BE Seminars & Events

Current Seminar Series: 2010-2011

Bioengineering Seminars are held on Thursdays at 12:00 pm in Room 337 Towne Building unless otherwise noted. For all Penn Engineering events, visit the Penn Calendar.

September 16  
Peter Cummings, John R. Hall Professor of Chemical & Biomedical Engineering, Vanderbilt University
"Combined Experimental and Modeling Approach to Cell Motility
and its Role in Tumor Growth Dynamics"
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In this talk, we describe our research aimed at developing multi-scale models of tumor growth dynamics, and to measure key cell motility parameters needed for input to the models.  Thus, the talk has three parts.  First, we describe experimental measurements of random cell motility in three, increasingly aggressive, cancer breast cell lines, MCF-10A pBabe, neuN and neuT on 2-D plastic substrates using videomicroscopy.  We find that the cells exhibit a bimodal correlated random walk, which is consistent with foraging behavior seen in whole organisms.  Second, we describe the development of a computational model for vascularized tumor growth in a framework that, in common with a number of models, is cell-based, but, unlike previous models, does not limit cell movement to a lattice. The motility measurements are some of the experimental data that this model is based on.  The model permits the contributions of the tumor microenvironment and cell motility to tumor morphology to be analyzed.  Finally, time permitting, we describe our recent work on simulating bone remodeling as part of a broader effort to model tumor metastasis to bone. This research has been supported by the National Cancer Institute Integrative Cancer Biology program.

September 23
Christopher R. Jacobs, Associate Professor, Biomedical Engineering, Columbia University
"Primary cilia as cellular mechanosensors"
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The ability of non-specialized non-excitable cells to sense and respond to mechanical stimulation is central to proper physiologic function in a surprisingly wide range of cell types including endothelial cells, liver, lung and kidney epithelial cells, chondrocytes, neurons, and osteocytes.  Cellular mechanosensation is critical in diseases responsible for enormous human suffering including atherosclerosis, osteoarthritis, cancer, and osteoporosis.  Primary cilia are solitary linear cellular extensions that extend from the surface of virtually all cells.  As a result, large local strains occur as they are deflected suggesting that they may act as a cellular strain concentrators. For decades, the biologic function of this enigmatic structure was elusive, however, recent data suggest that it functions as a complex nexus where both physical and chemical extracellular signals are sensed and coordinated responses initiated.  For example, it is important in sensing the biochemical signals hedgehog (Hh), wingless, and platelet derived growth factor, as well as mechanosensing in the kidney and embryonic node.  In our laboratory we have collected data that primary cilia act as molecular mechanical sensors in bone cells with both in vitro and in vivo models.  Furthermore, we have found that the intracellular signaling pathway activated by primary cilia in bone is distinct from those observed in other tissues such as kidney.  This suggests that the primary cilium has a rich potential to transduce many signals through multiple mechanisms and may undergo functional specialization as a function of tissue or cell type. 

Wednesday, September 29
Jennifer Cochran, Assistant Professor, Bioengineering, Stanford University
Joint BE/CBE Seminar, 3:00 to 4:00 pm, Wu and Chen Auditorium, Levine Hall
ngineered Protein Therapeutics and Diagnostic Agents Inspired by Nature"
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Proteins have long been recognized for their potential therapeutic applications in regenerative medicine and cancer. However, when produced recombinantly such proteins are often difficult to express and unstable, or suffer from low biological efficacy when introduced into the body. Using rational and combinatorial methods, we engineered natural proteins for enhanced biophysical and biological properties. Alternatively, we used these technologies to create novel proteins that are not found in nature. Applications of these engineered proteins in biomedical applications will be discussed. In particular, recent results will be presented on engineered growth factor ligands that function as agonists or antagonists for tissue engineering or cancer therapy, respectively, and novel engineered protein ligands that are being used to image tumors in living subjects.
October 14
Zeng-Rong Lu, M. Frank and Margaret Domiter Rudy Professor of Biomedical Engineering, Case Western Reserve University
"MRI Contrast Agents for Molecular Imaging of Tumor Microenvironment"
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Tumor microenvironment plays a critical role in cancer survival, angiogenesis, proliferation and metastasis.  Molecular imaging of biomarkers in tumor microenvironment provides accurate characterization of tumor angiogenesis, earlier detection and diagnosis of malignant tumors and non-invasive evaluation of anticancer therapeutics efficacy.  We have designed and developed polydisulfide-based biodegradable macromolecular MRI contrast agents for evaluating tumor angiogenesis and targeted nanoglobular MRI contrast agents for detecting a cancer-related biomarker expressed in the extracellular matrix of malignant tumors.  The biodegradable macromolecular contrast agents are effective for characterizing tumor angiogenesis and non-invasive evaluation of tumor response to cancer therapies in DCE-MRI.  The targeted contrast agents specifically bind to the biomarker in tumor extracellular matrix, resulting in strong and prolonged contrast enhancement in the tumor tissue, not in normal tissues.  The novel MRI contrast agents have shown a potential for accurate characterization of tumor angiogenesis, timely evaluation of anticancer therapeutic efficacy and specific cancer molecular imaging with MRI.

