Optimization of HIV-1 Envelope DNA Vaccine Candidates within Three Different Animal Models, Guinea Pigs, Rabbits and Cynomolgus Macaques by Roger Le Grand, Anders Fomsgaard, Marianne Jansson, Leo Heyndrickx, Gabriella Scarlatti, Priscilla Biswas, Guillaume Stewart-Jones, Emma Joanne Bowles, Nathalie Dereuddre-Bosquet, Frédéric Martinon, Rogier W Sanders, Mark Melchers, Tara Laura Elvang, Betina Skovgaard Andresen, Berit Grevstad, Johanna Repits, Marie Borggren, Lasse Vinner

“…Envelope genes from the prototype isolate HIV-1 Bx08 and two elite neutralizers were included. Codon-optimized genes, encoded secreted gp140 or membrane bound gp150, were modified for expression of stabilized soluble trimer gene products, and delivered individually or mixed. …”
Get full text

Complete mitochondrial genomes of two marine monogonont rotifer Brachionus manjavacas strains by Min-Sub Kim, Young Hwan Lee, Duck-Hyun Kim, Hee-Jin Kim, Un-Ki Hwang, Russell Shiel, Atsushi Hagiwara, Jae-Seong Lee

“…Of 12 PCGs of both B. manjavacas strains, three genes (ND1, ATP6, and ND5) had incomplete stop codon T. Furthermore, ATA was the start codon for ND4, ND5, and CO3 genes, whereas that for other PCGs was ATG in both strains. …”
Get full text

Analysis of genetic status of pivotal driver genes in pancreatic ductal adenocarcinoma and their correlation with clinicopathologic features by XIE Wen, LIANG Huaiyu, DONG Lei, YUAN Fei, WANG Chaofu, GUO Yan

“…KRAS mutations were missense mutations, of which 94.59% occurred in codon 12 of exon 2 and 5.41% in codon 61 in exon 3. …”
Get full text

Susceptibility to scrapie and disease phenotype in sheep: cross-<it>PRNP</it> genotype experimental transmissions with natural sources by González Lorenzo, Jeffrey Martin, Dagleish Mark P, Goldmann Wilfred, Sisó Sílvia, Eaton Samantha L, Martin Stuart, Finlayson Jeanie, Stewart Paula, Steele Philip, Pang Yvonne, Hamilton Scott, Reid Hugh W, Chianini Francesca

“…It was found that additional polymorphisms at codons 112 or 141 of AA₁₃₆ recipients resulted in a delayed appearance of clinical disease or even in protection from infection. …”
Get full text

First Complete Mitochondrial Genome of Melyridae(Coleoptera, Cleroidea): Genome Description and Phylogenetic Implications by Lilan Yuan, Xueying Ge, Guanglin Xie, Haoyu Liu, Yuxia Yang

“…Consistent with previous observations of Cleroidea species, the mitogenome of <i>Cordylepherus</i> sp. is highly conserved in gene size, organization and codon usage, and secondary structures of tRNAs. All protein-coding genes (PCGs) initiate with the standard start codon ATN, except ND1, which starts with TTG, and terminate with the complete stop codons of TAA and TAG, or incomplete forms, TA- and T-. …”
Get full text

First Draft Genome Assembly of the Malaysian Stingless Bee, <i>Heterotrigona itama</i> (Apidae, Meliponinae) by Chien-Yeong Wee, Amin-Asyraf Tamizi, Nazrul-Hisham Nazaruddin, Siuk-Mun Ng, Jia-Shiun Khoo, Rosliza Jajuli

Get full text

The Chloroplast Genome of the Lichen Photobiont <i>Trebouxiophyceae</i> sp. DW1 and Its Phylogenetic Implications by Lidan Wang, Shenglu Zhang, Jinjin Fang, Xinjie Jin, Reyim Mamut, Pan Li

“…The simple sequence repeats are all mononucleotide repeats. Codon usage analysis showed that the genome tended to use codon ending in A/U. …”
Get full text

Resurrection of a Viral Internal Ribosome Entry Site from a 700 Year Old Ancient Northwest Territories Cripavirus by Xinying Wang, Marli Vlok, Stephane Flibotte, Eric Jan

“…The dicistrovirus intergenic region internal ribosome entry site (IGR IRES) uses an unprecedented, streamlined mechanism whereby the IRES adopts a triple-pseudoknot (PK) structure to directly bind to the conserved core of the ribosome and drive translation from a non-AUG codon. The origin of this IRES mechanism is not known. …”
Get full text

The nucleotide landscape of polyXY regions by Pablo Mier, Miguel A. Andrade-Navarro

“…We observed that polyXY exacerbates the codon biases, and that the similarity between the X and Y codons is higher than in the background proteome. …”
Get full text

DnoisE: distance denoising by entropy. An open-source parallelizable alternative for denoising sequence datasets by Adrià Antich, Creu Palacín, Xavier Turon, Owen S. Wangensteen

“…DnoisE implements different merging procedures as options, and can incorporate codon entropy information either retrieved from the data or supplied by the user. …”
Get full text

A novel statistical method predicts mutability of the genomic segments of the SARS-CoV-2 virus by Amir Hossein Darooneh, Michelle Przedborski, Mohammad Kohandel

