Bioinformatic Analysis Reveals the Role of Translation Elongation Efficiency Optimisation in the Evolution of <i>Ralstonia</i> Genus by Aleksandra Y. Korenskaia, Yury G. Matushkin, Zakhar S. Mustafin, Sergey A. Lashin, Alexandra I. Klimenko

“…We found that the soil <i>Ralstonia</i> have a significantly lower number and energy of potential secondary structures in mRNA and an increased role of codon usage bias in the optimization of highly expressed genes’ translation elongation efficiency, not only compared to phytopathogenic <i>Ralstonia</i> but also to <i>Cupriavidus necator</i>, which is closely related to the <i>Ralstonia</i> genus. …”
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The complete chloroplast genome of Cicer reticulatum and comparative analysis against relative Cicer species by Ezgi Mehmetoğlu, Yasin Kaymaz, Duygu Ateş, Abdullah Kahraman, Muhammed Bahattin Tanyolaç

“…The study also included codon usage frequency analysis, hotspot divergence analysis, and phylogenetic analysis using various bioinformatics tools. …”
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Population Variability Generated during Rescue Process and Passaging of Recombinant Mumps Viruses by Anamarija Slović, Tanja Košutić-Gulija, Dubravko Forčić, Maja Šantak, Maja Jagušić, Mirna Jurković, Dorotea Pali, Jelena Ivančić-Jelečki

“…As we show for Pro408Leu mutation in L gene and a stop codon in one of ATUs, positively selected variants can rise to frequencies over 85% in only few passages.…”
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Morphological Correlates of KIT and PDGFRA Genotypes in Gastrointestinal Stromal Tumour by Valli PRIYA, Niraj KUMARI, Narendra KRISHNANI

“…KIT exon 11 deletion was associated with gastric location (60%) (p=0.04), spindle cells (63.3%), and high-risk stratification (66.6%) (p=0.01) while KIT exon 9 mutation was common in small intestine (66.7%) (p=0.04), in higher risk groups (66.7%) (p=0.01) and 75% of codon 502-503 duplications (p=0.03). PDGFRA 18 mutation was common in males (p=0.03), in gastric location (62.5%) (p=0.04), in cases showing mild to moderate atypia (62.5%) (p=0.01) and lower risk stratification (62.5%) (p=0.01). …”
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Effect of X-rays on Seedling Pigment, Biochemical Profile, and Molecular Variability in <i>Astrophytum</i> spp. by Piotr Licznerski, Justyna Lema-Rumińska, Emilia Michałowska, Alicja Tymoszuk, Janusz Winiecki

“…Remarkably high polymorphism rates were observed, ranging from 59.09% for primer S12 to a full 100.0% for S3 and S8, as determined by the SCoT (Start-Codon-Targeted) marker. In addition, a large variation in the content of plant pigments (anthocyanins, carotenoids, chlorophyll a, and chlorophyll b) was noted. …”
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The Nef Protein of the Macrophage Tropic HIV-1 Strain AD8 Counteracts Human BST-2/Tetherin by Sebastian Giese, Scott P. Lawrence, Michela Mazzon, Bernadien M. Nijmeijer, Mark Marsh

“…However, at least one M group HIV-1 strain, the macrophage-tropic primary AD8 isolate, is unable to express Vpu due to a mutation in its translation initiation codon. Here, using primary monocyte-derived macrophages (MDMs), we show that AD8 Nef protein can compensate for the absence of Vpu and restore virus release to wild type levels. …”
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Identifying two pathogenic variants in a patient with pigmented paravenous retinochoroidal atrophy by Liu Zeyuan, Wang He, He Xiaoli, Tao Dan, Li Li

“…Two heterozygous pathogenic variants were detected by WES according to the American college of medical genetics and genomics guidelines, including NM_020366.4: c.2592T > G: p.Y864* and NM_020366.4: c.154C > T: p.R52* in RPGRIP1 located in exon 17 and exon 3, leading to termination codon, respectively. This is the first study reporting pathogenic variants within RPGRIP1 as causal for PPRCA.…”
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Sign of APOBEC editing, purifying selection, frameshift, and in-frame nonsense mutations in the microevolution of lumpy skin disease virus by Perumal Arumugam Desingu, T. P. Rubeni, K. Nagarajan, K. Nagarajan, Nagalingam R. Sundaresan

“…Furthermore, the present study has brought to light that the selection pressure for codons usage bias is mostly exerted by purifying selection, and this process is possibly caused by APOBEC editing. …”
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Optimization of the Cry2Aa gene and development of insect-resistant and herbicide-tolerant photoperiod-sensitive genic male sterile rice by Lushui Weng, Lihua Deng, Fengxiang Lai, Guoying Xiao

“…In this study, an optimized Cry2Aa gene was obtained after codon optimization based on the preferred codons in rice. …”
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A novel fungal beta-propeller phytase from nematophagous Arthrobotrys oligospora: characterization and potential application in phosphorus and mineral release for feed processing by Xianjuan Hou, Zhen Shen, Na Li, Xiaowei Kong, Kangliang Sheng, Jingmin Wang, Yongzhong Wang

“…The heterologous expression of codon-optimized Aophytase gene in Pichia pastoris was successfully investigated to yield recombinant Aophytase (r-Aophytase) with high specific enzyme activity of 74.71 U/mg, much higher than those of recombinant BPP phytases derived bacteria. …”
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The Role of DND1 in Cancers by Yun Zhang, Jyotsna D. Godavarthi, Abie Williams-Villalobo, Shahrazad Polk, Angabin Matin

