Microtechnologies and nanotechnologies for single-cell analysis

Continuous microfluidic flow-through protocol for selective and image-activated electroporation of single cells

Electroporation of cells is a widely-used tool to transport molecules such as proteins or nucleic acids into cells or to extract cellular material. However, bulk methods for electroporation do not offer the possibility to selectively porate subpopulations or single cells in heterogeneous cell samples. To achieve this, either presorting or complex single-cell technologies are required currently. In this work, we present a microfluidic flow protocol for selective electroporation of predefined target cells identified in real-time by high-quality microscopic image analysis of fluorescence and transmitted light. While traveling through the microchannel, the cells are focused by dielectrophoretic forces into the microscopic detection area, where they are classified based on image analysis techniques. Finally, the cells are forwarded to a poration electrode and only the target cells are pulsed. By processing a heterogenically stained cell sample, we were able to selectively porate only target cells (green-fluorescent) while non-target cells (blue-fluorescent) remained unaffected. We achieved highly selective poration with >90% specificity at average poration rates of >50% and throughputs of up to 7200 cells per hour.

Micro-Technologies for Assessing Microbial Dynamics in Controlled Environments

With recent advances in microfabrication technologies, the miniaturization of traditional culturing techniques has provided ideal methods for interrogating microbial communities in a confined and finely controlled environment. Micro-technologies offer high-throughput screening and analysis, reduced experimental time and resources, and have low footprint. More importantly, they provide access to culturing microbes in situ in their natural environments and similarly, offer optical access to real-time dynamics under a microscope. Utilizing micro-technologies for the discovery, isolation and cultivation of "unculturable" species will propel many fields forward; drug discovery, point-of-care diagnostics, and fundamental studies in microbial community behaviors rely on the exploration of novel metabolic pathways. However, micro-technologies are still largely proof-of-concept, and scalability and commercialization of micro-technologies will require increased accessibility to expensive equipment and resources, as well as simpler designs for usability. Here, we discuss three different miniaturized culturing practices; including microarrays, micromachined devices, and microfluidics; advancements to the field, and perceived challenges.

Three-dimensional protein microarrays fabricated on reactive microsphere modified COC substrates

Fabrication of three-dimensional (3D) surface structures for the high density immobilization of biomolecules is an effective way to prepare highly sensitive biochips. In this work, a strategy to attach polymeric microspheres on a cyclic olefin copolymer (COC) substrate for the preparation of a 3D protein chip was developed. The COC surface was firstly functionalized by the photograft technique with epoxy groups, which were subsequently converted to amine groups. Then monodisperse poly(styrene-alt-maleic anhydride) (PSM) copolymer microspheres were prepared by self-stabilized precipitation polymerization and deposited as a single layer on a modified COC surface to form a 3D surface texture. The surface roughness of the COC support undergoes a significant increase from 1.4 nm to 37.1 nm after deposition of PSM microspheres with a size of 460 nm, and the modified COC still maintains a transmittance of more than 63% at the fluorescence excitation wavelengths (555 nm and 647 nm). The immobilization efficiency of immunoglobulin G (IgG) on the 3D surface reached 75.6% and the immobilization density was calculated to be 0.255 μg cm^-2, at a probe protein concentration of 200 μg mL^-1. The 3D protein microarray can be rapidly blocked by gaseous ethylenediamine within 10 minutes due to the high reactivity of anhydride groups in PSM microspheres. Immunoassay results show that the 3D protein microarray achieved specific identification of the target protein with a linear detection range from 6.25 ng mL^-1 to 250 ng mL^-1 (R² > 0.99) and a limit of detection of 8.87 ng mL^-1. This strategy offers a novel way to develop high performance polymer-based 3D protein chips.

Droplet flow cytometry for single-cell analysis

The interrogation of single cells has revolutionised biology and medicine by providing crucial unparalleled insights into cell-to-cell heterogeneity. Flow cytometry (including fluorescence-activated cell sorting) is one of the most versatile and high-throughput approaches for single-cell analysis by detecting multiple fluorescence parameters of individual cells in aqueous suspension as they flow past through a focus of excitation lasers. However, this approach relies on the expression of cell surface and intracellular biomarkers, which inevitably lacks spatial and temporal phenotypes and activities of cells, such as secreted proteins, extracellular metabolite production, and proliferation. Droplet microfluidics has recently emerged as a powerful tool for the encapsulation and manipulation of thousands to millions of individual cells within pico-litre microdroplets. Integrating flow cytometry with microdroplet architectures surrounded by aqueous solutions (e.g., water-in-oil-in-water (W/O/W) double emulsion and hydrogel droplets) opens avenues for new cellular assays linking cell phenotypes to genotypes at the single-cell level. In this review, we discuss the capabilities and applications of droplet flow cytometry (DFC). This unique technique uses standard commercially available flow cytometry instruments to characterise or select individual microdroplets containing single cells of interest. We explore current challenges associated with DFC and present our visions for future development.

