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1.
Chinese Journal of Biotechnology ; (12): 2939-2953, 2023.
Article in Chinese | WPRIM | ID: wpr-981242

ABSTRACT

The genomic DNA of Rubus rosaefolius was extracted and sequenced by Illumina NovaSeq platform to obtain the complete chloroplast genome sequence, and the sequence characteristics and phylogenetic analysis of chloroplast genes were carried out. The results showed that the complete chloroplast genome of the R. rosaefolius was 155 650 bp in length and had a typical tetrad structure, including two reverse repeats (25 748 bp each), a large copy region (85 443 bp) and a small copy region (18 711 bp). A total of 131 genes were identified in the whole genome of R. rosaefolius chloroplast, including 86 protein coding genes, 37 tRNA genes and 8 rRNA genes. The GC content of the whole genome was 36.9%. The genome of R. rosaefolius chloroplast contains 47 scattered repeats and 72 simple sequence repeating (SSR) loci. The codon preference is leucine codon, and the codon at the end of A/U is preferred. Phylogenetic analysis showed that R. rosaefolius had the closest relationship with R. taiwanicola, followed by R. rubraangustifolius and R. glandulosopunctatus. The chloroplast genome characteristics and phylogenetic analysis of R. rosaefolius provide a theoretical basis for its genetic diversity research and chloroplast development and utilization.


Subject(s)
Phylogeny , Rubus/genetics , Genome, Chloroplast , Fruit/genetics , Codon/genetics
2.
Chinese Journal of Biotechnology ; (12): 670-684, 2023.
Article in Chinese | WPRIM | ID: wpr-970399

ABSTRACT

The structure and size of the chloroplast genome of Castanopsis hystrix was determined by Illumina HiSeq 2500 sequencing platform to understand the difference between C. hystrix and the chloroplast genome of the same genus, and the evolutionary position of C. hystrix in the genus, so as to facilitate species identification, genetic diversity analysis and resource conservation of the genus. Bioinformatics analysis was used to perform sequence assembly, annotation and characteristic analysis. R, Python, MISA, CodonW and MEGA 6 bioinformatics software were used to analyze the genome structure and number, codon bias, sequence repeats, simple sequence repeat (SSR) loci and phylogeny. The genome size of C. hystrix chloroplast was 153 754 bp, showing tetrad structure. A total of 130 genes were identified, including 85 coding genes, 37 tRNA genes and 8 rRNA genes. According to codon bias analysis, the average number of effective codons was 55.5, indicating that the codons were highly random and low in bias. Forty-five repeats and 111 SSR loci were detected by SSR and long repeat fragment analysis. Compared with the related species, chloroplast genome sequences were highly conserved, especially the protein coding sequences. Phylogenetic analysis showed that C. hystrix is closely related to the Hainanese cone. In summary, we obtained the basic information and phylogenetic position of the chloroplast genome of red cone, which will provide a preliminary basis for species identification, genetic diversity of natural populations and functional genomics research of C. hystrix.


Subject(s)
Phylogeny , Genome, Chloroplast , Codon/genetics , Genomics , Chloroplasts/genetics
3.
Chinese Journal of Biotechnology ; (12): 882-892, 2022.
Article in Chinese | WPRIM | ID: wpr-927751

ABSTRACT

With the widespread application of genomics and transcriptomics in the genetics and cell biology of different species, synonymous codon usage bias has been gradually accepted and used to study the deep connection between biological evolution and biological phenotypes. It is an important part of the life activities that mRNA is expressed into proteins with normal biological activities. The synonymous codon usage patterns, which were named as 'the second genetic codon', can express genetic information carried by themselves at the levels of transcriptional regulations, translational regulations and metabolic activities through molecular mechanisms such as fine-tune translation selection. Some studies have shown that the length of mRNA half-life has significant impacts on mRNA activity and the process of transcription and translation. This review summarized the roles of synonymous codon usage patterns in transcription, translational regulation and post-translational modification, with the aim to better understand how organisms skillfully utilize the genetic effects caused by codon usage patterns to accurately synthesize different types of proteins, so as to ensure the growth or differentiation of the specific gene expression procedures to carry out smoothly and maintain the normal life cycle.