October 28
James E. Ferrell, Jr., Professor and Chair, Chemical and Systems Biology, Stanford University School of Medicine
"Dissecting the mitotic oscillator"
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The Xenopus embryonic cell cycle is driven by a system of regulatory proteins that functions as an autonomous, clock-like oscillator.  The oscillator is centered on the protein kinase cyclin-Cdk1, and is built out of interlinked positive and negative feedback loops.  We have been dissecting this circuit to understand how the robust oscillations of the embryonic cell cycle arise, and how the oscillations remain synchronized over the large distance scales of the Xenopus embryo.
November 4
Darrell J. Irvine, Associate Professor, Materials Science and Engineering, Biological Engineering, MIT
"New materials and new methods for cancer immunotherapy and vaccine delivery"
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A major focus of our laboratory is the development of new materials for drug and vaccine delivery, and two recent advances in our work in this area will be described.  Adoptive cell therapy (ACT) with tumor-specific T-cells is a promising approach for cancer therapy, but strategies to enhance the persistence and functionality of ACT T-cells are still sought.  Meanwhile, the use of synthetic nanoparticles as carriers to deliver drugs to tumor environments has become of increasing interest, with the goal of targeting drugs to tumor sites. We will describe a strategy combining these two approaches, based on stable chemical conjugation of drug-loaded nanoparticles (NPs) to the surfaces of live lymphocytes for ACT.  We demonstrate how ACT T-cells carrying cytokine-loaded NPs (to permit pseudo-autocrine self-stimulation following transfer into tumor-bearing hosts) are capable of massive in vivo expansion and robust anti-tumor responses, enabled by minimal doses of cytokines that by comparison have no therapeutic effect when given in a soluble form systemically.

In the second part of this talk, new materials for vaccine delivery will be described, employing a new class of nanoparticle drug carriers, dubbed interbilayer-crosslinked multilamellar vesicles (ICMVs).  These lipid-based capsules are formed by synthesizing multilamellar liposomes, stabilized by the introduction of covalent crosslinks connecting tightly stacked lipids bilayer-to-bilayer within the vesicle walls.  We show how these capsules enable the efficient loading and retention of both hydrophilic protein antigens (in the aqueous core) and lipophilic molecular adjuvants (in the vesicle walls).  By sequestering both adjuvant and antigen molecules within the particle structure in this way, we found that these lipid particles form an extremely potent vaccine for both humoral and cellular immunity, eliciting up to ~30% antigen-specific CD8+ T-cells for a single epitope and strong IgG responses in mice.  Notably, unlike live vaccine vectors that often must be used in so-called “heterologous” prime-boosting regimens due to anti-vector immunity, this nanoparticle vaccine could be repeatedly administered, boosting both CD8+ T-cell and antibody responses on each immunization.  Implications of this strategy for obtaining strong combined T-cell and antibody responses from subunit vaccines will be discussed.

