Microfabricated Two-Dimensional Electrophoresis Device for Differential Protein Expression Profiling

Flow Dynamics and Analyte Transfer in a Microfluidic Device for Spatial Two-Dimensional Separations

In the last decade, chip-based separations have become a major area of interest in the field of separation science, especially for the development of “spatial” two-dimensional liquid chromatography (xLC × xLC). In xLC × xLC, the analytes are first separated by migration to different positions in a first-dimension (1D) channel and subsequently transferred with the aid of a flow distributor in a perpendicular direction to undergo a second-dimension (2D) separation. In this study, several designs for 2D separations are explored with the aid of computational fluid dynamics simulations. There were several aims of this work, viz. (1) to investigate the possible anomalies arising from the location of analyte bands in the first-dimension channel before transfer to the second dimension induced by the flow distributor, (2) to study the distribution ratio of the analytes across the different outlets of the 1D channel, and (3) to study the flow behaviour confinement in the flow distributor. In all designs, the simulated absolute flow velocity was not equal in all regions of the 1D channel. The extreme segments showed higher velocities compared to the central zones. This will eventually influence the migration times (first moments) and the variances (second moments), as confirmed by CFD results. The study has contributed to the understanding of the effects of the peak locations and, ultimately, to progress in spatial 2D-LC separations.

Implementing Multi-Enzyme Biocatalytic Systems Using Nanoparticle Scaffolds

Interest in multi-enzyme synthesis outside of cells (in vitro) is becoming far more prevalent as the field of cell-free synthetic biology grows exponentially. Such synthesis would allow for complex chemical transformations based on the exquisite specificity of enzymes in a "greener" manner as compared to organic chemical transformations. Here, we describe how nanoparticles, and in this specific case-semiconductor quantum dots, can be used to both stabilize enzymes and further allow them to self-assemble into nanocomplexes that facilitate high-efficiency channeling phenomena. Pertinent protocol information is provided on enzyme expression, choice of nanoparticulate material, confirmation of enzyme attachment to nanoparticles, assay format and tracking, data analysis, and optimization of assay formats to draw the best analytical information from the underlying processes.

On-chip protein separation with single-molecule resolution

Accurate identification of both abundant and rare proteins hinges on the development of single-protein sensing methods. Given the immense variation in protein expression levels in a cell, separation of proteins by weight would improve protein classification strategies. Upstream separation facilitates sample binning into smaller groups while also preventing sensor overflow, as may be caused by highly abundant proteins in cell lysates or clinical samples. Here, we scale a bulk analysis method for protein separation, sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), to the single-molecule level using single-photon sensitive widefield imaging. Single-molecule sensing of the electrokinetically moving proteins is achieved by in situ polymerization of the PAGE in a low-profile fluidic channel having a depth of only ~ 0.6 µm. The polyacrylamide gel restricts the Brownian kinetics of the proteins, while the low-profile channel ensures that they remain in focus during imaging, allowing video-rate monitoring of single-protein migration. Calibration of the device involves separating a set of Atto647N-covalently labeled recombinant proteins in the size range of 14-70 kDa, yielding an exponential dependence of the proteins' molecular weights on the measured mobilities, as expected. Subsequently, we demonstrate the ability of our fluidic device to separate and image thousands of proteins directly extracted from a human cancer cell line. Using single-particle image analysis methods, we created detailed profiles of the separation kinetics of lysine and cysteine -labeled proteins. Downstream coupling of the device to single-protein identification sensors may provide superior protein classification and improve our ability to analyze complex biological and medical protein samples.

Immunomagnetic separation of circulating tumor cells with microfluidic chips and their clinical applications

Circulating tumor cells (CTCs) are tumor cells detached from the original lesion and getting into the blood and lymphatic circulation systems. They potentially establish new tumors in remote areas, namely, metastasis. Isolation of CTCs and following biological molecular analysis facilitate investigating cancer and coming out treatment. Since CTCs carry important information on the primary tumor, they are vital in exploring the mechanism of cancer, metastasis, and diagnosis. However, CTCs are very difficult to separate due to their extreme heterogeneity and rarity in blood. Recently, advanced technologies, such as nanosurfaces, quantum dots, and Raman spectroscopy, have been integrated with microfluidic chips. These achievements enable the next generation isolation technologies and subsequent biological analysis of CTCs. In this review, we summarize CTCs' separation with microfluidic chips based on the principle of immunomagnetic isolation of CTCs. Fundamental insights, clinical applications, and potential future directions are discussed.

