Genomic analysis of HIV type 1 strains derived from a mother and child pair of long-term nonprogressors. by Reinis, M, Weiser, B, Kuiken, C, Dong, T, Lang, D, Nachman, S, Zhang, Y, Rowland-Jones, S, Burger, H

“…Analysis of four genomic sequences demonstrated that all viral genes were intact, lacking major deletions or premature stop codons to easily explain the slow disease progression. …”

Analysis of antigenic surfaces of proteins. by Lea, S, Stuart, D

“…Although these changes may be rationalized in terms of the structure and chemistry of the different side chains, we suggest that there may be a further, genetic component behind the observations: point mutations in the respective codons for serine and threonine lead to markedly different forms of structural variability. …”

A locus on human chromosome 20 contains several genes expressing protease inhibitor domains with homology to whey acidic protein. by Clauss, A, Lilja, H, Lundwall, A

“…In most cases, there is also a separate exon encompassing a few terminal codons and the 3' untranslated nucleotides. There are also examples of mixed type inhibitors, that encode inhibitor domains of both WAP and Kunitz types. …”

Mutagenically separated PCR assay for rapid detection of M41L and K70R zidovudine resistance mutations in CRF01_AE (subtype E) human immunodeficiency virus type 1. by Myint, L, Ariyoshi, K, Yan, H, Frater, A, Auwanit, W, Pathipvanith, P, Yamada, K, Matsuda, M, Chiba, T, Fujita, K, McClure, M, Weber, J, Sugiura, W

“…The concordance of the two assays was 92 and 100% in codons 41 and 70, respectively. The MS-PCR assay is a rapid, simple, and inexpensive assay that is highly sensitive in detecting mutant targets, including minor populations. …”

X-linked hypophosphatemia attributable to pseudoexons of the PHEX gene. by Christie, P, Harding, B, Nesbit, M, Whyte, M, Thakker, R

“…One X-linked hypophosphatemia patient was found to have 3 abnormally large transcripts, resulting from 51-bp, 100-bp, and 170-bp insertions, all of which would lead to missense peptides and premature termination codons. The origin of these transcripts was a mutation (g to t) at position +1268 of intron 7, which resulted in the occurrence of a high quality novel donor splice site (ggaagg to gtaagg). …”

Combined molecular and clinical assessment of Plasmodium falciparum antimalarial drug resistance in the Lao People's Democratic Republic (Laos). by Mayxay, M, Nair, S, Sudimack, D, Imwong, M, Tanomsing, N, Pongvongsa, T, Phompida, S, Phetsouvanh, R, White, N, Anderson, T, Newton, P

“…Each sample was genotyped for 11 codons in the chloroquine resistance transporter (pfcrt), dihydrofolate reductase (pfdhfr), and dihydropteroate synthase (pfdhps) genes. …”

Expression and chromosomal localization of the Requiem gene. by Gabig, T, Crean, C, Klenk, A, Long, H, Copeland, N, Gilbert, D, Jenkins, N, Quincey, D, Parente, F, Lespinasse, F, Carle, G, Gaudray, P, Zhang, C, Calender, A, Hoeppener, J, Kas, K, Thakker, R, Farnebo, F, Teh, B, Larsson, C, Piehl, F, Lagercrantz, J, Khodaei, S, Carson, E, Weber, G

“…The human cDNA clone sequenced showed high homology to its murine counterpart and extended the open reading frame by 20 codons upstream. The gene is located in the proximal region of mouse Chromosome (Chr) 19. …”

A presenilin-1 truncating mutation is present in two cases with autopsy-confirmed early-onset Alzheimer disease. by Tysoe, C, Whittaker, J, Xuereb, J, Cairns, N, Cruts, M, Van Broeckhoven, C, Wilcock, G, Rubinsztein, D

“…The mutation was associated with two shortened transcripts, both with shifted reading frames resulting in premature-termination codons. All the PS-1 mutations described elsewhere have been missense or in-frame splice mutations, and recent data suggest that these result in disease by gain-of-function or dominant-negative mechanisms. …”

Genomic innovation of ATD alleviates mistranslation associated with multicellularity in Animalia by Santosh Kumar Kuncha, Vinitha Lakshmi Venkadasamy, Gurumoorthy Amudhan, Priyanka Dahate, Sankara Rao Kola, Sambhavi Pottabathini, Shobha P Kruparani, P Chandra Shekar, Rajan Sankaranarayanan

“…Therefore, ATD knockout cells display pronounced sensitivity through increased mistranslation of threonine codons leading to cell death. Strikingly, we identify the emergence of ATD along with the error inducing tRNA species starting from Choanoflagellates thus uncovering an important genomic innovation required for multicellularity that occurred in unicellular ancestors of animals. …”
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The Clinical Implications of KRAS Mutations and Variant Allele Frequencies in Pancreatic Ductal Adenocarcinoma by Faria Nusrat, Akshay Khanna, Aditi Jain, Wei Jiang, Harish Lavu, Charles J. Yeo, Wilbur Bowne, Avinoam Nevler

