GNN-Based Concentration Prediction With Variable Input Flow Rates for Microfluidic Mixers

Recent years have witnessed significant advances brought by microfluidic biochips in automating biochemical protocols. Accurate preparation of fluid samples is an essential component of these protocols, where concentration prediction and generation are critical. Equipped with the advantages of convenient fabrication and control, microfluidic mixers demonstrate huge potential in sample preparation. Although finite element analysis (FEA) is the most commonly used simulation method for accurate concentration prediction of a given microfluidic mixer, it is time-consuming with poor scalability for large biochip sizes. Recently, machine learning models have been adopted in concentration prediction, with great potential in enhancing the efficiency over traditional FEA methods. However, the state-of-the-art machine learning-based method can only predict the concentration of mixers with fixed input flow rates and fixed sizes. In this paper, we propose a new concentration prediction method based on graph neural networks (GNNs), which can predict output concentrations for microfluidic mixters with variable input flow rates. Moreover, a transfer learning method is proposed to transfer the trained model to mixers of different sizes with reduced training data. Experimental results show that, for microfluidic mixers with fixed input flow rates, the proposed method obtains an average reduction of 88% in terms of prediction errors compared with the state-of-the-art method. For microfluidic mixers with variable input flow rates, the proposed method reduces the prediction error by 85% on average. Besides, the proposed transfer learning method reduces the training data by 84% for extending the pre-trained model for microfluidic mixers of different sizes with acceptable prediction error.

Biomimetic gradient scaffolds for the tissue engineering and regeneration of rotator cuff enthesis

Rotator cuff tear is one of the most common musculoskeletal disorders, which often results in recurrent shoulder pain and limited movement. Enthesis is a structurally complex and functionally critical interface connecting tendon and bone that plays an essential role in maintaining integrity of the shoulder joint. Despite the availability of advanced surgical procedures for rotator cuff repair, there is a high rate of failure following surgery due to suboptimal enthesis healing and regeneration. Novel strategies based on tissue engineering are gaining popularity in improving tendon-bone interface (TBI) regeneration. Through incorporating physical and biochemical cues into scaffold design which mimics the structure and composition of native enthesis is advantageous to guide specific differentiation of seeding cells and facilitate the formation of functional tissues. In this review, we summarize the current state of research in enthesis tissue engineering highlighting the development and application of biomimetic scaffolds that replicate the gradient TBI. We also discuss the latest techniques for fabricating potential translatable scaffolds such as 3D bioprinting and microfluidic device. While preclinical studies have demonstrated encouraging results of biomimetic gradient scaffolds, the translation of these findings into clinical applications necessitates a comprehensive understanding of their safety and long-term efficacy.

High-throughput 3D microfluidic chip for generation of concentration gradients and mixture combinations

Concentration gradient generation and mixed combinations of multiple solutions are of great value in the field of biomedical research. However, existing concentration gradient generators for single or two-drug solutions cannot simultaneously achieve multiple concentration gradient formations and mixed solution combinations. Furthermore, the whole system was huge, and required expensive auxiliary equipment, which may lead to complex operations. To address this problem, we devised a novel 3D microchannel network design, which is capable of creating all the desired mixture combinations and concentration gradients of given small amounts of the input solutions. As a proof of concept, the device we presented was verified by both colorimetric and fluorescence detection methods to test the efficiency. This can enable the implementation of one to three solutions with no driving pump and facilitate unique multiple types of more concentration gradients and mixture combinations in a single operation. We envision that this will be a promising candidate for the development of simplified methods for screening of the appropriate concentration and combination, such as various drug screening applications.

Electrospun Aligned Nanofiber Yarns Constructed Biomimetic M-Type Interface Integrated into Precise Co-Culture System as Muscle-Tendon Junction-on-a-Chip for Drug Development

The incorporation of engineered muscle-tendon junction (MTJ) with organ-on-a-chip technology provides promising in vitro models for the understanding of cell-cell interaction at the interface between muscle and tendon tissues. However, developing engineered MTJ tissue with biomimetic anatomical interface structure remains challenging, and the precise co-culture of engineered interface tissue is further regarded as a remarkable obstacle. Herein, an interwoven waving approach is presented to develop engineered MTJ tissue with a biomimetic "M-type" interface structure, and further integrated into a precise co-culture microfluidic device for functional MTJ-on-a-chip fabrication. These multiscale MTJ scaffolds based on electrospun nanofiber yarns enabled 3D cellular alignment and differentiation, and the "M-type" structure led to cellular organization and interaction at the interface zone. Crucially, a compartmentalized co-culture system is integrated into an MTJ-on-a-chip device for the precise co-culture of muscle and tendon zones using their medium at the same time. Such an MTJ-on-a-chip device is further served for drug-associated MTJ toxic or protective efficacy investigations. These results highlight that these interwoven nanofibrous scaffolds with biomimetic "M-type" interface are beneficial for engineered MTJ tissue development, and MTJ-on-a-chip with precise co-culture system indicated their promising potential as in vitro musculoskeletal models for drug development and biological mechanism studies.

