Self-contained, fully integrated biochip for sample preparation, polymerase chain reaction amplification, and DNA microarray detection

Theoretical and Experimental Study of an Electrokinetic Micromanipulator for Biological Applications

The ability to control and manipulate biological fluids within microchannels is a fundamental challenge in biological diagnosis and pharmaceutical analyses, particularly when buffers with very high ionic strength are used. In this study, we investigate the numerical and experimental study of fluidic biochips driven by ac electrothermal flow for controlling and manipulating biological samples inside a microchannel, e.g., for fluid-driven and manipulation purposes such as concentrating and mixing. By appropriately switching the voltage on the electrode structures and inducing AC electrothermal forces within the channel, a fluidic network with pumping and manipulation capabilities can be achieved, enabling the control of fluid velocity/direction and also fluid rotation. By using finite element analysis, coupled physics of electrical, thermal, fluidic fields, and molecular diffusion transport were solved. AC electrothermal flow was studied for pumping and mixing applications, and the optimal model was extracted. The microfluidic chip was fabricated using two processes: electrode structure development on the chip and silicon mold fabrication in a cleanroom. PDMS was prepared as the microchannel material and bonded to the electrode structure. After implementing the chip holder and excitation circuit, a biological buffer with varying ionic strengths (0.2, 0.4, and 0.6 [S/m]) was prepared, mixed with fluorescent particles, and loaded into the microfluidic chip. Experimental results demonstrated the efficiency of the proposed chip for biological applications, showing that stronger flows were generated with increasing fluid conductivity and excitation voltage. The system behavior was characterized using an impedance analyzer. Frequency response analysis revealed that for a solution with an electrical conductivity of 0.6 [S/m], the fluid velocity remained almost constant within a frequency range of 100 kHz to 10 MHz. Overall, the experimental results showed good agreement with the simulation outcomes.

Reagent storage and delivery on integrated microfluidic chips for point-of-care diagnostics

Microfluidic-based point-of-care diagnostics offer several unique advantages over existing bioanalytical solutions, such as automation, miniaturisation, and integration of sensors to rapidly detect on-site specific biomarkers. It is important to highlight that a microfluidic POC system needs to perform a number of steps, including sample preparation, nucleic acid extraction, amplification, and detection. Each of these stages involves mixing and elution to go from sample to result. To address these complex sample preparation procedures, a vast number of different approaches have been developed to solve the problem of reagent storage and delivery. However, to date, no universal method has been proposed that can be applied as a working solution for all cases. Herein, both current self-contained (stored within the chip) and off-chip (stored in a separate device and brought together at the point of use) are reviewed, and their merits and limitations are discussed. This review focuses on reagent storage devices that could be integrated with microfluidic devices, discussing further issues or merits of these storage solutions in two different sections: direct on-chip storage and external storage with their application devices. Furthermore, the different microvalves and micropumps are considered to provide guidelines for designing appropriate integrated microfluidic point-of-care devices.

Multiplex detection of the big five carbapenemase genes using solid-phase recombinase polymerase amplification

Five carbapenemase enzymes, coined the 'big five', have been identified as the biggest threat to worldwide antibiotic resistance based on their broad substrate affinity and global prevalence. Here we show the development of a molecular detection method for the gene sequences from the five carbapenemases utilising the isothermal amplification method of recombinase polymerase amplification (RPA). We demonstrate the successful detection of each of the big five carbapenemase genes with femtomolar detection limits using a spatially separated multiplex amplification strategy. The approach uses tailed oligonucleotides for hybridisation, reducing the complexity and cost of the assay compared to classical RPA detection strategies. The reporter probe, horseradish peroxidase, generates the measureable output on a benchtop microplate reader, but more notably, our study leverages the power of a portable Raman spectrometer, enabling up to a 19-fold enhancement in the limit of detection. Significantly, the development approach employed a solid-phase RPA format, wherein the forward primers targeting each of the five carbapenemase genes are immobilised to a streptavidin-coated microplate. The adoption of this solid-phase methodology is pivotal for achieving a successful developmental pathway when employing this streamlined approach. The assay takes 2 hours until result, including a 40 minutes RPA amplification step at 37 °C. This is the first example of using solid-phase RPA for the detection of the big five and represents a milestone towards the developments of an automated point-of-care diagnostic for the big five using RPA.

Programmable magnetic robot (ProMagBot) for automated nucleic acid extraction at the point of need

Upstream sample preparation remains the bottleneck for point-of-need nucleic acid testing due to its complexity and time-consuming nature. Sample preparation involves extracting, purifying, and concentrating nucleic acids from various matrices. These processes are critical for ensuring the accuracy and sensitivity of downstream nucleic acid amplification and detection. However, current sample preparation methods are often laboratory-based, requiring specialized equipment, trained personnel, and several hours of processing time. As a result, sample preparation often limits the speed, portability, and cost-effectiveness of point-of-need nucleic acid testing. A universal, field-deployable sample preparation device is highly desirable for this critical need and unmet challenge. Here we reported a handheld, battery-powered, reconfigurable, and field-deployable nucleic acid sample preparation device. A programmable electromagnetic actuator was developed to drive a magnetic robot (ProMagBot) in X/Y 2D space, such that various magnetic bead-based sample preparations can be readily translated from the laboratory to point-of-need settings. The control of the electromagnetic actuator requires only a 3-phase unipolar voltage in X and Y directions, and therefore, the motion space is highly scalable. We validated the ProMagBot device with a model application by extracting HIV viral RNAs from plasma samples using two widely used magnetic bead kits: ChargeSwitch and MagMAX beads. In both cases, the ProMagBot could successfully extract viral RNAs from 50 μL plasma samples containing as low as 102 copies of viral RNAs in 20 minutes. Our results demonstrated the ability of ProMagBot to prepare samples from complex mediums at the point of need. We believe such a device would enable rapid and robust sample preparation in various settings, including resource-limited or remote environments, and accelerate the development of next-generation point-of-need nucleic acid testing.

