Term synonymous variation is widely used, but frequently in a wrong or misleading meaning and context. Twenty three point eight % of possible nucleotide substitution types in the universal genetic code are for synonymous amino acid changes, but when...
Synonymous variants, traditionally regarded as silent mutations due to their lack of impact on protein sequence, structure and function, have been the subject of increasing scrutiny. This commentary explores the emerging evidence challenging the noti...
Recent semantic communication methods explore effective ways to expand the communication paradigm and improve the performance of communication systems. Nonetheless, a common problem with these methods is that the essence of semantics is not explicitl...
Synonymous mutations result from the degeneracy of the genetic code. Most amino acids are encoded by two or more codons, and mutations that change a codon to another synonymous codon do not change the amino acid in the gene product. Historically, suc...
The family of Chlamydiaceae contains a group of obligate intracellular bacteria that can infect a wide range of hosts. The evolutionary trend of members in this family is a hot topic, which benefits our understanding of the cross-infection of these p...
Synonymous single nucleotide variants (sSNVs) are often considered functionally silent, but a few cases of cancer-causing sSNVs have been reported. From available databases, we collected four categories of sSNVs: germline, somatic in normal tissues,...
Single-nucleotide variants (SNVs) are a major form of genetic variation in the human genome that contribute to various disorders. There are two types of SNVs, namely non-synonymous (missense) variants (nsSNVs) and synonymous variants (sSNVs), predomi...
Synonymous codon bias in the viral genome affects protein translation and gene expression, suggesting that the synonymous codon mutant plays an essential role in influencing virulence and evolution. However, how the recessive mutant form contributes...
30 September 2015
Historically, owing to not changing amino acid composition of protein sequences, synonymous mutations are commonly assumed to be neutral during evolution and therefore have no effect on the phenotype and disease. Here, based on observations from larg...
Background: The most common form of monogenic diabetes is maturity onset diabetes of the young (MODY). This study investigates the molecular basis of MODY type 2 (GCK-MODY) in a group of Italian patients, focusing on the functional characterization o...
Synonymous mutations influence RNA splicing, mRNA stability, and translational efficiency without altering amino acid sequences, yet accurately identifying those that drive cancer remains a persistent challenge in cancer genetics. Current computation...
Synonymous codon pair deoptimization is an efficient strategy for virus attenuation; however, the underlying mechanism remains controversial. Here, we optimized and deoptimized the codon pair bias (CPB) of the human immunodeficiency virus type 1 (HIV...
Distinct patterns of dinucleotide representation, such as CpG and UpA suppression, are characteristic of certain viral genomes. Recent research has uncovered vertebrate immune mechanisms that select against specific dinucleotides in targeted viruses....
The domestication of wild rice occurred together with genomic variation, including the synonymous nucleotide substitutions that result in synonymous codon usage bias (SCUB). SCUB mirrors the evolutionary specialization of plants, but its characterist...
Protein phosphatase 2A (PP2A) functions as a tumor suppressor and consists of a scaffolding, catalytic, and regulatory subunit. The B56 gene family of regulatory subunits impart distinct functions onto PP2A. Codon usage bias (CUB) involves the select...
Synonymous variants within coding regions may influence protein expression and function. We have previously reported increased protein expression levels ex vivo (~120% in comparison to wild-type) from a synonymous polymorphism variant, c.354G>A [p...
Previous studies have shown that engineered mutants of cucumber mosaic virus (CMV) with synonymous changes in the coat protein (CP) open reading frame (ORF), accumulate de novo amino acid (aa) substitutions in the CP when passaged in planta. To explo...
Background/Objectives: Adenomyosis is a common estrogen-dependent gynecological condition with a largely undefined genetic architecture. Ciliary dysfunction has been implicated in its pathogenesis, positioning genes governing ciliary structure and mo...
Synonymous single nucleotide polymorphisms (sSNPs), which change a nucleotide, but not the encoded amino acid, are perceived as neutral to protein function and thus, classified as benign. We report a patient who was diagnosed with cystic fibrosis (CF...
Human fibroblast growth factor 19 (hFGF19) is a difficult-to-express protein that is frequently fused with another protein for soluble expression. However, residual amino acids after cleavage with protease represent one of the major problems in thera...
Pedestrianization is a significant discourse focus within urban planning and design research. However, the need for more clarity from the inconsistent use of near-synonym concepts or terms necessitates attention. This review article addresses this is...
Missense, nonsense, splice site and regulatory region variants in interferon regulatory factor 6 (IRF6) have been shown to contribute to both syndromic and non-syndromic forms of cleft lip and/or palate (CL/P). We report the diagnostic evaluation of...
5-Substituted 2-selenouridines (R5Se2U) are post-transcriptional modifications present in the first anticodon position of transfer RNA. Their functional role in the regulation of gene expression is elusive. Here, we present efficient syntheses of 5-m...
In most bacteria, synonymous codons are not used with equal frequencies. Different factors have been proposed to contribute to codon usage preference, including translational selection, GC composition, strand-specific mutational bias, amino acid co...
Synonyms and homonyms appear in all natural languages. We analyze their evolution within the framework of the signaling game. Agents in our model use reinforcement learning, where probabilities of selection of a communicated word or of its interpreta...
