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3101
Assembly and comparative analysis of the initial complete mitochondrial genome of Primulina hunanensis (Gesneriaceae): a cave-dwelling endangered plant
Published 2024-04-01“…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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3102
Establishment of Replication Deficient Vesicular Stomatitis Virus for Studies of PEDV Spike-Mediated Cell Entry and Its Inhibition
Published 2023-08-01“…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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3103
The first complete mitochondrial genome of the genus Echinolaelaps reveals mitochondrial genome rearrangement type and evolution of Gamasida
Published 2023-06-01“…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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3104
Phylogeny and Flow Cytometry of the Genus <i>Kalidium</i> Moq. (Amaranthaceae s.l.) in Kazakhstan
Published 2023-07-01“…To identify phylogenetic processes at the intraspecific level, the SCoT (Start codon targeted) fingerprinting method was used.…”
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3105
Altered Splicing of <i>LAMP2</i> in a Multigenerational Family from Latvia Affected by Danon Disease
Published 2024-01-01“…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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3106
Assembly and Comparative Analysis of the Complete Mitochondrial Genome of Two Species of Calla Lilies (<i>Zantedeschia</i>, Araceae)
Published 2023-05-01“…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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3107
Assessment of genetic variation and population structure in Iraqi barley accessions using ISSR, CDDP, and SCoT markers
Published 2023-06-01“…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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3108
An immunoinformatics study: designing multivalent T-cell epitope vaccine against canine circovirus
Published 2021-08-01“…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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3109
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3110
Restoring Dystrophin Expression in Duchenne Muscular Dystrophy: Current Status of Therapeutic Approaches
Published 2019-01-01“…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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3111
Lymantria Dispar Iflavirus 1 RNA Comprises a Large Proportion of RNA in Adult <i>L. dispar</i> Moths
Published 2023-05-01“…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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3112
A Mitochondrial Genome Phylogeny of Cleridae (Coleoptera, Cleroidea)
Published 2022-01-01“…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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3113
Genetic Differentiation of Five Sea Cucumber Species from the Red Sea, Hurghada, Egypt
Published 2023-06-01“…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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3114
Differential translation elongation directs protein synthesis in response to acute glucose deprivation in yeast
Published 2022-12-01“…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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3115
Detection of rifampin resistance patterns in Mycobacterium tuberculosis strains isolated in Iran by polymerase chain reaction-single-strand conformation polymorphism and direct seq...
Published 2006-09-01“…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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3116
Amino acid fermentation at the origin of the genetic code
Published 2012-02-01“…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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3117
DNA vaccination induced protective immunity against SARS CoV-2 infection in hamsterss.
Published 2021-05-01“…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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3118
PCR detection of <it>Plasmodium falciparum </it>in human urine and saliva samples
Published 2006-11-01“…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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3119
Improved SNV Discovery in Barcode-Stratified scRNA-seq Alignments
Published 2021-09-01“…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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3120
Deciphering the role of RNA structure in translation efficiency
Published 2022-12-01“…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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