“…Pathogenic KRAS mutations are mostly limited to codons 12, 13 and 61, with G12D, G12V, G12R, Q61H, and G13D accounting for approximately 95% of the mutant cases. …”
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Processing DNA Storage through Programmable Assembly in a Droplet‐Based Fluidics System by Minsang Yu, Doyeon Lim, Jungwoo Kim, Youngjun Song

“…Furthermore, eight 90 bps DNA pools with pixel information (png: 0.27–0.28 kB), encoded by codons, are synthesized to create eight 270 bps DNA pools with an animation movie chip file (mp4: 12 kB) in the DCF system.…”
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Immunodetection of Truncated Forms of the α6 Subunit of the nAChR in the Brain of Spinosad Resistant <i>Ceratitis capitata</i> Phenotypes by Ana Guillem-Amat, Elena López-Errasquín, Irene García-Ricote, José Luis Barbero, Lucas Sánchez, Sergio Casas-Tintó, Félix Ortego

“…Point mutations that result in premature stop codons in the <i>α6</i> gene of <i>Ceratitis capitata</i> flies have been previously associated with spinosad resistance, but it is unknown if these transcripts are translated and if so, what is the location of the putative truncated proteins. …”
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CHARACTERIZATION AT PROTEIN LEVEL OF THE NEW αS1 CASEIN ALLELE IRV DISCOVERED IN ROMANIAN GREY STEPPE CATTLE BREED MOLDAVIAN VARIETY by V.A. BALTEANU, A. VLAIC, F.D. POP, ANDA RALUCA RUSU, P. MARTIN, G. MIRANDA, S. CREANGA

“…The only possible substitution found is concerning the glutamine (Q) residue codified by codons from exons 8, 9 or 11. This is under study also at DNA level. …”
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The functional mutational landscape of the lacZ gene by Marc A. Beal, Matthew J. Meier, Angela Dykes, Carole L. Yauk, Iain B. Lambert, Francesco Marchetti

“…Those mutations affected 492 of the 1,023 lacZ codons, including most of the 21 previously known residues critical for catalytic activity. …”
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Photon Dissipation as the Origin of Information Encoding in RNA and DNA by Julián Mejía Morales, Karo Michaelian

“…Indeed, we show here that those amino acids with characteristics most relevant to fomenting UVC photon dissipation are precisely those with greatest chemical affinity to their codons or anticodons. This could provide a thermodynamic basis for the specificity in the amino acid-nucleic acid interaction and an explanation for the accumulation of information in nucleic acids since this information is relevant to the optimization of dissipation of the externally imposed thermodynamic potentials. …”
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Is Apolipoprotein E ε2 Associated with Delayed Onset of Non-Lesional Temporal Lobe Epilepsy? by Davor Sporiš, Silvio Bašić, Jadranka Sertić, Darija Mahović Lakušić, Tomislav Babić

“…ApoE alleles were determined by a procedure where genome DNA was amplified by chain reaction along with polymerase, using the LightCycler kit (Roche) for ApoE mutations on codons 112 and 158. There was a statistically significant difference between the groups of patients with ApoE ε2/3 and ε3/4 genotypes (p=0.03), but not between patients with ApoE ε2/3 and ε3/3, and those with ApoE ε3/4 and ε3/3. …”
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Impact of C‐terminal amino acid composition on protein expression in bacteria by Marc Weber, Raul Burgos, Eva Yus, Jae‐Seong Yang, Maria Lluch‐Senar, Luis Serrano

“…We then studied the impact of C‐terminal composition on protein levels in a library of Mycoplasma pneumoniae mutants, covering all possible combinations of the two last codons. We found that charged and polar residues, in particular lysine, led to higher expression, while hydrophobic and aromatic residues led to lower expression, with a difference in protein levels up to fourfold. …”
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Small open reading frames: a comparative genetics approach to validation by Niyati Jain, Felix Richter, Ivan Adzhubei, Andrew J. Sharp, Bruce D. Gelb

“…Abstract Open reading frames (ORFs) with fewer than 100 codons are generally not annotated in genomes, although bona fide genes of that size are known. …”
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Kinetic modeling predicts a stimulatory role for ribosome collisions at elongation stall sites in bacteria by Michael A Ferrin, Arvind R Subramaniam

“…To decipher ribosome kinetics at stall sites, we induced ribosome stalling at specific codons by starving the bacterium Escherichia coli for the cognate amino acid. …”
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Compromised nonsense-mediated RNA decay results in truncated RNA-binding protein production upon DUX4 expression by Amy E. Campbell, Michael C. Dyle, Roberto Albanese, Tyler Matheny, Kavitha Sudheendran, Michael A. Cortázar, Thomas Forman, Rui Fu, Austin E. Gillen, Marvin H. Caruthers, Stephen N. Floor, Lorenzo Calviello, Sujatha Jagannathan

“…Summary: Nonsense-mediated RNA decay (NMD) degrades transcripts carrying premature termination codons. NMD is thought to prevent the synthesis of toxic truncated proteins. …”
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