A portable droplet generation system for ultra-wide dynamic range digital PCR based on a vibrating sharp-tip capillary

Digital Sort-Enabled Counting Allows Absolute Electrical Quantification of Target Nucleic Acid

Quantitative nucleic acid amplification tests are of great importance for diagnostics, but current approaches require complex and costly optical setups that limit their nonlaboratory applications. Herein we describe the implementation of a microfluidics platform that can perform binary DNA-amplification-activated droplet sorting. The digital sort-enabled counting (DISCO) platform enables label-free absolute quantification of the nucleic acid. This is achieved by provoking a pH change in droplets through a loop-mediated isothermal amplification (LAMP) reaction, followed by using sorting by interfacial tension (SIFT) to direct positive and negative droplets to different outlets. With the use of on-chip electrodes at both outlets, we demonstrate that the digital electrical counting of target DNA and RNA can be realized. DISCO is a promising approach for realizing sensitive nucleic acid quantification in point-of-care settings.

Experimental investigation of confinement effect in single molecule amplification via real-time digital PCR on a multivolume droplet array SlipChip

BACKGROUND

Digital polymerase chain reaction (digital PCR) is an important quantitative nucleic acid analysis method in both life science research and clinical diagnostics. One important hypothesis is that by physically constraining a single nucleic acid molecule in a small volume, the relative concentration can be increased therefore further improving the analysis performance, and this is commonly defined as the confinement effect in digital PCR. However, experimental investigation of this confinement effect can be challenging since it requires a microfluidic device that can generate partitions of different volumes and an instrument that can monitor the kinetics of amplification. (96).

RESULTS

Here, we developed a real-time digital PCR system with a multivolume droplet array SlipChip (Muda-SlipChip) that can generate droplet of 125 nL, 25 nL, 5 nL, and 1 nL by a simple "load-slip" operation. In the digital region, by reducing the volume, the relative concentration is increased, the amplification kinetic can be accelerated, and the time to reach the fluorescence threshold, or Cq value, can be reduced. When the copy number per well is much higher than one, the relative concentration is independent of the partition volume, thus the amplification kinetics are similar in different volume partitions. This system is not limited to studying the kinetics of digital nucleic acid amplification, it can also extend the dynamic range of the digital nucleic acid analysis by additional three orders of magnitude by combining a digital and an analog quantification algorithm. (140).

SIGNIFICANCE

In this study, we experimentally investigated for the first time the confinement effect in the community of digital PCR via a new real-time digital PCR system with a multivolume droplet array SlipChip (Muda-SlipChip). And a wider dynamic range of quantification methods compared to conventional digital PCR was validated by this system. This system provides emerging opportunities for life science research and clinical diagnostics. (63).

Microfluidic strategies for engineering oxygen-releasing biomaterials

In the field of tissue engineering, local hypoxia in large-cell structures (larger than 1 mm3) poses a significant challenge. Oxygen-releasing biomaterials supply an innovative solution through oxygen ⁠ delivery in a sustained and controlled manner. Compared to traditional methods such as emulsion, sonication, and agitation, microfluidic technology offers distinct benefits for oxygen-releasing material production, including controllability, flexibility, and applicability. It holds enormous potential in the production of smart oxygen-releasing materials. This review comprehensively covers the fabrication and application of microfluidic-enabled oxygen-releasing biomaterials. To begin with, the physical mechanism of various microfluidic technologies and their differences in oxygen carrier preparation are explained. Then, the distinctions among diverse oxygen-releasing components in regards for oxygen-releasing mechanism, oxygen-carrying capacity, and duration of oxygen release are presented. Finally, the present obstacles and anticipated development trends are examined together with the application outcomes of oxygen-releasing biomaterials based on microfluidic technology in the biomedical area. STATEMENT OF SIGNIFICANCE: Oxygen is essential for sustaining life, and hypoxia (a condition of low oxygen) is a significant challenge in various diseases. Microfluidic-based oxygen-releasing biomaterials offer precise control and outstanding performance, providing unique advantages over traditional approaches for tissue engineering. However, comprehensive reviews on this topic are currently lacking. In this review, we provide a comprehensive analysis of various microfluidic technologies and their applications for developing oxygen-releasing biomaterials. We compare the characteristics of organic and inorganic oxygen-releasing biomaterials and highlight the latest advancements in microfluidic-enabled oxygen-releasing biomaterials for tissue engineering, wound healing, and drug delivery. This review may hold the potential to make a significant contribution to the field, with a profound impact on the scientific community.