Subject(s)
Codon/genetics , Codon Usage , Half-Life , Protein Processing, Post-Translational , RNA, Messenger/genetics
4.
Chinese Journal of Biotechnology ; (12): 1334-1345, 2021.
Article in Chinese | WPRIM | ID: wpr-878635

ABSTRACT

The main protease (Mpro) of SARS-CoV-2 is a highly conserved and mutation-resistant coronaviral enzyme, which plays a pivotal role in viral replication, making it an ideal target for the development of novel broad-spectrum anti-coronaviral drugs. In this study, a codon-optimized Mpro gene was cloned into pET-21a and pET-28a expression vectors. The recombinant plasmids were transformed into E. coli Rosetta(DE3) competent cells and the expression conditions were optimized. The highly expressed recombinant proteins, Mpro and Mpro-28, were purified by HisTrapTM chelating column and its proteolytic activity was determined by a fluorescence resonance energy transfer (FRET) assay. The FRET assay showed that Mpro exhibits a desirable proteolytic activity (25 000 U/mg), with Km and kcat values of 11.68 μmol/L and 0.037/s, respectively. The specific activity of Mpro is 25 times that of Mpro-28, a fusion protein carrying a polyhistidine tag at the N and C termini, indicating additional residues at the N terminus of Mpro, but not at the C terminus, are detrimental to its proteolytic activity. The preparation of active SARS-CoV-2 Mpro through codon-optimization strategy might facilitate the development of the rapid screening assays for the discovery of broad-spectrum anti-coronaviral drugs targeting Mpro.


Subject(s)
Humans , COVID-19 , Codon/genetics , Cysteine Endopeptidases/genetics , Escherichia coli/genetics , Peptide Hydrolases , SARS-CoV-2 , Viral Nonstructural Proteins/genetics
5.
Chinese Journal of Biotechnology ; (12): 4083-4094, 2021.
Article in Chinese | WPRIM | ID: wpr-921489

ABSTRACT

Vascular endothelial growth factor (VEGF165) is a highly specific vascular endothelial growth factor that can be used to treat many cardiovascular diseases. The development of anti-tumor drugs and disease detection reagents requires highly pure VEGF165 (at least 95% purity). To date, the methods for heterologous expression and purification of VEGF165 require multiple purification steps, but the product purity remains to be low. In this study, we optimized the codons of the human VEGF165 gene (vegf165) according to the yeast codon preference. Based on the Pichia pastoris BBPB vector, we used the Biobrick method to construct a five-copy rhVEGF165 recombinant expression vector using Pgap as the promoter. In addition, a histidine tag was added to the vector. Facilitated by the His tag and the heparin-binding domain of VEGF165, we were able to obtain highly pure rhVEGF165 (purity > 98%) protein using two-step affinity chromatography. The purified rhVEGF165 was biologically active, and reached a concentration of 0.45 mg/mL. The new design of the expression vector enables production of active and highly pure rhVEGF165 ) in a simplified purification process, the purity of the biologically active natural VEGF165 reached the highest reported to date.


Subject(s)
Humans , Codon/genetics , Pichia/genetics , Recombinant Proteins/genetics , Saccharomycetales , Vascular Endothelial Growth Factor A/genetics , Vascular Endothelial Growth Factors
6.
An. acad. bras. ciênc ; 89(1): 213-222, Jan,-Mar. 2017. tab, graf
Article in English | LILACS | ID: biblio-886631

ABSTRACT

ABSTRACT Cichlid fishes are an important group in evolutionary biology due to their fast speciation. This group depends widely of vision for feeding and reproduction. During the evolutionary process it plays a significant role in interspecific and intraspecific recognition and in its ecology. The molecular basis of vision is formed by the interaction of the protein opsin and retinal chromophore. Long-wavelength sensitive opsin (LWS) gene is the most variable among the opsin genes and it has an ecological significance. Current assay identifies interspecific variation of Neotropical cichlids that would modify the spectral properties of the LWS opsin protein and codons selected. Neotropical species present more variable sites for LWS gene than those of the African lakes species. The LWS opsin gene in Crenicichla britskii has a higher amino acid similarity when compared to that in the African species, but the variable regions do not overlap. Neotropical cichlids accumulate larger amounts of variable sites for LWS opsin gene, probably because they are spread over a wider area and submitted to a wider range of selective pressures by inhabiting mainly lotic environments. Furthermore, the codons under selection are different when compared to those of the African cichlids.


