Droplet barcoding for single-cell transcriptomics applied to embryonic stem cells.

It has long been the dream of biologists to map gene expression at the single-cell level. With such data one might track heterogeneous cell sub-populations, and infer regulatory relationships between genes and pathways. Recently, RNA sequencing has achieved single-cell resolution. What is limiting is an effective way to routinely isolate and process large numbers of individual cells for quantitative in-depth sequencing. We have developed a high-throughput droplet-microfluidic approach for barcoding the RNA from thousands of individual cells for subsequent analysis by next-generation sequencing. The method shows a surprisingly low noise profile and is readily adaptable to other sequencing-based assays. We analyzed mouse embryonic stem cells, revealing in detail the population structure and the heterogeneous onset of differentiation after leukemia inhibitory factor (LIF) withdrawal. The reproducibility of these high-throughput single-cell data allowed us to deconstruct cell populations and infer gene expression relationships. VIDEO ABSTRACT.

One-pot system for synthesis, assembly, and display of functional single-span membrane proteins on oil-water interfaces.

Single-span membrane proteins (ssMPs) represent approximately one-half of all membrane proteins and play important roles in cellular communications. However, like all membrane proteins, ssMPs are prone to misfolding and aggregation because of the hydrophobicity of transmembrane helices, making them difficult to study using common aqueous solution-based approaches. Detergents and membrane mimetics can solubilize membrane proteins but do not always result in proper folding and functionality. Here, we use cell-free protein synthesis in the presence of oil drops to create a one-pot system for the synthesis, assembly, and display of functional ssMPs. Our studies suggest that oil drops prevent aggregation of some in vitro-synthesized ssMPs by allowing these ssMPs to localize on oil surfaces. We speculate that oil drops may provide a hydrophobic interior for cotranslational insertion of the transmembrane helices and a fluidic surface for proper assembly and display of the ectodomains. These functionalized oil drop surfaces could mimic cell surfaces and allow ssMPs to interact with cell surface receptors under an environment closest to cell-cell communication. Using this approach, we showed that apoptosis-inducing human transmembrane proteins, FasL and TRAIL, synthesized and displayed on oil drops induce apoptosis of cultured tumor cells. In addition, we take advantage of hydrophobic interactions of transmembrane helices to manipulate the assembly of ssMPs and create artificial clusters on oil drop surfaces. Thus, by coupling protein synthesis with self-assembly at the water-oil interface, we create a platform that can use recombinant ssMPs to communicate with cells.

General route for the assembly of functional inorganic capsules.

Semipermeable, hollow capsules are attractive materials for the encapsulation and delivery of active agents in food processing, pharmaceutical and agricultural industries, and biomedicine. These capsules can be produced by forming a solid shell of close packed colloidal particles, typically polymeric particles, at the surface of emulsion droplets. However, current methods to prepare such capsules may involve multistep chemical procedures to tailor the surface chemistry of particles or are limited to particles that exhibit inherently the right hydrophobic-hydrophilic balance to adsorb around emulsion droplets. In this work, we describe a general and simple method to fabricate semipermeable, inorganic capsules from emulsion droplets stabilized by a wide variety of colloidal metal oxide particles. The assembly of particles at the oil-water interface is induced by the in situ hydrophobization of the particle surface through the adsorption of short amphiphilic molecules. The adsorption of particles at the interface leads to stable capsules comprising a single layer of particles in the outer shell. Such capsules can be used in the wet state or can be further processed into dry capsules. The permeability of the capsules can be modified by filling the interstices between the shell particles with polymeric or inorganic species. Functional capsules with biocompatible, bioresorbable, heat-resistant, chemical-resistant, and magnetic properties were prepared using alumina, silica, iron oxide, or tricalcium phosphate as particles in the shell.

Chemically induced coalescence in droplet-based microfluidics.

We present a new microfluidic method to coalesce pairs of surfactant-stabilized water-in-fluorocarbon oil droplets. We achieve this through the local addition of a poor solvent for the surfactant, perfluorobutanol, which induces cohesion between droplet interfaces causing them to merge. The efficiency of this technique is comparable to existing techniques providing an alternative method to coalesce pairs of droplets.

Stabilization of oil-in-water emulsions by colloidal particles modified with short amphiphiles.

Emulsions stabilized through the adsorption of colloidal particles at the liquid-liquid interface have long been used and investigated in a number of different applications. The interfacial adsorption of particles can be induced by adjusting the particle wetting behavior in the liquid media. Here, we report a new approach to prepare stable oil-in-water emulsions by tailoring the wetting behavior of colloidal particles in water using short amphiphilic molecules. We illustrate the method using hydrophilic metal oxide particles initially dispersed in the aqueous phase. The wettability of such particles in water is reduced by an in situ surface hydrophobization that induces particle adsorption at oil-water interfaces. We evaluate the conditions required for particle adsorption at the liquid-liquid interface and discuss the effect of the emulsion initial composition on the final microstructure of oil-water mixtures containing high concentrations of alumina particles modified with short carboxylic acids. This new approach for emulsion preparation can be easily applied to a variety of other metal oxide particles.

The stability of L3 sponge phase in acidic solutions.

In the synthesis of the disordered lyotropic liquid crystalline L3 sponge phase prepared with the cosurfactants cetylpyridinium chloride and hexanol, aqueous NaCl solution is used as the solvent. When this sponge phase is used as the template for L3 silica-phase processing, we replace NaCl with HCl to facilitate the acid catalysis of tetramethoxysilane in forming a templated silica gel, assuming that changing the solvent from NaCl(aq) to HCl(aq) of equivalent ionic strength does not affect the stability range of the L3 phase. In this work, we confirm that changing the pH of the solvent from neutral to acidic (with HCl) has negligible effect on the L3 phase region. Equivalent ionic strength is provided by either NaCl(aq) or HCl(aq) solvent; therefore, a similar phase behavior is observed regardless of which aqueous solvent is used.