PCR, clone and sequence analysis of rDNA-ITS of Nelumbo nucifera from different geographical origins in China / 中国中药杂志

<p><b>OBJECTIVE</b>To provide DNA molecular marker for identification of Nelumbo nucifera by exploring the differences of nrDNA-ITS sequence of N. nucifera originated from different habitats.</p><p><b>METHOD</b>To compare nrDNA-ITS base sequence using specific PCR-ITS.</p><p><b>RESULT</b>The completed sequence of ITS and 5.8 S rDNA, and the partial sequences of 18S rDNA and 26S rDNA, totally 750 bp, from N. nucifera were obtained. The differences among N. nucifera from different habitats and from different cultivars were found.</p><p><b>CONCLUSION</b>The method can be used to identify N. nucifera among different species and to distinguish their fakes. It provided the basis for identifying N. nucifera from different geographical regions by comparison of their ITS sequences.</p>

Uso del análisis de restricción en el control de calidad de cepa del biolarvicida cubano BACTIVEC / Use of the restriction analysis in the quality control of the strain of Cuban biolarvicide BACTIVEC

Se mostró la caracterización genómica de la cepa utilizada en la producción del biolarvicida Bactivec. Se compararon los patrones de digestión de la cepa de referencia 266 de Bacillus thuringiensis de la colección del Instituto Pushkin del antiguo Leningrado y 2 cepas aisladas de 2 lotes del biolarvicida. Las digestiones del ADN cromosomal se realizaron con las enzimas HindIII y EcoRI. En todos los casos se observó el mismo patrón de restricción, lo que muestra la estabilidad genética del ingrediente activo del biolarvicida Bactivec

Study on EcoR I fragment polymorphism of the subtelomeric domains within 4q35 and 10q26 with pulsed field gel electrophoresis in the Chinese population / 中华医学遗传学杂志

<p><b>OBJECTIVE</b>To elucidate the structural polymorphism of EcoR I fragment within chromosomes 4q35 and 10q26 in the Chinese population and investigate the relationship of plasticity, translocation and somatic mosaicism in these domains with deletion of D4Z4 repeated units.</p><p><b>METHODS</b>One hundred and ten unrelated healthy individuals from a random Chinese population were investigated. The genomic DNA was extracted from peripheral blood lymphocytes according to the specific procedure designed to minimize DNA shearing, then digested with EcoR I or double digested with EcoR I and Bln I. The cleaved DNA was separated by pulsed field gel electrophoresis (PFGE) and Southern blotted with the probe p13E-11. The sizes of EcoR I fragments were calculated by "curve fitting" according to the MidRange PFG marker and the alleles were assigned to their respective chromosomes based on their Bln I sensitivity. Data were analyzed using a commercially available statistical package (Version 11.0 SPSS).</p><p><b>RESULTS</b>Seventy-seven point three per cent (85/110) of the unrelated healthy individuals displayed a standard configuration distribution. The mean and median of 4q35 repeat arrays are (87.9+/-3.3) kb and 78.5 kb respectively, whereas the mean and median of 10q26 homologous arrays are (90.1+/-4.1) kb and 73.0 kb. Repeat size distributions between both of them were of no significance according to the t test (P>0.05). 19.1% (21/110) of the individuals displayed a translocation repeat array configuration on chromosomes 4 and 10. No significant difference was detected between 4q-->10q translocation and 10q-->4q translocation according to Chisquare test (Chi2 test=0.053, P>0.05). Somatic mosaicism was observed in 3.6% (4/110) of the subjects and less than 35 kb 10-type array was found in 14.5% (16/110) of the individuals.</p><p><b>CONCLUSION</b>The structural polymorphism and dynamic behaviors of EcoR I fragments within 4q35 and 10q26 were demonstrated in this study using PFGE. The occurrence of frequent translocations and somatic mosaicism between 4q35 and 10q26 subtelomeric domains in the Chinese population further confirmed that mitotic interchromosomal gene conversion or translocation might be a major mechanism relating to the deletion of D4Z4 units.</p>

The X-X-/E+E+ genotype of the XbaI/EcoRI polymorphisms of the apolipoprotein B gene as a marker of coronary artery disease in a Brazilian sample

