Influence of Recombinant Codon-Optimized Plasmid DNA Encoding VEGF and FGF2 on Co-Induction of Angiogenesis by Ilnur I. Salafutdinov, Ilnaz M. Gazizov, Dilara K. Gatina, Ruslan I. Mullin, Alexey A. Bogov, Rustem R. Islamov, Andrey P. Kiassov, Ruslan F. Masgutov, Albert A. Rizvanov

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A novel homozygous initiation codon variant associated with infantile alpha‐Bcrystallinopathy in a Chinese family by Keze Ma, Dong Luo, Tian Tian, Ning Li, Xiaoguang He, Chunbao Rao, Baimao Zhong, Xiaomei Lu

“…Mutation analysis of the proband identified a novel rare homozygous mutation in the initiation codon of the CRYAB gene, which was inherited from currently asymptomatic, heterozygous carrier parents, and his heterozygous biological brother is unaffected. …”
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Comprehensive Analysis of Codon Usage Patterns in Chinese Porcine Circoviruses Based on Their Major Protein-Coding Sequences by Hua Feng, Joaquim Segalés, Fangyu Wang, Qianyue Jin, Aiping Wang, Gaiping Zhang, Giovanni Franzo

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The Shift in Synonymous Codon Usage Reveals Similar Genomic Variation during Domestication of Asian and African Rice by Guilian Xiao, Junzhi Zhou, Zhiheng Huo, Tong Wu, Yingchun Li, Yajing Li, Yanxia Wang, Mengcheng Wang

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In Silico Analyses of the Role of Codon Usage at the Hemagglutinin Cleavage Site in Highly Pathogenic Avian Influenza Genesis by Mathis Funk, Anja C. M. de Bruin, Monique I. Spronken, Alexander P. Gultyaev, Mathilde Richard

“…The results of the present analyses suggest that the subtype restriction of HPAIV genesis to H5 and H7 influenza viruses might be due to the particular codon usage at the HA cleavage site in these subtypes.…”
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Ancestral inference and the study of codon bias evolution: implications for molecular evolutionary analyses of the Drosophila melanogaster subgroup. by Hiroshi Akashi, Piyush Goel, Anoop John

“…The effects of asymmetric and lineage-specific substitution rates (i.e., varying levels of codon usage bias and departures from equilibrium) on the reliability of ancestral codon usage was investigated. …”
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Structural features in the Rous sarcoma virus RNA stability element are necessary for sensing the correct termination codon by Withers Johanna B, Beemon Karen L

“…These data suggest that the minimal RSE is 155 nucleotides (nts) and functions independently of the nucleotide sequence of the stop codon or the first nucleotide following the stop codon. …”
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CHIKV infection reprograms codon optimality to favor viral RNA translation by altering the tRNA epitranscriptome by Jennifer Jungfleisch, René Böttcher, Marc Talló-Parra, Gemma Pérez-Vilaró, Andres Merits, Eva Maria Novoa, Juana Díez

“…Viruses completely depend on the host translational machinery, but their genomes are often enriched in rare codons and therefore should be translated with poor efficiency. …”
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Prediction of Premature Termination Codon Suppressing Compounds for Treatment of Duchenne Muscular Dystrophy Using Machine Learning by Kate Wang, Eden L. Romm, Valentina L. Kouznetsova, Igor F. Tsigelny

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Anaerobic Fungal Mevalonate Pathway Genomic Biases Lead to Heterologous Toxicity Underpredicted by Codon Adaptation Indices by Ethan T. Hillman, Elizabeth M. Frazier, Evan K. Shank, Adrian N. Ortiz-Velez, Jacob A. Englaender, Kevin V. Solomon

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Association of p53 codon 72 polymorphism with weight and metabolic diseases in a Central Indian population by Jessy Abraham, Deepak Mahapatra, Pratishtha Agrawal, Mary Jovita James

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Variability in Codon Usage in Coronaviruses Is Mainly Driven by Mutational Bias and Selective Constraints on CpG Dinucleotide by Josquin Daron, Ignacio G. Bravo

