Microfabrication meets microbiology

Selective factors in the evolution of multicellularity in choanoflagellates

Choanoflagellates, unicellular eukaryotes that can form multicellular colonies by cell division and that share a common ancestor with animals, are used as a model system to study functional consequences of being unicellular versus colonial. This review examines performance differences between unicellular and multicellular choanoflagellates in swimming, feeding, and avoiding predation, to provide insights about possible selective advantages of being multicellular for the protozoan ancestors of animals. Each choanoflagellate cell propels water by beating a single flagellum and captures bacterial prey on a collar of microvilli around the flagellum. Formation of multicellular colonies does not improve the swimming performance, but the flux of prey-bearing water to the collars of some of the cells in colonies of certain configurations can be greater than for single cells. Colony geometry appears to affect whether cells in colonies catch more prey per cell per time than do unicellular choanoflagellates. Although multicellular choanoflagellates show chemokinetic behavior in response to oxygen, only the unicellular dispersal stage (fast swimmers without collars) use pH signals to aggregate in locations where bacterial prey might be abundant. Colonies produce larger hydrodynamic signals than do single cells, and raptorial protozoan predators capture colonies while ignoring single cells. In contrast, ciliate predators entrain both single cells and colonies in their feeding currents, but reject larger colonies, whereas passive heliozoan predators show no preference. Thus, the ability of choanoflagellate cells to differentiate into different morphotypes, including multicellular forms, in response to variable aquatic environments might have provided a selective advantage to the ancestors of animals.

Droplet and Microchamber-Based Digital Loop-Mediated Isothermal Amplification (dLAMP)

Digital loop-mediated isothermal amplification (dLAMP) refers to compartmentalizing nucleic acids and LAMP reagents into a large number of individual partitions, such as microchambers and droplets. This compartmentalization enables dLAMP to be an excellent platform to quantify the absolute number of the target nucleic acids. Owing to its low requirement for instrumentation complexity, high specificity, and strong tolerance to inhibitors in the nucleic acid samples, dLAMP has been recognized as a simple and accurate technique to quantify pathogenic nucleic acid. Herein, the general process of dLAMP techniques is summarized, the current dLAMP techniques are categorized, and a comprehensive discussion on different types of dLAMP techniques is presented. Also, the challenges of the current dLAMP are illustrated together with the possible strategies to address these challenges. In the end, the future directions of the dLAMP developments, including multitarget detection, multisample detection, and processing nucleic acid extraction are outlined. With recently significant advances in dLAMP, this technology has the potential to see more widespread use beyond the laboratory in the future.

Simultaneous measurement of surface and bilayer tension in a microfluidic chip

Freestanding lipid bilayers are one of the most used model systems to mimic biological cell membranes. To form an unsupported bilayer, we employ two aqueous fingers in a microfluidic chip surrounded by an oily phase that contains lipids. Upon pushing two aqueous fingers forward, their interface becomes decorated with a lipid monolayer and eventually zip to form a bilayer when the monolayers have nanoscopic contact with each other. Using this straightforward approach, the quick and easy bilayer formation is facilitated by oil draining into the microfluidic device material consisting of polydimethylsiloxane. However, the oil drainage limits the lifetime of a bilayer to about 1 h. We demonstrate that this drainage can be managed, resulting in superior bilayer stability and an increased lifetime of several hours when using a pressure-controlled system. Applying different pressures to the aqueous fingers in the microfluidic chip, the formed bilayer can even be bent to a desired curvature. Extracting the contact angle and the resulting curvature of the bilayer region, for a given applied pressure difference, both the bilayer tension and the surface tension of each lipid monolayer can be derived from a single experiment using the Young Laplace pressure equation.

An array microhabitat device with dual gradients revealed synergistic roles of nitrogen and phosphorous in the growth of microalgae

Harmful algal blooms (HABs) are an emerging environmental problem contaminating water resources and disrupting the balance of the ecosystems. HABs are caused by the sudden growth of photosynthetic algal cells in both fresh and marine water, and have been expanding in extent and appearing more frequently due to the climate change and population growth. Despite the urgency of the problem, the exact environmental conditions that trigger HABs are unknown. This is in part due to the lack of high throughput tools for screening environmental parameters in promoting the growth of photosynthetic microorganisms. In this article, we developed an array microhabitat device with well defined dual nutrient gradients suitable for quantitative studies of multiple environmental parameters in microalgal cell growth. This device enabled an ability to provide 64 different nutrient conditions [nitrogen (N), phosphorous (P), and N : P ratio] at the same time, and the gradient generation took less than 90 min, advancing the current pond and test tube assays in terms of time and cost. Using a photosynthetic algal cell line, Chlamydomonas reinhardtii, preconditioned in co-limited media, we revealed that N and P synergistically promoted cell growth. Interestingly, no discernible response was observed when single P or N gradient was imposed. Our work demonstrated the enabling capability of the microfluidic platform for screening effects of multiple environmental factors in photosynthetic cell growth, and highlighted the importance of the synergistic roles of environmental factors in algal cell growth.

Prototyping a Versatile Two-Layer Multi-Channel Microfluidic Device for Direct-Contact Cell-Vessel Co-Culture

Microfluidic devices are gaining increasing popularity due to their wide applications in various research areas. Herein, we propose a two-layer multi-channel microfluidic device allowing for direct-contact cell-vessel co-culture. Using the device, we built a co-culture model of the outer blood-retina barrier (oBRB), mimicking the in vivo retinal pigment epithelial cells-Bruch membrane-fenestrated choroids. To demonstrate the versatility of the design, we further modified the device by inserting platinum electrodes for trans-epithelial electrical resistance (TEER) measurement, demonstrating the feasibility of on-chip assessment of the epithelial barrier integrity. Our proposed design allows for direct-contact co-culture of cell–cell or cell–vessel, modifiable for real-time evaluation of the state of the epithelial monolayers.

