Krishna K. Niyogi

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

Divisions

Environmental Genomics and Systems Biology

• Comparative and Functional Genomics

Research Interests

The Ryan lab studies mechanisms that regulate protein activity in bacteria. We have focused on the Gram-negative aquatic bacterium Caulobacter crescentus because it has a complex life cycle that is driven in large part by changes in the phosphorylation, proteolysis, localization, and interactions of proteins.

C. crescentus undergoes a developmental step during its division cycle from a motile cell unable to replicate its DNA to a nonmotile cell that is competent for chromosome replication. We use synchronized populations of motile G1-phase cells to study the events that occur during development. C. crescentus also divides asymmetrically, producing one motile and one nonmotile cell at each division. Proteins in the predivisional cell are segregated to opposite ends to mediate the differentiation of identity after division. We study the locations and movements of individual proteins using fluorescence microscopy.

Specific problems that we are investigating include the following: regulated degradation of a key transcription factor during the motile-sessile developmental step; the roles, locations, and interactions of enzymes that participate in cell wall biosynthesis; and the regulatory functions of protein phosphorylation on serine, threonine, or tyrosine residues.

Divisions

Biological Systems and Engineering

• Biodesign

Biography

In addition to directing the Biological Systems & Engineering Division, Blake Simmons serves as the Chief Scientific and Technology Officer and Vice President of the Deconstruction Division at the Joint BioEnergy Institute in Emeryville. After earning his BS in chemical engineering from the University of Washington, Simmons continued his studies at Tulane University and received his doctorate in the same field. For the past 15 years, Simmons has been part of the Senior Management team at Sandia National Laboratories, most recently serving as the Senior Manager of Advanced Biomanufacturing, Biomass Program Manager, as well as Adjunct Professor at the University of Queensland. His expertise includes biofuels, renewable chemicals, biomanufacturing, abiotic-biotic interfaces, biomass pretreatment, enzyme engineering, biofuel cells, templated nanomaterials, microfluidics, desalination, and biomineralization.

Research Interests

Bioenergy
A significant focus in my research program at the Joint BioEnergy Institute is the development of new scientific insights and novel technologies for biomass deconstruction, the process of breaking down and fractionating lignocellulos into targeted intermediates through the use of ionic liquids. This includes the development of microbes and enzymes that can tolerate and operate efficiently in the presence of these ionic liquids, and the advent of consolidated conversion operations in order to produce a scalable, sustainable, and affordable technology suitable for deployment in a biorefinery.

Biotechnology and Biomanufacturing
While the 21st century will undoubtedly be recognized for advances in the biological and life sciences, another important element in magnifying the positive impacts of these advances is to enable the US bioeconomy, especially in the realms of developing advanced biomanufacturing technologies to replace and displace current manufacturing techniques that are energy intensive and have a negative effect on the environment. My goal is to mature the science of biotechnology and synthetic biology into a BioFoundry, and to identify opportunities where biomanufacturing can have a positive impact on cost and sustainability profiles relative to conventional manufacturing approaches.

Nanotechnology and Nanostructured Materials
Another significant research interest is the development of templated nanomaterials that provide a superior performance attributes relative to bulk materials. I have worked with surfactant-based approaches for the production of tailored nanostructures with unique properties as semiconductors, photocatalysts, catalysts, and energy storage materials.

Selected publications

1. Sun, N., Xu, F., Sathitsuksanoh, N., Thompson, V.S., Cafferty, K., Li, C., Tanjore, D., Narani, A., Pray, T.R., Simmons, B.A., Singh, S. 2015. Blending municipal solid waste with corn stover for sugar production using ionic liquid process. Bioresour Technol, 186(0), 200-206.
2.  Cheng, G., Zhang, X., Simmons, B., Singh, S. 2015. Theory, practice and prospects of X-ray and neutron scattering for lignocellulosic biomass characterization: towards understanding biomass pretreatment. Energy Environ. Sci., 8(2), 436-455.
3. Papa, G., Rodriguez, S., George, A., Schievano, A., Orzi, V., Sale, K.L., Singh, S., Adani, F., Simmons, B.A. 2015. Comparison of different pretreatments for the production of bioethanol and biomethane from corn stover and switchgrass. Bioresour Technol, 183C(0), 101-110.
4. Socha, A.M., Parthasarathi, R., Shi, J., Pattathil, S., Whyte, D., Bergeron, M., George, A., Tran, K., Stavila, V., Venkatachalam, S., Hahn, M.G., Simmons, B.A., Singh, S. 2014. Efficient biomass pretreatment using ionic liquids derived from lignin and hemicellulose. Proc Natl Acad Sci U S A, 111(35), E3587-95.
5. Eudes, A., Sathitsuksanoh, N., Baidoo, E.E., George, A., Liang, Y., Yang, F., Singh, S., Keasling, J.D., Simmons, B.A., Loque, D. 2015. Expression of a bacterial 3-dehydroshikimate dehydratase reduces lignin content and improves biomass saccharification efficiency. Plant Biotechnol J.
6. Uppugundla, N., da Costa Sousa, L., Chundawat, S.P., Yu, X., Simmons, B., Singh, S., Gao, X., Kumar, R., Wyman, C.E., Dale, B.E., Balan, V. 2014. A comparative study of ethanol production using dilute acid, ionic liquid and AFEX pretreated corn stover. Biotechnol Biofuels, 7(1), 72.
7. Sun, N., Parthasarathi, R., Socha, A.M., Shi, J., Zhang, S., Stavila, V., Sale, K.L., Simmons, B.A., Singh, S. 2014. Understanding pretreatment efficacy of four cholinium and imidazolium ionic liquids by chemistry and computation. Green Chemistry, 16(5), 2546-2557.
8. Sathitsuksanoh, N., Holtman, K.M., Yelle, D.J., Morgan, T., Stavila, V., Pelton, J., Blanch, H., Simmons, B.A., George, A. 2014. Lignin fate and characterization during ionic liquid biomass pretreatment for renewable chemicals and fuels production. Green Chemistry, 16(3), 1236-1247.
9. Ruegg, T.L., Kim, E.M., Simmons, B.A., Keasling, J.D., Singer, S.W., Soon Lee, T., Thelen, M.P. 2014. An auto-inducible mechanism for ionic liquid resistance in microbial biofuel production. Nat Commun, 5, 3490.
10. Oleskowicz-Popiel, P., Klein-Marcuschamer, D., Simmons, B.A., Blanch, H.W. 2014. Lignocellulosic ethanol production without enzymes–technoeconomic analysis of ionic liquid pretreatment followed by acidolysis. Bioresour Technol, 158, 294-9.

