scholarly journals Molecular characterization of Malassezia sympodialis and Malassezia furfur from cattle with and without otitis

2008 ◽  
Vol 60 (4) ◽  
pp. 779-785 ◽  
Author(s):  
E.R. Duarte ◽  
J.S. Hamdan
Keyword(s):  
Genetic Heterogeneity ◽  
Inflammatory Process ◽  
Dna Analysis ◽  
Rapd Analysis ◽  
Random Amplified Polymorphic Dna ◽  
Molecular Study ◽  
Malassezia Furfur ◽  
Geographic Origins ◽  
Minas Gerais State

A molecular study of Malassezia strains isolated from cattle with or without otitis was carried out by random amplified polymorphic DNA analysis (RAPD). DNA was extracted and purified from nine strains of Malassezia sympodialis and fourteen of Malassezia furfur. These microorganisms were collected from eight different bovine herds in Minas Gerais state, Brazil. The RAPD analysis and phenograms did not show the formation of genetically distinct groups among the strain isolated from cattle with or without otitis raised in the same herds. Genetic heterogeneity was observed among Malassezia strains from different geographic origins. These data suggest that genetically similar M. sympodialis and M. furfur strains found as members of the normal ear microbiota could become opportunistically active in the inflammatory process in cattle.

scholarly journals Random Amplification of Polymorphic DNA Analysis for Genetic Characterization of Two Breeds of Dogs, German Shepherd and Japanese Spitz

2013 ◽  
Vol 13 (2) ◽  
pp. 73-78
Author(s):  
Jarina Joshsi ◽  
Lumanti Manandhar ◽  
Patima Shrestha ◽  
Rani Gupta ◽  
Rojlina Manadhar ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Rapd Markers ◽  
Dna Analysis ◽  
Genetic Characterization ◽  
Random Amplified Polymorphic Dna ◽  
Neighbor Joining ◽  
German Shepherd ◽  
Polymorphic Loci ◽  
Random Amplification

Random amplified polymorphic DNA (RAPD) markers were used to study genetic diversity in dog samples belonging to populations of German Shepherd and Japanese Spitz. A total of twelve samples were typed using eight RAPD primers. Out of eight primers, three primers gave result in six individuals of dogs. The phylogenetic tree constructed by the neighbor joining method based on Nei. Original measures revealed highest genetic identity found in German Shepherd as 0.9444 and highest genetic distance as 1.2809. The analysis predicts the number of polymorphic loci as 15 and the percentage of polymorphic loci as 83.3. Nepal Journal of Science and Technology Vol. 13, No. 2 (2012) 73-78 DOI: http://dx.doi.org/10.3126/njst.v13i2.7717

Comparison of repetitive-sequence-based polymerase chain reaction with random amplified polymorphic DNA analysis for rapid genotyping of nontuberculosis mycobacteria

2012 ◽  
Vol 58 (8) ◽  
pp. 953-964 ◽  
Author(s):  
Sara Christianson ◽  
Joyce Wolfe ◽  
Hafid Soualhine ◽  
Meenu K. Sharma
Keyword(s):  
Repetitive Sequence ◽  
Dna Analysis ◽  
Rapd Analysis ◽  
Random Amplified Polymorphic Dna ◽  
Gene Sequencing ◽  
Variable Number ◽  
Outbreak Investigations ◽  
Hsp65 Gene ◽  
Polymerase Chain ◽  
Clinically Significant

Nontuberculosis mycobacteria (NTM) are an important cause of human disease and infections. Though less notorious than tuberculosis, these infections are clinically significant and have been associated with outbreaks in various settings. To accommodate outbreak investigations for the numerous species of NTM, we evaluated a DiversiLab repetitive-sequence-based PCR (rep-PCR) kit for genotyping of mycobacteria. This kit was used to genotype both rapidly and slowly growing mycobacteria and was compared with other PCR-based genotyping methods, including random amplified polymorphic DNA (RAPD) analysis, hsp65 gene sequencing, and mycobacterial interspersed repetitive unit – variable number of tandem repeat (MIRU–VNTR) analysis. Compared with RAPD analysis, rep-PCR achieved better reproducibility in testing. When compared with hsp65 gene sequencing and MIRU–VNTR for Mycobacterium avium , rep-PCR provided results that agreed with these less discriminatory genotyping methods but provided a higher level of discrimination for situations such as outbreak investigations. We also evaluated the kit for its ability to identify closely related rapidly growing NTM. While rep-PCR was informative in some cases, a much larger library of isolates would be necessary to truly evaluate it as an identification tool. Overall, rep-PCR was able to provide improved reproducibility over RAPD and a discriminatory genotyping method for the isolates evaluated in this study.