Chemotactic Interactions of Scenedesmus sp. and Azospirillum brasilense Investigated by Microfluidic Methods

The use of algae for industrial, biotechnological, and agricultural purposes is spreading globally. Scenedesmus species can play an essential role in the food industry and agriculture due to their favorable nutrient content and plant-stimulating properties. Previous research and the development of Scenedesmus-based foliar fertilizers raised several questions about the effectiveness of large-scale algal cultivation and the potential effects of algae on associative rhizobacteria. In the microbiological practice applied in agriculture, bacteria from the genus Azospirillum are one of the most studied plant growth-promoting, associative, nitrogen-fixing bacteria. Co-cultivation with Azospirillum species may be a new way of optimizing Scenedesmus culturing, but the functioning of the co-culture system still needs to be fully understood. It is known that Azospirillum brasilense can produce indole-3-acetic acid, which could stimulate algae growth as a plant hormone. However, the effect of microalgae on Azospirillum bacteria is unclear. In this study, we investigated the behavior of Azospirillum brasilense bacteria in the vicinity of Scenedesmus sp. or its supernatant using a microfluidic device consisting of physically separated but chemically coupled microchambers. Following the spatial distribution of bacteria within the device, we detected a positive chemotactic response toward the microalgae culture. To identify the metabolites responsible for this behavior, we tested the chemoeffector potential of citric acid and oxaloacetic acid, which, according to our HPLC analysis, were present in the algae supernatant in 0.074 mg/ml and 0.116 mg/ml concentrations, respectively. We found that oxaloacetic acid acts as a chemoattractant for Azospirillum brasilense.

An embedded obstacle type micromixer-concentration gradient generator based on capillary driven

An embedded obstacle-type micromixer-concentration gradient generator based on capillary self-driven is proposed and studied. Herringbone structure (HS) for mixing and palisade-shape small channels at the outlet are designed in the device (named HS). Simulation and experimentation are done to study the liquid mixing efficiency in the small channels and concentration gradient at the outlet, and the experimental results agree with the simulation results. For three cases of liquid dripping (sequential, reverse, and delayed drippings), mixing analysis shows that the mixing efficiency increases along both mixing channel and palisade length, and is high in the middle small channel of the palisade-shape area and low on both sides. An obvious concentration gradient at the outlet can form compared with the device without the palisade-shape area. Finally, water pH value detection is done as one of the applications of HS. This study can provide guidance for the application of HS in biochemical detection, cell research, drug screening, etc. based on the capillary-driven effect.

Flexible Toolbox of High-Precision Microfluidic Modules for Versatile Droplet-Based Applications

Although the enormous potential of droplet-based microfluidics has been successfully demonstrated in the past two decades for medical, pharmaceutical, and academic applications, its inherent potential has not been fully exploited until now. Nevertheless, the cultivation of biological cells and 3D cell structures like spheroids and organoids, located in serially arranged droplets in micro-channels, has a range of benefits compared to established cultivation techniques based on, e.g., microplates and microchips. To exploit the enormous potential of the droplet-based cell cultivation technique, a number of basic functions have to be fulfilled. In this paper, we describe microfluidic modules to realize the following basic functions with high precision: (i) droplet generation, (ii) mixing of cell suspensions and cell culture media in the droplets, (iii) droplet content detection, and (iv) active fluid injection into serially arranged droplets. The robustness of the functionality of the Two-Fluid Probe is further investigated regarding its droplet generation using different flow rates. Advantages and disadvantages in comparison to chip-based solutions are discussed. New chip-based modules like the gradient, the piezo valve-based conditioning, the analysis, and the microscopy module are characterized in detail and their high-precision functionalities are demonstrated. These microfluidic modules are micro-machined, and as the surfaces of their micro-channels are plasma-treated, we are able to perform cell cultivation experiments using any kind of cell culture media, but without needing to use surfactants. This is even more considerable when droplets are used to investigate cell cultures like stem cells or cancer cells as cell suspensions, as 3D cell structures, or as tissue fragments over days or even weeks for versatile applications.

Liquid-liquid interfaces enable tunable cell confinement to recapitulate surrounding tissue deformations during neutrophil interstitial migration in vivo

Cell migration is regulated by an interplay between both chemical and mechanical cues. Immune cells navigate through interstitial spaces and generate forces to deform surrounding cells, which in turn exert opposing pressures that regulate cell morphology and motility mechanisms. Current in vitro systems to study confined cell migration largely utilize rigid materials orders of magnitude stiffer than surrounding cells, limiting insights into how these local physical interactions regulate interstitial cell motility. Here, we first characterize mechanical interactions between neutrophils and surrounding cells in larval zebrafish and subsequently engineer in vitro migration channels bound by a deformable liquid-liquid interface that responds to cell generated pressures yielding a gradient of confinement across the length of a single cell. Tuning confining pressure gradients replicates mechanical interactions with surrounding cells during interstitial migration in vivo . We find that neutrophils favor a bleb-based mechanism of force generation to deform a barrier applying cell-scale confining forces. This work introduces a biomimetic material interface that enables new avenues of exploring the influence of mechanical forces on cell migration.

Micro-engineering and nano-engineering approaches to investigate tumour ecosystems

The interactions among tumour cells, the tumour microenvironment (TME) and non-tumour tissues are of interest to many cancer researchers. Micro-engineering approaches and nanotechnologies are under extensive exploration for modelling these interactions and measuring them in situ and in vivo to investigate therapeutic vulnerabilities in cancer and extend a systemic view of tumour ecosystems. Here we highlight the greatest opportunities for improving the understanding of tumour ecosystems using microfluidic devices, bioprinting or organ-on-a-chip approaches. We also discuss the potential of nanosensors that can transmit information from within the TME or elsewhere in the body to address scientific and clinical questions about changes in chemical gradients, enzymatic activities, metabolic and immune profiles of the TME and circulating analytes. This Review aims to connect the cancer biology and engineering communities, presenting biomedical technologies that may expand the methodologies of the former, while inspiring the latter to develop approaches for interrogating cancer ecosystems.

