Colorectal tumors from APC*I1307K carriers principally harbor somatic APC mutations outside the A8 tract by Zauber, P, Bishop, T, Taylor, C, Sabbath-Solitare, M, Marotta, S, Tomlinson, I

“…METHODS: DNA from 82 colonic tumours and accompanying normal tissue collected from 29 carriers with multiple colorectal tumors was directly sequenced between codons 716 and 1604. We also assessed APC gene loss of heterozygosity. …”

The Omp85-related chloroplast outer envelope protein OEP80 is essential for viability in Arabidopsis. by Patel, R, Hsu, S, Bédard, J, Inoue, K, Jarvis, P

“…Surprisingly, the oep80-3 T-DNA (located in exon 1 between the first and second ATG codons of the open reading frame) did not cause any detectable developmental defects or affect the size of the AtOEP80 protein in chloroplasts. …”

Novel five nucleotide deletion in dysferlin leads to autosomal recessive limb‐girdle muscular dystrophy by Yen‐Lin Chen, Wen‐Bin Wu, Pei Wang, Ping‐Keung Yip, Yi‐No Wu, Ying‐Hung Lin, Wei‐Ning Lin

“…These mutations induced early stop codons; if translated, truncated DYSF proteins will be expressed. …”
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Development and Characterization of a cDNA-Launch Recombinant Simian Hemorrhagic Fever Virus Expressing Enhanced Green Fluorescent Protein: ORF 2b’ Is Not Required for In Vitro Vir... by Yingyun Cai, Shuiqing Yu, Ying Fang, Laura Bollinger, Yanhua Li, Michael Lauck, Elena N. Postnikova, Steven Mazur, Reed F. Johnson, Courtney L. Finch, Sheli R. Radoshitzky, Gustavo Palacios, Thomas C. Friedrich, Tony L. Goldberg, David H. O’Connor, Peter B. Jahrling, Jens H. Kuhn

“…To further demonstrate the investigative potential of the infectious clone system, we introduced stop codons into eight viral open reading frames (ORFs). …”
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Alzheimer’s disease pathogenetic progression is associated with changes in regulated retained introns and editing of circular RNAs by Karol Andrea Arizaca Maquera, Justin Ralph Welden, Giorgi Margvelani, Sandra C. Miranda Sardón, Samantha Hart, Noémie Robil, Alvaro Gonzalo Hernandez, Pierre de la Grange, Peter T. Nelson, Peter T. Nelson, Stefan Stamm

“…CircMAN2A1 expression correlated with AD progression and transfection experiments indicated that RNA editing promoted its translation using start codons out of frame with linear mRNAs, which generates novel proteins.DiscussionThus, we identified novel regulated retained introns that correlate with NFT Braak stages and provide evidence for a role of translated circRNAs in AD development.…”
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A Comprehensive Analysis of the <i>Fowleria variegata</i> (Valenciennes, 1832) Mitochondrial Genome and Its Phylogenetic Implications within the Family Apogonidae by Jiaqiao Wang, Weiyi He, Hao Huang, Danyun Ou, Lei Wang, Jun Li, Weiwen Li, Site Luo

“…Nearly all protein-coding genes started with ATG, while stop codons TAA/TAG/T were observed, along with evidence of strong functional constraints imposed via purifying selection. …”
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Characterization of Simple Sequence Repeats (SSRs) in Ciliated Protists Inferred by Comparative Genomics by Yuan Li, Xiao Chen, Kun Wu, Jiao Pan, Hongan Long, Ying Yan

“…We found that homopolymers are the most prevalent SSRs in these A/T-rich species, with AAA (lysine, charged amino acid; also seen as an SSR with one-adenine motif repeated three times) being the codons repeated at the highest frequencies in coding SSR regions, consistent with the widespread alveolin proteins rich in lysine repeats as found in <i>Tetrahymena</i>. …”
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Sex-Biased Gene Expression and Evolution in the Cerebrum and Syrinx of Chinese Hwamei (<i>Garrulax canorus</i>) by Hua Jiang, Jian-Qing Lin, Li Sun, Yan-Chun Xu, Sheng-Guo Fang

