Carolyn A. Larabell

Divisions

Molecular Biophysics and Integrated Bioimaging

• Cellular and Tissue Imaging

Research Interests

Carolyn Larabell is the Director of the National Center for X-ray Tomography, which develops novel imaging technologies for biological and biomedical research. In particular, NCXT staff and collaborators are spearheading the development of soft x-ray tomography as a new tool for visualizing cells. A major part of this development has been the design, construction and now operation of XM-2, the world’s first soft x-ray microscope for life science research. Located at the Advanced Light Source of Lawrence Berkeley National Laboratory, the microscope is fully operational and in high demand.

NCXT staff are also developing new light-based methods for imaging cells, for example high-numerical aperture cryo-light microscopy. This new modality allows cryopreserved cells to be sequentially imaged with light (fluorescence) and then X-rays. The latter visualizes the detailed, 3-dimensional sub-cellular architecture, whereas light-based imaging provides information on the positions of fluorescent-tagged molecules within the cell. These two pieces of data can be overlaid to form a single, information rich 3D image of a cell. This technique is now producing powerful insights into cell structure and the local environment of the fluorescent-labeled molecule. This information can be integrated with molecular biology, genetics and computer modeling to greatly increase our understanding of cell biology.

Programs & Initiatives

• National Center for X-ray Tomography
  

Divisions

Molecular Biophysics and Integrated Bioimaging

• Cellular and Tissue Imaging

Divisions

DOE Joint Genome Institute

• Genomic Technologies

Secondary Affiliation:

Environmental Genomics and Systems Biology

• Comparative and Functional Genomics

Divisions

Molecular Biophysics and Integrated Bioimaging

• Structural Biology

Research Interests

The long-term goal of our research is to understand the structural and dynamic information encoded in the linear sequence of amino acids. Proteins undergo an incredible transformation from one-dimensional sequence information into complex three-dimensional shapes that carry out intricate cellular functions. We still, however, don’t have enough biophysical knowledge to translate this sequence information into functional insights. For instance, many proteins share the same native structure yet their cellular dynamics and function, in other words their energy landscapes, are different. Our laboratory uses a combination of biophysical, structural and computational techniques to understand these features.

In addition to the native conformation, a protein sequence populates small fluctuations around the native state, partially unfolded forms and even the globally unfolded conformation. Such non-native states on the energy landscape are thought to play a determining function in many cellular processes such as translocation, protein synthesis, degradation, signaling and allostery. They are also prone to aggregation, a phenomena which has been implicated for many diseases (the so-called misfolding and amyloid diseases). Understanding the sequence determinants of the energy landscape is therefore fundamental to the biological process that proteins carry out as well as protein folding itself.

Divisions

Molecular Biophysics and Integrated Bioimaging

• Cellular and Tissue Imaging

Research Interests

The Marriott Lab operates at the interface of chemistry, biology, medicine and engineering, is focused on understanding the molecular regulation of cellular processes and function, and improving human health. Active research projects underway in my group include establishing new principles and techniques for high-contrast imaging and optical manipulation of specific proteins in living cells and tissue, developing new smart biomaterials that mimic the extracellular organisms. The ultimate goal of these studies is to understand the molecular regulation of specific processes within living systems over multiple scales of biological organization, space and time, and to use this knowledge to develop drugs and therapies to improve human health.

Divisions

Molecular Biophysics and Integrated Bioimaging

• Cellular and Tissue Imaging

Research Interests

Cynthia McMurray studies the biological progression of neurodegenerative diseases, such as Huntington Disease and Alzheimer Disease, by investigating changes in brain metabolism, DNA damage, and other cellular indicators.

Divisions

Molecular Biophysics and Integrated Bioimaging

• Structural Biology

Research Interests

I have a broad background in ion channel structural biology and functional characterization. My interest in the physical chemistry of biological phenomena began with my undergraduate study in biophysics and biochemistry at the University of Pennsylvania. As a graduate student in the Department of Chemistry at MIT with Prof. Peter S. Kim, I focused on understanding the basic principles of protein folding and molecular interactions. While at MIT, I developed a keen interest in the proteins involved in electrical signaling. To pursue this interest, I worked as a postdoctoral fellow with Dr. Nigel Unwin at the LMB Cambridge and with Prof. Lily Y. Jan at UCSF where I was able to apply my background in structural biology to specific questions regarding ion channel structure and regulation. As a PI, I have focused my laboratory’s efforts on structural and mechanistic understanding of ion channels and in the development of new pharmacological tools for orphaned channel classes. My lab is pursing a research program that combines structural biology, ion channel functional studies, and chemical biology approaches to develop new channel pharmacologies. I am a Professor of Biochemistry and Biophysics and Cellular and Molecular Pharmacology, an Investigator in the Cardiovascular Research Institute at UCSF, and a Faculty Scientist at LBNL. My laboratory has made many contributions to the structural understanding of the function of various classes of ion channels and development of new channel modulators using a multidisciplinary approach employing genetic selections, biophysical approaches, chemical biology, and X-ray crystallography.

