Deepanwita Banerjee

Divisions

Biological Systems and Engineering

• BioEngineering & BioMedical Sciences

Research Interests

Deepanwita Banerjee, PhD, is currently working on computationally driven host engineering for growth-coupled production of biofuels and bioproducts using the Product Substrate Pairing (PSP) approach. She uses computational strain optimization methods and genome scale metabolic models (GSM) to predict gene targets for engineering Pseudomonas putida. She is also working towards predicting PSP strategies in P. putida for utilization of lignocellulose derived carbon sources for bioenergy and biomanufacturing applications. The goal is to test and learn to better design robust and sustainable microbial hosts that maintain desirable phenotype across industrially relevant scales and conditions.

Deepanwita Banerjee’s research interests include understanding microbial systems for desirable phenotypes using multi-omics integrated systems biology approach. The applications are diverse ranging from improving production of value-added products or assessing microenvironments for a redox imbalance in vivo. She is also interested in understanding the emergent properties of a microbial hosts that are a result of the complex relationship between metabolism and transcriptional regulation. Currently there are digital resources available for model microbes that help inform such relationships but is lacking for non-model microbial systems. Genome-scale network reconstruction of a microbial system requires integration of more than one layer of biological networks (e.g., metabolism, regulation or signaling) as constraints to improve prediction power of such computational models for desirable phenotypes such as growth coupled production or maximum bioconversion of carbon sources.

Programs & Initiatives

• The Joint Bioenergy Institute
  

Divisions

DOE Joint Genome Institute

• Science Programs

Secondary Affiliation:

Environmental Genomics and Systems Biology

• Comparative and Functional Genomics

Biography

Stephen Mondo completed his PhD training at Cornell University in 2013, where he studied host-endosymbiont interactions with Dr. Teresa Pawlowska. After a brief postdoc in the Bogdanove lab at Cornell studying TAL effectors present in fungal endosymbiont he joined the Fungal and Algal Genomics team at the DOE Joint Genome Institute as a Data Scientist. Here, Stephen supports the fungal scientific community through annotation of fungal genomes, comparative genomic analyses for user-driven publications and tool development for improved quality of fungal genome annotations. Stephen also conducts his own independent research in support of DOE mission objectives, primarily in the areas of epigenomics an chromatin regulation. Additionally, he now leads multi-omics data analysis, integration and visualization efforts within the Fungal and Algal Genomics program.

Research Interests

Epigenetics, chromatin regulation, fungal comparative genomics, evolutionary & co-evolutionary theory, host-endosymbiont interactions, phylogenomics, early-diverging fungi

Divisions

Molecular Biophysics and Integrated Bioimaging

• Bioenergetics

Biography

From the Molecular Foundry page:

Dr. Ajo-Franklin has been a Staff Scientist at the Molecular Foundry since 2007. Before that, she received her Ph.D. in Chemistry from Stanford University with Prof. Steve Boxer and was a post-doctoral fellow with Prof. Pam Silver in the Department of Systems Biology at Harvard Medical School.

Dr. Ajo-Franklin is fascinated by the incredible, diverse functionality of biological molecules and nanoassemblies, and seeks to engineer these complexes and their host organisms to address global challenges in energy and the environment.

Research Interests

Dr. Ajo-Franklin’s research creates engineered bioassemblies–electron nanoconduits–that direct the flow of charge between living cells and non-living materials. Though a combinatorial approach, she has established an unparalleled ability to genetically program the enormously complex biosynthesis of these electron nanoconduits and to quantitatively characterize their function at the biological-inorganic nanointerface. These capabilities have allowed her to discover design principles that govern the emergent processes of nanoconduit assembly and function. In future work, she will expand the combinatorial space through designed genetic variants and adaptive evolution approaches to dissect fundamental controls on charge transfer at this hybrid nanointerface.

