Characterization ofFusarium verticillioides strains by PCR-RFLP analysis of the intergenic spacer region of the rDNA

2005 ◽  
Vol 86 (3) ◽  
pp. 429-435 ◽  
Author(s):  
Belén Patiño ◽  
Salvador Mirete ◽  
Covadonga Vázquez ◽  
Misericordia Jiménez ◽  
M Teresa Rodríguez ◽  
...  
Keyword(s):  
Intergenic Spacer ◽  
Rflp Analysis ◽  
Intergenic Spacer Region ◽  
Pcr Rflp

Characterization of Fusarium spp. isolates by PCR-RFLP analysis of the intergenic spacer region of the rRNA gene (rDNA)

2006 ◽  
Vol 106 (3) ◽  
pp. 297-306 ◽  
Author(s):  
A. Llorens ◽  
M.J. Hinojo ◽  
R. Mateo ◽  
M.T. González-Jaén ◽  
F.M. Valle-Algarra ◽  
...  
Keyword(s):  
Intergenic Spacer ◽  
Rflp Analysis ◽  
Rrna Gene ◽  
Fusarium Spp ◽  
Intergenic Spacer Region ◽  
Pcr Rflp

scholarly journals Isolation of Bartonella species from rodents in Taiwan including a strain closely related to ‘Bartonella rochalimae’ from Rattus norvegicus

2008 ◽  
Vol 57 (12) ◽  
pp. 1496-1501 ◽  
Author(s):  
Jen-Wei Lin ◽  
Chun-Yu Chen ◽  
Wan-Ching Chen ◽  
Bruno B. Chomel ◽  
Chao-Chin Chang
Keyword(s):  
Rattus Norvegicus ◽  
Phylogenetic Analyses ◽  
Intergenic Spacer ◽  
Rflp Analysis ◽  
23S Rrna ◽  
Human Pathogens ◽  
Bartonella Species ◽  
Intergenic Spacer Region ◽  
Pcr Rflp ◽  
Rodent Populations

An increasing number of Bartonella species originally isolated from small mammals have been identified as emerging human pathogens. During an investigation of Bartonella infection in rodent populations carried out in Taiwan in 2006, a total of 58 rodents were tested. It was determined that 10.3 % (6/58) of the animals were Bartonella bacteraemic. After PCR/RFLP analysis, four isolates were identified as Bartonella elizabethae and one isolate as Bartonella tribocorum. However, there was one specific isolate with an unrecognized PCR/RFLP pattern. After further sequence and phylogenetic analyses of the gltA, ftsZ and rpoB genes, and the 16S–23S rRNA intergenic spacer region, the results indicated that this specific isolate from Rattus norvegicus was closely related to human pathogenic ‘Bartonella rochalimae’. Further studies need to be conducted to evaluate whether this rodent species could be a reservoir for ‘B. rochalimae’.

scholarly journals Coyotes (Canis latrans) as the Reservoir for a Human Pathogenic Bartonella sp.: Molecular Epidemiology ofBartonella vinsonii subsp. berkhoffii Infection in Coyotes from Central Coastal California

2000 ◽  
Vol 38 (11) ◽  
pp. 4193-4200 ◽  
Author(s):  
Chao-Chin Chang ◽  
Rickie W. Kasten ◽  
Bruno B. Chomel ◽  
Darren C. Simpson ◽  
Carrie M. Hew ◽  
...  
Keyword(s):  
16S Rrna ◽  
Canis Latrans ◽  
Bacterial Genome ◽  
Clinical Signs ◽  
Rflp Analysis ◽  
Domestic Dog ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Intergenic Spacer Region ◽  
Pcr Rflp