Simultaneous label-free screening of G-quadruplex active ligands from natural medicine via a microfluidic chip electrophoresis-based energy transfer multi-biosensor strategy

Rapid screening of active compounds plays a crucial role in the research and application of complex natural medicines. Herein, a new method of simultaneous label-free multi-drug screening based on a selective aptamer-carboxyfluorescein/graphene oxide energy transfer optical sensor combined with microfluidic chip electrophoretic separation is reported. In this study, seven traditional Chinese medicinal monomers were chosen as targets for the screening of G-quadruplex ligands. The screening results of the G-quadruplex active ligands, including daidzein, berberine hydrochloride, jatrorrhizine hydrochloride, and fangchinoline, and non-active ligands, including geniposide and oxymatrine, were consistent with those reported in literature. Moreover, one new potential G4DNA active drug, jujuboside A, was identified. Molecular simulation of the interaction between G4DNA and drugs was also carried out using HyperChem and AutoDock to verify the results of the experimental screening. It further demonstrated the reliability of our strategy. This novel separation and concentration based multi-sensing strategy provides a simple, rapid, and sensitive tool for simultaneous multi-drug screening, which is very meaningful for drug screening and bio-interaction analysis.

Detecting Biothreat Agents: From Current Diagnostics to Developing Sensor Technologies

Although a fundamental understanding of the pathogenicity of most biothreat agents has been elucidated and available treatments have increased substantially over the past decades, they still represent a significant public health threat in this age of (bio)terrorism, indiscriminate warfare, pollution, climate change, unchecked population growth, and globalization. The key step to almost all prevention, protection, prophylaxis, post-exposure treatment, and mitigation of any bioagent is early detection. Here, we review available methods for detecting bioagents including pathogenic bacteria and viruses along with their toxins. An introduction placing this subject in the historical context of previous naturally occurring outbreaks and efforts to weaponize selected agents is first provided along with definitions and relevant considerations. An overview of the detection technologies that find use in this endeavor along with how they provide data or transduce signal within a sensing configuration follows. Current "gold" standards for biothreat detection/diagnostics along with a listing of relevant FDA approved in vitro diagnostic devices is then discussed to provide an overview of the current state of the art. Given the 2014 outbreak of Ebola virus in Western Africa and the recent 2016 spread of Zika virus in the Americas, discussion of what constitutes a public health emergency and how new in vitro diagnostic devices are authorized for emergency use in the U.S. are also included. The majority of the Review is then subdivided around the sensing of bacterial, viral, and toxin biothreats with each including an overview of the major agents in that class, a detailed cross-section of different sensing methods in development based on assay format or analytical technique, and some discussion of related microfluidic lab-on-a-chip/point-of-care devices. Finally, an outlook is given on how this field will develop from the perspective of the biosensing technology itself and the new emerging threats they may face.

Protein separation under a microfluidic regime

Lab-on-a-Chip (LoC), or micro-Total Analysis Systems (μTAS), is recognized as a powerful analytical technology with high capabilities, though end-user products for protein purification are still far from being available on the market. Remarkable progress has been achieved in the separation of nucleic acids and proteins using electrophoretic microfluidic devices, while pintsize devices have been developed for protein isolation according to miniaturized chromatography principles (size, charge, affinity, etc.). In this work, we review the latest advances in the fabrication of components, detection methods and commercial implementation for the separation of biological macromolecules based on microfluidic systems, with some critical remarks on the perspectives of their future development towards standardized microfluidic systems and protocols. An outlook on the current needs and future applications is also presented.

