Immunoinformatic-Based Multi-Epitope Vaccine Design for Co-Infection of <i>Mycobacterium tuberculosis</i> and SARS-CoV-2 by Cong Peng, Fengjie Tang, Jie Wang, Peng Cheng, Liang Wang, Wenping Gong

“…Immune simulation and codon optimization were carried out using immunoinformatics and molecular biology tools. (3) Results: The S7D5L4 vaccine showed good physical properties, such as solubility, stability, non-sensitization, and non-toxicity. …”
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Comparative Analysis of Complete Chloroplast Genome Sequences of Wild and Cultivated <i>Bougainvillea</i> (Nyctaginaceae) by Mary Ann C. Bautista, Yan Zheng, Zhangli Hu, Yunfei Deng, Tao Chen

“…They all exhibit quadripartite structures and all have the same numbers of genes and introns. Codon usage, RNA editing sites, and repeat analyses also revealed highly similar results for the six cp genomes. …”
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Complete Chloroplast Genome Sequence of the Endemic and Endangered Plant <i>Dendropanax oligodontus</i>: Genome Structure, Comparative and Phylogenetic Analysis by Yong Wang, Jing Yu, Yu-Kai Chen, Zhu-Cheng Wang

“…Furthermore, we identified 26,514 codons, 13 repetitive sequences, and 43 simple sequence repeat sites in the <i>D. oligodontus</i> cpDNA. …”
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Epidemiology and Genetic Diversity of PCV2 Reveals That PCV2e Is an Emerging Genotype in Southern China: A Preliminary Study by Quanming Xu, Yongyi Zhang, Wen Sun, Hong Chen, Dewen Zhu, Chang Lu, Yuanyuan Yin, Kul Raj Rai, Ji-Long Chen, Ye Chen

“…Additionally, we found two positively selected sites in the ORF2 region, located on the previously reported antigenic epitopes. Moreover, codon 63, one of the positively selected sites, has different types of amino acids in different genotypes. …”
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ORF-Interrupting Mutations in Monkeypox Virus Genomes from Washington and Ohio, 2022 by Jaydee Sereewit, Nicole A. P. Lieberman, Hong Xie, Shah A. K. Mohamed Bakhash, B. Ethan Nunley, Benjamin Chung, Margaret G. Mills, Pavitra Roychoudhury, Alexander L. Greninger

“…Additional mutations include a frameshift leading to an alternative C-terminus in MPXVgp010 (OPG023) and an insertion in an adenine homopolymer at the beginning of the annotated ORF for MPXVgp153 (OPG151), encoding a subunit of the RNA polymerase, suggesting the virus may instead use the start codon that encodes Met9 as annotated. Finally, we detected three samples with large (>900 bp) deletions. …”
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The Scrapie Prevalence in a Goat Herd Is Underestimated by Using a Rapid Diagnostic Test by Timm Konold, John Spiropoulos, Jemma Thorne, Laura Phelan, Louise Fothergill, Brenda Rajanayagam, Tobias Floyd, Beatriz Vidana, Judith Charnley, Nadya Coates, Marion Simmons

“…Significantly more goats that were scrapie-positive were isoleucine homozygous at codon 142 (II142). The results indicate that the sensitivity of the applied screening test is poor in goats compared to the confirmatory tests as gold standard, particularly for asymptomatic animals. …”
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Fine Mapping and Candidate Gene Analysis of the <i>Gv1</i> Locus Controlling Green-Peel Color in Eggplant (<i>Solanum melongena</i> L.) by Zijian Lv, Qingmin Jin, Zhiliang Li, Tao Li, Yikui Wang, Qian You, Chao Gong, Zhou Heng, Baojuan Sun

“…The results of cloning and sequencing of <i>SmAPPR2-like</i> showed that there might have been three types of mutation (large deletion, frameshift variant and premature stop codon) in white-peel accessions, and of these, the deletion mutation, such as that in inbred line 19141, was the most common. …”
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Droplet digital PCR of circulating tumor cells from colorectal cancer patients can predict KRAS mutations before surgery by Jérôme Alexandre Denis, Alexia Patroni, Erell Guillerm, Dominique Pépin, Naoual Benali-Furet, Janine Wechsler, Gilles Manceau, Maguy Bernard, Florence Coulet, Annette K. Larsen, Mehdi Karoui, Jean-Marc Lacorte

