Human immunodeficiency virus type 1: drug resistance in treated and untreated Brazilian children by SRR Simonetti, HG Schatzmayr, JP Simonetti

“…The children who presented alterations at polymorphism sites should be monitored for the development of additional mutations occurring at relevant resistance codons.…”
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Phylogenetic studies on three Helicotylenchus species based on 28S rDNA and mtCOI sequence data by Rybarczyk-Mydłowska K., Dmowska E., Kowalewska K.

“…Moreover, within the mtCOI sequences obtained from H. pseudorobustus, unlike from the other two, a simultaneous presence of TAG and TAA codons was identified. This may indicate mitochondrial genetic code alterations or other genomic rearrangements in H. pseudorobustus.…”
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The relationship between protein domains and homopeptides in the Plasmodium falciparum proteome by Yue Wang, Hsin Jou Yang, Paul M. Harrison

“…The most prevalent of these are made from residues encoded by adenine/thymidine (AT)-rich codons, in particular asparagine. We examined homopeptide occurrences within protein domains in P. falciparum. …”
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Autosomal dominant hereditary spastic paraplegia: Novel mutations in the <it>REEP1 </it>gene (SPG31) by Epplen Joerg T, Arning Larissa, Schlang Katharina J, Stemmler Susanne

“…</p> <p>Results</p> <p>Ten mutations were identified in the <it>REEP1 </it>gene, these included eight novel mutations comprising small insertions/deletions causing frame shifts and subsequently premature stop codons, one nonsense mutation and one splice site mutation as well as two missense mutations. …”
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Tobacco Transgenic for the Flax Rust Resistance Gene L Expresses Allele-Specific Activation of Defense Responses by Donna Frost, Heather Way, Paul Howles, Joanne Luck, John Manners, Adrienne Hardham, Jean Finnegan, Jeff Ellis

“…The truncated gene consisted of the promoter, the complete TIR region, and 39 codons of the NBS domain fused in-frame to a tobacco retrotransposon-like sequence. …”
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The pleiotropic functions of Pri smORF peptides synchronize leg development regulators. by Damien Markus, Aurore Pelletier, Muriel Boube, Fillip Port, Michael Boutros, François Payre, Benedikt Obermayer, Jennifer Zanet

“…The last decade witnesses the emergence of the abundant family of smORF peptides, encoded by small ORF (<100 codons), whose biological functions remain largely unexplored. …”
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Dhh1 promotes autophagy-related protein translation during nitrogen starvation. by Xu Liu, Zhiyuan Yao, Meiyan Jin, Sim Namkoong, Zhangyuan Yin, Jun Hee Lee, Daniel J Klionsky

“…The structured regions shortly after the start codons of the two ATG mRNAs are necessary for their translational regulation by Dhh1. …”
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Cryptic transcription mediates repression of subtelomeric metal homeostasis genes. by Isabelle Toesca, Camille R Nery, Cesar F Fernandez, Shakir Sayani, Guillaume F Chanfreau

“…Nonsense-mediated mRNA decay (NMD) prevents the accumulation of transcripts bearing premature termination codons. Here we show that Saccharomyces cerevisiae NMD mutants accumulate 5'-extended RNAs (CD-CUTs) of many subtelomeric genes. …”
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Genetic variation and selection in the major histocompatibility complex Class II gene in the Guizhou pony by Chang Liu, Hongmei Lei, Xueqin Ran, Jiafu Wang

“…Nine DQA, five DQB, nine DRA, and seven DRB codons were under significant positive selection at the antigen binding sites (ABS), suggesting that the selected residues in ABS may play a significant role in the innate immune system of the GZP. …”
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The vlhA gene sequencing of Iranian Mycoplasma synoviae isolates by Pourbakhsh, S.A., Maghami, M., Ashtari, A., Bayatzadeh, M.A., Ahangaran, S.

