Next-Generation Sequencing Revealed a Distinct Immunoglobulin Repertoire with Specific Mutation Hotspots in Acute Myeloid Leukemia by Miaoran Xia, Lina Wu, Xiaoping Sun, Xin Han, Huige Yan, Jing Huang, Youhui Zhang, Zhihong Hu, Youli Zu, C. Cameron Yin, Xiaoyan Qiu

“…Moreover, AML-derived IGK was different from classical IGK in B-cells for the high mutation rates and special mutation hotspots at serine codons. Findings of the distinct Ig repertoire in myeloblasts may facilitate the discovery of a new molecular marker for disease monitoring and target therapy.…”
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CRISPR/Cas9-Mediated Knockout of <i>HOS1</i> Reveals Its Role in the Regulation of Secondary Metabolism in <i>Arabidopsis thaliana</i> by Yury Shkryl, Yulia Yugay, Tatiana Avramenko, Valeria Grigorchuk, Tatiana Gorpenchenko, Olga Grischenko, Victor Bulgakov

“…DNA sequencing showed that frameshift indels introduced by genome editing of <i>HOS1</i> resulted in the appearance of premature stop codons, disrupting the open reading frame. Obtained <i>hos1</i>^Cas9 mutant plants were compared with the SALK T-DNA insertion mutant, line <i>hos1-3</i>, in terms of their tolerance to abiotic stresses, accumulation of secondary metabolites and expression levels of genes participating in these processes. …”
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Differentiating Pigs from Wild Boars Based on <i>NR6A1</i> and <i>MC1R</i> Gene Polymorphisms by Anna Koseniuk, Grzegorz Smołucha, Małgorzata Natonek-Wiśniewska, Anna Radko, Dominika Rubiś

“…Along the <i>MC1R</i> gene sequence, we identified four polymorphic loci comprising three codons. The “wild type” allele was primarily found in wild boar but also in the Duroc and Złotnicka White breeds. …”
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Drug resistance and the genotypic characteristics of and in rifampicin- and/or isoniazid-resistant isolates in central Vietnam by Thi Binh Nguyen Nguyen, Thi Kieu Diem Nguyen, Van Hue Trương, Thi Tuyet Ngoc Tran, van Bao Thang Phan, Thi Tuyen Nguyen, Hoang Bach Nguyen, Viet Quynh Tram Ngo, Van Tuan Mai, Paola Molicotti

“…The most frequently detected mutations were at codons 531 (37.5%), 526 (18.8%), and 516 (6.3%). Conclusion To help prevent new cases of DR-TB in Vietnam, it is crucial to gain a comprehensive understanding of the genotypic DR-TB isolates.…”
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Transcriptome-wide analyses of RNA m6A methylation in hexaploid wheat reveal its roles in mRNA translation regulation by Tao Huang, Tao Huang, Wei-Jie He, Wei-Jie He, Cheng Li, Jing-Bo Zhang, Jing-Bo Zhang, Yu-Cai Liao, Yu-Cai Liao, Bo Song, Peng Yang, Peng Yang, Peng Yang

“…Specifically, m6As within coding sequences and 3′UTRs repress the translation of mRNAs while the m6As within 5′UTRs and start codons could promote it. The m6A-containing mRNAs are significantly enriched in processes and pathways of “translation” and “RNA transport,” suggesting the potential role of m6As in regulating the translation of genes involved in translation regulation. …”
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Murine Long Noncoding RNA Morrbid Contributes in the Regulation of NRAS Splicing in Hepatocytes In Vitro by Anna Fefilova, Pavel Melnikov, Tatiana Prikazchikova, Tatiana Abakumova, Ilya Kurochkin, Pavel V. Mazin, Rustam Ziganshin, Olga Sergeeva, Timofei S. Zatsepin

“…The coupling of alternative splicing with the nonsense-mediated decay (NMD) pathway maintains quality control of the transcriptome in eukaryotes by eliminating transcripts with premature termination codons (PTC) and fine-tunes gene expression. Long noncoding RNA (lncRNA) can regulate multiple cellular processes, including alternative splicing. …”
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VNAR development through antigen immunization of Japanese topeshark (Hemitriakis japanica) by Hiroyuki Takeda, Tatsuhiko Ozawa, Tatsuhiko Ozawa, Hiroki Zenke, Yoh Ohnuki, Yuri Umeda, Wei Zhou, Honoka Tomoda, Akihiko Takechi, Kimiyoshi Narita, Takaaki Shimizu, Takuya Miyakawa, Yuji Ito, Tatsuya Sawasaki

