The Effect of the <i>BCO2</i> Genotype on the Expression of Genes Related to Carotenoid, Retinol, and α-Tocopherol Metabolism in Rabbits Fed a Diet with Aztec Marigold Flower Extra... by Janusz Strychalski, Andrzej Gugołek, Zofia Antoszkiewicz, Dorota Fopp-Bayat, Edyta Kaczorek-Łukowska, Anna Snarska, Grzegorz Zwierzchowski, Angelika Król-Grzymała, Paulius Matusevičius

“…Sixty male Termond White growing rabbits were divided into three groups based on their genotype at codon 248 of the <i>BCO2</i> gene (ins/ins, ins/del and del/del); each group was divided into two subgroups: one subgroup received a standard diet, and the other subgroup was fed a diet supplemented with 6 g/kg of marigold flower extract. …”
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Metabolic engineering of Ashbya gossypii for deciphering the de novo biosynthesis of γ-lactones by Rui Silva, Tatiana Q. Aguiar, Eduardo Coelho, Alberto Jiménez, José Luis Revuelta, Lucília Domingues

“…Further substitution of AgPOX1, encoding the exclusive acyl-CoA oxidase in A. gossypii, by a codon-optimized POX2 gene from Yarrowia lipolytica, which encodes a specific long chain acyl-CoA oxidase, fine-tuned the biosynthesis of γ-decalactone to a relative production of more than 99%. …”
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KRAS^G12C Can Either Promote or Impair Cap-Dependent Translation in Two Different Lung Adenocarcinoma Cell Lines by George Kyriakopoulos, Vicky Katopodi, Ilias Skeparnias, Eleni G. Kaliatsi, Katerina Grafanaki, Constantinos Stathopoulos

“…Downregulation of eIF1, eIF5 and eIF5B in the same cell line suggested a stringency loss of start codon selection during scanning of mRNAs. Puromycin staining and polysome profile analysis validated the enhanced translation rates in A549 cells and the impaired cap-dependent translation in CL1-5 cells. …”
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Comparative mitochondrial genome brings insights to slight variation in gene proportion and large intergenic spacer and phylogenetic relationship of mudskipper species by Valdemiro Muhala, Aurycéia Guimarães-Costa, Adam Rick Bessa-Silva, Luan Pinto Rabelo, Jeferson Carneiro, Isadola Eusébio Macate, Luciana Watanabe, Oscar David Balcázar, Grazielle Evangelista Gomes, Marcelo Vallinoto, Iracilda Sampaio

“…Most of the PCG showed similar codon usage bias. The gene length was found to be different specially for the CR, 12S rRNA gene and ND5 gene in some taxon. …”
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A de novo frameshift pathogenic variant in TBR1 identified in autism without intellectual disability by Laurie-Anne Sapey-Triomphe, Julie Reversat, Gaëtan Lesca, Nicolas Chatron, Marina Bussa, Sylvie Mazoyer, Christina Schmitz, Sandrine Sonié, Patrick Edery

“…Importantly, this patient presents with no intellectual disability or language impairment, despite a de novo heterozygous frameshift pathogenic variant in TBR1, leading to an early premature termination codon (c.26del, p.(Pro9Leufs*12)). Conclusion Based on this case report, we discuss the role of TBR1 in general brain development, language development, intellectual disability and other symptoms of ASD. …”
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A CHO-Based Cell-Free Dual Fluorescence Reporter System for the Straightforward Assessment of Amber Suppression and scFv Functionality by Simon K. Krebs, Simon K. Krebs, Nathanaël Rakotoarinoro, Nathanaël Rakotoarinoro, Marlitt Stech, Anne Zemella, Stefan Kubick, Stefan Kubick, Stefan Kubick

“…The positioning of the ncAA-responsive codon within the protein’s coding sequence is critical in order to maintain protein function, achieve high yields of ncAA-containing protein, and allow effective conjugation. …”
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Immunoinformatic-based design of immune-boosting multiepitope subunit vaccines against monkeypox virus and validation through molecular dynamics and immune simulation by Muhammad Suleman, Farooq Rashid, Shahid Ali, Hassan Sher, Sisi Luo, Sisi Luo, Sisi Luo, Liji Xie, Liji Xie, Liji Xie, Zhixun Xie, Zhixun Xie, Zhixun Xie

“…The strong binding of the constructed vaccines with human TLR-2 was verified by the molecular docking and determination of dissociation constant values. The GC content and codon adaptation index (CAI) values confirmed the high expression of the constructed vaccines in the pET-28a (+) expression vector. …”
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Ribosome profiling of porcine reproductive and respiratory syndrome virus reveals novel features of viral gene expression by Georgia M Cook, Katherine Brown, Pengcheng Shang, Yanhua Li, Lior Soday, Adam M Dinan, Charlotte Tumescheit, AP Adrian Mockett, Ying Fang, Andrew E Firth, Ian Brierley

