BE Seminars & Events

How cells pattern their shapes and distribution is critically important in many biological processes. The current theory is that cells follow extracellular biochemical cues (spatial scales: tens of μm) to create spatial patterns of intracellular signaling molecules, thereby patterning cell shape and cell distribution. How cell shapes in turn influence signaling molecule dynamics and whether cells can spontaneously organize large-scale distribution without the guidance of biochemical cues or preexisting scaffolds remain to be better characterized. Here, we first show that in the absence of biochemical cues, non-uniform cell shapes can spontaneously emerge without preceding patterning of signaling molecules including PIP₃ and Rac1. These spontaneously emerged shapes, however, can guide the patterning of PIP₃, Rac1, and actin filaments. Moreover, the rate of shape-guided patterning (time scales: ~ hours) is much slower than those induced by biochemical cues (time scales: seconds-minutes). Second, we show that without preexisting geometrical cues, epithelial cells and type I collagen molecules can self-organize into single, centimeter-long, hundred-micrometer-wide, and unbranched tubules. The geometrical cue of these tubules is created via sequential events including cell-aided assembly of collagen fibers, collagen-guided correlated cell motions, and long-range (~ 600 micrometers) mechanical interactions among cells. Our findings suggest a slow geometrical feedback in cell shape patterning and demonstrate the feasibility to engineer large-scale tissue patterns under scaffold-free conditions.

The goal of my lab is to form a quantitative narrative for the fundamental processes driving the living cell. This narrative is built upon precise measurements performed in individual cells, at the level of individual molecules and discrete events in space and time. To achieve this level of detail, we are using a synthesis of approaches: classical molecular biology and biochemistry; single-cell and single-molecule fluorescence microscopy; and advanced image- and data-analysis algorithms. By using simple, coarse-grained theoretical models, we are able to distill our result into general principles, which can then be directly compared to findings in other model systems. I will present a few examples from our work, focusing on the study of the life cycle of bacteriophage lambda, a simple paradigm for cellular decision making.

References
1. L. Zeng, S.O. Skinner, C. Zong, J. Sippy, M. Feiss and I. Golding, Cell 141(4):682-91 (2010)
2. L. H. So, A. Ghosh, C. Zong, L. A. Sepulveda, R. Segev and I. Golding, Nature Genetics 43(6):554-560 (2011)
3. I. Golding, Annual Review of Biophysics 40:63-80 (2011)

To adhere and migrate, cells exert traction stresses against their extracellular matrix. In addition to aiding cell movements and helping to maintain cell shape, cellular traction stresses also contribute to the ability of cells to probe and remodel their environment. In this talk, I will discuss my lab’s work investigating the role of cellular traction stresses in mediating cell health. Using in vitro and ex vivo models, we have shown that changes in cell contractility occur during the progression of two deadly diseases: atherosclerosis and cancer. Altered cellular mechanical forces can lead to changes in cell-cell and cell-matrix interactions that contribute to disorganized tissue structures, a hallmark of both cancer and atherosclerosis. Our data reveal that changes in cell contractility are linked to both atherosclerosis progression and metastasis, and that therapeutically targeting changes in cellular contractility may be one potential pathway to preventing disease progression.

Dendritic spines are sites of communication in excitatory neurons. Loss of these spines, and swelling along dendrites and axons at the area of injury, occur due to traumatic brain injury (TBI) and stroke, and this spine loss is correlated with the behavioral deficits that accompany TBI and stroke. Spontaneous or rehabilitative improvements in function following ischemic stroke are accompanied by a reemergence of dendritic spines. Very little is known about the molecular mechanisms and identities of molecular participants in dendritic spine loss and reemergence, with regard to TBI. One of our more recent discoveries is that two proteins, postsynaptic density-95 (PSD-95) and cytosolic PSD-95 interactor (cypin), play opposing roles in mediating the morphological changes that occur in response to sublethal NMDA glutamate-receptor activation, a secondary effect of TBI and ischemic stroke. Cypin promotes small and numerous varicosity formations and is necessary for NMDA-mediated spine retraction. Most importantly, it confers protection from NMDA-induced neurotoxicity. PSD-95 mediates the opposite effects. Furthermore, we have complemented our cellular studies with electrophysiological studies. We use microelectrode arrays to study cellular activity before and after injury in vitro. Our data show that treatment with different concentrations of glutamate results in different injury profiles. Thus, a future goal is to combine our morphological studies with microelectrode array recordings to understand how varicosity formation relates to neuronal function.

