Microfabricated bioprocessor for integrated nanoliter-scale Sanger DNA sequencing

DNA Origami-Enabled Gene Localization of Repetitive Sequences

Repetitive sequences, which make up over 50% of human DNA, have diverse applications in disease diagnosis, forensic identification, paternity testing, and population genetic analysis due to their crucial functions for gene regulation. However, representative detection technologies such as sequencing and fluorescence imaging suffer from time-consuming protocols, high cost, and inaccuracy of the position and order of repetitive sequences. Here, we develop a precise and cost-effective strategy that combines the high resolution of atomic force microscopy with the shape customizability of DNA origami for repetitive sequence-specific gene localization. "Tri-block" DNA structures were specifically designed to connect repetitive sequences to DNA origami tags, thereby revealing precise genetic information in terms of position and sequence for high-resolution and high-precision visualization of repetitive sequences. More importantly, we achieved the results of simultaneous detection of different DNA repetitive sequences on the gene template with a resolution of ∼6.5 nm (19 nt). This strategy is characterized by high efficiency, high precision, low operational complexity, and low labor/time costs, providing a powerful complement to sequencing technologies for gene localization of repetitive sequences.

The Development of Plant Genome Sequencing Technology and Its Conservation and Application in Endangered Gymnosperms

Genome sequencing is widely recognized as a fundamental pillar in genetic research and legal studies of biological phenomena, providing essential insights for genetic investigations and legal analyses of biological events. The field of genome sequencing has experienced significant progress due to rapid improvements in scientific and technological developments. These advancements encompass not only significant improvements in the speed and quality of sequencing but also provide an unparalleled opportunity to explore the subtle complexities of genomes, particularly in the context of rare species. Such a wide range of possibilities has successfully supported the validation of plant gene functions and the refinement of precision breeding methodologies. This expanded scope now includes a comprehensive exploration of the current state and conservation efforts of gymnosperm gene sequencing, offering invaluable insights into their genomic landscapes. This comprehensive review elucidates the trajectory of development and the diverse applications of genome sequencing. It encompasses various domains, including crop breeding, responses to abiotic stress, species evolutionary dynamics, biodiversity, and the unique challenges faced in the conservation and utilization of gymnosperms. It highlights both ongoing challenges and the unveiling of forthcoming developmental trajectories.

Advanced Omics Techniques for Understanding Cochlear Genome, Epigenome, and Transcriptome in Health and Disease

Advanced genomics, transcriptomics, and epigenomics techniques are providing unprecedented insights into the understanding of the molecular underpinnings of the central nervous system, including the neuro-sensory cochlea of the inner ear. Here, we report for the first time a comprehensive and updated overview of the most advanced omics techniques for the study of nucleic acids and their applications in cochlear research. We describe the available in vitro and in vivo models for hearing research and the principles of genomics, transcriptomics, and epigenomics, alongside their most advanced technologies (like single-cell omics and spatial omics), which allow for the investigation of the molecular events that occur at a single-cell resolution while retaining the spatial information.

Organ-on-a-chip: A new tool for in vitro research

Organ-on-a-chip (OOC, organ chip) technology can closely simulate the human microenvironment, synthesize organ-like functional units on a fluidic chip substrate, and simulate the physiology of tissues and organs. It will become an increasingly important platform for in vitro drug development and screening. Most importantly, organ-on-a-chip technology, incorporating 3D cell cultures, overcomes the traditional drawbacks of 2D (flat) cell-culture technology in vitro and in vivo animal trials, neither of which generate completely reliable results when it comes to the actual human subject. It is expected that organ chips will allow huge reductions in the incidence of failure in late-stage human trials, thus slashing the cost of drug development and speeding up the introduction of drugs that are effective. There have been three key enabling technologies that have made organ chip technology possible: 3D bioprinting, fluidic chips, and 3D cell culture, of which the last has allowed cells to be cultivated under more physiologically realistic growth conditions than 2D culture. The fusion of these advanced technologies and the addition of new research methods and algorithms has enabled the construction of chip types with different structures and different uses, providing a wide range of controllable microenvironments, both for research at the cellular level and for more reliable analysis of the action of drugs on the human body. This paper summarizes some research progress of organ-on-a-chip in recent years, outlines the key technologies used and the achievements in drug screening, and makes some suggestions concerning the current challenges and future development of organ-on-a-chip technology.

Advances and Trends in Omics Technology Development

The human history has witnessed the rapid development of technologies such as high-throughput sequencing and mass spectrometry that led to the concept of “omics” and methodological advancement in systematically interrogating a cellular system. Yet, the ever-growing types of molecules and regulatory mechanisms being discovered have been persistently transforming our understandings on the cellular machinery. This renders cell omics seemingly, like the universe, expand with no limit and our goal toward the complete harness of the cellular system merely impossible. Therefore, it is imperative to review what has been done and is being done to predict what can be done toward the translation of omics information to disease control with minimal cell perturbation. With a focus on the “four big omics,” i.e., genomics, transcriptomics, proteomics, metabolomics, we delineate hierarchies of these omics together with their epiomics and interactomics, and review technologies developed for interrogation. We predict, among others, redoxomics as an emerging omics layer that views cell decision toward the physiological or pathological state as a fine-tuned redox balance.

