. Presented are criteria for assessing the safety and hazard potential of island developments. (WB)
Pilkey, Orrin H.; Neal, William J.
This animation shows the power of computer graphics to explore data in the sense of virtual reality. In this scene, standard tools are applied to fly around the Galapagos Islands and the ocean floor surrounding the islands.
Pape, Dave; Feldman, Gene
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.
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;)
\\u000a We perform a meta-analysis on morphological data from four island rodent populations exhibiting microevolution ( 100 years).\\u000a 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
Oliver R. W. Pergams; Mary V. Ashley
This almost totally cloud free, photo of the island of Timor, Indonesia (9.0S, 125.0E) illustrates the volcanic origin of the over 1500 islands of Indonesia. Close examination of the photo reveals several eroded volcanoes on the Island of Timor and several of the adjacent islands. The linear alignment of the volcanoes, as seen from space, indicates the edges of the tectonic plates of the Earth's crust where volcanic activity is most common.
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.
This report summarises the issues related to the use of man-made ice islands as exploration drilling structures in the Canadian Arctic Islands and Beaufort Sea. The historical development of ice island technology has been reviewed with respect to design, ...
Streptococcus agalactiae causes a range of clinical syndromes in camels (Camelus dromedarius). We report the genome sequences of two S. agalactiae isolates that induce abscesses in Kenyan camels. These genomes provide novel data on the composition of the S. agalactiae “pan genome” and reveal the presence of multiple genomic islands.
de Villiers, Etienne P.; Younan, Mario; Andersson, Goran; Tettelin, Herve; Riley, David R.; Jores, Joerg; Bongcam-Rudloff, Erik; Bishop, Richard P.
Streptococcus agalactiae causes a range of clinical syndromes in camels (Camelus dromedarius). We report the genome sequences of two S. agalactiae isolates that induce abscesses in Kenyan camels. These genomes provide novel data on the composition of the S. agalactiae "pan genome" and reveal the presence of multiple genomic islands. PMID:23868134
Zubair, Saima; de Villiers, Etienne P; Younan, Mario; Andersson, Göran; Tettelin, Herve; Riley, David R; Jores, Joerg; Bongcam-Rudloff, Erik; Bishop, Richard P
Near the western end of Lake Superior lies a forested archipelago of twenty-two islands called the Apostles. The Apostle Islands National Lakeshore (est. 1970) is composed of 20 of the 22 islands as well as a 12 mile strip of shoreline on the mainland. This National Park Service site contains an Explore the Islands section to get to know the natural wonders and human history of the islands. It offers information about: the islands, including a list of flora; lighthouses and shipwrecks; eagles and bears; sea caves; old growth forests; Lake Superior, including a fish species list; and the formation of sandscapes. The history of farming, stone quarries, and fisheries on the islands are also covered.
The great ape families are the species most closely related to our own, comprising chimpanzees, bonobos, gorillas, and orangutans. They live exclusively in tropical rainforests in Central Africa and the islands of Southeast Asia. Due to their close evolutionary relationship with humans, great apes share many cognitive, physiological, and morphological similarities with humans. The members of the great ape family make obvious models to facilitate the further understanding about humans' biology and history. This review will discuss how the recent addition of genome-wide data from great apes has furthered humans' understanding of these species and humanity, especially in the realm of evolutionary genetics.
Wall, Jeffrey D.
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
As with most small island groups around the world, the Marquesas Island group 9.0S, 140.0W) is usually concealed by heavy cloud cover throughout the day making them very difficult to photograph in their entirety. Located in the south central Pacific Ocean, just north of the Tuamotu Archipelago, the islands partially seen in this view are: Nuku Hiva, Ua Huka and Ua Pu.
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
Daiya Takai; Peter A. Jones
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
With more than 200 bacterial and archaeal genomes completely sequenced, and more than 500 genomes at various stages of completion,\\u000a we begin to appreciate the enormous diversity of prokaryotic genomes in terms of chromosomal structure, gene content and organization,\\u000a and the abundance and fluidity of accessory and mobile genetic elements. The genome of a bacterial species is composed of\\u000a conserved
Voon Loong Chan
This report was compiled as part of a study to assess the hydrogeology and the quality and quantity of fresh ground water on Block Island, Rhode Island. Hydrologic data were collected on Block Island during 1988-91. The data are pre- sented in illustrations and tables. Data collec- ted include precipitation, surfae-water, ground- water, lithologic, and well-construction and dis- charge information. Precipitation data include total monthly precipitation values from 11 rain gages and water-quality analyses of 14 precipi- tation samples from one station. Surface-water data include water-level measurements at 12 ponds, water-quality data for five ponds, and field specific-conductance measurements at 56 surface- water sites (streams, ponds, and springs). Ground- water data include water-level measurements at 159 wells, water-quality data at 150 wells, and field specific-conductance data at 52 wells. Lithologic logs for 375 wells and test borings, and construc- tion and location data for 570 wells, springs, and test borings are included. In addition, the data set contains data on water quality of water samples, collected by the Rhode Island Department of Health during 1976-91, from Fresh and Sands Ponds and from wells at the Block Island Water Company well field north of Sands Pond.
Lying in the eastern Mediterranean Sea, the entire Island of Crete (35.0N, 25.0E) can be seen in great detail in this cloud free view. The volcanic origins of this island can also be observed in the many sharp and angular ridgelines and rugged coastal features.
Turkey abounds in both natural as well as cultural richness. Especially the natural assets located in developing regions have an important role to play in the economic life of such areas. The floating islands are one of these assets and have become an important research subject lately. Turkey is considered as a heaven of floating islands. Almost all geographical regions
The Hawaiian Islands are an ideal location to study basaltic sand provenance in that they are a series of progressively older basaltic shield volcanoes with arid to humid microclimates. Sixty-two sand samples were collected from beaches on the islands of Hawaii, Maui, Oahu and Kauai and petrographically analyzed. The major sand components are calcareous bioclasts, volcanic lithic fragments, and monomineralic grains of dense minerals and plagioclase. Proportions of these components vary from island to island, with bioclastic end members being more prevalent on older islands exhibiting well-developed fringing reef systems and volcanic end members more prevalent on younger, volcanically active islands. Climatic variations across the island of Hawaii are reflected in the percentage of weathered detritus, which is greater on the wetter, northern side of the island. The groundmass of glassy, basaltic lithics is predominantly black tachylite, with lesser brown sideromelane; microlitic and lathwork textures are more common than holohyaline vitric textures. Other common basaltic volcanic lithic fragments are holocrystalline aggregates of silt-sized pyroxene or olivine, opaque minerals and plagioclase. Sands derived from alkalic lavas are texturally and compositionally indistinguishable from sands derived from tholeiitic lavas. Although Hawaiian basaltic sands overlap in composition with magmatic arc-derived sands in terms of their relative QFL, QmPK and LmLvLs percentages, they are dissimilar in that they lack felsic components and are more enriched in lathwork volcanic lithic fragments, holocrystalline volcanic lithic fragments, and dense minerals.
Marsaglia, K.M. (Univ. of Texas, El Paso, TX (United States). Dept. of Geological Sciences)
In this article, the author presents the Treasure Island problem and some inquiry activities derived from the problem. Trying to find where pirates buried a treasure leads to a surprising answer, multiple solutions, and a discussion of problem solving. The Treasure Island problem is an example of an inquiry activity that can be implemented in…
Marine Corps recruits at a ceremony at the Parris Island Auditorium. The auditorium is part of the Marine Corps Recruit Depot in Parris Island, South Carolina. Over one million men and women have trained at the depot since 1915 and served all over the world.
Describes an ecology course which provides students with an opportunity to observe aquatic and terrestrial life in the Bahamas. States that students learn scientific methodology by measuring physical and chemical aspects of the island habitats. Provides information on the island, course description and objectives, transportation, facilities, and…
Stephens, Lawrence J.; And Others
Prepared for students in grade six attending the Island Natural Science School, Toronto, Ontario, Canada, this booklet offers information and suggests activities in the areas of ecology, conservation, natural resources, and outdoor recreation. Introductory material describes island lore, its formation and significant features, followed by units of…
Toronto Board of Education (Ontario).
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
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
Terezie Mandáková; Peter B Heenan; Martin A Lysak
...Wildlife Service [FWS-R1-R-2010-N131; 1265-0000-10137-S3] Protection Island and San Juan Islands National Wildlife Refuges, Jefferson, Island, San Juan, Skagit, and Whatcom Counties, WA AGENCY: Fish and Wildlife...
We report the complete genome sequence of Lactococcus lactis subsp. cremoris A76, a dairy strain isolated from a cheese production outfit. Genome analysis detected two contiguous islands fitting to the L. lactis subsp. lactis rather than to the L. lactis subsp. cremoris lineage. This indicates the existence of genetic exchange between the diverse subspecies, presumably related to the technological process.
Quinquis, Benoit; Ehrlich, Stanislas Dusko; Sorokin, Alexei
Here, we report the complete genome sequence of Psychrobacter sp. strain G, isolated from King George Island, Antarctica, which can produce lipolytic enzymes at low temperatures. The genomics information of this strain will facilitate the study of the physiology, cold adaptation properties, and evolution of this genus. PMID:24051316
Che, Shuai; Song, Lai; Song, Weizhi; Yang, Meng; Liu, Guiming; Lin, Xuezheng
We report the complete genome sequence of Lactococcus lactis subsp. cremoris A76, a dairy strain isolated from a cheese production outfit. Genome analysis detected two contiguous islands fitting to the L. lactis subsp. lactis rather than to the L. lactis subsp. cremoris lineage. This indicates the existence of genetic exchange between the diverse subspecies, presumably related to the technological process. PMID:22328746
Bolotin, Alexander; Quinquis, Benoit; Ehrlich, Stanislas Dusko; Sorokin, Alexei
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.
Manwani, Deepa; Bieker, James J.
The last three years have seen an escalation in the number of sequenced bacteriophage genomes with more than five hundred now in the NCBI phage database, representing a more than three-fold increase from 2005. These span at least 70 different bacterial hosts, with two-thirds of the sequenced genomes of phages representing only eight bacterial hosts. Three key features emerge from the comparative analysis of these genomes. First, they span a very high degree of genetic diversity, suggesting early evolutionary origins. Secondly, the genome architectures are mosaic, reflecting an unusually high degree of horizontal genetic exchange in their evolution. Thirdly, phage genomes contain a very high proportion of novel genetic sequences of unknown function, and likely represent the largest reservoir of unexplored genes. With an estimated 1031 bacterial and archael viruses in the in the biosphere, our view of the virosphere will draw into sharper focus as further bacteriophage genomes are characterized.
Hatfull, Graham F.
Since the completion of the Human Genome Project 10 years ago, the world has witnessed an incredible progress in human genetics and genomics.(1) This progress was largely driven by the availability of better, faster and cheaper sequencing technology.(2) While it took more than 10 years and more than 1 billion dollars to complete the Human Genome Project,(3-5) an individual in the year 2011 can have his whole genome sequenced within a week for less than $30,000. With cheaper and faster sequencing came a wealth of novel discoveries which makes it timely to review how these newly found insights into the human genome are relevant for perioperative medicine. This article summarises the basics of genetic inheritance, the human genome and modern sequencing methods, as well as genetic variation and how this knowledge may be applied to patient care and research in the perioperative setting. PMID:22099920
Since the completion of the Human Genome Project 10 years ago, the world has witnessed an incredible progress in human genetics and genomics.1 This progress was largely driven by the availability of better, faster and cheaper sequencing technology.2 While it took more than 10 years and more than 1 billion dollars to complete the Human Genome Project,3-5 an individual in the year 2011 can have his whole genome sequenced within a week for less than $30,000. With cheaper and faster sequencing came a wealth of novel discoveries which makes it timely to review how these newly found insights into the human genome are relevant for perioperative medicine. This review summarizes the basics of genetic inheritance, the human genome and modern sequencing methods, as well as genetic variation and how this knowledge may be applied to patient care and research in the perioperative setting.
This lesson plan is part of the DiscoverySchool.com lesson plan library for grades 6-8. It focuses on island formation through water level changes, coral growth, or volcanism. Through class demonstrations, worksheets, and research, students learn the different ways islands form as well as how different lifeforms develop on the islands. It includes objectives, materials, procedures, discussion questions, evaluation ideas, extensions, suggested readings, and vocabulary. There are videos available to order which complement this lesson, and links to teaching tools for making custom quizzes, worksheets, puzzles and lesson plans.
The majority of the bacterial genome sequences deposited in the National Center for Biotechnology Information database contain prophage sequences. Analysis of the prophages suggested that after being integrated into bacterial genomes, they undergo a complex decay process consisting of inactivating point mutations, genome rearrangements, modular exchanges, invasion by further mobile DNA elements, and massive DNA deletion. We review the technical difficulties in defining such altered prophage sequences in bacterial genomes and discuss theoretical frameworks for the phage-bacterium interaction at the genomic level. The published genome sequences from three groups of eubacteria (low- and high-G+C gram-positive bacteria and ?-proteobacteria) were screened for prophage sequences. The prophages from Streptococcus pyogenes served as test case for theoretical predictions of the role of prophages in the evolution of pathogenic bacteria. The genomes from further human, animal, and plant pathogens, as well as commensal and free-living bacteria, were included in the analysis to see whether the same principles of prophage genomics apply for bacteria living in different ecological niches and coming from distinct phylogenetical affinities. The effect of selection pressure on the host bacterium is apparently an important force shaping the prophage genomes in low-G+C gram-positive bacteria and ?-proteobacteria.