Rapid Assessment of Water Toxicity by Plasmonic Nanomechanical Sensing

The ability to rapidly and accurately detect water toxicity is crucial for monitoring water quality and assessing toxic risk, but such detection remains a great challenge. Here, we present a plasmonic nanomechanical sensing (PNMS) system for the rapid assessment of water toxicity. This technique is based on the plasmonic sensing of the nanomechanical movement of single bacterial cells, which could be inhibited upon exposure to potential toxicants. By correlating the amplitude of nanomechanical movement with bacterial activity, we detected a variety of toxic substances in water. The direct readout of bacterial activity via PNMS allowed for a high sensitivity to toxicants in water, thereby enabling us to evaluate the acute toxicological effect of chemical compounds rapidly. The PNMS method is promising for online alerts of water quality safety and for assessing chemical hazards. We anticipate that PNMS is also suitable for a wide range of other applications, including bacterial detection and high-throughput screening of antibacterial materials.

Micro and nanoscale technologies in oral drug delivery

Oral administration is a pillar of the pharmaceutical industry and yet it remains challenging to administer hydrophilic therapeutics by the oral route. Smart and controlled oral drug delivery could bypass the physiological barriers that limit the oral delivery of these therapeutics. Micro- and nanoscale technologies, with an unprecedented ability to create, control, and measure micro- or nanoenvironments, have found tremendous applications in biology and medicine. In particular, significant advances have been made in using these technologies for oral drug delivery. In this review, we briefly describe biological barriers to oral drug delivery and micro and nanoscale fabrication technologies. Micro and nanoscale drug carriers fabricated using these technologies, including bioadhesives, microparticles, micropatches, and nanoparticles, are described. Other applications of micro and nanoscale technologies are discussed, including fabrication of devices and tissue engineering models to precisely control or assess oral drug delivery in vivo and in vitro, respectively. Strategies to advance translation of micro and nanotechnologies into clinical trials for oral drug delivery are mentioned. Finally, challenges and future prospects on further integration of micro and nanoscale technologies with oral drug delivery systems are highlighted.

Microfluidic immobilized enzyme reactors for continuous biocatalysis

This review investigates strategies for employing μ-IMERs for continuous biocatalysis via a top-down approach.

Fabrication, Characterization and Application of Biomolecule Micropatterns on Cyclic Olefin Polymer (COP) Surfaces with Adjustable Contrast

Peptide and protein micropatterns are powerful tools for the investigation of various cellular processes, including protein–protein interactions (PPIs). Within recent years, various approaches for the production of functional surfaces have been developed. Most of these systems use glass as a substrate, which has several drawbacks, including high fragility and costs, especially if implemented for fluorescence microscopy. In addition, conventional fabrication technologies such as microcontact printing (µCP) are frequently used for the transfer of biomolecules to the glass surface. In this case, it is challenging to adjust the biomolecule density. Here, we show that cyclic olefin polymer (COP) foils, with their encouraging properties, including the ease of manufacturing, chemical resistance, biocompatibility, low water absorption, and optical clarity, are a promising alternative to glass substrates for the fabrication of micropatterns. Using a photolithography-based approach, we generated streptavidin/biotinylated antibody patterns on COPs with the possibility of adjusting the pattern contrast by varying plasma activation parameters. Our experimental setup was finally successfully implemented for the analysis of PPIs in the membranes of live cells via total internal reflection fluorescence (TIRF) microscopy.

Frontiers in Microfluidics, a Teaching Resource Review

This is a literature teaching resource review for biologically inspired microfluidics courses or exploring the diverse applications of microfluidics. The structure is around key papers and model organisms. While courses gradually change over time, a focus remains on understanding how microfluidics has developed as well as what it can and cannot do for researchers. As a primary starting point, we cover micro-fluid mechanics principles and microfabrication of devices. A variety of applications are discussed using model prokaryotic and eukaryotic organisms from the set of bacteria (Escherichia coli), trypanosomes (Trypanosoma brucei), yeast (Saccharomyces cerevisiae), slime molds (Physarum polycephalum), worms (Caenorhabditis elegans), flies (Drosophila melangoster), plants (Arabidopsis thaliana), and mouse immune cells (Mus musculus). Other engineering and biochemical methods discussed include biomimetics, organ on a chip, inkjet, droplet microfluidics, biotic games, and diagnostics. While we have not yet reached the end-all lab on a chip, microfluidics can still be used effectively for specific applications.

Engineering Strategies to Improve Islet Transplantation for Type 1 Diabetes Therapy

Type 1 diabetes is an autoimmune disease in which the immune system attacks insulin-producing beta cells of pancreatic islets. Type 1 diabetes can be treated with islet transplantation; however, patients must be administered immunosuppressants to prevent immune rejection of the transplanted islets if they are not autologous or not engineered with immune protection/isolation. To overcome biological barriers of islet transplantation, encapsulation strategies have been developed and robustly investigated. While islet encapsulation can prevent the need for immunosuppressants, these approaches have not shown much success in clinical trials due to a lack of long-term insulin production. Multiple engineering strategies have been used to improve encapsulation and post-transplantation islet survival. In addition, more efficient islet cryopreservation methods have been designed to facilitate the scaling-up of islet transplantation. Other islet sources have been identified including porcine islets and stem cell-derived islet-like aggregates. Overall, islet-laden capsule transplantation has greatly improved over the past 30 years and is moving towards becoming a clinically feasible treatment for type 1 diabetes.

