Photophysical image analysis: Unsupervised probabilistic thresholding for images from electron-multiplying charge-coupled devices

We introduce the concept photophysical image analysis (PIA) and an associated pipeline for unsupervised probabilistic image thresholding for images recorded by electron-multiplying charge-coupled device (EMCCD) cameras. We base our approach on a closed-form analytic expression for the characteristic function (Fourier-transform of the probability mass function) for the image counts recorded in an EMCCD camera, which takes into account both stochasticity in the arrival of photons at the imaging camera and subsequent noise induced by the detection system of the camera. The only assumption in our method is that the background photon arrival to the imaging system is described by a stationary Poisson process (we make no assumption about the photon statistics for the signal). We estimate the background photon statistics parameter, λbg, from an image which contains both background and signal pixels by use of a novel truncated fit procedure with an automatically determined image count threshold. Prior to this, the camera noise model parameters are estimated using a calibration step. Utilizing the estimates for the camera parameters and λbg, we then introduce a probabilistic thresholding method, where, for the first time, the fraction of misclassified pixels can be determined a priori for a general image in an unsupervised way. We use synthetic images to validate our a priori estimates and to benchmark against the Otsu method, which is a popular unsupervised non-probabilistic image thresholding method (no a priori estimates for the error rates are provided). For completeness, we lastly present a simple heuristic general-purpose segmentation method based on the thresholding results, which we apply to segmentation of synthetic images and experimental images of fluorescent beads and lung cell nuclei. Our publicly available software opens up for fully automated, unsupervised, probabilistic photophysical image analysis.

Geometry-Dependent Elastic Flow Dynamics in Micropillar Arrays

Regular device-scale DNA waves for high DNA concentrations and flow velocities have been shown to emerge in quadratic micropillar arrays with potentially strong relevance for a wide range of microfluidic applications. Hexagonal arrays constitute another geometry that is especially relevant for the microfluidic pulsed-field separation of DNA. Here, we report on the differences at the micro and macroscopic scales between the resulting wave patterns for these two regular array geometries and one disordered array geometry. In contrast to the large-scale regular waves visible in the quadratic array, in the hexagonal arrays, waves occur in a device-scale disordered zig-zag pattern with fluctuations on a much smaller scale. We connect the large-scale pattern to the microscopic flow and observe flow synchronization that switches between two directions for both the quadratic and hexagonal arrays. We show the importance of order using the disordered array, where steady-state stationary and highly fluctuating flow states persist in seemingly random locations across the array. We compare the flow dynamics of the arrays to that in a device with sparsely distributed pillars. Here, we observe similar vortex shedding, which is clearly observable in the quadratic and disordered arrays. However, the shedding of these vortices couples only in the flow direction and not laterally as in the dense, ordered arrays. We believe that our findings will contribute to the understanding of elastic flow dynamics in pillar arrays, helping us elucidate the fundamental principles of non-Newtonian fluid flow in complex environments as well as supporting applications in engineering involving e.g., transport, sorting, and mixing of complex fluids.

Fluorescence Microscopy of Nanochannel-Confined DNA

Stretching of DNA in nanoscale confinement allows for several important studies. The genetic contents of the DNA can be visualized on the single DNA molecule level, and the polymer physics of confined DNA and also DNA/protein and other DNA/DNA-binding molecule interactions can be explored. This chapter describes the basic steps to fabricate the nanostructures, perform the experiments, and analyze the data.

Using symmetry to control viscoelastic waves in pillar arrays

Solutions of macromolecules exhibit viscoelastic properties and unlike Newtonian fluids, they may break time-reversal symmetry at low Reynolds numbers resulting in elastic turbulence. Furthermore, under some conditions, instead of the chaotic turbulence, the result is large-scale waves in the form of cyclic spatial and temporal concentration variations, as has been shown for macromolecular DNA flowing in microfluidic pillar arrays. We here demonstrate how altering the symmetry of the individual pillars can be used to influence the symmetry of these waves. We control the extent of instabilities in viscoelastic flow by leveraging the effects of the symmetry of the pillars on the waves, demonstrating suppressed viscoelastic fluctuations with relevance for transport and sorting applications, or conversely opening up for enhanced viscoelasticity-mediated mixing. The onset of waves, which changes flow resistance, occurs at different Deborah numbers for flow in different directions through the array of triangular pillars, thus breaking the symmetry of the flow resistance along the device, opening up for using the occurrence of the waves to construct a fluidic diode.