Linguistic steganography can be utilized to establish covert communication channels on social media platforms, thus facilitating the dissemination of illegal messages, seriously compromising cyberspace security. Synonym substitution-based linguistic...
Investigations into crispy and crunchy in American English have demonstrated that these synonymic taste words have differing effects on perceived taste depending on association. To test the generalizability of these findings, category fluency tasks w...
Japanese medical device adverse events terminology, published by the Japan Federation of Medical Devices Associations (JFMDA terminology), contains entries for 89 terminology items, with each of the terminology entries created independently. It is ne...
Based on several sources of evidence from morphology, the micromorphology of the abaxial leaf epidermis, and a phylogenetic analysis using complete chloroplast genome data, a new combination and two new synonyms are reported in the genus Indocalamus...
In recent years, many studies have been devoted to discovering the inner workings of Transformer-based models, such as BERT, for instance, attempting to identify what information is contained within them. However, little is known about how these mode...
Classical information theory (CIT) characterizes the transmission limit for communication systems under syntactic accuracy, whereas semantic information theory (SIT) studies communication from the perspective of semantic fidelity induced by synonymou...
We recently examined specimens of the genus Paraleuctra Hanson, 1941, from Zhejiang Province and Sichuan Province, China, and two new synonyms are established based on morphological and molecular data. Paraleuctra sinica Yang and Yang, 1995, and Para...
Streptococcus agalactiae is an important human and animal pathogen. To better understand the genetic features and evolution of S. agalactiae, multiple factors influencing synonymous codon usage patterns in S. agalactiae were analyzed in this study. A...
Ranacris You & Lin, 1983, is a small genus in the subfamily Habrocneminae with an undefined phylogenetic position, exhibiting in previous molecular studies a distant relationship with the genera in the same subfamily but an extremely close relati...
Background/Objectives: Serum calcium concentrations have been associated with bone mineral density (BMD), but results seem to depend on sex. Genetic variants in the Ryanodine Receptor1 (RYR1) gene have been previously associated with low BMD in postm...
Narcissus degeneration virus (NDV), narcissus late season yellows virus (NLSYV) and narcissus yellow stripe virus (NYSV), which belong to the genus Potyvirus of the family Potyviridae, cause significant losses in the ornamental value and quality of n...
Intraspecific variation is ubiquitous from individual traits to population level and plays an important role in a variety of fields. However, it is often ignored by systematists and comparative evolutionary biologists. In view of the limited knowledg...
Triatoma guazu Lent and Wygodzinsky and Triatoma williami Galvão, Souza, and Lima (Hemiptera: Triatominae) are found in human dwellings and are potential vectors of the protozoan Trypanosoma cruzi, the etiological agent of Chagas disease. Tria...
Riemerella anatipestifer (RA) belongs to the Flavobacteriaceae family and can cause a septicemia disease in poultry. The synonymous codon usage patterns of bacteria reflect a series of evolutionary changes that enable bacteria to improve tolerance of...
Hypnum denticulatum var. obtusifolium was described by Turner in the early nineteenth century. This taxon, now known as Plagiothecium denticulatum var. obtusifolium, has not been studied in detail or received a detailed description. During the revisi...
The genus Peirates comprises important predatory assassin bugs that serve as vital biological control agents against agricultural and forestry pests. Thus, accurate species identification is critical for the utilization of these natural enemies. An i...
This study systematically evaluated the taxonomic relationship between Streptococcus taoyuanensis ST2T and Streptococcus caecimuris CLAAV18T. Comparative genomic analysis revealed a high 16S rRNA gene sequence similarity of 99.6%, with the two strain...
Polio viral proteinase 2A performs several essential functions in genome replication. Its inhibition prevents viral replication, thus making it an excellent substrate for drug development. In this study, the three-dimensional structure of 2A protease...
Feline panleukopenia virus (FPLV) is the primary causative agent of a highly contagious and often fatal disease affecting domestic cats and other felids. The increasing isolation of species-specific FPLV variants from multiple host species has garner...
Cowpea mild mottle virus (CpMMV) is an economically significant virus that causes severe disease on several legume crops. Aside from recombination, other factors driving its rapid evolution are elusive. In this study, the synonymous codon pattern of...
Joubert syndrome (OMIM #213300) is a rare neurodevelopmental disease characterized by abnormal breathing patterns, intellectual impairment, ocular findings, renal cysts, and hepatic fibrosis. It is classified as a ciliopathy disease, where cilia func...
Melanoma is characterized by a high mutational burden making it an established model for studying tumor neoantigens and developing strategies for personalized immunotherapy. In this study, a reproducible bioinformatics pipeline was developed and impl...
Synonymous codon usage can be influenced by mutations and/or selection, e.g., for speed of protein translation and correct folding. However, this codon bias can also be affected by a general selection at the amino acid level due to differences in the...
The S glycoprotein of coronaviruses is important for viral entry and pathogenesis with most variable sequences. Therefore, we analyzed the S gene sequences of SARS-CoV-2 to better understand the antigenicity and immunogenicity of this virus in this s...
Potato virus M (PVM) is a member of the genus Carlavirus of the family Betaflexviridae and causes large economic losses of nightshade crops. Several previous studies have elucidated the population structure, evolutionary timescale and adaptive evolut...
of 37