Microfluidics-based systems biology

Microfluidic technology for cell biology-related applications: a review

Fluid flow at the microscale level exhibits a unique phenomenon that can be explored to fabricate microfluidic devices integrated with components that can perform various biological functions. In this manuscript, the importance of physics for microscale fluid dynamics using microfluidic devices has been reviewed. Microfluidic devices provide new opportunities with regard to spatial and temporal control over cell growth. Furthermore, the manuscript presents an overview of cellular stimuli observed by combining surfaces that mimic the complex biochemistries and different geometries of the extracellular matrix, with microfluidic channels regulating the transport of fluids, soluble factors, etc. We have also explained the concept of mechanotransduction, which defines the relation between mechanical force and biological response. Furthermore, the manipulation of cellular microenvironments by the use of microfluidic systems has been highlighted as a useful device for basic cell biology research activities. Finally, the article focuses on highly integrated microfluidic platforms that exhibit immense potential for biomedical and pharmaceutical research as robust and portable point-of-care diagnostic devices for the assessment of clinical samples.

Adapting to ever-changing conditions

Experiments involving periodic stimuli shed light on the interplay between hyper-osmotic stress and glucose starvation in yeast cells.

Microfluidic Blood Separation: Key Technologies and Critical Figures of Merit

Blood is a complex sample comprised mostly of plasma, red blood cells (RBCs), and other cells whose concentrations correlate to physiological or pathological health conditions. There are also many blood-circulating biomarkers, such as circulating tumor cells (CTCs) and various pathogens, that can be used as measurands to diagnose certain diseases. Microfluidic devices are attractive analytical tools for separating blood components in point-of-care (POC) applications. These platforms have the potential advantage of, among other features, being compact and portable. These features can eventually be exploited in clinics and rapid tests performed in households and low-income scenarios. Microfluidic systems have the added benefit of only needing small volumes of blood drawn from patients (from nanoliters to milliliters) while integrating (within the devices) the steps required before detecting analytes. Hence, these systems will reduce the associated costs of purifying blood components of interest (e.g., specific groups of cells or blood biomarkers) for studying and quantifying collected blood fractions. The microfluidic blood separation field has grown since the 2000s, and important advances have been reported in the last few years. Nonetheless, real POC microfluidic blood separation platforms are still elusive. A widespread consensus on what key figures of merit should be reported to assess the quality and yield of these platforms has not been achieved. Knowing what parameters should be reported for microfluidic blood separations will help achieve that consensus and establish a clear road map to promote further commercialization of these devices and attain real POC applications. This review provides an overview of the separation techniques currently used to separate blood components for higher throughput separations (number of cells or particles per minute). We present a summary of the critical parameters that should be considered when designing such devices and the figures of merit that should be explicitly reported when presenting a device's separation capabilities. Ultimately, reporting the relevant figures of merit will benefit this growing community and help pave the road toward commercialization of these microfluidic systems.

Sub-wavelength acoustic stencil for tailored micropatterning

Acoustofluidic devices are ideal for biomedical micromanipulation applications, with high biocompatibility and the ability to generate force gradients down to the scale of cells. However, complex and designed patterning at the microscale remains challenging. In this work we report an acoustofluidic approach to direct particles and cells within a structured surface in arbitrary configurations. Wells, trenches and cavities are embedded in this surface. Combined with a half-wavelength acoustic field, together these form an 'acoustic stencil' where arbitrary cell and particle arrangements can be reversibly generated. Here a bulk-wavemode lithium niobate resonator generates multiplexed parallel patterning via a multilayer resonant geometry, where cell-scale resolution is accomplished via structured sub-wavelength microfeatures. Uniquely, this permits simultaneous manipulation in a unidirectional, device-spanning single-node field across scalable ∼cm² areas in a microfluidic device. This approach is demonstrated via patterning of 5, 10 and 15 μm particles and 293-F cells in a variety of arrangements, where these activities are enabling for a range of cell studies and tissue engineering applications via the generation of highly complex and designed acoustic patterns at the microscale.

