Mixing characteristics of a bubble mixing microfluidic chip for genomic DNA extraction based on magnetophoresis: CFD simulation and experiment

Air trap and removal on a pressure driven PDMS-based microfluidic device

With the development of microfluidic technology, microfluidic chips have played a positive role in applications such as cell culture, microfluidic PCR, and nanopore gene sequencing. However, the presence of bubbles interferes with fluid flow and has a significant impact on experimental results. There are many reasons for the generation of bubbles in microfluidic chips, such as pressure changes inside the chip, air vibration inside the chip, and the open chip guiding air into the chip when driving fluid. This study designed and prepared a microfluidic device based on polydimethylsiloxane. First, air was actively introduced into the microfluidic chip, and bubbles were captured through the microfluidic device to simulate the presence of bubbles inside the chip in biological experiments. To remove bubbles trapped in the microfluidic chip, distilled water, distilled water containing surfactants, and mineral oil were pumped into the microfluidic chip. We compared and discussed the bubble removal efficiency under different driving fluids, driving pressures, and open/closed channel configurations. This study helps to understand the mechanism of bubble formation and removal in microfluidic devices, optimize chip structure design and experimental reagent selection, prevent or eliminate bubbles, and reduce the impact of bubbles on experiments.

Rapid on-site nucleic acid testing: On-chip sample preparation, amplification, and detection, and their integration into all-in-one systems

As nucleic acid testing is playing a vital role in increasingly many research fields, the need for rapid on-site testing methods is also increasing. The test procedure often consists of three steps: Sample preparation, amplification, and detection. This review covers recent advances in on-chip methods for each of these three steps and explains the principles underlying related methods. The sample preparation process is further divided into cell lysis and nucleic acid purification, and methods for the integration of these two steps on a single chip are discussed. Under amplification, on-chip studies based on PCR and isothermal amplification are covered. Three isothermal amplification methods reported to have good resistance to PCR inhibitors are selected for discussion due to their potential for use in direct amplification. Chip designs and novel strategies employed to achieve rapid extraction/amplification with satisfactory efficiency are discussed. Four detection methods providing rapid responses (fluorescent, optical, and electrochemical detection methods, plus lateral flow assay) are evaluated for their potential in rapid on-site detection. In the final section, we discuss strategies to improve the speed of the entire procedure and to integrate all three steps onto a single chip; we also comment on recent advances, and on obstacles to reducing the cost of chip manufacture and achieving mass production. We conclude that future trends will focus on effective nucleic acid extraction via combined methods and direct amplification via isothermal methods.

Polydimethylsiloxane microstructure-induced acoustic streaming for enhanced ultrasonic DNA fragmentation on a microfluidic chip

Next-generation sequencing (NGS) is an essential technology for DNA identification in genomic research. DNA fragmentation is a critical step for NGS and doing this on-chip is of great interest for future integrated genomic solutions. Here we demonstrate fast acoustofluidic DNA fragmentation via ultrasound-actuated elastic polydimethylsiloxane (PDMS) microstructures that induce acoustic streaming and associated shear forces when placed in the field of an ultrasonic transducer. Indeed, acoustic streaming locally generates high tensile stresses that can mechanically stretch and break DNA molecule chains. The improvement in efficiency of the on-chip DNA fragmentation is due to the synergistic effect of these tensile stresses and ultrasonic cavitation phenomena. We tested these microstructure-induced effects in a DNA-containing microfluidic channel both experimentally and by simulation. The DNA fragmentation process was evaluated by measuring the change in the DNA fragment size over time. The chip works well with both long and short DNA chains; in particular, purified lambda (λ) DNA was cut from 48.5 kbp to 3 kbp in one minute with selected microstructures and further down to 300 bp within two and a half minutes. The fragment size of mouse genomic DNA was reduced from 1.4 kbp to 400 bp in one minute and then to 200 bp in two and a half minutes. The DNA fragmentation efficiency of the chip equipped with the PDMS microstructures was twice that of the chip without the microstructures. Exhaustive comparison shows that the on-chip fragmentation performance reaches the level of high-end professional standards. Recently, DNA fragmentation was shown to be enhanced using vibrating air microbubbles when the chip was placed in an acoustic field. We think the microbubble-free microstructure-based device we present is easier to operate and more reliable, as it avoids microbubble preparation and maintenance, while showing high DNA fragmentation performance.

Automatic feedback control by image processing for mixing solutions in a microfluidic device

Two approaches of an automatic control were studied through mathematical fitting obtained from color mixing saturation curves in polydimethylsiloxane microfluidic devices: The integrative control with variable integral gain and integrative control with constant integral gain. The aim of this work is to control the color percentage decrement when dye is injected. The results indicate that microfluidic systems are very sensitive to changes in flow and the control variable needs to change slowly; that is, it must be small (at least 100 times less than the theoretically calculated values). The control and stabilization of the microfluidic system were achieved for dye percentages above 60%. The controlling color percentage could provide a tool to regulate other parameters' concentration applied to cell culture and alkalinity control (pH) of solutions in microfluidic devices.