Different DNA Sequencing Using DNA Graphs: A Study

Natural genetic material may shed light on gene expression mechanisms and aid in the detection of genetic disorders. Single Nucleotide Polymorphism (SNP), small insertions and deletions (indels), and major chromosomal anomalies are all chromosomal abnormality-related disorders. As a result, several methods have been applied to analyze DNA sequences, which constitutes one of the most critical aspects of biological research. Thus, numerous mathematical and algorithmic contributions have been made to DNA analysis and computing. Cost minimization, deployment, and sensitivity analysis to many factors are all components of sequencing platforms built on a quantitative framework and their operating mechanisms. This study aims to investigate the role of DNA sequencing and its representation in the form of graphs in the analysis of different diseases by means of DNA sequencing.

Leakage pressures for gasketless superhydrophobic fluid interconnects for modular lab-on-a-chip systems

Chip-to-chip and world-to-chip fluidic interconnections are paramount to enable the passage of liquids between component chips and to/from microfluidic systems. Unfortunately, most interconnect designs add additional physical constraints to chips with each additional interconnect leading to over-constrained microfluidic systems. The competing constraints provided by multiple interconnects induce strain in the chips, creating indeterminate dead volumes and misalignment between chips that comprise the microfluidic system. A novel, gasketless superhydrophobic fluidic interconnect (GSFI) that uses capillary forces to form a liquid bridge suspended between concentric through-holes and acting as a fluid passage was investigated. The GSFI decouples the alignment between component chips from the interconnect function and the attachment of the meniscus of the liquid bridge to the edges of the holes produces negligible dead volume. This passive seal was created by patterning parallel superhydrophobic surfaces (water contact angle ≥ 150°) around concentric microfluidic ports separated by a gap. The relative position of the two polymer chips was determined by passive kinematic constraints, three spherical ball bearings seated in v-grooves. A leakage pressure model derived from the Young-Laplace equation was used to estimate the leakage pressure at failure for the liquid bridge. Injection-molded, Cyclic Olefin Copolymer (COC) chip assemblies with assembly gaps from 3 to 240 µm were used to experimentally validate the model. The maximum leakage pressure measured for the GSFI was 21.4 kPa (3.1 psig), which corresponded to a measured mean assembly gap of 3 µm, and decreased to 0.5 kPa (0.073 psig) at a mean assembly gap of 240 µm. The effect of radial misalignment on the efficacy of the gasketless seals was tested and no significant effect was observed. This may be a function of how the liquid bridges are formed during the priming of the chip, but additional research is required to test that hypothesis.

A fully integrated isotachophoresis with a programmable microfluidic platform

Conventional isotachophoresis (ITP) can be used for pre-concentration of a single analyte, but preconcentration of multiple analytes is time consuming due to handling and washing steps required for the extensive buffer optimization procedure. In this work, we present a programmable microfluidic platform (PMP) to demonstrate fully automated optimization of ITP of multiple analytes. By interfacing a PMP with ITP, buffer selection and repetitive ITP procedures were automated. Using lifting-gate microvalve technology, a PMP consisting of a two-dimensional microvalve array was designed and fabricated for seamless integration with an ITP chip. The microvalve array was used for basic liquid manipulation such as metering, mixing, selecting, delivering, and washing procedures to prime and run ITP. Initially, the performances of the PMP and ITP channel were validated individually by estimating volume per pumping cycle and preconcentrating Alexa Fluor 594 with appropriate trailing (TE) and leading (LE) buffers, respectively. After confirming basic functions, autonomous ITP was demonstrated using multiple analytes (Pacific blue, Alexa Fluor 594, and Alexa Fluor 488). The optimal buffer combination was was determined by performing multiple ITP runs with three different TEs (borate, HEPES, and phosphate buffers) and three different concentrations of Tris-HCl for the LE. We found that 40 mM borate and 100 mM Tris-HCl successfully preconcentrated all analytes during a single ITP run. The integrated PMP-ITP system can simplify overall buffer selection and validation procedures for various biological and chemical target samples. Furthermore, by incorporating analytical tools that interconnect with the PMP, it can provide high sample concentrations to aid in downstream analysis.

Eukaryotic and Prokaryotic Microbiota Interactions

The nature of the relationship between the communities of microorganisms making up the microbiota in and on a host body has been increasingly explored in recent years. Microorganisms, including bacteria, archaea, viruses, parasites and fungi, have often long co-evolved with their hosts. In human, the structure and diversity of microbiota vary according to the host’s immunity, diet, environment, age, physiological and metabolic status, medical practices (e.g., antibiotic treatment), climate, season and host genetics. The recent advent of next generation sequencing (NGS) technologies enhanced observational capacities and allowed for a better understanding of the relationship between distinct microorganisms within microbiota. The interaction between the host and their microbiota has become a field of research into microorganisms with therapeutic and preventive interest for public health applications. This review aims at assessing the current knowledge on interactions between prokaryotic and eukaryotic communities. After a brief description of the metagenomic methods used in the studies were analysed, we summarise the findings of available publications describing the interaction between the bacterial communities and protozoa, helminths and fungi, either in vitro, in experimental models, or in humans. Overall, we observed the existence of a beneficial effect in situations where some microorganisms can improve the health status of the host, while the presence of other microorganisms has been associated with pathologies, resulting in an adverse effect on human health.