Engineering High-Resolution Micropatterns Directly onto Titanium with Optimized Contact Guidance to Promote Osteogenic Differentiation and Bone Regeneration

Topographical cues play an important role in directing cell behavior, and thus, extensive research efforts have been devoted to fabrication of surface patterns and exploring the contact guidance effect. However, engineering high-resolution micropatterns directly onto metallic implants remains a grand challenge. Moreover, there still lacks evidence that allows translation of in vitro screening to in vivo tissue response. Herein, we demonstrate a fast, cost-effective, and feasible approach to the precise fabrication of shape- and size-controlled micropatterns on titanium substrates using a combination of photolithography and inductively coupled plasma-based dry etching. A titanium TopoChip containing 34 microgrooved patterns with varying geometry parameters and a flat surface as the control was designed for a high-throughput in vitro study of the contact guidance of osteoblasts. The correlation between the surface pattern dimensions, cell morphological characteristics, proliferation, and osteogenic marker expression was systematically investigated in vitro. Furthermore, the surface with the highest osteogenic potential in vitro along with representative controls was evaluated in rat cranial defect models. The results show that microgrooved pattern parameters have almost no effect on osteoblast proliferation but significantly regulate the cell morphology, orientation, focal adhesion (FA) formation, and osteogenic differentiation in vitro. In particular, a specific groove pattern with a ridge width of 3 μm, groove width of 7 μm, and depth of 2 μm can most effectively align the cells through regulating the distribution of FAs, resulting in an anisotropic actin cytoskeleton, and thereby promoting osteogenic differentiation. In vivo, microcomputed tomography and histological analyses show that the optimized pattern can apparently stimulate new bone formation. This study not only offers a microfabrication method that can be extended to fabricate various shape- and size-controlled micropatterns on titanium alloys but also provides insight into the surface structure design of orthopedic and dental implants for enhanced bone regeneration.

Fully Automated Microsystem for Unmediated Electrochemical Characterization, Visualization and Monitoring of Bacteria on Solid Media; E. coli K-12: A Case Study

In this paper, we present a non-fluidic microsystem for the simultaneous visualization and electrochemical evaluation of confined, growing bacteria on solid media. Using a completely automated platform, real-time monitoring of bacterial and image-based computer characterization of growth were performed. Electrochemical tests, using Escherichia coli K-12 as the model microorganism, revealed the development of a faradaic process at the bacteria-microelectrode interface inside the microsystem, as implied by cyclic voltammetry and electrochemical impedance spectrometry measurements. The electrochemical information was used to determine the moment in which bacteria colonized the electrode-enabled area of the microsystem. This microsystem shows potential advantages for long-term electrochemical monitoring of the extracellular environment of cell culture and has been designed using readily available technologies that can be easily integrated in routine protocols. Complementarily, these methods can help elucidate fundamental questions of the electron transfer of bacterial cultures and are potentially feasible to be integrated into current characterization techniques.

Continuous focusing, fractionation and extraction of anionic analytes in a microfluidic chip

Electrokinetic focusing and separation methods, specifically ion concentration polarization focusing (ICPF), provide a very powerful and easy to use analytical tool for several scientific fields. Nevertheless, the concentrated and separated analytes are effectively trapped inside the chip in picoliter volumes. In this article we propose an ICPF device that allows continuous and selective extraction of the focused analytes. A theoretical background is presented to understand the dynamics of the system and a 1D model was developed that describes the general behavior of the system. We demonstrate the selective extraction of three fluorescent model anionic analytes and we report selective extraction of the analytes at a 300-fold increased concentration.

DropSOAC: Stabilizing Microfluidic Drops for Time-Lapse Quantification of Single-Cell Bacterial Physiology

The physiological heterogeneity of cells within a microbial population imparts resilience to stresses such as antimicrobial treatments and nutrient limitation. This resilience is partially due to a subpopulation of cells that can survive such stresses and regenerate the community. Microfluidic approaches now provide a means to study microbial physiology and bacterial heterogeneity at the single cell level, improving our ability to isolate and examine these subpopulations. Drop-based microfluidics provides a high-throughput approach to study individual cell physiology within bacterial populations. Using this approach, single cells are isolated from the population and encapsulated in growth medium dispersed in oil using a 15 μm diameter drop making microfluidic device. The drops are arranged as a packed monolayer inside a polydimethylsiloxane (PDMS) microfluidic device. Growth of thousands of individual cells in identical microenvironments can then be imaged using confocal laser scanning microscopy (CLSM). A challenge for this approach has been the maintenance of drop stability during extended time-lapse imaging. In particular, the drops do not maintain their volume over time during incubation in PDMS devices, due to fluid transport into the porous PDMS surroundings. Here, we present a strategy for PDMS device preparation that stabilizes drop position and volume within a drop array on a microfluidic chip for over 20 h. The stability of water-in-oil drops is maintained by soaking the device in a reservoir containing both water and oil in thermodynamic equilibrium. This ensures that phase equilibrium of the drop emulsion fluids within the porous PDMS material is maintained during drop incubation and imaging. We demonstrate the utility of this approach, which we label DropSOAC (Drop Stabilization On A Chip), for time-lapse studies of bacterial growth. We characterize growth of Pseudomonas aeruginosa and its Δhpf mutant derivative during resuscitation and growth following starvation. We demonstrate that growth rate and lag time heterogeneity of hundreds of individual bacterial cells can be determined starting from single isolated cells. The results show that the DropSOAC capsule provides a high-throughput approach toward studies of microbial physiology at the single cell level, and can be used to characterize physiological differences of cells from within a larger population.

Flat and microstructured polymeric membranes in organs-on-chips

In recent years, organs-on-chips (OOCs) have been developed to meet the desire for more realistic in vitro cell culture models. These systems introduce microfluidics, mechanical stretch and other physiological stimuli to in vitro models, thereby significantly enhancing their descriptive power. In most OOCs, porous polymeric membranes are used as substrates for cell culture. The polymeric material, morphology and shape of these membranes are often suboptimal, despite their importance for achieving ideal cell functionality such as cell-cell interaction and differentiation. The currently used membranes are flat and thus do not account for the shape and surface morphology of a tissue. Moreover, the polymers used for fabrication of these membranes often lack relevant characteristics, such as mechanical properties matching the tissue to be developed and/or cytocompatibility. Recently, innovative techniques have been reported for fabrication of porous membranes with suitable porosity, shape and surface morphology matching the requirements of OOCs. In this paper, we review the state of the art for developing these membranes and discuss their application in OOCs.

Microfluidic epigenomic mapping technologies for precision medicine

Epigenomic mapping of tissue samples generates critical insights into genome-wide regulations of gene activities and expressions during normal development and disease processes. Epigenomic profiling using a low number of cells produced by patient and mouse samples presents new challenges to biotechnologists. In this review, we first discuss the rationale and premise behind profiling epigenomes for precision medicine. We then examine the existing literature on applying microfluidics to facilitate low-input and high-throughput epigenomic profiling, with emphasis on technologies enabling interfacing with next-generation sequencing. We detail assays on studies of histone modifications, DNA methylation, 3D chromatin structures and non-coding RNAs. Finally, we discuss what the future may hold in terms of method development and translational potential.

