Investigation of RNA viral genome amplification by multiple displacement amplification technique / 病毒学报

In order to facilitate the detection of newly emerging or rare viral infectious diseases, a negative-strand RNA virus-severe fever with thrombocytopenia syndrome bunyavirus, and a positive-strand RNA virus-dengue virus, were used to investigate RNA viral genome unspecific amplification by multiple displacement amplification technique from clinical samples. Series of 10-fold diluted purified viral RNA were utilized as analog samples with different pathogen loads, after a series of reactions were sequentially processed, single-strand cDNA, double-strand cDNA, double-strand cDNA treated with ligation without or with supplemental RNA were generated, then a Phi29 DNA polymerase depended isothermal amplification was employed, and finally the target gene copies were detected by real time PCR assays to evaluate the amplification efficiencies of various methods. The results showed that multiple displacement amplification effects of single-strand or double-strand cDNA templates were limited, while the fold increases of double-strand cDNA templates treated with ligation could be up to 6 X 10(3), even 2 X 10(5) when supplemental RNA existed, and better results were obtained when viral RNA loads were lower. A RNA viral genome amplification system using multiple displacement amplification technique was established in this study and effective amplification of RNA viral genome with low load was achieved, which could provide a tool to synthesize adequate viral genome for multiplex pathogens detection.

Association of metabolic and DNA repair enzyme gene polymorphisms and DNA damage in coke-oven workers / 中华预防医学杂志

<p><b>OBJECTIVE</b>To investigate the association of polymorphisms of metabolic and DNA repair enzyme genes and DNA damage in peripheral blood lymphocytes in coke-oven workers.</p><p><b>METHODS</b>One hundred and forty-four coke-oven workers and 50 controls were recruited in this study. Urinary 1-hydroxypyrene (1-OHP) levels were measured as the internal dose of polycyclic aromatic hydrocarbons exposure. DNA damage was detected by alkaline comet assay, and the value of 1.74 was used as the cut-off value to determine whether the individual's DNA damage was positive. The genotypes of CYP1A1, CYP2E1, GSTP1, NQO1, mEH and XRCC1 were determined by PCR-based methods. With adjustment for urinary 1-OHP, age, sex, multiple analysis of covariance was used to study the association between genotypes and the ln-transformed olive TM and multiple logistic regression was used to calculate the adjusted OR and the 95% CI for the risk of DNA damage.</p><p><b>RESULTS</b>In 144 coke-oven workers, with adjustment for urinary 1-OHP, coking history and sex, the olive TM was significantly higher with XRCC1 280His allele than those with Arg allele (5.6 vs. 2.8, P < 0.01). The subjects with XRCC1 280His allele also have significantly higher risk for DNA damage than subjects with Arg allele (adjusted OR = 2.66, 95% CI = 1.00-7.14, P = 0.05) and the subjects with GSTP1 104Val allele have higher risk for DNA damage than subjects with Ile allele (adjusted OR = 1.90, 95% CI = 0.94-3.85, P = 0.07).</p><p><b>CONCLUSION</b>XRCC1 and GSTP1 polymorphisms might influence the susceptibility of DNA damage in occupational PAH-exposed coke-oven workers.</p>

Preferred amino acids and thermostability

Most organisms grow at temperatures from 20 to 50 degrees C, but some prokaryotes, including Archaea and Bacteria, are capable of withstanding higher temperatures, from 60 to >100 degrees C. Their biomolecules, especially proteins, must be sufficiently stable to function under these extreme conditions; however, the basis for thermostability remains elusive. We investigated the preferential usage of certain groupings of amino acids and codons in thermally adapted organisms, by comparative proteome analysis, using 28 complete genomes from 18 mesophiles (M), 4 thermophiles (T), and 6 hyperthermophiles (HT). Whenever the percent of glutamate (E) and lysine (K) increased in the HT proteomes, the percent of glutamine (Q) and histidine (H) decreased, so that the E + K/Q + H ratio was >4.5; it was <2.5 in the M proteomes, and 3.2 to 4.6 in T. The E + K/Q + H ratios for chaperonins, potentially thermostable proteins, were higher than their proteome ratios, whereas for DNA ligases, which are not necessarily thermostable, they followed the proteome ratios. Analysis of codon usage revealed that HT had more AGR codons for Arg than they did CGN codons, which were more common in mesophiles. The E + K/Q + H ratio may provide a useful marker for distinguishing HT, T and M prokaryotes, and the high percentage of the amino acid couple E + K, consistently associated with a low percentage of the pair Q + H, could contribute to protein thermostability. The preponderance of AGR codons for Arg is a signature of all HT so far analyzed. The E + K/Q + H ratio and the codon bias for Arg are apparently not related to phylogeny. HT members of the Bacteria show the same values as the HT members of the Archaea; the values for T organisms are related to their lifestyle (intermediate temperature) and not to their domain (Archaea) and the values for M are similar in Eukarya, Bacteria and Archaea

DNA mismatch repair enzyme hMSH2 genetic polymorphism in southern Chinese Han population / 中华医学遗传学杂志

<p><b>OBJECTIVE</b>To study hMSH2 genetic polymorphism in southern Chinese Han population.</p><p><b>METHODS</b>The basic materials and blood samples from 163 southern Chinese were collected. The mutations of exon 6 and exon 7 of hMSH2 gene were investigated by PCR-SSCP, followed by DNA sequencing.</p><p><b>RESULTS</b>Fragments of 250 bp including exon 6 and fragments of 323 bp including exon 7 of hMSH2 gene were amplified by multiple PCR. The allele frequencies of C18, A82 and B39 type mutations were 0.0184, 0.0031, 0.0031, respectively. The gene frequencies and gene type frequencies of three polymorphism sites in normal population accorded with Hardy-Weinberg equilibrium (P>0.05). The heterozygosity of C18 type mutation (0.0361) was the highest.</p><p><b>CONCLUSION</b>There were three polymorphism sites in exon 7 of hMSH2 gene in southern Chinese Han population, among which the genotype frequency of C18 type was the highest, suggesting that C18 type mutation be a useful genetic mark.</p>

Optimización de las condiciones de purificación de T4 ADN ligasa / Optimization of the purification conditions for the T4 DNA ligase

El procedimiento reportado por Davis et al., 1980. para purificar T4 ADN ligasa, ha sido modificado con el objetivo de obtener una preparación de la enzima virtualmente libre de exonucleasas. Se modificaron las condiciones de elución de las columnas de P11 e hidroxilapatita: en vez de eludir en un paso, en ambos se aplicó un gradiente lineal, de 300 a 800 mM de cloruro de sodio en la columna de P11 y de 0 a 800 mM en la de hidroxilapatita. Este procedimiento permitió la eliminación de nucleasas y la obtención de una preparación enzimática de gran calidad

DNA repair aystems.

Sistemas de reparo do DNA tem merecido atencao, principalmente devido ao papel que exercem em mutagenese e carcinogenese. Sao revistos fatos ja estabelecidos e avancos recentes, no assunto, com enfase nos eventos enzimaticos, envolvidos nas celulas bacterianas