Magnetic-based Microfluidic Chip: A Powerful Tool for Pathogen Detection and Affinity Reagents Selection

The global outbreak of pathogen diseases has brought a huge risk to human lives and social development. Rapid diagnosis is the key strategy to fight against pathogen diseases. Development of detection methods and discovery of related affinity reagents are important parts of pathogen diagnosis. Conventional detection methods and affinity reagents discovery have some problems including much reagent consumption and labor intensity. Magnetic-based microfluidic chip integrates the unique advantages of magnetism and microfluidic technology, improving a powerful tool for pathogen detection and their affinity reagent discovery. This review provides a summary about the summary of pathogen detection through magnetic-based microfluidic chip, which refers to the pathogen nucleic acid detection (including extraction, amplification and signal acquisition), pathogen proteins and antibodies detection. Meanwhile, affinity reagents are served as the critical tool to specially capture pathogens. New affinity reagents are discovered to further facilitate the pathogen diagnosis. Microfluidic technology has also emerged as a powerful tool for affinity reagents discovery. Thus, this review further introduced the selection progress of aptamer as next generation affinity through the magnetic-based microfluidic technology. Using this selection technology shows great potential to improve selection performance, including integration and highly efficient selection. Finally, an outlook is given on how this field will develop on the basis of ongoing pathogen challenges.

An automated, fully-integrated nucleic acid analyzer based on microfluidic liquid handling robot technique

On-site nucleic acid testing (NAT) plays an important role for disease monitoring and pathogen diagnosis. In this work, we developed an automated and fully-integrated nucleic acid analyzer by combining the automated liquid handling robot technique with the microfluidic droplet-based real-time PCR assay technique. The present analyzer could achieve multiple operations including sample introduction, nucleic acid extraction based on magnetic solid-phase extraction, reverse transcription and, sample droplet generation, PCR amplification, real-time and dual fluorescence detection of droplet array. A strategy of constructing an integrated compact and low-cost system was adopted to minimize the analyzer size to 50 × 45 × 45 cm (length × width × height), and reduce the instrument cost to ca. $900 with a single analysis cost less than $5. A simple chip was also designed to pre-load reagents and carry oil-covered PCR reaction droplets. We applied the analyzer to identify eight types of influenza pathogens in human throat swabs, and the results were consistent with the colloidal gold method.

Innovative Quantification of Critical Quality Attributes

Potency testing is an important part of the evaluation of cellular therapy products. In vitro quantification of identified quality-related biomarkers is a technique often used at the laboratory. Nonetheless, the limited stability of most cellular therapy products, the lot variability and the limited time within which to perform testing are currently hindering their widespread use. Fortunately, within the last two decades, the evolution of material technology and miniaturisation processes has enabled the research community to shift the spotlight of attention towards the Lab-on-Chip concept for diagnostic applications. Such devices enable portable, rapid, sensitive, automated and affordable biochemical analyses aiming to advance the healthcare services across a broad application spectrum. However, it could be argued that the aspirations on their affordability are far from being exceeded, mainly due to the lack of a practical manufacturing technology. The Lab-on-Printed Circuit Board (Lab-on-PCB) approach has demonstrated enormous potential for developing economical diagnostic platforms leveraging the advantage provided by economy of scale manufacturing of the long-standing PCB industry. The integration capabilities that the PCB platform introduces to the Lab-on-Chip concept concerning the electronics and microfluidics seem to be unique. In this chapter, we will be reviewing the progress of Lab-on-PCB prototypes quantifying within miniaturised microchips a range of critical quality attributes with potential in potency testing. We will focus on their technology and applications whilst addressing the potential of this approach in practical use and commercialisation.

Microvalves for Applications in Centrifugal Microfluidics

Centrifugal microfluidic platforms (CDs) have opened new possibilities for inexpensive point-of-care (POC) diagnostics. They are now widely used in applications requiring polymerase chain reaction steps, blood plasma separation, serial dilutions, and many other diagnostic processes. CD microfluidic devices allow a variety of complex processes to transfer onto the small disc platform that previously were carried out by individual expensive laboratory equipment requiring trained personnel. The portability, ease of operation, integration, and robustness of the CD fluidic platforms requires simple, reliable, and scalable designs to control the flow of fluids. Valves play a vital role in opening/closing of microfluidic channels to enable a precise control of the flow of fluids on a centrifugal platform. Valving systems are also critical in isolating chambers from the rest of a fluidic network at required times, in effectively directing the reagents to the target location, in serial dilutions, and in integration of multiple other processes on a single CD. In this paper, we review the various available fluidic valving systems, discuss their working principles, and evaluate their compatibility with CD fluidic platforms. We categorize the presented valving systems into either "active", "passive", or "hybrid"-based on their actuation mechanism that can be mechanical, thermal, hydrophobic/hydrophilic, solubility-based, phase-change, and others. Important topics such as their actuation mechanism, governing physics, variability of performance, necessary disc spin rate for valve actuation, valve response time, and other parameters are discussed. The applicability of some types of valves for specialized functions such as reagent storage, flow control, and other applications is summarized.

Light Controlled 3D Crystal Morphology for Droplet Evaporative Crystallization on Photosensitive Hydrophobic Substrate

Controlling crystal morphology is crucial in analytical chemistry and smart materials synthesis, etc. However, flexible manipulation of 3D crystal morphology still remains challenging. Herein, we present a novel and facile light strategy for droplet evaporative crystallization to manipulate macroscopic crystal morphology on photosensitive hydrophobic substrate possessing photothermal conversion property. We demonstrate that the spherical coronal shell and alms bowl-like crystal skeletons can be achieved on smooth photosensitive hydrophobic substrate, depending on the salt concentration. Rough photosensitive hydrophobic substrate further creates a bubble-assisted light strategy, by which a cylindrical shell-like crystal skeleton with a directionally controllable cavity is achieved. Amazingly, the proper additive endows droplet evaporative crystallization to form a closed crystal skeleton with the solution wrapped inside. The present study provides new ideas for designing a novel optical droplet microfluidic platform for controlling crystal morphology.

