Isolation and amplification of mRNA within a simple microfluidic lab on a chip

Development of a Point-of-Care Microfluidic RNA Extraction Slide for Gene Expression Diagnosis after Irradiation

In times of war, radiological/nuclear emergency scenarios have become a reemphasized threat. However, there are challenges in transferring whole-blood samples to laboratories for specialized diagnostics using RNA. This project aims to miniaturize the process of unwieldy conventional RNA extraction with its stationed technical equipment using a microfluidic-based slide (MBS) for point-of-care diagnostics. The MBS is thought to be a preliminary step toward the development of a so-called lab-on-a-chip microfluidic device. A MBS would enable early and fast field care combined with gene expression (GE) analysis for the prediction of hematologic acute radiation syndrome (HARS) severity or identification of RNA microbes. Whole blood samples from ten healthy donors were irradiated with 0, 0.5 and 4 Gy, simulating different ARS severity degrees. RNA quality and quantity of a preliminary MBS was compared with a conventional column-based (CB) RNA extraction method. GE of four HARS severity-predicting radiation-induced genes (FDXR, DDB2, POU2AF1 and WNT3) was examined employing qRT-PCR. Compared to the CB method, twice as much total RNA from whole blood could be extracted using the MBS (6.6 ± 3.2 µg vs. 12.0 ± 5.8 µg) in half of the extraction time, and all MBS RNA extracts appeared DNA-free in contrast to the CB method (30% were contaminated with DNA). Using MBS, RNA quality [RNA integrity number equivalent (RINe)] values decreased about threefold (3.3 ± 0.8 vs. 9.0 ± 0.4), indicating severe RNA degradation, while expected high-quality RINe ≥ 8 were found using column-based method. However, normalized cycle threshold (Ct) values, as well as radiation-induced GE fold-changes appeared comparable for all genes utilizing both methods, indicating that no RNA degradation took place. In summary, the preliminary MBS showed promising features such as: 1. halving the RNA extraction time without the burden of heavy technical equipment (e.g., a centrifuge); 2. absence of DNA contamination in contrast to CB RNA extraction; 3. reduction in blood required, because of twice the biological output of RNA; and 4. equal GE performance compared to CB, thus, increasing its appeal for later semi-automatic parallel field applications.

Integrated nucleic acid purification technology based on amino-modified centrifugal microfluidic chip

Nucleic acid detection is an important tool for clinical diagnosis. The purification of the sample is the most time-consuming step in the nucleic acid testing process and will affect the results of the assay. Here, we developed a surface modification-based nucleic acid purification method and designed an accompanying set of centrifugation equipment and chips to integrate the steps of nucleic acid purification on a single platform. The results of experiments with HeLa cells and HPV type 16 as samples showed that the mentioned method had good nucleic acid purification capability and the accompanying equipment greatly simplified the operation of the experimenters in the whole process. Overall, our equipment can improve the efficiency of nucleic acid purification and is suitable for application in larger-scale clinical assays.

Miniaturized sensor for electroanalytical and electrochemiluminescent detection of pathogens enabled through laser-induced graphene electrodes embedded in microfluidic channels

High performance, laser-induced graphene (LIG) electrodes were integrated into adhesive tape-based microfluidic channels to realize both electrochemical (EC) and electrochemiluminescent (ECL) detection approaches. This provides strategies for low limits of detection, simple hardware requirements and inexpensive fabrication, which are characteristics required for assays in the competitive point-of-care (POC) sensor field. Here, electrode design and microchannel dimensions were studied and a DNA hybridization assay with liposomes for signal amplification was developed for the specific detection of DNA derived from Cryptosporidium parvum as the model analyte. Liposomes entrapped either Ru(bpy)₃²⁺ or K₄[Fe(CN)₆] generating ECL- and EC-signal amplification, respectively. This new microchip provided all desirable analytical figures of merit needed for POC applications. Specifically, a desirable one-step assay was designed which provided a limit of detection of 3 pmol L^-1 for the ECL and 47 pmol L^-1 for the EC approach and furthermore enabled highly specific detection considering that at room temperature in this simple setup a single nucleotide polymorphism resulted in a signal decrease of 58%, whereas a decrease of > 98% was observed for non-matching sequences present in 10-fold excess. Direct detection in various matrices ranging from drinking water to soil extracts was also achieved. It is concluded that the simple and inexpensive fabrication in combination with signal amplification strategies makes these concepts relevant for on-site pathogen detection in resource-limited environments.