“…VNARs that were primarily enriched in the phage display had CDR3 coding sequences with fewer E. coli rare codons, suggesting translation machinery on the selection and enrichment process during biopanning.…”
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Genetic manipulation of porcine deltacoronavirus reveals insights into NS6 and NS7 functions: a novel strategy for vaccine design by Mengjia Zhang, Wan Li, Peng Zhou, Dejian Liu, Rui Luo, Anan Jongkaewwattana, Qigai He

“…We further manipulated the infectious clone by replacing the NS6 gene with a green fluorescent protein (GFP) to generate rPDCoV-ΔNS6-GFP; likewise, rPDCoV-ΔNS7 was constructed by removing the ATG start codons of the NS7 gene. Growth kinetics studies suggest that rPDCoV-ΔNS7 could replicate similarly to that of the wild-type PDCoV, whereas rPDCoV-ΔNS6-GFP exhibited a substantial reduction of viral titer in vitro and in vivo. …”
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Uncovering a 500 million year old history and evidence of pseudogenization for TLR15 by Fabiana Neves, Fabiana Neves, Antonio Muñoz-Mérida, Antonio Muñoz-Mérida, Antonio Muñoz-Mérida, André M. Machado, André M. Machado, Tereza Almeida, Tereza Almeida, Arnaud Gaigher, Arnaud Gaigher, Arnaud Gaigher, Arnaud Gaigher, Pedro J. Esteves, Pedro J. Esteves, Pedro J. Esteves, Pedro J. Esteves, L. Filipe C. Castro, L. Filipe C. Castro, Ana Veríssimo, Ana Veríssimo

“…Holocephalans have long TLR15 protein sequences that disrupt the typical TLR structure, and some species display a pseudogene sequence due to the presence of frameshift mutations and early stop codons. Additionally, TLR15 has low expression levels in holocephalans when compared with other TLR genes. …”
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Genetic diversity across the mitochondrial genome of eastern oysters (Crassostrea virginica) in the northern Gulf of Mexico by Chani R. Rue, Jason D. Selwyn, Patricia M. Cockett, Bryan Gillis, Lauren Gurski, Philip Jose, Brandi L. Kutil, Sharon F. Magnuson, Luz Ángela López de Mesa, R Deborah Overath, Delbert Lee Smee, Christopher E. Bird

“…The pooled-genome-assembled-genomes (PAGs) from Texas exhibited several characteristics indicating that they were valid, including elevated nucleotide diversity in non-coding and the third position of codons, placement as the sister haplotype of the genome from Delaware in a phylogenetic reconstruction of Crassostrea mitochondrial genomes, and a lack of genetic structure in the ND4 gene among the three Texas bays as was found with Sanger amplicons in samples from the same bays several years prior. …”
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The usefulness of the genetic panel in the classification and refinement of diagnostic accuracy of Mexican patients with Marfan syndrome and other connective tissue disorders by Giovanny Fuentevilla-Álvarez, María Elena Soto, Yazmín Estela Torres-Paz, Sergio Enrique Meza-Toledo, Gilberto Vargas-Alarcón, Nadia González-Moyotl, Israel Pérez-Torres, Linaloe Manzano-Pech, Ana Maria Mejia, Claudia Huesca-Gómez, Ricardo Gamboa

“…We observed a high prevalence (65%) of more severe mutations, such as frameshift indels and stop codons, among patients requiring invasive treatments like aortic valve-sparing surgery, Bentall and de Bono procedures, or aortic valve replacement due to severe cardiovascular injury. …”
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Detection of <i>CTNNB1</i> Hotspot Mutations in Cell-Free DNA from the Urine of Hepatocellular Carcinoma Patients by Selena Y. Lin, Ting-Tsung Chang, Jamin D. Steffen, Sitong Chen, Surbhi Jain, Wei Song, Yih-Jyh Lin, Ying-Hsiu Su

“…Using a short amplicon qPCR assay targeting HCC mutational hotspot <i>CTNNB1</i> codons 32–37 (exon 3), we detected <i>CTNNB1</i> mutations in 25% (18/73) of HCC tissues and 24% (15/62) of pre-operative HCC urine samples in two independent cohorts. …”
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Pneumococcal BgaA Promotes Host Organ Bleeding and Coagulation in a Mouse Sepsis Model by Moe Takemura, Moe Takemura, Masaya Yamaguchi, Momoko Kobayashi, Tomoko Sumitomo, Yujiro Hirose, Daisuke Okuzaki, Masayuki Ono, Daisuke Motooka, Kana Goto, Kana Goto, Masanobu Nakata, Masanobu Nakata, Narikazu Uzawa, Shigetada Kawabata