Compact Microfluidic Platform with LED Light-Actuated Valves for Enzyme-Linked Immunosorbent Assay Automation

Lab-on-a-chip devices incorporating valves and pumps can perform complex assays involving multiple reagents. However, the instruments used to drive these chips are complex and bulky. In this article, a new wax valve design that uses light from a light emitting diode (LED) for both opening and closing is reported. The valves and a pumping chamber are integrated in lab-on-a-foil chips that can be fabricated at low cost using rapid prototyping techniques. A chip for the implementation of enzyme-linked immunosorbent assays (ELISA) is designed. A porous nitrocellulose material is used for the immobilization of capture antibodies in the microchannel. A compact generic instrument with an array of 64 LEDs, a linear actuator to drive the pumping chamber, and absorbance detection for a colorimetric readout of the assay is also presented. Characterization of all the components and functionalities of the platform and the designed chip demonstrate their potential for assay automation.

Printed Circuit Boards: The Layers' Functions for Electronic and Biomedical Engineering

This paper describes the fabrication opportunities that Printed Circuit Boards (PCBs) offer for electronic and biomedical engineering. Historically, PCB substrates have been used to support the components of the electronic devices, linking them using copper lines, and providing input and output pads to connect the rest of the system. In addition, this kind of substrate is an emerging material for biomedical engineering thanks to its many interesting characteristics, such as its commercial availability at a low cost with very good tolerance and versatility, due to its multilayer characteristics; that is, the possibility of using several metals and substrate layers. The alternative uses of copper, gold, Flame Retardant 4 (FR4) and silver layers, together with the use of vias, solder masks and a rigid and flexible substrate, are noted. Among other uses, these characteristics have been using to develop many sensors, biosensors and actuators, and PCB-based lab-on chips; for example, deoxyribonucleic acid (DNA) amplification devices for Polymerase Chain Reaction (PCR). In addition, several applications of these devices are going to be noted in this paper, and two tables summarizing the layers' functions are included in the discussion: the first one for metallic layers, and the second one for the vias, solder mask, flexible and rigid substrate functions.

Detection and separation of proteins using micro/nanofluidics devices

Microfluidics is the technology or system wherein the behavior of fluids' is studied onto a miniaturized device composed of chambers and tunnels. In biological and biomedical sciences, microfluidic technology/system or device serves as an ultra-high-output approach capable of detecting and separating the biomolecules present even in trace quantities. Given the essential role of protein, the identification and quantification of proteins help understand the various living systems' biological function regulation. Microfluidics has enormous potential to enable biological investigation at the cellular and molecular level and maybe a fair substitution of the sophisticated instruments/equipment used for proteomics, genomics, and metabolomics analysis. The current advancement in microfluidic systems' development is achieving momentum and opening new avenues in developing innovative and hybrid methodologies/technologies. This chapter attempts to expound the micro/nanofluidic systems/devices for their wide-ranging application to detect and separate protein. It covers microfluidic chip electrophoresis, microchip gel electrophoresis, and nanofluidic systems as protein separation systems, while methods such as spectrophotometric, mass spectrometry, electrochemical detection, magneto-resistive sensors and dynamic light scattering (DLS) are discussed as proteins' detection system.

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.

A Titratable Cell Lysis-on-Demand System for Droplet-Compartmentalized Ultrahigh-Throughput Screening in Functional Metagenomics and Directed Evolution

Water-in-oil emulsion droplets are an attractive format for ultrahigh-throughput screening in functional metagenomics and directed evolution applications that allow libraries with more than 10⁷ members to be characterized in a day. Single library members are compartmentalized in droplets that are generated in microfluidic devices and tested for the presence of target biocatalysts. The target proteins can be produced intracellularly, for example, in bacterial hosts in-droplet cell lysis is therefore necessary to allow the enzymes to encounter the substrate to initiate an activity assay. Here, we present a titratable lysis-on-demand (LoD) system enabling the control of the cell lysis rate in Escherichia coli. We demonstrate that the rate of cell lysis can be controlled by adjusting the externally added inducer concentration. This LoD system is evaluated both at the population level (by optical density measurements) and at the single-cell level (on single-cell arrays and in alginate microbeads). Additionally, we validate the LoD system by droplet screening of a phosphotriesterase expressed from E. coli, with cell lysis triggered by inducer concentrations in the μM range. The LoD system yields sufficient release of the intracellularly produced enzymes to bring about a detectable quantity of product (measured by fluorescence in flow cytometry of double emulsions), while leaving viable cells for the downstream recovery of the genetic material.

Lab-on-PCB and Flow Driving: A Critical Review

Lab-on-PCB devices have been developed for many biomedical and biochemical applications. However, much work has to be done towards commercial applications. Even so, the research on devices of this kind is rapidly increasing. The reason for this lies in the great potential of lab-on-PCB devices to provide marketable devices. This review describes the active flow driving methods for lab-on-PCB devices, while commenting on their main characteristics. Among others, the methods described are the typical external impulsion devices, that is, syringe or peristaltic pumps; pressurized microchambers for precise displacement of liquid samples; electrowetting on dielectrics; and electroosmotic and phase-change-based flow driving, to name a few. In general, there is not a perfect method because all of them have drawbacks. The main problems with regard to marketable devices are the complex fabrication processes, the integration of many materials, the sealing process, and the use of many facilities for the PCB-chips. The larger the numbers of integrated sensors and actuators in the PCB-chip, the more complex the fabrication. In addition, the flow driving-integrated devices increase that difficulty. Moreover, the biological applications are demanding. They require transparency, biocompatibility, and specific ambient conditions. All the problems have to be solved when trying to reach repetitiveness and reliability, for both the fabrication process and the working of the lab-on-PCB, including the flow driving system.