NGN2-based neuronal programming of hiPSCs in an automated microfluidic platform

The generation of induced pluripotent stem cells (iPSCs) via somatic cell reprogramming allowed to have an unlimited in vitro source of patient-specific cells. This achievement has introduced a new revolutionary way to create human in vitro models and to study human diseases starting from patient's own cells, especially important for inaccessible tissues like the brain. Recently, lab-on-a-chip technology has opened new reliable alternatives to conventional in vitro models able to replicate key aspects of human physiology, thanks to the intrinsic high surface-area-to-volume ratio, which allows fine control of the cellular microenvironment. The development of automated microfluidic platforms allowed the implementation of this technology to perform high-throughput, standardized and parallelized assays, suitable for drug screenings and developing new therapeutic approaches in a cost-effective way. However, the major challenges in the broad application of automated lab-on-a-chip in biological research are the lack of production robustness and ease of use of the devices. Here, we present an automated microfluidic platform able to host the rapid conversion of human iPSCs (hiPSCs) into neurons via viral-mediated overexpression of Neurogenin 2 (NGN2) in a user-friendly manner. The design of the platform, built with multilayer soft-lithography techniques, shows easiness in the fabrication and assembly thanks to the simple geometry and experimental reproducibility at the same time. All operations are managed automatically, from the cell seeding, medium change, doxycycline-mediated neuronal induction, selection of the genetically engineered cells, and analysis of the output of differentiation, including immunofluorescence assay. Our results show a high-throughput, efficient and homogenous conversion of hiPSCs into neurons in 10 days, characterized by the expression of the mature neuronal marker MAP2 and calcium signaling. The neurons-on-chip model here described represents a fully automated loop system able to address the challenges in the field of neurological diseases modelling in vitro and improve current preclinical models.

Biomedical Applications of Microfluidic Devices: A Review

Both passive and active microfluidic chips are used in many biomedical and chemical applications to support fluid mixing, particle manipulations, and signal detection. Passive microfluidic devices are geometry-dependent, and their uses are rather limited. Active microfluidic devices include sensors or detectors that transduce chemical, biological, and physical changes into electrical or optical signals. Also, they are transduction devices that detect biological and chemical changes in biomedical applications, and they are highly versatile microfluidic tools for disease diagnosis and organ modeling. This review provides a comprehensive overview of the significant advances that have been made in the development of microfluidics devices. We will discuss the function of microfluidic devices as micromixers or as sorters of cells and substances (e.g., microfiltration, flow or displacement, and trapping). Microfluidic devices are fabricated using a range of techniques, including molding, etching, three-dimensional printing, and nanofabrication. Their broad utility lies in the detection of diagnostic biomarkers and organ-on-chip approaches that permit disease modeling in cancer, as well as uses in neurological, cardiovascular, hepatic, and pulmonary diseases. Biosensor applications allow for point-of-care testing, using assays based on enzymes, nanozymes, antibodies, or nucleic acids (DNA or RNA). An anticipated development in the field includes the optimization of techniques for the fabrication of microfluidic devices using biocompatible materials. These developments will increase biomedical versatility, reduce diagnostic costs, and accelerate diagnosis time of microfluidics technology.

Organs-on-Chips Platforms Are Everywhere: A Zoom on Biomedical Investigation

Over the decades, conventional in vitro culture systems and animal models have been used to study physiology, nutrient or drug metabolisms including mechanical and physiopathological aspects. However, there is an urgent need for Integrated Testing Strategies (ITS) and more sophisticated platforms and devices to approach the real complexity of human physiology and provide reliable extrapolations for clinical investigations and personalized medicine. Organ-on-a-chip (OOC), also known as a microphysiological system, is a state-of-the-art microfluidic cell culture technology that sums up cells or tissue-to-tissue interfaces, fluid flows, mechanical cues, and organ-level physiology, and it has been developed to fill the gap between in vitro experimental models and human pathophysiology. The wide range of OOC platforms involves the miniaturization of cell culture systems and enables a variety of novel experimental techniques. These range from modeling the independent effects of biophysical forces on cells to screening novel drugs in multi-organ microphysiological systems, all within microscale devices. As in living biosystems, the development of vascular structure is the salient feature common to almost all organ-on-a-chip platforms. Herein, we provide a snapshot of this fast-evolving sophisticated technology. We will review cutting-edge developments and advances in the OOC realm, discussing current applications in the biomedical field with a detailed description of how this technology has enabled the reconstruction of complex multi-scale and multifunctional matrices and platforms (at the cellular and tissular levels) leading to an acute understanding of the physiopathological features of human ailments and infections in vitro.

3D Printed Microfluidic Bioreactors Used for the Preferential Growth of Bacterial Biofilms through Dielectrophoresis

A realistic modelling of the way biofilms form and evolve in time requests a dynamic approach. In this study, the proposed route uses continuous-flow bioreactors under controlled flow rates and temperature in the culture medium containing bacteria or fungi. 3D printed, Polylactic acid (PLA), flow-based bioreactors with integrated copper electrodes were used to investigate the effect of dielectrophoresis on the formation and growth of Staphylococcus aureus ATCC 25923, Enterococcus faecalis ATCC 29212, Pseudomonas aeruginosa ATCC 27853, and Klebsiella pneumoniae ATCC 13883 biofilms. Bacterial suspensions of 1McF turbidity have been prepared and circulated through the bioreactors. At the same time, a 30 V potential difference was applied on the system. The effect of the non-uniform electric field induced upon the bacterial cells was determined using quantitative methods, such as an adjusted microtiter plate technique, as well as spectral domain optical coherence tomography (SD-OCT) images. The morphology and the surface quality of the biofilms were investigated using Scanning Electron Microscopy (SEM) images. The results show that the different bacterial cells present a positive dielectrophoretic behaviour, with the preferential formation of biofilms in the high field gradient region.

