Stable diffusion gradients in microfluidic conduits bounded by fluid walls.

Assays mimicking in vitro the concentration gradients triggering biological responses like those involved in fighting infections and blood clotting are essential for biomedical research. Microfluidic assays prove especially attractive as they allow precise control of gradient shape allied to a reduction in scale. Conventional microfluidic devices are fabricated using solid plastics that prevent direct access to responding cells. Fluid-walled microfluidics allows the manufacture of circuits on standard Petri dishes in seconds, coupled to simple operating methods; cell-culture medium sitting in a standard dish is confined to circuits by fluid walls made of an immiscible fluorocarbon. We develop and experimentally validate an analytical model of diffusion between two or more aqueous streams flowing at different rates into a fluid-walled conduit with the cross-section of a circular segment. Unlike solid walls, fluid walls morph during flows as pressures fall, with wall shape changing down the conduit. The model is validated experimentally for Fourier numbers < 0.1 using fluorescein diffusing between laminar streams. It enables a priori prediction of concentration gradients throughout a conduit, so allowing rapid circuit design as well as providing bio-scientists with an accurate way of predicting local concentrations of bioactive molecules around responsive and non-responsive cells.

A fluid-walled microfluidic platform for human neuron microcircuits and directed axotomy.

In our brains, different neurons make appropriate connections; however, there remain few in vitro models of such circuits. We use an open microfluidic approach to build and study neuronal circuits in vitro in ways that fit easily into existing bio-medical workflows. Dumbbell-shaped circuits are built in minutes in standard Petri dishes; the aqueous phase is confined by fluid walls - interfaces between cell-growth medium and an immiscible fluorocarbon, FC40. Conditions are established that ensure post-mitotic neurons derived from human induced pluripotent stem cells (iPSCs) plated in one chamber of a dumbbell remain where deposited. After seeding cortical neurons on one side, axons grow through the connecting conduit to ramify amongst striatal neurons on the other - an arrangement mimicking unidirectional cortico-striatal connectivity. We also develop a moderate-throughput non-contact axotomy assay. Cortical axons in conduits are severed by a media jet; then, brain-derived neurotrophic factor and striatal neurons in distal chambers promote axon regeneration. As additional conduits and chambers are easily added, this opens up the possibility of mimicking complex neuronal networks, and screening drugs for their effects on connectivity.

Bridging condensins mediate compaction of mitotic chromosomes.

Eukaryotic chromosomes compact during mitosis into elongated cylinders-and not the spherical globules expected of self-attracting long flexible polymers. This process is mainly driven by condensin-like proteins. Here, we present Brownian-dynamic simulations involving two types of such proteins with different activities. One, which we refer to as looping condensins, anchors long-lived chromatin loops to create bottlebrush structures. The second, referred to as bridging condensins, forms multivalent bridges between distant parts of these loops. We show that binding of bridging condensins leads to the formation of shorter and stiffer mitotic-like cylinders without requiring any additional energy input. These cylinders have several features matching experimental observations. For instance, the axial condensin backbone breaks up into clusters as found by microscopy, and cylinder elasticity qualitatively matches that seen in chromosome pulling experiments. Additionally, simulating global condensin depletion or local faulty condensin loading gives phenotypes seen experimentally and points to a mechanistic basis for the structure of common fragile sites in mitotic chromosomes.

A platform for modular assembly and feeding of micro-organoids on standard Petri dishes.

Organoids grow in vitro to reproduce structures and functions of corresponding organs in vivo. As diffusion delivers nutrients over only ∼200 µm, refreshing flows through organoids are required to avoid necrosis at their cores; achieving this is a central challenge in the field. Our general aim is to develop a platform for culturing micro-organoids fed by appropriate flows that is accessible to bioscientists. As organs develop from layers of several cell types, our strategy is to seed different cells in thin modules (i.e. extra-cellular matrices in stronger scaffolds) in standard Petri dishes, stack modules in the required order, and overlay an immiscible fluorocarbon (FC40) to prevent evaporation. As FC40 is denser than medium, one might expect medium to float on FC40, but interfacial forces can be stronger than buoyancy ones; then, stacks remain attached to the bottom of dishes. After manually pipetting medium into the base of stacks, refreshing upward flows occur automatically (without the need for external pumps), driven mainly by differences in hydrostatic pressure. Proof-of-concept experiments show that such flows support clonal growth of human embryonic kidney cells at expected rates, even though cells may lie hundreds of microns away from surrounding fluid walls of the two immiscible liquids.

