Microfluidics: reframing biological enquiry

Liquid metal electrodes enabled cascaded on-chip dielectrophoretic separation of large-size-range particles

The separation of large-size-range particles of complex biological samples is critical but yet well resolved. As a label-free technique, dielectrophoresis (DEP)-based particle separation faces the challenge of how to configure DEP in an integrated microfluidic device to bring particles of various sizes into the effective DEP force field. Herein, we propose a concept that combines the passive flow fraction mechanism with the accumulative DEP deflection effect in a cascaded manner. This concept places DEP deflection segments and bypass outlets alternately. Each DEP deflection segment is configured with an array of side-wall liquid metal electrodes to exert effective DEP forces on the particles of a suitable size range. After each DEP deflection segment, the passive bypass flow fraction mechanism diverts part of the sample flow and target range of particles through the bypass outlet. Simultaneously, this flow fraction brings the remaining particles closer to the electrodes in the subsequent DEP deflection segment, causing the next size range of particles to deflect under effective DEP forces and thus making them separable. Repeating this process, particles would be separated from the bypass outlets one by one in the order of reducing size ranges. We present the concept design and modeling, and prove the concept through separating five different particles ranging from 16-0.5 μm mixed together to mimic blood composition, providing a powerful platform for separating multiple particles in diverse biomedical applications.

Experimental approaches to investigate biophysical interactions between homeodomain transcription factors and DNA

Homeodomain transcription factors (TFs) bind to specific DNA sequences to regulate the expression of target genes. Structural work has provided insight into molecular identities and aided in unraveling structural features of these TFs. However, the detailed affinity and specificity by which these TFs bind to DNA sequences is still largely unknown. Qualitative methods, such as DNA footprinting, Electrophoretic Mobility Shift Assays (EMSAs), Systematic Evolution of Ligands by Exponential Enrichment (SELEX), Bacterial One Hybrid (B1H) systems, Surface Plasmon Resonance (SPR), and Protein Binding Microarrays (PBMs) have been widely used to investigate the biochemical characteristics of TF-DNA binding events. In addition to these qualitative methods, bioinformatic approaches have also assisted in TF binding site discovery. Here we discuss the advantages and limitations of these different approaches, as well as the benefits of utilizing more quantitative approaches, such as Mechanically Induced Trapping of Molecular Interactions (MITOMI), Microscale Thermophoresis (MST) and Isothermal Titration Calorimetry (ITC), in determining the biophysical basis of binding specificity of TF-DNA complexes and improving upon existing computational approaches aimed at affinity predictions.

Periodic Flows in Microfluidics

Microfluidics, the science and technology of manipulating fluids in microscale channels, offers numerous advantages, such as low energy consumption, compact device size, precise control, fast reaction, and enhanced portability. These benefits have led to applications in biomedical assays, disease diagnostics, drug discovery, neuroscience, and so on. Fluid flow within microfluidic channels is typically in the laminar flow region, which is characterized by low Reynolds numbers but brings the challenge of efficient mixing of fluids. Periodic flows are time-dependent fluid flows, featuring repetitive patterns that can significantly improve fluid mixing and extend the effective length of microchannels for submicron and nanoparticle manipulation. Besides, periodic flow is crucial in organ-on-a-chip (OoC) for accurately modeling physiological processes, advancing disease understanding, drug development, and personalized medicine. Various techniques for generating periodic flows have been reported, including syringe pumps, peristalsis, and actuation based on electric, magnetic, acoustic, mechanical, pneumatic, and fluidic forces, yet comprehensive reviews on this topic remain limited. This paper aims to provide a comprehensive review of periodic flows in microfluidics, from fundamental mechanisms to generation techniques and applications. The challenges and future perspectives are also discussed to exploit the potential of periodic flows in microfluidics.

Quantitative Characterization of Gene Regulatory Circuits Associated With Fungal Secondary Metabolism to Discover Novel Natural Products

Microbial genetic circuits are vital for regulating gene expression and synthesizing bioactive compounds. However, assessing their strength and timing, especially in multicellular fungi, remains challenging. Here, an advanced microfluidic platform is combined with a mathematical model enabling precise characterization of fungal gene regulatory circuits (GRCs) at the single-cell level. Utilizing this platform, the expression intensity and timing of 30 transcription factor-promoter combinations derived from two representative fungal GRCs, using the model fungus Aspergillus nidulans are determined. As a proof of concept, the selected GRC combination is utilized to successfully refactor the biosynthetic pathways of bioactive molecules, precisely control their production, and activate the expression of the silenced biosynthetic gene clusters (BGCs). This study provides insights into microbial gene regulation and highlights the potential of platform in fungal synthetic biology applications and the discovery of novel natural products.

Droplet-based fluorescence anisotropy insulin immunoassay

Over the last several decades, multiple microfluidic platforms have been used for measurement of hormone secretion from islets of Langerhans. Most have used continuous flow systems where mixing of hormones with assay reagents is governed by diffusion, leading to long mixing times, especially for biomolecules like peptides and proteins which have large diffusion coefficients. Consequently, dispersion of rapidly changing signals can occur, reducing temporal resolution. Droplet microfluidic systems can be used to capture reagents into individual reactors, limiting dispersion and improving temporal resolution. In this study, we integrated a fluorescence anisotropy (FA) immunoassay (IA) for insulin into a droplet microfluidic system. Insulin IA reagents were mixed online with insulin and captured quickly into droplets prior to passing through a 200 mm incubation channel. Double etching of the glass device was used to increase the depth of the incubation channel compared to the IA channels to maintain proper flow of reagents. The droplet system produced highly precise FA results with relative standard deviations < 2% at all insulin concentrations tested, whereas the absolute fluorescence intensity precisions ranged between 5 and 6%. A limit of detection of 3 nM for insulin was obtained, similar to those found in conventional flow systems. The advantage of the system was in the increased temporal resolution using the droplet system where a 9.8 ± 2.6 s response time was obtained, faster than previously reported continuous flow systems. The improved temporal resolution aligns with continued efforts to resolve rapid signaling events in pancreatic islet biology.

Microfluidics for studying the deep underground biosphere: from applications to fundamentals

In this review, selected examples are presented to demonstrate how microfluidic approaches can be utilized for investigating microbial life from deep geological environments, both from practical and fundamental perspectives. Beginning with the definition of the deep underground biosphere and the conventional experimental techniques employed for these studies, the use of microfluidic systems for accessing critical parameters of deep life in geological environments at the microscale is subsequently addressed (high pressure, high temperature, low volume). Microfluidics can simulate a range of environmental conditions on a chip, enabling rapid and comprehensive studies of microbial behavior and interactions in subsurface ecosystems, such as simulations of porous systems, interactions among microbes/microbes/minerals, and gradient cultivation. Transparent microreactors allow real-time, noninvasive analysis of microbial activities (microscopy, Raman spectroscopy, FTIR microspectroscopy, etc.), providing detailed insights into biogeochemical processes and facilitating pore-scale analysis. Finally, the current challenges and opportunities to expand the use of microfluidic methodologies for studying and monitoring the deep biosphere in real time under deep underground conditions are discussed.