Single Cell Isolation and Analysis

Individual cell heterogeneity within a population can be critical to its peculiar function and fate. Subpopulations studies with mixed mutants and wild types may not be as informative regarding which cell responds to which drugs or clinical treatments. Cell to cell differences in RNA transcripts and protein expression can be key to answering questions in cancer, neurobiology, stem cell biology, immunology, and developmental biology. Conventional cell-based assays mainly analyze the average responses from a population of cells, without regarding individual cell phenotypes. To better understand the variations from cell to cell, scientists need to use single cell analyses to provide more detailed information for therapeutic decision making in precision medicine. In this review, we focus on the recent developments in single cell isolation and analysis, which include technologies, analyses and main applications. Here, we summarize the historical background, limitations, applications, and potential of single cell isolation technologies.

A novel microfluidic chip electrophoresis strategy for simultaneous, label-free, multi-protein detection based on a graphene energy transfer biosensor

A new type of high-throughput and parallel optical sensing platform with a single-color probe based on microfluidic chip electrophoresis combined with aptamer-carboxyfluorescein/graphene oxide energy transfer is reported here. Label-free protein multi-targets were detected, even in challenging complex samples without any pre-treatment.

Microchip with an open tubular immobilized ph gradient for UV whole column imaging detection

This study reports a new method for establishing an open tubular IPG in a microchip coupled with a whole column image detection (WCID) system for protein separation applications. This method allows a wider range of immobilized pH (2.6-9.5) to be established in a PDMS/quartz channel by controlling the diffusion of acidic and basic polymer solutions into the channel through well-designed channel dimensions. The developed pH gradient was experimentally validated by performing the separation of a mixture of standard pI markers. It was further validated by the separation of the hemoglobin control AFSC sample. This method is advantageous over existing IPG methods because it has a wider range of pH and maintains the open tubular feature that matches the UV WCID to improve the sensitivity.

Droplet-based in situ compartmentalization of chemically separated components after isoelectric focusing in a Slipchip

Isoelectric focusing (IEF) is a powerful and widely used technique for protein separation and purification. There are many embodiments of microscale IEF that use capillary or microfluidic chips for the analysis of small sample volumes. Nevertheless, collecting the separated sample volumes without causing remixing remains a challenge. Herein, we describe a microfluidic Slipchip device that is able to efficiently compartmentalize focused analyte bands in situ into microdroplets. The device contains a microfluidic "zig-zag" separation channel that is composed of a sequence of wells formed in the two halves of the Slipchip. The analytes are focused in the channel and then compartmentalised into droplets by slipping the chip. Importantly, sample droplets can be analysed on chip or collected for subsequent analysis using electrophoresis or mass spectrometry for example. To demonstrate this approach, we perform IEF separation using standard markers and protein samples, with on-chip post-processing. Compared to alternative approaches for sample collection, the method avoids remixing, is scalable and is easily hyphenated with the other analytical methods.

The future of microfluidic assays in drug development

BACKGROUND

Microfluidic technology emerges as a convenient route to applying automated and reliable assays in a high-throughput manner with low cost.

OBJECTIVE

This review aims to answer questions related to the capabilities and potential applications of microfluidic assays that can benefit the drug development process and extends an outlook on its future trends.

METHODS

This article reviews recent publications in the field of microfluidics, with an emphasis on novel applications for drug development.

RESULTS/CONCLUSION

Microfluidics affords unique capabilities in sample preparation and separation, combinatorial synthesis and array formation, and incorporating nanotechnology for more functionalities. The pharmaceutical industry, facing challenges from limited productivity and accelerated competition, can thus greatly benefit from applying new microfluidic assays in various drug development stages, from target screening and lead optimization to absorption distribution metabolism elimination and toxicity studies in preclinical evaluations, diagnostics in clinical trials and drug formulation and manufacturing process optimization.

Microscale 2D separation systems for proteomic analysis

Microscale 2D separation systems have been implemented in capillaries and microfabricated channels. They offer advantages of faster analysis, higher separation efficiency and less sample consumption than the conventional methods, such as liquid chromatography (LC) in a column and slab gel electrophoresis. In this article, we review their recent advancement, focusing on three types of platforms, including 2D capillary electrophoresis (CE), CE coupling with capillary LC, and microfluidic devices. A variety of CE and LC modes have been employed to construct 2D separation systems via sophistically designed interfaces. Coupling of different separation modes has also been realized in a number of microfluidic devices. These separation systems have been applied for the proteomic analysis of various biological samples, ranging from a single cell to tumor tissues.