Subject(s)
Animals , Genetic Variation , Rod Opsins/genetics , Cichlids/genetics , Phylogeny , Species Specificity , Brazil , Codon/genetics , Polymerase Chain Reaction , Sequence Analysis, DNA , Africa , Cichlids/classification
7.
Int. braz. j. urol ; 43(1): 36-46, Jan.-Feb. 2017. tab, graf
Article in English | LILACS | ID: biblio-840810

ABSTRACT

ABSTRACT Objectives The aim of this study was to assess the possible role of HPV in the development of prostate cancer (PCa) and investigate the distribution of the p53 codon 72 polymorphism in PCa in a Turkish population. Materials and methods A total of 96 tissues, which had been obtained using a radical surgery method, formalin-fixed and parafin-embedded, were used in this study. The study group consisted of 60 PCa tissues (open radical prostatectomy) and the control group contained 36 benign prostatic hyperplasia tissues (BPH) (transvesical open prostatectomy). The presence of HPV and the p53 codon 72 polymorphism was investigated in both groups using real-time PCR and pyrosequencing. Results The results of the real-time PCR showed no HPV DNA in any of the 36 BPH tissue samples. HPV-DNA was positive in only 1 of the 60 PCa samples (1.7%). The HPV type of this sample was identified as HPV-57. The distribution of the three genotypes, Arg/Arg, Arg/Pro and Pro/Pro was found to be 45.6, 45.6, and 8.8% in the PCa group and 57.1%, 34.3% and 8.6% in the control group, respectively. Compared with the control group, patients with PCa had a higher frequency of the Arg/Pro genotype and Proline allele (odds ratio (OR)=1.67, 95% confidence interval (CI)=0.68-4.09, p=0.044; OR=1.13, 95% CI=0.76-1.68, p=0.021, respectively). Conclusions The results of the study do not support the hyphothesis that prostate cancer is associated with HPV infection but indicated that Proline allele can be a risk factor in the development of PCa in the Turkish population.


Subject(s)
Humans , Male , Aged , Aged, 80 and over , Papillomaviridae/isolation & purification , Polymorphism, Genetic , Prostatic Neoplasms/genetics , Prostatic Neoplasms/virology , Tumor Suppressor Protein p53/genetics , Papillomavirus Infections/complications , Prostatectomy , Prostatic Hyperplasia/genetics , Prostatic Hyperplasia/pathology , Prostatic Hyperplasia/virology , Prostatic Neoplasms/surgery , Prostatic Neoplasms/pathology , Turkey , Codon/genetics , DNA, Viral , Proline/genetics , Retrospective Studies , Risk Factors , Paraffin Embedding , Genetic Association Studies , Neoplasm Grading , Genotyping Techniques , Real-Time Polymerase Chain Reaction , Genotype , Middle Aged
8.
The Korean Journal of Parasitology ; : 689-697, 2015.
Article in English | WPRIM | ID: wpr-91236

ABSTRACT

The tapeworm Taenia solium is an important human zoonotic parasite that causes great economic loss and also endangers public health. At present, an effective vaccine that will prevent infection and chemotherapy without any side effect remains to be developed. In this study, codon usage patterns in the T. solium genome were examined through 8,484 protein-coding genes. Neutrality analysis showed that T. solium had a narrow GC distribution, and a significant correlation was observed between GC12 and GC3. Examination of an NC (ENC vs GC3s)-plot showed a few genes on or close to the expected curve, but the majority of points with low-ENC (the effective number of codons) values were detected below the expected curve, suggesting that mutational bias plays a major role in shaping codon usage. The Parity Rule 2 plot (PR2) analysis showed that GC and AT were not used proportionally. We also identified 26 optimal codons in the T. solium genome, all of which ended with either a G or C residue. These optimal codons in the T. solium genome are likely consistent with tRNAs that are highly expressed in the cell, suggesting that mutational and translational selection forces are probably driving factors of codon usage bias in the T. solium genome.


