Serotype Prediction for Frequently Isolated Serotypes of Streptococcus Pneumoniae by Heteroduplex Analysis and Modification of This Technique to Real-Time Fluorometric Nucleic Acid Detection System

2010 ◽  
Vol 30 (5) ◽  
pp. 1487-1492
Author(s):  
Ahmet PINAR ◽  
Burçin ŞENER ◽  
Şemsettin USTAÇELEBİ
Keyword(s):  
Streptococcus Pneumoniae ◽  
Nucleic Acid ◽  
Real Time ◽  
Detection System ◽  
Heteroduplex Analysis ◽  
Nucleic Acid Detection

Improvement and Application of qPCR (Real-Time Quantitative Polymerase Chain Reaction) Data Processing Method for Home-Made Integrated Nucleic Acid Detection System

2020 ◽  
Vol 20 (12) ◽  
pp. 7369-7375
Author(s):  
Yile Fang ◽  
Pei Liao ◽  
Zhu Chen ◽  
Hui Chen ◽  
Yanqi Wu ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Data Processing ◽  
Real Time ◽  
Detection System ◽  
Disease Diagnosis ◽  
Processing Algorithm ◽  
Clinical Samples ◽  
Nucleic Acid Detection ◽  
Qpcr Data ◽  
Data Processing Algorithm

Because it has many advantages such as rapidity and accuracy, nucleic acid detection is applied to infectious disease diagnosis more and more. An automatic integrated nucleic acid detection system based on real-time PCR is developed by our research group to conduct point-of-care testing of infectious pathogens. The home-made detection system collects fluorescence data in each PCR cycle through an integrated dual-channel fluorescence detection module and then real-time fluorescence curves are drawn by the software, which can tell the results of the diagnostics after some processing and analysis. However, owing to the disturbance of the environment or the imperfect of nucleic acid extraction before PCR, the fluorescence curves sometimes may contain several abnormal points. For the purpose of enhancing its ability to deal with these iffy curves and improve the accuracy of the testing results, in this study, the SDM-based qPCR data processing algorithm was studied and 11 groups of qPCR data that have different flaws from the clinical samples detected by this system were chosen to prove the practicability of the method. In comparison with the conventional threshold-based method, the Cq values calculated by the SDM-based method were more close to the actual values, meaning it can overcome the shortcomings of the conventional methods such as being unable to accommodate noise and being unable to avoiding abnormal data. With the improvement of this data processing algorithm, the stability of our system and the reliability and accuracy of the results are greatly improved.

Identifying the etiologic role of Parvovirus B19 in non-immune hydrops fetalis by histopathology, immunohistochemistry and nucleic acid testing: a retrospective study

Open Medicine ◽  
2007 ◽  
Vol 2 (3) ◽  
pp. 271-279 ◽  
Author(s):  
Koray Ergunay ◽  
Gulcin Altinok ◽  
Bora Gurel ◽  
Ahmet Pinar ◽  
Arzu Sungur ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Real Time ◽  
San Francisco ◽  
Real Time Pcr ◽  
Nested Pcr ◽  
Parvovirus B19 ◽  
Etiologic Agent ◽  
Hydrops Fetalis ◽  
Nucleic Acid Detection

AbstractIntrauterine Parvovirus B19 infections may cause fetal anemia, non-immune hydrops fetalis or abortion. This study focuses on the pathogenic role of Parvovirus B19 in non-immune hydrops fetalis at Hacettepe University, a major reference hospital in Turkey. Twenty-two cases of non-immune hydrops fetalis were retrospectively selected out of a total of 431 hydrops fetalis specimens from the Department of Pathology archieves. Paraffine embedded tissue sections from placental and liver tissues from each case were evaluated by histopathology, immunohistochemistry, nested PCR and commercial quantitative Real-time PCR. Viral DNA was detected in placental tissues by Real-time PCR in 2 cases (2/22, 9.1%) where histopathology also revealed changes suggestive of Parvovirus B19 infection. No significant histopathologic changes were observed for the remaining sections. Nested PCR that targets the VP1 region of the viral genome and immunohistochemistry for viral capsid antigens were negative for all cases. As a result, Parvovirus B19 is identified as the etiologic agent for the development of non-immune hydrops fetalis for 9.1% of the cases in Hacettepe University, Turkey. Real-time PCR is observed to be an effective diagnostic tool for nucleic acid detection from paraffine embedded tissues. Part of this study was presented as a poster at XIIIth International Congress of Virology, San Francisco, USA (Abstract V-572).

scholarly journals Scanning single-molecule counting system for Eprobe with highly simple and effective approach

PLoS ONE ◽  
2020 ◽  
Vol 15 (12) ◽  
pp. e0243319
Author(s):  
Takeshi Hanami ◽  
Tetsuya Tanabe ◽  
Takuya Hanashi ◽  
Mitsushiro Yamaguchi ◽  
Hidetaka Nakata ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Single Molecule ◽  
Detection System ◽  
Signal To Noise Ratio ◽  
High Sensitivity ◽  
Nucleic Acid Detection ◽  
Digital Measurement ◽  
Excitation Light ◽  
Target Nucleic Acid ◽  
Fluorescent Molecules

