Thermally multiplexed polymerase chain reaction

Amplification of multiple unique genetic targets using the polymerase chain reaction (PCR) is commonly required in molecular biology laboratories. Such reactions are typically performed either serially or by multiplex PCR. Serial reactions are time consuming, and multiplex PCR, while powerful and widely used, can be prone to amplification bias, PCR drift, and primer-primer interactions. We present a new thermocycling method, termed thermal multiplexing, in which a single heat source is uniformly distributed and selectively modulated for independent temperature control of an array of PCR reactions. Thermal multiplexing allows amplification of multiple targets simultaneously—each reaction segregated and performed at optimal conditions. We demonstrate the method using a microfluidic system consisting of an infrared laser thermocycler, a polymer microchip featuring 1 μl, oil-encapsulated reactions, and closed-loop pulse-width modulation control. Heat transfer modeling is used to characterize thermal performance limitations of the system. We validate the model and perform two reactions simultaneously with widely varying annealing temperatures (48 °C and 68 °C), demonstrating excellent amplification. In addition, to demonstrate microfluidic infrared PCR using clinical specimens, we successfully amplified and detected both influenza A and B from human nasopharyngeal swabs. Thermal multiplexing is scalable and applicable to challenges such as pathogen detection where patients presenting non-specific symptoms need to be efficiently screened across a viral or bacterial panel.     

Rapid multi sample DNA amplification using rotary-linear polymerase chain reaction device (PCRDisc)

Multiple sample DNA amplification was done by using a novel rotary-linear motion polymerase chain reaction (PCR) device. A simple compact disc was used to create the stationary sample chambers which are individually temperature controlled. The PCR was performed by shuttling the samples to different temperature zones by using a combined rotary-linear movement of the disc. The device was successfully used to amplify up to 12 samples in less than 30 min with a sample volume of 5 μl. A simple spring loaded heater mechanism was introduced to enable good thermal contact between the samples and the heaters. Each of the heater temperatures are controlled by using a simple proportional–integral–derivative pulse width modulation control system. The results show a good improvement in the amplification rate and duration of the samples. The reagent volume used was reduced to nearly 25% of that used in conventional method.     

Detection ofNeisseria Gonorrhoeae by polymerase chain reaction (PCR)

Three different sets of primers were designed using FASTA homology search and PRIMERSELECT for the specific detection ofNeisseria gonorrhoeae using polymerase chain reaction (PCR). These primers amplified the highly conserved regions of genes for Open Reading Frame (ORF), Outer Membrane Protein (OMP) and 23S rRNA sequences ofN. gonorrhoeae. Each of the PCR primer set was evaluated using the DNA samples isolated from eight different positive isolates ofN. gonorrhoeae cultured from urethral swabs of patients visiting Maulana Azad Medical College and Safdarjung Hospital. Amplification products were analyzed on agarose gel electrophoresis. Two sets of PCR primers, designated as Ngu1/Ngu2 and Ngu5/Ngu6, specific for ORF and OMP gene respectively, amplified four regions of the gene which may help to differentiate the various strains ofN. gonorrhoeae infecting indigenous population. In contrast, a single, specific PCR product of 650 bp was visualized on agarose gel with primers Ngu3/Ngu4, amplifying the 23S rRNA gene. Under optimum conditions, as low as 25ng of DNA isolated from eight different clinical strains ofN. gonorrhoeae could be detected by PCR using Ngu3/Ngu4 set of primers. Our results suggested that Ngu3/Ngu4 could serve as good primers for the specific, reproducible and sensitive diagnosis ofNeisseria gonorrhoeae from clinical samples.     

Amplification of SPPS150 and Salmonella typhi DNA with a high throughput oscillating flow polymerase chain reaction device

In this paper, a novel oscillating flow polymerase chain reaction (PCR) device was designed and fabricated to amplify SPPS150 and salmonella typhi. In this new design, the samples are shuttled (oscillating flow) inside a microfluidic chip to three different temperature zones required for DNA amplification. The amplification cycle time has markedly been reduced as the reagent volume used was only about 25% of that used in conventional PCRs. Bubble formation and adsorption issues commonly associated to chip based PCR were also eliminated. Based on the performance evaluated, it is demonstrated that this oscillating flow PCR has the advantages of both the stationary chamber and continuous flow PCR devices.     

