Encryption of Stereo Image Based on Fractional Chaotic System and RNA Encoding by Zhenyu LI, Hao ZHANG, Li WANG, Xiufang FENG

“…After that, the plain image is permuted by cycle shifting the rows and columns and the permuted image is encoded dynamically using RNA rules and then the Codon sequence is obtained. Then the generated S-box is used for translating RNA sequence. …”
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A proteogenomic analysis of <it>Shigella flexneri </it>using 2D LC-MALDI TOF/TOF by Wei Candong, Leng Wenchuan, Liu Liguo, Zhao Lina, Jin Qi

“…Two genes, which could not be translated to their full length because of stop codon 'mutations' induced by genome sequencing errors, were revised and annotated as fully functional genes. …”
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Selenoprotein: Potential Player in Redox Regulation in <i>Chlamydomonas reinhardtii</i> by Sandip A. Ghuge, Ulhas Sopanrao Kadam, Jong Chan Hong

“…It is obtained from the 21st amino acid selenocysteine (Sec, U), genetically encoded by the UGA codon. Proteins containing Sec are known as selenoproteins. …”
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Transcriptional analysis in bacteriophage Fc02 of Pseudomonas aeruginosa revealed two overlapping genes with exclusion activity by Irais Ramírez-Sánchez, Marco Magos-Castro, Gabriel Guarneros

“…The other ORF, placed in an alternate reading frame with a possible AUG initiation codon at 25 nucleotide downstream of the AUG of the first gene, is expected to encode a 20.7 kDa polypeptide of yet an unknown function. …”
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Cotranscription and intergenic splicing of the <it>PPARG </it>and <it>TSEN2 </it>genes in cattle by Amarger Valérie, Levéziel Hubert, Roux Matthieu

“…One of these transcripts harbors a premature STOP codon and the other encodes a putative chimeric protein combining most of the PPARγ protein and the entire TSEN2 protein, but we could not establish the existence of this protein.…”
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Ribosome Profiling Provides Evidence that Large Noncoding RNAs Do Not Encode Proteins by Guttman, Mitchell, Russell, Pamela, Ingolia, Nicholas T., Weissman, Jonathan S., Lander, Eric S., Lander, Eric Steven

“…Instead, we define a metric based on the known property of translation whereby translating ribosomes are released upon encountering a bona fide stop codon. We show that this metric accurately discriminates between protein-coding transcripts and all classes of known noncoding transcripts, including lincRNAs. …”
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A Proteomics Approach to Profiling the Temporal Translational Response to Stress and Growth by Rothenberg, Daniel Abram, Taliaferro, Jefferson Matthew, Huber, Sabrina M, Dedon, Peter C, White, Forest M.

“…Temporal delays between ribosome occupancy and protein synthesis were observed and found to correlate with altered codon usage in significantly delayed proteins.…”
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High-Performance Computational Genomics by Shajii, Ariya

“…Finally, we also generalize many of the principles used by Seq to create a domain-configurable compiler called Codon, which can be applied to other domains with similar results.…”
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Optimizing recombineering in Corynebacterium glutamicum by Li, Cheng, Swofford, Charles A., Rückert, Christian, Sinskey, Anthony J.

“…By optimizing the homologous arm length and the amount of dsDNA transformed, as well as eliminating codon bias, a dsDNA recombineering efficiency of 13,250 transformed colonies/10 viable cells was achieved, the highest efficiency currently reported in the literature. …”
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Enhanced Expression of Alcohol Dehydrogenase I in Pichia pastoris Reduces the Content of Acetaldehyde in Wines by Geng, Kun, Lin, Ying, Zheng, Xueyun, Li, Cheng, Chen, Shuting, Ling, He, Yang, Jun, Zhu, Xiangyu, Liang, Shuli

“…In this study, <i>ADH1</i> was successfully expressed in <i>Pichia pastoris</i> GS115 based on codon optimization. Then, the expression level of <i>ADH1</i> was enhanced by replacing its promoter with optimized promoters and increasing the copy number of the expression cassette, with ADH1 being purified using nickel column affinity chromatography. …”
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A systematic and extensible approach to DNA primer design for whole gene synthesis by Wozniak, Amanda Victrix Allen

