Altaf Sarker
Biologist Research Scientist
Divisions
Molecular Biophysics and Integrated Bioimaging
- Structural Biology
Secondary Affiliation:
Biological Systems and Engineering
- BioEngineering & BioMedical Sciences
Recent Publications
Related News
Thirdhand Smoke Harms the Body More Than We Ever Realized
A new study found that concentrations of toxic chemicals lingering indoors where cigarettes have been smoked can exceed risk guidelines from the State of California. This means that non-smokers can be exposed to health risks by living in contaminated spaces.
Research Interests
We are interested in understanding how constituents of the remodeled extracellular matrix and tumor stroma contribute resistance to therapy. ECM comprise the main ligands for integrins, which transmit extracellular cues to effect cell fate. We have investigated integrin signaling in pre-clinical models of breast cancer, showing its promise as a therapeutic target alone and with radiation therapy. In addition to the molecular aspects of ECM-induced signaling via integrins, recent developments point to the physical and mechanical aspects of the ECM and malignant stroma in cancer progression, and now, possibly resistance. We are interested in understanding how mechanical features of stroma may enhance resistance through integrin-dependent and independent pathways.
Recent Publications
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.
Normal is Good: Breast Cells Produced in Novel Media Resemble Those In Vivo
When studying human cells in a laboratory, it is important that the media, or the broth that bathes the cells, contains all of the nutrients necessary to support cells through their normal growth and division phases even though they are outside of the body. Bioscientists at Berkeley Lab have a long history of studying breast cancer, and Martha Stampfer, senior scientist in the Biological Systems & Engineering (BSE) Division, has spent decades developing media now widely used by the community. Today, PLOS ONE published a study describing a comprehensive analysis of three kinds of media used to grow human mammary epithelial cells (HMEC).
Recent Publications
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Two Scientists Named AAAS Fellows
Two scientists in the Biosciences Area, Abby Dernburg and Blake Simmons, have been elected into the 2025 class of the American Association for the Advancement of Science (AAAS).
Abby Dernburg Elected Into National Academy of Sciences
Abby Dernburg, a senior faculty scientist in the Biological Systems and Engineering (BSE) Division, has been elected into the National Academy of Sciences (NAS) in recognition of her distinguished and continuing achievements in meiosis research.
Dernburg and Nogales Named Fellows of the American Society for Cell Biology
Biosciences’ Abby Dernburg and Eva Nogales--both of whom are also UC Berkeley professors and HHMI Investigators--have been selected as 2017 Fellows of the American Society for Cell Biology (ASCB). Election as a Fellow is an honor bestowed upon ASCB members by their peers. The award is a lifetime recognition of meritorious efforts to advance cell biology and/or its applications, work in service to the Society, and ongoing loyalty to ASCB.
Research Interests
My research interests lie in the use of metabolomics analyses to characterize engineered biosynthetic and metabolic pathways to understand primary and secondary cellular metabolism and their regulation, in vivo. This is directed towards addressing key environmental challenges and engineering robust microbial platforms for producing valuable renewable bioproducts.
Recent Publications
Related News
Biomanufacturing Increases Available Supply of Anti-cancer Drug
Thanks to a leap forward in synthetic biology, the plant-derived chemotherapy vinblastine has a new source.
Finding the Missing Step of an Important Molecular Process
Lysine is an important amino acid that must be supplied in our diets, as our bodies can’t produce lysine on their own. Most cereal grains have low levels of lysine, and scientists have worked to breed crops with higher lysine levels. However, the biochemical processes that break down lysine in plants weren’t fully understood. New Joint BioEnergy Institute (JBEI) research, published in Nature Communications, reveals this last missing step of lysine catabolism.
Building: 90, Room 2012
Mail Stop: R2002
Phone: (510) 486-4507
cdscown@lbl.gov
http://www.cscown.com
Links
Divisions
Energy Analysis and Environmental Impacts
Secondary Affiliation:
Biological Systems and Engineering
- Process Engineering & Analytics
Research Interests
Technoeconomic analysis, life-cycle assessment, bioenergy scenario modeling, energy-water nexus, uncertainty analysis, infrastructure systems modeling, economic input-output modeling, transportation fleet modeling, comparative analysis of energy carriers/energy storage technologies
Recent Publications
Related News
Turning Agricultural Trash to Treasure
New funding will help Berkeley Lab and partners improve how the diverse agricultural waste in California’s Northern San Joaquin Valley can be used to make sustainable bioproducts and biofuels.
