Polymorphism of Sakini Chicken Population From Different Locations/Altitudes of Nepal Using Randomly Amplified Polymorphic Dna Markers

A study was conducted to evaluate genetic polymorphism in three Sakini chicken populations using random amplification of polymorphic DNA (RAPD) with seven highly polymorphic primers. All populations showed polymorphism with these primers that generates 59 different bands with an average of 8.4 bands per primer with 78.6% polymorphism nature. Primer OPA-16 produced the highest number of polymorphism bands 47 % and the lowest number of bands was produced by the OPA-05 primer 24 %. Differences for genetic distance (D) among populations were significant (P<0.05). A consensus dendogram was therefore developed to show the phylogenetic relationship among the populations. The cluster pattern is well supported by the principle component analysis that also separates all three populations of Sakini chicken into six major groups. The results provide evidence of the applicability of RAPD to determining genetic relatedness within and among different poultry populations and in developing reproducible markers useful in evaluating individual variation in poultry. SAARC J. Agri., 18(2): 115-124 (2020)

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An Outbreak of ESBL-producing Klebsiella pneumoniae in an Iranian Referral Hospital: Epidemiology and Molecular Typing

Infectious Disorders - Drug Targets ◽

10.2174/1871526518666180507121831 ◽

2019 ◽

Vol 19 (1) ◽

pp. 46-54 ◽

Cited By ~ 4

Author(s):

Shima Mahmoudi ◽

Babak Pourakbari ◽

Aliakbar Rahbarimanesh ◽

Mohammad Reza Abdosalehi ◽

Keyghobad Ghadiri ◽

...

Keyword(s):

Klebsiella Pneumoniae ◽

Nosocomial Infections ◽

Molecular Typing ◽

Genetic Relatedness ◽

Referral Hospital ◽

Limited Information ◽

Hospital Epidemiology ◽

Rapd Pcr ◽

Published Report ◽

Random Amplification

Introduction: Klebsiella pneumoniae is a common cause of nosocomial infections; however, there is limited information in Iran regarding nosocomial outbreaks due to extended-spectrum &#946;–lactamase (ESBL) producing K pneumoniae strains, particularly using molecular methods. The present study focused on the molecular mechanism of ESBL resistance and genetic relatedness in K. pneumoniae isolates causing nosocomial infections in an Iranian referral hospital. Material and Methods: This study evaluated the antimicrobial resistance and molecular epidemiology of K. pneumoniae causing nosocomial infections in children between October 2013 and March 2014. The ESBL detection was carried out for all the isolates by the CLSI method and PCR was carried out for the detection of the blaSHV, blaTEM, and blaCTX-M genes among ESBL-producing K. pneumonia. Molecular typing of the K. pneumoniae was performed using random amplification of polymorphic DNA-polymerase chain reaction (RAPD-PCR). Results: A total of 30 isolates of K. pneumoniae were used for epidemiological analysis. High rates of resistance to cefotaxime (n=29, 97%), cefazolin (n=29, 97%), cefepime (n=25, 83%) and gentamicin (n=23, 77%) were observed. A total of 29 strains (97%) produced ESBLs. The frequency of blaSHV, blaCTX-M and blaTEM genes among these isolates was 83% (n=25), 70% (n=21) and 57% (n=17), respectively. Surprisingly 11 isolated (37%) carried blaSHV, blaCTX-M and blaTEM genes simultaneously. Moreover, the concurrent presence of “blaSHV and blaCTX-M” and “blaSHV and blaTEM” was seen in 8 (27%) and 4 (13%) isolates, respectively. RAPDPCR analyses revealed that K. pneumoniae isolates belonged to 2 RAPD-PCR types among which one cluster counted for 28 isolates. Conclusion: To our knowledge, this is the first published report of a nosocomial outbreak of ESBL-producing K. pneumoniae in children in Iran. Although the epidemiology of nosocomial infections with ESBL-producing organisms has not yet been explored in depth in Iran, our findings suggest that ESBL-producing organisms are already an established public health threat in our country.

