Research Focus of PMB Scientists
PMB scientists engage in a wide range of research, collaborate on a large number of projects and are affiliated with other scientists and research projects both on and off the UC Berkeley campus. Below is a list of scientists and their specialties, with keywords that note areas of emphasis at a glance. For a more complete, detailed look at each lab's research please visit the faculty pages on this site at pmb.berkeley.edu/faculty directory.
|Barbara Baker||Plant Disease, Disease Resistance|
Professor Barbara Baker researches microbe interactions with their hosts. She is interested in the biology and chemistry behind these interactions. In particular, her lab studies how pathogens cause disease and how the host builds up disease resistance. The Baker Lab specifically studies bacterial, viral and oomycete pathogens and their plant hosts. Their research has important practical benefits and might lead to better disease resistant crops and plants.
|Ben Blackman||Evolutionary Processes||The Blackman lab takes developmental, genomic, and evolutionary approaches to studying how plant interactions with the environment evolve during domestication, adaptation, and speciation. Working in two systems, sunflower and monkey flower, his research focuses on identifying natural genetic variants and ecological factors important as plants adapt to thrive in local seasonal habitats. His work also investigates the mechanisms important for sunflower domestication and environment-sensitive aspects of growth and reproductive development. Together, these findings reveal the molecular and evolutionary basis of processes by which new traits evolve and through which diversity is maintained within and among natural populations.|
|Rachel Brem||Principles of Molecular Evolution in Fungi|
The goal of work in the Brem lab is to interpret natural genetic variation at the molecular level, using fungi as a model system. Lab members survey the molecular differences between fungal individuals and species, and infer which differences manifest phenotypically, or have been important in evolutionary history. Experimental tests then validate these predictions. Together, these findings reveal how organisms acquire new traits, and what evolutionary forces have driven them.
|Steven E. Brenner|
Computational Biology, Genomics, Protein Function Prediction
Professor Steven Brenner researches computational and experimental genomics (the study of an organism's genome). His research focuses on gene regulation, protein function and structure and personal genomics, among other things. He studies structural genomics, which aims to provide a high-quality model for every protein. In addition, he has worked with a number of collaborators to understand Crohn’s disease and how microbes in the gut can cause the disease.
|Tom Bruns||Mushrooms, Fungi|
Professor Tom Bruns researches the ecology and evolution of mycorrhizal fungi. Mycorrhizal fungi are fungi that form symbiotic (close and mutually beneficial) associations with plants. The fungi receive carbohydrates from the plant roots while the plant benefits from increased water absorption and mineral uptake. The Bruns Lab’s past work studied the effect of the plant host and disturbance on fungal community structure. His research group has also developed molecular tools for the identification of fungi from environmental samples.
|Zac Cande||Cell Division, Cytoskeleton Development|
Professor W. Zacheus Cande studies the evolution of eukaryotic cells and the mechanism behind chromosome segregation during mitosis (cell division) and meiosis (two cell division). The Cande Lab also uses phylogenomic and cell biological approaches to investigate cytoskeleton and chromatin evolution in basal eukaryotic microbes. The cytoskeleton is essentially the protein scaffolding within a cell’s cytoplasm that supports and gives shape to the cell. The chromatin is the mass of DNA and proteins in the nucleus of a eukaryotic cell. The development of both the cytoskeleton and the chromatin were important innovations in the evolution of eukaryotes. Their research has revealed the complex mechanisms behind cell division and eukaryotic evolution.
