An analysis of structural influences on selection in RNA genes. by Mimouni, N, Lyngsø, R, Griffiths-Jones, S, Hein, J

“…By analogy to the different properties of codon positions based on the genetic code, we use a well-developed energy model for RNA structure to classify stem positions into structural classes and argue that they are under different selective constraints. …”

Simple detection of point mutations associated with HIV-1 drug resistance. by Frater, A, Chaput, C, Beddows, S, Weber, J, McClure, M

“…MS--PCR is sensitive and specific for the detection of mutations in HIV-1, and can be adapted easily to test for resistance at any codon of interest.…”

Intronic L1 insertion and F268S, novel mutations in RPS6KA3 (RSK2) causing Coffin-Lowry syndrome. by Martínez-Garay, I, Ballesta, M, Oltra, S, Orellana, C, Palomeque, A, Moltó, MD, Prieto, F, Martínez, F

“…The first mutation consists of a de novo insertion of a 5'-truncated LINE-1 element at position -8 of intron 3, which leads to a skipping of exon 4, leading to a shift of the reading frame and a premature stop codon. The L1 fragment (2800 bp) showed a rearrangement with a small deletion, a partial inversion of the ORF 2, flanked by short direct repeats which duplicate the acceptor splice site. …”

Characterisation of a novel lyssavirus isolated from Pteropid bats in Australia. by Gould, A, Hyatt, A, Lunt, R, Kattenbelt, J, Hengstberger, S, Blacksell, S

“…The nucleotide sequence of the prototype strain of ABLV was determined from the initiator methionine codon for the nucleocapsid protein (N protein) to the amino terminus of the polymerase gene (L protein), a distance of 5344 nucleotides. …”

Viral vectors for malaria vaccine development. by Li, S, Locke, E, Bruder, J, Clarke, D, Doolan, D, Havenga, M, Hill, A, Liljestrom, P, Monath, T, Naim, H, Ockenhouse, C, Tang, D, Van Kampen, K, Viret, J, Zavala, F, Dubovsky, F

“…Those studies have also revealed that optimization of Plasmodium genes for mammalian expression is an important aspect of vaccine design. Codon-optimization, surface-trafficking, de-glycosylation and removal of toxic domains can lead to improved immunogenicity. …”

Mutagenesis of the human IgA1 heavy chain tailpiece that prevents dimer assembly. by Atkin, J, Pleass, R, Owens, R, Woof, J

“…Deletion of the entire tailpiece by stop codon introduction completely prevented dimer formation. …”

Germline mutations in the EXT1 and EXT2 genes in Korean patients with hereditary multiple exostoses. by Park, K, Shin, K, Ku, J, Cho, T, Lee, S, Choi, I, Phillipe, C, Monaco, A, Porter, D, Park, J

“…The EXT2 mutation identified in the SNU-OC15 family was a missense mutation at codon 85 of exon 2 (TGC-->CGC), resulting in an amino acid change from cysteine to arginine. …”

Effective knockdown of Drosophila long noncoding RNAs by CRISPR interference by Ghosh, S, Tibbit, C, Liu, J

“…Additionally, we find that the human and Drosophila codon optimised dCas9 genes are functional and show similar transcription repressive activity. …”

Current status of pharmaceutical and genetic therapeutic approaches to treat DMD. by Pichavant, C, Aartsma-Rus, A, Clemens, P, Davies, K, Dickson, G, Takeda, S, Wilton, S, Wolff, J, Wooddell, C, Xiao, X, Tremblay, J

“…This led to several clinical trials for gentamicin and ataluren (PTC124) allowing stop codon read-through. An alternative approach is to induce the expression of an internally deleted, partially functional dystrophin protein through exon skipping. …”

Beta 2-microglobulin gene mutations: a study of established colorectal cell lines and fresh tumors. by Bicknell, D, Rowan, A, Bodmer, W

“…In the related cell lines, DLD-1 and HCT-15, two similar mutations were identified, a C-->A substitution in codon 10 and a G-->T mutation in the splice sequence of intron 1. …”

The structure of a human alpha-globin pseudogene and its relationship to alpha-globin gene duplication. by Proudfoot, N, Maniatis, T

“…Comparison of this sequence with a normal human alpha-globin gene (alpha 2) reveals that psi alpha 1 contains both an initiator codon mutation and frameshift deletions which would prevent the production of an alpha-globin polypeptide. psi alpha 1 contains two intervening sequences with sizes and locations characteristic of mammalian alpha-globin genes. …”

CpG and UpA dinucleotides in both coding and non-coding regions of echovirus 7 inhibit replication initiation post-entry. by Fros, JJ, Dietrich, I, Alshaikhahmed, K, Passchier, TC, Evans, DJ, Simmonds, P