Canchaya, Carlos; Proux, Caroline; Fournous, Ghislain; Bruttin, Anne; Brussow, Harald
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…
Hofmeister, Philip; Sag, Ivan A.
Pseudomonas putida S16 is an efficient degrader of nicotine. The complete genome of strain S16 (5,984,790 bp in length) includes genes related to catabolism of aromatic and heterocyclic compounds. The genes of enzymes in the core genome and a genomic island encode the proteins responsible for nicotine catabolism.
Yu, Hao; Tang, Hongzhi; Wang, Lijuan; Yao, Yuxiang; Wu, Geng; Xu, Ping
We report the draft genome sequence of Achromobacter arsenitoxydans SY8, the first reported arsenite-oxidizing bacterium belonging to the genus Achromobacter and containing a genomic arsenic island, an intact type III secretion system, and multiple metal(loid) transporters. The genome may be helpful to explore the mechanisms intertwining metal(loid) resistance and pathogenicity.
Li, Xiangyang; Hu, Yao; Gong, Jing; Lin, Yanbing; Johnstone, Laurel; Rensing, Christopher
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 insigh...
D. C. Robinson
Describes a 90-minute "Island Watershed" activity to help earth science students understand the concept of the water cycle. Introduces a surface waters unit appropriate for students in grades 7-10. Includes watershed project guidelines. (Author/KHR)
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.
In this online interactive game about shark biodiversity, learners investigate some strange things happening on Apo Island, in the Philippines. Learners collect clues to identify the animal species that attacked their boat's propeller.
Aquarium, Shedd; Educational Web Adventures (Eduweb)
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)
The dedicated librarians at the Stony Brook University Library have created this most excellent research guide and digital archive that covers all things Long Island. On their homepage, visitors can use the Long Island Documents area to view recently acquired items from key figures in local (and national) history, such as George Clinton, James Jay, and Benjamin Tallmadge. Also on the site is the Books, Pamphlets, and Journals area. Here visitors can make their way through key documents, such as "Early Long Island: A Colonial Study" and "The Evolution of Long Island: A Story of Land and Sea." Also, the site pays tribute to a very exciting new acquisition: several letters from George Washington, donated by Dr. Henry Laufer, a history enthusiast. This site is a tremendously valuable resource and one that will serve as a model to other institutions seeking to do similar work.
Since 1983, the Island Institute has employed a wide range of individuals, including photographers, artists, policy experts, and others, all in the name of maintaining the viability of the fifteen year-round island communities in the Gulf of Maine. They have become well-known for their outreach efforts, and their website will be of great value to anyone interested in this region, or how various island communities remain economically, culturally, and ecologically sustainable. Resources located on the Institute's homepage include information about fellowship opportunities and links to full and annual reports on the Atlantic herring spawning project. Visitors who are hoping to get a sense of the flavor of this unique region should definitely peruse their monthly publication, "The Working Waterfront." Recent articles include opinion pieces on fish hatcheries, the lobster business, and news profiles of local islanders.
The article announces the formation of family planning associations on the Tonga, Tahiti, Gilbert and Ellice Island groups. The administrative structures of the Associations are briefly described and organizational methods and directions to involve all islands of a particular groups are reported. All of the territories are within the area served by the South Pacific Commission which has set up a family planning seminar for the areas involved. PMID:12305000
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 ...
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.
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
Wheat is the largest produced grain crop world-wide and has been extensively studied for a wide range of agronomic traits located across the genome. Its large chromosomes and the capacity of the polyploid genome to tolerate the addition or loss of chromosomes facilitated a fast progress in early wheat genetics using cytogenetic techniques. However, these same characteristics have limited the
Evans S Lagudah; Jorge Dubcovsky; Wayne Powell
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.
Wung, Shu-Fen; Hickey, Kathleen T.; Taylor, Jacquelyn Y.; Gallek, Matthew J.
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.
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.
This article reviews recent advances in genomics and informatics relevant to cardiovascular research. In particular, we review the status of (1) whole genome sequencing efforts in human, mouse, rat, zebrafish, and dog; (2) the development of data mining and analysis tools; (3) the launching of the National Heart, Lung, and Blood Institute Programs for Genomics Applications and Proteomics Initiative; (4) efforts to characterize the cardiac transcriptome and proteome; and (5) the current status of computational modeling of the cardiac myocyte. In each instance, we provide links to relevant sources of information on the World Wide Web and critical appraisals of the promises and the challenges of an expanding and diverse information landscape.
Winslow, Raimond L.; Boguski, Mark S.
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
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.
Unique DNA sequences can be determined directly from mouse genomic DNA. A denaturing gel separates by size mixtures of unlabeled DNA fragments from complete restriction and partial chemical cleavages of the entire genome. These lanes of DNA are transferred and UV-crosslinked to nylon membranes. Hybridization with a short 32P-labeled single-stranded probe produces the image of a DNA sequence "ladder" extending from the 3' or 5' end of one restriction site in the genome. Numerous different sequences can be obtained from a single membrane by reprobing. Each band in these sequences represents 3 fg of DNA complementary to the probe. Sequence data from mouse immunoglobulin heavy chain genes from several cell types are presented. The genomic sequencing procedures are applicable to the analysis of genetic polymorphisms, DNA methylation at deoxycytidines, and nucleic acid-protein interactions at single nucleotide resolution. Images
Church, G M; Gilbert, W
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.
Saltatory changes in genomic technologies have driven successive eras of discovery of loci underlying human traits. The development of complete genetic maps of the human genome in the 1980's fueled the mapping of Mendelian loci in extended kindreds for dominant traits and predominantly in consanguineous kindreds for recessive traits. Further accelerated by the acquisition of the sequence of the human genome in 2001, this first Mendelian era identified over 2800 disease loci and profoundly changed our understanding of the biology and pathophysiology of every organ system. A second era, examining the contribution of common variants to common disease, was driven by the identification of more than 10 million common variants in the human genome sequence recognition of substantial linkage disequilibrium in the human genome, and methods to rapidly and relatively inexpensively genotype 500,000 – 1,000,000 SNPs in large cohorts. This led to identification of more than 1000 loci that show robust association with diverse human traits, a number of which have also drastically changed our understanding of disease biology. We have recently entered a third era of discovery, this one driven by spectacular reductions in the cost of DNA sequencing from ?$100,000 per million bases in 1998 to less than $0.10 today on the HiSeq instrument. Coupled with our development of robust methods for selectively sequencing complete coding regions of the genome, which harbor the overwhelming majority of Mendelian loci, and analytic methods to rapidly and with high sensitivity and specificity identify variations from the reference sequence, one can now sequence ostensibly all the genes in the human genome (the exome) to high levels of completion for ?$ 700. This has provided fundamental new opportunities for identifying Mendelian loci that were previously elusive. Drs. Shrikant Mane, Kaya Bilguvar and Martin Kircher will present the efforts being made at Yale and at University of Washington to discover Mendelian loci using cutting edge genomic technologies.
Mane, Shrikant; Bilgvar, Kaya; Kircher, Martin; Mane, Shrikant
In this north to south view of the Island of Luzon, Philippines (13.0N, 120.0E), the prominent Cordillera Central mountain range where gold, copper and silver are mined. The several large rivers that drain this region normally carry a heavy silt load to the sea but the absence of sediment plumes in this view is evidence of hot dry weather and lack of recent rains. Manila, the capital city is just visible at the south end of the island.
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.
This National Park Service (NPS) site covers the geology of Buck Island Reef National Monument in the Virgin Islands. It discusses coral reef formation and characteristics, as well as the history of Buck Island. There are links for maps, visitor information, and more details about this monument.
Contextual view of Treasure Island from Yerba Buena Island, showing Palace of Fine and Decorative Arts (Building 3), far right, Hall of Transportation (Building 2), middle, and The Administration Building (Building 1), far left, Port of Trade Winds is in foreground, camera facing northwest - Golden Gate International Exposition, Treasure Island, San Francisco, San Francisco County, CA
Examines the economic activity, language, world view, kinship patterns, and religion of contemporary Sea Islanders in order to illustrate the Islands' cultural conservatism and, thus, their appropriateness for the study of Africanism in the United States. (GC)
Twining, Mary A.; Baird, Keith E.
Lactobacillus casei, L. paracasei, and L. rhamnosus form a closely related taxonomic group (Lactobacillus casei group) within the facultatively heterofermentative lactobacilli. Here, we report the complete genome sequences of L. paracasei JCM 8130 and L. casei ATCC 393, and the draft genome sequence of L. paracasei COM0101, all of which were isolated from daily products. Furthermore, we re-annotated the genome of L. rhamnosus ATCC 53103 (also known as L. rhamnosus GG), which we have previously reported. We confirmed that ATCC 393 is distinct from other strains previously described as L. paracasei. The core genome of 10 completely sequenced strains of the L. casei group comprised 1,682 protein-coding genes. Although extensive genome-wide synteny was found among the L. casei group, the genomes of ATCC 53103, JCM 8130, and ATCC 393 contained genomic islands compared with L. paracasei ATCC 334. Several genomic islands, including carbohydrate utilization gene clusters, were found at the same loci in the chromosomes of the L. casei group. The spaCBA pilus gene cluster, which was first identified in GG, was also found in other strains of the L. casei group, but several L. paracasei strains including COM0101 contained truncated spaC gene. ATCC 53103 encoded a higher number of proteins involved in carbohydrate utilization compared with intestinal lactobacilli, and extracellular adhesion proteins, several of which are absent in other strains of the L. casei group. In addition to previously fully sequenced L. rhamnosus and L. paracasei strains, the complete genome sequences of L. casei will provide valuable insights into the evolution of the L. casei group. PMID:24116025
Toh, Hidehiro; Oshima, Kenshiro; Nakano, Akiyo; Takahata, Muneaki; Murakami, Masaru; Takaki, Takashi; Nishiyama, Hidetoshi; Igimi, Shizunobu; Hattori, Masahira; Morita, Hidetoshi
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.
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...
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
The response of a finite conductivity plasma to resonant magnetic perturbations is studied. The equations, which are derived for the time development of magnetic islands, help one interpret the singular currents which occur under the assumption of perfect plasma conductivity. The relation to the Rutherford regime of resistive instabilities is given.
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...
The IT2000 project, Singapore's national information technology (IT) effort to create the intelligent island, is introduced. The motivation for Singapore's government and other parties in taking an active role in the development of the National Information Infrastructure (NII) is outlined, and a strategic framework for coordinating the development of different aspects of the NII is presented. The architectural framework of
Juzar Motiwalla; Michael Yap; L. H. Ngoh
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.
The entrance to the Marine Corps Recruit Depot in Parris Island, South Carolina. Training of Marine Corps recruits began here in 1915. The base has been training recruits for every major U.S. conflict of the 20th and 21st century.
An island groin flap was used for satisfactory reconstruction of defects in the anterior thigh, lower abdomen, or perineal regions in 9 patients. This flap has several advantages: simple operation, wide range of coverage, large rotation arc, direct closure of the donor site, and no sacrifice of muscle. Comparison with tensor fascia lata and other musculocutaneous flaps is made. PMID:4091467
Ohtsuka, H; Nakaoka, H; Saeki, N; Miki, Y
As a result of the accident in March 1979, the Three Mile Island Unit 2 (TMI-2) reactor vessel sustained significant internal damage. Approximately half of the reactor core suffered some degree of melting, with 10 to 20 tons of molten core material relocating inside the vessel and flowing down onto the reactor vessel's lower head. The resulting damage and the
B. L. Lipford; N. M. Cole; T. J. Friderichs
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
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.
Purpose of review Imaging genomics is an emerging field that is rapidly identifying genes that influence the brain, cognition, and risk for disease. Worldwide, thousands of individuals are being scanned with high-throughput genotyping (genome-wide scans), and new imaging techniques [high angular resolution diffusion imaging and resting state functional magnetic resonance imaging (MRI)] that provide fine-grained measures of the brain’s structural and functional connectivity. Along with clinical diagnosis and cognitive testing, brain imaging offers highly reproducible measures that can be subjected to genetic analysis. Recent findings Recent studies of twin, pedigree, and population-based datasets have discovered several candidate genes that consistently show small to moderate effects on brain measures. Many studies measure single phenotypes from the images, such as hippocampal volume, but voxel-wise genomic methods can plot the profile of genetic association at each 3D point in the brain. This exploits the full arsenal of imaging statistics to discover and replicate gene effects. Summary Imaging genomics efforts worldwide are now working together to discover and replicate many promising leads. By studying brain phenotypes closer to causative gene action, larger gene effects are detectable with realistic sample sizes obtainable from meta-analysis of smaller studies. Imaging genomics has broad applications to dementia, mental illness, and public health.
