Synonymous sites are generally considered to be functionally neutral. However, there are recent contradictory findings suggesting that synonymous alleles might have functional roles in various molecular aspects. For instance, a recent study demonstrated that synonymous single nucleotide polymorphisms have a similar effect size as nonsynonymous single nucleotide polymorphisms in human disease association studies. Researchers have recognized synonymous codon usage bias (SCUB) in the genomes of almost all species and have investigated whether SCUB is due to random nucleotide compositional bias or to natural selection of any functional exposure generated by synonymous mutations. One of the most prominent observations on the non-neutrality of synonymous codons is the correlation between SCUB and levels of gene expression, such that highly expressed genes tend to have a higher preference toward so-called optimal codons than lowly expressed genes. In relation, it is known that amounts of cognate tRNAs that bind to optimal codons are significantly higher than the amounts of cognate tRNAs that bind to non-optimal codons in genomes. In the present paper, we review various functions that synonymous codons might have other than regulating expression levels.
Alleles ; Bias (Epidemiology) ; Codon* ; Gene Expression ; Genome ; Humans ; Polymorphism, Single Nucleotide ; RNA, Transfer ; Selection, Genetic ; Silent Mutation

The genomic diversity of Avian leukosis virus subgroup J (ALV-J) was investigated in an experimentally infected chicken. ALV-J variants in tissues from four different organs of the same bird were re-isolated in DF-1 cells, and their gp85 gene was amplified and cloned. Ten clones from each organ were sequenced and compared with the original inoculum strain, NX0101. The minimum homology of each organ ranged from 96.7 to 97.6%, and the lowest homology between organs was only 94.9%, which was much lower than the 99.1% homology of inoculum NX0101, indicating high diversity of ALV-J, even within the same bird. The gp85 mutations from the left kidney, which contained tumors, and the right kidney, which was tumor-free, had higher non-synonymous to synonymous mutation ratios than those in the tumor-bearing liver and lungs. Additionally, the mutational sites of gp85 gene in the kidney were similar, and they differed from those in the liver and lung, implying that organ- or tissue-specific selective pressure had a greater influence on the evolution of ALV-J diversity. These results suggest that more ALV-J clones from different organs and tissues should be sequenced and compared to better understand viral evolution and molecular epidemiology in the field.
Animals ; Avian Leukosis Virus* ; Avian Leukosis* ; Birds ; Chickens* ; Clone Cells ; Kidney ; Liver ; Lung ; Molecular Epidemiology ; Silent Mutation

Male breast cancer (MBC) is a rare and poorly studied disease that is a growing global health problem. Interestingly, both the molecular basis of MBC and its histological profile are often quite distinct from the far more prevalent female breast cancer, emphasizing the need for increased focus on MBC. Here, we present a case report of an MBC patient from India with a strong familial history of breast cancer. This patient was normal for BRCA1/2 and many other common breast cancer-associated genes. However, upon further analysis, the individual was found to possess two mutations in the DNA helicase and tumor suppressor gene BRIP1, including a silent mutation at residue 879 as well as a P919S variant. Other family members were also screened for these mutations. To the best of our knowledge, this is the first report of BRIP1 mutation in MBC in the Indian population.
Breast Neoplasms* ; Breast Neoplasms, Male ; Breast* ; DNA ; Female* ; Genes, Tumor Suppressor ; Global Health ; Humans ; India* ; Male* ; Silent Mutation