Biography: Darrell Irvine, Ph.D., is an Associate Professor at the Massachusetts Institute of Technology and an Investigator of the Howard Hughes Medical Institute. His research is focused on the application of engineering tools to problems in cellular immunology and the development of new materials for vaccine and drug delivery.  These efforts largely focus on cellular immunology and vaccine development for HIV and immunotherapy of cancer.  This interdisciplinary work has been recognized in numerous awards, including a Beckman Young Investigator award, an NSF CAREER award, selection for Technology Review’s ‘TR35’ most promising scientists under age 35, and appointment as an investigator of the Howard Hughes Medical Institute in 2008.  He is the author of over 50 publications, reviews, and book chapters and an inventor on numerous patents.
November 11
Andres J. Garcia, Professor and Woodruff Faculty Fellow, Woodruff School of Mechanical Engineering, Georgia Institute of Technology
"BioArtificial Materials for Harnessing Host Repair"
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Cell adhesion to extracellular matrices plays central roles in the formation, maintenance and repair of numerous tissues. Moreover, cell adhesion to adsorbed proteins or adhesive sequences engineered on surfaces is important to biomaterials, tissue engineering, and biotechnological applications. Cell adhesion to extracellular matrix proteins is primarily mediated by the integrin family of adhesion receptors. We have established biomolecular strategies for the engineering of bioartificial materials to direct integrin binding specificity and signaling. These materials regulate cell adhesion and signaling to direct in vitro cell function (adhesion, proliferation, and differentiation) and in vivo healing responses for tissue repair and integration. Notably, these surface engineering strategies focus on modifying clinically relevant materials and are translatable to existing biomedical devices. In one application, we have engineered polymeric brush coatings on titanium that present controlled densities of engineered ligands that enhance implant osseointegration and bone repair. In another application, we have synthesized synthetic hydrogels presenting defined densities of adhesive ligands, vasculogenic growth factors, and protease degradable sequences that direct in vivo vascular growth and therapeutic vascularization. These approaches provide a basis for the rational design of robust bioinstructive materials that tailor adhesive interactions and elicit specific cellular responses for the development of 3D hybrid scaffolds for enhanced tissue reconstruction, "smart" biomaterials, and cell growth supports. 

December 2
Paul Sajda, Associate Professor of Biomedical Engineering, Columbia University
"Single-trial Analysis of Simultaneously Acquired fMRI and EEG: A Window into Latent Brain States"
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A relatively new non-invasive neuroimaging modality is simultaneous EEG/fMRI. Though such a multi-modal acquisition is attractive given that it can exploit the temporal resolution of EEG and spatial resolution of fMRI, it comes with unique signal processing and pattern classification challenges, specifically a principled methodology for fusing the two data types. In this talk I will review our work at developing a custom-made simultaneous EEG/fMRI system for detecting and tracking latent brain states.  I will describe our signal processing and machine learning approaches for analysis of simultaneous EEG and fMRI, with a focus on those algorithms enabling a single-trial analysis of the neural signals. In general, these algorithms exploit the multivariate nature of the EEG, removing MR induced artifacts and classifying event-related signals that then can be correlated with the BOLD signal to yield specific fMRI activations. I will present our experimental results which suggest that trial-to-trial variability of latent brain states, unobservable via behavioral measures, can be spatially and temporally tracked to yield insight into how the brain shifts attention and monitors its sensory input.
James Moon December 9
James Moon, Postdoctoral Associate, Department of Biological Engineering and Materials Science & Engineering, Massachusetts Institute of Technology
"Novel lipid-based nanoparticles for antigen delivery and vaccine applications"
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Currently licensed vaccine adjuvants promote immunity by primarily eliciting humoral immune responses, whereas the cellular arm of adaptive immunity is largely unaffected by these adjuvants. As strong cellular CD8+ T‐cell responses may be required for vaccines against cancer or intracellular pathogens such as malaria, there is great interest in technologies to promote concerted humoral and cellular immune responses. To this end, synthetic particles carrying antigens and adjuvant molecules have been developed, but in general, their immunogenicity is poor, particularly for CD8+ T‐cell responses. In this seminar, I will describe development of novel interbilayer‐crosslinked multilamellar vesicles (ICMVs) that can promote robust humoral and cellular immune responses. ICMVs are formed by fusing liposomes into multilamellar vesicles and subsequent crosslinking of adjacent lipid headgroups across lipid bilayers within multilamellar vesicles. ICMVs exhibit substantially enhanced protein antigen loading compared to traditional drug delivery vehicles (e.g. liposomes and polymeric particles). Protein antigens are stably entrapped in ICMVs under extracellular conditions, but rapidly released in the presence of endolysosomal lipase. ICMVs encapsulating antigen and adjuvant elicit potent antibody and CD8+ T‐cell responses comparable to the strongest viral vector vaccines currently in clinical trials. Efforts to translate these promising results into effective malaria vaccines will be discussed.
Daniel A. Heller December 16
Daniel A. Heller, Damon Runyon Fellow, Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology
"Single-Walled Carbon Nanotube Optical Biosensor Technologies"
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Real-time, spatially resolved detection and identification of analytes in biological media, and at the single-molecule level, present worthy goals for nanoscale sensors.  Encapsulation of single-walled carbon nanotubes in synthetic polymers and biopolymers creates a handle for the transduction of analyte binding.  By wrapping nanotubes with short sequences of ssDNA, reactive oxygen species (ROS) are detected via DNA chemistry in the vicinity of the nanotube.  Nitroaromatic compounds, such as pesticides, can be detected by the conformational change of a peptide upon binding to the analyte.  In both cases, analyte identification is possible by observing variations in the nanotube’s spectral response, resulting in distinctive optical fingerprints.  Nanotubes undergo wavelength and intensity modulation, permitting identification of analytes which are difficult to differentiate via conventional methods, such as certain types of ROS.  The analyte responses can be spatially mapped in live cells and tissues, measured with sensitivity down to the single-molecule level, and detected in real-time, facilitating new and unprecedented biological measurements.