Thompson, Paul M.; Martin, Nicholas G.; Wright, Margaret J.
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.
The opportunistic intracellular foodborne pathogen Listeria monocytogenes has become a paradigm for the study of host-pathogen interactions and bacterial adaptation to mammalian hosts. Analysis of L. monocytogenes infection has provided considerable insight into how bacteria invade cells, move intracellularly, and disseminate in tissues, as well as tools to address fundamental processes in cell biology. Moreover, the vast amount of knowledge that has been gathered through in-depth comparative genomic analyses and in vivo studies makes L. monocytogenes one of the most well-studied bacterial pathogens. This chapter provides an overview of progress in the exploration of genomic, transcriptomic, and proteomic data in Listeria spp. to understand genome evolution and diversity, as well as physiological aspects of metabolism used by bacteria when growing in diverse environments, in particular in infected hosts.
Cabanes, Didier; Sousa, Sandra; Cossart, Pascale
The ubiquitous bacterium Pseudomonas aeruginosa is the quintessential opportunistic pathogen. Certain isolates infect a broad range of host organisms, from plants to humans. The pathogenic promiscuity of particular variants may reflect an increased virulence gene repertoire beyond the core P. aeruginosa genome. We have identified and characterized two P. aeruginosa pathogenicity islands (PAPI-1 and PAPI-2) in the genome of PA14,
Jianxin He; Regina L. Baldini; Eric Déziel; Maude Saucier; Qunhao Zhang; Nicole T. Liberati; Daniel Lee; Jonathan Urbach; Howard M. Goodman; Laurence G. Rahme
Near-infrared (near-IR) excitation produces little background signal from biological molecules, making near-IR fluorescence technology highly useful in proteomic and genomic applications. To increase the emissions of near-IR fluorophores, we examined the use of metal-enhanced fluorescence on these longer wavelength dyes. IRDye700- and IRDye800-labeled DNA oligonucleotides and proteins were spotted onto silver island film (SIF)-coated glass slides, and analyzed using a
Jon P. Anderson; Mark Griffiths; Vince R. Boveia
Genomic signature tags (GSTs) are the products of a method we have developed for identifying and quantitatively analyzing genomic DNAs. The DNA is initially fragmented with a type II restriction enzyme. An oligonucleotide adaptor containing a recognition site for MmeI, a type IIS restriction enzyme, is then used to release 21-bp tags from fixed positions in the DNA relative to the sites recognized by the fragmenting enzyme. These tags are PCR-amplified, purified, concatenated, and then cloned and sequenced. The tag sequences and abundances are used to create a high-resolution GST sequence profile of the genomic DNA. GSTs are shown to be long enough for use as oligonucleotide primers to amplify adjacent segments of the DNA, which can then be sequenced to provide additional nucleotide information or used as probes to identify specific clones in metagenomic libraries. GST analysis of the 4.7-Mb Yersinia pestis EV766 genome using BamHI as the fragmenting enzyme and NlaIII as the tagging enzyme validated the precision of our approach. The GST profile predicts that this strain has several changes relative to the archetype CO92 strain, including deletion of a 57-kb region of the chromosome known to be an unstable pathogenicity island. [The following individuals kindly provided reagents, samples, or unpublished information as indicated in the paper: W. Crockett, K. Pellechi, J. Paparelli, J. Romeo, and K. Thompson.
Dunn, John J.; McCorkle, Sean R.; Praissman, Laura A.; Hind, Geoffrey; van der Lelie, Daniel; Bahou, Wadie F.; Gnatenko, Dmitri V.; Krause, Maureen K.
BACKGROUND: Hypermethylation of promoter CpG islands is strongly correlated to transcriptional gene silencing and epigenetic maintenance of the silenced state. As well as its role in tumor development, CpG island methylation contributes to the acquisition of resistance to chemotherapy. Differential Methylation Hybridisation (DMH) is one technique used for genome-wide DNA methylation analysis. The study of such microarray data sets should
Wei Dai; Jens M. Teodoridis; Janet Graham; Constanze Zeller; Tim Hui-ming Huang; Pearlly Yan; J. Keith Vass; Robert Brown; Jim Paul
The publication of the complete genome sequences of four clinical Listeria monocytogenes isolates and one of its apathogenic relative, Listeria innocua, in 2001 and 2003 has paved the way for major breakthroughs in understanding the biology of L. monocytogenes. The availability of these sequences allowed applying postgenomics analysis to understand virulence and ecology of L. monocytogenes and evolution of the
Philippe Glaser; Christophe Rusniok; Carmen Buchrieser
For more than 50 years, those engineering genetic material have pursued increasingly challenging targets. During that time, the tools and resources available to the genetic engineer have grown to encompass new extremes of both scale and precision, opening up new opportunities in genome engineering. Today, our capacity to generate larger de novo assemblies of DNA is increasing at a rapid
George M Church; Peter A Carr
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.
This animation is a sequence showing the formation of the Pine Island iceberg and the glacial seaward flow upstream from the crack. It is a series of MISR images from the Terra satellite on top of the continental Radarsat view of Antarctica. The Pine Island Glacier is the largest discharger of ice in Antarctica and the continents fastest moving glacier. Even so, when a large crack formed across the glacier in mid 2000, it was surprising how fast the crack expanded, 15 meters per day, and how soon the resulting iceberg broke off, mid-November, 2001. This iceberg, called B-21, is 42 kilometers by 17 kilometers and contains seven years of glacier outflow released to the sea in a single event.
Perkins, Lori; Bindschadler, Bob; Diner, Dave
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.
The effects of Tropical Storm Thelma in November 1991, three weeks prior to the taking of this photo can still be seen on Leyte, (10.5N, 125.0E). Flash floods and mud slides triggered by the heavy rainfall and aggravated by logging operations on the mountain slopes, added to the general destruction caused by the storm. Fresh water runoff (lens) into the ocean are still evident as numerous bright semi circles around the island perimeter.
Dauphin Island Sea Lab is Alabama's marine education and research center. Lab also provides a public aquarium that focuses solely on the native eco-systems of the Mobile Bay estuary. Site provides information on graduate programs, undergraduate opportunities, faculty, facilities, and news and events. Explore the Education and Aquarium sections for teacher resources and information on workshops, student summer camps, and academic-year programs.
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.
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.
Landsat satellite images of Southern Vancouver Island are among the collection of the Canada Centre for Remote Sensing's Images of Canada series (reviewed in the June 7, 2000 Scout Report for Science and Engineering). Below the full-color .jpeg images are tables documenting the satellites and sensors used, date of acquisition, image resolution, area (km), and links to a reference map. Educational, hyperlinked text about the featured region and close-ups of important topographic features accompany the images.
Dengue-1 viruses responsible for the dengue fever outbreak in Easter Island in 2002 were isolated from acute-phase sera of dengue fever patients. In order to analyze the complete genome sequence, we designed primers to amplify contiguous segments across the entire sequence of the viral genome. RT-PCR products obtained were cloned, and complete nucleotide and deduced amino acid sequences were determined. This report constitutes the first complete genetic characterization of a DENV-1 isolate from Chile. Phylogenetic analysis shows that an Easter Island isolate is most closely related to Pacific DENV-1 genotype IV viruses. PMID:18815724
Cáceres, C; Yung, V; Araya, P; Tognarelli, J; Villagra, E; Vera, L; Fernández, J
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 Ã¢ÂÂÃ¢ÂÂ¦there is no direct connection between them except for the languages, the time period, and place.Ã¢ÂÂ 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.
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
Single copy probes derived from CpG-rich island clones from Eag I and Not I linking libraries and nine rare-cutter restriction endonucleases were used to investigate the methylation status of CpG-rich islands on the inactive and active X chromosomes (Chr) of the mouse. Thirteen of the 14 probes used detected CpG-rich islands in genomic DNA. The majority of island CpGs detected by rare-cutter restriction endonucleases were methylated on the inactive X Chr and unmethylated on the active X Chr, but some heterogeneity within the cell population used to make genomic DNA was detected. The CpG-rich islands detected by two putative pseudoautosomal probes remained unmethylated on both the active and inactive X Chrs. Otherwise, distance from the X Chr inactivation center did not affect the methylation profile of CpG-rich islands. We conclude that methylation of CpG-rich islands is a general feature of X Chr inactivation. PMID:1799791
Norris, D P; Brockdorff, N; Rastan, S
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.
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.
New companies offering personal whole-genome information services over the internet are dynamic and highly visible players in the personal genomics field. For fees currently ranging from US$399 to US$2500 and a vial of saliva, individuals can now purchase online access to their individual genetic information regarding susceptibility to a range of chronic diseases and phenotypic traits based on a genome-wide SNP scan. Most of the companies offering such services are based in the United States, but their clients may come from nearly anywhere in the world. Although the scientific validity, clinical utility and potential future implications of such services are being hotly debated, several ethical and regulatory questions related to direct-to-consumer (DTC) marketing strategies of genetic tests have not yet received sufficient attention. For example, how can we minimize the risk of unauthorized third parties from submitting other people's DNA for testing? Another pressing question concerns the ownership of (genotypic and phenotypic) information, as well as the unclear legal status of customers regarding their own personal information. Current legislation in the US and Europe falls short of providing clear answers to these questions. Until the regulation of personal genomics services catches up with the technology, we call upon commercial providers to self-regulate and coordinate their activities to minimize potential risks to individual privacy. We also point out some specific steps, along the trustee model, that providers of DTC personal genomics services as well as regulators and policy makers could consider for addressing some of the concerns raised below.
Gurwitz, David; Bregman-Eschet, Yael
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.
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.
Talon, Manuel; Gmitter Jr., Fred G.
...Kelley's Island Swim, Lake Erie; Kelley's Island, Lakeside...movement in portions of Lake Erie during the annual Kelley's...Temporary Final Rule A. Regulatory History and Information On June 5...Kelley's Island Swim, Lake Erie; Kelley's Island,...
...2120-AA66 Amendment of Class E Airspace; Kwajalein Island, Marshall Islands, RMI AGENCY: Federal Aviation Administration (FAA...description of the Class E airspace areas for Kwajalein Island, Bucholz AAF, Marshall Islands, RMI. The...
...Zone; Bostock 50th Anniversary Fireworks, Long Island Sound; Manursing Island, NY AGENCY: Coast Guard, DHS. ACTION: Notice...temporary safety zone on the navigable waters of Long Island Sound in the vicinity of Manursing Island, NY...
...FWS-R4-R-2010-N051; 40136-1265-0000-S3] Pine Island, Matlacha Pass, Island Bay, and Caloosahatchee National Wildlife Refuges...environmental assessment (Draft CCP/EA) for Pine Island, Matlacha Pass, Island Bay, and...
...Zone; Bostock 50th Anniversary Fireworks, Long Island Sound; Manursing Island, NY AGENCY: Coast Guard, DHS. ACTION: Final...temporary safety zone on the navigable waters of Long Island Sound in the vicinity of Manursing Island, NY...
In the framework of the NESCOIL code, a method analogous to the procedure of Cary and Hanson was developed to eliminate islands and more generally to control the size and phase of islands. The method was applied to Helias stellerator vacuum fields in order to determine configurations with a dense set of flux surfaces in the plasma region and an island chain at the boundary which may serve as a basis for a divertor concept.
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; López, Nancy I
We report the complete genome sequence of Pseudomonas putida strain H8234, which was isolated from a hospital patient presenting with bacteremia. This strain has a single chromosome (6,870,827 bp) that contains 6,305 open reading frames. The strain is not a pathogen but exhibits multidrug resistance associated with 40 genomic islands.
Bernal, Patricia; Udaondo, Zulema; Segura, Ana; Ramos, Juan-Luis
The genome of Enterococcus faecalis 62, a commensal isolate from a healthy Norwegian infant, revealed multiple adaptive traits to the gastrointestinal tract (GIT) environment and the milk-containing diet of breast-fed infants. Adaptation to a commensal existence was emphasized by lactose and other carbohydrate metabolism genes within genomic islands, accompanied by the absence of virulence traits. PMID:21398545
Brede, Dag Anders; Snipen, Lars Gustav; Ussery, David Wayne; Nederbragt, Alexander J; Nes, Ingolf F
AT-rich minisatellites (AT islands) are sites of genomic instability in cancer cells and targets for extremely lethal AT-specific drugs, such as biz- elesin. Here we investigated the AT islands in the FRA16B fragile site region for their possible roles in the organization of DNA on the nuclear matrix. The FRA16B AT island nominally spans ~3 kb of mostly >90% A\\/T
Jennifer A. Jackson; Alex V. Trevino; Maryanne C. Herzig; Terence S. Herman; Jan M. Woynarowski
Genome plasticity resulting from frequent rearrangement of the bacterial genome is a fascinating but poorly understood phenomenon. First reported in Salmonella typhi, it has been observed only in a small number of Salmonella serovars, although the over 2,500 known Salmonella serovars are all very closely related. To gain insights into this phenomenon and elucidate its roles in bacterial evolution, especially those involved in the formation of particular pathogens, we systematically analyzed the genomes of 127 wild-type S. typhi strains isolated from many places of the world and compared them with the two sequenced strains, Ty2 and CT18, attempting to find possible associations between genome rearrangement and other significant genomic features. Like other host-adapted Salmonella serovars, S. typhi contained large genome insertions, including the 134 kb Salmonella pathogenicity island, SPI7. Our analyses showed that SPI7 disrupted the physical balance of the bacterial genome between the replication origin (ori) and terminus (ter) when this DNA segment was inserted into the genome, and rearrangement in individual strains further changed the genome balance status, with a general tendency toward a better balanced genome structure. In a given S. typhi strain, genome diversification occurred and resulted in different structures among cells in the culture. Under a stressed condition, bacterial cells with better balanced genome structures were selected to greatly increase in proportion; in such cases, bacteria with better balanced genomes formed larger colonies and grew with shorter generation times. Our results support the hypothesis that genome plasticity as a result of frequent rearrangement provides the opportunity for the bacterial genome to adopt a better balanced structure and thus eventually stabilizes the genome during evolution. PMID:16237205
Liu, Gui-Rong; Liu, Wei-Qiao; Johnston, Randal N; Sanderson, Kenneth E; Li, Shao-Xian; Liu, Shu-Lin
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
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
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.