Revolutionizing IBD research with on-chip models of disease modeling and drug screening

Inflammatory bowel disease (IBD) comprises chronic inflammatory conditions with complex mechanisms and diverse manifestations, posing significant clinical challenges. Traditional animal models and ethical concerns in human studies necessitate innovative approaches. This review provides an overview of human intestinal architecture in health and inflammation, emphasizing the role of microfluidics and on-chip technologies in IBD research. These technologies allow precise manipulation of cellular and microbial interactions in a physiologically relevant context, simulating the intestinal ecosystem microscopically. By integrating cellular components and replicating 3D tissue architecture, they offer promising models for studying host-microbe interactions, wound healing, and therapeutic approaches. Continuous refinement of these technologies promises to advance IBD understanding and therapy development, inspiring further innovation and cross-disciplinary collaboration.

Development of a mix-and-read assay for human asprosin using antibody-oligonucleotide probes and thermofluorimetric analysis

Adipose tissue, or fat tissue, can now be classified as an endocrine organ as it responds to stimuli by secreting a range of hormones, termed adipokines, which regulate the functions of various other tissues and organs. Because novel adipokines continue to be discovered and characterized by researchers, there is an enduring need for the development of new analytical assays that target these hormones. Discovered recently, asprosin is an adipokine hormone secreted by white adipose tissue (WAT) during fasting which has been implicated for its important effects on the liver, skeletal muscle, hypothalamus, pancreas, and possibly other tissues. While standard immunoassays have been developed, the continued surge in research on asprosin's function would greatly benefit from an assay with homogeneous, mix-and-read workflow, and the nanomolar clinical range makes this goal more feasible. In this work, we developed such an assay for asprosin using our thermofluorimetric analysis (TFA) methods with antibody-oligonucleotide conjugate probes. The assay, achievable in less than one hour, was successfully validated by quantifying native levels of asprosin in human serum collected from fasting, nonfasting, type II diabetic, and obese donors.

Can We Simplify Liposome Manufacturing Using a Complex DoE Approach?

Microfluidic liposome production presents a streamlined pathway for expediting the translation of liposomal formulations from the laboratory setting to clinical applications. Using this production method, resultant liposome characteristics can be tuned through the control of both the formulation parameters (including the lipids and solvents used) and production parameters (including the production speed and mixing ratio). Therefore, the aim of this study was to investigate the relationship between not only total flow rate (TFR), the fraction of the aqueous flow rate over the organic flow rate (flow rate ratio (FRR)), and the lipid concentration, but also the solvent selection, aqueous buffer, and production temperature. To achieve this, we used temperature, applying a design of experiment (DoE) combined with machine learning. This study demonstrated that liposome size and polydispersity were influenced by manipulation of not only the total flow rate and flow rate ratio but also through the lipids, lipid concentration, and solvent selection, such that liposome attributes can be in-process controlled, and all factors should be considered within a manufacturing process as impacting on liposome critical quality attributes.

Aided Porous Medium Emulsification for Functional Hydrogel Microparticles Synthesis

Despite the substantial advancement in developing various hydrogel microparticle (HMP) synthesis methods, emulsification through porous medium to synthesize functional hybrid protein-polymer HMPs has yet to be addressed. Here, the aided porous medium emulsification for hydrogel microparticle synthesis (APME-HMS) system, an innovative approach drawing inspiration from porous medium emulsification is introduced. This method capitalizes on emulsifying immiscible phases within a 3D porous structure for optimal HMP production. Using the APME-HMS system, synthesized responsive bovine serum albumin (BSA) and polyethylene glycol diacrylate (PEGDA) HMPs of various sizes are successfully synthesized. Preserving protein structural integrity and functionality enable the formation of cytochrome c (cyt c) - PEGDA HMPs for hydrogen peroxide (H2O2) detection at various concentrations. The flexibility of the APME-HMS system is demonstrated by its ability to efficiently synthesize HMPs using low volumes (≈50 µL) and concentrations (100 µm) of proteins within minutes while preserving proteins' structural and functional properties. Additionally, the capability of the APME-HMS method to produce a diverse array of HMP types enriches the palette of HMP fabrication techniques, presenting it as a cost-effective, biocompatible, and scalable alternative for various biomedical applications, such as controlled drug delivery, 3D printing bio-inks, biosensing devices, with potential implications even in culinary applications.

Exploring the unmapped cysteine redox proteoform landscape

Cysteine redox proteoforms define the diverse molecular states that proteins with cysteine residues can adopt. A protein with one cysteine residue must adopt one of two binary proteoforms: reduced or oxidized. Their numbers scale: a protein with 10 cysteine residues must assume one of 1,024 proteoforms. Although they play pivotal biological roles, the vast cysteine redox proteoform landscape comprising vast numbers of theoretical proteoforms remains largely uncharted. Progress is hampered by a general underappreciation of cysteine redox proteoforms, their intricate complexity, and the formidable challenges that they pose to existing methods. The present review advances cysteine redox proteoform theory, scrutinizes methodological barriers, and elaborates innovative technologies for detecting unique residue-defined cysteine redox proteoforms. For example, chemistry-enabled hybrid approaches combining the strengths of top-down mass spectrometry (TD-MS) and bottom-up mass spectrometry (BU-MS) for systematically cataloguing cysteine redox proteoforms are delineated. These methods provide the technological means to map uncharted redox terrain. To unravel hidden redox regulatory mechanisms, discover new biomarkers, and pinpoint therapeutic targets by mining the theoretical cysteine redox proteoform space, a community-wide initiative termed the "Human Cysteine Redox Proteoform Project" is proposed. Exploring the cysteine redox proteoform landscape could transform current understanding of redox biology.

Dielectrophoretic bead-droplet reactor for solid-phase synthesis

Solid-phase synthesis underpins many advances in synthetic and combinatorial chemistry, biology, and material science. The immobilization of a reacting species on the solid support makes interfacing of reagents an important challenge in this approach. In traditional synthesis columns, this leads to reaction errors that limit the product yield and necessitates excess consumption of the mobile reagent phase. Although droplet microfluidics can mitigate these problems, its adoption is fundamentally limited by the inability to controllably interface microbeads and reagent droplets. Here, we introduce Dielectrophoretic Bead-Droplet Reactor as a physical method to implement solid-phase synthesis on individual functionalized microbeads by encapsulating and ejecting them from microdroplets by tuning the supply voltage. Proof-of-concept demonstration of the enzymatic coupling of fluorescently labeled nucleotides onto the bead using this reactor yielded a 3.2-fold higher fidelity over columns through precise interfacing of individual microreactors and beads. Our work combines microparticle manipulation and droplet microfluidics to address a long-standing problem in solid-phase synthesis with potentially wide-ranging implications.