Taking Flight with Biofuels and Carbon Crops
A recent study by Joint BioEnergy Institute (JBEI) researchers reveals which crop-based feedstocks offer the greatest potential for a plentiful, cost-competitive, renewable alternative to petroleum-based jet fuel, while also maximizing atmospheric carbon removal.
Bacteria Can Make Infinitely Recyclable Plastic with Renewable Materials
A collaboration among experts at the Molecular Foundry, the Joint BioEnergy Institute (JBEI), and the Advanced Light Source has shown that the starting ingredients in an infinitely recyclable plastic known as poly(diketoenamine), or PDK, can be successfully made by microbes. The new approach shows that renewable, recyclable plastics are not only possible, but also outperform those from petrochemicals.
Building: 978, Room 4462-L
Mail Stop: 978
Phone: (408) 623-4867
syuzawa@lbl.gov
Links
Research Interests
My research has focused on understanding mechanistic and structural features of modular polyketide synthases and exploiting that knowledge for producing a variety of high-value chemicals in microbes from renewable carbon sources. 
Related News
Scientists Develop Higher-performance Fuels, Biofuels and Bioproducts
Researchers at the Joint BioEnergy Institute (JBEI) and the Advanced Biofuels & Bioproducts Process Development Unit (ABPDU), part of the Biological Systems and Engineering (BSE) Division, have developed a new polyketide synthase-based platform and prototyped efficient production of potential biofuels, gasoline additives, and commodity chemicals.
Building: 310 (JGI)
Phone: (510) 486-5327
NMouncey@lbl.gov
https://jgi.doe.gov/about-us/organization/strategic-management/nigel-mouncey/
Divisions
Secondary Affiliation:
Environmental Genomics and Systems Biology
- Molecular EcoSystems Biology
Biography
Nigel Mouncey joined us on March 15, 2017 as the Director of the DOE Joint Genome Institute. Hailing from England, Mouncey earned his Bachelor of Science degree in microbiology with honors from the University of Glasgow and received his Doctor of Philosophy in biochemistry at the University of Sussex. He completed post-doctoral research at Harvard Medical School and the University of Texas Medical School in Houston. Mouncey spent 10 years at Roche Vitamins in New Jersey and DSM Nutritional Products in Switzerland before joining Dow AgroSciences in Indianapolis, Indiana. He has a demonstrated strong track record in microbiology and management, in both the academic and industry sectors.
Recent Publications
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Advancing the Frontiers of Genetic Science
As a Department of Energy user facility, the Joint Genome Institute offers scientists access to advanced genomic capabilities, large-scale data and professional expertise. They help us understand biology today and develop breakthroughs for tomorrow.
New Strategic Plan: JGI’s Next 5 Years
The DOE Joint Genome Institute (JGI) has released its newest 5-Year Strategic Plan: Innovating Genomics to Serve the Changing Planet. Aside from aligning the DOE Office of Science user facility with broader national efforts to promote and stimulate a bioeconomy, it lays out how users and the global research community will bridge fundamental knowledge gaps to advance biotechnology and biomanufacturing.
University of Duisburg-Essen Delegation Explores Collaborative Opportunities with Lawrence Berkeley National Laboratory
Building on a Memorandum of Understanding signed between UDE and Berkeley Lab researchers, a kick-off meeting focused on future collaborations in the fields of genomics, structural biology, bioimaging, and water research.
Building: 70A, Room 3317F
Mail Stop: MS-70A3317F
Phone: (510) 486-4091
Fax: (510) 486-7152
rchakraborty@lbl.gov
https://profiles.lbl.gov/20463-romy-chakraborty
Divisions
Climate & Ecosystems
Secondary Affiliation:
Environmental Genomics and Systems Biology
- Molecular EcoSystems Biology
Biography
As an environmental microbiologist, Chakraborty has pioneered identification of unique microbes mediating critical carbon and nitrogen metabolisms in diverse ecosystems. She is involved in extensive outreach and mentorship and her efforts have led to very positive impacts in the community, at the Laboratory, and on the career trajectories of a wide range of early career scientists.