Improved Canker Processing and Viability Droplet Digital PCR Allow Detection of Erwinia amylovora Viable Nonculturable Cells in Apple Bark

The bacterium Erwinia amylovora causes fire blight and continues to threaten global commercial apple and pear production. Conventional microbiology techniques cannot accurately determine the presence of live pathogen cells in fire blight cankers. Several factors may prevent E. amylovora from growing on solid culture media, including competing microbiota and the release of bacterial-growth-inhibitory compounds by plant material during sample processing. We previously developed a canker processing methodology and a chip-based viability digital PCR (v-dPCR) assay using propidium monoazide (PMA) to bypass these obstacles. However, sample analysis was still time-consuming and physically demanding. In this work, we improved the previous protocol using an automatic tissue homogenizer and transferred the chip-based v-dPCR to the BioRad QX200 droplet dPCR (ddPCR) platform. The improved sample processing method allowed the simultaneous, fast, and effortless processing of up to six samples. Moreover, the transferred v-ddPCR protocol was compatible with the same PMA treatment and showed a similar dynamic range, from 7.2 × 102 to 7.6 × 107 cells mL-1, as the previous v-dPCR. Finally, the improved protocol allowed, for the first time, the detection of E. amylovora viable but nonculturable (VBNC) cells in cankers and bark tissues surrounding cankers. Our v-ddPCR assay will enable new ways to evaluate resistant pome fruit tree germplasm, further dissect the E. amylovora life cycle, and elucidate E. amylovora physiology, epidemiology, and new options for canker management.

Free-Boundary Microfluidic Platform for Advanced Materials Manufacturing and Applications

Microfluidics, with its remarkable capacity to manipulate fluids and droplets at the microscale, has emerged as a powerful platform in numerous fields. In contrast to conventional closed microchannel microfluidic systems, free-boundary microfluidic manufacturing (FBMM) processes continuous precursor fluids into jets or droplets in a relatively spacious environment. FBMM is highly regarded for its superior flexibility, stability, economy, usability, and versatility in the manufacturing of advanced materials and architectures. In this review, a comprehensive overview of recent advancements in FBMM is provided, encompassing technical principles, advanced material manufacturing, and their applications. FBMM is categorized based on the foundational mechanisms, primarily comprising hydrodynamics, interface effects, acoustics, and electrohydrodynamic. The processes and mechanisms of fluid manipulation are thoroughly discussed. Additionally, the manufacturing of advanced materials in various dimensions ranging from zero-dimensional to three-dimensional, as well as their diverse applications in material science, biomedical engineering, and engineering are presented. Finally, current progress is summarized and future challenges are prospected. Overall, this review highlights the significant potential of FBMM as a powerful tool for advanced materials manufacturing and its wide-ranging applications.

Profiling DNA Cargos in Single Extracellular Vesicles via Hydrogel-Based Droplet Digital Multiple Displacement Amplification

Due to the substantial heterogeneity among extracellular vesicle (EV) subpopulations, single-EV analysis has the potential to elucidate the mechanisms behind EV biogenesis and shed light on the myriad functions, leading to the development of novel diagnostics and therapeutics. While many studies have been devoted to reveal between-EV variations in surface proteins and RNAs, DNA cargos (EV-DNA) have received little attention. Here, we report a hydrogel-based droplet digital multiple displacement amplification approach for the comprehensive analysis of EV-DNA at the single-EV level. Single EVs are dispersed in thousands of hydrogel droplets and lysed for DNA amplification and identification. The droplet microfluidics strategy empowers the assay with single-molecule sensitivity and capability for absolute quantification of DNA-containing EVs. In particular, our findings indicate that 5-40% EVs are associated with DNA, depending on the cell of origin. Large EVs exhibit a higher proportion of DNA-containing EVs and a more substantial presence of intraluminal DNA, compared to small EVs. These DNA-containing EVs carry multiple DNA fragments on average. Furthermore, both double-stranded DNA and single-stranded DNA were able to be detected at the single-EV level. Utilizing this method, the abundance, distribution, and biophysical properties of EV-DNA in various EV populations are evaluated. The DNA level within EVs provides insight into the status of the originating cells and offers valuable information on the outcomes of anticancer treatments. The utilization of single-EV analysis for EV-DNA holds significant promise for early cancer detection and treatment response monitoring.