A modular, easy-to-use microcapillary electrophoresis system with laser-induced fluorescence for quantitative compositional analysis of trace organic molecules

Microcapillary electrophoresis (μCE) enables high-resolution separations in miniaturized, automated microfluidic devices. Pairing this powerful separation technique with laser-induced fluorescence (LIF) enables a highly sensitive, quantitative, and compositional analysis of organic molecule monomers and short polymers, which are essential, ubiquitous components of life on Earth. Improving methods for their detection has applications to multiple scientific fields, particularly those related to medicine, industry, and space science. Here, a modular benchtop system using μCE with LIF detection was constructed and tested by analyzing standard amino acid samples of valine, serine, alanine, glycine, glutamic acid, and aspartic acid in multiple borate buffered solutions of increasing concentrations from 10 mM to 50 mM, all pH 9.5. The 35 mM borate buffer solution generated the highest resolution before Joule heating dominated. The limits of detection of alanine and glycine using 35 mM borate buffer were found to be 2.12 nM and 2.91 nM, respectively, comparable to other state-of-the-art μCE-LIF instruments. This benchtop system is amenable to a variety of detectors, including a photomultiplier tube, a silicon photomultiplier, or a spectrometer, and currently employs a spectrometer for facile multi-wavelength detection. Furthermore, the microdevice is easily exchanged to fit the desired application of the system, and optical components within the central filter cube can be easily replaced to target alternative fluorescent dyes. This work represents a significant step forward for the analysis of small organic molecules and biopolymers using μCE-LIF systems.

Micro- and Nanostructured Polyaniline for Instant Identification of Metal Ions in Solution

The unique properties of nanomaterials enable the creation new analytical devices. Polyaniline (PANI) micro- and nanofiber network, freestanding in the gap between two gold microelectrodes, has been used in a new nanodetector for metal ions in solutions. The gold electrodes were modified with the aid of alkanethiols, forming a self-assembled monolayer (SAM), which is able to block the ion current flow, but also to interact with metal ions when specific functional molecules are incorporated into the layer. The electric field of the trapped metal ions induces change of the electrical conductivity of polyaniline nanofibers in vicinity. A small injected sample (75 μL) of a solution of salt (about 0.5 μg of salt) was enough to induce a reproducible change in the electrical conductivity of polyaniline nano-network, which was registered as a function of time within 10⁻20 s. The response was proportional to the concentration of ions. It also depends on properties of ions, e.g., the ionic radius, which allows for identification of metal ions by analyzing the parameters of the signal: the retention time (RT), half width (HW), amplitude (A) and integral intensity (INT). The advantage of the new device is the instant responsiveness and easy operation, but also the simple construction based on organic (polymer) technology. The system is "open"-when learned and calibrated adequately, other metal ions can be analyzed. The nanodetector can be used in cases where monitoring of the presence and concentration of metal ions is important.

Selection of highly specific aptamers to Vibrio parahaemolyticus using cell-SELEX powered by functionalized graphene oxide and rolling circle amplification

Cell-SELEX is a powerful tool to screen aptamers binding to living cellular organisms such as bacteria, fungi and even oncocytes. Here, we developed an advanced cell-SELEX strategy featuring functionalized graphene oxide (GO) and isothermal rolling circle amplification (RCA) to select aptamers against a prevailing foodborne pathogen, Vibrio parahaemolyticus. Polyethyleneglycol (PEG) and chitosan (CTS) were grafted onto the sheet-like GO molecules to synthesize a PC-GO material. TEM and FT-IR characterization demonstrated that the PC-GO composites were near-nanometric scale and tethered with PEG and CTS moieties, a property that significantly improved its solubility in biological buffer solutions used in cell-SELEX process. PC-GO could bind with ssDNAs with lower affinities to target cells, therefore the selection efficiency is greatly enhanced. The cell-binding aptamer candidates (CACs) were amplified by 10⁷ fold using complementary ring mediated (CRM-RCA), a created amplification method that generate single-stranded products, which could be directly used in the next round selection. As fueled by PC-GO and CRM-RCA, four highly specific aptamers with lowest K_d value of 10.3 ± 2.5 nM were obtained. Flow cytometry analysis showed that all the four aptamers exhibited more than 75% binding affinity to V. parahaemolyticus than to other foodborne bacteria (less than 18%). Simple procedure, high efficiency, and free from expensive thermal cycler (required by PCR amplification) will enable the established strategy to find its applications in aptamer selecting against fungi, stem and cancerous cells as well.

Advancements and Potential Applications of Microfluidic Approaches—A Review

A micro-level technique so-called “microfluidic technology or simply microfluidic” has gained a special place as a powerful tool in bioengineering and biomedical engineering research due to its core advantages in modern science and engineering. Microfluidic technology has played a substantial role in numerous applications with special reference to bioscience, biomedical and biotechnological research. It has facilitated noteworthy development in various sectors of bio-research and upsurges the efficacy of research at the molecular level, in recent years. Microfluidic technology can manipulate sample volumes with precise control outside cellular microenvironment, at micro-level. Thus, enable the reduction of discrepancies between in vivo and in vitro environments and reduce the overall reaction time and cost. In this review, we discuss various integrations of microfluidic technologies into biotechnology and its paradigmatic significance in bio-research, supporting mechanical and chemical in vitro cellular microenvironment. Furthermore, specific innovations related to the application of microfluidics to advance microbial life, solitary and co-cultures along with a multiple-type cell culturing, cellular communications, cellular interactions, and population dynamics are also discussed.

