Form and function of Poly(A) tails by Eisen, Timothy J.(Timothy Jonas)

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Translational regulation by short RNAs in mammalian cells by Petersen, Christian Paul

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Development of new tools for the production of plasmid DNA biopharmaceuticals by Bower, Diana M. (Diana Morgan)

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Alkbh8 Regulates Selenocysteine-Protein Expression to Protect against Reactive Oxygen Species Damage by Endres, Lauren, Begley, Ulrike, Clark, Ryan, Gu, Chen, Dziergowska, Agnieszka, Małkiewicz, Andrzej, Melendez, J. Andres, Dedon, Peter C., Begley, Thomas J.

“…We also show that, in response to oxidative stress, the tRNA modification 5-methoxycarbonylmethyl-2′-O-methyluridi​ne(mcm[superscript 5]Um) increases in normal MEFs to drive the expression of ROS detoxification enzymes, with this damage-induced reprogramming of tRNA and stop-codon recoding corrupted in Alkbh8[superscript -/-] MEFS. …”
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Quantitative analysis of tRNA modifications by HPLC-coupled mass spectrometry by Su, Dan, Gu, Chen, Lim, Kok Seong, Chionh, Yok Hian, Chan, Clement T. Y., McBee, Megan E., Russell, Brandon S., Ramesh Babu, I., Begley, Thomas J., Dedon, Peter C.

“…This is illustrated by the observation of toxicant-specific changes in the spectrum of tRNA modifications in a stress-response mechanism involving selective translation of codon-biased mRNA for crucial proteins. To facilitate systems-level studies of RNA modifications, we developed a liquid chromatography–mass spectrometry (LC-MS) technique for the quantitative analysis of modified ribonucleosides in tRNA. …”
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Robust RNAi enhancement via human Argonaute-2 overexpression from plasmids, viral vectors and cell lines by Börner, Kathleen, Niopek, Dominik, Cotugno, Gabriella, Kaldenbach, Michaela, Pankert, Teresa, Willemsen, Joschka, Zhang, Xian, Schürmann, Nina, Streetz, Konrad, Kräusslich, Hans-Georg, Mockenhaupt, Stefan, Serva, Andrius, Grimm, Dirk, Hiet, Marie-Sophie, Wiedtke, Ellen, Binder, Marco, Castoldi, Mirco, Starkuviene, Vytaute, Erfle, Holger, Bartenschlager, Ralf, Boutros, Michael, Gilbert, Daniel F.

“…Specifically, we engineered plasmids and viral vectors to co-encode a codon-optimized human Ago2 cDNA along with custom shRNAs. …”
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A novel fluorinated probe for medical imaging by Robinson, M, Matthew Dominic Robinson

“…The fluorinated amino acid trifluoromethionine (TFM) was incorporated into the Qβ coat protein by the sense codon reassignment method using auxotrophic <em>E. coli</em>. …”

Multivariate time-series analysis of biomarkers from a dengue cohort offers new approaches for diagnosis and prognosis by Vasey, B, Shankar, AH, Herrera, BB, Becerra, A, Xhaja, K, Echenagucia, M, Machado, SR, Caicedo, D, Miller, J, Amedeo, P, Naumova, EN, Bosch, I, Norma Blumenfeld deBosch

“…Based on partial analysis of 31 viral complete genomes, a high frequency of C-to-T transitions located at the third codon position was observed, suggesting deamination events with five major hot spots of amino acid polymorphic sites outside in non-structural proteins. …”

Potential for immune-driven viral polymorphisms to compromise antiretroviral-based preexposure prophylaxis for prevention of HIV-1 infection by Gatanaga, H, Brumme, Z, Adland, E, Reyes-Terán, G, Avila-Rios, S, Mejía-Villatoro, C, Hayashida, T, Chikata, T, Van Tran, G, Van Nguyen, K, Meza, R, Palou, E, Valenzuela-Ponce, H, Pascale, J, Porras-Cortés, G, Manzanero, M, Lee, G, Martin, J, Carrington, M, John, M, Mallal, S, Poon, A, Goulder, P, Takiguchi, M, Oka, S

“…However, rilpivirine resistance mutations at reverse transcriptase codon 138 (RT-E138X) occur naturally in a minority of HIV-1-infected persons; in particular those expressing Human Leukocyte Antigen (HLA)-B*18 where RT-E138X arises as an immune escape mutation. …”

Investigating the effect of melanopsin gene therapy in the degenerate retina by De Silva, S

“…Further evaluation of the vector was then performed to identify whether delivery using a ubiquitous or bipolar cell specific promoter gave optimal expression, and that comparing a wild type to a codon optimised sequence was also assessed. Longevity of expression was also assessed with robust levels of melanopsin seen in the degenerate retina fifteen months after a single subretinal injection. …”

Frequencies distribution of dihydrofolate reductase and dihydropteroate synthetase mutant alleles associated with sulfadoxine-pyrimethamine resistance in Plasmodium falciparum popu... by Bamaga, O.A.A., Mahdy, M.A.K., Lim, Y.A.L.

