Evolutionary rate analyses of orthologs and paralogs from 12 Drosophila genomes. by Heger, A, Ponting, C

“…Constraints on amino acid sequences appear to have been most pronounced on D. ananassae and least pronounced on D. simulans and D. erecta terminal lineages. Codons predicted to have been subject to positive selection were found to be significantly over-represented among genes with roles in immune response and RNA metabolism, with the latter category including each subunit of the Dicer-2/r2d2 heterodimer. …”

Exclusion of ZFM1 as a candidate gene for multiple endocrine neoplasia type 1 (MEN1). by Lloyd, SE, Pang, J, Pearce, S, Leigh, SE, Thakker, R

“…A 6-bp deletion that resulted in the loss of two proline residues at codons 479 and 480 in exon 12 was found in one MEN1 patient. …”

Low prevalence of genotypic drug resistance mutations among antiretroviral-naive HIV type 1 patients in Malaysia by Tee, K.K., Kamarulzaman, A., Ng, K.P.

“…The majority of the patients were recently diagnosed. Codons 20-255 of the RT and 1-96 of the protease gene were examined for major and minor mutations associated with antiretroviral resistance reported by the International AIDS Society-USA (IAS-USA) Drug Resistance Mutations Group. …”

The Translated Amino Acid Sequence of an Insertion in the Hepatitis E Virus Strain 47832c Genome, But Not the RNA Sequence, Is Essential for Efficient Cell Culture Replication by Johannes Scholz, Alexander Falkenhagen, Reimar Johne

“…A mutant encoding a frameshift of the inserted sequence was not infectious, whereas a mutant carrying synonymous codons in this region replicated similar like the wild type. …”
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Efficient and Safe Editing of Porcine Endogenous Retrovirus Genomes by Multiple-Site Base-Editing Editor by Shuwen Zheng, Haiwen Zhong, Xiaoqing Zhou, Min Chen, Wansheng Li, Yin Zi, Yue Chi, Jinling Wang, Wei Zheng, Qingjian Zou, Liangxue Lai, Chengcheng Tang

“…Seven sgRNAs were set to target <i>gag</i> and <i>pol</i> loci of PERVs to induce premature stop codons. We found that approximately 10% of cell clones were completely inactivated for PERVs in pig ST cells, and the plasmid that was used for editing the PERVs did not integrate into host genome and influence the karyotype of the modified cells. …”
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PCR-Based Detection and Genetic Characterization of Parainfluenza Virus 5 Detected in Pigs in Korea from 2016 to 2018 by Ha-Thai Truong, Van-Giap Nguyen, Le-Bich-Hang Pham, Thi-My-Le Huynh, Jasper Lee, Su-Jin Hwang, Jae-Myun Lee, Hee-Chun Chung

“…The evolution of two structural protein-coding genes was largely under purifying selection. A few codons (6/9 for the F gene, 7/8 for the HN gene) had elevated dN/dS values, which were loaded on internal branches and were predicted to be related to beneficial trait(s) of the virus.…”
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The VP53 protein encoded by RNA2 of a fabavirus, broad bean wilt virus 2, is essential for viral systemic infection by Myung-Hwi Kim, Boram Choi, Seok-Yeong Jang, Ji-Soo Choi, Sora Kim, Yubin Lee, Suejin Park, Sun-Jung Kwon, Jin-Ho Kang, Jang-Kyun Seo

“…It is hypothesized that BBWV2 RNA2 possesses two alternative in-frame translation initiation codons, resulting in the production of two largely overlapping proteins, VP53 and VP37. …”
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Examination of Factors Affecting Site-Directed RNA Editing by the MS2-ADAR1 Deaminase System by Md Thoufic Anam Azad, Umme Qulsum, Toshifumi Tsukahara

“…Using this system in transfected HEK-293 cells, we evaluated the effects of changing the length and position of the guide RNA on the efficiency of conversion of amber (TAG) and ochre (TAA) stop codons to tryptophan (TGG) in the target. Guide RNAs of 19, 21 and 23 nt were positioned upstream and downstream of the MS2-RNA, providing a total of six guide RNAs. …”
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Designing and comparison study of rapid detection methods of resistance to injectable drugs in clinical strains of Mycobacterium tuberculosis by Fatemeh Salehi, Bahareh Rahimiyan Zarif, Azam Ahmadi, Mana Shojapour, Toktam Polad, Mohammad Arjomandzadegan

“…Furthermore, allele specific method (as PCR) was designed for detection mutations in codons 1401 and 1402 gene rrs. Some selected isolates were sequenced.Results: In PCR-RFLP method, among the 70 strains examined by BstFNI enzyme, could detect 17 mutant strains among 24 phenotypicaly resistant and 44 non-mutant isolates from 46 susceptible isolates. …”
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Prevalence of rifampicin-resistant Mycobacterium tuberculosis among human-immunodeficiency-virus-seropositive patients and their treatment outcomes by C.K. Vidyaraj, A. Chitra, S. Smita, M. Muthuraj, S. Govindarajan, B. Usharani, S. Anbazhagi