Microfluidic technology and its application in the point-of-care testing field

Since the outbreak of the coronavirus disease 2019 (COVID-19), countries around the world have suffered heavy losses of life and property. The global pandemic poses a challenge to the global public health system, and public health organizations around the world are actively looking for ways to quickly and efficiently screen for viruses. Point-of-care testing (POCT), as a fast, portable, and instant detection method, is of great significance in infectious disease detection, disease screening, pre-disease prevention, postoperative treatment, and other fields. Microfluidic technology is a comprehensive technology that involves various interdisciplinary disciplines. It is also known as a lab-on-a-chip (LOC), and can concentrate biological and chemical experiments in traditional laboratories on a chip of several square centimeters with high integration. Therefore, microfluidic devices have become the primary implementation platform of POCT technology. POCT devices based on microfluidic technology combine the advantages of both POCT and microfluids, and are expected to shine in the biomedical field. This review introduces microfluidic technology and its applications in combination with other technologies.

Recent advances and challenges of biosensing in point-of-care molecular diagnosis

Molecular diagnosis, which plays a major role in infectious disease screening with successful understanding of the human genome, has attracted more attention because of the outbreak of COVID-19 recently. Since point-of-care testing (POCT) can expand the application of molecular diagnosis with the benefit of rapid reply, low cost, and working in decentralized environments, many researchers and commercial institutions have dedicated tremendous effort and enthusiasm to POCT-based biosensing for molecular diagnosis. In this review, we firstly summarize the state-of-the-art techniques and the construction of biosensing systems for POC molecular diagnosis. Then, the application scenarios of POCT-based biosensing for molecular diagnosis were also reviewed. Finally, several challenges and perspectives of POC biosensing for molecular diagnosis are discussed. This review is expected to help researchers deepen comprehension and make progresses in POCT-based biosensing field for molecular diagnosis applications.

Developments in integrating nucleic acid isothermal amplification and detection systems for point-of-care diagnostics

Early disease detection through point-of-care (POC) testing is vital for quickly treating patients and preventing the spread of harmful pathogens. Disease diagnosis is generally accomplished using quantitative polymerase chain reaction (qPCR) to amplify nucleic acids in patient samples, permitting detection even at low target concentrations. However, qPCR requires expensive equipment, trained personnel, and significant time. These resources are not available in POC settings, driving researchers to instead utilize isothermal amplification, conducted at a single temperature, as an alternative. Common isothermal amplification methods include loop-mediated isothermal amplification, recombinase polymerase amplification, rolling circle amplification, nucleic acid sequence-based amplification, and helicase-dependent amplification. There has been a growing interest in combining such amplification methods with POC detection methods to enable the development of diagnostic tests that are well suited for resource-limited settings as well as developed countries performing mass screenings. Exciting developments have been made in the integration of these two research areas due to the significant impact that such approaches can have on healthcare. This review will primarily focus on advances made by North American research groups between 2015 and June 2020, and will emphasize integrated approaches that reduce user steps, reliance on expensive equipment, and the system's time-to-result.