PURPOSE: The aim of the current study is to assess the spectrum of genetic variation in the BRIP1 gene among Korean high-risk breast cancer patients who tested negative for the BRCA1/2 mutation. MATERIALS AND METHODS: Overall, 235 Korean patientswith BRCA1/2 mutation-negative high-risk breast cancerwere screened for BRIP1 mutations. The entire BRIP1 gene was analyzed using fluorescent-conformation sensitive gel electrophoresis. In silico analysis of BRIP1 variants was performed using PolyPhen-2 and SIFT. RESULTS: A total of 20 sequence alterations including 12 exonic and eight intronic variantswere found. Among the 12 exonic variants, 10 were missense and two were silent mutations. No protein-truncating mutation was found among the tested patients. Among the 10 missense variants, four (p.L263F, p.L340F, p.L474P, and p.R848H) were predicted to be pathogenic by both PolyPhen-2 and SIFT, and these variants were found in five patients. Of the four missense variants, p.L263F, p.L474P, and p.R848H localize to regions between the helicase motifs, while p.L340F resides in an iron-sulfur domain of BRIP1. CONCLUSION: No protein-truncating mutation in BRIP1 was found among the tested patients. The contribution of BRIP1 variants is thought to be minor in Korean non-BRCA1/2 high-risk breast cancer.
Breast Neoplasms* ; Breast* ; Computer Simulation ; Electrophoresis ; Exons ; Genetic Variation ; Hereditary Breast and Ovarian Cancer Syndrome ; Humans ; Introns ; Korea ; Silent Mutation

Plasmodium vivax merozoite surface protein-1 (PvMSP1) gene codes for a major malaria vaccine candidate antigen. However, its polymorphic nature represents an obstacle to the design of a protective vaccine. In this study, we analyzed the genetic polymorphism and natural selection of the C-terminal 42 kDa fragment within PvMSP1 gene (Pv MSP142) from 77 P. vivax isolates, collected from imported cases of China-Myanmar border (CMB) areas in Yunnan province and the inland cases from Anhui, Yunnan, and Zhejiang province in China during 2009–2012. Totally, 41 haplotypes were identified and 30 of them were new haplotypes. The differences between the rates of non-synonymous and synonymous mutations suggest that PvMSP142 has evolved under natural selection, and a high selective pressure preferentially acted on regions identified of PvMSP133. Our results also demonstrated that PvMSP142 of P. vivax isolates collected on China-Myanmar border areas display higher genetic polymorphisms than those collected from inland of China. Such results have significant implications for understanding the dynamic of the P. vivax population and may be useful information towards China malaria elimination campaign strategies.
China ; Genetic Variation* ; Haplotypes ; Malaria ; Merozoite Surface Protein 1* ; Merozoites* ; Myanmar ; Plasmodium vivax* ; Plasmodium* ; Polymorphism, Genetic ; Selection, Genetic* ; Silent Mutation

BACKGROUND: We investigated the molecular epidemiological characteristics and antimicrobial susceptibility pattern of penicillinase-producing Neisseria gonorrhoeae (PPNG) isolates to monitor the change in distribution of bla(TEM) in Korea. METHODS: We collected 804 PPNG isolates from diverse hospitals and clinics mainly located in Seoul, Korea, over a period of 11 years (2005–2015). Isolate susceptibility to seven antimicrobials was determined using the agar dilution test. The molecular epidemiological characteristics of the isolates were determined by Sanger sequencing of bla(TEM), N. gonorrhoeae multiantigen sequence typing (NG-MAST) and plasmid typing. RESULTS: Among 72 fully sequenced PPNG isolates, sixteen (22.2%) possessed TEM-135. All TEM-135 isolates had a common silent mutation (c.18C>T), which was previously unreported. We observed a pattern of continuous increase in the number of TEM-135 isolates since 2012. The median and 90% minimum inhibitory concentration of azithromycin were substantially lower in the TEM-135 group than in the non-PPNG and TEM-1 groups. All TEM-135 isolates showed different NG-MAST types and predominantly harbored Toronto/Rio (75%) plasmids. A comprehensive comparative analysis of PPNG with TEM-135 according to NG-MAST, plasmid type, and year of isolation revealed a wide distribution. CONCLUSIONS: The proportion of TEM-135 PPNG has continuously increased since 2012, in association with clonal spread. The difference at position 18 of the TEM-135 sequence can be interpreted as the existence of multiple clonal complexes. The possibility that TEM-135 was acquired via foreign plasmids requires careful follow-up and continuous monitoring of TEM-135 to ascertain whether it constitutes a step towards evolutionary change.
Agar ; Azithromycin ; Drug Resistance, Microbial ; Follow-Up Studies ; Incidence* ; Korea* ; Microbial Sensitivity Tests ; Neisseria gonorrhoeae* ; Neisseria* ; Plasmids ; Seoul ; Silent Mutation