A Novel Feature Fusion Method Based on RSCU and K-mer to Classify the SARS-Cov-2 DOI Creative Commons
Fuqiang Ye, Jianhua Zhou, Hao Zhang

et al.

Academic Journal of Science and Technology, Journal Year: 2024, Volume and Issue: 13(3), P. 334 - 342

Published: Dec. 26, 2024

The SARS-Cov-2 virus exhibits a high mutation rate, which makes the prediction and classification of its genetic evolution variation trends highly significant. Accurate methods not only contribute to epidemiological studies virus, but also play crucial role in vaccine development antiviral drug discovery. This study aims systematically evaluate accuracy generalization capability RSCU (Relative Synonymous Codon Usage) K-mer encoding techniques SARS-CoV-2 genome. We extracted genomic data from two major variants, Alpha Beta, applied Support Vector Machine (SVM) algorithm train assess impact different feature on performance. Furthermore, we introduce novel multi-feature fusion method, KRSCU, combines sequence position information with synonymous codon compositions RSCU. method effectively captures subtle differences data, significantly improving both model. Experimental results demonstrate that KRSCU outperforms traditional single-feature approaches subtype tasks. Our research offers new insights into analysis, potential applications viral monitoring.

Language: Английский

A deep learning model trained on expressed transcripts across different tissue types reveals cell-type codon-optimization preferences DOI Creative Commons

S K RAVI,

Tapan Sharma, Mitchell Yip

et al.

Nucleic Acids Research, Journal Year: 2025, Volume and Issue: 53(6)

Published: March 20, 2025

Abstract Species-specific differences in protein translation can affect the design of protein-based drugs. Consequently, efficient expression recombinant proteins often requires codon optimization. Publicly available optimization tools do not always result higher levels and lead to misfolding reduced expression. Here, we aimed develop a novel deep learning (DL) tool using recurrent neural network (RNN) define cell type-dependent biases. Using gene data from three different tissue types (brain, liver, muscle) all secretory genes, trained DL models predict optimal usage. Codon-optimized sequences for test reporter genes exhibited enhanced compared their original those optimized publicly tool. Interestingly, on expressed liver cells (hepatocytes) resulted highest when tested vitro, irrespective type. Our findings also demonstrate that DL-based algorithms significantly enhance translation, particularly proteins, which are crucial therapeutic applications. This research represents approach with broader implications pharmaceuticals, vaccine manufacturing, therapy, other DNA products.

Language: Английский

Citations

0
Molecular characterization of virulent genes in Pseudomonas aeruginosa based on componential usage divergence DOI Creative Commons
Qian Huang, Keding Yan, Gun Li

et al.

Scientific Reports, Journal Year: 2025, Volume and Issue: 15(1)

Published: April 2, 2025

Language: Английский

Citations

0
Codon-dependent regulation of mRNA translation and stability by ZC3H7A and ZC3H7B RNA-binding proteins DOI Creative Commons
Patric Harris Snell,

Parisa Naeli,

Aitor Garzia

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2025, Volume and Issue: unknown

Published: April 23, 2025

Summary Decelerated translation elongation caused by non-optimal codons can reduce mRNA stability through codon optimality-mediated degradation . A key element of this process is the coupling sensing usage with regulation efficiency and stability. We report that two paralog RNA-binding proteins (ZC3H7A ZC3H7B), which are only found in Chordates, preferentially bind to mRNAs enriched A/U at their wobble sites (A/U3 codons). ZC3H7A/B engage ribosomes lack factors induce or block initiation interactions CCR4-NOT GIGYF2/4EHP repressor complex, respectively. Depletion 4EHP impairs repression A/U3-rich mRNAs. This study provides insights into a unique mechanism higher eukaryotes couples

Language: Английский

Citations

0
Natural Selection Primarily Shaping Codon Usage Bias in Glycine max (soybean) WRKY Genes DOI Creative Commons
Krishnendu Sinha,

Sourav Jana,

Payel Pramanik

et al.

