Microfluidics for biological measurements with single-molecule resolution

A machine learning based method for tracking of simultaneously imaged neural activity and body posture of freely moving maggot

To understand neural basis of animal behavior, it is necessary to monitor neural activity and behavior in freely moving animal before building relationship between them. Here we use light sheet fluorescence microscope (LSFM) combined with microfluidic chip to simultaneously capture neural activity and body movement in small freely behaving Drosophila larva. We develop a transfer learning based method to simultaneously track the continuously changing body posture and activity of neurons that move together using a sub-region tracking network with a precise landmark estimation network for the inference of target landmark trajectory. Based on the tracking of each labelled neuron, the activity of the neuron indicated by fluorescent intensity is calculated. For each video, annotation of only 20 frames in a video is sufficient to yield human-level accuracy for all other frames. The validity of this method is further confirmed by reproducing the activity pattern of PMSIs (period-positive median segmental interneurons) and larval movement as previously reported. Using this method, we disclosed the correlation between larval movement and left-right asymmetry in activity of a group of unidentified neurons labelled by R52H01-Gal4 and further confirmed the roles of these neurons in bilateral balance of body contraction during larval crawling by genetic inhibition of these neurons. Our method provides a new tool for accurate extraction of neural activities and movement of freely behaving small-size transparent animals.

When Super-Resolution Microscopy Meets Microfluidics: Enhanced Biological Imaging and Analysis with Unprecedented Resolution

Super-resolution microscopy is rapidly developed in recent years, allowing biologists to extract more quantitative information on subcellular processes in live cells that is usually not accessible with conventional techniques. However, super-resolution imaging is not fully exploited because of the lack of an appropriate and multifunctional experimental platform. As an important tool in life sciences, microfluidics is capable of cell manipulation and the regulation of the cellular environment because of its superior flexibility and biocompatibility. The combination of microfluidics and super-resolution microscopy revolutionizes the study of complex cellular properties and dynamics, providing valuable insights into cellular structure and biological functions at the single-molecule level. In this perspective, an overview of the main advantages of microfluidic technology that are essential to the performance of super-resolution microscopy are offered. The main benefits of performing super-resolution imaging with microfluidic devices are highlighted and perspectives on the diverse applications that are facilitated by combining these two powerful techniques are provided.

Pressure-controlled microfluidics for automated single-molecule sample preparation

Sample preparation is a crucial step in single-molecule experiments and involves passivating the microfluidic sample chamber, immobilizing the molecules, and setting experimental buffer conditions. The efficiency of the experiment depends on the quality and speed of sample preparation, which is often performed manually and relies on the experience of the experimenter. This can result in inefficient use of single-molecule samples and time, especially for high-throughput applications. To address this, a pressure-controlled microfluidic system is proposed to automate single-molecule sample preparation. The hardware is based on microfluidic components from ElveFlow and is designed to be cost-effective and adaptable to various microscopy applications. The system includes a reservoir pressure adapter and a reservoir holder designed for additive manufacturing. Two flow chamber designs Ibidi µ-slide and Grace Bio-Labs HybriWell chamber are characterized, and the flow characteristics of the liquid at different volume flow rates V˙ are simulated using CFD-simulations and compared to experimental and theoretical values. The goal of this work is to establish a straightforward and robust system for single-molecule sample preparation that can increase the efficiency of experiments and reduce the bottleneck of manual sample preparation, particularly for high-throughput applications.

Microfluidic Gradient Culture Arrays for Cell Pro-oxidation Analysis Using Bipolar Electrochemiluminescence

A microfluidic gradient array is a widely used screening and analysis device, which has characteristics of high efficiency, high automation, and low consumption. Bipolar electrode electrochemiluminescence (BPE-ECL) has special value in microfluidic array chips. The combination of the microfluidic gradient and BPE arrays has potential for high-throughput screening. In this article, a microfluidic BPE array chip for gradient culture and conditional screening of cancer cells was designed. The generation of concentration gradients, continuous culture of cancer cells with high throughput, and drug screening through BPE-ECL of the Ru(bpy)₃²⁺/TPrA system can be performed in one chip. We tested gradient pro-oxidation of MCF-7 by ascorbic acid and the synergistic effect of pro-oxidation on doxorubicin. The method achieves high analysis efficiency through a BPE array while simplifying the tedious procedures required by cell culture methods.

Direct digital sensing of protein biomarkers in solution

The detection of proteins is of central importance to biomolecular analysis and diagnostics. Typical immunosensing assays rely on surface-capture of target molecules, but this constraint can limit specificity, sensitivity, and the ability to obtain information beyond simple concentration measurements. Here we present a surface-free, single-molecule microfluidic sensing platform for direct digital protein biomarker detection in solution, termed digital immunosensor assay (DigitISA). DigitISA is based on microchip electrophoretic separation combined with single-molecule detection and enables absolute number/concentration quantification of proteins in a single, solution-phase step. Applying DigitISA to a range of targets including amyloid aggregates, exosomes, and biomolecular condensates, we demonstrate that the assay provides information beyond stoichiometric interactions, and enables characterization of immunochemistry, binding affinity, and protein biomarker abundance. Taken together, our results suggest a experimental paradigm for the sensing of protein biomarkers, which enables analyses of targets that are challenging to address using conventional immunosensing approaches.

