scholarly journals RAPD-PCR Fingerprinting for Some RhodotorulaSpecies Isolated from Natural Sources and their Antagonistic Potential Against Erwinia Carotovora and Erwinia Chrysanthem

2019 ◽  
Vol 21 (1) ◽  
Author(s):  
Abd El Latif Hesham
Keyword(s):  
Erwinia Carotovora ◽  
Natural Sources ◽  
Pcr Fingerprinting ◽  
Rapd Pcr ◽  
Antagonistic Potential

Diversity and symbiotic effectiveness of Rhizobium leguminosarum bv. trifolii isolates from pasture soils in south-western Australia

Soil Research ◽  
2002 ◽  
Vol 40 (8) ◽  
pp. 1319 ◽  
Author(s):  
M. T. Collins ◽  
J. E. Thies ◽  
L. K. Abbott
Keyword(s):  
Western Australia ◽  
Rhizobium Leguminosarum ◽  
Subterranean Clover ◽  
Most Probable Number ◽  
Enzyme Linked Immunosorbent Assay ◽  
Symbiotic Effectiveness ◽  
Probable Number ◽  
Pcr Fingerprinting ◽  
Rapd Pcr ◽  
Inoculant Strain

The abundance of the Australian inoculant strain of Rhizobium leguminosarum bv. trifolii for subterraneum clover (WU95) and the diversity of naturalised rhizobia were assessed in 3 subterranean clover pastures in the Albany region of south-western Western Australia. Most probable number, enzyme linked immunosorbent assay (ELISA), and polymerase chain reaction (PCR) techniques were used. A putative strain similar to inoculant strain WU96 was uncommon at one site (South Stirling) and not isolated at 2 other sites. Randomly amplified polymorphic DNA (RAPD) PCR fingerprinting using the RPO1 primer identified 45 different profiles amongst the 208 isolates examined. RAPD-PCR fingerprinting using the primers RPO4 and RPO5 confirmed most groupings based on RPO1 fingerprint patterns and revealed further genetic diversity within some groups. Overall, 54 putative strains were defined by RAPD-PCR fingerprint profiles across the 3 sites. Subterranean clover rhizobia at the Manypeaks and Mount Shadforth sites were dominated by isolates with 1 or 2 RPO1 RAPD profiles at 2 sampling times, while the population at South Stirling was much more diverse. The symbiotic effectiveness of 11 rhizobial isolates, representing the major RPO1 RAPD profile groups within naturalised rhizobial populations, were compared in pot culture with those of the 2 commercial inoculant strains for subterranean clover, WU95 and TA1, on 3 cultivars. Differences in effectiveness among 3 of the 11 isolates were observed in comparison to both the commercial strains and other naturalised isolates. The nitrogen fixing effectiveness of 8 isolates representing different subgroups from one RP01 group was not the same. The use of all 3 primers increased the precision in defining putative strains of Rhizobium leguminosarum bv. trifolii, and although naturalised rhizobia from these pastures are saprophytically competent, their dominance in nodules does not appear to be linked to symbiotic effectiveness.

scholarly journals Characterization of verocytotoxin-producingEscherichia coliO157 isolates from patients with haemolytic uraemic syndrome in Western Europe

1995 ◽  
Vol 115 (1) ◽  
pp. 1-3 ◽  
Author(s):  
A. E. Heuvelink ◽  
N. C. A. J. van de Kar ◽  
J. F. G. M. Meis ◽  
L. A. H. Monnens ◽  
W. J. G. Melchers
Keyword(s):  
Haemolytic Uraemic Syndrome ◽  
Western Europe ◽  
Random Amplified Polymorphic Dna ◽  
E Coli ◽  
Pcr Fingerprinting ◽  
Phage Types ◽  
Rapd Pcr ◽  
Typing Methods ◽  
Dna Pcr

SummaryFifty verocytotoxin (VT)-producingEscherichia coli(VTEC) strains of serogroup O157 were characterized by phage typing, polymerase chain reaction (PCR) for VT genes and theE. coliattaching and effacing (eae) gene, and random amplified polymorphic DNA–PCR (RAPD–PCR) fingerprinting. The collection represented isolates obtained from patients with diarrhoea-associated haemolytic-uraemic syndrome (D+ HUS) and their family contacts, isolated in the Netherlands, Belgium and Germany between 1989 and 1993. Based on isolates from separate families (n= 27) seven different phage types were identified, types 2 (44%) and 4 (33%) were predominant. Eighty-five percent of the strains contained only VT2 gene sequences and 15% both VT1 and VT2. All strains of the dominant phage types 2 and 4 carried the VT2 gene. Strains that belonged to the minor phage types 8, 14, 32 carried both VT1 and VT2 genes, with the exception of two isolates identified as phage types 49 and 54 which contained only VT2 genes. All O157 VTEC strains possessed the chromosomally-locatedeaegene, which indicates its usefulness as virulence marker. RAPD–PCR fingerprinting identified four distinct banding patterns, with one profile found among 79% of the strains. Based on the combined results of all typing methods used in this study, the collection of 50 O157 VTEC strains could be divided into nine distinct groups. Strains isolated from different persons within one family could not be distinguished by any of these methods. The data suggest that O157 VTEC strains are members of one clone that has become widely distributed.

