Publications

2016
Cowan, M. L. ; Page, J. H. ; Norisuye, T. ; Weitz, D. A. Dynamic sound scattering: Field fluctuation spectroscopy with singly scattered ultrasound in the near and far fields. The Journal of the Acoustical Society of America 2016, 140, 1992. Publisher's VersionAbstract

Dynamic sound scattering (DSS) is a powerful acoustic technique for investigating the motion of particles or other inclusions inside an evolving medium. In DSS, this dynamic information is obtained by measuring the field autocorrelation function of the temporal fluctuations of singly scattered acoustic waves. The technique was initially introduced 15 years ago, but its technical aspects were not adequately discussed then. This paper addresses the need for a more complete account of the method by describing in detail two different implementations of this sound scattering technique, one of which is specifically adapted to a common experimental situation in ultrasonics. The technique is illustrated by the application of DSS to measure the mean square velocity fluctuations of particles in fluidized suspensions, as well as the dynamic velocity correlation length. By explaining the experimental and analytical methods involved in realizing the DSS technique in practice, the use of DSS will be facilitated for future studies of particulate suspension dynamics and particle properties over a wide range of particle sizes and concentrations, from millimeters down to nanometers, where the use of optical techniques is often limited by the opacity of the medium.

cowan2016.pdf
Massenburg, S. S. ; Amstad, E. ; Weitz, D. A. Clogging in parallelized tapered microfluidic channels. Microfluidics and Nanofluidics 2016, 20, 1–5. Publisher's VersionAbstract

Nearly all tubes and pores used to transport solids in fluids, such as arteries and filters, are subject to clogging. The length scales and geometries of these tubes are well defined. In spite of this knowledge, the collective clogging behavior of multiple tubes has not yet been connected to their shapes and sizes. We investigate the clogging behavior of ten parallel tubes, which we model with ten parallel tapered microchannels using poly(styrene) beads to induce clogging events. The clogging behavior depends on the channel geometry as well as the shear stress particles are subjected to. Although our microchannels model filters, our results can be applied to the clogging behavior of a broad range of applications such as the clogging in arteries, inkjets, or xylem in trees.

massenburg2016.pdf
Michaels, T. C. T. ; Dear, A. J. ; Kirkegaard, J. B. ; Saar, K. L. ; Weitz, D. A. ; Knowles, T. P. J. Fluctuations in the Kinetics of Linear Protein Self-Assembly. Physical Review Letters 2016, 116, 258103. Publisher's VersionAbstract

Biological systems are characterized by compartmentalization from the subcellular to the tissue level, and thus reactions in small volumes are ubiquitous in living systems. Under such conditions, statistical number fluctuations, which are commonly negligible in bulk reactions, can become dominant and lead to stochastic behavior. We present here a stochastic model of protein filament formation in small volumes. We show that two principal regimes emerge for the system behavior, a small fluctuation regime close to bulk behavior and a large fluctuation regime characterized by single rare events. Our analysis shows that in both regimes the reaction lag-time scales inversely with the system volume, unlike in bulk. Finally, we use our stochastic model to connect data from small-volume microdroplet experiments of amyloid formation to bulk aggregation rates, and show that digital analysis of an ensemble of protein aggregation reactions taking place under microconfinement provides an accurate measure of the rate of primary nucleation of protein aggregates, a process that has been challenging to quantify from conventional bulk experiments.

    michaels2016.pdf
    Amstad, E. ; Spaepen, F. A. ; Weitz, D. A. Stabilization of the Amorphous Structure of Spray-dried Drug Nanoparticles. The Journal of Physical Chemistry B 2016, 120, 9161–9165. Publisher's VersionAbstract

    The bioavailability of hydrophobic drugs strongly increases if they are formulated as amorphous materials because the solubility of the amorphous phase is much higher than that of the crystal. Moreover, the stability of these particles against crystallization during storage increases with decreasing particle size. Hence, it is advantageous to formulate poorly water soluble drugs as amorphous nanoparticles. The formulation of an amorphous structure is often difficult because many of these drugs have a high propensity to crystallize. This difficulty can be overcome if drugs are spray-dried using a microfluidic nebulator we recently developed. However, these nanoparticles agglomerate when they come in contact with each other, and this compromises the stability of their amorphous structure through crystallization. To improve their stability, we coat the nanoparticles with a sterically stabilizing polymer layer; this can be accomplished by co-spraying them with an excipient. However, this excipient must meet strict solubility limits, which severely limit the choice of polymers. Alternatively, the nanoparticles can be sterically stabilized by spraying them directly into a polymeric matrix; this enables a much wider choice of stabilizing polymers.