Subject(s)
Animals , Base Sequence , Codon/genetics , Evolution, Molecular , Genome, Helminth , Helminth Proteins/genetics , Molecular Sequence Data , Taenia solium/genetics
9.
Indian J Biochem Biophys ; 2013 Dec; 50(6): 537-547
Article in English | IMSEAR | ID: sea-154210

ABSTRACT

Phytic acid, the major storage form of phosphorus in plant seeds is degraded by the phytases to yield inositol and free phosphate, contributing thereby to the improved bioavailability of phytate phosphorus and essential minerals in plant foods and simultaneous reduction in phosphorus pollution of the terrestrial and aquatic ecosystems. As a possible strategy for altering seed phytate levels, the approach involving reduction of phytate content by ectopically expressing endogenous phytase gene during seed development of soybean (Glycine max L. cv. Pusa-20) was attempted in the present study. Semi-quantitative RT-PCR revealed the maximum expression of phytase gene transcripts in germinating cotyledons (~10 days after germinations), compared to other vegetative tissues. A full-length phytase cDNA was amplified from the germinating seedlings by splicing by overlap extension (SOE)-PCR and its sequence analysis revealed an open-reading-frame of 1644 bp, including an N terminal signal peptide of 28 amino acids. Predicted amino acid sequence (547-aa) of molecular mass 62 kDa on alignment with related purple acid phosphatases in other plants shared five conserved domains and seven invariant amino acids involved in coordination of the metals in the binuclear center of purple acid phosphatases. Owing to a large number of E. coli low-usage codons in soybean phytase gene, the modified gene was cloned into a prokaryotic expression vector pET-28a (+) and its expression in E. coli was confirmed by SDS-PAGE and Western blot analysis. Bioassay of the crude expression product in E. coli revealed a functional phytase gene, showing a great potential for developing low phytate transgenic soybean through its seed-specific overexpression in the early stages of seed development.


Subject(s)
6-Phytase/biosynthesis , 6-Phytase/chemistry , 6-Phytase/genetics , Amino Acid Sequence , Cloning, Molecular , Codon/genetics , DNA, Complementary/genetics , Escherichia coli/genetics , Gene Expression , Gene Expression Regulation, Plant , Genetic Engineering/methods , Minerals/metabolism , Molecular Sequence Data , Organ Specificity , Phosphorus/metabolism , Phylogeny , Seedlings/genetics , Sequence Homology , Glycine max/enzymology , Glycine max/genetics , Glycine max/metabolism
10.
Medicina (B.Aires) ; 73(5): 417-422, oct. 2013. tab
Article in Spanish | LILACS | ID: lil-708527

ABSTRACT

El cáncer colorrectal es el tercer cáncer más frecuente en hombres y el segundo más frecuente en mujeres, con una incidencia mundial aproximada de 1.2 millones de casos nuevos por año. Nuestro objetivo primario fue estudiar la relación existente entre las características clínico-histológicas en individuos con cáncer colorrectal y el estado mutacional de los codones 12 y 13 del gen KRAS (7 mutaciones validadas), con el fin de hallar un marcador histopatológico para los tumores mutados. El objetivo secundario fue determinar cuántos pacientes tenían mutaciones adicionales en los codones 15 y 61 del gen KRAS y 600 del gen BRAF que podrían modificar el fenotipo tumoral. Fueron seleccionados 60 individuos con cáncer colorrectal (30 wild-type y 30 con mutaciones validadas en los codones 12 y 13 del gen KRAS). Se amplificaron y secuenciaron del gen KRAS los exones 2 y 3, y del gen BRAF el exón 15. La información recolectada se examinó mediante un análisis descriptivo, análisis univariado y/o análisis multivariado, según correspondiese. En conclusión, no se encontró relación entre las características clínico-histológicas de los tumores de individuos con diagnóstico de cáncer colorrectal y el estado mutacional de los codones 12 y 13 del gen KRAS. No hallamos un marcador histopatológico para los tumores mutados. En pacientes con adenocarcinomas colorrectales avanzados y KRAS wild-type resulta de interés considerar el estudio del codón 600 del gen BRAF.


Colorectal cancer is the third most frequent cancer in men and the second most frequent in women, with a worldwide incidence of approximately 1.2 million new cases per year. Our primary objective was to study the relationship between clinical and histological features of individuals with colorectal cancer and the mutational status of codons 12 and 13 of the KRAS gene (7 validated mutations), in order to find a histopathological marker to mutated tumors. The secondary objective was to determine how many patients had additional mutations in codons 15 and 61 of the KRAS gene, and codon 600 of the BRAF gene, which could modify the tumor phenotype. Sixty individuals with colorectal cancer (30 wild-type subjects and 30 with validated mutations in codons 12 and 13 of the KRAS gene) were selected. Exons 2 and 3 of the KRAS gene, and exon 15 of the BRAF gene were amplified and sequenced. The data collected were reviewed by a descriptive, univariate and/or multivariate analysis, as appropriate. In conclusion, no relation was found between clinical and histological features of individuals with colorectal cancer and their mutational status for codons 12 and 13 of the KRAS gene. This suggests that those easily available data do not allow predicting the response to anti-EGFR therapy. In patients with advanced colorectal adenocarcinomas and KRAS wild-type status, further study of codon 600 of the BRAF gene could be required.


