Design and Construction of a Synthetic Nanobody Library: Testing Its Potential with a Single Selection Round Strategy by María Angélica Contreras, Yunier Serrano-Rivero, Alaín González-Pose, Julieta Salazar-Uribe, Marcela Rubio-Carrasquilla, Matheus Soares-Alves, Natalie C. Parra, Frank Camacho-Casanova, Oliberto Sánchez-Ramos, Ernesto Moreno

“…The constructed library has a clonal diversity of 10⁸ and an amino acid variability that matches the codon distribution set by design at each randomized position. …”
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Variation suggestive of horizontal gene transfer at a lipopolysaccharide (<it>lps</it>) biosynthetic locus in <it>Xanthomonas oryzae </it>pv. <it>oryzae</it>, the bacterial leaf bl... by Sonti Ramesh V, Patil Prabhu B

“…All six open reading frames (ORFs) have atypical G+C content and altered codon usage, which are the hallmarks of genomic islands that are acquired by horizontal gene transfer. …”
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Heterologous expression of pediocin/papA in Bacillus subtilis by Genyu Wang, Zhijun Guo, Xueqian Zhang, Hao Wu, XiuMei Bai, Hailiang Zhang, Richa Hu, Shaoliang Han, Yuanxiang Pang, Zi’ang Gao, Lili Yan, Cuiying Huang, Le Zhang, Chunli Pan, Xuelian Liu

“…In this study, two vectors carrying the codon sequence of the mature PapA peptide were constructed, one with and one without a His tag. …”
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Quality of Life of Patients on Peritoneal Dialysis and Contributing Factors by Niloofar Nili, Shiva Seirafian, Sayed Mohsen Hosseini, Abdolamir Atapour, Maryam Kazemi Naeini, Mojgan Mortazavi

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Immunoinformatics-Aided Design and Evaluation of a Potential Multi-Epitope Vaccine against <i>Klebsiella Pneumoniae</i> by Hamza Arshad Dar, Tahreem Zaheer, Muhammad Shehroz, Nimat Ullah, Kanwal Naz, Syed Aun Muhammad, Tianyu Zhang, Amjad Ali

“…<i>In silico</i> reverse translation and codon optimization also confirmed its high expression in <i>E. coli</i> K12 strain. …”
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Understanding Insulin in the Age of Precision Medicine and Big Data: Under-Explored Nature of Genomics by Taylor W. Cook, Amy M. Wilstermann, Jackson T. Mitchell, Nicholas E. Arnold, Surender Rajasekaran, Caleb P. Bupp, Jeremy W. Prokop

“…Moreover, a rare, poorly characterized African population-enriched variant of INS–IGF2 results in a loss of the stop codon. <i>INS</i> transcript UTR variants rs689 and rs3842753, associated with type 1 diabetes, are found in many pancreatic RNAseq datasets with an elevation of the 3′UTR alternatively spliced <i>INS</i> transcript. …”
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β-Globin Gene Cluster Haplotypes in Iranian Patients with β-Thalassemia by Z Rahimi, A Merat, M Akhzari, M Haghshenass, Nagel Ronald L, Gerard Nathalie, Krish-namoorthy Rajagopal

“…IVS I.110 (G→A) mutation was linked to haplotype I. Mutation in codon 30 (G→A) was associated with haplotype V. …”
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Determination of Pathogenicity of Breast Cancer 1 Gene Variants using the American College of Medical Genetics and Genomics and the Association for Molecular Pathology Guidelines by Angela Brown, Mansour Zamanpoor, Donald R. Love, Debra O. Prosser

“…Keywords: BRCA1 Gene; Bioinformatics; DNA Sequencing; Nonsense Codon; Splice Donor Site; New Zealand.…”
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Comprehensive genomic analysis of the SARS-CoV-2 Omicron variant BA.2.76 in Jining City, China, 2022 by Qiang Yin, Wei Liu, Yajuan Jiang, Qiang Feng, Xiaoyu Wang, Huixin Dou, Zanzan Liu, Feifei He, Yingying Fan, Baihai Jiao, Boyan Jiao

“…A total of 69 amino acid variant sites, 9 amino acid deletions, and 1 stop codon mutation were identified across 18 proteins. …”
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Nonsense-mediated decay machinery in Plasmodium falciparum is inefficient and non-essential by Emma McHugh, Michaela S. Bulloch, Steven Batinovic, Cameron J. Patrick, Drishti K. Sarna, Stuart A. Ralph

“…ABSTRACT Nonsense-mediated decay (NMD) is a conserved mRNA quality control process that eliminates transcripts bearing a premature termination codon. In addition to its role in removing erroneous transcripts, NMD is involved in post-transcriptional regulation of gene expression via programmed intron retention in metazoans. …”
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Adsorption of Hg2+/Cr6+ by metal-binding proteins heterologously expressed in Escherichia coli by Shuting Hu, Zixiang Wei, Teng Liu, Xinyu Zuo, Xiaoqiang Jia

