Publications

2015
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.

2015_jvirmeth_fischer.pdf
Köster, S. ; Weitz, D. A. ; Goldman, R. D. ; Aebi, U. ; Herrmann, H. Intermediate filament mechanics in vitro and in the cell: from coiled coils to filaments, fibers and networks. Current Opinion in Cell Biology 2015, 32, 82-91.Abstract

Intermediate filament proteins form filaments, fibers and networks both in the cytoplasm and the nucleus of metazoan cells. Their general structural building plan accommodates highly varying amino acid sequences to yield extended dimeric α-helical coiled coils of highly conserved design. These ‘rod’ particles are the basic building blocks of intrinsically flexible, filamentous structures that are able to resist high mechanical stresses, that is, bending and stretching to a considerable degree, both in vitro and in the cell. Biophysical and computer modeling studies are beginning to unfold detailed structural and mechanical insights into these major supramolecular assemblies of cell architecture, not only in the ‘test tube’ but also in the cellular and tissue context.

2015_currentopinioncellbiology_koster.pdf
Zieringer, M. A. ; Carroll, N. J. ; Abbaspourrad, A. ; Koehler, S. A. ; Weitz, D. A. Microcapsules for Enhanced Cargo Retention and Diversity. Small 2015, n/a–n/a. Publisher's Version 2015_small_microcapsules_for_cargo_retention.pdf
Polenz, I. ; Weitz, D. A. ; Baret, J. - C. Polyurea Microcapsules in Microfluidics: Surfactant Control of Soft Membranes. Langmuir 2015, 31, 1127–1134. Publisher's Version 2015_langmuir_polyurea_microcapsules.pdf

PMID: 25531127

Akartuna, I. ; Aubrecht, D. M. ; Kodger, T. E. ; Weitz, D. A. Chemically induced coalescence in droplet-based microfluidics. Lab Chip 2015, -. Publisher's VersionAbstract

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.

2015_labchip_coalescence.pdf
Shimanovich, U. ; Efimov, I. ; Mason, T. O. ; Flagmeier, P. ; Buell, A. K. ; Gedanken, A. ; Linse, S. ; Åkerfeldt, K. S. ; Dobson, C. M. ; Weitz, D. A. ; et al. Protein Microgels from Amyloid Fibril Networks. ACS Nano 2015, Article ASAP. Publisher's Version [PDF]

PMID: 25469621

2014
Ostafe, R. ; Prodanovic, R. ; Lloyd Ung, W. ; Weitz, D. A. ; Fischer, R. A high-throughput cellulase screening system based on droplet microfluidics. Biomicrofluidics 2014, 8 041102. Publisher's Version [PDF]
Jensen, M. H. *; Morris, E. J. *; Goldman, R. D. ; Weitz, D. A. Emergent properties of composite semiflexible biopolymer networks. BioArchitecture 2014, 4 138-143. Publisher's Version 2015_bioarchitecture_composite_semiflexible_biopolymer_networks.pdf

[*Equal contribution]

Thon, J. N. ; Mazutis, L. ; Wu, S. ; Sylman, J. L. ; Ehrlicher, A. ; Machlus, K. R. ; Feng, Q. ; Lu, S. ; Lanza, R. ; Neeves, K. B. ; et al. Platelet bioreactor-on-a-chip. Blood 2014, 124, 1857–1867.Abstract

Jonathan N. Thon1,2,3, Linas Mazutis3,4,5, Stephen Wu1, Joanna L. Sylman6, Allen Ehrlicher4,7, Kellie R. Machlus1,2, Qiang Feng8, Shijiang Lu8, Robert Lanza8, Keith B. Neeves6,9, David A. Weitz4, and Joseph E. Italiano Jr1,2,3,101Department of Medicine, Brigham and Women’s Hospital, Boston, MA; 2Harvard Medical School, Boston, MA; 3Platelet BioGenesis, Chestnut Hill, MA; 4School of Engineering and Applied Sciences, Harvard University, Cambridge, MA; 5Institute of Biotechnology, Vilnius University, Vilnius, Lithuania; 6Department of Chemical and Biological Engineering, Colorado School of Mines, Golden, CO; 7Department of Bioengineering, McGill University, Montreal, Canada; 8Advanced Cell Technologies, Marlborough, MA; 9Department of Pediatrics, University of Colorado, Denver, Aurora, CO; and 10Department of Surgery, Vascular Biology Program, Boston Children’s Hospital, Boston, MAKey PointsWe have developed a biomimetic microfluidic platelet bioreactor that recapitulates bone marrow and blood vessel microenvironments.Application of shear stress in this bioreactor triggers physiological proplatelet production, and platelet release.AbstractPlatelet transfusions total >2.17 million apheresis-equivalent units per year in the United States and are derived entirely from human donors, despite clinically significant immunogenicity, associated risk of sepsis, and inventory shortages due to high demand and 5-day shelf life. To take advantage of known physiological drivers of thrombopoiesis, we have developed a microfluidic human platelet bioreactor that recapitulates bone marrow stiffness, extracellular matrix composition, micro-channel size, hemodynamic vascular shear stress, and endothelial cell contacts, and it supports high-resolution live-cell microscopy and quantification of platelet production. Physiological shear stresses triggered proplatelet initiation, reproduced ex vivo bone marrow proplatelet production, and generated functional platelets. Modeling human bone marrow composition and hemodynamics in vitro obviates risks associated with platelet procurement and storage to help meet growing transfusion needs.Submitted May 9, 2014.Accepted July 8, 2014.© 2014 by The American Society of Hematology

