scholarly journals Genetic Heterogeneity ofAlicyclobacillusStrains Revealed by RFLP Analysis ofvdcRegion andrpoBGene

2018 ◽  
Vol 2018 ◽  
pp. 1-12 ◽  
Author(s):  
Agnieszka Dekowska ◽  
Jolanta Niezgoda ◽  
Barbara Sokołowska
Keyword(s):  
Cluster Analysis ◽  
16S Rdna ◽  
Genetic Heterogeneity ◽  
Reference Strain ◽  
Rflp Analysis ◽  
The Other ◽  
16S Rdna Gene ◽  
Restriction Patterns ◽  
Pcr Rflp ◽  
Reference Strains

PCR-RFLP targeting of the 16S rDNA andrpoBgenes, as well as thevdcregion, was applied to identify and differentiate between the spoilage and non-spoilageAlicyclobacillusspecies. Eight reference strains and 75 strains isolated from spoiled juices, juice concentrates, drinks, its intermediates, and fresh apples were subject to study. Hin6I restriction patterns of the 16S rDNA gene enabled distinguishing between all the species analyzed, while therpoBgene andvdcgene cluster analysis also revealed that there were two major types among theA. acidoterrestrisisolates, one similar to the reference strainA. acidoterrestrisDSM 2498, and the other similar to the reference strainA. acidoterrestrisATCC 49025. Heterogeneity was also observed among theA. acidocaldariusisolates. RFLP analysis of the 16S rDNA andrpoBgenes, as well asvdcregion, can be used successfully in the identification and research of intraspecies heterogeneity of theAlicyclobacillusspecies.

scholarly journals Usefulness of ribotyping in a molecular epidemiology study of shigellosis

1996 ◽  
Vol 116 (2) ◽  
pp. 127-135 ◽  
Author(s):  
M. C. Mendoza ◽  
M. C. Martín ◽  
M. A. González-Hevia
Keyword(s):  
Molecular Epidemiology ◽  
Genetic Heterogeneity ◽  
Reference Strain ◽  
Shigella Sonnei ◽  
The Other ◽  
Epidemiology Study ◽  
Sporadic Cases ◽  
Clonal Lines ◽  
Reference Strains ◽  
Discriminatory Index

SUMMARYRibotyping performed with six restriction endonucleases was used to study the molecular epidemiology of shigellosis in Asturias, Spain. The series includedShigella sonneifrom 34 sporadic cases, 3 outbreaks and 3 reference strains, andS. flexnerifrom 13 sporadic cases and 1 reference strain. TheS. sonneistrains were grouped into 5 ribotypes withSalI, 4 withHindIII andPvuII, 3 withBglII andEcoR I and 2 withHincII (Discriminatory Index (DI) between 0·54 and 0·14); theS. flexneriinto 5 ribotypes withSalI, Hinc II andHindIII, and 4 with the other enzymes (DI = 0·71–0·63). The combination of results for 2 or more enzymes facilitated an additional discrimination, the highest values inS. sonneiwere for the 6 enzymes (16 types, DI = 0·91) and inS. flexnerifor some combinations of 3 or more enzymes (7 types, DI = 0·81). Ribotypes with the 6 enzymes defined 16 clonal lines inS. sonneiand 7 inS. flexneri, which showed a different degree of genetic heterogeneity, and all the lines of each species falling into a different cluster. No line appeared as clearly endemic in the bowels of Asturian people.

scholarly journals Characterisation of avian Pasteurella multocida strains with PCR-RFLP analysis of the ompH gene

2013 ◽  
Vol 61 (1) ◽  
pp. 1-8 ◽  
Author(s):  
Boglárka Sellyei ◽  
Éva Ivanics ◽  
Tibor Magyar
Keyword(s):  
Restriction Fragment Length Polymorphism ◽  
Pasteurella Multocida ◽  
Fragment Length Polymorphism ◽  
Rflp Analysis ◽  
The Other ◽  
Pcr Rflp ◽  
H Gene ◽  
Geographic Regions ◽  
Type Strains ◽  
Restriction Fragment Length

