Stop codon readthrough generates a C-terminally extended variant of the human vitamin D receptor with reduced calcitriol response by Loughran, Gary, Jungreis, Irwin, Tzani, Ioanna, Power, Michael, Dmitriev, Ruslan I, Ivanov, Ivaylo P, Kellis, Manolis, Atkins, John F

“…Previously, our analysis of conserved protein coding signatures that extend beyond annotated stop codons predicted stop codon readthrough of several mammalian genes, all of which have been validated experimentally. …”
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Stop codon readthrough generates a C-terminally extended variant of the human vitamin D receptor with reduced calcitriol response by Loughran, Gary, Jungreis, Irwin, Tzani, Ioanna, Power, Michael, Dmitriev, Ruslan I, Ivanov, Ivaylo P, Kellis, Manolis, Atkins, John F

“…Previously, our analysis of conserved protein coding signatures that extend beyond annotated stop codons predicted stop codon readthrough of several mammalian genes, all of which have been validated experimentally. …”
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Increased tRNA modification and gene-specific codon usage regulate cell cycle progression during the DNA damage response by Patil, Ashish, Dyavaiah, Madhu, Joseph, Fraulin, Rooney, John P., Chan, Tsz Yan Clement, Dedon, Peter C., Begley, Thomas J.

“…In support, we demonstrate that the Trm9-dependent tRNA modification 5-methoxycarbonylmethyluridine (mcm⁵U) is increased in hydroxyurea (HU)-induced S-phase cells, relative to G₁ and G₂, and that mcm⁵U is one of 16 tRNA modifications whose levels oscillate during the cell cycle. Codon-reporter data matches the mcm⁵U increase to Trm9 and the efficient translation of AGA codons and RNR1. …”
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Crystal structures of HIV-1 reverse transcriptases mutated at codons 100, 106 and 108 and mechanisms of resistance to non-nucleoside inhibitors. by Ren, J, Nichols, C, Chamberlain, P, Weaver, K, Short, SA, Stammers, D

Identification of the functional initiation codons of a phase-variable gene of Haemophilus influenzae, lic2A, with the potential for differential expression. by Dixon, K, Bayliss, C, Makepeace, K, Moxon, E, Hood, D

“…The lic2A 5' CAAT repeat tract is preceded by four 5' ATG codons (x, y, z1, and z2) in two reading frames. Each of these initiation codons was inactivated by site-directed mutagenesis. …”

The MSPDBL2 codon 591 polymorphism is associated with lumefantrine in vitro drug responses in Plasmodium falciparum isolates from Kilifi, Kenya. by Ochola-Oyier, L, Okombo, J, Mwai, L, Kiara, S, Pole, L, Tetteh, K, Nzila, A, Marsh, K

“…The high frequency of Pfmspdbl2 codon 591S in Kenya, may be driven by the widespread use of lumefantrine in the artemisinin combination therapy, Coartem.…”

Tenderness and physicochemical characteristics of meat treated by recombinant bromelain of MD2 pineapple from a codon-optimized synthetic gene by Rafida Razali, Vijay Kumar Subbiah, Cahyo Budiman

“…To address this, MD2-MBro was over-expressed in Escherichia coli BL21 Codon Plus(DE3), followed by purification using a single step of Ni-NTA affinity chromatography. …”
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Estrogen receptor-α gene codon 10 (T392C) polymorphism in Iranian women with breast cancer: a case study by Abbasi, Sakineh, Azimi, Cyrus, Othman, Fauziah, Daloii, Mohammad Reza Noori, Ashtiani, Zahra Ousati, Mojarrad, Majid, Oskouei, S. A., Nejad, F. M., Ismail, Patimah

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Topical gentamicin 0.1% promotes collagen 7 expression in recessive dystrophic epidermolysis bullosa by Rahul Mahajan, Seema Manjunath, Manoj G Madakshira, Dipankar De, Sanjeev Handa, Debajyoti Chatterjee, Bishan D Radotra

