Amy E. Herr

Divisions

Biological Systems and Engineering

• Process Engineering & Analytics

Secondary Affiliation:

Molecular Biophysics and Integrated Bioimaging

Biography

Amy E. Herr is the Lester John & Lynne Dewar Lloyd Distinguished Professor of Bioengineering at the University of California, Berkeley and a Chan Zuckerberg (CZ) Biohub Investigator. Prof. Herr joined UC Berkeley as Assistant Professor of Bioengineering in 2007, was promoted to Associate Professor with tenure in 2012, and promoted to Full Professor in 2015. Prior to joining UC Berkeley, she was a staff member in the Biosystems Research Group at Sandia National Laboratories (Livermore, CA; 2002-2007). She earned her PhD in Mechanical Engineering at Stanford with Profs. Tom Kenny & Juan Santiago as an NSF Graduate Research Fellow, an MS in Mechanical Engineering also from Stanford, and a BS in Engineering & Applied Science from Caltech.

Professor Herr is an elected Fellow of the National Academy of Inventors and the American Institute of Medical and Biological Engineering (AIMBE), a Board Member of the Chemical & Biological Microsystems Society (CBMS) which oversees the microTAS conferences, is a standing member of the NIH Nanotechnology Study Section, and is an Advisory Board Member for the UCSF Rosenman Institute and the journals Analytical Chemistry and ACS Sensors. She has served as a Co-Director of the Cold Spring Harbor Laboratory’s Single Cell Analysis summer course (2015 & 2016), both Chair (2009) and Vice-chair (2007) of the Gordon Research Conference (GRC) on the Physics & Chemistry of Microfluidics. She is faculty advisor to the UC Berkeley chapter of the Society of Women Engineers (SWE) and the Graduate Women in Engineering (GWE).

Professor Herr’s research has been recognized by: the 2016 Mid-career Achievement Award from the American Electrophoresis Society, the 2015 Georges Guiochon Faculty Fellow from HPLC, the 2012 Young Innovator Award from Analytical Chemistry/CBMS, the 2012 Ellen Weaver Award from the Association for Women in Science (AWIS, for mentoring), a 2011 NSF CAREER award, a 2010 NIH New Innovator Award, a 2010 Alfred P. Sloan Research Fellowship in chemistry, a 2010 New Investigator Award in Analytical Chemistry from Eli Lilly & Co., a 2009 Defense Advanced Research Projects Agency (DARPA) Young Faculty Award, a 2009 Hellman Family Faculty Fund Award from UC Berkeley, a 2008 Regents’ Junior Faculty Fellowship from the University of California. Professor Herr has also been recognized by the 2012 Outstanding Instructor Award in Bioengineering (Bioengineering Honor Society student vote) and a 2007 Outstanding Mentor Award from Sandia National Laboratories.

Research Interests

Scale-dependent Phenomena Underpinning Technology Development

Large-scale study of protein structure, function, and expression (proteomics) is instrumental to molecular biomarker discovery.  Due to the constantly changing nature of protein expression and state, these profiles are notoriously difficult to study.   High-resolution analytical assays such as two-dimensional electrophoresis and mass spectrometry have proven essential to proteomics; nevertheless, these information-rich methods can be slow and labor intensive.  With these considerations in mind, our group is developing  techniques, implemented via microfluidic technologies, as a means to achieve a rapid, yet still quantitative, assessment of protein expression & state variations in complex samples.

Biomarker Validation

In spite of significant advances in proteomic technology, few new protein biomarkers have emerged from the proteomic discovery pool, progressed though the scrutiny of validation studies, and become incorporated in diagnostic tools.  The long-term goal of our work is development of flexible instruments for the rapid validation of putative disease-specific biomarkers in promising diagnostic fluids. An urgent need exists for robust bioanalytical capability that delivers high-throughput validation of putative biomarkers, thus allowing subsequent incorporation of validated markers into diagnostics. To achieve this aim, our group employs nascent microfluidic technologies to seamlessly integrate complex sample preparation, sample handling, and quantitative bioanalytical assays into tools amenable to automation.

