scholarly journals Accelerating DNA Computing via PLP-qPCR Answer Read out to Solve Traveling Salesman Problems

2020 ◽  
Author(s):  
Fusheng Xiong ◽  
Michael Kuby ◽  
Wayne D. Frasch
Keyword(s):  
Polymerase Chain Reaction ◽  
High Throughput ◽  
Dna Computing ◽  
High Specificity ◽  
Traveling Salesman ◽  
Traveling Salesman Problems ◽  
Node Pair ◽  
Polymerase Chain ◽  
Time Required ◽  
Fully Connected

An asymmetric, fully-connected 8-city traveling salesman problem (TSP) was solved by DNA computing using the ordered node pair abundance (ONPA) approach through the use of pair ligation probe quantitative real time polymerase chain reaction (PLP-qPCR). The validity of using ONPA to derive the optimal answer was confirmed by in silico computing using a reverse-engineering method to reconstruct the complete tours in the feasible answer set from the measured ONPA. The high specificity of the sequence-tagged hybridization, and ligation that results from the use of PLPs significantly increased the accuracy of answer determination in DNA computing. When combined with the high throughput efficiency of qPCR, the time required to identify the optimal answer to the TSP was reduced from days to 25 min.

High-Throughput Polymerase Chain Reaction in Parallel Circular Loops Using Magnetic Actuation

2008 ◽  
Vol 80 (15) ◽  
pp. 6127-6130 ◽  
Author(s):  
Yi Sun ◽  
Nam-Trung Nguyen ◽  
Yien Chian Kwok
Keyword(s):  
Polymerase Chain Reaction ◽  
High Throughput ◽  
Magnetic Actuation ◽  
Chain Reaction ◽  
Polymerase Chain

scholarly journals Sustained high-throughput polymerase chain reaction diagnostics during the European epidemic of Bluetongue virus serotype 8

2012 ◽  
Vol 24 (3) ◽  
pp. 469-478 ◽  
Author(s):  
Piet A. van Rijn ◽  
René G. Heutink ◽  
Jan Boonstra ◽  
Hans A. Kramps ◽  
René G. P. van Gennip
Keyword(s):  
Polymerase Chain Reaction ◽  
High Throughput ◽  
Bluetongue Virus ◽  
Chain Reaction ◽  
Virus Serotype ◽  
Polymerase Chain

Quantum dots for a high-throughput Pfu polymerase based multi-round polymerase chain reaction (PCR)

The Analyst ◽  
2018 ◽  
Vol 143 (5) ◽  
pp. 1259-1267 ◽  
Author(s):  
Fuming Sang ◽  
Zhizhou Zhang ◽  
Lin Yuan ◽  
Deli Liu
Keyword(s):  
Polymerase Chain Reaction ◽  
Quantum Dots ◽  
High Throughput ◽  
Chain Reaction ◽  
Round Polymerase Chain Reaction ◽  
Polymerase Chain

We developed a Pfu polymerase based multi-round PCR technique assisted by quantum dots (QDs).

scholarly journals Evaluation of a 384–Well Format for High-Throughput Real-Time Reverse Transcription Polymerase Chain Reaction for Avian Influenza Testing

2009 ◽  
Vol 21 (5) ◽  
pp. 679-683 ◽  
Author(s):  
Pamela J. Ferro ◽  
Jason Osterstock ◽  
Bo Norby ◽  
Geoffrey T. Fosgate ◽  
Blanca Lupiani
Keyword(s):  
Polymerase Chain Reaction ◽  
Avian Influenza ◽  
Real Time ◽  
High Throughput ◽  
Reverse Transcription ◽  
Virus Isolation ◽  
Rt Pcr ◽  
Chain Reaction ◽  
Response Planning ◽  
Polymerase Chain

