Identification of Bartonella strains isolated from wild and domestic ruminants by a single-step PCR analysis of the 16S–23S intergenic spacer region

2004 ◽  
Vol 98 (1) ◽  
pp. 63-69 ◽  
Author(s):  
R. Maillard ◽  
M. Vayssier-Taussat ◽  
C. Bouillin ◽  
C. Gandoin ◽  
L. Halos ◽  
...  
Keyword(s):  
Intergenic Spacer ◽  
Single Step ◽  
Pcr Analysis ◽  
Intergenic Spacer Region ◽  
Domestic Ruminants

scholarly journals Barcoding of ToLCV Resistant Tomato Germplasm in Bangladesh

2020 ◽  
Vol 30 (1) ◽  
pp. 107-117
Author(s):  
Mahbubah Jannat ◽  
Umma Homaira Eva ◽  
RH Sarker ◽  
Mohammad Nurul Islam
Keyword(s):  
Nuclear Genome ◽  
Intergenic Spacer ◽  
Pcr Analysis ◽  
Correct Identification ◽  
Potential Donor ◽  
Breeding Programs ◽  
Intergenic Spacer Region ◽  
Mitochondrial Region ◽  
Successful Amplification ◽  
Modern Breeding

The current study was carried out to confirm the existence of the ToLCV resistant genes (Ty-1 to Ty-5) in the germplasm using molecular markers and to identify at the genomic level following phylogenetic relationships analysis among some local tomato germplasm using DNA barcoding. Most of the tomato germplasm (Ten out of 14) contain the dominant Ty-genes as revealed by PCR analysis. “Barcoding” of the non-coding plastid trnH-psbA intergenic spacer region, three plastidal regions: rbcL, rpoB, rpoC1, spacer region of nuclear genome ITS and a mitochondrial region matK were employed following PCR and sequence analysis of the germplasm. Among all the barcode genes, rpoB, rbcL, trnH-psbA and ITS were leading candidates for successful amplification and used for the identification of the germplasm as S. lycopersicum in multi-locus identification based on their sequences. Neighbor-Joining phylogenetic tree was constructed in which the germplasm were clustered into five main clades. The current study was successful to establish an efficient barcoding protocol for the correct identification of tomatoes and was capable of establishing elite gene source(s) for biotic stress resistance tomato varieties which would serve as potential donor plants in modern breeding programs. Plant Tissue Cult. & Biotech. 30(1): 107-117, 2020 (June)

scholarly journals VARIASI GENETIK Lactobacillus fermentum Beijerink ASAL SAYUR ASIN BERDASARKAN ANALISIS RFLP 16S-23S rDNA ISR, RAPD-PCR DAN ERIC-PCR

2017 ◽  
Vol 16 (2) ◽  
Author(s):  
Sulistiani Sulistiani ◽  
Wibowo Mangunwardoyo ◽  
Abinawanto Abinawanto ◽  
Endang Sukara ◽  
Achmad Dinoto ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Random Amplified Polymorphic Dna ◽  
Intergenic Spacer ◽  
Molecular Techniques ◽  
Lactobacillus Fermentum ◽  
Pcr Analysis ◽  
Intergenic Spacer Region ◽  
Rapd Pcr ◽  
Upgma Cluster Analysis ◽  
Process Combination

Molecular analysis of Lactobacillus fermentum isolates is essential to understand their genetic variation in relations to their roles in sayur asin fermentation process. Combination of three molecular techniques which is restriction fragment length polymorphism (RFLP) of 16S23S rDNA intergenic spacer region (ISR), random amplified polymorphic DNA (RAPD-PCR) and an enterobacterial repetitive intergenic consensus (ERIC-PCR) analysis were performed to discriminate 19 representative isolates of L. fermentum isolated from sayur asin. The result showed that L. fermentum strain D11 is distantly related to other isolates based on RFLP using HhaI restriction enzyme and RAPDPCR analyses. In addition, both of RAPD-PCR and ERIC-PCR successfully determined the genetic variation among L. fermentum strains by exhibiting distinct 4-8 bands (800-2080 bp) and 4-10 bands (280-3050 bp), respectively. A dendogram generated from UPGMA cluster analysis of both RAPD-PCR and ERIC-PCR data showed two distinct genotypic groups exist among L. fermentum isolated from sayur asin in Indonesia.

