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RAPD Patterns (rapd + pattern)
Selected AbstractsMicrobiota analysis of Caspian Sea yogurt, a ropy fermented milk circulated in JapanANIMAL SCIENCE JOURNAL, Issue 2 2009Kenji UCHIDA ABSTRACT We analyzed the microbiota of domestic ropy fermented milk, Caspian Sea yogurt (or ,kasupikai yohguruto' in Japanese), circulated in Japan. We collected six varieties from five localities. Lactococcus (L) lactis ssp. cremoris was isolated from all samples as the dominant strain at levels of 108,109 CFU/g. We show this strain produces an extracellular polysaccharide (EPS) that causes the unique characteristic viscosity of the product. From analysis of the RAPD pattern of 60 bacterial isolates from the six samples, we found that 59 strains from a total of 60 isolates were identical and produced this viscosity. Furthermore, PFGE analysis of representative strains from each sample indicated that the isolates could be classified into four subgroups. This suggests these L. lactis ssp. cremoris strains found in Caspian Sea yogurt may have been slightly mutated during subculture in Japan. In addition, Lactobacillus (L.) sakei ssp. sakei were isolated from three samples; L. plantarum, Gluconoacetobacter sacchari and Acetobacter aceti were isolated from two samples; and L. paracasei, L. kefiri, Leuconostoc (Leu.) mesenteroides were isolated from one sample. [source] Different portions of the maize root system host Burkholderia cepacia populations with different degrees of genetic polymorphismENVIRONMENTAL MICROBIOLOGY, Issue 1 2000Luigi Chiarini In order to acquire a better understanding of the spatial and temporal variations of genetic diversity of Burkholderia cepacia populations in the rhizosphere of Zea mays, 161 strains were isolated from three portions of the maize root system at different soil depths and at three distinct plant growth stages. The genetic diversity among B. cepacia isolates was analysed by means of the random amplified polymorphic DNA (RAPD) technique. A number of diversity indices (richness, Shannon diversity, evenness and mean genetic distance) were calculated for each bacterial population isolated from the different root system portions. Moreover, the analysis of molecular variance ( amova) method was applied to estimate the genetic differences among the various bacterial populations. Our results showed that, in young plants, B. cepacia colonized preferentially the upper part of the root system, whereas in mature plants, B. cepacia was mostly recovered from the terminal part of the root system. This uneven distribution of B. cepacia cells among different root system portions partially reflected marked genetic differences among the B. cepacia populations isolated along maize roots on three distinct sampling occasions. In fact, all the diversity indices calculated indicated that genetic diversity increased during plant development and that the highest diversity values were found in mature maize plants, in particular in the middle and terminal portions of the root system. Moreover, the analysis of RAPD patterns by means of the amova method revealed highly significant divergences in the degree of genetic polymorphism among the various B. cepacia populations. [source] Evaluation of DNA polymorphisms amplified by arbitrary primers (RAPD) as genetically associated elements to differentiate virulent and non-virulent Paracoccidioides brasiliensis isolatesFEMS IMMUNOLOGY & MEDICAL MICROBIOLOGY, Issue 3 2002Teresa R Motta Abstract Randomly amplified polymorphic DNA (RAPD) analysis of 35 Paracoccidioides brasiliensis isolates was carried out to evaluate the correlation of RAPD profiles with the virulence degree or the type of the clinical manifestations of human paracoccidioidomycosis. The dendrogram presented two main groups sharing 64% genetic similarity. Group A included two isolates from patients with chronic paracoccidioidomycosis; group B comprised the following isolates showing 65% similarity: two non-virulent, six attenuated, five virulent, eight from patients with chronic paracoccidioidomycosis and two from patients with acute paracoccidioidomycosis. The virulent Pb18 isolate and six attenuated or non-virulent samples derived from it were genetically indistinguishable (100% of similarity). Thus, in our study, RAPD patterns could not discriminate among 35 P. brasiliensis isolates according to their differences either in the degree of virulence or in the type of the clinical manifestation of this fungal infection. [source] Genotypic and phenotypic characteristics of antibiotic-producing soil Streptomyces investigated by RAPD-PCRJOURNAL OF BASIC MICROBIOLOGY, Issue 1 2003Raad Gharaibeh Random amplified polymorphic DNA (RAPD) analysis has been used to determine the relatedness of 73 antibiotic-producing soil Streptomyces isolates that were recovered from different soil habitats in Jordan based on their RAPD-PCR fingerprints. Genetic