Electromagnetic fields alter the motility of metastatic breast cancer cells

Interactions between cells and their environment influence key physiologic processes such as their propensity to migrate. However, directed migration controlled by extrinsically applied electrical signals is poorly understood. Using a novel microfluidic platform, we found that metastatic breast cancer cells sense and respond to the net direction of weak (∼100 µV cm-1), asymmetric, non-contact induced Electric Fields (iEFs). iEFs inhibited EGFR (Epidermal Growth Factor Receptor) activation, prevented formation of actin-rich filopodia, and hindered the motility of EGF-treated breast cancer cells. The directional effects of iEFs were nullified by inhibition of Akt phosphorylation. Moreover, iEFs in combination with Akt inhibitor reduced EGF-promoted motility below the level of untreated controls. These results represent a step towards isolating the coupling mechanism between cell motility and iEFs, provide valuable insights into how iEFs target multiple diverging cancer cell signaling mechanisms, and demonstrate that electrical signals are a fundamental regulator of cancer cell migration.

Using Wool Keratin as a Basic Resist Material to Fabricate Precise Protein Patterns

The ability to pattern natural polymers at different scales is extremely important for many research areas, such as cell culture, regenerative medicine, bioelectronics, tissue engineering, degradable implants, and photonics. For the first time, the use of wool keratin (WK) as a structural biomaterial for fabricating precise protein microarchitectures is presented. Through straightforward biochemical processes, modified WK proteins become intrinsically photoreactive without significant changes in protein structure or function. Under light irradiation, intermolecular chemical crosslinking between WK molecules can be successfully initiated by using commercially available photoinitiators. As a result, high-performance WK patterning on the micrometer scale (µm) can be achieved through a combination of water-based photolithography techniques. By simply mixing with nanoparticles, enzymes, and other dopants, various "functional WK resists" can be generated. In addition, without the addition of any cell-adhesive ligands, these patterned protein microstructures are demonstrated as bio-friendly cellular substrates for the spatial guidance of cells on their surface. Furthermore, periodic microfabricated WK structures in complex patterns that display typical iridescent behavior can be designed and formed over macroscale areas (cm).

Design of Sealable Custom-Shaped Cell Mimicries Based on Self-Assembled Monolayers on CYTOP Polymer

In bottom-up synthetic biology, one of the major methodological challenges is to provide reaction spaces that mimic biological systems with regard to topology and surface functionality. Of particular interest are cell- or organelle-shaped membrane compartments, as many protein functions unfold at lipid interfaces. However, shaping artificial cell systems using materials with non-intrusive physicochemical properties, while maintaining flexible lipid interfaces relevant to the reconstituted protein systems, is not straightforward. Herein, we develop micropatterned chambers from CYTOP, a less commonly used polymer with good chemical resistance and a refractive index matching that of water. By forming a self-assembled lipid monolayer on the polymer surface, we dramatically increased the biocompatibility of CYTOP-fabricated systems. The phospholipid interface provides an excellent passivation layer to prevent protein adhesion to the hydrophobic surface, and we succeeded in cell-free protein synthesis inside the chambers. Importantly, the chambers could be sealed after loading by a lipid monolayer, providing a novel platform to study encapsulated systems. We successfully reconstituted pole-to-pole oscillations of the Escherichia coli MinDE system, which responds dramatically to compartment geometry. Furthermore, we present a simplified fabrication of our artificial cell compartments via replica molding, making it a readily accessible technique for standard cleanroom facilities.

Microfluidic-Based Nucleic Acid Amplification Systems in Microbiology

Rapid, sensitive, and selective bacterial detection is a hot topic, because the progress in this research area has had a broad range of applications. Novel and innovative strategies for detection and identification of bacterial nucleic acids are important for practical applications. Microfluidics is an emerging technology that only requires small amounts of liquid samples. Microfluidic devices allow for rapid advances in microbiology, enabling access to methods of amplifying nucleic acid molecules and overcoming difficulties faced by conventional. In this review, we summarize the recent progress in microfluidics-based polymerase chain reaction devices for the detection of nucleic acid biomarkers. The paper also discusses the recent development of isothermal nucleic acid amplification and droplet-based microfluidics devices. We discuss recent microfluidic techniques for sample preparation prior to the amplification process.

Invariance properties of bacterial random walks in complex structures

Motile cells often explore natural environments characterized by a high degree of structural complexity. Moreover cell motility is also intrinsically noisy due to spontaneous random reorientations and speed fluctuations. This interplay of internal and external noise sources gives rise to a complex dynamical behavior that can be strongly sensitive to details and hard to model quantitatively. In striking contrast to this general picture we show that the mean residence time of swimming bacteria inside artificial complex microstructures is quantitatively predicted by a generic invariance property of random walks. We find that while external shape and internal disorder have dramatic effects on the distributions of path lengths and residence times, the corresponding mean values are constrained by the sole free surface to perimeter ratio. As a counterintuitive consequence, bacteria escape faster from structures with higher density of obstacles due to the lower accessible surface.

It has been previously shown theoretically that the average path length of random walks inside a closed domain is invariant. Here the authors demonstrate that this invariance property can be used to predict the mean residence time of swimming bacteria exploring structured micro-environments.