Bartonella vinsonii subsp. berkhoffii was originally isolated from a dog suffering infectious endocarditis and was recently identified as a zoonotic agent causing human endocarditis. Following the coyote bite of a child who developed clinical signs compatible with Bartonella infection in Santa Clara County, Calif., this epidemiological study was conducted. Among 109 coyotes (Canis latrans) from central coastal California, 31 animals (28%) were found to be bacteremic with B. vinsonii subsp.berkhoffii and 83 animals (76%) had B. vinsonii subsp. berkhoffii antibodies. These findings suggest these animals could be the wildlife reservoir of B. vinsonii subsp. berkhoffii. PCR-restriction fragment length polymorphism (PCR-RFLP) analysis of the gltA and 16S rRNA genes for these 31 isolates yielded similar profiles that were identical to those of B. vinsonii subsp.berkhoffii. Partial sequencing of the gltA and 16S rRNA genes, respectively, indicated 99.5 and 100% homology between the coyote isolate and B. vinsonii subsp.berkhoffii (ATCC 51672). PCR-RFLP analysis of the 16S-23S intergenic spacer region showed the existence of two different strain profiles, as has been reported in dogs. Six (19%) of 31Bartonella bacteremic coyotes exhibited the strain profile that was identified in the type strain of a canine endocarditis case (B. vinsonii subsp. berkhoffii ATCC 51672). The other 25 bacteremic coyotes were infected with a strain that was similar to the strains isolated from healthy dogs. Based on whole bacterial genome analysis by pulsed-field gel electrophoresis (PFGE) with SmaI restriction endonuclease, there was more diversity in fingerprints for the coyote isolates, which had at least 10 major variants compared to the two variants described for domestic dog isolates from the eastern United States. By PFGE analysis, threeBartonella bacteremic coyotes were infected by a strain identical to the one isolated from three healthy dog carriers. Further studies are necessary to elucidate the mode of transmission of B. vinsonii subsp. berkhoffii, especially to identify potential vectors, and to determine how humans become infected.

scholarly journals Development of a multilocus sequence typing method for analysis of Lactobacillus plantarum strains

Microbiology ◽  
2006 ◽  
Vol 152 (1) ◽  
pp. 85-93 ◽  
Author(s):  
Blanca de las Rivas ◽  
Ángela Marcobal ◽  
Rosario Muñoz
Keyword(s):  
Lactobacillus Plantarum ◽  
Multilocus Sequence Typing ◽  
Population Biology ◽  
Decomposition Analysis ◽  
Intergenic Spacer ◽  
Rflp Analysis ◽  
Culture Collection ◽  
Future Application ◽  
Typing Method ◽  
Intergenic Spacer Region

Lactobacillus plantarum is a species of considerable industrial and medical interest. To date, the lack of reliable molecular methods for definite identification at strain level has hindered studies of the population biology of this organism. Here, a multilocus sequence typing (MLST) system for this organism is described, which exploits the genetic variation present in six housekeeping loci to determine the genetic relationship among isolates. The MLST system was established using 16 L. plantarum strains that were also characterized by ribotyping and restriction fragment length polymorphism (RFLP) analysis of the PCR-amplified 16S–23S rDNA intergenic spacer region (ISR). Ribotyping grouped the strains into four groups; however, RFLP analysis of the ISRs showed no differences in the strains analysed. In contrast, MLST had a good discriminatory ability. The sequence analysis of the six genes showed 14 different allelic combinations, with 12 of them represented by only one strain. By using this MLST approach we were able to confirm the identity of two strains deposited in the Spanish Type Culture Collection as different strains. Phylogenetic analysis indicated a panmictic population structure of L. plantarum and split decomposition analysis indicated that recombination plays a role in creating genetic heterogeneity in L. plantarum. As MLST allows precise identification, and easy comparison and exchange of results obtained in different laboratories, the future application of this new molecular method could be useful for the identification of valuable L. plantarum strains.

scholarly journals First Report of Oat as Host of a Phytoplasma Belonging to Group 16SrI, Subgroup A

Plant Disease ◽  
2002 ◽  
Vol 86 (4) ◽  
pp. 443-443 ◽  
Author(s):  
R. Jomantiene ◽  
R. E. Davis ◽  
A. Alminaite ◽  
D. Valiunas ◽  
R. Jasinskaite
Keyword(s):  
16S Rdna ◽  
Plant Species ◽  
Nested Pcr ◽  
Sequence Similarity ◽  
Intergenic Spacer ◽  
Rflp Analysis ◽  
23S Rrna ◽  
Universal Primer ◽  
Intergenic Spacer Region ◽  
Group I