Study on the Sugar-Producing Effect of High-Temperature Anaerobic Straw Biosaccharification Strain

The utilization of straw waste cellulose will be beneficial by economic, social, and environmental means. The present study sought to screen the high-efficiency cellulose sugar-producing strain from corn straw. The 16S high-throughput sequencing method and the combination of morphological, physiological, and biochemical characteristics of the strain confirmed the strain to be Clostridium thermocellum, which was named Clostridium thermocellum FC811. Moreover, the single factor experiment was conducted to investigate the effect of environmental factors on saccharification efficiency. The optimal saccharification conditions of cellulose saccharification of FC811 strain selected through response surface analysis were as follows: temperature of 58.9 °C, pH of 7.21, culture time of 6.60 d, substrate concentration of 5.01 g/L, and yeast powder concentration of 2.15 g/L. The soluble sugar yield was 3.11 g/L, and the conversion rate of reducing sugar was 62.2%. This study will provide a reference for resource and energy utilization of straw materials, simultaneous fermentation of sugar and hydrogen production, and their large-scale production and application.

The enhancement of DNA fragmentation in a bench top ultrasonic water bath with needle-induced air bubbles: Simulation and experimental investigation

Shearing DNA to a certain size is the first step in many medical and biological applications, especially in next-generation gene sequencing technology. In this article, we introduced a highly efficient ultrasonic DNA fragmentation method enhanced by needle-induced air bubbles, which is easy to operate with high throughput. The principle of the bubble-enhanced sonication system is introduced and verified by flow field and acoustic simulations and experiments. Lambda DNA long chains and mouse genomic DNA short chains are used in the experiments for testing the performance of the bubble-enhanced ultrasonic DNA fragmentation system. Air bubbles are an effective enhancement agent for ultrasonic DNA fragmentation; they can obviously improve the sound pressure level in the whole solution, thus, achieving better absorption of ultrasound energy. Growing bubbles also have a stretched function on DNA molecule chains and form a huge pressure gradient in the solution, which is beneficial to DNA fragmentation. Purified λDNA is cut from 48.5 to 2 kbp in 5 min and cut to 300 bp in 30 min. Mouse genomic DNA (≈1400 bp) decreases to 400 bp in 5 min and then reduces to 200 bp in 30 min. This bubble-enhanced ultrasonic method enables widespread access to genomic DNA fragmentation in a standard ultrasonic water bath for many virus sequencing demands even without good medical facilities.

Microfluidics-based strategies for molecular diagnostics of infectious diseases

Traditional diagnostic strategies for infectious disease detection require benchtop instruments that are inappropriate for point-of-care testing (POCT). Emerging microfluidics, a highly miniaturized, automatic, and integrated technology, are a potential substitute for traditional methods in performing rapid, low-cost, accurate, and on-site diagnoses. Molecular diagnostics are widely used in microfluidic devices as the most effective approaches for pathogen detection. This review summarizes the latest advances in microfluidics-based molecular diagnostics for infectious diseases from academic perspectives and industrial outlooks. First, we introduce the typical on-chip nucleic acid processes, including sample preprocessing, amplification, and signal read-out. Then, four categories of microfluidic platforms are compared with respect to features, merits, and demerits. We further discuss application of the digital assay in absolute nucleic acid quantification. Both the classic and recent microfluidics-based commercial molecular diagnostic devices are summarized as proof of the current market status. Finally, we propose future directions for microfluidics-based infectious disease diagnosis.

Design and operation of magnetophoretic systems at microscale: Device and particle approaches

Combining both device and particle designs are the essential concepts to be considered in magnetophoretic system development. Researcher efforts are often dedicated to only one of these design aspects and neglecting the interplay between them. Herein, to bring out importance of the idea of integration between device and particle, we reviewed the working principle of magnetophoretic system (includes both device and particle design concepts). Since, the magnetophoretic force is influenced by both field gradient and magnetization volume, hence, accurate prediction of the magnetophoretic force is relying on the availability of information on both parameters. In device design, we focus on the different strategies used to create localized high-field gradient. For particle design, we emphasize on the scaling between hydrodynamic size and magnetization volume. Moreover, we also briefly discussed the importance of magnetoshape anisotropy related to particle design aspect of magnetophoretic systems. Next, we illustrated the need for integration between device and particle design using microscale applications of magnetophoretic systems, include magnetic tweezers and microfluidic systems, as our working example. On the basis of our discussion, we highlighted several promising examples of microscale magnetophoretic systems which greatly utilized the interplay between device and particle design. Further, we concluded the review with several factors that possibly resulted in the lack of research efforts related to device and particle design integration.