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Sunday, September 22, 2019

High-Resolution Full-Length HLA Typing Method Using Third Generation (Pac-Bio SMRT) Sequencing Technology.

The human HLA genes are among the most polymorphic genes in the human genome. Therefore, it is very difficult to find two unrelated individuals with identical HLA molecules. As a result, HLA Class I and Class II genes are routinely sequenced or serotyped for organ transplantation, autoimmune disease-association studies, drug hypersensitivity research, and other applications. However, these methods were able to give two or four digit data, which was not sufficient enough to understand the completeness of haplotypes of HLA genes. To overcome these limitations, we here described end-to-end workflow for sequencing of HLA class I and class II genes…

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Friday, July 19, 2019

Comparative analyses of low, medium and high-resolution HLA typing technologies for human populations

Human Leukocyte Antigen (HLA) encoding genes are part of the major histocompatibility complex (MHC) on human chromosome 6. This region is one of the most polymorphic regions in the human genome. Prior knowledge of HLA allelic polymorphisms is clinically important for matching donor and recipient during organ/tissue transplantation. HLA allelic information is also useful in predicting immune responses to various infectious diseases, genetic disorders and autoimmune conditions. India harbors over a billion people and its population is untapped for HLA allelic diversity. In this study, we explored and compared three HLA typing methods for South Indian population, using Sequence-Specific Primers…

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Sunday, July 7, 2019

Complete genome sequencing of protease-producing novel Arthrobacter sp. strain IHBB 11108 using PacBio Single-Molecule Real-Time Sequencing technology.

A previously uncharacterized species of the genus Arthrobacter, strain IHBB 11108 (MCC 2780), is a Gram-positive, strictly aerobic, nonmotile, cold-adapted, and protease-producing alkaliphilic actinobacterium, isolated from shallow undersurface water from Chandra Tal Lake, Lahaul-Spiti, India. The complete genome of the strain is 3.6 Mb in size with an average 58.97% G+C content.

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Sunday, July 7, 2019

Complete genome sequence of the rhizobacterium Pseudomonas trivialis strain IHBB745 with multiple plant growth-promoting activities and tolerance to desiccation and alkalinity

The complete genome sequence of 6.45 Mb is reported here for Pseudomonas trivialis strain IHBB745 (MTCC 5336), which is an efficient, stress-tolerant, and broad-spectrum plant growth-promoting rhizobacterium. The gene-coding clusters predicted the genes for phosphate solubilization, siderophore production, 1-aminocyclopropane-1-carboxylate (ACC) deaminase activity, indole-3-acetic acid (IAA) production, and stress response. Copyright © 2015 Gulati et al.

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Sunday, July 7, 2019

Complete genome sequence of Arthrobacter sp. ERGS1:01, a putative novel bacterium with prospective cold active industrial enzymes, isolated from East Rathong glacier in India.

We report the complete genome sequence of Arthrobacter sp. ERGS1:01, a novel bacterium which produces industrial enzymes at low temperature. East Rathong glacier in Sikkim Himalayas is untouched and unexplored for microbial diversity though it has a rich source of glaciers, alpine and meadows. Genome sequence has provided the basis for understanding its adaptation under harsh condition of Himalayan glacier, its ability to produce cold active industrial enzymes and has unlocked opportunities for microbial bioprospection from East Rathong glacier. Copyright © 2015. Published by Elsevier B.V.

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Sunday, July 7, 2019

Genome assembly of Chryseobacterium polytrichastri ERMR1:04, a psychrotolerant bacterium with cold active proteases, isolated from East Rathong Glacier in India.

We report here the genome assembly of a psychrotolerant bacterium, Chryseobacterium polytrichastri ERMR1:04, which secretes cold-active proteases. The bacterium was isolated from a pristine location, the East Rathong Glacier in the Sikkim Himalaya. The 5.53-Mb genome provides insight into the cold-active industrial enzyme and adaptation in the cold environment. Copyright © 2015 Kumar et al.