Separation of nanoparticles via surfing on chemical wavefronts

The separation of micro and nanoscale colloids is a necessary step in most biological microassay techniques, and is a common practice in microchemical processing. Chemical waves are frequently encountered in biochemical systems driven far from equilibrium. Here, we put forward a strategy for separating small suspending colloids by means of their surfing on substrate chemical wavefronts. The colloids with catalytic activities sensitive to the substrates are activated to show self-propulsion and consequently exhibit a chemotactic response to the traveling wavefronts, which results in their spontaneous separation from the multicomponent complex mixture via self-diffusiophoresis. The dynamics of the process is analyzed through a particle-based simulation. In addition, it is found that separation can be carried out according to particle size. The mechanisms underpinning the chemical and physical separation processes are discussed, and the dependencies on the reaction rate constant and particle size are presented. The results may prove relevant for further experimental and theoretical studies of separation in complex active environments.

Functionalized multiscale visual models to unravel flow and transport physics in porous structures

The fluid flow, species transport, and chemical reactions in geological formations are the chief mechanisms in engineering the exploitation of fossil fuels and geothermal energy, the geological storage of carbon dioxide (CO₂), and the disposal of hazardous materials. Porous rock is characterized by a wide surface area, where the physicochemical fluid-solid interactions dominate the multiphase flow behavior. A variety of visual models with differences in dimensions, patterns, surface properties, and fabrication techniques have been widely utilized to simulate and directly visualize such interactions in porous media. This review discusses the six categories of visual models used in geological flow applications, including packed beds, Hele-Shaw cells, synthesized microchips (also known as microfluidic chips or micromodels), geomaterial-dominated microchips, three-dimensional (3D) microchips, and nanofluidics. For each category, critical technical points (such as surface chemistry and geometry) and practical applications are summarized. Finally, we discuss opportunities and provide a framework for the development of custom-built visual models.

Split Dapoxyl Aptamer for Sequence-Selective Analysis of Nucleic Acid Sequence Based Amplification Amplicons

Hybridization probes have been used for the detection of single nucleotide variations (SNV) in DNA and RNA sequences in the mix-and-read formats. Among the most conventional are Taqman probes, which require expensive quantitative polymerase chain reaction (qPCR) instruments with melting capabilities. More affordable isothermal amplification format requires hybridization probes that can selectively detect SNVs isothermally. Here we designed a split DNA aptamer (SDA) hybridization probe based on a recently reported DNA sequence that binds a dapoxyl dye and increases its fluorescence ( Kato, T.; Shimada, I.; Kimura, R.; Hyuga, M., Light-up fluorophore-DNA aptamer pair for label-free turn-on aptamer sensors. Chem. Commun. 2016 , 52 , 4041 - 4044 ). SDA uses two DNA strands that have low affinity to the dapoxyl dye unless hybridized to abutting positions at a specific analyte and form a dye-binding site, which is accompanied by up to a 120-fold increase in fluorescence. SDA differentiates SNV in the  inhA gene of Mycobacterium tuberculosis at ambient temperatures and detects a conserved region of the Zika virus after isothermal nucleic acid sequence based amplification (NASBA) reaction. The approach reported here can be used for detection of isothermal amplification products in the mix-and-read format as an alternative to qPCR.

SD-chip enabled quantitative detection of HIV RNA using digital nucleic acid sequence-based amplification (dNASBA)

Quantitative detection of RNA is important in molecular biology and clinical diagnostics. Nucleic acid sequence-based amplification (NASBA), a single-step method to amplify single-stranded RNA, is attractive for use in point-of-care (POC) diagnostics because it is an isothermal technique that is as sensitive as RT-PCR with a shorter reaction time. However, NASBA is limited in its ability to provide accurate quantitative information, such as viral load or RNA copy number. Here we test a digital format of NASBA (dNASBA) using a self-digitization (SD) chip platform, and apply it to quantifying HIV-1 RNA. We demonstrate that dNASBA is more sensitive and accurate than the real-time quantitative NASBA, and can be used to quantify HIV-1 RNA in plasma samples. Digital NASBA is thus a promising POC diagnostics tool for use in resource-limited settings.