3D Multi-Microchannel Helical Mixer Fabricated by Femtosecond Laser inside Fused Silica

Three-dimensional (3D) multi-microchannel mixers can meet the requirements of different combinations according to actual needs. Rapid and simple creation of 3D multi-microchannel mixers in a "lab-on-a-chip" platform is a significant challenge in micromachining. In order to realize the complex mixing functions of microfluidic chips, we fabricated two kinds of complex structure micromixers for multiple substance mixes simultaneously, separately, and in proper order. The 3D multi-microchannel mixers are fabricated by femtosecond laser wet etch technology inside fused silica. The 3D multi-microchannel helical mixers have desirable uniformity and consistency, which will greatly expand their utility and scope of application.

Emerging Droplet Microfluidics

Droplet microfluidics generates and manipulates discrete droplets through immiscible multiphase flows inside microchannels. Due to its remarkable advantages, droplet microfluidics bears significant value in an extremely wide range of area. In this review, we provide a comprehensive and in-depth insight into droplet microfluidics, covering fundamental research from microfluidic chip fabrication and droplet generation to the applications of droplets in bio(chemical) analysis and materials generation. The purpose of this review is to convey the fundamentals of droplet microfluidics, a critical analysis on its current status and challenges, and opinions on its future development. We believe this review will promote communications among biology, chemistry, physics, and materials science.

Genome Sequencing

Genome sequencing is an important step toward correlating genotypes with phenotypic characters. Sequencing technologies are important in many fields in the life sciences, including functional genomics, transcriptomics, oncology, evolutionary biology, forensic sciences, and many more. The era of sequencing has been divided into three generations. First generation sequencing involved sequencing by synthesis (Sanger sequencing) and sequencing by cleavage (Maxam-Gilbert sequencing). Sanger sequencing led to the completion of various genome sequences (including human) and provided the foundation for development of other sequencing technologies. Since then, various techniques have been developed which can overcome some of the limitations of Sanger sequencing. These techniques are collectively known as "Next-generation sequencing" (NGS), and are further classified into second and third generation technologies. Although NGS methods have many advantages in terms of speed, cost, and parallelism, the accuracy and read length of Sanger sequencing is still superior and has confined the use of NGS mainly to resequencing genomes. Consequently, there is a continuing need to develop improved real time sequencing techniques. This chapter reviews some of the options currently available and provides a generic workflow for sequencing a genome.

Optical fiber LPG biosensor integrated microfluidic chip for ultrasensitive glucose detection

An optical fiber sensor integrated microfluidic chip is presented for ultrasensitive detection of glucose. A long-period grating (LPG) inscribed in a small-diameter single-mode fiber (SDSMF) is employed as an optical refractive-index (RI) sensor. With the layer-by-layer (LbL) self-assembly technique, poly (ethylenimine) (PEI) and poly (acrylic acid) (PAA) multilayer film is deposited on the SDSMF-LPG sensor for both supporting and signal enhancement, and then a glucose oxidase (GOD) layer is immobilized on the outer layer for glucose sensing. A microfluidic chip for glucose detection is fabricated after embedding the SDSMF-LPG biosensor into the microchannel of the chip. Experimental results reveal that the SDSMF-LPG biosensor based on such a hybrid sensing film can ultrasensitively detect glucose concentration as low as 1 nM. After integration into the microfluidic chip, the detection range of the sensor is extended from 2 µM to 10 µM, and the response time is remarkablely shortened from 6 minutes to 70 seconds.

Multiplexed Sequence Encoding: A Framework for DNA Communication

Synthetic DNA has great propensity for efficiently and stably storing non-biological information. With DNA writing and reading technologies rapidly advancing, new applications for synthetic DNA are emerging in data storage and communication. Traditionally, DNA communication has focused on the encoding and transfer of complete sets of information. Here, we explore the use of DNA for the communication of short messages that are fragmented across multiple distinct DNA molecules. We identified three pivotal points in a communication-data encoding, data transfer & data extraction-and developed novel tools to enable communication via molecules of DNA. To address data encoding, we designed DNA-based individualized keyboards (iKeys) to convert plaintext into DNA, while reducing the occurrence of DNA homopolymers to improve synthesis and sequencing processes. To address data transfer, we implemented a secret-sharing system-Multiplexed Sequence Encoding (MuSE)-that conceals messages between multiple distinct DNA molecules, requiring a combination key to reveal messages. To address data extraction, we achieved the first instance of chromatogram patterning through multiplexed sequencing, thereby enabling a new method for data extraction. We envision these approaches will enable more widespread communication of information via DNA.

High-performance detection of somatic D-loop mutation in urothelial cell carcinoma patients by polymorphism ratio sequencing

Utilizing a polymorphism ratio sequencing platform, we performed a complete somatic mutation analysis of the mitochondrial D-loop region in 14 urothelial cell carcinomas. A total of 28 somatic mutations, all heteroplasmic, were detected in 8 of 14 individuals (57.1 %). Insertion/deletion changes in unstable mono- and dinucleotide repeat segments comprise the most pervasive class of mutations (9 of 28), while two recurring single-base substitution loci were identified. Seven variants, mostly insertion/deletions, represent population shifts from a heteroplasmic germline toward dominance in the tumor. In four cases, DNA from matched urine samples was similarly analyzed, with all somatic variants present in associated tumors readily detectable in the bodily fluid. Consistent with previous findings, mutant populations in urine were similar to those detected in tumor and in three of four cases were more prominent in urine.