Microtechnology-enabled filtration-based liquid biopsy: challenges and practical considerations

Liquid biopsy, an important enabling technology for early diagnosis and dynamic monitoring of cancer, has drawn extensive attention in the past decade. With the rapid developments of microtechnology, it has been possible to manipulate cells at the single-cell level, which dramatically improves the liquid biopsy capability. As the microtechnology-enabled liquid biopsy matures from proof-of-concept demonstrations towards practical applications, a main challenge it is facing now is to process clinical samples which are usually of a large volume while containing very rare targeted cells in complex backgrounds. Therefore, a high-throughput liquid biopsy which is capable of processing liquid samples with a large volume in a reasonable time along with a high recovery rate of rare targeted cells from complex clinical liquids is in high demand. Moreover, the purity, viability and release feasibility of recovered targeted cells are the other three key impact factors requiring careful considerations. To date, among the developed techniques, micropore-type filtration has been acknowledged as the most promising solution to address the aforementioned challenges in practical applications. However, the presently reported studies about micropore-type filtration are mostly based on trial and error for device designs aiming at different cancer types, which requires lots of efforts. Therefore, there is an urgent need to investigate and elaborate the fundamental theories of micropore-type filtration and key features that influence the working performances in the liquid biopsy of real clinical samples to promote the application efficacy in practical applications. In this review, the state of the art of microtechnology-enabled filtration is systematically and comprehensively summarized. Four key features of the filtration, including throughput, purity, viability and release feasibility of the captured targeted cells, are elaborated to provide the guidelines for filter designs. The recent progress in the filtration mode modulation and sample standardization to improve the filtration performance of real clinical samples is also discussed. Finally, this review concludes with prospective views for future developments of filtration-based liquid biopsy to promote its application efficacy in clinical practice.

A Numerical Investigation on the Collision Behavior of Unequal-Sized Micro-Nano Droplets

Micro-nano droplet collisions are fundamental phenomena in the applications of nanocoating, nano spray, and microfluidics. Detailed investigations of the process of the droplet collisions under higher Weber are still lacking when compared with previous research studies under a low Weber number below 120. Collision dynamics of unequal-sized micro-nano droplets are simulated by a coupled level-set and volume of fluid (CLSVOF) method with adaptive mesh refinement (AMR). The effects of the size ratio (from 0.25 to 0.75) and different initial collision velocities on the head-on collision process of two unequal-sized droplets at We = 210 are studied. Complex droplets will form the filament structure and break up with satellite droplets under higher Weber. The filament structure is easier to disengage from the complex droplet as the size ratio increases. The surface energy converting from kinetic energy increases with the size ratio, which promotes a better spreading effect. When two droplets keep the constant relative velocity, the motion tendency of the droplets after the collision is mainly dominated by the large droplet. On one hand, compared with binary equal-sized droplet collisions, a hole-like structure can be observed more clearly since the initial velocity of a large droplet decreases in the deformation process of binary unequal-sized droplets. On the other hand, the rim spreads outward as the initial velocity of the larger droplet increases, which leads to its thickening.

Emerging technologies for profiling extracellular vesicle heterogeneity

Extracellular vesicles (EVs) are membrane-bound vesicles secreted by most cell types and exist in virtually all bodily fluids. They carry on a wealth of proteomic and genetic information including proteins, lipids, miRNAs, mRNA, non-coding RNA and other molecules from parental cells. Increasing evidence shows that within populations of EVs, their biogenesis, physical characteristics (e.g. size, density, morphology) and cargos (e.g. protein, lipid content, nucleic acids) may vary substantially, which accordingly change their biological properties. To fully exploit the potential of EVs, it requires qualified methods to profile EV heterogeneity. In this review, we survey recent approaches for EV isolation with innovative discoveries in heterogeneity. The main challenges in EV heterogeneity research are identified, and the roles of single cell EV profiling and single EV imaging are highlighted. We further discuss promising opportunities for resolving the underlying complexity of EV heterogeneity.

Single-Probe Mass Spectrometry Analysis of Metabolites in Single Cells

Mass spectrometry (MS) is an indispensable analytical technique for bioanalysis. Based on the measurement of mass/charge ratios (m/z) of ions, MS can be used for sensitive detection and accurate identification of species of interest. In traditional studies, MS is utilized to measure analytes in prepared solutions or gas-phase samples. Benefited from recent development of sampling and ionization approaches, MS has been extensively applied to the analysis of broad ranges of biological samples. We have developed a new device, the Single-probe, that can be used for in situ, real-time MS analysis of metabolites inside individual living cells. The Single-probe is a miniaturized multifunctional sampling and ionization device that is directly coupled to the mass spectrometer. With a sampling tip size smaller than 10 μm, we can insert the Single-probe tip into single cells to extract intracellular compounds, which are analyzed using MS in real-time. We have successfully used the Single-probe MS technique to detect a variety of endogenous and exogenous cellular metabolites in individual eukaryotic cells. Single cell mass spectrometry (SCMS) is a new scientific technology that has the potential to reshape approaches in biological and pharmaceutical bioanalytical research.