Reconfigurable Microfluidic Circuits for Isolating and Retrieving Cells of Interest.

Microfluidic devices are widely used in many fields of biology, but a key limitation is that cells are typically surrounded by solid walls, making it hard to access those that exhibit a specific phenotype for further study. Here, we provide a general and flexible solution to this problem that exploits the remarkable properties of microfluidic circuits with fluid walls─transparent interfaces between culture media and an immiscible fluorocarbon that are easily pierced with pipets. We provide two proofs of concept in which specific cell subpopulations are isolated and recovered: (i) murine macrophages chemotaxing toward complement component 5a and (ii) bacteria (Pseudomonas aeruginosa) in developing biofilms that migrate toward antibiotics. We build circuits in minutes on standard Petri dishes, add cells, pump in laminar streams so molecular diffusion creates attractant gradients, acquire time-lapse images, and isolate desired subpopulations in real time by building fluid walls around migrating cells with an accuracy of tens of micrometers using 3D printed adaptors that convert conventional microscopes into wall-building machines. Our method allows live cells of interest to be easily extracted from microfluidic devices for downstream analyses.

Microfluidics on Standard Petri Dishes for Bioscientists.

Few microfluidic devices are used in biomedical labs, despite the obvious potential; reasons given include the devices are rarely made with cell-friendly materials, and liquids are inaccessibly buried behind solid confining walls. An open microfluidic approach is reviewed in which aqueous circuits with almost any imaginable 2D shape are fabricated in minutes on standard polystyrene Petri dishes by reshaping two liquids (cell-culture media plus an immiscible and bioinert fluorocarbon, FC40). Then, the aqueous phase becomes confined by fluid FC40 walls firmly pinned to the dish by interfacial forces. Such walls can be pierced at any point with pipets and liquids added or removed through them, while flows can be driven actively using external pumps or passively by exploiting local differences in Laplace pressure. As walls are robust, permeable to O2 plus CO2 , and transparent, cells are grown in incubators and monitored microscopically as usual. It is hoped that this simple, accessible, and affordable fluid-shaping technology provides bioscientists with an easy entrée into microfluidics.

Predicting flows through microfluidic circuits with fluid walls.

The aqueous phase in traditional microfluidics is usually confined by solid walls; flows through such systems are often predicted accurately. As solid walls limit access, open systems are being developed in which the aqueous phase is partly bounded by fluid walls (interfaces with air or immiscible liquids). Such fluid walls morph during flow due to pressure gradients, so predicting flow fields remains challenging. We recently developed a version of open microfluidics suitable for live-cell biology in which the aqueous phase is confined by an interface with an immiscible and bioinert fluorocarbon (FC40). Here, we find that common medium additives (fetal bovine serum, serum replacement) induce elastic no-slip boundaries at this interface and develop a semi-analytical model to predict flow fields. We experimentally validate the model's accuracy for single conduits and fractal vascular trees and demonstrate how flow fields and shear stresses can be controlled to suit individual applications in cell biology.

Creating wounds in cell monolayers using micro-jets.

Many wound-healing assays are used in cell biology and biomedicine; they are often labor intensive and/or require specialized and costly equipment. We describe a contactless method to create wounds with any imaginable 2D pattern in cell monolayers using the micro-jets of either media or an immiscible and biocompatible fluorocarbon (i.e., FC40). We also combine this with another method that allows automation and multiplexing using standard Petri dishes. A dish is filled with a thin film of media overlaid with FC40, and the two liquids are reshaped into an array of microchambers within minutes. Each chamber in such a grid is isolated from others by the fluid walls of FC40. Cells are now added, allowed to grow into a monolayer, and wounds are created using the microjets; then, healing is monitored by microscopy. As arrays of chambers can be made using media and Petri dishes familiar to biologists, and as dishes fit seamlessly into their incubators, microscopes, and workflows, we anticipate that this assay will find wide application in wound healing.

