Highly Parallel Single-Molecule Amplification Approach Based on Agarose Droplet Polymerase Chain Reaction for Efficient and Cost-Effective Aptamer Selection

2011 ◽  
Vol 84 (1) ◽  
pp. 350-355 ◽  
Author(s):  
Wei Yun Zhang ◽  
Wenhua Zhang ◽  
Zhiyuan Liu ◽  
Cong Li ◽  
Zhi Zhu ◽  
...  
Keyword(s):  
Polymerase Chain Reaction ◽  
Single Molecule ◽  
Cost Effective ◽  
Chain Reaction ◽  
Aptamer Selection ◽  
Polymerase Chain

scholarly journals Development of a Genoserotyping Method for Salmonella Infantis Detection on the Basis of Pangenome Analysis

2020 ◽  
Vol 9 (1) ◽  
pp. 67
Author(s):  
Seung-Min Yang ◽  
Jiwon Baek ◽  
Eiseul Kim ◽  
Hyeon-Be Kim ◽  
Seyoung Ko ◽  
...  
Keyword(s):  
Public Health ◽  
Polymerase Chain Reaction ◽  
Bacterial Species ◽  
Cost Effective ◽  
The Other ◽  
Gene Marker ◽  
Diagnostic Assay ◽  
Chain Reaction ◽  
Polymerase Chain ◽  
Substantial Economic Burden

In recent years, Salmonella Infantis has become a predominant serovariant in clinical and poultry isolates, thereby imposing a substantial economic burden on both public health and the livestock industry. With the aim of coping with the steep increase in serovar Infantis prevalence, a polymerase chain reaction (PCR)-based rapid and accurate diagnostic assay was developed in this study through pangenome profiling of 60 Salmonella serovars. A gene marker, SIN_02055, was identified, which is present in the S. Infantis genome but not in the pangenome of the other serovars. Primers specific to SIN_02055 were used to accurately detect serovar Infantis, and to successfully differentiate Infantis from the other 59 serovars in real-time PCR with a R2 of 0.999 and an efficiency of 95.76%. The developed method was applied to 54 Salmonella strains belonging to eight dominant serovars, and distinguished Infantis from the other seven serovars with an accuracy of 100%. The diagnostic primer set also did not show false positive amplification with 32 strains from eight non-Salmonella bacterial species. This cost-effective and rapid method can be considered an alternative to the classic serotyping using antisera.

scholarly journals High-Resolution Melting-Based Quantitative Analysis of RASSF1 Methylation in Breast Cancer

Medicina ◽  
2013 ◽  
Vol 49 (2) ◽  
pp. 14 ◽  
Author(s):  
Kristina Stuopelytė ◽  
Kristina Daniūnaitė ◽  
Aida Laurinavičienė ◽  
Valerijus Ostapenko ◽  
Sonata Jarmalaitė
Keyword(s):  
Breast Cancer ◽  
Polymerase Chain Reaction ◽  
High Resolution ◽  
Quantitative Methods ◽  
High Resolution Melting ◽  
Cost Effective ◽  
Chain Reaction ◽  
Specific Polymerase Chain Reaction ◽  
Polymerase Chain ◽  
Breast Tissues

Background and Objective. Breast cancer is the leading cause of death from cancer among women worldwide. The aberrant promoter methylation of tumor suppressor genes is a typical epigenetic alteration for breast cancer and can be detected in early carcinogenesis. High-throughput and cost-effective methods are needed for the early and sensitive detection of epigenetic changes in clinical material. The main purpose of our study was to optimize a high-resolution melting (HRM) assay for the reliable and quantitative assessment of RASSF1 gene methylation, which is considered one of the earliest epigenetic alterations in breast cancer. Material and Methods. A total of 76 breast carcinomas and 10 noncancerous breast tissues were studied by means of HRM and compared with the results obtained by means of quantitative methylation-specific polymerase chain reaction (QMSP) and methylation-specific polymerase chain reaction (MSP). Results. Both quantitative methods, HRM and QMSP, showed a similar specificity and sensitivity for the detection of RASSF1 methylation in breast cancer (about 80% and 70%, respectively). In breast cancer, the mean methylation intensity of RASSF1 was 42.5% and 48.6% according to HRM and QMSP, respectively. Both methods detected low levels of methylation (less than 5%) in noncancerous breast tissues. In comparison with quantitative methods, MSP showed a lower sensitivity (70%), but a higher specificity (80%) for the detection of RASSF1 methylation in breast cancer. Conclusions. HRM is as a simple, cost-effective method for the reliable high-throughput quantification of DNA methylation in clinical material.