Direct diagnosis ofMycobacterium tuberculosis in blood samples of HIV infected patients by polymerase chain reaction

We have developed a simple, economical and reproducible method for processing blood samples from HIV infected patients for diagnosis of tuberculosis. The procedure was validated on 55 samples selected for tuberculosis based on clinical criteria. 52 patients had radiological changes indicative of pulmonary tuberculosis of which only 28 were positive for AFB in sputum (sensitivity 54%) and 27 for tuberculin (sensitivity 52%). 26 HIV positive patients who showed positive X-ray did not react to tuberculin. The genus PCR probe missed 3 samples (sensitivity 94%) compared to X-ray.M.tuberculosis was detected in the blood of all X-ray positive cases by PCR using TB400 probe (sensitivity 100%) and another probe forM. tuberculosis, IS6110, missed 6 of them (sensitivity 88% compared to X-ray and 89% compared to TB400). It is proposed that this simple sample processing method could be used to screen all blood samples quickly for mycobacteremia using the genus PCR and only those positive for mycobacteria need to be tested forM.tuberculosis. This would save the scarce resources and time by reducing significantly the number of samples to be screened for species confirmation.     

Evaluation of polymerase chain reaction for rapid diagnosis of clinically suspected tuberculous pleurisy

Pleural effusion is one of the commonest presentations of tuberculosis, the clinical manifestations being typically abrupt resembling bacterial pneumonia. Since delayed hypersensitivity is the underlying immune response, bacterial load is very low. Owing to these facts, tuberculous pleurisy as an extra-pulmonary disease poses a diagnostic dilemma. The conventional bacteriological methods rarely detect Mycobacterium tuberculosis in pleural fluid and are of limited use in diagnosis of tuberculous pleurisy. We evaluated the efficacy of polymerase chain reaction (PCR) in the diagnosis of tuberculous pleurisy by targeting the gene segment coding for MPB64 protein specific forMycobacterium tuberculosis. Based on the clinical criteria, 82 patients with lymphocytic exudative pleural effusion were included in the study. Patients were analyzed in two groups; one group consisting of 48 patients of tubercular pleural effusion confimed by various diagnostic procedures and another group of 34 patients comprising of non-tubercular pleural effusion. There were no false positive results by PCR and the specificity worked out to be 100%. Twenty two patients tested positive for Mantoux with a sensitivity of 45%. ZN-staining for AFB was found in samples from 15 patients (20% sensitivity). ADA was positive for 28 patients with a sensitivity of 53%. PCR was positive for 32/48 patients (67% sensitivity). Thus, PCR was found to be more sensitive than any other conventional method in diagnosis of clinically suspected tubercular pleurisy.     

Single molecule analysis of bacterial polymerase chain reaction products in submicrometer fluidic channels

Laser induced fluorescence in submicrometer fluidic channels was used to characterize the synthesis of polymerase chain reaction (PCR) products from a model bacterial system in order to explore the advantages and limitations of on chip real time single molecule PCR analysis. Single oligonucleotide universal bacterial primers and PCR amplicons from the 16S rDNA of Thermobifida fusca (325 bp) were directly detected at all phases of the reaction with low sample consumption and without post-amplification purification or size screening. Primers were fluorescently labeled with single Alexa Fluor 488 or Alexa Fluor 594 fluorophores, resulting in double labeled, two color amplicons. PCR products were driven electrokinetically through a fused silica channel with a 250 nm by 500 nm rectangular cross section. Lasers with 488 nm and 568 nm wavelengths were focused and overlapped on the channel for fluorescence excitation. All molecules entering the channel were rapidly and uniformly analyzed. Photon burst analysis was used to detect and identify individual primers and amplicons, and fluorescence correlation and cross-correlation spectroscopy were used to account for analyte flow speed. Conventional gel and capillary electrophoresis were also used to characterize the PCR amplification, and the results of differences in detection sensitivity and analyte discrimination were examined. Limits were imposed by the purity and labeling efficiency of the PCR reagents, which must be improved in parallel with increases in detection sensitivity.     