Quantitative measurement of acute myocardial infarction cardiac biomarkers by "All-in-One" immune microfluidic chip for early diagnosis of myocardial infarction

Acute myocardial infarction (AMI) is a life-threatening condition with a narrow treatment window, necessitating rapid and accurate diagnostic methods. We present an "all-in-one" convenient and rapid immunoassay system that combines microfluidic technology with a colloidal gold immunoassay. A degassing-driven chip replaces a bulky external pump, resulting in a user-friendly and easy-to-operate immunoassay system. The chip comprises four units: an inlet reservoir, an immunoreaction channel, a waste pool, and an immunocomplex collection chamber, allowing single-channel flow for rapid and accurate AMI biomarker detection. In this study, we focused on cardiac troponin I (cTnI). With a minimal sample of just 4 μL and a total detection time of under 3 min, the chip enabled a quantitative visual analysis of cTnI concentration within a range of 0.5 ∼ 60.0 ng mL-1. This all-in-one integrated microfluidic chip with colloidal gold immunoassay offers a promising solution for rapid AMI diagnosis. The system's portability, small sample requirement, and quantitative visual detection capabilities make it a valuable tool for AMI diagnostics.

Bidirectional linkage of DNA barcodes for the multiplexed mapping of higher-order protein interactions in cells

Capturing the full complexity of the diverse hierarchical interactions in the protein interactome is challenging. Here we report a DNA-barcoding method for the multiplexed mapping of pairwise and higher-order protein interactions and their dynamics within cells. The method leverages antibodies conjugated with barcoded DNA strands that can bidirectionally hybridize and covalently link to linearize closely spaced interactions within individual 3D protein complexes, encoding and decoding the protein constituents and the interactions among them. By mapping protein interactions in cancer cells and normal cells, we found that tumour cells exhibit a larger diversity and abundance of protein complexes with higher-order interactions. In biopsies of human breast-cancer tissue, the method accurately identified the cancer subtype and revealed that higher-order protein interactions are associated with cancer aggressiveness.

Surface Acoustic Wave-Driven Enhancement of Enzyme-Linked Immunosorbent Assays: ELISAW

Enzyme-linked immunosorbent assays (ELISAs) are widely used in biology and clinical diagnosis. Relying on antigen-antibody interaction through diffusion, the standard ELISA protocol can be time-consuming, preventing its use in rapid diagnostics. We present a time-saving and more sensitive ELISA without changing the standard setup and protocol, using surface acoustic waves (SAWs) to enhance performance. Each step of the assay, from the initial antibody binding onto the walls of the well plate to the target analyte molecules' binding for detection─except, notably, for the blocking step─is improved principally via acoustic streaming-driven advection. Using SAWs, the time required for one step of an example ELISA is reduced from 60 to 15 min to achieve the same binding amount. By extending the duration of SAW exposure to 20 min, the sensitivity can be significantly improved over the 60 min, 35 °C ELISA without SAWs. It is also possible to confer beneficial improvements to bead-based ELISA by combining it with SAWs to further reduce the time required for binding to 2 min. By significantly increasing the speed of ELISA, its utility may be improved for a wide range of point-of-care diagnostics applications.

Microfluidic isolation of extrachromosomal circular DNA through selective digestion of plasmids and linear DNA using immobilized nucleases

Extrachromosomal circular DNA (eccDNA) refers to small circular DNA molecules that are distinct from chromosomal DNA and play diverse roles in various biological processes. They are also explored as potential biomarkers for disease diagnosis and precision medicine. However, isolating eccDNA from tissues and plasma is challenging due to low abundance and the presence of interfering linear DNA, requiring time-consuming processes and expert handling. Our study addresses this by utilizing a microfluidic chip tailored for eccDNA isolation, leveraging microfluidic principles for enzymatic removal of non-circular DNA. Our approach involves integrating restriction enzymes into the microfluidic chip, enabling selective digestion of mitochondrial and linear DNA fragments while preserving eccDNA integrity. This integration is facilitated by an in situ photo-polymerized emulsion inside microchannels, creating a porous monolithic structure suitable for immobilizing restriction and exonuclease enzymes (restriction enzyme MssI and exonuclease ExoV). Evaluation using control DNA mixtures and plasma samples with artificially introduced eccDNA demonstrated that our microfluidic chips reduce linear DNA by over 99%, performing comparable to conventional off-chip methods but with substantially faster digestion times, allowing for a remarkable 76-fold acceleration in overall sample preparation time. This technological advancement holds great promise for enhancing the isolation and analysis of eccDNA from tissue and plasma and the potential for increasing the speed of other molecular methods with multiple enzymatic steps.

Superimposed Electric Field Enhanced Electrospray for High-Throughput and Consistent Cell Encapsulation

Cell encapsulation technology, crucial for advanced biomedical applications, faces challenges in existing microfluidic and electrospray methods. Microfluidic techniques, while precise, can damage vulnerable cells, and conventional electrospray methods often encounter instability and capsule breakage during high-throughput encapsulation. Inspired by the transformation of the working state from unstable dripping to stable jetting triggered by local electric potential, this study introduces a superimposed electric field (SEF)-enhanced electrospray method for cell encapsulation, with improved stability and biocompatibility. Utilizing stiffness theory, the stability of the electrospray, whose stiffness is five times stronger under conical confinement, is quantitatively analyzed. The SEF technique enables rapid, continuous production of ≈300 core-shell capsules per second in an aqueous environment, significantly improving cell encapsulation efficiency. This method demonstrates remarkable potential as exemplified in two key applications: (1) a 92-fold increase in human-derived induced pluripotent stem cells (iPSCs) expansion over 10 d, outperforming traditional 2D cultures in both growth rate and pluripotency maintenance, and (2) the development of liver capsules for steatosis modeling, exhibiting normal function and biomimetic lipid accumulation. The SEF-enhanced electrospray method presents a significant advancement in cell encapsulation technology. It offers a more efficient, stable, and biocompatible approach for clinical transplantation, drug screening, and cell therapy.

Advancing Intelligent Organ-on-a-Chip Systems with Comprehensive In Situ Bioanalysis

In vitro models are essential to a broad range of biomedical research, such as pathological studies, drug development, and personalized medicine. As a potentially transformative paradigm for 3D in vitro models, organ-on-a-chip (OOC) technology has been extensively developed to recapitulate sophisticated architectures and dynamic microenvironments of human organs by applying the principles of life sciences and leveraging micro- and nanoscale engineering capabilities. A pivotal function of OOC devices is to support multifaceted and timely characterization of cultured cells and their microenvironments. However, in-depth analysis of OOC models typically requires biomedical assay procedures that are labor-intensive and interruptive. Herein, the latest advances toward intelligent OOC (iOOC) systems, where sensors integrated with OOC devices continuously report cellular and microenvironmental information for comprehensive in situ bioanalysis, are examined. It is proposed that the multimodal data in iOOC systems can support closed-loop control of the in vitro models and offer holistic biomedical insights for diverse applications. Essential techniques for establishing iOOC systems are surveyed, encompassing in situ sensing, data processing, and dynamic modulation. Eventually, the future development of iOOC systems featuring cross-disciplinary strategies is discussed.

