Yan Liang
Research Associate Principal
Research Interests
Recent Publications
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Biosciences Staff Honored with Director’s Awards
Several Biosciences Area personnel have been named as recipients of 2016 Berkeley Lab Director's Awards. Yan Liang (Biological Systems & Engineering), Eva Nogales, and William Jagust (Molecular Biophysics & Integrated Bioimaging, MBIB) were honored with individual awards in Early Career, Scientific Achievement, and Societal Impact, respectively. Jill Fuss and Steven Yannone (MBIB) were the recipients of a team award in Technology Transfer for the launch of their company CinderBio. Jim Bristow (Biosciences Area Office, Trent Northen (Environmental Genomics & Systems Biology & Joint Genome Institute, JGI), and Susannah Tringe (JGI), along with Eoin Brodie and Peter Nico of the Earth and Environmental Sciences Area, were named in a team award in Service.
Recent Publications
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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.
Get a Move On: Protein Translates Chemistry into Motion
The protein CheY plays a role in relaying sensory signals from chemoreceptors to the rotary motor at the base of the tail-like appendage, or flagellum, that protrudes from the cell body of certain bacteria and eukaryotic cells. It has been studied as a model for dissecting the mechanism of allostery—the process by which the binding of biological macromolecules (mainly proteins) at one location regulates activity at another, often distant, functional site. When it is transiently phosphorylated in response to chemotactic cues, CheY’s binding affinity for a flagellar motor switch protein called FliM is enhanced. CheY binding to FliM changes the direction of flagellar rotation from counterclockwise to clockwise. Using X-ray footprinting with mass spectroscopy (XFMS), a team led by Shahid Khan, a senior scientist with the Molecular Biology Consortium, established that CheY changes shape when it tethers to the motor, and further parsed the contribution of phosphorylation to this shape change. The results of the XFMS experiments validated atomistic molecular dynamics (MD) predictions of the architecture of the allosteric communication network, marking the first time that XFMS has been used to validate protein dynamics simulations at single-residue resolution sampled over the complete protein.
X-ray Footprinting Reveals Secrets of ‘Metal-Breathing’ Bacterium
A team of Berkeley Lab researchers conducted X-ray footprinting mass spectrometry (XFMS) experiments at the Lab’s Advanced Light Source (ALS) to pinpoint how a protein of the bacterium Shewanella oneidensis transfers electrons to a metal oxide substrate. The research was led by Caroline Ajo-Franklin, whose lab is part of the Molecular Foundry and who holds a secondary appointment in the Molecular Biophysics and Integrated Bioimaging (MBIB) division, in collaboration with Corie Ralston, also of MBIB. Tatsuya Fukushima, a former postdoc in Ajo-Franklin’s lab, and Sayan Gupta, a member of Ralston’s lab, were co-first authors on the paper published in the Journal of the American Chemical Society. The study, which identified an unexpectedly small and weak binding site, also benefitted from expertise and tools contributed by Joint BioEnergy Institute (JBEI) and Biological Systems and Engineering (BSE) researchers Christopher Petzold and Leanne Jade Chan. Read more at the Berkeley Lab News Center.
Recent Publications
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Another Successful Year for Biotech Partners Interns at Biosciences Area
The Biosciences Area partnered once again with Biotech Partners to provide paid summer internships to high school students. This year six high school students worked side by side with Biosciences researchers across the Area’s laboratories. The mission of the non-profit Biotech Partners is to educate underserved youth in the Bay Area with personal, academic and professional development experiences that increase participation in higher education and access to fulfilling science careers.
Recent Publications
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Foundational AI Models to Accelerate Biological Discovery
Berkeley Lab is helping build AI models for autonomous research that will enable prediction and precise design of biological systems.
Get a Move On: Protein Translates Chemistry into Motion
The protein CheY plays a role in relaying sensory signals from chemoreceptors to the rotary motor at the base of the tail-like appendage, or flagellum, that protrudes from the cell body of certain bacteria and eukaryotic cells. It has been studied as a model for dissecting the mechanism of allostery—the process by which the binding of biological macromolecules (mainly proteins) at one location regulates activity at another, often distant, functional site. When it is transiently phosphorylated in response to chemotactic cues, CheY’s binding affinity for a flagellar motor switch protein called FliM is enhanced. CheY binding to FliM changes the direction of flagellar rotation from counterclockwise to clockwise. Using X-ray footprinting with mass spectroscopy (XFMS), a team led by Shahid Khan, a senior scientist with the Molecular Biology Consortium, established that CheY changes shape when it tethers to the motor, and further parsed the contribution of phosphorylation to this shape change. The results of the XFMS experiments validated atomistic molecular dynamics (MD) predictions of the architecture of the allosteric communication network, marking the first time that XFMS has been used to validate protein dynamics simulations at single-residue resolution sampled over the complete protein.
Building: 84, Room 238
Mail Stop: 84R0171
Phone: (510) 495-2300
Fax: (510) 486-4229
yzhu@lbl.gov
Links
Research Interests
• Studying genes or non-coding DNA and enhancers and their functional significance in mammalian gene regulation and diseases using targeted knock-out, knock-in or transgenic mouse models via in vivo CRISPR/Cas9 genome editing.
• Understanding the functional necessity of enhancers, noncoding sequences that activate gene expression using single-cell transcriptomics tools (DropSeq 10X Chromium Single cell and Chromium Single Cell ATAC technologies).
Recent Publications
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AI Helps Decode Gene Regulation
A combination of comprehensive experiments and machine learning is uncovering hidden complexities of gene expression during development.