Functionalization and Patterning of Self-Assembled Monolayers and Polymer Brushes Using Microcontact Chemistry

Because the surface connects a material to its environment, the functionalization, modification, and patterning of surfaces is key to a wide range of materials applied in microelectronics, displays, sensing, microarrays, photovoltaics, catalysis, and other fields. Self-assembled monolayers (SAMs), which can be deposited on a wide range of inorganic materials, are only a few nanometers thick, yet they can radically change the properties of the resulting interface. Alternatively, thin polymer films composed of polymer brushes grown from the surface provide a more robust molecular modification of inorganic materials. For many applications, patterned SAMs or polymer brushes are desired. Over the past decade, our group has shown that both SAMs as well as polymer brushes can be patterned very efficiently using microcontact printing. In microcontact printing, a molecular "ink" is deposited on a suitable substrate using a microstructured elastomer stamp, which delivers the ink exclusively in the area of contact between stamp and substrate. In contrast to most types of lithography, microcontact printing does not require expensive equipment. Our work has shown that "microcontact chemistry" is a powerful additive surface patterning method, in which molecular inks react with a precursor SAM during printing so that surfaces can be modified with various orthogonal functional groups or molecular recognition sites in microscale patterns. Functional groups include reactive groups for click chemistry or photochemistry and initiators for radical polymerization. Molecular recognition sites include host-guest chemistry as well as biochemical ligands such as carbohydrates and biotin. In this Account, we present an overview of our research in this area including selected examples of work by other groups. In the first part, we review our work on the patterning of SAMs using microcontact chemistry, with a focus on click chemistry and photochemistry. We will show how cycloadditions, thiol-ene reactions, and tetrazole chemistry can be used to obtain versatile surface patterns. In the second part, we demonstrate that microcontact chemistry can be used to pattern polymer brushes. Among others, initiators for surface-induced nitroxide-mediated polymerization and atom transfer polymerization were printed and used to grow patterned polymer brushes with molecular recognition groups suitable for responsive surface adhesion. In the third part, we describe how SAMs and polymer brushes can be printed on microparticles instead of flat substrates so that Janus particles with functional patches can be obtained. Finally, we present a brief outlook on further developments expected in this field.

Integrating Microfabrication into Biological Investigations: the Benefits of Interdisciplinarity

The advent of micro and nanotechnologies, such as microfabrication, have impacted scientific research and contributed to meaningful real-world applications, to a degree seen during historic technological revolutions. Some key areas benefitting from the invention and advancement of microfabrication platforms are those of biological and biomedical sciences. Modern therapeutic approaches, involving point-of-care, precision or personalized medicine, are transitioning from the experimental phase to becoming the standard of care. At the same time, biological research benefits from the contribution of microfluidics at every level from single cell to tissue engineering and organoids studies. The aim of this commentary is to describe, through proven examples, the interdisciplinary process used to develop novel biological technologies and to emphasize the role of technical knowledge in empowering researchers who are specialized in a niche area to look beyond and innovate.

Diagnosis of feline filariasis assisted by a novel semi-automated microfluidic device in combination with high resolution melting real-time PCR

BACKGROUND

The diagnosis of filariasis traditionally relies on the detection of circulating microfilariae (mf) using Giemsa-stained thick blood smears. This approach has several limitations. We developed a semi-automated microfluidic device to improve and simplify the detection of filarial nematodes.

METHODS

The efficiency and repeatability of the microfluidic device was evaluated. Human EDTA blood samples were 'spiked' with B. malayi mf at high, moderate, and low levels, and subsequently tested 10 times. The device was also used for a field survey of feline filariasis in 383 domesticated cats in an area of Narathiwat Province, Thailand, the endemic area of Brugia malayi infection.

RESULTS

In the control blood arbitrarily spiked with mf, the high level, moderate level and low level mf-positive controls yielded coefficient variation (CV) values of 4.44, 4.16 and 4.66%, respectively, at the optimized flow rate of 6 µl/min. During the field survey of feline filariasis in Narathiwat Province, the device detected mf in the blood of 34 of 383 cats (8.9%) whereas mf were detected in 28 (7.3%) cats using the blood smear test. Genomic DNA was extracted from mf trapped in the device after which high-resolution melting (HRM) real-time PCR assay was carried out, which enabled the simultaneous diagnosis of filarial species. Among the 34 mf-positive samples, 12 were identified as B. malayi, 15 as Dirofilaria immitis and 7 as| D. repens.

CONCLUSIONS

We developed a semi-automated microfluidic device to detect mf of filarial parasites that could be used to diagnose lymphatic filariasis in human populations. This novel device facilitates rapid, higher-throughput detection and identification of infection with filariae in blood samples.

Chemotactic screening of imidazolinone-degrading bacteria by microfluidic SlipChip

The group of imidazolinone herbicides, widely used for weed control, is hazardous to some sensitive rotational crops. Thus, rapid elimination of imidazolinones from contaminated soil is significant for the environment. Biodegradation studies have demonstrated the ability of chemotaxis to enhance the biodegradation of pollutants. In this study, we used our newly developed SlipChip device for chemotactic sorting and a microfluidic streak plate device for bacterial cultivation as a new pipeline for screening imidazolinone degraders. The degradation efficiencies of an enrichment consortium and a chemotaxis consortium were determined by HPLC-MS/MS. Both consortia degraded all tested imidazolinones, with the highest efficiency (71.8%) for imazethapyr, and the chemotaxis consortium degraded these compounds approximately 10% more efficiently than the enrichment consortium. Moreover, the community diversities of the enrichment consortium and the chemotaxis consortium were analyzed by 16S rRNA gene amplicon sequencing. The results indicated that members of genus Ochrobactrum primarily contribute to the degradation of imidazolinones. This work proved that chemotaxis toward biodegradable pollutants increases their bioavailability and enhances the biodegradation rate. It also provided a new way to screen effective pollutant degraders and can be applied for the selective isolation of other chemotactic species from environmental samples.

Efficiency of the flagellar propulsion of Escherichia coli in confined microfluidic geometries

Bacterial movement in confined spaces is routinely encountered either in a natural environment or in artificial structures. Consequently, the ability to understand and predict the behavior of motile bacterial cells in confined geometries is essential to many applications, spanning from the more classical, such as the management complex microbial networks involved in diseases, biomanufacturing, mining, and environment, to the more recent, such as single cell DNA sequencing and computation with biological agents. Fortunately, the development of this understanding can be helped by the decades-long advances in semiconductor microfabrication, which allow the design and the construction of complex confining structures used as test beds for the study of bacterial motility. To this end, here we use microfabricated channels with varying sizes to study the interaction of Escherichia coli with solid confining spaces. It is shown that an optimal channel size exists for which the hydrostatic potential allows the most efficient movement of the cells. The improved understanding of how bacteria move will result in the ability to design better microfluidic structures based on their interaction with bacterial movement.