CMOS Enabled Microfluidic Systems for Healthcare Based Applications

With the increased global population, it is more important than ever to expand accessibility to affordable personalized healthcare. In this context, a seamless integration of microfluidic technology for bioanalysis and drug delivery and complementary metal oxide semiconductor (CMOS) technology enabled data-management circuitry is critical. Therefore, here, the fundamentals, integration aspects, and applications of CMOS-enabled microfluidic systems for affordable personalized healthcare systems are presented. Critical components, like sensors, actuators, and their fabrication and packaging, are discussed and reviewed in detail. With the emergence of the Internet-of-Things and the upcoming Internet-of-Everything for a people-process-data-device connected world, now is the time to take CMOS-enabled microfluidics technology to as many people as possible. There is enormous potential for microfluidic technologies in affordable healthcare for everyone, and CMOS technology will play a major role in making that happen.

Review: Microfluidics technologies for blood-based cancer liquid biopsies

Blood-based liquid biopsies provide a minimally invasive alternative to identify cellular and molecular signatures that can be used as biomarkers to detect early-stage cancer, predict disease progression, longitudinally monitor response to chemotherapeutic drugs, and provide personalized treatment options. Specific targets in blood that can be used for detailed molecular analysis to develop highly specific and sensitive biomarkers include circulating tumor cells (CTCs), exosomes shed from tumor cells, cell-free circulating tumor DNA (cfDNA), and circulating RNA. Given the low abundance of CTCs and other tumor-derived products in blood, clinical evaluation of liquid biopsies is extremely challenging. Microfluidics technologies for cellular and molecular separations have great potential to either outperform conventional methods or enable completely new approaches for efficient separation of targets from complex samples like blood. In this article, we provide a comprehensive overview of blood-based targets that can be used for analysis of cancer, review microfluidic technologies that are currently used for isolation of CTCs, tumor derived exosomes, cfDNA, and circulating RNA, and provide a detailed discussion regarding potential opportunities for microfluidics-based approaches in cancer diagnostics.

Enabling miniaturised personalised diagnostics: from lab-on-a-chip to lab-in-a-drop

The concept of personalised diagnostics is to direct accurate clinical decisions based on an individual's unique disease molecular profile. Lab-on-a-chip (LOC) systems are prime personalised diagnostics examples which seek to perform an entire sample-to-outcome detection of disease nucleic acid (NA) biomarkers on a single miniaturised platform with minimal user handling. Despite the great potential of LOC devices in providing rapid, portable, and inexpensive personalised diagnosis at the point-of-care (POC), the translation of this technology into widespread use has still been hampered by the need for sophisticated and complex engineering. As an alternative miniaturised diagnostics platform free of precision fabrication, there have been recent developments towards a solution-based lab-in-a-drop (LID) system by which an entire laboratory-based diagnostics workflow could be downscaled and integrated within a singular fluid droplet for POC detection of NA biomarkers. In contrast to existing excellent reviews on miniaturised LOC fabrication and individual steps of NA biomarker sensing, we herein focus on miniaturised solution-based NA biosensing strategies suited for integrated LID personalised diagnostics development. In this review, we first evaluate the three fundamental bioassay steps for miniaturised NA biomarker detection: crude sample preparation, isothermal target amplification, and detection readout of amplicons. Then, we provide insights into research advancements towards a functional LID system which integrates all three of the above-mentioned fundamental steps. Finally, we discuss perspectives and future directions of LID diagnostic platforms in personalised medicine applications.

Advances in microfluidic devices made from thermoplastics used in cell biology and analyses

Silicon and glass were the main fabrication materials of microfluidic devices, however, plastics are on the rise in the past few years. Thermoplastic materials have recently been used to fabricate microfluidic platforms to perform experiments on cellular studies or environmental monitoring, with low cost disposable devices. This review describes the present state of the development and applications of microfluidic systems used in cell biology and analyses since the year 2000. Cultivation, separation/isolation, detection and analysis, and reaction studies are extensively discussed, considering only microorganisms (bacteria, yeast, fungi, zebra fish, etc.) and mammalian cell related studies in the microfluidic platforms. The advantages/disadvantages, fabrication methods, dimensions, and the purpose of creating the desired system are explained in detail. An important conclusion of this review is that these microfluidic platforms are still open for research and development, and solutions need to be found for each case separately.