|John Coates||Bioremediation, Pollution Clean-Up||Professor John Coates researches the chemical interactions between microbes and certain compounds. He studies oxidization and reduction reactions the microbes perform and the pathways behind the reactions. He uses a variety of cutting-edge molecular and chemical techniques in his research. His lab was the first to isolate a microbe that would degrade benzene, a contaminant and carcinogen that is produced in large amounts by industry.|
|Devin Coleman-Derr||Plant-associated Microbial Communities, Abiotic Stress Tolerance||Adjunct Assistant Professor Devin Coleman-Derr studies how abiotic stress affects plant- associated microbial communities, and the role of plant growth promoting microrganisms in improving abiotic stress response in cereals, with a major focus on Sorghum bicolor, an important forage and biofuels crop. A goal of this work is the development of microbial-based strategies of increasing yield and resilience in the face of drought, an issue of growing importance for California agriculture. He seeks to identify the rules that govern microbial community assembly in the rhizospheres of diverse grass species, including both host, microbe, and environment derived factors.|
|Lew Feldman||Plant Development, Root Development|
Professor Lewis J. Feldman researches plant development, especially root development. The root cap is the site of perception for many environmental stimuli, including gravity and light. Plants have much of their physiology and biochemistry devoted to the perception and transduction of environmental stimuli. The Feldman lab investigates how the cap communicates with the rest of the root.
|Bob Fischer||DNA Demethylation, Gene Imprinting|
Professor Robert Fischer studies how DNA demethylation regulates gene imprinting. Gene imprinting is when gene expression occurs from only one allele, as opposed to the usual two. Instead of producing the proteins for each separate allele, organisms with an imprinted gene will only produce protein for one. Gene imprinting has important consequences in the reproduction of plants and how they develop.
|Jennifer Fletcher||Plant Stem Cells, Developmental Signaling|
Associate Professor Jennifer Fletcher studies stem cell biology in plants. Stem cell reservoirs reside at the growing tips of all plants and are the source of cells that make the leaves, stems, flowers and fruits. The transition between stem cell activity and organ formation involves complex cell signaling and gene regulation processes. The Fletcher lab uses genetic, molecular and biochemical tools to characterize these processes during plant development.
|Michael Freeling||Evolutionary History of Plants|
Professor Michael Freeling studies the evolutionary history of vascular plants. Vascular plants are a highly successful and diverse group of plants that have lignified tissues for carrying water and nutrients.The Freeling Lab compares the genomes of different plant lineages to infer their evolutionary relationship. The lab seeks to explain what drives evolutionary trends in vascular plants and the roles of regulatory genes and environmental stress tolerance in shaping evolution.
|N. Louise Glass||Biofuels, Fungi|
Professor N. Louise Glass studies how cells specialize, communicate and recognize each other. Her work is especially important for microbial organisms, which live in a complex community of cells. She seeks to understand the mechanisms that mediate cell fusion and how cells recognize each other before and after fusion. She uses the fungus Neurospora crassa as an experimental system to study these mechanisms. Her lab also focuses on how plant cell walls are degraded by fungi. This particular project has the potential to improve plant biomass degradation, which is important for the production of biofuels.
|Britt Glaunsinger||Virus-Host Interactions, RNA-Based Regulation|
Associate Professor Britt A. Glaunsinger studies how viruses manipulate gene expression in infected host cells. Glaunsinger focuses on the RNA-based regulation and viral factors that target RNA. The Glaunsinger Lab seeks to understand how viral manipulation of host cell gene expression pathways influences viral replication and disease. Her lab specifically studies gammaherpesviruses, which can cause cancers in people with weakened immune systems. Her work has also shed light on the regulation of gene expression in human cells.
|Igor Grigoriev||Genomics of Eukaryotes, Computational Biology|
Adjunct Professor Igor Grigoriev is affiliated with the US Department of Energy Joint Genome Institute. His research focuses on genomics of eukaryotes, from protists to plants. At the JGI he leads the Fungal Genomics program to explore fungal diversity, evolution and interactions.
|Sarah Hake||Plant Development and Plant Architecture|
Professor Sarah C. Hake, director of the Plant Gene Expression Center, uses genetics to study plant development. Depending on the experimental question, the Hake Lab works on maize, Arabidopsis and tomato. The lab uses mutant plants that differ from normal plants to identify genes responsible for forming different parts of the plants. Once the gene is identified, the Hake Lab uses a variety of genetic and biological techniques to understand the developmental mechanisms underlying plant development.