Reduction of water evaporation in polymerase chain reaction microfluidic devices based on oscillating-flow

Producing polymeric or hybrid microfluidic devices operating at high temperatures with reduced or no water evaporation is a challenge for many on-chip applications including polymerase chain reaction (PCR). We study sample evaporation in polymeric and hybrid devices, realized by glass microchannels for avoiding water diffusion toward the elastomer used for chip fabrication. The method dramatically reduces water evaporation in PCR devices that are found to exhibit optimal stability and effective operation under oscillating-flow. This approach maintains the flexibility, ease of fabrication, and low cost of disposable chips, and can be extended to other high-temperature microfluidic biochemical reactors.     

Detection of Helicobacter pylori using nested polymerase chain reaction in gastric biopsy samples

Helicobacter pylori remains a controversial organism with regards to humans, its epidemiology still unclear nearly two decades after discovery. The present study was undertaken to estimate the prevalence of the organism in the gastrointestinal tract in symptomatic and asymptomatic subjects to understand its precise natural history in India. A total of 154 specimens were a part of the study. These included gastric biopsies from peptic ulcer disease and Non ulcer dyspepsia subjects, as visualized on endoscopy, saliva and stool samples from apparently normal healthy adults. Nested polymerase chain reaction was performed using the primers Hp1, Hp2, Hp3 targeting 16S rRNA gene. A prevalence of 65.1%, 100%, 66.7%, and 73.3% respectively was observed by polymerase chain reaction. No association was observed between the H.pylori status and the disease condition of the patient.     

DNA capture-probe based separation of double-stranded polymerase chain reaction amplification products in poly(dimethylsiloxane) microfluidic channels

Herein, we describe the development of a novel primer system that allows for the capture of double-stranded polymerase chain reaction (PCR) amplification products onto a microfluidic channel without any preliminary purification stages. We show that specially designed PCR primers consisting of the main primer sequence and an additional “tag sequence” linked through a poly(ethylene glycol) molecule can be used to generate ds-PCR amplification products tailed with ss-oligonucleotides of two forensically relevant genes (amelogenin and human c-fms (macrophage colony-stimulating factor) proto-oncogene for the CSF-1 receptor (CSF1PO). Furthermore, with a view to enriching and eluting the ds-PCR products of amplification on a capillary electrophoretic-based microfluidic device we describe the capture of the target ds-PCR products onto poly(dimethylsiloxane) microchannels modified with ss-oligonucleotide capture probes.     

Detection of hemoglobin E in Endhra Pradesh: Mutational analysis using polymerase chain reaction and restriction enzyme Mnl 1

Hemoglobin E (beta-26^{Glutamic acid→Lysine}) is the second most prevalent hemoglobin variant in the world. 293 blood samples from cases referred from several hospitals in the region of Andhra Pradesh were screened for the detection of hemoglobinopathies. Four samples were found to be in heterozygous state for Hb E condition. Mutation in two of these heterozygotes was analysed using a 722 base pair (bp) amplified DNA fragment from beta-globin gene and restriction enzyme Mnl 1. A 232bp DNA fragment was found to be associated with the Hb E mutation.     

Experimental validation of numerical study on thermoelectric-based heating in an integrated centrifugal microfluidic platform for polymerase chain reaction amplification

A comprehensive study involving numerical analysis and experimental validation of temperature transients within a microchamber was performed for thermocycling operation in an integrated centrifugal microfluidic platform for polymerase chain reaction (PCR) amplification. Controlled heating and cooling of biological samples are essential processes in many sample preparation and detection steps for micro-total analysis systems. Specifically, the PCR process relies on highly controllable and uniform heating of nucleic acid samples for successful and efficient amplification. In these miniaturized systems, the heating process is often performed more rapidly, making the temperature control more difficult, and adding complexity to the integrated hardware system. To gain further insight into the complex temperature profiles within the PCR microchamber, numerical simulations using computational fluid dynamics and computational heat transfer were performed. The designed integrated centrifugal microfluidics platform utilizes thermoelectrics for ice-valving and thermocycling for PCR amplification. Embedded micro-thermocouples were used to record the static and dynamic thermal responses in the experiments. The data collected was subsequently used for computational validation of the numerical predictions for the system response during thermocycling, and these simulations were found to be in agreement with the experimental data to within ∼97%. When thermal contact resistance values were incorporated in the simulations, the numerical predictions were found to be in agreement with the experimental data to within ∼99.9%. This in-depth numerical modeling and experimental validation of a complex single-sided heating platform provide insights into hardware and system design for multi-layered polymer microfluidic systems. In addition, the biological capability along with the practical feasibility of the integrated system is demonstrated by successfully performing PCR amplification of a Group B Streptococcus gene.     