Microfluidic Technology for Antibacterial Resistance Study and Antibiotic Susceptibility Testing: Review and Perspective

A review on microfluidic technology for antibacterial resistance study and antibiotic susceptibility testing (AST) is presented here. Antibiotic resistance has become a global health crisis in recent decades, severely threatening public health, patient care, economic growth, and even national security. It is extremely urgent that antibiotic resistance be well looked into and aggressively combated in order for us to survive this crisis. AST has been routinely utilized in determining bacterial susceptibility to antibiotics and identifying potential resistance. Yet conventional methods for AST are increasingly incompetent due to unsatisfactory test speed, high cost, and deficient reliability. Microfluidics has emerged as a powerful and very promising platform technology that has proven capable of addressing the limitation of conventional methods and advancing AST to a new level. Besides, potential technical challenges that are likely to hinder the development of microfluidic technology aimed at AST are observed and discussed. To conclude, it is noted that (1) the translation of microfluidic innovations from laboratories to be ready AST platforms remains a lengthy journey and (2) ensuring all relevant parties engaged in a collaborative and unified mode is foundational to the successful incubation of commercial microfluidic platforms for AST.

Printed Circuit Board (PCB) Technology for Electrochemical Sensors and Sensing Platforms

The development of various biosensors has revolutionized the healthcare industry by providing rapid and reliable detection capability. Printed circuit board (PCB) technology has a well-established industry widely available around the world. In addition to electronics, this technology has been utilized to fabricate electrical parts, including electrodes for different biological and chemical sensors. High reproducibility achieved through long-lasting standard processes and low-cost resulting from an abundance of competitive manufacturing services makes this fabrication method a prime candidate for patterning electrodes and electrical parts of biosensors. The adoption of this approach in the fabrication of sensing platforms facilitates the integration of electronics and microfluidics with biosensors. In this review paper, the underlying principles and advances of printed board circuit technology are discussed. In addition, an overview of recent advancements in the development of PCB-based biosensors is provided. Finally, the challenges and outlook of PCB-based sensors are elaborated.

The vision of point-of-care PCR tests for the COVID-19 pandemic and beyond

Infectious diseases, such as the most recent case of coronavirus disease 2019, have brought the prospect of point-of-care (POC) diagnostic tests into the spotlight. A rapid, accurate, low-cost, and easy-to-use test in the field could stop epidemics before they develop into full-blown pandemics. Unfortunately, despite all the advances, it still does not exist. Here, we critically review the limited number of prototypes demonstrated to date that is based on a polymerase chain reaction (PCR) and has come close to fulfill this vision. We summarize the requirements for the POC-PCR tests and then go on to discuss the PCR product-detection methods, the integration of their functional components, the potential applications, and other practical issues related to the implementation of lab-on-a-chip technologies. We conclude our review with a discussion of the latest findings on nucleic acid-based diagnosis.

Construction of the Nickel Oxide Nanocoral Structure on Microscope Slides for Total Self-Assembly-Oriented Probe Immobilization and Signal Enhancement

Proper orientation of probes and the binding capacity of surfaces will determine the performance of bio-applications. It has been reported that immobilizing through bio-/chemical affinity is an efficient but gentle strategy to solve the above-mentioned issue. Herein, we introduce a total self-assembly approach via the strong affinity of nickel oxide (NiO) to the polyhistidine-tag (His-tag). It allows the efficient immobilizing His-tagged proteins with orientation. Furthermore, we find that the nanocoral structure can be formed after applying rapid thermal annealing at 1100 °C, which could increase the His-tagged protein binding capacity efficiently by the enhanced surface-to-volume ratio. Lastly, we demonstrate the NiO thin film with the nanocoral structure, which has great potential for universal biosensing with a wide range of biomolecules, including DNA, protein, and bacteria. Through His-tagged monomer streptavidin (His₆-mSA) or His-tagged protein G (His₆-protein G), the biotinylated DNA or antibody could be immobilized with proper orientation on the surface consequently to complete a sensitive biomolecule detection. Moreover, the NiO nanocoral structure has the advantages of high hydrophilicity, transmittance, and pH stability that are promising to develop into several kinds of bio-applications in the near future.

Label-Free cDNA Detection Based on Radiofrequency Scattering Parameters: A New Approach for an Inexpensive Gene Sensor

A new gene detection technique that is fast, inexpensive, and easy-to-use is urgently needed in hospitals, clinics, and laboratories without access to expensive equipments. The lack of a practical, minimally invasive, and economical method constitutes the main impediment to the promotion of genetic medicine in developing countries. Radiofrequency scattering parameters are an inexpensive gene sensor potentially capable of noninvasively identifying biological materials. They represent a quantitative value for the electromagnetic reflection/transmission characteristics of certain molecular markers in a given frequency domain. The S21 parameter is the difference between the signal received and that transmitted. The aim of this study is to evaluate the S21 transmittance parameters (magnitude and phase) as an indirect impedance measurement for detecting the label-free complementary deoxyribonucleic acid (cDNA) amplification of the 16S ribosomal subunit gene. S21 values showed differences associated with distinct cDNA concentrations. Hence, this technique could possibly facilitate the design of an inexpensive, label-free, and easy-to-use gene sensor.

One-step liquid molding based modular microfluidic circuits

We present an easy-to-follow modular method that combines liquid molding with standard SU-8 lithography to create customized integrated microfluidic devices for the changing needs of users.

Ultrasensitive THz biosensor for PCR-free cDNA detection based on frequency selective surfaces

THz technologies are a powerful tool for label-free detection of biomolecules. However, significant reduction of the lower detection limit is required to apply THz-sensors in biomedical diagnosis. This paper reports an ultrasensitive THz-biosensor based on asymmetric double split ring resonators (aDSRR) for the direct label- and PCR-free detection of DNA at physiologically relevant concentrations. We introduce selective functionalization and localized electric field concentration to enhance aDSRR sensitivity and specificity. The sensor characteristics are demonstrated using the human tumor marker MIA in cDNA samples produced from total RNA without PCR-amplification. Measurements of DNA samples with concentrations as low as 1.55 × 10^-12 mol/l are presented.