New PCR-based assay for the identification of Pectobacterium carotovorum causing potato soft rot

Plant Disease ◽  
2021 ◽  
Author(s):  
M. Belén Suárez ◽  
Marta Diego ◽  
F. J. Feria ◽  
M J Martín-Robles ◽  
Sergio Moreno ◽  
...  
Keyword(s):  
Real Time ◽  
Dna Sequences ◽  
Real Time Pcr ◽  
Bacterial Species ◽  
Intergenic Spacer ◽  
Soft Rot ◽  
Pcr Analysis ◽  
Rrna Gene ◽  
Accurate Identification ◽  
Intergenic Spacer Region

Soft rot on potato tuber is a destructive disease caused by pathogenic bacterial species of the genera Pectobacterium and Dickeya. Accurate identification of the causal agent is necessary to ensure adequate disease management, since different species may have distinct levels of aggressiveness and host range. One of the most important potato pathogens is P. carotovorum, a highly heterogeneous species capable of infecting multiple hosts. The complexity of this species, until recently divided into several subspecies, has made it difficult to develop precise diagnostic tests. This study proposes a PCR assay based on the new pair of primers Pcar1F/R to facilitate the identification of potato isolates of P. carotovorum according to the most recent taxonomic description of this species. The new primers were designed on a variable segment of the 16S rRNA gene and the intergenic spacer region (ITS) of available DNA sequences from classical and recently established species in the genus Pectobacterium. The results of the PCR analysis of genomic DNA from 32 Pectobacterium and Dickeya strains confirmed that the Pcar1F/R primers have sufficient nucleotide differences to discriminate between P. carotovorum and other Pectobacterium species associated with damage to potato crops, with the exception of P. versatile, which improves the specificity of the currently available primers. The proposed assay was originally developed as a conventional PCR but was later adapted to the real-time PCR format for application in combination with the existing real-time PCR test for the potato-specific pathogen P. parmentieri. This should be useful for the routine diagnosis of potato soft rot.

scholarly journals Use of 16S-23S rRNA Intergenic Spacer Region PCR and Repetitive Extragenic Palindromic PCR Analyses of Escherichia coli Isolates To Identify Nonpoint Fecal Sources

2003 ◽  
Vol 69 (8) ◽  
pp. 4942-4950 ◽  
Author(s):  
Sylvie Seurinck ◽  
Willy Verstraete ◽  
Steven D. Siciliano
Keyword(s):  
Escherichia Coli ◽  
Natural Waters ◽  
Average Rate ◽  
Intergenic Spacer ◽  
23S Rrna ◽  
Pcr Analysis ◽  
Factors Affecting ◽  
Intergenic Spacer Region ◽  
E Coli ◽  
Repetitive Extragenic Palindromic