Jet-Printing Microfluidic Devices on Demand.

There is an unmet demand for microfluidics in biomedicine. This paper describes contactless fabrication of microfluidic circuits on standard Petri dishes using just a dispensing needle, syringe pump, three-way traverse, cell-culture media, and an immiscible fluorocarbon (FC40). A submerged microjet of FC40 is projected through FC40 and media onto the bottom of a dish, where it washes media away to leave liquid fluorocarbon walls pinned to the substrate by interfacial forces. Such fluid walls can be built into almost any imaginable 2D circuit in minutes, which is exploited to clone cells in a way that beats the Poisson limit, subculture adherent cells, and feed arrays of cells continuously for a week. This general method should have wide application in biomedicine.

Using Fluid Walls for Single-Cell Cloning Provides Assurance in Monoclonality.

Single-cell isolation and cloning are essential steps in many applications, ranging from the production of biotherapeutics to stem cell therapy. Having confidence in monoclonality in such applications is essential from both research and commercial perspectives, for example, to ensure that data are of high quality and regulatory requirements are met. Consequently, several approaches have been developed to improve confidence in monoclonality. However, ensuring monoclonality using standard well plate formats remains challenging, primarily due to edge effects; the solid wall around a well can prevent a clear view of how many cells might be in a well. We describe a method that eliminates such edge effects: solid confining walls are replaced by transparent fluid ones, and standard low-cost optics can confirm monoclonality.

Raising fluid walls around living cells.

An effective transformation of the cell culture dishes that biologists use every day into microfluidic devices would open many avenues for miniaturizing cell-based workflows. In this article, we report a simple method for creating microfluidic arrangements around cells already growing on the surface of standard petri dishes, using the interface between immiscible fluids as a "building material." Conventional dishes are repurposed into sophisticated microfluidic devices by reshaping, on demand, the fluid structures around living cells. Moreover, these microfluidic arrangements can be further reconfigured during experiments, which is impossible with most existing microfluidic platforms. The method is demonstrated using workflows involving cell cloning, the selection of a particular clone from among others in a dish, drug treatments, and wound healing. The versatility of the approach and its biologically friendly aspects may hasten uptake by biologists of microfluidics, so the technology finally fulfills its potential.

Transcription-driven genome organization: a model for chromosome structure and the regulation of gene expression tested through simulations.

Current models for the folding of the human genome see a hierarchy stretching down from chromosome territories, through A/B compartments and topologically-associating domains (TADs), to contact domains stabilized by cohesin and CTCF. However, molecular mechanisms underlying this folding, and the way folding affects transcriptional activity, remain obscure. Here we review physical principles driving proteins bound to long polymers into clusters surrounded by loops, and present a parsimonious yet comprehensive model for the way the organization determines function. We argue that clusters of active RNA polymerases and their transcription factors are major architectural features; then, contact domains, TADs and compartments just reflect one or more loops and clusters. We suggest tethering a gene close to a cluster containing appropriate factors-a transcription factory-increases the firing frequency, and offer solutions to many current puzzles concerning the actions of enhancers, super-enhancers, boundaries and eQTLs (expression quantitative trait loci). As a result, the activity of any gene is directly influenced by the activity of other transcription units around it in 3D space, and this is supported by Brownian-dynamics simulations of transcription factors binding to cognate sites on long polymers.

Microfluidic chambers using fluid walls for cell biology.