Efforts to extend nanoparticle residence time in vivo have inspired many strategies in particle surface modifications to bypass macrophage uptake and systemic clearance. Herein I report a top-down biomimetic approach in particle functionalization by coating biocompatible nanoparticles with natural red blood cell (RBC) membranes including both membrane lipids and associated membrane proteins for long-circulating cargo delivery. This approach aims to camouflage the nanoparticle surface with the erythrocyte exterior for long circulation while retaining the applicability of the cores that support the RBC membrane shell. In vivo results revealed superior pharmacokinetics and biodistribution by the RBC-mimicking nanoparticles, as compared to control particles coated with the state-of-the-art synthetic stealth materials.

This lecture will describe a new concept in high speed ground transportation that may make it possible for jet powered trains to glide on frictionless soft porous tracks at speeds approaching current commercial jet aircraft. The jet train employs a nearly frictionless,

lift mechanism first described for red cells gliding on the endothelial glycocalyx (Feng and Weinbaum, JFM 2000) and subsequently used to predict the lift forces generated in skiing and snowboarding by the transiently trapped air beneath their planing surfaces. Using an

asymptotic analysis for large values of the dimensionless permeability parameter H/√KP , where H is the porous layer thickness and KP the Darcy permeability, we show that it is possible to support a 70 metric ton jet train carrying 200 passengers on a giant ski that is 30m long and 3 m wide using a soft porous material whose KP is approximately 5

x 10-9 m2 . Quite remarkably, for an angle of attack of < 0.1 degrees the entire weight of the train plus its passengers can be achieved at a velocity of < 5 m/s if lateral leakage of air at the edges of the ski can be eliminated. This value of KP can be satisfied by inexpensive

soft fiber materials commonly used in body pillows (fiber radius 5 µm, void fraction of 0.995). Compression tests for these fiber-fill materials show that the fibers contribute < 0.2 percent of the total lift and hence the friction force of the fiber phase is negligible. Using jet engines of 10,000 lbf thrust, about 1/5 that of a 200 passenger jet aircraft, one is able to obtain a cruising velocity approaching 700 km/hr. This would allow for huge fuel savings, especially on short flights where much of the energy expenditure is used to climb to altitude and overcome lift-induced drag.

Sessile marine organisms are very effective at adhering to substrates under wet conditions and in harsh environments. The proteins employed by mussels, for example, have very specialized amino acid compositions undoubtedly related to the particular challenges of achieving permanent adhesion in the wet marine environment. Mussel adhesive proteins (MAPs) are known to contain high levels of 3,4-dihydroxy-L-alanine (DOPA), a catecholic amino acid that is believed to confer cohesive and adhesive properties to these proteins. I will summarize the adhesive and cohesive roles of DOPA, and describe our efforts to develop biomimetic polymer hydrogels and coatings from synthetic catechol-containing polymers. Synthetic mimics of MAPs take the form of linear or branched polymers with catecholic endgroups or side chains, where the catechols serve the role of a cross-linking component, or surface anchor for attachment to surfaces. These biologically inspired polymers have a variety of functional uses, including tissue repair, drug delivery and antifouling coatings.