Fluid dynamic design for mitigating undesired cell effects and its application to testis cell response testing to endocrine disruptors

Microfluidic devices have emerged as powerful tools for cell-based experiments, offering a controlled microenvironment that mimic the conditions within the body. Numerous cell experiment studies have successfully utilized microfluidic channels to achieve various new scientific discoveries. However, it has been often overlooked that undesired and unnoticed propagation of cellular molecules in such bio-microfluidic channel systems can have a negative impact on the experimental results. Thus, more careful designing is required to minimize such unwanted issues through deeper understanding and careful control of chemically and physically predominant factors at the microscopic scale. In this paper, we introduce a new approach to improve microfluidic channel design, specifically targeting the mitigation of the aforementioned challenges. To minimize the occurrence of undesired cell positioning upstream from the main test section where a concentration gradient field locates, an additional narrow port structure was devised between the microfluidic upstream channel and each inlet reservoir. This port also functioned as a passive lock that hold the flow at rest via fluid-air surface tension, which facilitated manual movement of the device even when cell attachment was not achieved completely. To demonstrate the practicability of the system, we conducted experiments and diffusion simulations on the effect of endocrine disruptors on germ cells. To this end, a bisphenol-A (BPA) concentration gradient was generated in the main channel of the system at BPA concentrations ranging from 120.8 μM to 79.3 μM, and the proliferation of GC-1 cells in the BPA gradient environment was quantitatively evaluated. The features and concepts of the introduced design is to minimize unexpected and ignored error sources, which will be one of the issues to be considered in the development of microfluidic systems to explore extremely delicate cellular phenomena.

When Super-Resolution Microscopy Meets Microfluidics: Enhanced Biological Imaging and Analysis with Unprecedented Resolution

Super-resolution microscopy is rapidly developed in recent years, allowing biologists to extract more quantitative information on subcellular processes in live cells that is usually not accessible with conventional techniques. However, super-resolution imaging is not fully exploited because of the lack of an appropriate and multifunctional experimental platform. As an important tool in life sciences, microfluidics is capable of cell manipulation and the regulation of the cellular environment because of its superior flexibility and biocompatibility. The combination of microfluidics and super-resolution microscopy revolutionizes the study of complex cellular properties and dynamics, providing valuable insights into cellular structure and biological functions at the single-molecule level. In this perspective, an overview of the main advantages of microfluidic technology that are essential to the performance of super-resolution microscopy are offered. The main benefits of performing super-resolution imaging with microfluidic devices are highlighted and perspectives on the diverse applications that are facilitated by combining these two powerful techniques are provided.

Microfluidic Gradient Culture Arrays for Cell Pro-oxidation Analysis Using Bipolar Electrochemiluminescence

A microfluidic gradient array is a widely used screening and analysis device, which has characteristics of high efficiency, high automation, and low consumption. Bipolar electrode electrochemiluminescence (BPE-ECL) has special value in microfluidic array chips. The combination of the microfluidic gradient and BPE arrays has potential for high-throughput screening. In this article, a microfluidic BPE array chip for gradient culture and conditional screening of cancer cells was designed. The generation of concentration gradients, continuous culture of cancer cells with high throughput, and drug screening through BPE-ECL of the Ru(bpy)₃²⁺/TPrA system can be performed in one chip. We tested gradient pro-oxidation of MCF-7 by ascorbic acid and the synergistic effect of pro-oxidation on doxorubicin. The method achieves high analysis efficiency through a BPE array while simplifying the tedious procedures required by cell culture methods.

Efficient Synthesis of a Schiff Base Copper(II) Complex Using a Microfluidic Device

The efficient synthesis of amino acid Schiff base copper(II) complexes using a microfluidic device was successfully achieved. Schiff bases and their complexes are remarkable compounds due to their high biological activity and catalytic function. Conventionally, products are synthesized under reaction conditions of 40 °C for 4 h using a beaker-based method. However, in this paper, we propose using a microfluidic channel to enable quasi-instantaneous synthesis at room temperature (23 °C). The products were characterized using UV-Vis, FT-IR, and MS spectroscopy. The efficient generation of compounds using microfluidic channels has the potential to significantly contribute to the efficiency of drug discovery and material development due to high reactivity.

Construction of multiple concentration gradients for single-cell level drug screening

Isolation and manipulation of single cells play a crucial role in drug screening. However, previously reported single-cell drug screening lacked multiple-dose concentration gradient studies, which limits their ability to predict drug performance accurately. To solve this problem, we constructed a multiconcentration gradient generator in which a Tai Chi-spiral mixer can accelerate solution mixing in a short time and produce a linear concentration gradient. Later, a gradient generator combined with a single-cell capture array was adopted to investigate the effects of single or combined doses of 5-fluorouracil and cisplatin on human hepatoma cells and human breast carcinoma cells (at the single-cell level). The results showed that both drugs were effective in inhibiting the growth of cancer cells, and the combination was more effective for human hepatoma cells. In addition, the relationship between the biomechanical heterogeneity (e.g., deformability and size) of tumor cells and potential drug resistance at the single-cell level was investigated, indicating that small and/or deformable cells were more resistant than large and/or less deformable cells. The device provides a simple and reliable platform for studying the optimal dosage of different drug candidates at the single-cell level and effectively screening single-agent chemotherapy regimens and combination therapies.

Modular microfluidics for life sciences

The advancement of microfluidics has enabled numerous discoveries and technologies in life sciences. However, due to the lack of industry standards and configurability, the design and fabrication of microfluidic devices require highly skilled technicians. The diversity of microfluidic devices discourages biologists and chemists from applying this technique in their laboratories. Modular microfluidics, which integrates the standardized microfluidic modules into a whole, complex platform, brings the capability of configurability to conventional microfluidics. The exciting features, including portability, on-site deployability, and high customization motivate us to review the state-of-the-art modular microfluidics and discuss future perspectives. In this review, we first introduce the working mechanisms of the basic microfluidic modules and evaluate their feasibility as modular microfluidic components. Next, we explain the connection approaches among these microfluidic modules, and summarize the advantages of modular microfluidics over integrated microfluidics in biological applications. Finally, we discuss the challenge and future perspectives of modular microfluidics.