KEY MESSAGES

PRS accurately detects high mtDNA mutations in UCCs and their body fluids. mtDNA mutations are universally heteroplasmic and often appear at low levels. The PRS technology could be a viable approach to develop mitochondrial biomarkers.

Pneumatically actuated microvalve circuits for programmable automation of chemical and biochemical analysis

Programmable microfluidic platforms (PMPs) are enabling significant advances in the utility of microfluidics for chemical and biochemical analysis. Traditional microfluidic devices are analogous to application-specific devices--a new device is needed to implement each new chemical or biochemical assay. PMPs are analogous to digital electronic processors--all that is needed to implement a new assay is a change in the order of operations conducted by the device. In this review, we introduce PMPs based on normally-closed microvalves. We discuss recent applications of PMPs in diverse fields including genetic analysis, antibody-based biomarker analysis, and chemical analysis in planetary exploration. Prospects, challenges, and future concepts for this emerging technology will also be presented.

Solvent compatible microfluidic platforms for pharmaceutical solid form screening

The use of SIFEL in the crystallization fluid layers renders the microfluidic crystallization array compatible with solvents such as tetrahydrofuran, acetonitrile, chloroform, hexane, and toluene.

Single-use thermoplastic microfluidic burst valves enabling on-chip reagent storage

A simple and reliable method for fabricating single-use normally closed burst valves in thermoplastic microfluidic devices is presented, using a process flow that is readily integrated into established workflows for the fabrication of thermoplastic microfluidics. An experimental study of valve performance reveals the relationships between valve geometry and burst pressure. The technology is demonstrated in a device employing multiple valves engineered to actuate at different inlet pressures that can be generated using integrated screw pumps. On-chip storage and reconstitution of fluorescein salt sealed within defined reagent chambers are demonstrated. By taking advantage of the low gas and water permeability of cyclic olefin copolymer, the robust burst valves allow on-chip hermetic storage of reagents, making the technology well suited for the development of integrated and disposable assays for use at the point of care.

Future of portable devices for plant pathogen diagnosis

The demand for rapid and accurate diagnosis of plant diseases has risen in the last decade. On-site diagnosis of single or multiple pathogens using portable devices is the first step in this endeavour. Despite extensive attempts to develop portable devices for pathogen detection, current technologies are still restricted to detecting known pathogens with limited detection accuracy. Developing new detection techniques for rapid and accurate detection of multiple plant pathogens and their associated variants is essential. Recent single DNA sequencing technologies are a promising new avenue for developing future portable devices for plant pathogen detection. In this review, we detail the current progress in portable devices and technologies used for detecting plant pathogens, the current position of emerging sequencing technologies for analysis of plant genomics, and the future of portable devices for rapid pathogen diagnosis.

Recent developments in microfluidics for cell studies

As a technique for precisely manipulating fluid at the micrometer scale, the field of microfluidics has experienced an explosive growth over the past two decades, particularly owing to the advances in device design and fabrication. With the inherent advantages associated with its scale of operation, and its flexibility in being incorporated with other microscale techniques for manipulation and detection, microfluidics has become a major enabling technology, which has introduced new paradigms in various fields involving biological cells. A microfluidic device is able to realize functions that are not easily imaginable in conventional biological analysis, such as highly parallel, sophisticated high-throughput analysis, single-cell analysis in a well-defined manner, and tissue engineering with the capability of manipulation at the single-cell level. Major advancements in microfluidic device fabrication and the growing trend of implementing microfluidics in cell studies are presented, with a focus on biological research and clinical diagnostics.

New tools and new biology: recent miniaturized systems for molecular and cellular biology

Recent advances in applied physics and chemistry have led to the development of novel microfluidic systems. Microfluidic systems allow minute amounts of reagents to be processed using μm-scale channels and offer several advantages over conventional analytical devices for use in biological sciences: faster, more accurate and more reproducible analytical performance, reduced cell and reagent consumption, portability, and integration of functional components in a single chip. In this review, we introduce how microfluidics has been applied to biological sciences. We first present an overview of the fabrication of microfluidic systems and describe the distinct technologies available for biological research. We then present examples of microsystems used in biological sciences, focusing on applications in molecular and cellular biology.