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.
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.
Friedlaender, Jonathan S; Friedlaender, Francoise 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
...FWS-R4-R-2010-N240; 40136-1265-0000-S3] Pine Island, Matlacha Pass, Island Bay, and...for the environmental assessment for Pine Island, Matlacha Pass, Island Bay, and...notice, we finalize the CCP process for Pine Island, Matlacha Pass, Island Bay,...
A population survey of southern elephant seals (Mirounga leonina Linnaeus, 1758) was conducted at Nelson Island, South Shetland Islands, Antarctica, during the 2001 breeding season. Two breeding sites were identified, one of which had not been previously re? ported. The largest breeding site was located at Duthoit Point, with a total of 128 females, 111 pups and 7 weanlings distributed
Alejandro R. CARLINI; Sebastián POLJAK; Ricardo CASAUX; Gustavo Adolfo DANERI; Miguel GASCO
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.
Genomic islands (GIs) and integrative conjugative elements (ICEs) are major players in bacterial evolution since they encode genes involved in adaptive functions of medical or environmental importance. Here we performed the genomic analysis of ICEVchBan8, an unusual ICE found in the genome of a clinical non-toxigenic Vibrio cholerae O37 isolate. ICEVchBan8 shares most of its genetic structure with SXT/R391 ICEs. However, this ICE codes for a different integration/excision module is located at a different insertion site, and part of its genetic cargo shows homology to other pathogenicity islands of V. cholerae.
Taviani, Elisa; Spagnoletti, Matteo; Ceccarelli, Daniela; Haley, Bradd J.; Hasan, Nur A.; Chen, Arlene; Colombo, Mauro M.; Huq, Anwar; Colwell, Rita R.
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
Bohle, U R; Hilger, H H; Martin, W F
IN my notice (NATURE, p. 623) of Dr. Baur's botanical collections from the Galapagos Islands, I intended to add a few words respecting the Cactaceæ, but forgot it at the last moment. This natural order of plants forms the most conspicuous feature in the vegetation of some of the islands, as may be seen in the excellent views illustrating the
W. Botting Hemsley
Island populations are more prone to extinction than mainland populations, with island endemic species having higher extinction rates than nonendemic species. Inbreeding depression is one possible expla- nation for this. Insular populations are expected to suffer increased inbreeding relative to mainland popula- tions due to bottlenecks at foundation and to lower subsequent population sizes. Inbreeding coefficients for 182 nonendemic and
Whole-genome shotgun sequencing was used to study the sequence variation of three Pseudomonas aeruginosa isolates, two from clonal infections of cystic fibrosis patients and one from an aquatic environment, relative to the genomic sequence of reference strain PAO1. The majority of the PAO1 genome is represented in these strains; however, at least three prominent islands of PAO1-specific sequence are apparent.
David H. Spencer; Arnold Kas; Eric E. Smith; Christopher K. Raymond; Elizabeth H. Sims; Michele Hastings; Jane L. Burns; Rajinder Kaul; Maynard V. Olson
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
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.
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
Grigoriev; Igor V
Helicobacter pylori colonizes the human gastric mucosa, leading to a spectrum of gastric diseases in susceptible populations. Here we announce the draft genome sequences of strains HPARG8G and HPARG63. The data for both genome sequences provide insights regarding the diversity in gene content and rearrangement of the genomic islands commonly harbored by H. pylori.
Armitano, Rita Ines; Zerbetto De Palma, Gerardo; Matteo, Mario Jose; Revale, Santiago; Romero, Soledad; Traglia, German Matias
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.
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.
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
It is now clear that aberrant DNA methylation observed in cancer cells is not restricted to a few CpG islands, but affects multiple loci. When this epigenetic event occurs at the 5-end of the regulatory region of genes, it is frequently associated with transcriptional silencing. To investigate fur- ther this widespread event in the tumor genome, we developed a novel
Pearlly S. Yan; Chuan-Mu Chen; Huidong Shi; Farahnaz Rahmatpanah; Susan H. Wei; Charles W. Caldwell; Tim Hui-Ming Huang
In an attempt to understand the origin of CpG islands (CGIs) in mammalian genomes, we have studied their location and structure according to the expression pattern of genes and to the G + C content of isochores in which they are embedded. We show that CGIs located over the transcription start site (named start CGIs) are very different structurally from
Loïc Ponger; Laurent Duret; Dominique Mouchiroud
Pedicled tongue flaps have proved to be an effective method of repairing defects due to tissue loss in the oral cavity. Their central position, mobility, and excellent blood supply make their use feasible in a variety of sites. This paper describes the use and applications of central island tongue flaps to reconstruct defects of anterior floor of the mouth. This procedure was conducted at the Department of Oral and Maxillofacial Surgery, Medical University Hanover, introducing an improved surgical method and presenting the actual operation performed in our department. This method is considered superior for resurfacing the anterior floor of mouth defects because it is easy to perform and results in recovery of function and cosmetics. PMID:9927907
Shibahara, T; Noma, H; Fujikawa, M; Miyao, T; Ishikawa, M; Takasaki, Y
The Sovereign Democratic Republic of the Fiji Islands, commonly known as Fiji, is an independent nation consisting of some 332 islands surrounding the Koro Sea in the South Pacific Ocean. This topographic image shows Viti Levu, the largest island in the group. With an area of 10,429 square kilometers (about 4000 square miles), it comprises more than half the area of the Fiji Islands. Suva, the capital city, lies on the southeast shore. The Nakauvadra, the rugged mountain range running from north to south, has several peaks rising above 900 meters (about 3000 feet). Mount Tomanivi, in the upper center, is the highest peak at 1324 meters (4341 feet). The distinct circular feature on the north shore is the Tavua Caldera, the remnant of a large shield volcano that was active about 4 million years ago. Gold has been mined on the margin of the caldera since the 1930s. The Nadrau plateau is the low relief highland in the center of the mountain range. The coastal plains in the west, northwest and southeast account for only 15 percent of Viti Levu's area but are the main centers of agriculture and settlement.This shaded relief anaglyph image was generated using preliminary topographic data from the Shuttle Radar Topography Mission. A computer-generated artificial light source illuminates the elevation data from the top (north) to produce a pattern of light and shadows. Slopes facing the light appear bright, while those facing away are shaded. The stereoscopic effect was created by first draping the shaded relief image back over the topographic data and then generating two differing perspectives, one for each eye. When viewed through special glasses, the result is a vertically exaggerated view of the Earth's surface in its full three dimensions. Anaglyph glasses cover the left eye with a red filter and cover the right eye with a blue filter.This image was acquired by SRTM aboard the Space Shuttle Endeavour, launched on February 11, 2000. SRTM used the same radar instrument that comprised the Spaceborne Imaging Radar-C/X-Band Synthetic Aperture Radar (SIR-C/X-SAR) that flew twice on the Space Shuttle Endeavour in 1994. SRTM was designed to collect three-dimensional measurements of the Earth's surface. To collect the 3-D data, engineers added a 60-meter-long (about 200 feet) mast, installed additional C-band and X-band antennas, and improved tracking and navigation devices. The mission is a cooperative project between the National Aeronautics and Space Administration (NASA), the National Imagery and Mapping Agency (NIMA) of the U.S. Department of Defense (DoD), and the German and Italian space agencies. It is managed by NASA's Jet Propulsion Laboratory, Pasadena, CA, for NASA's Earth Science Enterprise, Washington, DC.Size: 192 km (119 miles) x 142 km (88 miles) Location: 17.8 deg. South lat., 178.0 deg. East lon. Orientation: North at top Date Acquired: February 19, 2000 Image: NASA/JPL/NIMA
...Islands have been designated as adversely affected by this major disaster: The islands of St. Croix, St. John, and St. Thomas, including Water Island for Public Assistance. All islands within the Territory of the U.S. Virgin Islands are...
...Islands have been designated as adversely affected by this major disaster: The islands of St. Croix, St. John, and St. Thomas, including Water Island for Public Assistance. All islands in the Territory of the U.S. Virgin Islands are...
Three new non-indigenous springtail species are recorded in recent collections made on Deception Island, South Shetland Islands, maritime Antarctic: Deuteraphorura (Deuteraphorura) cebennaria (Gisin) (Collembola: Onychiuridae), Mesaphorura macrochaeta Rusek (Tullbergiidae), and Proisotoma minuta Axelson (Isotomidae). One of these, D. (D.) cebennaria, is described. Additionally, two new indigenous species, Mesaphorura macrochaeta Rusek and Proisotoma minuta Axelson, are also recorded. The total number of Collembola species now known from the island is 14, comprised of eight native species and six non-indigenous species. This number of non-indigenous species recorded at Deception Island compares with only a single non-indigenous springtail recorded at any other maritime or continental Antarctic location. The reason underlying this high level of occurrence of non-indigenous species on Deception Island is likely to be a combination of the island's high level of human visitation and the presence of relatively benign terrestrial habitats associated with areas of geothermal activity. Two of the new records represent species recently assessed as being of the highest risk to become invaders in the less extreme environments of the subantarctic, thereby emphasising the importance and urgency of adopting and applying effective biosecurity measures to protect the unique and vulnerable ecosystems of this region. Also documented are the impacts on the soil fauna of the island from human trampling, which drastically reduced densities of both native and non-indigenous species to 1% of the abundance typical of non-trampled sites.
Greenslade, Penelope; Potapov, Mikhail; Russell, David; Convey, Peter
Three new non-indigenous springtail species are recorded in recent collections made on Deception Island, South Shetland Islands, maritime Antarctic: Deuteraphorura (Deuteraphorura) cebennaria (Gisin) (Collembola: Onychiuridae), Mesaphorura macrochaeta Rusek (Tullbergiidae), and Proisotoma minuta Axelson (Isotomidae). One of these, D. (D.) cebennaria, is described. Additionally, two new indigenous species, Mesaphorura macrochaeta Rusek and Proisotoma minuta Axelson, are also recorded. The total number of Collembola species now known from the island is 14, comprised of eight native species and six non-indigenous species. This number of non-indigenous species recorded at Deception Island compares with only a single non-indigenous springtail recorded at any other maritime or continental Antarctic location. The reason underlying this high level of occurrence of non-indigenous species on Deception Island is likely to be a combination of the island's high level of human visitation and the presence of relatively benign terrestrial habitats associated with areas of geothermal activity. Two of the new records represent species recently assessed as being of the highest risk to become invaders in the less extreme environments of the subantarctic, thereby emphasising the importance and urgency of adopting and applying effective biosecurity measures to protect the unique and vulnerable ecosystems of this region. Also documented are the impacts on the soil fauna of the island from human trampling, which drastically reduced densities of both native and non-indigenous species to 1% of the abundance typical of non-trampled sites. PMID:23438196
Greenslade, Penelope; Potapov, Mikhail; Russell, David; Convey, Peter
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.
\\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
...the Northern Mariana Islands, the Commonwealth of Puerto Rico, and the Island of...the Northern Mariana Islands, the Commonwealth of Puerto Rico, and the Island of...Northern Mariana Islands, and the Commonwealth of Puerto Rico are quarantined....
Methylation of CpG islands associated with genes can affect the expression of the proximal gene, and methylation of non-associated CpG islands cor- relates to genomic instability. This epigenetic mod- ification has been shown to be important in many pathologies, from development and disease to cancer. We report the development of a novel high-resolution microarray that detects the methyla- tion status
Sitharthan Kamalakaran; Jude Kendall; Xiaoyue Zhao; Chunlao Tang; Sohail Khan; Kandasamy Ravi; Theresa Auletta; Michael Riggs; Yun Wang; Aslaug Helland; Bjørn Naume; Nevenka Dimitrova; A.-L. Borresen-Dale; Jim Hicks; Robert Lucito
To shed light on the breadth of the host range of Mesorhizobium loti strain NZP2037, we determined the sequence of the NZP2037 symbiosis island and compared it with those of strain MAFF303099 and R7A islands. The determined 533 kb sequence of NZP2037 symbiosis island, on which 504 genes were predicted, implied its integration into a phenylalanine-tRNA gene and subsequent genome rearrangement. Comparative analysis revealed that the core regions of the three symbiosis islands consisted of 165 genes. We also identified several NZP2037-specific genes with putative functions in nodulation-related events, suggesting that these genes contribute to broaden the host range of NZP2037.