A One-Sided Acoustic Trap for Cell Immobilization Using 30-MHz Array Transducer

Biological studies often involve the investigation of immobilized (or trapped) particles and cells. Various trapping methods without touching, such as optical, magnetic, and acoustic tweezers, have been developed to trap small particles. Here, we present the manipulation of a single cell or multiple cells using ultrasound-array-based single-beam acoustic tweezers (UA-SBATs). In SBATs, only a one-sided tightly focused acoustic beam produces a high acoustic gradient force-a mechanism that mirrors that of optical tweezers. As a result, targeted cells can be attracted to the beam center and immobilized within its trapping zone. Since an array transducer allows acoustic beam steering and scanning electronically instead of mechanical translation, it can manipulate cells more simply and quickly compared with single-element transducers, especially in biocompatible setup. In this experiment, a customized 30-MHz array transducer with an interdigitally bonded (IB) 2-2 piezocomposite was employed to immobilize MCF-12F cells. Cells were attracted to the center of the beam and laterally displaced with the array transducer without any damages to the cells. These findings suggest that UA-SBAT can be a promising tool for cell manipulation and may pave the way for exploring new biological applications.

A versatile cancer cell trapping and 1D migration assay in a microfluidic device

Highly migratory cancer cells often lead to metastasis and recurrence and are responsible for the high mortality rates in many cancers despite aggressive treatment. Recently, the migratory behavior of patient-derived glioblastoma multiforme cells on microtracks has shown potential in predicting the likelihood of recurrence, while at the same time, antimetastasis drugs have been developed which require simple yet relevant high-throughput screening systems. However, robust in vitro platforms which can reliably seed single cells and measure their migration while mimicking the physiological tumor microenvironment have not been demonstrated. In this study, we demonstrate a microfluidic device which hydrodynamically seeds single cancer cells onto stamped or femtosecond laser ablated polystyrene microtracks, promoting 1D migratory behavior due to the cells' tendency to follow topographical cues. Using time-lapse microscopy, we found that single U87 glioblastoma multiforme cells migrated more slowly on laser ablated microtracks compared to stamped microtracks of equal width and spacing (p < 0.05) and exhibited greater directional persistence on both 1D patterns compared to flat polystyrene (p < 0.05). Single-cell morphologies also differed significantly between flat and 1D patterns, with cells on 1D substrates exhibiting higher aspect ratios and less circularity (p < 0.05). This microfluidic platform could lead to automated quantification of single-cell migratory behavior due to the high predictability of hydrodynamic seeding and guided 1D migration, an important step to realizing the potential of microfluidic migration assays for drug screening and individualized medicine.

Mass Spectrometry Measurement of Single Suspended Cells Using a Combined Cell Manipulation System and a Single-Probe Device

Existing single cell mass spectrometry (SCMS) sampling platforms are largely designed to work only with immobilized cells and not the suspended cells isolated from patient samples. Here, we present a novel method that integrates a commercially available cell manipulation system commonly used for in vitro fertilization with the Single-probe SCMS sampling technology. The combined Single-probe SCMS/cell manipulating platform is capable of rapidly analyzing intracellular species in real time from a suspension leukemia cell line. A broad range of molecular species was detected, and species of interest were verified using tandem MS (MS/MS). Experimental results were analyzed utilizing statistical analyses such as principle component analysis (PCA) and  t-tests. The developed SCMS/cell manipulation system is a versatile tool to provide rapid single cell analysis of broad types of patient cell samples.

True one cell chemical analysis: a review

The constantly growing field of True One Cell (TOC) analysis has provided important information on the direct chemical composition of various cells and cellular components.

Fluorescent analysis of bioactive molecules in single cells based on microfluidic chips

Single-cell analysis of bioactive molecules is an essential strategy for a better understanding of cell biology, exploring cell heterogeneity, and improvement of the ability to detect early diseases. In single-cell analysis, highly efficient single-cell manipulation techniques and high-sensitive detection schemes are in urgent need. The rapid development of fluorescent analysis techniques combined with microfluidic chips have offered a widely applicable solution. Thus, in this review, we mainly focus on the application of fluorescence methods in components analysis on microchips at a single-cell level. By targeting different types of biological molecules in cells such as nucleic acids, proteins, and active small molecules, we specially introduce and comment on their corresponding fluorescent probes, fluorescence labelling and sensing strategies, and different fluorescence detection instruments used in single-cell analysis on a microfluidic chip. We hope that through this review, readers will have a better understanding of single-cell fluorescence analysis, especially for single-cell component fluorescence analysis based on microfluidic chips.