scholarly journals Rep-PCR and RAPD-PCR fingerprinting ofAspergillus terreus

2013 ◽  
Vol 51 (8) ◽  
pp. 876-879 ◽  
Author(s):  
Wolfgang Mutschlechner ◽  
Katharina Grif ◽  
Gerhard Blum ◽  
Cornelia Lass-Flörl
Keyword(s):  
Pcr Fingerprinting ◽  
Rapd Pcr

scholarly journals Macrobrachium amazonicum: an alternative for microbiological monitoring of aquatic environments in Brazil

2014 ◽  
Vol 44 (11) ◽  
pp. 2029-2034 ◽  
Author(s):  
Raimunda Sâmia Nogueira Brilhante ◽  
Manoel de Araújo Neto Paiva ◽  
Célia Maria de Souza Sampaio ◽  
Carlos Eduardo Cordeiro Teixeira ◽  
Joyce Fonteles Ribeiro ◽  
...  
Keyword(s):  
Gastrointestinal Tract ◽  
Surface Water ◽  
Aquatic Environment ◽  
Candida Spp ◽  
Pcr Fingerprinting ◽  
Water And Sediment ◽  
Rapd Pcr ◽  
Molecular Comparison ◽  
Macrobrachium Amazonicum ◽  
M13 Pcr Fingerprinting

This study aimed to evaluate the role of the Amazon River prawn, Macrobrachium amazonicum, as carrier of Candida spp., by analyzing the correlation between Candida spp. from these prawns and their environment (surface water and sediment), through M13-PCR fingerprinting and RAPD-PCR. For this purpose, 27 strains of Candida spp. were evaluated. These strains were recovered from the gastrointestinal tract of adult M. amazonicum (7/27) from Catú Lake, Ceará State, Brazil and from the aquatic environment (surface water and sediment) of this lake (20/27). Molecular comparison between the strains from prawns and the aquatic environment was conducted by M13-PCR fingerprinting and RAPD-PCR, utilizing the primers M13 and OPQ16, respectively. The molecular analysis revealed similarities between the band patterns of eight Candida isolates with the primer M13 and 11 isolates with the primer OPQ16, indicating that the same strains are present in the digestive tract of M. amazonicum and in the aquatic environment where these prawns inhabit. Therefore, these prawns can be used as sentinels for environmental monitoring through the recovery of Candida spp. from the aquatic environment in their gastrointestinal tract

Microevolution between paired antral and paired antrum and corpus Helicobacter pylori isolates recovered from individual patients

2004 ◽  
Vol 53 (7) ◽  
pp. 669-677 ◽  
Author(s):  
Ian M. Carroll ◽  
Niyaz Ahmed ◽  
Sarah M. Beesley ◽  
Aleem A. Khan ◽  
Sheikh Ghousunnissa ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Helicobacter Pylori ◽  
Length Polymorphism ◽  
Fragment Length Polymorphism ◽  
Signal Sequence ◽  
Mixed Infections ◽  
Pcr Fingerprinting ◽  
Sequence Variations ◽  
Rapd Pcr ◽  
Random Amplification

Sequence variations located at the signal sequence and mid-region within the vacA gene, the 3′-end of the cagA gene, the indel motifs at the 3′-end of the cag pathogenicity island and the regions upstream of the vacA and ribA genes were determined by PCR in 19 paired antral or antrum and corpus Helicobacter pylori isolates obtained at the same endoscopic session, and three antral pairs taken sequentially. Random amplification of polymorphic DNA (RAPD)-PCR and fluorescent amplified fragment length polymorphism (FAFLP)-PCR fingerprinting were applied to these paired clinical isolates. The FAFLP-PCR profiles generated were phylogenetically analysed. For the 22 paired isolates there were no differences within pairs at five of the genetic loci studied. However, six pairs of isolates (27 %), of which four were antrum and corpus pairs, showed differences in the numbers of repeats located at the 3′-end of the cagA gene. RAPD-PCR fingerprinting showed that 16 (73 %) pairs, nine of which were antrum and corpus pairs, possessed identical profiles, while six (27 %) displayed distinctly different profiles, indicating mixed infections. Three of the six pairs showing differences at the 3′-end of the cagA gene yielded identical RAPD-PCR fingerprints. FAFLP-PCR fingerprinting and phylogenetic analysis revealed that all 16 pairs that displayed identical RAPD-PCR profiles had highly similar, but not identical, fingerprints, demonstrating that these pairs were ancestrally related but had undergone minor genomic alterations. Two antrum and corpus pairs of isolates, within the latter group, were isolates obtained from two siblings from the same family. This analysis demonstrated that each sibling was colonized by ancestrally related strains that exhibited differences in vacA genotype characteristics.