Clinical & Point-of-Care Diagnostics

Appropriate, effective biomolecular analysis mechanisms are identified for diagnostic development based upon the physicochemical characteristics of putative, disease-specific biomarkers. Most disease states are complex — diagnosis & monitoring require more than simple binary detection of a small set of proteins. To compound the difficulty in assessing disease state, analytical grade quantitation and specificity are difficult to achieve as part of a disease diagnostic, especially diagnostics employed in near-patient environments.   Consequently, our group is exploring the use of electrophoretic microfluidic formats, as such formats have been demonstrated to allow rapid, analytical-grade quantitation of small sample volumes through enhanced resolving power and high-efficiency operation.

Divisions

Molecular Biophysics and Integrated Bioimaging

• Structural Biology

Research Interests

The Holmes Lab brings techniques from machine learning, statistical linguistics, phylogenetics, and web development to bear on the interpretation and analysis of genomic data. Examples include the application of context-free grammars to understanding DNA and RNA structure; the use of phylogenetic methods in genome annotation, and to detect recombination breakpoints; the development of machine learning algorithms for bioinformatics models; the reconstruction of insertion, deletion and transposition events in genome evolutionary histories; statistical algorithms for metagenomics species distribution analysis; and dynamic-HTML web applications for collaborative genomic data analysis.

Divisions

Molecular Biophysics and Integrated Bioimaging

• Structural Biology

Biography

Dr. Holton is currently an Associate Adjunct Professor at the University of California San Francisco with a Faculty Associate appointment at Lawrence Berkeley National Laboratory, where he serves as the Director for the Macromolecular Crystallography (MX) X-ray Diffraction Beamline 8.3.1 at the Advanced Light Source. He is an expert in optimizing sample preparation and diffraction techniques with particular focus on radiation damage, detector performance and x-ray scattering physics. He has written several absolute-scale simulators for both “conventional” MX and femtosecond nanocrystallography that have been instrumental in designing these experiments.

Dr. Holton earned a B.S., in Biology from the California Institute of Technology and his Ph.D., in Molecular and Cell Biology from the University of California at Berkeley.

Divisions

Molecular Biophysics and Integrated Bioimaging

• Structural Biology

Research Interests

Mechanisms of biological macromolecules inspire nanoscale engineering strategies and provide insights into disease.

The speed of genomic sequencing has rapidly increased; opening up 3 billion years of evolutionary engineering, new disease treatment opportunities and providing a perspective on the complex networks involved in most biological processes. Enabled by high throughput approaches, rather than focusing on a single system or pathway I study multiple pathways and processes. I work with the view that in cellular networks there are only a few degrees of separation between the actions of any two molecules. Of particular interest are hub proteins which, through multiple interactions or adopting specific conformations, signal alternate cellular outcomes. By developing an intuition in diverse bio-macromolecular systems I also work on engineering macromolecules for new functions.

Building intuition on the large networks and multi-level feedback loops in cellular systems requires many measurements which current capabilities cannot deliver.

An understanding of mechanism has fallen behind the rate at which new molecules of interest are being identified. I utilize and develop high throughput solution based techniques to characterize the conformations biomolecules adopt in the many contexts they encounter. A primary technique has been small angle X-ray scattering or SAXS. X-rays provide access to high resolution. New light sources provide exponentially increasing power. The two aspects combined provide insights into conformations of a macromolecule in high throughput. I also develop approaches to combine crystallographic results with SAXS. Crystallography is low throughput but provides un-paralleled resolution. SAXS provides access to conformational changes in high throughput.

Divisions

Molecular Biophysics and Integrated Bioimaging

• Cellular and Tissue Imaging

Research Interests

Our lab’s research is focused in four intersecting and complementary areas: mechanisms of ion channel function, synapse development and plasticity, neural circuit function, and the design of novel probes for the optical detection of neuronal signaling.