    amstad2016.pdf
    Lee, H. ; Choi, C. - H. ; Abbaspourrad, A. ; Wesner, C. ; Caggioni, M. ; Zhu, T. ; Nawar, S. ; Weitz, D. A. Fluorocarbon Oil Reinforced Triple Emulsion Drops. Advanced Materials 2016, 28, 8425-8430. Publisher's VersionAbstract

    Fluorocarbon oil reinforced triple emulsion drops are prepared to encapsulate a broad range of polar and non‐polar cargoes in a single platform. In addition, it is demonstrated that the fluorocarbon oil within the emulsion drop acts as an effective diffusion barrier, as well as a non‐adhesive layer, enabling highly efficient encapsulation and retention of small molecules and active biomolecules in microcapsules.

    lee2016.pdf
    Mashaghi, S. ; Abbaspourrad, A. ; Weitz, D. A. ; van Oijen, A. M. Droplet microfluidics: A tool for biology, chemistry and nanotechnology. TrAC Trends in Analytical Chemistry 2016, 82, 118-125. Publisher's VersionAbstract
    The ability to perform laboratory operations on small scales using miniaturized devices provides numerous benefits, including reduced quantities of reagents and waste as well as increased portability and controllability of assays. These operations can involve reaction components in the solution phase and as a result, their miniaturization can be accomplished through microfluidic approaches. One such approach, droplet microfluidics, provides a high-throughput platform for a wide range of assays and approaches in chemistry, biology and nanotechnology. We highlight recent advances in the application of droplet microfluidics in chip-based technologies, such as single-cell analysis tools, small-scale cell cultures, in-droplet chemical synthesis, high-throughput drug screening, and nanodevice fabrication.
    mashaghi2016.pdf
    Burger, J. A. ; Landau, D. A. ; Taylor-Weiner, A. ; Bozic, I. ; Zhang, H. ; Sarosiek, K. ; Wang, L. ; Stewart, C. ; Fan, J. ; Hoellenriegel, J. ; et al. Clonal evolution in patients with chronic lymphocytic leukaemia developing resistance to BTK inhibition. Nature communications 2016, 7 11589. Publisher's VersionAbstract

    Resistance to the Bruton’s tyrosine kinase (BTK) inhibitor ibrutinib has been attributed solely to mutations in BTK and related pathway molecules. Using whole-exome and deep-targeted sequencing, we dissect evolution of ibrutinib resistance in serial samples from five chronic lymphocytic leukaemia patients. In two patients, we detect BTK-C481S mutation or multiple PLCG2 mutations. The other three patients exhibit an expansion of clones harbouring del(8p) with additional driver mutations (EP300, MLL2 and EIF2A), with one patient developing trans-differentiation into CD19-negative histiocytic sarcoma. Using droplet-microfluidic technology and growth kinetic analyses, we demonstrate the presence of ibrutinib-resistant subclones and estimate subclone size before treatment initiation. Haploinsufficiency of TRAIL-R, a consequence of del(8p), results in TRAIL insensitivity, which may contribute to ibrutinib resistance. These findings demonstrate that the ibrutinib therapy favours selection and expansion of rare subclones already present before ibrutinib treatment, and provide insight into the heterogeneity of genetic changes associated with ibrutinib resistance.

    burger2016.pdf
    do Nascimento, D. F. ; Arriaga, L. R. ; Eggersdorfer, M. ; Ziblat, R. ; de Marques, M. F. V. ; Reynaud, F. ; Koehler, S. A. ; Weitz, D. A. Microfluidic Fabrication of Pluronic Vesicles with Controlled Permeability. Langmuir 2016, 32, 5350–5355. Publisher's VersionAbstract