Platforms for Single-Cell Collection and Analysis

Single-cell analysis has become an established method to study cell heterogeneity and for rare cell characterization. Despite the high cost and technical constraints, applications are increasing every year in all fields of biology. Following the trend, there is a tremendous development of tools for single-cell analysis, especially in the RNA sequencing field. Every improvement increases sensitivity and throughput. Collecting a large amount of data also stimulates the development of new approaches for bioinformatic analysis and interpretation. However, the essential requirement for any analysis is the collection of single cells of high quality. The single-cell isolation must be fast, effective, and gentle to maintain the native expression profiles. Classical methods for single-cell isolation are micromanipulation, microdissection, and fluorescence-activated cell sorting (FACS). In the last decade several new and highly efficient approaches have been developed, which not just supplement but may fully replace the traditional ones. These new techniques are based on microfluidic chips, droplets, micro-well plates, and automatic collection of cells using capillaries, magnets, an electric field, or a punching probe. In this review we summarize the current methods and developments in this field. We discuss the advantages of the different commercially available platforms and their applicability, and also provide remarks on future developments.

Potential applications and human biosafety of nanomaterials used in nanomedicine

With the rapid development of nanotechnology, potential applications of nanomaterials in medicine have been widely researched in recent years. Nanomaterials themselves can be used as image agents or therapeutic drugs, and for drug and gene delivery, biological devices, nanoelectronic biosensors or molecular nanotechnology. As the composition, morphology, chemical properties, implant sites as well as potential applications become more and more complex, human biosafety of nanomaterials for clinical use has become a major concern. If nanoparticles accumulate in the human body or interact with the body molecules or chemical components, health risks may also occur. Accordingly, the unique chemical and physical properties, potential applications in medical fields, as well as human biosafety in clinical trials are reviewed in this study. Finally, this article tries to give some suggestions for future work in nanomedicine research. Copyright © 2017 John Wiley & Sons, Ltd.

Digital Assays Part II: Digital Protein and Cell Assays

A digital assay is one in which the sample is partitioned into many containers such that each partition contains a discrete number of biological entities (0, 1, 2, 3, . . .). A powerful technique in the biologist’s toolkit, digital assays bring a new level of precision in quantifying nucleic acids, measuring proteins and their enzymatic activity, and probing single-cell genotype and phenotype. Where part I of this review focused on the fundamentals of partitioning and digital PCR, part II turns its attention to digital protein and cell assays. Digital enzyme assays measure the kinetics of single proteins with enzymatic activity. Digital enzyme-linked immunoassays (ELISAs) quantify antigenic proteins with 2 to 3 log lower detection limit than conventional ELISA, making them well suited for low-abundance biomarkers. Digital cell assays probe single-cell genotype and phenotype, including gene expression, intracellular and surface proteins, metabolic activity, cytotoxicity, and transcriptomes (scRNA-seq). These methods exploit partitioning to 1) isolate single cells or proteins, 2) detect their activity via enzymatic amplification, and 3) tag them individually by coencapsulating them with molecular barcodes. When scaled, digital assays reveal stochastic differences between proteins or cells within a population, a key to understanding biological heterogeneity. This review is intended to give a broad perspective to scientists interested in adopting digital assays into their workflows.

Multifunctional, inexpensive, and reusable nanoparticle-printed biochip for cell manipulation and diagnosis

Isolation and characterization of rare cells and molecules from a heterogeneous population is of critical importance in diagnosis of common lethal diseases such as malaria, tuberculosis, HIV, and cancer. For the developing world, point-of-care (POC) diagnostics design must account for limited funds, modest public health infrastructure, and low power availability. To address these challenges, here we integrate microfluidics, electronics, and inkjet printing to build an ultra-low-cost, rapid, and miniaturized lab-on-a-chip (LOC) platform. This platform can perform label-free and rapid single-cell capture, efficient cellular manipulation, rare-cell isolation, selective analytical separation of biological species, sorting, concentration, positioning, enumeration, and characterization. The miniaturized format allows for small sample and reagent volumes. By keeping the electronics separate from microfluidic chips, the former can be reused and device lifetime is extended. Perhaps most notably, the device manufacturing is significantly less expensive, time-consuming, and complex than traditional LOC platforms, requiring only an inkjet printer rather than skilled personnel and clean-room facilities. Production only takes 20 min (vs. up to weeks) and $0.01-an unprecedented cost in clinical diagnostics. The platform works based on intrinsic physical characteristics of biomolecules (e.g., size and polarizability). We demonstrate biomedical applications and verify cell viability in our platform, whose multiplexing and integration of numerous steps and external analyses enhance its application in the clinic, including by nonspecialists. Through its massive cost reduction and usability we anticipate that our platform will enable greater access to diagnostic facilities in developed countries as well as POC diagnostics in resource-poor and developing countries.