Microtoxicology by microfluidic instrumentation: a review

Microtoxicology is concerned with the toxic effects of small amounts of substances. This review paper discusses the application of small amounts of noxious substances for toxicological investigation in small volumes. The vigorous development of miniaturized methods in microfluidics over the last two decades involves chip-based devices, micro droplet-based procedures, and the use of micro-segmented flow for microtoxicological studies. The studies have shown that the microfluidic approach is particularly valuable for highly parallelized and combinatorial dose-response screenings. Accurate dosing and mixing of effector substances in large numbers of microcompartments supplies detailed data of dose-response functions by highly concentration-resolved assays and allows evaluation of stochastic responses in case of small separated cell ensembles and single cell experiments. The investigations demonstrate that very different biological targets can be studied using miniaturized approaches, among them bacteria, eukaryotic microorganisms, cell cultures from tissues of multicellular organisms, stem cells, and early embryonic states. Cultivation and effector exposure tests can be performed in small volumes over weeks and months, confirming that the microfluicial strategy is also applicable for slow-growing organisms. Here, the state of the art of miniaturized toxicology, particularly for studying antibiotic susceptibility, drug toxicity testing in the miniaturized system like organ-on-chip, environmental toxicology, and the characterization of combinatorial effects by two and multi-dimensional screenings, is discussed. Additionally, this review points out the practical limitations of the microtoxicology platform and discusses perspectives on future opportunities and challenges.

Advances in microfluidics devices and its applications in personalized medicines

Microfluidics is an exponentially growing area and is being used for numerous applications from basic science to advanced biotechnology and medicines. Microfluidics provides a platform to the research community for studying and building new strategies for the diagnosis and therapeutics applications. In the last decade, microfluidic have enriched the field of diagnostics by providing new solutions which was not possible with conventional detection and treatment methods. Microfluidics has the ability to precisely control and perform high-throughput functions. It has been proven as an efficient and rapid method for biological sample preparation, analysis and controlled drug delivery system. Microfluidics plays significant role in personalized medicine. These personalized medicines are used for medical decisions, practices and other interventions as well as for individual patients based on their predicted response or risk of disease. This chapter highlights microfluidics in developing personalized medical applications for its applications in diseases such as cancer, cardiovascular disease, diabetes, pulmonary disease and several others.

A microfluidic generator of dynamic shear stress and biochemical signals based on autonomously oscillatory flow

Biological cells in vivo typically reside in a dynamic flowing microenvironment with extensive biomechanical and biochemical cues varying in time and space. These dynamic biomechanical and biochemical signals together act to regulate cellular behaviors and functions. Microfluidic technology is an important experimental platform for mimicking extracellular flowing microenvironment in vitro. However, most existing microfluidic chips for generating dynamic shear stress and biochemical signals require expensive, large peripheral pumps and external control systems, unsuitable for being placed inside cell incubators to conduct cell biology experiments. This study has developed a microfluidic generator of dynamic shear stress and biochemical signals based on autonomously oscillatory flow. Further, based on the lumped-parameter and distributed-parameter models of multiscale fluid dynamics, the oscillatory flow field and the concentration field of biochemical factors has been simulated at the cell culture region within the designed microfluidic chip. Using the constructed experimental system, the feasibility of the designed microfluidic chip has been validated by simulating biochemical factors with red dye. The simulation results demonstrate that dynamic shear stress and biochemical signals with adjustable period and amplitude can be generated at the cell culture chamber within the microfluidic chip. The amplitudes of dynamic shear stress and biochemical signals is proportional to the pressure difference and inversely proportional to the flow resistance, while their periods are correlated positively with the flow capacity and the flow resistance. The experimental results reveal the feasibility of the designed microfluidic chip. Conclusively, the proposed microfluidic generator based on autonomously oscillatory flow can generate dynamic shear stress and biochemical signals without peripheral pumps and external control systems. In addition to reducing the experimental cost, due to the tiny volume, it is beneficial to be integrated into cell incubators for cell biology experiments. Thus, the proposed microfluidic chip provides a novel experimental platform for cell biology investigations.

Bio-conversion of CO2 into biofuels and other value-added chemicals via metabolic engineering

Carbon dioxide (CO₂) occurs naturally in the atmosphere as a trace gas, which is produced naturally as well as by anthropogenic activities. CO₂ is a readily available source of carbon that in principle can be used as a raw material for the synthesis of valuable products. The autotrophic organisms are naturally equipped to convert CO₂ into biomass by obtaining energy from sunlight or inorganic electron donors. This autotrophic CO₂ fixation has been exploited in biotechnology, and microbial cell factories have been metabolically engineered to convert CO₂ into biofuels and other value-added bio-based chemicals. A variety of metabolic engineering efforts for CO₂ fixation ranging from basic copy, paste, and fine-tuning approaches to engineering and testing of novel synthetic CO₂ fixing pathways have been demonstrated. In this paper, we review the current advances and innovations in metabolic engineering for bio-conversion of CO₂ into bio biofuels and other value-added bio-based chemicals.

