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Genome-wide analysis of codon usage bias patterns in an enterotoxigenic Escherichia coli F18 strain
Ri Wei Xia,Wen Bin Bao,Xue Mei Yin,Wei Yun Qin,Guo Qiang Zhu,Sheng Long Wu 한국유전학회 2017 Genes & Genomics Vol.39 No.11
Enterogenic Escherichia coli (ETEC) F18 strains are the main pathogenic bacteria causing severe diarrhea in humans and domestic animals. However, the information about synonymous codon usage pattern of ETEC F18 genome remains unclear. We conducted a genome-wide analysis of synonymous codon usage patterns in the ETEC F18 strain SRA: SAMN02471895. After filtering of the complete genome sequence, 4327 coding sequences were analyzed using multivariate statistical methods to calculate synonymous codon usage patterns and to evaluate the influence of various factors in shaping the codon usage. The mean GC content was 51.38%, with a slight preference for G/C-ending codons. Twenty-two codons were determined as ‘‘optimal codons”. ENC plots showed some of the genes were on or close to the expected curve, while only points with low-ENC values were below the curve. PR2 analysis showed that GC and AT were not used proportionally, suggesting major roles for mutational pressure and natural selection in shaping usage. Neutrality plots showed a significant correlation between GC12 and GC3, suggesting that mutational pressure is responsible for nucleotide composition in shaping the strength of codon usage. Translational selection was the main factor shaping the codon usage pattern of ETEC F18 genome, while other factors such as protein length, GRAVY and ARO values also influenced codon usage to some extent. We analyzed the codon usage pattern systematically and identified the factors shaping codon usage bias in the ETEC F18 genome. Such information further elucidates the mechanisms of synonymous codon usage bias and provides the basis of molecular genetic engineering and evolutionary studies.
Wei Li,Chang-Ji Zheng,Liang-Peng Sun,Ming-Xia Song,Yan Wu,Yin-Jing Li,Yi Liu,Hu-Ri Piao 대한약학회 2014 Archives of Pharmacal Research Vol.37 No.7
A series of arylhydrazone derivatives bearing arhodanine moiety have been synthesized, characterized, andevaluated as antibacterial agents. Some of these compoundsshowed potent antibacterial activities against several differentstrains of Gram-positive bacteria, including multidrug-resistant clinical isolates. Of the compounds tested, IIkand IIIk were identified as the most effective, with minimuminhibitory concentration values of 2–4 lg/mL against multidrug-resistant Gram-positive organisms, including methicillin-resistant and quinolone-resistant Staphylococcusaureus. None of the compounds exhibited any activityagainst the Gram-negative bacteria Escherichia coli 1356 at64 lg/mL.
Li, Wei,Zheng, Chang-Ji,Sun, Liang-Peng,Song, Ming-Xia,Wu, Yan,Li, Yin-Jing,Liu, Yi,Piao, Hu-Ri 대한약학회 2014 Archives of Pharmacal Research Vol.37 No.7
A series of arylhydrazone derivatives bearing a rhodanine moiety have been synthesized, characterized, and evaluated as antibacterial agents. Some of these compounds showed potent antibacterial activities against several different strains of Gram-positive bacteria, including multidrug-resistant clinical isolates. Of the compounds tested, IIk and IIIk were identified as the most effective, with minimum inhibitory concentration values of $2-4{\mu}g/mL$ against multidrug-resistant Gram-positive organisms, including methicillin-resistant and quinolone-resistant Staphylococcus aureus. None of the compounds exhibited any activity against the Gram-negative bacteria Escherichia coli 1356 at $64{\mu}g/mL$.
Song, Ming-Xia,Deng, Xian-Qing,Wei, Zhi-Yu,Zheng, Chang-Ji,Wu, Yan,An, Chang-Shan,Piao, Hu-Ri Shaheed Beheshti University of Medical Sciences 2015 Iranian journal of pharmaceutical research Vol.14 No.1
<P>The microbial resistance has become a global hazard with the irrational use of antibiotics. Infection of drug-resistant bacteria seriously threatens human health. Currently, there is an urgent need for the development of novel antimicrobial agents with new mechanisms and lower levels of toxicity. In this paper, a series of (<I>S</I><I>,Z</I>)-4-methyl-2-(4-oxo-5-((5-substitutedphenylfuran-2-yl) methylene)-2-thioxothiazolidin-3-yl)pentanoic acids via a Knoevenagel condensation were synthesized and evaluated for their antibacterial activity <I>in</I><I>-</I><I>vitro</I>. The synthesized compounds were characterized by IR, <SUP>1</SUP>H NMR and MS. The antibacterial test<I> in</I><I>-</I><I>vitro</I> showed that all of the synthesized compounds had good antibacterial activity against several Gram-positive bacteria (including multidrug-resistant clinical isolates) with minimum inhibitory concentration (MIC) values in the range of 2–4 µg/mL. Especially compounds 4c, 4d, 4e and 4f were the most potent, with MIC values of 2 µg/mL against four multidrug-resistant Gram-positive bacterial strains.</P>