2014_blood_platelet_bioreactor_on_a_chip.pdf
Schmid, L. ; Weitz, D. A. ; Franke, T. Sorting drops and cells with acoustics: acoustic microfluidic fluorescence-activated cell sorter. Lab Chip 2014, 14, 3710-3718. Publisher's VersionAbstract

We describe a versatile microfluidic fluorescence-activated cell sorter that uses acoustic actuation to sort cells or drops at ultra-high rates. Our acoustic sorter combines the advantages of traditional fluorescence-activated cell (FACS) and droplet sorting (FADS) and is applicable for a multitude of objects. We sort aqueous droplets{,} at rates as high as several kHz{,} into two or even more outlet channels. We can also sort cells directly from the medium without prior encapsulation into drops; we demonstrate this by sorting fluorescently labeled mouse melanoma cells in a single phase fluid. Our acoustic microfluidic FACS is compatible with standard cell sorting cytometers{,} yet{,} at the same time{,} enables a rich variety of more sophisticated applications.

2014_labchip_franke-acoustic.pdf
Fan, J. ; Li, Y. ; Bisoyi, H. K. ; Zola, R. S. ; Yang, D. -ke; Bunning, T. J. ; Weitz, D. A. ; Li, Q. Light-Directing Omnidirectional Circularly Polarized Reflection from Liquid-Crystal Droplets. Angewandte Chemie 2014, n/a–n/a. Publisher's Version 2014_angewchem_liquid_crystal_droplets.pdf
Lin, T. ; Rubinstein, S. M. ; Korchev, A. ; Weitz, D. A. Pattern Formation of Charged Particles in an Electric Field. Langmuir 2014, 30, 12119-12123. Publisher's Version 2014_langmuir_charged_particles_in_e_field.pdf

PMID: 25227689

Rowat, A. C. ; Sinha, N. N. ; Sörensen, P. M. ; Campàs, O. ; Castells, P. ; Rosenberg, D. ; Brenner, M. P. ; Weitz, D. A. The kitchen as a physics classroom. Physics Education 2014, 49, 512. Publisher's VersionAbstract

Cooking is a tangible, familiar, and delicious tool for teaching physics, which is easy to implement in a university setting. Through our courses at Harvard and UCLA, each year we are engaging hundreds of undergraduate students, primarily non-science majors, in science concepts and the scientific research process. We find that weekly lectures by chefs and professors, paired with edible lab experiments, generate enthusiasm and provide strong motivation for students to learn physics. By the end of the course, students are able to conduct independent scientific research and present their results in a final science fair. Given the considerable broad appeal of food and cooking, the topic could be adapted to other post-secondary as well as secondary-level courses.

2014_physedu_kitch_as_physics_classroom.pdf
Polenz, I. ; Datta, S. S. ; Weitz, D. A. Controlling the Morphology of Polyurea Microcapsules Using Microfluidics. Langmuir 2014, ASAP. Publisher's Version 2014_langmuir_polyurea_microcapsules.pdf

doi: 10.1021/la503234z

Duncanson, W. J. ; Arriaga, L. R. ; Ung, L. W. ; Kopechek, J. ; Porter, T. ; Weitz, D. A. Microfluidic Fabrication of Perfluorohexane-Shelled Double Emulsions for Controlled Loading and Acoustic-Triggered Release of Hydrophilic Agents. Langmuir 2014, null. Publisher's Version 2014_langmuir_perfluorohexane_shelled_double_emulsions.pdf