Short and long-range cyclic patterns in flows of DNA solutions in microfluidic obstacle arrays

We observe regular patterns emerging across multiple length scales with high-concentration DNA solutions in microfluidic pillar arrays at low Reynolds numbers and high Deborah numbers. Interacting vortices between pillars lead to long-range order in the form of large travelling waves consisting of DNA at high concentration and extension. Waves are formed in quadratic arrays of pillars, while randomizing the position of the pillar in each unit cell of a quadratic array leads to suppression of the long-range patterns. We find that concentrations exceeding the overlap concentration of the DNA enables the waves, and exploring the behavior of the waves as a function of flow rate, buffer composition, concentration and molecular length, we identify elastic effects as central to the origin of the waves. Our work may not only help increase the low throughput that often limits sample processing in microfluidics, it may also provide a platform for further studies of the underlying viscoelastic mechanisms.

High-Throughput Separation of Long DNA in Deterministic Lateral Displacement Arrays

Length-based separation of DNA remains as relevant today as when gel electrophoresis was introduced almost 100 years ago. While new, long-read genomics technologies have revolutionised accessibility to powerful genomic data, the preparation of samples has not proceeded at the same pace, with sample preparation often constituting a considerable bottleneck, both in time and difficulty. Microfluidics holds great potential for automated, sample-to-answer analysis via the integration of preparatory and analytical steps, but for this to be fully realised, more versatile, powerful and integrable unit operations, such as separation, are essential. We demonstrate the displacement and separation of DNA with a throughput that is one to five orders of magnitude greater than other microfluidic techniques. Using a device with a small footprint (23 mm × 0.5 mm), and with feature sizes in the micrometre range, it is considerably easier to fabricate than parallelized nano-array-based approaches. We show the separation of 48.5 kbp and 166 kbp DNA strands achieving a significantly improved throughput of 760 ng/h, compared to previous work and the separation of low concentrations of 48.5 kbp DNA molecules from a massive background of sub 10 kbp fragments. We show that the extension of DNA molecules at high flow velocities, generally believed to make the length-based separation of long DNA difficult, does not place the ultimate limitation on our method. Instead, we explore the effects of polymer rotations and intermolecular interactions at extremely high DNA concentrations and postulate that these may have both negative and positive influences on the separation depending on the detailed experimental conditions.

Use of dielectrophoresis for directing T cells to microwells before nanostraw transfection: modelling and experiments†

Nanostraw substrates have great potential for achieving minimally invasive cell transfection. Cells located on the nanostraw substrate are subjected to mild DC electric pulses applied across the nanostraw substrate, which open pores in the cell membrane on top of the nanostraws and drives charged cargo through these pores via electrophoresis. However, with this method, the current may leak through uncovered nanostraws, thereby decreasing the desired effect in the cell-covered nanostraws. A minimization of the number of uncovered nanostraws could be achieved by high cell coverage, but this is challenging when working with small cell populations. Nanostraw substrates of smaller area could be covered by smaller cell populations but are hard to integrate into fluidics systems. Here, we use simulations and experiments to show that this issue can be addressed by covering the nanostraw substrate with an insulating layer containing pores of similar size to cells. The pores act as traps into which cells can be guided using dielectrophoresis, ensuring a high degree of occupancy while maintaining a high cell viability, even if the total number of cells is low.

Dielectrophoresis can be used to guide cells to microwells with nanostraws at the bottom. This ensures a high nanostraw occupancy, minimizing the current leak through unoccupied nanostraws while maintaining a high cell viability, even if the total number of cells is low.

Charge-Based Separation of Micro- and Nanoparticles

Deterministic Lateral Displacement (DLD) is a label-free particle sorting method that separates by size continuously and with high resolution. By combining DLD with electric fields (eDLD), we show separation of a variety of nano and micro-sized particles primarily by their zeta potential. Zeta potential is an indicator of electrokinetic charge-the charge corresponding to the electric field at the shear plane-an important property of micro- and nanoparticles in colloidal or separation science. We also demonstrate proof of principle of separation of nanoscale liposomes of different lipid compositions, with strong relevance for biomedicine. We perform careful characterization of relevant experimental conditions necessary to obtain adequate sorting of different particle types. By choosing a combination of frequency and amplitude, sorting can be made sensitive to the particle subgroup of interest. The enhanced displacement effect due to electrokinetics is found to be significant at low frequency and for particles with high zeta potential. The effect appears to scale with the square of the voltage, suggesting that it is associated with either non-linear electrokinetics or dielectrophoresis (DEP). However, since we observe large changes in separation behavior over the frequency range at which DEP forces are expected to remain constant, DEP can be ruled out.