Single-Cell Analysis of circRNA Using ddPCR

Droplet digital polymerase chain reaction (ddPCR) is a new quantitative PCR method based on water-oil emulsion droplet technology. ddPCR enables highly sensitive and accurate quantification of nucleic acid molecules, especially when their copy numbers are low. In ddPCR, a sample is fractionated into ~20,000 droplets, and every nanoliter-sized droplet undergoes PCR amplification of the target molecule. The fluorescence signals of droplets are then recorded by an automated droplet reader. Circular RNAs (circRNAs) are single-stranded, covalently closed RNA molecules that are ubiquitously expressed in animals and plants. CircRNAs are promising as biomarkers for cancer diagnosis and prognosis and as therapeutic targets or agents to inhibit oncogenic microRNAs or proteins (Kristensen LS, Jakobsen T, Hager H, Kjems J, Nat Rev Clin Oncol 19:188-206, 2022). In this chapter, the procedures for the quantitation of a circRNA in single pancreatic cancer cells using ddPCR are described.

A Critical Review on the Sensing, Control, and Manipulation of Single Molecules on Optofluidic Devices

Single-molecule techniques have shifted the paradigm of biological measurements from ensemble measurements to probing individual molecules and propelled a rapid revolution in related fields. Compared to ensemble measurements of biomolecules, single-molecule techniques provide a breadth of information with a high spatial and temporal resolution at the molecular level. Usually, optical and electrical methods are two commonly employed methods for probing single molecules, and some platforms even offer the integration of these two methods such as optofluidics. The recent spark in technological advancement and the tremendous leap in fabrication techniques, microfluidics, and integrated optofluidics are paving the way toward low cost, chip-scale, portable, and point-of-care diagnostic and single-molecule analysis tools. This review provides the fundamentals and overview of commonly employed single-molecule methods including optical methods, electrical methods, force-based methods, combinatorial integrated methods, etc. In most single-molecule experiments, the ability to manipulate and exercise precise control over individual molecules plays a vital role, which sometimes defines the capabilities and limits of the operation. This review discusses different manipulation techniques including sorting and trapping individual particles. An insight into the control of single molecules is provided that mainly discusses the recent development of electrical control over single molecules. Overall, this review is designed to provide the fundamentals and recent advancements in different single-molecule techniques and their applications, with a special focus on the detection, manipulation, and control of single molecules on chip-scale devices.

Coronavirus Disease 2019 (COVID-19): Emerging detection technologies and auxiliary analysis

The ongoing COVID-19 pandemic constitutes a new challenge for public health. Prevention and control of infection have become urgent and serious issues. To meet the clinical demand for higher accuracy of COVID-19 detection, the development of fast and efficient methods represents an important step. The most common methods of COVID-19 diagnosis, relying on real-time fluorescent quantitative PCR(RT-qPCR), computed tomography, and new-generation sequencing technologies, have a series of advantages, especially for early diagnosis and screening. In addition, joint efforts of researchers all over the world have led to the development of other rapid detection methods with high sensitivity, ease of use, cost-effectiveness, or allowing multiplex analysis based on technologies such as dPCR, ELISA, fluorescence immunochromatography assay, and the microfluidic detection chip method. The main goal of this review was to provide a critical discussion on the development and application of these different analytical methods, which based on etiology, serology, and molecular biology, as well as to compare their respective advantages and disadvantages. In addition to these methods, hematology and biochemistry, as well as auxiliary analysis based on pathological anatomy, ultrasonography, and cytokine detection, will help understand COVID-19 pathogenesis. Together, these technologies may promote and open new windows to unravel issues surrounding symptomatic and asymptomatic COVID-19 infections and improve clinical strategies toward reducing mortality.

Real-Time Monitoring of the In Situ Microfluidic Synthesis of Ag Nanoparticles on Solid Substrate for Reliable SERS Detection

A sharpened control over the parameters affecting the synthesis of plasmonic nanostructures is often crucial for their application in biosensing, which, if based on surface-enhanced Raman spectroscopy (SERS), requires well-defined optical properties of the substrate. In this work, a method for the microfluidic synthesis of Ag nanoparticles (NPs) on porous silicon (pSi) was developed, focusing on achieving a fine control over the morphological characteristics and spatial distribution of the produced nanostructures to be used as SERS substrates. To this end, a pSi membrane was integrated in a microfluidic chamber in which the silver precursor solution was injected, allowing for the real-time monitoring of the reaction by UV-Vis spectroscopy. The synthesis parameters, such as the concentration of the silver precursor, the temperature, and the flow rate, were varied in order to study their effects on the final silver NPs' morphology. Variations in the flow rate affected the size distribution of the NPs, whereas both the temperature and the concentration of the silver precursor strongly influenced the rate of the reaction and the particle size. Consistently with the described trends, SERS tests using 4-MBA as a probe showed how the flow rate variation affected the SERS enhancement uniformity, and how the production of larger NPs, as a result of an increase in temperature or of the concentration of the Ag precursor, led to an increased SERS efficiency.