From research lab to standard environmental analysis tool: Will NASBA make the leap?

Nucleic acid sequence-based amplification (NASBA) is a sensitive and efficient molecular tool for amplification of RNA and has been widely adopted in clinical diagnostics. Monitoring of water and other environmental samples demands sensitive techniques, as potential pathogens may be in low concentrations and require only a few infectious units to infect their host. NASBA has qualities that should be advantageous for analysis of environmental samples, such as short reaction times, high sensitivity, and not readily affected by inhibitory substances that are often abundant in environmental samples. NASBA is well suited for incorporation into lab-on-a-chip (LOC) devices, as part of analysis systems that can be taken into the field for on-site screening. In this review, we explore advantages and drawbacks of NASBA as a tool for environmental analyses, and try to answer the question of whether it will be a recognised technique in the same manner as in clinical diagnostics.

Real-time nucleic acid sequence-based amplification (NASBA) assay targeting MIC1 for detection of Cryptosporidium parvum and Cryptosporidium hominis oocysts

Both Cryptosporidium parvum and Cryptosporidium hominis are often associated with cryptosporidiosis in humans, but whereas humans are the main host for C. hominis, C. parvum is zoonotic and able to infect a variety of species. The oocyst transmission stages of both species of parasites are morphologically identical and molecular techniques, usually polymerase chain reaction (PCR), are required to distinguish between oocysts detected by standard methods in environmental samples, such as water. In this study, we developed two primer sets for real-time nucleic acid sequence-based amplification (NASBA), targeting the MIC1 transcript in C. parvum (CpMIC1) and C. hominis (ChMIC1). Using these primer sets, we were not only able to detect low numbers of C. parvum and C. hominis oocysts (down to 5 oocysts in 10 μl, and down to 1 oocyst using diluted RNA samples), but also distinguish between them. One of the primer sets targeted an exon only occurring in CpMIC1, thereby providing a tool for distinguishing C. parvum from other Cryptosporidium species. Although mRNA has been suggested as a tool for assessing viability of Cryptosporidium oocysts, as it is short-lived and may have high transcription, this NASBA assay detected MIC1 mRNA in inactivated oocysts. RNA within the oocysts seems to be protected from degradation, even when the oocysts have been killed by heating or freeze-thawing. Thus, our approach detects both viable and non-viable oocysts, and RNA does not seem to be a suitable marker for assessing oocyst viability.

Photoelectrocatalytic microfluidic reactors utilizing hierarchical TiO2 nanotubes for determination of chemical oxygen demand

A novel and highly sensitive microfluidic device which integrated hierarchical TiO₂ nanotubes exhibited an improved detection efficiency for determination of COD.

Isothermal Amplification of Nucleic Acids

Isothermal amplification of nucleic acids is a simple process that rapidly and efficiently accumulates nucleic acid sequences at constant temperature. Since the early 1990s, various isothermal amplification techniques have been developed as alternatives to polymerase chain reaction (PCR). These isothermal amplification methods have been used for biosensing targets such as DNA, RNA, cells, proteins, small molecules, and ions. The applications of these techniques for in situ or intracellular bioimaging and sequencing have been amply demonstrated. Amplicons produced by isothermal amplification methods have also been utilized to construct versatile nucleic acid nanomaterials for promising applications in biomedicine, bioimaging, and biosensing. The integration of isothermal amplification into microsystems or portable devices improves nucleic acid-based on-site assays and confers high sensitivity. Single-cell and single-molecule analyses have also been implemented based on integrated microfluidic systems. In this review, we provide a comprehensive overview of the isothermal amplification of nucleic acids encompassing work published in the past two decades. First, different isothermal amplification techniques are classified into three types based on reaction kinetics. Then, we summarize the applications of isothermal amplification in bioanalysis, diagnostics, nanotechnology, materials science, and device integration. Finally, several challenges and perspectives in the field are discussed.

