Search results for "random amplified polymorphic DNA"
showing 10 items of 62 documents
A genomic study of the inter-ORF distances in Saccharomyces cerevisiae.
2006
The genome of eukaryotic microbes is usually quite compacted. The yeast Saccharomyces cerevisiae is one of the best-known examples. Open reading frames (ORFs) occupy about 75% of the total DNA sequence. The existence of other, non-protein coding genes and other genetic elements leaves very little space for gene promoters and terminators. We have performed an in silico study of inter-ORF distances that shows that there is a minimum distance between two adjacent ORFs that depends on the relative orientation between them. Our analyses suggest that different kinds of promoters and terminators exist with regard to their length and ability to overlap each other. The experimental testing of some p…
Phenotypic and genotypic characterization of a new fish-virulent Vibrio vulnificus serovar that lacks potential to infect humans.
2007
Vibrio vulnificus is a bacterial species that is virulent for humans and fish. Human isolates are classified into biotypes 1 and 3 (BT1 and BT3) and fish isolates into biotype 2 (BT2). However, a few human infections caused by BT2 isolates have been reported worldwide (zoonosis). These BT2 human isolates belong to serovar E (SerE), which is also present in diseased fish. The aim of the present work was to characterize a new BT2 serovar [serovar A (SerA)], which emerged in the European fish-farming industry in 2000, by means of phenotypic, serological and genetic [plasmid profiling, ribotyping and random amplified polymorphic DNA (RAPD)] methodologies. The results confirmed that SerA constit…
Evaluation of a modified single-enzyme amplified fragment length polymorphism (SE-AFLP) technique for subtyping Salmonella enterica serotype Enteriti…
2006
Salmonella enterica subsp. enterica serotype Enteritidis is not readily subtyped beyond the level of phage type (PT). Pulsed field gel electrophoresis (PFGE) is generally acknowledged to be the most discriminating typing method for Salmonella, but only a restricted variety of PFGE types has been described for S. enterica serotype Enteritidis. In the present study, a modification of the SE-AFLP typing method was used to investigate both outbreak and apparently sporadic isolates of S. enterica serotype Enteritidis belonging to different PTs and/or PFGE types. The method proved to be as discriminatory as PFGE when combined with phage typing, and provided subtyping data consistent with epidemio…
In vivo application and dynamics of lactic acid bacteria for the four-season production of Vastedda-like cheese.
2014
article Twelve lactic acid bacteria (LAB), previously selected in vitro (Gaglio et al., 2014), were evaluated in situ for their potential to act as starter cultures for the continuous four-season production of Vastedda-like cheese, made with raw ewes' milk. The strains belonged to Lactobacillus delbrueckii, Lactococcus lactis subsp. cremoris, Leuconostoc mesenteroides subsp. mesenteroides and Streptococcus thermophilus .L AB werefirst inoculated in multiple-strain combinations on the basis of their optimal growth temperatures in three process conditions which differed for milk treatment and medium for strain development: process 1, growth of strains in the optimal synthetic media and pasteu…
Cryopreservation of Digitalis obscura selected genotypes by encapsulation-dehydration
2001
Shoot-tips from several genotypes of the cardenolide-producing perennial shrub Digitalis obscura L. were successfully cryopreserved using the encapsulation-dehydration technique. Precultivation on MS medium containing 0.5 M sucrose, followed by 2.5 h dehydration (final weight 30 %) induced shoot regrowth in 42 % of cryopreserved shoot-tips. Cold-hardening of the in vitro cultures before sucrose treatment dramatically increased shoot recovery up to 86 %. The optimized cryopreservation protocol was then employed using different shoot cultures from five D. obscura genotypes. Responses to cryopreservation depended mainly on the genotype, best results being obtained when shoot tips from HU3 and …