Expanding CAR-T cell immunotherapy horizons through microfluidics

Chimeric antigen receptor (CAR)-T cell therapies have revolutionized cancer treatment, particularly in hematological malignancies. However, their application to solid tumors is limited, and they face challenges in safety, scalability, and cost. To enhance current CAR-T cell therapies, the integration of microfluidic technologies, harnessing their inherent advantages, such as reduced sample consumption, simplicity in operation, cost-effectiveness, automation, and high scalability, has emerged as a powerful solution. This review provides a comprehensive overview of the step-by-step manufacturing process of CAR-T cells, identifies existing difficulties at each production stage, and discusses the successful implementation of microfluidics and related technologies in addressing these challenges. Furthermore, this review investigates the potential of microfluidics-based methodologies in advancing cell-based therapy across various applications, including solid tumors, next-generation CAR constructs, T-cell receptors, and the development of allogeneic "off-the-shelf" CAR products.

Transforming Static Barrier Tissue Models into Dynamic Microphysiological Systems

Microphysiological systems are miniaturized cell culture platforms used to mimic the structure and function of human tissues in a laboratory setting. However, these platforms have not gained widespread adoption in bioscience laboratories where open-well, membrane-based approaches serve as the gold standard for mimicking tissue barriers, despite lacking fluid flow capabilities. This issue can be primarily attributed to the incompatibility of existing microphysiological systems with standard protocols and tools developed for open-well systems. Here, we present a protocol for creating a reconfigurable membrane-based platform with an open-well structure, flow enhancement capability, and compatibility with conventional protocols. This system utilizes a magnetic assembly approach that enables reversible switching between open-well and microfluidic modes. With this approach, users have the flexibility to begin an experiment in the open-well format using standard protocols and add or remove flow capabilities as needed. To demonstrate the practical usage of this system and its compatibility with standard techniques, an endothelial cell monolayer was established in an open-well format. The system was reconfigured to introduce fluid flow and then switched to the open-well format to conduct immunostaining and RNA extraction. Due to its compatibility with conventional open-well protocols and flow enhancement capability, this reconfigurable design is expected to be adopted by both engineering and bioscience laboratories.

Microfluidic-assisted single-cell RNA sequencing facilitates the development of neutralizing monoclonal antibodies against SARS-CoV-2

As a class of antibodies that specifically bind to a virus and block its entry, neutralizing monoclonal antibodies (neutralizing mAbs) have been recognized as a top choice for combating COVID-19 due to their high specificity and efficacy in treating serious infections. Although conventional approaches for neutralizing mAb development have been optimized for decades, there is an urgent need for workflows with higher efficiency due to time-sensitive concerns, including the high mutation rate of SARS-CoV-2. One promising approach is the identification of neutralizing mAb candidates via single-cell RNA sequencing (RNA-seq), as each B cell has a unique transcript sequence corresponding to its secreted antibody. The state-of-the-art high-throughput single-cell sequencing technologies, which have been greatly facilitated by advances in microfluidics, have greatly accelerated the process of neutralizing mAb development. Here, we provide an overview of the general procedures for high-throughput single-cell RNA-seq enabled by breakthroughs in droplet microfluidics, introduce revolutionary approaches that combine single-cell RNA-seq to facilitate the development of neutralizing mAbs against SARS-CoV-2, and outline future steps that need to be taken to further improve development strategies for effective treatments against infectious diseases.

Spiral Large-Dimension Microfluidic Channel for Flow-Rate- and Particle-Size-Insensitive Focusing by the Stabilization and Acceleration of Secondary Flow

Inertial microfluidics has demonstrated its ability to focus particles in a passive and straightforward manner. However, achieving flow-rate- and particle-size-insensitive focusing in large-dimension channels with a simple design remains challenging. In this study, we developed a spiral microfluidic with a large-dimension channel to achieve inertial focusing. By designing a unique "big buffering area" and a "small buffering area" in the spiral microchannel, we observed the stabilization and acceleration of secondary flow. Our optimized design allowed for efficient (>99.9%) focusing of 15 μm particles within a wide range of flow rates (0.5-4.5 mL/min) during a long operation duration (0-60 min). Additionally, we achieved effective (>95%) focusing of different-sized particles (7, 10, 15, and 30 μm) and three types of tumor cells (K562, HeLa, and MCF-7) near the inner wall of the 1 mm wide outlet when applying different flow rates (1-3 mL/min). Finally, successful 3D cell focusing was achieved within an optimized device, with the cells positioned at a distance of 50 μm from the wall. Our strategy of stabilizing and accelerating Dean-like secondary flow through the unique configuration of a "big buffering area" and a "small buffering area" proved to be highly effective in achieving inertial focusing that is insensitive to the flow rate and particle size, particularly in large-dimension channels. Consequently, it shows great potential for use in hand-operated microfluidic tools for flow cytometry.

Microfluidics for adaptation of microorganisms to stress: design and application

Microfluidic systems have fundamentally transformed the realm of adaptive laboratory evolution (ALE) for microorganisms by offering unparalleled control over environmental conditions, thereby optimizing mutant generation and desired trait selection. This review summarizes the substantial influence of microfluidic technologies and their design paradigms on microbial adaptation, with a primary focus on leveraging spatial stressor concentration gradients to enhance microbial growth in challenging environments. Specifically, microfluidic platforms tailored for scaled-down ALE processes not only enable highly autonomous and precise setups but also incorporate novel functionalities. These capabilities encompass fostering the growth of biofilms alongside planktonic cells, refining selection gradient profiles, and simulating adaptation dynamics akin to natural habitats. The integration of these aspects enables shaping phenotypes under pressure, presenting an unprecedented avenue for developing robust, stress-resistant strains, a feat not easily attainable using conventional ALE setups. The versatility of these microfluidic systems is not limited to fundamental research but also offers promising applications in various areas of stress resistance. As microfluidic technologies continue to evolve and merge with cutting-edge methodologies, they possess the potential not only to redefine the landscape of microbial adaptation studies but also to expedite advancements in various biotechnological areas. KEY POINTS: • Microfluidics enable precise microbial adaptation in controlled gradients. • Microfluidic ALE offers insights into stress resistance and distinguishes between resistance and persistence. • Integration of adaptation-influencing factors in microfluidic setups facilitates efficient generation of stress-resistant strains.

