Spontaneous Mutations in HIV-1 Gag, Protease, RT p66 in the First Replication Cycle and How They Appear: Insights from an In Vitro Assay on Mutation Rates and Types by Joshua Yi Yeo, Darius Wen-Shuo Koh, Ping Yap, Ghin-Ray Goh, Samuel Ken-En Gan

“…Mutational free energies of the ‘A to G’ mutations revealed an avoidance of destabilizing effects, with the natural p66 gene codon usage providing barriers to disruptive amino acid changes. …”
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Improving Expression of Pepsinogen A from <i>Homo sapiens</i> in <i>Aspergillus niger</i> by Using a Multi-Copy Gene Knock-in Strategy by Jie Chen, Ling Gui, Boyu Chen, Yuang Sun, Yongcan Zhao, Fuping Lu, Ming Li

“…The <i>hPGA5</i> gene codon was optimized according to the codon bias of <i>A. niger</i> and then connected to a strong promoter and signal peptide to construct an <i>hPGA5</i> expression cassette. …”
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The complete chloroplast genome of Hibiscus syriacus using long-read sequencing: Comparative analysis to examine the evolution of the tribe Hibisceae by Hyunjin Koo, Ah-Young Shin, Ah-Young Shin, Seongmin Hong, Yong-Min Kim, Yong-Min Kim, Yong-Min Kim

“…Among them, ndhD and rpoC1, containing traces of RNA-editing events associated with adaptive evolution, were identified by analysis of putative RNA-editing sites. Codon usage analysis revealed a preference for A/U-terminated codons. …”
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MicroRNAs control mRNA fate by compartmentalization based on 3′ UTR length in male germ cells by Ying Zhang, Chong Tang, Tian Yu, Ruirui Zhang, Huili Zheng, Wei Yan

“…Result Among all small noncoding RNAs studied, miRNAs displayed the most dynamic changes in both abundance and subcytoplasmic localization. mRNAs with shorter 3′ UTRs became increasingly enriched in RNPs from pachytene spermatocytes to round spermatids, and the enrichment of shorter 3′ UTR mRNAs in RNPs coincided with newly synthesized miRNAs that target these mRNAs at sites closer to the stop codon. In contrast, the translocation of longer 3′ UTR mRNAs from RNPs to polysomes correlated with the production of new miRNAs that target these mRNAs at sites distal to the stop codon. …”
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Case Report: β-thalassemia major on the East African coast [version 1; peer review: 2 approved] by Neema Mturi, Alexander W. Macharia, George Mochamah, Anna Färnert, Thad Howard, Thomas N. Williams, Russell E. Ware, Johnstone Makale, Peter Olupot-Olupot

“…One of the mutations identified was a rare β-globin gene initiation codon mutation (ATG➝ACG) (rs33941849). Here we present a patient with β-thalassemia major resulting from this mutation, only the second homozygous patient to have been reported.  …”
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Structural organization and sequence diversity of the complete nucleotide sequence encoding the Plasmodium malariae merozoite surface protein-1 by Chaturong Putaporntip, Napaporn Kuamsab, Rattanaporn Rojrung, Sunee Seethamchai, Somchai Jongwutiwes

“…The rate of nonsynonymous nucleotide substitutions significantly exceeded that of synonymous nucleotide substitutions in block IV, suggesting positive selection in this region. Codon-based analysis of deviation from neutrality has identified a codon under purifying selection located in close proximity to the homologous region of the 38 kDa/42 kDa cleavage site of P. falciparum MSP1. …”
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Resistance to thyroid hormone due to a novel mutation in the thyroid beta receptor (THRβ) gene coexisting with autoimmune thyroid disease—A case report by Elżbieta Skowrońska-Jóźwiak, Elżbieta Skowrońska-Jóźwiak, Agnieszka Gach, Anna Cyniak-Magierska, Anna Nykel, Monika Jurkowska, Andrzej Lewiński, Andrzej Lewiński

“…The mutation has not been described in the literature yet; however, THRβ codon 453 represents a mutational hot spot, frequently altered in the TH receptor ß gene. …”
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Conserved Double Translation Initiation Site for Δ160p53 Protein Hints at Isoform’s Key Role in Mammalian Physiology by Maria José López-Iniesta, Shrutee N. Parkar, Ana Catarina Ramalho, Rafaela Lacerda, Inês F. Costa, Jingyuan Zhao, Luísa Romão, Marco M. Candeias

“…Here, we identified a translation initiation site nine codons downstream of codon 160—the known initiation codon for the translation of Δ160p53—that is recognized by the translation machinery. …”
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Patterns of Genetic Diversity among Alphasatellites Infecting <i>Gossypium</i> Species by Muhammad Mubin, Arzoo Shabbir, Nazia Nahid, Iram Liaqat, Muhammad Hassan, Nada H. Aljarba, Ahmed Al Qahtani, Claude M. Fauquet, Jian Ye, Muhammad Shah Nawaz-ul-Rehman

“…However, unlike other begomoviruses and satellites, the first codon position of alpha-Rep rapidly changed compared to the second and third codon positions. …”
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Association of P53 (+16ins-Arg) Haplotype with the Increased Susceptibility to Breast Cancer in Iranian-Azeri Women by Nasser Pouladi, Roghayeh dehghan, Mohammadali Hosseinpour Feizi, Narges dastmalchi

“…Results: Our findings did not show a significant association of P53 intron 3 and codon 72 polymorphisms with the risk of breast neoplastic tumors among Iranian-Azeri women. …”
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Novel Polymorphisms and Genetic Features of the Prion Protein Gene (<i>PRNP</i>) in Cats, Hosts of Feline Spongiform Encephalopathy by Hyeon-Ho Kim, Yong-Chan Kim, Kiwon Kim, An-Dang Kim, Byung-Hoon Jeong