“…Sequences were analysed for mutations in Pfdhfr gene codons 51, 59, 108, and 164 and in Pfdhps gene codons 436, 437, and 540. …”

<i>Rindera graeca</i> (A. DC.) Boiss. & Heldr. (Boraginaceae) In Vitro Cultures Targeting Lithospermic Acid B and Rosmarinic Acid Production by Katarzyna Sykłowska-Baranek, Małgorzata Gaweł, Łukasz Kuźma, Beata Wileńska, Mateusz Kawka, Małgorzata Jeziorek, Konstantia Graikou, Ioanna Chinou, Ewa Szyszko, Piotr Stępień, Patryk Zakrzewski, Agnieszka Pietrosiuk

“…A genetic analysis performed using random amplified polymorphic DNA and start codon targeted markers revealed genetic variation of 62.8% to 96.5% among the investigated shoots and roots. …”
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Deep Characterization of Circular RNAs from Human Cardiovascular Cell Models and Cardiac Tissue by Tobias Jakobi, Dominik Siede, Jessica Eschenbach, Andreas W. Heumüller, Martin Busch, Rouven Nietsch, Benjamin Meder, Patrick Most, Stefanie Dimmeler, Johannes Backs, Hugo A. Katus, Christoph Dieterich

“…Moreover, we describe, for the first time in cardiac model systems, a sub class of circRNAs containing the start codon of their primary transcript (AUG circRNAs) and observe an enrichment for m⁶A-methylation for AUG circRNAs.…”
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Combined Locked Nucleic Acid Probes and High-Resolution Melting Curve Analysis for Detection of Rifampicin-Resistant Tuberculosis in Northern Thailand by Yee Mon Thant, Sukanya Saikaew, Chayada Sitthidet Tharinjaroen, Ponrut Phunpae, Rodjana Pongsararuk, Kanya Preechasuth, Bordin Butr-Indr, Sorasak Intorasoot, Khajornsak Tragoolpua, Angkana Chaiprasert, Usanee Wattananandkul

“…Furthermore, this is the first report of the rare mutation profiles, S531W, and a triple codon deletion (510–512) in northern Thailand. According to high accuracy, the RIF-RDp assay may render an easy-to-use, low-cost, and promising diagnostics of RR-TB in the future.…”
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Identifying Potent Nonsense-Mediated mRNA Decay Inhibitors with a Novel Screening System by Julie Carrard, Fiona Ratajczak, Joséphine Elsens, Catherine Leroy, Rebekah Kong, Lucie Geoffroy, Arnaud Comte, Guy Fournet, Benoît Joseph, Xiubin Li, Sylvie Moebs-Sanchez, Fabrice Lejeune

“…Nonsense-mediated mRNA decay (NMD) is a quality control mechanism that degrades mRNAs carrying a premature termination codon. Its inhibition, alone or in combination with other approaches, could be exploited to develop therapies for genetic diseases caused by a nonsense mutation. …”
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Genetic analysis of Chinese families reveals a novel truncation allele of the retinitis pigmentosa GTPase regulator gene by Fang Hu, Xiang-Yun Zeng, Lin-Lin Liu, Yao-Ling Luo, Yi-Ping Jiang, Hui Wang, Jing Xie, Cheng-Quan Hu, Lin Gan, Liang Huang

“…<b>RESULTS:</b> Capture-NGS in one affected 47-year-old male reveals a novel mutation, c.2417_2418insG:p.E806fs, in exon ORF15 of RP GTPase regulator (RPGR) gene results in a frameshift change that results in a premature stop codon and a truncated protein product. The mutation was further validated in three of four affected males and two of four female carriers but not in the other unaffected family members. …”
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Widespread Alternative Splicing Changes in Metastatic Breast Cancer Cells by Jagyeong Oh, Davide Pradella, Changwei Shao, Hairi Li, Namjeong Choi, Jiyeon Ha, Sonia Ruggiero, Xiang-Dong Fu, Xuexiu Zheng, Claudia Ghigna, Haihong Shen

“…Among SRSF1-regulated targets we found <i>DCUN1D5</i>, a gene for which skipping of exon 4 in its pre-mRNA introduces a premature termination codon (PTC), thus generating an unstable transcript degraded by nonsense-mediated mRNA decay (NMD). …”
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Transcriptomic Analysis Reveals the Role of tmRNA on Biofilm Formation in <i>Bacillus subtilis</i> by Shanshan Xu, Qianqian Cao, Zengzhi Liu, Junpeng Chen, Peiguang Yan, Bingyu Li, Ying Xu

“…In bacteria, tmRNA, encoded by the <i>ssrA</i> gene, catalyzes <i>trans</i>-translation that can rescue ribosomes stalled on mRNA transcripts lacking a functional stop codon. tmRNA also affects physiological bioprocesses in some bacteria. …”
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A Simple CRISPR/Cas9 System for Efficiently Targeting Genes of Aspergillus Section Flavi Species, Aspergillus nidulans, Aspergillus fumigatus, Aspergillus terreus, and Aspergillus... by Perng-Kuang Chang

“…It contained a shortened Aspergillus nidulans AMA1 autonomously replicating sequence that maintained good transformation frequencies and Aspergillus oryzae ptrA as the selection marker for pyrithiamine resistance. Expression of the codon-optimized cas9 gene was driven by the A. nidulans gpdA promoter and trpC terminator. …”
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Contriving multi-epitope vaccine ensemble for monkeypox disease using an immunoinformatics approach by Shahkaar Aziz, Fahad Nasser Almajhdi, Muhammad Waqas, Muhammad Waqas, Inam Ullah, Muhammad Adil Salim, Muhammad Adil Salim, Nasir Ali Khan, Amjad Ali

“…Three multi-epitope vaccines were constructed (MPXV-1–3) by fusing finalized epitopes with the aid of appropriate linkers and adjuvant (beta-defensin 3, 50S ribosomal protein L7/L12, and Heparin-binding hemagglutinin). Codon optimization and in silico cloning in the pET28a (+) expression vector ensure the optimal expression of each construct in the Escherichia Coli system. …”
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