Subject(s)
Adult , Aged , Aged, 80 and over , Female , Humans , Male , Middle Aged , Adenocarcinoma/genetics , Codon/genetics , Colorectal Neoplasms/genetics , Genes, ras/genetics , Mutation/genetics , Adenocarcinoma/pathology , Colorectal Neoplasms/pathology , Genetic Markers , Genetic Predisposition to Disease , Multivariate Analysis , Polymorphism, Genetic , Predictive Value of Tests
11.
Arq. neuropsiquiatr ; 71(7): 423-427, July/2013. tab
Article in English | LILACS | ID: lil-679173

ABSTRACT

Interaction of prion protein and amyloid-b oligomers has been demonstrated recently. Homozygosity at prion protein gene (PRNP) codon 129 is associated with higher risk for Creutzfeldt-Jakob disease. This polymorphism has been addressed as a possible risk factor in Alzheimer disease (AD). Objective To describe the association between codon 129 polymorphisms and AD. Methods We investigated the association of codon 129 polymorphism of PRNP in 99 AD patients and 111 controls, and the association between this polymorphism and cognitive performance. Other polymorphisms of PRNP and additive effect of apolipoprotein E gene (ApoE) were evaluated. Results Codon 129 genotype distribution in AD 45.5% methionine (MM), 42.2% methionine valine (MV), 12.1% valine (VV); and 39.6% MM, 50.5% MV, 9.9% VV among controls (p>0.05). There were no differences of cognitive performance concerning codon 129. Stratification according to ApoE genotype did not reveal difference between groups. Conclusion Codon 129 polymorphism is not a risk factor for AD in Brazilian patients.


Polimorfismo do códon 129 do gene da proteína priônica não é fator de risco para doença de Alzheimer A interação entre proteína priônica e oligômeros b-amiloide foi demonstrada recentemente. Homozigose no códon 129 do gene da proteína priônica (PRNP) é fator de risco para doença de Creutzfeldt-Jakob. Este polimorfismo foi estudado como possível fator de risco para doença de Alzheimer (DA). Objetivo Estudar uma possível associação entre o polimorfismo do códon 129 e DA. Métodos Foram investigados 99 pacientes com DA e 111 controles em relação ao polimorfismo do códon 129 e sua associação com desempenho cognitivo. Foram pesquisados outros polimorfismos do PRNP e efeito aditivo do gene da apolipoproteína E (ApoE). Resultados Distribuição no códon 129: 45,5% metionina (MM), 42,2% metionina valina (MV), 12,1% valina (VV) nos pacientes com DA; e 39,6% MM, 50,5% MV, 9,9% VV, nos controles (p >0.05). Não houve diferença no desempenho cognitivo em relação ao códon 129. Estratificação pelo genótipo do ApoE não mostrou diferença entre grupos. Conclusão Polimorfismo do códon 129 não é fator de risco para DA em pacientes brasileiros.


Subject(s)
Aged , Aged, 80 and over , Female , Humans , Male , Alzheimer Disease/genetics , Codon/genetics , Polymorphism, Genetic/genetics , Prions/genetics , Age Factors , Apolipoproteins E/genetics , Brazil , Case-Control Studies , Cognition , Gene Frequency , Risk Factors , Sex Factors
13.
Rev. argent. microbiol ; 45(1): 21-6, mar. 2013.
Article in Spanish | LILACS, BINACIS | ID: biblio-1171772

ABSTRACT

The relation of ethambutol resistance to embB mutations remains unclear, and there are no reports on ethambutol resistance from the caribbean. We examined the sequence of embB in 57 distinct Multi-Drug Resistant (MDR) and non-MDR strains of Mycobacterium tuberculosis, mostly from Cuba and the Dominican Republic. embB306 codon mutations were found exclusively in MDR-TB, but in both ethambutol sensitive and resistant strains. Valine substitutions predominated in ethambutol resistant strains, while isoleucine replacements were more common in sensitive strains. Three ethambutol resistant MDR strains without embB306 substitutions had replacements in embB406 or embB497, but these were also found in ethambutol sensitive MDR strains. The results confirm previous findings that amino acid substitutions in EmbB306, EmbB406 and EmbB497 are found only in MDR-TB strains but in both phenotypically resistant and sensitive strains. One ethambutol resistant non-MDR strain did not have any embB mutation suggesting that other undefined mutations can also confer ethambutol resistance.