Isolation of Genotype- and Chromosome-specific DNA Markers in a Biotype of Colletotrichum gloeosporioides Using Random Amplified Polymorphic DNA Analysis

1998 ◽  
Vol 46 (1) ◽  
pp. 143
Author(s):  
Agnieszka M. Poplawski ◽  
John A. G. Irwin ◽  
John M. Manners
Keyword(s):  
Dna Sequences ◽  
Fungal Pathogen ◽  
Rapd Markers ◽  
Dna Analysis ◽  
Colletotrichum Gloeosporioides ◽  
Rapd Analysis ◽  
Random Amplified Polymorphic Dna ◽  
Dna Probes ◽  
Race 2 ◽  
Biotype B

Genetic markers that distinguish fungal genotypes are important tools for genetic analysis of heterokaryosis and parasexual recombination in fungi. Random amplified polymorphic DNA (RAPD) markers that distinguish two races of biotype B of Colletotrichum gloeosporioides infecting the legume Stylosanthes guianensis were sought. Eighty-five arbitrary oligonucleotide primers were used to generate 895 RAPD bands but only two bands were found to be specifically amplified from DNA of the race 3 isolate. These two RAPD bands were used as DNA probes and hybridised only to DNA of the race 3 isolate. Both RAPD bands hybridised to a dispensable 1.2 Mb chromosome of the race 3 isolate. No other genotype-specific chromosomes or DNA sequences were identified in either the race 2 or race 3 isolates. The RAPD markers hybridised to a 2 Mb chromosome in all races of the genetically distinct biotype A pathogen which infects other species of Stylosanthes as well as S. guianensis. The experiments indicate that RAPD analysis is a potentially useful tool for obtaining genotype- and chromosome-specific DNA probes in closely related isolates of one biotype of this fungal pathogen.

scholarly journals 678 PB 186 RAPD GENETIC MARKERS FOR CHARACTERIZATION OF MUSA GENETIC RESOURCES

HortScience ◽  
1994 ◽  
Vol 29 (5) ◽  
pp. 530a-530
Author(s):  
R.L. Jarret ◽  
K.V. Bhat
Keyword(s):  
Genetic Markers ◽  
Size Range ◽  
Rapd Analysis ◽  
Random Amplified Polymorphic Dna ◽  
Dna Amplification ◽  
Principal Coordinate Analysis ◽  
Phenetic Analysis ◽  
Similarity Coefficients ◽  
Primer Sequence

Fifty-seven accessions of Musa including cultivated clones Of 6 genomic groups (AA, AB, AAA, AAB, ABB, ABBB), M. balbisiana (BB), M. acuminata ssp. banksii (AA), M. acuminata ssp. malaccensis (AA) and M. velutina were examined for random amplified polymorphic DNA (RAPD) genetic markers using PCR with sixty 10-mer random primers. Forty-nine of 60 tested primers gave reproducible DNA amplification patterns. The number of bands resolved per amplification was primer dependent and varied from 1 to a maximum of 24. The size range of the amolification products also differed with the select& primer sequence/genotype and ranged from 0.29 to 3.0 kb. RAPD data were used to generate Jaccard's similarity coefficients which were analyzed phenetically. Phenetic analysis separated clones into distinct groupings that were in agreement with clusterings revealed when data were subsequently analyzed by principal coordinate analysis (PCO). In both the phenetic and the PCO analyses, previously unclassified cultivars grouped with cultivars previously classified for their genomic group based on morphological keys. The implications of RAPD analysis for Musa germplasm classification, clonal identification, and management are discussed.