Predictive Value and Cost-Effectiveness Analysis of a Rapid Polymerase Chain Reaction for Preoperative Detection of Nasal Carriage of Staphylococcus aureus

2003 ◽  
Vol 24 (5) ◽  
pp. 327-333 ◽  
Author(s):  
Nabin K. Shrestha ◽  
Kenneth M. Shermock ◽  
Steven M. Gordon ◽  
Marion J. Tuohy ◽  
Deborah A. Wilson ◽  
...  
Keyword(s):  
Staphylococcus Aureus ◽  
Polymerase Chain Reaction ◽  
Cost Effectiveness ◽  
Cost Effective ◽  
Nasal Carriage ◽  
Initial Therapy ◽  
Cost Effectiveness Analysis ◽  
Chain Reaction ◽  
Effectiveness Analysis ◽  
Polymerase Chain

AbstractObjective:To determine the accuracy and cost-effectiveness of a polymerase chain reaction (PCR) for detecting nasal carriage of Staphylococcus aureus directly from clinical specimens.Cross-Sectional Study:This occurred in a tertiary-care hospital in Cleveland, Ohio, and included 239 consecutive patients who were scheduled for a cardiothoracic surgical procedure. Conventional cultures and a PCR for S. aureus from nasal swabs were used as measurements.Cost-Effectiveness Analysis:Data sources were market prices and Bureau of Labor Statistics. The time horizon was the maximum period for availability of culture results (3 days). Interventions included universal mupirocin therapy without testing; initial therapy, with termination if PCR negative (treat-PCR); initial therapy, with termination if culture negative (treat-culture); treat PCR-positive carriers (PCR-guided treatment); and treat culture-positive carriers (culture-guided treatment). The perspective was institutional and costs and the length of time to treatment were outcome measures.Results:Sixty-seven (28%) of the 239 swabs grew S. aureus. Rapid PCR was 97.0% sensitive and 97.1% specific for the detection of S. aureus. For populations with prevalences of nasal S. aureus carriage of up to 50%, the PCR assay had negative predictive values of greater than 97%. PCR-guided treatment had the lowest incremental cost-effectiveness ratio ($1.93 per additional day compared with the culture strategy). Among immediate treatment strategies, treat-PCR was most cost-effective. The universal therapy strategy cost $38.19 more per additional day gained with carrier identification compared with the PCR strategy.Conclusion:Rapid real-time PCR is an accurate, rapid, and cost-effective method for identifying S. aureus carriers for preoperative intervention.

scholarly journals Novel Dual Labeled Fluorescence Probe Based Assay to Measure the Telomere Length

2018 ◽  
Author(s):  
Itty Sethi ◽  
Gh. Rasool Bhat ◽  
Rakesh Kumar ◽  
Ekta Rai ◽  
Swarkar Sharma
Keyword(s):  
Polymerase Chain Reaction ◽  
Telomere Length ◽  
Fluorescence Probe ◽  
Quantitative Polymerase Chain Reaction ◽  
Cost Effective ◽  
Sybr Green ◽  
Telomeric Dna ◽  
Chain Reaction ◽  
Specific Pcr ◽  
Polymerase Chain

ABSTRACTTelomeres are highly repetitive regions capping the chromosomes and composed of multiple units of hexa-nucleotides, TTAGGG, making their quantification difficult. Most of the methods developed to estimate telomeres are extensively cumbersome and expensive. The quantitative polymerase chain reaction (qPCR) based assay is relatively easy and cheaper method that applies SyBr Green dye chemistry to measure telomere length. As SyBr Green dye fluoresces after intercalation into the dsDNA, lack of differentiation between specific PCR target products and unspecific products is a limitation and it affects accuracy in quantitation of telomeres. To overcome the limitations of SyBr Green, we developed a dual labeled fluorescence probe based quantitative polymerase chain reaction (qPCR) to measure the telomere length. This robust, accurate and highly reproducible (R2=0.96) proprietary method (patent pending), yet cost effective and easy, utilizes a probe that targets specifically the telomeric DNA.

scholarly journals A new single run polymerase chain reaction assay for cyclosporiasis in immunocompromised patients

2021 ◽  
Vol 7 (3) ◽  
pp. 207-212
Author(s):  
Rakesh Singh ◽  
Manish Katiyar ◽  
Reena Gulati ◽  
Sreejith Parameswaran ◽  
Abdoul Hamide ◽  
...  
Keyword(s):  
Polymerase Chain Reaction ◽  
Tertiary Care ◽  
Cost Effective ◽  
People Living With Hiv ◽  
Immunocompromised Patients ◽  
Chain Reaction ◽  
Pcr Assay ◽  
Cross Sectional ◽  
Stool Samples ◽  
Polymerase Chain

causes human intestinal cyclosporiasis. It is more common in the immunocompromised patients and mainly seen in people living with HIV/AIDS (PLHA), post-renal transplant (PRT) patients and immunocompromised children (IC). Diagnostic microscopy for the oocysts of the parasite is less sensitive, requiring examination of multiple stool samples. Here we developed a new single run polymerase chain reaction (PCR) assay for the detection of and it was used to know the hospital based prevalence of cyclosporiasis. A cross-sectional study was conducted from June 2016 to October 2020 in a tertiary care teaching hospital. A new single run amplification PCR-based diagnostic assay was developed for . Stool samples were collected from 121 PLHA, 135 PRT and 79 immunocompromised children (IC) other than PLHA and PRT. All stool samples were examined for the presence of oocysts as well as tested with new PCR assay. Modified Ziehl-Neelsen staining of the concentrated stool smear did not reveal oocysts of species in any stool specimen. However, new PCR assay detected in 2 stool specimens – one from a PLHA patient and another from a PRT patient, giving a prevalence of 0.6% (2/335), 0.8% (1/121) in PLHA and 0.7% (1/135) in PRT. It was not detected in IC. Cyclosporiasis is infrequent in southern part of India. The new single run PCR assay developed by us is simple and cost effective molecular assay for the detection of .

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