Analysis of PCR Kinetics inside a Microfluidic DNA Amplification System

Assessing Different PCR Master Mixes for Ultrarapid DNA Amplification: Important Analytical Parameters

The basic principles of ultrafast plasmonic PCR have been promulgated in the scientific and technological literature for over a decade. Yet, its everyday diagnostic utility remains unvalidated in pre-clinical and clinical settings. Although the impressive speed of plasmonic PCR reaction is well-documented, implementing this process into a device form compatible with routine diagnostic tasks has been challenging. Here, we show that combining careful system engineering and process control with innovative and specific PCR biochemistry makes it possible to routinely achieve a sensitive and robust "10 min" PCR assay in a compact and lightweight system. The critical analytical parameters of PCR reactions are discussed in the current instrument setting.

An integrated microfluidic chip for nucleic acid extraction and continued cdPCR detection of pathogens

This paper introduces an enclosed microfluidic chip that integrates sample preparation and the chamber-based digital polymerase chain reaction (cdPCR). The sample preparation of the chip includes nucleic acid extraction and purification based on magnetic beads, which adsorb nucleic acids by moving around the reaction chambers to complete the reactions including lysis, washing, and elution. The cdPCR area of the chip consists of tens of thousands of regularly arranged microchambers. After the sample preparation processes are completed, the purified nucleic acid can be directly introduced into the microchambers for amplification and detection on the chip. The nucleic acid extraction performance and digital quantification performance of the system were examined using synthetic SARS-CoV-2 plasmid templates at concentrations ranging from 10¹-10⁵ copies per μL. Further on, a simulated clinical sample was used to test the system, and the integrated chip was able to accurately detect SARS-CoV-2 virus particle samples doped with interference (saliva) with a detection limit of 10 copies per μL. This integrated system could provide a promising tool for point-of-care testing of pathogenic infections.

Low-Temperature Loop-Mediated Isothermal Amplification Operating at Physiological Temperature

Loop-mediated isothermal amplification (LAMP) is one of the most widely used isothermal amplification technologies in molecular diagnostics. However, LAMP operates at a high temperature of 65 °C; thus, operating LAMP at a lower temperature is desirable to maximize its usefulness for on-site diagnosis. In this study, we propose a new version of LAMP, termed low-temperature LAMP, which operates at the physiological temperature of 37 °C. Low-temperature LAMP differs from conventional LAMP operating at 65 °C in terms of the concentrations of MgSO₄ and deoxyribonucleoside triphosphates (dNTPs), as well as the lengths of DNA probes, which are crucial for the execution of low-temperature LAMP. Under the optimal conditions, the amplification efficiency of low-temperature LAMP is comparable to that of conventional LAMP. In addition, the ligation reaction at 37 °C, which is necessary to detect actual target nucleic acids, is combined without altering the temperature, enabling the identification of miR-21, a cancer-promoting oncogenic miRNA, with high sensitivity and selectivity. The method described in this paper does not require expensive DNA modifications or special additives and would facilitate the widespread application of LAMP in facility-limited or point-of-care settings, paving the way to improvements in other isothermal-amplification-based techniques.

Detection Method for Tomato Leaf Mildew Based on Hyperspectral Fusion Terahertz Technology

Leaf mildew is a common disease of tomato leaves. Its detection is an important means to reduce yield loss from the disease and improve tomato quality. In this study, a new method was developed for the multi-source detection of tomato leaf mildew by THz hyperspectral imaging through combining internal and external leaf features. First, multi-source information obtained from tomato leaves of different disease grades was extracted by near-infrared hyperspectral imaging and THz time-domain spectroscopy, while the influence of low-frequency noise was removed by the Savitzky Golay (SG) smoothing algorithm. A genetic algorithm (GA) was used to optimize the selection of the characteristic near-infrared hyperspectral band. Principal component analysis (PCA) was employed to optimize the THz characteristic absorption spectra and power spectrum dimensions. Recognition models were developed for different grades of tomato leaf mildew infestation by incorporating near-infrared hyperspectral imaging, THz absorbance, and power spectra using the backpropagation neural network (BPNN), and the models had recognition rates of 95%, 96.67%, and 95%, respectively. Based on the near-infrared hyperspectral features, THz time-domain spectrum features, and classification model, the probability density of the posterior distribution of tomato leaf health parameter variables was recalculated by a Bayesian network model. Finally, a fusion diagnosis and health evaluation model of tomato leaf mildew with hyperspectral fusion THz was established, and the recognition rate of tomato leaf mildew samples reached 97.12%, which improved the recognition accuracy by 0.45% when compared with the single detection method, thereby achieving the accurate detection of facility diseases.

