Laminin and hyaluronan supplementation of collagen hydrogels enhances endothelial function and tight junction expression on three-dimensional cylindrical microvessel-on-a-chip.

Vasculature-on-chip (VoC) models have become a prominent tool in the study of microvasculature functions because of their cost-effective and ethical production process. These models typically use a hydrogel in which the three-dimensional (3D) microvascular structure is embedded. Thus, VoCs are directly impacted by the physical and chemical cues of the supporting hydrogel. Endothelial cell (EC) response in VoCs is critical, especially in organ-specific vasculature models, in which ECs exhibit specific traits and behaviors that vary between organs. Many studies customize the stimuli ECs perceive in different ways; however, customizing the hydrogel composition accordingly to the target organ's extracellular matrix (ECM), which we believe has great potential, has been rarely investigated. We explored this approach to organ-specific VoCs by fabricating microvessels (MVs) with either human umbilical vein ECs or human brain microvascular ECs in a 3D cylindrical VoC using a collagen hydrogel alone or one supplemented with laminin and hyaluronan, components found in the brain ECM. We characterized the physical properties of these hydrogels and analyzed the barrier properties of the MVs. Barrier function and tight junction (ZO-1) expression improved with the addition of laminin and hyaluronan in the composite hydrogel.

Size Fractionation of Milliliter DNA Samples in Minutes Controlled by an Electric Field of ∼10 V.

DNA size fractionation is an essential tool in molecular biology and is used to isolate targets in a mixture characterized by a broad molecular-weight distribution. Microfluidics was thought to provide the opportunity to create devices capable of enhancing and speeding up the classical fractionation processes. However, this conjecture met limited success due to the low mass or volume throughput of these technologies. We describe the µLAF (µ-laboratory for DNA fractionation) technology for DNA size selection based on the stacking of molecules on films of ∼100 µm in thickness with 105 cm-2 pores ∼2 µm in diameter. Size selection is achieved by controlling the regime of electrohydrodynamic migration through the temporal modulation of an electric field. This technology allows the processing of milliliter-scale samples containing a DNA mass of several hundreds of ng within ∼10 min and the selection of DNA in virtually any size window spanning 200 to 1000 bp. We demonstrate that one operation suffices to fractionate sheared genomic DNA in up to six fractions with collection efficiencies of ∼20-40% and enrichment factors of ∼1.5-3-fold. These performances compare favorably in terms of speed and versatility to those of the current standards.

µLAS technology for DNA isolation coupled to Cas9-assisted targeting for sequencing and assembly of a 30 kb region in plant genome.

Cas9-assisted targeting of DNA fragments in complex genomes is viewed as an essential strategy to obtain high-quality and continuous sequence data. However, the purity of target loci selected by pulsed-field gel electrophoresis (PFGE) has so far been insufficient to assemble the sequence in one contig. Here, we describe the µLAS technology to capture and purify high molecular weight DNA. First, the technology is optimized to perform high sensitivity DNA profiling with a limit of detection of 20 fg/µl for 50 kb fragments and an analytical time of 50 min. Then, µLAS is operated to isolate a 31.5 kb locus cleaved by Cas9 in the genome of the plant Medicago truncatula. Target purification is validated on a Bacterial Artificial Chromosome plasmid, and subsequently carried out in whole genome with µLAS, PFGE or by combining these techniques. PacBio sequencing shows an enrichment factor of the target sequence of 84 with PFGE alone versus 892 by association of PFGE with µLAS. These performances allow us to sequence and assemble one contig of 29 441 bp with 99% sequence identity to the reference sequence.

Rouse model with transient intramolecular contacts on a timescale of seconds recapitulates folding and fluctuation of yeast chromosomes.