“…KRAS genotyping was successful for 86% (30/35) of samples with a KRAS codon 12/13 mutant ratio of 57% (17/30). In contrast, only one patient was identified as KRAS mutant when size‐based isolation was combined with HRM or TaqMeltPCR. …”
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Determination of the native features of the exoglucanase Cel48S from Clostridium thermocellum by Ya-Jun Liu, Shiyue Liu, Sheng Dong, Renmin Li, Yingang Feng, Qiu Cui

“…Using a previously developed seamless genome-editing system for C. thermocellum, we achieved direct purification of Cel48S_CD from the culture supernatant of C. thermocellum DSM1313 by inserting a sequence encoding 12 successive histidine residues and a TAA stop codon immediately behind the GH domain of Cel48S. …”
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Systematically identifying genetic signatures including novel SNP-clusters, nonsense variants, frame-shift INDELs, and long STR expansions that potentially link to unknown phenotyp... by Zicheng Li, Zuoheng Wang, Zhiyuan Chen, Heidi Voegeli, Judith H. Lichtman, Peter Smith, Ju Liu, Andrew T. DeWan, Josephine Hoh

“…Four INDELs resulting in either frame-shift or codon disruptions were found in the Norwich Terrier, Airedale Terrier, Chow Chow and Bernese Mountain Dog, respectively. …”
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NT1-Tau Is Increased in CSF and Plasma of CJD Patients, and Correlates with Disease Progression by David Mengel, Tze How Mok, Akin Nihat, Wen Liu, Robert A. Rissman, Douglas Galasko, Henrik Zetterberg, Simon Mead, John Collinge, Dominic M. Walsh

“…Moreover, in CJD plasma (<i>n</i> = 145) NT1-tau levels correlated with stage and rate of disease progression, and the effect on clinical progression was modified by the <i>PRNP</i> codon 129. Our findings suggest that plasma NT1-tau shows promise as a minimally invasive diagnostic and prognostic biomarker of CJD, and should be further investigated for its potential to monitor disease progression and response to therapies.…”
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Expression, purification, and functional characterization of soluble recombinant full-length simian immunodeficiency virus (SIV) Pr55Gag by Vineeta N. Pillai, Lizna Mohamed Ali, Suresha G. Prabhu, Anjana Krishnan, Saeed Tariq, Farah Mustafa, Tahir A. Rizvi

“…In the process, we identified within Gag, a second in-frame start codon downstream of a putative Shine-Dalgarno-like sequence resulting in an additional truncated form of Gag. …”
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Development of a high-throughput TR-FRET screening assay for a fast-cycling KRAS mutant by Jacob E. Larson, P. Brian Hardy, Noah K. Schomburg, Xiaodong Wang, Dmitri Kireev, Kent L. Rossman, Kenneth H. Pearce

“…However, there are currently no FDA approved inhibitors that target KRAS mutations occurring at non-codon 12 positions. Herein, we focused on the KRAS mutant A146T, found in colorectal cancers, that exhibits a “fast-cycling” nucleotide mechanism as a driver for oncogenic activation. …”
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Complete Mitochondrial Genome and Phylogenetic Analysis of <i>Tarsiger indicus</i> (Aves: Passeriformes: Muscicapidae) by Guanwei Lan, Jiaojiao Yu, Juan Liu, Yue Zhang, Rui Ma, Yanshan Zhou, Biqing Zhu, Wei Wei, Jiabin Liu, Guilan Qi

“…Most PCGs of <i>T. indicus</i> were initiated strictly with the typical start codon ATG, while <i>COX1</i> and <i>ND2</i> were started with GTG. …”
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Mitochondrial genome characteristics and phylogenetic analysis of the medicinal and edible plant Mesona chinensis Benth by Danfeng Tang, Danfeng Tang, Suhua Huang, Changqian Quan, Changqian Quan, Yuan Huang, Yuan Huang, Jianhua Miao, Jianhua Miao, Fan Wei, Fan Wei