“…Our previous molecular evolutionary analysis revealed that the S. pneumoniae gene bgaA, encoding the enzyme β-galactosidase (BgaA), had a high proportion of codons under negative selection among the examined pneumococcal genes and that deletion of bgaA significantly reduced host mortality in a mouse intravenous infection assay. …”
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Genetically manipulating endogenous Kras levels and oncogenic mutations in vivo influences tissue patterning of murine tumorigenesis by Özgün Le Roux, Nicole LK Pershing, Erin Kaltenbrun, Nicole J Newman, Jeffrey I Everitt, Elisa Baldelli, Mariaelena Pierobon, Emanuel F Petricoin, Christopher M Counter

“…To attempt to separate these two effects, we generated four novel Cre-inducible (LSL) Kras alleles in mice with the biochemically distinct G12D or Q61R mutations and encoded by native (nat) rare or common (com) codons to produce low or high protein levels. While there were similarities, each allele also induced a distinct transcriptional response shortly after activation in vivo. …”
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Fluoroquinolone heteroresistance, antimicrobial tolerance, and lethality enhancement by Amit Singh, Amit Singh, Xilin Zhao, Xilin Zhao, Karl Drlica

“…Rapid DNA-based detection methods exploit the finding that fluoroquinolone-resistant substitutions occur largely in a few codons of DNA gyrase. A second approach for restricting the emergence of resistance involves understanding fluoroquinolone lethality through studies of antimicrobial tolerance, a condition in which bacteria fail to be killed even though their growth is blocked by lethal agents. …”
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The Complete Mitochondrial Genome of a Neglected Breed, the Peruvian Creole Cattle (<i>Bos taurus</i>), and Its Phylogenetic Analysis by Carlos I. Arbizu, Rubén D. Ferro-Mauricio, Julio C. Chávez-Galarza, Héctor V. Vásquez, Jorge L. Maicelo, Carlos Poemape, Jhony Gonzales, Carlos Quilcate, Flor-Anita Corredor

“…The most frequently used codons were CUA (leucine), AUA (isoleucine), AUU (isoleucine), AUC (isoleucine), and ACA (threonine). …”
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Autosomal recessive primary microcephaly type 2 associated with a novel WDR62 splicing variant that disrupts the expression of the functional transcript by Haizhu Chen, Haizhu Chen, Ying Zheng, Ying Zheng, Hua Wu, Hua Wu, Naiqing Cai, Naiqing Cai, Guorong Xu, Guorong Xu, Yi Lin, Yi Lin, Jin-Jing Li, Jin-Jing Li

“…A molecular analysis uncovered a novel homozygous variant c.4154–6 C &gt; G in the WDR62 intron, and a functional analysis confirmed the pathogenicity of this mutation, resulting in the formation of an abnormal transcript with premature termination codons.ConclusionThis study enhances our understanding of the genetic heterogeneity associated with MCPH and highlights the pivotal role of genetic testing in the diagnosing and managing of rare neurodevelopmental disorders. …”
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Molecular Pharming of the Recombinant Protein hEGF-hEGF Concatenated with Oleosin Using Transgenic <i>Arabidopsis</i> by Weidong Qiang, Tingting Gao, Xinxin Lan, Jinnan Guo, Muhammad Noman, Yaying Li, Yongxin Guo, Jie Kong, Haiyan Li, Linna Du, Jing Yang

“…Under a phaseolin promoter, we concatenated oleosin gene to double hEGF (hEGF–hEGF) with plant-preferred codons in the expression vectors and the construct was transformed into <i>Arabidopsis thaliana</i> (Arabidopsis). …”
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Structure-Based Redesign of the Binding Specificity of Anti-Apoptotic Bcl-x[subscript L] by Chen, T. Scott, Palacios, Hector, Keating, Amy E.

“…Sequence features were identified using structure-based modeling, and an optimization algorithm based on integer programming was used to select degenerate codons that maximally covered these features. A constraint on library size was used to ensure thorough sampling. …”
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Prion induction involves an ancient system for the sequestration of aggregated proteins and heritable changes in prion fragmentation by Tyedmers, Jens, Treusch, Sebastian, Dong, Jijun, McCaffery, J. Michael, Bevis, Brooke J., Lindquist, Susan

“…When the translation termination factor Sup35 adopts the prion state, [PSI+], the read-through of stop codons increases, uncovering hidden genetic variation and giving rise to new, often beneficial, phenotypes. …”
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