[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

Enteric microbiome composition and structure varies widely between individuals, and has been associated with multiple health conditions and differences in productivity in farm animals. Enteric microbial communities are clearly influenced by environmental factors and food, but host genotype may also have an impact. This study is part of an effort to comprehensively profile interactions between chicken genetic variation and the composition of the gut microbial ecosystem on a genome-wide scale. We collected blood and caecal lumen contents from 150 indigenous Indian Kadaknath chickens and 150 commercial-type Cobb400 broilers, raised in groups together under the same farm conditions. All chickens were genotyped with the 600K Affymetrix HD SNP array and the caecal lumen microbiome was defined using Illumina 16s rDNA amplicon sequencing. Single marker regression genomewide association analysis was conducted. Using this dataset, we identified significant associations at genome-wide level (P<0.05 Bonferroni corrected) between host genetic variation and gut microbiome composition.

/pdf/identification-of-snp-markers-associated-with-gut-microbiome-3q9wr19jez.pdf

Identification of SNP markers associated with gut microbiome composition in chicken

Periodontitis is a multi-factorial disease which has affected mankind since the dawn of an era. Prevalence of periodontal disease has considerably increased over a period of time. Periodontal research has progressed tremendously worldwide. In India in spite of increased periodontal research, many problems are faced by the clinicians. It leads to improper recording of the results and resultant failure to spread the knowledge that would help in understanding the subject better. This is a major setback in the current era of evidenced based clinical practice. Hence in this review, an attempt is made to discuss and emphasize these unsolved issues pertaining to epidemiology, disease activity and therapy.

/pdf/issues-in-periodontal-research-in-india-1pbxihzucq.pdf

Issues in Periodontal Research in India

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. aureus.

IDENTIFICATION OF PUTATIVE DRUG TARGETS IN MASTITIS CAUSING STAPHYLOCOCCUS AUREUS BY IN SILICO APPROACH Original Article

Horn cancer is most prevalent in Bos indicus and poorly defined genetic landscape makes disease diagnosis and treatment difficult. In this study, RNA-Seq and data analysis using CLC Genomics Workbench was employed to identify biomarkers associated with horn cancer. As a result, a total of 149 genes were found significant differentially expressed in horn cancer samples compared to horn normal samples. The study revealed ‘keratins’ and ‘interleukins’ as apex groups of significant differentially expressed genes (DEGs). Functional analysis showed that the upregulated keratins support metastasis of tumor via cell proliferation, migration, and affecting cell stability, while downregulated interleukins along with other associated chemokine receptors deprive the immune response to tumor posing clear path for metastasis of horn cancer. Combi-action of both the group facilitates the tumor microenvironment to reproduce tumorigenesis. Analysis of pathways enriched in DEGs and exemplified protein–protein interaction network indicated actual role of DEGs in horn cancer at a fine level. Important effect of deregulated expression of keratin and interleukin genes in horn cancer enrolling their candidacy as potential biomarkers for horn cancer prognosis. This study appraises the possibility to mitigate horn cancer at fine resolution to extract attainable identification of prognostic molecular portraits.

Expression profiling revealed keratins and interleukins as potential biomarkers in squamous cell carcinoma of horn in Indian bullocks (Bos indicus)

Recently tuberculosis has assumed primacy as a global health emergency due to upsurge of AIDS demographic explosion environmental pollution poverty and poor housing. Clinically Mycobacterium bovis possesses a very high degree of virulence in cattle as well as in human beings compared to Mycobacterium tuberculosis. Detection of the early infection is often very difficult with conventional method of diagnosis. Feasibility of using PCR technique for the detection of Mycobacterium tuberculosis is investigated in the present study. (authors)

Chaitanya G. Joshi

Papers

Identification of SNP markers associated with gut microbiome composition in chicken

Issues in Periodontal Research in India

IDENTIFICATION OF PUTATIVE DRUG TARGETS IN MASTITIS CAUSING STAPHYLOCOCCUS AUREUS BY IN SILICO APPROACH Original Article

Expression profiling revealed keratins and interleukins as potential biomarkers in squamous cell carcinoma of horn in Indian bullocks (Bos indicus)

PCR based detection of tuberculosis from blood using oligo primers in cattle.