Coins in microfluidics: From mere scale objects to font of inspiration for microchannel circuits

The fabrication of microfluidic chips remains a complex and expensive process requiring specific equipment and protocols, often if not always limited to the most privileged laboratories. As an alternative to the most sophisticated methods, the present paper describes the fabrication of microfluidic chips by an approach that uses coins as positive master for the rapid production of multigeometry chips. All steps of chip production were carried out using inexpensive approaches by low-cost chemicals and equipment. The chips were validated by different "classic" microfluidic tasks, such as hydrodynamic focusing, droplets generation, micromixing, and on-chip cell culture. The use of coins is not only an efficient method for rapid prototyping but also represents an inspiring possibility for the design of new microfluidic chips. Finally, coin-inspired chips could represent a laboratory experiment doable at a high school level.

Interference Disturbance Analysis Enables Single-Cell Level Growth and Mobility Characterization for Rapid Antimicrobial Susceptibility Testing

To support the emerging battle against antimicrobial resistance (AMR), detection methods that allow fast and accurate antimicrobial susceptibility testing (AST) are urgently needed. The early identification and application of an appropriate antibiotic treatment leads to lower mortality rates and substantial cost savings and prevents the development of resistant pathogens. In this work, we present a diffraction-based method, which is capable of quantitative bacterial growth, mobility, and susceptibility measurements. The method is based on the temporal analysis of the intensity of a light diffraction peak, which arises due to interference at a periodic pattern of gold nanostructures. The presence of bacteria disturbs the constructive interference, leading to an intensity decrease and thus allows the monitoring of bacterial growth in very low volumes. We demonstrate the direct correlation of the decrease in diffraction peak intensity with bacterial cell number starting from single cells and show the capability for rapid high-throughput AST measurements by determining the minimum inhibitory concentration for three different antimicrobials in less than 2-3 h as well as the susceptibility in less than 30-40 min. Furthermore, bacterial mobility is obtained from short-term fluctuations of the diffraction peak intensity and is shown to decrease by a factor of 3 during bacterial attachment to a surface. This multiparameter detection method allows for rapid AST of planktonic and of biofilm-forming bacterial strains in low volumes and in real-time without the need of high initial cell numbers.

Engineering Bacterial Shape Using Soft Matter Microchambers

This article describes the design and fabrication of microchambers that are used for the study of bacterial cells. The design allows for the confinement and precise manipulation of bacterial cell shape. The application of fluorescent dyes and fluorescent proteins enables the precise analysis of the localization of biomolecules within confined bacterial cell. This article also outlines three methods to engineer cell shape from a filamentous cell type and from spheroplasts without a cell wall using soft lithography-based technologies. © 2018 by John Wiley & Sons, Inc.

Correlative light and electron microscopy for complex cellular structures on PDMS substrates with coded micro-patterns

Fluorescence light microscopy (FLM) is commonly used for localizing specific cellular and subcellular targets. Electron microscopy (EM), on the other hand, can reveal ultrastructural details of cellular architectures beyond the limit of optical resolution. Correlative light and electron microscopy (CLEM) that combines the two techniques has proven valuable in various cell biological applications that require both specificity and resolution. Here, we report an efficient and easy-to-use CLEM system, and its applications in studying neuronal synapses. The system utilizes patterned symbols to encode coordinates on micro-fabricated polydimethylsiloxane (PDMS) substrates, on which dissociated primary hippocampal neurons grow and form synaptic connections. After imaging and localizing specifically labeled synapses with FLM, samples are embedded in resin blocks and sectioned for EM analysis. The patterned symbols on PDMS substrates provide coordinate information, allowing efficient co-registration between FLM and EM images with high precision. A custom-developed software package achieves automated EM image collection, FLM/EM alignment, and EM navigation. With this CLEM system, we have obtained high quality electron tomograms of fluorescently labeled synapses along dendrites of hippocampal neurons and analyzed docking statistics of synaptic vesicles (SVs) in different subtypes of excitatory synapses. This technique provides an efficient approach to combine functional studies with ultrastructural analysis of heterogeneous neuronal synapses, as well as other subcellular structures in general.

Surface Modification by Combination of Dip-Pen Nanolithography and Soft Lithography for Reduction of Bacterial Adhesion

Dip-pen nanolithography (DPN) and soft lithography are techniques suitable to modify the surface of biomaterials. Modified surfaces might play a role in modulating cells and reducing bacterial adhesion and biofilm formation. The main objective of this study was threefold: first, to create patterns at microscale on model surfaces using DPN; second, to duplicate and transfer these patterns to a real biomaterial surface using a microstamping technique; and finally, to assess bacterial adhesion to these developed patterned surfaces using the cariogenic species Streptococcus mutans. DPN was used with a polymeric adhesive to create dot patterns on model surfaces. Elastomeric polydimethylsiloxane was used to duplicate the patterns and silica sol to transfer them to the medical grade stainless steel 316L surface by microstamping. Optical microscopy and atomic force microscopy (AFM) were used to characterize the patterns. S. mutans adhesion was assessed by colony-forming units (CFUs), MTT viability assay, and scanning electron microscopy (SEM). DPN allowed creating microarrays from 1 to 5 µm in diameter on model surfaces that were successfully transferred to the stainless steel 316L surface via microstamping. A significant reduction up to one order of magnitude in bacterial adhesion to micropatterned surfaces was observed. The presented experimental approach may be used to create patterns at microscale on a surface and transfer them to other surfaces of interest. A reduction in bacterial adhesion to patterned surfaces might have a major impact since adhesion is a key step in biofilm formation and development of biomaterial-related infections.