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PhyloCSF: a comparative genomics method to distinguish protein coding and non-coding regions by Lin, Michael F., Jungreis, Irwin, Kellis, Manolis

“…We present PhyloCSF, a novel comparative genomics method that analyzes a multispecies nucleotide sequence alignment to determine whether it is likely to represent a conserved protein-coding region, based on a formal statistical comparison of phylogenetic codon models. Results: We show that PhyloCSF's classification performance in 12-species Drosophila genome alignments exceeds all other methods we compared in a previous study. …”
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Loss of a Conserved tRNA Anticodon Modification Perturbs Cellular Signaling by Zinshteyn, Boris, Gilbert, Wendy

“…We found accumulations at AAA, CAA, and GAA codons, suggesting that translation is slow when these codons are in the ribosomal A site, but these changes appeared too small to affect protein output. …”
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Hemoglobin M-Saskatoon clarified at molecular level by DNA sequencing of the 13-globin gene by Perpustakaan UGM, i-lib

“…At 10 years of age blood sample was withdrawn and enzymatic sequencing of blood lympocyte DNA showed a mutation at Codon 63 (CAT->TAT). Therefore, hemoglobin M-Saskatoon was diagnosed. …”

High-resolution analysis of intrahost genetic diversity in dengue virus serotype 1 infection identifies mixed infections. by Thai, K, Henn, MR, Zody, M, Tricou, V, Nguyet, N, Charlebois, P, Lennon, N, Green, L, de Vries, P, Hien, T, Farrar, J, Van Doorn, H, Jong, d, Birren, B, Holmes, E, Simmons, C

“…Despite such sequence conservation, we observed clear evidence for mixed infection, with the presence of multiple phylogenetically distinct lineages present within the same host, while the presence of stop codon mutations in some samples suggests the action of complementation. …”

Regulatory region single nucleotide polymorphisms of the apolipoprotein E gene and the rate of cognitive decline in Alzheimer's disease. by Belbin, O, Dunn, J, Ling, Y, Morgan, L, Chappell, S, Beaumont, H, Warden, D, Smith, D, Kalsheker, N, Morgan, K

“…We report here that in a case-control association study (N=719) of the seven SNPs, the genotype at codon 112 captures all the information required to assess disease risk. …”

Characterisation of renal chloride channel, CLCN5, mutations in hypercalciuric nephrolithiasis (kidney stones) disorders. by Lloyd, SE, Gunther, W, Pearce, S, Thomson, A, Bianchi, M, Bosio, M, Craig, I, Fisher, S, Scheinman, S, Wrong, O, Jentsch, T, Thakker, R

“…The G57V and 30:H insertion mutations represent the first CLCN5 mutations to be identified in the N-terminus region, and the R648Stop mutation, which has been observed previously in an unrelated family, suggests that this codon may be particularly prone to mutations. Heterologous expression of the mutations resulted in a marked reduction or abolition of the chloride currents, thereby establishing their functional importance. …”

Inferring the translation speed and determining its relationship to the protein structure produced by Martin, A

“…This thesis investigates whether the speed with which a codon is translated biases the protein structure produced. …”

The genetic diversity and phenotypic associations of feline caliciviruses from cats in Switzerland by Spiri, A, Thézé, J, Meli, M, Cattori, V, Berger, A, Steinrigl, A, Pybus, O, Hofmann-Lehmann, R, Willi, B

“…Sequences from 66 FCV samples were used to investigate the correlation between viral phylogeny and several traits, including geographic origin, signalment, husbandry, FCV vaccination, and co-infections. Codon-based nucleotide alignment showed that individual nucleotides and their corresponding amino acid sites were either invariant or highly variable. …”

Mutations in the gamma(2) subunit of AMP-activated protein kinase cause familial hypertrophic cardiomyopathy: evidence for the central role of energy compromise in disease pathogen... by Blair, E, Redwood, C, Ashrafian, H, Oliveira, M, Broxholme, J, Kerr, B, Salmon, A, Ostman-Smith, I, Watkins, H

“…The mutations, one missense and one in-frame single codon insertion, occur in highly conserved regions. …”