DNA folding and dynamics along with major nuclear functions are determined by chromosome structural properties, which remain, thus far, elusive in vivo. Here, we combine polymer modeling and single particle tracking experiments to determine the physico-chemical parameters of chromatin in vitro and in living yeast. We find that the motion of reconstituted chromatin fibers can be recapitulated by the Rouse model using mechanical parameters of nucleosome arrays deduced from structural simulations. Conversely, we report that the Rouse model shows some inconsistencies to analyze the motion and structural properties inferred from yeast chromosomes determined with chromosome conformation capture techniques (specifically, Hi-C). We hence introduce the Rouse model with Transient Internal Contacts (RouseTIC), in which random association and dissociation occurs along the chromosome contour. The parametrization of this model by fitting motion and Hi-C data allows us to measure the kinetic parameters of the contact formation reaction. Chromosome contacts appear to be transient; associated to a lifetime of seconds and characterized by an attractive energy of -0.3 to -0.5 kBT. We suggest attributing this energy to the occurrence of histone tail-DNA contacts and notice that its amplitude sets chromosomes in 'theta' conditions, in which they are poised for compartmentalization and phase separation.

Characterization and minimization of band broadening in DNA electrohydrodynamic migration for enhanced size separation.

The combination of hydrodynamic actuation with an opposing electrophoretic force in viscoelastic liquids enables the separation, concentration, and purification of DNA. Obtaining good analytical performances despite the use of hydrodynamic flow fields, which dramatically enhance band broadening due to Taylor dispersion, constitutes a paradox that remains to be clarified. Here, we study the mechanism of band broadening in electrohydrodynamic migration with an automated microfluidic platform that allows us to track the migration of a 600 bp band in the pressure-electric field parameter space. We demonstrate that diffusion in the electrohydrodynamic regime is controlled predominantly by the electric field and marginally by the hydrodynamic flow velocity. We explain this response with an analytical model of diffusion based on Taylor dispersion arguments. Furthermore, we demonstrate that the electric field can be modulated over time to monitor and minimize the breadth of a DNA band, and suggest guidelines to enhance the resolution of DNA separation experiments. Altogether, our report is a leap towards to the development of high-performance analytical technologies based on electrohydrodynamic actuation.

BIABooster: Online DNA Concentration and Size Profiling with a Limit of Detection of 10 fg/µL and Application to High-Sensitivity Characterization of Circulating Cell-Free DNA.

We describe a technology to perform sizing and concentration analysis of double stranded DNA with a sensitivity of 10 fg/µL in an operating time of 20 min. The technology is operated automatically on a commercial capillary electrophoresis instrument using electro-hydrodynamic actuation. It relies on a new capillary device that achieves online concentration of DNA at the junction between two capillaries of different diameters, thanks to viscoelastic lift forces. Using a set of DNA ladders in the range of 100-1500 bp, we report a sizing accuracy and precision better than 3% and a concentration quantification precision of ∼20%. When the technology is applied to the analysis of clinical samples of circulating cell-free DNA (cfDNA), the measured cfDNA concentrations are in good correlation with those measured by digital PCR. Furthermore, the cfDNA size profiles indicate that the fraction of low molecular weight cfDNA in the range of 75-240 bp is a candidate biomarker to discriminate between healthy subjects and cancer patients. We conclude that our technology is efficient in analyzing highly diluted DNA samples and suggest that it will be helpful in translational and clinical research involving cfDNA.

DNA polymerase ν gene expression influences fludarabine resistance in chronic lymphocytic leukemia independently of p53 status.

Alteration in the DNA replication, repair or recombination processes is a highly relevant mechanism of genomic instability. Despite genomic aberrations manifested in hematologic malignancies, such a defect as a source of biomarkers has been underexplored. Here, we investigated the prognostic value of expression of 82 genes involved in DNA replication-repair-recombination in a series of 99 patients with chronic lymphocytic leukemia without detectable 17p deletion or TP53 mutation. We found that expression of the POLN gene, encoding the specialized DNA polymerase ν (Pol ν) correlates with time to relapse after first-line therapy with fludarabine. Moreover, we found that POLN was the only gene up-regulated in primary patients' lymphocytes when exposed in vitro to proliferative and pro-survival stimuli. By using two cell lines that were sequentially established from the same patient during the course of the disease and Pol ν knockout mouse embryonic fibroblasts, we reveal that high relative POLN expression is important for DNA synthesis and cell survival upon fludarabine treatment. These findings suggest that Pol ν could influence therapeutic resistance in chronic lymphocytic leukemia. (Patients' samples were obtained from the CLL 2007 FMP clinical trial registered at: clinicaltrials.gov identifer: 00564512).

