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Evolution of Herpes Simplex Viruses
Published in Marie Studahl, Paola Cinque, Tomas Bergström, Herpes Simplex Viruses, 2017
Rory J. Bowden, Duncan J. McGeoch
Heterogeneity in the constraint on amino acid replacements is evident in the widely variable ratio of nonsynonymous to synonymous substitutions (Ka/Ks) amongst HSV-1 genes. Data from genes belonging to different functional classes fit with broad expectations: Ka/KS ranges from 0.05 in UL40, encoding the small subunit of ribonucleotide reductase, a protein that is highly conserved on evolutionary timescales, to 0.5–0.6 in the virion glycoproteins US4 (gG) and US5 (gJ) (92). Constraint on the gene for gC, a glycoprotein with an essential role in virus entry, is stronger than in US4 and US5. Variation in the rate of nonsynonymous substitution rather than in overall mutation rate therefore appears to be primarily responsible for observed differences in gene diversity in HSV-1. Ka/Ks measures from intraspecific comparisons seem consistent with the genome-wide ratio of nonsynonymous to synonymous divergences of c. 0.3 for the comparison of HSV-1 and HSV-2 earlier in the chapter.
Polymorphisms within vitamin D binding protein gene within a Preeclamptic South African population
Published in Hypertension in Pregnancy, 2019
Yeshnee Naidoo, Jagidesa Moodley, Veron Ramsuran, Thajasvarie Naicker
The vitamin D binding protein (VDBP) is encoded by a highly polymorphic gene GC which is located on chromosome 4q13 and has 13 exons encoding 474 amino acids (15). Two common (rs4588 and rs7041) positioned at codons 416 and 420 in exon 11 are associated with 25 (OH) D deficiencies. The rs4588 polymorphism substitutes nucleic acid A for C, which results in a nonsynonymous substitution altering the amino acid from lysine to threonine, while the rs7041 polymorphism substitutes G to T, which also results in a nonsynonymous change from glutamate to aspartate. The amino acid changes result in variant proteins that differ in their affinity for vitamin D (16).
Sequence analysis of the N-acetyltransferase 2 gene (NAT2) among Jordanian volunteers
Published in Libyan Journal of Medicine, 2018
Yazun Bashir Jarrar, Ayat Ahmed Balasmeh, Wassan Jarrar
The current study applied three different software programs, PolyPhen 2.0, SIFT, and Mutpred, in order to predict the effect of amino acid substitution, caused by the novel NAT2 436G>C nonsynonymous genetic variant on NAT2 protein’s stability and function [19,20]. These software programs used numerical scores representing the probability that nonsynonymous substitution is damaging. PolyPhen-2, Mutpred, and SIFT scores use the same range, 0.0–1.0, but with opposite meanings. A variant with PolyPhen-2 and Mutpred score of 0.0 is predicted to be benign, whereas it is not tolerated in SIFT software.
FC gamma receptor polymorphisms in patients with immune thrombocytopenia
Published in Hematology, 2018
Marica Pavkovic, Aleksandar Petlichkovski, Oliver Karanfilski, Lidija Cevreska, Aleksandar Stojanovic
Another FCGR polymorphism that could be associated with ITP and is not analyzed in our study is FCGR2B-I232T. FCGR2B-I232T was identified by Kyogoku et al. [40] as a single nucleotide polymorphism in FcγRIIB gene, coding for a nonsynonymous substitution within the transmembrane domain, Ile232Thr (I232T). Kyogoku et al. [40] demonstrated that FCGR2B-232T/T genotype was significantly increased in Japanese patients with SLE.