“…The <i>Ter</i> mutation in Dead-End 1 (<i>Dnd1</i>), <i>Dnd1^Ter</i>, which leads to a premature stop codon, has been determined to be the cause for primordial germ cell deficiency, accompanied with a high incidence of congenital testicular germ cell tumors (TGCTs) or teratomas in the 129/Sv-<i>Ter</i> mice. …”
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Safe use of the ketogenic diet in an infant with microcephaly, epilepsy, and diabetes syndrome: a case report by Walter A. Zegarra, William B. Gallentine, Maura R. Ruzhnikov, Catherine A. McAndrews, Anna L. Gloyn, Ananta Addala

“…An epilepsy gene panel identified bi-allelic variants, c.239T > G (p.Leu80*) and c.2T > A (initiator codon), in IER3IP1 that were subsequently shown to be inherited in trans. …”
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Minimal Contribution of APOBEC3-Induced G-to-A Hypermutation to HIV-1 Recombination and Genetic Variation. by Krista A Delviks-Frankenberry, Olga A Nikolaitchik, Ryan C Burdick, Robert J Gorelick, Brandon F Keele, Wei-Shau Hu, Vinay K Pathak

“…Confounding factors contributing to the debate include the extent of lethal (stop codon) and sublethal hypermutation induced by different APOBEC3 proteins, the inability to distinguish between G-to-A mutations induced by APOBEC3 proteins and error-prone viral replication, the potential impact of hypermutation on the frequency of retroviral recombination, and the extent to which viral recombination occurs in vivo, which can reassort mutations in hypermutated genomes. …”
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Proteome analysis of high affinity mouse saliva proteins to hydroxyapatite by Keijiro Ohshima, Tomoko Ohshima, Karen Meyer, Eisuke Takai, Shunsuke Yoshizawa, Kentaro Shiraki, Nobuko Maeda

“…Total RNA from the salivary glands of both mouse strains, PCR amplification of cDNA with a CAVI specific primer, and sequence analysis revealed one different base in codon 96, resulting in one different amino acid. …”
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High-Resolution Ribosome Profiling Reveals Gene-Specific Details of UGA Re-Coding in Selenoprotein Biosynthesis by Simon Bohleber, Noelia Fradejas-Villar, Wenchao Zhao, Uschi Reuter, Ulrich Schweizer

“…Co-translational incorporation of selenocysteine (Sec) into selenoproteins occurs at UGA codons in a process in which translational elongation competes with translational termination. …”
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A Homozygous Deep Intronic Variant Causes Von Willebrand Factor Deficiency and Lack of Endothelial-Specific Secretory Organelles, Weibel–Palade Bodies by Hamideh Yadegari, Muhammad Ahmer Jamil, Natascha Marquardt, Johannes Oldenburg

“…This would lead to an aberrant mRNA that contains a premature stop codon, targeting it to nonsense-mediated mRNA decay. …”
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An unmodified wobble uridine in tRNAs specific for Glutamine, Lysine, and Glutamic acid from Salmonella enterica Serovar Typhimurium results in nonviability-Due to increased missen... by Kristina Nilsson, Gunilla Jäger, Glenn R Björk

“…Accordingly, it was suggested that the primary function of mcm5s2U34 in these yeast tRNAs is to improve cognate codon reading rather than prevents missense errors. …”
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The Phylogenetic Relationship of Lamiinae (Coleoptera: Cerambycidae) Using Mitochondrial Genomes by Ke Li, Sheng-Wu Yu, Hao Hu, Yu-Feng Feng, Kenneth B. Storey, Yue Ma, Jia-Yong Zhang, Dan-Na Yu

“…Other mitochondrial structural features were also observed: the start codon in the nad1 gene of all 11 mitochondrial genomes is TTG; 17–22 bp intergenic spacers (IGS) with a ‘TACTA’ motif were found between <i>trnS2</i> and nad1. …”
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Pathogenic Variant Rs1471414348of the TTN Gene in the Patient with Familial Left Venticular Noncompaction Cardiomyopathy by O. V. Kulikova, A. N. Meshkov, R. P. Myasnikov, A. V. Kiseleva, S. N. Koretsky, A. A. Zharikova, M. S. Kharlap, E. A. Mershina, V. E. Sinitsyn, O. P. Skirko, I. A. Efimova, M. S. Pokrovskaya, S. A. Boytsov, O. M. Drapkina

“…One likely pathogenic variant (rs1471414348, stop codon) in the TTN gene was detected. The discovered variant was validated by Sanger sequencing and was detected only in the proband and his mother, and was absent in other relatives. …”
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Improving growth properties of Corynebacterium glutamicum by implementing an iron‐responsive protocatechuate biosynthesis by Felix Thoma, Christof Appel, Dominik Russ, Janine Huber, Felix Werner, Bastian Blombach

“…Reduction of the degradation was achieved by mitigating expression of the pcaG and pcaH genes through a start codon exchange. The final strain C. glutamicum IRON+ showed in the absence of PCA a significantly increased intracellular Fe2+ availability, exhibited improved growth properties on glucose and acetate, retained a wild type‐like biomass yield but did not accumulate PCA in the supernatant. …”
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