scholarly journals A revisit to a low-cost method for the isolation of microsatellite markers: the case of the endangered Malayan tapir (Tapirus indicus)

2018 ◽  
Author(s):  
Qi Luan Lim ◽  
Nurul Adilah Ismail ◽  
Ramitha Arumugam ◽  
Wei Lun Ng ◽  
Christina Seok Yien Yong ◽  
...  
Keyword(s):  
Microsatellite Markers ◽  
Microsatellite Loci ◽  
Low Cost ◽  
Pcr Cloning ◽  
Chain Reaction ◽  
Sequencing Method ◽  
Rapid Polymerase Chain Reaction ◽  
Pcr Method ◽  
Polymerase Chain ◽  
Tapirus Indicus

AbstractThere are many approaches to develop microsatellite markers. We revisited an easy and rapid Polymerase Chain Reaction (PCR)-cloning-sequencing method to design microsatellite markers for Tapirus indicus. Using six random amplified microsatellite (RAM) markers, this study had rapidly generated 45 unique genomic sequences containing microsatellites. After screening 15 terminal and seven intermediate microsatellite loci, we shortlisted five and seven which were amplified either by single- or multiplex PCR using the economical three-primer PCR method. Genotyping attempts were made with ten Tapirus indicus individuals using three of the terminal microsatellite loci and all seven intermediate loci. However, none of the terminal microsatellite loci were considered useful for population genotyping studies, while the seven intermediate loci showed good amplification but were monomorphic in the ten samples. Despite successful detection of amplified loci, we would like to highlight that, researchers who are interested in this alternative method for isolation of microsatellite loci to be cautious and be aware of the limitations and downfalls reported herein that could render these loci unsuitable for population genotyping.

Immuno-capture PCR method for detecting Acidovorax avenae subsp. citrulli from watermelon

2007 ◽  
Vol 4 (2) ◽  
pp. 173-179 ◽  
Author(s):  
Wang Xiao ◽  
Zhang Le ◽  
Xu Fu-Shou ◽  
Zhao Li-Han ◽  
Xie Guan-Lin
Keyword(s):  
Polymerase Chain Reaction ◽  
Low Cost ◽  
Chain Reaction ◽  
Direct Pcr ◽  
Causal Organism ◽  
Bacterial Fruit Blotch ◽  
Pcr Method ◽  
Polymerase Chain ◽  
Honeydew Melon ◽  
Melon Seeds

AbstractAn immuno-capture polymerase chain reaction (IC-PCR) method for detection of Acidovorax avenae subsp. citrulli (AAC), the causal organism of bacterial fruit blotch (BFB) of watermelon, was developed by combining the immunosorbent enrichment (ISE) method with classical PCR and comparing with the direct PCR and growth check methods. The results showed that all A. avenae subsp. citrulli strains tested have produced 360 bp specific fragments using IC-PCR and direct PCR methods, while other strains from 10 different genera showed negative PCR results. The minimum detection concentration was about 50–100 cfu/ml and 104 cfu/ml, respectively. The IC-PCR sensitivity was 100 times higher than that of direct PCR. The examination of seven batches of different melon seeds from the markets by IC-PCR showed that one cantaloupe, two honeydew melon and two watermelon seed varieties carried the pathogen, indicating that the IC-PCR is an accurate, sensitive, rapid and low-cost technique.

A low-cost, disposable card for rapid polymerase chain reaction

2007 ◽  
Vol 58 (1) ◽  
pp. 52-60 ◽  
Author(s):  
Guangyao Jia ◽  
Jonathan Siegrist ◽  
Chengwu Deng ◽  
Jim V. Zoval ◽  
Gale Stewart ◽  
...  
Keyword(s):  
Polymerase Chain Reaction ◽  
Low Cost ◽  
Chain Reaction ◽  
Rapid Polymerase Chain Reaction ◽  
Polymerase Chain

Variability of thirteen microsatellite markers in American mink (Mustela vison)

2003 ◽  
Vol 83 (3) ◽  
pp. 597-599 ◽  
Author(s):  
I. R. Vincent ◽  
A. Farid ◽  
C. J. Otieno
Keyword(s):  
Polymerase Chain Reaction ◽  
Microsatellite Markers ◽  
Microsatellite Loci ◽  
Genomic Library ◽  
American Mink ◽  
Pine Marten ◽  
Chain Reaction ◽  
Polymerase Chain ◽  
Polymerase Chain Reaction Primers ◽  
Wild Mink

A mink genomic library was screened with an (AC)15 oligonucleotide as the probe. Thirteen microsatellite loci were identified and primer sequences and amplification conditions were determined. All the 13 loci were polymorphic in black, brown, pastel and wild mink (n = 86), generating between 4 to 12 alleles per locus. Six of the primer pairs revealed polymorphisms in American pine marten. Key words: Mink, pine marten, microsatellite, polymorphism, polymerase chain reaction, primers

Identification of Bacteroides forsythus in Subgingival Dental Plaque with the Aid of a Rapid PCR Method

1997 ◽  
Vol 76 (7) ◽  
pp. 1376-1380 ◽  
Author(s):  
J.H. Meurman ◽  
J. Wahlfors ◽  
A. Korhonen ◽  
P. Alakuijala ◽  
P. Väisänen ◽  
...  
Keyword(s):  
Dental Plaque ◽  
Subgingival Plaque ◽  
Chain Reaction ◽  
Rapid Pcr ◽  
Microbiological Methods ◽  
Pcr Method ◽  
Polymerase Chain ◽  
Pre Treatment ◽  
Culture Positive ◽  
Positive Results

Bacteroides forsythus has been shown to be prevalent among patients with periodontitis. Conventional microbiological methods used to identify this bacterium, however, are laborious and time-consuming and are therefore not well-suited for screening purposes. We have developed a polymerase chain-reaction (PCR) method which is rapid, specific, and simple to perform and does not require other sample pre-treatment except a brief centrifugation. This method was applied to the detection of B. forsythus in subgingival plaque of 58 periodontitis patients. When compared with the results of conventional culturing, the PCR method always confirmed the culture-positive results, while none of the PCR negative samples was shown to be culture-positive. The PCR method appeared to give more than double the number of samples positive for B. forsythus than culturing (89.7% vs. 37.9%). The analysis requires less than 4 hrs to perform, and is specific only to B. forsythus and sensitive enough to detect fewer than 5 bacteria.

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