[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

Ruminants, cloven-hoofed mammals of the order Artiodactyla, obtain their food by grazing on plant material. The ruminants are distinguished from other mammals as they possess peculiarities for cud chewing, the process which is called rumination; hence ruminants. After the description given by Aristotle about the four compartments of the ruminant stomach, several experiments were performed to test the rate of passage of material through the alimentary tract (Spallanzani, 1776). In 1831, Tiedemann and Gmelin concluded that fermentation occurred in the rumen that leads to production of acetic and butyric acid in rumen contents. Another important product of rumen fermentation, propionic acid, was not identified until Elsden s research (1945) ISSN: 2319-7706 Volume 4 Number 7 (2015) pp. 105-121 http://www.ijcmas.com

https://ijcmas.com/vol-4-7/Nidhi%20R.%20Parmar,%20et%20al.pdf

Advancements in Bovine Rumen Microbial Ecology: A Review

Post surgical adhesion development remains a frequent occurrence and is often unrecognized by surgeons. Peritoneal adhesions are the leading cause of pelvic pain, bowel obstruction and infertility. The prevention of adhesion till date is speculative due to lack of understanding of mechanisms involved in adhesion development. Adhesions are proposed to the disorder of wound healing and imbalance between fibrinogenesis and fibrinolysis. The unprecedented advancement in Molecular Biology has led us to identify molecules involved in both wound healing and adhesion development. The role of these molecules in peritoneal biological functions is not well understood. Hypoxia is proposed to be major contributing factor for the development of adhesions. The major mechanisms behind adhesion development are increased fibrinogenesis, reduced fibrinolysis, increased Extra Cellular Matrix deposition, increased cytokine production, increased angiogenesis and reduced apoptosis. Better understanding of these events will make efficient management of adhesions possible.

/pdf/molecular-basis-of-post-surgical-peritoneal-adhesions-an-fhv6osfl20.pdf

Molecular basis of Post-surgical Peritoneal adhesions - An Overview

The water buffalo ( Bubalus bubalis) has shown enormous milk production potential in many Asian countries. India is considered as the home tract of some of the best buffalo breeds. However, genetic structure of the Indian river buffalo is poorly understood. Hence, for selection and breeding strategies, there is a need to characterize the populations and understand the genetic structure of various buffalo breeds. In this study, we have analysed genetic variability and population structure of seven buffalo breeds from their respective geographical regions using Axiom ® Buffalo Genotyping Array having 124,030 Single Nucleotide Polymorphisms (SNPs). Blood samples were obtained from 302 buffaloes comprising Murrah, Nili-Ravi, Mehsana, Jaffarabadi, Banni, Pandharpuri and Surti breeds. Diversity, as measured by expected heterozygosity (H e ) ranged from 0.364 in the Surti to 0.384 in the Murrah breed. All the breeds showed negligible inbreeding coefficient. Pair-wise F ST values revealed the lowest genetic distance between Mehsana and Nili-Ravi (0.0022) while highest between Surti and Pandharpuri (0.030). Principal component analysis and structure analysis unveiled the differentiation of Surti, Pandharpuri and Jaffarabadi in first two PCs, while remaining breeds were grouped together as a separate single cluster. Murrah and Mehsana showed early linkage disequilibrium decay while Surti breed showed late decay, similarly LD based Ne was drastically declined for Murrah and Mehsana since last 100 generations. In LD blocks to QTLs concordance analysis, 14.19 per cent of concordance was observed with 873 (out of 1144) LD blocks overlapped with 8912 (out of 67804) QTLs. Overall, total 4090 markers were identified from all LD blocks for six types of traits. Results of this study indicated that these SNP markers could differentiate phenotypically distinct breeds like Surti,Pandharpuri and Jaffarabadi but not others. So, there is a need to develop SNP chip based on SNP markers identified by sequence information of local breeds. Author Summary Indian buffaloes, through 13 recognised breeds, contribute about 49% in total milk production and play a vital role in enhancing the economic condition of Indian farmers. High density genotyping these breeds will allow us to study differences at the molecular level. Evolutionary relationship and phenotypes relations with genotype could be tested with high density genotyping. Breed structure analysis helps to take effective breeding policy decision. In the present study, we have used the high-throughput microarray based genotyping technology for SNP markers. These markers were used for breed differentiation using various genetic parameters. Population structure reflected the proportion of breed admixture among studied breeds. We have also tried to dig the markers associated with traits based LD calculation. However, these SNPs couldn’t explain obvious variation up to the expected level, hence, there is need to develop an indigenous SNP chip based on Indian buffalo populations.

https://www.biorxiv.org/content/biorxiv/early/2018/08/19/395681.full.pdf

High-throughput Genotype based Population Structure Analysis of Selected Buffalo Breeds

The present study was carried out for the identifi cation of cattle and buffalo meat from a mixed meat sample using cyt b gene variability by Real Time PCR. In Real Time PCR, the common forward primer with cattle specifi c reverse primer showed melting peak 76.2oC on cattle DNA while the common forward primer with buffalo specifi c reverse primers showed melting peak at 78.2oC on buffalo DNA. Even in duplex PCR it showed only species specifi c melting peaks in respective species DNA. But when duplex PCR was evaluated on cattlebuffalo mixed DNA template in equal proportion it exhibited two peaks, a major buffalo specifi c and a minor cattle specifi c, merging into one broader peak at 78.2oC. However it was possible to know presence of mixed DNA by Real Time PCR duplex primers. The duplex Real Time PCR showed only a single broader peak at 78.2oC at 1: 10 and all further ratios. Hence all independent cattle specifi c Real Time PCR was run on mixed DNA which produced cattle specifi c melting peak at 76.2oC upto 1:1000 dilutions. Thus, it was possible to detect and differentiate cattle meat mixed in buffalo meat upto 1:1000 fraction i.e. 9 pg of cattle DNA adulterated in buffalo DNA by running a duplex PCR followed by cattle specifi c Real Time PCR. Duplex Real Time PCR did not produce any amplifi cation and melting peaks on DNA templates from sheep, goat and chicken. Thus, Real Time PCR was found to be successful in differentiating cattle and buffalo mixed meat samples.

Real time pcr- an approach to detect meat adulteration

Paenibacillus sp. strain DMB20, in cometabolism with other Proteobacteria and Firmicutes, exhibits azoreduction of textile dyes. Here, we report the draft genome sequence of this bacterium, consisting of 6,647,181 bp with 7,668 coding sequences (CDSs). The data presented highlight multiple sets of functional genes associated with xenobiotic compound degradation.

https://journals.asm.org/doi/pdf/10.1128/genomeA.00554-15

Chaitanya G. Joshi

Papers

Advancements in Bovine Rumen Microbial Ecology: A Review

Molecular basis of Post-surgical Peritoneal adhesions - An Overview

High-throughput Genotype based Population Structure Analysis of Selected Buffalo Breeds

Real time pcr- an approach to detect meat adulteration

Draft Genome Sequence of Paenibacillus sp. Strain DMB20, Isolated from Alang Ship-Breaking Yard, Which Harbors Genes for Xenobiotic Degradation.