The control of gene expression in cells and organisms allows to unveil gene to function relationships and to reprogram biological responses. Several systems, such as Zinc fingers, TALE (Transcription activator-like effectors), and siRNAs (small-interfering RNAs), have been exploited to achieve this. However, recent advances in Clustered Regularly Interspaced Short Palindromic Repeats and Cas9 (CRISPR-Cas9) have overshadowed them due to high specificity, compatibility with many different organisms, and design flexibility. In this review we summarize state-of-the art for CRISPR-Cas9 technology for large scale gene perturbation studies, including single gene and multiple genes knock-out, knock-down, knock-up libraries, and their associated screening assays. We feature in particular the combination of these methods with single-cell transcriptomics approaches. Finally, we highlight the application of CRISPR-Cas9 systems in building synthetic circuits that can be interfaced with gene networks to control cellular states.

The development of new therapies for surgical adhesions has proven to be difficult as there is no consistently effective way to assess treatment efficacy in clinical trials without performing a second surgery, which can result in additional adhesions. We have developed lipid microbubble formulations that use a short peptide sequence, CREKA, to target fibrin, the molecule that forms nascent adhesions. These targeted polymerized shell microbubbles (PSMs) are designed to allow ultrasound imaging of early adhesions for diagnostic purposes and for evaluating the success of potential treatments in clinical trials while acting as a possible treatment. In this study, we show that CREKA-targeted microbubbles preferentially bind fibrin over fibrinogen and are stable for long periods of time (~48 h), that these bound microbubbles can be visualized by ultrasound, and that neither these lipid-based bubbles nor their diagnostic-ultrasound-induced vibrations damage mesothelial cells in vitro. Moreover, these bubbles show the potential to identify adhesionlike fibrin formations and may hold promise in blocking or breaking up fibrin formations in vivo.

We investigate the kinetics of irreversible adsorption under the van der Waals regime, i.e. weakly Brownian polydisperse colloidal suspensions injected into shallow microchannels at high ionic strengths, where each suspension is represented by populations of particles with different particle sizes. We find that each population size of the particle in the suspension can be treated independently using an analytical solution based on the advection–diffusion equation and that the distribution of the adsorbed particles along the channel axis behaves according to a power law. The experimental measurements agree with Langevin simulations and are well accounted for by theory valid in the van der Waals regime. Operating in the van der Waals regime permits the present study to confirm the use of microfluidics as an effective in situ method to measure the Hamaker constant of particles under aqueous conditions.

The onset of liquid crystal (LC) phases in concentrated aqueous solutions of DNA oligomers crucially depends on the end-to-end interaction between the DNA duplexes, which can be provided by the aromatic stacking of the terminal base-pairs or by the pairing of complementary dangling-ends. Here we investigated the LC behavior of three blunt-end 12-base-long DNA duplexes synthesized with hydroxyl, phosphate and triphosphate 5’-termini. We experimentally characterized the concentration-temperature phase diagrams and we quantitatively estimated the end-to-end stacking free energy, by comparing the empirical data with the predictions of coarse-grained linear aggregation models. The preservation of LC ordering, even in presence of the bulky and highly charged triphosphate group, indicates that attractive stacking interactions are still present and capable of induce linear aggregation of the DNA duplexes. This finding strengthens the potential role of chromonic like self-assembly for the prebiotic formation of linear polymeric nucleic acids.