scholarly journals Characterization of Alstroemeria Species using Random Amplified Polymorphic DNA (RAPD) Analysis

HortScience ◽  
1997 ◽  
Vol 32 (3) ◽  
pp. 482F-482 ◽  
Author(s):  
Deric D. Picton ◽  
Harrison G. Hughes
Keyword(s):  
Rapd Analysis ◽  
Random Amplified Polymorphic Dna ◽  
Randomly Amplified Polymorphic Dna ◽  
Banding Patterns ◽  
Extraction Buffer ◽  
Rapd Pcr ◽  
High Degree ◽  
Species Hybrids ◽  
Color Variants

In this study, 11 species, hybrids, and color variants were characterized using randomly amplified polymorphic DNA (RAPD) analysis. Total genomic DNA was extracted using a 2% CTAB extraction buffer using fresh or frozen leaf material. The DNA was amplified using standard RAPD-PCR protocols utilizing 10-mer primers. All primers utilized exhibited a high degree of polymorphism in their banding patterns among the species and hybrids studied. The primers used produced ≈40 reproducible bands. It was possible to identify and uniquely distinguish all species and hybrids investigated using these bands.

scholarly journals Co-Isolation and Characterization of Two Pandoraviruses and a Mimivirus from a Riverbank in Japan

Viruses ◽  
2019 ◽  
Vol 11 (12) ◽  
pp. 1123 ◽  
Author(s):  
Motohiro Akashi ◽  
Masaharu Takemura
Keyword(s):  
Phylogenetic Analysis ◽  
Dna Analysis ◽  
Virus Isolation ◽  
Random Amplified Polymorphic Dna ◽  
Isolation And Characterization ◽  
The Family ◽  
Complete Sequences ◽  
Infected Amoeba ◽  
Giant Viruses

Giant viruses, like pandoraviruses and mimiviruses, have been discovered from diverse environments, and their broad global distribution has been established. Here, we report two new isolates of Pandoravirus spp. and one Mimivirus sp., named Pandoravirus hades, Pandoravirus persephone, and Mimivirus sp. isolate styx, co-isolated from riverbank soil in Japan. We obtained nearly complete sequences of the family B DNA polymerase gene (polB) of P. hades and P. persephone; the former carried two known intein regions, while the latter had only one. Phylogenetic analysis revealed that the two new pandoravirus isolates are closely related to Pandoravirus dulcis. Furthermore, random amplified polymorphic DNA analysis revealed that P. hades and P. persephone might harbor different genome structures. Based on phylogenetic analysis of the partial polB sequence, Mimivirus sp. isolate styx belongs to mimivirus lineage A. DNA staining suggested that the Pandoravirus spp. asynchronously replicates in amoeba cells while Mimivirus sp. replicates synchronously. We also observed that P. persephone- or Mimivirus sp. isolate styx-infected amoeba cytoplasm is extruded by the cells. To the best of our knowledge, we are the first to report the isolation of pandoraviruses in Asia. In addition, our results emphasize the importance of virus isolation from soil to reveal the ecology of giant viruses.

Isolation and Characterization of a New Arthrospira Strain

2008 ◽  
Vol 63 (1-2) ◽  
pp. 144-150 ◽  
Author(s):  
Michele Greque de Morais ◽  
Carolina da Cruz Reichert ◽  
Francieli Dalcanton ◽  
Andrei José Durante ◽  
Luís Fernando Marins ◽  
...  
Keyword(s):  
Growth Rate ◽  
Specific Growth Rate ◽  
Specific Growth ◽  
Rapd Analysis ◽  
Random Amplified Polymorphic Dna ◽  
Arthrospira Platensis ◽  
Central Point ◽  
Filamentous Microorganism ◽  
Isolation And Characterization