January 13
Sophie Dumont, Postdoctoral Fellow, Systems Biology Department, Harvard Medical School
"Mechanical Forces in Cell Division"
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Cell division is a mechanical process.  Although we now have a nearly complete list of molecular players, our understanding of the underlying mechanical principles and interactions is still poor.  How do nanometer-scale molecules work together to generate micrometer-scale movements?  To gain insight into the mechanical design principles of cell division, we developed a system to perform conventional and super-resolution live imaging of dividing mammalian cells while mechanically and molecularly perturbing them.  First, I will discuss the mechanical design of kinetochores, the macromolecular machine attaching chromosomes to dynamic microtubules.  We developed and imaged a two-color sensor to measure structural dynamics of individual kinetochores at 10 nm and 10 s scales as they generate and respond to natural force fluctuations.  We show, for the first time, that kinetochores make two distinct mechanical interactions with microtubules: an active, force-generating interface is located near the DNA at the microtubule tip, and a passive, frictional interface is located further out along the microtubule.  Second, I will discuss how spindle mechanical architecture supports chromosome movement.  Using laser ablation of kinetochore-attached microtubules, we show that kinetochores are very locally anchored to the spindle.  Kinetochores are mechanically isolated from forces generated far away and this may facilitate robust chromosome segregation.  Together, the framework and approaches developed here should help reveal the nanometer and micrometer mechanical design principles of cell division and other mechanical processes essential to life.
Grace Hopper Lecture, January 20
Christine Ortiz, Professor of Materials Science and Engineering, Dean for Graduate Education, Massachusetts Institute of Technology
"Natural Armor: An Encyclopedia of Protective Engineering Designs"
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Biological exoskeletons or "natural armor" systems are multilayered,  hierarchical structures that serve many functions, in particular protective mechanical roles such as; penetration, wear, and scratch resistance, minimization of back deflection and potential blunt trauma, damage detection and sensing, self-repair and regeneration, and, in certain cases, flexibility and mobility. We can learn much from biological organisms that have evolved over millions of years a veritable encyclopedia of environmentally friendly engineering designs for protection against specific predatory and environmental threats. Natural armor functions efficiently by elegantly balancing protection, tissue damage tolerance, weight, and mobility requirements to maximize survivability. In order to elucidate the design principles of these fascinating materials, nanomechanics methodologies have been employed including: the measurement and prediction of extremely small forces and displacements, the quantification of nanoscale spatially varying mechanical properties, the identification of local constitutive laws, the formulation of molecular-level structure-property relationships, and the investigation of new mechanical phenomena existing at small-length scales. This talk will focus on a  number of classes of natural armor: flexible; transparent; and those that exhibit resistance to biochemical toxins, kinetic attacks, extreme thermal fluctuations, and blast. Model systems to be discussed include "living fossils," such as armored fish, deep sea hydrothermal vent and antarctic molluscs, echinoderms and molluscs with articulating plates (e.g., chitons, urchins), and the transparent exoskeletons of certain crustaceans and pteropods, etc.
January 27
Jeanne Stachowiak, Senior Member, Technical Staff, Sandia National Laboratories
"Reverse Engineering Biological Membranes"
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My research employs micro- and nanotechnology to build biological membranes component-by-component from the bottom up.  By reconstructing membranes from known components under controlled conditions, we can simultaneously model the biophysical mechanisms that underlie membrane function in cells and employ cell-like synthetic membranes for practical applications in medicine, materials science, and energy.