polymorphisms between these isolates showed three common bands of 2777, 800 and 250 bp shared by approximately (95%) of them. Some specific bands were also observed. Further analysis of RAPD patterns with the UPGMA resulted in clustering the tested isolates into two main super clusters. Super cluster I was more homogenous than super cluster II and contained all the reference strains. However, super cluster II consists of unrelated isolates within five small groups. As RAPD fingerprints of the tested isolates linked to their phenotypes, differentiation between isolates with different cultural properties was observed. [source] Heteropogon triticeus, a New Host of Claviceps sorghi in IndiaJOURNAL OF PHYTOPATHOLOGY, Issue 4-5 2002OUTOVÁ, S. PA Abstract Claviceps sorghi occurred on Heteropogon triticeus in Gulbarga, Karnataka, India. Its external sphacelial morphology on this species differed from that on sorghum in having long white sphacelial tips that protruded from spikelets or wound around awns. The tips were formed by parallel synnema-like hyphae and were covered by a phialide layer that produced elongated macroconidia (7,18 ,m) and rounded to oval microconidia (3,5 ,m). Unlike the macroconidia, the microconidia failed to germinate. Plated macroconidia underwent secondary sporulation. The white sclerotial stroma consisted of parallel hyphae with cylindrical cells that later became rounded due to accumulation of reserve metabolites. Some of these cells differentiated into a sclerotial rind that accumulated a terracotta-coloured pigment. RAPD patterns and the rDNA nucleotide sequence confirmed the identity of the species. [source] RAPD variation and population genetic structure in Prunus mahaleb (Rosaceae), an animal-dispersed treeMOLECULAR ECOLOGY, Issue 9 2000Pedro Jordano Abstract We examined the patterns of random amplified polymorphic DNA (RAPD) variation among seven Prunus mahaleb (Rosaceae) populations extending over , 100 km2 to examine local differentiation in relation to spatial isolation due to both geographical distance and differences in elevation. No less than 51.4% of the RAPD loci were polymorphic, but very few were fixed and among-population variation accounted for 16.46% of variation in RAPD patterns. Mean gene diversity was 0.1441, with mean Nei's genetic diversity for individual populations ranging between 0.089 and 0.149. Mean GST value across loci was 0.1935 (range, 0.0162,0.4685), giving an average estimate for Nm of 1.191. These results suggest extensive gene flow among populations, but higher GST and lower Nm values relative to other outcrossing, woody species with endozoochorous dispersal, also suggest a process of isolation by distance. The combined effect of both geographical and elevation distances and nonoverlapping flowering and fruiting phenophases on the GST matrix was partially significant, revealing only marginal isolation of the P. mahaleb populations. The matrix correlation between estimated Nm values among populations and the geographical + elevation distance matrices (r = ,0.4623, P = 0.07), suggests a marginal trend for more isolated populations to exchange less immigrants. Long-distance seed dispersal by efficient medium-sized frugivorous birds and mammals is most likely associated to the high levels of within-population genetic diversity. However, vicariance factors and demographic bottlenecks (high postdispersal seed and seedling mortality) explain comparatively high levels of local differentiation. [source] Biotype stability of Candida albicans isolates after culture storage determined by randomly amplified polymorphic DNA and phenotypical methodsMYCOSES, Issue 6 2010Katia Leston Bacelo Summary Typing methods to evaluate isolates in relation to their phenotypical and molecular characteristics are essential in epidemiological studies. In this study, Candida albicans biotypes were determined before and after storage in order to verify their stability. Twenty C. albicans isolates were typed by Randomly Amplified Polymorphic DNA (RAPD), production of phospholipase and proteinase exoenzymes (enzymotyping) and morphotyping before and after 180 days of storage in Sabouraud dextrose agar (SDA) and sterilised distilled water. Before the storage, 19 RAPD patterns, two enzymotypes and eight morphotypes were identified. The fragment patterns obtained by RAPD, on the one hand, were not significantly altered after storage. On the other hand, the majority of the isolates changed their enzymotype and morphotype after storage. RAPD typing provided the better discriminatory index (DI) among isolates (DI = 0.995) and maintained the profile identified, thereby confirming its utility in epidemiological surveys. Based on the low reproducibility observed after storage in SDA and distilled water by morphotyping (DI = 0.853) and enzymotyping (DI = 0.521), the use of these techniques is not recommended on stored isolates. [source] | |||||||||||||