Intraspecific diversity of Lactobacillus curvatus, Lactobacillus plantarum, Lactobacillus sakei, and Leuconostoc mesenteroides associated with vacuum…
2006
The intraspecific diversity of Leuconostoc mesenteroides, Lactobacillus curvatus, Lactobacillus sakei, and Lactobacillus plantarum was analyzed by randomly amplified polymorphic DNA (RAPD) PCR with universal primers M13 and T3. The study included 100 reference strains and 210 isolates recovered from two vacuum-packed Spanish meat products, fiambre de magro adobado and morcilla, previously identified by rDNA-restriction fragment length polymorphism profiles. The RAPD-M13 profiles identified isolates at species level in L. plantarum and L. mesenteroides, while RAPD-T3 provided profiles in L. sakei. The combination of RAPD-M13 and RAPD-T3 fingerprints revealed a total of 17 profiles in L. mese…
HSP70 gene expression in Mytilus galloprovincialis hemocytes is triggered by moderate heat shock and Vibrio anguillarum, but not by V. splendidus or …
2005
Complete sequence of HSP70 cDNA from the mussel, Mytilus galloprovincialis was established before quantifying its expression following moderate heat shock or injection of heat-killed bacteria. HSP70 cDNA is comprised of 2378 bp including one ORF of 654 aa, with a predicted 70 bp 5'-UTR and a 343 bp 3'-UTR (GenBank, 18 Jan 05, AY861684). Alignment identity ranged from 89% for Crassostrea ariakensis to 72% for C. virginica. Curiously, HSP70 gene and cDNA sequences from M. galloprovincialis, deposited later (03 and 27 May), show only 73% identity with the present sequence. Meanwhile, characteristic motifs of the HSP70 family were located in conserved positions. Expression of HSP70 gene was qua…
Genetic relatedness among environmental, clinical, and diseased-eel Vibrio vulnificus isolates from different geographic regions by ribotyping and ra…
1998
ABSTRACT Genetic relationships among 132 strains of Vibrio vulnificus (clinical, environmental, and diseased-eel isolates from different geographic origins, as well as seawater and shellfish isolates from the western Mediterranean coast, including reference strains) were analyzed by random amplified polymorphic DNA (RAPD) PCR. Results were validated by ribotyping. For ribotyping, DNAs were digested with Kpn I and hybridized with an oligonucleotide probe complementary to a highly conserved sequence in the 23S rRNA gene. Random amplification of DNA was performed with M13 and T3 universal primers. The comparison between ribotyping and RAPD PCR revealed an overall agreement regarding the high l…
Pyrosequencing vs. culture-dependent approaches to analyze lactic acid bacteria associated to chicha, a traditional maize-based fermented beverage fr…
2015
The diversity of lactic acid bacteria (LAB) associated with chicha, a traditional maize-based fermented alcoholicbeverage from Northwestern Argentina, was analyzed using culture-dependent and culture-independent approaches.Samples corresponding to 10 production steps were obtained from two local producers at Maimará(chicha M) and Tumbaya (chicha T). Whereas by culture-dependent approach a few number of species(Lactobacillus plantarum and Weissella viridescens in chicha M, and Enterococcus faecium and Leuconostocmesenteroides in chicha T) were identified, a higher quantitative distribution of taxa was found in both beveragesby pyrosequencing. The relative abundance of OTUs was higher in chic…
Characterization of sourdough lactic acid bacteria based on genotypic and cell-wall protein analyses
2003
Abstract Aims: To evaluate the effectiveness of two independent methods in differentiating a large population of lactic acid bacteria (LAB) isolated from wheat flours and sourdoughs and to correlate eventual differences/similarities among strains with their geographical origin and/or process parameters. Methods and Results: One hundred fifty strains belonging to Lactobacillus spp. and Weissella spp., plus eight type strains, one for each species, and two unidentified isolates, were characterized by randomly amplified polymorphic DNA (RAPD) and SDS-PAGE of cell-wall proteins. The RAPD analysis separated the eight type strains but did not always assign all the strains of a species to the same…