The first part of the talk will discuss development of a microfluidic method for direct encapsulation of biomolecular solutions in lipid vesicles.  Construction of vesicle-encapsulated systems has been limited by the difficulty of forming vesicles with controlled size and composition. We have recently developed a method for forming and loading lipid vesicles using a pulsed microfluidic jet. Akin to blowing a bubble, the microfluidic jet deforms a planar lipid bilayer into a vesicle that is filled with solution from the jet and separates from the planar bilayer. In contrast to existing techniques, this method rapidly generates multiple monodisperse vesicles with controlled membrane composition and virtually unrestricted internal contents, creating broad opportunities for the construction of biomimetic devices. 

The second part of the talk will discuss the use of synthetic membrane systems to explore a new mechanism of membrane curvature induction that can define membrane architecture at the nano-scale.  While critical to cellular function, deformation of lipid membranes into highly curved structures remains poorly understood.  Using lipid vesicles that contain phase-separated lipid regions with engineered affinity for proteins, we observed that protein crowding on membrane surfaces created a protein layer that buckled outward, spontaneously bending the membrane to form stable buds and tubules. These observations may help explain how lipids and proteins collaborate to create the highly curved structures observed in cellular membranes, and could be used to build synthetic nano-scale containers and dynamic membrane networks.

The talk will conclude with a brief discussion of research opportunities at the intersection of micro/nano technology, membrane biophysics, and biomedical applications of membrane-encapsulated systems. 

February 3
Sotiris Masmanidis, Broad Senior Research Fellow in Brain Circuitry, Division of Biology, California Institute of Technology
"Probing brain activity with micro and nanoscale neural interfaces"
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In vivo electrophysiology has revealed a wealth of information about the responses of individual neurons to stimuli.  Yet studying the brain one cell at a time inherently constrains our ability to understand how the complex interplay of neurons gives rise to behavior.  Carrying out large-scale neuronal recordings – simultaneously monitoring the activity of hundreds to thousands of cells across multiple brain areas – will be a transformative advance in systems neuroscience.  I will describe the development of implantable microelectrode arrays for massively parallel extracellular readout of brain activity.  A new MEMS fabrication and assembly technique has allowed us to increase the spatial density of recording sites via dual-sided and three-dimensional electrode arrays.  I will present some applications of such devices in electrophysiological measurements in insects and rodents.  In addition, in order to create minimally invasive structures we have utilized nanofabrication techniques to wire up high-density arrays containing a large number of recording sites.  I will describe the development 64-channel neural probe with submicron features that is operated by a commercially available application specific integrated circuit.  I will also discuss some of the measurements we are carrying out with such devices in mice to resolve feedback interactions within dopaminergic brain pathways.