“…Resultantly, male-biased genes in both tissues had significantly higher Ka/Ks and effective number of codons (ENCs) than unbiased genes, and this suggested that male-biased genes which exhibit accelerated divergence may have resulted from positive selection. …”
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Genetic features of Mycobacterium tuberculosis modern Beijing sublineage by Qingyun Liu, Tao Luo, Xinran Dong, Gang Sun, Zhu Liu, Mingyun Gan, Jie Wu, Xin Shen, Qian Gao

“…For example, 4 genes were frameshifted due to premature stop mutation or genomic deletions, 19 nonsynonymous SNPs located in conservative codons, and there is a significant enrichment in regulatory network for all nonsynonymous mutations. …”
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Hepatitis B Virus Variants with Multiple Insertions and/or Deletions in the X Open Reading Frame 3′ End: Common Members of Viral Quasispecies in Chronic Hepatitis B Patients by Selene García-García, Andrea Caballero-Garralda, David Tabernero, Maria Francesca Cortese, Josep Gregori, Francisco Rodriguez-Algarra, Josep Quer, Mar Riveiro-Barciela, Maria Homs, Ariadna Rando-Segura, Beatriz Pacin-Ruiz, Marta Vila, Roser Ferrer-Costa, Tomas Pumarola, Maria Buti, Francisco Rodriguez-Frias

“…Of those Indels, 101 (98.1%) caused 44 different altered stop codons, the most commonly observed were at positions 128, 129, 135, and 362 (putative position). …”
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SARS-CoV-2 infection engenders heterogeneous ribonucleoprotein interactions to impede translation elongation in the lungs by Junsoo Kim, Daehwa Youn, Seunghoon Choi, Youn Woo Lee, Dulguun Sumberzul, Jeongeun Yoon, Hanju Lee, Jong Woo Bae, Hyuna Noh, Dain On, Seung-Min Hong, Se-Hee An, Hui Jeong Jang, Seo Yeon Kim, Young Been Kim, Ji-Yeon Hwang, Hyo-Jung Lee, Hong Bin Kim, Jun Won Park, Jun-Won Yun, Jeon-Soo Shin, Jun-Young Seo, Ki Taek Nam, Kang-Seuk Choi, Ho-Young Lee, Hyeshik Chang, Je Kyung Seong, Jun Cho

“…Analyses of canonical Ribo-seq reads (ribosome footprints) highlighted two obstructive characteristics to host gene expression: ribosome stalling on codons within transmembrane domain-coding regions and compromised translation of immunity- and metabolism-related genes with upregulated transcription. …”
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Novel and recurrent FBN1 mutations causing Marfan syndrome in two Chinese families by Dandan Li, Jun Qiao, Dandan Huang, Ruru Guo, Jian Ji, Wei Liu

“…Evolutionary conservation analysis showed that codons 723 and 1,687 were highly conserved among several species. …”
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Evaluation of two new highly multiplexed PCR assays as an alternative to next‐generation sequencing for IDH1/2 mutation detection by Loetitia Favre, Nouhoum Sako, Sihem Tarfi, Violaine Tran Quang, Corine Joy, Aurélie Dupuy, Erell Guillerm, Philippe Gaulard, Orianne Wagner‐Ballon, Anaïs Pujals, Ivan Sloma

“…The ddPCR assay had better analytical performances than the PGX assay with 100% specificity, 100% sensitivity and a detection limit down to 0.5% on IDH1R132, IDH2R140 and IDH2R172 codons, and a high correlation with NGS results. Therefore, the new highly multiplexed ddPCR is a fast and cost‐effective assay that meets most clinical needs to identify and follow cancer patients in the era of anti‐IDH1/2‐targeted therapies.…”
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Translational Read-Through Therapy of <i>RPGR</i> Nonsense Mutations by Christine Vössing, Marta Owczarek-Lipska, Kerstin Nagel-Wolfrum, Charlotte Reiff, Christoph Jüschke, John Neidhardt