Nanophotonic Cell Lysis and Polymerase Chain Reaction with Gravity-Driven Cell Enrichment for Rapid Detection of Pathogens

Rapid and precise detection of pathogens is a critical step in the prevention and identification of emergencies related to health and biosafety as well as the clinical management of community-acquired urinary tract infections or sexually transmitted diseases. However, a conventional culture-based pathogen diagnostic method is time-consuming, permitting physicians to use antibiotics without ample clinical data. Here, we present a nanophotonic Light-driven Integrated cell lysis and polymerase chain reaction (PCR) on a chip with Gravity-driven cell enrichment Health Technology (LIGHT) for rapid precision detection of pathogens (<20 min). We created the LIGHT, which has the three functions of (1) selective enrichment of pathogens, (2) photothermal cell lysis, and (3) photonic PCR on a chip. We designed the gravity-driven cell enrichment via a nanoporous membrane on a chip that allows an effective bacterial enrichment of 40 000-fold from a 1 mL sample in 2 min. We established a light-driven photothermal lysis of preconcentrated bacteria within 1 min by designing the network of nanoplasmonic optical antenna on a chip for ultrafast light-to-heat conversion, created the nanoplasmonic optical antenna network-based ultrafast photonic PCR on a chip, and identified Escherichia coli. Finally, we demonstrated the end-point detection of up to 10³ CFU/mL of E. coli in 10 min. We believe that our nanophotonic LIGHT will provide rapid and precise identification of pathogens in both developing and developed countries.

Cell lysis via acoustically oscillating sharp edges

In this article, we demonstrate an acoustofluidic device for cell lysis using the acoustic streaming effects induced by acoustically oscillating sharp-edged structures. The acoustic streaming locally generates high shear forces that can mechanically rupture cell membranes. With the acoustic-streaming-derived shear forces, our acoustofluidic device can perform cell lysis in a continuous, reagent-free manner, with a lysis efficiency of more than 90% over a range of sample flow rates. We demonstrate that our acoustofluidic lysis device works well on both adherent and non-adherent cells. We also validate it using clinically relevant samples such as red blood cells infected with malarial parasites. Additionally, the unique capability of our acoustofluidic device was demonstrated by performing downstream protein analysis and gene profiling without additional washing steps post-lysis. Our device is simple to fabricate and operate while consuming a relatively low volume of samples. These advantages and other features including the reagent-free nature and controllable lysis efficiency make our platform valuable for many biological and biomedical applications, particularly for the development of point-of-care platforms.

A self-contained and fully integrated fluidic cassette system for multiplex nucleic acid detection of bacteriuria

The gold standard for diagnosing infectious diseases is culture-based identification of bacterial pathogens, which is time-consuming and labour-intensive. Current advances in molecular diagnostics and microfluidic technologies have made the rapid detection of bacteria or viruses in clinical specimens possible. However, the need for rapid, sensitive and multiplex detection of pathogens in a "sample-in and answer-out" manner has not been fully satisfied. In this study, a self-contained and fully integrated fluidic cassette and its supporting analyser were constructed for multiplex detection of bacteria to accelerate the diagnosis of urinary tract infections (UTIs). The fully integrated cassette contains all the necessary components and reagents for bacterial analysis. All of the bacterial analysis processes, including bacterial lysis, magnetic silica bead-based DNA extraction, DNA elution and multiplex loop-mediated amplification (LAMP), are automatically conducted in the cassette. This cassette was successfully applied for the detection of four major pathogenic bacteria in UTIs, i.e., Escherichia coli, Proteus mirabilis, Salmonella typhimurium and Staphylococcus aureus. The first three were successfully detected with a limit of detection (LoD) of 1 colony-forming unit (CFU) μL^-1 and the last was with a LoD of 10 CFU μL^-1 in urine samples, demonstrating that the cassette has similar sensitivity compared to that of the manual protocol, which is lower than that required by UTIs. The turnaround time for this cassette-based sample-to-answer system was approximately 100 minutes, and the detection is sensitive, fully automated, and accurate, demonstrating the potential to be a useful diagnostic tool for UTIs.

A highly sensitive and selective fluorescence biosensor for hepatitis C virus DNA detection based on δ-FeOOH and exonuclease III-assisted signal amplification

Developing the high selectivity and sensitivity strategy for nucleic acid detection is crucial for early diagnosis and therapy of diseases. In this work, a novel low back-ground fluorescent sensor platform for the detection of nucleic acid has been developed based on δ-FeOOH nanosheets integrating with exonuclease III-assisted target-recycling signal amplification. Because of the strong binding ability between the single-strand DNA (ssDNA) and the δ-FeOOH nanosheets, the dye-labeled ssDNA probe would be quenched by δ-FeOOH nanosheets through fluorescence resonance energy transfer (FRET). By using magnetic separate properties of δ-FeOOH, the background signal was separated from the sensor system, and the low background sensor system was obtained. After adding the target DNA, a double-strand DNA complex (dsDNA) would be formed between the target DNA and dye-labeled ssDNA probe. Then, the dye-labeled ssDNA probe in the dsDNA complex would be stepwise hydrolyzed into short fragments from 3'-terminus by Exonuclease III, and the fluorescence signal was recovered due to the weak bind affinity between the short fragments and δ-FeOOH nanosheets. By using the fluorescence quenching ability of δ-FeOOH nanosheets and enzyme-assisted target-recycling signal amplification, this strategy could show an excellent selectivity toward hepatitis C virus DNA with a low detection limit of 10 pM. By simply changing the dye-labeled ssDNA probe sequence, this sensing platform can be developed as a universal approach for the simple, sensitive, and selective detection of different target DNA.

Microfluidics-Based Organism Isolation from Whole Blood: An Emerging Tool for Bloodstream Infection Diagnosis

The diagnosis of bloodstream infections presents numerous challenges, in part, due to the low concentration of pathogens present in the peripheral bloodstream. As an alternative to existing time-consuming, culture-based diagnostic methods for organism identification, microfluidic devices have emerged as rapid, high-throughput and integrated platforms for bacterial and fungal enrichment, detection, and characterization. This focused review serves to highlight and compare the emerging microfluidic platforms designed for the isolation of sepsis-causing pathogens from blood and suggest important areas for future research.

Modern Approach to Medical Diagnostics - the Use of Separation Techniques in Microorganisms Detection

Background:

Analytical chemistry and biotechnology as an interdisciplinary fields of science have been developed during many years and are experiencing significant growth, to cover a wide range of microorganisms separation techniques and methods, utilized for medical therapeutic and diagnostic purposes. Currently scientific reports contribute by introducing electrophoretical and immunological methods and formation of devices applied in food protection (avoiding epidemiological diseases) and healthcare (safety ensuring in hospitals).