ABSTRACT Despite efforts to minimize fecal input into waterways, this kind of pollution continues to be a problem due to an inability to reliably identify nonpoint sources. Our objective was to find candidate source-specific Escherichia coli fingerprints as potential genotypic markers for raw sewage, horses, dogs, gulls, and cows. We evaluated 16S-23S rRNA intergenic spacer region (ISR)-PCR and repetitive extragenic palindromic (rep)-PCR analyses of E. coli isolates as tools to identify nonpoint fecal sources. The BOXA1R primer was used for rep-PCR analysis. A total of 267 E. coli isolates from different fecal sources were typed with both techniques. E. coli was found to be highly diverse. Only two candidate source-specific E. coli fingerprints, one for cow and one for raw sewage, were identified out of 87 ISR fingerprints. Similarly, there was only one candidate source-specific E. coli fingerprint for horse out of 59 BOX fingerprints. Jackknife analysis resulted in an average rate of correct classification (ARCC) of 83% for BOX-PCR analysis and 67% for ISR-PCR analysis for the five source categories of this study. When nonhuman sources were pooled so that each isolate was classified as animal or human derived (raw sewage), ARCCs of 82% for BOX-PCR analysis and 72% for ISR-PCR analysis were obtained. Critical factors affecting the utility of these methods, namely sample size and fingerprint stability, were also assessed. Chao1 estimation showed that generally 32 isolates per fecal source individual were sufficient to characterize the richness of the E. coli population of that source. The results of a fingerprint stability experiment indicated that BOX and ISR fingerprints were stable in natural waters at 4, 12, and 28°C for 150 days. In conclusion, 16S-23S rRNA ISR-PCR and rep-PCR analyses of E. coli isolates have the potential to identify nonpoint fecal sources. A fairly small number of isolates was needed to find candidate source-specific E. coli fingerprints that were stable under the simulated environmental conditions.

scholarly journals Detection and Characterization of an Elm Yellows (16SrV) Group Phytoplasma Infecting Virginia Creeper Plants in Southern Florida

Plant Disease ◽  
2001 ◽  
Vol 85 (10) ◽  
pp. 1055-1062 ◽  
Author(s):  
N. A. Harrison ◽  
H. M. Griffiths ◽  
M. L. Carpio ◽  
P. A.. Richardson
Keyword(s):  
Intergenic Spacer ◽  
23S Rrna ◽  
Pcr Analysis ◽  
Polymorphism Analysis ◽  
Intergenic Spacer Region ◽  
Flavescence Dorée ◽  
Specific Pcr ◽  
Rdna Sequences ◽  
Elm Yellows ◽  
Southern Florida

The polymerase chain reaction (PCR) employing phytoplasma-specific ribosomal RNA primer pair P1/P7 consistently amplified a product of expected size (1.8 kb) from 29 of 36 symptom-less Virginia creeper (Parthenocissus quinquefolia) plants growing in southern Florida. Restriction fragment length polymorphism analysis of P1/P7-primed PCR products indicated that most phytoplasmas detected in Virginia creeper were similar to phytoplasmas composing the elm yellows (16SrV) group. This relationship was verified by reamplification of P1/P7 products using an elm yellows (EY) group-specific rRNA primer pair fB1/rULWS1. rDNA products (1,571 bp) were generated by group-specific PCR from 28 phytoplasma-positive plants and 1 negatively testing plant identified by earlier P1/P7-primed PCR. Analysis of 16S rDNA sequences determined the Virginia creeper (VC) phytoplasma to be phylogenetically closest to the European alder yellows (ALY) agent, an established 16SrV-C subgroup strain. However, presence or absence of restriction sites for endonucleases AluI, BfaI, MspI, RsaI, and TaqI in the 16S rRNA and 16-23S rRNA intergenic spacer region of the VC phytoplasma collectively differentiated this strain from ALY and other 16SrV group phytoplasmas. Failure to detect the VC phytoplasma by PCR employing nonribosomal primer pair FD9f/FD9r suggests that this newly characterized agent varies from known European grapevine yellows (flavescence dorée) phyto-plasmas previously classified as 16SrV subgroup C or D strains.

scholarly journals One Health Approach: An Overview of Q Fever in Livestock, Wildlife and Humans in Asturias (Northwestern Spain)

