[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

Firfty serum and fifty semen samples collected from cattle and buffalo bulls were subjected to ELISA and gB gene based PCR, respectively to detect antibodies in serum and viral DNA in the semen against BHV 1. Out of 50 bulls, 15 (30%) serum samples were detected positive by ELISA while 21 (42%) semen samples were positive by gB gene based PCR. While correlating the results of ELISA and PCR, some seronegative bulls revealed presence of viral genome in semen whereas few seropositive bulls could not reveal viral genome in semen, thus, suggesting application of combined serological assay and PCR assay to detect the presence of BHV-1 infection in bulls.

Detection of Bovine Herpesvirus 1 Infection in Breeding Bulls by ELISA and PCR Assay.

Emergence of a genotype I variant of avian infectious bronchitis virus from Northern part of India.

The aim of this study was to develop a simple method for simultaneous identification of multiple meat species. During this study, six raw meat samples from each species including cattle, buffalo, sheep, goat, pig and poultry in fresh and cooked state were subjected for DNA extraction. The amplification of extracted DNA was done through conventional polymerase chain reaction with actin gene primers. The results of conventional polymerase chain reaction with actin gene primers revealed a clear cut differentiation of pig and poultry with that of bovine, ovine and caprine meat. However, it could not differentiate the meat of sheep from that of goat and meat of cattle from that of buffalo.

Detection of meat species by polymerase chain reaction of actin gene family.

Bacterial line of defense in Dirinaria lichen from two different ecosystems: First genomic insights of its mycobiont Dirinaria sp. GBRC AP01.

/pdf/metagenomic-analysis-of-bacterial-communities-during-estrous-2s4r5pwjx4.pdf

Chaitanya G. Joshi

Papers

Detection of Bovine Herpesvirus 1 Infection in Breeding Bulls by ELISA and PCR Assay.

Emergence of a genotype I variant of avian infectious bronchitis virus from Northern part of India.

Detection of meat species by polymerase chain reaction of actin gene family.

Bacterial line of defense in Dirinaria lichen from two different ecosystems: First genomic insights of its mycobiont Dirinaria sp. GBRC AP01.

Metagenomic Analysis of Bacterial Communities During Estrous Cycle in Bos Indicus