On-Chip Isoniazid Exposure of Mycobacterium smegmatis Penicillin-Binding Protein (PBP) Mutant Using Time-Lapse Fluorescent Microscopy

Antibiotic resistance has been one of the biggest threats to global health. Despite the available prevention and control strategies and efforts in developing new antibiotics, the need remains for effective approaches against antibiotic resistance. Efficient strategies to cope with antimicrobial resistance require a quantitative and deeper understanding of microbial behavior, which can be obtained using different techniques to provide the missing pieces of the current antibiotic-resistance puzzle. Microfluidic-microscopy techniques are among the most promising methods that contribute modernization of traditional assays in microbiology. They provide monitoring and manipulation of cells at micro-scale volumes. Here, we combined population-level, culture-based assays with single-cell resolution, microfluidic-microscopy systems to investigate isoniazid response of Mycobacterium smegmatis penicillin-binding protein (PBP) mutant. This mutant exhibited normal growth in plain medium and sensitivity to stress responses when treated with thermal stress (45 °C), detergent stress (0.1% sodium dodecyl sulfate), acid stress (pH 4.5), and nutrient starvation (1XPBS). The impact of msm0031 transposon insertion on drug-mediated killing was determined for isoniazid (INH, 50 µg/mL), rifampicin (RIF, 200 µg/mL), ethionamide (ETH, 200 µg/mL), and ethambutol (EMB, 5 µg/mL). The PBP mutant demonstrated remarkable isoniazid-killing phenotype in batch culture. Therefore, we hypothesized that single-cell analysis will show increased lysis kinetics and fewer intact cells after drug treatment. However, the single-cell analysis data showed that upon isoniazid exposure, the percentage of the intact PBP mutant cells was 24%, while the percentage of the intact wild-type cells was 4.6%. The PBP mutant cells exhibited decreased cell-lysis profile. Therefore, the traditional culture-based assays were not sufficient to provide insights about the subpopulation of viable but non-culture cells. Consequently, we need more adequate tools to be able to comprehend and fight the antibiotic resistance of bacteria.

A novel approach to create an antibacterial surface using titanium dioxide and a combination of dip-pen nanolithography and soft lithography

Soft lithography and Dip-Pen Nanolithography (DPN) are techniques that have been used to modify the surface of biomaterials. Modified surfaces play a role in reducing bacterial adhesion and biofilm formation. Also, titanium dioxide has been reported as an antibacterial substance due to its photocatalytic effect. This work aimed at creating patterns on model surfaces using DPN and soft lithography combined with titanium dioxide to create functional antibacterial micropatterned surfaces, which were tested against Streptococcus mutans. DPN was used to create a master pattern onto a model surface and microstamping was performed to duplicate and transfer such patterns to medical-grade stainless steel 316L using a suspension of TiO₂. Modified SS316L plates were subjected to UVA black light as photocatalytic activator. Patterns were characterized by atomic force microscopy and biologically evaluated using S. mutans. A significant reduction of up to 60% in bacterial adhesion to TiO₂ -coated and -micropatterned surfaces was observed. Moreover, both TiO₂ surfaces reduced the viability of adhered bacteria after UV exposure. TiO₂ micropatterned demonstrated a synergic effect between physical and chemical modification against S. mutans. This dual effect was enhanced by increasing TiO₂ concentration. This novel approach may be a promising alternative to reduce bacterial adhesion to surfaces.

Functional detection of the original generation of hippocampal cells planted on to the micro-fluidic chip with artificial neuronal network using the patch clamp recording technique: a preliminary study

PURPOSE

The design of pattern that limits the hippocampal cells growth is an important explore for realizing a simplified artificial neuronal network in vitro.

MATERIALS AND METHODS

In this study, we examined the pattern in micro-fluidic chip to stipulate the hippocampal cells adhesion, growth and the formation of a functional neuronal network in vitro. Patch clamp recording technique was used to detect the growth situation and biological function of the haippocampal cells on the micro-fluidic chip which could simulate environment in vivo.

RESULTS

We showed that the number of neurons cultured was about 5000-6000 cells on the micro-fluidic chip, which was conductive to the hippocampal cells growth. The result of patch clamp recording technique showed the signals of sodium and potassium channels, meanwhile, it also revealed the signals of synaptic connection.

CONCLUSIONS

These findings involve placing cells in specific locations to create organized structures, and explore the spread function of synaptic on the micro-fluidic chip.

Point-of-care microfluidic devices for pathogen detection

The rapid diagnosis of pathogens is crucial in the early stages of treatment of diseases where the choice of the correct drug can be critical. Although conventional cell culture-based techniques have been widely utilized in clinical applications, newly introduced optical-based, microfluidic chips are becoming attractive. The advantages of the novel methods compared to the conventional techniques comprise more rapid diagnosis, lower consumption of patient sample and valuable reagents, easy application, and high reproducibility in the detection of pathogens. The miniaturized channels used in microfluidic systems simulate interactions between cells and reagents in microchannel structures, and evaluate the interactions between biological moieties to enable diagnosis of microorganisms. The overarching goal of this review is to provide a summary of the development of microfluidic biochips and to comprehensively discuss different applications of microfluidic biochips in the detection of pathogens. New types of microfluidic systems and novel techniques for viral pathogen detection (e.g. HIV, HVB, ZIKV) are covered. Next generation techniques relying on high sensitivity, specificity, lower consumption of precious reagents, suggest that rapid generation of results can be achieved via optical based detection of bacterial cells. The introduction of smartphones to replace microscope based observation has substantially improved cell detection, and allows facile data processing and transfer for presentation purposes.

Lift-off cell lithography for cell patterning with clean background

We developed a highly efficient method for patterning cells by a novel and simple technique called lift-off cell lithography (LCL). Our approach borrows the key concept of lift-off lithography from microfabrication and utilizes a fully biocompatible process to achieve high-throughput, high-efficiency cell patterning with nearly zero background defects across a large surface area. Using LCL, we reproducibly achieved >70% patterning efficiency for both adherent and non-adherent cells with <1% defects in undesired areas.