Animals ◽  
2021 ◽  
Vol 11 (5) ◽  
pp. 1395
Author(s):  
Alberto Espí ◽  
Ana del Cerro ◽  
Álvaro Oleaga ◽  
Mercedes Rodríguez-Pérez ◽  
Ceferino M. López ◽  
...  
Keyword(s):  
One Health ◽  
Roe Deer ◽  
Q Fever ◽  
Close Contact ◽  
Acute Infection ◽  
Pcr Analysis ◽  
Wild Ungulates ◽  
Domestic Ruminants ◽  
Iberian Red Deer ◽  
Northwestern Spain

This study aimed to investigate the seroprevalence of C. burnetii in domestic ruminants, wild ungulates, as well as the current situation of Q fever in humans in a small region in northwestern Spain where a close contact at the wildlife–livestock–human interface exists, and information on C. burnetii infection is scarce. Seroprevalence of C. burnetii was 8.4% in sheep, 18.4% in cattle, and 24.4% in goats. Real-time PCR analysis of environmental samples collected in 25 livestock farms detected Coxiella DNA in dust and/or aerosols collected in 20 of them. Analysis of sera from 327 wild ungulates revealed lower seroprevalence than that found in domestic ruminants, with 8.4% of Iberian red deer, 7.3% chamois, 6.9% fallow deer, 5.5% European wild boar and 3.5% of roe deer harboring antibodies to C. burnetii. Exposure to the pathogen in humans was determined by IFAT analysis of 1312 blood samples collected from patients admitted at healthcare centers with Q fever compatible symptoms, such as fever and/or pneumonia. Results showed that 15.9% of the patients had IFAT titers ≥ 1/128 suggestive of probable acute infection. This study is an example of a One Health approach with medical and veterinary institutions involved in investigating zoonotic diseases.

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 The Western Progression of Lyme Disease: Infectious and NonclonalBorrelia burgdorferi Sensu LatoPopulations in Grand Forks County, North Dakota

2014 ◽  
Vol 81 (1) ◽  
pp. 48-58 ◽  
Author(s):  
Brandee L. Stone ◽  
Nathan M. Russart ◽  
Robert A. Gaultney ◽  
Angela M. Floden ◽  
Jefferson A. Vaughan ◽  
...  
Keyword(s):  
Lyme Disease ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
North Dakota ◽  
Intergenic Spacer ◽  
Rrna Gene ◽  
Content Type ◽  
Intergenic Spacer Region ◽  
Grand Forks ◽  
The 16S Rrna Gene

ABSTRACTScant attention has been paid to Lyme disease,Borrelia burgdorferi,Ixodes scapularis, or reservoirs in eastern North Dakota despite the fact that it borders high-risk counties in Minnesota. Recent reports ofB. burgdorferiandI. scapularisin North Dakota, however, prompted a more detailed examination. Spirochetes cultured from the hearts of five rodents trapped in Grand Forks County, ND, were identified asB. burgdorferi sensu latothrough sequence analyses of the 16S rRNA gene, the 16S rRNA gene-ileTintergenic spacer region,flaB,ospA,ospC, andp66. OspC typing revealed the presence of groups A, B, E, F, L, and I. Two rodents were concurrently carrying multiple OspC types. Multilocus sequence typing suggested the eastern North Dakota strains are most closely related to those found in neighboring regions of the upper Midwest and Canada. BALB/c mice were infected withB. burgdorferiisolate M3 (OspC group B) by needle inoculation or tick bite. Tibiotarsal joints and ear pinnae were culture positive, andB. burgdorferiM3 was detected by quantitative PCR (qPCR) in the tibiotarsal joints, hearts, and ear pinnae of infected mice. Uninfected larvalI. scapularisticks were able to acquireB. burgdorferiM3 from infected mice; M3 was maintained inI. scapularisduring the molt from larva to nymph; and further, M3 was transmitted from infectedI. scapularisnymphs to naive mice, as evidenced by cultures and qPCR analyses. These results demonstrate that isolate M3 is capable of disseminated infection by both artificial and natural routes of infection. This study confirms the presence of unique (nonclonal) and infectiousB. burgdorferipopulations in eastern North Dakota.

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