Publications by Year: 2015

Soft Poly(dimethylsiloxane) Elastomers from Architecture-Driven Entanglement Free Design
Cai*, L. - H. ; Kodger*, T. E. ; Guerra, R. E. ; Pegoraro, A. F. ; Rubinstein, M. ; Weitz, D. A. Soft Poly(dimethylsiloxane) Elastomers from Architecture-Driven Entanglement Free Design. Advanced Materials 2015, 27, 5132-5140. Publisher's Version 2015_Cai&Kodger_soft Elastomer.pdf

[*Equal contribution] [Featured as Cover Article; Media]

Duncanson, W. J. ; Kodger, T. E. ; Babaee, S. ; Gonzalez, G. ; Weitz, D. A. ; Bertoldi, K. Microfluidic Fabrication and Micromechanics of Permeable and Impermeable Elastomeric Microbubbles. Langmuir 2015, 31, 3489-3493. Publisher's Version 2015_langmuire_duncanson.pdf

PMID: 25730159

Park, J. ; Elmlund, H. ; Ercius, P. ; Yuk, J. M. ; Limmer, D. T. ; Chen, Q. ; Kim, K. ; Han, S. H. ; Weitz, D. A. ; Zettl, A. ; et al. 3D structure of individual nanocrystals in solution by electron microscopy. Science 2015, 349, 290-295. Publisher's Version 2015_science_park.pdf
Park, J. ; Park, H. ; Ercius, P. ; Pegoraro, A. F. ; Xu, C. ; Kim, J. W. ; Han, S. H. ; Weitz, D. A. Direct Observation of Wet Biological Samples by Graphene Liquid Cell Transmission Electron Microscopy. Nano Letters 2015, 15, 4737-4744. Publisher's Version 2015_nanoletter_park.pdf

PMID: 26065925

Rotem, A. ; Ram, O. ; Shoresh, N. ; Sperling, R. A. ; Schnall-Levin, M. ; Zhang, H. ; Basu, A. ; Bernstein, B. E. ; Weitz, D. A. High-Throughput Single-Cell Labeling (Hi-SCL) for RNA-Seq Using Drop-Based Microfluidics. PLoS ONE 2015, 10, e0116328. Publisher's VersionAbstract

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.

Jensen, M. H. ; Morris, E. J. ; Weitz, D. A. Mechanics and dynamics of reconstituted cytoskeletal systems. Biochimica et Biophysica Acta (BBA) - Molecular Cell Research 2015, doi:10.1016/j.bbamcr.2015.06.013. Publisher's Version 2015_bba_jensen.pdf
Akamatsu, K. ; Kanasugi, S. ; Nakao, S. -ichi; Weitz, D. A. Membrane-Integrated Glass Capillary Device for Preparing Small-Sized Water-in-Oil-in-Water Emulsion Droplets. Langmuir 2015, 31, 7166-7172. Publisher's Version 2015_langmuir_akamatsu.pdf

PMID: 26057203

Kong, F. ; Zhang, X. ; Zhang, H. ; Qu, X. ; Chen, D. ; Servos, M. ; Mäkilä, E. ; Salonen, J. ; Santos, H. A. ; Hai, M. ; et al. Inhibition of Multidrug Resistance of Cancer Cells by Co-Delivery of DNA Nanostructures and Drugs Using Porous Silicon Nanoparticles@Giant Liposomes. Advanced Functional Materials 2015, 25, 3330–3340. Publisher's Version 2015_adfm_kong.pdf
Fodor, É. ; Guo, M. ; Gov, N. S. ; Visco, P. ; Weitz, D. A. ; van Wijland, F. Activity-driven fluctuations in living cells. EPL (Europhysics Letters) 2015, 110, 48005. Publisher's VersionAbstract

We propose a model for the dynamics of a probe embedded in a living cell, where both thermal fluctuations and nonequilibrium activity coexist. The model is based on a confining harmonic potential describing the elastic cytoskeletal matrix, which undergoes random active hops as a result of the nonequilibrium rearrangements within the cell. We describe the probe's statistics and we bring forth quantities affected by the nonequilibrium activity. We find an excellent agreement between the predictions of our model and experimental results for tracers inside living cells. Finally, we exploit our model to arrive at quantitative predictions for the parameters characterizing nonequilibrium activity, such as the typical time scale of the activity and the amplitude of the active fluctuations.

Ehrlicher, A. J. ; Krishnan, R. ; Guo, M. ; Bidan, C. M. ; Weitz, D. A. ; Pollak, M. R. Alpha-actinin binding kinetics modulate cellular dynamics and force generation. Proceedings of the National Academy of Sciences 2015, 112, 6619-6624. Publisher's VersionAbstract

The actin cytoskeleton is a key element of cell structure and movement whose properties are determined by a host of accessory proteins. Actin cross-linking proteins create a connected network from individual actin filaments, and though the mechanical effects of cross-linker binding affinity on actin networks have been investigated in reconstituted systems, their impact on cellular forces is unknown. Here we show that the binding affinity of the actin cross-linker α-actinin 4 (ACTN4) in cells modulates cytoplasmic mobility, cellular movement, and traction forces. Using fluorescence recovery after photobleaching, we show that an ACTN4 mutation that causes human kidney disease roughly triples the wild-type binding affinity of ACTN4 to F-actin in cells, increasing the dissociation time from 29 ± 13 to 86 ± 29 s. This increased affinity creates a less dynamic cytoplasm, as demonstrated by reduced intracellular microsphere movement, and an approximate halving of cell speed. Surprisingly, these less motile cells generate larger forces. Using traction force microscopy, we show that increased binding affinity of ACTN4 increases the average contractile stress (from 1.8 ± 0.7 to 4.7 ± 0.5 kPa), and the average strain energy (0.4 ± 0.2 to 2.1 ± 0.4 pJ). We speculate that these changes may be explained by an increased solid-like nature of the cytoskeleton, where myosin activity is more partitioned into tension and less is dissipated through filament sliding. These findings demonstrate the impact of cross-linker point mutations on cell dynamics and forces, and suggest mechanisms by which such physical defects lead to human disease.