Deterministic Lateral Displacement: Challenges and Perspectives

The advent of microfluidics in the 1990s promised a revolution in multiple industries from healthcare to chemical processing. Deterministic lateral displacement (DLD) is a continuous-flow microfluidic particle separation method discovered in 2004 that has been applied successfully and widely to the separation of blood cells, yeast, spores, bacteria, viruses, DNA, droplets, and more. Deterministic lateral displacement is conceptually simple and can deliver consistent performance over a wide range of flow rates and particle concentrations. Despite wide use and in-depth study, DLD has not yet been fully elucidated or optimized, with different approaches to the same problem yielding varying results. We endeavor here to provide up-to-date expert opinion on the state-of-art and current fundamental, practical, and commercial challenges with DLD as well as describe experimental and modeling opportunities. Because these challenges and opportunities arise from constraints on hydrodynamics, fabrication, and operation at the micro- and nanoscale, we expect this Perspective to serve as a guide for the broader micro- and nanofluidic community to identify and to address open questions in the field.

Preparation of colloidal molecules with temperature-tunable interactions from oppositely charged microgel spheres

The self-assembly of small colloidal clusters, so-called colloidal molecules, into crystalline materials has proven extremely challenging, the outcome often being glassy, amorphous states where positions and orientations are locked. In this paper, a new type of colloidal molecule is therefore prepared, assembled from poly(N-isopropylacrylamide) (PNIPAM)-based microgels that due to their well documented softness and temperature-response allow for greater defect tolerance compared to hard spheres and for convenient in situ tuning of size, volume fraction and inter-particle interactions with temperature. The microgels (B) are assembled by electrostatic adsorption onto oppositely charged, smaller-sized microgels (A), where the relative size of the two determines the valency (n) of the resulting core-satellite ABn-type colloidal molecules. Following assembly, a microfluidic deterministic lateral displacement (DLD) device is used to effectively isolate AB4-type colloidal molecules of tetrahedral geometry that possess a repulsive-to-attractive transition on crossing the microgels' volume phase transition temperature (VPTT). These soft, temperature-responsive colloidal molecules constitute highly promising building blocks for the preparation of new materials with emergent properties, and their optical wavelength-size makes them especially interesting for optical applications.

A Droplet-Based Microfluidics Route to Temperature-Responsive Colloidal Molecules

Small clusters of spherical colloids that mimic real molecules, so-called colloidal molecules, hold great promise as building blocks in bottom-up routes to new materials. However, their typical hard sphere nature has hampered their assembly into ordered structures, largely due to a lack of control in the interparticle interactions. To provide easy external control of the interactions, the present work focuses on the preparation of colloidal molecules from temperature-responsive microgel particles that undergo a transition from a soft repulsive to a short-range attractive state as their characteristic volume phase transition temperature (VPTT) is crossed. Preparation of the colloidal molecules starts with the use of a droplet-based microfluidics device to form highly uniform water-in-oil (W/O) emulsion droplets containing, on average and with a narrow distribution, four microgels per droplet. Evaporation of the water then leads to the formation of colloidal molecule-like clusters, which can be harvested following cross-linking and phase transfer. We use a mixture of two types of microgels, one based on poly(N-isopropylacrylamide) (PNIPAM) and the other on poly(N-isopropylmethacrylamide) (PNIPMAM), to prepare bicomponent colloidal molecules, and show that the difference in VPTT between the two allows for induction of attractive interparticle interactions between the PNIPAM interaction sites at temperatures in between the two VPTTs, analogous to the interactions among patchy biomacromolecules such as many proteins.

Label-free enrichment of primary human skeletal progenitor cells using deterministic lateral displacement

Skeletal stem cells (SSCs) are present in bone marrow (BM) and offer great potential for bone regenerative therapies. However, in the absence of a unique marker, current sorting approaches remain challenging in the quest for simple strategies to deliver SSCs with consistent regeneration and differentiation capacities. Microfluidics offers the possibility to sort cells marker-free, based on intrinsic biophysical properties. Recent studies indicate that SSCs are stiffer than leukocytes and are contained within the larger cell fraction in BM. This paper describes the use of deterministic lateral displacement (DLD) to sort SSCs based on cell size and stiffness. DLD is a technology that uses arrays of micropillars to sort cells based on their diameter. Cell deformation within the device can change the cell size and affect sorting - here evidenced using human cell lines and by fractionation of expanded SSCs. Following sorting, SSCs remained viable and retained their capacity to form clonogenic cultures (CFU-F), indicative of stem cell potential. Additionally, larger BM cells showed enhanced capacity to form CFU-F. These findings support the theory that SSCs are more abundant within the larger BM cell fraction and that DLD, or other size-based approaches, could be used to provide enriched SSC populations with significant implications for stem cell research and translation to the clinic.