Accelerated Transport of Particles in Confined Channels with a High Roughness Amplitude.

We investigate the pressure-driven transport of particles 200 or 300 nm in diameter in shallow microfluidic channels ∼1 µm in height with a bottom wall characterized by a high roughness amplitude of ∼100 nm. This study starts with the description of an assay to generate cracks in hydrophilic thin polymer films together with a structural characterization of these corrugations. Microfluidic chips of variable height are then assembled on top of these rough surfaces, and the transport of particles is assessed by measuring the velocity distribution function for a set of pressure drops. We specifically detect anomalous transport properties for rough surfaces. The maximum particle velocity at the centerline of the channel is comparable to that obtained with smooth surfaces, but the average particle velocity increases nonlinearly with the flow rate. We suggest that the change in the boundary condition at the rough wall is not sufficient to account for our data and that the occurrence of contacts between the particle and the surface transports the particle away from the wall and speeds up its motion. We finally draw perspectives for the separation by field-flow fractionation.

Real-Time Imaging of a Single Gene Reveals Transcription-Initiated Local Confinement.

Genome dynamics are intimately linked to the regulation of gene expression, the most fundamental mechanism in biology, yet we still do not know whether the very process of transcription drives spatial organization at specific gene loci. Here, we have optimized the ANCHOR/ParB DNA-labeling system for real-time imaging of a single-copy, estrogen-inducible transgene in human cells. Motion of an ANCHOR3-tagged DNA locus was recorded in the same cell before and during the appearance of nascent MS2-labeled mRNA. We found that transcription initiation by RNA polymerase 2 resulted in confinement of the mRNA-producing gene domain within minutes. Transcription-induced confinement occurred in each single cell independently of initial, highly heterogeneous mobility. Constrained mobility was maintained even when inhibiting polymerase elongation. Chromatin motion at constant step size within a largely confined area hence leads to increased collisions that are compatible with the formation of gene-specific chromatin domains, and reflect the assembly of functional protein hubs and DNA processing during the rate-limiting steps of transcription.

DNA Grafting and Arrangement on Oxide Surfaces for Self-Assembly of Al and CuO Nanoparticles.

DNA-directed assembly of nano-objects as a means to manufacture advanced nanomaterial architectures has been the subject of many studies. However, most applications have dealt with noble metals as there are fundamental difficulties to work with other materials. In this work, we propose a generic and systematic approach for functionalizing and characterizing oxide surfaces with single-stranded DNA oligonucleotides. This protocol is applied to aluminum and copper oxide nanoparticles due to their great interest for the fabrication of highly energetic heterogeneous nanocomposites. The surface densities of streptavidin and biotinylated DNA oligonucleotides are precisely quantified combining atomic absorption spectroscopy with conventional dynamic light scattering and fluorometry and maximized to provide a basis for understanding the grafting mechanism. First, the streptavidin coverage is consistently below 20% of the total surface for both nanoparticles. Second, direct and unspecific grafting of DNA single strands onto Al and CuO nanoparticles largely dominates the overall functionalization process: ∼95% and 90% of all grafted DNA strands are chemisorbed on the CuO and Al nanoparticle surfaces, respectively. Measurements of hybridization efficiency indicate that only ∼5 and ∼10% of single-stranded oligonucleotides grafted onto the CuO and Al surfaces are involved in the hybridization process, corresponding precisely to the streptavidin coverage, as evidenced by the occupancy of 0.9 and 1.2 oligonucleotides per protein. The hybridization efficiency of single-stranded oligonucleotides chemisorbed on CuO and Al without streptavidin coating decreases to only ∼2%, justifying the use of streptavidin despite its poor surface occupancy. Finally, the structure of directly chemisorbed DNA strands onto oxide surfaces is examined and discussed.

High-throughput chromatin motion tracking in living yeast reveals the flexibility of the fiber throughout the genome.