February 10
William Greenleaf, Postdoctoral Fellow, Department of Chemistry and Chemical Biology, Harvard University
"Making light work in biology: Observing transcription with high‐resolution optical tweezers, and sequencing DNA with fluorogenic nucleotides"
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Optical tweezers have proven a powerful tool for the investigation biomolecular mechanisms. I will describe the development of high resolution optical tweezers that allow sub‐nanometer motions of individual molecules to be observed under physiological conditions and under controlled loads. This technology has allowed the direct observation of single‐nucleotide translocations of RNA polymerase, the investigation of the hierarchical folding pathway of an adenine riboswitch, as well as single‐molecule sequencing of DNA using the motion of an RNA polymerase molecule. Finally, I will discuss recent work on a parallelizable DNA sequencing technology that takes advantage of reversibly sealable polydimethylsiloxane (PDMS) microreactors and fluorogenic nucleotides to sequence DNA. This "fluorogenic pyrosequencing" method is simple, rapid, inexpensive, and has the potential to be elegantly interfaced with a variety of PDMS‐based microfluidic devices suitable for the preparation and amplification of nucleic acids for sequencing.
Tuesday, February 15, 12:15 p.m. - 1:15 p.m. in 337 Towne
Sai Reddy,Postdoctoral Fellow, Department of Chemical Engineering, University of Texas, Austin
"Integrating immunology and engineering for biopharmaceutical drug development"
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Nearly half of all clinically approved biopharmaceuticals are comprised of subunit vaccine and antibody-based therapeutics which have been heavily reliant on immunology techniques (i.e., hybridomas and vaccine antigens). I describe novel approaches that exploit immune function and response for vaccine and antibody engineering.

Subunit vaccine development is often focused on antigen targeting and adjuvancy schemes that respectively facilitate delivery of antigen to dendritic cells and elicit their activation. Here I will present a novel polymer nanoparticle-based vaccine platform, which targets lymph node– residing dendritic cells via interstitial flow and activates these cells by in situ complement activation. After intradermal injection, interstitial flow transported ultra-small nanoparticles (25 nm) highly efficiently into lymphatic capillaries and their draining lymph nodes. The surface chemistry of these nanoparticles activated the complement cascade, generating a danger signal in situ and potently activating dendritic cells. Using nanoparticles conjugated to the model antigen ovalbumin, the generation of humoral and cellular immunity was shown in mice in a size- and complement- dependent manner. Such a vaccine technology platform is both effective and inexpensive, and therefore allows it to be explored in global health applications.

The ability of humoral B cell immunity to generate a vastly diverse antibody repertoire as a response to stimuli (i.e., immunization) has been substantially exploited for monoclonal antibody discovery. Here I present a novel platform for monoclonal antibody discovery, by exploiting high-throughput DNA sequencing of plasma cell antibody gene repertoires from immunized mice. We found that antigen-specificity of antibodies could be identified based on bioinformatic analysis of the antibody repertoire; subsequently we utilized automated synthetic gene construction for the production of antigen-specific antibodies in mammalian and bacterial expression systems. Taken within the context of the rapid advances and declining costs for DNA sequencing and gene synthesis, this technology offers a powerful alternative to conventional methodologies for monoclonal antibody discovery (e.g., hybridoma and phage/microbial display screening). Furthermore, we have used immune repertoire analysis and a systems immunology approach for answering basic questions about immune response.  This includes quantitative determination of various B cell repertoires in secondary lymphoid organs of immunized mice and precise mapping of naïve repertoires in a humanized mouse model.

