Jan Florian Kern
Department Head, Bioenergetics
Chemist Senior Scientist
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.
Recent Publications
Related News
Biosciences FY26 LDRD Projects
The Laboratory Directed Research and Development program at Berkeley Lab produces cutting-edge research for the DOE and the nation. Read about the Biosciences Area–led projects and multi-Area collaborations with Biosciences co-investigators receiving funding this cycle.
Atomic X-ray Laser Opens Door to Attosecond Imaging
A newly discovered X-ray laser approach is fast and powerful enough to capture details about the movement of electrons.
Congratulations to Biosciences Area Director’s Award Recipients
Several Biosciences Area personnel are among the 2024 recipients of Berkeley Lab Director’s Achievement Awards. The program recognizes outstanding contributions by employees to all aspects of Lab activities.
Building: 977, Room 142E
Mail Stop: 977
Phone: (510) 486-4983
Fax: (510) 486-4545
TKohwi-Shigematsu@lbl.gov
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.
Recent Publications
Building: 977, Room 180D
Mail Stop: 977
Phone: (510) 486-6449
Fax: (510) 486-4475
A_Kronenberg@lbl.gov
Recent Publications
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.
Recent Publications
Related News
Three from Biosciences Area Named AAAS Fellows
The American Association for the Advancement of Science (AAAS), which was founded in 1848 and is the world’s largest general scientific society, announced that 489 of its members—among them nine scientists at Berkeley Lab—have been named Fellows. This lifetime honor, which follows a nomination and review process, recognizes scientists, engineers, and innovators for their distinguished achievements toward the advancement or applications of science. The three newly named Fellows from the Biosciences Area are: Sanjay Kumar, a faculty scientist in the Biological Systems and Engineering (BSE) Division; Mary Maxon, the Associate Laboratory Director for the Biosciences Area; and Len Pennacchio, a senior scientist in the Environmental Genomics and Systems Biology (EGSB) Division and the Deputy of Genomic Technologies at the DOE Joint Genome Institute (JGI).
Brown Fat Flexes its Muscle to Burn Energy—and Calories
A multidisciplinary team of bioengineers and metabolic researchers led Andreas Stahl, a professor in the Department of Nutritional Sciences & Toxicology at UC Berkeley, has figured out a new pathway that triggers brown fat to consume calories and radiate them away as heat. Sanjay Kumar, a faculty scientist in Biological Systems and Engineering (BSE) and assistant professor of bioengineering at UC Berkeley, was a co-author on the study published March 6 in Cell Metabolism. One unexpected finding was that muscle-like myosin is responsible for causing brown fat cells to stiffen in response to signals from the brain; it is this increased tension that triggers a biochemical pathway that ends with these cells burning calories for heat. “This study offers a remarkable example of how mechanical and other physical forces can influence physiology and disease in powerful, unexpected ways,” Kumar said. Understanding how brown fat is activated could unlock new ways to combat obesity. Read more from UC Berkeley News.
‘Tug of War’ Among Skin Cells Key to Development of Chicken Feathers
Sanjay Kumar, a Berkeley Lab faculty scientist in Biological Systems and Engineering (BSE), and Elena Kassianidou, a graduate student working in his lab, are co-authors on a UC Berkeley-led study published in the journal Science which for the first time linked mechanical forces acting on skin cells in a developing organism to the activation of specific genes that make the cells differentiate into more specialized types, such feathers. The researchers grew skin taken from week-old chicken eggs on artificial substrates generated by Kumar and Kassianidou to mimic the stiffness of tissues that underlie the skin in the bird. The work could pave the way to growing artificial skin for grafts that looks like normal human skin with proper spacing of hair follicles and sweat pores. Read more from the UC Berkeley News Center.
Building: 6, Room 2138
Phone: (510) 486-5890
Fax: 510-486-5664
CALarabell@lbl.gov
http://ncxt.lbl.gov/
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.
Recent Publications
Related News
Larabell Shares AAAS Outstanding Paper Prize
The American Association for the Advancement of Science (AAAS) presented the Newcomb Cleveland prize to an international team of researchers, including senior faculty scientist Carolyn Larabell. They were recognized for their Science journal article describing the discovery of a novel organelle, the nitroplast, in single-celled algae.
Scientists Discover Nitrogen-fixing Organelle
After years of work, an international team found evidence that a once-independent nitrogen-fixing microbe has become a permanent resident within algae cells.
A New Pathway for Clearing Misfolded Proteins
Stanford researchers have used cryogenic 3D imaging at the National Center for X-ray Tomography (NCXT) to identify a new pathway for clearing misfolded proteins from cells. This work presents a potential therapy target for age-related disorders like Alzheimer, Parkinson, and Huntington Diseases.
Recent Publications
Related News
Scientists Discover Nitrogen-fixing Organelle
After years of work, an international team found evidence that a once-independent nitrogen-fixing microbe has become a permanent resident within algae cells.
A New Pathway for Clearing Misfolded Proteins
Stanford researchers have used cryogenic 3D imaging at the National Center for X-ray Tomography (NCXT) to identify a new pathway for clearing misfolded proteins from cells. This work presents a potential therapy target for age-related disorders like Alzheimer, Parkinson, and Huntington Diseases.