Multiplex bacteria detection using one-pot CRISPR/Cas13a-based droplet microfluidics

High-throughput detection of bacteria at low levels is critical in public health, food safety, and first response. Herein, for the first time, we present a platform based on droplet microfluidics coupling with the recombinase aided amplification (RAA)-assisted one-pot clustered regularly interspaced short palindromic repeats together with CRISPR-associated proteins 13a (CRISPR/Cas13a) assay, and droplet encoding strategy for accurate and sensitive determination of nucleic acids from various foodborne pathogens. The workflow takes full advantage of CRISPR/Cas13a signal amplification and droplet confinement effects, which enhances the detection sensitivity and enables end-point quantitation. Meanwhile, by varying the color of droplets, the number of bacteria detected at the same time is greatly improved. It possesses the capability to simultaneously detect seven different types of foodborne pathogens. Notably, the system is also applied to real food samples with satisfactory results. Overall, in view of superiorities in high sensitivity, outstanding selectivity, and large-scale multiplexing, the one-pot CRISPR/Cas13a-based droplet microfluidic system could be expanded and universalized for identifying other bacteria.

Fluorescence-coded logarithmic-dilution digital droplet PCR for ultrawide-dynamic-range nucleic acid quantification

Digital PCR (dPCR) is considered the next generation of nucleic acid detection for its ability of absolute quantification and high sensitivity. However, when compared to the current gold standard, quantitative PCR (qPCR), dPCR is falling behind by several orders of magnitude in dynamic range, which limits its clinical applicability. Here we present fluorescence-coded logarithmic-dilution digital droplet PCR (Flodd-PCR) that features a dynamic range across 7 orders of magnitude, over 2 orders higher than conventional dPCR (4-5 log range) and approaching that of qPCR (7-8 log range). Flodd-PCR realizes such a wide dynamic range by dividing ∼20,000 droplets into 4 groups, each featuring a unique dilution factor of the loaded DNA template and thus a shifted dynamic range. This is achieved by a microfluidic chip that performs multi-step serial dilution (20-925 folds) and droplet generation. The post-PCR droplets can be clustered in silico based on their dilution indicator fluorescence and analyzed independently. Experimentally, Flodd-PCR can detect 4-20,000,000 copies/μL (cp./μL) of the synthetic human papillomavirus (HPV) DNA and outperforms standard dPCR when analyzing clinical HPV samples. Furthermore, Flodd-PCR can be implemented with existing dPCR system set-up with minimal adjustment, and therefore will also have wide practicality in different applications which conventional dPCR has already demonstrated.

Fully integrated sample-in-answer-out platform for viral detection using digital reverse transcription recombinase polymerase amplification (dRT-RPA)

Recombinase polymerase amplification (RPA) is one of the most promising diagnostic methods for pathogen detection, owing to the simplified isothermal amplification technique. Using one-step digital reverse transcription RPA (dRT-RPA) to detect viral RNA provides a fast diagnosis and absolute quantification. Here, we present a chip that purifies, digitalizes, and detects viral RNA of SARS-CoV-2 in a fully automated and sensitive manner. The chip purifies the RNA using the surface charge concept of magnet bead-RNA binding, then mixes the RNA with the amplification reagents, digitalizes the amplification mixture, and performs dRT-RPA. RNA-bead complex is transported among purification buffers that are separated by an oil phase. For reagent manipulation and mixing, a magnetic valve system is integrated on the chip, where an external magnet controls the reagent direction and time of addition. Besides, a novel vacuum system is suggested to drive and regulate the reagents into two fluid systems simultaneously in ∼2 min. We also developed a cost-effective way to perform fluorescent detection for dRT-RPA on chip by using EvaGreen® dye. With integrated heating and optical detection system, the on-chip dRT-RPA presents a sample-to-answer detection platform for absolute viral RNA quantitation in 37 min and a sensitivity as low as 10 RNA copies/μL. Hence, this platform is expected to be a useful tool for accurate and automated diagnosis of infectious diseases.