“…Host-cells thus possess intrinsic defence pathways that prevent replication of viruses with increased CpG/UpA frequencies independently of codon usage.…”

Delaying emergence of resistance to KRAS inhibitors with adaptive therapy: “treatment-to-contain” instead of “treatment-to-cure” by Hamdi, Amir Imran Faisal, Stanslas, Johnson

“…Specific KRAS inhibitors, such as sotorasib and adagrasib, which bind covalently to codon 12 of substituted glycine to cysteine residue of the protein (G12C), have been approved by the FDA recently for the treatment of lung cancers. …”

Complete mitochondrial genome sequence of the Indian pipistrelle Pipistrellus coromandra (Vespertilioninae) by Rahman, Md. Mafizur, Yoon, Kwang Bae, Kim, Ji Young, Hussin, Mohamed Zakaria, Park, Yung Chul

“…The mitochondrial protein-coding genes in P. coromandra use the standard start codon (ATN), two stop codons (TAA and AGA), and two incomplete stop codons (TA- and T--). …”
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Synthetic BXN gene utilization in the resistance of crops to the herbicide bromoxynil - a review by Taghipour, Farhad, Huyop, Fahrul Zaman

“…This review described the application of synthetic and codon-optimized bxn gene for the efficient transformation into plant resistance to Bromoxynil.…”
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Reduced polymorphism of Plasmodium vivax early transcribed membrane protein (PvETRAMP) 11.2 by Edvige Perrotti, Mariangela L’Episcopia, Michela Menegon, Irene S. Soares, Angel Rosas-Aguirre, Niko Speybroeck, Alejandro LLanos-Cuentas, Didier Menard, Marcelo Urbano Ferreira, Carlo Severini

“…Plasmodium vivax populations from Latin America showed a marked inter-population genetic differentiation (fixation index [Fst]) in contrast to SEA/PNG populations. Codon bias measures (effective number of codons [ENC] and Codon bias index [CBI]) indicated preferential use of synonymous codons, suggesting selective pressure at the translation level. …”
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Novel homozygous pathogenic mitochondrial DNAJC19 variant in a patient with dilated cardiomyopathy and global developmental delay by Abeer Al Tuwaijri, Yusra Alyafee, Mashael Alharbi, Maryam Ballow, Mohammed Aldrees, Qamre Alam, Rola A. Sleiman, Muhammad Umair, Majid Alfadhel

“…Results Whole‐exome sequencing followed by Sanger sequencing revealed a homozygous frameshift variant in the reading frame starting at codon 54 in exon 4 in the DNAJC19 gene (c.159del [Phe54Leufs*5]), which results in a stop codon four positions downstream. …”
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Adaptive Thermogenesis in a Mouse Model Lacking Selenoprotein Biosynthesis in Brown Adipocytes by Lucia A. Seale, Ashley N. Ogawa-Wong, Ligia M. Watanabe, Vedbar S. Khadka, Mark Menor, Daniel J. Torres, Bradley A. Carlson, Dolph L. Hatfield, Marla J. Berry

“…Sec is incorporated into selenoproteins via recoding of the stop codon UGA, with specific <i>cis</i> and <i>trans</i> factors required during translation to avoid UGA recognition as a stop codon, including a Sec-specific tRNA, tRNA^[Ser]Sec, encoded in mice by the gene <i>Trsp</i>. …”
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Complete Plastid Genome Sequencing of Eight Species from <i>Hansenia</i>, <i>Haplosphaera</i> and <i>Sinodielsia</i> (Apiaceae): Comparative Analyses and Phylogenetic Implications by Wei Gou, Sheng-Bin Jia, Megan Price, Xian-Lin Guo, Song-Dong Zhou, Xing-Jin He

“…</i> There was no evident divergence of codon usage frequency between the three genera, where codons ranged from 21,134 to 21,254. …”
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IGF2-tagging of GAA promotes full correction of murine Pompe disease at a clinically relevant dosage of lentiviral gene therapy by Qiushi Liang, Fabio Catalano, Eva C. Vlaar, Joon M. Pijnenburg, Merel Stok, Yvette van Helsdingen, Arnold G. Vulto, Ans T. van der Ploeg, Niek P. van Til, W.W.M. Pim Pijnappel

“…Here, we fused insulin-like growth factor 2 (IGF2) to a codon-optimized version of GAA (LV-IGF2.GAAco) to improve cellular uptake by the cation-independent mannose 6-phosphate/IGF2 (CI-M6P/IGF2) receptor. …”
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