DNA barcoding of Lates calcarifer (Bloch, 1970) by John, Akbar, Kumar, C. Prasanna, Lyla, P.S., Khan, S. Ajmal, Khan Chowdhury, Ahmed Jalal

“…The phylogenetic and genetic distance data showed that the maximum genetic distance is present in 3rd codon position in all the selected species. It is apparent from the genetic distance that the GD between L. calcarifer and L. niloticus was observed to be higher than the GD between P. waigiensis and L. niloticus in all the codon positions. …”
Get full text

Persistence of attenuated rev genes in a human immunodeficiency virus type 1-infected asymptomatic individual. by Iversen, A, Shpaer, E, Rodrigo, A, Hirsch, MS, Walker, B, Sheppard, H, Merigan, T, Mullins, J

“…Similarly, mutagenesis of rev codon 78 of NL4-3 from Leu to Ile partially attenuated this virus. …”

Screen for IDH1, IDH2, IDH3, D2HGDH and L2HGDH mutations in glioblastoma. by Krell, D, Assoku, M, Galloway, M, Mulholland, P, Tomlinson, I, Bardella, C

“…Mutations in IDH2 at codon 172 are present in grade II-III gliomas at a low frequency. …”

The Mu subunit of Plasmodium falciparum Clathrin-associated adaptor protein 2 modulates in vitro parasite response to Artemisinin and Quinine by Henriques, G, van Schalkwyk, D, Burrow, R, Warhurst, D, Thompson, E, Baker, D, Fidock, D, Hallett, R, Flueck, C, Sutherland, C

“…Here, we characterize the role of pfap2-mu in mediating the in vitro antimalarial drug response of P. falciparum by generating transgenic parasites constitutively expressing codon 160 encoding either the wild-type Ser (Ser160) or the Asn mutant (160Asn) form of pfap2-mu. …”

Targeted amplicon deep sequencing for monitoring antimalarial resistance markers in western Kenya by Osoti, V, Akinyi, M, Wamae, K, Kimenyi, KM, de Laurent, Z, Ndwiga, L, Gichuki, P, Okoyo, C, Kepha, S, Mwandawiro, C, Kandie, R, Bejon, P, Snow, RW, Ochola-Oyier, LI

“…TADS highlighted the low-frequency variants, allowing the early identification of new mutations, <i>Pfmdr1</i> codon 199S and <i>Pfdhfr</i> codon 85I and emerging 164L mutations. …”

Hydroxylation of the eukaryotic ribosomal decoding center affects translational accuracy. by Loenarz, C, Sekirnik, R, Thalhammer, A, Ge, W, Spivakovsky, E, Mackeen, M, McDonough, M, Cockman, M, Kessler, B, Ratcliffe, P, Wolf, A, Schofield, C

“…In contrast to most previously characterized accuracy modulators, including antibiotics and the prion state of the S. cerevisiae translation termination factor eRF3, Rps23p hydroxylation can either increase or decrease translational accuracy in a stop codon context-dependent manner. We identify conditions where Rps23p hydroxylation status determines viability as a consequence of nonsense codon suppression. …”

Novel DAX1 mutations in X-linked adrenal hypoplasia congenita and hypogonadotrophic hypogonadism. by Bassett, J, O'Halloran, D, Williams, G, Beardwell, C, Shalet, S, Thakker, R

“…These consisted of an insertional mutation at codon 183 that led to a frameshift and a premature Stop at codon 184, and a missense mutation Leu278Pro that involved a highly conserved leucine residue within the proposed ligand binding domain. …”

Agonist-independent interactions between β-arrestins and mutant vasopressin type ii receptors associated with nephrogenic syndrome of inappropriate antidiuresis by Kocan, M, See, H, Sampaio, N, Eidne, K, Feldman, B, Pfleger, K

“…It was found that each infant had a different mutation of the vasopressin type II receptor (V2R) at codon 137 where arginine was converted to cysteine or leucine (R137C or R137L), resulting in constitutive signaling. …”

TLR5 as an anti-inflammatory target and modifier gene in cystic fibrosis. by Blohmke, C, Park, J, Hirschfeld, A, Victor, R, Schneiderman, J, Stefanowicz, D, Chilvers, M, Durie, P, Corey, M, Zielenski, J, Dorfman, R, Sandford, A, Daley, D, Turvey, SE

“…Adults with CF carrying the TLR5 premature stop codon (CT or TT genotype) had a higher body mass index than did CF patients homozygous for the fully functional allele (CC genotype) (p = 0.044); however, similar improvements in lung function associated with the T allele were not statistically significant. …”

Mitogenome of Gymnothorax minor and phylogenetic relationship with its congeners and related genera (Anguilliformes: Muraenidae) by Song, Sze-Looi, Yong, Hoi-Sen, Loh, Kar-Hoe, Lim, Phaik-Eem, Yee, Amy Hui Then, Praphathip Eamsobhana

“…Excepting cox1 with GTG, the other 12 PCGs had ATG start codon. Seven of its PCGs had incomplete stop codon - five (nad2; cox1; cox2; nad3 and nad4) with T and two (atp6 and cox3) with TA. …”
Get full text

Complete mitochondrial genome of Angiostrongylus malaysiensis lungworm and molecular phylogeny of Metastrongyloid nematodes by Yong, Hoi Sen, Song, Sze Looi, Eamsobhana, Praphathip, Lim, Phaik Eem

“…A. malaysiensis and A. cantonensis had identical start codon for the 12 PCGs, but four PCGs (atp6, cob, nad2, nad6) had different stop codon. …”