The engineering of complex in-vitro models that more accurately recapitulate the formation of vascular networks has the potential to improve our understanding and targeting of key events that control vasculogenesis and angiogenesis. Our lab focuses on the development and employment of models to investigate how low oxygen concentration (hypoxia) and cues from the extracellular matrix (ECM) instigate vascular morphogenesis. We demonstrate how dissolved oxygen levels during 2-D and 3-D culture of endothelial progenitors and cells vary and affect cellular responses including tube formation and ECM deposition. Developing and applying a microbioreactor for long-term cell cultures under controlled dissolved oxygen levels and flow rates, we found alteration in endothelial responses to healthy or diseased conditions. Using 3-D polymeric hydrogels we show how synthetic, tunable polysaccharide hydrogels can be utilized to determine physical and biological parameters that enable formation of functional vascular networks. One type of hydrogel enables human vascular network formation in vitro, and further supports the integration of the vascular networks with the host’s circulation and blood flow into the hydrogel following transplantation.

All animals search for prey, whether they graze, peck, hunt or shop, and selection pressure under common environmental constraints has yielded conserved-search strategies that can be highly efficient. When prey items are sparse, randomly distributed and undetectable at a distance, random search can be moreefficient than systematic search. However, little is known about the neuronal basis of random search because of the difficulty of recording from neurons infreely moving animals under field conditions. To address this problem, we made an exhaustive kinetic analysis of random search in a simple foragingorganism, the nematode C. elegans. Our analysis is formalized in terms of a hidden Markov model that is isomorphic with a mathematically tractable neuronalcircuit comprised of two binary, stochastic, neuron-like elements. The model predicts that cross connections between the two elements are inhibitory. Thisprediction is supported by direct optophysiological measurements of synaptic connectivity between neurons in the underlying biological circuit, suggestingthat it functions as a neuronal flip-flop device. The model also predicts the counterintuitive behavioral effects of neuronal ablations, and previouslyundescribed effects of genetic manipulations of neuronal membrane potential. Finally, the model can be generalized to explain other behaviors includingdeterministic escape responses and biased random walks. These findings validate a neuronal flip-flop as a universal module for a wide range of behaviors inC. elegans and as a source of testable hypotheses for the mechanism of search behaviors in other organisms.

In the first part of talk, I will present biophotonic nanosatellites that have multiple functions: targeting, imaging, gene delivery & regulations in living systems. For the remote optical control of gene regulations and therapeutic applications, we have developed Oligonucleotides on a Nanoplasmonic Carrier Optical Switch (ONCOS). We also accomplished photonic gene circuits that utilized RNA-medicated gene silencing to multistep bidirectional control of specific gene expression by taking advantage of the tunability of the longitudinal plasmon resonance wavelength in gold optical nanoantennas.

In the second part of the talk, I will discuss (1) Cellular BASICs (Biologic Application Specific Integrated Circuits) for single stem cell analysis, dynamic cell culture array, and self-powered integrated microfluidic blood analysis system; (2) Biologically inspired 3D tissue chips: disease-specific integrated microphysiological human tissue models via normal and patient-specific human induced pluripotent stem cells for drug development and safety; (3) Integrated Molecular Diagnostic Systems (iMDx) for global healthcare. In summary, I will share my vision for the convergence of science, engineering, and medicine to transform life sciences, and finding the solutions for preventive personalized medicine and low-cost healthcare systems.

Highly regulated signals in the stem cell microenvironment, such as growth factor presentation and concentration, matrix stiffness, and ligand adhesion density have been implicated in modulating stem cell proliferation and maturation. Therefore, it is desirable to have independent control over both the biochemical and mechanical cues presented to the cell to analyze their relative and combined effects on stem cell function. Accordingly, we have developed synthetic hydrogels, novel three-dimensional filamentous matrices, and biointerfaces to assess the effects of adhesion ligand presentation, material moduli, and matrix architecture on stem cell function and fate determination. Employing these soft materials we have demonstrated that the mechanical, structural, and biochemical properties of a stem cell microenvironment can be tuned to regulate the self-renewal, differentiation, and morphological features of different stem cells including human embryonic, neural, cardiac progenitor, and mesenchymal stem cells. We have further modified these tunable hydrogels with matrix metalloproteinase labile crosslinkers (e.g. MMP-2, 9 &13), to be used as an assistive microenvironment for transplantation of stem cells into diseased or damaged tissue such as the infracted myocardium. These biomimetic hydrogels provide a foundation for systematic development of “pro-survival” microenvironments for cell transplantation and the potential improvement in the long-term results of stem cell based regenerative therapies. Various examples from our work will be discussed during this presentation.