Diseased plants of oat (Avena sativa L.) exhibiting abnormal proliferation of spikelets were observed in the field in Raseniai, Lithuania. The possible association of a phytoplasma with the disease, termed oat proliferation (OatP), was determined using polymerase chain reaction (PCR) for amplification of phytoplasmal ribosomal (r) RNA gene (rDNA) sequences from template DNA extracted from the diseased oats. DNA extractions and nested PCRs were conducted as previously described (2). In the nested PCRs, the first reaction was primed by phytoplasma-universal primer pair P1/P7, and the second (nested) PCR was primed by primer pair R16F2n/R16R2 (F2n/R2). Phytoplasmal rDNA was amplified in the nested PCR, indicating that the plants contained a phytoplasma, designated oat proliferation (OatP) phytoplasma. The OatP phytoplasma was identified and classified according to the system of Lee et al. (2) through restriction fragment length polymorphism (RFLP) analysis of 16S rDNA amplified in the PCR primed by F2n/R2. On the basis of collective RFLP patterns of the 16S rDNA, the OatP phytoplasma was classified as a member of group 16SrI (group I, aster yellows phytoplasma group). The RFLP patterns of the 16S rDNA were indistinguishable from those of 16S rDNA from tomato big bud (BB) phytoplasma and other phytoplasmas classified in group I, subgroup A (subgroup I-A, tomato big bud phytoplasma subgroup). The 1.8-kbp rDNA product of PCR primed by primer pair P1/P7 was cloned, and its nucleotide sequence was determined. The sequence was deposited in GenBank under Accession No. AF453416. Results from putative restriction site analysis of the cloned and sequenced rDNA were in excellent agreement with the results from enzymatic RFLP analysis of uncloned rDNA from OatP-diseased oat plants. Sequence similarity between the 1.8-kbp rDNA of OatP phytoplasma and that of BB phytoplasma (GenBank No. AF222064) was 99.2%; 9 of the 14 base changes were in the 16S-23S rRNA intergenic spacer region. The base differences in rDNA may signal that the OatP and BB phytoplasmas are mutually distinct in their biologies. Phytoplasmas classified in subgroup I-A have previously been reported in a broad range of plant species in North America and Europe, although there are no previous definitive reports of oat as a host of a subgroup I-A phytoplasma (3,4). In 1977, Fedotina (1) reported electron microscopy of a mycoplasma-like organism (phytoplasma) in pseudorosette-diseased oat plants in Siberia, but the identity of that phytoplasma remains unknown. Subgroup I-A phytoplasma strains are geographically widespread and have been found in numerous plant species (3,4). The discovery reported here, of a subgroup I-A phytoplasma in diseased oats in Lithuania, provokes questions concerning possible impacts of this phytoplasma on oat cultivation in central Europe and other regions. References: (1) V. L. Fedotina. Arch. Phytopathol. Pflanzenschutz 13:177, 1977. (2) I.-M. Lee et al. Int. J. Syst. Bacteriol. 48:1153, 1998. (3) C. Marcone et al. Int. J. Syst. Evol. Microbiol. 50:1703, 2000. (4) D. Valiunas et al. Plant Dis. 85:804, 2001.

scholarly journals Morphological, Pathogenic, and Molecular Characterization of Alternaria Isolates Associated with Alternaria Late Blight of Pistachio

2002 ◽  
Vol 92 (4) ◽  
pp. 406-416 ◽  
Author(s):  
Barry M. Pryor ◽  
Themis J. Michailides
Keyword(s):  
Sequence Data ◽  
Morphological Characteristics ◽  
Intergenic Spacer ◽  
Rflp Analysis ◽  
Species Group ◽  
Molecular Characteristics ◽  
Pcr Rflp ◽  
Species Groups ◽  
Selection Of