Stochastic unfolding of nanoconfined DNA: Experiments, model and Bayesian analysis

Nanochannels provide a means for detailed experiments on the effect of confinement on biomacromolecules, such as DNA. Here we introduce a model for the complete unfolding of DNA from the circular to linear configuration. Two main ingredients are the entropic unfolding force and the friction coefficient for the unfolding process, and we describe the associated dynamics by a non-linear Langevin equation. By analyzing experimental data where DNA molecules are photo-cut and unfolded inside a nanochannel, our model allows us to extract values for the unfolding force as well as the friction coefficient for the first time. In order to extract numerical values for these physical quantities, we employ a recently introduced Bayesian inference framework. We find that the determined unfolding force is in agreement with estimates from a simple Flory-type argument. The estimated friction coefficient is in agreement with theoretical estimates for motion of a cylinder in a channel. We further validate the estimated friction constant by extracting this parameter from DNA's center-of-mass motion before and after unfolding, yielding decent agreement. We provide publically available software for performing the required image and Bayesian analysis.

Open channel deterministic lateral displacement for particle and cell sorting

We present the use of capillary driven flow over patterned surfaces to achieve cheap and simple, but powerful separation of biologically relevant particle systems. The wide use of microfluidics is often hampered by the propensity for devices to clog due to the small channel sizes and the inability to access the interior of devices for cleaning. Often the devices can only be used for a limited duration and most frequently only once. In addition the cost and power requirements of flow control equipment limits the wider spread of the devices. We address these issues by presenting a simple particle- and cell-sorting scheme based on controlled fluid flow on a patterned surface. The open architecture makes it highly robust and easy to use. If clogging occurs it is straightforward to rinse the device and reuse it. Instead of external mechanical pumps, paper is used as a capillary pump. The different fractions are deposited in the paper and can subsequently be handled independently by simply cutting the paper for downstream processing and analyses. The sorting, based on deterministic lateral displacement, performs equivalently well in comparison with standard covered devices. We demonstrate successful separation of cancer cells and parasites from blood with good viability and with relevance for diagnostics and sample preparation. Sorting a mixture of soil and blood, we show the potential for forensic applications.

Sorting cells by their dynamical properties

Recent advances in cell sorting aim at the development of novel methods that are sensitive to various mechanical properties of cells. Microfluidic technologies have a great potential for cell sorting; however, the design of many micro-devices is based on theories developed for rigid spherical particles with size as a separation parameter. Clearly, most bioparticles are non-spherical and deformable and therefore exhibit a much more intricate behavior in fluid flow than rigid spheres. Here, we demonstrate the use of cells’ mechanical and dynamical properties as biomarkers for separation by employing a combination of mesoscale hydrodynamic simulations and microfluidic experiments. The dynamic behavior of red blood cells (RBCs) within deterministic lateral displacement (DLD) devices is investigated for different device geometries and viscosity contrasts between the intra-cellular fluid and suspending medium. We find that the viscosity contrast and associated cell dynamics clearly determine the RBC trajectory through a DLD device. Simulation results compare well to experiments and provide new insights into the physical mechanisms which govern the sorting of non-spherical and deformable cells in DLD devices. Finally, we discuss the implications of cell dynamics for sorting schemes based on properties other than cell size, such as mechanics and morphology.

Extension of nanoconfined DNA: Quantitative comparison between experiment and theory

The extension of DNA confined to nanochannels has been studied intensively and in detail. However, quantitative comparisons between experiments and model calculations are difficult because most theoretical predictions involve undetermined prefactors, and because the model parameters (contour length, Kuhn length, effective width) are difficult to compute reliably, leading to substantial uncertainties. Here we use a recent asymptotically exact theory for the DNA extension in the "extended de Gennes regime" that allows us to compare experimental results with theory. For this purpose, we performed experiments measuring the mean DNA extension and its standard deviation while varying the channel geometry, dye intercalation ratio, and ionic strength of the buffer. The experimental results agree very well with theory at high ionic strengths, indicating that the model parameters are reliable. At low ionic strengths, the agreement is less good. We discuss possible reasons. In principle, our approach allows us to measure the Kuhn length and the effective width of a single DNA molecule and more generally of semiflexible polymers in solution.

New technologies for DNA analysis--a review of the READNA Project

The REvolutionary Approaches and Devices for Nucleic Acid analysis (READNA) project received funding from the European Commission for 41/2 years. The objectives of the project revolved around technological developments in nucleic acid analysis. The project partners have discovered, created and developed a huge body of insights into nucleic acid analysis, ranging from improvements and implementation of current technologies to the most promising sequencing technologies that constitute a 3(rd) and 4(th) generation of sequencing methods with nanopores and in situ sequencing, respectively.