A digitalized isothermal nucleic acid testing platform based on a pump-free open droplet array microfluidic chip

Digital PCR has shown great potential for quantitative nucleic acid testing (NAT), but most existing platforms are dependent on large auxiliary equipment (e.g., vacuum pump, amplification instrument, fluorescence microscope) to achieve target dispersion, amplification, signal capture and result analysis. Such complex, expensive and bulky NAT platforms have limited their applications in resource-limited areas, especially for point-of-care testing (POCT). In this work, we designed a digital isothermal NAT platform based on a pump-free open droplet array microfluidic chip. A pump-free microfluidic chip was developed based on an open microdroplet array in the form of thousands of independent microdroplets for spontaneous sample dispersion, without the need for external power. Combined with a handheld fluorescent signal reader based on a smartphone, this digital NAT platform can accurately quantify as low as 1 copy per μL of λDNA. Therefore, our integrated NAT platform, as a potable, robust and low-cost tool for highly accurate NA quantitative analysis, holds great potential for POCT applications.

Different Microfluidic Environments for In Vitro Testing of Lipid Nanoparticles against Osteosarcoma

The use of lipid nanoparticles as biodegradable shells for controlled drug delivery shows promise as a more effective and targeted tumor treatment than traditional treatment methods. Although the combination of target therapy with nanotechnology created new hope for cancer treatment, methodological issues during in vitro validation of nanovehicles slowed their application. In the current work, the effect of methotrexate (MTX) encapsulated in different matrices was evaluated in a dynamic microfluidic platform. Effects on the viability of osteosarcoma cells in the presence of recirculation of cell media, free MTX and two types of blank and drug-containing nanoparticles were successfully assessed in different tumor-mimicking microenvironments. Encapsulated MTX was more effective than the equal dose free drug treatment, as cell death significantly increased under the recirculation of both types of drug-loaded nanoparticles in all concentrations. In fact, MTX-nanoparticles reduced cell population 50 times more than the free drug when 150-µM drug dose was recirculated. Moreover, when compared to the equivalent free drug dose recirculation, cell number was reduced 60 and 100 points more under recirculation of each nanoparticle with a 15-µM drug concentration. Thus, the results obtained with the microfluidic model present MTX-lipid nanoparticles as a promising and more effective therapy for pediatric osteosarcoma treatment than current treatment options.

A Molecular Approach to Quantum Sensing

The second quantum revolution hinges on the creation of materials that unite atomic structural precision with electronic and structural tunability. A molecular approach to quantum information science (QIS) promises to enable the bottom-up creation of quantum systems. Within the broad reach of QIS, which spans fields ranging from quantum computation to quantum communication, we will focus on quantum sensing. Quantum sensing harnesses quantum control to interrogate the world around us. A broadly applicable class of quantum sensors would feature adaptable environmental compatibility, control over distance from the target analyte, and a tunable energy range of interaction. Molecules enable customizable "designer" quantum sensors with tunable functionality and compatibility across a range of environments. These capabilities offer the potential to bring unmatched sensitivity and spatial resolution to address a wide range of sensing tasks from the characterization of dynamic biological processes to the detection of emergent phenomena in condensed matter. In this Outlook, we outline the concepts and design criteria central to quantum sensors and look toward the next generation of designer quantum sensors based on new classes of molecular sensors.

Ultra-precise quantification of mRNA targets across a broad dynamic range with nanoreactor beads

Precise quantification of molecular targets in a biological sample across a wide dynamic range is a key requirement in many diagnostic procedures, such as monitoring response to therapy or detection of measurable residual disease. State of the art digital PCR assays provide for a dynamic range of four orders of magnitude. However digital assays are complex and require sophisticated microfluidic tools. Here we present an assay format that enables ultra-precise quantification of RNA targets in a single measurement across a dynamic range of more than six orders of magnitude. The approach is based on hydrogel beads that provide for microfluidic free compartmentalization of the sample as they are used as nanoreactors for reverse transcription, PCR amplification and combined real time and digital detection of gene transcripts. We have applied these nanoreactor beads for establishing an assay for the detection and quantification of BCR-ABL1 fusion transcripts. The assay has been characterized for its precision and linear dynamic range. A comparison of the new method against conventional real time RT-PCR analysis (reference method) with clinical samples from patients with chronic myeloid leukemia (CML) revealed excellent concordance with Pearsons correlation coefficient of 0.983 and slope of 1.08.

Characterizing microfluidic approaches for a fast and efficient reagent exchange in single-molecule studies

Single-molecule experiments usually take place in flow cells. This experimental approach is essential for experiments requiring a liquid environment, but is also useful to allow the exchange of reagents before or during measurements. This is crucial in experiments that need to be triggered by ligands or require a sequential addition of proteins. Home-fabricated flow cells using two glass coverslips and a gasket made of paraffin wax are a widespread approach. The volume of the flow cell can be controlled by modifying the dimensions of the channel while the reagents are introduced using a syringe pump. In this system, high flow rates disturb the biological system, whereas lower flow rates lead to the generation of a reagent gradient in the flow cell. For very precise measurements it is thus desirable to have a very fast exchange of reagents with minimal diffusion. We propose the implementation of multistream laminar microfluidic cells with two inlets and one outlet, which achieve a minimum fluid switching time of 0.25 s. We additionally define a phenomenological expression to predict the boundary switching time for a particular flow cell cross section. Finally, we study the potential applicability of the platform to study kinetics at the single molecule level.