CRISPR Assays for Disease Diagnosis: Progress to and Barriers Remaining for Clinical Applications

Numerous groups have employed the special properties of CRISPR/Cas systems to develop platforms that have broad potential applications for sensitive and specific detection of nucleic acid (NA) targets. However, few of these approaches have progressed to commercial or clinical applications. This review summarizes the properties of known CRISPR/Cas systems and their applications, challenges associated with the development of such assays, and opportunities to improve their performance or address unmet assay needs using nano-/micro-technology platforms. These include rapid and efficient sample preparation, integrated single-tube, amplification-free, quantifiable, multiplex, and non-NA assays. Finally, this review discusses the current outlook for such assays, including remaining barriers for clinical or point-of-care applications and their commercial development.

Manipulation with sound and vibration: A review on the micromanipulation system based on sub-MHz acoustic waves

Manipulation of micro-objects have been playing an essential role in biochemical analysis or clinical diagnostics. Among the diverse technologies for micromanipulation, acoustic methods show the advantages of good biocompatibility, wide tunability, a label-free and contactless manner. Thus, acoustic micromanipulations have been widely exploited in micro-analysis systems. In this article, we reviewed the acoustic micromanipulation systems that were actuated by sub-MHz acoustic waves. In contrast to the high-frequency range, the acoustic microsystems operating at sub-MHz acoustic frequency are more accessible, whose acoustic sources are at low cost and even available from daily acoustic devices (e.g. buzzers, speakers, piezoelectric plates). The broad availability, with the addition of the advantages of acoustic micromanipulation, make sub-MHz microsystems promising for a variety of biomedical applications. Here, we review recent progresses in sub-MHz acoustic micromanipulation technologies, focusing on their applications in biomedical fields. These technologies are based on the basic acoustic phenomenon, such as cavitation, acoustic radiation force, and acoustic streaming. And categorized by their applications, we introduce these systems for mixing, pumping and droplet generation, separation and enrichment, patterning, rotation, propulsion and actuation. The diverse applications of these systems hold great promise for a wide range of enhancements in biomedicines and attract increasing interest for further investigation.

Auto Flow-Focusing Droplet Reinjection Chip-Based Integrated Portable Droplet System (iPODs)

Droplet microfluidics provides powerful tools for biochemical applications. However, precise fluid control is usually required in the process of droplet generation and detection, which hinders droplet-based applications in point-of-care testing (POCT). Here, we present a droplet reinjection method capable of droplet distribution without precise fluid control and external pumps by which the droplets can be passively aligned and detected one by one at intervals. By further integrating the surface-wetting-based droplet generation chip, an integrated POrtable Droplet system (iPODs) is developed. The iPODs integrates multiple functions such as droplet generation, online reaction, and serial reading. Using the iPODs, monodisperse droplets can be generated at a flow rate of 800 Hz with a narrow size distribution (CV <2.2%). Droplets are kept stable, and the fluorescence signal can be significantly identified after the reaction. The spaced droplet efficiency in the reinjection chip is nearly 100%. In addition, we validate digital loop-mediated isothermal amplification (dLAMP) within 80 min with a simple operation workflow. The results show that iPODs has good linearity (R² = 0.999) at concentrations ranging from 10¹ to 10⁴ copies/μL. Thus, the developed iPODs highlights its potential to be a portable, low-cost, and easy-to-deploy toolbox for droplet-based applications.

dDrop-Chip: disposable film-chip microfluidic device for real-time droplet feedback control