A versatile micromodel technology to explore biofilm development in porous media flows

Bacterial biofilms that grow in porous media are critical to ecosystem processes and applications ranging from soil bioremediation to bioreactors for treating wastewater or producing value-added products. However, understanding and engineering the complex phenomena that drive the development of biofilms in such systems remains a challenge. Here we present a novel micromodel technology to explore bacterial biofilm development in porous media flows. The technology consists of a set of modules that can be combined as required for any given experiment and conveniently tuned for specific requirements. The core module is a 3D-printed micromodel where biofilm is grown into a perfusable porous substrate. High-precision additive manufacturing, in particular stereolithography, is used to fabricate porous scaffolds with precisely controlled architectures integrating flow channels with diameters down to several hundreds of micrometers. The system is instrumented with: ultraviolet-C light-emitting diodes; on-line measurements of oxygen consumption and pressure drop across the porous medium; camera and spectrophotometric cells for the detection of biofilm detachment events at the outlet. We demonstrate how this technology can be used to study the development of Pseudomonas aeruginosa biofilm for several days within a network of flow channels. We find complex dynamics whereby oxygen consumption reaches a steady-state but not the pressure drop, which instead features a permanent regime with large fluctuations. We further use X-ray computed microtomography to image the spatial distribution of biofilms and computational fluid dynamics to link biofilm development with local flow properties. By combining the advantages of additive manufacturing for the creation of reproducible 3D porous microarchitectures with the flow control and instrumentation accuracy of microfluidics, our system provides a platform to study the dynamics of biofilm development in 3D porous media and to rapidly test new concepts in process engineering.

Prospects of single-cell nuclear magnetic resonance spectroscopy with quantum sensors

Single-cell analysis can unravel functional heterogeneity within cell populations otherwise obscured by ensemble measurements. However, noninvasive techniques that probe chemical entities and their dynamics are still lacking. This challenge could be overcome by novel sensors based on nitrogen-vacancy (NV) centers in diamond, which enable nuclear magnetic resonance (NMR) spectroscopy on unprecedented sample volumes. In this perspective, we briefly introduce NV-based quantum sensing and review the progress made in microscale NV-NMR spectroscopy. Last, we discuss approaches to enhance the sensitivity of NV ensemble magnetometers to detect biologically relevant concentrations and provide a roadmap toward their application in single-cell analysis.

Assessment of stored red blood cells through lab-on-a-chip technologies for precision transfusion medicine

Transfusion of red blood cells (RBCs) is one of the most valuable and widespread treatments in modern medicine. Lifesaving RBC transfusions are facilitated by the cold storage of RBC units in blood banks worldwide. Currently, RBC storage and subsequent transfusion practices are performed using simplistic workflows. More specifically, most blood banks follow the "first-in-first-out" principle to avoid wastage, whereas most healthcare providers prefer the "last-in-first-out" approach simply favoring chronologically younger RBCs. Neither approach addresses recent advances through -omics showing that stored RBC quality is highly variable depending on donor-, time-, and processing-specific factors. Thus, it is time to rethink our workflows in transfusion medicine taking advantage of novel technologies to perform RBC quality assessment. We imagine a future where lab-on-a-chip technologies utilize novel predictive markers of RBC quality identified by -omics and machine learning to usher in a new era of safer and precise transfusion medicine.

SpectIR-fluidics: completely customizable microfluidic cartridges for high sensitivity on-chip infrared spectroscopy with point-of-application studies on bacterial biofilms

We present a generalizable fabrication method for a new class of analytical devices that merges virtually any microfluidic design with high-sensitivity on-chip attenuated total reflection (ATR) sampling using any standard Fourier transform infrared (FTIR) spectrometer. Termed "spectIR-fluidics", a major design feature is the integration of a multi-groove silicon ATR crystal into a microfluidic device, compared with previous approaches in which the ATR surface served as a structural support for the entire device. This was accomplished by the design, fabrication, and aligned bonding of a highly engineered ATR sensing layer, which con```tains a seamlessly embedded ATR crystal on the channel side and an optical access port that matched the spectrometer light path characteristics at the device exterior. The refocused role of the ATR crystal as a dedicated analytical element, combined with optimized light coupling to the spectrometer, results in limits of detection as low as 540 nM for a D-glucose solution, arbitrarily complex channel features that are fully enclosed, and up to 18 world-to-chip connections. Three purpose-built spectIR-fluidic cartridges are used in a series of validation experiments followed by several point-of-application studies on biofilms from the gut microbiota of plastic-consuming insects using a small portable spectrometer.

Recent Advances on Cell Culture Platforms for In Vitro Drug Screening and Cell Therapies: From Conventional to Microfluidic Strategies

The clinical translations of drugs and nanomedicines depend on coherent pharmaceutical research based on biologically accurate screening approaches. Since establishing the 2D in vitro cell culture method, the scientific community has improved cell-based drug screening assays and models. Those advances result in more informative biochemical assays and the development of 3D multicellular models to describe the biological complexity better and enhance the simulation of the in vivo microenvironment. Despite the overall dominance of conventional 2D and 3D cell macroscopic culture methods, they present physicochemical and operational challenges that impair the scale-up of drug screening by not allowing a high parallelization, multidrug combination, and high-throughput screening. Their combination and complementarity with microfluidic platforms enable the development of microfluidics-based cell culture platforms with unequivocal advantages in drug screening and cell therapies. Thus, this review presents an updated and consolidated view of cell culture miniaturization's physical, chemical, and operational considerations in the pharmaceutical research scenario. It clarifies advances in the field using gradient-based microfluidics, droplet-based microfluidics, printed-based microfluidics, digital-based microfluidics, SlipChip, and paper-based microfluidics. Finally, it presents a comparative analysis of the performance of cell-based methods in life research and development to achieve increased precision in the drug screening process.

The Quantification of Bacterial Cell Size: Discrepancies Arise from Varied Quantification Methods

The robust regulation of the cell cycle is critical for the survival and proliferation of bacteria. To gain a comprehensive understanding of the mechanisms regulating the bacterial cell cycle, it is essential to accurately quantify cell-cycle-related parameters and to uncover quantitative relationships. In this paper, we demonstrate that the quantification of cell size parameters using microscopic images can be influenced by software and by the parameter settings used. Remarkably, even if the consistent use of a particular software and specific parameter settings is maintained throughout a study, the type of software and the parameter settings can significantly impact the validation of quantitative relationships, such as the constant-initiation-mass hypothesis. Given these inherent characteristics of microscopic image-based quantification methods, it is recommended that conclusions be cross-validated using independent methods, especially when the conclusions are associated with cell size parameters that were obtained under different conditions. To this end, we presented a flexible workflow for simultaneously quantifying multiple bacterial cell-cycle-related parameters using microscope-independent methods.