Thermoplastic microfluidic devices and their applications in protein and DNA analysis

Microfluidics is a platform technology that has been used for genomics, proteomics, chemical synthesis, environment monitoring, cellular studies, and other applications. The fabrication materials of microfluidic devices have traditionally included silicon and glass, but plastics have gained increasing attention in the past few years. We focus this review on thermoplastic microfluidic devices and their applications in protein and DNA analysis. We outline the device design and fabrication methods, followed by discussion on the strategies of surface treatment. We then concentrate on several significant advancements in applying thermoplastic microfluidic devices to protein separation, immunoassays, and DNA analysis. Comparison among numerous efforts, as well as the discussion on the challenges and innovation associated with detection, is presented.

Microfluidics in protein chromatography

The development of microfluidics and its utilization in a myriad of applications has grown exponentially over the past 15 years. One area that has benefited from the great strides in fabrication of microelectromechanical systems (MEMS) is separations chemistry. Most studies have focused on small molecule and DNA separations; few on protein chromatographic techniques on microchips. This review details recent developments in protein separations on microfluidic platforms and how MEMS have the potential for revolutionizing protein chromatography.

2D separations on a 1D chip: gradient elution moving boundary electrophoresis-chiral capillary zone electrophoresis

A new method is described for two-dimensional (2D) separations using a microfluidic chip normally employed for single dimension electrophoresis. The method employs a combination of gradient elution moving boundary electrophoresis (GEMBE) and chiral capillary zone electrophoresis (CZE). The simplicity of the first dimension GEMBE method enables its implementation in the injection channel of a conventional electrophoresis chip, simplifying the design and operation of the device. The method was used for high resolution 2D chiral separations of a mixture of amino acids considered as possible signatures of extant or extinct life for solar system exploration. The enantiomers of aspartic acid, glutamic acid, serine, alanine, and valine were all resolved as well as glycine (achiral) and several unidentified impurities, giving an estimated peak capacity of 35 for the region between valine and glycine. The results highlight the need for high peak capacity separations for chiral amino acid analysis if accurate enantiomeric ratios are to be determined.

Toward point-of-care microchip profiling of proteins

Profiling of protein biomarkers is powerful for the analysis of complex proteomes altered during the progression of diseases. Lab-on-a-chip technologies can potentially provide the throughput and efficiency required for point-of-care and clinical applications. While initial studies utilized 1D microchip separation techniques, researchers have recently developed novel 2D microchip separation platforms with the ability to profile thousands of proteins more effectively. Despite advancements in lab-on-a-chip technologies, very few reports have demonstrated a point-of-care microchip-based profiling of proteins. In this review, recent progress in 1D and 2D microchip profiling of protein mixtures of a biological sample with potential point-of-care applications are discussed. A selection of recent microchip immunoassay-based techniques is also highlighted.

Mixed-mode electrokinetic and chromatographic peptide separations in a microvalve-integrated polymer chip

A cycloolefin polymer chip supporting the concatenation of isoelectric focusing (IEF) and reversed-phase liquid chromatography (RPLC) is demonstrated for high throughput two dimensional peptide separations. A unique benefit of the mixed-mode platform is the ability of IEF to act as a highly concentrating electrokinetic separation mode for effective isolation of sample components prior to RPLC. The thermoplastic chip contains integrated high pressure microvalves, enabling uniform sample transfer from the IEF channel to multiple parallel RPLC channels, gradient elution from each RPLC column, and hydrodynamic isolation between the separation dimensions. The reusable system is shown to provide efficient 2-D separations together with facile interfacing with MALDI-MS, suggesting a new path towards effective peptide analysis from complex samples.