Research Square (Research Square), Journal Year: 2024, Volume and Issue: unknown

Published: May 29, 2024

Abstract Background: Codon usage biases in genomes emerge from the interaction of two prominent evolutionary factors: mutational pressure and natural selection. Studying codon bias facilitates understanding fundamental mechanisms influencing genetic structure. Glycine max (soybean) holds considerable agricultural industrial significance as a widely cultivated crop. Despite pivotal role WRKY transcription factors plant regulation stress responses, investigations these are limited, providing an opportunity to probe trends within this gene family. Results: Examination base composition genes revealed average GC content 44.85% GC3 42.01%, indicating preference for A/T(U)-ending codons. Relative synonymous (RSCU) analysis identified 27 codons with RSCU > 1, predominantly ending A U bases. The effective number (NC) ranged 42.17 61, adaptation index (CAI) values ranging 0.713 0.904, suggesting phenomenon weak yet high expression levels genes. Neutrality indicated significantly correlation between GC12 GC3, while NC plot predominant selection shaping pattern. Parity rule 2 (PR2) highlighted disproportionate AT One optimal was identified. Conclusion: Natural is primary driving force preferences These findings provide new insights into landscape translational efficiency max, contributing enhancement resources soybeans.

Language: Английский

Citations

1
Revealing Molecular Patterns of Alzheimer’s Disease Risk Gene Expression Signatures in COVID-19 Brains DOI
Yan Liu,

Weiyue Xu,

Yang Pan

et al.

Journal of Alzheimer s Disease, Journal Year: 2024, Volume and Issue: 101(1), P. 31 - 48

Published: July 23, 2024

Background: Various virus infections are known to predispose Alzheimer’s disease (AD), and a linkage between COVID-19 AD has been established. infection modulates the gene expression of genes implicated in progression AD. Objective: Determination molecular patterns codon usage context analysis for that modulated during was target study. Methods: Our study employed comprehensive array research methods, including relative synonymous usage, Codon adaptation index analysis, Neutrality parity Rare analyses, analysis. This meticulous approach crucial determining present up or downregulated infection. Results: G/C ending codons were preferred upregulated while not genes, both sets, longer have high expressivity. Similarly, T over A nucleotide preferred, selection major evolutionary force shaping sets. Apart from stops codons, CGU – Arg, AUA Ile, UUA Leu, UCG Ser, GUA Val, CGA Arg CUA Leu below 0.5%. Glutamine-initiated pairs residual values genes. Identical GAG-GAG GUG-GUG Conclusions: The shared unique features up- sets provide insights into complex interplay Further studies required elucidate relationship these with pathology.

Language: Английский

Citations

1
Comparative Analysis of Codon Usage Bias in Six Eimeria Genomes DOI Open Access
Yu Zhao,

Shicheng Zhang

International Journal of Molecular Sciences, Journal Year: 2024, Volume and Issue: 25(15), P. 8398 - 8398

Published: Aug. 1, 2024

The codon usage bias (CUB) of genes encoded by different species’ genomes varies greatly. analysis patterns enriches our comprehension genetic and evolutionary characteristics across diverse species. In this study, we performed a genome-wide CUB its influencing factors in six sequenced Eimeria species that cause coccidiosis poultry: acervulina, necatrix, brunetti, tenella, praecox, maxima. GC content protein-coding between 52.67% 58.24% among the distribution trend at positions follows GC1 > GC3 GC2. Most high-frequency codons tend to end with C/G, except E. Additionally, there is positive correlation GC3s/C3s, but significantly negative A3s. Analysis ENC-Plot, neutrality plot, PR2-bias plot suggests selection pressure has stronger influence than mutational on genomes. Finally, identified from 11 15 optimal codons, GCA, CAG, AGC being most commonly used these This study offers thorough exploration relationships pressures within Genetic evolution appears be influenced mutations pressures. findings shed light unique traits specific

Language: Английский

Citations

1
Selection on synonymous codon usage in soybean (Glycine max) WRKY genes DOI Creative Commons
Krishnendu Sinha,

Sourav Jana,

Payel Pramanik

et al.

