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

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.

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Identification of Pneumococcal Serotypes by PCR–Restriction Fragment Length Polymorphism

Diagnostics ◽

10.3390/diagnostics9040196 ◽

2019 ◽

Vol 9 (4) ◽

pp. 196 ◽

Cited By ~ 1

Author(s):

García-Suárez ◽

González-Rodríguez ◽

Cima-Cabal ◽

Yuste ◽

Vazquez ◽

...

Keyword(s):

Restriction Fragment Length Polymorphism ◽

Restriction Fragment ◽

Length Polymorphism ◽

Dna Sequences ◽

Fragment Length ◽

Fragment Length Polymorphism ◽

Rflp Analysis ◽

Restriction Enzymes ◽

Pcr Rflp ◽

Restriction Fragment Length

Streptococcus pneumoniae shows more than 90 capsular serotypes that can be distinguished by their reactivity against antisera. The main objective of this work was the development of a molecular method for serotyping without the use of antisera. A computer program containing an algorithm was used to search in a database for potentially useful enzymes for Restriction Fragment Length Polymorphism-RFLP typing, in order to maximize the discrimination between different serotypes. DNA sequences of 90 serotypes for the region between dexB and aliA genes were compiled, and a computer screening of restriction enzymes was performed. The wzg–wzh–wzd–wze region and Sse9I restriction predicted unique PCR-RFLP patterns for 39 serotypes and eight serogroups. A second restriction enzyme resolved fragment specific patterns for 25 serotypes. The method was tested with 98 serotype-unknown clinical isolates. PCR-RFLP analysis deduced correct serotypes that were confirmed by Quellung reaction for 78.5% of the isolates.

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Phylogenetic relationships of the pigeonpea (Cajanus cajan) based on nuclear restriction fragment length polymorphisms

Genome ◽

10.1139/g93-030 ◽

1993 ◽

Vol 36 (2) ◽

pp. 216-223 ◽

Cited By ~ 37

Author(s):

Ram G. Nadimpalli ◽

R. L. Jarret ◽

Sharad C. Phatak ◽

Gary Kochert

Keyword(s):

Restriction Fragment ◽

Fragment Length ◽

Phylogenetic Relationships ◽

Seed Protein ◽

Restriction Enzymes ◽

Restriction Fragment Length Polymorphisms ◽

Length Polymorphisms ◽

Genomic Probes ◽

Clustering Patterns ◽

Restriction Fragment Length

Nuclear restriction fragment length polymorphisms (RFLPs) were used to determine phylogenetic relationships in the genus Cajanus using 15 random genomic probes and six restriction enzymes. Twenty-four accessions representing 12 species of four genera (Cajanus, Dunbaria, Eriosema, and Rhynchosia) were examined to determine phylogenetic relationships in the genus Cajanus. Eriosema parviflorum was selected as the out-group. Sufficient RFLP polymorphisms were detected among species to resolve in-group taxa into distinct clusters. Topologies of trees from parsimony and similarity matrix analyses were similar but not identical, and clustering patterns agreed broadly with published phylogenies based on seed protein data and, to a lesser extent, data from cytology and breeding experiments. Accessions of cultivated C. cajan shared more DNA fragments with C. scarabaeoides than with C. cajanifolia. Inconsistencies in taxonomic relationships based on data from morphology, cytology, crossability, and RFLPs are discussed.Key words: pigeonpea, systematics, taxonomy, evolution, germplasm.

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Directed terminal restriction analysis tool (DRAT): an aid to enzyme selection for directed terminal-restriction fragment length polymorphisms

Methods in Ecology and Evolution ◽

10.1111/j.2041-210x.2011.00139.x ◽

2011 ◽

Vol 3 (1) ◽

pp. 24-28 ◽

Cited By ~ 4

Author(s):

David M. Roberts ◽

Pietà G. Schofield ◽

Suzanne Donn ◽

Tim J. Daniell

Keyword(s):