“…For example, we found a highly expressed 125-codon ORF overlapping nsp12, which is likely translated from novel subgenomic RNA transcripts that overlap the 3′ end of ORF1b. …”
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Emerging Perspectives on the Rare Tubulopathy Dent Disease: Is Glomerular Damage a Direct Consequence of ClC-5 Dysfunction? by Giovanna Priante, Monica Ceol, Lisa Gianesello, Dario Bizzotto, Paola Braghetta, Lorenzo Arcangelo Calò, Dorella Del Prete, Franca Anglani

“…CRISPR/Cas9 (Clustered Regularly Interspaced Short Palindromic Repeats/Caspase9) gene editing of <i>CLCN5</i> in conditionally immortalized human podocytes was used to obtain clones with the stop codon mutation p.(R34Efs*14). We showed that ClC-5 and nephrin expression, analyzed by quantitative Reverse Transcription/Polymerase Chain Reaction (qRT/PCR) and In-Cell Western (ICW), was significantly downregulated in mutant clones compared to the wild type ones. …”
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Comparative Analysis of the Complete Plastid Genome of Five <i>Bupleurum</i> Species and New Insights into DNA Barcoding and Phylogenetic Relationship by Jun Li, Deng-Feng Xie, Xian-Lin Guo, Zhen-Ying Zheng, Xing-Jin He, Song-Dong Zhou

“…The five <i>Bupleurum</i> species had nearly the same codon usages, and eight regions (<i>petN-psbM</i>, <i>rbcL-accD</i>, <i>ccsA-ndhD</i>, <i>trnK(UUU)-rps16</i>, <i>rpl32-trnL(UAG)-ccsA</i>, <i>petA-psbJ</i>, <i>ndhF-rpl32,</i> and <i>trnP(UGG)-psaJ-rpl33</i>) were found to possess relatively higher nucleotide diversity, which may be the promising DNA barcodes in <i>Bupleurum</i>. …”
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Zebrafish polg2 knock-out recapitulates human POLG-disorders; implications for drug treatment by Raquel Brañas Casas, Alessandro Zuppardo, Giovanni Risato, Alberto Dinarello, Rudy Celeghin, Camilla Fontana, Eleonora Grelloni, Alexandru Ionut Gilea, Carlo Viscomi, Andrea Rasola, Luisa Dalla Valle, Tiziana Lodi, Enrico Baruffini, Nicola Facchinello, Francesco Argenton, Natascia Tiso

“…Considering the paucity of POLG2 models, we have generated a stable zebrafish polg2 mutant line (polg2 ia304 ) by CRISPR/Cas9 technology, carrying a 10-nucleotide deletion with frameshift mutation and premature stop codon. Zebrafish polg2 homozygous mutants present slower development and decreased viability compared to wild type siblings, dying before the juvenile stage. …”
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Complete Chloroplast Genome of <i>Cnidium monnieri</i> (Apiaceae) and Comparisons with Other Tribe Selineae Species by Ting Ren, Xueyimu Aou, Rongming Tian, Zhenbing Li, Chang Peng, Xingjin He

“…A total of 129 genes were contained in the cp genome, including 85 protein-coding genes, 36 tRNA genes, and eight rRNA genes. We also investigated codon usage, RNA editing, repeat sequences, simple sequence repeats (SSRs), IR boundaries, and pairwise Ka/Ks ratios. …”
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A case of McLeod syndrome caused by a nonsense variation c.942G>A in the XK gene: A case report by Yanling Ying, Yanling Ying, Shifang Yu, Jingjing Zhang, Jingjing Zhang, Ji He, Ji He, Xianguo Xu, Xianguo Xu, Xiaozhen Hong, Xiaozhen Hong, Faming Zhu, Faming Zhu

“…Sequencing of the coding region of the XK gene showed a hemizygous c.942G&gt;A variation in the XK gene, which resulted in a premature stop codon at position 314 (p.Trp314Ter). Therefore, the patient was diagnosed with McLeod syndrome. …”
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Annotation of Potential Vaccine Targets and Designing of mRNA-Based Multi-Epitope Vaccine against Lumpy Skin Disease Virus via Reverse Vaccinology and Agent-Based Modeling by Sehrish Kakakhel, Abbas Ahmad, Wael A. Mahdi, Sultan Alshehri, Sara Aiman, Sara Begum, Sulaiman Shams, Mehnaz Kamal, Mohd. Imran, Faiyaz Shakeel, Asifullah Khan

