BE Seminars & Events

The brain is a complex, densely wired circuit made out of heterogeneous cells, which vary in their shapes, molecular composition, and patterns of connectivity. In order to help discover how neural circuits implement brain functions, and how these computations go awry in brain disorders, we invent technologies to enable the scalable, systematic observation and control of biological structures and processes in the living brain. We have developed genetically-encoded reagents that, when expressed in specific neuron types in the nervous system, enable their electrical activities to be precisely driven or silenced in response to millisecond timescale pulses of light. I will give an overview of these “optogenetic” tools, adapted from natural photosensory and photosynthetic proteins, and discuss new tools we are developing, including molecules with novel color sensitivities and other unique capabilities. Often working in interdisciplinary collaborations, we have developed microfabricated hardware to enable complex and distributed neural circuits to be controlled and observed in a fully 3-D fashion, as well as robots that can automatically record neurons intracellularly and integratively in live brain. These tools are in widespread use to enable systematic analysis of neural circuit functions, are also opening up new frontiers on the understanding and treatment of brain disorders, and may serve as components of new platforms for diagnosing and treating brain disease.

Abstract forthcoming.

Abstract: Technology advances have driven a genomics revolution with sweeping impact on our understanding of life processes. Nevertheless, the arguably more important “proteomics revolution” remains unrealized. While microfluidic technology has advanced separations science, progress lags in the multi-stage separations that are a hallmark of proteomics. This talk will summarize new microengineering design for critical multi-stage protein assays. I will detail our tunable photopatterned materials for switchable function, microfluidic architectures for seamless integration of discrete stages, and multiplexed readouts for quantitation. As specific case studies, we will discuss a spectrum of demonstrated assays from diagnostics for HIV confirmation to biomarker validation of protein isoforms to single-cell Western blotting for stem cell differentiation studies. Performance and operational gains will be discussed, including quantitation capability, total assay automation, integration of sample preparation, and workflows that require minutes not days. Ultimately, we aim to infuse engineering advances into the biological and biomedical sciences.

Bio: Amy E. Herr received her BS degree from Caltech and her MS (1999) and PhD (2002) degrees from Stanford in Mechanical Engineering. From 2002-2007, Dr. Herr was a Biosystems Research staff member at Sandia National Laboratories (Livermore). At UC Berkeley since 2007, Prof. Herr’s research focuses on instrumentation innovation to advance quantitation in life sciences and clinical problems – impact spans from tools for fundamental research (cell signaling) to near-patient disease diagnostics. Her major awards include: the 2012 Young Innovator Award from Analytical Chemistry and the Chemical & Biological Microsystems Society, the 2012 Ellen Weaver Award from the Association for Women in Science (AWIS), a 2012 Bakar Fellowship at UC Berkeley, a 2011 NSF CAREER Award, the 2011 Eli Lilly & Co. New Investigator Award in analytical chemistry, a 2010 NIH New Innovator Award, a 2010 Alfred P. Sloan Research Fellowship (chemistry), a 2009 DARPA Young Faculty Award, the 2009 Hellman Family Faculty Fund Award from UC Berkeley, and the 2008 Regents’ Junior Faculty Fellowship from UC. She Chaired (2009) & Vice-chaired (2007) the Gordon Research Conference (GRC) on the Physics & Chemistry of Microfluidics, has served on the technical program committee for several international conferences and is on the Editorial Board of the peer-reviewed international journal Electrophoresis.

Environmental cues regulate many biological processes, controlling pathways used by cells to respond to changing conditions. Such regulation is often initiated by sensory protein domains that use internally-bound ligands to convert environmentally-triggered changes into altered protein/protein interactions. Several families of these domains have evolved with remarkable diversity in the stimuli they sense and outputs that they control. Using a combination of biophysics, biochemistry and synthetic chemistry, we seek insight into the fundamental protein structure/function principles of such environmental-sensing domains.

Here I will discuss examples of our work from one such regulatory domain family: the Per-ARNT-Sim (PAS) domains, found in thousands of proteins throughout biology. I will present results from studies of PAS domains that respond to radically different stimuli – ranging from blue light illumination to the presence of metabolites – showing how these share a common transduction mechanism as revealed by solution NMR, X-ray crystallography and other biophysical and biochemical approaches. I will further discuss how we have taken advantage of this mechanistic understanding to search for artificial PAS-binding ligands using NMR-oriented fragment-based approaches and high-throughput screens. Importantly, our studies demonstrate how these natural proteins can be artificially regulated, both in vitro and in living cells. Taken together, our work provides an integrated view of a fascinating class of natural switches and suggests routes by which these can be manipulated to achieve desired therapeutic and/or technological outcomes.