Chromosome dynamics are recognized to be intimately linked to genomic transactions, yet the physical principles governing spatial fluctuations of chromatin are still a matter of debate. Using high-throughput single-particle tracking, we recorded the movements of nine fluorescently labeled chromosome loci located on chromosomes III, IV, XII, and XIV of Saccharomyces cerevisiae over an extended temporal range spanning more than four orders of magnitude (10(-2)-10(3) sec). Spatial fluctuations appear to be characterized by an anomalous diffusive behavior, which is homogeneous in the time domain, for all sites analyzed. We show that this response is consistent with the Rouse polymer model, and we confirm the relevance of the model with Brownian dynamics simulations and the analysis of the statistical properties of the trajectories. Moreover, the analysis of the amplitude of fluctuations by the Rouse model shows that yeast chromatin is highly flexible, its persistence length being qualitatively estimated to <30 nm. Finally, we show that the Rouse model is also relevant to analyze chromosome motion in mutant cells depleted of proteins that bind to or assemble chromatin, and suggest that it provides a consistent framework to study chromatin dynamics. We discuss the implications of our findings for yeast genome architecture and for target search mechanisms in the nucleus.

Analysis of DNA Replication by Optical Mapping in Nanochannels.

DNA replication is essential to maintain genome integrity in S phase of the cell division cycle. Accumulation of stalled replication forks is a major source of genetic instability, and likely constitutes a key driver of tumorigenesis. The mechanisms of regulation of replication fork progression have therefore been extensively investigated, in particular with DNA combing, an optical mapping technique that allows the stretching of single molecules and the mapping of active region for DNA synthesis by fluorescence microscopy. DNA linearization in nanochannels has been successfully used to probe genomic information patterns along single chromosomes, and has been proposed to be a competitive alternative to DNA combing. Yet this conjecture remains to be confirmed experimentally. Here, two complementary techniques are established to detect the genomic distribution of tracks of newly synthesized DNA in human cells by optical mapping in nanochannels. Their respective advantages and limitations are compared, and applied them to detect deregulations of the replication program induced by the antitumor drug hydroxyurea. The developments here thus broaden the field of applications accessible to nanofluidic technologies, and can be used in the future as part for molecular diagnostics in the context of high throughput cancer drug screening.

A fractal model for nuclear organization: current evidence and biological implications.

Chromatin is a multiscale structure on which transcription, replication, recombination and repair of the genome occur. To fully understand any of these processes at the molecular level under physiological conditions, a clear picture of the polymorphic and dynamic organization of chromatin in the eukaryotic nucleus is required. Recent studies indicate that a fractal model of chromatin architecture is consistent with both the reaction-diffusion properties of chromatin interacting proteins and with structural data on chromatin interminglement. In this study, we provide a critical overview of the experimental evidence that support a fractal organization of chromatin. On this basis, we discuss the functional implications of a fractal chromatin model for biological processes and propose future experiments to probe chromatin organization further that should allow to strongly support or invalidate the fractal hypothesis.

DNA Sizing with pg/µL Sensitivity for Cell-Free DNA Analysis with the µLAS Technology.

The µLAS technology enables in-line DNA concentration and separation in a microchannel. Here, we describe its operation to analyze the size profile of cell-free DNA (cfDNA) extracted from blood plasma. Operated on commercial systems for capillary electrophoresis, we provide the size distribution of healthy individuals or patients using an input of 10 µL.

Protocol for fabricating and characterizing microvessel-on-a-chip for human umbilical vein endothelial cells.

Organ-on-a-chip technologies enable the fabrication of endothelial tissues, so-called microvessels (MVs), which emulate the endothelial barrier function in healthy or disease conditions. In this protocol, we describe the fabrication of perfusable open-chamber style MVs embedded in collagen gels. We then report a simple technology to characterize the MV barrier properties in static or under pressure based on fluorescence confocal imaging. Finally, we provide quantification techniques that enable us to infer the structure of MV paracellular pores. For complete details on the use and execution of this protocol, please refer to Cacheux et al.1.

Molecular crowding affects diffusion and binding of nuclear proteins in heterochromatin and reveals the fractal organization of chromatin.

