Search
Search Results
-
Incorporating mutational heterogeneity to identify genes that are enriched for synonymous mutations in cancer
BackgroundSynonymous mutations, which change the DNA sequence but not the encoded protein sequence, can affect protein structure and function, mRNA...
-
In silico methods for predicting functional synonymous variants
Single nucleotide variants (SNVs) contribute to human genomic diversity. Synonymous SNVs are previously considered to be “silent,” but mounting...
-
Non-random Codon Usage of Synonymous and Non-synonymous Mutations in the Human HLA-A Gene
The structure and function of human leucocyte antigen (HLA-A) is well known and is an extremely variable protein. From the public HLA-A database, we...
-
Fitness difference between two synonymous mutations of Phytophthora infestans ATP6 gene
BackgroundSequence variation produced by mutation provides the ultimate source of natural selection for species adaptation. Unlike nonsynonymous...
-
Genome-wide sequencing identifies a thermal-tolerance related synonymous mutation in the mussel, Mytilisepta virgata
The roles of synonymous mutations for adapting to stressful thermal environments are of fundamental biological and ecological interests but poorly...
-
Molecular bases for strong phenotypic effects of single synonymous codon substitutions in the E. coli ccdB toxin gene
BackgroundSingle synonymous codon mutations typically have only minor or no effects on gene function. Here, we estimate the effects on cell growth...
-
Identification and in silico characterization of CSRP3 synonymous variants in dilated cardiomyopathy
BackgroundSynonymous variations have always been ignored while studying the underlying genetic mechanisms for most of the human diseases. However,...
-
Suppression of the dwarf phenotype of an Arabidopsis mutant defective in thermospermine biosynthesis by a synonymous codon change in the SAC51 uORF
Thermospermine plays a critical role in negatively regulating xylem development in angiosperms. A mutant of Arabidopsis thaliana that is defective in...
-
Intraspecific and interspecific variations in the synonymous codon usage in mitochondrial genomes of 8 pleurotus strains
In this study, we investigated the codon bias of twelve mitochondrial core protein coding genes (PCGs) in eight Pleurotus strains, two of which are...
-
Two isoleucyl tRNAs that decode synonymous codons divergently regulate breast cancer metastatic growth by controlling translation of proliferation-regulating genes
The human genome contains 61 codons encoding 20 amino acids. Synonymous codons representing a given amino acid are decoded by a set of transfer RNAs...
-
High heteroplasmy is associated with low mitochondrial copy number and selection against non-synonymous mutations in the snail Cepaea nemoralis
Molluscan mitochondrial genomes are unusual because they show wide variation in size, radical genome rearrangements and frequently show high...
-
Prediction of the most deleterious non-synonymous SNPs in the human IL1B gene: evidence from bioinformatics analyses
BackgroundPolymorphisms in IL1B play a significant role in depression, multiple inflammatory-associated disorders, and susceptibility to infection....
-
Context-dependent and -independent selection on synonymous mutations revealed by 1,135 genomes of Arabidopsis thaliana
BackgroundSynonymous mutations do not alter the amino acids and therefore are regarded as neutral for a long time. However, they do change the tRNA...
-
In-silico assessment of high-risk non-synonymous SNPs in ADAMTS3 gene associated with Hennekam syndrome and their impact on protein stability and function
Hennekam Lymphangiectasia–Lymphedema Syndrome 3 (HKLLS3) is a rare genetical disorder caused by mutations in a few genes including ADAMTS3. It is...
-
Massively parallel gene expression variation measurement of a synonymous codon library
BackgroundCell-to-cell variation in gene expression strongly affects population behavior and is key to multiple biological processes. While codon...
-
Synonymous point mutation of gtfB gene caused by therapeutic X-rays exposure reduced the biofilm formation and cariogenic abilities of Streptococcus mutans
BackgroundThe shift of oral microbiota is a critical factor of radiation caries in head and neck cancer patients after the radiotherapy. However, the...
-
Genome-wide analysis on the maize genome reveals weak selection on synonymous mutations
BackgroundSynonymous mutations are able to change the tAI (tRNA adaptation index) of a codon and consequently affect the local translation rate....
-
SARS-CoV-2 continuously optimizes its codon usage to adapt to human lung environment
Viruses need to utilize the resources from host cells to reproduce themselves. RNA translation rate, which is largely determined by codon usage, is...
-
Climate change affects multiple dimensions of well-being through impacts, information and policy responses
The consequences of climate change and responses to climate change interact with multiple dimensions of human well-being in ways that are emerging or...
-
Comparative mitochondrial genomics in Nematoda reveal astonishing variation in compositional biases and substitution rates indicative of multi-level selection
BackgroundNematodes are the most abundant and diverse metazoans on Earth, and are known to significantly affect ecosystem functioning. A better...