PCR past, present and future

PCR has become one of the most valuable techniques currently used in bioscience, diagnostics and forensic science. Here we review the history of PCR development and the technologies that have evolved from the original PCR method. Currently, there are two main areas of PCR utilization in bioscience: high-throughput PCR systems and microfluidics-based PCR devices for point-of-care (POC) applications. We also discuss the commercialization of these techniques and conclude with a look into their modifications and use in innovative areas of biomedicine. For example, real-time reverse transcription PCR is the gold standard for SARS-CoV-2 diagnoses. It could also be used for POC applications, being a key component of the sample-to-answer system.

Double Emulsion Picoreactors for High-Throughput Single-Cell Encapsulation and Phenotyping via FACS

In the past five years, droplet microfluidic techniques have unlocked new opportunities for the high-throughput genome-wide analysis of single cells, transforming our understanding of cellular diversity and function. However, the field lacks an accessible method to screen and sort droplets based on cellular phenotype upstream of genetic analysis, particularly for large and complex cells. To meet this need, we developed Dropception, a robust, easy-to-use workflow for precise single-cell encapsulation into picoliter-scale double emulsion droplets compatible with high-throughput screening via fluorescence-activated cell sorting (FACS). We demonstrate the capabilities of this method by encapsulating five standardized mammalian cell lines of varying sizes and morphologies as well as a heterogeneous cell mixture of a whole dissociated flatworm (5-25 μm in diameter) within highly monodisperse double emulsions (35 μm in diameter). We optimize for preferential encapsulation of single cells with extremely low multiple-cell loading events (<2% of cell-containing droplets), thereby allowing direct linkage of cellular phenotype to genotype. Across all cell lines, cell loading efficiency approaches the theoretical limit with no observable bias by cell size. FACS measurements reveal the ability to discriminate empty droplets from those containing cells with good agreement to single-cell occupancies quantified via microscopy, establishing robust droplet screening at single-cell resolution. High-throughput FACS screening of cellular picoreactors has the potential to shift the landscape of single-cell droplet microfluidics by expanding the repertoire of current nucleic acid droplet assays to include functional phenotyping.

Utilization of Digital PCR in Quantity Verification of Plasmid Standards Used in Quantitative PCR

Quantitative PCR (qPCR) is a widely used method for nucleic acid quantification of various pathogenic microorganisms. For absolute quantification of microbial load by qPCR, it is essential to create a calibration curve from accurately quantified quantification standards, from which the number of pathogens in a sample is derived. Spectrophotometric measurement of absorbance is a routine method for estimating nucleic acid concentration, however, it may be affected by presence of other potentially contaminating nucleic acids or proteins and salts. Therefore, absorbance measurement is not reliable for estimating the concentration of stock solutions of quantification standards, based on which they are subsequently diluted. In this study, we utilized digital PCR (dPCR) for absolute quantification of qPCR plasmid standards and thus detecting possible discrepancies in the determination of the plasmid DNA number of standards derived from UV spectrophotometry. The concept of dPCR utilization for quantification of standards was applied on 45 qPCR assays using droplet-based and chip-based dPCR platforms. Using dPCR, we found that spectrophotometry overestimated the concentrations of standard stock solutions in the majority of cases. Furthermore, batch-to-batch variation in standard quantity was revealed, as well as quantitative changes in standards over time. Finally, it was demonstrated that droplet-based dPCR is a suitable tool for achieving defined quantity of quantification plasmid standards and ensuring the quantity over time, which is crucial for acquiring homogenous, reproducible and comparable quantitative data by qPCR.

Stochastic thermodynamics of a harmonically trapped colloid in linear mixed flow

In this paper, motivated by a general interest in the stochastic thermodynamics of small systems, we derive an exact expression-via path integrals-for the conditional probability density of a two-dimensional harmonically confined Brownian particle acted on by linear mixed flow. This expression is a generalization of the expression derived earlier by Foister and Van De Ven [J. Fluid Mech. 96, 105 (1980)10.1017/S0022112080002042] for the case of the corresponding free Brownian particle, and reduces to it in the appropriate unconfined limit. By considering the long-time limit of our calculated probability density function, we show that the flow-driven Brownian oscillator attains a well-defined steady state. We also show that, during the course of a transition from an initial flow-free thermal equilibrium state to the flow-driven steady state, the integral fluctuation theorem, the Jarzynski equality, and the Bochkov-Kuzovlev relation are all rigorously satisfied. Additionally, for the special cases of pure rotational flow we derive an exact expression for the distribution of the heat dissipated by the particle into the medium, and for the special case of pure elongational flow we derive an exact expression for the distribution of the total entropy change. Finally, by examining the system's stochastic thermodynamics along a reverse trajectory, we also demonstrate that in elongational flow the total entropy change satisfies a detailed fluctuation theorem.