Recent Publications
Related News
Managing Microbes for More Resilient Plants
Scientists curated a microbial community that helped a species of grass better recover from drought.
EcoFABs Could Help Fuel AI in Agriculture
A first-of-its-kind global study showed that EcoFABs can deliver consistent results across labs on three continents, supported by open protocols, tools, and datasets. The reliable, large-scale data EcoFABs generate are ideal for training AI, which could help accelerate discoveries in crop development, soil health, and agriculture.
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.
Building: 977, Room 227
Mail Stop: 977
Phone: (510) 486-4365
Fax: (510) 486-5586
mjbissell@lbl.gov
http://www2.lbl.gov/LBL-Programs/lifesciences/BissellLab/main.html
Links
Research Interests
Breast Cancer Research
3-Dimensional Tissue Research
Programs & Initiatives
- Senior Advisor to the Laboratory Director on Biology, Berkeley Lab
- University California, Berkeley, Faculty of Four Graduate Groups: Graduate Groups in Comparative Biochemistry, Endocrinology, Molecular Toxicology, and Joint Graduate Group in Bioengineering (with UCSF)
Recent Publications
Related News
Commemorating Judy Campisi
Judith (Judy) Campisi, a leader in the field of cell senescence and a researcher at Berkeley Lab for just over 30 years, died on January 19, 2024. She was 75.
Bissell to Receive Cancer Research Award
Distinguished Senior Scientist awarded the American Association for Cancer Research Award for describing ways in which the microenvironment of cells can influence tumor growth.
Mina Bissell Delivers Gairdner Laureate Talk Virtually, Receives Medal at Home
This spring, Mina Bissell, distinguished senior scientist in the Biological Systems and Engineering (BSE) Division, was awarded the 2020 Canada Gairdner International Award for Biomedical Research. Due to the ongoing coronavirus pandemic, the Gairdner Foundation held their annual Laureate Lectures and Gala Celebration—normally hosted in Toronto, Ontario, Canada—virtually this year. Bissell presented her talk, entitled “Why Don’t We Get More Cancer?”, about a signaling pathway she and her research group discovered that doesn’t get turned off in cancer and leads to uncontrolled growth. She received her medal surrounded by family at home in Berkeley, and spoke about the power of empathy.
Building: 977, Room 107
Mail Stop: 977
Phone: (510) 495-2795
Fax: (510) 486-7152
glandersen@lbl.gov
http://esd1.lbl.gov/research/facilities/andersenlab/
Links
Divisions
Environmental Genomics and Systems Biology
- Molecular EcoSystems Biology
Secondary Affiliation:
Biography
I received my undergraduate training at Northwestern University where I majored in Biology. While at Northwestern, I worked for Dr. James A. Lippincott on Agrobacterium tumefaciens Ti plasmid transfer and integration. It was here that I first developed an interest in molecular biology and plant pathology. I then went to the University of California at Berkeley were I eventually ended up working the laboratory of Dr. Steven Lindow as a staff research associate for almost eight years. I was rapidly educated in the workings of the news media and public perceptions of scientific research with the lab’s release of Ice Minus Pseudomonas syringae into the environment. I went to graduate school in the Department of Plant Pathology at UC Berkeley with Dr. Lindow as my advisor and Dr. Andy O. Jackson as my mentor in molecular biology. My interest was in the bacterium’s response to stress in the environment and received my Ph.D. under Steve Lindow in the characterization of epiphytic fitness mutants of P. syringae subjected to UV and desiccation stresses. The mid-90s was not the best time for agricultural research funding, so for my post-doc I changed fields, still keeping my interest in bacterial interactions in the environment. I joined Dr. Ken Wilson’s lab in the Infectious Diseases Division of Duke University Medical Center where I studied culture-resistant human pathogens and the epidemiology of the anthrax pathogen, Bacillus anthracis. While at Duke University I was fortunate enough to be the first to discover sequence-based differences for the differentiation of strains of B. anthracis. The variable number tandem repeats (VNTR) that I discovered became the basis for a strain identification system for B. anthracis that is still in use today. I joined Lawrence Livermore National Laboratory as a Principle Investigator in the Biology and Biotechnology Research Program. While at LLNL, I set up a research program in bacterial diagnostics and environmental monitoring of pathogens. I joined Lawrence Berkeley National Laboratory in 2003 as a Scientist in the Earth Sciences Division. I have set up a laboratory to study bacterial responses to selected environments. I have been very excited to be at a place where I am exposed to the latest technological breakthroughs and to be right next door to the UC Berkeley campus where I am able to interact with the leaders in the field of microbiology. I am the former Head of the Ecology Department at LBNL.