Identification of an N-terminal tag (580N) that improves the biosynthesis of fluorescent proteins in Francisella tularensis and other Gram-negative bacteria by Kristen Haggerty, Stuart Cantlay, Emily Young, Mariah K. Cashbaugh, Elio F. Delatore III, Rori Schreiber, Hayden Hess, Daniel R. Komlosi, Sarah Butler, Dalton Bolon, Theresa Evangelista, Takoda Hager, Claire Kelly, Katherine Phillips, Jada Voellinger, Robert M.Q. Shanks, Joseph Horzempa

“…In support, expression of emGFPFt that had been codon-optimized for F. tularensis, yielded significantly enhanced fluorescence than its non-optimized counterpart. …”
Get full text

Distribution patterns of molecular markers of antimalarial drug resistance in Plasmodium falciparum isolates on the Thai-Myanmar border during the periods of 1993–1998 and 2002–200... by Phunuch Muhamad, Papichaya Phompradit, Wanna Chaijaroenkul, Kesara Na-Bangchang

“…Results Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) were used to detect pfcrt mutations at codons 76, 220, 271, 326, 356, and 371 as well as pfmdr1 mutation at codon 86. …”
Get full text

Open Reading Frame 4 Is Not Essential in the Replication and Infection of Genotype 1 Hepatitis E Virus by Huimin Bai, Yasushi Ami, Yuriko Suzaki, Yen Hai Doan, Masamichi Muramatsu, Tian-Cheng Li

“…The second construct had ACG instead of the ATG codon (T2837C), introducing an M→T mutation in ORF4. …”
Get full text

Sustainable and high-level microbial production of plant hemoglobin in Corynebacterium glutamicum by Mengmeng Wang, Zhong Shi, Ning Gao, Yingyu Zhou, Xiaomeng Ni, Jiuzhou Chen, Jiao Liu, Wenjuan Zhou, Xuan Guo, Bo Xin, Yanbing Shen, Yu Wang, Ping Zheng, Jibin Sun

“…Hemoglobin genes from different sources including soybean and maize were selected and subjected to codon optimization. Interestingly, some candidates optimized for the codon usage bias of Escherichia coli outperformed those for C. glutamicum regarding the heterologous expression in C. glutamicum. …”
Get full text

A simple geometrical model of the electrostatic environment around the catalytic center of the ribosome and its significance for the elongation cycle kinetics by Marc Joiret, Frederic Kerff, Francesca Rapino, Pierre Close, Liesbet Geris

“…The hypo-exponential distribution fits the residence time observed distribution of the ribosome on a codon. An educated deconvolution of this distribution is used to estimate the rates of each elongation step in a codon specific manner. …”
Get full text

Sporadic Creutzfeldt-Jakob disease VM1: phenotypic and molecular characterization of a novel subtype of human prion disease by Ellen Gelpi, Simone Baiardi, Carlos Nos, Sofia Dellavalle, Iban Aldecoa, Raquel Ruiz-Garcia, Lourdes Ispierto, Domingo Escudero, Virgina Casado, Elena Barranco, Anuncia Boltes, Laura Molina-Porcel, Nuria Bargalló, Marcello Rossi, Angela Mammana, Dorina Tiple, Luana Vaianella, Elisabeth Stoegmann, Ingrid Simonitsch-Klupp, Gregor Kasprian, Sigrid Klotz, Romana Höftberger, Herbert Budka, Gabor G. Kovacs, Isidre Ferrer, Sabina Capellari, Raquel Sanchez-Valle, Piero Parchi

“…Abstract The methionine (M)—valine (V) polymorphic codon 129 of the prion protein gene (PRNP) plays a central role in both susceptibility and phenotypic expression of sporadic Creutzfeldt-Jakob diseases (sCJD). …”
Get full text

The metazoan landscape of mitochondrial DNA gene order and content is shaped by selection and affects mitochondrial transcription by Noam Shtolz, Dan Mishmar

“…The analysis of mitochondrial DNA from over 8000 metazoans shows gene content conservation, association between preference for mtDNA-encoded tRNAs and codon usage, selective constraint for mtDNA rearrangements and their impact on mtDNA transcription.…”
Get full text

Gibberellin Oxidase Gene Family in <i>L. chinense</i>: Genome-Wide Identification and Gene Expression Analysis by Lingfeng Hu, Pengkai Wang, Zhaodong Hao, Ye Lu, Guoxia Xue, Zijian Cao, Haoxian Qu, Tielong Cheng, Jisen Shi, Jinhui Chen

“…Furthermore, evidence for purifying selection was detected between orthologous <i>GAox</i> genes in rice, grape, Arabidopsis, and <i>L. chinense</i>. Analysis of the codon usage patterns showed that mutation pressure and natural selection might have induced codon usage bias in angiosperms; however, the <i>LcGAox</i> genes in mosses, lycophytes, and ambarella plants exhibited no obvious codon usage preference. …”
Get full text

Novel Structural Variation and Evolutionary Characteristics of Chloroplast tRNA in <i>Gossypium</i> Plants by Ting-Ting Zhang, Yang Yang, Xiao-Yu Song, Xin-Yu Gao, Xian-Liang Zhang, Jun-Jie Zhao, Ke-Hai Zhou, Chang-Bao Zhao, Wei Li, Dai-Gang Yang, Xiong-Feng Ma, Zhong-Hu Li

“…The cp tRNAs of <i>Gossypium</i> L. contained introns, and cp tRNA^Ile contained the anti-codon (C-A-U), which was generally the anti-codon of tRNA^Met. …”
Get full text