The 16 somatic serotype type strains and 60 field isolates of Pasteurella multocida, representing various avian species and geographic regions in Hungary, were characterised by PCR-restriction fragment length polymorphism (PCR-RFLP) analysis of the ompH gene with DraI restriction endonuclease. The type strains yielded eight different (I-VIII) profiles. Strains whose PCR fragment was uncut by DraI (profile IV) could be differentiated with HindIII and PvuII restriction endonucleases. Five of the eight PCR-RFLP profiles (I, III, V, VI and VII) were detected among the field strains. Only a correlation of limited strength was found between the classical somatic serotypes and the PCR-RFLP profiles. However, the results confirmed that molecular methods could confidently distinguish serotype A:1 strains from the other serotypes. Moreover, the specific relationship between somatic serotypes and PCR-RFLP types among isolates from turkey raises the possibility of the existence of host-specific clones within the P. multocida population.

scholarly journals 16S rDNA Genotyping of Lactic Acid Bacteria Using PCR-RFLP Analysis

2017 ◽  
Vol 64 (7) ◽  
pp. 355-364
Author(s):  
Hideyuki Tamakawa ◽  
Yoshihito Ito
Keyword(s):  
Lactic Acid ◽  
Lactic Acid Bacteria ◽  
16S Rdna ◽  
Rflp Analysis ◽  
Pcr Rflp

A rapid method for identification of typical Leuconostoc species by 16S rDNA PCR-RFLP analysis

2003 ◽  
Vol 55 (1) ◽  
pp. 295-302 ◽  
Author(s):  
Jichan Jang ◽  
Bongjoon Kim ◽  
Jongho Lee ◽  
Hongui Han
Keyword(s):  
16S Rdna ◽  
Rapid Method ◽  
Rflp Analysis ◽  
16S Rdna Pcr ◽  
Pcr Rflp

scholarly journals Molecular characterization of stolbur phytoplasmas in pepper and tomato from Bulgaria

2020 ◽  
Vol 18 ◽  
pp. 00025
Author(s):  
Dimitriyka Sakalieva
Keyword(s):  
Molecular Characterization ◽  
Reference Strain ◽  
Rflp Analysis ◽  
Plant Diseases ◽  
Vegetable Crops ◽  
Disease Symptoms ◽  
Natural Plant ◽  
Conserved Genes ◽  
Reference Strains

Tomato and pepper are the main vegetable crops cultivated in Bulgaria. Phytoplasma diseases, mainly stolbur, are important plant diseases for these crops in Bulgaria. The goal of the present paper was to verify association of phytoplasmas with the observed disease symptoms in tomato and pepper and to identify the phytoplasmas detected using RFLP analysis of conserved genes and other uncharacterised phytoplasma chromosomal regions. The presence of phytoplasmas was confirmed in all the samples of tomato and pepper showing typical stolbur symptoms. A phytoplasm sample, which caused severe symptoms, showed the same pattern as the reference strain Mol, while all other phytoplasmic reference strains showed different polymorphisms. RFLP profiles were found useful in distinguishing phytoplasmas in stolbur subgroup (16SrXII-A) in natural plant hosts.

scholarly journals Phenotypic and genotypic characterization of Xanthomonas campestris strains isolated from cabbage, kale and broccoli

2013 ◽  
Vol 65 (2) ◽  
pp. 585-593 ◽  
Author(s):  
Tatjana Popovic ◽  
Dragana Josic ◽  
Mira Starovic ◽  
P. Milovanovic ◽  
N. Dolovac ◽  
...  
Keyword(s):  
16S Rdna ◽  
Xanthomonas Campestris ◽  
Reference Strain ◽  
Tween 80 ◽  
Genotypic Characterization ◽  
Hypodermic Syringe ◽  
Xanthomonas Campestris Pv Campestris ◽  
Reference Strains ◽  
Phenotypic And Genotypic Characterization

Thirty-six strains of Xanthomonas campestris pv. campestris (Xcc) isolated from cabbage, kale and broccoli were identified according to their pathogenicity, phenotypic and genotypic characterization. Pathogenicity was confirmed by the injection method with a hypodermic syringe into the mesophilic tissue of cabbage leaves. All strains were Gramnegative, aerobic, catalase-positive, oxidase-negative, grew at 35?C, produced levan, H2S and indole, did not reduce nitrate, hydrolyzed Tween 80, starch, gelatin and esculin and did not show tolerance to 0.1 and 0.02% TTC. The strains produced acid from d-arabinose, arginine, dulcitol, galactose, d-glucose, maltose, mannose, sorbitol, sucrose and xylose. The genetic characterization was based on the sequence analyses of 16S rDNA and ERIC and BOX PCR. Strains of different pathovars were also used to compare PCR resulting patterns. BOX-PCR of the strains from kale and broccoli, obtained using (GTG)5 primer, yielded patterns with a high similarity level to pathovar reference strain Xcc. The strains from cabbage yielded BOX and ERIC product patterns, distinguishing them from the other tested strains and reference strains. 16S rDNA of the representative strains was closely related to Xcc strain ATCC 33913. ERIC PCR and BOX using (GTG)5 primer generated different Xcc patterns and were effective in distinguishing strains from different plant hosts.