Research interests from EESA’s webpage:
My research focus is in the area of microbial ecology and includes the examination of phylogenetic diversity in natural environments. My laboratory uses molecular approaches to study the dynamics of microbial community structure under changing environmental conditions. This includes the development of new techniques to dissect the microbial diversity of complex ecosystems. The long-term goal of this research is to integrate different fields of biology (i.e., genomics, ecology, molecular biology, proteomics and bioinformatics) to provide insight into the interactions of environmental microorganisms under stressful conditions. We hope to harness the existing capabilities of beneficial microbes to improve water quality, reduce contamination and limit the amount of carbon released into the atmosphere. My current research focuses on the remediation of oil spills, limiting sulfate reduction in oil reservoirs, tracking sources of fecal pollution in marine and freshwater systems and using thermophilic composting to reduce the impact of wastes on watersheds and to improve land use productivity. My laboratory has developed Greengenes, a 16S rRNA gene sequence repository and online toolset, for aligning/annotating novel sequences, interpreting microarray results and developing phylogenetically specific probes. We have been part of the Data Analysis and Coordination Center for the Human Microbiome Project and have examined the tremendous diversity of human-associated microbes. We have developed numerous microarray systems, including the third-generation (G3) PhyloChip, for the measurement of microbial diversity and the identification of bacterial communities by 16S rRNA gene sequences. We have also developed additional microarray systems, including microarrays for whole-genome expression profiling in response to various environmental stimuli.
A complete listing of current research projects can be found on The Andersen Lab website or on UC Berkeley’s Gary Andersen Page
Research Interests
I am interested in using molecular approaches to study the dynamics of microbial community structure in the environment. This includes the development of new techniques to dissect the microbial diversity of complex ecosystems. The long-term goal of this research is to integrate different fields of biology (i.e., genomics, ecology, molecular biology, proteomics and bioinformatics) to provide insight into the interactions of environmental microorganisms under stressful conditions. My current research focuses on the microbial ecology of airborne and aquatic bacteria with an emphasis on the natural distribution of pathogens in the environment. I have developed numerous microarray systems for the measurement of microbial diversity and the identification of bacterial communities by 16S and other gene sequences. I have also used microarrays for whole genome expression of genes in response to environmental stimuli.
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.
From the Molecular to the Mesoscale: The EcoPOD Provides A New Way to Link Plants, Soil, and Microbes
On May 25, Berkeley Lab and Biosciences Area leadership officially welcomed the EcoPOD to its home at Potter Street in West Berkeley. The Lab's Deputy Director for Research Horst Simon and Associate Laboratory Director for Biosciences Mary Maxon opened the doors of the EcoPOD after Maxon cut the ceremonial ribbon.
PhyloChip Provides Clarity Amid Hawaiian Water Contamination Concerns
To better understand the cause of high counts of potentially pathogenic fecal indicator bacteria (FIB) in the watersheds of the Mahaulepu Valley and Waikomo Stream in southeast Kauai, the Hawaii Department of Health (DOH) commissioned a study by Berkeley Lab microbial ecologists Gary Andersen and Eric Dubinsky. The duo is frequently invited to lead microbial water assessment projects thanks to their expertise and the PhyloChip, a credit card-sized microbial detection technology invented by Andersen and others at Berkeley Lab.
Building: 33, Room 349
Mail Stop: 33R0345
Phone: (510) 221-7384
Fax: (510) 486-5909
PAfonine@lbl.gov
Links
Research Interests
1) New algorithms and methods development for crystallographic structure determination of small- and macro(bio)-molecules.
2) Software (Phenix) development for automated crystallographic structure solution, analysis and validation using X-ray, neutron and cryo-EM data.
3) Three-dimensional structure determination of macro-molecules.
Recent Publications
Related News
Cracking the Code: Using AI to Solve Difficult-to-map Proteins
Leveraging artificial intelligence and quantum calculations, scientists developed a new tool that yielded higher-quality structural information and solved notoriously elusive proteins.
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.