Bone-on-a-chip: microfluidic technologies and microphysiologic models of bone tissue

Bone is an active organ that continuously undergoes an orchestrated process of remodeling throughout life. Bone tissue is uniquely capable of adapting to loading, hormonal, and other changes happening in the body, as well as repairing bone that becomes damaged to maintain tissue integrity. On the other hand, diseases such as osteoporosis and metastatic cancers disrupt normal bone homeostasis leading to compromised function. Historically, our ability to investigate processes related to either physiologic or diseased bone tissue has been limited by traditional models that fail to emulate the complexity of native bone. Organ-on-a-chip models are based on technological advances in tissue engineering and microfluidics, enabling the reproduction of key features specific to tissue microenvironments within a microfabricated device. Compared to conventional in-vitro and in-vivo bone models, microfluidic models, and especially organs-on-a-chip platforms, provide more biomimetic tissue culture conditions, with increased predictive power for clinical assays. In this review, we will report microfluidic and organ-on-a-chip technologies designed for understanding the biology of bone as well as bone-related diseases and treatments. Finally, we discuss the limitations of the current models and point toward future directions for microfluidics and organ-on-a-chip technologies in bone research.

Miniaturization and 3D Printing of Bioreactors: A Technological Mini Review

Many articles have been published on scale-down concepts as well as additive manufacturing techniques. However, information is scarce when miniaturization and 3D printing are applied in the fabrication of bioreactor systems. Therefore, garnering information for the interfaces between miniaturization and 3D printing becomes important and essential. The first goal is to examine the miniaturization aspects concerning bioreactor screening systems. The second goal is to review successful modalities of 3D printing and its applications in bioreactor manufacturing. This paper intends to provide information on anaerobic digestion process intensification by fusion of miniaturization technique and 3D printing technology. In particular, it gives a perspective on the challenges of 3D printing and the options of miniature bioreactor systems for process high-throughput screening.

Art-on-a-Chip: Preserving Microfluidic Chips for Visualization and Permanent Display

"After a certain high level of technical skill is achieved, science and art tend to coalesce in aesthetics, plasticity, and form. The greatest scientists are always artists as well." said Albert Einstein. Currently, photographic images bridge the gap between microfluidic/lab-on-a-chip devices and art. However, the microfluidic chip itself should be a form of art. Here, novel vibrant epoxy dyes are presented in combination with a simple process to fill and preserve microfluidic chips, to produce microfluidic art or art-on-a-chip. In addition, this process can be used to produce epoxy dye patterned substrates that preserve the geometry of the microfluidic channels-height within 10% of the mold master. This simple approach for preserving microfluidic chips with vibrant, colorful, and long-lasting epoxy dyes creates microfluidic chips that can easily be visualized and photographed repeatedly, for at least 11 years, and hence enabling researchers to showcase their microfluidic chips to potential graduate students, investors, and collaborators.

Design and Fabrication of Low-cost Microfluidic Channel for Biomedical Application

This paper presents the design, simulation and low-cost fabrication of microfluidic channel for biomedical application. Channel is fabricated using soft lithography technique. Printed Circuit Board (PCB) is used to make the master for the channel. Channel pattern is transferred on PCB plate using toner transfer technique followed by ferric chloride etching. Paper also discusses, the issues involved in PCB based master fabrication and their viable solutions. Glass is used as substrate material and the channel is made of Sylgard 184 Polydimethylsiloxane (PDMS). Channel is interfaced with a syringe pump to observe the fluid flow. To predict the behavior of the channel, FEM simulation is performed using COMSOL Multiphysics 5.2a. There is a good match between the theoretical, simulation and test results. Finally, to test the biocompatibility of the channel, genomic DNA is passed through the channel and gel electrophoresis analysis is performed.

Microbioreactors for Process Development and Cell-Based Screening Studies

Microbioreactors (MBRs) have emerged as potent cultivation devices enabling automated small-scale experiments in parallel while enhancing their cost efficiency. The widespread use of MBRs has contributed to recent advances in industrial and pharmaceutical biotechnology, and they have proved to be indispensable tools in the development of many modern bioprocesses. Being predominantly applied in early stage process development, they open up new fields of research and enhance the efficacy of biotechnological product development. Their reduced reaction volume is associated with numerous inherent advantages - particularly the possibility for enabling parallel screening operations that facilitate high-throughput cultivations with reduced sample consumption (or the use of rare and expensive educts). As a result, multiple variables can be examined in a shorter time and with a lower expense. This leads to a simultaneous acceleration of research and process development along with decreased costs.MBRs range from simple miniaturized cultivations vessels (i.e., in the milliliter scale with limited possibilities for process control) to highly complex and automated small-scale microreactors with integrated sensors that allow for comprehensive screenings in very short time or a precise reflection of large-scale cultivation conditions. Progressive developments and improvements in manufacturing and automation techniques are already helping researchers to make use of the advantages that MBRs offer. This overview of current MBR systems surveys the diverse application for microbial and mammalian cell cultivations that have been developed in recent years.