PMID: 25340527

Jensen, K. E. ; Weitz, D. A. ; Spaepen, F. Local shear transformations in deformed and quiescent hard-sphere colloidal glasses. Physical Review E 2014, 90, 042305 -. Publisher's Version [PDF]
Zaburdaev, V. ; Biais, N. ; Schmiedeberg, M. ; Eriksson, J. ; Jonsson, A. - B. ; Sheetz, M.  P. ; Weitz, D.  A. Uncovering the Mechanism of Trapping and Cell Orientation during Neisseria gonorrhoeae Twitching Motility. 2014, 107, 1523 - 1531. Publisher's VersionAbstract

AbstractNeisseria gonorrheae bacteria are the causative agent of the second most common sexually transmitted infection in the world. The bacteria move on a surface by means of twitching motility. Their movement is mediated by multiple long and flexible filaments, called type IV pili, that extend from the cell body, attach to the surface, and retract, thus generating a pulling force. Moving cells also use pili to aggregate and form microcolonies. However, the mechanism by which the pili surrounding the cell body work together to propel bacteria remains unclear. Understanding this process will help describe the motility of N. gonorrheae bacteria, and thus the dissemination of the disease which they cause. In this article we track individual twitching cells and observe that their trajectories consist of alternating moving and pausing intervals, while the cell body is preferably oriented with its wide side toward the direction of motion. Based on these data, we propose a model for the collective pili operation of N. gonorrheae bacteria that explains the experimentally observed behavior. Individual pili function independently but can lead to coordinated motion or pausing via the force balance. The geometry of the cell defines its orientation during motion. We show that by changing pili substrate interactions, the motility pattern can be altered in a predictable way. Although the model proposed is tangibly simple, it still has sufficient robustness to incorporate further advanced pili features and various cell geometries to describe other bacteria that employ pili to move on surfaces.

[PDF]
Larsen, R. J. ; Kim, J. - W. ; Zukoski, C. F. ; Weitz, D. A. Fluctuations in flow produced by competition between apparent wall slip and dilatancy. Rheologica Acta 2014, 53, 333-347. Publisher's Version [PDF]
Jarosz, D.  F. ; Brown, J.  C. S. ; Walker, G.  A. ; Datta, M.  S. ; Ung, W.  L. ; Lancaster, A.  K. ; Rotem, A. ; Chang, A. ; Newby, G.  A. ; Weitz, D.  A. ; et al. Cross-Kingdom Chemical Communication Drives a Heritable, Mutually Beneficial Prion-Based Transformation of Metabolism. Cell 2014, 158, 1083 - 1093. Publisher's VersionAbstract

Summary In experimental science, organisms are usually studied in isolation, but in the wild, they compete and cooperate in complex communities. We report a system for cross-kingdom communication by which bacteria heritably transform yeast metabolism. An ancient biological circuit blocks yeast from using other carbon sources in the presence of glucose. [GAR+], a protein-based epigenetic element, allows yeast to circumvent this “glucose repression” and use multiple carbon sources in the presence of glucose. Some bacteria secrete a chemical factor that induces [GAR+]. [GAR+] is advantageous to bacteria because yeast cells make less ethanol and is advantageous to yeast because their growth and long-term viability is improved in complex carbon sources. This cross-kingdom communication is broadly conserved, providing a compelling argument for its adaptive value. By heritably transforming growth and survival strategies in response to the selective pressures of life in a biological community, [GAR+] presents a unique example of Lamarckian inheritance.

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Wang, B. L. ; Ghaderi, A. ; Zhou, H. ; Agresti, J. ; Weitz, D. A. ; Fink, G. R. ; Stephanopoulos, G. Microfluidic high-throughput culturing of single cells for selection based on extracellular metabolite production or consumption. Nat Biotech 2014, 32, 473 - 478. Publisher's VersionAbstract

Phenotyping single cells based on the products they secrete or consume is a key bottleneck in many biotechnology applications, such as combinatorial metabolic engineering for the overproduction of secreted metabolites. Here we present a flexible high-throughput approach that uses microfluidics to compartmentalize individual cells for growth and analysis in monodisperse nanoliter aqueous droplets surrounded by an immiscible fluorinated oil phase. We use this system to identify xylose-overconsuming Saccharomyces cerevisiae cells from a population containing one such cell per 104 cells and to screen a genomic library to identify multiple copies of the xylose isomerase gene as a genomic change contributing to high xylose consumption, a trait important for lignocellulosic feedstock utilization. We also enriched L-lactate-producing Escherichia coli clones 5,800[times] from a population containing one L-lactate producer per 104D-lactate producers. Our approach has broad applications for single-cell analyses, such as in strain selection for the overproduction of fuels, chemicals and pharmaceuticals.

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