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Sunday, July 7, 2019

Genome assembly of Chryseobacterium sp. strain IHBB 10212 from glacier top-surface soil in the Indian trans-Himalayas with potential for hydrolytic enzymes

The cold-active esterases are gaining importance due to their catalytic activities finding applications in chemical industry, food processes and detergent industry as additives, and organic synthesis of unstable compounds as catalysts. In the present study, the complete genome sequence of 4,843,645 bp with an average 34.08% G + C content and 4260 protein-coding genes are reported for the low temperature-active esterase-producing novel strain of Chrysobacterium isolated from the top-surface soil of a glacier in the cold deserts of the Indian trans-Himalayas. The genome contained two plasmids of 16,553 and 11,450 bp with 40.54 and 40.37% G + C contents, respectively.…

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Sunday, July 7, 2019

Paenibacillus ihbetae sp. nov., a cold-adapted antimicrobial producing bacterium isolated from high altitude Suraj Tal Lake in the Indian trans-Himalayas.

The assessment of bacterial diversity and bioprospection of the high-altitude lake Suraj Tal microorganisms for potent antimicrobial activities revealed the presence of two Gram-stain-variable, endospore-forming, rod-shaped, aerobic bacteria, namely IHBB 9852(T) and IHBB 9951. Phylogenetic analysis based on 16S rRNA gene sequence showed the affiliation of strains IHBB 9852(T) and IHBB 9951 within the genus Paenibacillus, exhibiting the highest sequence similarity to Paenibacillus lactis DSM 15596(T) (97.8% and 97.7%) and less than 95.9% similarity to other species of the genus Paenibacillus. DNA-DNA relatedness among strains IHBB 9852(T) and IHBB 9951 was 90.2%, and with P. lactis DSM 15596(T), was 52.7%…

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Sunday, July 7, 2019

Complete genome sequence of Arthrobacter alpinus ERGS4:06, a yellow pigmented bacterium tolerant to cold and radiations isolated from Sikkim Himalaya.

Arthrobacter alpinus ERGS4:06, a yellow pigmented bacterium which exhibited tolerance to cold and UV radiations was isolated from the glacial stream of East Rathong glacier in Sikkim Himalaya. Here we report the 4.3 Mb complete genome assembly that has provided the basis for potential role of pigments as a survival strategy to combat stressed environment of cold and high UV-radiation and additionally the ability to produce cold active industrial enzymes. Copyright © 2016. Published by Elsevier B.V.

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Sunday, July 7, 2019

First complete genome sequence of a species in the genus Microterricola, an extremophilic cold active enzyme producing bacterial strain ERGS5:02 isolated from Sikkim Himalaya.

Here, we report the first ever complete genome sequence of any species in the genus Microterricola. The bacterium Microterricola viridarii ERGS5:02 isolated from the glacial stream of Sikkim Himalaya survived at low temperature and exhibited enhanced growth upon UV treatment, in addition, it also produced cold active enzymes. The complete genome assembly of 3.7 Mb suggested for the presence of genetic elements favoring the survival of bacterium under extreme conditions of UV and low temperature besides producing amylase, lipase and protease of industrial relevance. Copyright © 2016 Elsevier B.V. All rights reserved.

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Sunday, July 7, 2019

Complete genome sequence of a low-temperature active and alkaline-stable endoglucanase-producing Paenibacillus sp. strain IHB B 3084 from the Indian Trans-Himalayas.

A genome of 5.88Mb with 46.83% G+C content is reported for an endoglucanase-producing bacterium Paenibacillus sp. strain IHB B 3084 isolated from the cold environments of the Indian Trans-Himalayas. The psychrotrophic bacterium produces low-temperature active and alkaline-stable endoglucanases of industrial importance. The genomic data has provided insight into genomic basis of cellulase production and survival of the bacterium in the cold environments. Copyright © 2016. Published by Elsevier B.V.

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Sunday, July 7, 2019

Strategies for high-altitude adaptation revealed from high-quality draft genome of non-violacein producing Janthinobacterium lividum ERGS5:01.

A light pink coloured bacterial strain ERGS5:01 isolated from glacial stream water of Sikkim Himalaya was affiliated to Janthinobacterium lividum based on 16S rRNA gene sequence identity and phylogenetic clustering. Whole genome sequencing was performed for the strain to confirm its taxonomy as it lacked the typical violet pigmentation of the genus and also to decipher its survival strategy at the aquatic ecosystem of high elevation. The PacBio RSII sequencing generated genome of 5,168,928 bp with 4575 protein-coding genes and 118 RNA genes. Whole genome-based multilocus sequence analysis clustering, in silico DDH similarity value of 95.1% and, the ANI value of…

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