A cost-effective, simple to use, and automated technique that can provide real-time feedback control for droplet generation is required to obtain droplets with high-throughput, stability, and uniformity. This study introduces a disposable droplet generation microfluidic device (dDrop-Chip) that can simultaneously control both droplet size and production rate in real time. The dDrop-Chip consists of a reusable sensing substrate and a disposable microchannel that can be assembled using vacuum pressure. It also integrates a droplet detector and a flow sensor on-chip, enabling real-time measurement and feedback control of droplet size and sample flow rate. The dDrop-Chip has the additional advantage of being disposable, which can prevent chemical and biological contamination, due to low manufacturing cost by the film-chip technique. We demonstrate benefits of the dDrop-Chip by controlling droplet size at a fixed sample flow rate and the production rate at a fixed droplet size using real-time feedback control. The experimental results show that the dDrop-Chip consistently generates monodisperse droplets with a length of 219.36 ± 0.08 μm (CV 0.036%) at a production rate of 32.38 ± 0.48 Hz using the feedback control, while without feedback control, there is a significant deviation in droplet length (224.18 ± 6.69 μm, CV 2.98%) and production rate (33.94 ± 1.72 Hz) despite the use of identical devices. Therefore, the dDrop-Chip is a reliable, cost-effective, and automated technique for generating droplets of controlled size and production rate in real time, making it suitable for various droplet-based applications.

Advances in droplet digital polymerase chain reaction on microfluidic chips

The PCR technique has been known to the general public since the pandemic outbreak of COVID-19. This technique has progressed through three stages: from simple PCR to real-time fluorescence PCR to digital PCR. Among them, the microfluidic-based droplet digital PCR technique has attracted much attention and has been widely applied due to its advantages of high throughput, high sensitivity, low reagent consumption, low cross-contamination, and absolute quantification ability. In this review, we introduce various designs of microfluidic-based ddPCR developed within the last decade. The microfluidic-based droplet generation methods, thermal cycle strategies, and signal counting approaches are described, and the applications in the fields of single-cell analysis, disease diagnosis, and pathogen detection are introduced. Further, the challenges and prospects of microfluidic-based ddPCR are discussed. We hope that this review can contribute to the further development of the microfluidic-based ddPCR technique.

Bent-Capillary-Centrifugal-Driven Monodisperse Droplet Generator with Its Application for Digital LAMP Assay

We developed a bent-capillary-centrifugal-driven (BCCD) monodisperse droplet generator, which could achieve a perfect combination of driving and segmentation for the dispersed phase only using a rotating bent capillary immersed in the continuous phase (mineral oil). The sample could flow continuously to the bent-capillary outlet to form the droplet precursors, which were segmented into homogeneous droplets in the continuous phase. Through the investigation of influence factors on droplet size and stability, we found that the droplet size could be conveniently controlled by the rotational speed of the bent capillary. The droplet volumes could be adjusted with the range from 34 pL to 1 μL, and the coefficient variations (CVs) were less than 3%. Meanwhile, the BCCD droplet generator could realize the controllable droplet output with a high-efficiency sample utilization of 99.75 ± 1.15%, which offered a significant advantage in reducing the waste of precious samples in the droplet generation process. We validated this system with a digital loop-mediated isothermal amplification (dLAMP) assay for the absolute quantification of Mycobacterium tuberculosis complex nucleic acids. The results demonstrated that the BCCD droplet generator was easy to build, was of low cost, and was convenient to operate, as well as avoided sample loss and cross-contamination by coupling with a 96-well plate. Overall, the present platform, as a simple chip-free droplet generator, will provide an especially valuable droplet generation solution for biochemical applications based on droplets.

Recent Advances in Digital Biosensing Technology

Digital biosensing assays demonstrate remarkable advantages over conventional biosensing systems because of their ability to achieve single-molecule detection and absolute quantification. Unlike traditional low-abundance biomarking screening, digital-based biosensing systems reduce sample volumes significantly to the fL-nL level, which vastly reduces overall reagent consumption, improves reaction time and throughput, and enables high sensitivity and single target detection. This review presents the current technology for compartmentalizing reactions and their applications in detecting proteins and nucleic acids. We also analyze existing challenges and future opportunities associated with digital biosensing and research opportunities for developing integrated digital biosensing systems.