Numerical investigation of ternary particle separation in a microchannel with a wall-mounted obstacle using dielectrophoresis

In recent years, microfluidic-based particle/cell manipulation techniques have catalyzed significant advances in several fields of science. As an efficient, precise, and label-free particle/cell manipulation technique, dielectrophoresis (DEP) has recently attracted widespread attention. This paper presents the design and investigation of a straight sheathless 3D microchannel with a wall-mounted trapezoidal obstacle for continuous-flow separation of three different populations of polystyrene (PS) particles (5, 10 and 20 µm) using DEP. An OpenFOAM code is developed to simulate and investigate the movement of particles in the microchannel. Then, the code is validated by performing various experimental tests using a microdevice previously fabricated in our lab. By comparing the numerical simulation results with the experimental tests, it can be claimed that the newly developed solver is highly accurate, and its results agree well with experimental tests. Next, the effect of various operational and geometrical parameters such as obstacle height, applied voltage, electrode pairs angle, and flow rate on the efficient focusing and separation of particles are numerically investigated. The results showed that efficient particle separation could only be achieved for obstacle heights of more than 350 µm. Furthermore, the appropriate voltage range for efficient particle separation is increased by decreasing the electrode angle as well as increasing the flow rate. Moreover, the results showed that by employing the appropriate channel design and operational conditions, at a maximum applied voltage of 10V, a sample flow rate of 2.5μL/min could be processed. The proposed design can be beneficial for integrating with lab-on-a-chip and clinical diagnosis applications due to advantages, such as simple design, no need for sheath flow, the simultaneous ternary separation of particles, and providing precise particle separation.

Performance benchmarking microplate-immunoassays for quantifying target-specific cysteine oxidation reveals their potential for understanding redox-regulation and oxidative stress

The antibody-linked oxi-state assay (ALISA) for quantifying target-specific cysteine oxidation can benefit specialist and non-specialist users. Specialists can benefit from time-efficient analysis and high-throughput target and/or sample n-plex capacities. The simple and accessible "off-the-shelf" nature of ALISA brings the benefits of oxidative damage assays to non-specialists studying redox-regulation. Until performance benchmarking establishes confidence in the "unseen" microplate results, ALISA is unlikely to be widely adopted. Here, we implemented pre-set pass/fail criteria to benchmark ALISA by evaluating immunoassay performance in diverse contexts. ELISA-mode ALISA assays were accurate, reliable, and sensitive. For example, the average inter-assay CV for detecting 20%- and 40%-oxidised PRDX2 or GAPDH standards was 4.6% (range: 3.6-7.4%). ALISA displayed target-specificity. Immunodepleting the target decreased the signal by ∼75%. Single-antibody formatted ALISA failed to quantify the matrix-facing alpha subunit of the mitochondrial ATP synthase. However, RedoxiFluor quantified the alpha subunit displaying exceptional performance in the single-antibody format. ALISA discovered that (1) monocyte-to-macrophage differentiation amplified PRDX2-oxidation in THP-1 cells and (2) exercise increased GAPDH-specific oxidation in human erythrocytes. The "unseen" microplate data were "seen-to-be-believed" via orthogonal visually displayed immunoassays like the dimer method. Finally, we established target (n = 3) and sample (n = 100) n-plex capacities in ∼4 h with 50-70 min hands-on time. Our work showcases the potential of ALISA to advance our understanding of redox-regulation and oxidative stress.

A 'print-pause-print' protocol for 3D printing microfluidics using multimaterial stereolithography

Methods to make microfluidic chips using 3D printers have attracted much attention because these simple procedures allow rapid fabrication of ready-to-use products from digital 3D designs with minimal human intervention. Printing high-resolution chips that are simultaneously transparent, biocompatible and contain regions of dissimilar materials is an ongoing challenge. Transparency allows for the optical inspection of specimens containing cells and labeled biomolecules inside the chip. Being able to use different materials for different layers in the product increases the number of potential applications. In this 'print-pause-print' protocol, we describe detailed strategies for fabricating transparent biomicrofluidic devices and multimaterial chips using stereolithographic 3D printing. To print transparent biomicrofluidic chips, we developed a transparent resin based on poly(ethylene glycol) diacrylate (PEG-DA) (average molecular weight: 250 g/mol, PEG-DA-250) and a smooth chip surface technique achieved using glass. Cells can be successfully cultured and visualized on PEG-DA-250 prints and inside PEG-DA-250 microchannels. The multimaterial potential of the technique is exemplified using a molecular diffusion device that comprises parts made of two different materials: the channel walls, which are water impermeable, and a porous barrier structure, which is permeable to small molecules that diffuse through it. The two materials were prepared from two different molecular-weight PEG-DA-based printing resins. Alignment of the two dissimilar material structures is performed automatically by the printer during the printing process, which only requires a simple pause step to exchange the resins. The procedure takes less than 1 h and can facilitate chip-based applications including biomolecule analysis, cell biology, organ-on-a-chip and tissue engineering.

Recent advances in microfluidics for single-cell functional proteomics

Single-cell proteomics (SCP) reveals phenotypic heterogeneity by profiling individual cells, their biological states and functional outcomes upon signaling activation that can hardly be probed via other omics characterizations. This has become appealing to researchers as it enables an overall more holistic view of biological details underlying cellular processes, disease onset and progression, as well as facilitates unique biomarker identification from individual cells. Microfluidic-based strategies have become methods of choice for single-cell analysis because they allow facile assay integrations, such as cell sorting, manipulation, and content analysis. Notably, they have been serving as an enabling technology to improve the sensitivity, robustness, and reproducibility of recently developed SCP methods. Critical roles of microfluidics technologies are expected to further expand rapidly in advancing the next phase of SCP analysis to reveal more biological and clinical insights. In this review, we will capture the excitement of the recent achievements of microfluidics methods for both targeted and global SCP, including efforts to enhance the proteomic coverage, minimize sample loss, and increase multiplexity and throughput. Furthermore, we will discuss the advantages, challenges, applications, and future prospects of SCP.

Functional precision oncology using patient-derived assays: bridging genotype and phenotype

Genomics-based precision medicine has revolutionized oncology but also has inherent limitations. Functional precision oncology is emerging as a complementary approach that aims to bridge the gap between genotype and phenotype by modelling individual tumours in vitro. These patient-derived ex vivo models largely preserve several tumour characteristics that are not captured by genomics approaches and enable the functional dissection of tumour vulnerabilities in a personalized manner. In this Review, we discuss several examples of personalized functional assays involving tumour organoids, spheroids and explants and their potential to predict treatment responses and drug-induced toxicities in individual patients. These developments have opened exciting new avenues for precision oncology, with the potential for successful clinical applications in contexts in which genomic data alone are not informative. To implement these assays into clinical practice, we outline four key barriers that need to be overcome: assay success rates, turnaround times, the need for standardized conditions and the definition of in vitro responders. Furthermore, we discuss novel technological advances such as microfluidics that might reduce sample requirements, assay times and labour intensity and thereby enable functional precision oncology to be implemented in routine clinical practice.