Kinetics of elementary steps in loop-mediated isothermal amplification (LAMP) show that strand invasion during initiation is rate-limiting

Loop-mediated isothermal amplification (LAMP) has proven to be easier to implement than PCR for point-of-care diagnostic tests. However, the underlying mechanism of LAMP is complicated and the kinetics of the major steps in LAMP have not been fully elucidated, which prevents rational improvements in assay development. Here we present our work to characterize the kinetics of the elementary steps in LAMP and show that: (i) strand invasion / initiation is the rate-limiting step in the LAMP reaction; (ii) the loop primer plays an important role in accelerating the rate of initiation and does not function solely during the exponential amplification phase and (iii) strand displacement synthesis by Bst-LF polymerase is relatively fast (125 nt/s) and processive on both linear and hairpin templates, although with some interruptions on high GC content templates. Building on these data, we were able to develop a kinetic model that relates the individual kinetic experiments to the bulk LAMP reaction. The assays developed here provide important insights into the mechanism of LAMP, and the overall model should be crucial in engineering more sensitive and faster LAMP reactions. The kinetic methods we employ should likely prove useful with other isothermal DNA amplification methods.

Application of Microfluidics for Bacterial Identification

Bacterial infections continue to pose serious public health challenges. Though anti-bacterial therapeutics are effective remedies for treating these infections, the emergence of antibiotic resistance has imposed new challenges to treatment. Often, there is a delay in prescribing antibiotics at initial symptom presentation as it can be challenging to clinically differentiate bacterial infections from other organisms (e.g., viruses) causing infection. Moreover, bacterial infections can arise from food, water, or other sources. These challenges have demonstrated the need for rapid identification of bacteria in liquids, food, clinical spaces, and other environments. Conventional methods of bacterial identification rely on culture-based approaches which require long processing times and higher pathogen concentration thresholds. In the past few years, microfluidic devices paired with various bacterial identification methods have garnered attention for addressing the limitations of conventional methods and demonstrating feasibility for rapid bacterial identification with lower biomass thresholds. However, such culture-free methods often require integration of multiple steps from sample preparation to measurement. Research interest in using microfluidic methods for bacterial identification is growing; therefore, this review article is a summary of current advancements in this field with a focus on comparing the efficacy of polymerase chain reaction (PCR), loop-mediated isothermal amplification (LAMP), and emerging spectroscopic methods.

A Portable Continuous-Flow Polymerase Chain Reaction Chip Device Integrated with Arduino Boards for Detecting Colla corii asini

Food security is a significant issue in modern society. Because morphological characters are not reliable enough to distinguish authentic traditional Chinese medicines, it is essential to establish an effective and applicable method to identify them to protect people's health. Due to the expensive cost of the manufacturing process and the large volume of the analytical system, the need to build a portable and cheap device is urgent. This work describes the development of a portable nucleic acid amplification device integrated with thermal control and liquid pumping connecting to Arduino boards. We present a novel microfluidic polymerase chain reaction (PCR) chip with symmetric isothermal zones. The total chip volume is small, and only one Arduino board is needed for thermal control. We assemble a miniaturized liquid pump and program an Arduino file to push the sample mixture into the chip to implement the PCR process. In the proposed operation, the Nusselt number of the sample flow is less than one, and the heat transfer is conduction only. Then we can ensure temperature uniformity in specific reaction regions. A Colla corii asini DNA segment of 200 bp is amplified to evaluate the PCR performance under the various operational parameters. The initial concentration for accomplishing the PCR process is at least 20 ng/μL at the flow rate of 0.4 μL/min in the portable continuous flow PCR (CFPCR) device. To our knowledge, our group is the first to introduce Arduino boards into the heat control and sample pumping modules for a CFPCR device.