Microfluidic Generation of Amino-Functionalized Hydrogel Microbeads Capable of On-Bead Bioassay

Microfluidic generation of hydrogel microbeads is a highly efficient and reproducible approach to create various functional hydrogel beads. Here, we report a method to prepare crosslinked amino-functionalized polyethylene glycol (PEG) microbeads using a microfluidic channel. The microbeads generated from a microfluidic device were evaluated by scanning electron microscopy (SEM), energy dispersive X-ray spectroscopy (EDS) and confocal laser scanning microscopy, respectively. We found that the microbeads were monodisperse and the amino groups were localized on the shell region of the microbeads. A swelling test exhibited compatibility with various solvents. A cell binding assay was successfully performed with RGD peptide-coupled amino-functionalized hydrogel microbeads. This strategy will enable the large production of the various functional microbeads, which can be used for solid phase peptide synthesis and on-bead bioassays.

Understanding conformational and dynamical evolution of semiflexible polymers in shear flow

A clear description of the conformational and dynamical evolution of polymer chains in shear flow is the fundamental basis of microfluidic separations and macroscopic rheological behaviors. We employ graph theory analysis to analyze the local deformation and dynamics of linear polymer chains with different rigidities in shear flow based on the simulation trajectories that record the instantaneous conformations and dynamics. Our results show that all semiflexible chains experience quasi-periodic tumbling motions when the shear strain overwhelms the U-shape (or S-shape) deformation energy barrier. More interestingly, the contact map provides solid evidence for the asymmetric deformation in the whole tumbling motion. In the stretching process: at small and intermediate shear strength, flexible polymers show a quasi-affine deformation while semiflexible ones are initially unfolded from the center of the chains, then both of them follow the extension with half dumbbell- or dumbbell-like ends; at high shear strength, all polymer chains present only a dumbbell-like extension. In the collapse process, all chains prefer to initiate the folding from chain ends. This finding can facilitate our understanding on how semiflexible polymer chains relax and dissipate the stress in shear flow.

High-throughput smFRET analysis of freely diffusing nucleic acid molecules and associated proteins

Single-molecule Förster resonance energy transfer (smFRET) is a powerful technique for nanometer-scale studies of single molecules. Solution-based smFRET, in particular, can be used to study equilibrium intra- and intermolecular conformations, binding/unbinding events and conformational changes under biologically relevant conditions without ensemble averaging. However, single-spot smFRET measurements in solution are slow. Here, we detail a high-throughput smFRET approach that extends the traditional single-spot confocal geometry to a multispot one. The excitation spots are optically conjugated to two custom silicon single photon avalanche diode (SPAD) arrays. Two-color excitation is implemented using a periodic acceptor excitation (PAX), allowing distinguishing between singly- and doubly-labeled molecules. We demonstrate the ability of this setup to rapidly and accurately determine FRET efficiencies and population stoichiometries by pooling the data collected independently from the multiple spots. We also show how the high throughput of this approach can be used o increase the temporal resolution of single-molecule FRET population characterization from minutes to seconds. Combined with microfluidics, this high-throughput approach will enable simple real-time kinetic studies as well as powerful molecular screening applications.

Mobile Microfluidics

Microfluidics platforms can program small amounts of fluids to execute a bio-protocol, and thus, can automate the work of a technician and also integrate a large part of laboratory equipment. Although most microfluidic systems have considerably reduced the size of a laboratory, they are still benchtop units, of a size comparable to a desktop computer. In this paper, we argue that achieving true mobility in microfluidics would revolutionize the domain by making laboratory services accessible during traveling or even in daily situations, such as sport and outdoor activities. We review the existing efforts to achieve mobility in microfluidics, and we discuss the conditions mobile biochips need to satisfy. In particular, we show how we adapted an existing biochip for mobile use, and we present the results when using it during a train ride. Based on these results and our systematic discussion, we identify the challenges that need to be overcome at technical, usability and social levels. In analogy to the history of computing, we make some predictions on the future of mobile biochips. In our vision, mobile biochips will disrupt how people interact with a wide range of healthcare processes, including medical testing and synthesis of on-demand medicine.

Single Cell Proteomics for Molecular Targets in Lung Cancer: High-Dimensional Data Acquisition and Analysis

In the proteomic and genomic era, lung cancer researchers are increasingly under challenge with traditional protein analyzing tools. High output, multiplexed analytical procedures are in demand for disclosing the post-translational modification, molecular interactions and signaling pathways of proteins precisely, specifically, dynamically and systematically, as well as for identifying novel proteins and their functions. This could be better realized by single-cell proteomic methods than conventional proteomic methods. Using single-cell proteomic tools including flow cytometry, mass cytometry, microfluidics and chip technologies, chemical cytometry, single-cell western blotting, the quantity and functions of proteins are analyzed simultaneously. Aside from deciphering disease mechanisms, single-cell proteomic techniques facilitate the identification and screening of biomarkers, molecular targets and promising compounds as well. This review summarized single-cell proteomic tools and their use in lung cancer.