The flow of two immiscible liquids or fluids in bounded systems where confinement
geometry varies can lead to drop or bubble formation. This phenomenon has been reported
in the context of oil recovery and named snap-off, or exploited for making emulsions,
and then foams, by using microfluidic systems, namely, microchannel emulsification or
step emulsification. We report a comprehensive experimental investigation of such an
emulsification process occurring at the end of a glass rectangular tube filled with oil and
immersed in a water bath. This allows us to clearly visualize the breakup event of the
dispersed phase liquid finger at the capillary’s end. Below a critical flow rate, the drop size
varies slowly with the flow rate and it is linked to the pinching time of the dispersed phase.
A semiempirical law that gives the resulting drop size as a function of fluid and geometrical
properties is proposed. However, this feature is altered for an aspect ratio of the rectangular
tube below 2.5 where the forming drop hinders the counterflow of the continuous phase
leading to larger drops. Then, above a critical flow rate, or capillary number that weakly
depends on the viscosity ratio of the two liquids, the neck adopts a quasistatic shape well
accounted for by a model based on a Hele-Shaw flow. In that case, drop formation is
driven by gravity and a transition from a dripping regime to a jetting regime is observed
at higher flow rates. Monodisperse foam can also be formed by injecting air. While the
overall dynamics of bubble formation shares similarities with an incompressible fluid, the
bubble size and the critical capillary number do not follow the same scaling laws.

Convective dispersion of solutes is inherent to flow in channels because of the nonuniformity of the velocity profile. When diffusion is negligible, for large particles for example,
the trajectory of particles can be solely described by a kinematic approach. Here, we
investigate such a phenomenon for micrometer-size beads flowing in a circular pipe. We
show that the presence of large bubbles, namely in the case of a segmented flow, either
prevents the convective dispersion or leads to the accumulation of particles at the rear of
the bubble moving in front. The destabilization of the initially homogeneous suspension
occurs when liquid inertia comes into play. Indeed, for moderate Reynolds number of
the particles, particles move away from the wall, thus exploring different flow lines that
finally impact the axial dispersion features. Moreover, since the bubbles impose an axial
boundary condition of the mean velocity, a net flux of particles directed along the flow
direction is built up above a critical particle Reynolds number. This work is motivated by
the understanding of the flow behavior of biological samples, and especially in the context
of cell encapsulation.

In many cell types, migration can be oriented towards a chemical stimulus. In mammals, for example, embryonic cells migrate to follow developmental cues, immune cells migrate toward sites of inflammation, and cancer cells migrate away from the primary tumour and toward blood vessels during metastasis. Understanding how cells migrate in 3D environments in response to chemical cues is thus crucial to understanding directed migration in normal and disease states. To date, chemotaxis in mammalian cells has been primarily studied using 2D migration models. However, it is becoming increasingly clear that the mechanisms by which cells migrate in 2D and 3D environments dramatically differ, and cells in their native environments are confronted with a complex chemical milieu. To address these issues, we developed a microfluidic device to monitor the behaviour of cells embedded in a 3D collagen matrix in the presence of complex concentration fields of chemoattractants. This tuneable microsystem enables the generation of (1) homogeneous, stationary gradients set by a purely diffusive mechanism, or (2) spatially evolving, stationary gradients, set by a convection-diffusion mechanism. The device allows for stable gradients over several days and is large enough to study the behaviour of large cell aggregates. We observe that primary mature dendritic cells respond uniformly to homogeneous diffusion gradients, while cell behaviour is highly position-dependent in spatially variable convection-diffusion gradients. In addition, we demonstrate a directed response of cancer cells migrating away from tumour-like aggregates in the presence of soluble chemokine gradients. Together, this microfluidic device is a powerful system to observe the response of different cells and aggregates to tuneable chemical gradients.

A microfluidic method to specifically capture and detect infectious bacteria based on immunorecognition and proliferative power is presented. It involves a microscale fluidized bed in which magnetic and drag forces are balanced to retain antibody-functionalized superparamagnetic beads in a chamber during sample perfusion. Captured cells are then cultivated in situ by infusing nutritionally-rich medium. The system was validated by the direct one-step detection of Salmonella Typhimurium in undiluted unskimmed milk, without pre-treatment. The growth of bacteria induces an expansion of the fluidized bed, mainly due to the volume occupied by the newly formed bacteria. This expansion can be observed with the naked eye, providing simple low-cost detection of only a few bacteria and in a few hours. The time to expansion can also be measured with a low-cost camera, allowing quantitative detection down to 4 cfu (colony forming unit), with a dynamic range of 100 to 107 cfu ml−1 in 2 to 8 hours, depending on the initial concentration. This mode of operation is an equivalent of quantitative PCR, with which it shares a high dynamic range and outstanding sensitivity and specificity, operating at the live cell rather than DNA level. Specificity was demonstrated by controls performed in the presence of a 500× excess of non-pathogenic Lactococcus lactis. The system's versatility was demonstrated by its successful application to the detection and quantitation of Escherichia coli O157:H15 and Enterobacter cloacae. This new technology allows fast, low-cost, portable and automated bacteria detection for various applications in food, environment, security and clinics.