ENGINEERING ELECTRONIC COMMUNICATION

Cellular-electrical connections would enable devices to combine specialties of the living world and the non-living technological world. This new class of smart, self-renewing nanostructured systems has the potential to revolutionize environmental sensing and energy harvesting applications and to open new avenues to program cellular behavior. Building towards this vision, the long-term objectives of the our research are to develop understanding of the principles which govern electron flow across living-non-living interfaces and to use those principles to create electron transfer pathways between individual living microbial cells and non-living electrodes. Our overall strategy is both to explore how naturally-occurring microbes achieve electron transfer to inorganic surfaces and to use genetic and materials surface engineering to create new ‘domesticated’ hybrid cell-electrode systems.

ASSEMBLY & APPLICATIONS OF S-LAYER PROTEINS

S (`surface’)-layer proteins form crystalline lattices on the outsides of many bacteria and archaea. These nearly ubquitous structures play a number of crucial biological roles: they serve as structural scaffolds, effect selective transport of ions and proteins, serve as templates for mineralization, and protect against phagocytosis. While the lattice structures of many S-layers are known, the dynamical mechanisms through which they form are poorly understood. A molecular-level picture of the assembly of the S-layer protein SbpA from Lysinibacillus sphaericus on lipid bilayers was obtained only recently by using in situ atomic force microscopy. AFM images elucidated the phase transition of amorphous precursors into the crystalline clusters composed of folded tetramers and subsequent growth without disappearance of any crystal clusters. Such a system demonstrates the non-classical crystallization behaviors in the S-layer assembly. Molecular dynamic simulations of the S-layer assembly using a coarse grain model also supported the non-classical nucleation arising from a dense liquid precursor, and subsequent growth of the crystal2. The long-term objectives of our research are to develop predictive understanding of S-layer protein nucleation and growth, so as to advance basic knowledge of the dynamics of coupled nanoscale phase separation and self-assembly and to enable control of the nanoscale structures. Together with the Whitelam, DeYoreo, and Bertozzi groups, we are using a combination of fluorescence microscopy, atomic force microscopy, and computer modeling to reveal the mechanisms underlying S-layer crystallization and to identify strategies for its control.

Divisions

Molecular Foundry

Secondary Affiliation:

Molecular Biophysics and Integrated Bioimaging

• Cellular and Tissue Imaging

Biography

Bruce Cohen, Ph.D. is a Staff Scientist at the Molecular Foundry and the Division of Molecular Biophysics & Integrated Bioimaging at Lawrence Berkeley National Laboratory in Berkeley, California (USA), where his research focuses on the design and synthesis of novel luminescent nanomaterials for bioimaging. He graduated with honors in Chemistry from Princeton and earned his Ph.D. in Chemistry and Biophysics from UC Berkeley working with Daniel E. Koshland, Jr.  He earned a certificate in Neurobiology from Woods Hole Institute before working as a Howard Hughes Medical Association postdoctoral fellow in the laboratory of Lily Y. Jan (UCSF) developing organic and protein-based fluorescent probes for addressing problems in protein biophysics and bioimaging. He has a broad background covering nanoscience, biophysics, neuroscience, photophysics, and chemical biology.  His current research interests include development of novel organic fluorophores for imaging and sensing, nanoparticle-based biosensors, and lanthanide-based upconverting nanoparticles as single molecule, quantitative, and deep tissue imaging probes.

Research Interests

Optical microscopy is the primary means of studying live cells in real time, enabling analysis of individual cellular components at high spatial and temporal resolution.  Inorganic nanocrystals have shown promise as transformative probes for these imaging studies, with exceptional optical properties not found in other materials.   Along these lines, we are developing novel nanocrystals as biosensors and single-molecule probes, improving bioconjugation and targeting chemistries, and imaging live cells with these reagents.  We aim to integrate the development of novel luminescent nanomaterials into multidisciplinary efforts to address significant biological questions of cell function.