Design and validation of a flowless gradient generating microfluidic device for high-throughput drug testing

Drug testing is a vital step in the identification of the potential efficacy of any new/existing drug and/or combinations of drugs. The conventional methods of testing the efficacy of new drugs using multiwell plates are time consuming and prone to evaporation loss and manual error. Microfluidic devices with automated generation of concentration gradients provide a promising alternative. The implementation of such microfluidic devices is still limited owing to the additional expertise and facilities required to fabricate and run these devices. Conventional microfluidic devices also need pumps, tubing, valves, and other accessories, making them bulky and non-portable. To address these problems, we have developed a method for fabricating microfluidic structures using a nonconventional technique by exploiting the Saffman-Taylor instability in lifted Hele-Shaw cells. Multi-channel structure molds with varying dimensions were fabricated by shaping ceramic polymer slurry and retaining the shape. Further using the mold thus made, polydimethyl siloxane (PDMS) devices offering static, stable, diffusion-based gradients were casted using soft lithography. We have demonstrated with COMSOL simulation, as well as using fluorescein isothiocyanate (FITC), a fluorescent dye, that the concentration gradient can be generated in this device, which remains stable for at least 5 days. Using this multichannel device, in vitro drug efficacy was validated with two drugs namely, temozolomide (TMZ) and curcumin, one FDA approved and one under research, on glioblastoma cells (U87MG). The resulting IC50 values were consistent with those reported in the literature. We have also demonstrated the possibility of conducting molecular assays post-drug testing in the device by microtubule staining after curcumin treatment on cervical cancer cells (HeLa). In summary, we have demonstrated a i) user-friendly, ii) portable, static drug testing platform that iii) does not require further accessories and can create iv) a stable gradient for a long duration. Such a device can reduce the time, manual errors, fabrication and running expenditure, and resources needed to a great extent in drug testing.

Organoids

Organoids have attracted increasing attention because they are simple tissue-engineered cell-based in vitro models that recapitulate many aspects of the complex structure and function of the corresponding in vivo tissue. They can be dissected and interrogated for fundamental mechanistic studies on development, regeneration, and repair in human tissues. Organoids can also be used in diagnostics, disease modeling, drug discovery, and personalized medicine. Organoids are derived from either pluripotent or tissue-resident stem (embryonic or adult) or progenitor or differentiated cells from healthy or diseased tissues, such as tumors. To date, numerous organoid engineering strategies that support organoid culture and growth, proliferation, differentiation and maturation have been reported. This Primer serves to highlight the rationale underlying the selection and development of these materials and methods to control the cellular/tissue niche; and therefore, structure and function of the engineered organoid. We also discuss key considerations for generating robust organoids, such as those related to cell isolation and seeding, matrix and soluble factor selection, physical cues and integration. The general standards for data quality, reproducibility and deposition within the organoid community is also outlined. Lastly, we conclude by elaborating on the limitations of organoids in different applications, and key priorities in organoid engineering for the coming years.

Microfluidic-based dynamic BH3 profiling predicts anticancer treatment efficacy

Precision medicine is starting to incorporate functional assays to evaluate anticancer agents on patient-isolated tissues or cells to select for the most effective. Among these new technologies, dynamic BH3 profiling (DBP) has emerged and extensively been used to predict treatment efficacy in different types of cancer. DBP uses synthetic BH3 peptides to measure early apoptotic events ('priming') and anticipate therapy-induced cell death leading to tumor elimination. This predictive functional assay presents multiple advantages but a critical limitation: the cell number requirement, that limits drug screening on patient samples, especially in solid tumors. To solve this problem, we developed an innovative microfluidic-based DBP (µDBP) device that overcomes tissue limitations on primary samples. We used microfluidic chips to generate a gradient of BIM BH3 peptide, compared it with the standard flow cytometry based DBP, and tested different anticancer treatments. We first examined this new technology's predictive capacity using gastrointestinal stromal tumor (GIST) cell lines, by comparing imatinib sensitive and resistant cells, and we could detect differences in apoptotic priming and anticipate cytotoxicity. We then validated µDBP on a refractory GIST patient sample and identified that the combination of dactolisib and venetoclax increased apoptotic priming. In summary, this new technology could represent an important advance for precision medicine by providing a fast, easy-to-use and scalable microfluidic device to perform DBP in situ as a routine assay to identify the best treatment for cancer patients.

Scalable large-area mesh-structured microfluidic gradient generator for drug testing applications

Microfluidic concentration gradient generators are useful in drug testing, drug screening, and other cellular applications to avoid manual errors, save time, and labor. However, expensive fabrication techniques make such devices prohibitively costly. Here, in the present work, we developed a microfluidic concentration gradient generator (μCGG) using a recently proposed non-conventional photolithography-less method. In this method, ceramic suspension fluid was shaped into a square mesh by controlling Saffman Taylor instability in a multiport lifted Hele-Shaw cell (MLHSC). Using the shaped ceramic structure as the template, μCGG was prepared by soft lithography. The concentration gradient was characterized and effect of the flow rates was studied using COMSOL simulations. The simulation result was further validated by creating a fluorescein dye (fluorescein isothiocanate) gradient in the fabricated μCGG. To demonstrate the use of this device for drug testing, we created various concentrations of an anticancer drug-curcumin-using the device and determined its inhibitory concentration on cervical cancer cell-line HeLa. We found that the IC50 of curcumin for HeLa matched well with the conventional multi-well drug testing method. This method of μCGG fabrication has multiple advantages over conventional photolithography such as: (i) the channel layout and inlet-outlet arrangements can be changed by simply wiping the ceramic fluid before it solidifies, (ii) it is cost effective, (iii) large area patterning is easily achievable, and (iv) the method is scalable. This technique can be utilized to achieve a broad range of concentration gradient to be used for various biological and non-biological applications.