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Strain Typing of Trichosporon asahii Clinical Isolates by Random Amplification of Polymorphic DNA (RAPD) Analysis

Journal of Laboratory Physicians ◽

10.1055/s-0041-1731111 ◽

2021 ◽

Author(s):

Thayanidhi Premamalini ◽

Vijayaraman Rajyoganandh ◽

Ramaraj Vijayakumar ◽

Hemanth Veena ◽

Anupma Jyoti Kindo ◽

...

Keyword(s):

Genetic Relatedness ◽

Rapd Analysis ◽

Clinical Isolates ◽

Clinical Samples ◽

Strain Typing ◽

Trichosporon Asahii ◽

Pcr Fingerprinting ◽

Specific Pcr ◽

Rapd Primer ◽

Random Amplification

Abstract Objective The aim of this study was to identify and isolate Trichosporon asahii (T. asahii) from clinical samples and to assess the genetic relatedness of the most frequently isolated strains of T. asahii using random amplification of polymorphic DNA (RAPD) primers GAC-1 and M13. Methods All the clinical samples that grew Trichosporon species, identified and confirmed by polymerase chain reaction (PCR) using Trichosporon genus-specific primers, were considered for the study. Confirmation of the species T. asahii was carried out by T. asahii-specific PCR. Fingerprinting of the most frequently isolated T. asahii isolates was carried out by RAPD using random primers GAC-1 and M13. Results Among the 72 clinical isolates of Trichosporon sp. confirmed by Trichosporon-specific PCR, 65 were found to be T. asahii as identified by T. asahii-specific PCR. Fingerprinting of the 65 isolates confirmed as T. asahii using GAC-1 RAPD primer yielded 11 different patterns, whereas that of M13 primer produced only 5 patterns. The pattern I was found to be the most predominant type (29.2%) followed by pattern III (16.9%) by GAC-1 primer. Conclusions This study being the first of its kind in India on strain typing of T. asahii isolates by adopting RAPD analysis throws light on genetic diversity among the T. asahii isolates from clinical samples. Fingerprinting by RAPD primer GAC-1 identified more heterogeneity among the T. asahii isolates than M13.

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Genetic Variation among and within United States Collard Cultivars and Landraces as Determined by Randomly Amplified Polymorphic DNA Markers

Journal of the American Society for Horticultural Science ◽

10.21273/jashs.121.3.374 ◽

1996 ◽

Vol 121 (3) ◽

pp. 374-379 ◽

Cited By ~ 17

Author(s):

Mark W. Farnham

Keyword(s):

Genetic Variation ◽

Dna Markers ◽

Crop Improvement ◽

Similarity Index ◽

Randomly Amplified Polymorphic Dna ◽

Brussels Sprouts ◽

Breeding Lines ◽

Intrapopulation Variation ◽

Similarity Indices ◽

Systematic Collection

A collection of collard (Brassica oleracea L., Acephala group) germplasm, including 13 cultivars or breeding lines and 5 landraces, was evaluated using randomly amplified polymorphic DNA (RAPD) markers and compared to representatives of kale (Acephala group), cabbage (Capitata group), broccoli (Italica group), Brussels sprouts (Gemmifera group), and cauliflower (Botrytis group). Objectives were to assess genetic variation and relationships among collard and other crop entries, evaluate intrapopulation variation of open-pollinated (OP) collard lines, and determine the potential of collard landraces to provide new B. oleracea genes. Two hundred nine RAPD bands were scored from 18 oligonucleotide decamer primers when collard and other B. oleracea entries were compared. Of these, 147 (70%) were polymorphic and 29 were specific to collard. Similarity indices between collard entries were computed from RAPD data and these ranged from 0.75 to 0.99 with an average of 0.83. Collard entries were most closely related to cabbage (similarity index = 0.83) and Brussels sprouts entries (index = 0.80). Analysis of individuals of an OP cultivar and landrace indicated that intrapopulation genetic variance accounts for as much variation as that observed between populations. RAPD analysis identified collard landraces as unique genotypes and showed them to be sources of unique DNA markers. The systematic collection of collard landraces should enhance diversity of the B. oleracea germplasm pool and provide genes for future crop improvement.

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