Multiparameter mechanical and morphometric screening of cells

We introduce a label-free method to rapidly phenotype and classify cells purely based on physical properties. We extract 15 biophysical parameters from cells as they deform in a microfluidic stretching flow field via high-speed microscopy and apply machine-learning approaches to discriminate different cell types and states. When employing the full 15 dimensional dataset, the technique robustly classifies individual cells based on their pluripotency, with accuracy above 95%. Rheological and morphological properties of cells while deforming were critical for this classification. We also show the application of this method in accurate classifying cells based on their viability, drug screening and detecting populations of malignant cells in mixed samples. We show that some of the extracted parameters are not linearly independent, and in fact we reach maximum classification accuracy by using only a subset of parameters. However, the informative subsets could vary depending on cell types in the sample. This work shows the utility of an assay purely based on intrinsic biophysical properties of cells to identify changes in cell state. In addition to a label-free alternative to flow cytometry in certain applications, this work, also can provide novel intracellular metrics that would not be feasible with labeled approaches (i.e. flow cytometry).

Serial weighting of micro-objects with resonant microchanneled cantilevers

Atomic force microscopy (AFM) cantilevers have proven to be very effective mass sensors. The attachment of a small mass to a vibrating cantilever produces a resonance frequency shift that can be monitored, providing the ability to measure mass changes down to a few molecules resolution. Nevertheless, the lack of a practical method to handle the catch and release process required for dynamic weighting of microobjects strongly hindered the application of the technology beyond proof of concept measurements. Here, a method is proposed in which FluidFM hollow cantilevers are exploited to overcome the standard limitations of AFM-based mass sensors, providing high throughput single object weighting with picogram accuracy. The extension of the dynamic models of AFM cantilevers to hollow cantilevers was discussed and the effectiveness of mass weighting in air was validated on test samples.

In vivo acoustic and photoacoustic focusing of circulating cells

In vivo flow cytometry using vessels as natural tubes with native cell flows has revolutionized the study of rare circulating tumor cells in a complex blood background. However, the presence of many blood cells in the detection volume makes it difficult to count each cell in this volume. We introduce method for manipulation of circulating cells in vivo with the use of gradient acoustic forces induced by ultrasound and photoacoustic waves. In a murine model, we demonstrated cell trapping, redirecting and focusing in blood and lymph flow into a tight stream, noninvasive wall-free transportation of blood, and the potential for photoacoustic detection of sickle cells without labeling and of leukocytes targeted by functionalized nanoparticles. Integration of cell focusing with intravital imaging methods may provide a versatile biological tool for single-cell analysis in circulation, with a focus on in vivo needleless blood tests, and preclinical studies of human diseases in animal models.

Materiomics for Oral Disease Diagnostics and Personal Health Monitoring: Designer Biomaterials for the Next Generation Biomarkers

We live in exciting times for a new generation of biomarkers being enabled by advances in the design and use of biomaterials for medical and clinical applications, from nano- to macro-materials, and protein to tissue. Key challenges arise, however, due to both scientific complexity and compatibility of the interface of biology and engineered materials. The linking of mechanisms across scales by using a materials science approach to provide structure-process-property relations characterizes the emerging field of 'materiomics,' which offers enormous promise to provide the hitherto missing tools for biomaterial development for clinical diagnostics and the next generation biomarker applications towards personal health monitoring. Put in other words, the emerging field of materiomics represents an essentially systematic approach to the investigation of biological material systems, integrating natural functions and processes with traditional materials science perspectives. Here we outline how materiomics provides a game-changing technology platform for disruptive innovation in biomaterial science to enable the design of tailored and functional biomaterials--particularly, the design and screening of DNA aptamers for targeting biomarkers related to oral diseases and oral health monitoring. Rigorous and complementary computational modeling and experimental techniques will provide an efficient means to develop new clinical technologies in silico, greatly accelerating the translation of materiomics-driven oral health diagnostics from concept to practice in the clinic.

Nanochannel Electroporation as a Platform for Living Cell Interrogation in Acute Myeloid Leukemia

A living cell interrogation platform based on nanochannel electroporation is demonstrated with analysis of RNAs in single cells. This minimally invasive process is based on individual cells and allows both multi-target analysis and stimulus-response analysis by sequential deliveries. The unique platform possesses a great potential to the comprehensive and lysis-free nucleic acid analysis on rare or hard-to-transfect cells.

