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Dec 29
Love4

dBBQs: dataBase of Bacterial Quality scores

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Visanu Wanchai, Preecha Patumcharoenpol, Intawat Nookaew and David Ussery
From The 14th Annual MCBIOS Conference
Little Rock, AR, USA. 23-25 March 2017

Abstract

Background:
It is well-known that genome sequencing technologies are becoming significantly cheaper and faster. As a result of this, the exponential growth in sequencing data in public databases allows us to explore ever growing large collections of genome sequences. However, it is less known that the majority of available sequenced genome sequences in public databases are not complete, drafts of varying qualities. We have calculated quality scores for around 100,000 bacterial genomes from all major genome repositories and put them in a fast and easy-to-use database.
Dec 28
Love0

Suggested mechanisms for Zika virus causing microcephaly: what do the genomes tell us?

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Se-Ran Jun, Trudy M. Wassenaar, Visanu Wanchai, Preecha Patumcharoenpol, Intawat Nookaew and David W. Ussery.

©  The Author(s). 2017

Published: 28 December 2017

Abstract

Background

Zika virus (ZIKV) is an emerging human pathogen. Since its arrival in the Western hemisphere, from Africa via Asia, it has become a serious threat to pregnant women, causing microcephaly and other neuropathies in developing fetuses. The mechanisms behind these teratogenic effects are unknown, although epidemiological evidence suggests that microcephaly is not associated with the original, African lineage of ZIKV. The sequences of 196 published ZIKV genomes were used to assess whether recently proposed mechanistic explanations for microcephaly are supported by molecular level changes that may have increased its virulence since the virus left Africa. For this we performed phylogenetic, recombination, adaptive evolution and tetramer frequency analyses, and compared protein sequences for the presence of protease cleavage sites, Pfam domains, glycosylation sites, signal peptides, trans-membrane protein domains, and phosphorylation sites.

Read more: https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-017-1894-3

Jan 10
Love0

Integrated omics analyses reveal the details of metabolic adaptation of Clostridium thermocellum to lignocellulose-derived growth inhibitors released during the deconstruction of switchgrass. Biotechnol Biofuels

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Poudel S, Giannone RJ, Rodriguez M Jr, Raman B, Martin MZ, Engle NL, Mielenz JR, Nookaew I, Brown SD, Tschaplinski TJ, Ussery D, Hettich RL.
2017 Jan 10;10:14. doi: 10.1186/s13068-016-0697-5. PubMed PMID: 28077967; PubMed Central PMCID: PMC5223564.

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