Miniaturized devices for the extraction of DNA have been used for assessing genetic material in biological, forensic and environmental samples. However, the ability to isolate trace amounts of highly fragmented DNA from biological fluids remains a challenge. The current work reports a microfluidic approach that combines on line a dynamic magnetic extraction procedure with droplet-based digital PCR (ddPCR). This strategy maximizes the surface area for DNA binding within the chip, in order to capture short DNA fragments, with the possibility of
recovering the purified samples into picoliter volumes for high sensitivity mutation detection. The application of this technology to capture circulating cell-free DNA (ccfDNA) from serum samples of cancer patients is demonstrated herein, with efficiencies comparable to standard column-based DNA extraction methods. This technology uses lesser amounts of required material and reagents, and has a higher potential for automation and multiplex DNA analysis. Furthermore, this approach can also be extended for the detection of other circulating biomarkers, such as nucleic acid sequences with aberrant methylation patterns or miRNA.

This study reports on the conception of magneto-Capillary Electrophoresis (magneto-CE), an approach integrating immuno-capture on circulating bio-functionalized magnetic beads into a unique capillary for preconcentration and electrokinetic separation. This hybrid mode is an evolution of in-capillary magnetic bead-based operation from static cluster format to dynamic configuration where beads are allowed to controllably circulate inside a CE capillary for interaction improvement. To implement the magneto-CE operation, a purpose-made instrument was constructed, allowing visual observation of the movement of the magnetic beads. We applied a new methodological strategy for determination of the amyloid β peptide (Aβ 1–42), which is as an established biomarker for molecular diagnosis of Alzheimer's disease (AD). The methodology is based on magneto-immuno-capture of fluorescently labeled Aβ 1–42 followed by a chemical elution with a basic solution prior to CE separation with laser induced fluorescent (LIF) detection. The superiority of this dynamic configuration of magneto-CE was demonstrated for this target analyte, with sample pretreatment and separation being performed in-capillary without any delay in between and without any waste of pretreated sample, which otherwise would not be the case with offline/batch-wise operation.

In mammalian embryos, cortical interneurons travel long distances among complex three-dimensional tissues before integrating into cortical circuits. Several molecular guiding cues involved in this migration process have been identified, but the influence of physical parameters remains poorly understood. In the present study, we have investigated in vitro the influence of the topography of the microenvironment on the migration of primary cortical interneurons released from mouse embryonic explants. We found that arrays of PDMS micro-pillars of 10 μm size and spacing, either round or square, influenced both the morphology and the migratory behavior of interneurons. Strikingly, most interneurons exhibited a single and long leading process oriented along the diagonals of the square pillared array, whereas leading processes of interneurons migrating in-between round pillars were shorter, often branched and oriented in all available directions. Accordingly, dynamic studies revealed that growth cone divisions were twice more frequent in round than in square pillars. Both soma and leading process tips presented forward directed movements within square pillars, contrasting with the erratic trajectories and more dynamic movements observed among round pillars. In support of these observations, long interneurons migrating in square pillars displayed tight bundles of stable microtubules aligned in the direction of migration. Overall, our results show that micron-sized topography provides global spatial constraints promoting the establishment of different morphological and migratory states. Remarkably, these different states belong to the natural range of migratory behaviors of cortical interneurons, highlighting the potential importance of topographical cues in the guidance of these embryonic neurons, and more generally in brain development.