Here, we report a rapid and ultra-sensitive detection technique for fluorescent molecules called scanning single molecular counting (SSMC). The method uses a fluorescence-based digital measurement system to count single molecules in a solution. In this technique, noise is reduced by conforming the signal shape to the intensity distribution of the excitation light via a circular scan of the confocal region. This simple technique allows the fluorescent molecules to freely diffuse into the solution through the confocal region and be counted one by one and does not require statistical analysis. Using this technique, 28 to 62 aM fluorescent dye was detected through measurement for 600 s. Furthermore, we achieved a good signal-to-noise ratio (S/N = 2326) under the condition of 100 pM target nucleic acid by only mixing a hybridization-sensitive fluorescent probe, called Eprobe, into the target oligonucleotide solution. Combination of SSMC and Eprobe provides a simple, rapid, amplification-free, and high-sensitive target nucleic acid detection system. This method is promising for future applications to detect particularly difficult to design primers for amplification as miRNAs and other short oligo nucleotide biomarkers by only hybridization with high sensitivity.

scholarly journals Schnellnachweis von SARS-CoV-2 mit recombinase polymerase amplification

BIOspektrum ◽  
2020 ◽  
Vol 26 (6) ◽  
pp. 624-627
Author(s):  
Ole Behrmann ◽  
Iris Bachmann ◽  
Frank Hufert ◽  
Gregory Dame
Keyword(s):  
Nucleic Acid ◽  
Real Time ◽  
Dna Polymerase ◽  
Fluorescent Probes ◽  
Reverse Transcription ◽  
Nucleic Acid Detection ◽  
Detection Scheme ◽  
Recombination Proteins ◽  
Target Dna ◽  
Rapid Amplification

Abstract The COVID-19 pandemic highlights the need for fast and simple assays for nucleic acid detection. As an isothermal alternative to RT-qPCR, we outline the development of a detection scheme for SARS-CoV-2 RNA based on reverse transcription recombinase polymerase amplification (RT-RPA) technology. RPA uses recombination proteins in combination with a DNA polymerase for rapid amplification of target DNA at a constant temperature (39–42 °C) within 10 to 20 minutes and can be monitored in real-time with fluorescent probes.

Design and Implementation of Experimental Consumable Management Device for the Automatic Nucleic Acid Detection System

2016 ◽  
Vol 16 (7) ◽  
pp. 7069-7076
Author(s):  
Jun Yu ◽  
Zhu Chen ◽  
Chao Wang ◽  
Yana Hu ◽  
Hongming Dong ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Detection System ◽  
Nucleic Acid Detection ◽  
Design And Implementation

Mechanical Gripper Design and Force Analysis of Microplates for Automated High-Throughput Nucleic Acid Detection System

2020 ◽  
Vol 20 (3) ◽  
pp. 1401-1408 ◽  
Author(s):  
Chao Wang ◽  
Zhukang Guo ◽  
He Zhu ◽  
Nongyue He ◽  
Zhu Chen ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
High Throughput ◽  
Detection System ◽  
Nucleic Acid Detection ◽  
Force Analysis ◽  
Control Board ◽  
Absolute Position ◽  
Element Analysis ◽  
Position Data ◽  
Master Control

In the automated high-throughput nucleic acid detection system, we need to grip and transfer consumables frequently when carrying out multichannel nucleic acid detection. In order to ensure the efficiency of experiments and solve problems of the deflection and drop when transferring microplates, we design a self-locking mechanical gripper which consists of a rotary positioning module and a gripping module. The absolute position encoder fixed on the top of the stepper motor can collect the position data of the mechanical gripper in real time and send them to the master control board based on STM32 for processing, which ensures the accuracy of the movement of the mechanical gripper. We used SolidWorks to build models of the mechanical gripper and different microplates, and we carried on finite element analysis of microplates to find the suitable gripping position. Through the force analysis, we obtained the pressure distribution and the deformation of different microplates, and defined the effective gripping areas, which is important to the grip and transfer of microplates.

scholarly journals High-throughput HTLV-1 proviral DNA detection system using a nucleic acid extraction robot and real-time PCR detection.

2001 ◽  
Vol 47 (3) ◽  
pp. 378-383 ◽  
Author(s):  
Chieko Matsumoto ◽  
Rieko Shiozawa ◽  
Shigeki Mitsunaga ◽  
Akiko Ichikawa ◽  
Rika Ishiwatari ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Real Time ◽  
High Throughput ◽  
Real Time Pcr ◽  
Detection System ◽  
Dna Detection ◽  
Pcr Detection ◽  
Acid Extraction ◽  
Nucleic Acid Extraction ◽  
Proviral Dna

scholarly journals A Chemical-Enhanced System for CRISPR-Based Nucleic Acid Detection

2021 ◽  
Author(s):  
Zihan Li ◽  
Wenchang Zhao ◽  
Shixin Ma ◽  
Zexu Li ◽  
Yingjia Yao ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Detection System ◽  
Point Of Care ◽  
Detection Sensitivity ◽  
Nucleic Acid Detection ◽  
Chemical Additives ◽  
Lateral Flow Strip ◽  
Viral Pathogens ◽  
Detection Systems ◽  
System Robustness

The CRISPR-based nucleic acid detection systems such as SHERLOCK, DETECTR and HOLMES have shown great potential for point-of-care testing of viral pathogens, especially in the context of COVID-19 pandemic. Here we optimize several key parameters of reaction chemistry and develop a Chemical Enhanced CRISPR Detection system for nucleic acid (termed CECRID). For the Cas12a/Cas13a-based signal detection phase, we determine buffer conditions and substrate range for optimal detection performance. By comparing several chemical additives, we find that addition of L-proline can secure or enhance Cas12a/Cas13a detection capability. For isothermal amplification phase with typical LAMP and RPA methods, inclusion of L-proline can also enhance specific target amplification as determined by CRISPR detection. Using SARS-CoV-2 pseudovirus, we demonstrate CECRID has enhanced detection sensitivity over chemical additive-null method with either fluorescence or lateral flow strip readout. Thus, CECRID provides an improved detection power and system robustness towards practical application of CRISPR-based diagnostics.

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