Determinants of associations between codon and amino acid usage patterns of microbial communities and the environment inferred based on a cross-biome metagenomic analysis by Arup Panda, Tamir Tuller

“…Abstract Codon and amino acid usage were associated with almost every aspect of microbial life. …”
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Interface between 40S exit channel protein uS7/Rps5 and eIF2α modulates start codon recognition in vivo by Jyothsna Visweswaraiah, Alan G Hinnebusch

“…The eukaryotic pre-initiation complex (PIC) bearing the eIF2·GTP·Met-tRNAiMet ternary complex (TC) scans the mRNA for an AUG codon in favorable context. AUG recognition evokes rearrangement of the PIC from an open, scanning to a closed, arrested conformation. …”
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Optimization of codon composition and regulatory elements for expression of human insulin like growth factor-1 in transgenic chloroplasts and evaluation of structural identity and function by Sandberg Laurence, Denes Bela, Ruiz Gricel, Daniell Henry, Langridge William

“…The <it>IGF-1n </it>plants contained 9.5% TSP as <it>IGF-1n</it>, suggesting that the chloroplast translation machinery is more flexible than <it>E. coli </it>in codon preference and usage. The expression of <it>IGF-1 </it>was increased up to 32% TSP under continuous illumination by the chloroplast light regulatory elements. …”
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Relocalization of Translation Termination and Ribosome Recycling Factors to Stress Granules Coincides with Elevated Stop-Codon Readthrough and Reinitiation Rates upon Oxidative Stress by Desislava S. Makeeva, Claire L. Riggs, Anton V. Burakov, Pavel A. Ivanov, Artem S. Kushchenko, Dmitri A. Bykov, Vladimir I. Popenko, Vladimir S. Prassolov, Pavel V. Ivanov, Sergey E. Dmitriev

“…Here we show that arsenite-induced stress causes a dramatic increase in the stop-codon readthrough rate and significantly elevates translation reinitiation levels on uORF-containing and bicistronic mRNAs. …”
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Codon-level co-occurrences of germline variants and somatic mutations in cancer are rare but often lead to incorrect variant annotation and underestimated impact prediction. by Amanda Koire, Young Won Kim, Jarey Wang, Panagiotis Katsonis, Haijing Jin, Olivier Lichtarge

“…Cancer cells explore a broad mutational landscape, bringing the possibility that tumor-specific somatic mutations could fall in the same codons as germline SNVs and leverage their presence to produce substitutions with a larger impact on protein function. …”
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Readthrough Activators and Nonsense-Mediated mRNA Decay Inhibitor Molecules: Real Potential in Many Genetic Diseases Harboring Premature Termination Codons by Nesrine Benslimane, Camille Loret, Pauline Chazelas, Frédéric Favreau, Pierre-Antoine Faye, Fabrice Lejeune, Anne-Sophie Lia

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Investigating the Diversity and Host Range of Novel Parvoviruses from North American Ducks Using Epidemiology, Phylogenetics, Genome Structure, and Codon Usage Analysis by Marta Canuti, Joost T. P. Verhoeven, Hannah J. Munro, Sheena Roul, Davor Ojkic, Gregory J. Robertson, Hugh G. Whitney, Suzanne C. Dufour, Andrew S. Lang

“…While DACs were included in a highly supported clade of avian viruses, no definitive conclusions could be drawn about the host type of DAAD because it was phylogenetically close to viruses found in vertebrates and invertebrates and analyses of codon usage bias and nucleotide frequencies of viruses within the family <i>Parvoviridae</i> showed no clear host-based viral segregation. …”
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Natural selection plays a significant role in governing the codon usage bias in the novel SARS-CoV-2 variants of concern (VOC) by Neetu Tyagi, Rahila Sardar, Dinesh Gupta

Subjects: “…Codon usage bias…”
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A Simple and Affordable Method to Create Nonsense Mutation Clones of p53 for Studying the Premature Termination Codon Readthrough Activity of PTC124 by Chia-Chi Chen, Ruo-Yu Liao, Fang-Yu Yeh, Yu-Rou Lin, Tze-You Wu, Alexa Escobar Pastor, Danny Danilo Zul, Yun-Chien Hsu, Kuan-Yo Wu, Ke-Fang Liu, Reiji Kannagi, Jang-Yi Chen, Bi-He Cai

“…(1) Background: A premature termination codon (PTC) can be induced by a type of point mutation known as a nonsense mutation, which occurs within the coding region. …”
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In silico prediction of mtDNA Gene Expression Based on Codon Usage Bias in Ants (Formicidae Latreille, 1802) that Inhabit Limestone Quarry Ecosystems by Semir Dorić, Dinko Osmanković, Lada Lukić Bilela

Subjects: “…codon usage bias…”
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Chloroplast gene expression level is negatively correlated with evolutionary rates and selective pressure while positively with codon usage bias in Ophioglossum vulgatum L by Jing Hao, Yingyi Liang, Jingyao Ping, Jinye Li, Wanxin Shi, Yingjuan Su, Ting Wang

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Crystal structures of Zidovudine- or Lamivudine-resistant human immunodeficiency virus type 1 reverse transcriptases containing mutations at codons 41, 184, and 215. by Chamberlain, P, Ren, J, Nichols, C, Douglas, L, Lennerstrand, J, Larder, B, Stuart, D, Stammers, D

Evaluation of codon optimized recombinant plasmodium knowlesi merozoite surface protein-1(19) (pkMSP-1(19)) expressed in pichia pastoris by Lau, Y.L., Cheong, F.W., Chin, L.C., Mahmud, R., Chen, Y., Fong, M.Y.

“…Merozoite surface protein-1(19) (MSP-1(19)) appears as a potential candidate for malaria blood stage vaccine as it could induce protective immunity. In this study, codon optimized P. knowlesi MSP-1(19) (pkMSP-1(19)) was expressed and purified in yeast Pichia pastoris expression system. …”

An Unsupervised Algorithm for Host Identification in Flaviviruses by Phuoc Truong Nguyen, Santiago Garcia-Vallvé, Pere Puigbò

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Determination of the Amino Acid Recruitment Order in Early Life by Genome-Wide Analysis of Amino Acid Usage Bias by Mingxiao Zhao, Ruofan Ding, Yan Liu, Zhiliang Ji, Yufen Zhao

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Genotype-Phenotype Correlations of &#946;-Thalassemia Mutations in an Azerbaijani Population by Chingiz Asadov, Eldar Abdulalimov, Tahira Mammadova, Surmaya Gafarova, Yegana Guliyeva, Gunay Aliyeva

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The prevalence, genetic diversity and evolutionary analysis of cachavirus firstly detected in northeastern China by Nuowa Li, Nuowa Li, Yue Bai, Xin Yan, Zhiyuan Guo, Kongrui Xiang, Zaixing Yang, Haikun Shangguan, Junwei Ge, Junwei Ge, Lili Zhao

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GENE EXPRESSION AND mRNA SECONDARY STRUCTURES IN DIFFERENT Mycoplasma SPECIES by V. S. Sokolov, V. A. Likhoshvai, Yu. G. Matushkun

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High-throughput sequencing-based assembly of chloroplast genomes of five pine tree species by Qunfeng Luo, Zhangqi Yang, Yuanheng Feng, Jie Jia, Jianhui Tan, Peidong Yan

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A computational screen for alternative genetic codes in over 250,000 genomes by Yekaterina Shulgina, Sean R Eddy

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