Preeclampsia is a hypertensive pregnancy disease associated with a massive increase in sFlt-1 (soluble form of the vascular endothelial growth factor 1) in the maternal circulation, responsible for angiogenic imbalance and endothelial dysfunction. Pilot studies suggest that extracorporeal apheresis may reduce circulating sFlt-1 and prolong pregnancy. Nonspecific apheresis systems have potential adverse effects because of the capture of many other molecules. Our concept is based on a specific and competitive apheresis approach using VEGF (vascular endothelial growth factor) functionalized magnetic beads to capture sFlt-1 while releasing endogenous PlGF (placental growth factor) to restore a physiological angiogenic balance. Magnetic beads were functionalized with VEGF to capture sFlt-1. Experiments were performed using PBS, conditioned media from human trophoblastic cells, and human plasma. The proof of concept was validated in dynamic conditions in a microfluidic device as an approach mimicking real apheresis. Magnetic beads were functionalized with VEGF and characterized to evaluate their surface ligand density and recognition capabilities. VEGF-coated magnetic beads proved to be an efficient support in capturing sFlt-1 and releasing PlGF. In static conditions, sFlt-1 concentration decreased by 33±13%, whereas PlGF concentration increased by 27±10%. In dynamic conditions, the performances were improved, with 40% reduction of sFlt-1 and up to 2-fold increase of free PlGF. The sFlt-1/PlGF ratio was reduced by 63% in the plasma of preeclamptic patients. Apheresis was also associated with VEGF release. A ligand-based approach using VEGF-coated beads is an effective approach to the capture of sFlt-1 and the release of endogenous PlGF. It offers new perspectives for the treatment of preeclampsia.

Droplet microfluidics is a powerful technology that finds many applications in chemistry and biomedicine. Among different configurations, droplets confined in a capillary (or plugs) present a number of advantages: they allow positional identification and simplify the integration of complex multi-steps protocols. However, these protocols rely on the control of droplet speed, which is affected by a complex and still debated interplay of various physico-chemical parameters like droplet length, viscosity ratio between droplets and carrier fluid, flow rate and interfacial tension. We present here a systematic investigation of the droplet speed as a function of their length and interfacial tension, and propose a novel, simple and robust methodology to control the relative distance between consecutive droplets flowing in microfluidic channels through the addition of surfactants either into the dispersed and/or into the continuous phases. As a proof of concept application, we present the possibility to accurately trigger in space and time the merging of two confined droplets flowing in a uniform cross-section circular capillary. This approach is further validated by monitoring a conventional enzymatic reaction used to quantify the concentration of H2O2 in a biological sample, showing its potentialities in both continuous and stopped assay methods.

Tumor initiation and growth is associated with significant changes in the surrounding tissue. During carcinoma progression, a global stiffening of the extracellular matrix is observed and is interpreted as a signature of aggressive invasive tumors. However, it is still unknown whether this increase in matrix rigidity promotes invasion and whether this effect is constant along the course of invasion. Here we have developed a biomimetic in vitro assay that enabled us to address the question of the importance of tissue rigidity in the chronology of tumor invasion. Using low concentrations of the sugar threose, we can effectively stiffen reconstituted collagen I matrices and control the stiffening in time with no direct effect on residing cells. Our findings demonstrate that, depending on the timing of its stiffening, the extracellular matrix could either inhibit or promote cancer cell invasion and subsequent metastasis: while matrix stiffening after the onset of invasion promotes cancer cell migration and tumor spreading, stiff matrices encapsulate the tumor at an early stage and prevent cancer cell invasion. Our study suggests that adding a temporal dimension in in vitro models to analyze biological processes in four dimensions is necessary to fully capture their complexity.