A Rapid Detection Method for Fungal Spores from Greenhouse Crops Based on CMOS Image Sensors and Diffraction Fingerprint Feature Processing

The detection and control of fungal spores in greenhouse crops are important for stabilizing and increasing crop yield. At present, the detection of fungal spores mainly adopts the method of combining portable volumetric spore traps and microscope image processing. This method is problematic as it is limited by the small field of view of the microscope and has low efficiency. This study proposes a rapid detection method for fungal spores from greenhouse crops based on CMOS image sensors and diffraction fingerprint feature processing. We built a diffraction fingerprint image acquisition system for fungal spores of greenhouse crops and collected diffraction fingerprint images of three kinds of fungal spores. A total of 13 diffraction fingerprint features were selected for the classification of fungal spores. These 13 characteristic values were divided into 3 categories, main bright fringe, main dark fringe, and center fringe. Then, these three features were calculated to obtain the Peak to Center ratio (PCR), Valley to Center ratio, and Peak to Valley ratio (PVR). Based on these features, logistics regression (LR), K nearest neighbor (KNN), random forest (RF), and support vector machine (SVM) classification models were built. The test results show that the SVM model has a better overall classification performance than the LR, KNN, and RF models. The average accuracy rate of the recognition of three kinds of fungal spores from greenhouse crops under the SVM model was 92.72%, while the accuracy rates of the LR, KNN, and RF models were 84.97%, 87.44%, and 88.72%, respectively. The F1-Score value of the SVM model was higher, and the overall average value reached 89.41%, which was 11.12%, 7.18%, and 5.57% higher than the LR, KNN, and RF models, respectively. Therefore, the method proposed in this study can be used for the remote identification of three fungal spores which can provide a reference for the identification of fungal spores in greenhouse crops and has the advantages of low cost and portability.

Multi-objective optimisation of polymerase chain reaction continuous flow systems

A surrogate-enabled multi-objective optimisation methodology for a continuous flow Polymerase Chain Reaction (CFPCR) systems is presented, which enables the effect of the applied PCR protocol and the channel width in the extension zone on four practical objectives of interest, to be explored. High fidelity, conjugate heat transfer (CHT) simulations are combined with Machine Learning to create accurate surrogate models of DNA amplification efficiency, total residence time, total substrate volume and pressure drop throughout the design space for a practical CFPCR device with sigmoid-shape microfluidic channels. A series of single objective optimisations are carried out which demonstrate that DNA concentration, pressure drop, total residence time and total substrate volume within a single unitcell can be improved by up to [Formula: see text]5.7%, [Formula: see text]80.5%, [Formula: see text]17.8% and [Formula: see text]43.2% respectively, for the practical cases considered. The methodology is then extended to a multi-objective problem, where a scientifically-rigorous procedure is needed to allow designers to strike appropriate compromises between the competing objectives. A series of multi-objective optimisation results are presented in the form of a Pareto surface, which show for example how manufacturing and operating cost reductions from device miniaturisation and reduced power consumption can be achieved with minimal impact on DNA amplification efficiency. DNA amplification has been found to be strongly related to the residence time in the extension zone, but not related to the residence times in denaturation and annealing zones.

Integrated microdevice with a windmill-like hole array for the clog-free, efficient, and self-mixing enrichment of circulating tumor cells

Circulating tumor cells (CTCs) have tremendous potential to indicate disease progression and monitor therapeutic response using minimally invasive approaches. Considering the limitations of affinity strategies based on their cost, effectiveness, and simplicity, size-based enrichment methods that involve low-cost, label-free, and relatively simple protocols have been further promoted. Nevertheless, the key challenges of these methods are clogging issues and cell aggregation, which reduce the recovery rates and purity. Inspired by the natural phenomenon that the airflow around a windmill is disturbed, in this study, a windmill-like hole array on the SU-8 membrane was designed to perturb the fluid such that cells in a fluid would be able to self-mix and that the pressure acting on cells or the membrane would be dispersed to allow a greater velocity. In addition, based on the advantages of fluid coatings, a lipid coating was used to modify the membrane surface to prevent cell aggregation and clogging of the holes. Under the optimal conditions, recovery rates of 93% and 90% were found for A549 and HeLa cells in a clinical simulation test of our platform with a CTC concentration of 20-100 cells per milliliter of blood. The white blood cell (WBC) depletion rate was 98.7% (n = 15), and the CTC detection limit was less than 10 cells per milliliter of blood (n = 6). Moreover, compared with conventional membrane filtration, the advantages of the proposed device for the rapid (2 mL/min) and efficient enrichment of CTCs without clogging were shown both experimentally and theoretically. Due to its advantages in the efficient, rapid, uniform, and clog-free enrichment of CTCs, our platform offers great potential for metastatic detection and therapy analyses.