Methods:

Electrophoretic as well as nucleic-acid-based or specific immunological methods have contributed tremendously to the advance of analyses in recent three decades, particularly in relation to bacteria, viruses and fungi identifications, especially in medical in vitro diagnostics, as well as in environmental or food protection.

Results:

The paper presents the pathogen detection competitiveness of these methods against conventional ones, which are still too time consuming and also labor intensive. The review is presented in several parts following the current trends in improved pathogens separation and detection methods and their subsequent use in medical diagnosis.

Discussion:

Part one, consists of elemental knowledge about microorganisms as an introduction to their characterization: descriptions of divisions, sizes, membranes (cells) components. Second section includes the development, new technological and practical solution descriptions used in electrophoretical procedures during microbes analyses, with special attention paid to bio-samples analyses like blood, urine, lymph or wastewater. Third part covers biomolecular areas that have created a basis needed to identify the progress, limitations and challenges of nucleic-acid-based and immunological techniques discussed to emphasize the advantages of new separative techniques in selective fractionating of microorganisms.

An automated microfluidic DNA microarray platform for genetic variant detection in inherited arrhythmic diseases

In this study, we developed an automated microfluidic DNA microarray (AMDM) platform for point mutation detection of genetic variants in inherited arrhythmic diseases. The platform allows for automated and programmable reagent sequencing under precise conditions of hybridization flow and temperature control. It is composed of a commercial microfluidic control system, a microfluidic microarray device, and a temperature control unit. The automated and rapid hybridization process can be performed in the AMDM platform using Cy3 labeled oligonucleotide exons of SCN5A genetic DNA, which produces proteins associated with sodium channels abundant in the heart (cardiac) muscle cells. We then introduce a graphene oxide (GO)-assisted DNA microarray hybridization protocol to enable point mutation detection. In this protocol, a GO solution is added after the staining step to quench dyes bound to single-stranded DNA or non-perfectly matched DNA, which can improve point mutation specificity. As proof-of-concept we extracted the wild-type and mutant of exon 12 and exon 17 of SCN5A genetic DNA from patients with long QT syndrome or Brugada syndrome by touchdown PCR and performed a successful point mutation discrimination in the AMDM platform. Overall, the AMDM platform can greatly reduce laborious and time-consuming hybridization steps and prevent potential contamination. Furthermore, by introducing the reciprocating flow into the microchannel during the hybridization process, the total assay time can be reduced to 3 hours, which is 6 times faster than the conventional DNA microarray. Given the automatic assay operation, shorter assay time, and high point mutation discrimination, we believe that the AMDM platform has potential for low-cost, rapid and sensitive genetic testing in a simple and user-friendly manner, which may benefit gene screening in medical practice.

Mobile Microfluidics

Microfluidics platforms can program small amounts of fluids to execute a bio-protocol, and thus, can automate the work of a technician and also integrate a large part of laboratory equipment. Although most microfluidic systems have considerably reduced the size of a laboratory, they are still benchtop units, of a size comparable to a desktop computer. In this paper, we argue that achieving true mobility in microfluidics would revolutionize the domain by making laboratory services accessible during traveling or even in daily situations, such as sport and outdoor activities. We review the existing efforts to achieve mobility in microfluidics, and we discuss the conditions mobile biochips need to satisfy. In particular, we show how we adapted an existing biochip for mobile use, and we present the results when using it during a train ride. Based on these results and our systematic discussion, we identify the challenges that need to be overcome at technical, usability and social levels. In analogy to the history of computing, we make some predictions on the future of mobile biochips. In our vision, mobile biochips will disrupt how people interact with a wide range of healthcare processes, including medical testing and synthesis of on-demand medicine.

Integrated Microfluidic System for Rapid DNA Fingerprint Analysis: A Miniaturized Integrated DNA Analysis System (MiDAS)-Swab Sample-In to DNA Profile-Out

A fully automated rapid DNA analysis system requires integrating several operational elements performing multiple steps onto one single microfluidic platform. The functions to include on the microfluidic platform consist of substrate lysis, lysate DNA extraction, single or multiplexed PCR amplification, amplicon separation, and product readout. Here we describe a fully automated integrated system for forensic short tandem repeat (STR) analysis of reference samples, achieving buccal swab-in and DNA profile-out.

Microbiome 101: Studying, Analyzing, and Interpreting Gut Microbiome Data for Clinicians

Advances in technical capabilities for reading complex human microbiomes are leading to an explosion of microbiome research, leading in turn to intense interest among clinicians in applying these techniques to their patients. In this review, we discuss the content of the human microbiome, including intersubject and intrasubject variability, considerations of study design including important confounding factors, and different methods in the laboratory and on the computer to read the microbiome and its resulting gene products and metabolites. We highlight several common pitfalls for clinicians, including the expectation that an individual's microbiome will be stable, that diet can induce rapid changes that are large compared with the differences among subjects, that everyone has essentially the same core stool microbiome, and that different laboratory and computational methods will yield essentially the same results. We also highlight the current limitations and future promise of these techniques, with the expectation that an understanding of these considerations will help accelerate the path toward routine clinical application of these techniques developed in research settings.