Subject(s)
Antitubercular Agents/pharmacology , Ethambutol/pharmacology , Mycobacterium tuberculosis/genetics , Pentosyltransferases/genetics , Drug Resistance, Microbial/genetics , Tuberculosis, Multidrug-Resistant/microbiology , DNA Mutational Analysis , Cuba/epidemiology , Codon/genetics , DNA, Bacterial/genetics , Drug Resistance, Multiple, Bacterial/genetics , Humans , Mutation , Mycobacterium tuberculosis/drug effects , Pentosyltransferases/physiology , Dose-Response Relationship, Drug , Reproducibility of Results , Dominican Republic/epidemiology , Sensitivity and Specificity , Amino Acid Substitution , Microbial Sensitivity Tests , Tuberculosis, Multidrug-Resistant/epidemiology
14.
Journal of Veterinary Science ; : 441-447, 2013.
Article in English | WPRIM | ID: wpr-43063

ABSTRACT

Rabbit hemorrhagic disease (RHD) is contagious and highly lethal. Commercial vaccines against RHD are produced from the livers of experimentally infected rabbits. Although several groups have reported that recombinant subunit vaccines against rabbit hemorrhagic disease virus (RHDV) are promising, application of the vaccines has been restricted due to high production costs or low yield. In the present study, we performed codon optimization of the capsid gene to increase the number of preference codons and eliminate rare codons in Spodoptera frugiperda 9 (Sf9) cells. The capsid gene was then subcloned into the pFastBac plasmid, and the recombinant baculoviruses were identified with a plaque assay. As expected, expression of the optimized capsid protein was markedly increased in the Sf9 cells, and the recombinant capsid proteins self-assembled into virus-like particles (VLPs) that were released into the cell supernatant. Rabbits inoculated with the supernatant and the purified VLPs were protected against RHDV challenge. A rapid, specific antibody response against RHDV was detected by an ELISA in all of the experimental groups. In conclusion, this strategy of producing a recombinant subunit vaccine antigen can be used to develop a low-cost, insect cell-derived recombinant subunit vaccine against RHDV.


Subject(s)
Animals , Rabbits , Antigens, Viral/genetics , Caliciviridae Infections/prevention & control , Capsid Proteins/genetics , Cell Culture Techniques/methods , Codon/genetics , Enzyme-Linked Immunosorbent Assay/veterinary , Gene Expression Regulation, Viral , Hemorrhagic Disease Virus, Rabbit/genetics , Recombinant Proteins/genetics , Sf9 Cells , Spodoptera , Viral Structural Proteins/genetics , Viral Vaccines/genetics
15.
Braz. j. med. biol. res ; 45(11): 1011-1016, Nov. 2012. ilus, tab
Article in English | LILACS | ID: lil-650577

ABSTRACT

Polymorphisms of the p53 gene, which participates in DNA repair, can affect the functioning of the p53 protein. The Arg and Pro variants in p53 codon 72 were shown to have different regulation properties of p53-dependent DNA repair target genes that can affect various levels of cytogenetic aberrations in chronic hepatitis B patients. The present study aimed to examine the frequency of chromosomal aberrations and the mitotic index in patients with chronic hepatitis B and their possible association with p53 gene exon 4 codon 72 Arg72Pro (Ex4+119 G>C; rs1042522) polymorphism. Fifty-eight patients with chronic hepatitis B and 30 healthy individuals were genotyped in terms of the p53 gene codon 72 Arg72Pro polymorphism by PCR-RFLP. A 72-h cell culture was performed on the same individuals and evaluated in terms of chromosomal aberrations and mitotic index. A high frequency of chromosomal aberrations and low mitotic index were detected in the patient group compared to the control group. A higher frequency of chromosomal aberrations was detected in both the patient and the control groups with a homozygous proline genotype (13 patients, 3 control subjects) compared to patients and controls with other genotypes [Arg/Pro (38 patients, 20 control subjects) and Arg/Arg (7 patients, 7 control subjects)]. We observed an increased frequency of cytogenetic aberrations in patients with chronic hepatitis B. In addition, a higher frequency of cytogenetic aberrations was observed in p53 variants having the homozygous proline genotype compared to variants having other genotypes both in patients and healthy individuals.