“…In addition, asparagine at codon 166 of cat PrP was predicted to have longer hydrogen bond than aspartic acid at codon 163 of canine PrP. …”
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A Listeria monocytogenes ST2 clone lacking chitinase ChiB from an outbreak of non-invasive gastroenteritis by Sven Halbedel, Rita Prager, Sangeeta Banerji, Sylvia Kleta, Eva Trost, Gopala Nishanth, Georg Alles, Christina Hölzel, Friederike Schlesiger, Ariane Pietzka, Dirk Schlüter, Antje Flieger

“…A comparative genomic approach identified a premature stop codon in the chiB gene, encoding one of the two L. monocytogenes chitinases, which clustered with disease outcome. …”
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Caracterização de Mutações no Gene BRCA1 em Pacientes com Câncer de Mama e ou Ovário Hereditários do Instituto Nacional de Câncer-RJ by Juliano Javert Lourenço

“…Sete mutações (15%) foram encontradas em BRCA1 entre os 47 pacientes incluídos na investigação: uma idêntica inserção (insC 5382) foi encontrada no éxon 20 de quatro pacientes, uma deleção de quatro pares de bases (3450 del4 CAAG) no éxon 11, resultando em um códon de parada, no quinto paciente; uma transição (T>C IVS 17+2) no íntron 17, afetando o sítio de processamento do ARNm no sexto paciente; e uma transição C>T resultante em um códon de parada (Q1135X) no éxon 11 do sétimo paciente. …”
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Gain of function in somatic TP53 mutations is associated with immune‐rich breast tumors and changes in tumor‐associated macrophages by Michael Behring, Ana I. Vazquez, Xiangqin Cui, Marguerite R. Irvin, Akinyemi I. Ojesina, Sumit Agarwal, Upender Manne, Sadeep Shrestha

“…Results Within TP53‐mutated samples, a mutation at codon p.R175H was shown to be present at higher frequency in immune‐rich tumors. …”
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Monoallelic variants resulting in substitutions of MAB21L1 Arg51 Cause Aniridia and microphthalmia. by Hildegard Nikki Hall, Hemant Bengani, Robert B Hufnagel, Giuseppe Damante, Morad Ansari, Joseph A Marsh, Graeme R Grimes, Alex von Kriegsheim, David Moore, Lisa McKie, Jamalia Rahmat, Catia Mio, Moira Blyth, Wee Teik Keng, Lily Islam, Meriel McEntargart, Marcel M Mannens, Veronica Van Heyningen, Joe Rainger, Brian P Brooks, David R FitzPatrick

“…Substitutions of the same codon (Arg51) in MAB21L2, a close homolog of MAB21L1, cause severe ocular and skeletal malformations in humans and mice. …”
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<i>Microbacterium</i> Cluster EA Bacteriophages: Phylogenomic Relationships and Host Range Predictions by Mark Milhaven, Cyril J. Versoza, Aman Garg, Lindsey Cai, Sanjana Cherian, Kamalei Johnson, Kevin Salas Perez, Madison Blanco, Jackelyn Lobatos, Corinne Mitra, Maria Strasser, Susanne P. Pfeifer

“…Interestingly, bacteriophages of all sub-clusters exhibit codon usage preference patterns that resemble those of bacterial strains different from ones used for isolation, suggesting that they might be able to infect additional hosts. …”
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Prevalence and mutations of β-thalassemia trait and abnormal hemoglobins in premarital screening in Çanakkale province, Turkey by Uludağ A, Uysal A, Uludağ A, Ertekin YH, Tekin M, Kütük B, Silan F, Özdemir Ö

“…These mutations were found to be HBB: c.93-21G>A [IVS-I-110 (G>A)], 26.08% (12/46); HBB: c.17_ 18delCT [codon 5 (‒CT)], 10.85% (5/46); HBB: c.20delA [codon 6 (‒A)] 8.69% (4/46). …”
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Complete Mitogenome Analysis of Five Leafhopper Species of Idiocerini (Hemiptera: Cicadellidae) by Lili Tian, Wenxin Yang, Chengyan Si, Xianguang Guo, Bin Zhang

“…The less pronounced genes (0.5 < dN/dS < 1) were <i>nad5</i> and <i>nad4l</i> in Idiocerin, whereas in the family Cicadellidae including the sequences of Idiocerin, <i>nad1</i>-<i>nad6</i> and <i>cox1</i> genes were less pronounced. The codon encoding leucine was the most common in all species, and the codon encoding serine 1 was the most common in all species except for <i>P. opacus</i>. …”
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Expression and enzymatic activity analysis of non-structure protein 14 of SARS-CoV-2 by CHEN Shuang, XU Jingwen, DING Kaiyun, LIU Jiansheng, PENG Xiaozhong, LIU Hongqi

“…Methods This study firstly analyzed the rare codons in the gene of nsp14 according to the codon usage bias of E. coli, followed by codon optimization. …”
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Characterization and phylogenetic implications of newly sequenced mitogenomes of Five Mileewa and Processina species from China (Hemiptera: Cicadellidae: Mileewinae) by Hongli He, Bin Yan, Xiaofei Yu, Maofa Yang

“…For protein-coding genes (PCGs), ATN was the start codon, while atp8 and nad5 genes were initiated with TTG, and a great majority of them used TAA or TAG as stop codons, whereas cox2 and nad1 ended with an incomplete codon T–. …”
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