No abstract available.
Breast* ; Codon*

Translocation ribonucleic acid (tRNA) is one of the important components in protein synthesis. In order to explore the effect of the changes of tRNAs corresponding to rare codons (rarity tRNAs) on the expression of exogenous genes, the co-expression system of rare tRNA gene and exogenous gene in Pichia pastoris was constructed. The expression of GFP in P. pastoris can be greatly reduced when a repressor region composed of four continuous proline rare codon CCG was added into the GFP gene. The expression amount of the repressed GFP could be increased about 4.9% when tRNAProCCG gene was cointegrated to the 3' of the repressed GFP gene through pPIC9K to the genome of P. pastoris GS115. Meanwhile, the expression amount of the repressed GFP increased about 12.5% by integrating the repressed GFP gene and tRNAProCCG gene to the genome of P. pastoris GS115 through pPIC9K and pFLDα, respectively. Using the same method, NFATc3T-GFP fusion gene and tRNAProCCG gene were co-expressed in P. pastoris GS115 resulting in 21.3% increased of the expression amount of NFATc3T-GFP fusion protein. In conclusion, tRNAProCCG gene has been confirmed to be a kind of rare tRNAs in P. pastoris GS115. Through co-expression of tRNAProCCG gene and heterologous genes which containing the continuous rare codon CCG, the expression of the repressed heterologous genes could be increased significantly. Furthermore, this co-expression system would contribute to screening and determining the other rare tRNAs.
Codon ; Pichia ; Recombinant Proteins

No abstract available.
Codon ; Hallucinations ; Illusions

Enzymes are widely used in medical and biopharmaceuticals. They can be used not only for various disease treatments, but also clinical diagnosis. The use of microorganisms to express heterologous proteins has become the easiest and fastest way to obtain enzymes. In order to obtain high concentration and high-quality heterologous proteins, a common method is codon optimization of gene sequences. The traditional codon optimization strategy is mainly based on codon bias and GC content, ignoring complex and varied factors such as translational dynamics and metabolic levels. We provide here comprehensive codon optimization strategy based on gene level, transcriptional level, translational level, post-translational level and metabolic level, mainly including codon bias, codon harmonization, codon sensitivity, adjustment of gene sequence structure and some other influencing factors. We also summarize the aspects of strategy content, theoretical support and application. Besides, the advantages and disadvantages of each strategy are also systematically compared, providing an all-round, multi-level and multi-selection optimization strategy for heterogeneous protein expression, and also providing references for the enzyme industry and biopharmaceuticals.
Base Composition ; Codon

BACKGROUND: Mutations in the KRAS gene have been identified in approximately 50% of colorectal cancers (CRCs). KRAS mutations are well established biomarkers in anti–epidermal growth factor receptor therapy. Therefore, assessment of KRAS mutations is needed in CRC patients to ensure appropriate treatment. METHODS: We compared the analytical performance of the cobas test to Sanger sequencing in 264 CRC cases. In addition, discordant specimens were evaluated by 454 pyrosequencing. RESULTS: KRAS mutations for codons 12/13 were detected in 43.2% of cases (114/264) by Sanger sequencing. Of 257 evaluable specimens for comparison, KRAS mutations were detected in 112 cases (43.6%) by Sanger sequencing and 118 cases (45.9%) by the cobas test. Concordance between the cobas test and Sanger sequencing for each lot was 93.8% positive percent agreement (PPA) and 91.0% negative percent agreement (NPA) for codons 12/13. Results from the cobas test and Sanger sequencing were discordant for 20 cases (7.8%). Twenty discrepant cases were subsequently subjected to 454 pyrosequencing. After comprehensive analysis of the results from combined Sanger sequencing–454 pyrosequencing and the cobas test, PPA was 97.5% and NPA was 100%. CONCLUSIONS: The cobas test is an accurate and sensitive test for detecting KRAS-activating mutations and has analytical power equivalent to Sanger sequencing. Prescreening using the cobas test with subsequent application of Sanger sequencing is the best strategy for routine detection of KRAS mutations in CRC.
Biomarkers ; Codon ; Colorectal Neoplasms* ; Humans