Subject(s)
Adult , Female , Humans , Male , Codon/genetics , Hepatitis B, Chronic/genetics , Polymorphism, Genetic/genetics , /genetics , Arginine/genetics , Case-Control Studies , Chromosome Aberrations , Genetic Predisposition to Disease , Genotype , Mitotic Index , Proline/genetics
16.
Govaresh. 2012; 17 (1): 25-32
in Persian | IMEMR | ID: emr-124798

ABSTRACT

Colorectal cancer is the second cause of mortality in developed countries. The p53 gene and some of it's polymorphisms are among the causes for cancer development. The purpose of this study is to evaluate the relationship between the p53 codon 72 polymorphism in colorectal adenocarcinoma specimens compared with controls. We performed a case-control study among 112 patients with colorectal carcinoma and 112 controls in Rasht, Iran. Different genotypes of codon 72 were determined by allele-specific polymerase chain reaction [PCR]. The frequency of the Arg/Arg genotype of the p53 codon 72 polymorphism was 35.7%, for Arg/Pro it was 50.9%, and for Pro/Pro it was 13.4% in colorectal cancer patients. Among controls, the Arg/Arg genotype was seen 37.5%, Arg/Pro was noted in 50%, and Pro/Pro was seen in 12.5% [p = 0.95]. When tumor location was taken into consideration, 68.8% of the Arg/Arg carrier genotypes were associated with an increased incidence of left colon cancer. There was a significant statistical relationship between expression of the Arg allele in colorectal cancer samples and metastases [p=0.003]. The majority of colorectal cancer patients with p53 Arg homozygosity had left-sided colon cancer. There was also a relation between p53 Arg homozygosity, lymph node involvement, and metastases. Thus, we have suggested that the correlation between this polymorphism, tumor risk, and metastasis should be studied to determine its effectiveness as a diagnostic factor


Subject(s)
Humans , Polymorphism, Genetic , Codon/genetics , Colorectal Neoplasms/genetics , Genetic Predisposition to Disease , Case-Control Studies , Polymerase Chain Reaction , Genes, p53 , Neoplasm Metastasis
17.
Clinics ; 67(supl.1): 33-36, 2012. ilus
Article in English | LILACS | ID: lil-623128

ABSTRACT

Medullary thyroid carcinoma currently accounts for 5-8% of all thyroid cancers. The clinical course of this disease varies from extremely indolent tumors that can go unchanged for years to an extremely aggressive variant that is associated with a high mortality rate. As many as 75% of all medullary thyroid carcinomas are sporadic, with an average age at presentation reported as 60 years, and the remaining 25% are hereditary with an earlier age of presentation, ranging from 20 to 40 years. Germline RET proto-oncogene mutations are the genetic causes of multiple endocrine neoplasia type 2 and a strong genotype-phenotype correlation exists, particularly between a specific RET codon mutation and the (a) age-related onset and (b) thyroid tumor progression, from C-cell hyperplasia to medullary thyroid carcinoma and, ultimately, to nodal metastases. RET mutations predispose an individual to the development of medullary thyroid carcinomas and can also influence the individual response to RET protein receptor-targeted therapies. RET codon 609point mutations are rare genetic events belonging to the intermediate risk category for the onset of medullary thyroid carcinoma. A large genealogy resulting in a less aggressive form of medullary thyroid carcinoma is associated with the high penetrance of pheochromocytoma and has been reported in the literature. In this short review article, we comment on our previous report of a large multiple endocrine neoplasia type 2A kindred with the same Cys609Ser germline RET mutation in which, conversely, the syndrome was characterized by a slightly aggressive, highly penetrant form of medullary thyroid carcinoma that was associated with low penetrance of pheochromocytoma and primary hyperparathyroidism.