Machine-Learning-Enabled Design and Manipulation of a Microfluidic Concentration Gradient Generator

Microfluidics concentration gradient generators have been widely applied in chemical and biological fields. However, the current gradient generators still have some limitations. In this work, we presented a microfluidic concentration gradient generator with its corresponding manipulation process to generate an arbitrary concentration gradient. Machine-learning techniques and interpolation algorithms were implemented to help researchers instantly analyze the current concentration profile of the gradient generator with different inlet configurations. The proposed method has a 93.71% accuracy rate with a 300× acceleration effect compared to the conventional finite element analysis. In addition, our method shows the potential application of the design automation and computer-aided design of microfluidics by leveraging both artificial neural networks and computer science algorithms.

Advances in Concentration Gradient Generation Approaches in a Microfluidic Device for Toxicity Analysis

This systematic review aimed to analyze the development and functionality of microfluidic concentration gradient generators (CGGs) for toxicological evaluation of different biological organisms. We searched articles using the keywords: concentration gradient generator, toxicity, and microfluidic device. Only 33 of the 352 articles found were included and examined regarding the fabrication of the microdevices, the characteristics of the CGG, the biological model, and the desired results. The main fabrication method was soft lithography, using polydimethylsiloxane (PDMS) material (91%) and SU-8 as the mold (58.3%). New technologies were applied to minimize shear and bubble problems, reduce costs, and accelerate prototyping. The Christmas tree CGG design and its variations were the most reported in the studies, as well as the convective method of generation (61%). Biological models included bacteria and nematodes for antibiotic screening, microalgae for pollutant toxicity, tumor and normal cells for, primarily, chemotherapy screening, and Zebrafish embryos for drug and metal developmental toxicity. The toxic effects of each concentration generated were evaluated mostly with imaging and microscopy techniques. This study showed an advantage of CGGs over other techniques and their applicability for several biological models. Even with soft lithography, PDMS, and Christmas tree being more popular in their respective categories, current studies aim to apply new technologies and intricate architectures to improve testing effectiveness and reduce common microfluidics problems, allowing for high applicability of toxicity tests in different medical and environmental models.

Microfluidics for antibiotic susceptibility testing

The rise of antibiotic resistance is a threat to global health. Rapid and comprehensive analysis of infectious strains is critical to reducing the global use of antibiotics, as informed antibiotic use could slow down the emergence of resistant strains worldwide. Multiple platforms for antibiotic susceptibility testing (AST) have been developed with the use of microfluidic solutions. Here we describe microfluidic systems that have been proposed to aid AST. We identify the key contributions in overcoming outstanding challenges associated with the required degree of multiplexing, reduction of detection time, scalability, ease of use, and capacity for commercialization. We introduce the reader to microfluidics in general, and we analyze the challenges and opportunities related to the field of microfluidic AST.

Bacterial chemotaxis in static gradients quantified in a biopolymer membrane-integrated microfluidic platform

Chemotaxis is a fundamental bacterial response mechanism to changes in chemical gradients of specific molecules known as chemoattractant or chemorepellent. The advancement of biological platforms for bacterial chemotaxis research is of significant interest for a wide range of biological and environmental studies. Many microfluidic devices have been developed for its study, but challenges still remain that can obscure analysis. For example, cell migration can be compromised by flow-induced shear stress, and bacterial motility can be impaired by nonspecific cell adhesion to microchannels. Also, devices can be complicated, expensive, and hard to assemble. We address these issues with a three-channel microfluidic platform integrated with natural biopolymer membranes that are assembled in situ. This provides several unique attributes. First, a static, steady and robust chemoattractant gradient was generated and maintained. Second, because the assembly incorporates assembly pillars, the assembled membrane arrays connecting nearby pillars can be created longer than the viewing window, enabling a wide 2D area for study. Third, the in situ assembled biopolymer membranes minimize pressure and/or chemiosmotic gradients that could induce flow and obscure chemotaxis study. Finally, nonspecific cell adhesion is avoided by priming the polydimethylsiloxane (PDMS) microchannel surfaces with Pluronic F-127. We demonstrated chemotactic migration of Escherichia coli as well as Pseudomonas aeruginosa under well-controlled easy-to-assemble glucose gradients. We characterized motility using the chemotaxis partition coefficient (CPC) and chemotaxis migration coefficient (CMC) and found our results consistent with other reports. Further, random walk trajectories of individual cells in simple bright field images were conveniently tracked and presented in rose plots. Velocities were calculated, again in agreement with previous literature. We believe the biopolymer membrane-integrated platform represents a facile and convenient system for robust quantitative assessment of cellular motility in response to various chemical cues.

Formation and Parallel Manipulation of Gradient Droplets on a Self-Partitioning SlipChip for Phenotypic Antimicrobial Susceptibility Testing

Flexible, robust, and user-friendly screening systems with a large dynamic range are highly desired in scientific research, industrial development, and clinical diagnostics. Droplet-based microfluidic systems with gradient concentrations of chemicals have been demonstrated as promising tools to provide confined microenvironments for screening tests with small reaction volumes. However, the generation and manipulation of gradient droplets, such as droplet merging, generally require sophisticated fluidic manipulation systems, potentially limiting their application in decentralized settings. We present a gradient-droplet SlipChip (gd-SlipChip) microfluidic device that enables instrument-free gradient droplet formation and parallel manipulation. The device can establish a gradient profile by free interfacial diffusion in a continuous fluidic channel. With a simple slipping step, gradient droplets can be generated by a surface tension-driven self-partitioning process. Additional reagents can be introduced in parallel to these gradient droplets with further slipping operations to initiate screening tests of the droplets over a large concentration range. To profile the concentration in the gradient droplets, we establish a numerical simulation model and verify it with hydrogen chloride (HCl) diffusion, as tested with a dual-color pH indicator (methyl orange and aniline blue). As a proof of concept, we tested this system with a gradient concentration of nitrofurantoin for the phenotypic antimicrobial susceptibility testing (AST) of Escherichia coli. The results of our gd-SlipChip-based AST on both reference and clinical strains of E. coli can be indicated by the bacterial growth profile within 3 h and are consistent with the clinical culture-based AST.