Viable cell culture in PDMS-based microfluidic devices

Microfluidics has played a vital role in developing novel methods to investigate biological phenomena at the molecular and cellular level during the last two decades. Microscale engineering of cellular systems is nevertheless a nascent field marked inherently by frequent disruptive advancements in technology such as PDMS-based soft lithography. Viable culture and manipulation of cells in microfluidic devices requires knowledge across multiple disciplines including molecular and cellular biology, chemistry, physics, and engineering. There has been numerous excellent reviews in the past 15 years on applications of microfluidics for molecular and cellular biology including microfluidic cell culture (Berthier et al., 2012; El-Ali, Sorger, & Jensen, 2006; Halldorsson et al., 2015; Kim et al., 2007; Mehling & Tay, 2014; Sackmann et al., 2014; Whitesides, 2006; Young & Beebe, 2010), cell culture models (Gupta et al., 2016; Inamdar & Borenstein, 2011; Meyvantsson & Beebe, 2008), cell secretion (Schrell et al., 2016), chemotaxis (Kim & Wu, 2012; Wu et al., 2013), neuron culture (Millet & Gillette, 2012a, 2012b), drug screening (Dittrich & Manz, 2006; Eribol, Uguz, & Ulgen, 2016; Wu, Huang, & Lee, 2010), cell sorting (Autebert et al., 2012; Bhagat et al., 2010; Gossett et al., 2010; Wyatt Shields Iv, Reyes, & López, 2015), single cell studies (Lecault et al., 2012; Reece et al., 2016; Yin & Marshall, 2012), stem cell biology (Burdick & Vunjak-Novakovic, 2009; Wu et al., 2011; Zhang & Austin, 2012), cell differentiation (Zhang et al., 2017a), systems biology (Breslauer, Lee, & Lee, 2006), 3D cell culture (Huh et al., 2011; Li et al., 2012; van Duinen et al., 2015), spheroids and organoids (Lee et al., 2016; Montanez-Sauri, Beebe, & Sung, 2015; Morimoto & Takeuchi, 2013; Skardal et al., 2016; Young, 2013), organ-on-chip (Bhatia & Ingber, 2014; Esch, Bahinski, & Huh, 2015; Huh et al., 2011; van der Meer & van den Berg, 2012), and tissue engineering (Andersson & Van Den Berg, 2004; Choi et al., 2007; Hasan et al., 2014). In this chapter, we provide an overview of PDMS-based microdevices for microfluidic cell culture. We discuss the advantages and challenges of using PDMS-based soft lithography for microfluidic cell culture and highlight recent progress and future directions in this area.

Microstructured Photo-Crosslinked Poly(Trimethylene Carbonate) for Use in Soft Lithography Applications: A Biodegradable Alternative for Poly(Dimethylsiloxane)

Photo-crosslinkable poly(trimethylene carbonate) (PTMC) macromers were used to fabricate microstructured surfaces. Microstructured PTMC surfaces were obtained by hot embossing the macromer against structured silicon masters and subsequent photo-crosslinking, resulting in network formation. The microstructures of the master could be precisely replicated, limiting the shrinkage. Microstructured PTMC was investigated for use in two different applications: as stamping material to transfer a model protein to another surface and as structured substrate for cell culture. Using the flexible and elastic materials as stamps, bovine serum albumin labelled with fluorescein isothiocyanate was patterned on glass surfaces. In cell culture experiments, the behavior of human mesenchymal stem cells on nonstructured and microstructured PTMC surfaces was investigated. The cells strongly adhered to the PTMC surfaces and proliferated well. Compared to poly(dimethylsiloxane) (PDMS), which is commonly used in soft lithography, the PTMC networks offer significant advantages. They show better compatibility with cells, are biodegradable, and have much better mechanical properties. Both materials are transparent, flexible, and elastic at room temperature, but the tear resistance of PTMC networks is much higher than that of PDMS. Thus, PTMC might be an alternative material to PDMS in the fields of biology, medicine, and tissue engineering, in which microfabricated devices are increasingly being applied.

Microtechnology applied to stem cells research and development

Microfabrication and microfluidics contribute to the research of cellular functions of cells and their interaction with their environment. Previously, it has been shown that microfluidics can contribute to the isolation, selection, characterization and migration of cells. This review aims to provide stem cell researchers with a toolkit of microtechnology (mT) instruments for elucidating complex stem cells functions which are challenging to decipher with traditional assays and animal models. These microdevices are able to investigate about the differentiation and niche interaction, stem cells transcriptomics, therapeutic functions and the capture of their secreted microvesicles. In conclusion, microtechnology will allow a more realistic assessment of stem cells properties, driving and accelerating the translation of regenerative medicine approaches to the clinic.