Visualizing the entire DNA from a chromosome in a single frame

The contiguity and phase of sequence information are intrinsic to obtain complete understanding of the genome and its relationship to phenotype. We report the fabrication and application of a novel nanochannel design that folds megabase lengths of genomic DNA into a systematic back-and-forth meandering path. Such meandering nanochannels enabled us to visualize the complete 5.7 Mbp (1 mm) stained DNA length of a Schizosaccharomyces pombe chromosome in a single frame of a CCD. We were able to hold the DNA in situ while implementing partial denaturation to obtain a barcode pattern that we could match to a reference map using the Poland-Scheraga model for DNA melting. The facility to compose such long linear lengths of genomic DNA in one field of view enabled us to directly visualize a repeat motif, count the repeat unit number, and chart its location in the genome by reference to unique barcode motifs found at measurable distances from the repeat. Meandering nanochannel dimensions can easily be tailored to human chromosome scales, which would enable the whole genome to be visualized in seconds.

Fluidic switching in nanochannels for the control of Inchworm: a synthetic biomolecular motor with a power stroke

Synthetic molecular motors typically take nanometer-scale steps through rectification of thermal motion. Here we propose Inchworm, a DNA-based motor that employs a pronounced power stroke to take micrometer-scale steps on a time scale of seconds, and we design, fabricate, and analyze the nanofluidic device needed to operate the motor. Inchworm is a kbp-long, double-stranded DNA confined inside a nanochannel in a stretched configuration. Motor stepping is achieved through externally controlled changes in salt concentration (changing the DNA's extension), coordinated with ligand-gated binding of the DNA's ends to the functionalized nanochannel surface. Brownian dynamics simulations predict that Inchworm's stall force is determined by its entropic spring constant and is ∼ 0.1 pN. Operation of the motor requires periodic cycling of four different buffers surrounding the DNA inside a nanochannel, while keeping constant the hydrodynamic load force on the DNA. We present a two-layer fluidic device incorporating 100 nm-radius nanochannels that are connected through a few-nm-wide slit to a microfluidic system used for in situ buffer exchanges, either diffusionally (zero flow) or with controlled hydrodynamic flow. Combining experiment with finite-element modeling, we demonstrate the device's key performance features and experimentally establish achievable Inchworm stepping times of the order of seconds or faster.

Competitive binding-based optical DNA mapping for fast identification of bacteria--multi-ligand transfer matrix theory and experimental applications on Escherichia coli

We demonstrate a single DNA molecule optical mapping assay able to resolve a specific Escherichia coli strain from other strains. The assay is based on competitive binding of the fluorescent dye YOYO-1 and the AT-specific antibiotic netropsin. The optical map is visualized by stretching the DNA molecules in nanofluidic channels. We optimize the experimental conditions to obtain reproducible barcodes containing as much information as possible. We implement a multi-ligand transfer matrix method for calculating theoretical barcodes from known DNA sequences. Our method extends previous theoretical approaches for competitive binding of two types of ligands to many types of ligands and introduces a recursive approach that allows long barcodes to be calculated with standard computer floating point formats. The identification of a specific E. coli strain (CCUG 10979) is based on mapping of 50-160 kilobasepair experimental DNA fragments onto the theoretical genome using the developed theory. Our identification protocol introduces two theoretical constructs: a P-value for a best experiment-theory match and an information score threshold. The developed methods provide a novel optical mapping toolbox for identification of bacterial species and strains. The protocol does not require cultivation of bacteria or DNA amplification, which allows for ultra-fast identification of bacterial pathogens.

Fibroblasts cultured on nanowires exhibit low motility, impaired cell division, and DNA damage

Nanowires are commonly used as tools for interfacing living cells, acting as biomolecule-delivery vectors or electrodes. It is generally assumed that the small size of the nanowires ensures a minimal cellular perturbation, yet the effects of nanowires on cell migration and proliferation remain largely unknown. Fibroblast behaviour on vertical nanowire arrays is investigated, and it is shown that cell motility and proliferation rate are reduced on nanowires. Fibroblasts cultured on long nanowires exhibit failed cell division, DNA damage, increased ROS content and respiration. Using focused ion beam milling and scanning electron microscopy, highly curved but intact nuclear membranes are observed, showing no direct contact between the nanowires and the DNA. The nanowires possibly induce cellular stress and high respiration rates, which trigger the formation of ROS, which in turn results in DNA damage. These results are important guidelines to the design and interpretation of experiments involving nanowire-based transfection and electrical characterization of living cells.