Restriction Fragment ◽

Fragment Length ◽

Restriction Analysis ◽

Restriction Fragment Length Polymorphisms ◽

Analysis Tool ◽

Length Polymorphisms ◽

Selection For ◽

Restriction Fragment Length

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Restriction Fragment Length Polymorphism Analysis Using Random Chromosomal Gene Probes for Epidemiological Analysis ofCampylobacter jejuni Infections

Journal of Clinical Microbiology ◽

10.1128/jcm.38.4.1664-1667.2000 ◽

2000 ◽

Vol 38 (4) ◽

pp. 1664-1667 ◽

Cited By ~ 1

Author(s):

Shuji Fujimoto ◽

Kenichi Umene ◽

Mitsumasa Saito ◽

Kazumi Horikawa ◽

Martin J. Blaser

Keyword(s):

Restriction Fragment ◽

Fragment Length ◽

Restriction Enzymes ◽

Polymorphism Analysis ◽

Chromosomal Gene ◽

Epidemiological Analysis ◽

Gene Probes ◽

Length Polymorphisms ◽

Ofcampylobacter Jejuni ◽

Restriction Fragment Length

We have evaluated the ability of a new genotyping method forCampylobacter jejuni based on restriction fragment length polymorphisms using random chromosomal gene probes. DNAs from C. jejuni strains digested with each of three restriction enzymes,HhaI, HaeIII, and HpaII, were analyzed by Southern hybridization using each of two unrelated cosmid clones, P14 and P15 (respectively containing 30- and 35-kb genomic DNA fragments of C. jejuni strain OH4384). The method reported provides a stable and discriminating means for identifying C. jejuni strains and should be useful for epidemiological analyses.

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Molecular cloning of a bovine ornithine decarboxylase cDNA and its use in the detection of restriction fragment length polymorphisms in Holsteins

Genome ◽

10.1139/g95-041 ◽

1995 ◽

Vol 38 (2) ◽

pp. 325-331 ◽

Cited By ~ 12

Author(s):

Jianbo Yao ◽

David Zadworny ◽

Urs Kühnlein ◽

J. Flan Hayes

Keyword(s):

Ornithine Decarboxylase ◽

Restriction Fragment ◽

Fragment Length ◽

Molecular Size ◽

Restriction Enzymes ◽

Bovine Liver ◽

Single Species ◽

Restriction Fragment Length Polymorphisms ◽

Length Polymorphisms ◽

Restriction Fragment Length

A cDNA coding for ornithine decarboxylase (ODC) was isolated from a bovine liver cDNA library. The clone (1758 base pairs) consisted of 5′- and 3′-untranslated regions of 185 and 187 nucleotides, respectively, and an open reading frame of 1383 nucleotides encoding an ODC protein (Mr 51 342 daltons) of 461 amino acids. Comparison of the nucleotide and the predicted amino acid of the cDNA with other mammalian ODCs showed a very high degree of homology both at the DNA and protein levels. The bovine ODC mRNA was identified by northern blot to be a single species with a molecular size of 2.35 kilobase pairs. Primer extension analysis indicated that the 5′-untranslated region of the bovine ODC mRNA was 312 nucleotides long. Southern blot analysis of bovine genomic DNA revealed restriction fragment length polymorphisms when cleaved with restriction enzymes PstI, MspI, TaqI, and BglI.Key words: bovine, ornithine decarboxylase, cloning, restriction fragment length polymorphism.

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Restriction Fragment Length Polymorphisms in Chloroplast DNA From Six Species of Eucalyptus

Australian Journal of Botany ◽

10.1071/bt9910399 ◽

1991 ◽

Vol 39 (5) ◽

pp. 399 ◽

Cited By ~ 9

Author(s):

DA Steane ◽

AK West ◽

BM Potts ◽

JR Ovenden ◽

JB Reid

Keyword(s):