In the past two decades, tremendous advances in medical device technology, imaging systems and interventional techniques have enabled minimally invasive, endovascular treatment of cerebrovascular disease. Brain surgery from a small puncture in the leg can be used to address deadly diseases such as aneurysms, arteriovenous malformations and acute ischemic stroke. Critical to this evolution has been the miniaturization of medical devices to be safely navigated into tortuous and fragile vessels that often measure less than 2mm. Our laboratory engineers solutions to accomplish numerous tasks that include access into the brain’s arteries, embolization of delicate structures that are prone to rupture and cause devastating bleeding, and removal of emboli that starve the brain of critical blood flow. Our research at the New England Center for Stroke Research at the University of Massachusetts Medical School is an interdisciplinary center that focuses on model systems to develop imaging and device technology that enables physicians to safely and effectively treat vascular diseases of the brain. This presentation will survey the technology that has made this evolution possible, from bench to brain.

Many biological systems employ physically constrained networks of chemical, electrical, or mechanical signals to perform complex functions. Recent advances across multiple disciplines have begun to elucidate the role that these embedded networks play in guiding and enabling system dynamics. A critical remaining challenge is to harness the predictive role of complex networks in tissue, brain, and behavior to support the control, rescue, and imitation of system function. Such predictions can be extracted from network structure, network dynamics, or the properties of the signals that propagate through the network. I will illustrate these efforts and the associated mathematical tools they employ using examples drawn from material, biomedical and population systems. For example, the network structure of soft materials constrains sound propagation, informing the development of non-destructive testing and design techniques. The network dynamics of human brain activity predicts adaptive behaviors like learning, potentially enabling the monitoring of disease progression and rehabilitation. The information passed between individuals on a social network drives behavioral variability in the population, impacting information dissemination policies. I will discuss the ramifications of these findings for critical questions in bio- and systems engineering and outline some of the outstanding conceptual, experimental, and mathematical challenges that will propel research in the coming years.

The Stanford Microsystems Lab works on custom measurements and analysis systems for small-scale metrologies, including scanning probe microscopy, biomechanics and mechanotransduction assays. We study the mechanics and biology of the sense of touch in C. elegans, the mechanisms and forces of cell adhesion, and the development and response of stem cells and cardiac myocytes to mechanical loading. We design and fabricate most of our own tools and sensors, and are interested in the reliable manufacture and operation of micromachined sensors and actuators in harsh environments; measuring nanoscale mechanical behavior; and the analysis, design, and control of integrated electromechanical systems. We leverage new tools and answer novel questions in our lab in the areas of physiology, biology, stem cells, neuroscience and cardiology, with an eye toward quantitative and fundamental biophysics.

Osteoarthritis is a painful and debilitating disease of the joints that is characterized by progressive degeneration of the articular cartilage. The etiology of osteoarthritis is not fully understood, but it is now well accepted that biomechanical factors play an important role in the onset and progression of this disease. In recent studies, we have focused on the identification of several mechanical signal transduction pathways in chondrocytes that involve the activation of mechano- and osmo-sensitive ion channels, such as those in the transient receptor potential (TRP) family. These pathways may provide novel pharmacologic targets for the modification of biomechanically-induced cartilage degeneration in osteoarthritis. Additionally, other studies in our lab have focused on tissue engineering approaches for resurfacing entire joints using adult stem cells and biomimetic 3D woven fiber scaffolds. Bioreactor studies have shown that mechanical factors can play an important role in accelerating cartilage regeneration, but this approach may not be feasible for scaffolds with complex shapes and architectures. In this regard, we have found that artificial activation of mechanical signaling pathways can enhance cartilage development similar to direct mechanical loading. Taken together, these studies emphasize the critical role that biomechanics plays in the physiology as well as pathology of the joint, and demonstrate the importance of biomechanical factors in functional tissue engineering of cartilage and other joint tissues.