Towards single-cell LC-MS phosphoproteomics

Protein phosphorylation is a ubiquitous posttranslational modification, which is heavily involved in signal transduction. Misregulation of protein phosphorylation is often associated with a decrease in cell viability and complex diseases such as cancer. The dynamic and low abundant nature of phosphorylated proteins makes studying phosphoproteome a challenging task. In this review, we summarize state of the art proteomic techniques to study and quantify peptide phosphorylation in biological systems and discuss their limitations. Due to its short-lived nature, the phosphorylation event cannot be precisely traced in a heterogonous cell population, which highlights the importance of analyzing phosphorylation events at the single cell level. Mainly, we focus on the methodical and instrumental developments in proteomics and nanotechnology, which will help to build more accurate and robust systems for the feasibility of phosphorylation analysis at the single cell level. We propose that an automated and miniaturized construction of analytical systems holds the key to the future of phosphoproteomics; therefore, we highlight the benchmark studies in this direction. Having advanced and automated microfluidic chip LC systems will allow us to analyze single-cell phosphoproteomics and quantitatively compare it with others. The progress in the microfluidic chip LC systems and feasibility of the single-cell phosphoproteomics will be beneficial for early diagnosis and detection of the treatment response of many crucial diseases.

3D liver models on a microplatform: well-defined culture, engineering of liver tissue and liver-on-a-chip

The liver, the largest organ in the human body, is a multi-functional organ with diverse metabolic activities that plays a critical role in maintaining the body and sustaining life. Although the liver has excellent regenerative and recuperative properties, damages caused by chronic liver diseases or viral infection may lead to permanent loss of liver functions. Studies of liver disease mechanism have focused on drug screening and liver tissue engineering techniques, including strategies based on in vitro models. However, conventional liver models are plagued by a number of limitations, which have motivated the development of 'liver-on-a-chip' and microplatform-based bioreactors that can provide well-defined microenvironments. Microtechnology is a promising tool for liver tissue engineering and liver system development, as it can mimic the complex in vivo microenvironment and microlevel ultrastructure, by using a small number of human cells under two-dimensional (2D) and three-dimensional (3D) culture conditions. These systems provided by microtechnology allow improved liver-specific functions and can be expanded to encompass diverse 3D culture methods, which are critical for the maintenance of liver functions and recapitulation of the features of the native liver. In this review, we provide an overview of microtechnologies that have been used for liver studies, describe biomimetic technologies for constructing microscale 2D and 3D liver models as well as liver-on-a-chip systems and microscale bioreactors, and introduce applications of liver microtechnology and future trends in the field.

Sub-population analysis of deformability distribution in heterogeneous red blood cell population

We present a method for sub-population analysis of deformability distribution using single-cell microchamber array (SiCMA) technology. It is a unique method allowing the correlation of overall cellular characteristics with surface and cytosolic characteristics to define the distribution of individual cellular characteristics in heterogeneous cell populations. As a proof of principle, reticulocytes, the immature sub-population of red blood cells (RBC), were recognized from RBC population by a surface marker and different characteristics on deformability between these populations were characterized. The proposed technology can be used in a variety of applications that would benefit from the ability to measure the distribution of cellular characteristics in complex populations, especially important to define hematologic disorders.

High-throughput microfluidic platform for adherent single cells non-viral gene delivery

Microfluidic platform for the high-throughput screening of gene delivery vectors and optimization of the transfection protocols at a single cell level.

The Single-Cell Lab or How to Perform Single-Cell Molecular Analysis

The increasing interest towards cellular heterogeneity within cell populations has pushed the development of new protocols to isolate and analyze single cells. PCR-based amplification techniques are widely used in this field. However, setting up an experiment and analyzing the results can sometimes be challenging. The aim of this chapter is to provide a general overview on single-cell PCR analysis focusing on the potential pitfalls and on the possible solutions to successfully perform the analysis.

Microbial cell lysis and nucleic acid extraction via nanofluidic channel

This paper presents a microfluidic device with a nano-channel prepared by focused ion beam (FIB) milling for microbial cell lysis and nucleic acid extraction.

Co-detection and sequencing of genes and transcripts from the same single cells facilitated by a microfluidics platform

Despite the recent advance of single-cell gene expression analyses, co-measurement of both genomic and transcriptional signatures at the single-cell level has not been realized. However such analysis is necessary in order to accurately delineate how genetic information is transcribed, expressed, and regulated to give rise to an enormously diverse range of cell phenotypes. Here we report on a microfluidics-facilitated approach that allows for controlled separation of cytoplasmic and nuclear contents of a single cell followed by on-chip amplification of genomic DNA and cytoplasmic mRNA. When coupled with off-chip polymerase chain reaction, gel electrophoresis and Sanger sequencing, a panel of genes and transcripts from the same single cell can be co-detected and sequenced. This platform is potentially an enabling tool to permit multiple genomic measurements performed on the same single cells and opens new opportunities to tackle a range of fundamental biology questions including non-genetic cell-to-cell variability, epigenetic regulation, and stem cell fate control. It also helps address clinical challenges such as diagnosing intra-tumor heterogeneity and dissecting complex cellular immune responses.

