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1421
Optimization of HIV-1 Envelope DNA Vaccine Candidates within Three Different Animal Models, Guinea Pigs, Rabbits and Cynomolgus Macaques
Published 2013-07-01“…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. …”
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1422
Complete mitochondrial genomes of two marine monogonont rotifer Brachionus manjavacas strains
Published 2021-07-01“…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. …”
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1423
Analysis of genetic status of pivotal driver genes in pancreatic ductal adenocarcinoma and their correlation with clinicopathologic features
Published 2022-10-01“…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. …”
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1424
Susceptibility to scrapie and disease phenotype in sheep: cross-<it>PRNP</it> genotype experimental transmissions with natural sources
Published 2012-07-01“…It was found that additional polymorphisms at codons 112 or 141 of AA<sub>136</sub> recipients resulted in a delayed appearance of clinical disease or even in protection from infection. …”
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1425
First Complete Mitochondrial Genome of Melyridae(Coleoptera, Cleroidea): Genome Description and Phylogenetic Implications
Published 2021-01-01“…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-. …”
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1426
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1427
The Chloroplast Genome of the Lichen Photobiont <i>Trebouxiophyceae</i> sp. DW1 and Its Phylogenetic Implications
Published 2022-10-01“…The simple sequence repeats are all mononucleotide repeats. Codon usage analysis showed that the genome tended to use codon ending in A/U. …”
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1428
Resurrection of a Viral Internal Ribosome Entry Site from a 700 Year Old Ancient Northwest Territories Cripavirus
Published 2021-03-01“…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. …”
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1429
The nucleotide landscape of polyXY regions
Published 2023-01-01“…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. …”
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1430
DnoisE: distance denoising by entropy. An open-source parallelizable alternative for denoising sequence datasets
Published 2022-01-01“…DnoisE implements different merging procedures as options, and can incorporate codon entropy information either retrieved from the data or supplied by the user. …”
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1431
A novel statistical method predicts mutability of the genomic segments of the SARS-CoV-2 virus
Published 2022-01-01“…Importantly, these correlations are found to hold at the codon and gene levels, as well as for gene coding regions. …”
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1432
Detection of Amino Acid Mutations in Dihydrofolate Reductase & Dihydro Pteroate Synthase Gene in Plasmodium Vivax Isolates
Published 2020-06-01“…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. …”
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1433
<i>E. coli</i> MnmA Is an Fe-S Cluster-Independent 2-Thiouridylase
Published 2024-02-01“…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. …”
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1434
A statistical analysis of the three-fold evolution of genomic compression through frame overlaps in prokaryotes
Published 2007-09-01“…Some phases seem to reflect codon pairings reducing the probability of non-synonymous substitution. …”
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1435
The complete mitochondrial genome of Poecilia formosa (Poecilia, Cyprinodontidae) and phylogenetic studies of cyprinodontiformes
Published 2019-07-01“…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. …”
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1436
The mitochondrial genome of one ‘twisted-wing parasite’ Xenos cf. moutoni (Insecta, Strepsiptera, Xenidae) from Gaoligong Mountains, Southwest of China
Published 2021-02-01“…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. …”
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1437
A gene optimization strategy that enhances production of fully functional P-glycoprotein in Pichia pastoris.
Published 2011-01-01“…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. …”
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1438
The Versatile Roles of the tRNA Epitranscriptome during Cellular Responses to Toxic Exposures and Environmental Stress
Published 2019“…Keywords: epitranscriptomics; tRNA modifications; stress response mechanisms; codon-biased translation…”
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1439
Arsenite toxicity is regulated by queuine availability and oxidation-induced reprogramming of the human tRNA epitranscriptome
Published 2023“…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. …”
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1440
KLONING DAN EKSPRESI PROTEASE DegP DARI BAKTERI Halomonas sp. BKL-5
Published 2013“…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. …”
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