[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

River buffalo (Bubalus bubalis) milk plays an important role in economy and nutritious diet in several developing countries. However, reliable milk-yield genomic markers and their functional insights remain unexposed. Here, we have used a target capture sequencing approach in three economically important buffalo breeds namely: Banni, Jafrabadi and Mehsani, belonging to either high or low milk-yield group. Blood samples were collected from the milk-yield/breed balanced group of 12 buffaloes, and whole exome sequencing was performed using Roche 454 GS-FLX Titanium sequencer. Using an innovative approach namely, MultiCom; we have identified high-quality SNPs specific for high and low-milk yield buffaloes. Almost 70% of the reported genes in QTL regions of milk-yield and milk-fat in cattle were present among the buffalo milk-yield gene candidates. Functional analysis highlighted transcriptional regulation category in the low milk-yield group, and several new pathways in the two groups. Further, the discovered SNP candidates may account for more than half of mammary transcriptome changes in high versus low-milk yielding cattle. Thus, starting from the design of a reliable strategy, we identified reliable genomic markers specific for high and low-milk yield buffalo breeds and addressed possible downstream effects.

Comparative analysis of SNP candidates in disparate milk yielding river buffaloes using targeted sequencing.

Background: The protective effect of the chloroform extract of Cyperus rotundus (CHCR) is attributed to its anti-inflammatory and antioxidant activities. Cytokines, important regulators of inflammation and repair, play a key role in the pathogenesis of inflammatory bowel disease (IBD). Targeting these cytokines can effectively ameliorate the symptoms of IBD. The aim of the present study was to unravel the molecular mechanism through cytokine regulation in rats in experimental IBD. Methods: Sprague Dawley rats were randomly allocated to 5 groups (n=6). Group I served as the normal control. Group II served as the vehicle control and received 50% ethanol intracolonically on day 11 of the study. Group III served as the model control. Group IV and Group V were given standard drug 5-aminosalicylic acid (100 mg/kg) and CHCR (800 mg/kg), respectively, for 18 days once a day orally. Colitis was induced with dinitrobenzene sulfonic acid (180 mg/kg in 50% ethanol) intracolonically in groups III–V on day 11 of the study. On day 18, the rats were euthanized and colon tissues were removed for IL-4, IL-6, IL-12, and IFN-gamma gene expression studies using quantitative RT-PCR. Results: The expression levels of proinflammatory cytokines IL-4, IL-6, IL-12, and IFN-gamma were upregulated in the model control rats. Pretreatment with 5-aminosalicylic acid (100 mg/kg) and CHCR (800 mg/kg) significantly decreased the fold of the expression of the above cytokines. Conclusion: CHCR acts as a molecular brake and downregulates the expression of proinflammatory cytokine genes; this is beneficial for reducing the severity of the experimental IBD. Thus, Cyperus rotundus is a safe, economical, and effective alternative for the treatment of patients with IBD.

https://ijms.sums.ac.ir/article_40393_f358fd4831d9e22f3de483d1fe0defda.pdf

Effect of Cyperus Rotundus on Cytokine Gene Expression in Experimental Inflammatory Bowel Disease.

Revised on: Accepted on: Published on: make comparative studyshowed only one variation (a>G) in exon I of a soviet chinchilla (S11) and one variation (g>A) in exon III of a resequencing; codon Corresponding author: Email: drajais@gmail.com; Tel: +91–2692 261201, 261486; Fax: +91–2692 261201, 261486 [I] INTRODUCTION Rabbits are small mammals in the family Leporidea of the order Lagomorpha found in several parts of the world and used for many purposes mainly meat, fur production etc. Several DNA markers associated with production traits in livestock have been already identified through candidate gene approach [1], which is based on the fact that variability within genes coding for protein products involved in key physiological mechanisms and metabolic pathways directly or indirectly involved in determining an economic trait (e.g. feed efficiency, muscle mass accretion, reproduction efficiency, disease resistance, etc.) and might probably explain a fraction of the genetic variability for the production trait itself [2]. differentiation factor 8), is specifically expressed during embryonic development, expressed at high level in adult skeletal muscle and controls skeletal muscle growth [3]. Molecular analysis of the myostatin gene in different species has showed that it consists of three exons and two introns

/pdf/molecular-cloning-and-characterization-of-rabbit-myostatin-4lcsa1vgdk.pdf

Molecular cloning and characterization of rabbit myostatin gene

Proteases form nematophagous fungi are most important extracellular hydrolytic enzymes paying a centra l role in cuticle degradation. In the present study, prote ase from two nematode-trapping fungi, A. conoides GenBank accession no. JX979095 and D. flagrans JX979096 were studied at biochemical and molecular level. Crude protease of A. conoides showed maximum activity at pH 7 and temperature 50°C while protese of D. flagrans was functioning best at pH 8 and temperature 55°C. 726 and 716 bp serine protease gene fragment from each fungus was amplified and sequences were submitted to GenBank under the accession No. KC769585 and KC862257. Phylogenetic relationships showed homology with serine proteases of other nematode-trapping fungi. Moreover protease activity in culture broth of fungi inoculated with nematodes was increased. Biochemical assay demonstrated 2.14 and 6.4 fold increase in protease activity in induced culture of A. conoides and D. flagrans respectively. Real Time-PCR assay confirmed 4.27 and 23.8 fold increase in serine protease gene activity in A. conoides and D. flagrans respectively. Thus like other nematode trapping fu ngi, serine protease of these two fungi plays important role in virulence against nematodes.

Biochemical and Molecular Characterization of Protease from Arthrobotrys conoides And Duddingtonia flagrans

The present study describes the isolation and pheno-genotypic analysis of anaerobic Clostridium sartagoforme strain AAU1 from buffalo rumen, having major role in cellulose and chitin degradation. The isolate was cultured between 37°C and 42°C (optimum 40°C) temperature with an optimum pH of 7.5 in Hungate's medium supplemented with cellulose. Whole genome sequencing was performed using ion torrent PGM platforms. Local BLAST showed highest phylogenetic relation with C. sartagoforme DSM 1292 strain based on comparison of the 16S rDNA sequences. Comparison of sequences coding for housekeeping genes phosphoglycerate kinase (pgk) and gyrase B (gyrB) confirmed its taxonomic position within Clostridium genus. The fermentation ability analysed biochemically using AN-Biolog plate showed that the strain utilized more than 30 different substrates as metabolite precursors. Pathway analysis based on Rapid Annotation using Subsystem Technology reveals the organism to be highly active in the production of volati...

Correlation between genomic analyses with metatranscriptomic study reveals various functional pathways of Clostridium sartagoforme AAU1, a buffalo rumen isolate

Chaitanya G. Joshi

Papers

Comparative analysis of SNP candidates in disparate milk yielding river buffaloes using targeted sequencing.

Effect of Cyperus Rotundus on Cytokine Gene Expression in Experimental Inflammatory Bowel Disease.

Molecular cloning and characterization of rabbit myostatin gene

Biochemical and Molecular Characterization of Protease from Arthrobotrys conoides And Duddingtonia flagrans

Correlation between genomic analyses with metatranscriptomic study reveals various functional pathways of Clostridium sartagoforme AAU1, a buffalo rumen isolate