Specific Ionic Recognition Using Fig's Xylem/Phloem Vessel as a Novel and Applicable Device: Lab-on-a Xylem/Phloem

A novel and specific detection system using voltage-stimulating ion transport through fig xylem/phloem vessels as a new lab-on-a xylem/phloem substrate was introduced. The voltage drove the ion flux through the vessels by a sinusoidal waveform with very low frequency (2.70 ± 0.05 kHz, n = 10) and voltage amplitude between 0.0 and 1.0 kV (vs total applied potential) with positive and negative polarities depending on cation and anion separation, respectively. The recorded potential induced by the applied potential was considered as a fingerprint electrical potential stimulator during reliable recognition of different ionic species. The system possessed some different characteristics such as (i) prominent figures of merit with linear ranges between 5.0 and 1200.0 (±0.7, n = 10) ng mL^-1 (correlation coefficient, R ², >0.99) for each ionic species and (ii) improved detection limits via tracing electrical current and conductance gradient (as the sensitive detection systems), while testing 50.0 ng mL^-1 of different salts as cationic and anionic species. The reliability of the system was evidenced via focusing on at least 60 independent cationic and anionic species during introducing a 70-membered distinct array-based bio-substrate device. This process not only showed great method applicability for specific determination with acceptable figures of merit but also resulted in introducing a software database for direct detection and recognition of various ionic analyses. The introduced detection/separation device competed with other spectroscopic/electrochemical systems due to the specific and simultaneous recognition of great ranges of ionic species in different real samples at ultratrace levels.

Conventional and Microfluidic Methods for the Detection of Nucleic Acid of SARS-CoV-2

Nucleic acid testing (NAT) played a crucial role in containing the spread of SARS-CoV-2 during the epidemic. The gold standard technique, the quantitative real-time polymerase chain reaction (qRT-PCR) technique, is currently used by the government and medical boards to detect SARS-CoV-2. Due to the limitations of this technology, it is not capable of meeting the needs of large-scale rapid detection. To solve this problem, many new techniques for detecting nucleic acids of SARS-CoV-2 have been reported. Therefore, a review that systematically and comprehensively introduces and compares various detection technologies is needed. In this paper, we not only review the traditional NAT but also provide an overview of microfluidic-based NAT technologies and summarize and discuss the characteristics and development prospects of these techniques.

Emergence of Resistant Escherichia coli Mutants in Microfluidic On-Chip Antibiotic Gradients

Spatiotemporal structures and heterogeneities are common in natural habitats, yet their role in the evolution of antibiotic resistance is still to be uncovered. We applied a microfluidic gradient generator device to study the emergence of resistant bacteria in spatial ciprofloxacin gradients. We observed biofilm formation in regions with sub-inhibitory concentrations of antibiotics, which quickly expanded into the high antibiotic regions. In the absence of an explicit structure of the habitat, this multicellular formation led to a spatial structure of the population with local competition and limited migration. Therefore, such structures can function as amplifiers of selection and aid the spread of beneficial mutations. We found that the physical environment itself induces stress-related mutations that later prove beneficial when cells are exposed to antibiotics. This shift in function suggests that exaptation occurs in such experimental scenarios. The above two processes pave the way for the subsequent emergence of highly resistant specific mutations.

Oxygen control: the often overlooked but essential piece to create better in vitro systems

Variations in oxygen levels play key roles in numerous physiological and pathological processes, but are often not properly controlled in in vitro models, introducing a significant bias in experimental outcomes. Recent developments in microfluidic technology have introduced a paradigm shift by providing new opportunities to better mimic physiological and pathological conditions, which is achieved by both regulating and monitoring oxygen levels at the micrometre scale in miniaturized devices. In this review, we first introduce the nature and relevance of oxygen-dependent pathways in both physiological and pathological contexts. Subsequently, we discuss strategies to control oxygen in microfluidic devices, distinguishing between engineering approaches that operate at the device level during its fabrication and chemical approaches that involve the active perfusion of fluids oxygenated at a precise level or supplemented with oxygen-producing or oxygen-scavenging materials. In addition, we discuss readout approaches for monitoring oxygen levels at the cellular and tissue levels, focusing on electrochemical and optical detection schemes for high-resolution measurements directly on-chip. An overview of different applications in which microfluidic devices have been utilized to answer biological research questions is then provided. In the final section, we provide our vision for further technological refinements of oxygen-controlling devices and discuss how these devices can be employed to generate new fundamental insights regarding key scientific problems that call for emulating oxygen levels as encountered in vivo. We conclude by making the case that ultimately emulating physiological or pathological oxygen levels should become a standard feature in all in vitro cell, tissue, and organ models.

Hand-powered vacuum-driven microfluidic gradient generator for high-throughput antimicrobial susceptibility testing

The growth of bacterial resistance to antimicrobials is a serious problem attracting much attention nowadays. To prevent the misuse and abuse of antimicrobials, it is important to carry out antibiotic susceptibility testing (AST) before clinical use. However, conventional AST methods are relatively laborious and time-consuming (18-24 h). Here, we present a hand-powered vacuum-driven microfluidic (HVM) device, in which a syringe is used as the only vacuum source for rapid generating concentration gradient of antibiotics in different chambers. The HVM device can be preassembled with various amounts of antibiotics, lyophilized, and stored for ready-to-use. Bacterial samples can be loaded into the HVM device through a simple suction step. With the assistance of Alamar Blue, the AST assay and the minimum inhibitory concentration (MIC) of different antibiotics can be investigated by comparing the growth results of bacteria in different culture chambers. In addition, a parallel HVM device was proposed, in which eight AST assays can be performed simultaneously. The results of MIC of three commonly used antibiotics against E. coli K-12 in our HVM device were consistent with those obtained by traditional method while the detection time was shortened to less than 8 h. We believe that our platform is high-throughput, cost-efficient, easy to use, and suitable for POCT applications.