A digital microfluidic platform for the automation of quantitative biomolecular assays

A digital microfluidic platform for the automation of quantitative, multi-step biomolecular assays is developed and optimized. The platform consists of a 2-dimensional array of microvalves that can be programmed to perform reagent routing, mixing, rinsing, serial dilution, and many other operations using nanolitre scale volumes of sample. Discrete transfer of fluid between microvalves is characterized using gravimetric flow analysis and optimized to achieve maximum efficiency. Protocols for on-chip reagent mixing and serial dilution are optimized to achieve linearity over a 1000-fold dilution range. These optimized programs are used to develop a rapid, quantitative assay for hydrogen peroxide, a biomarker of oxidative stress. A sub-micromolar limit of detection is demonstrated with an 8.5 min program runtime, thus establishing this platform as an effective tool for the automation of multi-step bioassays. The programmability of this system enables rapid development of diverse assay protocols on a common chip format.

Microchip isoelectric focusing with monolithic immobilized pH gradient materials for proteins separation

Monolithic immobilized pH gradient (M-IPG) materials were prepared in microchannles by photoinitiated polymerization of acrylamide, glycidylmethacrylate and Bis, followed by the attachment of focused Ampholine onto the surface of porous monoliths via epoxide groups. With M-IPG materials as matrix, FITC-labeled ribonuclease B, myoglobin and alpha-casein were well separated by microchip isoelectric focusing (muCIEF) without carrier amphocytes (CAs) added in the buffer. Both chemical and pressure mobilization were applied to drive focused zones for LIF detection. Our experimental results showed that pressure mobilization was preferable with neglectable band broadening, and good peak shape and high detection sensitivity were obtained. All these results demonstrate that muCIEF with M-IPG materials is not only an efficient mode for protein enrichment and separation but also attractive to couple with other CE modes to achieve multi-dimensional separation or MS for further identification, without the interference of mobile CAs.

On-chip technologies for multidimensional separations

We review microfluidic devices designed for multidimensional sample analysis, with a primer on relevant theory, an emphasis on protein analysis, and an eye towards future improvements and challenges to the field. Image shows results of an on-chip IEF-CE separation of a protein mixture; unpublished surface plot data from A. E. Herr.

Serial-to-parallel interfaces for efficient sample transfer on microfluidic devices

We report serial-to-parallel interfaces for rapidly and efficiently transferring samples from a single microfluidic channel to multiple parallel channels. Three designs and operation modes were evaluated to determine the most efficient transfer process. All designs employed two routing channels to direct the sample into the parallel channels and to prevent sample from leaking into adjacent channels. For two of the three designs, a tee valve and gated valve were added to the interface prior to routing the samples to assist with sample injections into the parallel channels. Injection times as short as 20 ms and injection frequencies up to 10 Hz were achieved with relative standard deviations less than 0.5% for the injected area. With an injection time of 50 ms and injection frequency of 10 Hz, up to 50% of the sample is efficiently transferred. Among the three designs, the interface with the gated valve provided the highest performance and reproducibility.

Microfluidic 2-D PAGE using multifunctional in situ polyacrylamide gels and discontinuous buffers

A two-dimensional microfluidic system is presented for intact protein separations combining isoelectric focusing (IEF) and sodium dodecyl sulfate (SDS) polyacrylamide gel electrophoresis (PAGE) employing in situ photopolymerized polyacrylamide (PAAm) gels. The PAAm gels are used for multiple functions. In addition to serving as a highly-resolving separation medium for gel electrophoresis, discrete polyacrylamide gel plugs are used to enable the efficient isolation of different on-chip media including anolyte, catholyte, and sample/ampholyte solutions for IEF. The gel plugs are demonstrated as on-chip reagent containers, holding defined quantities of SDS for on-chip SDS-protein complexation, and enabling the use of a discontinuous buffer system for sample band sharpening during SDS-PAGE. The 2-D chip also employs several unique design features including an angled isoelectric focusing channel to minimize sample tailing, and backbiasing channels designed to achieve uniform interdimensional sample transfer. Separation results using E. coli cell lysate are presented using a 10-channel chip with and without the discontinuous buffer system, with resolving power more than doubled in the former case. Further improvements in separation resolution are demonstrated using a 20-channel chip design.