Studies that consider polymorphisms within the apolipoprotein B (apo B) gene as risk factors for coronary artery disease (CAD) have reported conflicting results. The aim of the present study was to search for associations between two DNA RFLPs (XbaI and EcoRI) of the apo B gene and CAD diagnosed by angiography. In the present study we compared 116 Brazilian patients (92 men) with CAD (CAD+) to 78 control patients (26 men) without ischemia or arterial damage (CAD-). The allele frequencies at the XbaI (X) and EcoRI (E) sites did not differ between groups. The genotype distributions of CAD+ and CAD- patients were different (chi²(1) = 6.27, P = 0.012) when assigned to two classes (X-X-/E+E+ and the remaining XbaI/EcoRI genotypes). Multivariate logistic regression analysis showed that individuals with the X-X-/E+E+ genotype presented a 6.1 higher chance of developing CAD than individuals with the other XbaI/EcoRI genotypes, independently of the other risk factors considered (sex, tobacco consumption, total cholesterol, hypertension, and triglycerides). We conclude that the X-X-/E+E genotype may be in linkage disequilibrium with an unknown variation in the apo B gene or with a variation in another gene that affects the risk of CAD

Gene diagnosis of facioscapulohumeral muscular dystrophy / 中华医学遗传学杂志

<p><b>OBJECTIVE</b>To observe the characteristics of changes of p13E-11 labelled 4q35 EcoRI fragments and to make a gene diagnosis of facioscapulohumeral muscular dystrophy(FSHD).</p><p><b>METHODS</b>Genomic DNA was extracted and was digested by EcoR I /Bln I. After pulsed field gel electrophoresis, it was hybridized with probe p13E-11 by Southern blot. The illness was diagnosed as FSHD when the 4q35 EcoRI fragment was smaller than 38 kb.</p><p><b>RESULTS</b>In 26 cases of FSHD, the fragments of 20 cases were smaller than 38 kb. The positive rate was 76.92%. In 12 cases of FSHD family members, the fragments of 2 cases were smaller than 38 kb. All fragments of the 21 controls were greater than 38 kb.</p><p><b>CONCLUSION</b>It was rather good to use <38 kb as a standard for diagnosis of FSHD. The positive rate of FSHD was similar to that from the references.</p>

Association between EcoRI fragment-length polymorphism of the immunoglobulin lambda variable 8 (IGLV8) gene family with rheumatoid arthritis and systemic lupus erythematosus

The human immunoglobulin lambda variable 8 (IGLV8) subgroup is a gene family containing three members, one of them included in a monomorphic 3.7-kb EcoRI genomic fragment located at the major lambda variable locus on chromosome 22q11.1 (gene IGLV8a, EMBL accession No. Z73650) at 100 percent frequency in the normal urban population. The second is a polymorphic RFLP allele included in a 6.0-kb EcoRI fragment at 10 percent frequency, and the third is located in a monomorphic 8.0-kb EcoRI fragment at 100 percent frequency, the last being translocated to chromosome 8q11.2 and considered to be an orphan gene. Our Southern blot-EcoRI-RFLP studies in normal individuals and in patients with rheumatoid arthritis (RA) or with systemic lupus erythematosus (SLE), using a specific probe for the IGLV8 gene family (probe pVL8, EMBL accession No. X75424), have revealed the two monomorphic genomic fragments containing the IGLV8 genes, i.e., the 3.7-kb fragment from chromosome 22q11.1 and the 8.0-kb fragment from 8q11.2, both occurring at 100 percent frequency (103 normal individuals, 48 RA and 28 SLE patients analyzed), but absence of the 6.0-kb IGLV8 polymorphic RFLP allele in all RA or SLE patients. As expected, the frequency of the 6.0-kb allele among the normal individuals was 10 percent. These findings suggest an association between the absence of the 6.0-kb EcoRI fragment and rheumatoid arthritis and systemic lupus erythematosus

Relationship of Xba1 and EcoR1 polymorphisms of apolipoprotein-B gene to dyslipidemia and obesity in Asian Indians in North India.