Developing Tools to Study Neurons
Elucidating structural and functional connectivity between neurons is one of today’s greatest challenges of systems neuroscience. We have developed a family of genetically-encoded photoactivatable calcium sensors that allow us to simultaneously visualize the morphology and activity of individual neurons, including fine structures such as dendritic spines.

Divisions

DOE Joint Genome Institute

• Science Programs

Secondary Affiliation:

Environmental Genomics and Systems Biology

• Comparative and Functional Genomics

Divisions

Biological Systems and Engineering

• BioEngineering & BioMedical Sciences

Biography

Gary started his scientific career in 1978 as a research technician in the Schubiger lab at the University of Washington, where he worked on imaginal disc formation in Drosophila. He obtained his PhD in the lab of Charles Laird at the University of Washington, where he worked on the role of nucleolus organization in rDNA function. He finished his PhD in Genetics in 1987 and continued to work with Drosophila during his postdoc in the lab of Allan Spradling at the Carnegie Institute.

His work in the Spradling lab spurred his interest in heterochromatin formation and 4 years later he started his own lab at The Salk Institute, La Jolla in 1991. After being in San Diego for 12 years, during which he obtained his professorship at The Salk Institute for Biological Studies, Gary and his lab moved to the Lawrence Berkeley National Lab (LBNL) in 2003. Gary has been an adjunct professor at UC Berkeley since 2003 and became director of the LBNL Life Sciences Division in 2011.

The Karpen lab has a long-standing interest in chromatin structure and function, with a special emphasis on heterochromatic DNA regions. The current projects in the lab range from centromere formation and function, to the role of lncRNAs, ageing, and DNA repair in heterochromatin formation and maintenance.

Research Interests

Our studies are focused on understanding inheritance, chromatin structure, gene expression, and the organization of chromosomes in the nucleus. Most of our studies have focused on the fruit fly Drosophila melanogaster as a model for chromosome function in metazoans, which allows us to address mechanisms in animals by synergistically combining molecular, genetic, cell biological and biochemical approaches. Additionally, we have examined the relevance of our findings to human chromosomes, and have demonstrated surprising similarities between these evolutionarily-distant species.

Divisions

Molecular Biophysics and Integrated Bioimaging

• Bioenergetics

Research Interests

The Katz group applies emerging principles of supramolecular chemistry on solid surfaces towards the synthesis of functional advanced materials, involving catalysis and adsorption. We lead in the synthesis of organic-inorganic active sites, which are at the state-of-the-art in structural control. Our modular and generalizable engineering approach aims to roughly mimic principles of active site connectivity found in biological catalysts.

This approach leads to the highly refined design of heterogeneous catalysts, which function with an activity and selectivity that cannot be achieved using conventional approaches.

The group has most recently invented approaches for (i) mild zeolite precursor delamination, preseving framework cystallinity for applications benefiting from crystalline supports, (ii) the hydrolysis of glycosidic bonds under the mildest (i.e. close to pH 7) pH conditions that have ever been achieved, and (iii) design and synthesis of robust metal clusters that consist of an unprecedented amount of catalytic surface. Area (i) impacts catalytic applications where zeolitic supports are beneficial over traditional amorhous ones (see Grosso-Giordano et al. JACS 2018, 140, 4956—4960). Area (ii) broadly impacts the depolymerization and pretreatment of biomass to biofuels using less harsh chemicals. Area (iii) improves on the major limitation to cluster catalysts in industry—lack of stability (see Gates et al. Nature 1994, 372, 346—348).

Divisions

Molecular Biophysics and Integrated Bioimaging

• Bioenergetics

Research Interests

My research is focused on elucidating the structure and function of metalloenzymes using a combination of X-ray methods. The main emphasis is on understanding the mechanism of light-driven water oxidation in Photosystem II, a large membrane protein present in all organisms that conduct oxygenic photosynthesis. For this purpose, we use very intense femtosecond X-ray pulses as delivered by the X-ray free electron laser, Linac Coherent Light Source (LCLS), at Stanford. This technique allows us to record X-ray diffraction and X-ray spectroscopic data from the enzyme under working (physiological) conditions and provide information about the geometric and electronic structure of the catalytic site (a Mn₄CaO₅ cluster) of the enzyme during the water oxidation reaction. Also, we are working on generalizing these approaches to other metalloenzymes to study reaction intermediates not accessible with conventional X-ray methods.