Real-Time Study of Rapid Spread of Antibiotic Resistance Plasmid in Biofilm Using Microfluidics

Gene transfer in biofilms is known to play an important role in antibiotic resistance dissemination. However, the process remains poorly understood. In this study, microfluidics with time-lapse imaging was used for real-time monitoring of plasmid-mediated horizontal gene transfer (HGT) in biofilms. Pseudomonas putida KT2440 harboring an antibiotic resistance plasmid RP4 was chosen as the donor while Escherichia coli and activated sludge bacteria were used as the recipient cells. Dynamic features of the transfer process, including the transfer rate, cell growth rate and kinetic changes of the transfer frequency, were determined. It was found that the routes for gene transfer strongly depend on the structure and composition of a biofilm. While intraspecies HGT is essential to initiate a transfer event, the secondary retransfer from transconjugants to the same species is more efficient and can cause cascading gene spread in single-strain biofilms. For the activated sludge biofilm, only small and scattered colonies formed and vertical gene transfer appears to be the dominant route after initial intraspecies transfer. Furthermore, more than 46% of genera in the activated sludge were permissive to plasmid RP4, many of which are associated with human pathogens. These phenomena imply early prevention and interruptions to biofilm structure could provide an effect way to inhibit rapid antibiotic resistance gene spread and reduce the likelihood of catastrophic events associated with antibiotic resistance.

Bacterial Sexuality at the Nanoscale

Understanding the basic mechanisms of bacterial sexuality is an important topic in current microbiology and biotechnology. While classical methods used to study gene transfer provide information on whole cell populations, nanotechnologies offer new opportunities for analyzing the behavior of individual mating partners. We introduce an innovative atomic force microscopy (AFM) platform to study and mechanically control DNA transfer between single bacteria, focusing on the large conjugative pXO16 plasmid of the Gram-positive bacterium Bacillus thuringiensis. We demonstrate that the adhesion forces between single donor and recipient cells are very strong (∼2 nN). Using a mutant plasmid, we find that these high forces are mediated by a pXO16 aggregation locus that contains two large surface protein genes. Notably, we also show that AFM can be used to mechanically induce plasmid transfer between single partners, revealing that transfer is very fast (<15 min) and triggers major cell surface changes in transconjugant cells. We anticipate that the single-cell technology developed here will enable researchers to mechanically control gene transfer among a wide range of Gram-positive and Gram-negative bacterial species and to understand the molecular forces involved. Also, the method could be useful in nanomedicine for the design of antiadhesion compounds capable of preventing intimate cell-cell contacts, therefore providing a means to control the resistance and virulence of bacterial pathogens.

A self-sufficient pressure pump using latex balloons for microfluidic applications

Here, we demonstrate a self-sufficient, inexpensive and disposable pressure pump using commercially available latex balloons. The versatility of the pump is demonstrated against various microfluidic structures, liquid viscosities, and ambient temperatures. The flow rate of the pump can be controlled by varying the size and thickness of the balloon. Importantly, the soft structure of the balloon allows for almost instantaneous change of the flow rate upon manual squeezing of the balloon. This feature has been used for dynamically changing the flow ratio of parallel streams in a T-shaped channel or varying the size of droplets in a droplet generation system. The self-sufficiency, simplicity of fabrication and operation, along with the low-cost of the balloon pump facilitate the widespread application of microfluidic technologies for various research, education, and in situ monitoring purposes.

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.

A bacterial antibiotic resistance accelerator and applications

The systematic emergence of drug resistance remains a major problem in the treatment of infectious diseases (antibiotics) and cancer (chemotherapy), with possible common fundamental origins linking bacterial antibiotic resistance and emergence of chemotherapy resistance. The common link may be evolution in a complex fitness landscape with connected small population niches. We report a detailed method for observing bacterial adaptive behavior in heterogeneous microfluidic environment designed to mimic the environmental heterogeneity found in natural microbial niches. First, the device is structured with multiple connected micro-chambers that allow the cell population to communicate and organize into smaller populations. Second, bacteria evolve within an antibiotic gradient generated throughout the micro-chambers that creates a wide range of fitness landscapes. High-resolution images of the adaptive response to the antibiotic stress are captured by epifluorescence microscopy at various levels of the bacterial organization for quantitative analysis. Thus, the experimental setup we have developed provides a powerful frame for visualizing evolution at work: bacterial movement, survival and death. It also presents a basis for exploring the rates at which drug resistance arises in bacteria and other biological contexts such as cancer.

Simple and Precise Counting of Viable Bacteria by Resazurin-Amplified Picoarray Detection

Simple, fast, and precise counting of viable bacteria is fundamental to a variety of microbiological applications such as food quality monitoring and clinical diagnosis. To this end, agar plating, microscopy, and emerging microfluidic devices for single bacteria detection have provided useful means for counting viable bacteria, but they also have their limitations ranging from complexity, time, and inaccuracy. We present herein our new method RAPiD (Resazurin-Amplified Picoarray Detection) for addressing this important problem. In RAPiD, we employ vacuum-assisted sample loading and oil-driven sample digitization to stochastically confine single bacteria in Picoarray, a microfluidic device with picoliter-sized isolation chambers (picochambers), in <30 s with only a few minutes of hands-on time. We add AlamarBlue, a resazurin-based fluorescent dye for bacterial growth, in our assay to accelerate the detection of "microcolonies" proliferated from single bacteria within picochambers. Detecting fluorescence in picochambers as an amplified surrogate for bacterial cells allows us to count hundreds of microcolonies with a single image taken via wide-field fluorescence microscopy. We have also expanded our method to practically test multiple titrations from a single bacterial sample in parallel. Using this expanded "multi-RAPiD" strategy, we can quantify viable cells in E. coli and S. aureus samples with precision in ∼3 h, illustrating RAPiD as a promising new method for counting viable bacteria for microbiological applications.

"Do-it-in-classroom" fabrication of microfluidic systems by replica moulding of pasta structures

Here, we describe a novel method for fabrication of microfluidic structures in classroom environments. This method is based on replica moulding of pasta structures in polydimethylsiloxane. Placing pasta structures on a petroleum jelly base layer enables templating round-shaped structures with controllable cross-sectional profiles. The pasta structures can be easily deformed and combined to create more complex 3D microfluidic structures. Proof-of-concept experiments indicate the capability of this method for studying the mixing of neighbouring flows, generation of droplets, lateral migration of particles, as well as culturing, shear stress stimulation, and imaging of cells. Our "do-it-in-classroom" method bridges the gap between the classroom and the laboratory.