Microfluidic Screening-Assisted Machine Learning to Investigate Vertical Phase Separation of Small Molecule:Polymer Blend

Solution-based thin-film processing is a widely utilized technique for the fabrication of various devices. In particular, the tunability of the ink composition and coating condition allows precise control of thin-film properties and device performance. Despite the advantage of having such tunability, the sheer number of possible combinations of experimental parameters render it infeasible to efficiently optimize device performance and analyze the correlation between experimental parameters and device performance. In this work, a microfluidic screening-embedded thin-film processing technique is developed, through which thin-films of varying ratios of small molecule semiconductor:polymer blend are simultaneously generated and screened in a time- and resource-efficient manner. Moreover, utilizing the thin-films of varying combinations of experimental parameters, machine learning models are trained to predict the transistor performance. Gaussian Process Regression (GPR) algorithms tuned by Bayesian optimization shows the best predictive accuracy amongst the trained models, which enables narrowing down of the combinations of experimental parameters and investigation of the degree of vertical phase separation under the predicted parameter space. The technique can serve as a guideline for elucidating the underlying complex parameter-property-performance correlations in solution-based thin-film processing, thereby accelerating the optimization of various thin-film devices in the future.

Reaction-diffusion phenomena in antagonistic bipolar diffusion fields

Operating natural or artificial chemical systems requires nonequilibrium conditions under which temporal and spatial control of the process is realizable. Open reaction-diffusion systems provide a general way to create such conditions. A key issue is the proper design of reactors in which the nonequilibrium conditions can be maintained. A hydrogel with flow-through channels is a simple, flexible, and easy-to-make device in which chemical reactions are performed in the diffusion field of localized separated sources of reactants. Two reactants separated in two channels create a bipolar antagonistic diffusion field, where the reaction intermediates firmly separate in space. Numerical simulations and corresponding experiments are performed to present this inhomogeneous diffusion field-induced chemical separation in sequential reactions. A remarkable result of this bipolar spatial control is localized wave phenomena in a nonlinear activatory-inhibitory reaction. These findings may help design functioning artificial nonequilibrium systems with the desired spatial separation of chemicals.

Active matter dynamics in confined microfluidic environments

The field of active matter is a nascent area of research in soft condensed matter physics, which is drawing on the expertise of researchers from diverse disciplines. Small scale active particles-both inorganic and biological-display non-trivial emergent dynamics and interactions that could help us understand complex biological processes and phenomena. Recently, using microfluidic technologies, several research groups have performed important experimental and theoretical studies to understand the behavior of self-propelled particles and molecular active matter within confined environments-to glean a fundamental understanding of the cellular processes occurring under ultra-low Reynolds number conditions. In this chapter, we would like to review applications of microfluidics in active matter research, highlighting a few important theoretical and experimental investigations. We will conclude the discussion with a note on the future of this field mentioning a few open questions that are at the forefront of our minds.

Digital Light Processing Based Bioprinting with Composable Gradients

Recapitulation of complex tissues signifies a remarkable challenge and, to date, only a few approaches have emerged that can efficiently reconstruct necessary gradients in 3D constructs. This is true even though mimicry of these gradients is of great importance to establish the functionality of engineered tissues and devices. Here, a composable-gradient Digital Light Processing (DLP)-based (bio)printing system is developed, utilizing the unprecedented integration of a microfluidic mixer for the generation of either continual or discrete gradients of desired (bio)inks in real time. Notably, the precisely controlled gradients are composable on-the-fly by facilely by adjusting the (bio)ink flow ratios. In addition, this setup is designed in such a way that (bio)ink waste is minimized when exchanging the gradient (bio)inks, further enhancing this time- and (bio)ink-saving strategy. Various planar and 3D structures exhibiting continual gradients of materials, of cell densities, of growth factor concentrations, of hydrogel stiffness, and of porosities in horizontal and/or vertical direction, are exemplified. The composable fabrication of multifunctional gradients strongly supports the potential of the unique bioprinting system in numerous biomedical applications.

Complete experimental and theoretical characterization of nonlinear concentration gradient generator microfluidic device for analytical purposes

Microfluidic devices that generate stable concentration gradients are efficient instruments for automated calibration for analytical and bioanalytical systems. However, little attention has been paid to the development of reusable microfluidic concentration gradient generators, which can be useful for a range of species through mathematical characterization. In this work, we develop a microfluidic device based on three steps of serial dilution that were able to generate nonlinear concentration gradient for dyes and biomolecules. The microfluidic device was described mathematically, statistically and was suitable for reusable analytical and bioanalytical analysis. The device reproducibility was assessed by experimental tests, which have shown the same gradient concentration profile for different dyes and statistical reproducibility with 95% confidence interval for bovine serum albumin (BSA). Moreover, the experimental data converged well with those  obtained by computational fluid dynamics simulation. Applicability was verified by coupling the microfluidic device to a surface plasmon resonance (SPR) biosensor, based on nanohole arrays with sensitivity of 358.7 nm RIU^-1 determined by white-light SPR excitation exposed to different D-(+)-glucose aqueous solutions with 1.3361-1.4035 refractive index interval. The transmission light intensities obtained by the array of images allowed to quantify a pseudo-unknown BSA sample (160 µg mL^-1) at 138 µg mL^-1. The SPR analysis has been validated in parallel by fluorescence emissions, which showed a concentration of 154.8 ± 16.6 µg mL^-1.