Kasai-Maita, Hiroko; Hirakawa, Hideki; Nakamura, Yasukazu; Kaneko, Takakazu; Miki, Kumiko; Maruya, Jumpei; Okazaki, Shin; Tabata, Satoshi; Saeki, Kazuhiko; Sato, Shusei
A paleomagnetic study was carried out on recent volcanic rocks exposed on Deception Island (63.0°S, 60.6°W), Antarctica. Sampling comprised all stratigraphic units exposed on the island, which include basaltic, andesitic and trachytic lavas, basaltic dykes and pyroclastic flows. Following stepwise thermal and alternating field demagnetization procedures, consistent characteristic remanence directions were determined at 21 sites, using principal-component analysis. The overall
Andrés Baraldo; Augusto E. Rapalini; Harald Böhnel; Mabel Mena
After establishing its present location around 9.5 ka, Mustang Island aggraded, stacking over 20 m of barrier-island sand in the same location. Throughout Mustang Island's history, tidal inlets shifted within nearly the same location from 7.5 ka to the present, leaving 10-15 m thick deposits of clean, well-sorted, quartz sand deposited within only a few centuries. These deposits lack some of the sedimentary features normally associated with tidal inlets, such as tidal couplets and shell hash. The lack of such features is attributed to the uniform nature of the deposits cut by the inlets during the island's relatively long period of aggradation. Mustang Island was able to maintain an aggradation character throughout most of the Holocene due to the sediment eroded from three sources: Pleistocene headlands, the transgressive Colorado River delta of Texas, and the OIS 3 shoreline of the central-Texas shelf. Each of these sources was exposed to waves and accompanying longshore drift during the island's early history when sea level rose quickly, but was flooded or capped by transgressive muds by the time sea-level rise slowed during the middle Holocene.
Simms, Alexander R.; Anderson, John B.; Blum, Michael
Previous laboratory and numerical experiments show that the nonlinear heat island circulation has two different flow regimes: One has two maximums of updraft at both edges of the heat island (type E), while the other has a single maximum of updraft at the center of the island (type C). Our theoretical consideration shows that the heat island circulation is principally
Hiroshi Niino; Atsushi Mori; Takehiko Satomura; Sayaka Akiba
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
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
For the past decade, education has been experiencing meltdown, explosions, radiation leaks, heat pollution, and management crises, just like the Three Mile Island disaster. This article offers suggestions on how to deal with these problems. (Author/LD)
On January 16, the aging Ecuadorean tanker "Jessica" ran aground on San Cristobal Island, threatening the delicate ecosystem of the Galapagos Islands, famous as the location for much of Charles Darwin's key research. The Galapagos, 97 percent of which is a national park, is perhaps the last complete and preserved island archipelago. The captain of the ship has since accepted responsibility for misjudging his entry into the bay and running the ship aground, spilling approximately 160,000 gallons of oil. Efforts continue to refloat the ship and remove the 10,000 gallons left inside. Fortunately, favorable winds and currents have limited the amount of oil washing up on the Galapagos Islands, but the long-term effects remain to be seen.
De Nie, Michael W.
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
Invasive mammals are the greatest threat to island biodiversity and invasive rodents are likely responsible for the greatest number of extinctions and ecosystem changes. Techniques for eradicating rodents from islands were developed over 2 decades ago. Since that time there has been a significant development and application of this conservation tool. We reviewed the literature on invasive rodent eradications to assess its current state and identify actions to make it more effective. Worldwide, 332 successful rodent eradications have been undertaken; we identified 35 failed eradications and 20 campaigns of unknown result. Invasive rodents have been eradicated from 284 islands (47,628 ha). With the exception of two small islands, rodenticides were used in all eradication campaigns. Brodifacoum was used in 71% of campaigns and 91% of the total area treated. The most frequent rodenticide distribution methods (from most to least) are bait stations, hand broadcasting, and aerial broadcasting. Nevertheless, campaigns using aerial broadcast made up 76% of the total area treated. Mortality of native vertebrates due to nontarget poisoning has been documented, but affected species quickly recover to pre-eradication population levels or higher. A variety of methods have been developed to mitigate nontarget impacts, and applied research can further aid in minimizing impacts. Land managers should routinely remove invasive rodents from islands <100 ha that lack vertebrates susceptible to nontarget poisoning. For larger islands and those that require nontarget mitigation, expert consultation and greater planning effort are needed. With the exception of house mice (Mus musculus), island size may no longer be the limiting factor for rodent eradications; rather, social acceptance and funding may be the main challenges. To be successful, large-scale rodent campaigns should be integrated with programs to improve the livelihoods of residents, island biosecurity, and reinvasion response programs. PMID:17883491
Howald, Gregg; Donlan, C Josh; Galván, Juan Pablo; Russell, James C; Parkes, John; Samaniego, Araceli; Wang, Yiwei; Veitch, Dick; Genovesi, Piero; Pascal, Michel; Saunders, Alan; Tershy, Bernie
We present an ontology for describing genomes, genome comparisons, their evolution and biological function. This ontology will support the development of novel genome comparison algorithms and aid the community in discussing genomic evolution. It provides a framework for communication about comparative genomics, and a basis upon which further automated analysis can be built. The nomenclature defined by the ontology will foster clearer communication between biologists, and also standardize terms used by data publishers in the results of analysis programs. The overriding aim of this ontology is the facilitation of consistent annotation of genomes through computational methods, rather than human annotators. To this end, the ontology includes definitions that support computer analysis and automated transfer of annotations between genomes, rather than relying upon human mediation.
Flanagan, Keith; Stevens, Robert; Pocock, Matthew; Lee, Pete
The year 2004 was an exciting one for the Phytophthora research community. The United States Department of Energy Joint Genome Institute (JGI) completed the draft genome sequence of two Phytophthora species, Phytophthora sojae and Phytophthora ramorum. In August of that year over 50 people gathered at JGI in Walnut Creek, California, for an annotation jamboree and searched for the secrets and surprises that the two genomes have in petto. This culminated in a paper in Science in September of this year describing the highlights of the sequencing project and emphasizing the power of having the genome sequences of two closely related organisms. This MPMI Focus issue on Phytophthora genomics contains a number of more specialized manuscripts centered on gene annotation and genome organization, and complemented with manuscripts that rely on genomics resources. PMID:17153913
Govers, Francine; Gijzen, Mark
As a result of the accident in March 1979, the Three Mile Island Unit 2 (TMI-2) reactor vessel sustained significant internal damage. Approximately half of the reactor core suffered some degree of melting, with 10 to 20 tons of molten core material relocating inside the vessel and flowing down onto the reactor vessel's lower head. The resulting damage and the margin to failure of the lower head are of interest to the nuclear industry. In early 1988 the owner and operator of the TMI facility, had completed a large portion of the defueling work in the reactor core region and was preparing to remove the lower structural internals in order to defuel the area within the lower head. At that point the U.S. Nuclear Regulatory Commission's Office of Nuclear Regulatory Research (NRC-Res) in Washington, D.C., initiated a project to remove metallurgical specimens from the reactor vessel's lower head region. The goal was to determine the extent of damage to the pressure-retaining boundary in the lower head and to learn what happened during the accident.
Lipford, B.L.; Cole, N.M.; Friderichs, T.J. (MPR Associates Inc., Washington, DC (US))
West Nile virus (WNV) first emerged in the US in 1999 and has since spread across the Americas. Here, we report the continued expansion of WNV to the British Virgin Islands following its emergence in a flock of free-roaming flamingos. Histologic review of a single chick revealed lesions consistent with WNV infection, subsequently confirmed with PCR, immunohistochemistry and in situ hybridization. Full genome analysis revealed 99% sequence homology to strains circulating in the US over the past decade. This study highlights the need for rapid necropsy of wild bird carcasses to fully understand the impact of WNV on wild populations. PMID:24504904
Anthony, S J; Garner, M M; Palminteri, L; Navarrete-Macias, I; Sanchez-Leon, M D; Briese, T; Daszak, P; Lipkin, W I
Points out the importance of genomes other than the human genome project and provides information on the identified bacterial genomes Pseudomonas aeuroginosa, Leprosy, Cholera, Meningitis, Tuberculosis, Bubonic Plague, and plant pathogens. Considers the computer's use in genome studies. (Contains 14 references.) (YDS)
Flannery, Maura C.
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.
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 6.1 Mb sequence indicates that 30% of the traits are unique and distributed over 5 genomic islands, a prophage and two plasmids.
Archana Chauhan; Alice Layton; Daniel W Williams; Abby E. Smart; Steven Anthony Ripp; Tatiana V Karpinets; Steven D Brown; Gary Steven Sayler
The genome of Aeromonas salmonicida subsp. pectinolytica strain 34melT, isolated from a heavily polluted river, contains several genomic islands and putative virulence genes. The identification of genes involved in resistance to different kinds of stress sheds light on the mechanisms used by this strain to thrive in an extreme environment.
Pavan, M. Elisa; Pavan, Esteban E.; Lopez, Nancy I.; Levin, Laura
The genome of Aeromonas salmonicida subsp. pectinolytica strain 34mel(T), isolated from a heavily polluted river, contains several genomic islands and putative virulence genes. The identification of genes involved in resistance to different kinds of stress sheds light on the mechanisms used by this strain to thrive in an extreme environment. PMID:24029754
Pavan, M Elisa; Pavan, Esteban E; López, Nancy I; Levin, Laura; Pettinari, M Julia
This research project focuses on Aquidneck Island in the State of Rhode Island. The research project has two primary objectives. First, the project builds the foundation for coordinated transportation and land use planning on Aquidneck Island using TransC...
F. Atash K. Woodward J. Boyce S. Eisenbeiser
...Service [FWS-R1-R-2010-N222; 10137-1265-0000 S3] Protection Island and San Juan Islands National Wildlife Refuges, Jefferson, San Juan, Skagit, Island, and Whatcom Counties, WA; Final Comprehensive Conservation Plan,...
...2120-AA66 Amendment of Class D Airspace; Kwajalein Island, Marshall Islands, RMI AGENCY: Federal Aviation Administration (FAA...SUMMARY: This action amends the Kwajalein Island Class D airspace description by amending the...
Plant mitochondria share a functional role with their fungal and animal counterparts, and their genomes have a number of genes\\u000a in common. In almost every other aspect, however, plant mitochondrial genomes differ. Whereas animal genomes are very small\\u000a (14-18 kb) and fungal genomes somewhat larger (70-100 kb), known plant mitochondrial genomes range in size from 187 kb to\\u000a over 2400
C. Fauron; J. Allen; S. Clifton; K. Newton
Genome-scale scans have revealed highly heterogeneous levels of divergence between closely related taxa in many systems. Generally, a small number of regions show high differentiation, with the rest of the genome showing no or only low levels of divergence. These patterns have been interpreted as evidence for ongoing speciation-with-gene-flow, with introgression homogenizing the whole genome except loci involved in reproductive isolation. However, as the number of selected loci increases, the probability of introgression at unselected loci decreases unless there is a transmission ratio distortion causing an over-representation of specific combinations of alleles. Here we examine the transmission of three ‘speciation islands’ that contain fixed differences between the M and S forms of the mosquito, Anopheles gambiae. We made reciprocal crosses between M and S parents and genotyped over 2000 F2 individuals, developing a hierarchical likelihood model to identify specific genotypes that are under- or over-represented among the recombinant offspring. Though our overall results did not match the expected number of F2 genotypes, we found no biased co-transmission among M or S alleles in the three islands. Our likelihood model did identify transmission ratio distortion at two of the three islands, but this distortion was small (approx. 3%) and in opposite directions for the two islands. We discuss how our results impinge on hypotheses of current gene flow between M and S and ongoing speciation-with-gene-flow in this system.
Hahn, Matthew W.; White, Bradley J.; Muir, Christopher D.; Besansky, Nora J.
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.
Medina, Ignacio; Salavert, Francisco; Sanchez, Ruben; de Maria, Alejandro; Alonso, Roberto; Escobar, Pablo; Bleda, Marta; Dopazo, Joaquin
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
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.
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.