No abstract available.
Codon, Nonsense* ; Pemphigus, Benign Familial*

BACKGROUND: Despite the emerging danger of MDR-TB to human beings, there have only been a limited number of drugs developed to treat MDR-TB since 1970. This study investigated the cross-resistance rate between rifampicin (RFP) and rifabutin (RBU) in order to determine the efficacy of rifabutin in treating MDR-TB. In addition, the results of rifabutin were correlated with the rpoB mutations, which are believed to be markers for MDR-TB and RFP resistance. METHODS: The MICs of RBU were tested against 126 clinical isolates of MDR-TB submitted to the clinical laboratory of National Masan TB Hospital in 2004. Five different concentrations (10-160 microgram/ml) were used for the MICs. The detection of the rpoB mutations was performed using a RFP resistance detection kit with a line probe assay(LiPA), which contains the oligonucleotide probes for 5 wide type and 3 specific mutations (513CCA, 516GTC, and 531TTG). The rpoB mutation was determined by direct sequencing. RESULTS: The rate of cross-resistance between RFP and RBU was 70.5%(74/105) at 20 microgram/ml RBU(ed note: How much RFP?) Most mutations (86.3%) occurred in the 524~534 codons. The His526Gln, His526Leu, Leu533Pro, Gln513Glu, and Leu511Pro mutations(Ed note: Is this correct?) were associated with the susceptibilty to RBU. CONCLUSION: Based on the cross-resistance rate between RFP and RBU, RBU may be used effectively in some MDR-TB patients. Therefore, a conventional drug susceptibility test for RBU and a determination of the critical concentration are needed. However, rpoB gene mutation test may be have limited clinical applications in detecting RBU resistance.
Codon ; Humans ; Oligonucleotide Probes ; Rifabutin* ; Rifampin*

BACKGROUND: Development of rapid drug susceptibility testing provides the opportunity for rapid identification of individuals with drug resistant tubercle bacilli, allowing selection of appropriate therapeutic regimens. METHODS: A total of 502 drug resistant isolates were subjected to reverse blot hybridization assay to detect mutations within genes (rpoB, katG, inhA, and ahpC) associated with rifampicin (RMP) and isoniazid (INH) resistance. RESULTS: Among the 264 RMP resistant strains (RMPR) tested, the most prevalent mutation was the Ser531Leu seen in 121 strains (46%). The second common mutation occurred in 84 strains (32%) at codon 526. And 27 strains (10%) showed the mutation at codon 516. Among all 469 INH resistant strains (INHR), the katG mutation was responsible for INH. The inhA mutation was present in 88 strains (19%). In 11 isolates (2%), coexisting of the katG and inhA mutations were identified. Reverse hybridization assay successfully detected over 80% of INHR and over 92% of RMPR among Korean isolates. CONCLUSION: Reverse hybridization was useful for rapid detection of INHR and RMPR.
Codon ; Genotype ; Isoniazid* ; Korea ; Mycobacterium tuberculosis ; Rifampin*

Different mechanisms, including transcriptional and post transcriptional processes, regulate tissue specific expression of genes. In this study, we report differences in gene/protein compositional features between apoptosis involved genes selectively expressed in human tissues. We found some correlations between codon/amino acid usage and tissue specific expression level of genes. The findings can be significant for understanding the translational selection on these features. The selection may play an important role in the differentiation of human tissues and can be considered for future studies in diagnosis of some diseases such as cancer.
Apoptosis* ; Codon* ; Diagnosis ; Gene Expression Regulation ; Humans

No abstract available.
Codon, Nonsense* ; Epilepsy, Temporal Lobe* ; Temporal Lobe*