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A serine sensor for multicellularity in a bacterium by Arvind R Subramaniam, Aaron DeLoughery, Niels Bradshaw, Yun Chen, Erin O’Shea, Richard Losick, Yunrong Chai

Subjects: “…codon usage…”
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ABPEPserver: a web application for documentation and analysis of substitutants by Abhijeet Pataskar, Jasmine Montenegro Navarro, Reuven Agami

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Comparative analysis of codon usage patterns and phylogenetic implications of five mitochondrial genomes of the genus Japanagallia Ishihara, 1955 (Hemiptera, Cicadellidae, Megophthalminae) by Min Li, Jiajia Wang, Renhuai Dai, Guy Smagghe, Xianyi Wang, Siying You

Subjects: “…Codon usage…”
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ASSOCIATION OF TLR 5 AND ESCHERICHIA COLI FLIC POLYMORPHISMS WITH RECURRENT URINARY TRACT INFECTIONS IN WOMEN by Z. J. Kadhim, G. A. Abdulhasan

Subjects: “…stop codon, flagellin, SNPs, 1174 C>T.…”
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Chronic intermittent ethanol exposure-induced m6A modifications around mRNA stop codons of opioid receptor genes by Ying Liu, Ji Sun Koo, Huiping Zhang

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Codon Optimization Enables the Geneticin Resistance Gene to Be Applied Efficiently to the Genetic Manipulation of the Plant Pathogenic Fungus <i>Botrytis cinerea</i> by Maoyao Tang, Yangyizhou Wang, Kexin Wang, Yuanhang Zhou, Enshuang Zhao, Hao Zhang, Mingzhe Zhang, Hang Yu, Xi Zhao, Guihua Li

“…Our data show that the codon-optimized <i>BcNPTII</i> is an efficient positive selection marker for <i>B. cinerea</i> transformation and can be used for various genetic manipulations in <i>B. cinerea</i>, including field wild-type strains.…”
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The surprising negative correlation of gene length and optimal codon use - disentangling translational selection from GC-biased gene conversion in yeast by Stoletzki Nina

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Saturation genome editing of 11 codons and exon 13 of BRCA2 coupled with chemotherapeutic drug response accurately determines pathogenicity of variants. by Sounak Sahu, Teresa L Sullivan, Alexander Y Mitrophanov, Mélissa Galloux, Darryl Nousome, Eileen Southon, Dylan Caylor, Arun Prakash Mishra, Christine N Evans, Michelle E Clapp, Sandra Burkett, Tyler Malys, Raj Chari, Kajal Biswas, Shyam K Sharan

“…As a proof-of-principle, we have saturated 11 codons encoded by BRCA2 exons 3, 18, 19 and all possible single-nucleotide variants in exon 13 and multiplexed these variants for their functional categorization. …”
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Destabilization of Eukaryote mRNAs by 5′ Proximal Stop Codons Can Occur Independently of the Nonsense-Mediated mRNA Decay Pathway by Barbara Gorgoni, Yun-Bo Zhao, J. Krishnan, Ian Stansfield

“…We show that in a yeast disabled for nonsense mediated mRNA decay (NMD), a <i>PGK1</i> mRNA with an early stop codon at codon 22 of the reading frame is still highly unstable, and that this instability cannot be significantly countered even when 50% stop codon readthrough is triggered. …”
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1100 Immunovirotherapy with the codon-modified influenza virus CodaLytic™ modulates the quality of the tumor immune infiltrate in support of anti-tumor immunity by Nusrat Jahan, Katarina Blagovic, Steffen Mueller, J Robert Coleman, Yiwen Zhao, Johanna K Kaufmann

Plasmid Curing and Exchange Using a Novel Counter-Selectable Marker Based on Unnatural Amino Acid Incorporation at a Sense Codon by Yusuke Kato

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