Hypoxia-enhanced adhesion of red blood cells in microscale flow

OBJECTIVES

The advancement of microfluidic technology has facilitated the simulation of physiological conditions of the microcirculation, such as oxygen tension, fluid flow, and shear stress in these devices. Here, we present a micro-gas exchanger integrated with microfluidics to study RBC adhesion under hypoxic flow conditions mimicking postcapillary venules.

METHODS

We simulated a range of physiological conditions and explored RBC adhesion to endothelial or subendothelial components (FN or LN). Blood samples were injected into microchannels at normoxic or hypoxic physiological flow conditions. Quantitative evaluation of RBC adhesion was performed on 35 subjects with homozygous SCD.

RESULTS

Significant heterogeneity in RBC adherence response to hypoxia was seen among SCD patients. RBCs from a HEA population showed a significantly greater increase in adhesion compared to RBCs from a HNA population, for both FN and LN.

CONCLUSIONS

The approach presented here enabled the control of oxygen tension in blood during microscale flow and the quantification of RBC adhesion in a cost-efficient and patient-specific manner. We identified a unique patient population in which RBCs showed enhanced adhesion in hypoxia in vitro. Clinical correlates suggest a more severe clinical phenotype in this subgroup.

Microfluidics in systems biology-hype or truly useful?

Systems biology often relies on large-scale measurements and model-building to understand how complex biological systems function. Microfluidic technology has been touted as a tool for high-throughput experiments and has been a valuable tool to some systems biology research. This review focuses on applications where microfluidics can enhance experimental sensitivity and throughput, particularly in recent development in single-cell analyses and analyses on multi-cellular or complex biological entities. We conclude that microfluidics is not necessarily always useful for systems biology, but when used appropriately can greatly enhance experimentalists' ability to measure and control, and thereby enhance the understanding of and expand the utility of biological systems.

Cell Microarray Technologies for High-Throughput Cell-Based Biosensors

Due to the recent demand for high-throughput cellular assays, a lot of efforts have been made on miniaturization of cell-based biosensors by preparing cell microarrays. Various microfabrication technologies have been used to generate cell microarrays, where cells of different phenotypes are immobilized either on a flat substrate (positional array) or on particles (solution or suspension array) to achieve multiplexed and high-throughput cell-based biosensing. After introducing the fabrication methods for preparation of the positional and suspension cell microarrays, this review discusses the applications of the cell microarray including toxicology, drug discovery and detection of toxic agents.

Amphiphilic nanoparticles suppress droplet break-up in a concentrated emulsion flowing through a narrow constriction

This paper describes the break-up behavior of a concentrated emulsion comprising drops stabilized by amphiphilic silica nanoparticles flowing in a tapered microchannel. Such geometry is often used in serial droplet interrogation and sorting processes in droplet microfluidics applications. When exposed to high viscous stresses, drops can undergo break-up and compromise their physical integrity. As these drops are used as micro-reactors, such compromise leads to a loss in the accuracy of droplet-based assays. Here, we show droplet break-up is suppressed by replacing the fluoro-surfactant similar to the one commonly used in current droplet microfluidics applications with amphiphilic nanoparticles as droplet stabilizer. We identify parameters that influence the break-up of these drops and demonstrate that break-up probability increases with increasing capillary number and confinement, decreasing nanoparticle size, and is insensitive to viscosity ratio within the range tested. Practically, our results reveal two key advantages of nanoparticles with direct applications to droplet microfluidics. First, replacing surfactants with nanoparticles suppresses break-up and increases the throughput of the serial interrogation process to 3 times higher than that in surfactant system under similar flow conditions. Second, the insensitivity of break-up to droplet viscosity makes it possible to process samples having different composition and viscosities without having to change the channel and droplet geometry in order to maintain the same degree of break-up and corresponding assay accuracy.

A minimal model of burst-noise induced bistability

We investigate the influence of intrinsic noise on stable states of a one-dimensional dynamical system that shows in its deterministic version a saddle-node bifurcation between monostable and bistable behaviour. The system is a modified version of the Schlögl model, which is a chemical reaction system with only one type of molecule. The strength of the intrinsic noise is varied without changing the deterministic description by introducing bursts in the autocatalytic production step. We study the transitions between monostable and bistable behavior in this system by evaluating the number of maxima of the stationary probability distribution. We find that changing the size of bursts can destroy and even induce saddle-node bifurcations. This means that a bursty production of molecules can qualitatively change the dynamics of a chemical reaction system even when the deterministic description remains unchanged.