“…Importantly, these correlations are found to hold at the codon and gene levels, as well as for gene coding regions. …”
Get full text

Detection of Amino Acid Mutations in Dihydrofolate Reductase & Dihydro Pteroate Synthase Gene in Plasmodium Vivax Isolates by Rizwana Yasmin, Musarrat Jehan, Mehwish Kalam, Syeda Mariam Siddiqa, Mahadev Harani

“…In pvdhfr gene, common mutations were observed in ‘S’ amino acids at codons 58 &117 and ‘D’ at codons 105 &157. Regarding pvdhps gene, common mutations were observed in ‘V’ amino acids at codon 398 and ‘K’ at codon 590. …”
Get full text

<i>E. coli</i> MnmA Is an Fe-S Cluster-Independent 2-Thiouridylase by Moses Ogunkola, Lennart Wolff, Eric Asare Fenteng, Benjamin R. Duffus, Silke Leimkühler

“…These changes are necessary for the proper codon recognition and stability of tRNA. In <i>Escherichia coli</i>, sulfur modification at the wobble uridine (34) of lysine, glutamic acid, and glutamine is essential for codon and anticodon binding and prevents frameshifting during translation. …”
Get full text

A statistical analysis of the three-fold evolution of genomic compression through frame overlaps in prokaryotes by Lillo Fabrizio, Krakauer David C

“…Some phases seem to reflect codon pairings reducing the probability of non-synonymous substitution. …”
Get full text

The complete mitochondrial genome of Poecilia formosa (Poecilia, Cyprinodontidae) and phylogenetic studies of cyprinodontiformes by Youkun Huang, Bingjian Liu, Fang Meng, Qi Wang, Kehua Zhu, Jianshe Zhang, Fei Jing, Liping Xia, Yifan Liu

“…All protein-coding genes started with Met, ND1, CO1, ATP8, ATP6, CO3, ND4L, ND5, ND6 and CytB ended by TAA as a stop codon, ND2 and ND3 ended by TAG as a stop codon, CO3 and ND4 ended by a single T. …”
Get full text

The mitochondrial genome of one ‘twisted-wing parasite’ Xenos cf. moutoni (Insecta, Strepsiptera, Xenidae) from Gaoligong Mountains, Southwest of China by Ru Zhang, Jun Li, Chuyang Mao, Zhiwei Dong, Jinwu He, Guichun Liu, Ruoping Zhao, Wen Wang, Xueyan Li

“…All of the 13 PCGs are initiated with canonical ATN (N represents A, T, G, C) as start codons; 8 PCGs are terminated with a complete typical stop codon TAA, and the remaining five PCGs (cox2, cox3, nad3, nad4 and nad5) have an incomplete stop codon with just a T. …”
Get full text

A gene optimization strategy that enhances production of fully functional P-glycoprotein in Pichia pastoris. by Jiangping Bai, Douglas J Swartz, Irina I Protasevich, Christie G Brouillette, Patina M Harrell, Ellen Hildebrandt, Brigitte Gasser, Diethard Mattanovich, Andrew Ward, Geoffrey Chang, Ina L Urbatsch

“…Structural and biochemical studies of mammalian membrane proteins remain hampered by inefficient production of pure protein. We explored codon optimization based on highly expressed Pichia pastoris genes to enhance co-translational folding and production of P-glycoprotein (Pgp), an ATP-dependent drug efflux pump involved in multidrug resistance of cancers.Codon-optimized "Opti-Pgp" and wild-type Pgp, identical in primary protein sequence, were rigorously analyzed for differences in function or solution structure. …”
Get full text

The Versatile Roles of the tRNA Epitranscriptome during Cellular Responses to Toxic Exposures and Environmental Stress by Huber, Sabrina M, Leonardi, Andrea, Dedon, Peter C, Begley, Thomas J.

“…Keywords: epitranscriptomics; tRNA modifications; stress response mechanisms; codon-biased translation…”
Get full text

Arsenite toxicity is regulated by queuine availability and oxidation-induced reprogramming of the human tRNA epitranscriptome by Huber, Sabrina M, Begley, Ulrike, Sarkar, Anwesha, Gasperi, William, Davis, Evan T, Surampudi, Vasudha, Lee, May, Melendez, J Andres, Dedon, Peter C, Begley, Thomas J

“…The ∼50 modified ribonucleotides of the human epitranscriptome contribute to the latter, with mounting evidence that dynamic regulation of transfer RNA (tRNA) wobble modifications leads to selective translation of stress response proteins from codon-biased genes. Here we show that the response of human hepatocellular carcinoma cells to arsenite exposure is regulated by the availability of queuine, a micronutrient and essential precursor to the wobble modification queuosine (Q) on tRNAs reading GUN codons. …”
Get full text

KLONING DAN EKSPRESI PROTEASE DegP DARI BAKTERI Halomonas sp. BKL-5 by , Dewi Fitriani, , M. Saifur Rohman, M.Eng., Ph.D.

“…Analysis of nucleotide sequence showed open reading frame of the gene consists of 1356 bp, with ATG as start codon and TGA as stop codon. The deduced amino acid of the gene has 99% similarity to DegP from Chromohalobacter salexigen DSM 3043. …”