Photosymbiotic ascidian fauna were surveyed in the subtidal zone off Pari Island in the Thousand Islands (Java Sea, Indonesia). Nine species were recorded: Didemnum molle, Trididemnum miniatum, Lissoclinum patella, L. punctatum, L. timorense, Diplosoma gumavirens, D. simile, D. simileguwa, and D. virens. All of these species have been previously recorded in the Ryukyu Archipelago, Japan. Diplosoma gumavirens and D. simileguwa were originally described from the Ryukyu Archipelago in 2009 and 2005, respectively, and all of the observed species are potentially widely distributed in Indo-West Pacific coral reefs. PMID:25061385
Hirose, Euichi; Iskandar, Budhi Hascaryo; Wardiatno, Yusli
Abstract Photosymbiotic ascidian fauna were surveyed in the subtidal zone off Pari Island in the Thousand Islands (Java Sea, Indonesia). Nine species were recorded: Didemnum molle, Trididemnum miniatum, Lissoclinum patella, L. punctatum, L. timorense, Diplosoma gumavirens, D. simile, D. simileguwa, and D. virens. All of these species have been previously recorded in the Ryukyu Archipelago, Japan. Diplosoma gumavirens and D. simileguwa were originally described from the Ryukyu Archipelago in 2009 and 2005, respectively, and all of the observed species are potentially widely distributed in Indo–West Pacific coral reefs.
Hirose, Euichi; Iskandar, Budhi Hascaryo; Wardiatno, Yusli
A collection of 9,990 single-pass nuclear genomic sequences, corresponding to 5 Mb of tomato DNA, were obtained using methylation filtration (MF) strategy and reduced to 7,053 unique undermethylated genomic islands (UGIs) distributed as follows: (1) 59% non-coding sequences, (2) 28% coding sequences, (3) 12% transposons—96% of which are class I retroelements, and (4) 1% organellar sequences integrated into the nuclear genome
Y. Wang; R. S. van der Hoeven; R. Nielsen; L. A. Mueller; S. D. Tanksley
Bacterial blight, caused by Pseudomonas savastanoi pv. glycinea (Psg), is a common disease of soybean. In an effort to compare a current field isolate with one isolated in the early 1960s, the genomes of two Psg strains, race 4 and B076, were sequenced using 454 pyrosequencing. The genomes of both Psg strains share more than 4,900 highly conserved genes, indicating very low genetic diversity between Psg genomes. Though conserved, genome rearrangements and recombination events occur commonly within the two Psg genomes. When compared to each other, 437 and 163 specific genes were identified in B076 and race 4, respectively. Most specific genes are plasmid-borne, indicating that acquisition and maintenance of plasmids may represent a major mechanism to change the genetic composition of the genome and even acquire new virulence factors. Type three secretion gene clusters of Psg strains are near identical with that of P. savastanoi pv. phaseolicola (Pph) strain 1448A and they shared 20 common effector genes. Furthermore, the coronatine biosynthetic cluster is present on a large plasmid in strain B076, but not in race 4. In silico subtractive hybridization-based comparative genomic analyses with nine sequenced phytopathogenic pseudomonads identified dozens of specific islands (SIs), and revealed that the genomes of Psg strains are more similar to those belonging to the same genomospecies such as Pph 1448A than to other phytopathogenic pseudomonads. The number of highly conserved genes (core genome) among them decreased dramatically when more genomes were included in the subtraction, suggesting the diversification of pseudomonads, and further indicating the genome heterogeneity among pseudomonads. However, the number of specific genes did not change significantly, suggesting these genes are indeed specific in Psg genomes. These results reinforce the idea of a species complex of P. syringae and support the reclassification of P. syringae into different species.
Qi, Mingsheng; Wang, Dongping; Bradley, Carl A.; Zhao, Youfu
Vancomycin-resistant enterococci (VRE) are one of the leading causes of nosocomial infections in health care facilities around the globe. In particular, infections caused by vancomycin-resistant Enterococcus faecium are becoming increasingly common. Comparative and functional genomic studies of E. faecium isolates have so far been limited owing to the lack of a fully assembled E. faecium genome sequence. Here we address this issue and report the complete 3.0-Mb genome sequence of the multilocus sequence type 17 vancomycin-resistant Enterococcus faecium strain Aus0004, isolated from the bloodstream of a patient in Melbourne, Australia, in 1998. The genome comprises a 2.9-Mb circular chromosome and three circular plasmids. The chromosome harbors putative E. faecium virulence factors such as enterococcal surface protein, hemolysin, and collagen-binding adhesin. Aus0004 has a very large accessory genome (38%) that includes three prophage and two genomic islands absent among 22 other E. faecium genomes. One of the prophage was present as inverted 50-kb repeats that appear to have facilitated a 683-kb chromosomal inversion across the replication terminus, resulting in a striking replichore imbalance. Other distinctive features include 76 insertion sequence elements and a single chromosomal copy of Tn1549 containing the vanB vancomycin resistance element. A complete E. faecium genome will be a useful resource to assist our understanding of this emerging nosocomial pathogen.
Lam, Margaret M. C.; Seemann, Torsten; Bulach, Dieter M.; Gladman, Simon L.; Chen, Honglei; Haring, Volker; Moore, Robert J.; Ballard, Susan; Grayson, M. Lindsay; Johnson, Paul D. R.; Howden, Benjamin P.
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.
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.
The Staphylococcus carnosus genome has the highest GC content of all sequenced staphylococcal genomes, with 34.6%, and therefore represents a species that is set apart from S. aureus, S. epidermidis, S. saprophyticus, and S. haemolyticus. With only 2.56 Mbp, the genome belongs to a family of smaller staphylococcal genomes, and the ori and ter regions are asymmetrically arranged with the replichores I (1.05 Mbp) and II (1.5 Mbp). The events leading up to this asymmetry probably occurred not that long ago in evolution, as there was not enough time to approach the natural tendency of a physical balance. Unlike the genomes of pathogenic species, the TM300 genome does not contain mobile elements such as plasmids, insertion sequences, transposons, or STAR elements; also, the number of repeat sequences is markedly decreased, suggesting a comparatively high stability of the genome. While most S. aureus genomes contain several prophages and genomic islands, the TM300 genome contains only one prophage, ?TM300, and one genomic island, ?SCA1, which is characterized by a mosaic structure mainly composed of species-specific genes. Most of the metabolic core pathways are present in the genome. Some open reading frames are truncated, which reflects the nutrient-rich environment of the meat starter culture, making some functions dispensable. The genome is well equipped with all functions necessary for the starter culture, such as nitrate/nitrite reduction, various sugar degradation pathways, two catalases, and nine osmoprotection systems. The genome lacks most of the toxins typical of S. aureus as well as genes involved in biofilm formation, underscoring the nonpathogenic status.
Rosenstein, Ralf; Nerz, Christiane; Biswas, Lalitha; Resch, Alexandra; Raddatz, Guenter; Schuster, Stephan C.; Gotz, Friedrich
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
Pathogenicity islands (PAIs) are genetic elements whose products are essential to the process of disease development. They have been horizontally (laterally) transferred from other microbes and are important in evolution of pathogenesis. In this study, a comprehensive database and search engines specialized for PAIs were established. The pathogenicity island database (PAIDB) is a comprehensive relational database of all the reported PAIs and potential PAI regions which were predicted by a method that combines feature-based analysis and similarity-based analysis. Also, using the PAI Finder search application, a multi-sequence query can be analyzed onsite for the presence of potential PAIs. As of April 2006, PAIDB contains 112 types of PAIs and 889 GenBank accessions containing either partial or all PAI loci previously reported in the literature, which are present in 497 strains of pathogenic bacteria. The database also offers 310 candidate PAIs predicted from 118 sequenced prokaryotic genomes. With the increasing number of prokaryotic genomes without functional inference and sequenced genetic regions of suspected involvement in diseases, this web-based, user-friendly resource has the potential to be of significant use in pathogenomics. PAIDB is freely accessible at .
Yoon, Sung Ho; Park, Young-Kyu; Lee, Soohyun; Choi, Doil; Oh, Tae Kwang; Hur, Cheol-Goo; Kim, Jihyun F.
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.
Pathogenicity islands are chromosomal clusters of pathogen-specific virulence genes often found at tRNA loci. We have determined the molecular genetic structure of SPI-3, a 17-kb pathogenicity island located at the selC tRNA locus of Salmonella enterica serovar Typhimurium. The G+C content of SPI-3 (47.5%) differs from that of the Salmonella genome (52%), consistent with the notion that these sequences have been horizontally acquired. SPI-3 harbors 10 open reading frames organized in six transcriptional units, which include the previously described mgtCB operon encoding the macrophage survival protein MgtC and the Mg2+ transporter MgtB. Among the newly identified open reading frames, one exhibits sequence similarity to the ToxR regulatory protein of Vibrio cholerae and one is similar to the AIDA-I adhesin of enteropathogenic Escherichia coli. The distribution of SPI-3 sequences varies among the salmonellae: the right end of the island, which harbors the virulence gene mgtC, is present in all eight subspecies of Salmonella; however, a four-gene cluster at the center of SPI-3 is found in only some of the subspecies and is bracketed by remnants of insertion sequences, suggesting a multistep process in the evolution of SPI-3 sequences. PMID:9922266
Blanc-Potard, A B; Solomon, F; Kayser, J; Groisman, E A
WAKE ISLAND AIRFIELD TERMINAL, BUILDING 1502 LOOKING EAST WITH PHOTO SCALE CENTERED ON BUILDING (12/30/2008) - Wake Island Airfield, Terminal Building, West Side of Wake Avenue, Wake Island, Wake Island, UM
21. Photograph of a photograph in possession of Rock Island Arsenal Historical Office. ORIGINAL HORIZONTAL SHAFTING OF GENERAL ELECTRIC GENERATORS. ORIGINALLY PUBLISHED IN 1905. - Rock Island Arsenal, Building No. 160, Sylvan Drive, Rock Island, Rock Island County, IL
The nucleation and growth of islands during deposition or etching produces subtle correlations between island size and separation, which control the island size distribution . These correlations develop early on, motivating detailed analysis of the island nucleation regime. Once a \\
J. W. Evans; J. B. Hannon; M. C. Bartelt; G. L. Kellogg
5. Photograph of a photograph in possession of Rock Island Arsenal Historical Office. INTERIOR AFTER REMODELING INTO OFFICE SPACE. DATED FEBRUARY 13, 1943. - Rock Island Arsenal, Building No. 67, Rodman Avenue & Fourth Street, Rock Island, Rock Island County, IL
7. Photograph of a photograph in possession of Rock Island Arsenal Historical Office. SOUTH AND EAST ELEVATIONS. DATED MARCH 19, 1945. - Rock Island Arsenal, Building No. 62, Rodman Avenue between First & Second Streets, Rock Island, Rock Island County, IL
8. Photograph of a photograph in possession of Rock Island Arsenal Historical Office. SOUTH ELEVATON IN UNALTERED CONDITION. ORIGINALLY PUBLISHED 1898. - Rock Island Arsenal, Building No. 68, Rodman Avenue between Fourth Street & East Avenue, Rock Island, Rock Island County, IL
9. Photograph of photograph in possession of Rock Island Arsenal Historical Office. WEST AND NORTH ELEVATIONS. ORIGINALLY PUBLISHED 1887. - Rock Island Arsenal, Building No. 90, East Avenue between North Avenue & King Drive, Rock Island, Rock Island County, IL
10. Photograph of a photograph in possession of Rock Island Arsenal Historical Office. INTERIOR, LOOKING WEST. DATED OCTOBER 2, 1945. - Rock Island Arsenal, Building No. 138, Second Avenue between South Avenue & Ramsey Street, Rock Island, Rock Island County, IL
11. Photograph of a photograph in possession of Rock Island Arsenal Historical Office. BASEMENT, SHOWING ORIGINAL OPEN INTERIOR PLAN. DATED APRIL 7, 1942. - Rock Island Arsenal, Building No. 56, North Avenue & East Avenue, Rock Island, Rock Island County, IL
5. Photograph of a photograph in possession of Rock Island Arsenal Historical Office. WEST ELEVATION IN UNALTERED CONDITION. ORIGINALLY PUBLISHED 1898. - Rock Island Arsenal, Building No. 280, Sylvan Drive, Rock Island, Rock Island County, IL
4. Photograph of a photograph in possession of Rock Island Arsenal Historical Office. NORTH ELEVATION IN UNALTERED CONDITION. DATED NOVEMBER 21, 1944. - Rock Island Arsenal, Building No. 109, Rodman Avenue & Fourth Street, Rock Island, Rock Island County, IL
4. Photograph of a photograph in possession of Rock Island Arsenal Historical Office. LOOKING NORTH AFTER ADDITION OF CONICAL ROOF. ORIGINALLY PUBLISHED 1887. - Rock Island Arsenal, Building No. 53, North Avenue North of Midpoint, Rock Island, Rock Island County, IL
10. Photograph of a photograph in possession of Rock Island Arsenal Historical Office. SOUTH AND WEST ELEVATIONS IN UNALTERED CONDITION. DATED APRIL 18, 1941. - Rock Island Arsenal, Building No. 56, North Avenue & East Avenue, Rock Island, Rock Island County, IL
4. Photograph of a photograph in possession of Rock Island Arsenal Historical Office. NORTH AND WEST ELEVATIONS. DATED NOVEMBER 21, 1944. - Rock Island Arsenal, Building No. 108, Rodman Avenue between Third & Fourth Streets, Rock Island, Rock Island County, IL
3. Photograph of a photograph in possession of Rock Island Arsenal Historical Office. NORTH ELEVATION IN UNALTERED CONDITION. DATED NOVEMBER 21, 1944. - Rock Island Arsenal, Building No. 103, Rodman Avenue & First Street, Rock Island, Rock Island County, IL
3. Photograph of a photograph in possession of Rock Island Arsenal Historical Office. SOUTH ELEVATION IN UNALTERED CONDITION. DATED MARCH 19, 1945. - Rock Island Arsenal, Building No. 61, Rodman Avenue & First Street, Rock Island, Rock Island County, IL
A small ice cap (covering about 12 square kilometers) and at least two--probably four--cirque glaciers (each covering less than 1 square kilometer) occurred on St. George Island, Pribilof Islands, probably during the Illinoian Glaciation. Snowbanks persis...