The role of DNA diffusion in solid phase polymerase chain reaction with gel-immobilized primers in planar and capillary microarray format

The solid phase polymerase chain reaction (PCR) on a gel-based microarray system was studied under various durations of individual stages of the PCR cycle and spatial restriction of the reaction volume. Combining the experimental study with numerical modeling, we demonstrated that the diffusion of the PCR product in and out of a microarray element during the annealing and melting stages, respectively, is the main factor responsible for distinctive features of the studied type of PCR. The restriction of reaction volume leads to faster PCR signal growth. Particularly, the capillary array, whereby gel-based microarray elements are located on a glass bar inserted into capillary chamber, was found to be a suitable format for the development of the platform.     

Inter-laboratory ring trial to evaluate real-time reverse transcription polymerase chain reaction methods used for detection of infectious pancreatic necrosis virus in Chile

BackgroundInfectious Pancreatic Necrosis Virus (IPNV) is the etiological agent of a highly contagious disease that affects salmonids. In Chile, the second worldwide salmon producer, IPNV causes great economic loss and is one of the most frequently detected pathogens. Due to its high level of persistence and the lack of information about the efficiency of its diagnostic techniques, the National Reference Laboratory (NRL) for IPNV in Chile performed the first inter-laboratory ring trial, to evaluate the sensitivity, specificity and repeatability of the qRT-PCR detection methods used in the country.ResultsResults showed 100% in sensitivity and specificity in most of the laboratories. Only three of the twelve participant laboratories presented problems in sensitivity and one in specificity. Problems in specificity (false positives) were most likely caused by cross contamination of the samples, while errors in sensitivity (false negatives) were due to detection problems of the least concentrated viral sample. Regarding repeatability, many of the laboratories presented great dispersion of the results (Ct values) for replicate samples over the three days of the trial. Moreover, large differences in the Ct values for each sample were detected among all the laboratories.ConclusionsOverall, the ring trial showed high values of sensitivity and specificity, with some problems of repeatability and inter-laboratory variability. This last issue needs to be addressed in order to allow harmonized diagnostic of IPNV within the country. We recommend the use of the NRL methods as validated and reliable qRT-PCR protocols for the detection of IPNV.     

Cool down computer chips with liquid metal device driven by the heat of chips

With the soaring advances in computational speed, thermal management becomes a major concern in computer systems. To remove heat generated by computer chips or very large scale integrated circuits, a research team headed by Prof. LIU Jing with the CAS Technical Institute of Physics and Chemistry in Beijing has developed a novel liquid metal cooling system that can be powered by the very heat produced by computer chips.     

Polymerase chain reaction: It’s diagnostic application

The development of the Polymerase Chain Reaction (PCR) has been a major technical milestone in molecular genetics with the greatest impact on research, in rapid medical diagnosis and in studying the pathogenesis of disease. This study highlights the practical applications of polymerase chain reaction in diagnosis and includes a recent application of PCR in differentiating polio from other nonpolio enteroviruses.     

浅谈钛在海水冷却换热器中的应用优势

海水容易对传统的换热器产生腐蚀作用,缩短设备的使用寿命。长时间的腐蚀,不仅增加设备维护工作,造成经济损失,而且容易造成设备漏泄,产生安全事故,具有极大的安全隐患,寻找一种适当的材质,从源头上防止海水腐蚀势在必行。通过大量的研究,钛因其具有的特殊性能从众多的材质中脱颖而出,成为海水冷却换热器的首选。     

太阳能空气集热器应用于建筑供暖的研究

本文从国内外太阳能空气集热器的研究、技术水平和应用现状,结合自身对太阳能空气集热器的研究所取得的阶段成果,分析此种集热器应用于西藏地区建筑供暖的可行性,并对所需要进一步开展的研究以及方法、未来市场前景进行了技术描述.