    Block copolymers with a low hydrophilic-to-lipophilic balance form membranes that are highly permeable to hydrophilic molecules. Polymersomes with this type of membrane enable the controllable release of molecules without membrane rupture. However, these polymersomes are difficult to assemble because of their low hydrophobicity. Here, we report a microfluidic approach to the production of these polymersomes using double-emulsion drops with ultrathin shells as templates. The small thickness of the middle oil phase enables the attraction of the hydrophobic blocks of the polymers adsorbed at each of the oil/water interfaces of the double emulsions; this results in the dewetting of the oil from the surface of the innermost water drops of the double emulsions and the ultimate formation of the polymersome. This approach to polymersome fabrication enables control of the vesicle size and results in the efficient encapsulation of hydrophilic ingredients that can be released through the polymer membrane without membrane rupture. We apply our approach to the fabrication of Pluronic L121 vesicles and characterize the permeability of their membranes. Furthermore, we show that membrane permeability can be tuned by blending different Pluronic polymers. Our work thus describes a route to producing Pluronic vesicles that are useful for the controlled release of hydrophilic ingredients.

    donascimento2016.pdf
    Xu, Z. ; Huang, X. ; Wang, P. ; Wang, H. ; Weitz, D. A. Optimization and development of a universal flow-based microfluidic gradient generator. Microfluidics and Nanofluidics 2016, 20, 1–10. Publisher's VersionAbstract

    Generation of concentration gradients of reactive molecules is of fundamental importance for many applications including biology, pharmaceutical and chemical engineering. By numerically simulating the flow behaviour, we reveal the possible factors that cause significant error in the gradients generated by the conventional universal microfluidic gradient generator (MGG) device reported previously. Based on these computational analyses, we optimize the geometrical design of the conventional 2-inlet MGG devices and improve the accuracy of the generated gradients. Moreover, we innovatively propose a 3-inlet MGG design showing desirable accuracy and versatility on creating various gradient profiles using the one single device. We further demonstrate our numerical simulation by fabricating the MGG devices by soft lithography and experimentally produce concentration gradients of diverse power functions. In general, the current study substantially improves the performance of universal MGG devices, which can serve as powerful tools for widespread applications in biology and chemistry.

    2016_microfluid_nanofluid_xu.pdf
    Choi, C. - H. ; Wang, H. ; Lee, H. ; Kim, J. H. ; Zhang, L. ; Mao, A. ; Mooney, D. J. ; Weitz, D. A. One-step generation of cell-laden microgels using double emulsion drops with a sacrificial ultra-thin oil shell. Lab on a Chip 2016, 16, 1549–1555. Publisher's VersionAbstract

    Cell-laden microgels with highly uniform sizes have significant potential in tissue engineering and cell therapy due to their capability to provide a physiologically relevant three-dimensional (3D) microenvironment for living cells. In this work, we present a simple and efficient microfluidic approach to produce monodisperse cell-laden microgels through the use of double emulsion drops with an ultra-thin oil shell as the sacrificial template. Specifically, the thin oil shell in double emulsion spontaneously dewets upon polymerization of the innermost precursor drop and subsequent transfer into an aqueous solution, resulting in direct dispersion of microgels in the aqueous phase. Compared to conventional single emulsion-based techniques for cell encapsulation, this one-step approach prevents prolonged exposure of cells to the oil phase, leading to high-throughput cell encapsulation in microgels without compromising the cell viability. Moreover, this approach allows us to culture cells within a 3D microgel which mimics the extracellular matrix, thus enabling long-term cell functionality. This microfluidic technique represents a significant step forward in high-throughput cell microencapsulation technology and offers a potentially viable option to produce cell-laden microgels for widespread applications in tissue engineering and cell therapies.

    2016_labchip_choi.pdf
    Choi, C. - H. ; Lee, H. ; Abbaspourrad, A. ; Kim, J. H. ; Fan, J. ; Caggioni, M. ; Wesner, C. ; Zhu, T. ; Weitz, D. A. Triple Emulsion Drops with An Ultrathin Water Layer: High Encapsulation Efficiency and Enhanced Cargo Retention in Microcapsules. Advanced Materials 2016, 28, 3340–3344. Publisher's VersionAbstract

    Triple emulsion drops with an ultrathin water layer are developed to achieve high encapsulation efficiency of hydrophobic cargo in a hydrophobic polymeric shell, directly dispersed in water. Furthermore, enhanced retention of volatile hydrophobic cargo is achieved by forming a hydrogel network within this water layer that serves as a physical barrier.

    2016_advmater_choi.pdf
    Chen, Q. ; Utech, S. ; Chen, D. ; Prodanovic, R. M. ; Lin, J. - M. ; Weitz, D. A. Controlled Assembly of Heterotypic cells in a Core-Shell Scaffold: Organ in a Droplet. Lab on a Chip 2016, 16, 1346-1349. Publisher's VersionAbstract

    This paper reports a droplet-based microfluidic approach to fabricate a large number of monodisperse, portable microtissues, each in an individual drop. We use water–water–oil double emulsions as templates and spatially assemble hepatocytes in the core and fibroblasts in the shell, forming a 3D liver model in a drop.