A Rapid Detection Method for Tomato Gray Mold Spores in Greenhouse Based on Microfluidic Chip Enrichment and Lens-Less Diffraction Image Processing

It is of great significance to find tomato gray mold in time and take corresponding control measures to ensure the production of tomato crops. This study proposed a rapid detection method for spores of Botrytis cinerea in green-house based on microfluidic chip enrichment and lens-free diffraction image processing. Microfluidic chip with a regular triangular inner rib structure was designed to achieve the enrichment of Botrytis cinerea spores. In order to obtain the diffraction image of the diseased spores, a lens-less diffraction imaging system was built. Furthermore, the collected spore diffraction images were processed and counted. The simulation results showed that the collection efficiency of 16 μm particles was 79%, 100%, and 89% at the inlet flow rate of 12, 14 and 16 mL/min, respectively. The experimental verification results were observed under a microscope. The results showed that when the flow rate of the microfluidic chip was 12, 14 and 16 mL/min, the collection efficiency of Botrytis cinerea spores was 70.65%, 87.52% and 77.96%, respectively. The Botrytis cinerea spores collected in the experiment were placed under a microscope for manual counting and compared with the automatic counting results based on diffraction image processing. A total of 10 sets of experiments were carried out, with an error range of the experiment was 5.13~8.57%, and the average error of the experiment was 6.42%. The Bland–Altman method was used to analyze two methods based on diffraction image processing and manual counting under a microscope. All points are within the 95% consistency interval. Therefore, this study can provide a basis for the research on the real-time monitoring technology of tomato gray mold spores in the greenhouse.

Miniaturized and IoT enabled Continuous-flow based Microfluidic PCR Device for DNA Amplification

Herein, a continuous-flow driven microfluidic device has been designed and fabricated using the CO2 laser ablation method for polymerase chain reaction (PCR). The device consists of a polymethyl methacrylate (PMMA) microfluidic channel with 30 serpentine thermal cycles, an arduino board, two custom-made cartridge heaters, and thermocouple sensors. The portable thermal management system, with aluminium blocks placed on a wooden substrate, working on the PID controller principle, is low-cost, battery-powered, automated, integrated, and IoT-enabled. The device with dimensions 80 × 72 × 36 mm3 (L x W x H) has a temperature accuracy of ±0.2°C. The IoT module enables accessing and storage of real-time temperature values directly onto the smartphone through ThingSpeak analytics. It was developed to achieve desirable accurate temperature at two thermal zones, denaturation and annealing (95°C and 60°C) on the microfluidic thermal management platform. A PCR mixture of 20 μ l was infused into the serpentine-based microchannel using a syringe pump. Amplification of DNA template with 594-base pair (bp) fragment of the rat GAPDH gene was successfully performed on the miniaturized thermal management system. The total time required for a complete PCR reaction was 32 min at an optimum flow rate of 5 μ l/min. The amplified sample of the target DNA obtained from the PCR microchannel was then separated by agarose gel electrophoresis and was further analyzed using a gel-doc system. Finally, the obtained results were compared to the conventional PCR instrument showing excellent performance.

Portable Rice Disease Spores Capture and Detection Method Using Diffraction Fingerprints on Microfluidic Chip

Crop diseases cause great harm to food security, 90% of these are caused by fungal spores. This paper proposes a crop diseases spore detection method, based on the lensfree diffraction fingerprint and microfluidic chip. The spore diffraction images are obtained by a designed large field of view lensless diffraction detection platform which contains the spore enrichment microfluidic chip and lensless imaging module. By using the microfluidic chip to enrich and isolate spores in advance, the required particles can be captured in the chip enrichment area, and other impurities can be filtered to reduce the interference of impurities on spore detection. The light source emits partially coherent light and irradiates the target to generate diffraction fingerprints, which can be used to distinguish spores and impurities. According to the theoretical analysis, two parameters, Peak to Center ratio (PCR) and Peak to Valley ratio (PVR), are found to quantify these spores. The correlation coefficient between the detection results of rice blast spores by the constructed device and the results of microscopic artificial identification was up to 0.99, and the average error rate of the proposed device was only 5.91%. The size of the device is only 4 cm × 4 cm × 5 cm, and the cost is less than $150, which is one thousandth of the existing equipment. Therefore, it may be widely used as an early detection method for crop disease caused by spores.