Hackelbusch, S. ; Rossow, T. ; Steinhilber, D. ; Weitz, D. A. ; Seiffert, S. Hybrid Microgels with Thermo-Tunable Elasticity for Controllable Cell Confinement. Advanced Healthcare Materials 2015, n/a–n/a. Publisher's Version 2015_advhealthcaremater_hackelbusch.pdf
Gaudreault, R. ; Di Cesare, N. ; van de Ven, T. G. M. ; Weitz, D. A. Structure and Strength of Flocs of Precipitated Calcium Carbonate Induced by Various Polymers Used in Papermaking. Industrial & Engineering Chemistry Research 2015, null. Publisher's Version 2015_iec_caudreault.pdf
Klein, A.  M. ; Mazutis, L. ; Akartuna, I. ; Tallapragada, N. ; Veres, A. ; Li, V. ; Peshkin, L. ; Weitz, D.  A. ; Kirschner, M.  W. Droplet Barcoding for Single-Cell Transcriptomics Applied to Embryonic Stem Cells. Cell 2015, 161, 1187 - 1201. Publisher's Version 2015_cell_klein.pdf
Macosko, E.  Z. ; Basu, A. ; Satija, R. ; Nemesh, J. ; Shekhar, K. ; Goldman, M. ; Tirosh, I. ; Bialas, A.  R. ; Kamitaki, N. ; Martersteck, E.  M. ; et al. Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets. Cell 2015, 161, 1202 - 1214. Publisher's Version 2015_cell_macosko.pdf
Zhou, Y. ; Park, J. ; Shi, J. ; Chhowalla, M. ; Park, H. ; Weitz, D. A. ; Ramanathan, S. Control of Emergent Properties at a Correlated Oxide Interface with Graphene. Nano Letters 2015, 15, 1627-1634. Publisher's Version 2015_nanoletter_zhou.pdf
Russell, E. R. ; Spaepen, F. ; Weitz, D. A. Anisotropic elasticity of experimental colloidal Wigner crystals. Phys. Rev. E 2015, 91, 032310. Publisher's Version 2015_pre_russell.pdf
Bannwarth, M. B. ; Utech, S. ; Ebert, S. ; Weitz, D. A. ; Crespy, D. ; Landfester, K. Colloidal Polymers with Controlled Sequence and Branching Constructed from Magnetic Field Assembled Nanoparticles. ACS Nano 2015, 9 2720-2728. Publisher's Version 2015_acsnano_bannwarth.pdf

PMID: 25695858

Kanai, T. ; Boon, N. ; Lu, P. J. ; Sloutskin, E. ; Schofield, A. B. ; Smallenburg, F. ; van Roij, R. ; Dijkstra, M. ; Weitz, D. A. Crystallization and reentrant melting of charged colloids in nonpolar solvents. Phys. Rev. E 2015, 91, 030301. Publisher's Version 2015_pre_kanai.pdf
Lee, W. C. ; Kim, K. ; Park, J. ; Koo, J. ; Jeong, H. Y. ; Lee, H. ; Weitz, D. A. ; Zettl, A. ; Takeuchi, S. Graphene-templated directional growth of an inorganic nanowire. Nature Nanotechnology 2015, 10, 423-428. 2015_natnanotech_lee.pdf
Fischer, A. E. ; Wu, S. K. ; Proescher, J. B. G. ; Rotem, A. ; Chang, C. B. ; Zhang, H. ; Tao, Y. ; Mehoke, T. S. ; Thielen, P. M. ; Kolawole, A. O. ; et al. A high-throughput drop microfluidic system for virus culture and analysis. Journal of Virological Methods 2015, 213, 111-117.Abstract

High mutation rates and short replication times lead to rapid evolution in RNA viruses. New tools for high-throughput culture and analysis of viral phenotypes will enable more effective studies of viral evolutionary processes. A water-in-oil drop microfluidic system to study virus–cell interactions at the single event level on a massively parallel scale is described here. Murine norovirus (MNV-1) particles were co-encapsulated with individual RAW 264.7 cells in 65 pL aqueous drops formed by flow focusing in 50 μm microchannels. At low multiplicity of infection (MOI), viral titers increased greatly, reaching a maximum 18 h post-encapsulation. This system was employed to evaluate MNV-1 escape from a neutralizing monoclonal antibody (clone A6.2). Further, the system was validated as a means for testing escape from antibody neutralization using a series of viral point mutants. Finally, the replicative capacity of single viral particles in drops under antibody stress was tested. Under standard conditions, many RNA virus stocks harbor minority populations of genotypic and phenotypic variants, resulting in quasispecies. These data show that when single cells are encapsulated with single viral particles under antibody stress without competition from other virions, the number of resulting infectious particles is nearly equivalent to the number of viral genomes present. These findings suggest that lower fitness virions can infect cells successfully and replicate, indicating that the microfluidics system may serve as an effective tool for isolating mutants that escape evolutionary stressors.