Improved microfluidic platform for simultaneous multiple drug screening towards personalized treatment

Development of new targeted therapies is a challenge in the battle against cancer. Although a variety of treatments is currently available, there is no technique for rapidly evaluating the response of cancer patients to the drug. In this work, a microfluidic platform for the real-time simultaneous analysis of the success rate of different nanoparticle based chemotherapeutic drugs is presented. Based on a previous planar chamber and a reported sensitivity enhancing strategy, linear and cross shape microstructures were integrated into the chamber dome of the microfluidic polydimethylsiloxane and glass platform in order to provide a higher fluid mixing and treatment-cell interaction. Several methotrexate (MTX) based treatments (free MTX, MTX loaded Lecithin-PVA nanoparticles, MTX loaded Lecithin-Tween 80 nanoparticles) as well as their respective controls (cell media and both blank nanoparticles) were recirculated through the microchamber over an osteosarcoma cell monolayer. These nanovehicles reduced cell population to less than 20% (LEC-PVA nanoparticles) and 2.3% (LEC-Tween nanoparticles), demonstrating that nanoparticles are a promising target therapy for cancer treatment. Moreover, microstructured platforms demonstrated a higher efficacy in the drug-screening process: due to the liquid folding a higher amount of nanoparticles was internalized by the cells and, therefore, results were observed faster. In fact, the time required to reduce cell viability to the half was nearly a 75% faster. Furthermore, this microfluidic platform offers the capability to test up to five different drugs simultaneously, making it a powerful tool to evaluate the effect of multiple drugs and determine the most effective and personalized treatment.

Cell-Free Approaches in Synthetic Biology Utilizing Microfluidics

Synthetic biology is a rapidly growing multidisciplinary branch of science which aims to mimic complex biological systems by creating similar forms. Constructing an artificial system requires optimization at the gene and protein levels to allow the formation of entire biological pathways. Advances in cell-free synthetic biology have helped in discovering new genes, proteins, and pathways bypassing the complexity of the complex pathway interactions in living cells. Furthermore, this method is cost- and time-effective with access to the cellular protein factory without the membrane boundaries. The freedom of design, full automation, and mimicking of in vivo systems reveal advantages of synthetic biology that can improve the molecular understanding of processes, relevant for life science applications. In parallel, in vitro approaches have enhanced our understanding of the living system. This review highlights the recent evolution of cell-free gene design, proteins, and cells integrated with microfluidic platforms as a promising technology, which has allowed for the transformation of the concept of bioprocesses. Although several challenges remain, the manipulation of biological synthetic machinery in microfluidic devices as suitable 'homes' for in vitro protein synthesis has been proposed as a pioneering approach for the development of new platforms, relevant in biomedical and diagnostic contexts towards even the sensing and monitoring of environmental issues.

Target Confinement in Small Reaction Volumes Using Microfluidic Technologies: A Smart Approach for Single-Entity Detection and Analysis

Over the last decades, the study of cells, nucleic acid molecules, and proteins has evolved from ensemble measurements to so-called single-entity studies. The latter offers huge benefits, not only as biological research tools to examine heterogeneities among individual entities within a population, but also as biosensing tools for medical diagnostics, which can reach the ultimate sensitivity by detecting single targets. Whereas various techniques for single-entity detection have been reported, this review focuses on microfluidic systems that physically confine single targets in small reaction volumes. We categorize these techniques as droplet-, microchamber-, and nanostructure-based and provide an overview of their implementation for studying single cells, nucleic acids, and proteins. We furthermore reflect on the advantages and limitations of these techniques and highlight future opportunities in the field.

Microfluidic Devices for Drug Delivery Systems and Drug Screening

Microfluidic devices present unique advantages for the development of efficient drug carrier particles, cell-free protein synthesis systems, and rapid techniques for direct drug screening. Compared to bulk methods, by efficiently controlling the geometries of the fabricated chip and the flow rates of multiphase fluids, microfluidic technology enables the generation of highly stable, uniform, monodispersed particles with higher encapsulation efficiency. Since the existing preclinical models are inefficient drug screens for predicting clinical outcomes, microfluidic platforms might offer a more rapid and cost-effective alternative. Compared to 2D cell culture systems and in vivo animal models, microfluidic 3D platforms mimic the in vivo cell systems in a simple, inexpensive manner, which allows high throughput and multiplexed drug screening at the cell, organ, and whole-body levels. In this review, the generation of appropriate drug or gene carriers including different particle types using different configurations of microfluidic devices is highlighted. Additionally, this paper discusses the emergence of fabricated microfluidic cell-free protein synthesis systems for potential use at point of care as well as cell-, organ-, and human-on-a-chip models as smart, sensitive, and reproducible platforms, allowing the investigation of the effects of drugs under conditions imitating the biological system.