A filamentous microorganism, morphologically similar to the cyanobacterium Arthrospira, was isolated from Mangueira Lagoon in Brazil, from which Arthrospira has not previously been isolated. Random amplified polymorphic DNA (RAPD) comparison with the standard Arthrospira platensis strains LEB 52 and Paracas indicated that the organism isolated was an Arthrospira isolate, which we denominated strain LEB 18. The RAPD analysis showed conserved sequences which indicated that the three strains belonged to the same genus, and were all Arthrospira species, but there were sufficient differences between them suggesting that they were separate strains. The strain LEB 18 was cultivated in undiluted Zarrouk medium and in 60% and 20% (v/v) Zarrouk medium diluted with sterilized Mangueira Lagoon water (MLW) using illuminance rates of 32.5, 45.5 and 58.5 μmol m−2 s−1 according to a complete 32 factorial design with a triplicate central point. The strains LEB 52 and Paracas were cultived in the conditions central point. Our new isolate produced the highest specific growth rate (μmax = 0.22 d−1) in 60% Zarrouk medium diluted with MLW and illuminated with 58.5 μmol m−2 s−1 and the highest protein content (86.0% w/w).

scholarly journals Genetic Characterization ofStreptococcus iniaein Diseased Farmed Rainbow Trout (Onchorhynchus mykiss) in Iran

2012 ◽  
Vol 2012 ◽  
pp. 1-6 ◽  
Author(s):  
A. Erfanmanesh ◽  
M. Soltani ◽  
E. Pirali ◽  
S. Mohammadian ◽  
A. Taherimirghaed
Keyword(s):  
Rainbow Trout ◽  
Phylogenetic Tree ◽  
Genetic Characterization ◽  
Rapd Analysis ◽  
Random Amplified Polymorphic Dna ◽  
Streptococcus Iniae ◽  
The North ◽  
North Part ◽  
Gram Positive Cocci

Genetic characterization of strains ofStreptococcus iniaerecovered from morbidity and mortality of farmed rainbow trout in different provinces of Iran were studied. The Gram-positive cocci isolates were obtained from the kidney tissues of diseased rainbow trout on blood agar at25°Cfor 72 h. The grown bacteria were then characterized using biochemical and molecular works. The identified 26 isolates ofS. iniaeproducing a 513 bp in PCR procedure were then compared using random amplified polymorphic DNA (RAPD) analysis using 9 random primers. The phylogenetic tree of the RAPD product using UPMGA software included these strains in one genetic group but into two clusters. The results of this study show thatS. iniaestrains from the diseased rainbow trout in the north part of Iran are genetically similar to those strains in the south and west parts of the country.

Characterization of Giardia lamblia groups A and B from North India by isoenzyme and random amplified polymorphic DNA analysis

1999 ◽  
Vol 85 (6) ◽  
pp. 510-512 ◽  
Author(s):  
Ajaib Singh Paintlia ◽  
Ramesh Chander Mahajan ◽  
Anuradha Chakraborti ◽  
Rakesh Sehgal ◽  
Nirmal Kumar Ganguly
Keyword(s):  
Giardia Lamblia ◽  
Dna Analysis ◽  
Random Amplified Polymorphic Dna ◽  
North India

Emergence of group B Streptococcus serotype IV in women of child-bearing age in Ireland

2010 ◽  
Vol 139 (2) ◽  
pp. 236-238 ◽  
Author(s):  
R. A. KIELY ◽  
L. COTTER ◽  
A. M. MOLLAGHAN ◽  
B. CRYAN ◽  
A. COFFEY ◽  
...  
Keyword(s):  
Genetic Heterogeneity ◽  
Dna Analysis ◽  
Random Amplified Polymorphic Dna ◽  
Group B Streptococcus ◽  
Serotype Distribution ◽  
Carriage Rate ◽  
Child Bearing ◽  
High Prevalence ◽  
Vaginal Swabs ◽  
Group B

SUMMARYThis study determined the carriage rate and serotype distribution of group B Streptococcus (GBS) in women of child-bearing age in the southern region of Ireland. A total of 2000 vaginal swabs collected in two periods in 2004 and 2006 were examined and revealed a GBS carriage rate of 16·1%. Serotyping of isolates showed that serotypes Ia, II, III, IV, and V were the most prevalent. A high prevalence of serotype IV was found, increasing from 7·6% to 15·2% between 2004 and 2006. Random amplified polymorphic DNA analysis demonstrated considerable genetic heterogeneity in the serotype IV isolates. This serotype should be considered for inclusion in potential vaccines for use in Ireland.

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