“…Furthermore, these data indicated that changes in the vlhA gene sequence could introduce into the expressed vlhA gene amino acid codons and effective in pathogenesis rate in flocks.…”
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Suggested role for G4 DNA in recombinational switching at the antigenic variation locus of the Lyme disease spirochete. by Rupali Walia, George Chaconas

“…We found that runs of G, three nucleotides and longer occur at a very high density, with a greater than 100-fold strand-specific distribution in the vls locus of three B. burgdorferi strains as well as in B. afzelii and B. garinii, in spite of the bias for the use of A-T rich codons in Borrelia species. Our findings suggest the possibility that G4 DNA may be a mediator of recombinational switching at the vlsE locus in the Lyme spirochetes.…”
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Putative Promoter Motif Analyses Reinforce the Evolutionary Relationships Among Faustoviruses, Kaumoebavirus, and Asfarvirus by Graziele P. Oliveira, Isabella L. M. de Aquino, Ana P. M. F. Luiz, Jônatas S. Abrahão

“…Here, we demonstrate that TATTT and TATATA are mostly present in faustovirus and kaumoebavirus genomic intergenic regions (IRs) and that they are widely distributed at 0 to -100 bp upstream to the start codons. We observed that putative promoter motifs are present as one to dozens of repetitions in IRs of faustovirus, kaumoebavirus, and asfarvirus, which is similar to that described previously for marseilleviruses. …”
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Computing Genomic Signatures Using de Bruijn Chains by Lenwood S. Heath, Amrita Pati

“…<p style="text-align: justify;">Genomic DNA sequences have both deterministic and random aspects and exhibit features at numerous scales, from codons to regions of conserved or divergent gene order. …”
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Extensive Changes in Transcription Dynamics Reflected on Alternative Splicing Events in Systemic Lupus Erythematosus Patients by Sofia Papanikolaou, George K. Bertsias, Christoforos Nikolaou

“…We found a predominance of intron retention events, with the majority introducing premature stop codons, suggestive of gene repression, in both inactive and active SLE patient samples. …”
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More-SPEED: Enhancing Protein Activity Prediction from DNA Sequences by Samaher Al-Janabi, Zena A. Kadhuim

“…The BDLSTM layer plays a crucial role in matching codons and predicting protein names, reducing computational complexity without compromising accuracy. …”
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From diagnosis to therapy in Duchenne muscular dystrophy by Babbs, A, Chatzopoulou, M, Edwards, B, Squire, SE, Wilkinson, IVL, Wynne, GM, Russell, AJ, Davies, KE

“…However, there are several promising genetic therapeutic approaches at the preclinical stage or in clinical trials including read-through of stop codons, exon skipping, delivery of dystrophin minigenes and the modulation of expression of the dystrophin related protein, utrophin. …”

Explaining variation in familial adenomatous polyposis: relationship between genotype and phenotype and evidence for modifier genes. by Crabtree, MD, Tomlinson, I, Hodgson, S, Neale, K, Phillips, R, Houlston, R

“…Formal modelling of the segregation of disease severity in families was performed RESULTS: There was strong evidence for a relationship between site of mutation and the number of colorectal polyps, with germline mutations in the "cluster region" causing the most severe disease and those with mutations between codons 1020 and 1169 having the mildest disease. In addition to this genotype-phenotype relationship, we found evidence for non-APC linked genetic modifiers of disease expression. …”

Comparative phylogenies of yellow fever isolates from Peru and Brazil. by Bryant, J, Barrett, A

“…Sequences were obtained for two genomic regions from 50 strains of YFV collected between 1954 and 2000 comprising 223 codons of the structural proteins (premembrane and envelope genes, 'prM/E'), and a distal region spanning the carboxy terminus of NS5 and part of the 3' non-coding region ('EMF'). …”

The first co-opted endogenous foamy viruses and the evolutionary history of reptilian foamy viruses by Aiewsakun, P, Simmonds, P, Katzourakis, A

“…Numerous copies of full length ERV-Spuma-Spu elements were found in the tuatara genome littered with in-frame stop codons and transposable elements, suggesting that they are indeed endogenous and are not functional. …”

Evolutionary dynamics of Oropouche virus in South America by Gutierrez, B, Wise, E, Pullan, S, Logue, C, Bowden, T, Escalera-Zamudio, M, Trueba, G, Nunes, M, Faria, N, Pybus, O

“…We also present the discovery of previously unobserved putative N-linked glycosylation sites, as well as codons that evolve under positive selection on the viral surface proteins, and discuss the potential role of these features in the evolution of OROV through a combined phylogenetic and structural approach.…”