Single-molecule techniques in biophysics: a review of the progress in methods and applications

Single-molecule biophysics has transformed our understanding of biology, but also of the physics of life. More exotic than simple soft matter, biomatter lives far from thermal equilibrium, covering multiple lengths from the nanoscale of single molecules to up to several orders of magnitude higher in cells, tissues and organisms. Biomolecules are often characterized by underlying instability: multiple metastable free energy states exist, separated by levels of just a few multiples of the thermal energy scale k _B T, where k _B is the Boltzmann constant and T absolute temperature, implying complex inter-conversion kinetics in the relatively hot, wet environment of active biological matter. A key benefit of single-molecule biophysics techniques is their ability to probe heterogeneity of free energy states across a molecular population, too challenging in general for conventional ensemble average approaches. Parallel developments in experimental and computational techniques have catalysed the birth of multiplexed, correlative techniques to tackle previously intractable biological questions. Experimentally, progress has been driven by improvements in sensitivity and speed of detectors, and the stability and efficiency of light sources, probes and microfluidics. We discuss the motivation and requirements for these recent experiments, including the underpinning mathematics. These methods are broadly divided into tools which detect molecules and those which manipulate them. For the former we discuss the progress of super-resolution microscopy, transformative for addressing many longstanding questions in the life sciences, and for the latter we include progress in 'force spectroscopy' techniques that mechanically perturb molecules. We also consider in silico progress of single-molecule computational physics, and how simulation and experimentation may be drawn together to give a more complete understanding. Increasingly, combinatorial techniques are now used, including correlative atomic force microscopy and fluorescence imaging, to probe questions closer to native physiological behaviour. We identify the trade-offs, limitations and applications of these techniques, and discuss exciting new directions.

Toward dynamic structural biology: Two decades of single-molecule Förster resonance energy transfer

Classical structural biology can only provide static snapshots of biomacromolecules. Single-molecule Förster resonance energy transfer (smFRET) paved the way for studying dynamics in macromolecular structures under biologically relevant conditions. Since its first implementation in 1996, smFRET experiments have confirmed previously hypothesized mechanisms and provided new insights into many fundamental biological processes, such as DNA maintenance and repair, transcription, translation, and membrane transport. We review 22 years of contributions of smFRET to our understanding of basic mechanisms in biochemistry, molecular biology, and structural biology. Additionally, building on current state-of-the-art implementations of smFRET, we highlight possible future directions for smFRET in applications such as biosensing, high-throughput screening, and molecular diagnostics.

Droplet Microfluidics for the Production of Microparticles and Nanoparticles

Droplet microfluidics technology is recently a highly interesting platform in material fabrication. Droplets can precisely monitor and control entire material fabrication processes and are superior to conventional bulk techniques. Droplet production is controlled by regulating the channel geometry and flow rates of each fluid. The micro-scale size of droplets results in rapid heat and mass-transfer rates. When used as templates, droplets can be used to develop reproducible and scalable microparticles with tailored sizes, shapes and morphologies, which are difficult to obtain using traditional bulk methods. This technology can revolutionize material processing and application platforms. Generally, microparticle preparation methods involve three steps: (1) the formation of micro-droplets using a microfluidics generator; (2) shaping the droplets in micro-channels; and (3) solidifying the droplets to form microparticles. This review discusses the production of microparticles produced by droplet microfluidics according to their morphological categories, which generally determine their physicochemical properties and applications.

Advances in digital polymerase chain reaction (dPCR) and its emerging biomedical applications

Since the invention of polymerase chain reaction (PCR) in 1985, PCR has played a significant role in molecular diagnostics for genetic diseases, pathogens, oncogenes and forensic identification. In the past three decades, PCR has evolved from end-point PCR, through real-time PCR, to its current version, which is the absolute quantitive digital PCR (dPCR). In this review, we first discuss the principles of all key steps of dPCR, i.e., sample dispersion, amplification, and quantification, covering commercialized apparatuses and other devices still under lab development. We highlight the advantages and disadvantages of different technologies based on these steps, and discuss the emerging biomedical applications of dPCR. Finally, we provide a glimpse of the existing challenges and future perspectives for dPCR.

The effect of pressure and temperature on microthermoforming thermoplastic films integrated in the injection moulding process

Injection moulding is a widespread large-scale production technology for the manufacturing of thermoplastic parts, with small wall thicknesses limiting the feasible flow length. Introducing microthermoforming into the injection moulding process with dynamic mould temperature control enables the production of film-based, plane microstructured parts with further three-dimensional functional structures (e.g. for handling or for fitting in devices/assembly groups). Investigations show that considerable forming is possible with pressures up to 140 bar and forming temperatures far below the glass transition temperature of 50-μm-thick polycarbonate films in cycle times of <3 min. Generally speaking, the novel technology is expected to allow for multifunctional, thin-walled microstructured parts at large scales with short cycle times.

Female fertility preservation strategies: cryopreservation and ovarian tissue in vitro culture, current state of the art and future perspectives

In the present review, the main strategies of female fertility preservation are covered. Procedures of fertility preservation are necessary for women who suffer from diseases whose treatment requires the use of aggressive therapies, such as chemotherapy and radiotherapy. These kinds of therapy negatively influence the health of gametes and their progenitors. The most commonly used method of female fertility preservation is ovarian tissue cryopreservation, followed by the retransplantation of thawed tissue. Another approach to female fertility preservation that has been actively developed lately is the ovarian tissue in vitro culture. The principal methods, advantages and drawbacks of these two strategies are discussed in this article.

