Assembly and comparative analysis of the initial complete mitochondrial genome of Primulina hunanensis (Gesneriaceae): a cave-dwelling endangered plant by Lingling Chen, Xiang Dong, Hang Huang, Haixia Xu, Peninah Cheptoo Rono, Xiuzhen Cai, Guangwan Hu

“…Furthermore, an exploration of PCGs relative synonymous codon usage, identification of RNA editing events, and an investigation of collinearity with closely related species were conducted. …”
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Establishment of Replication Deficient Vesicular Stomatitis Virus for Studies of PEDV Spike-Mediated Cell Entry and Its Inhibition by Huaye Luo, Lilei Lv, Jingxuan Yi, Yanjun Zhou, Changlong Liu

“…In this study, we used a codon-optimized PEDV S protein to generate recombinant pseudotyped vesicular stomatitis virus (VSV) particles (rVSV-ΔG-EGFP-S). …”
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The first complete mitochondrial genome of the genus Echinolaelaps reveals mitochondrial genome rearrangement type and evolution of Gamasida by Bili Yuan, Gangxian He, Wenge Dong

“…The mitochondrial genome is 15 736 bp in length and contains 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and a control region of 1561 bp in length. Codon analysis of 13 protein-coding genes revealed that UUU, UUA, AUU, AUA and AAU were the most frequently used, while cox2 had the fastest evolutionary rate and cob the slowest. …”
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Phylogeny and Flow Cytometry of the Genus <i>Kalidium</i> Moq. (Amaranthaceae s.l.) in Kazakhstan by B. B. Osmonali, P. V. Vesselova, G. M. Kudabayeva, M. V. Skaptsov, A. I. Shmakov, N. Friesen

“…To identify phylogenetic processes at the intraspecific level, the SCoT (Start codon targeted) fingerprinting method was used.…”
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Altered Splicing of <i>LAMP2</i> in a Multigenerational Family from Latvia Affected by Danon Disease by Janis Stavusis, Ieva Micule, Ieva Grinfelde, Anna Zdanovica, Janis Pudulis, Sandra Valeina, Svetlana Sepetiene, Baiba Lace, Inna Inashkina

“…This alteration was predicted to cause a shift of the reading frame, consequently introducing a premature stop codon downstream in the sequence. <i>Conclusions</i>: Based on our data, we propose that c.928+3A>G is a pathogenic variant associated with Danon disease.…”
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Assembly and Comparative Analysis of the Complete Mitochondrial Genome of Two Species of Calla Lilies (<i>Zantedeschia</i>, Araceae) by Yanbing Guo, Ziwei Li, Shoulin Jin, Shuying Chen, Fei Li, Hongzhi Wu

“…Both mitogenomes harbored similar gene compositions, with 56 and 58 genes identified in <i>Z. aethiopica</i> and <i>Z. odorata</i>, respectively. Analyses of codon usage, sequence repeats, gene migration from chloroplast to mitochondrial, and RNA editing were conducted for both <i>Z. aethiopica</i> and <i>Z. odorata</i> mt genomes. …”
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Assessment of genetic variation and population structure in Iraqi barley accessions using ISSR, CDDP, and SCoT markers by Nawroz Tahir, Djshwar Lateef, Kamaran Rasul, Didar Rahim, Kamil Mustafa, Shokhan Sleman, Avin Mirza, Rebwar Aziz

“…The objective of this study was to investigate the diversity of 59 accessions of barley using inter simple sequence repeat (ISSR), conserved DNA-derived polymorphism (CDDP), and start codon targeted (SCoT) markers. A total of 391 amplified polymorphic bands were generated using 44 ISSR, 9 CDDP, and 12 SCoT primers that produced 255, 35, and 101 polymorphic bands, respectively. …”
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An immunoinformatics study: designing multivalent T-cell epitope vaccine against canine circovirus by Pankaj Jain, Amit Joshi, Nahid Akhtar, Sunil Krishnan, Vikas Kaushik

“…The molecular docking and molecular dynamics simulation studies show that these epitopes can bind with DLA molecules with stability. The codon adaptation and in silico cloning studies show that the vaccine can be expressed by Escherichia coli K12 strain. …”
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Differences in Urinary Calculi Characteristics among the Three Main Racial Groups in KwaZulu-Natal, South Africa by Dhesigan Naidoo, Vishan Ramloutan

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Restoring Dystrophin Expression in Duchenne Muscular Dystrophy: Current Status of Therapeutic Approaches by Yuko Shimizu-Motohashi, Hirofumi Komaki, Norio Motohashi, Shin’ichi Takeda, Toshifumi Yokota, Yoshitsugu Aoki

“…In 2014, ataluren, a drug that can promote ribosomal read-through of mRNA containing a premature stop codon, was conditionally approved in Europe. In 2016, eteplirsen, a morpholino-based chemical capable of skipping exon 51 in premature mRNA, received conditional approval in the USA. …”
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Lymantria Dispar Iflavirus 1 RNA Comprises a Large Proportion of RNA in Adult <i>L. dispar</i> Moths by Michael E. Sparks, Yi-Ming Wang, Juan Shi, Robert L. Harrison