scholarly journals Evaluation of Two Approaches for Assessing the Genetic Similarity of Virioplankton Populations as Defined by Genome Size

2012 ◽  
Vol 78 (24) ◽  
pp. 8773-8783 ◽  
Author(s):  
Sanchita Jamindar ◽  
Shawn W. Polson ◽  
Sharath Srinivasiah ◽  
Lisa Waidner ◽  
K. Eric Wommack
Keyword(s):  
Genome Size ◽  
Spatial Scales ◽  
Low Cost ◽  
Geographic Location ◽  
Host Interactions ◽  
Pcr Fingerprinting ◽  
Rapd Pcr ◽  
Turn Over ◽  
Viral Host Interactions ◽  
Dna Pcr

ABSTRACTViral production estimates show that virioplankton communities turn over rapidly in aquatic ecosystems. Thus, it is likely that the genetic identity of viral populations comprising the virioplankton also change over temporal and spatial scales, reflecting shifts in viral-host interactions. However, there are few approaches that can provide data on the genotypic identity of viral populations at low cost and with the sample throughput necessary to assess dynamic changes in the virioplankton. This study examined two of these approaches—T4-like major capsid protein (g23) gene polymorphism and randomly amplified polymorphic DNA-PCR (RAPD-PCR) fingerprinting—to ask how well each technique could track differences in virioplankton populations over time and geographic location. Seasonal changes in overall virioplankton composition were apparent from pulsed-field gel electrophoresis (PFGE) analysis. T4-like phages containing similar g23 proteins were found within both small- and large-genome populations, including populations from different geographic locations and times. The surprising occurrence of T4-like g23 within small genomic groups (23 to 64 kb) indicated that the genome size range of T4-like phages may be broader than previously believed. In contrast, RAPD-PCR fingerprinting detected high genotypic similarity within PFGE bands from the same location, time, and genome size class without the requirement for DNA sequencing. Unlike g23 polymorphism, RAPD-PCR fingerprints showed a greater temporal than geographic variation. Thus, while polymorphism in a viral signature gene, such as g23, can be a powerful tool for inferring evolutionary relationships, the degree to which this approach can capture fine-scale variability within virioplankton populations is less clear.

scholarly journals Microevolution in the sicilian shrewcrocidura sicula(Mammalia, Soricidae) tested by RAPD‐PCR fingerprinting

1997 ◽  
Vol 64 (1) ◽  
pp. 41-48
Author(s):  
Maurizio Sarà ◽  
Cinzia Aiuto ◽  
Goffredo Cognetti
Keyword(s):  
Pcr Fingerprinting ◽  
Rapd Pcr

scholarly journals The ProbioticBifidobacterium breveB632 Inhibited the Growth ofEnterobacteriaceaewithin Colicky Infant Microbiota Cultures

2014 ◽  
Vol 2014 ◽  
pp. 1-7 ◽  
Author(s):  
Marta Simone ◽  
Caterina Gozzoli ◽  
Andrea Quartieri ◽  
Giuseppe Mazzola ◽  
Diana Di Gioia ◽  
...  
Keyword(s):  
Steady State ◽  
Gut Microbiota ◽  
Probiotic Strain ◽  
Gastrointestinal Disorder ◽  
Continuous Cultures ◽  
Bifidobacterium Breve ◽  
Pcr Fingerprinting ◽  
Rapd Pcr ◽  
Infant Colic

Infant colic is a common gastrointestinal disorder of newborns, mostly related to imbalances in the composition of gut microbiota and particularly to the presence of gas-producing coliforms and to lower levels of Bifidobacteria and Lactobacilli. Probiotics could help to contain this disturbance, with formulations consisting ofLactobacillusstrains being the most utilized. In this work, the probiotic strainBifidobacterium breveB632 that was specifically selected for its ability to inhibit gas-producing coliforms, was challenged against theEnterobacteriaceaewithin continuous cultures of microbiota from a 2-month-old colicky infant. As confirmed by RAPD-PCR fingerprinting,B. breveB632 persisted in probiotic-supplemented microbiota cultures, accounting for the 64% of Bifidobacteria at the steady state. The probiotic succeeded in inhibiting coliforms, since FISH and qPCR revealed that the amount ofEnterobacteriaceaeafter 18 h of cultivation was 0.42 and 0.44 magnitude orders lower(P<0.05)in probiotic-supplemented microbiota cultures than in the control ones. These results support the possibility to move to another level of study, that is, the administration ofB. breveB632 to a cohort of colicky newborns, in order to observe the behavior of this strainin vivoand to validate its effect in colic treatment.

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