I will discuss the use of microfluidic techniques for two different applications: controlling 3D microenvironments of cells and tissues, and for developing low-cost point-of-care diagnostics for use in U.S. and in developing countries.

1. A number of microfluidic techniques have been developed in our group for controlling the 3D microenvironments of cells and tissues to high resolution. These techniques are useful for studying microvascularization in a number of organ systems, and for engineering implantable devices.
2. In the second half of the talk, I will discuss the development of lab-on-a-chip devices for improving the health of people in developing countries, which presents unique and challenging design criteria. I will discuss our lab's current efforts, in conjunction with partners in industry, public health, and local governments, to develop new rapid diagnostic tests for use in sub-Saharan Africa.

Brain-computer interfaces provide a defined link between neural activity and devices, allowing a detailed study of the neural adaptive responses generating behavioral output. Our research is centered on two aspects of motor control: cerebral mechanisms of volitional arm movement and cortical control of neural prosthetics. We use electrode arrays to record action potentials from populations of individual neurons in motor cortical areas of monkeys while they perform tasks related to reaching and drawing and a variety of hand movements. A number of signal-processing and statistical analyses are performed on these data to extract movement-related information from the recorded activity. We are currently developing prostheses capable of restoring reaching, grasping and manipulation to immobilized individuals.

A better understanding neural population function would be an important advance in systems neuroscience. The change in emphasis from the single neuron to the neural ensemble has made it possible to extract high-fidelity information about movements that will occur in the near future. This ability is due to the distributed nature of information processing in the brain.

Neurons encode many parameters simultaneously, but the fidelity of encoding at the level of individual neurons is weak. However, because encoding is redundant and consistent across the population, extraction methods based on multiple neurons are capable of generating a faithful representation of intended movement. The realization that useful information is embedded in the population has spawned the current success of brain- computer interfaces. Since multiple movement parameters are encoded simultaneously in the same population of neurons, we have been gradually increasing the degrees of freedom (DOF) that a subject can control through the interface. Our early work showed that 3-dimensions could be controlled in a virtual reality task. We then demonstrated control of an anthropomorphic physical device with 4 DOF in a self-feeding task. Currently, monkeys in our laboratory are using this interface to control a very realistic, prosthetic arm with a wrist and hand to grasp objects in different locations and orientations. Our recent data show that we can extract 10-DOF to add hand shape and dexterity to our control set. This technology has now been has been extended to patients who are paralyzed and cannot move their arms or hands.

The extracellular matrix (ECM) is a complex organization of structural proteins such as collagens and proteoglycans. Understanding that the ECM is dynamic and often spatially patterned or heterogeneous over the length-scale of traditional biomaterials, we are developing instructive biomaterials that present microenvironmental cues in spatially and temporally defined manners. I will describe development of a collagen biomaterial to address critical barriers preventing regeneration of orthopedic insertions such as the osteotendinous (tendon-bone) junction. Here, replicating spatial gradients in mineral content and matrix anisotropy across a single biomaterial construct enables us to drive mesenchymal stem cell (MSC) differentiation down osteotendinous lineages in a spatially-selective manner. Further, we have created bioinspired core-shell structures (e.g., porcupine quills) in order to balance bioactivity and mechanical competence concerns. I will subsequently describe a microfluidic forming technique to create libraries of optically-translucent hydrogels containing overlapping patterns of cell, matrix, and biomolecule cues. We are using this ‘tissue biochip’ platform to dissect the coordinated impact of spatially-organized cell and matrix signals on (1) niche-mediated regulation of hematopoietic stem cell fate; and (2) the malignancy and therapeutic response of human glioblastoma multiforme cells. I will show how these biomaterial platforms can be used as rheostats to regulate critical cellular processes such as stem cell self-renewal vs. differentiation; tissue regeneration and vascularization; and the etiology and malignancy of cancer.

Living cells encounter a variety of mechanical signals encoded within their microenvironment, and these inputs can strongly regulate many fundamental cell and tissue behaviors. Here we present a set of complementary approaches we have recently created and applied to dissect and genetically manipulate this force-based signaling in living cells. First, we have used laser nanosurgery to spatially map the nanomechanical properties of actomyosin stress fibers. We have combined this approach with advanced molecular imaging tools (FRAP, FRET) to relate intracellular tensile forces to the conformational activation of mechanosensory proteins at the cell-microenvironment interface and the activities of specific myosin activators and isoforms. Second, we have used the tools of synthetic biology to precisely control the expression and activation of mechanoregulatory proteins in single cells using multiple mutually orthogonal inducer/repressor systems. This capability has enabled us to quantitatively elucidate relationships between signal activation and phenotype and to deconstruct complex signaling networks. By combining these genetic approaches with advanced culture paradigms and in vivo models, we have been able to explore how mechanobiological signals may contribute to stem cell differentiation and tumor invasion in the central nervous system. In addition to improving our understanding of force-based signaling, these approaches are allowing us to “rewire" how cells communicate with their physical microenvironment in vitro and in vivo, which we view as an important first step towards instructing cell behavior at interfaces between living and nonliving systems.