Materials for microfluidic chip fabrication

Through manipulating fluids using microfabricated channel and chamber structures, microfluidics is a powerful tool to realize high sensitive, high speed, high throughput, and low cost analysis. In addition, the method can establish a well-controlled microenivroment for manipulating fluids and particles. It also has rapid growing implementations in both sophisticated chemical/biological analysis and low-cost point-of-care assays. Some unique phenomena emerge at the micrometer scale. For example, reactions are completed in a shorter amount of time as the travel distances of mass and heat are relatively small; the flows are usually laminar; and the capillary effect becomes dominant owing to large surface-to-volume ratios. In the meantime, the surface properties of the device material are greatly amplified, which can lead to either unique functions or problems that we would not encounter at the macroscale. Also, each material inherently corresponds with specific microfabrication strategies and certain native properties of the device. Therefore, the material for making the device plays a dominating role in microfluidic technologies. In this Account, we address the evolution of materials used for fabricating microfluidic chips, and discuss the application-oriented pros and cons of different materials. This Account generally follows the order of the materials introduced to microfluidics. Glass and silicon, the first generation microfluidic device materials, are perfect for capillary electrophoresis and solvent-involved applications but expensive for microfabriaction. Elastomers enable low-cost rapid prototyping and high density integration of valves on chip, allowing complicated and parallel fluid manipulation and in-channel cell culture. Plastics, as competitive alternatives to elastomers, are also rapid and inexpensive to microfabricate. Their broad variety provides flexible choices for different needs. For example, some thermosets support in-situ fabrication of arbitrary 3D structures, while some perfluoropolymers are extremely inert and antifouling. Chemists can use hydrogels as highly permeable structural material, which allows diffusion of molecules without bulk fluid flows. They are used to support 3D cell culture, to form diffusion gradient, and to serve as actuators. Researchers have recently introduced paper-based devices, which are extremely low-cost to prepare and easy to use, thereby promising in commercial point-of-care assays. In general, the evolution of chip materials reflects the two major trends of microfluidic technology: powerful microscale research platforms and low-cost portable analyses. For laboratory research, chemists choosing materials generally need to compromise the ease in prototyping and the performance of the device. However, in commercialization, the major concerns are the cost of production and the ease and reliability in use. There may be new growth in the combination of surface engineering, functional materials, and microfluidics, which is possibly accomplished by the utilization of composite materials or hybrids for advanced device functions. Also, significant expanding of commercial applications can be predicted.

Innovations in studying in vivo cell behavior and pharmacology in complex tissues--microvascular endothelial cells in the spotlight

Many studies on the molecular control underlying normal cell behavior and cellular responses to disease stimuli and pharmacological intervention are conducted in single-cell culture systems, while the read-out of cellular engagement in disease and responsiveness to drugs in vivo is often based on overall tissue responses. As the majority of drugs under development aim to specifically interact with molecular targets in subsets of cells in complex tissues, this approach poses a major experimental discrepancy that prevents successful development of new therapeutics. In this review, we address the shortcomings of the use of artificial (single) cell systems and of whole tissue analyses in creating a better understanding of cell engagement in disease and of the true effects of drugs. We focus on microvascular endothelial cells that actively engage in a wide range of physiological and pathological processes. We propose a new strategy in which in vivo molecular control of cells is studied directly in the diseased endothelium instead of at a (far) distance from the site where drugs have to act, thereby accounting for tissue-controlled cell responses. The strategy uses laser microdissection-based enrichment of microvascular endothelium which, when combined with transcriptome and (phospho)proteome analyses, provides a factual view on their status in their complex microenvironment. Combining this with miniaturized sample handling using microfluidic devices enables handling the minute sample input that results from this strategy. The multidisciplinary approach proposed will enable compartmentalized analysis of cell behavior and drug effects in complex tissue to become widely implemented in daily biomedical research and drug development practice.

Radiation resistance of sequencing chips for in situ life detection

Life beyond Earth may be based on RNA or DNA if such life is related to life on Earth through shared ancestry due to meteoritic exchange, such as may be the case for Mars, or if delivery of similar building blocks to habitable environments has biased the evolution of life toward utilizing nucleic acids. In this case, in situ sequencing is a powerful approach to identify and characterize such life without the limitations or expense of returning samples to Earth, and can monitor forward contamination. A new semiconductor sequencing technology based on sensing hydrogen ions released during nucleotide incorporation can enable massively parallel sequencing in a small, robust, optics-free CMOS chip format. We demonstrate that these sequencing chips survive several analogues of space radiation at doses consistent with a 2-year Mars mission, including protons with solar particle event-distributed energy levels and 1 GeV oxygen and iron ions. We find no measurable impact of irradiation at 1 and 5 Gy doses on sequencing quality nor on low-level hardware characteristics. Further testing is required to study the impacts of soft errors as well as to characterize performance under neutron and gamma irradiation and at higher doses, which would be expected during operation in environments with significant trapped energetic particles such as during a mission to Europa. Our results support future efforts to use in situ sequencing to test theories of panspermia and/or whether life has a common chemical basis.

Fabrication and multifunction integration of microfluidic chips by femtosecond laser direct writing

In the pursuit of modern microfluidic chips with multifunction integration, micronanofabrication techniques play an increasingly important role. Despite the fact that conventional fabrication approaches such as lithography, imprinting and soft lithography have been widely used for the preparation of microfluidic chips, it is still challenging to achieve complex microfluidic chips with multifunction integration. Therefore, novel micronanofabrication approaches that could be used to achieve this end are highly desired. As a powerful 3D processing tool, femtosecond laser fabrication shows great potential to endow general microfluidic chips with multifunctional units. In this review, we briefly introduce the fundamental principles of femtosecond laser micronanofabrication. With the help of laser techniques, both the preparation and functionalization of advanced microfluidic chips are summarized. Finally, the current challenges and future perspective of this dynamic field are discussed based on our own opinion.