As concerns over the global spread of highly pathogenic avian influenza H5N1 have heightened, more countries are faced with increased surveillance efforts and incident response planning for handling a potential outbreak. The incorporation of molecular techniques in most diagnostic laboratories has enabled fast and efficient testing of many agents of concern, including avian influenza. However, the need for high-throughput testing remains. In this study, the use of a 384–well format for high-throughput real-time reverse transcription polymerase chain reaction (real-time RT-PCR) testing for avian influenza is described. The analytical sensitivity of a real-time RT-PCR assay for avian influenza virus matrix gene with the use of both 96– and 384–well assay formats and serial dilutions of transcribed control RNA were comparable, resulting in similar limits of detection. Of 28 hunter-collected cloacal swabs that were positive by virus isolation, 26 (92.9%) and 27 (96.4%) were positive in the 96– and 384–well assays, respectively; of the 340 hunter-collected swabs that were negative by virus isolation, 45 (13.2%) and 23 (6.8%) were positive in the 96– and 384–well assays, respectively. The data presented herein supports the utility of the 384–well format in the event of an avian influenza outbreak for high-throughput real-time RT-PCR testing.

scholarly journals Positive nasal Staphylococcus aureus polymerase chain reaction assay is not sensitive in predicting concurrent or subsequent Staphylococcus aureus infection in critically ill patients

2020 ◽  
Vol 48 (3) ◽  
pp. 196-202
Author(s):  
Kalai C Kanagasingham ◽  
Kwok M Ho ◽  
J Owen Robinson
Keyword(s):  
Staphylococcus Aureus ◽  
Polymerase Chain Reaction ◽  
Critically Ill ◽  
Sensitivity And Specificity ◽  
Critically Ill Patients ◽  
High Specificity ◽  
Chain Reaction ◽  
Pcr Assay ◽  
Polymerase Chain ◽  
Mssa Infection

Staphylococcal infection is associated with significant morbidity and mortality in critically ill patients. Using data from 16,681 patients who had a nasal Staphylococcus aureus polymerase chain reaction (PCR) assay on admission to the intensive care unit (ICU) of Royal Perth Hospital between March 2006 and September 2016, this retrospective cohort study assessed whether nasal S. aureus colonisation on admission to an ICU was predictive of concurrent or subsequent S. aureus infections. Culture-proven S. aureus infections were identified using the hospital microbiology database. Of the 16,681 patients included, 565 (3.4%) had a positive methicillin-resistant S. aureus (MRSA) assay, 146 (0.9%) had a positive methicillin-sensitive S. aureus (MSSA) assay and eight (0.05%) had both positive MRSA and MSSA assays. Of those 565 patients with a positive MRSA PCR assay, 79 (13.8%) had concurrent or subsequent MRSA infections. Of those 146 patients with a positive MSSA PCR assay, only 5 (3.4%) had MSSA infection. The sensitivity and specificity for the MRSA PCR assay in predicting concurrent or subsequent MRSA infection were 72.7% (95% confidence intervals (CI) 63.4%–80.8%) and 97.0% (95% CI 96.8%–97.3%), respectively. The sensitivity and specificity for the MSSA PCR assay in predicting concurrent or subsequent MSSA infection were 3.3% (95% CI 1.1%–7.6%) and 99.1% (95% CI 98.9%–99.2%), respectively. Both nasal MRSA and MSSA PCR assays had a high specificity and negative predictive value in predicting MRSA and MSSA infections, respectively, suggesting that in centres without endemic S. aureus infections, a negative nasal MRSA or MSSA PCR assay may be useful to reduce unnecessary empirical antibiotic therapy against S. aureus.

scholarly journals Amplification of SPPS150 andSalmonella typhiDNA with a high throughput oscillating flow polymerase chain reaction device

2010 ◽  
Vol 4 (2) ◽  
pp. 024103 ◽  
Author(s):  
D. Sugumar ◽  
Asma Ismail ◽  
Manickam Ravichandran ◽  
Ismail Aziah ◽  
L. X. Kong
Keyword(s):  
Polymerase Chain Reaction ◽  
High Throughput ◽  
Oscillating Flow ◽  
Chain Reaction ◽  
Polymerase Chain ◽  
Reaction Device
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