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Aims:The aim of this study was to develop and demonstrate an approach for describing the diversity of human pathogenic viruses in an environmentally isolated viral metagenome.Methods and Results:In silico bioinformatic experiments...
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Aims:The aim of this study was to develop and demonstrate an approach for describing the diversity of human pathogenic viruses in an environmentally isolated viral metagenome.Methods and Results:In silico bioinformatic experiments were used to select an optimum annotation strategy for discovering human viruses in virome data sets and applied to annotate a class B biosolid virome. Results from the in silico study indicated that < 1% errors in virus identification could be achieved when nucleotide-based search programs (BLASTn or tBLASTx), viral genome only databases and sequence reads > 200 nt were considered. Within the 51 925 annotated sequences, 94 DNA and 19 RNA sequences were identified as human viruses. Virus diversity included environmentally transmitted agents such as parechovirus, coronavirus, adenovirus and aichi virus, as well as viruses associated with chronic human infections such as human herpes and hepatitis C viruses.Conclusions:This study provided a bioinformatic approach for identifying pathogens in a virome data set and demonstrated the human virus diversity in a relevant environmental sample.Significance and Impact of the Study:As the costs of next-generation sequencing decrease, the pathogen diversity described by virus metagenomes will provide an unbiased guide for subsequent cell culture and quantitative pathogen analyses and ensures that highly enriched and relevant pathogens are not neglected in exposure and risk assessments.
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Arsenate is a common toxic metalloid found in drinking water worldwide that causes several human diseases. The biochemical action underlying cellular response to arsenate, however, is not yet completely understood. Here we used Sa...
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Arsenate is a common toxic metalloid found in drinking water worldwide that causes several human diseases. The biochemical action underlying cellular response to arsenate, however, is not yet completely understood. Here we used Saccharomyces cerevisiae as an eukaryotic model system to identify proteins essential for adaptation to arsenate treatment. Previous studies have demonstrated a function for Hog1 MAPK in modulating the cellular response to arsenite. Our results, however, showed that cells deficient in Hog1 did not show increased sensitivity to arsenate, suggesting that perhaps other MAPKs may be involved in the response to this particular arsenic species. Here, we found that Slt2 MAPK and several of its upstream regulators are essential in modulating the response to arsenate, and that Slt2 is phosphorylated after arsenate treatment. Furthermore, whole-genome transcriptional analysis showed that Slt2 is required for the induction of several genes in response to arsenate exposure. Many of these genes are involved in the cellular response to heat, suggesting an overlap between these two stress response pathways, and pointing toward a common response to both arsenate and heat exposure in Saccharomyces cerevisiae. Furthermore, our results support the idea that cellular exposure to arsenate results in induction of cellular signalling pathways different from those induced under arsenite treatment.
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The 454 Sequencer has dramatically increased the volume of sequencing conducted by the scientific community and expanded the range of problems that can be addressed by the direct readouts of DNA sequence. Key breakthroughs in the ...
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The 454 Sequencer has dramatically increased the volume of sequencing conducted by the scientific community and expanded the range of problems that can be addressed by the direct readouts of DNA sequence. Key breakthroughs in the development of the 454 sequencing platform included higher throughput, simplified all in vitro sample preparation and the miniaturization of sequencing chemistries, enabling massively parallel sequencing reactions to be carried out at a scale and cost not previously possible. Together with other recently released next-generation technologies, the 454 platform has started to democratize sequencing, providing individual laboratories with access to capacities that rival those previously found only at a handful of large sequencing centers. Over the past 18 months, 454 sequencing has led to a better understanding of the structure of the human genome, allowed the first non-Sanger sequence of an individual human and opened up new approaches to identify small RNAs. To make next-generation technologies more widely accessible, they must become easier to use and less costly. In the longer term, the principles established by 454 sequencing might reduce cost further, potentially enabling personalized genomics.
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Sideroxylon majus (Sapotaceae) is an endangered endemic tree of La R,union Island that has suffered from human actions. It is present in small and isolated populations that encounter severe difficulties to regenerate. To have powe...
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Sideroxylon majus (Sapotaceae) is an endangered endemic tree of La R,union Island that has suffered from human actions. It is present in small and isolated populations that encounter severe difficulties to regenerate. To have powerful tools for population genetic studies, we have isolated and characterized 14 polymorphic microsatellite markers from S. majus. The 14 loci were tested on 57 individuals from 6 populations. The number of alleles per locus varied from 2 to 20, with an average of 11.8. The observed and expected heterozygosity levels ranged from 0.053 to 1.000, and 0.116 to 0.917, respectively. Six of the 14 loci deviated from Hardy-Weinberg equilibrium. These polymorphic microsatellite markers constitute new tools to study the genetic diversity and spatial genetic structure of S. majus. The cross-species amplifications indicate that most of these loci can be used to investigate population genetic structure in S. grandiflorum, S. boutonianum and S. sessiliflorum. These studies will provide useful results for the elaboration of effective conservation strategies.
