Codon Usage Bias: A Potential Factor Affecting VGLUT Developmental Expression and Protein Evolution

Molecular Neurobiology, Journal Year: 2024, Volume and Issue: unknown

Published: Sept. 21, 2024

Language: Английский

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A detailed analysis of codon usages bias and influencing factors in the nucleocapsid gene of Nipah Virus

The Microbe, Journal Year: 2023, Volume and Issue: 1, P. 100014 - 100014

Published: Nov. 2, 2023

Several outbreaks of Nipah Virus (NiV) have recently been reported in various parts the world including India. The 18.2-kb size single-stranded negative-sense RNA genome NiV has six genes that encode nine proteins. Among nine, nucleoprotein (N) protein is most abundant viral protein. relative availability N a determining factor for activation encapsidation, replicase activity, and regulating synthesis. In this study, we conducted codon usage analysis protein-encoding gene (N gene) NiV. synonymous (RSCU) values, combination with an ENC value 51.048, represented low bias gene. effect mutational pressure on was confirmed by significant correlations GC3s, G3s, C3s, A3s, U3s, values whole nucleotide contents (GC%, G%, C%, A%, U%). Correlation study U3s axis correspondence (CA) also supported role pressure. correlation Gravy revealed presence natural selection addition to bias. Moreover, adaptation index (CAI) higher than their corresponding expected CAI (eCAI) against human (CAI, 0.726; eCAI, 0.715), pig 0.837; 0.819), bat 0.762; 0.750) indicated play Additionally, geographical distribution, evolutionary processes influenced some extent.

Language: Английский

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Reexamination of Aspergillus cristatus phylogeny in dark tea: Characteristics of the mitochondrial genome

Open Life Sciences, Journal Year: 2024, Volume and Issue: 19(1)

Published: Jan. 1, 2024

Abstract To enhance our understanding of Aspergillus cristatus , an important functional microorganism, the characteristics its mitochondrial genome were analyzed and compared with related species. The A. was determined to be 77,649 bp in length, 15 protein-coding regions. Notably, length surpassed that other species, primarily attributable intron length. Gene order exhibited significant variations, greater conservation observed genus Penicillium . Phylogenetic tree analyses indicated genera are closely but monophyletic. Furthermore, phylogenetic constructed based on genes effectively distinguished all strains high branching confidence. This approach provides a robust reflection evolutionary relationship between offering potential for development molecular markers suitable

Language: Английский

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Exploring Codon Usage Patterns and Influencing Factors in Ranavirus DNA Polymerase Genes

Journal of Basic Microbiology, Journal Year: 2024, Volume and Issue: 64(10)

Published: Aug. 4, 2024

ABSTRACT Ranaviruses, members of the genus Ranavirus within family Iridoviridae , have become a significant concern for amphibian populations globally, along with other cold‐blooded vertebrates, due to their emergence as threat. We employed bioinformatics tools examine codon usage patterns in 61 DNA pol genes from Lymphocystivirus Megalocytivirus and two unclassified ranaviruses, no prior studies had been conducted on this topic. The results showed slight or low level bias (CUB) . Relative synonymous (RSCU) analysis indicated that predominant codons favored terminate C G. Correlation examining nucleotide content, third position, effective number (ENC), correspondence (COA), Aroma values, GRAVY values CUB across could be influenced by both mutation pressure natural selection. neutrality plot selection is primary factor driving usage. Furthermore, adaptation index (CAI) illustrated robust adaptability hosts. Analysis relative deoptimization (RCDI) suggested underwent greater These findings will aid comprehending factors influencing evolution its

Language: Английский

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The role of coumarin, hespertin and liquritigenin against oral cancer novel drug target FAP protein

Annals of Phytomedicine An International Journal, Journal Year: 2022, Volume and Issue: 11(Special Issue 1)

Published: Nov. 1, 2022

The study of codon usage bias (CUB) can be seen as a platform for identifying the gene composition, effect evolutionary forces and other traits influencing pattern.It is natural some codons to chosen over others in coding sequences; however, disorders may result from quiet modification synonymous codons.One fatal diseases that has recently expanded world oral cancer.According certain research, cancer linked unhealthy practices these areas, like smoking chewing tobacco.Here, we investigated CUB 677 down-regulated cancer-related genes.The bases CDs were composed following order: C > G A T third-place are: C3 G3 T3 A3.Genes also GC-rich order three locations' total GC content was: GC3 GC1 GC2.For genes, effective number their values computed average value was >35, indicating low CUB.The more commonly used predominantly ending, according RSCU values.Ten under represented, while there 2 represented codons.Based on GC12 versus concentrations, neutrality plot demonstrated superiority selection directed mutation pressure creating genes leads new target FAP protein.Using docking tools, could detect good interaction between products; coumarin, hespertin liquiritgenin.

Language: Английский

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