BACKGROUND: Genetic investigation of dyslipidemia and obesity prevalent in the Indian population form the basis of this study. METHODS AND RESULTS: The frequency of restriction fragment length polymorphisms (Xba1 and EcoR1) of the apolipoprotein-B gene was investigated in a case-control study of 30 hyperlipidemic and 40 normolipidemic subjects. By univariate analysis, old age, higher body mass index, waist-hip ratio and sum of four skinfolds were found to be significantly associated with hyperlipidemia. The frequencies of X- and E+ alleles of the apolipoprotein-B gene were significantly higher in North Indians in the state of New Delhi (0.83 and 0.91, respectively) as compared to the observations made in Caucasians in previous studies, but was similar to the frequency reported in Indians settled in Singapore and the UK. There were no significant differences in the allele or genotype frequencies of either Xba1 or EcoR1 polymorphisms between the hyperlipidemic and normolipidemic groups. On multiple logistic regression analysis considering body mass index, waist-hip ratio, percentage body fat and genotypes as independent variables, no association was observed between the apolipoprotein-B genotypes and serum lipid components. Further, there were no associations between apolipoprotein-B polymorphisms and generalized obesity (as assessed by body mass index, sum of four skinfolds, and percentage total body fat) and abdominal obesity (as measured by waist circumference and waist-hip ratio). CONCLUSIONS: We conclude that apolipoprotein-B (Xba1 and EcoR1) polymorphisms do not appear to influence serum lipid levels and parameters of generalized andregional obesity in the study sample.

Molecular Genetic Characteristics of Trimethoprim Resistance in Clinical and Normal Fecal Isolates of Escherichia coli

One hundred and thirty trimethoprim-resistant R plasmids derived from of Escherichia coli isolated from clinical specimens and feces of healthy collegians were examined for incompatibility, EcoRI endonuclease restriction fragment pattern, and Southern hybridization with DHFR I, II, III, V, and VII probe. 1. Most trimethoprim-resistant R plasmids were resistant to ampicillin, tetracycline, chloramphenicol, gentamicin, and kanamycin, and showed multiple drug resistance and various antimicrobial resistance patterns. 2. Trimethoprim-resistant R plasmids ranged from 90 to 50 kilobase and 42.3% of R plasmids tested were classified to incompatibilty group Inc FI, Inc FII or Inc FIV, 3. Among 48 random selected R plasmids from various origin, 14 R plasmids (including 9 of 14 Inc FII plasmids and 3 of 14 Inc FI plasmids) hybridized with DHFR VII oligonucleotide probe but others did not respond to any of DHFR probes used. 4. Most R plasmids showed various EcoRI endonuclease fragments and different reaction sites by Southern hybridization. Six plasmids showed identical or nearly identical molecular weight, EcoRI endonuclease fragment patterns and different sites of Southern hybridization. But 2 Inc FII plasmids derived from urine and feces showed identical pattern. These findings, if confirmed by further studies, suggest that normal flora E. coli can act as reservoir of resistant genes and, consequently, as a factor in the dissemination of these genes among enteric pathogens and need to be examined further.

Transferable Trimethoprim Resistance in Urine Isolates of Escherichia coli

One hundred and twenty-two strains of E. coli isolated from urinary tract infection were examined for antibiogram, transferability of trimethoprim (Tp) resistance, incompatibility with F group plasmid and southem hybridization with DHFR I, II, and III probe of Tp-resistant R plasmids. 1. Among 172 Gram negative bacilli isolated from urinary tract infection, 122 (70.9%) were E. coli and 75 strains of them were resistant to trimethoprim (Tp). Most of Tp-resistant isolates were also resistant to penicillins (ampicillin, carbenicillin, and ticarcillin), aminoglycosides (kanamycin and gentamicin), and sulfisoxazole but almost all strains were susceptible to cephalosporins. 2. Most of Tp-resistant strains and E. coli transconjugant derived from them showed multiple drug resistance and various antimicrobial resistance patterns. 3. Thirty-three Tp-resistant strains (45.2%) transferred 35 Tp-resistant plasmids to E. coli recipients but among them 6 transconjugants did not show retransfer of resistance and plasmid DNA were not detected in 2 transconjugants after resistance transfer. 4. Tp-resistant R plasmids ranged from 157 to 67 kb and 8 R plasmids were classified to incompatibilty group IncFI or IncFII ranging from 120 to 83 kb. Three and two R plasmids belonged to IncFII showed similar molecular weight, resistance pattern, and reaction site by southern hybridization with DHFR I probe. Twenty-five plasmids specifically responded on various EcoRI endonuclease fragments to DHFR I probe but not to DHFR II or DHFR III probe. These findings suggest that most of Tp- resistant R plasmids from urine isolates of E. coli were derived from various sources but some plasmids including IncFII R plasmids were probably originated from same or similar sources.