A comparative study of three different nucleic acid amplification techniques combined with microchip electrophoresis for HPV16 E6/E7 mRNA detection

The development of a high-throughput and automatic system by combining gene amplification with MCE for HPV16 E6/E7 mRNA screening is reported.

Chemotactic separation of enzymes

We demonstrate a procedure for the separation of enzymes based on their chemotactic response toward an imposed substrate concentration gradient. The separation is observed within a two-inlet, five-outlet microfluidic network, designed to allow mixtures of active (ones that catalyze substrate turnover) and inactive (ones that do not catalyze substrate turnover) enzymes, labeled with different fluorophores, to flow through one of the inlets. Substrate solution prepared in phosphate buffer was introduced through the other inlet of the device at the same flow rate. The steady-state concentration profiles of the enzymes were obtained at specific positions within the outlets of the microchannel using fluorescence microscopy. In the presence of a substrate concentration gradient, active enzyme molecules migrated preferentially toward the substrate channel. The excess migration of the active enzyme molecules was quantified in terms of an enrichment coefficient. Experiments were carried out with different pairs of enzymes. Coupling the physics of laminar flow of liquid and molecular diffusion, multiphysics simulations were carried out to estimate the extent of the chemotactic separation. Our results show that, with appropriate microfluidic arrangement, molecular chemotaxis leads to spontaneous separation of active enzyme molecules from their inactive counterparts of similar charge and size.

A dual-amplified electrochemical detection of mRNA based on duplex-specific nuclease and bio-bar-code conjugates

On the basis of strong preference for cleaving double-stranded DNA or DNA in DNA:RNA heteroduplexes of duplex-specific nuclease (DSN), a dual-amplified electrochemical detection of mRNA was developed in this article, by coupling the enhancement of DSN and bio-bar-code conjugates. Capture probe was linked with magnetic nanoparticles (MNPs) at its 5' end and bio-bar-code at its 3' end. In the presence of target surviving mRNA, all hybridized S1 strands were cleaved off the biosensor by the DSN, and the bio-bar-code probe with CdS nanoparticles (CdS NPs) was released into the solution. The metal sulfide nanoparticles were measured by anodic stripping voltammetry (ASV) subsequently. This assay exhibited high sensitivity and selectivity with a detection limit of 0.48fM. In addition, we proved that this simple and cost-effective strategy is capable of detecting the target in complicated biological samples and holds great potential application in biomedical research and clinical diagnostics.

Visual and sensitive detection of viable pathogenic bacteria by sensing of RNA markers in gold nanoparticles based paper platform

Food-borne pathogens have been recognized as a major cause of human infections worldwide. Their identification needs to be simpler, cheaper and more reliable than the traditional methods. Here, we constructed a low-cost paper platform for viable pathogenic bacteria detection with the naked eye. In this study, an effective isothermal amplification method was used to amplify the hlyA mRNA gene, a specific RNA marker in Listeria monocytogenes. The amplification products were applied to the paper-based platform to perform a visual test using sandwich hybridization assays. When the RNA products migrated along the platform by capillary action, the gold nanoparticles accumulated at the designated area. Under optimized experimental conditions, as little as 0.5 pg/μL genomic RNA from L. monocytogenes could be detected. It could also be used to specifically detect 20 CFU/mL L. monocytogenes from actual samples. The whole assay process, including RNA extraction, amplification, and visualization, can be completed within several hours. This method is suitable for point-of-care applications to detect food-borne pathogens, as it can overcome the false-positive results caused by amplifying nonviable L. monocytogenes. Furthermore, the results can be imaged and transformed into a two-dimensional bar code through an Android-based smart phone for further analysis or in-field food safety tracking.