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Next-generation RNA-sequencing (RNA-Seq) is rapidly outcompeting microarrays as the technology of choice for whole-transcriptome studies. However, the bioinformatics skills required for RNA-Seq data analysis often pose a significa...
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Next-generation RNA-sequencing (RNA-Seq) is rapidly outcompeting microarrays as the technology of choice for whole-transcriptome studies. However, the bioinformatics skills required for RNA-Seq data analysis often pose a significant hurdle for many biologists. Here, we put forward the concepts and considerations that are critical for RNA-Seq data analysis and provide a generic tutorial with example data that outlines the whole pipeline from next-generation sequencing output to quantification of differential gene expression.
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Premise of the study: We developed microsatellite markers to investigate genetic diversity within and among populations of Capsella rubella and Capsella bursa-pastoris and between these two species.Methods and Results: Fourteen po...
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Premise of the study: We developed microsatellite markers to investigate genetic diversity within and among populations of Capsella rubella and Capsella bursa-pastoris and between these two species.Methods and Results: Fourteen polymorphic microsatellite loci were identified in the two species and one more polymorphic microsatellite locus only in C. rubella. Samples from different European localities were genotyped. Up to six alleles per locus were observed in C. rubella, and up to 22 alleles per locus in C. bursa-pastoris. Observed heterozygosities were low, indicating high selfing rates, especially in C. rubella.Conclusions: The results provide valuable information on genetic diversity for future studies of population genetics in C. rubella and C. bursa-pastoris.
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We developed and characterized nine microsatellite markers for Livistona rigida, a species endemic to northern Australia, and confirmed the transferability of these markers for five other Australian Livistona species. The number o...
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We developed and characterized nine microsatellite markers for Livistona rigida, a species endemic to northern Australia, and confirmed the transferability of these markers for five other Australian Livistona species. The number of alleles per locus ranged from 1 to 6 with an average of 2.1, and the expected heterozygosity ranged from 0.00 to 0.73 with averages of 0.23. Most of the loci were successfully amplified and showed moderate to high polymorphism for five other Livistona species sampled. The microsatellite markers described here will be useful for investigating the speciation and range formation processes of the recent radiation of the Livistona genus in Australia, and the results obtained from them will provide crucial information for conservation of Australian Livistona species.
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Caenorhabditis elegans is a premier model organism upon which considerable knowledge of basic cell and developmental biology has been built. Yet, as is true for many traditional model systems, we have limited knowledge of the ecol...
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Caenorhabditis elegans is a premier model organism upon which considerable knowledge of basic cell and developmental biology has been built. Yet, as is true for many traditional model systems, we have limited knowledge of the ecological context in which these systems evolved, severely limiting our understanding of gene function. A better grasp of the ecology of model systems would help us immensely in understanding the functionality of genes and evolution of genomes in an environmental context. Consequently, there are ongoing efforts to uncover natural populations of this model system globally. Here, we describe the discovery of a Caenorhabditis briggsae strain and its bacterial associate (Serratia sp.) that form an entomopathogenic complex in the wild. Laboratory experiments confirm that this nematode and its natural bacterial associate can penetrate, kill and reproduce in an insect host and that the bacterial associate can induce this insect pathogenic life cycle in other Caenorhabditis species, including C. elegans. Our findings suggest that this life history may be widespread in nature and critical to the understanding of the biology of this important model organism. Caenorhabditis-insect interaction could be a key factor in our quest for a better grasp of gene functionality in this important model species. The discovered association, consequently, would provide an ecological framework for functional genomics of Caenorhabditis.
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The increasing speed and decreasing cost of generating DNA sequence data has transformed experimental approaches in many fields of biology. In this review we describe some of the new technologies commercially available and in deve...
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The increasing speed and decreasing cost of generating DNA sequence data has transformed experimental approaches in many fields of biology. In this review we describe some of the new technologies commercially available and in development, and discuss how plant taxonomy could benefit from the possible data generated. These benefits include better resolved phylogenies, potential for dealing with the difficulties posed by polyploidy and hybridisation, and new options for studying species boundaries and species relationships in recent radiations.
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The complexity of gene expression data generated from microarrays and high-throughput sequencing make their analysis challenging. One goal of these analyses is to define sets of co-regulated genes and identify patterns of gene exp...
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The complexity of gene expression data generated from microarrays and high-throughput sequencing make their analysis challenging. One goal of these analyses is to define sets of co-regulated genes and identify patterns of gene expression. To date, however, there is a lack of easily implemented methods that allow an investigator to visualize and interact with the data in an intuitive and flexible manner. Here, we show that combining a nonlinear dimensionality reduction method, t-statistic Stochastic Neighbor Embedding (t-SNE), with a novel visualization technique provides a graphical mapping that allows the intuitive investigation of transcriptome data. This approach performs better than commonly used methods, offering insight into underlying patterns of gene expression at both global and local scales and identifying clusters of similarly expressed genes. A freely available MATLAB-implemented graphical user interface to perform t-SNE and nearest neighbour plots on genomic data sets is available at www.nimr.mrc.ac.uk/research/james-briscoe/visgenex.
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