scholarly journals Estrus Behaviour and Reproductive Traits of Pulawska Gilts Associated with Selected Gene Polymorphisms

2021 ◽  
Vol 21 (1) ◽  
pp. 159-172
Author(s):  
Marek Babicz ◽  
Marcin Pastwa ◽  
Magdalena Szyndler-Nędza ◽  
Anna Kozubska-Sobocińska ◽  
Barbara Danielak-Czech ◽  
...  
Keyword(s):  
Genetic Structure ◽  
Gene Polymorphisms ◽  
Rflp Analysis ◽  
Reproductive Traits ◽  
The Other ◽  
Molecular Analyses ◽  
Native Breed ◽  
Hair Roots ◽  
Pcr Rflp ◽  
Pcr Conditions

Abstract Searching for the associations between the gene polymorphism and the reproductive traits is essential in defining the genetic native breed specificity, which distinguishes them from the other breeds. The aim of our study was to determine the associations between mutations in the PRL, PRLR, PTGS2, FUT1 genes and sexual and periparturient activity in native Pulawska gilts. The analysis included 72 animals which gave birth to the first litter. Evaluation of the productive value of gilts accounted for indicators of sexual and periparturient activity as well as reproductive traits. The biological material for molecular analyses was obtained from the hair roots of the gilts. The genotype was verified by PCR RFLP analysis. The primers and PCR conditions were determined on the basis of available literature data. Statistically significant differences (P≤0.05) were found at the PRL locus: gilts of AA genotypes (Ins/Ins) at the PRL locus were characterised by longest farrowing duration compared to gilts of AB genotype (P≤0.05). The analysis of PRLR gene showed that gilts of TT genotype revealed a tendency for later occurrence of estrus signs (first and second estrus) and for the markedly longest farrowings (P≤0.05). With regard to PTGS2 and FUT1 loci, no significant differences were found in the parameters of sexual and periparturient activity of the gilts. However, gilts of FUT1 GG genotype gave birth to and reared the largest first litters (P≤0.05). The results of the studies expand the knowledge about the genetic structure and productivity of Pulawska gilts.

scholarly journals Genotypic Characterization ofBradyrhizobium Strains Nodulating Endemic Woody Legumes of the Canary Islands by PCR-Restriction Fragment Length Polymorphism Analysis of Genes Encoding 16S rRNA (16S rDNA) and 16S-23S rDNA Intergenic Spacers, Repetitive Extragenic Palindromic PCR Genomic Fingerprinting, and Partial 16S rDNA Sequencing

1998 ◽  
Vol 64 (6) ◽  
pp. 2096-2104 ◽  
Author(s):  
Pablo Vinuesa ◽  
Jan L. W. Rademaker ◽  
Frans J. de Bruijn ◽  
Dietrich Werner
Keyword(s):  
Cluster Analysis ◽  
16S Rrna ◽  
16S Rdna ◽  
Canary Islands ◽  
Computer Assisted ◽  
Woody Legumes ◽  
Repetitive Extragenic Palindromic Pcr ◽  
Reference Strains ◽  
Restriction Fragment Length ◽  
Repetitive Extragenic Palindromic