The single-probe: a miniaturized multifunctional device for single cell mass spectrometry analysis

We have developed a new mass spectrometry (MS) technology, the Single-probe MS, capable of real-time, in situ metabolomic analysis of individual living cells. The Single-probe is a miniaturized multifunctional sampling and ionization device that is directly coupled to the mass spectrometer. With a sampling tip smaller than individual eukaryotic cells (<10 μm), the Single-probe can be inserted into single cells to sample the intracellular compounds for real-time MS analysis. We have used the Single-probe to detect several cellular metabolites and the anticancer small molecules paclitaxel, doxorubicin, and OSW-1 in individual cervical cancer cells (HeLa). Single cell mass spectrometry (SCMS) is an emerging scientific technology that could reshape the analytical science of many research disciplines, and the Single-probe MS technology is a novel method for SCMS that, through its accessible fabrication protocols, can be broadly applied to different research areas.

Saturated vs. unsaturated hydrocarbon interactions with carbon nanostructures

The interactions of various acyclic and cyclic hydrocarbons in both saturated and unsaturated forms with the carbon nanostructures (CNSs) have been explored by using density functional theory (DFT) calculations. Model systems representing armchair and zigzag carbon nanotubes (CNTs) and graphene have been considered to investigate the effect of chirality and curvature of the CNSs toward these interactions. Results of this study reveal contrasting binding nature of the acyclic and cyclic hydrocarbons toward CNSs. While the saturated molecules show stronger binding affinity in acyclic hydrocarbons; the unsaturated molecules exhibit higher binding affinity in cyclic hydrocarbons. In addition, acyclic hydrocarbons exhibit stronger binding affinity toward the CNSs when compared to their corresponding cyclic counterparts. The computed results excellently corroborate the experimental observations. The interaction of hydrocarbons with graphene is more favorable when compared with CNTs. Bader's theory of atoms in molecules has been invoked to characterize the noncovalent interactions of saturated and unsaturated hydrocarbons. Our results are expected to provide useful insights toward the development of rational strategies for designing complexes with desired noncovalent interaction involving CNSs.

Quantification of single-cell nanoparticle concentrations and the distribution of these concentrations in cell population

Quantification of nanoparticle uptake into cells is necessary for numerous applications in cellular imaging and therapy. Herein, synchrotron X-ray fluorescence (SXRF) microscopy, a promising tool to quantify elements in plant and animal cells, was employed to quantify and characterize the distribution of titanium dioxide (TiO2) nanosphere uptake in a population of single cells. These results were compared with average nanoparticle concentrations per cell obtained by widely used inductively coupled plasma mass spectrometry (ICP-MS). The results show that nanoparticle concentrations per cell quantified by SXRF were of one to two orders of magnitude greater compared with ICP-MS. The SXRF results also indicate a Gaussian distribution of the nanoparticle concentration per cell. The results suggest that issues relevant to the field of single-cell analysis, the limitation of methods to determine physical parameters from large population averages leading to potentially misleading information and the lack of any information about the cellular heterogeneity are equally relevant for quantification of nanoparticles in cell populations.

Optimization of light delivery by a nanowire-based single cell optical endoscope

Here we present a new design and FDTD simulations of light delivery by a nanowire-based intracellular endoscope. Nanowires can be used for minimally invasive and very local light delivery inside cells. One of the main challenges is coupling of light into the nanowire. We propose a new plasmonic coupler interface between cleaved optical fiber and a nanowire, and optimize light coupling efficiency and contrast.

Microfluidic parallel patterning and cellular delivery of molecules with a nanofountain probe

This brief report describes a novel tool for microfluidic patterning of biomolecules and delivery of molecules into cells. The microdevice is based on integration of nanofountain probe (NFP) chips with packaging that creates a closed system and enables operation in liquid. The packaged NFP can be easily coupled to a micro/nano manipulator or atomic force microscope for precise position and force control. We demonstrate here the functionality of the device for continuous direct-write parallel patterning on a surface in air and in liquid. Because of the small volume of the probes (~3 pL), we can achieve flow rates as low as 1 fL/s and have dispensed liquid drops with submicron to 10 µm diameters in a liquid environment. Furthermore, we demonstrate that this microdevice can be used for delivery of molecules into single cells by transient permeabilization of the cell membrane (i.e., electroporation). The significant advantage of NFP-based electroporation compared with bulk electroporation and other transfection techniques is that it allows for precise and targeted delivery while minimizing stress to the cell. We discuss the ongoing development of the tool toward automated operation and its potential as a multifunctional device for microarray applications and time-dependent single-cell studies.