“…To improve the adsorption performance, surface display and codon optimization were carried out. Results In this study, we constructed 24 adsorption engineering strains for Hg2+ and Cr6+, utilizing different strategies. …”
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Impact of β-2 Thr164Ile and combined β-adrenergic receptor polymorphisms on prognosis in a cohort of heart failure outpatients by A. Biolo, R. Salvaro, N. Clausell, D. Silvello, K.G. Santos, L.E. Rohde

“…We evaluated the role of the β2-AR Thr164Ile polymorphism at codon 164 on prognosis in a prospective study on 315 adult Brazilian HF patients, predominantly middle-aged Caucasian men in functional class I-II, with severe left ventricular systolic dysfunction. …”
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K65R in subtype C HIV-1 isolates from patients failing on a first-line regimen including d4T or AZT: comparison of Sanger and UDP sequencing data. by Patricia Recordon-Pinson, Jennifer Papuchon, Sandrine Reigadas, Alaka Deshpande, Hervé Fleury

“…METHODS: 27 subtype C HIV-1 isolates from treated patients failing on a regimen with d4T or AZT plus lamivudine (3TC) plus nevirapine (NVP) or efavirenz (EFV) and who had been sequenced by Sanger were investigated by UDPS at codon 65 of the reverse transcriptase (RT). 18 isolates from naïve patients and dilutions of a control K65R plasmid were analysed by Sanger plus UDPS. …”
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A Possible Pathogenic PSEN2 Gly56Ser Mutation in a Korean Patient with Early-Onset Alzheimer’s Disease by Kyu-Hwan Shim, Min-Ju Kang, Heewon Bae, Danyeong Kim, Jiwon Park, Seong-Soo A. An, Da-Eun Jeong

“…Here, a heterozygous <i>PSEN2</i> point mutation from G to A nucleotide change at position 166 (codon 56; c.166G>A, Gly56Ser) was identified in a 64-year-old Korean female with AD with progressive cognitive memory impairment for the 4 years prior to the hospital visit. …”
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IRF8 Regulates Intrinsic Ferroptosis through Repressing p53 Expression to Maintain Tumor Cell Sensitivity to Cytotoxic T Lymphocytes by Dakota B. Poschel, Mercy Kehinde-Ige, John D. Klement, Dafeng Yang, Alyssa D. Merting, Natasha M. Savage, Huidong Shi, Kebin Liu

“…To restore IRF8 expression in tumor cells, we designed and synthesized codon usage-optimized IRF8-encoding DNA to generate IRF8-encoding plasmid NTC9385R-mIRF8. …”
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Genome of Rhodnius prolixus, an insect vector of Chagas disease, reveals unique adaptations to hematophagy and parasite infection by Mesquita, Rafael D., Waterhouse, Robert

“…The genome contained actively transcribed, horizontally transferred genes from Wolbachia sp., which showed evidence of codon use evolution toward the insect use pattern. …”
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Improved vectors and genome-wide libraries for CRISPR screening by Sanjana, Neville E, Shalem, Ophir, Zhang, Feng

“…To create a new vector capable of producing higher-titer virus (lentiCRISPRv2), we made several modifications, including removal of one of the nuclear localization signals, human-codon optimization of the remaining nuclear localization signal and P2A bicistronic linker sequences, and repositioning of the U6-driven sgRNA cassette (Fig. 1a). …”
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A supervised learning approach for taxonomic classification of core-photosystem-II genes and transcripts in the marine environment by Tzahor, Shani, Man-Aharonovich, Dikla, Kirkup, Benjamin, Yogev, Tali, Berman-Frank, Ilana, Polz, Martin F., Beja, Oded, Mandel-Gutfreund, Yael

“…Results To achieve an accurate and rapid taxonomic classification, we employed a computational approach combining a multi-class Support Vector Machine (SVM) with a codon usage position specific scoring matrix (cuPSSM). …”
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Intragenic and Extragenic Suppressors of Temperature Sensitive Mutations in the Replication Initiation Genes dnaD and dnaB of Bacillus subtilis by Rokop, Megan E., Grossman, Alan Davis

“…These suppressor mutations caused a change in the anticodon of an alanine tRNA so that it would recognize the mutant codon (threonine) in dnaB and likely insert the wild type amino acid (alanine). …”
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Intragenic and extragenic suppressors of temperature sensitive mutations replication initiation genes dnaD and dnaB of Bacillus subtilis by Rokop, Megan E., Grossman, Alan Davis

“…These suppressor mutations caused a change in the anticodon of an alanine tRNA so that it would recognize the mutant codon (threonine) in dnaB and likely insert the wild type amino acid (alanine). …”
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