Dynamic Vortex Generation, Pulsed Injection, and Rapid Mixing of Blood Samples in Microfluidics Using the Tube Oscillation Mechanism

Here, we describe the generation of dynamic vortices in micro-scale cavities at low flow rates. The system utilizes a computer-controlled audio speaker to axially oscillate the inlet tube of the microfluidic system at desired frequencies and amplitudes. The oscillation of the tube induces transiently high flow rates in the system, which facilitates the generation of dynamic vortices inside the cavity. The size of the vortices can be modulated by varying the tube oscillation frequency or amplitude. The vortices can be generated in single or serial cavities and in a wide range of cavity sizes. We demonstrate the suitability of the tube oscillation mechanism for the pulsed injection of water-based solutions or whole blood into the cavity. The injection rate can be controlled by the oscillation characteristics of the tube, enabling the injection of liquids at ultralow flow rates. The dynamic vortices facilitate the rapid mixing of the injected liquid with the main flow. The controllability and versatility of this technology allow for the development of programmable inertial microfluidic systems for performing multistep biological assays.

Fully Automated Characterization of Protein-Peptide Binding by Microfluidic 2D NMR

We demonstrate an automated microfluidic nuclear magnetic resonance (NMR) system that quantitatively characterizes protein-ligand interactions without user intervention and with minimal sample needs through protein-detected heteronuclear 2D NMR spectroscopy. Quantitation of protein-ligand interactions is of fundamental importance to the understanding of signaling and other life processes. As is well-known, NMR provides rich information both on the thermodynamics of binding and on the binding site. However, the required titrations are laborious and tend to require large amounts of sample, which are not always available. The present work shows how the analytical power of NMR detection can be brought in line with the trend of miniaturization and automation in life science workflows.

Advances in Microfluidics for Single Red Blood Cell Analysis

The utilizations of microfluidic chips for single RBC (red blood cell) studies have attracted great interests in recent years to filter, trap, analyze, and release single erythrocytes for various applications. Researchers in this field have highlighted the vast potential in developing micro devices for industrial and academia usages, including lab-on-a-chip and organ-on-a-chip systems. This article critically reviews the current state-of-the-art and recent advances of microfluidics for single RBC analyses, including integrated sensors and microfluidic platforms for microscopic/tomographic/spectroscopic single RBC analyses, trapping arrays (including bifurcating channels), dielectrophoretic and agglutination/aggregation studies, as well as clinical implications covering cancer, sepsis, prenatal, and Sickle Cell diseases. Microfluidics based RBC microarrays, sorting/counting and trapping techniques (including acoustic, dielectrophoretic, hydrodynamic, magnetic, and optical techniques) are also reviewed. Lastly, organs on chips, multi-organ chips, and drug discovery involving single RBC are described. The limitations and drawbacks of each technology are addressed and future prospects are discussed.

Genomic medicine in Africa: a need for molecular genetics and pharmacogenomics experts

The large-scale implementation of genomic medicine in Africa has not been actualized. This overview describes how routine molecular genetics and advanced protein engineering/structural biotechnology could accelerate the implementation of genomic medicine. By using data-mining and analysis approaches, we analyzed relevant information obtained from public genomic databases on pharmacogenomics biomarkers and reviewed published studies to discuss the ideas. The results showed that only 68 very important pharmacogenes currently exist, while 867 drug label annotations, 201 curated functional pathways, and 746 annotated drugs have been catalogued on the largest pharmacogenomics database (PharmGKB). Only about 5009 variants of the reported ∼25,000 have been clinically annotated. Predominantly, the genetic variants were derived from 43 genes that contribute to 2318 clinically relevant variations in 57 diseases. Majority (∼60%) of the clinically relevant genetic variations in the pharmacogenes are missense variants (1390). The enrichment analysis showed that 15 pharmacogenes are connected biologically and are involved in the metabolism of cardiovascular and cancer drugs. The review of studies showed that cardiovascular diseases are the most frequent non-communicable diseases responsible for approximately 13% of all deaths in Africa. Also, warfarin pharmacogenomics is the most studied drug on the continent, while CYP2D6, CYP2C9, DPD, and TPMT are the most investigated pharmacogenes with allele activities indicated in African and considered to be intermediate metaboliser for DPD and TPMT (8.4% and 11%). In summary, we highlighted a framework for implementing genomic medicine starting from the available resources on ground.

Fluidic Device System for Mechanical Processing and Filtering of Human Lipoaspirate Enhances Recovery of Mesenchymal Stem Cells

BACKGROUND

Adipose tissue is an easily accessible source of stem and progenitor cells that offers exciting promise as an injectable autologous therapeutic for regenerative applications. Mechanical processing is preferred over enzymatic digestion, and the most common method involves shuffling lipoaspirate between syringes and filtering to produce nanofat. Although nanofat has shown exciting clinical results, the authors hypothesized that new device designs could enhance recovery of stem/progenitor cells through optimization of fluid dynamics principles, integration, and automation.

METHODS

The authors designed and fabricated the emulsification and micronization device (EMD) and the filtration device (FD) to replace the manual nanofat procedures. Using human lipoaspirate samples, the EMD and the FD were optimized and compared to traditional nanofat using ex vivo measurements of cell number, viability, and percentage of mesenchymal stem cells and endothelial progenitor cells.

RESULTS

The EMD produced results statistically similar to nanofat, and these findings were confirmed for a cohort of diabetic patients. Combining the FD with the EMD was superior to manually filtered nanofat in terms of both recovered cell percentages (>1.5-fold) and numbers (two- to three-fold). Differences were statistically significant for total mesenchymal stem cells and a DPP4 + /CD55 + subpopulation linked to improved wound healing in diabetes.

CONCLUSIONS

The new EMD and the FD improved mechanical processing of human lipoaspirate in terms of mesenchymal stem cell enrichment and number compared to traditional nanofat. Future work will seek to investigate the wound healing response both in vitro and in vivo, and to refine the technology for automated operation within clinical settings.

CLINICAL RELEVANCE STATEMENT

The new devices improved mechanical processing of human lipoaspirate in terms of stem cell enrichment and number compared to traditional methods. Future work will seek to validate wound healing response and refine the technology for automated operation within clinical settings.

Advances in Regenerative Medicine and Biomaterials

The low regenerative potential of the human body hinders proper regeneration of dysfunctional or lost tissues and organs due to trauma, congenital defects, and diseases. Tissue or organ transplantation has hence been a major conventional option for replacing the diseased or dysfunctional body parts of the patients. In fact, a great number of patients on waiting lists would benefit tremendously if tissue and organs could be replaced with biomimetic spare parts on demand. Herein, regenerative medicine and advanced biomaterials strive to reach this distant goal. Tissue engineering aims to create new biological tissue or organ substitutes, and promote regeneration of damaged or diseased tissue and organs. This approach has been jointly evolving with the major advances in biomaterials, stem cells, and additive manufacturing technologies. In particular, three-dimensional (3D) bioprinting utilizes 3D printing to fabricate viable tissue-like structures (perhaps organs in the future) using bioinks composed of special hydrogels, cells, growth factors, and other bioactive contents. A third generation of multifunctional biomaterials could also show opportunities for building biomimetic scaffolds, upon which to regenerate stem cells in vivo. Besides, decellularization technology based on isolation of extracellular matrix of tissue and organs from their inhabiting cells is presented as an alternative to synthetic biomaterials. Today, the gained knowledge of functional microtissue engineering and biointerfaces, along with the remarkable advances in pluripotent stem cell technology, seems to be instrumental for the development of more realistic microphysiological 3D in vitro tissue models, which can be utilized for personalized disease modeling and drug development. This chapter will discuss the recent advances in the field of regenerative medicine and biomaterials, alongside challenges, limitations, and potentials of the current technologies.