February 17
Neal K. Devaraj, Postdoctoral Fellow, Harvard Medical School
"Biomedical Applications of Tetrazine Cycloadditions: Live Cell Microscopy, Clinical Diagnostics, and In-Vivo Imaging"
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Disease mechanisms are increasingly being resolved at the molecular level.  This presents opportunities for combining specifically engineered synthetic reactions with biology for applications in imaging, diagnostics, and therapy.   I will discuss our recent efforts to design coupling reactions between tetrazines and strained alkenes that can proceed extremely rapidly in whole serum or blood. These selective reactions were used to label biomarkers on living breast and lung cancer cells with near infrared emitting fluorophores.  We subsequently discovered fluorogenic probes that increase in intensity after chemical reaction leading to improved signal to background and the ability to react and image chemotherapeutics, such as taxol analogs, inside of live cells.  Since the coupling partners are small molecules (<300 daltons) they offer unique steric advantages in multistep amplification.   We have labelled cells with magnetic nanoparticles using two step protocols and can significantly amplify signals over one step labeling procedures as well as two step procedures using more sterically hindered biotin-avidin interactions.  This method is now being used routinely at Mass General Hospital for nanoparticle based biomarker profiling of patient clinical samples.  Finally, I will discuss recent results in our efforts to use in-vivo chemical reactions for multistep targeting of fluorine-18 radionuclides to colon cancer xenografts in live mice for PET/CT imaging.

March 3
Gabriel  A. Silva, Associate Professor, Bioengineering, Ophthalmology, University of California San Diego
"Engineering methods for making sense of the function of neural circuits and networks from cell signaling"
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Our lab's goal is to understand cell signaling and information processing in biological cellular neural networks in the brain, and how the break down of these processes contribute to neurological disorders. A broad goal is understanding how the complex dynamics of the brain at a systems level emerge from (often stereotyped and ubiquitous) molecular and cellular foundational processes. We approach these questions by developing and using experimental and computational methods in order to reverse engineer how the nervous system is built, so that we can understand how it functions. Our lab operates at the interface between experiment, theory, and computation. Experimentally we rely on optical imaging methods, as well as traditional molecular and cellular neurobiology methods. More technologically intensive, we are very engaged in the development of nanotechnologies as biosensors for neural cells in order to study both individual cells and neural circuits and networks. Theoretically and computationally we are developing mathematical and physical models for identifying and mapping functional signaling and information propagation in biological neural networks, and neurophysiological and biophysical models that provide mechanistic insights. Computer science and engineering comes into all of this by providing the theory and tools necessary to computationally implement the models, and our lab is engaged in using and pushing the limits of graphics processing unit (GPU) computing in systems neuroscience. This talk will discuss some of the challenges associated with these goals, and provide an update on the development of our methods and scientific progress to date.

March 10
Viviana Gradinaru, Research Associate, CNC Center, Stanford University
"Bioengineering tools for mapping and mending dysfunctional brain circuits"
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How is the brain wired and how does the wiring contribute to its function, in health and in disease? Dr. Gradinaru will present: 1) the development of potent neuronal optogenetic activators and inhibitors and promoter-free projection-based targeting of optogenes in genetically non-tractable brain circuits; 2) disease-relevant applications of optogenetics; and 3) translational directions for optogenetics. Optogenetics was successfully used to provide insight into the mechanism behind deep brain stimulation (DBS) for Parkinson's disease. Unlike electrical stimulation, optogenetic manipulations are highly cell-type specific. Combined with detailed connectivity maps, information about the roles of specific cell types in DBS mechanisms can be used to improve the parameters for electrode placement and stimulation in patients.

March 17
Lena H. Ting, Associate Professor, WH Coulter Department of Biomedical Engineering, Emory University and Georgia Institute of Technology
"Neuromechanics of muscle coordination in normal and impaired posture and locomotion"
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How do humans and animals move so elegantly through unpredictable and dynamic environments? And why does this question continue to pose such a challenge? We have a wealth of data on the action of neurons, muscles, and limbs during a wide variety of motor behaviors, yet these data are difficult to interpret, as there is no one-to-one correspondence between a desired movement goal, limb motions, or muscle activity. Using combined experimental and computational approaches, we are teasing apart the neural and biomechanical influences on muscle coordination during standing balance control and walking in animals and humans.