Fluorescent nanowire heterostructures as a versatile tool for biology applications

Nanowires are increasingly used in biology, as sensors, as injection devices, and as model systems for toxicity studies. Currently, in situ visualization of nanowires in biological media is done using organic dyes, which are prone to photobleaching, or using microscopy methods which either yield poor resolution or require a sophisticated setup. Here we show that inherently fluorescent nanowire axial heterostructures can be used to localize and identify nanowires in cells and tissue. By synthesizing GaP-GaInP nanowire heterostructures, with nonfluorescent GaP segments and fluorescent GaInP segments, we created a barcode labeling system enabling the distinction of the nanowire morphological and chemical properties using fluorescence microscopy. The GaInP photoluminescence stability, combined with the fact that the nanowires can be coated with different materials while retaining their fluorescence, make these nanowires promising tools for biological and nanotoxicological studies.

Controlled microfluidic switching in arbitrary time-sequences with low drag

The ability to test the response of cells and proteins to a changing biochemical environment is of interest for studies of fundamental cell physiology and molecular interactions. In a common experimental scheme the cells or molecules of interest are attached to a surface and the composition of the surrounding fluid is changed. It is desirable to be able to switch several different biochemical reagents in any arbitrary order, and to keep the flow velocity low enough so that the cells and molecules remain attached and can be expected to retain their function. Here we develop a device with these capabilities, using U-shaped access channels. We use total-internal reflection fluorescence microscopy to characterize the time-dependent change in concentration during switching of solutions near the device surface. Well-defined fluid interfaces are formed in the immediate vicinity of the surface ensuring distinct switching events. We show that the experimental data agrees well with Taylor-Aris theory in its range of validity. In addition, we find that well-defined interfaces are achieved also in the immediate vicinity of the surface, where analytic approaches and numerical models become inaccurate. Assisted by finite-element modelling, the details of our device were designed for use with a specific artificial protein motor, but the key results are general and can be applied to a wide range of biochemical studies in which switching is important.

Solute transport on the sub 100 ms scale across the lipid bilayer membrane of individual proteoliposomes

Screening assays designed to probe ligand and drug-candidate regulation of membrane proteins responsible for ion-translocation across the cell membrane are wide spread, while efficient means to screen membrane-protein facilitated transport of uncharged solutes are sparse. We report on a microfluidic-based system to monitor transport of uncharged solutes across the membrane of multiple (>100) individually resolved surface-immobilized liposomes. This was accomplished by rapidly switching (<10 ms) the solution above dye-containing liposomes immobilized on the floor of a microfluidic channel. With liposomes encapsulating the pH-sensitive dye carboxyfluorescein (CF), internal changes in pH induced by transport of a weak acid (acetic acid) could be measured at time scales down to 25 ms. The applicability of the set up to study biological transport reactions was demonstrated by examining the osmotic water permeability of human aquaporin (AQP5) reconstituted in proteoliposomes. In this case, the rate of osmotic-induced volume changes of individual proteoliposomes was time resolved by imaging the self quenching of encapsulated calcein in response to an osmotic gradient. Single-liposome analysis of both pure and AQP5-containing liposomes revealed a relatively large heterogeneity in osmotic permeability. Still, in the case of AQP5-containing liposomes, the single liposome data suggest that the membrane-protein incorporation efficiency depends on liposome size, with higher incorporation efficiency for larger liposomes. The benefit of low sample consumption and automated liquid handling is discussed in terms of pharmaceutical screening applications.

Orientational correlations in confined DNA

We study how the orientational correlations of DNA confined to nanochannels depend on the channel diameter D by means of Monte Carlo simulations and a mean-field theory. This theory describes DNA conformations in the experimentally relevant regime where the Flory-de Gennes theory does not apply. We show how local correlations determine the dependence of the end-to-end distance of the DNA molecule upon D. Tapered nanochannels provide the necessary resolution in D to study experimentally how the extension of confined DNA molecules depends upon D. Our experimental and theoretical results are in qualitative agreement.

Lipid-based passivation in nanofluidics

Stretching DNA in nanochannels is a useful tool for direct, visual studies of genomic DNA at the single molecule level. To facilitate the study of the interaction of linear DNA with proteins in nanochannels, we have implemented a highly effective passivation scheme based on lipid bilayers. We demonstrate virtually complete long-term passivation of nanochannel surfaces to a range of relevant reagents, including streptavidin-coated quantum dots, RecA proteins, and RecA-DNA complexes. We show that the performance of the lipid bilayer is significantly better than that of standard bovine serum albumin-based passivation. Finally, we show how the passivated devices allow us to monitor single DNA cleavage events during enzymatic degradation by DNase I. We expect that our approach will open up for detailed, systematic studies of a wide range of protein-DNA interactions with high spatial and temporal resolution.

Sorting cells by size, shape and deformability

While size has been widely used as a parameter in cellular separations, in this communication we show how shape and deformability, a mainly untapped source of specificity in preparative and analytical microfluidic devices can be measured and used to separate cells.