“…Repeat sequence analysis revealed 305 repeat sequences (158 forward and 147 palindromic repeats) ranging from 30 bp to 48,383 bp and the 30–39 bp repeats were the majority type. Relative synonymous codon usage (RSCU) analysis uncovered that in total, 9,947 codons were encoding the protein-coding genes (PCGs). …”
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A single vaccination of nucleoside-modified Rabies mRNA vaccine induces prolonged highly protective immune responses in mice by Shimeng Bai, Tianhan Yang, Cuisong Zhu, Meiqi Feng, Li Zhang, Ziling Zhang, Xiang Wang, Rui Yu, Xinghao Pan, Chen Zhao, Jianqing Xu, Jianqing Xu, Xiaoyan Zhang, Xiaoyan Zhang

“…Although inactivated rabies vaccines are available, multiple-dose regimensare recommended for pre-exposure prophylaxis or post-exposure prophylaxis,which cuts down the cost- and time-effectiveness, especially in low- and middle incomecountries.MethodsWe developed a nucleoside-modified Rabies mRNA-lipid nanoparticle vaccine (RABV-G mRNA-LNP) encoding codon-optimized viral glycoprotein and assessed the immunogenicity and protective efficacy of this vaccine in mice comparing to a commercially available inactivated vaccine.ResultsWe first showed that, when evaluated in mice, a single vaccination of RABV-G mRNA with a moderate or high dose induces more potent humoral and T-cell immune responses than that elicited by three inoculations of the inactivated vaccine. …”
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Runx3 Restoration Regresses K-Ras-Activated Mouse Lung Cancers and Inhibits Recurrence by Ja-Yeol Lee, Jung-Won Lee, Tae-Geun Park, Sang-Hyun Han, Seo-Yeong Yoo, Kyoung-Mi Jung, Da-Mi Kim, Ok-Jun Lee, Dohun Kim, Xin-Zi Chi, Eung-Gook Kim, You-Soub Lee, Suk-Chul Bae

“…Oncogenic <i>K-RAS</i> mutations occur in approximately 25% of human lung cancers and are most frequently found in codon 12 (G12C, G12V, and G12D). Mutated K-RAS inhibitors have shown beneficial results in many patients; however, the inhibitors specifically target K-RAS<i>^G12C</i> and acquired resistance is a common occurrence. …”
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Immunoinformatics design of multivalent epitope vaccine against monkeypox virus and its variants using membrane-bound, enveloped, and extracellular proteins as targets by Muhammad Waqas, Muhammad Waqas, Shahkaar Aziz, Pietro Liò, Yumna Khan, Amjad Ali, Aqib Iqbal, Aqib Iqbal, Faizullah Khan, Faizullah Khan, Fahad Nasser Almajhdi

“…Bioinformatics tools were employed to carry out codon adaptation and computational cloning. The tertiary structure of the chimeric vaccine construct was modeled via I-TASSER, and its interaction with Toll-like receptor 4 (TLR4) was evaluated using molecular docking and molecular dynamics simulation. …”
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Strain specific properties of Escherichia coli can prevent non-canonical amino acid misincorporation caused by scale-related process heterogeneities by Florian Mayer, Monika Cserjan-Puschmann, Benedikt Haslinger, Anton Shpylovyi, Thomas Dalik, Christian Sam, Rainer Hahn, Gerald Striedner

“…Norleucine incorporation was not random and certain positions were preferred over others, even though only a single codon exists. Differences in biomass and Fab production between the strains during scale-down cultivations could be observed as well. …”
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Detection of Knockdown-Resistance Homozygous Mutant C1534C using Allele-Specific Polymerase Chain Reaction in Aedes Albopictus and Aedes Aegypti by Syananda Zahra Fadila, Ahmad Rudi Setiawan, Shifa Fauziyah, Safira Madaniyah, Eryantika Cipta Dewi, Sin War Naw, Sari Edi Cahyaningrum, Tukiran, Teguh Hari Sucipto

“…Cysteine-to-cysteine (C/C) mutations and phenylalanine-to-phenylalanine (F/F) mutations at codon 1534 were observed in Aedes aegypti and Aedes albopictus mosquitoes. …”
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