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DESIGN OF HEPATITIS E VIRUS GENOTYPE 1 RECOMBINANT ORF3 PROTEIN BY CODON OPTIMIZATION METHOD by G. I. Alatortseva, A. V. Sidorov, L. N. Nesterenko, L. N. Luhverchik, M. V. Zhukina, I. I. Amiantova, A. V. Milovanova, D. S. Vorobev, Yu. I. Ammur, M. I. Mikhailov, K. K. Kyuregyan, V. S. Kichatova, I. A. Potemkin, O. V. Isaeva, E. Yu. Malinnikova, A. A. Karlsen, V. M. Blinov, Z. Sh. Nurmatov, A. Z. Nurmatov, O. T. Kasymov, S. V. Zhavoronok, V. V. Zverev

“…DNA copy of subgenomic virus RNA had been cloned and used for further development of E.coli strains producing full-size recombinant protein ORF3 fused to E.coli beta-galactosidase. Codons optimization method was used in aim to increase expression level of recombinant protein. …”
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Phylogenetic Analysis and Codon Usage Bias Reveal the Base of Feline and Canine Chaphamaparvovirus for Cross-Species Transmission by Xu Guo, Yingying Zhang, Yang Pan, Kankan Yang, Xinxin Tong, Yong Wang

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Metabolic Specialization and Codon Preference of Lignocellulolytic Genes in the White Rot Basidiomycete <i>Ceriporiopsis subvermispora</i> by Alex Gonzalez, Gino Corsini, Sergio Lobos, Daniela Seelenfreund, Mario Tello

Subjects: “…Codon bias…”
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Molecular characterizations of genes in chloroplast genomes of the genus Arachis L. (Fabaceae) based on the codon usage divergence. by Shuwei Yang, Gun Li, Hao Li

“…The base composition, the effective number of codons, the relative synonymous codon usage, the codon bias index, and their correlation coefficients of a total of 41 genes in 21 chloroplast genomes of the genus Arachis were investigated to further perform the correspondence and clustering analyses, revealing significantly higher variations in genomes of wild species than those of the cultivated taxa. …”
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Improved tropoelastin synthesis in the skin by codon optimization and nucleotide modification of tropoelastin-encoding synthetic mRNA by Sonia Golombek, Thomas Hoffmann, Ludmilla Hann, Markus Mandler, Sabine Schmidhuber, Josefin Weber, Young-Tae Chang, Roman Mehling, Andrea Ladinig, Christian Knecht, Johanna Leyens, Christian Schlensak, Hans Peter Wendel, Achim Schneeberger, Meltem Avci-Adali

“…In this study, de novo tropoelastin (TE) synthesis is investigated in vitro and in vivo using different TE-encoding synthetic mRNA variants after codon optimization and nucleotide modification. Codon optimization shows a strong effect on protein synthesis without affecting cell viability in vitro, whereas nucleotide modifications strongly modulate translation and reduce cell toxicity. …”
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Trm9-Catalyzed tRNA Modifications Regulate Global Protein Expression by Codon-Biased Translation by Deng, Wenjun, Babu, I. Ramesh, Su, Dan, Yin, Shanye, Begley, Thomas J., Dedon, Peter C.

“…Moreover, we show that AGA and GAA codons occur with high frequency in clusters along the transcripts, which may play a role in modulating translation. …”
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Lifestyle modifications: coordinating the tRNA epitranscriptome with codon bias to adapt translation during stress responses by Chan, Cheryl, Begley, Thomas J., Pham, Phuong M., Dedon, Peter C

“…In this model, auxiliary genetic information contained in synonymous codon usage enables regulation of codon-biased and functionally related transcripts by dynamic changes in the tRNA epitranscriptome. …”
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The helicase Ded1p controls use of near-cognate translation initiation codons in 5′ UTRs by Guenther, Ulf-Peter, Weinberg, David E., Zubradt, Meghan M., Tedeschi, Frank A., Stawicki, Brittany N., Zagore, Leah L., Brar, Gloria A., Licatalosi, Donny D., Bartel, David, Weissman, Jonathan S., Jankowsky, Eckhard

“…Our observations indicate that Ded1p affects translation initiation by controlling the use of near-cognate initiation codons that are proximal to mRNA structure in 5′ untranslated regions.…”
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