Building: 978, Room 320
Mail Stop: 978-3200
Phone: (510) 495-8037
esundstrom@lbl.gov
https://abpdu.lbl.gov/
Links
Research Interests
Process development and scale-up for biomanufacturing
Bioconversion of gaseous feedstocks and products
Programs & Initiatives
Recent Publications
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ABF, ABPDU Scale up Acrylic Acid Precursor with Industrial Microbes
Researchers at the Agile BioFoundry (ABF) and the Advanced Biofuels and Bioproducts Process Development Unit (ABPDU), have successfully scaled up a bio-based process that converts ethanol into a valuable precursor for consumer products, such as paints, coatings, and diapers. The researchers worked with industry partner, Industrial Microbes, to develop the process.
Nurturing STEM Opportunities for Native Americans
A Berkeley Lab internship program aims to help increase Native American representation in graduate programs.
New ABPDU Capabilities Provide Resource for Gas Fermentation Development
Gas fermentation, a process in which microorganisms convert waste gases into commodity chemicals, has the potential to inexpensively manufacture sustainable bio-based materials and fuels to help create a circular bioeconomy.
Building: 33, Room 349
Mail Stop: 33R0345
Phone: (510) 486-5709
Fax: (510) 486-5909
osobolev@lbl.gov
https://www.phenix-online.org/
Links
Research Interests
Methods development for macromolecular crystallography and cryo-electron microscopy.
Recent Publications
Related News
Congratulations to Biosciences Area Director’s Award Recipients
Numerous Biosciences Area personnel are among the 2021 Berkeley Lab Director’s Awards honorees. This annual program recognizes outstanding contributions by employees to all facets of Lab activities. A complete list of winners can be found here. The 10th annual Director’s Awards ceremony will take place on November 18 at noon.
Revealing the Shapes of Molecular Machines
Within each cell of the human body, thousands of molecular machines are at work. They transport nutrients and biochemicals into and out of our cells, build other tiny machines, and even move our cells around. To understand how these molecular machines work, scientists create three-dimensional pictures using electron cryomicroscopy (cryo-EM), catching these machines in different shapes that give insight into their function. Now researchers at Berkeley Lab and their international collaborators who write and distribute the Phenix software suite have developed a new set of computational tools for automated structure determination from cryo-EM data.
Recent Publications
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Upgrading Plants’ Immune System with the Aid of AI
Predictive design and synthetic biology can give plants an edge in the arms race with pathogens, which may lead to new ways to protect crops.
Caught in the Actinium
Berkeley Center for Structural Biology beamline scientists contributed their expertise to a structural study of the radioactive metal actinium led by the Chemical Sciences Division's Rebecca Abergel. The team to learn how the radioactive metal binds with other elements. That information could help design better cancer treatments.
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.
Research Interests
I am interested in understanding how biosynthetic enzymes work on the molecular level, and engineering them for novel applications. My focus is on polyketide synthase and closely related fatty acid synthase enzymes, which we are reprogramming to produce new materials with improved properties.
Recent Publications
Building: 33, Room 0345
Mail Stop: M/S 33R0345
Phone: (510) 486-5709
dcliebschner@lbl.gov
http://cci.lbl.gov/people/dorothee_liebschner.html
Links
Research Interests
Macromolecular Crystallography
Neutron diffraction
Hydrogen atoms in crystallography
Teaching
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.
Congratulations to Biosciences Area Director’s Award Recipients
Numerous Biosciences Area personnel are among the 2021 Berkeley Lab Director’s Awards honorees. This annual program recognizes outstanding contributions by employees to all facets of Lab activities. A complete list of winners can be found here. The 10th annual Director’s Awards ceremony will take place on November 18 at noon.
X-rays Capture Unprecedented Images of Photosynthesis in Action
An international team of scientists is getting closer to discovering how plants split water during photosynthesis and produce nearly all of the oxygen in our atmosphere. Thanks to unprecedented, atomic-scale images of a protein complex found in plants, algae, and cyanobacteria captured by ultrafast X-ray lasers, researchers conducted atomic-level experiments to help delineate the mechanism of this system that also yields the protons and electrons used to reduce carbon dioxide to carbohydrates later in the photosynthesis cycle. The effort to uncover the secrets of this protein complex, photosystem II, was led by Vittal Yachandra and Junko Yano in the Molecular Biophysics & Integrated Bioimaging (MBIB) Division and the team's findings were published this week in Nature.
Research Interests
I work on the m-CAFEs SFA to find microbial genes that are essential for microbes collaborating with plants and how the microbiome might be edited or altered to benefit DOE relevant crops.
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.
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.
Biosciences Area FY24 LDRD Projects
The projects of 21 Biosciences Area scientists and engineers received funding through the FY24 Laboratory Directed Research and Development (LDRD) program.
Building: 91, Room 450F1
Mail Stop: 91R0183
Phone: (860) 373-1929
dwudwary@lbl.gov
http://naturalprodcast.com
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Divisions
Secondary Affiliation:
Environmental Genomics and Systems Biology
- Comparative and Functional Genomics
Research Interests
Secondary Metabolism, Bioinformatics, Microbial Genomics, Bioactive Compound Discovery
Recent Publications
Related News
A Community Resource for Secondary Metabolite Researchers
The Secondary Metabolism Collaboratory includes BGC sequence data from over 1.3 million publicly available sources.
JGI Adds Actinobacteria Chapter in the Genomic Encyclopedia of Bacteria and Archaea
Large-scale comparative analysis leads to identification of biosynthetic gene clusters for novel secondary metabolites for multiple applications
Biosciences Researchers Part of Genomic Analysis of Giant Bacteria Found in Guadeloupe Mangroves
Though visible to the naked eye, microscopy reveals unexpected complexity.