“…A comprehensive listing of synonymous and non-synonymous mutations, as well as indels, among the polyprotein coding sequences of these seven LdIV1 variants was compiled and a codon-level phylogram was computed using polyprotein sequences of these, and 50 additional iflaviruses placed LdIV1 in a large clade consisting mostly of iflaviruses from other species of Lepidoptera. …”
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A Mitochondrial Genome Phylogeny of Cleridae (Coleoptera, Cleroidea) by Lilan Yuan, Haoyu Liu, Xueying Ge, Ganyan Yang, Guanglin Xie, Yuxia Yang

“…In addition to phylogenomic analysis, we have leveraged our new sources to study the mitochondrial biology in terms of nucleotide composition, codon usage and substitutional rate, to understand how these vital cellular components may have contributed to the divergence of the Cleridae. …”
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Genetic Differentiation of Five Sea Cucumber Species from the Red Sea, Hurghada, Egypt by F. M. Abdelghany, A. W. A. Abdel-Warith, E. M. Younis, S. J. Davies, M. A. Elnakeeb, M. M. El-Nawasany, A. A. El-Bahlol, M. A. Bauomi, A. H. Abu-Almaaty, M. Y. Omer

“…Abstract This study aimed to assess the genetic differentiation and relationship among five sea cucumber species from the Red Sea in Egypt, namely Holothuria atra, H. impatiens, H. leucospilota, Actinopyga crassa and A. mauritiana, using Inter Simple Sequence Repeated (ISSR) and Start Codon Targeted (SCoT) markers. A collection of 100 specimens, with 20 individuals per species, was gathered for the analysis. …”
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Differential translation elongation directs protein synthesis in response to acute glucose deprivation in yeast by Anna R. Guzikowski, Alex T. Harvey, Jingxiao Zhang, Shihui Zhu, Kyle Begovich, Molly H. Cohn, James E. Wilhelm, Brian M. Zid

“…Abbreviations: AUG: start codon, bp: base pair(s), CDS: coding sequence, CHX: cycloheximide, eEF2: eukaryotic elongation factor 2, LTM: lactimidomycin, nt: nucleotide, PGK1: 3-phosphoglycerate kinase, ribosomal biogenesis: ribi, RO: ribosome occupancy, RPF: ribosome protected fragment, TE: translational efficiency…”
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Detection of rifampin resistance patterns in Mycobacterium tuberculosis strains isolated in Iran by polymerase chain reaction-single-strand conformation polymorphism and direct seq... by Bahram Nasr Isfahani, Akbar Tavakoli, Mansoor Salehi, Mehdi Tazhibi

“…There were seen six different mutations in the amplified region of rpoB gene: codon 516(GAC/GTC), 523(GGG/GGT), 526(CAC/TAC), 531(TCG/TTG), 511(CTG/TTG), and 512(AGC/TCG). …”
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Amino acid fermentation at the origin of the genetic code by de Vladar Harold P

“…Monte Carlo simulations are performed to evaluate the establishment of these simple proto-codes, based on amino acid substitutions and codon swapping. In all cases, donor amino acids are assigned to anticodons composed of U+G, and have low redundancy (1-2 codons), whereas acceptor amino acids are assigned to the the remaining codons. …”
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DNA vaccination induced protective immunity against SARS CoV-2 infection in hamsterss. by Kit Man Chai, Tsai-Teng Tzeng, Kuan-Yin Shen, Hung-Chun Liao, Jhe-Jhih Lin, Mei-Yu Chen, Guann-Yi Yu, Horng-Yunn Dou, Ching-Len Liao, Hsin-Wei Chen, Shih-Jen Liu

“…The spike genes of SARS-CoV and SARS-CoV-2 were codon optimized for mammalian cell expression and then cloned into mammalian cell expression vectors, called pSARS-S and pSARS2-S, respectively. …”
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PCR detection of <it>Plasmodium falciparum </it>in human urine and saliva samples by Thuma Philip E, Shiff Clive J, Simoloka Christopher, Mharakurwa Sungano, Sullivan David J

“…Amplicons from the various sample types were examined for MSP2 polymorphisms and restriction fragment patterns on DHFR amino acid codon 59.</p> <p>Results and discussion</p> <p>Malaria infections exhibited primarily low-grade parasite densities, with a geometric mean of 775 asexual parasites/μl. …”
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Improved SNV Discovery in Barcode-Stratified scRNA-seq Alignments by Prashant N. M., Hongyu Liu, Christian Dillard, Helen Ibeawuchi, Turkey Alsaeedy, Hang Chan, Anelia Dafinova Horvath

“…Our analysis shows that variant calls on individual cell alignments identify at least a two-fold higher number of SNVs as compared to the pooled scRNA-seq; these SNVs are enriched in novel variants and in stop-codon and missense substitutions. Our study indicates an immense potential of SNV calls from individual cell scRNA-seq data and emphasizes the need for cell-level variant detection approaches and tools, which can contribute to the understanding of the cellular heterogeneity and the relationships to phenotypes, and help elucidate somatic mutation evolution and functionality.…”
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Deciphering the role of RNA structure in translation efficiency by Jianan Lin, Yang Chen, Yuping Zhang, Haifan Lin, Zhengqing Ouyang

“…The reduced stability of secondary structures near the translation initiation site/start codon of the coding region promotes the efficiency of translation in both prokaryotic and eukaryotic species. …”
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