[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

In the current scenario, great emphasis is being made on the recovery, recycling, and reconditioning of organic solid waste. With a focus on the bioconversion of organic waste into value-added products, municipal vegetable waste was fractionated into liquid and solid part. The solid fraction was subjected to biodegradation in the presence of different microbial consortia and different enzymes were extracted. The remaining solid stuff was converted into animal feed, followed by the evaluation of its microbiological and chemical indices. Liquid fraction separated from waste was used as a crude medium to grow different bio-fertilizer strains. Among the three consortia, consortium C (Aspergillus terreus and Myrothecium verrucaria) showed the maximum production of amylase, cellulase, xylanase and pectinase after 4 days. Results of the microbiological and chemical parameters of the animal feed prepared from the fermented vegetable waste showed that the various parameters were found to be within the permissible limit. The average concentrations of heavy metals in the compost was found to be within the permissible limit of FCO standard, therefore, it can also be used for agricultural application. For using liquid extract of the vegetable waste, maximum CFU count 1.9 × 106, 1.1 × 106, and 8.7 × 10 5 was achieved in BAB 1980, BAB 662, and BAB 267 strain, respectively after 30 h of incubation. Thus, the present study demonstrated the bioconversion of vegetable waste into crude enzymes, animal feed, compost, and liquid biofertilizer.

Creating wealth from waste: An approach for converting organic waste in to value-added products using microbial consortia

Genomic analysis of Clostridium sp. NCR, an anaerobic Gram positive bacterium which was isolated from rumen fluid of Mehsani breed of buffalo revealed presence of various environmental gene tags (EGTs) involved in pathways for utilizing a wide range of substrates. Here we report the sequence of this rumen isolate, its whole genome sequence has been deposited in DDBJ/EMBL/GenBank under the accession number JQHY00000000. The genome comprises of a 3.62-Mb draft genome with a G + C content of 28.10%, which encodes a total of 3126 proteins. Functional analysis provides information about the microbe's role in maintaining host homeostasis and its fiber degradation potential.

Isolation of chitinolytic Clostridium sp. NCR from Mehsani buffalo rumen, its genomic analysis and potential role in rumen.

In India, during the second wave of the COVID-19 pandemic, the breakthrough infections were mainly caused by the SARS-COV-2 delta variant (B.1.617.2). It was reported that, among majority of the infections due to the delta variant, only 9.8% percent cases required hospitalization, whereas only 0.4% fatality was observed. Sudden dropdown in COVID-19 infections cases were observed within a short timeframe, suggesting better host adaptation with evolved delta variant. Downregulation of host immune response against SARS-CoV-2 by ORF8 induced MHC-I degradation has been reported earlier. The Delta variant carried mutations (deletion) at Asp119 and Phe120 amino acids which are critical for ORF8 dimerization. The deletions of amino acids Asp119 and Phe120 in ORF8 of delta variant resulted in structural instability of ORF8 dimer caused by disruption of hydrogen bonds and salt bridges as revealed by structural analysis and MD simulation studies. Further, flexible docking of wild type and mutant ORF8 dimer revealed reduced interaction of mutant ORF8 dimer with MHC-I as compared to wild-type ORF8 dimer with MHC-1, thus implicating its possible role in MHC-I expression and host immune response against SARS-CoV-2. We thus propose that mutant ORF8 of SARS-CoV-2 delta variant may not be hindering the MHC-I expression thereby resulting in a better immune response against the SARS-CoV-2 delta variant, which partly explains the possible reason for sudden drop of SARS-CoV-2 infection rate in the second wave of SARS-CoV-2 predominated by delta variant in India. 

/pdf/defective-orf8-dimerization-in-sars-cov-2-delta-variant-2zaevc55.pdf

Defective ORF8 dimerization in SARS-CoV-2 delta variant leads to a better adaptive immune response due to abrogation of ORF8-MHC1 interaction

Isolation and molecular identification of staphylococcus spp. from bovine mastitis milk samples.

Deoxyribonucleic acid was influenced by sperm ageing and sperm storage temperature. In this study, the effect on DNA integrity at prefreeze and postfree ze stages was analyzed by single cell gel electrophoresis during winter and summer seasons. Traditionally, the diagnosis of male infertility depends on microscopic assessment and biochemical assays to evaluate quality of semen. These tests are needed to provide the basic information for initial diagnosis. However, none of these parameters gives information about sperm function and their fertilization capability. The fertility of these sperms is questionable. The evaluation of sperm DNA damage is a promising technique to diagnose the male infertility. It has been shown to be closely associated with negative relationships with fertilization, embryo quality, implantation and positive relationships with abortion. Here we report the effect of preservation temperature and season on sperm DNA damage, using the single cell gel electrophoresis to measure DNA fragmentation. The significant difference (P<0.05) in DNA damage among Surti buffalo bulls spermatozoa were more pronounced at postfreeze stage as compared to the prefreeze stage. In addition, the significant difference (P<0.05) in DNA damage was observed among Surti buffalo bulls spermatozoa during summer season as compared to the winter season. The changes on DNA integrity were dependant on temperature of preservation, period of storage and seasonal variation. The single cell gel electrophoresis can be used to detect low levels of DNA damage in Surti buffalo bulls spermatozoa. Therefore, screening of the sperm DNA damage may be used as an additional test of sperm quality that can have diagnostic importance in the male infertility.

Chaitanya G. Joshi

Papers

Creating wealth from waste: An approach for converting organic waste in to value-added products using microbial consortia

Isolation of chitinolytic Clostridium sp. NCR from Mehsani buffalo rumen, its genomic analysis and potential role in rumen.

Defective ORF8 dimerization in SARS-CoV-2 delta variant leads to a better adaptive immune response due to abrogation of ORF8-MHC1 interaction

Isolation and molecular identification of staphylococcus spp. from bovine mastitis milk samples.

Evaluation of buffalo bull spermatozoal dna damage using single cell gel electrophoresis