Congratulations to Biosciences Area Director’s Award Recipients
Several Biosciences Area personnel are among the 2022 recipients of Berkeley Lab Director’s Achievement Awards. The program recognizes outstanding contributions by employees to all aspects of Lab activities.
Divisions
- Genomic Technologies
Secondary Affiliation:
Environmental Genomics and Systems Biology
- Comparative and Functional Genomics
Recent Publications
Related News
Biosciences FY25 LDRD Projects
The projects of 23 Biosciences Area scientists and engineers received funding through the FY25 Laboratory Directed Research and Development (LDRD) program.
How Plants and Mycorrhizal Fungi Cooperate
Researchers have studied both sides of plant-fungi symbiosis in one of the first cross-kingdom spatially-resolved transcriptomics studies to date.
Super-charged Stable Isotope Probing in the Fungal Hyphosphere
High-throughput stable isotope probing (SIP) proved to vastly reduce labor and improve results. Applying this method to the study of a particular fungi, researchers identified novel interactions between bacteria and the fungi.
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.
Recent Publications
Related News
Marqusee Recipient of Protein Society Award
Susan Marqusee, faculty scientist in the Molecular Biophysics and Integrated Bioimaging Division, will receive the Dorothy Crowfoot Hodgkin Award, sponsored by Genentech, which is granted in recognition of exceptional contributions in protein science that profoundly influence our understanding of biology. Marqusee, a biophysical chemist whose work focuses on protein folding and dynamics, is one of the world's top experimental scientists in the field of protein folding.
Three MBIB Scientists Named to the National Academy of Sciences
Three scientists affiliated with the Molecular Biophysics & Integrated Bioimaging Division - Robert Glaeser, Krishna Niyogi, and Susan Marqusee - were among four Lawrence Berkeley National Laboratory (Berkeley Lab)-affiliated researchers elected as members to the National Academy of Sciences (NAS) this week. The election to the NAS recognizes their distinguished and continuing achievements in original research.
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.
Recent Publications
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.
Recent Publications
Related News
Unraveling the Mysteries of DNA Damage in the Brain
A first-of-its-kind study led by Cynthia McMurray and Aris Polyzos in the Molecular Biophysics and Integrated Bioimaging (MBIB) Division integrated cell type– and brain region–specific features of DNA repair in normal brains, setting a benchmark for the field. Their results, recently published in Nature Communications, suggest that DNA damage itself serves as the checkpoint, limiting the accumulation of genomic errors in cells during natural aging.
R&D 100 Awards Are In!
Seven innovative technologies from Berkeley Lab have been honored with a 2022 R&D 100 Award, presented by R&D Magazine. Biosciences Area researchers contributed to two different products that were awarded.
Cell ‘Fingerprinting’ Could Yield Disease Diagnostic
A technology developed shows great promise for diagnosing Alzheimer disease before symptoms arise.
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.
Recent Publications
Related News
A Frog Worth Kissing: Natural Defense Against Red Tide Toxin Found in Bullfrogs
A team led by Berkeley Lab faculty biochemist Daniel Minor has discovered how a protein produced by bullfrogs binds to and inhibits the action of saxitoxin, the deadly neurotoxin made by cyanobacteria and dinoflagellates that causes paralytic shellfish poisoning. The findings, published this week in Science Advances, could lead to the first-ever antidote for the compound, which blocks nerve signaling in animal muscles, causing death by asphyxiation when consumed in sufficient quantities.
ALS-ENABLE Helps Decode a Calcium-dependent Switch
The Kv7 family of voltage-gated potassium channels control excitability in the heart, brain, and ear, and harbor mutations associated with arrhythmias, epilepsy, and deafness. A recent study, led by Molecular Biophysics and Integrated Bioimaging (MBIB) faculty scientist Daniel Minor’s group in the Cardiovascular Research Institute at UCSF, used both diffraction and scattering beamlines of ALS-ENABLE to reveal a universal switch mechanism by which the calcium sensor protein calmodulin controls the action of these channels. The findings, reported in the journal Neuron, provide a key link between Kv7 channel activity and cellular signaling pathways. Greg Hura, a research scientist in MBIB, was also a co-author on the paper. Watch a video detailing the work.
Building: 978, Room 4112
Mail Stop: 978-4121
Phone: (510) 495-2628
Fax: (510) 486-4252
AMukhopadhyay@lbl.gov
http://m-group.lbl.gov/
Links
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.
Recent Publications
Related News
AI, Automation, and Biosensors Speed the Path to Synthetic Jet Fuel
Two breakthrough strategies are rewriting the playbook for designing microbes that make synthetic aviation fuels.
Mukhopadhyay Elected American Academy of Microbiology Fellow
Aindrila Mukhopadhyay has been elected to the American Academy of Microbiology fellows in recognition of her achievements in functional genomics and systems biology.
Speeding up Biomanufacturing with a Turnkey Framework
Researchers from the Joint BioEnergy Institute (JBEI) developed a new framework that reduces the time of developing novel bioproducts. This new workflow, called Product Substrate Pairing (PSP), has already shown great promise for engineering strains that can convert common bacterial food sources into target molecules.