The nucleus of eukaryotes is organized into functional compartments, the two most prominent being heterochromatin and nucleoli. These structures are highly enriched in DNA, proteins or RNA, and thus thought to be crowded. In vitro, molecular crowding induces volume exclusion, hinders diffusion and enhances association, but whether these effects are relevant in vivo remains unclear. Here, we establish that volume exclusion and diffusive hindrance occur in dense nuclear compartments by probing the diffusive behaviour of inert fluorescent tracers in living cells. We also demonstrate that chromatin-interacting proteins remain transiently trapped in heterochromatin due to crowding induced enhanced affinity. The kinetic signatures of these crowding consequences allow us to derive a fractal model of chromatin organization, which explains why the dynamics of soluble nuclear proteins are affected independently of their size. This model further shows that the fractal architecture differs between heterochromatin and euchromatin, and predicts that chromatin proteins use different target-search strategies in the two compartments. We propose that fractal crowding is a fundamental principle of nuclear organization, particularly of heterochromatin maintenance.

Single molecule study of DNA collision with elliptical nanoposts conveyed by hydrodynamics.

Periodic arrays of micro- or nanopillars constitute solid-state matrices with excellent properties for DNA size separation. Nanofabrication technologies offer many solutions to tailor the geometry of obstacle arrays, yet most studies have been conducted with cylinders arranged in hexagonal lattices. In this report, we investigate the dynamics of single DNA collision with elliptical nanoposts using hydrodynamic actuation. Our data show that the asymmetry of the obstacles has minor effect on unhooking dynamics, and thus confirm recent predictions obtained by Brownian dynamics simulations. In addition, we show that the disengagement dynamics are correctly predicted by models of electrophoresis, and propose that this consistency is associated to the confinement in slit-like channels. We finally conclude that elliptical posts are expected to marginally improve the performances of separation devices.

Solute transport in the brain tissue: what are the key biophysical parameters tying in vivo and in vitro studies together?

The mechanisms of solute transport in brain tissues are still under debate. The medical relevance of this topic has put the blood-brain barrier and the mechanisms of solute transport through the brain parenchyma in the spotlight, notably in the context of brain clearance. In the last decade, the classical view of pure diffusive flow across the brain parenchyma was tested against the recent proposal of an active, convectional fluid flow model known as the glymphatic model. Experimental studies of brain transport on living humans and animals have temporal and spatial limitations to validate any of these models. Therefore, detailed microscopic observations, mostly ex vivo tissue and simplified in vitro brain models with the support from computational models, are necessary to understand transport mechanisms in brain tissues. However, standardization is lacking between these experimental approaches, which tends to limit the generality of conclusions. In this review, we provide an overview of the output and limitations of modern brain solute transport studies to search for key parameters comparable across experimental setups. We emphasize that in vitro models relying on physiological material and reproducing the biophysical setting of the brain, as well as computational/mathematical models constitute powerful solutions to understand the solute transport phenomena inside of the brain tissue. Finally, we suggest the blood-brain barrier permeability and the apparent diffusion coefficient through the brain parenchyma to be robust biophysical parameters for the extraction of cross-model conclusion.

Asymmetry of tensile versus compressive elasticity and permeability contributes to the regulation of exchanges in collagen gels.

The Starling principle describes exchanges between blood and tissues based on the balance of hydrostatic and osmotic flows. However, the permeation properties of the main constituent of tissues, namely, collagen, in response to the stress exerted by blood pressure remain poorly characterized. Here, we develop an instrument to determine the elasticity and permeability of collagen gels under tensile and compressive stress based on measuring the temporal change in pressure in an air cavity sealed at the outlet of a collagen slab. Data analysis with an analytical model reveals a drop in the permeability and enhanced strain stiffening of native collagen gels under compression versus tension, both effects being essentially lost after chemical cross-linking. Furthermore, we report the control of the permeability of native collagen gels using sinusoidal fluid injection, an effect explained by the asymmetric response in tension and compression. We lastly suggest that blood-associated pulsations could contribute to exchanges within tissues.