    2016_labchip_chen.pdf
    Zhao, X. ; Liu, S. ; Yildirimer, L. ; Zhao, H. ; Ding, R. ; Wang, H. ; Cui, W. ; Weitz, D. Injectable Stem Cell-Laden Photocrosslinkable Microspheres Fabricated Using Microfluidics for Rapid Generation of Osteogenic Tissue Constructs. Advanced Functional Materials 2016, 26. Publisher's VersionAbstract

    Direct injection is a minimally invasive method of stem cell transplantation for numerous injuries and diseases. However, despite its promising potential, its clinical translation is difficult due to the low cell retention and engraftment after injection. With high versatility, high‐resolution control and injectability, microfabrication of stem‐cell laden biomedical hydrogels holds great potential as minimally invasive technology. Herein, a strategy of microfluidics‐assisted technology entrapping bone marrow‐derived mesenchymal stem cells (BMSCs) and growth factors in photocrosslinkable gelatin (GelMA) microspheres to ultimately generate injectable osteogenic tissue constructs is presented. Additionally, it is demonstrated that the GelMA microspheres can sustain stem cell viability, support cell spreading inside the microspheres and migration from the interior to the surface as well as enhance cell proliferation. This finding shows that encapsulated cells have the potential to directly and actively participate in the regeneration process. Furthermore, it is found that BMSCs encapsulated in GelMA microspheres show enhanced osteogenesis in vitro and in vivo, associated with a significant increase in mineralization. In short, the proposed strategy can be utilized to facilitate bone regeneration with minimum invasiveness, and can potentially be applied along with other matrices for extended applications.

    2016_adfm_zhao.pdf
    Cui, N. ; Zhang, H. ; Schneider, N. ; Tao, Y. ; Asahara, H. ; Sun, Z. ; Cai, Y. ; Koehler, S. A. ; de Greef, T. F. A. ; Abbaspourrad, A. ; et al. A mix-and-read drop-based in vitro two-hybrid method for screening high-affinity peptide binders. Scientific reports 2016, 6 22575. Publisher's VersionAbstract

    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.

    2016_srep_cui.pdf
    Ridge, K. M. ; Shumaker, D. ; Robert, A. ; Hookway, C. ; Gelfand, V. I. ; Janmey, P. A. ; Lowery, J. ; Guo, M. ; Weitz, D. A. ; Kuczmarski, E. ; et al. Chapter Fourteen - Methods for Determining the Cellular Functions of Vimentin Intermediate Filaments. In Intermediate Filament Proteins; Omary, M. B. ; Liem, R. K. H., Ed. Academic Press, 2016; Vol. 568, pp. 389 - 426. Publisher's VersionAbstract

    The type III intermediate filament protein vimentin was once thought to function mainly as a static structural protein in the cytoskeleton of cells of mesenchymal origin. Now, however, vimentin is known to form a dynamic, flexible network that plays an important role in a number of signaling pathways. Here, we describe various methods that have been developed to investigate the cellular functions of the vimentin protein and intermediate filament network, including chemical disruption, photoactivation and photoconversion, biolayer interferometry, soluble bead binding assay, three-dimensional substrate experiments, collagen gel contraction, optical-tweezer active microrheology, and force spectrum microscopy. Using these techniques, the contributions of vimentin to essential cellular processes can be probed in ever further detail.

      2016_methods_in_enzymology_ridge.pdf
      Keita, E. ; Koehler, S. A. ; Faure, P. ; Weitz, D. A. ; Coussot, P. Drying kinetics driven by the shape of the air/water interface in a capillary channel. The European Physical Journal E 2016, 39, 23. Publisher's VersionAbstract

      We look at the drying process in a simple glass channel with dominant capillary effects as is the case in microfluidics. We find drying kinetics commonly observed for confined geometry, namely a constant period followed by a falling rate period. From visualization of the air/water interface with high resolution, we observe that the drying rate decreases without a drying front progression although this is the usually accepted mechanism for confined geometries. We show with FEM that in our specific geometry the falling rate period is due to changes in the shape of the air-water interface at the free surface where most evaporation occurs. Our simulations show that the sensitivity of the drying rate to the shape of the first air-water interface from the sample free surface implies that slight changes of the wetting or pinning conditions can significantly modify the drying rate.