Subject(s)
Humans , Carcinoma, Medullary/genetics , Codon/genetics , Germ-Line Mutation/genetics , /genetics , Proto-Oncogene Proteins c-ret/genetics , Thyroid Neoplasms/genetics , Cysteine/genetics , Genetic Association Studies , Hyperparathyroidism/genetics , Italy , Pedigree , Serine/genetics
18.
Electron. j. biotechnol ; 14(4): 7-7, July 2011. ilus, tab
Article in English | LILACS | ID: lil-640502

ABSTRACT

The gene dhaT from Klebsiella pneumoniae encoding 1,3-propanediol oxidoreductase (PDOR) was de novo synthesized by splicing overlap extension polymerase chain reaction (SOE-PCR) primarily according to Escherichia coli’s codon usage, as well as mRNA secondary structure. After optimization, Codon Adaptation Index (CAI) value was improved from 0.75 to 0.83, meanwhile energy of mRNA secondary structure was increased from -400.1 to -86.8 kcal/mol. This synthetic DNA was under control by phage T7 promoter in the expression vector pET-15b and transformed into the E. coli BL21 (DE3) strain. Inducers such as isopropyl beta-D-thiogalactoside (IPTG) and lactose were compared by activity at different inducing time. The activity of PDOR after codon optimized was 385.4 +/- 3.6 U/mL, which was almost 5-fold higher than wild type (82.3 +/- 1.5 U/ml) under the flask culture at 25ºC for 10 hrs. Then his-tagged enzyme was separated by using Ni-IDA column. The favorite environment for enzyme activity was at 5°C and pH 10.0, PDOR showed a certainly stability in potassium carbonate buffer for 2 hrs at diverse temperatures, enzyme activity was significantly improved by Mn2+.


Subject(s)
Alcohol Dehydrogenase , Codon/genetics , Escherichia coli/genetics , Propylene Glycols , Adaptation, Physiological , Escherichia coli/enzymology , Gene Expression , Genes, Bacterial , RNA, Messenger , Polymerase Chain Reaction/methods
19.
Rev. Soc. Bras. Med. Trop ; 44(3): 392-394, May-June 2011. ilus, tab
Article in English | LILACS | ID: lil-593370

ABSTRACT

Amino acid insertions in the protease have rarely been described in HIVinfected patients. One of these insertions has recently been described in codon 35, although its impact on resistance remains unknown. This study presents a case of an HIV variant with an insertion in codon 35 of the protease, described for the first time in Bauru, State of Sao Paulo, Brazil, circulating in a 38-year-old caucasian male with asymptomatic HIV infection since 1997. The variant isolated showed a codon 35 insertion of two amino acids in the protease: a threonine and an aspartic acid, resulting in the amino acid sequence E35E_TD.


Inserções de aminoácidos na protease têm sido raramente descritas em pacientes infectados pelo HIV. Uma destas inserções foi, recentemente, descrita no codon 35, embora seu impacto na resistência mantém-se pouco conhecido. Este trabalho apresenta um caso de uma variante viral com inserção no codon 35 da protease, descrita pela primeira vez em Bauru, São Paulo, Brasil, circulante em um homem, caucasiano, com 38 anos, o qual apresenta infecção assintomática pelo HIV desde 1997. A variante isolada mostrou uma inserção no codon 35 da protease de dois aminoácidos: uma treonina e um ácido aspártico, resultando na sequência de aminoácidos E35E_TD.


Subject(s)
Adult , Humans , Male , Codon/genetics , HIV Infections/virology , HIV Protease/genetics , HIV-1 , Mutagenesis, Insertional/genetics , Amino Acid Sequence , Brazil , Molecular Sequence Data
20.
Braz. j. microbiol ; 42(1): 211-215, Jan.-Mar. 2011. ilus, tab
Article in English | LILACS | ID: lil-571391

ABSTRACT

Mutations into codons Aspartate-87 (62 percent) and Serine-83 (38 percent) in QRDR of gyrA were identified in 105 Salmonella strains resistant to nalidixic acid (94 epidemic and 11 of poultry origin). The results show a high incidence of mutations associated to quinolone resistance but suggest association with others mechanisms of resistance.


Subject(s)
Animals , Chick Embryo , Anti-Bacterial Agents/analysis , Base Sequence , Codon/genetics , Drug Resistance, Microbial , Fluoroquinolones/analysis , In Vitro Techniques , Polymerase Chain Reaction , Polymorphism, Restriction Fragment Length , Poultry , Quinolones/analysis , Salmonella/isolation & purification , Methods , Methods
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