Adaptive microfluidic gradient generator for quantitative chemotaxis experiments

Chemotactic motion in a chemical gradient is an essential cellular function that controls many processes in the living world. For a better understanding and more detailed modelling of the underlying mechanisms of chemotaxis, quantitative investigations in controlled environments are needed. We developed a setup that allows us to separately address the dependencies of the chemotactic motion on the average background concentration and on the gradient steepness of the chemoattractant. In particular, both the background concentration and the gradient steepness can be kept constant at the position of the cell while it moves along in the gradient direction. This is achieved by generating a well-defined chemoattractant gradient using flow photolysis. In this approach, the chemoattractant is released by a light-induced reaction from a caged precursor in a microfluidic flow chamber upstream of the cell. The flow photolysis approach is combined with an automated real-time cell tracker that determines changes in the cell position and triggers movement of the microscope stage such that the cell motion is compensated and the cell remains at the same position in the gradient profile. The gradient profile can be either determined experimentally using a caged fluorescent dye or may be alternatively determined by numerical solutions of the corresponding physical model. To demonstrate the function of this adaptive microfluidic gradient generator, we compare the chemotactic motion of Dictyostelium discoideum cells in a static gradient and in a gradient that adapts to the position of the moving cell.

Control and automation of multilayered integrated microfluidic device fabrication

Integrated microfluidics is a sophisticated three-dimensional (multi layer) solution for high complexity serial or parallel processes. Fabrication of integrated microfluidic devices requires soft lithography and the stacking of thin-patterned PDMS layers. Precise layer alignment and bonding is crucial. There are no previously reported standards for alignment of the layers, which is mostly performed using uncontrolled processes with very low alignment success. As a result, integrated microfluidics is mostly used in academia rather than in the many potential industrial applications. We have designed and manufactured a semiautomatic Microfluidic Device Assembly System (μDAS) for full device production. μDAS comprises an electrooptic mechanical system consisting of four main parts: optical system, smart media holder (for PDMS), a micropositioning xyzθ system and a macropositioning XY mechanism. The use of the μDAS yielded valuable information regarding PDMS as the material for device fabrication, revealed previously unidentified errors, and enabled optimization of a robust fabrication process. In addition, we have demonstrated the utilization of the μDAS technology for fabrication of a complex 3 layered device with over 12 000 micromechanical valves and an array of 64 × 64 DNA spots on a glass substrate with high yield and high accuracy. We increased fabrication yield from 25% to about 85% with an average layer alignment error of just ∼4 μm. It also increased our protein expression yields from 80% to over 90%, allowing us to investigate more proteins per experiment. The μDAS has great potential to become a valuable tool for both advancing integrated microfluidics in academia and producing and applying microfluidic devices in the industry.

Direct Correlation between Motile Behavior and Protein Abundance in Single Cells

Understanding how stochastic molecular fluctuations affect cell behavior requires the quantification of both behavior and protein numbers in the same cells. Here, we combine automated microscopy with in situ hydrogel polymerization to measure single-cell protein expression after tracking swimming behavior. We characterized the distribution of non-genetic phenotypic diversity in Escherichia coli motility, which affects single-cell exploration. By expressing fluorescently tagged chemotaxis proteins (CheR and CheB) at different levels, we quantitatively mapped motile phenotype (tumble bias) to protein numbers using thousands of single-cell measurements. Our results disagreed with established models until we incorporated the role of CheB in receptor deamidation and the slow fluctuations in receptor methylation. Beyond refining models, our central finding is that changes in numbers of CheR and CheB affect the population mean tumble bias and its variance independently. Therefore, it is possible to adjust the degree of phenotypic diversity of a population by adjusting the global level of expression of CheR and CheB while keeping their ratio constant, which, as shown in previous studies, confers functional robustness to the system. Since genetic control of protein expression is heritable, our results suggest that non-genetic diversity in motile behavior is selectable, supporting earlier hypotheses that such diversity confers a selective advantage.

Cell-to-cell variations in protein numbers due to random fluctuations at the molecular level lead to cell-to-cell variations in behavior. To maintain predictable responses, signaling networks have evolved robustness against noise, but in some situations phenotypic diversity in a clonal population can be beneficial as a bet hedging or division of labor strategy. Investigating of how random molecular fluctuations affect cell behavior requires to measure biological parameters at different scales. Here, we report a new experiment that allows the measure of both protein numbers and behavior in cells that are free to move in their environment. Using Escherichia coli, a model system for the study of cellular behavior, we investigated the effects variations in the numbers of the chemo-receptor modification enzymes on single-cell swimming behavior. We found that the mean and variance of the behavior can be adjusted independently in the population by adjusting protein expression. This mechanism allows for the genetic selection of phenotypic diversity without disrupting correlations in protein expression that are important for the overall robustness of the chemotaxis system.