Quantitative Measurement of Hepatitis B Virus DNA by Competitive Nested Polymerase Chain Reaction / 대한임상병리학회지

BACKGROUND: We performed competitive nested polymerase chain reaction (PCR) to evaluate the clinical utility of quantitative measurement of HBV DNA by PCR and it's correlation with other serologic hepatits B markers. Because hepatitis markers such as HBsAg, HBeAg, anti-HBe can not accurately reflect the replication of hepatitis B virus (HBV). METHODS: The internal standard was generated from the HBV core gene by point mutation, which would result in restriction site for the restriction enzyme Eco RI and performed competitive nested PCR followed by densitometric scanning of the amplified products of agarose gel. RESULTS: The sensitivity of nested PCR was 5 molecules in direct observation of agarose gel, but because of the background effect as taking polaroid photo graph it was 50 molecules by using densitometer. When DNA pellets for original 250 microL serum were diluted with 40 microL distilled water the low detection limit was 5.0 x10(3) molecules/microL, however it could be lowered when less diluted. Lower detection limit of densitometer was 6.25 pg by twofold serial dilution of 100 pg of purified HBV DNA PCR products, and regression showed y=0.93x-0.33 (y : density, x : concentration, 6.25 pg considered as 6.25 density). The reproducibility of the densitometer from high concentration was 4.3 +/-0.6 x10(6) molecules/microL(mean +/-SD, CV 14%), and low concentration was 3.7 +/-0.7 x10(4) molecules/microL(mean +/-SD, CV : 20%) Higher concentration of HBV DNA in HBeAg positive cases comparing with HBeAg negative cases was statistically significant (p<0.01). There was no correlation between HBV DNA concentration and serum value of alanine aminotransferase. CONCLUSION: Quantification of HBV DNA should be very useful in clinical follow-up of Post-therapy Patients and in anticipating Prognosis and infectivity of the disease, especially in cases of atypical hepatitis B and hepatitis B without seroconversion of routine hepatitis B markers. The shortcoming of the method seemed to be a rough estimate of HBV concentration as measuring the ratio of specimen/internal standard of two consecutive concentration among 10 folds serially diluted internal standard.

Rapid identification of the association of hemoglobin D Punjab and hemoglobin S (HbD Punjab/HbS) by the polymerase chain reaction

A hemoglobina D-Punjab foi descrita em vários grupos étnicos, tanto em heterozigose simples quanto em associaçäo com Hb S ou ß-talassemia. Neste trabalho descrevemos uma paciente brasileira, negra de 10 anos de idade que apresentava características clínicas de doença falciforme. O padräo eletroforético sugeriu a associaçäo Hb S/Hb D. A mutaçäo da Hb D foi confirmada através da digestäo do fragmento amplificado do gene da globina ß com a enzima EcoRI e sequencialmente direto do fragmento amplificado. A mutaçäo muda uma base no codon 121 e abole o sítio de reconhecimento normal da enzima, possibilitando o reconhecimento do gene anormal em electroforese de gel de agarose. Estes dados representam a segunda descriçäo comprovada da associaçäo Hb S/Hb D no Brasil e indicam que a presença da Hb D deve ser investigada, pelo método aqui descrito, em casos de doença falciforme com padräo eletroforético anômalo

Heterogeneous plasmid population from enterotoxigenic Escherichia coli strains isolated in Venezuelan children with acute diarrhea

Con el objetivo de estudiar la presencia de posibles asociaciones entre enteroxigenicidad y otras características patógenas medidas por plásmidos cmo son resistencia a los antibióticos, producción de colicinas (Col V), hemolisinas (Hly) y factores de colonización (CFA/1), se analizaron 38 cepas de Escherichia coli enterotoxigénicas (ETEC) aisladas de niños con diarrea aguda. El 84% de las cepas enterotoxigénicas fueron multiresistentes. Veinte cepas (52,63%) fueron capaces de transferir una o más de las características estudiadas y 92,68% de las transcojugantes fueron mutiresistentes. Se encontró una baja frecuencia en la transferencia simultánea de ST y Col V, Hly o CEA/I (1,82%). El análisis de plásmidos reveló la presencia de una población heterogénea de plásmidios asociados a toxigenicidad. Se encontró un plásmido de aproximadamente 31 megadaltons (Md) de peso molecular que codifica pra ST y reistencia para ampicilina, Kanamicina y estreptomicina. Sin embargo este plásmidio no se encontró en todas las cepas. Estos resultados muestran la existencia de una población heterogénea de plásmidos que codifican para la producción de enterotoxinas, esta diversidad probablemente sea una consecuencia del uso indiscriminado de antibióticos y de los mecanismos moleculares de transposición de ST y resistencia a drogas en la evolución de estas enterobacterias