Many proofs of concept have demonstrated the potential of microfluidics in cell biology. However, the technology remains inaccessible to many biologists, as it often requires complex manufacturing facilities (such as soft lithography) and uses materials foreign to cell biology (such as polydimethylsiloxane). Here, we present a method for creating microfluidic environments by simply reshaping fluids on a substrate. For applications in cell biology, we use cell media on a virgin Petri dish overlaid with an immiscible fluorocarbon. A hydrophobic/fluorophilic stylus then reshapes the media into any pattern by creating liquid walls of fluorocarbon. Microfluidic arrangements suitable for cell culture are made in minutes using materials familiar to biologists. The versatility of the method is demonstrated by creating analogs of a common platform in cell biology, the microtiter plate. Using this vehicle, we demonstrate many manipulations required for cell culture and downstream analysis, including feeding, replating, cloning, cryopreservation, lysis plus RT-PCR, transfection plus genome editing, and fixation plus immunolabeling (when fluid walls are reconfigured during use). We also show that mammalian cells grow and respond to stimuli normally, and worm eggs develop into adults. This simple approach provides biologists with an entrée into microfluidics.

Shaping epigenetic memory via genomic bookmarking.

Reconciling the stability of epigenetic patterns with the rapid turnover of histone modifications and their adaptability to external stimuli is an outstanding challenge. Here, we propose a new biophysical mechanism that can establish and maintain robust yet plastic epigenetic domains via genomic bookmarking (GBM). We model chromatin as a recolourable polymer whose segments bear non-permanent histone marks (or colours) which can be modified by 'writer' proteins. The three-dimensional chromatin organisation is mediated by protein bridges, or 'readers', such as Polycomb Repressive Complexes and Transcription Factors. The coupling between readers and writers drives spreading of biochemical marks and sustains the memory of local chromatin states across replication and mitosis. In contrast, GBM-targeted perturbations destabilise the epigenetic patterns. Strikingly, we demonstrate that GBM alone can explain the full distribution of Polycomb marks in a whole Drosophila chromosome. We finally suggest that our model provides a starting point for an understanding of the biophysics of cellular differentiation and reprogramming.

Microfluidics with fluid walls.

Microfluidics has great potential, but the complexity of fabricating and operating devices has limited its use. Here we describe a method - Freestyle Fluidics - that overcomes many key limitations. In this method, liquids are confined by fluid (not solid) walls. Aqueous circuits with any 2D shape are printed in seconds on plastic or glass Petri dishes; then, interfacial forces pin liquids to substrates, and overlaying an immiscible liquid prevents evaporation. Confining fluid walls are pliant and resilient; they self-heal when liquids are pipetted through them. We drive flow through a wide range of circuits passively by manipulating surface tension and hydrostatic pressure, and actively using external pumps. Finally, we validate the technology with two challenging applications - triggering an inflammatory response in human cells and chemotaxis in bacterial biofilms. This approach provides a powerful and versatile alternative to traditional microfluidics.The complexity of fabricating and operating microfluidic devices limits their use. Walsh et al. describe a method in which circuits are printed as quickly and simply as writing with a pen, and liquids in them are confined by fluid instead of solid walls.

Ephemeral Protein Binding to DNA Shapes Stable Nuclear Bodies and Chromatin Domains.

Fluorescence microscopy reveals that the contents of many (membrane-free) nuclear bodies exchange rapidly with the soluble pool while the underlying structure persists; such observations await a satisfactory biophysical explanation. To shed light on this, we perform large-scale Brownian dynamics simulations of a chromatin fiber interacting with an ensemble of (multivalent) DNA-binding proteins able to switch between an "on" (binding) and an "off" (nonbinding) state. This system provides a model for any DNA-binding protein that can be posttranslationally modified to change its affinity for DNA (e.g., through phosphorylation). Protein switching is a nonequilibrium process, and it leads to the formation of clusters of self-limiting size, where individual proteins in a cluster exchange with the soluble pool with kinetics similar to those seen in photobleaching experiments. This behavior contrasts sharply with that exhibited by nonswitching proteins, which are permanently in the on-state; when these bind to DNA nonspecifically, they form clusters that grow indefinitely in size. To explain these findings, we propose a mean-field theory from which we obtain a scaling relation between the typical cluster size and the protein switching rate. Protein switching also reshapes intrachromatin contacts to give networks resembling those seen in topologically associating domains, as switching markedly favors local (short-range) contacts over distant ones. Our results point to posttranslational modification of chromatin-bridging proteins as a generic mechanism driving the self-assembly of highly dynamic, nonequilibrium, protein clusters with the properties of nuclear bodies.