A microfluidic platform for evaporation-based salt screening of pharmaceutical parent compounds

We describe a microfluidic platform to screen for salt forms of pharmaceutical compounds (PCs) via controlled evaporation. The platform enables on-chip combinatorial mixing of PC and salt former solutions in a 24-well array (~200 nL/well), which is a drastic reduction in the amount of PC needed per condition screened compared to traditional screening approaches that require ~100 μL/well. The reduced sample needs enable salt screening at a much earlier stage in the drug development process, when only limited quantities of PCs are available. Compatibility with (i) solvents commonly used in the pharmaceutical industry, and (ii) Raman spectroscopy for solid form identification was ensured by using a hybrid microfluidic platform. A thin layer of elastomeric PDMS was utilized to retain pneumatic valving capabilities. This layer is sandwiched between layers of cyclic-olefin copolymer, a material with low air and solvent permeability and low Raman background to yield a physically rigid and Raman compatible chip. A solvent-impermeable thiolene layer patterned with evaporation channels permits control over the rate of solvent evaporation. Control over the rate of solvent evaporation (2-15 nL h(-1)) results in consistent, known rates of increase in the supersaturation levels attained on-chip, and increases the probability for crystalline solids to form. The modular nature of the platform enables on-chip Raman and birefringence analysis of the solid forms. Model compounds, tamoxifen and ephedrine, were used to validate the platform's ability to screen for salts. On-chip Raman analysis helped to identify six different salts each of tamoxifen and ephedrine.

Digitally programmable microfluidic automaton for multiscale combinatorial mixing and sample processing

A digitally programmable microfluidic Automaton consisting of a 2-dimensional array of pneumatically actuated microvalves is programmed to perform new multiscale mixing and sample processing operations. Large (μL-scale) volume processing operations are enabled by precise metering of multiple reagents within individual nL-scale valves followed by serial repetitive transfer to programmed locations in the array. A novel process exploiting new combining valve concepts is developed for continuous rapid and complete mixing of reagents in less than 800 ms. Mixing, transfer, storage, and rinsing operations are implemented combinatorially to achieve complex assay automation protocols. The practical utility of this technology is demonstrated by performing automated serial dilution for quantitative analysis as well as the first demonstration of on-chip fluorescent derivatization of biomarker targets (carboxylic acids) for microchip capillary electrophoresis on the Mars Organic Analyzer. A language is developed to describe how unit operations are combined to form a microfluidic program. Finally, this technology is used to develop a novel microfluidic 6-sample processor for combinatorial mixing of large sets (>2(6) unique combinations) of reagents. The digitally programmable microfluidic Automaton is a versatile programmable sample processor for a wide range of process volumes, for multiple samples, and for different types of analyses.

Miniaturized technology for protein and nucleic acid point-of-care testing

The field of point-of-care (POC) testing technology is developing quickly and producing instruments that are increasingly reliable, while their size is being gradually reduced. Proteins are a common target for POC analyses and the detection of protein markers typically involves immunoassays aimed at detecting different groups of proteins such as tumor markers, inflammation proteins, and cardiac markers; but other techniques can also be used to analyze plasma proteins. In the case of nucleic acids, hybridization and amplification strategies can be used to record electromagnetic or electric signals. These techniques allow for the identification of specific viral or bacterial infections as well as specific cancers. In this review, we consider some of the latest advances in the analysis of specific nucleic acid and protein biomarkers, taking into account their trend toward miniaturization and paying special attention to the technology that can be implemented in future applications, such as lab-on-a-chip instruments.

Microfluidic 3D cell culture: potential application for tissue-based bioassays

Current fundamental investigations of human biology and the development of therapeutic drugs commonly rely on 2D monolayer cell culture systems. However, 2D cell culture systems do not accurately recapitulate the structure, function or physiology of living tissues, nor the highly complex and dynamic 3D environments in vivo. Microfluidic technology can provide microscale complex structures and well-controlled parameters to mimic the in vivo environment of cells. The combination of microfluidic technology with 3D cell culture offers great potential for in vivo-like tissue-based applications, such as the emerging organ-on-a-chip system. This article will review recent advances in the microfluidic technology for 3D cell culture and their biological applications.

Theory, fabrication and applications of microfluidic and nanofluidic biosensors

Biosensors are a broad array of devices that detect the type and amount of a biological species or biomolecule. Several different types of biosensors have been developed that rely on changes to mechanical, chemical or electrical properties of the transduction or sensing element to induce a measurable signal. Often, a biosensor will integrate several functions or unit operations such as sample extraction, manipulation and detection on a single platform. This review begins with an overview of the current state-of-the-art biosensor field. Next, the review delves into a special class of biosensors that rely on microfluidics and nanofluidics by presenting the underlying theory, fabrication and several examples and applications of microfluidic and nanofluidic sensors.

Divergent dispersion behavior of ssDNA fragments during microchip electrophoresis in pDMA and LPA entangled polymer networks

Resolution of DNA fragments separated by electrophoresis in polymer solutions ("matrices") is determined by both the spacing between peaks and the width of the peaks. Prior research on the development of high-performance separation matrices has been focused primarily on optimizing DNA mobility and matrix selectivity, and gave less attention to peak broadening. Quantitative data are rare for peak broadening in systems in which high electric field strengths are used (>150 V/cm), which is surprising since capillary and microchip-based systems commonly run at these field strengths. Here, we report results for a study of band broadening behavior for ssDNA fragments on a glass microfluidic chip, for electric field strengths up to 320 V/cm. We compare dispersion coefficients obtained in a poly(N,N-dimethylacrylamide) (pDMA) separation matrix that was developed for chip-based DNA sequencing with a commercially available linear polyacrylamide (LPA) matrix commonly used in capillaries. Much larger DNA dispersion coefficients were measured in the LPA matrix as compared to the pDMA matrix, and the dependence of dispersion coefficient on DNA size and electric field strength were found to differ quite starkly in the two matrices. These observations lead us to propose that DNA migration mechanisms differ substantially in our custom pDMA matrix compared to the commercially available LPA matrix. We discuss the implications of these results in terms of developing optimal matrices for specific separation (microchip or capillary) platforms.