Microfluidic Systems for Cancer Diagnosis and Applications

Microfluidic devices have led to novel biological advances through the improvement of micro systems that can mimic and measure. Microsystems easily handle sub-microliter volumes, obviously with guidance presumably through laminated fluid flows. Microfluidic systems have production methods that do not need expert engineering, away from a centralized laboratory, and can implement basic and point of care analysis, and this has attracted attention to their widespread dissemination and adaptation to specific biological issues. The general use of microfluidic tools in clinical settings can be seen in pregnancy tests and diabetic control, but recently microfluidic platforms have become a key novel technology for cancer diagnostics. Cancer is a heterogeneous group of diseases that needs a multimodal paradigm to diagnose, manage, and treat. Using advanced technologies can enable this, providing better diagnosis and treatment for cancer patients. Microfluidic tools have evolved as a promising tool in the field of cancer such as detection of a single cancer cell, liquid biopsy, drug screening modeling angiogenesis, and metastasis detection. This review summarizes the need for the low-abundant blood and serum cancer diagnosis with microfluidic tools and the progress that has been followed to develop integrated microfluidic platforms for this application in the last few years.

Analysis of Static Molecular Gradients in a High-Throughput Drug Screening Microfluidic Assay

In this study, we thoroughly analyzed molecular gradient generation, its stability over time, and linearity in our high-throughput drug screening microfluidic assay (HTS). These parameters greatly affect the precision and accuracy of the device's analytical protocol. As part of the research, we developed a mathematical model of dependence of the concentration profile on the initial concentrations of active substances in reservoirs and the number of tilts, as well as the dependence of the active substance concentration profiles in the culture chambers on the concentration profile of the reference dye in the indicator chamber. The mean concentration prediction error of the proposed equations ranged from 1.4% to 2.4% for the optimized parameters of the procedure and did not increase with the incubation time. The concentration profile linearity index, Pearson's correlation coefficient reached -0.997 for 25 device tilts. The observed time stability of the profiles was very good. The mean difference between the concentration profile after 5 days of incubation and the baseline profile was only 7.0%. The newly created mathematical relationships became part of the new HTS biochip operating protocols, which are detailed in the article.

Protamine-Controlled Reversible DNA Packaging: A Molecular Glue

Packaging paternal genome into tiny sperm nuclei during spermatogenesis requires 10⁶-fold compaction of DNA, corresponding to a 10-20 times higher compaction than in somatic cells. While such a high level of compaction involves protamine, a small arginine-rich basic protein, the precise mechanism at play is still unclear. Effective pair potential calculations and large-scale molecular dynamics simulations using a simple idealized model incorporating solely electrostatic and steric interactions clearly demonstrate a reversible control on DNA condensates formation by varying the protamine-to-DNA ratio. Microscopic states and condensate structures occurring in semidilute solutions of short DNA fragments are in good agreement with experimental phase diagram and cryoTEM observations. The reversible microscopic mechanisms induced by protamination modulation should provide valuable information to improve a mechanistic understanding of early and intermediate stages of spermatogenesis where an interplay between condensation and liquid-liquid phase separation triggered by protamine expression and post-translational regulation might occur. Moreover, recent vaccines to prevent virus infections and cancers using protamine as a packaging and depackaging agent might be fine-tuned for improved efficiency using a protamination control.

Microfluidic Network Simulations Enable On-Demand Prediction of Control Parameters for Operating Lab-on-a-Chip-Devices

Reliable operation of lab-on-a-chip systems depends on user-friendly, precise, and predictable fluid management tailored to particular sub-tasks of the microfluidic process protocol and their required sample fluids. Pressure-driven flow control, where the sample fluids are delivered to the chip from pressurized feed vessels, simplifies the fluid management even for multiple fluids. The achieved flow rates depend on the pressure settings, fluid properties, and pressure-throughput characteristics of the complete microfluidic system composed of the chip and the interconnecting tubing. The prediction of the required pressure settings for achieving given flow rates simplifies the control tasks and enables opportunities for automation. In our work, we utilize a fast-running, Kirchhoff-based microfluidic network simulation that solves the complete microfluidic system for in-line prediction of the required pressure settings within less than 200 ms. The appropriateness of and benefits from this approach are demonstrated as exemplary for creating multi-component laminar co-flow and the creation of droplets with variable composition. Image-based methods were combined with chemometric approaches for the readout and correlation of the created multi-component flow patterns with the predictions obtained from the solver.

Microfluidics for Microswimmers: Engineering Novel Swimmers and Constructing Swimming Lanes on the Microscale, a Tutorial Review

This paper provides an updated review of recent advances in microfluidics applied to artificial and biohybrid microswimmers. Sharing the common regime of low Reynolds number, the two fields have been brought together to take advantage of the fluid characteristics at the microscale, benefitting microswimmer research multifold. First, microfluidics offer simple and relatively low-cost devices for high-fidelity production of microswimmers made of organic and inorganic materials in a variety of shapes and sizes. Microscale confinement and the corresponding fluid properties have demonstrated differential microswimmer behaviors in microchannels or in the presence of various types of physical or chemical stimuli. Custom environments to study these behaviors have been designed in large part with the help of microfluidics. Evaluating microswimmers in increasingly complex lab environments such as microfluidic systems can ensure more effective implementation for in-field applications. The benefits of microfluidics for the fabrication and evaluation of microswimmers are balanced by the potential use of microswimmers for sample manipulation and processing in microfluidic systems, a large obstacle in diagnostic and other testing platforms. In this review various ways in which these two complementary technology fields will enhance microswimmer development and implementation in various fields are introduced.