      2016_eurphysje_keita.pdf
      Lee, H. ; Choi, C. - H. ; Abbaspourrad, A. ; Wesner, C. ; Caggioni, M. ; Zhu, T. ; Weitz, D. A. Encapsulation and Enhanced Retention of Fragrance in Polymer Microcapsules. ACS Applied Materials & Interfaces 2016, 8 4007-4013. Publisher's VersionAbstract

      Fragrances are amphiphilic and highly volatile, all of which makes them a challenging cargo to efficiently encapsulate and retain in microcapsules using traditional approaches. We address these limitations by introducing a new strategy that combines bulk and microfluidic emulsification: a stable fragrance-in-water (F/W) emulsion that is primarily prepared from bulk emulsification is incorporated within a polymer microcapsule via microfluidic emulsification. On the basis of the in-depth study of physicochemical properties of the microcapsules on fragrance leakage, we demonstrate that enhanced retention of fragrance can be achieved by using a polar polymeric shell and forming a hydrogel network within the microcapsule. We further extend the utility of these microcapsules by demonstrating the enhanced retention of encapsulated fragrance in powder state.

      2016_acsappliedmaterialsinterface_lee.pdf
      Verissimo, C. ; Abbaspourrad, A. ; Sunter, K. ; Capasso, F. ; Moshkalev, S. ; Weitz, D. Hydrothermal Synthesis and Properties of Hierarchical ZnO and Eu-doped ZnO 3D Structures. In une; 2016; Vol. 13, pp. 15. 2016_verissimo.pdf
      Spencer, S. J. ; Tamminen, M. V. ; Preheim, S. P. ; Guo, M. T. ; Briggs, A. W. ; Brito, I. L. ; Weitz, D. A. ; Pitkanen, L. K. ; Vigneault, F. ; Virta, M. P. J. ; et al. Massively parallel sequencing of single cells by epicPCR links functional genes with phylogenetic markers. ISME JOURNAL 2016, 10, 427-436. Publisher's VersionAbstract

      Many microbial communities are characterized by high genetic diversity. 16S ribosomal RNA sequencing can determine community members, and metagenomics can determine the functional diversity, but resolving the functional role of individual cells in high throughput remains an unsolved challenge. Here, we describe epicPCR (Emulsion, Paired Isolation and Concatenation PCR), a new technique that links functional genes and phylogenetic markers in uncultured single cells, providing a throughput of hundreds of thousands of cells with costs comparable to one genomic library preparation. We demonstrate the utility of our technique in a natural environment by profiling a sulfate-reducing community in a freshwater lake, revealing both known sulfate reducers and discovering new putative sulfate reducers. Our method is adaptable to any conserved genetic trait and translates genetic associations from diverse microbial samples into a sequencing library that answers targeted ecological questions. Potential applications include identifying functional community members, tracing horizontal gene transfer networks and mapping ecological interactions between microbial cells.

      2016_isme_spencer.pdf
      Wagner, O. ; Thiele, J. ; Weinhart, M. ; Mazutis, L. ; Weitz, D. A. ; Huck, W. T. S. ; Haag, R. Biocompatible fluorinated polyglycerols for droplet microfluidics as an alternative to PEG-based copolymer surfactants. Lab on a Chip 2016, 16, 65–69. Publisher's VersionAbstract

      In droplet-based microfluidics, non-ionic, high-molecular weight surfactants are required to stabilize droplet interfaces. One of the most common structures that imparts stability as well as biocompatibility to water-in-oil droplets is a triblock copolymer surfactant composed of perfluoropolyether (PFPE) and polyethylene glycol (PEG) blocks. However, the fast growing applications of microdroplets in biology would benefit from a larger choice of specialized surfactants. PEG as a hydrophilic moiety, however, is a very limited tool in surfactant modification as one can only vary the molecular weight and chain-end functionalization. In contrast, linear polyglycerol offers further side-chain functionalization to create custom-tailored, biocompatible droplet interfaces. Herein, we describe the synthesis and characterization of polyglycerol-based triblock surfactants with tailored side-chain composition, and exemplify their application in cell encapsulation and in vitro gene expression studies in droplet-based microfluidics.

      2016_labchip_wagner.pdf

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