Spontaneous adsorption of poly(lysine)-g-poly(ethylene glycol) comb-like copolymers (PLL-g-PEG) is a versatile mean to coat substrates with polymer layers that resist cell adhesion. We prepared redox cleavable PLL-g-PEG to switch adhesion on demand. Redox sensitivity was obtained by introducing disulfide linkers between the PLL backbone and PEG strands. This modification was done alone or in combination with an azide end on the PEG strands that enabled in situ conjugations of adhesion peptides or fluorescent labels (by a simple application of commercially available molecules for copper-free click chemistry compatible with cell survival). To balance the functional (adhesion-promoting) vs cell-repellent copolymers, mixed layers of adjusted compositions were obtained by coadsorption from mixed solutions of the cleavable copolymer with noncleavable and repellant PLL-g-PEG. The deposition of copolymers and quantitative cleavage as triggered by reductive conditions (application of solutions of tris(carboxyethyl)phosphine, dithiothreitol, or glutathione) were characterized by QCM-D, XPS, and fluorescence microscopy. In cell culture conditions, redox-triggered cleavage was obtained by a nontoxic application of TCEP for a few minutes, enabling either to release cell attachment points (i.e., cleavage of RGD-presenting areas) or to “open” nonspecific adherent areas (i.e., transition from PEG-presenting areas to adherent PLL-like coatings).

COOH-functionalized multi-walled carbon nanotubes (f-MWCNTs) film coated on glassy carbon electrode (GCE) were prepared, and the detection of diclofenac (DCF) was investigated on by cyclic voltammetry and amperometry. The results showed that the nano-structured electrodes exhibit good analytical performances towards the electrochemical oxidation of DCF with a detection limit of 0.1 µM and a sensitivity of 0.06 µA . µM-1 within a dynamic concentration range varying from 2 μM to 15 µM. Keywords: diclofenac; multi-walled carbon nanotubes; amperometry, detection

We study experimentally and theoretically the thickness of the coating obtained by pulling out a rod from a reservoir of yield-stress fluid. Opposite to Newtonian fluids, the coating thickness for a fluid of large enough yield stress is determined solely by the flow inside the reservoir and not by the flow inside the meniscus. The stress field inside the reservoir determines the thickness of the coating layer. The thickness is observed to increase nonlinearly with the sizes of the rod and of the reservoir. We develop a theoretical framework that describes this behavior and allows us to precisely predict the coating thickness.

Aqueous biphasic systems (ABSs), in which two aqueous phases with different compositions coexist as separate liquids, were first reported more than a century ago with polymer solutions. Recent observations of ABS forming from concentrated mixtures of inorganic salts and ionic liquids raise the fundamental question of how “different” the components of such mixtures should be for a liquid–liquid phase separation to occur. Here we show that even two monovalent salts sharing a common cation (lithium) but with different anions, namely, LiCl and lithium bis(trifluoromethanesulfonyl)imide (LiTFSI), may result in the formation of ABSs over a wide range of compositions at room temperature. Using a combination of experimental techniques and molecular simulations, we analyze the coexistence diagram and the mechanism driving the phase separation, arising from the different anion sizes. The understanding and …

Micro-energy storage devices are appealing, and highly demanded for diverse miniaturized electronic devices, ranging from microelectromechanical system, robotics, to sensing microsystems and wearable electronics. However, making high-energy microcapacitors with currently available printing technologies remains challenging. Herein, we show the possibility to use latex polyvinylidene fluoride (PVDF) as aqueous ink for making dielectric capacitors on the microscale. The dielectric properties of printed microcapacitors can be optimized based on a novel approach, i.e., mixing PVDF latex with polyvinyl alcohol (PVA) to realize dielectric organic nanocomposites. The PVA prevents the coalescence of PVDF nanoparticles and serves as a continuous matrix phase with high dielectric breakdown strength. While the well-dispersed PVDF nanoparticles serve as highly polarizable and isolated domains, providing large electric displacement under high fields. Consequently, a high discharged energy density of 12 Jcm-3 is achieved at 550 MVm-1. These printed microcapacitors demonstrate mechanical robustness and dielectric stability over time.