Alternaria isolates were obtained from various pistachio tissues collected in five orchards in California. For all isolates, morphological characteristics of the colony and sporulation apparatus were determined and compared with those of representative isolates of A. alternata, A. tenuissima, A. arborescens, and A. infectoria. A selection of the pistachio isolates and the representative Alternaria isolates were evaluated for pathogenicity to pistachio. Molecular characteristics of these isolates were determined using random amplified polymorphism DNA (RAPD) analysis, polymerase chain reaction restriction fragment length polymorphism (PCR-RFLP) analysis of nuclear intergenic spacer rDNA, and sequence analysis of nuclear internal transcribed spacer (ITS) rDNA. Based on morphological characteristics, the pistachio isolates were grouped as identical or very similar to either A. alternata, A. tenuissima, A. arborescens, or A. infectoria. Isolates from the alternata, tenuissima, and arborescens species-groups were pathogenic to pistachio and no significant differences in pathogenicity were observed. Isolates from the infectoria species-group were only weakly pathogenic to pistachio. Based on cluster analysis of RAPD and PCR-RFLP data, three distinct clusters were evident; the infectoria cluster, the arborescens cluster, and a combined alternata/tenuissima cluster. Based on analysis of ITS sequence data, the infectoria species-group was phylogenetically distinct from the other species-groups. Isolates of the alternata, tenuissima, and arborescens species-groups comprised a monophyletic clade in which the three species-groups could not be further resolved.

scholarly journals Molecular Analysis of Vitex Species Using Candidate DNA Barcoding and PCR-RFLP of the matK Gene for Authentication of Vitex glabrata

2013 ◽  
Vol 8 (1) ◽  
pp. 1934578X1300800 ◽  
Author(s):  
Waranyoo Phoolcharoen ◽  
Suchada Sukrong
Keyword(s):  
Folk Medicine ◽  
Intergenic Spacer ◽  
Rflp Analysis ◽  
Size Difference ◽  
Dna Barcodes ◽  
Pcr Rflp ◽  
Matk Gene ◽  
Pcr Products ◽  
The Difference ◽  
Vitex Species

Several species of the Vitex genus, family Lamiaceae, are used in folk medicine for a variety of remedies. V. glabrata is unique among Vitex species because its main effect is sexual enhancement. However, crude drugs derived from different Vitex species might not be easily distinguishable, which could lead to their misidentification and misuse. Therefore, the accurate authentication of V. glabrata is critical for its effective medicinal use. In this study, the mat K gene and the psbA- trnH intergenic spacer candidate DNA barcodes were sequenced and analyzed to identify five different Vitex species that are medicinally used in Thailand: V. negundo, V. trifolia, V. rotundifolia, V. limonifolia, and V. glabrata. Each region was successfully amplified from the leaves of the five species using a single set of primers, and the sequences determined. The size difference in PCR products of psb A- trn H and PCR restriction fragment length polymorphism (PCR-RFLP) of the matK gene sequences were used to differentiate V. glabrata from other Vitex species. These results indicate both the matK gene and the psbA-trnH intergenic spacer as candidate DNA barcodes of Vitex species and suggest that the difference of psbA-trnH PCR products and PCR-RFLP analysis based on the mat K gene are effective for the authentication of V. glabrata.

scholarly journals Corn with Symptoms of Reddening: New Host of Stolbur Phytoplasma

Plant Disease ◽  
2006 ◽  
Vol 90 (10) ◽  
pp. 1313-1319 ◽  
Author(s):  
B. Duduk ◽  
A. Bertaccini
Keyword(s):  
16S Rdna ◽  
Intergenic Spacer ◽  
Rflp Analysis ◽  
Gene Sequences ◽  
New Host ◽  
Intergenic Spacer Region ◽  
New Finding ◽  
Polymerase Chain ◽  
Stolbur Phytoplasma ◽  
Uncertain Etiology

Recurrent epiphytotic outbreaks of a disease of uncertain etiology known as reddening of corn (Zea mays) have occurred in some areas of Serbia during the last 50 years. Affected plants show early and abnormal ripening, dry precociously, and have poor, shriveled grains. Using molecular tools, phytoplasmas were detected in diseased plants and their identity was subsequently deduced as a subgroup 16SrXII-A strain by a variety of supporting assays involving restriction fragment length polymorphism (RFLP) analysis of polymerase chain reaction (PCR)-amplified 16S rDNA and tuf gene sequences, selective amplification of phytoplasma DNA using primer pair G35p/m, similarity of 16-23S intergenic spacer region (SR) sequences, and similarity and phylogenetic analysis of 16S rDNA gene sequences. Presence of stolbur phytoplasmas in corn with reddening symptoms is a new finding not only for Serbia: it is the first report of stolbur phytoplasma in this species worldwide.

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