3D printed selectable dilution mixer pumps

In this paper, we demonstrate the ability to 3D print tightly integrated structures with active valves, pumps, and mixers, and we use our compact chip-to-chip interconnects [Gong et al., Lab Chip 18, 639-647 (2018)] to move bulky world-to-chip connections to separate interface chips for both post-print flushing and post-cure device operation. As example devices, we first examine 3D printed pumps, followed by two types of selectable ratio mixer pumps, a linear dilution mixer pump (LDMP) and a parallelized dilution mixer pump (PDMP), which occupy volumes of only 1.5 mm 3 and 2.6 mm 3 , respectively. The LDMP generates a selectable dilution ratio from a linear set of possibilities, while the PDMP generates a denser set of possible dilutions with a maximum dilution ratio of 1/16. The PDMP also incorporates a new 4-to-1 valve to simultaneously control 4 inlet channels. To characterize LDMP and PDMP operation and performance, we present a new, low-cost video method to directly measure the relative concentration of an absorptive dye on a pixel-by-pixel basis for each video frame. Using this method, we find that 6 periods of the active mixer that forms the core of the LDMP and PDMP are sufficient to fully mix the fluid, and that the generated concentrations track the designed dilution ratios as expected. The LDMP mixes 20 nl per 4.6 s mixer pump period, while the PDMP uses parallelized input pumps to process the same fluid volume with greater choice of dilution ratios in a 3.6 s period.

dCas9-mediated Nanoelectrokinetic Direct Detection of Target Gene for Liquid Biopsy

The-state-of-the-art bio- and nanotechnology have opened up an avenue to noninvasive liquid biopsy for identifying diseases from biomolecules in bloodstream, especially DNA. In this work, we combined sequence-specific-labeling scheme using mutated clustered regularly interspaced short palindromic repeats associated protein 9 without endonuclease activity (CRISPR/dCas9) and ion concentration polarization (ICP) phenomenon as a mechanism to selectively preconcentrate targeted DNA molecules for rapid and direct detection. Theoretical analysis on ICP phenomenon figured out a critical mobility, elucidating two distinguishable concentrating behaviors near a nanojunction, a stacking and a propagating behavior. Through the modulation of the critical mobility to shift those behaviors, the C-C chemokine receptor type 5 ( CCR5) sequences were optically detected without PCR amplification. Conclusively, the proposed dCas9-mediated genetic detection methodology based on ICP would provide rapid and accurate micro/nanofluidic platform of liquid biopsies for disease diagnostics.

A Novel Microfluidic Point-of-Care Biosensor System on Printed Circuit Board for Cytokine Detection

Point of Care (PoC) diagnostics have been the subject of considerable research over the last few decades driven by the pressure to detect diseases quickly and effectively and reduce healthcare costs. Herein, we demonstrate a novel, fully integrated, microfluidic amperometric enzyme-linked immunosorbent assay (ELISA) prototype using a commercial interferon gamma release assay (IGRA) as a model antibody binding system. Microfluidic assay chemistry was engineered to take place on Au-plated electrodes within an assay cell on a printed circuit board (PCB)-based biosensor system. The assay cell is linked to an electrochemical reporter cell comprising microfluidic architecture, Au working and counter electrodes and a Ag/AgCl reference electrode, all manufactured exclusively via standard commercial PCB fabrication processes. Assay chemistry has been optimised for microfluidic diffusion kinetics to function under continual flow. We characterised the electrode integrity of the developed platforms with reference to biological sampling and buffer composition and subsequently we demonstrated concentration-dependent measurements of H₂O₂ depletion as resolved by existing FDA-validated ELISA kits. Finally, we validated the assay technology in both buffer and serum and demonstrate limits of detection comparable to high-end commercial systems with the addition of full microfluidic assay architecture capable of returning diagnostic analyses in approximately eight minutes.

On-chip pressure generation using a gel membrane fabricated outside of the microfluidic network

On-chip generation of pressure gradients via electrokinetic means can offer several advantages to microfluidic assay design and operation in a variety of applications. In this article, we describe a simple approach to realizing this capability by employing a polyacrylamide-based gel structure fabricated within a fluid reservoir located at the terminating end of a microchannel. Application of an electric field across this membrane has been shown to block a majority of the electroosmotic flow generated within the open duct yielding a high pressure at the channel-membrane junction. Experiments show the realization of higher pressure-driven velocities in an electric field-free separation channel integrated to the micropump with this design compared to other similar micropumps described in the literature. In addition, the noted velocity was found to be less sensitive to the extent of Debye layer overlap in the channel network, and therefore more impressive when working with background electrolytes having higher ionic strengths. With the current system, pressure-driven velocities up to 3.6 mm/s were realized in a 300-nm-deep separation channel applying a maximum voltage of 3 kV at a channel terminal. To demonstrate the separative performance of our device, a nanofluidic pressure-driven ion-chromatographic analysis was subsequently implemented that relied on the slower migration of cationic analytes relative to the neutral and anionic ones in the separation channel likely due to their strong electrostatic interaction with the channel surface charges. A mixture of amino acids was thus separated with resolutions greater than those reported by our group for a similar analysis previously.

A fully-integrated and automated testing device for PCR-free viral nucleic acid detection in whole blood

Integrated devices for automated nucleic acid testing (NAT) are critical for infectious disease diagnosis to be performed outside of centralized laboratories. The gold standard methods for NAT are enzymatic amplification methods like the polymerase chain reaction that typically require expensive equipment and highly-trained personnel, limiting use in low-resource settings. A low-cost, integrated, rapid, portable and user-friendly point-of-care (POC) nucleic acid diagnostic device will improve the accessibility of NAT. Here, we present a fully integrated and simple-to-use POC device operated by a passive fluidic method that is able to perform a sequential multi-step assay to detect viral nucleic acids in blood. This simple device enabled the rapid detection of hepatitis C virus in blood in approximately 30 minutes with minimal sample handling by the user.

DNA Electrochemistry and Electrochemical Sensors for Nucleic Acids

Sensitive, specific, and fast analysis of nucleic acids (NAs) is strongly needed in medicine, environmental science, biodefence, and agriculture for the study of bacterial contamination of food and beverages and genetically modified organisms. Electrochemistry offers accurate, simple, inexpensive, and robust tools for the development of such analytical platforms that can successfully compete with other approaches for NA detection. Here, electrode reactions of DNA, basic principles of electrochemical NA analysis, and their relevance for practical applications are reviewed and critically discussed.