“…High death rate (13, 36.1%, 95% confidence interval 20.8–53.8) was observed in this study among the patients who had mutations at the 530–533 codons. The present study emphasized the prerequisite to monitor the trend of drug-resistant TB in various mutant populations in order to timely implement appropriate interventions to curb the threat of MDR-TB.…”
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Perspective in Alternative Splicing Coupled to Nonsense-Mediated mRNA Decay by Juan F. García-Moreno, Luísa Romão

“…Nonsense-mediated RNA decay (NMD) is an mRNA surveillance pathway that recognizes and selectively degrades transcripts containing premature translation-termination codons (PTCs), thereby preventing the production of truncated proteins. …”
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Evaluating the effects of non-neutral molecular markers on phylogeny inference. by Dawn M Roje

“…To evaluate the possible effect(s) of positively versus negatively selected sites, the three non-neutral markers were analyzed to determine the presence of positively and negatively selected codons. To determine congruence in topology among ML trees inferred by individual neutral and non-neutral markers, as well as the combined (concatenated) dataset, tree, comparisons of distances among trees and hypothesis (topology) testing were carried out. …”
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The complete plastid genome of the endangered shrub Brassaiopsis angustifolia (Araliaceae): Comparative genetic and phylogenetic analysis. by Zhanghong Dong, Ruli Zhang, Ming Shi, Yu Song, Yaxuan Xin, Feng Li, Jianzhong Ma, Peiyao Xin

“…All protein-coding genes consisted of 21,582 codons. Among the nine species of Araliaceae, simple sequence repeats (SSRs) and five large repeat sequences were identified with total numbers ranging from 37 to 46 and 66 to 78, respectively. …”
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Exploring the selective constraint on the sizes of insertions and deletions in 5' untranslated regions in mammals by Chen Feng-Chi, Liao Ben-Yang, Chen Chun-Hsi

“…In 5'untranslated regions (5'UTRs) in mammalian genomes, upstream start codons (uAUGs) and upstream open reading frames (uORFs) can regulate protein translation. …”
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Viral and Cellular Factors Contributing to the Hematogenous Dissemination of Human Cytomegalovirus via Polymorphonuclear Leukocytes by Berenike Braun, Kerstin Laib Sampaio, Anna K. Kuderna, Miriam Widmann, Christian Sinzger

“…We aimed to identify viral components that contribute to PMN-mediated transmission and test the hypothesis that cellular adhesion molecules shield transmission sites from entry inhibitors. Stop codons were introduced into the genome of HCMV strain Merlin to delete pUL74 of the trimeric and pUL128 of the pentameric glycoprotein complex and the tegument proteins pp65 and pp71. …”
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Variability among the Isolates of Broad Bean Mottle Virus and Encapsidation of Host RNAs by Nipin Shrestha, Melvin R. Duvall, Jozef J. Bujarski

“…Both the 5′ and 3′ untranslated terminal regions (UTRs) among the corresponding RNAs are highly conserved, reflecting their functionality in virus replication. The AUG initiation codons are within suboptimal contexts, possibly to adjust/regulate translation. …”
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The selection pressure on the neuraminidase gene of influenza viruses isolated in Ukraine from 2009 to 2015 by Svetlana V. Babii, Liudmyla V. Leibenko, Larysa V. Radchenko, Olga S. Golubka, Nataliia V. Teteriuk, Alla P. Mironenko

“…With the help of this method, we showed that only a few codons in the NA gene were under positive selection resulting in mutations at the following sites: for influenza A viruses of the A(H1N1)pdm09 subtype – site 40, for viruses of the A(H3N2) subtype – sites 93 and 402, for Influenza B viruses of the B/Yamagata lineage – sites 74, 99, and 268, and for the viruses of the B/Victoria lineage – sites 358, 288, and 455. …”
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Mini-dCas13X–mediated RNA editing restores dystrophin expression in a humanized mouse model of Duchenne muscular dystrophy by Guoling Li, Ming Jin, Zhifang Li, Qingquan Xiao, Jiajia Lin, Dong Yang, Yuanhua Liu, Xing Wang, Long Xie, Wenqin Ying, Haoqiang Wang, Erwei Zuo, Linyu Shi, Ning Wang, Wanjin Chen, Chunlong Xu, Hui Yang

“…Approximately 10% of monogenic diseases are caused by nonsense point mutations that generate premature termination codons (PTCs), resulting in a truncated protein and nonsense-mediated decay of the mutant mRNAs. …”
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The Complete Mitogenome of the Wood-Feeding Cockroach Cryptocercus meridianus (Blattodea: Cryptocercidae) and Its Phylogenetic Relationship among Cockroach Families by Weijun Li, Zongqing Wang, Yanli Che

“…The protein-coding genes are initiated with typical mitochondrial start codons except for cox1 with TTG. The gene order of the C. meridianus mitogenome differs from the typical insect pattern for the translocation of tRNA-SerAGN, while the mitogenomes of the other two Cryptocercus species, C. relictus and C. kyebangensis, are consistent with the typical insect pattern. …”
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Uncovering natural allelic and structural variants of OsCENH3 gene by targeted resequencing and in silico mining in genus Oryza by Karminderbir Kaur, Kumari Neelam, Jasdeep Singh, Palvi Malik, Kuldeep Singh

“…O. longistaminata accessions carry SNPs in four codons along with indels in introns 3 and 6. Fifteen haplotypes were mined from our panel; representative mutant alleles exhibited structural variations upon modeling. …”
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