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Mesoscopic Systems
Published in James J Y Hsu, Nanocomputing, 2017
Chen, Su, and Mou (2006) proposed a mechanism to explain the folding of proteins. The model includes the essential effects of water in an effective potential. The electrical dipole-dipole interaction and the local hydrophobic interaction are introduced and are shown to be as crucial as the hydrogen bonding. The model allows successful folding of α-helix and β-sheet, the two important motifs of proteins. Hsieh, Luo, Ji and Lee (2003) proposed a minimal model for genome evolution and growth. The analysis of typical microbial genomes reveals that microbial DNA sequences have the statistical characteristics of being much shorter. This peculiar property supports an evolutionary model in which a genome evolves by random mutation and that it primarily grows by random segmental duplication. That genomes grew mostly by duplication is consistent with the observation that repeat sequences in all genomes are widespread and that intragenomic and intergenomic homologous genes are preponderant across all life forms. Most of the recent protein discoveries may be found from reading the Nobel press release and lectures. Students are encouraged to visit the website http://nobelprize.org/ of the Nobel Foundation whose press release details most of the recent awards for the breakthough discoveries on proteins. The Nobel lectures are most inspiring.
Tetramethylpyrazine production from edible materials by the probiotic Bacillus coagulans
Published in Preparative Biochemistry & Biotechnology, 2020
Haoxuan Zhong, Jie Shen, Zhe Meng, Jing-yi Zhao, Zijun Xiao
Then, we selected strains ATCC 7050, GBI-30 and S-Lac, the three strains with the most extensive applications among the 11 strains of B. coagulans, and conducted gene family analysis with strain CICC 20138. During genome evolution, a gene can be duplicated to two or more copies, and multiple copies of similar genes make up a gene family. Usually, each gene within a gene family has similar biochemical functions. All the sequences to be analyzed were merged into one file to build the database, all-vs-all BLASTP analysis was performed, and the threshold for serial alignment was set to 1e-5. The sequence alignment were performed using OrthoMCL (version 1.4) software and processed for gene family analysis,[17] and then the results were represented by a Venn diagram.
Next generation sequencing for pandemic preparedness
Published in Indian Chemical Engineer, 2020
Genome Evolution Analysis Resourcefor COVID-19 (GEAR-19) is an effort towards collating information towards all the SARS-CoV-2 sequenced genomes of India with data towards total sequenced genomes, clades, geographical distribution vis-a-vis states of India, total number of variants, contributing labs and sample demographics (https://data.ccmb.res.in/gear19/). As on 28 October 2020, 3154 genomes have been sequenced with 4493 variants and contribution by 35 labs with sample coverage from 19 states of India. The information captured here would be a great help towards analysis for genomic variants linked with disease severity and mortality (Figure 2).