Biocompatibility of fluids for multiphase drops-in-drops microfluidics.

This paper addresses the biocompatibility of fluids and surfactants in the context of microfluidics and more specifically in a drops-in-drops system for mammalian cell based drug screening. In the drops-in-drops approach, three immiscible fluids are used to manipulate the flow of aqueous microliter-sized drops; it enables merging of drops containing cells with drops containing drugs within a Teflon tube. Preliminary tests showed that a commonly-used fluid and surfactant combination resulted in significant variability in gene expression levels in Jurkat cells after exposure to a drug for four hours. This result led to further investigations of potential fluid and surfactant combinations that can be used in microfluidic systems for medium to long-term drug screening. Results herein identify a fluid combination, HFE-7500 and 5-cSt silicone oil + 0.25% Abil EM180, which enabled the drops-in-drops approach; this combination also allowed gene expression at normal levels comparable with the conventional drug screening in both magnitude and variability.

Binding of nuclear factor κB to noncanonical consensus sites reveals its multimodal role during the early inflammatory response.

Mammalian cells have developed intricate mechanisms to interpret, integrate, and respond to extracellular stimuli. For example, tumor necrosis factor (TNF) rapidly activates proinflammatory genes, but our understanding of how this occurs against the ongoing transcriptional program of the cell is far from complete. Here, we monitor the early phase of this cascade at high spatiotemporal resolution in TNF-stimulated human endothelial cells. NF-κB, the transcription factor complex driving the response, interferes with the regulatory machinery by binding active enhancers already in interaction with gene promoters. Notably, >50% of these enhancers do not encode canonical NF-κB binding motifs. Using a combination of genomics tools, we find that binding site selection plays a key role in NF-κΒ-mediated transcriptional activation and repression. We demonstrate the latter by describing the synergy between NF-κΒ and the corepressor JDP2. Finally, detailed analysis of a 2.8-Mbp locus using sub-kbp-resolution targeted chromatin conformation capture and genome editing uncovers how NF-κΒ that has just entered the nucleus exploits pre-existing chromatin looping to exert its multimodal role. This work highlights the involvement of topology in cis-regulatory element function during acute transcriptional responses, where primary DNA sequence and its higher-order structure constitute a regulatory context leading to either gene activation or repression.

Formation of droplet interface bilayers in a Teflon tube.

Droplet-interface bilayers (DIBs) have applications in disciplines ranging from biology to computing. We present a method for forming them manually using a Teflon tube attached to a syringe pump; this method is simple enough it should be accessible to those without expertise in microfluidics. It exploits the properties of interfaces between three immiscible liquids, and uses fluid flow through the tube to pack together drops coated with lipid monolayers to create bilayers at points of contact. It is used to create functional nanopores in DIBs composed of phosphocholine using the protein α-hemolysin (αHL), to demonstrate osmotically-driven mass transfer of fluid across surfactant-based DIBs, and to create arrays of DIBs. The approach is scalable, and thousands of DIBs can be prepared using a robot in one hour; therefore, it is feasible to use it for high throughput applications.

Simulated binding of transcription factors to active and inactive regions folds human chromosomes into loops, rosettes and topological domains.

Biophysicists are modeling conformations of interphase chromosomes, often basing the strengths of interactions between segments distant on the genetic map on contact frequencies determined experimentally. Here, instead, we develop a fitting-free, minimal model: bivalent or multivalent red and green 'transcription factors' bind to cognate sites in strings of beads ('chromatin') to form molecular bridges stabilizing loops. In the absence of additional explicit forces, molecular dynamic simulations reveal that bound factors spontaneously cluster-red with red, green with green, but rarely red with green-to give structures reminiscent of transcription factories. Binding of just two transcription factors (or proteins) to active and inactive regions of human chromosomes yields rosettes, topological domains and contact maps much like those seen experimentally. This emergent 'bridging-induced attraction' proves to be a robust, simple and generic force able to organize interphase chromosomes at all scales.