Chloroplast Dna ◽

Chloroplast Genome ◽

Restriction Fragment ◽

Fragment Length ◽

Restriction Enzymes ◽

Restriction Fragment Length Polymorphisms ◽

Taxonomic Distance ◽

Length Polymorphisms ◽

Well Differentiated ◽

Restriction Fragment Length

Chloroplast DNA was extracted from six species of Eucalyptus (E. perriniana, E. nitens, E. ovata, E. regnans, E. amygdalina and E. risdonii). Digests with four restriction enzymes (Hind III, Xho I, Nco I and Eco RV) revealed restriction fragment length polymorphisms (RFLPs) between subgenera, between species and within species. However, no variation in fragment pattern was detected with Sac II or Pst I. The subgenera Monocalyptus and Symphyomyrtus were clearly differentiated by their RFLP patterns where, with the exception of one outlying specimen of E. amygdalina, 45% of all polymorphic fragments were specific to one or other subgenus. While species from different subgenera and series were well differentiated, it was more difficult to differentiate species within series with the low sample sizes used. However, the average net divergence between species increased with increasing taxonomic distance between species, from 0.02% within series and 0.20% between species from different series within subgenera, to 0.99% of nucleotides per nucleotide site for species from different subgenera. Based on Eco RV digests, the eucalypt chloroplast genome was estimated at 143 kb.

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Differentiation of porcine reproductive and respiratory syndrome virus European vaccine strains from Czech field isolates by restriction fragment length polymorphism analysis of ORF5 gene

Veterinární Medicína ◽

10.17221/5838-vetmed ◽

2012 ◽

Vol 47 (No. 10 - 11) ◽

pp. 295-301 ◽

Cited By ~ 2

Author(s):

S. Indik ◽

L. Valíček

Keyword(s):

Restriction Fragment Length Polymorphism ◽

Restriction Fragment ◽

Length Polymorphism ◽

Fragment Length ◽

Fragment Length Polymorphism ◽

Rflp Analysis ◽

Restriction Enzymes ◽

Respiratory Syndrome Virus ◽

Field Isolates ◽

Restriction Fragment Length

Restriction fragment length polymorphism (RFLP) analysis of open reading frame 5 was developed for typing of Czech strains of porcine reproductive and respiratory syndrome virus (PRRSV). The set of restriction enzymes Acc I, Hae II and SnaB I allowed the differentiation of heterogeneous Czech strains of PRRSV clustered separately in the phylogenetic tree. The high-passage strain V-502 (164) was also differentiated from its parent strain V-502. The same restriction enzymes could distinguish the European-type vaccine strains Porcilis PRRS and Pyrsvac-183, registered inCzechRepublic, from the Czech field isolates. The published ORF5 nucleotide sequences allowed us to presume that it will also be possible to distinguish most of European field strains from vaccine strains. PCR-based RFLP analysis can become a valuable tool in epidemiological studies of PRRSV inEurope.

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A survey of restriction fragment length polymorphisms in tall fescue and its relatives

Genome ◽

10.1139/g91-106 ◽

1991 ◽

Vol 34 (5) ◽

pp. 686-692 ◽

Cited By ~ 31

Author(s):

W. W. Xu ◽

David A. Sleper ◽

David A. Hoisington

Keyword(s):

Restriction Fragment ◽

Tall Fescue ◽

Fragment Length ◽

Festuca Arundinacea ◽

Genomic Library ◽

Restriction Enzymes ◽

Single Copy ◽

Restriction Fragment Length Polymorphisms ◽

Length Polymorphisms ◽

Restriction Fragment Length

Restriction fragment length polymorphisms (RFLPs) have several advantages over conventional genetic markers and as a result have received increased attention from plant breeders and geneticists. The objective of this study was to construct a tall fescue (Festuca arundinacea Schreb.) genomic library and to survey RFLPs in tall fescue and its relatives. Using plasmid pUC19 as a vector and Escherichia coli XL1-Blue cells as hosts, the first reported PstI genomic DNA library has been established from hexaploid (2n = 6x = 42) tall fescue. The genomic clones were evaluated using nine genotypes from three species of Festuca and three restriction enzymes (BamHI, EcoRI, and HindIII). One hundred and seventy-four probes gave readable results, of which 21% were repetitive and 79% single-copy. The single-copy probes revealed good polymorphism in tall fescue. Approximately 21% of the probes did not cross hybridize to any of the diploids or tetraploids or both and, therefore, represented genome-specific clones.Key words: tall fescue, genome-specific probes, genomic library, polyploids, genomic relationships

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