Person:

Weitz, David

Quantitative protein analysis of single cells is rarely achieved due to technical difficulties of detecting minute amounts of proteins present in one cell. We develop a mix-and-read assay for drop-based label-free protein analysis of single cells. This high-throughput method quantifies absolute, rather than relative, amounts of proteins and does not involve antibody labeling or mass spectrometry.

Face-centered cubic single crystals of (σ=1.55 μm) diameter hard-sphere silica colloidal particles were prepared by sedimentation onto (100) and (110) oriented templates. The crystals had a wide interface with the overlaying liquid that was parallel to the template. The location of the interface was determined by confocal microscopic location of the particles, followed by identification of the crystalline and liquid phases by a bond-orientation order parameter. Fluctuations in the height of the interface about its average position were recorded for several hundred configurations. The interfacial stiffness (γ̃) was determined from the slope of the inverse squared Fourier components of the height profile vs the square of the wave number, according to the continuum capillary fluctuation method. The offset of the fit from the origin could quantitatively be accounted for by gravitational damping of the fluctuations. For the (100) interface, (γ̃ =(1.3±0.3)k_{B}T/σ^{2}); for the (110) interface, (γ̃ =(1.0±0.2)k_{B}T/σ^{2}). The interfacial stiffness of both interfaces was found to be isotropic in the plane. This is surprising for the (110), where crystallography predicts twofold symmetry. Sedimentation onto a (111) template yielded a randomly stacked hexagonal crystal with isotropic (γ̃ =0.66k_{B}T/σ^{2}). This value, however, is less reliable than the two others due to imperfections in the crystal.

Colloidal capsules can sustain an external osmotic pressure; however, for a sufficiently large pressure, they will ultimately buckle. This process can be strongly influenced by structural inhomogeneities in the capsule shells. We explore how the time delay before the onset of buckling decreases as the shells are made more inhomogeneous; this behavior can be quantitatively understood by coupling shell theory with Darcy’s law. In addition, we show that the shell inhomogeneity can dramatically change the folding pathway taken by a capsule after it buckles.

We performed a series of deformation experiments on a monodisperse, hard-sphere colloidal glass while simultaneously following the 3D trajectories of roughly 50,000 individual particles with a confocal microscope. In each experiment, we deformed the glass in pure shear at a constant strain rate (1 − 5 × 10−5s−1) to maximum macroscopic strains (5 − 10%), then reversed the deformation at the same rate to return to zero macroscopic strain. We also measured 3D particle trajectories in an identically-prepared quiescent glass in which the macroscopic strain was always zero. We find that shear transformation zones exist and are active in both sheared and quiescent colloidal glasses, revealed by a distinctive four-fold signature in spatial autocorrelations of the local shear strain. With increasing shear, the population of local shear transformations develops more quickly than in a quiescent glass, and many of these transformations are irreversible. When the macroscopic strain is reversed, we observe partial elastic recovery, followed by plastic deformation of the opposite sign, required to compensate for the irreversibly transformed regions. The average diameter of the shear transformation zones at maximum strain is 2.3 particle diameters.

Human noroviruses (HuNoVs) are positive-sense RNA viruses that can cause severe, highly infectious gastroenteritis. HuNoV outbreaks are frequently associated with recombination between circulating strains. Strain genotyping and phylogenetic analyses show that noroviruses often recombine in a highly conserved region near the junction of the viral polyprotein (open reading frame 1 [ORF1]) and capsid (ORF2) genes and occasionally within the RNA-dependent RNA polymerase (RdRP) gene. Although genotyping methods are useful for tracking changes in circulating viral populations, they report only the dominant recombinant strains and do not elucidate the frequency or range of recombination events. Furthermore, the relatively low frequency of recombination in RNA viruses has limited studies to cell culture or in vitro systems, which do not reflect the complexities and selective pressures present in an infected organism. Using two murine norovirus (MNV) strains to model coinfection, we developed a microfluidic platform to amplify, detect, and recover individual recombinants following in vitro and in vivo coinfection. One-step reverse transcriptase PCR (RT-PCR) was performed in picoliter drops with primers that identified the wild-type and recombinant progenies and scanned for recombination breakpoints at ∼1-kb intervals. We detected recombination between MNV strains at multiple loci spanning the viral protease, RdRP, and capsid ORFs and isolated individual recombinant RNA genomes that were present at a frequency of 1/300,000 or higher. This study is the first to examine norovirus recombination following coinfection of an animal and suggests that the exchange of RNA among viral genomes in an infected host occurs in multiple locations and is an important driver of genetic diversity.

