Bruce Cohen

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 Strategic Programs Development Group (SPDG) 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

I am broadly interested in using computational methods to extract actionable knowledge from biomedical and biological data. I am particularly interested in using these methods to address human disease.

My current research focuses on developing performant machine learning algorithms to extract knowledge from biomedical data. This involves for example applying unsupervised machine learning on EHR data for identifying subtypes of human diseases such as long COVID, and constructing and performing graph machine learning on knowledge graphs such as KG-COVID-19 (https://github.com/Knowledge-Graph-Hub/kg-covid-19) and using this knowledge to identify drugs that may have an effect on COVID-19 outcome.

I am also developing and applying epidemiological methods to validate knowledge extracted from computational experiments using EHR and other clinical data, for example describing the effect of metformin on COVID-19 outcome.

Programs & Initiatives

• National COVID Cohort Collaborative (N3C)
  
• RECOVER
  
• National Virtual Biotechnology Laboratory
  

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.

Divisions

Molecular Biophysics and Integrated Bioimaging

• Cellular and Tissue Imaging

Research Interests

Mustafa Janabi directs and manages operations of the Biomedical Isotope Facility, which means that he:
• Coordinates production schedule,
• Operates and maintains medical cyclotron (RDS-111),
• Hires, trains, and supervises new employees, and
• Coordinates with researchers on collaborative projects.

Divisions

Environmental Genomics and Systems Biology

• Molecular EcoSystems Biology

Research Interests

EcoFAB and EcoBOT development, environmental microbiology including plant-microbial interactions

Divisions

Molecular Biophysics and Integrated Bioimaging

• Bioenergetics

Research Interests

• Unravelling the relationship between structure, dynamics and function of enzymes using
  • Time-resolved structural studies at X-ray free-electron lasers (XFEL)
  • Simulating biological systems using Molecular Dynamics/Quantum mechanical methods
• X-ray crystallography data analysis – developing new methods for active sites of metalloenzymes
• Current systems of interest include Photosystem II, a multi-subunit membrane enzyme catalyzing the water oxidation reaction.