D. M. Hopkins T. Einarsson
The Comprehensive Conservation and Management Plan for Long Island Sound characterizes the priority problems affecting the Sound and identifies specific commitments and recommendations developed by the Long Island Sound Study (LISS) Management Conference. The CCMP provides a hist...
The Hawaiian Islands are classified as a distinct floristic region by phytogeographers because oftheir unique flora (Takhtajan 1986). Plants ancestral to Hawaii arrived by long distance dispersal, colonizing the islands at a rate of about one species per ...
Most of it functions DNA methylation realizes as an integral part of the mechanism of remodeling and modification of chromatin structure. At the same time the global pattern of this complex reaction's net is still to be determined and we are just approaching to studying the mechanisms controlling epigenetic processes of histone modification and DNA methylation. Though cytosine methylation occurs predominantly at CpG sequences of eukaryotic genome, it also takes place at symmetric CpHpG and non-symmetric CpHpH sites (where H-A, T, or C). Various modification efficiency for these three site-specific DNA methylation types is observed depending on their genome localization. Different regions in eukaryotic genome are remarkable for their methylation features: CpG-islands, CpG-islands shores, differentially methylated regions of imprinted genes, and regions of non-alternative site-specific modification. Dependence of three canonical types (CpG, CpHpG, and CpHpH) of DNA methylation efficiency on their surrounding nucleotide context is noted. Existence of epigenetic code of DNA methylation, in which these context differences play specific functional role, has been supposed. The present review summarizes main up-to-date data on structural-functional features of site-specific cytosine methylation in eukaryotic genomes. Pathogenesis-related alterations of eukaryotic genome methylation pattern are considered as well. PMID:20586180
Diachenko, O V; Shevchuk, T V; Bur'ianov, Ia I
Dr. Brenner discusses the techniques of cloning and sequencing DNA which enables large-scale analysis of complex genomes. The opportunities and challenges of the human genome project are reviewed. Primary audience: health professionals and researchers.
By the end of 2002, we witnessed the landmark submission of the 100th complete genome sequence in the databases. An overview of these genomes reveals certain interesting trends and provides valuable insights into possible future developments. PMID:12734008
Janssen, Paul; Audit, Benjamin; Cases, Ildefonso; Darzentas, Nikos; Goldovsky, Leon; Kunin, Victor; Lopez-Bigas, Nuria; Peregrin-Alvarez, José Manuel; Pereira-Leal, José B; Tsoka, Sophia; Ouzounis, Christos A
(Released 10 June 2002) The Science Although liquid water is not stable on the surface of Mars today, there is substantial geologic evidence that large quantities of water once flowed across the surface in the distant past. Streamlined islands, shown here, are one piece of evidence for this ancient water. The tremendous force of moving water, possibly from a catastrophic flood, carved these teardrop-shaped islands within a much larger channel called Ares Valles. The orientation of the islands can be used as an indicator of the direction the water flowed. The islands have a blunt end that is usually associated with an obstacle, commonly an impact crater. The crater is resistant to erosion and creates a geologic barrier around which the water must flow. As the water flows past the obstacle, its erosive power is directed outward, leaving the area in the lee of the obstacle relatively uneroded. However, some scientists have also argued that the area in the lee of the obstacle might be a depositional zone, where material is dropped out of the water as it briefly slows. The ridges observed on the high-standing terrain in the leeward parts of the islands may be benches carved into the rock that mark the height of the water at various times during the flood, or they might be indicative of layering in the leeward rock. As the water makes its way downstream, the interference of the water flow by the obstacle is reduced, and the water that was diverted around the obstacle rejoins itself at the narrow end of the island. Therefore, the direction of the water flow is parallel to the orientation of the island, and the narrow end of the island points downstream. In addition to the streamlined islands, the channel floor exhibits fluting that is also suggestive of flowing water. The flutes (also known as longitudinal grooves) are also parallel to the direction of flow, indicating that the water flow was turbulent and probably quite fast, which is consistent with the hypothesized catastrophic floods that came through Ares Valles. The Story In symbolism only, these guppy-shaped islands and current-like flutes of land beside them may conjure up a mental image of a flowing Martian river. This picture would only be half-right. Scientifically, no fish ever swam this channel, but these landforms do reveal that catastrophic floods of rushing water probably patterned the land in just this way. Geologists who study flood areas believe that a tremendous force of moving water probably carved both the islands and the small, parallel, 'current-like' ridges around them. The blunt end of the islands (the 'heads' of the 'fish') are probably ancient impact craters that posed obstacles to the water as it rushed down the channel in torrents. Because a crater is resistant to erosion, it creates a geologic barrier around which the water must flow. As the water makes its way downstream, the crater's interference with the water flow is reduced, so the water that was diverted around the obstacle rejoins at the narrow end of the island (the 'tail' of the 'fish'). Therefore, from this information, you can tell that the water flowed from the southeast to the northwest. As a rule of thumb for the future, you can say that the narrow end of the island points downstream. The result may be the island behind the crater, but geologists disagree about the exact process by which the island forms. Some scientists argue that the erosive power of the water is directed outward, leaving the area behind, or in the lee of, the obstacle relatively untouched. Other scientists argue that the water slows when it encounters the crater obstacle, and small particles of sand and 'dirt' drop out of the water and are deposited in the lee. There's another small associated uncertainty too. Look closely at the edges of the islands and notice how the land is terraced. These ledges might mark the height of the water at various times during the flood . . . or they might be an indication that layering occurred. It all depends on your hypothesis. Like the stream
We describe here a comparative genome analysis of three dairy product isolates of Lactobacillus rhamnosus GG (LGG) and the ATCC 53103 reference strain to the published genome sequence of L. rhamnosus GG. The analysis showed that in two of three isolates, major DNA segments were missing from the genomic islands LGGISL1,2. The deleted DNA segments consist of 34 genes in one isolate and 84 genes in the other and are flanked by identical insertion elements. Among the missing genes are the spaCBA genes, which encode pilin subunits involved in adhesion to mucus and persistence of the strains in the human intestinal tract. Subsequent quantitative PCR analyses of six commercial probiotic products confirmed that two more products contain a heterogeneous population of L. rhamnosus GG variants, including genotypes with or without spaC. These results underline the relevance for quality assurance and control measures targeting genome stability in probiotic strains and justify research assessing the effect of genetic rearrangements in probiotics on the outcome of in vitro and in vivo efficacy studies. PMID:23354703
Sybesma, Wilbert; Molenaar, Douwe; van IJcken, Wilfred; Venema, Koen; Kort, Remco
We describe here a comparative genome analysis of three dairy product isolates of Lactobacillus rhamnosus GG (LGG) and the ATCC 53103 reference strain to the published genome sequence of L. rhamnosus GG. The analysis showed that in two of three isolates, major DNA segments were missing from the genomic islands LGGISL1,2. The deleted DNA segments consist of 34 genes in one isolate and 84 genes in the other and are flanked by identical insertion elements. Among the missing genes are the spaCBA genes, which encode pilin subunits involved in adhesion to mucus and persistence of the strains in the human intestinal tract. Subsequent quantitative PCR analyses of six commercial probiotic products confirmed that two more products contain a heterogeneous population of L. rhamnosus GG variants, including genotypes with or without spaC. These results underline the relevance for quality assurance and control measures targeting genome stability in probiotic strains and justify research assessing the effect of genetic rearrangements in probiotics on the outcome of in vitro and in vivo efficacy studies.
Molenaar, Douwe; van IJcken, Wilfred; Venema, Koen
Most known virulence determinants of Pseudomonas aeruginosa are remarkably conserved in this bacterium's core genome, yet individual strains differ significantly in virulence. One explanation for this discrepancy is that pathogenicity islands, regions of DNA found in some strains but not in others, contribute to the overall virulence of P. aeruginosa. Here we employed a strategy in which the virulence of
Scott E. Battle; Folker Meyer; Jordi Rello; Vanderlene L. Kung; Alan R. Hauser
Dalma Island can be broadly defined as an emergent salt diapir formed through the halokinetic emplacement of the Precambrian-Cambrian Hormuz Complex. The outline of the island, as seen today, has been much modified by anthropogenic dredge-and-fill activities. The lithofacies of Dalma Island can be subdivided into three distinct geological and geographical provinces. The core of the island is dominated by
...2013-07-01 2013-07-01 false Morris Island, SC to Hilton Head Island, SC. 80.712 Section 80.712 Navigation...DEMARCATION LINES Seventh District Â§ 80.712 Morris Island, SC to Hilton Head Island, SC. (a) A...
... 2013-07-01 2013-07-01 false Tybee Island, GA to St. Simons Island, GA. 80.717 Section 80.717 Navigation...DEMARCATION LINES Seventh District Â§ 80.717 Tybee Island, GA to St. Simons Island, GA. (a) A...
...2013-07-01 2013-07-01 false St. Simons Island, GA to Amelia Island, FL. 80.720 Section 80.720 Navigation...LINES Seventh District Â§ 80.720 St. Simons Island, GA to Amelia Island, FL. (a) A line...
... 2013-10-01 2013-10-01 false Caribbean Island/Island Group Management Areas E Appendix E to Part 622...622, App. E Appendix E to Part 622âCaribbean Island/Island Group Management Areas Table 1 of...
...2013-10-01 2013-10-01 false St. Simons Island, GA to Little Talbot Island, FL. 7.85 Section 7.85 Shipping ...LINES Atlantic Coast Â§ 7.85 St. Simons Island, GA to Little Talbot Island, FL. (a) A line...
Deception Island is the largest volcano in the actively extending Bransfield Basin, a marginal basin situated behind the extinct South Shetland Islands arc. Deception Island has been well studied but its submerged flanks have not. A multibeam bathymetry survey was conducted around the island in 2005. Data from the flooded caldera show no evidence for recent localized resurgence. The gently-sloped
A. H. Barclay; W. S. D. Wilcock; J. M. Ibáñez
The use of novel technologies, the need to integrate different data types and the immense quantity of data generated by The Cancer Genome Atlas (TCGA) Research Network has led to an expansion of the TCGA Research Network to include new centers devoted to data analysis. The Genome Data Analysis Centers (GDACs) work hand-in-hand with the Genome Characterization Centers (GCCs) to develop state-of-the-art tools that assist researchers with processing and integrating data analyses across the entire genome.
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.
Three independent databases of eukaryotic genome size information have been launched or re-released in updated form since 2005: the Plant DNA C-values Database (www.kew.org\\/genomesize\\/homepage. html), the Animal Genome Size Database (www. genomesize.com) and the Fungal Genome Size Database (www.zbi.ee\\/fungal-genomesize\\/). In total, these databases provide freely accessible genome size data for >10 000 species of eukaryotes assem- bled from more than
T. Ryan Gregory; James A. Nicol; Heidi Tamm; Bellis Kullman; Kaur Kullman; Ilia J. Leitch; Brian G. Murray; Donald F. Kapraun; Johann Greilhuber; Michael D. Bennett
...Harbor, Portland, Maine (between Little Diamond Island and Great Diamond Island). 110.6 Section 110.6 Navigation and...Harbor, Portland, Maine (between Little Diamond Island and Great Diamond Island). Beginning at...
...2013-07-01 false San Francisco Bay between Treasure Island and Yerba Buena Island; naval restricted area. 334.1070 Section...334.1070 San Francisco Bay between Treasure Island and Yerba Buena Island; naval restricted...
... Pacific Ocean off Orote Point, Apra Harbor, Island of Guam, Marianas Islands; small arms firing range. 334.1420 Section... Pacific Ocean off Orote Point, Apra Harbor, Island of Guam, Marianas Islands; small arms firing...
Genomics is a highly cross-disciplinary field that creates paradigm shifts in such diverse areas as medicine and agriculture. It is believed that many significant scientific and technological endeavors in the 21st century will be related to the processing and interpretation of the vast information that is currently revealed from sequencing the genomes of many living organisms, including humans. Genomic information
Whole genome shotgun assembly is the process of taking many short sequenced segments (reads) and reconstructing the genome from which they originated. We demonstrate how the technique of bidirected network flow can be used to explicitly model the double-stranded nature of DNA for genome assembly. By combining an algorithm for the Chinese Postman Problem on bidirected graphs with the construction
Paul Medvedev; Michael Brudno
Diseases of the vascular system result from a complex mixture of genetic and environmental factors. Data sets, technologies and strategies emanating from the human genome programme have been applied to the analysis of both rare single-gene and common multigenic vascular disorders. Genomic approaches including inter- and intraspecies sequence comparisons, genotyping with dense marker sets spanning the genome, large-scale mutagenesis screens
Alan Tall; Edward M. Rubin
Block Island, an area of 11 square miles lies 15 miles off the Rhode Island Coast. Biennially since 1965, the Storm Trysail Club of New York has sponsored a week of yacht races at Block Island. The event, which takes place in the third week of June, comes...