Divisions

Biological Systems and Engineering

• BioEngineering & BioMedical Sciences

Research Interests

We have been studying a protein, SATB1, which functions as a chromatin organizer in thymocytes and activated T cells. SATB1 has a nuclear distribution resembling a cage-like structure, surrounding heterochromatin. SATB1 folds chromatin by tethering specialized genomic DNA segments, which bear an unusual physical property (base-unpairing region; BURs), to the SATB1 cage-like structure. SATB1 targets chromatin remodeling/modifying enzymes, such as HDAC1 and ISWI to BURs, and thereby regulates regional histone modification status and nucleosome positioning. Having such a function, SATB1 ablation leads to disruption of hundreds of genes, resulting in an arrest in T cell development. Our laboratory is examining the function of SATB1, its homolog SATB2, and other proteins with DNA binding specificity similar to the SATB family proteins, to see if any of them has the ability to reorganize chromatin as ES cells commit to specific cell lineages. We are interested in determining which sets of genes are targeted, how chromatin is functionally organized via looping, and how chromatin structure is marked by epigenetic modification during ES cell differentiation into the neuronal and T cell lineages.

Divisions

Biological Systems and Engineering

• BioEngineering & BioMedical Sciences

Divisions

Biological Systems and Engineering

• BioEngineering & BioMedical Sciences

Biography

Sanjay Kumar, M.D., Ph.D., was appointed Assistant Professor of Bioengineering at UC Berkeley in 2005, promoted to Associate Professor with tenure in 2011, and promoted to Full Professor in 2014. He is also Professor of Chemical and Biomolecular Engineering at UC Berkeley and a Faculty Scientist in the Biological Systems & Engineering Division of Lawrence Berkeley National Laboratory.  Dr. Kumar is an elected Fellow of AIMBE and BMES. He and his research group have been fortunate to receive a number of honors, including the Presidential Early Career Award for Scientists and Engineers (PECASE), The NIH Director’s New Innovator Award, The Arnold and Mabel Beckman Young Investigator Award, the NSF CAREER Award, and the Stem Cells Young Investigator Award. Dr. Kumar has also received awards by student vote for Excellence in Graduate Advising (UCSF/UC Berkeley Joint Graduate Group in Bioengineering) and Outstanding Teaching (Bioengineering Honor Society) and has served as a Presidential Chair Teaching Fellow.  Work in his laboratory has been sponsored by grants and fellowships from NIH, NSF, DOD, AHA, CRCC, LBNL, CIRM, The Beckman Foundation, the Keck Foundation, the Siebel Scholars Program, the DOE Molecular Foundry and the University of California.

Dr. Kumar earned a B.S. in chemical engineering (1996) from the University of Minnesota, where he studied lipid self-assembly in the laboratory of Matt Tirrell. He then moved on to Johns Hopkins University, where he earned an M.D. (2003) and a Ph.D. in molecular biophysics (2003) as a fellow of the NIH Medical Scientist Training Program. During the graduate portion of his training, he investigated the structure and energetics of neuronal intermediate filaments in the laboratories of Jan Hoh of the School of Medicine and Mike Paulaitis of the Department of Chemical Engineering. From 2003-2005, he served as an NIH research fellow with Don Ingber at Children’s Hospital Boston and Harvard Medical School, where he examined the nanoscale mechanics and dynamics of cytoskeletal structures in living cells and developed nanomagnetic technologies to control receptor-mediated signaling.

Research Interests

Our research team seeks to understand and control biophysical communication between cells and their surroundings. In addition to investigating fundamental aspects of this problem, we are especially interested in understanding the role played by cellular mechanobiological signaling in tumor and stem cell biology in the central nervous system.