A review on microscale polymerase chain reaction based methods in molecular diagnosis, and future prospects for the fabrication of fully integrated portable biomedical devices

Since the advent of microfabrication technology and soft lithography, the lab-on-a-chip concept has emerged as a state-of-the-art miniaturized tool for conducting the multiple functions associated with micro total analyses of nucleic acids, in series, in a seamless manner with a miniscule volume of sample. The enhanced surface-to-volume ratio inside a microchannel enables fast reactions owing to increased heat dissipation, allowing rapid amplification. For this reason, PCR has been one of the first applications to be miniaturized in a portable format. However, the nature of the basic working principle for microscale PCR, such as the complicated temperature controls and use of a thermal cycler, has hindered its total integration with other components into a micro total analyses systems (μTAS). This review (with 179 references) surveys the diverse forms of PCR microdevices constructed on the basis of different working principles and evaluates their performances. The first two main sections cover the state-of-the-art in chamber-type PCR microdevices and in continuous-flow PCR microdevices. Methods are then discussed that lead to microdevices with upstream sample purification and downstream detection schemes, with a particular focus on rapid on-site detection of foodborne pathogens. Next, the potential for miniaturizing and automating heaters and pumps is examined. The review concludes with sections on aspects of complete functional integration in conjunction with nanomaterial based sensing, a discussion on future prospects, and with conclusions. Graphical abstract In recent years, thermocycler-based PCR systems have been miniaturized to palm-sized, disposable polymer platforms. In addition, operational accessories such as heaters and mechanical pumps have been simplified to realize semi-automatted stand-alone portable biomedical diagnostic microdevices that are directly applicable in the field. This review summarizes the progress made and the current state of this field.

Methods for the detection and identification of pathogenic bacteria: past, present, and future

In order to retard the rate of development of antibacterial resistance, the causative agent must be identified as rapidly as possible, so that directed patient treatment and/or contact precautions can be initiated. This review highlights the challenges associated with the detection and identification of pathogenic bacteria, by providing an introduction to the techniques currently used, as well as newer techniques that are in development. Focusing on the chemical basis for these techniques, the review also provides a comparison of their advantages and disadvantages.

Fully 3D printed integrated reactor array for point-of-care molecular diagnostics

Molecular diagnostics that involve nucleic acid amplification tests (NAATs) are crucial for prevention and treatment of infectious diseases. In this study, we developed a simple, inexpensive, disposable, fully 3D printed microfluidic reactor array that is capable of carrying out extraction, concentration and isothermal amplification of nucleic acids in variety of body fluids. The method allows rapid molecular diagnostic tests for infectious diseases at point of care. A simple leak-proof polymerization strategy was developed to integrate flow-through nucleic acid isolation membranes into microfluidic devices, yielding a multifunctional diagnostic platform. Static coating technology was adopted to improve the biocompatibility of our 3D printed device. We demonstrated the suitability of our device for both end-point colorimetric qualitative detection and real-time fluorescence quantitative detection. We applied our diagnostic device to detection of Plasmodium falciparum in plasma samples and Neisseria meningitides in cerebrospinal fluid (CSF) samples by loop-mediated, isothermal amplification (LAMP) within 50 min. The detection limits were 100 fg for P. falciparum and 50 colony-forming unit (CFU) for N. meningitidis per reaction, which are comparable to that of benchtop instruments. This rapid and inexpensive 3D printed device has great potential for point-of-care molecular diagnosis of infectious disease in resource-limited settings.

Microfluidic "Pouch" Chips for Immunoassays and Nucleic Acid Amplification Tests

Microfluidic cassettes ("chips") for processing and analysis of clinical specimens and other sample types facilitate point-of-care (POC) immunoassays and nucleic acid based amplification tests. These single-use test chips can be self-contained and made amenable to autonomous operation-reducing or eliminating supporting instrumentation-by incorporating laminated, pliable "pouch" and membrane structures for fluid storage, pumping, mixing, and flow control. Materials and methods for integrating flexible pouch compartments and diaphragm valves into hard plastic (e.g., acrylic and polycarbonate) microfluidic "chips" for reagent storage, fluid actuation, and flow control are described. We review several versions of these pouch chips for immunoassay and nucleic acid amplification tests, and describe related fabrication techniques. These protocols thus offer a "toolbox" of methods for storage, pumping, and flow control functions in microfluidic devices.

Simple Approaches to Minimally-Instrumented, Microfluidic-Based Point-of-Care Nucleic Acid Amplification Tests

Designs and applications of microfluidics-based devices for molecular diagnostics (Nucleic Acid Amplification Tests, NAATs) in infectious disease testing are reviewed, with emphasis on minimally instrumented, point-of-care (POC) tests for resource-limited settings. Microfluidic cartridges ('chips') that combine solid-phase nucleic acid extraction; isothermal enzymatic nucleic acid amplification; pre-stored, paraffin-encapsulated lyophilized reagents; and real-time or endpoint optical detection are described. These chips can be used with a companion module for separating plasma from blood through a combined sedimentation-filtration effect. Three reporter types: Fluorescence, colorimetric dyes, and bioluminescence; and a new paradigm for end-point detection based on a diffusion-reaction column are compared. Multiplexing (parallel amplification and detection of multiple targets) is demonstrated. Low-cost detection and added functionality (data analysis, control, communication) can be realized using a cellphone platform with the chip. Some related and similar-purposed approaches by others are surveyed.

Bubble removal with the use of a vacuum pressure generated by a converging-diverging nozzle

Bubbles are an intrinsic problem in microfluidic devices and they can appear during the initial filling of the device or during operation. This report presents a generalizable technique to extract bubbles from microfluidic networks using an adjacent microfluidic negative pressure network over the entire microfluidic channel network design. We implement this technique by superimposing a network of parallel microchannels with a vacuum microfluidic channel and characterize the bubble extraction rates as a function of negative pressure applied. In addition, we generate negative pressure via a converging-diverging (CD) nozzle, which only requires inlet gas pressure to operate. Air bubbles generated during the initial liquid filling of the microfluidic network are removed within seconds and their volume extraction rate is calculated. This miniaturized vacuum source can achieve a vacuum pressure of 7.23 psi which corresponds to a bubble extraction rate of 9.84 pL/s, in the microfluidic channels we characterized. Finally, as proof of concept it is shown that the bubble removal system enables bubble removal on difficult to fill microfluidic channels such as circular or triangular shaped channels. This method can be easily integrated into many microfluidic experimental protocols.