J. F. Farrell
Water resources in small islands, such as atoll islands, are limited and threatened by climate change such as changes in precipitation and sea level rise. Groundwater is the main water resources in many atoll islands, and the freshwater in aquifers in coral atolls, where the average elevations are a few meters above the sea level, exists as lenses f1oating on
M. Taniguchi; S. Nakada; Y. Umezawa; H. Yamano
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...
...2013-07-01 2013-07-01 false Virgin Islands. 81.432 Section 81.432...Visibility Is an Important Value Â§ 81.432 Virgin Islands. Area name Acreage Public Law establishing Federal land manager Virgin Islands NP 12,295 84-925...
The purpose of this article is to discuss islanding operation and to provide end-users with items to consider when determining distributed generation plant and equipment design requirements. Islanding is operating an electric generating plant without an external voltage and frequency reference. Operating in parallel is the opposite of islanding. This article attempts to describe the valid concerns that grid operators
P. L. Villenueve
By using Landsat-7-ETM+ data and USGS DEM Elevation data, we are able to take a virtual tour of the Channel Islands and the coast of California. For more information on the Channel Islands, please visit (http:--www.channel.islands.national-park.com).
Snodgrass, Stuart; Williams, Darrel
...2013-10-01 2013-10-01 false Rhode Island. 32.59 Section 32.59 Wildlife...Hunting and Fishing Â§ 32.59 Rhode Island. The following refuge units have...refuge-specific regulations. Block Island National Wildlife Refuge A....
Christmas Island, or 'Kiritimati', is the world's largest coral atoll. It is located in the Line Island group, some 3240 km (2015 miles) from Tarawa, Kiribati's main island. About 4810 people (2002 fig- ures) live scattered around the atoll, mainly in four villages on the eastern side. The atoll covers 575 square km (222 square miles), but land resources are
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
The influence of the 'heat island' in the atmospheric transmittance and in the contrast of thermal images was studied. The transmittance and contrast were calculated for a real atmospheric and for an atmosphere with a simulated heat island. As a result of these calculation, it was possible to verify that the influence of the heat island in the transmittance and
M. A. Lombardo; A. E. C. Pereira; G. C. Neto; L. A. V. Dias
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
To a botanist or zoologist the birth of a new island from beneath the sea is an event of considerable interest. A number of questions occur to him and he will almost inevitably speculate as to the first forms of life to colonise it, and the date of their appearance. In Dr. W. Docters van Leeuwen's interesting letter, published in
W. S. Bristowe
Shortly after the March 28, 1979, accident at the Three Mile Island (TMI) nuclear plant outside Harrisburg, Pa., the Pennsylvania Department of Health, in conjunction with the Centers for Disease Control and the U.S. Bureau of the Census, conducted a census of the 35,930 persons residing within 5 miles of the plant. With the help of 150 enumerators, demographic and
M. K. Goldhaber; G. K. Tokuhata; E. Digon; G. G. Caldwell; G. F. Stein; G. Lutz; D. Gur
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
The purpose of this investigation was to determine the endemic areas for malayan filariasis in the island of Mindanao by means of spot or selective surveys. Night blood smears were taken from individuals whose dwellings are located close to fresh water sw...
B. D. Cabrera
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...
Describes a space education program in rural Manitoulin Island, Ontario. Reports that gifted and talented students examined space exploration, built models, met with astronauts, and designed multimedia presentations. Explains that the students also hosted a one-day conference on space for students, teachers, and parents and later visited…
The use of teledermatology as an adjunct to conventional clinical dermatology on the Faroe Islands is described. The service is based on a nurse-led dermatological clinic, and teledermatology is combined with specialist visits for more complex diagnosis or procedures. PMID:18937650
Jemec, Gregor B E; Heidenheim, Michael; Dam, Tomas N; Vang, Edith
Describes science curriculum facilitated through hands-on marine science activities correlated with the California Science Framework. Curriculum focuses on major ocean concepts and Catalina Island. Program involves overnight field trip to Wrigley Institute. Teacher training component is in development. Two student activities focusing on garibaldi and kelp are available on the site.
Since the March 1979 accident at the Three Mile Island (TMI) nuclear power plant, many studies have assessed its impacts. Compiled and summarized in this book are the results of five related surveys, all aimed at the scientific assessment of the psycho-socio-economic behavior of the residents around the TMI facility. These studies are based on a randomly selected, large sample
P. S. Houts; P. D. Cleary; T. W. Hu
Soils of Banks Island, Northwest Territories, Canada, are predominantly well-drained with many high arctic affinities. Because of the dry desert-like appearance of most of the soils, they are designated collectively as polar desert rather than tundra. Man...
J. C. F. Tedrow L. A. Douglas
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
BACKGROUND: Mid-range inhomogeneity or MRI is the significant enrichment of particular nucleotides in genomic sequences extending from 30 up to several thousands of nucleotides. The best-known manifestation of MRI is CpG islands representing CG-rich regions. Recently it was demonstrated that MRI could be observed not only for G+C content but also for all other nucleotide pairings (e.g. A+G and G+T)
Ashwin Prakash; Samuel S Shepard; Jie He; Benjamin Hart; Miao Chen; Surya P Amarachintha; Olga Mileyeva-Biebesheimer; Jason Bechtel; Alexei Fedorov
Background Haemophilus influenzae (Hi) colonizes the human respiratory tract and is an important pathogen associated with chronic obstructive pulmonary disease (COPD). Bacterial factors that interact with the human host may be important in the pathogenesis of COPD. These factors, however, have not been well defined. The overall goal of this study was to identify bacterial genetic elements with increased prevalence among H. influenzae strains isolated from patients with COPD compared to those isolated from the pharynges of healthy individuals. Methodology/Principal Findings Four nontypeable H. influenzae (NTHi) strains, two isolated from the airways of patients with COPD and two from a healthy individual, were subjected to whole genome sequencing using 454 FLX Titanium technology. COPD strain-specific genetic islands greater than 500 bp in size were identified by in silico subtraction. Open reading frames residing within these islands include known Hi virulence genes such as lic2b, hgbA, iga, hmw1 and hmw2, as well as genes encoding urease and other enzymes involving metabolic pathways. The distributions of seven selected genetic islands were assessed among a panel of 421 NTHi strains of both disease and commensal origins using a Library-on-a-Slide high throughput dot blot DNA hybridization procedure. Four of the seven islands screened, containing genes that encode a methyltransferase, a dehydrogenase, a urease synthesis enzyme, and a set of unknown short ORFs, respectively, were more prevalent in COPD strains than in colonizing strains with prevalence ratios ranging from 1.21 to 2.85 (p?0.0002). Surprisingly, none of these sequences show increased prevalence among NTHi isolated from the airways of patients with cystic fibrosis. Conclusions/Significance Our data suggest that specific bacterial genes, many involved in metabolic functions, are associated with the ability of NTHi strains to survive in the lower airways of patients with COPD.
Zhang, Lixin; Xie, Jingping; Patel, Mayuri; Bakhtyar, Arsala; Ehrlich, Garth D.; Ahmed, Azad; Earl, Josh; Marrs, Carl F.; Clemans, Daniel; Murphy, Timothy F.; Gilsdorf, Janet R.
"This width of the territorial sea of the People?s Republic of China is twelve national miles. This provision applies to all Territories of the People?s Republic of China including the mainland China and offshore islands Taiwan (separated from the mainland and offshore islands by high seas) and its surrounding islands the Pongo Archipelago the Dongsha Islands the Lisha islands the Zhongsha Islands the Nasha Islands and other islands belonging to China."
Did you mean: "This width of the territorial sea of the People?s Republic of China is twelve national miles. This provision applies to all Territories of the People?s Republic of China including the mainland China and offshore islands Taiwan (separated from the mainland and offshore islands by high seas) and its surrounding islands the Pongo Archipelago the Dongsha Islands the Lisha islands the Zhongsha Islands the Nasha Islands and other islands belonging to China." ?
This study collected data on rates of cigarette smoking in the following Pacific Islands: Cook Islands, Fiji, Kiribati, Nauru, New Caledonia, Niue, Tuvalu, and Western Samoa. The data were collected in 1975-81 as part of a diabetes-cardiovascular diseases survey. A large variation in the prevalence of smoking was found in the populations surveyed. 90% of men and 74% of women on Kiribati were daily smokers compared with 38% of men and 19% of women on the Cook Islands and only 4% of the female population of Fiji. There was no association between age and the prevalence of smoking. Smoking tended to be more common in rural areas than urban areas and was higher among men than women in all populations studied. For both men and women, the prevalence of smoking was higher among lower income groups and those who reported moderate or heavy alcohol consumption. There was no clear association between smoking and marital status. Overall, the data on the prevalence of cigarette smoking indicate that this has become a significant public health problem in Pacific island communities. The data further suggest that the prevalence of smoking differs markedly in culturally and ethnically different populations. Somewhat unexpected was the greater proportion of smokers among traditional communities in rural areas compared with urban areas. This finding can be explained in part by the widespread practice of cultivating tobacco in many rural areas of the Pacific. It is recommended that a reliable survey of smoking patterns in the Pacific islands and prospective surveys that correlate the results of such a study with the distribution of cardiovascular diseases and cancer be conducted. PMID:3490322
Tuomilehto, J; Zimmet, P; Taylor, R; Bennet, P; Wolf, E; Kankaanpää, J
Aberrant DNA methylation patterns may be the earliest somatic genome changes in prostate cancer. Using real-time methylation-specific PCR, we assessed the extent of hypermethylation at 16 CpG islands in DNA from seven prostate cancer cell lines (LNCaP, PC-3, DU-145, LAPC-4, CWR22Rv1, VCaP, and C42B), normal prostate epithelial cells, normal prostate stromal cells, 73 primary prostate cancers, 91 metastatic prostate cancers, and 25 noncancerous prostate tissues. We found that CpG islands at GSTP1, APC, RASSF1a, PTGS2, and MDR1 were hypermethylated in >85% of prostate cancers and cancer cell lines but not in normal prostate cells and tissues; CpG islands at EDNRB, ESR1, CDKN2a, and hMLH1 exhibited low to moderate rates of hypermethylation in prostate cancer tissues and cancer cell lines but were entirely unmethylated in normal tissues; and CpG islands at DAPK1, TIMP3, MGMT, CDKN2b, p14/ARF, and CDH1 were not abnormally hypermethylated in prostate cancers. Receiver operator characteristic curve analyses suggested that CpG island hypermethylation changes at GSTP1, APC, RASSF1a, PTGS2, and MDR1 in various combinations can distinguish primary prostate cancer from benign prostate tissues with sensitivities of 97.3-100% and specificities of 92-100%. Hypermethylation of the CpG island at EDNRB was correlated with the grade and stage of the primary prostate cancers. PTGS2 CpG island hypermethylation portended an increased risk of recurrence. Furthermore, CpG island hypermethylation patterns in prostate cancer metastases were very similar to the primary prostate cancers and tended to show greater differences between cases than between anatomical sites of metastasis. PMID:15026333
Yegnasubramanian, Srinivasan; Kowalski, Jeanne; Gonzalgo, Mark L; Zahurak, Marianna; Piantadosi, Steven; Walsh, Patrick C; Bova, G Steven; De Marzo, Angelo M; Isaacs, William B; Nelson, William G
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
Razafindratsimandresy, Richter; Joffret, Marie-Line; Delpeyroux, Francis; Heraud, Jean-Michel
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.
Joffret, Marie-Line; Delpeyroux, Francis; Heraud, Jean-Michel
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
The main statistical distributions applicable to the analysis of genome architecture and genome tracks are briefly discussed and critically assessed. Although the observed features in distributions of element lengths can be equally well fitted by the different statistical approximations, the interpretation of observed regularities may strongly depend on the chosen scheme. We discuss the possible evolution scenarios and describe the main characteristics obtained with different distributions. The expression for the assessment of levels in hierarchical chromatin folding is derived and the quantitative measure of genome architecture inhomogeneity is suggested. This theory provides the ground for the regular statistical study of genome architecture and genome tracks.
Chechetkin, V. R.
The virulence determinants of uropathogenic Escherichia coli have been studied extensively over the years, but relatively little is known about what differentiates isolates causing various types of urinary tract infections. In this study, we compared the genomic profiles of 45 strains from a range of different clinical backgrounds, i.e., urosepsis, pyelonephritis, cystitis, and asymptomatic bacteriuria (ABU), using comparative genomic hybridization analysis. A microarray based on 31 complete E. coli sequences was used. It emerged that there is little correlation between the genotypes of the strains and their disease categories but strong correlation between the genotype