Relatedness of Strains of Xanthomonas fragariae by Restriction Fragment Length Polymorphism, DNA-DNA Reassociation, and Fatty Acid Analyses

1998 ◽  
Vol 64 (10) ◽  
pp. 3961-3965 ◽  
Author(s):  
P. D. Roberts ◽  
N. C. Hodge ◽  
H. Bouzar ◽  
J. B. Jones ◽  
R. E. Stall ◽  
...  
Keyword(s):  
Fatty Acid ◽  
Restriction Fragment ◽  
Fragment Length ◽  
Restriction Analysis ◽  
Acid Methyl Ester ◽  
The United States ◽  
Fatty Acid Profiles ◽  
Dna Reassociation ◽  
Xanthomonas Fragariae ◽  
Restriction Fragment Length

ABSTRACT The levels of relatedness of strains of Xanthomonas fragariae collected over several years from locations in Canada and the United States were compared by determining fatty acid methyl ester profiles, restriction fragment length polymorphisms (RFLP) based on pulsed-field gel electrophoresis (PFGE) analysis, and DNA-DNA reassociation values. Based on qualitative and quantitative differences in fatty acid profiles, the strains were divided into nine groups and four groups by the MIDI “10% rule” and unweighted pair analysis, respectively. Restriction analysis of genomic DNA by PFGE with two endonucleases (XbaI and SpeI) revealed four distinct profiles. When a third endonuclease (VspI) was used, one group was divided into three subgroups. The profile of the American Type Culture Collection type strain differed from the profile of every other strain of X. fragariae. Considerable diversity was observed within X. fragariae, although the majority of the strains represented a clonal population. The four groups based on fatty acid profiles were similar to the four groups based on RFLP, but neither method related groups to the geographic origins of the strains. The DNA-DNA reassociation values were high for representative strains, providing evidence that all of the strains belong to the same species.

scholarly journals Computerized Analysis of Restriction Fragment Length Polymorphism Patterns: Comparative Evaluation of Two Commercial Software Packages

1998 ◽  
Vol 36 (5) ◽  
pp. 1318-1323 ◽  
Author(s):  
P. Gerner-Smidt ◽  
L. M. Graves ◽  
Susan Hunter ◽  
B. Swaminathan
Keyword(s):  
Restriction Fragment Length Polymorphism ◽  
Restriction Fragment ◽  
Length Polymorphism ◽  
Fragment Length ◽  
Fragment Length Polymorphism ◽  
Molecular Size ◽  
The United States ◽  
Reference Pattern ◽  
Two Systems ◽  
Restriction Fragment Length

Two computerized restriction fragment length polymorphism pattern analysis systems, the BioImage system and the GelCompar system (Molecular Analyst Fingerprinting Plus in the United States), were compared. The two systems use different approaches to compare patterns from different gels. In GelCompar, a standard reference pattern in one gel is used to normalize subsequent gels containing lanes with the same reference pattern. In BioImage, the molecular sizes of the fragments are calculated from size standards present in each gel. The molecular size estimates obtained with the two systems for 12 restriction fragments of phage λ were between 97 and 101% of their actual sizes, with a standard deviation of less than 1% of the average estimated size for most fragments. At the window sizes used for analysis, the GelCompar system performed somewhat better than BioImage in identifying visually identical patterns generated by electrophoretic separation ofHhaI-restricted DNA of Listeria monocytogenes. Both systems require the user to make critical decisions in the analysis. It is very important to visually verify that the systems are finding all bands in each lane and that no artifacts are being detected; both systems allow manual editing. It is also important to verify results obtained in the pattern matching or clustering portions of the analysis.

scholarly journals Plasmid profiles, restriction fragment length polymorphisms and O-serotypes amongVibrio anguillarumisolates

1996 ◽  
Vol 117 (3) ◽  
pp. 471-478 ◽  
Author(s):  
K. Pedersen ◽  
T. Tiainen ◽  
J. L. Larsen
Keyword(s):  
Restriction Fragment ◽  
Fragment Length ◽  
Restriction Analysis ◽  
Vibrio Anguillarum ◽  
Rflp Analysis ◽  
Restriction Enzymes ◽  
Plasmid Profile ◽  
Length Polymorphisms ◽  
Environmental Bacteria ◽  
Restriction Fragment Length

SummaryA total of 279Vibrio anguillarumstrains were serotyped and examined for plasmid content. Plasmids were subjected to digestion with restriction enzymes. Most strains belonged to serogroup O1 (39%) and O2 (16%). In total 164 strains (53%) carried plasmids. Of the O1 and O2 isolates, 92% and 30%, respectively, carried one or more plasmids. Restriction fragment length polymorphism (RFLP) analysis of plasmid DNA indicated that plasmids belonged to several groups. Each group seemed to be restricted to a single O-serovar. The largest group was the pJM1-like plasmids among most serovar O1 strains. Most of these plasmids were about 67 kb like the pJM1 plasmid, but various derivatives ranged from 26–77 kb. RFLP studies of the 67 kb plasmids revealed 17 different restriction patterns. Some patterns were dominant among European strains whereas others were dominant among North American strains. The results confirmed the applicability of O-serotyping together with plasmid profile and restriction analysis of plasmids for typing ofV. anguillarum. They also indicated that plasmids among strains which belonged to the traditional fish pathogenic serogroups, O1 and O2, showed more homology than did strains from most other serogroups, that were usually non-pathogenic, environmental bacteria.

scholarly journals Identification of Bartonella Species Directly in Clinical Specimens by PCR-Restriction Fragment Length Polymorphism Analysis of a 16S rRNA Gene Fragment

1999 ◽  
Vol 37 (12) ◽  
pp. 4045-4047 ◽  
Author(s):  
Ghassan M. Matar ◽  
Jane E. Koehler ◽  
Georgia Malcolm ◽  
Mary Ann Lambert-Fair ◽  
Jordan Tappero ◽  
...  
Keyword(s):  
Restriction Fragment Length Polymorphism ◽  
Restriction Fragment ◽  
Length Polymorphism ◽  
Fragment Length ◽  
Fragment Length Polymorphism ◽  
Restriction Analysis ◽  
Clinical Samples ◽  
Polymorphism Analysis ◽  
Clinical Specimens ◽  
Restriction Fragment Length

It is now established that two species of Bartonella, namely, Bartonella henselae and B. quintana, cause bacillary angiomatosis in human immunodeficiency virus-infected patients. In addition, B. henselae causes cat scratch disease and B. quintana, B. henselae, andB. elizabethae can cause bacteremia and endocarditis in immunocompetent persons. We have developed a PCR-restriction fragment length polymorphism-based assay for direct detection and identification to species level of Bartonella in clinical specimens. This is accomplished by PCR amplification of Bartonella DNA using primers derived from conserved regions of the gene carrying the 16S ribosomal DNA, followed by restriction analysis usingDdeI and MseI restriction endonucleases. We amplified a Bartonella genus-specific 296-bp fragment from 25 clinical samples obtained from 25 different individuals. Restriction analysis of amplicons showed that identical patterns were seen from digestion of B. henselae and B. quintanaamplicons with DdeI, whereas a different unique pattern was seen by using the same enzyme with B. vinsonii and B. elizabethae. With MseI digestion, B. henselae and B. vinsonii gave nearly identical patterns while B. quintana and B. elizabethaegave a different pattern. By combining the restriction analysis data generated with MseI and DdeI, unique “signature” restriction patterns characteristic for each species were obtained. These patterns were useful in identifying theBartonella species associated with each tissue specimen.

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