A single-step competitive binding assay for mapping of single DNA molecules

Optical mapping of genomic DNA is of relevance for a plethora of applications such as scaffolding for sequencing and detection of structural variations as well as identification of pathogens like bacteria and viruses. For future clinical applications it is desirable to have a fast and robust mapping method based on as few steps as possible. We here demonstrate a single-step method to obtain a DNA barcode that is directly visualized using nanofluidic devices and fluorescence microscopy. Using a mixture of YOYO-1, a bright DNA dye, and netropsin, a natural antibiotic with very high AT specificity, we obtain a DNA map with a fluorescence intensity profile along the DNA that reflects the underlying sequence. The netropsin binds to AT-tetrads and blocks these binding sites from YOYO-1 binding which results in lower fluorescence intensity from AT-rich regions of the DNA. We thus obtain a DNA barcode that is dark in AT-rich regions and bright in GC-rich regions with kilobasepair resolution. We demonstrate the versatility of the method by obtaining a barcode on DNA from the phage T4 that captures its circular permutation and agrees well with its known sequence.

Separation of parasites from human blood using deterministic lateral displacement

We present the use of a simple microfluidic technique to separate living parasites from human blood. Parasitic trypanosomatids cause a range of human and animal diseases. African trypanosomes, responsible for human African trypanosomiasis (sleeping sickness), live free in the blood and other tissue fluids. Diagnosis relies on detection and due to their often low numbers against an overwhelming background of predominantly red blood cells it is crucial to separate the parasites from the blood. By modifying the method of deterministic lateral displacement, confining parasites and red blood cells in channels of optimized depth which accentuates morphological differences, we were able to achieve separation thus offering a potential route to diagnostics.

Fluorescence microscopy of nanochannel-confined DNA

Stretching of DNA in nanoscale confinement allows for direct visualization of the genetic contents of the DNA on the single DNA molecule level. DNA stretched in nanoscale confinement also allows for studies of DNA-protein interactions and DNA polymer physics in confined environments. This chapter describes the basic steps to fabricate the nanostructures, to perform the experiments, and to analyze the data.

Fluorescence enhancement of single DNA molecules confined in Si/SiO2 nanochannels

We demonstrate that the detected emission intensity from YOYO-labeled DNA molecules confined in 180 nm deep Si/SiO2 nanofunnels changes significantly and not monotonically with the width of the funnel. This effect may be of importance for quantitative fluorescence microscopy and for experiments with a tight photon budget.

Single-molecule denaturation mapping of DNA in nanofluidic channels

Here we explore the potential power of denaturation mapping as a single-molecule technique. By partially denaturing YOYO-1-labeled DNA in nanofluidic channels with a combination of formamide and local heating, we obtain a sequence-dependent "barcode" corresponding to a series of local dips and peaks in the intensity trace along the extended molecule. We demonstrate that this structure arises from the physics of local denaturation: statistical mechanical calculations of sequence-dependent melting probability can predict the barcode to be observed experimentally for a given sequence. Consequently, the technique is sensitive to sequence variation without requiring enzymatic labeling or a restriction step. This technique may serve as the basis for a new mapping technology ideally suited for investigating the long-range structure of entire genomes extracted from single cells.

Nanofluidics in hollow nanowires

We present a novel scheme for producing nanotube membranes using free-standing hollow nanowires, with easily controllable dimensions. GaAs-AlInP core-shell nanowires were grown by metal-organic vapor phase epitaxy and were partially embedded in a polymer film. The GaAs core and substrate were etched selectively, leaving tubes with open access to both sides of the membrane. Electrophoretic transport of T4-phage DNA through the hollow nanowires was demonstrated using epifluorescence microscopy.

DNA in nanochannels--directly visualizing genomic information

The power of nanofluidic channels to analyze DNA is described along with practical experimental hints. As an introduction, a general overview is given on conventional DNA analysis tools, as well as tools under development towards the $1000 genome. The focus of this tutorial review is the stretching of DNA in nanoscale channels for coarse-grained mapping of DNA. To understand the behavior of the DNA, basic theory is discussed. Experimental details are revealed so that the reader, with the proper equipment, should be able to perform experiments. Basic approaches to the analysis of the data are discussed. Finally, potential future directions are discussed including the application of melting mapping as a simple barcode for the DNA.