Imaging single molecules

Lanthanide-based upconverting nanoparticles (UCNPs) sum the energies of 2 incident NIR photons to emit one at visible wavelengths, an unusual property unlike anything found in the cell.  UCNPs have significant advantages over other luminescent reporters, including an absence of on–off blinking, single-molecule multiphoton NIR excitation at powers approaching those used for standard one-photon confocal imaging, no overlap with cellular autofluorescence, and no measurable photobleaching under prolonged single-particle excitation. Our synthetic efforts have established control over UCNP size to produce smaller nanocrystals more compatible with many imaging applications. Current efforts are aimed at optimizing single nanocrystal brightness for extended single-molecule imaging in live cells, and developing UCNPs capable of chemical sensing for studying cellular biochemistry.

Optical biosensors

Many nanocrystals exhibit brightness and stability far superior to conventional fluorophores, making them ideal as the bases for biosensing reagents.   We have developed quantum dot and UCNP energy transfer-based systems for the sensitive detection of cellular chemistry and protein motions.  Our current work focuses on developing bright, selective sensors for studying neuronal activity, including voltage sensors, sensors of neurotransmission in the brain, and ion sensors.

Nanocrystal biocompatibility and targeting

Broadening the scope of nanocrystal surface conjugation chemistry is essential to expand their reach for imaging applications.   High-quality UCNPs and quantum dots are synthesized in hydrophobic solvent and must be transferred to water and made biocompatible to have any utility as imaging probes or biosensors. An ongoing challenge in applying nanocrystals as probes for cellular imaging is improving their aqueous passivation and developing new reactions that work on nanocrystal surfaces.  A growing area of research for us is development of new bioconjugation chemistries, including click reactions, SpyCatcher ligation, and bioorthonganol reactions for immunotargeting.

Divisions

DOE Joint Genome Institute

• Science Programs

Secondary Affiliation:

Environmental Genomics and Systems Biology

• Comparative and Functional Genomics

Biography

I received my B.S. in Bioinformatics and Molecular Biology at Rensselaer Polytechnic Institute in 2006. From there, I went on to pursue a Ph.D in Biological Sciences at UCSD, where I trained in the laboratory of Dr. Joanne Chory at the Salk Institute, studying morphometric features associated with shade avoidance in Arabidopsis thaliana. I then undertook a postdoctoral position in Dr. Steve Kay’s laboratory at UCSD to study circadian and diurnal growth and transcriptome profiles of the model grass, Brachypodium distachyon, before taking on a second postdoctoral position at the DOE-Joint Genome Institute using genome-wide mutagenesis surveys to investigate root colonization by soil bacteria. I became a Research Scientist at LBNL in 2020, and received a DOE Early Career Award in 2021.

Research Interests

Plants are phenomenal in their ability to adapt to adverse conditions, harboring an incredible diversity of responses to environmental stress. I am broadly interested in studying exactly how plants interact with their environment, from their relationships with soil micoorganisms to their reactions to drought, light, and nutrient scarcity. At the Joint Genome Institute, my research focus has been on understanding how microbes can colonize plant roots, focusing on genetic components required for effective colonization. In addition, I am now focusing on how individual plant cells respond to their biotic and abiotic environment using emerging single-cell characterization technologies (scRNA-seq and Spatial Transcriptomics).

Divisions

DOE Joint Genome Institute

• Science Programs

Secondary Affiliation:

Environmental Genomics and Systems Biology

• Biosystems Data Science

Research Interests

• Annotation of fungal genomes to better understand their roles in interactions with e.g. plants, algae, and other fungi
• Comparative phylogenomics to help resolve the Fungal Tree of Life, particularly untangling the lesser studied basal fungal clades
• Elucidation of the underlying biological mechanisms of efficient biomass degradation by fungi

Divisions

DOE Joint Genome Institute

• Science Programs

Secondary Affiliation:

Environmental Genomics and Systems Biology

• Comparative and Functional Genomics

Research Interests

• Comparative analysis of fungal and algal genomes
• Annotation and prediction of gene function
• Integration of diverse biological data