Nanotechnology has been used in cancer therapy and diagnosis for quite some time. This talk introduces various novel tools for molecular imaging and therapy of cancer based on nanoparticles. Chemotherapy (adjuvant or primary) is next to surgery one of the main stem therapies for many cancers but is inefficient due to poor bioavailability, toxicity and evolving resistance of many of the used drugs. A new approach to improve therapy of cancer is our self-reporting, environment-sensitive drug delivery system that combines novel aspects of nanotechnology with recent insights into cancer biology. We recently demonstrated that the clinically used nanoparticle Feraheme provides an excellent drug delivery system, which releases its payload upon sensing the tumor environment. This system provides better therapy efficacy compared to the same dose of free drugs in vivo and in vivo, especially for poorly soluble drugs. Importantly, Feraheme is capable of delivering several drugs simultaneously into the tumor, enabling facile combinatorial therapy. We also demonstrated that the same particle could be used for a novel way to identify sentinel lymph nodes with MRI, offering possible additional opportunities to treat tumor-ridden lymph nodes. Another entirely novel modality is provided by Cerenkov radiation, the low level of blue-light produced by particles traveling faster than the speed of a light through a diaelectric medium such as tissue. Cerenkov Luminescence Imaging (CLI) is a new, emerging modality that merges nuclear and optical imaging since it allows for optical imaging of radio-tracers used for Positron Emission Tomography (PET) and radiotherapy. It requires highly sensitive optical equipment to detect the low amount of photons emitted compared to other optical imaging modalities. However, it offers several compelling advantages. CLI utilizes clinical approved tracers, thus avoiding significant hurdles for approval of the imaging agent. It is able to image radionuclides that cannot be imaged otherwise such as [90)Y or 225[Ac]. By reverting to PET of the very same agent an internal standard is provided that allows for quantification as well as true multimodality imaging from the same imaging label. We used nanoparticles and fluorochromes to shift the light from blue to greater penetrating red light and have created the first switchable agent based on a radionuclide. Recently, clinical applications for this new entity emerged and first clinical images have been obtained, among them through an ongoing study at MSKCC to evaluate clinical Cerenkov imaging.

The external world is represented in the brain as spatiotemporal patterns of electrical activity. Sensory signals, such as light, sound, and touch, are transduced at the periphery and subsequently transformed by various stages of neural circuitry, resulting in increasingly abstract representations through the sensory pathways of the brain. It is these representations that ultimately give rise to sensory perception. Deciphering the messages conveyed in the representations is often referred to as "reading the neural code." True understanding of the neural code requires knowledge of not only the representation of the external world at one particular stage of the neural pathway, but ultimately how sensory information is communicated from the periphery to successive downstream brain structures. Our laboratory has focused on various challenges posed by this problem, some of which I will discuss. In contrast, prosthetic devices designed to augment or replace sensory function rely on the principle of artificially activating neural circuits to induce a desired perception, which we might refer to as "writing the neural code." This requires not only significant challenges in biomaterials and interfaces, but also in knowing precisely what to tell the brain to do. Our laboratory has begun some preliminary work in this direction that I will discuss. Taken together, an understanding of these complexities and others is critical for understanding how information about the outside world is acquired and communicated to downstream brain structures, in relating spatiotemporal patterns of neural activity to sensory perception, and for the development of engineered devices for replacing or augmenting sensory function lost to trauma or disease.

Using custom synthetic methods, we have prepared block copolypeptides containing a variety of both hydrophilic and hydrophobic domains. Recently we have also developed strategies to attach or incorporate biologically active functionality to these materials in a straightforward scalable process. In these copolypeptides, we have used ordered ?-helical chain conformations present in the block domains to dictate their self-assembly in aqueous solution, resulting in the formation of a variety of structures, such as micelles, membranes, and fibrils. One family of assemblies, diblock copolypeptide hydrogels (DCH) are synthetic materials whose properties can be varied by altering copolymer chain length or composition and are of potential interest for biomaterial applications. We have studied the biocompatibility of DCH in the central nervous system (CNS) of mice using light microscopy, immunohistochemistry and electron microscopy. Our findings show that DCH are injectable, form 3-dimensional deposits in vivo, are biocompatible in brain and spinal cord tissue and represent a new class of synthetic biomaterials with potential as depots or scaffolds in the CNS. Details of the design, application and optimization of DCH for biological uses will be presented.