Scientific Reports, Journal Year: 2024, Volume and Issue: 14(1)

Published: Nov. 3, 2024

The WRKY transcription factor gene family in soybean [Glycine max (L.) Merr.] (GmWRKY) is critical for the plant's development and stress responses. This study examines evolutionary dynamics of GmWRKY family, focusing on its synonymous codon usage bias (CUB) a comprehensive set 179 coding sequences. CUB was analyzed using various indices, revealing preference A/T-ending codons relatively low bias. Codon adaptation index (CAI) analysis suggested that these genes are optimized efficient translation despite bias, reflecting balance between diversity efficiency. Neutrality NC plots indicated selective forces dominate over mutational shaping usage, while selection signature showed purifying being prevalent across family. However, episodic positive also detected certain clades, highlighting potential adaptive diversification response to environmental stress. Additionally, promoter binding site uncovered correlations transcriptional regulation, indicating context-dependent relationship expression. Phylogenetic identified 11 well-supported clades modern ancestral sequence reconstruction revealed more relaxed preferences reduced constraints genes, potentially linked neofunctionalization changes. These findings provide framework optimizing expression transgenic crops with resilience. Further functional validation positively selected recommended elucidate their role

Language: Английский

Citations

1
Analysis of Synonymous Codon Usage Bias in the Chloroplast Genome of Rhododendron farrerae DOI

Xianlin Rong,

Lu Huang,

Jianshuang Shen

et al.

Published: July 12, 2024

Abstract In this study, the codon usage patterns of chloroplast genome Rhododendron farrerae were analyzed to provide genetic information for conservation and innovation Rhododendron germplasm resources. Codon preferences 54 protein coding sequences (CDS) from R. using software such as Codon, R package, EMBOSS. The results showed that average GC content CDS in was 38.10%, with GC1 (46.11%), GC2 (39.68%), GC3 (28.51%) representing contents at different positions, indicating third base codons is predominantly composed A T. ENC-plot, PR2-plot, neutral plotting analysis revealed natural selection pressure most significant factor influencing synonymous preference farrerae, leading identification 16 optimal codons. This study provides serves a reference improvement innovation.

Language: Английский

Citations

0
Analysis of Preferred Codon Usage in the ZIKA Virus Genome and Their Implications for Genome Evolution and Vaccine Design DOI

Shaikh Kaleem,

Anu Bansal

Indian Journal of Microbiology, Journal Year: 2024, Volume and Issue: unknown

Published: Nov. 8, 2024

Language: Английский

Citations

0
Brain-derived neurotrophic factor in the pathogenesis of comorbid coronary artery disease and depression: a review DOI Creative Commons
O. Yu. Kytikovа, М. V. Аntonyuk, Т. П. Новгородцева

et al.

Russian Journal of Cardiology, Journal Year: 2024, Volume and Issue: 29(11S), P. 5945 - 5945

Published: Sept. 24, 2024

Coronary artery disease (CAD) and depression are characterized by high bilateral comorbidity, but its pathogenesis is practically not studied. In the last decade, neurogenic mechanisms of inflammatory response brain-derived neurotrophic factor (BDNF), which can explain relationship between CAD, have been The review summarizes available information on BDNF role in CAD depression, as well their comorbid course for period 2019-2024. Based literature review, we identified components systems that most promising studying these multifactorial diseases (genetics, inflammation, neuroinflammation, endothelial dysfunction platelet hyperactivation, hypothalamic-pituitary-adrenal system, low-density lipoproteins triglycerides). emphasizes important development need further research this area.

Language: Английский

Citations

0