Divisions

DOE Joint Genome Institute

Secondary Affiliation:

Environmental Genomics and Systems Biology

• Comparative and Functional Genomics

Research Interests

Dr. Blaby joined the JGI in 2019 as the lead of the DNA synthesis platform, where he manages production for approved user projects as well as leading computational and lab-based R&D efforts for synthetic biology and functional genomics. Prior to JGI, he was a group lead at Brookhaven National Laboratory where he focused on functional genomics of phototrophs. Through this and post-doctoral positions at University of Florida and UCLA he has worked with a wide range of eukaryotic algae, archaea and bacteria with a view to developing a deeper understanding of sequence-based gene function.

Biography

As Area Deputy, Katy Christiansen supports Biosciences ALD Paul Adams, helping to plan and execute long-range strategies to advance the Area’s scientific mission. After earning her PhD in plant science from Indiana University, Bloomington, Christiansen first joined Berkeley Lab in 2008 as a postdoctoral researcher in the plant systems biology group at JBEI. After two years as a AAAS Science & Technology Policy Fellow at the DOE Bioenergy Technologies Office, where she served as a technical adviser and assisted in development of funding opportunities, she returned to the Biosciences Area in 2014 to help lead strategic planning efforts. Her efforts resulted in direct funding from DOE that established the multimillion dollar Agile BioFoundry (ABF) and Trial Ecosystem Advancement for Microbiome Science (TEAMS) programs. As Head of the Biosciences Program Development Group (BPDG) since its inception in 2020, she now leads program development activities and strategic planning for the Area, including building new multi-institutional research programs with other national laboratories. Christiansen is also responsible for the Biosciences Strategic Plan (BSP), a 10-year scientific strategic plan that describes biosciences research aspirations in energy, environment, health, biomanufacturing, and technology development.

Divisions

Environmental Genomics and Systems Biology

• Biosystems Data Science

Research Interests

Dr. Justin Reese is a Research Scientist in the Environmental Genomics and Systems Biology Division at Lawrence Berkeley National Laboratory. His research seeks to understand how complex biological systems give rise to health and disease, and how diverse data can be harnessed to accelerate biological discovery. He is particularly interested in questions that bridge biology and biomedicine, with an emphasis on translating biological knowledge into tools that improve human health.

He develops and applies computational approaches that include artificial intelligence, machine learning, knowledge graphs, and ontologies. His work spans molecular, clinical, and environmental biosciences. He leads and co-leads multi-institutional collaborations that combine structured biological knowledge with modern AI systems to derive insights from complex biological datasets. His projects include constructing large-scale knowledge graphs and applying graph machine learning algorithms to them, using large language models to extract and organize information from scientific literature and clinical data, and developing AI systems that assist scientists in discovery, including applications such as improving rare disease diagnosis, using AI to accelerate research in neurodegenerative diseases, and building tools to suggest better candidates for drug repurposing.

Programs & Initiatives

• C-BRAIN - Consortium for Biomedical Research & AI in Neurodegeneration
  
• Exomiser
  
• Bridge2AI
  
• Monarch Initiative and Phenomics First
  

Divisions

Molecular Biophysics and Integrated Bioimaging

• Structural Biology

Research Interests

High-performance computing
Anomalous diffraction
XFEL diffraction
Chemical crystallography

Divisions

Environmental Genomics and Systems Biology

• Molecular EcoSystems Biology

Research Interests

I am interested in using integrative system biology and high throughput approaches to understand plant specialized metabolism in plant environmental stress interactions. One of his projects is focused on plant microbiome interactions. Plants utilize chemicals to communicate with microorganisms, favoring beneficial microbes and killing harmful ones. I use integrative approaches, including metabolomics, genetics, transcriptomics, proteomics and others to identify novel secondary metabolites involved in plant microbe interactions and explore how plants use these metabolites to benefit their own.