Design considerations for electrostatic microvalves with applications in poly(dimethylsiloxane)-based microfluidics

Microvalves are critical in the operation of integrated microfluidic chips for a wide range of applications. In this paper, we present an analytical model to guide the design of electrostatic microvalves that can be integrated into microfluidic chips using standard fabrication processes and can reliably operate at low actuation potentials (<250 V). Based on the analytical model, we identify design guidelines and operational considerations for elastomeric electrostatic microvalves and formulate strategies to minimize their actuation potentials, while maintaining the feasibility of fabrication and integration. We specifically explore the application of the model to design microfluidic microvalves fabricated in poly(dimethylsiloxane), using only soft-lithographic techniques. We discuss the electrostatic actuation in terms of several microscale phenomena, including squeeze-film damping and adhesion-driven microvalve collapse. The actuation potentials predicted by the model are in good agreement with experimental data obtained with a microfabricated array of electrostatic microvalves actuated in air and oil. The model can also be extended to the design of peristaltic pumps for microfluidics and to the prediction of actuation potentials of microvalves in viscous liquid environments. Additionally, due to the compact ancillaries required to generate low potentials, these electrostatic microvalves can potentially be used in portable microfluidic chips.

Integrated allele-specific polymerase chain reaction-capillary electrophoresis microdevice for single nucleotide polymorphism genotyping

An integrated allele-specific (AS) polymerase chain reaction (PCR) and capillary electrophoresis (CE) microdevice has been developed for multiplex single nucleotide polymorphism (SNP) genotyping on a portable instrumentation, which was applied for on-site identification of HANWOO (Korean indigenous beef cattle). Twelve sets of primers were designed for targeting beef cattle's eleven SNP loci for HANWOO verification and one primer set for a positive PCR control, and the success rate for identification of HANWOO was demonstrated statistically. The AS PCR and CE separation for multiplex SNP typing was carried out on a glass-based microchip consisting of four layers: a microchannel plate for microfluidic control, a Pt-electrode plate for a resistance temperature detector (RTD), a poly(dimethylsiloxane) (PDMS) membrane and a manifold glass for microvalve function. The operation of the sample loading, AS PCR, microvalve, and CE on a chip was automated with a portable genetic analyzer, and the laser-induced fluorescence detection was performed on a miniaturized fluorescence detector. The blind samples were correctly identified as a HANWOO by showing one or two amplicon peaks in the electropherogram, while the imported beef cattle revealed more than five peaks. Our genetic analysis platform provides rapid, accurate, and on-site multiplex SNP typing.

Lifting gate polydimethylsiloxane microvalves and pumps for microfluidic control

We describe the development and characterization of pneumatically actuated "lifting gate" microvalves and pumps. A fluidic layer containing the gate structure and a pneumatic layer are fabricated by soft-lithography in PDMS and bonded permanently with an oxygen plasma treatment. The microvalve structures are then reversibly bonded to a featureless glass or plastic substrate to form hybrid glass-PDMS and plastic-PDMS microchannel structures. The break-through pressures of the microvalve increase linearly up to 65 kPa as the closing pressure increases. The pumping capability of these structures ranges from the nanoliter to microliter scale depending on the number of cycles and closing pressure employed. The micropump structures exhibit up to 86.2% pumping efficiency from flow rate measurements. The utility of these structures for integrated sample processing is demonstrated by performing an automated immunoassay. These lifting gate valve and pump structures enable facile integration of complex microfluidic control systems with a wide range of lab-on-a-chip substrates.

Integrated microdevice of reverse transcription-polymerase chain reaction with colorimetric immunochromatographic detection for rapid gene expression analysis of influenza A H1N1 virus

An integrated microdevice of a reverse transcription-polymerase chain reaction (RT-PCR) reactor and an immunochromatographic strip was constructed for colorimetric detection of gene expression of influenza A virus subtype H1N1. An RT-PCR cocktail, which included Texas Red-labeled primers, dNTP including biotin-labeled dUTP, and RNA templates of influenza A H1N1 virus, was filled in the PCR chamber through the micropump, and the RT-PCR was performed to amplify the target H1 gene (102 bp). The resultant amplicons bearing biotin moieties and Texas Red haptens were subsequently eluted to the immunochromatographic strip, in which they were first conjugated with the gold nanoparticle labeled anti-hapten antibody in the conjugation pad, and then captured on the streptavidin coated test line through the biotin–streptavidin interaction. By observing a violet color in the test line which was derived from the gold nanoparticle, we confirmed the H1N1 target virus. The entire process on the integrated microdevice consisting of a micropump, a 2 μL PCR chamber, and an immunochromatographic strip was carried out on the portable genetic analyzer within 2.5 h, enabling on-site colorimetric pathogen identification with detection sensitivity of 14.1 pg RNA templates.