Divisions

Biological Systems and Engineering

• Biodesign

Secondary Affiliation:

Environmental Genomics and Systems Biology

• Molecular EcoSystems Biology

Biography

Aindrila Mukhopadhyay received an MSc in chemistry from the Indian Institute of Technology, Bombay, and has a PhD in organic chemistry from the University of Chicago.  She is a senior scientist and a principal investigator in the Ecosystems and Networks Integrated with Genes Molecular Assemblies (ENIGMA) (https://enigma.lbl.gov) Scientific Focus Area. Mukhopadhyay leads a multidisciplinary team to study stress response in bacteria using microbiological, biochemical, and systems biology tools. Additionally, she is the Vice President of the Fuels Synthesis Division and the Director of the Host Engineering group at the Joint BioEnergy Institute.
Her group develops tools of engineering E. coli and S. cerevisiae strains, and specifically focuses on developing robust strains that show high tolerance and productivity during biofuels and chemicals production.

Research Interests

Dr. Mukhopadhyay’s work is focused on understanding membrane transport, signaling, stress response and tolerance phenotypes in microbial systems. She studies both engineered and environmental microbes. She utilizes a wide variety of microbiological, biochemical and systems biology tools to examine environmentally important organisms such as sulfate and metal reducing bacteria as well as cyanobacteria. She has specific interest in signaling mechanisms in novel non-model organisms like Pseudomonas stuzeri, Desulfovibrio vulgaris and Microcoleus vaginatus and has conducted detailed studies in model organisms such as Agrobacterium tumefaciens. She develops tools, and uses host engineering and protein engineering strategies, to improve the production of fuel and chemicals production, and conduct bioremediation, using model microbes such as Escherichia coli, Corynebacterium glutamicum and Saccharomyces cerevisiae.

Divisions

Molecular Biophysics and Integrated Bioimaging

• Bioenergetics

Research Interests

My long-term research goals are to understand how photosynthetic energy conversion works, how it is regulated, and how it might be improved to help meet the world’s needs for food and fuel. We use a wide array of experimental organisms and interdisciplinary approaches to investigate fundamental questions about assembly, regulation, and dynamics of photosynthesis. Current lab members study the biosynthesis and function of photosynthetic pigments, assembly and repair of photosynthetic reaction centers, structure and dynamics of the photosynthetic membrane, mechanisms involved in sensing excess light, singlet oxygen signaling, transcriptional regulation of photosynthesis and photoprotection by light and carbon, and regulation of photosynthetic light harvesting in saturating light. By comparing how photosynthesis works in diverse organisms, we hope to uncover general design principles of natural photosynthesis as well as unique adaptations to different environments.

Divisions

Environmental Genomics and Systems Biology

• Molecular EcoSystems Biology

Secondary Affiliation:

DOE Joint Genome Institute

Biography

Metabolomics Program Lead
Deputy Division Director, Environmental Genomics and Systems Biology
Senior Scientist, Berkeley Lab

Education
B.S. in Chemical Engineering, University of California Santa Barbara;
Ph.D. in Chemistry and Biochemistry, Arizona State University;
Post-doc in Metabolomics, The Scripps Research Institute;
Executive Education, UC Berkeley Haas School of Business;
DOE Oppenheimer Science and Energy Leadership

Summary
Dr. Trent Northen is currently a Senior Staff Scientist at Berkeley Lab. Since joining Berkeley lab in 2008 Dr. Northen has had leadership roles within large DOE funded research programs using mass spectrometry for energy and environmental research including through the Joint BioEnergy Institute and the ENIGMA SFA project. In 2015, he founded what is now the JGI Metabolomics Program to provide advanced metabolomic methods available to JGI users. Dr. Northen’s research is focused on using metabolomics to link genomes with environments to understand how webs of microbes cycle carbon and sustain biomes via the development and application of advanced mass spectrometry approaches and model laboratory ecosystems (EcoFABs).

Recent Awards and Service
2019 R&D100 Award, 2016 Berkeley Lab Director Exceptional Achievement Award, 2014 DOE Early Career Award, 2013 R&D100 award, 2009 Presidential Award for Science and Engineering PECASE awarded by President Obama, A JBEI Excellence Award, multiple LBNL SPOT Awards, and two NIH SPORE Career Development Awards. Dr. Northen currently serves as the Deputy Director of the Environmental Genomics and Systems Biology at Lawrence Berkeley National Laboratory, he was the interim Division Director within this same organization during the formation of the Division in 2015-2016. Dr. Northen regularly chairs workshops, organizes conference sessions, and serves on review panels. At Berkeley Lab he serves on a number of committees and is the Strategy Mentor for the Berkeley Lab Biosciences Environmental Strategy.

Research Interests

Please see our lab’s website for more detail on our research.

Summary: The combined impact of changing climate, population growth, environmental contamination, and soil degradation represent one of the greatest challenges facing humanity. Harnessing microbes will be a cornerstone of future sustainable agricultural and land management practices. Our laboratory uses mass spectrometry and fabricated ecosystem approaches to study the dynamic and reciprocal processes by which microbes interact to transform the organic molecules within their environment. Through the use of exometabolite profiling, we predict microbial metabolic webs in soils, sediment, and the rhizosphere for testing in fabricated ecosystems (EcoFABs) through the use of synthetic communities. Together these studies are providing insights into how microbes can be used to restore soil carbon, promote plant growth, and remove environmental contaminants.

Programs & Initiatives

• ENIGMA
  
• Joint BioEnergy Institute
  
• m-CAFEs
  
• EcoFABs
  
• TEAMS
  

Divisions

DOE Joint Genome Institute

• Science Programs

Secondary Affiliation:

Environmental Genomics and Systems Biology

• Comparative and Functional Genomics

Divisions

Environmental Genomics and Systems Biology

• Comparative and Functional Genomics