Recent advances in micro-/nanostructure array integrated microfluidic devices for efficient separation of circulating tumor cells

Circulating tumor cells (CTCs) released from the primary tumor to peripheral blood are promising targets for liquid biopsies. Their biological information is vital for early cancer detection, efficacy assessment, and prognostic monitoring. Despite the tremendous clinical applications of CTCs, development of effective separation techniques are still demanding. Traditional separation methods usually use batch processing for enrichment, which inevitably destroy cell integrity and affect the complete information acquisition. Considering the rarity and heterogeneity of CTCs, it is urgent to develop effective separation methods. Microfluidic chips with precise fluid control at the micron level are promising devices for CTC separation. Their further combination with micro-/nanostructure arrays adds more biomolecule binding sites and exhibit unique fluid barrier effect, which significantly improve the CTC capture efficiency, purity, and sensitivity. This review summarized the recent advances in micro-/nanostructure array integrated microfluidic devices for CTC separation, including microrods, nanowires, and 3D micro-/nanostructures. The mechanisms by which these structures contribute to improved capture efficiency are discussed. Two major categories of separation methods, based on the physical and biological properties of CTCs, are discussed separately. Physical separation includes the design and preparation of micro-/nanostructure arrays, while chemical separation additionally involves the selection and modification of specific capture probes. These emerging technologies are expected to become powerful tools for disease diagnosis in the future.

Microfluidic dose-response platform to track the dynamics of drug response in single mycobacterial cells

Preclinical analysis of drug efficacy is critical for drug development. However, conventional bulk-cell assays statically assess the mean population behavior, lacking resolution on drug-escaping cells. Inaccurate estimation of efficacy can lead to overestimation of compounds, whose efficacy will not be confirmed in the clinic, or lead to rejection of valuable candidates. Time-lapse microfluidic microscopy is a powerful approach to characterize drugs at high spatiotemporal resolution, but hard to apply on a large scale. Here we report the development of a microfluidic platform based on a pneumatic operating principle, which is scalable and compatible with long-term live-cell imaging and with simultaneous analysis of different drug concentrations. We tested the platform with mycobacterial cells, including the tubercular pathogen, providing the first proof of concept of a single-cell dose-response assay. This dynamic in-vitro model will prove useful to probe the fate of drug-stressed cells, providing improved predictions of drug efficacy in the clinic.

High-throughput screening paradigms in ecotoxicity testing: Emerging prospects and ongoing challenges

The rapidly increasing number of new production chemicals coupled with stringent implementation of global chemical management programs necessities a paradigm shift towards boarder uses of low-cost and high-throughput ecotoxicity testing strategies as well as deeper understanding of cellular and sub-cellular mechanisms of ecotoxicity that can be used in effective risk assessment. The latter will require automated acquisition of biological data, new capabilities for big data analysis as well as computational simulations capable of translating new data into in vivo relevance. However, very few efforts have been so far devoted into the development of automated bioanalytical systems in ecotoxicology. This is in stark contrast to standardized and high-throughput chemical screening and prioritization routines found in modern drug discovery pipelines. As a result, the high-throughput and high-content data acquisition in ecotoxicology is still in its infancy with limited examples focused on cell-free and cell-based assays. In this work we outline recent developments and emerging prospects of high-throughput bioanalytical approaches in ecotoxicology that reach beyond in vitro biotests. We discuss future importance of automated quantitative data acquisition for cell-free, cell-based as well as developments in phytotoxicity and in vivo biotests utilizing small aquatic model organisms. We also discuss recent innovations such as organs-on-a-chip technologies and existing challenges for emerging high-throughput ecotoxicity testing strategies. Lastly, we provide seminal examples of the small number of successful high-throughput implementations that have been employed in prioritization of chemicals and accelerated environmental risk assessment.

Quantification of Intracellular Proteins in Single Cells Based on Engineered Picoliter Droplets

Unlike conventional bulk measurements, single-cell protein analysis permits quantification of protein expression in individual cells. This has shed light on the cell-to-cell variation in heterogeneous biological systems, such as solid tumors, brain tissues, and developing embryos. Herein, a microfluidic method is developed to profile protein expression in individual cells by performing single-cell intracellular protein immunoassay in picoliter paired droplets. The high sensitivity of single-cell protein analysis on a chip is achieved by the confined reaction volume of picoliter droplets, efficient kinetic characteristics of the immunoassay through active mixing, and minimum single-cell protein loss by integrated operations. The abundance of an intracellular prostate specific antigen at the single-cell level is measured, and then the platform is applied to identify cell types and investigate heterogeneity within cell populations. Overall, a paired chip for single-cell immunoassay establishes a foundation for parallel, sensitive, and integrated protein quantification at the single-cell level and will find wide applications in the field of single-cell proteomics.

New Views of Old Proteins: Clarifying the Enigmatic Proteome

All human diseases involve proteins, yet our current tools to characterize and quantify them are limited. To better elucidate proteins across space, time, and molecular composition, we provide a >10 years of projection for technologies to meet the challenges that protein biology presents. With a broad perspective, we discuss grand opportunities to transition the science of proteomics into a more propulsive enterprise. Extrapolating recent trends, we describe a next generation of approaches to define, quantify, and visualize the multiple dimensions of the proteome, thereby transforming our understanding and interactions with human disease in the coming decade.

A Critical Review on the Sensing, Control, and Manipulation of Single Molecules on Optofluidic Devices

Single-molecule techniques have shifted the paradigm of biological measurements from ensemble measurements to probing individual molecules and propelled a rapid revolution in related fields. Compared to ensemble measurements of biomolecules, single-molecule techniques provide a breadth of information with a high spatial and temporal resolution at the molecular level. Usually, optical and electrical methods are two commonly employed methods for probing single molecules, and some platforms even offer the integration of these two methods such as optofluidics. The recent spark in technological advancement and the tremendous leap in fabrication techniques, microfluidics, and integrated optofluidics are paving the way toward low cost, chip-scale, portable, and point-of-care diagnostic and single-molecule analysis tools. This review provides the fundamentals and overview of commonly employed single-molecule methods including optical methods, electrical methods, force-based methods, combinatorial integrated methods, etc. In most single-molecule experiments, the ability to manipulate and exercise precise control over individual molecules plays a vital role, which sometimes defines the capabilities and limits of the operation. This review discusses different manipulation techniques including sorting and trapping individual particles. An insight into the control of single molecules is provided that mainly discusses the recent development of electrical control over single molecules. Overall, this review is designed to provide the fundamentals and recent advancements in different single-molecule techniques and their applications, with a special focus on the detection, manipulation, and control of single molecules on chip-scale devices.