“…The model constructs were back-translated to nucleotide sequences and codons were optimized. The Kozak sequence with a start codon along with MITD, tPA, Goblin 5′, 3′ UTRs, and a poly(A) tail sequences were added to design a stable and highly immunogenic mRNA vaccine. …”
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Analysis of whole chloroplast genomes from three medicinal Amomum species by Chang Su, Hong Wang, Shuhong Wang, Jie Zhao, Xiangxiao Meng, Wenxian Zhang, Bing Wang

“…However, they also varied in terms of gene content, the expansion of inverted repeats, codon usage, repeat sequences, and simple sequence repeats. …”
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A comparison of classical and H-type bovine spongiform encephalopathy associated with E211K prion protein polymorphism in wild type and EK211 cattle following intracranial inoculat... by Jo Moore, M. Heather West Greenlee, M. Heather West Greenlee, Jodi D. Smith, Catherine E. Vrentas, Eric M Nicholson, Justin J Greenlee

“…In 2006, a case of H-type bovine spongiform encephalopathy (BSE-H) was diagnosed in a cow that was associated with a heritable polymorphism in the bovine prion protein gene (PRNP) resulting in a lysine for glutamine amino acid substitution at codon 211 (called E211K) of the prion protein. Although the prevalence of this polymorphism is low, cattle carrying the K211 allele may be predisposed to rapid onset of BSE-H when exposed or to the potential development of a genetic BSE. …”
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Genotype Phenotype Correlation in Dent Disease 2 and Review of the Literature: <i>OCRL</i> Gene Pleiotropism or Extreme Phenotypic Variability of Lowe Syndrome? by Lisa Gianesello, Jennifer Arroyo, Dorella Del Prete, Giovanna Priante, Monica Ceol, Peter C. Harris, John C. Lieske, Franca Anglani

“…Analysis of the distribution of mutations revealed (1) truncating mutations map in the PH and linker domain, while missense mutations map in the 5-phosphatase domain, and only occasionally in the ASH-RhoGAP module; (2) five <i>OCRL</i> mutations cause both DD2 and LS phenotypes; (3) codon 318 is a DD2 mutational hot spot; (4) a correlation was found between the presence of ES and the position of the mutations along OCRL domains. …”
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Dynamic expression of HSP90B1 mRNA in the hypothalamus of two Chinese chicken breeds under heat stress and association analysis with a SNP in Huainan chickens by Yi Wan, Chendong Ma, Peipei Wei, Qi Fang, Xing Guo, Bangyuan Zhou, Runshen Jiang

“…In Huainan chickens, we identified a SNP (NC_006088.3:g.6798G&gt;A) in exon 14 of HSP90B1 which did not cause amino acid variation but caused a codon for glutamic acid change from GAG to GAA. The frequencies for genotypes AA, GA, and GG were 0.49, 0.27, and 0.24, respectively. …”
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Translation efficiency driven by CNOT3 subunit of the CCR4-NOT complex promotes leukemogenesis by Maryam Ghashghaei, Yilin Liu, James Ettles, Giuseppe Bombaci, Niveditha Ramkumar, Zongmin Liu, Leo Escano, Sandra Spencer Miko, Yerin Kim, Joseph A. Waldron, Kim Do, Kyle MacPherson, Katie A. Yuen, Thilelli Taibi, Marty Yue, Aaremish Arsalan, Zhen Jin, Glenn Edin, Aly Karsan, Gregg B. Morin, Florian Kuchenbauer, Fabiana Perna, Martin Bushell, Ly P. Vu

“…Global analysis of mRNA features demonstrates that CNOT3 selectively influences expression of target genes in a codon usage dependent manner. Furthermore, CNOT3 associates with the protein network largely consisting of ribosomal proteins and translation elongation factors in leukemia cells. …”
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A Novel Truncating Mutation in HOMER2 Causes Nonsyndromic Progressive DFNA68 Hearing Loss in a Spanish Family by María Lachgar, Matías Morín, Manuela Villamar, Ignacio del Castillo, Miguel Ángel Moreno-Pelayo

“…This frameshift mutation produces a premature stop codon that may lead in the absence of NMD to a shorter variant (p.Pro278Alafs*10) that truncates HOMER2 at the CDC42 binding domain (CBD) of the coiled-coil structure, a region that is essential for protein multimerization and HOMER2-CDC42 interaction. c.832_836delCCTCA mutation is placed close to the previously identified c.840_840dup mutation found in a Chinese family that truncates the protein (p.Met281Hisfs*9) at the CBD. …”
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