ABSTRACT We present a phylogenetic analysis of nine strains of symbiotic nitrogen-fixing bacteria isolated from nodules of tagasaste (Chamaecytisus proliferus) and other endemic woody legumes of the Canary Islands, Spain. These and several reference strains were characterized genotypically at different levels of taxonomic resolution by computer-assisted analysis of 16S ribosomal DNA (rDNA) PCR-restriction fragment length polymorphisms (PCR-RFLPs), 16S-23S rDNA intergenic spacer (IGS) RFLPs, and repetitive extragenic palindromic PCR (rep-PCR) genomic fingerprints with BOX, ERIC, and REP primers. Cluster analysis of 16S rDNA restriction patterns with four tetrameric endonucleases grouped the Canarian isolates with the two reference strains, Bradyrhizobium japonicum USDA 110spc4 and Bradyrhizobium sp. strain (Centrosema) CIAT 3101, resolving three genotypes within these bradyrhizobia. In the analysis of IGS RFLPs with three enzymes, six groups were found, whereas rep-PCR fingerprinting revealed an even greater genotypic diversity, with only two of the Canarian strains having similar fingerprints. Furthermore, we show that IGS RFLPs and even very dissimilar rep-PCR fingerprints can be clustered into phylogenetically sound groupings by combining them with 16S rDNA RFLPs in computer-assisted cluster analysis of electrophoretic patterns. The DNA sequence analysis of a highly variable 264-bp segment of the 16S rRNA genes of these strains was found to be consistent with the fingerprint-based classification. Three different DNA sequences were obtained, one of which was not previously described, and all belonged to the B. japonicum/Rhodopseudomonas rDNA cluster. Nodulation assays revealed that none of the Canarian isolates nodulatedGlycine max or Leucaena leucocephala, but all nodulated Acacia pendula, C. proliferus,Macroptilium atropurpureum, and Vigna unguiculata.

scholarly journals Abiotrophia elegans Strains Comprise 8% of the Nutritionally Variant Streptococci Isolated from the Human Mouth

1999 ◽  
Vol 37 (8) ◽  
pp. 2553-2556 ◽  
Author(s):  
Setsuko Sato ◽  
Taisei Kanamoto ◽  
Masakazu Inoue
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Rflp Analysis ◽  
The Other ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Biochemical Tests ◽  
Pcr Rflp ◽  
Adh Activity

Ninety-one isolates of nutritionally variant streptococci (NVS) that were previously isolated from the human mouth were regarded as consisting of 7 Streptococcus defectivus isolates, 78Streptococcus adjacens isolates, and 6 Gemella morbillorum isolates. However, recent references to the taxonomic reclassification of NVS, from S. defectivusto Abiotrophia defectiva and from S. adjacensto Abiotrophia adiacens, and the newly introduced speciesAbiotrophia elegans as a third Abiotrophiaspecies, emphasize the need for genetic analyses for identification of NVS. When PCR-restriction fragment length polymorphism (RFLP) and phylogenetic distances were examined based on 16S rRNA gene sequences, the results indicated that 7 of the 91 NVS isolates were closely related to A. elegans. These seven isolates consisted of four isolates previously identified as G. morbillorum and three isolates previously identified as S. adjacens. Two isolates previously identified as G. morbillorum were related to A. adiacens. In biochemical tests, A. elegans and the seven isolates related to it possessed arginine dihydrolase (ADH) activity but the other Abiotrophia species did not. As a result, A. elegans strains comprised 8% of the 91 NVS isolates. Our findings suggest that A. elegans, A. adiacens, and A. defectiva exist in the human mouth in proportions of about 1:11:1 and that A. elegans can be genetically distinguished from the other twoAbiotrophia species by PCR-RFLP analysis of 16S rRNA gene sequences and can be biochemically distinguished by ADH activity.

scholarly journals Proposal to accommodate Burkholderia cepacia genomovar VI as Burkholderia dolosa sp. nov.

2004 ◽  
Vol 54 (3) ◽  
pp. 689-691 ◽  
Author(s):  
Karen Vermis ◽  
Tom Coenye ◽  
John J. LiPuma ◽  
Eshwar Mahenthiralingam ◽  
Hans J. Nelis ◽  
...  
Keyword(s):  
16S Rdna ◽  
Burkholderia Cepacia ◽  
Type Strain ◽  
Rflp Analysis ◽  
Selective Medium ◽  
Complex Species ◽  
Burkholderia Multivorans ◽  
Restriction Patterns ◽  
Specific Identification ◽  
Pcr Assays

Phenotypic and genotypic studies revealed new tools for differentiating Burkholderia cepacia genomovar VI from Burkholderia multivorans and other B. cepacia-complex species. Hence, the name Burkholderia dolosa sp. nov. is proposed, with LMG 18943T (=CCUG 47727T) as the type strain. B. dolosa can be differentiated from other B. cepacia-complex bacteria by its inability to assimilate tryptamine, azelaic acid and salicin and by its failure to grow on the B. cepacia-selective medium PCAT. Both 16S rDNA and recA RFLP analysis revealed unique B. dolosa restriction patterns. In addition, new 16S rDNA- and recA-based PCR assays allowed its specific identification.

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