“…We evaluated the potential of PTC124 (Ataluren, Translama^TM) treatment to promote ribosomal read-through of premature termination codons (PTC) in <i>RPGR</i>. Expression constructs in HEK293T cells showed that the efficacy of read-through reagents is higher for UGA than UAA PTCs. …”
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Mitochondrial polymorphism m.3017C>T of SHLP6 relates to heterothermy by Sarah V. Emser, Sarah V. Emser, Clemens P. Spielvogel, Eva Millesi, Ralf Steinborn, Ralf Steinborn

“…Public mass spectrometric (MS) data of human SHLP6 indicated a canonical size of 20 amino acids, but not the use of alternative translation initiation codons that would expand the peptide. The shorter isoform of SHLP6 was found in heterothermic rodents at higher frequency compared to homeothermic rodents (p &lt; 0.001). …”
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Phylogeny and Comparative Analysis of Chinese <i>Chamaesium</i> Species Revealed by the Complete Plastid Genome by Xian-Lin Guo, Hong-Yi Zheng, Megan Price, Song-Dong Zhou, Xing-Jin He

“…We also found 20,953–21,115 codons from 53 coding sequence (CDS) regions, 38.4–38.7% GC content of the total genome and low Ka/Ks (0.27–0.43) ratios of 53 aligned CDS. …”
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Usefulness and Limitations of Comprehensive Characterization of mRNA Splicing Profiles in the Definition of the Clinical Relevance of BRCA1/2 Variants of Uncertain Significance by Elisa Gelli, Mara Colombo, Anna Maria Pinto, Giovanna De Vecchi, Claudia Foglia, Sara Amitrano, Valeria Morbidoni, Valentina Imperatore, Siranoush Manoukian, Margherita Baldassarri, Caterina Lo Rizzo, Lorenza Catania, Elisa Frullanti, Enrico Tagliafico, Laura Cortesi, Federica Spaggiari, Maria Antonietta Mencarelli, Eva Trevisson, Paolo Radice, Alessandra Renieri, Francesca Ariani

“…Transcripts with premature stop codons or in-frame loss of functionally important residues were generated. …”
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<i>KRAS</i> p.G12C Mutation in Metastatic Colorectal Cancer: Prognostic Implications and Advancements in Targeted Therapies by Alessandro Ottaiano, Francesco Sabbatino, Francesco Perri, Marco Cascella, Roberto Sirica, Renato Patrone, Maurizio Capuozzo, Giovanni Savarese, Monica Ianniello, Nadia Petrillo, Luisa Circelli, Vincenza Granata, Massimiliano Berretta, Mariachiara Santorsola, Guglielmo Nasti

“…Mutations in <i>KRAS</i> are frequently observed in codons 12 and 13, and these mutations have oncogenic properties. …”
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<i>Halobacterium salinarum</i> and <i>Haloferax volcanii</i> Comparative Transcriptomics Reveals Conserved Transcriptional Processing Sites by Amr Galal Abd El-Raheem Ibrahim, Ricardo Z. N. Vêncio, Alan P. R. Lorenzetti, Tie Koide

“…Of the 244 conserved TPS sites found, the majority were located around start and stop codons of orthologous genes. Specific genes are highlighted when discussing antisense, ribosome and insertion sequence associated TPS. …”
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STRIPAK Dependent and Independent Phosphorylation of the SIN Kinase DBF2 Controls Fruiting Body Development and Cytokinesis during Septation and Ascospore Formation in <i>Sordaria... by Maria Shariatnasery, Valentina Stein, Ines Teichert, Ulrich Kück

“…Furthermore, we constructed <i>dbf2</i> mutants carrying phospho-mimetic and phospho-deficient codons for two conserved phosphorylation sites. Growth tests of the phosphorylation mutants showed that coordinated phosphorylation is crucial for controlling vegetative growth rates and maintaining proper septum distances. …”
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