Our work demonstrates that variability in motor patterns both within and across subjects during balance control and walking in humans and animals can be characterized by a low-dimensional set of parameters related to abstract, task-level variables. Temporal patterns of muscle activation across the body can be characterized by a 3-parameter, delayed-feedback model on center-of-mass kinematic variables. Moreover, over a period of learning, subjects  improve their response to resemble that predicted by an optimal tradeoff between mechanical stability and energetic expenditure. Spatial patterns of muscle activation can also be characterized by a small set of muscle synergies (identified using non-negative matrix factorization) that are like motor building blocks, defining characteristic patterns of activation across multiple muscles. We demonstrate that each muscle synergy performs a task-level function, thereby providing a mechanism by which task-level motor intentions are translated into detailed, low-level muscle activation patterns. Moreover, these same muscle synergies are identified in subjects with post-stroke hemiplegia. Functional differences across subjects are related to the number of motor modules that subjects are able to independently control. Our results suggest a common modular organization of muscle coordination underlying walking in both healthy and post-stroke subjects. Our work demonstrates how both neural and biomechanical properties of the body constrain our patterns of movement, but at the same time also allow for flexibility and robustness that may lead to individual differences in how we move as well as motor deficits in neuropathologies.

March 24
Linda Watkins, Distinguished Professor of Psychology, University of Colorado at Boulder
"'Listening' and 'talking' to neurons: Clinical Implications of glial dysregulation of pain and opioid actions"
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Work over the past 15 years has challenged classical views of pain & opioid actions. Glia (microglia & astrocytes) in the central nervous system are now recognized as key players in: pain amplification, including pathological pain such as neuropathic pain; compromising the ability of opioids, such as morphine, for suppressing pain; causing chronic morphine to lose effect, contributing to opioid tolerance; driving morphine dependence/withdrawal; driving morphine reward, linked to drug craving & drug abuse; & even driving negative side effects such as respiratory depression.  Atop this, what is both fascinating & fundamentally important is that these opioid effects on glia are via the activation of a non-classical, non-stereoselective opioid receptor distinct from the receptor expressed by neurons that suppresses pain. This implies that the effects of opioids on glia & neurons should be pharmacologically separable so to lead to new drugs for the control of chronic pain & to increase the clinical efficacy of pain therapeutics.

March 31
Mark Churchland, Research Associate, Stanford University
"Conserved principles of movement generation: A dynamical systems perspective"
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Many studies, across many species, have examined the neural underpinnings of rhythmic motor behavior.  Yet for the primate, most studies involve discrete reaches, and have thus focused on how neural activity relates to quantities – direction, velocity – that naturally parameterize reaches.  Despite that focus, motor cortex responses remain poorly explained by all current hypotheses regarding what neural activity might be tuned for.  Employing novel theoretical and experimental approaches, we find that cortical responses during reaching exhibit many of the fundamental properties seen during rhythmic movement in simpler organisms.  These findings suggest that motor cortex should be thought of not as an organ for representing movement parameters, but as an engine for generating movement.  That neural engine exploits simple principles that are readily recognizable under dynamical systems theory and that persist across disparate species and varieties of movement.

April 7
Daria A. Narmoneva, Assistant Professor, Biomedical Engineering, University of Cincinnati
"Regulation of Angiogenesis by Extracellular Microenvironment"
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Vascular tissue engineering is a subset of regenerative medicine which focuses on establishing a blood supply to the regenerating tissue, essential for the tissue survival and functioning. Creating a functional microvasculature remains one of the major challenges in regenerative medicine. The difficulties arise mainly from the complexity of the local cell-cell and cell-matrix signaling involved in the process of capillary formation (angiogenesis), which is not well understood. The underlying premise of our work is that angiogenesis by microvascular endothelial cells can be controlled through the manipulation of the extracellular environment, including scaffold material, endothelial cell interactions with other vascular cells and with the external factors, including electromagnetic fields. We have developed a comprehensive approach which utilizes self-assembling peptide nanofiber technology to activate and regulate angiogenic responses of endothelial cells. This approach has been applied to study the mechanisms for angiogenic signaling in vitro, and to develop a new treatment strategy for chronic diabetic ulcers in the mouse model in vivo, where rapid neovascularization is the key factor for improving healing outcome. This talk will discuss how these results advance our mechanistic understanding of fundamental biological responses of endothelial cells to extracellular signals and foster enabling technology for angiogenic therapies for tissue regeneration.