Establishment of DNA fingerprints for Chrysosplenium using SRAP Markers / 中国中药杂志

As a traditional Chinese medicinal material, Chrysosplenium is urgently needed for genetic resource investigation and protection research due to the decrease of its wild resources in recent years. After investigating the wild resources, we conducted genetic polymorphism and clustering studies of 24 species(a total of 36 samples) of Chrysosplenium using SRAP technique. The results showed that a total of 374 polymorphic bands were obtained using 18 pairs of SRAP primers to amplify these samples, on average of 20.7 bands for each primer pair. We used the biological software to analyze the population's genetic parameter and got the N_a value as 2.000 0, N_(e )value as 1.408 4, the average Nei's index as 0.263 5, and the average Shannon information index as 0.419 1. UPGMA cluster analysis showed that all the samples can be divided into three major groups at the genetic similarity coefficient of 0.70: there are 18 species(24 samples) gathered for the Ⅰ groups, 3 species or variation(7 samples) for Ⅱ groups, and 3 species(5 samples) for Ⅲ groups. The differences of these Chrysosplenium species at the molecular level are consistent with that of their geographical and ecological distribution. At the same time, we used SRAP technology to construct 36 DNA digital fingerprints of Chrysosplenium and obtained the unique molecular identification band type of each material. These results will provide effective methods and reliable basis for the identification, protection and genetic diversity analysis of the germplasm resources of Chrysosplenium, and lay a foundation for the further development and utilization of them.

AFLP analysis of Xanthomonas axonopodis and X arboricola strains used in xanthan production studies reveal high levels of polymorphism

Amplified fragment length polymorphism (AFLP) was used to analyze the genetic diversity of 14 strains of Xanthomonas arboricola pv. pruni and seven strains of X. axonopodis pv. phaseoli, which are used in xanthan production studies. Relationships identified by the AFLP profiles were assessed for xanthan production capacity, geographical location and host plant. Strains were isolated from 10 different geographic regions in South and Southeast States in Brazil. Data were analyzed for genetic similarity using the Dice coefficient and subjected to UPGMA cluster analysis. A total of 128 AFLP fragments were generated from four primer combinations: EcoRI+C/MseI+0, EcoRI+A/MseI+0, EcoRI+G/MseI+T and EcoRI+G/MseI+A. Of these, 96.1 percent were polymorphic. X. axonopodis pv. phaseoli (S D = 0.27) was shown to be more polymorphic than X. arboricola pv. pruni (S D = 0.58). All 14 pathovar pruni strains were included in a single main group (S D = 0.58), while the pathovar phaseoli strains were divided into three separate groups, with one group containing five strains (S D = 0.38) and two isolated groups (S D = 0.31 and 0.27) composed of only one strain each. Species were distinguished by three and eight specific AFLP markers present in the pathovar phaseoli and the pathovar pruni, respectively. For the unique strain without xanthan production capacity (X. axonopodis pv. phaseoli str. 48), nine specific AFLP bands were found. There was no evidence that geographic area or host plant influenced genetic heterogeneity. Correlations between AFLP patterns and xanthan production capacity were found in some strains, but were not consistent enough to establish a relationship.

Análise das impressões digitais de DNA e de fatores de virulência de linhagens de Helicobacter pylori / Analysis of molecular fingerprint and virulence factors of Helicobacter pylori strains

RACIONAL: Helicobacter pylori é hoje aceito como o principal agente etiológico de gastrite em seres humanos e fator de risco para úlcera péptica e câncer gástrico. A evolução da infecção está relacionada a diversos fatores, inclusive bacterianos, como presença do gene cagA e o genótipo vacA s1m1, associados ao desenvolvimento de úlcera e adenocarcinoma gástrico. A técnica de RAPD ("random amplified polimorphic") tem sido amplamente utilizada para obtenção de impressões digitais de DNA para examinar a similaridade entre linhagens. OBJETIVOS: Avaliar a presença de cagA e alelos do vacA em amostras de H. pylori e associar os achados com a doença apresentada e também investigar possível clonicidade entre os fatores de virulência e as doenças com a impressão digital de DNA gerada pelo RAPD-PCR. MÉTODOS: Foram incluídas 112 amostras provenientes de pacientes com diferentes laudos endoscópicos: gastrite (n = 41), esofagite de refluxo (n = 14), úlcera gástrica (n = 19) e úlcera duodenal (n = 38). A análise dos fatores de virulência da bactéria foi feita por PCR e as impressões digitais de DNA foram estabelecidas pelo método de RAPD-PCR. RESULTADOS: Os resultados obtidos indicam que houve uma associação significativa entre úlcera duodenal e o mosaico vacA s1m1. Analisando-se os padrões de bandas geradas pelo RAPD-PCR, sete diferentes dendogramas foram construídos e não foi possível detectar associação significativa entre os agrupamentos, sugerindo que as amostras não possuem perfil clonal. CONCLUSÃO: Os resultados reforçam a importância do gene vacA como um marcador de virulência do H. pylori. O RAPD da impressão digital de DNA realizado foi incapaz de associar o padrão de bandas com as enfermidades e os genótipos de vacA e cagA.

BACKGROUND: Helicobacter pylori is now accepted as the most important agent of gastritis in humans, as well as a risk factor for peptic ulcer disease and gastric carcinoma. The outcome of the infection is related to several factors, among them bacterial ones such as cagA and vacA s1m1 genotype. Random amplified polymorphic DNA (RAPD)-PCR, has been used to generate DNA fingerprints to evaluate similarity among strains within a bacterial species. AIM: To assess the association between RAPD fingerprinting, virulence factors and the disease. METHODS: H. pylori was isolated from 112 patients (41 with gastritis; 19 with gastric ulcers; 38 with duodenal ulcer disease; and 14 with gastroesophageal reflux disease). Allelic variants of cagA and vacA were identified using the polymerase chain reaction (PCR) and the fingerprints were generated by RAPD-PCR. RESULTS: There was a strong association between the genotype vacA s1m1 and duodenal ulcers. Although RADP-PCR is a very useful tool in genotyping H. pylori, no significant correlation between the diseases studied and DNA fingerprint was detected neither with fingerprint and different vacA and, cagA genotypes. CONCLUSIONS: The extension of our analysis to patients with well-characterized gastric diseases may provide significant information on the relationship between vacA genotypes and clinical outcomes of H. pylori infection.