Drop-based microfluidics have recently become a novel tool by providing a stable linkage between phenotype and genotype for high throughput screening. However, use of drop-based microfluidics for screening high-affinity peptide binders has not been demonstrated due to the lack of a sensitive functional assay that can detect single DNA molecules in drops. To address this sensitivity issue, we introduced in vitro two-hybrid system (IVT2H) into microfluidic drops and developed a streamlined mix-and-read drop-IVT2H method to screen a random DNA library. Drop-IVT2H was based on the correlation between the binding affinity of two interacting protein domains and transcriptional activation of a fluorescent reporter. A DNA library encoding potential peptide binders was encapsulated with IVT2H such that single DNA molecules were distributed in individual drops. We validated drop-IVT2H by screening a three-random-residue library derived from a high-affinity MDM2 inhibitor PMI. The current drop-IVT2H platform is ideally suited for affinity screening of small-to-medium-sized libraries (103–106). It can obtain hits within a single day while consuming minimal amounts of reagents. Drop-IVT2H simplifies and accelerates the drop-based microfluidics workflow for screening random DNA libraries, and represents a novel alternative method for protein engineering and in vitro directed protein evolution.

Perfluoroalkyl-functionalized, hyperbranched polyglycerols that produce stable microbubbles are integrated into a microfluidic emulsion to create porous microspheres. In a previously-presented work a dendrimer with a perfluorinated shell was used. By replacing this dendrimer core with a hyperbranched core and evaluating different core sizes and degrees of fluorinated shell functionalization, we optimized the process to a more convenient synthesis and higher porosities. The new hyperbranched polyglycerol porogens produced more pores and can be used to prepare microspheres with porosity up to 12% (v/v). The presented preparation forms pores with a perfluoroalkyl-functionalized surface that enables the resulting microspheres to act as supramolecular host systems. The microspheres can incorporate gases into the pores and actives in the polymer matrix, while the perfluoroalkylated pore surface can be used to immobilize perfluoro-tagged molecules onto the pores by fluorous-fluorous interaction.

From coffee beans flowing in a chute to cells remodelling in a living tissue, a wide variety of close-packed collective systems— both inert and living—have the potential to jam. The collective can sometimes flow like a fluid or jam and rigidify like a solid. The unjammed-to-jammed transition remains poorly understood, however, and structural properties characterizing these phases remain unknown. Using primary human bronchial epithelial cells, we show that the jamming transition in asthma is linked to cell shape, thus establishing in that system a structural criterion for cell jamming. Surprisingly, the collapse of critical scaling predicts a counter-intuitive relationship between jamming, cell shape and cell–cell adhesive stresses that is borne out by direct experimental observations. Cell shape thus provides a rigorous structural signature for classification and investigation of bronchial epithelial layer jamming in asthma, and potentially in any process in disease or development in which epithelial dynamics play a prominent role.

The importance of single-cell level data is increasingly appreciated, and significant advances in this direction have been made in recent years. Common to these technologies is the need to physically segregate individual cells into containers, such as wells or chambers of a micro-fluidics chip. High-throughput Single-Cell Labeling (Hi-SCL) in drops is a novel method that uses drop-based libraries of oligonucleotide barcodes to index individual cells in a population. The use of drops as containers, and a microfluidics platform to manipulate them en-masse, yields a highly scalable methodological framework. Once tagged, labeled molecules from different cells may be mixed without losing the cell-of-origin information. Here we demonstrate an application of the method for generating RNA-sequencing data for multiple individual cells within a population. Barcoded oligonucleotides are used to prime cDNA synthesis within drops. Barcoded cDNAs are then combined and subjected to second generation sequencing. The data are deconvoluted based on the barcodes, yielding single-cell mRNA expression data. In a proof-of-concept set of experiments we show that this method yields data comparable to other existing methods, but with unique potential for assaying very large numbers of cells.

We describe a microfluidic device with an integrated microwave heater specifically designed to dielectrically heat non-aqueous droplets using time-varying electrical fields with the frequency range between 700 and 900 MHz. The precise control of frequency, power, temperature and duration of the applied field opens up new vistas for experiments not attainable by conventional microwave heating. We use a non-contact temperature measurement system based on fluorescence to directly determine the temperature inside a single droplet. The maximum temperature achieved of the droplets is 50 °C in 15 ms which represents an increase of about 25 °C above the base temperature of the continuous phase. In addition we use an infrared camera to monitor the thermal characteristics of the device allowing us to ensure that heating is exclusively due to the dielectric heating and not due to other effects like non-dielectric losses due to electrode or contact imperfection. This is crucial for illustrating the potential of dielectric heating of benzyl alcohol droplets for the synthesis of metal oxides. We demonstrate the utility of this technology for metal oxide nanoparticle synthesis, achieving crystallization of tungsten oxide nanoparticles and remarkable microstructure, with a reaction time of 64 ms, a substantial improvement over conventional heating methods.