Tipping the balance of deterministic lateral displacement devices using dielectrophoresis

We report the use of dielectrophoresis (DEP) to achieve tunability, improve dynamic range and open up for the separation of particles with regard to parameters other than hydrodynamic size in deterministic lateral displacement (DLD) devices. DLD devices have been shown capable of rapidly and continuously separating micrometer sized plastic spheres by size with a resolution of 20 nm in diameter and of being able to handle the separation of biological samples as wide ranging as bacterial artificial chromosomes and blood cells. DEP, while not exhibiting the same resolution in size separation as DLD, has the benefit of being easy to tune and can, by choosing the frequency, be used to probe a variety of particle properties. By combining DLD and DEP we open up for the advantages, while avoiding the drawbacks, of the two techniques. We present a proof of principle in which the critical size for separation of polystyrene beads is tuned in the range 2-6 microm in a single device by the application of moderate (100 V cm(-1)), low frequency (100 Hz) AC electric fields. The behaviour of the device was further investigated by performing simulations of particle trajectories, the results of which were in good qualitative agreement with experiments, indicating the potential of the method for tunable, high-resolution separations with respect to both size and polarisability.

Shear-driven motion of supported lipid bilayers in microfluidic channels

In this work, we demonstrate how a lateral motion of a supported lipid bilayer (SLB) and its constituents can be created without relying on self-spreading forces. The force driving the SLB is instead a viscous shear force arising from a pressure-driven bulk flow acting on the SLB that is formed on a glass wall inside a microfluidic channel. In contrast to self-spreading bilayers, this method allows for accurate control of the bilayer motion by altering the bulk flow in the channel. Experiments showed that an egg yolk phosphatidylcholine SLB formed on a glass support moved in a rolling motion under these shear forces, with the lipids in the upper leaflet of the bilayer moving at twice the velocity of the bilayer front. The drift velocity of different lipid probes in the SLB was observed to be sensitive to the interactions between the lipid probe and the surrounding molecules, resulting in drift velocities that varied by up to 1 order of magnitude for the different lipid probes in our experiments. Since the method provides a so far unattainable control of the motion of all molecules in an SLB, we foresee great potential for this technique, alone or in combination with other methods, for studies of lipid bilayers and different membrane-associated molecules.

Mechanical behavior of a supported lipid bilayer under external shear forces

Shear forces from a pressure-driven bulk flow in a microfluidic channel can be used to induce and control the motion of a supported lipid bilayer (SLB) formed on the walls of the channel. We here present a theoretical model that relates the experimentally observed drift velocities of an egg yolk phosphatidylcholine (egg PC) SLB to the hydrodynamic drag force from the bulk flow, the intermonolayer friction coefficient, b, of the bilayer, and the friction coefficient, bls, between the lower leaflet of the bilayer and the supporting substrate. The drift velocity and diffusivity of the lipids in the SLB were obtained by photobleaching a delimited area of fluorescently labeled lipids and subsequently monitoring the recovery and convective motion of the bleached spot. A striking observation was that the drift velocity of the lipids was observed to be nearly 6 orders of magnitude smaller than the bulk velocity at the center of the channel. This predicts a value for bls that is at least 25 times as high as predicted by the traditional model with the SLB and the support spaced by a homogeneous 1 nm thick film of water. In addition, the intermonolayer friction coefficient was estimated to 2x10(7) Pa s/m, a value that increased after addition of glycerol to the bulk solution. This increase was accompanied by an equal decrease in the lipid diffusivity, with both observations indicating an increased viscous drag within the bilayer when glycerol was added to the bulk solution.

Multidirectional sorting modes in deterministic lateral displacement devices

Deterministic lateral displacement (DLD) devices separate micrometer-scale particles in solution based on their size using a laminar microfluidic flow in an array of obstacles. We investigate array geometries with rational row-shift fractions in DLD devices by use of a simple model including both advection and diffusion. Our model predicts multidirectional sorting modes that could be experimentally tested in high-throughput DLD devices containing obstacles that are much smaller than the separation between obstacles.

Field-dependent DNA mobility in 20 nm high nanoslits

The transport behavior of lambda-DNA (48 kbp) in fused silica nanoslits is investigated upon application of electrical fields of different strengths. The slit dimensions are 20 nm in height, 3 microm in width, and 500 microm in length. With fields of 30 kV/m or below, the molecules move fluently through the slits, while at higher electrical fields, the DNA molecules move intermittently, resulting in a strongly reduced mobility. We propose that the behavior can be explained by mechanical and/or field-induced dielectrophoretic DNA trapping due to the surface roughness in the nanoslits. The observation of preferential pathways and trapping sites of the lambda-DNA molecules through the nanoslits supports this hypothesis and indicates that the classical viscous friction models to explain the DNA movement in nanoslits needs to be modified to include these effects. Preliminary experiments with the smaller XbaI-digested litmus-DNA (2.8 kbp) show that the behavior is size-dependent, suggesting that the high field electrophoresis in nanoslits can be used for DNA separation.