Nanofountain probe electroporation (NFP-E) of single cells

The ability to precisely deliver molecules into single cells is of great interest to biotechnology researchers for advancing applications in therapeutics, diagnostics, and drug delivery toward the promise of personalized medicine. The use of bulk electroporation techniques for cell transfection has increased significantly in the past decade, but the technique is nonspecific and requires high voltage, resulting in variable efficiency and low cell viability. We have developed a new tool for electroporation using nanofountain probe (NFP) technology, which can deliver molecules into cells in a manner that is highly efficient and gentler to cells than bulk electroporation or microinjection. Here we demonstrate NFP electroporation (NFP-E) of single HeLa cells within a population by transfecting them with fluorescently labeled dextran and imaging the cells to evaluate the transfection efficiency and cell viability. Our theoretical analysis of the mechanism of NFP-E reveals that application of the voltage creates a localized electric field between the NFP cantilever tip and the region of the cell membrane in contact with the tip. Therefore, NFP-E can deliver molecules to a target cell with minimal effect of the electric potential on the cell. Our experiments on HeLa cells confirm that NFP-E offers single cell selectivity, high transfection efficiency (>95%), qualitative dosage control, and very high viability (92%) of transfected cells.

Deciphering the single-cell omic: innovative application for translational medicine

Traditional technologies to investigate system biology are limited by the detection of parameters resulting from the averages of large populations of cells, missing cells produced in small numbers, and attempting to uniform the heterogeneity. The advent of proteomics and genomics at a single-cell level has set the basis for an outstanding improvement in analytical technology and data acquisition. It has been well demonstrated that cellular heterogeneity is closely related to numerous stochastic transcriptional events leading to variations in patterns of expression among single genetically identical cells. The new-generation technology of single-cell analysis is able to better characterize a cell's population, identifying and differentiating outlier cells, in order to provide both a single-cell experiment and a corresponding bulk measurement, through the identification, quantification and characterization of all system biology aspects (genomics, transcriptomics, proteomics, metabolomics, degradomics and fluxomics). The movement of omics into single-cell analysis represents a significant and outstanding shift.

Micro-nanopatterning as tool to study the role of physicochemical properties on cell-surface interactions

The current nano-biotechnologies interfacing synthetic materials and cell biology requires a better understanding of cell-surface interactions on the micro-to-nanometer scale. Cell-substrate interactions are mediated by the presence of proteins adsorbed from biological fluids to the substrate. The effect of nanotopography and surface chemistry on protein adsorption as well as the mediation effect on subsequent cellular communication with substratum is not well documented. This review discusses the role of physicochemical properties of cell-surface interactions and state-of-the-art methods currently available for micro-nanoscale surface fabrication and patterning. We also briefly discuss the current surface patterning techniques that allow the combination of a fine and independent control on nanotopography and chemistry to understand the effect of surface nanoscale substrate morphology on cell-surface interactions which has never been realized in previous reports. In addition, we discuss the influence of various chemical patterning and modulation of the nano-topography of surfaces on cell functionality and phenotype.

Round-tip dielectrophoresis-based tweezers for single micro-object manipulation

In this paper, we present an efficient methodology to manipulate a single micro-object using round-tip positive dielectrophoresis-based tweezers. The tweezers consist of a glass needle with a round-tip and a pair of thin gold-film electrodes. The round-tip, which has a radius of 3µm, is formed by melting a finely pulled glass needle and concentrates the electric field at the tip of the tweezers, which allows the individual manipulation of single micro-objects. The tweezers successfully captured, conveyed, and positioned single cell-sized liposomes with diameters of 5-23µm, which are difficult to manipulate with conventional manipulation methodologies, such as optical tweezers or glass micropipettes, due to the similarities between their optical properties and those of the media, as well as the ease with which they are deformed or broken. We used Stokes' drag theory to experimentally evaluate the positive dielectrophoresis (pDEP) force generated by the tweezers as a function of the liposome size, the content of the surrounding media, and the applied AC voltage and frequency. The results agreed with the theoretically deduced pDEP force. Finally, we demonstrated the separation of labeled single cells from non-labeled cells with the tweezers. This device can be used as an efficient tool for precisely and individually manipulating biological micro-objects that are typically transparent and flexible.

Microfluidic devices for cell cultivation and proliferation

Microfluidic technology provides precise, controlled-environment, cost-effective, compact, integrated, and high-throughput microsystems that are promising substitutes for conventional biological laboratory methods. In recent years, microfluidic cell culture devices have been used for applications such as tissue engineering, diagnostics, drug screening, immunology, cancer studies, stem cell proliferation and differentiation, and neurite guidance. Microfluidic technology allows dynamic cell culture in microperfusion systems to deliver continuous nutrient supplies for long term cell culture. It offers many opportunities to mimic the cell-cell and cell-extracellular matrix interactions of tissues by creating gradient concentrations of biochemical signals such as growth factors, chemokines, and hormones. Other applications of cell cultivation in microfluidic systems include high resolution cell patterning on a modified substrate with adhesive patterns and the reconstruction of complicated tissue architectures. In this review, recent advances in microfluidic platforms for cell culturing and proliferation, for both simple monolayer (2D) cell seeding processes and 3D configurations as accurate models of in vivo conditions, are examined.