[신간의 별자리x] 우리/미술, 그리고 ‘슬픔의 박물관’

The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.

SPAdes, a new genome assembly algorithm and its applications to single-cell sequencing ( 7th Annual SFAF Meeting, 2012)

Prospective Cohort Study

KEGG(Kyoto Encyclopedia of Genes and Genomes)〔和文〕 (特集 ゲノム医学の現在と未来--基礎と臨床) -- (データベース)

Most common human traits and diseases have a polygenic pattern of inheritance: DNA sequence variants at many genetic loci influence the phenotype. Genome-wide association (GWA) studies have identified more than 600 variants associated with human traits, but these typically explain small fractions of phenotypic variation, raising questions about the use of further studies. Here, using 183,727 individuals, we show that hundreds of genetic variants, in at least 180 loci, influence adult height, a highly heritable and classic polygenic trait. The large number of loci reveals patterns with important implications for genetic studies of common human diseases and traits. First, the 180 loci are not random, but instead are enriched for genes that are connected in biological pathways (P = 0.016) and that underlie skeletal growth defects (P < 0.001). Second, the likely causal gene is often located near the most strongly associated variant: in 13 of 21 loci containing a known skeletal growth gene, that gene was closest to the associated variant. Third, at least 19 loci have multiple independently associated variants, suggesting that allelic heterogeneity is a frequent feature of polygenic traits, that comprehensive explorations of already-discovered loci should discover additional variants and that an appreciable fraction of associated loci may have been identified. Fourth, associated variants are enriched for likely functional effects on genes, being over-represented among variants that alter amino-acid structure of proteins and expression levels of nearby genes. Our data explain approximately 10% of the phenotypic variation in height, and we estimate that unidentified common variants of similar effect sizes would increase this figure to approximately 16% of phenotypic variation (approximately 20% of heritable variation). Although additional approaches are needed to dissect the genetic architecture of polygenic human traits fully, our findings indicate that GWA studies can identify large numbers of loci that implicate biologically relevant genes and pathways.

Hundreds of variants clustered in genomic loci and biological pathways affect human height

Objective: In the present study an attempt has been made by the use of a computational approach to investigate putative drug targets in Staphylococcus aureus . Methods: In silico comparative analysis of the metabolic pathways between the pathogen and the Bos taurus was carried out. Further detection of bacterial genes that are non homologous to host, but are essential for the survival of the pathogen represents a promising means of identifying novel drug targets. Metabolic pathways were obtained from the metabolic pathway database Kyoto Encyclopedia of Genes and Genomes (KEGG) and were compared to identify unique pathways present only in the pathogen and absent in the host. Results: We have identified total 1930 proteins, which are non homologous to Bos taurus protein sequences and among them 374 enzymes are found to be essential for survival of the S. aureus according to the database of essential genes (DEG) database. Further, 10 proteins were predicted as cytoplasmic and cell wall associated proteins, which could serve as potential drug target candidates. Conclusion: The identified potential drug targets form a platform for further investigation in discovery of novel therapeutic agents against S. aur eus.

Identification of putative drug targets in mastitis causing staphylococcus aureus by in silico approach

Exploring bacteriome diversity of coral Goniopora sp. and Favia favus from the Gulf of Kutch, Gujarat

RNA-sequencing attest increased sperm motility in bovine spermatozoa treated with ethanolic extract of Putranjiva roxburghii

The present chapter describes the microbial diversity of faecal microbiomes of pack ani‐ mals. The sequencing data generated through ion semiconductor sequencing technology were analysed using EBI metagenomics and MG‐RAST server tools. Bacteria were the major domain in all the pack animals. At the phylogenetic level, Firmicutes was the major phylum. Clostridiales was the major order. Ruminococcus flavefaciens was the major species in camel, whereas the top‐most species existing in Equidae family was Streptococcus equinus. Among the 28 major functional categories, protein metabolism functionality was dominant in pack animals. The genes associated with protein processing and modification as well as for protein folding are higher in mules and in camel they are lowest. Central carbohydrate metabolism was the major functional group under carbohydrate metabolism in pack ani‐ mals. Variation in the amino acids and its derivatives was seen in pack animals. Genes asso‐ ciated with proline and 4‐hydroxy prolines were present in Equidae family only. Clustering using ward with Bray‐Curtis distance matrix for the functional categories showed that don‐ key and mule are most closely related and clustered with the horse metagenome.

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Chaitanya G. Joshi

Papers

Identification of putative drug targets in mastitis causing staphylococcus aureus by in silico approach

Exploring bacteriome diversity of coral Goniopora sp. and Favia favus from the Gulf of Kutch, Gujarat

RNA-sequencing attest increased sperm motility in bovine spermatozoa treated with ethanolic extract of Putranjiva roxburghii

Phylogenetic and Functional Diversity of Faecal Microbiome of Pack Animals

Identification of novel exonic variants contributing to hereditary breast and ovarian cancer in West Indian population.