Microfluidic System for Automated Cell-based Assays

Microfluidic cell culture is a promising technology for applications in the drug screening industry. Key benefits include improved biological function, higher quality cell-based data, reduced reagent consumption, and lower cost. In this work, we demonstrate how a microfluidic cell culture design was adapted to be compatible with the standard 96-well plate format. Key design features include the elimination of tubing and connectors, the ability to maintain long term continuous perfusion cell culture using a passive gravity driven pump, and direct analysis on the outlet wells of the microfluidic plate. A single microfluidic culture plate contained 8 independent flow units, each with 10(4) cells at a flow rate of 50 μl/day (6 minute residence time). The cytotoxicity of the anti-cancer drug etoposide was measured on HeLa cells cultured in this format, using a commercial lactate dehydrogenase (LDH) plate reader assay. The integration of microfluidic cell culture methods with commercial automation capabilities offers an exciting opportunity for improved cell-based screening.

Entrainment and Control of Bacterial Populations: An in Silico Study over a Spatially Extended Agent Based Model

We extend a spatially explicit agent based model (ABM) developed previously to investigate entrainment and control of the emergent behavior of a population of synchronized oscillating cells in a microfluidic chamber. Unlike most of the work in models of control of cellular systems which focus on temporal changes, we model individual cells with spatial dependencies which may contribute to certain behavioral responses. We use the model to investigate the response of both open loop and closed loop strategies, such as proportional control (P-control), proportional-integral control (PI-control) and proportional-integral-derivative control (PID-control), to heterogeinities and growth in the cell population, variations of the control parameters and spatial effects such as diffusion in the spatially explicit setting of a microfluidic chamber setup. We show that, as expected from the theory of phase locking in dynamical systems, open loop control can only entrain the cell population in a subset of forcing periods, with a wide variety of dynamical behaviors obtained outside these regions of entrainment. Closed-loop control is shown instead to guarantee entrainment in a much wider region of control parameter space although presenting limitations when the population size increases over a certain threshold. In silico tracking experiments are also performed to validate the ability of classical control approaches to achieve other reference behaviors such as a desired constant output or a linearly varying one. All simulations are carried out in BSim, an advanced agent-based simulator of microbial population which is here extended ad hoc to include the effects of control strategies acting onto the population.

Use of Microfluidic Technology to Monitor the Differentiation and Migration of Human ESC-Derived Neural Cells

Microfluidics forms the basis of unique experimental approaches that visualize the development of neural structure using micro-scale devices and aids the guidance of neurite growth in an axonal isolation compartment. We utilized microfluidics technology to monitor the differentiation and migration of neural cells derived from human embryonic stems cells (hESC). We cocultured hESC with PA6 stromal cells and isolated neural rosette-like structures, which subsequently formed neurospheres in a suspension culture. We found that Tuj1-positive neural cells but not nestin-positive neural precursor cells (NPC) were able to enter the microfluidics grooves (microchannels), suggesting a neural cell-migratory capacity that was dependent on neuronal differentiation. We also showed that bundles of axons formed and extended into the microchannels.Taken together, these results demonstrated that microfluidics technology can provide useful tools to study neurite outgrowth and axon guidance of neural cells, which are derived from human embryonic stem cells.

Microfluidics Integrated Biosensors: A Leading Technology towards Lab-on-a-Chip and Sensing Applications

A biosensor can be defined as a compact analytical device or unit incorporating a biological or biologically derived sensitive recognition element immobilized on a physicochemical transducer to measure one or more analytes. Microfluidic systems, on the other hand, provide throughput processing, enhance transport for controlling the flow conditions, increase the mixing rate of different reagents, reduce sample and reagents volume (down to nanoliter), increase sensitivity of detection, and utilize the same platform for both sample preparation and detection. In view of these advantages, the integration of microfluidic and biosensor technologies provides the ability to merge chemical and biological components into a single platform and offers new opportunities for future biosensing applications including portability, disposability, real-time detection, unprecedented accuracies, and simultaneous analysis of different analytes in a single device. This review aims at representing advances and achievements in the field of microfluidic-based biosensing. The review also presents examples extracted from the literature to demonstrate the advantages of merging microfluidic and biosensing technologies and illustrate the versatility that such integration promises in the future biosensing for emerging areas of biological engineering, biomedical studies, point-of-care diagnostics, environmental monitoring, and precision agriculture.

Dynamic control and quantification of bacterial population dynamics in droplets

Culturing and measuring bacterial population dynamics are critical to develop insights into gene regulation or bacterial physiology. Traditional methods, based on bulk culture to obtain such quantification, have the limitations of higher cost/volume of reagents, non-amendable to small size of population and more laborious manipulation. To this end, droplet-based microfluidics represents a promising alternative that is cost-effective and high-throughput. However, difficulties in manipulating the droplet environment and monitoring encapsulated bacterial population for long-term experiments limit its utilization. To overcome these limitations, we used an electrode-free injection technology to modulate the chemical environment in droplets. This ability is critical for precise control of bacterial dynamics in droplets. Moreover, we developed a trapping device for long-term monitoring of population dynamics in individual droplets for at least 240 h. We demonstrated the utility of this new microfluidic system by quantifying population dynamics of natural and engineered bacteria. Our approach can further improve the analysis for systems and synthetic biology in terms of manipulability and high temporal resolution.