High-Content Screening for Quantitative Cell Biology

High-content screening (HCS), which combines automated fluorescence microscopy with quantitative image analysis, allows the acquisition of unbiased multiparametric data at the single cell level. This approach has been used to address diverse biological questions and identify a plethora of quantitative phenotypes of varying complexity in numerous different model systems. Here, we describe some recent applications of HCS, ranging from the identification of genes required for specific biological processes to the characterization of genetic interactions. We review the steps involved in the design of useful biological assays and automated image analysis, and describe major challenges associated with each. Additionally, we highlight emerging technologies and future challenges, and discuss how the field of HCS might be enhanced in the future.

Characterizing Nanoscale Transient Communication

We consider the novel paradigm of nanoscale transient communication (NTC), where certain components of the small-scale communication link are physically transient. As such, the transmitter and the receiver may change their properties over a prescribed lifespan due to their time-varying structures. The NTC systems may find important applications in the biomedical, environmental, and military fields, where system degradability allows for benign integration into life and environment. In this paper, we analyze the NTC systems from the channel-modeling and capacity-analysis perspectives and focus on the stochastically meaningful slow transience scenario, where the coherence time of degeneration Td is much longer than the coding delay Tc. We first develop novel and parsimonious models to characterize the NTC channels, where three types of physical layers are considered: electromagnetism-based terahertz (THz) communication, diffusion-based molecular communication (DMC), and nanobots-assisted touchable communication (TouchCom). We then revisit the classical performance measure of ϵ-outage channel capacity and take a fresh look at its formulations in the NTC context. Next, we present the notion of capacity degeneration profile (CDP), which describes the reduction of channel capacity with respect to the degeneration time. Finally, we provide numerical examples to demonstrate the features of CDP. To the best of our knowledge, the current work represents a first attempt to systematically evaluate the quality of nanoscale communication systems deteriorating with time.

Analysis of single nucleic acid molecules in micro- and nano-fluidics

Nucleic acid analysis has enhanced our understanding of biological processes and disease progression, elucidated the association of genetic variants and disease, and led to the design and implementation of new treatment strategies. These diverse applications require analysis of a variety of characteristics of nucleic acid molecules: size or length, detection or quantification of specific sequences, mapping of the general sequence structure, full sequence identification, analysis of epigenetic modifications, and observation of interactions between nucleic acids and other biomolecules. Strategies that can detect rare or transient species, characterize population distributions, and analyze small sample volumes enable the collection of richer data from biosamples. Platforms that integrate micro- and nano-fluidic operations with high sensitivity single molecule detection facilitate manipulation and detection of individual nucleic acid molecules. In this review, we will highlight important milestones and recent advances in single molecule nucleic acid analysis in micro- and nano-fluidic platforms. We focus on assessment modalities for single nucleic acid molecules and highlight the role of micro- and nano-structures and fluidic manipulation. We will also briefly discuss future directions and the current limitations and obstacles impeding even faster progress toward these goals.

Microthermoforming Integrated in the Injection Molding Process for Fabrication of Film-Based Microstructured Parts

Thermoplastic micro parts are commonly manufactured by the large-scale production technology of micro injection molding, with small wall thicknesses limiting the feasible flow length. In contrast, microthermoforming is an inexpensive technology to manufacture thin-walled microstructured parts, but connecting three-dimensional solid bodies, e.g. functional structures, is impossible. The novel combination of processing techniques, i.e. microthermoforming integrated in the injection molding process with dynamic mold temperature control enables the use of non-adhesive polymer melt to form thermoplastic films via back molding and employ adhesive melt to connect further structures. Additional heating the film with the back molding component represents a particular benefit in terms of reaching the required film temperature and leads to low temperatures prevailing in the mold. Simulative tools facilitate the understanding of film temperatures after back molding and can be used in a further step for the adaption of homogenous temperature distributions across areally distributed microstructures. Generally speaking, the technology is expected to allow for multifunctional, thin-walled microstructured parts produced in short cycle times.

In Vitro Mouse Ovarian Follicle Growth and Maturation in Alginate Hydrogel: Current State of the Art

This review describes the main factors affecting the in vitro development of mouse ovarian follicles under conditions of three-dimensional alginate hydrogel system. The factors discussed include concentration of alginate hydrogel, presence of additives (collagen, fibrin) influencing substrate rigidity; culture conditions; composition of culture media; substances that act like antioxidants (salts of ascorbic acid, glutathione) and contribute to the improvement of lipid metabolism (L-carnitine), hormones and growth factors. The methods for follicle group cultivation in alginate hydrogel and cocultivation of different cell populations with follicles encapsulated in alginate hydrogel are covered in the present article.

Recent advances and current issues in single-cell sequencing of tumors

Intratumoral heterogeneity is a recently recognized but important feature of cancer that underlies the various biocharacteristics of cancer tissues. The advent of next-generation sequencing technologies has facilitated large scale capture of genomic data, while the recent development of single-cell sequencing has allowed for more in-depth studies into the complex molecular mechanisms of intratumoral heterogeneity. In this review, the recent advances and current challenges in single-cell sequencing methodologies are discussed, highlighting the potential power of these data to provide insights into oncological processes, from tumorigenesis through progression to metastasis and therapy resistance.