Programs & Initiatives

• Joint BioEnergy Institute
  

Divisions

Biological Systems and Engineering

• Biodesign

Divisions

Biological Systems and Engineering

• BioEngineering & BioMedical Sciences

Biography

Antoine Snijders is the Division Leader of the Biosciences and Biotechnology (BBTD) Division in the Physical and Life Sciences Directorate. Antoine holds a Ph.D. in Cancer and Molecular Biology from Utrecht University and an M.S. in Biomedical Sciences from VU University Amsterdam (both in the Netherlands). After appointments as a Postgraduate Researcher and Postdoctoral Scholar at the Cancer Research Institute at the University of California, San Francisco, Antoine joined Lawrence Berkeley National Lab where he served as the Head of the Bioengineering and Biomedical Sciences Department. Antoine’s research focused on understanding the complex interactions among genetic background, environmental exposures, and the microbiome in determining disease risk.

Research Interests

My research goals are to understand cancer tumorigenesis specifically addressing key questions concerning the contribution of host genetics, environmental exposures and their interactions in cancer risk and tumor progression. My laboratory uses a systems biology approach, together with novel mouse models to identify genetic networks controlling susceptibility to cancer risk.

Precision medicine is an emerging approach for disease treatment and prevention that takes into account individual variability in environment, lifestyle and genes for each person. Genetic susceptibility is a major component that contributes to the variability in disease susceptibility. Thus, identifying the genes involved in susceptibility to cancer may have potential utility in developing novel personalized medicines, lead to greater understanding of the biological pathways involved in cancer development, and elucidate how environmental factors exert their effects in combination with genetic variants. 

The broad and long-term goals of my laboratory are to identify how the interactions of combinations of genes and their functional polymorphisms and environmental exposures (including for example thirdhand smoke) contribute to disease susceptibility of individual human subjects. Major problems in assessing human cancer risk are that humans are genetically heterogeneous and exposures are pervasive and difficult to quantitate. Parallel exposures to multiple chemicals and lifestyle factors that can negatively impact health further confound efforts to assess risk.

Population-based mouse models offer many advantages for the study of the genetic basis of complex traits, including cancer, because of our ability to control both the genetic and environmental components of risk. My lab exploits the power of mouse genetics using Collaborative Cross (CC) mice, together with OMICS analyses to determine the influence of individual variations in disease susceptibility. This comprehensive systems biology approach will likely identify specific genes or pathways that are differentially controlled between mouse strains, and contribute to human variation in susceptibility to environment factor-induced carcinogenesis.

To learn more about thirdhand smoke, visit the Thirdhand Smoke Resource Center (www.thirdhandsmoke.org).

Divisions

Molecular Biophysics and Integrated Bioimaging

• Structural Biology

Biography

Education & Training
PhD, Duke University, 1982

Research Interests

We focus on structural biology methods and applications for analysis and design projects that concern fundamental questions of molecular cell biology and biochemistry relevant to biological mechanisms and human disease.

DNA damage responses provide master keys to unlock oncogenic synthetic lethality and activate innate immunity for cancer biology and medicine going forward. Our research focuses on applying structural biochemistry and biophysics to molecular and cellular oncology and cancer biology for predictive molecular mechanisms and innovative strategies that target DNA damage responses in cancer. By solving and building upon >350 macromolecular structures, our group is developing and applying methods for integrating X-ray and cryo-EM data to build quantitative and foundational knowledge resulting in publications and patents aimed at advanced patient care.

Programs & Initiatives

• The SIBYLS Beamline
  

Divisions

Molecular Biophysics and Integrated Bioimaging

• Cellular and Tissue Imaging

Research Interests

My lab is interested in the general question of how signaling circuits generate complex cellular behaviors such as cell polarity, motility, growth, and differentiation. Because these processes have been difficult to understand with standard techniques, we are developing new approaches to isolate and quantitatively interrogate individual steps in the signaling cascade.  We are particularly interested in four areas:

1. Understanding the self-organizing circuits that underlie cell polarity, directed migration, and morphogenesis.

2. Developing optogenetic tools to probe the spatial and temporal logic of signal transduction cascades.

3. Investigating how mechanotransduction integrates the local and global organization of migrating cells.

4. Probing how the three-dimensional structure of the eukaryotic genome regulates gene expression.

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