|Frank Harmon||Circadian Clock|
Adjunct Associate Professor Frank G. Harmon studies circadian clocks in plants. A circadian clock is a biochemical mechanism that drives circadian rhythms, built-in biological cycles that repeat every 24 hours. Organisms use these cycles to keep time, allowing them to perform functions at the proper time. Plants use circadian rhythms to coordinate growth and respond to environmental conditions. External factors like temperature and light affect clock rhythms and therefore the plant’s response. The Harmon lab uses genetic, biochemical, molecular, and genomic approaches to study the proteins in the plant’s clock.
|Cheryl Kerfeld||Structural Biology|
Adjunct Associate Professor Cheryl A. Kerfeld studies the structure and function of microcompartments in bacteria. Although bacteria and prokaryotes were once thought not to have organelles, that is no longer the case. Microcompartments are one example of a prokaryotic organelle. Microcomparments enclose various enzymes used for metabolism. The Kerfeld Lab also studies photoprotection in photosynthetic organisms. Photoprotection is the mechanism by which organisms protect themselves from harmful UV light.
Associate Professor Arash Komeili studies prokaryotic organelles. Organelles are structures in cells that have a specific function. For example, ribosomes are organelles that make proteins in cells. The Komeili Lab focuses on how organelles are produced within cells and how they are maintained. To do this, the lab uses magnetotactic bacteria, a diverse group of bacteria that can orient along magnetic fields. Their magnetic properties are due to special organelles called magnetosomes, which contain nanocrystalline magnetic compounds. Using a variety of biological and chemical tools, the lab identifies and investigates genes involved in controlling organelle formation and function.
|Peggy Lemaux||Crop Biotechnology|
Cooperative Extension Specialist Peggy Lemaux’s laboratory performs both basic and applied research focused primarily on cereal crops, like sorghum, wheat and barley. Objectives are to better understand crop plants and to use that knowledge to improve their performance and quality. Recent efforts with others from PMB, ANR, JGI and PNNL involve studying a variety of omic changes in sorghum in the field during drought. Studies will also follow changes over time in the microbiome associated with sorghum during drought. Lemaux is also involved in developing educational resources on food and agriculture that is disseminated to professionals, the media and consumers. These include middle school curricula, educational displays, games, and videos. Outreach activities increasingly involve undergrad and grad students and postdocs in the CLEAR (Communication, Literacy and Education for Agricultural Research) project.
|Jennifer Lewis||Plant Disease and Immunity|
Adjunct Assistant Professor Jennifer D. Lewis studies the interaction between plants and the bacterial pathogen Pseudomonas syringae, and downstream host defense responses. Pathogen-encoded virulence proteins are excellent tools to probe immune signaling pathways in plants. The Lewis Lab’s work will lead to a greater understanding of plant immunity and will help devise strategies to protect plants from disease.
|Steven Lindow||Ecology of Plant-Associated Microorganisms|
Professor Steven Lindow studies the interactions that occur between bacteria and fungi and the plants on which they live. Most of his research emphasize the study of various bacteria, including plant pathogenic and ice nucleation active species that live on the surfaces of plants as epiphytes. The Lindow lab also uses molecular approaches to study the traits that bacteria utilize to colonize the stressful habitat of plant surfaces. His work also addresses cell density-dependent expression of genes by quorum sensing in these bacteria as well as those that colonize the vascular system of plants. In addition, molecular ecological approaches are being used to study the effects of endophytic alkaloid-producing fungi on the bacterial communities on plants.
|Sheng Luan||Plant Responses to the Environment|
Professor Sheng Luan researches how plants respond and adapt to their environment. Unlike most animals, plants are immobile and cannot move when conditions become unfavorable. Therefore, plants have evolved complex mechanisms to perceive and respond to environmental change. The Luan Lab studies the molecular mechanisms and biochemical pathways behind these mechanisms. Some of his research deals with metabolic regulation in chloroplast and environmental sensing in plants.
|Sheila McCormick||Pollen, Plant Fertilization;|
Professor Sheila McCormick researches plant reproduction. The McCormick Lab studies pollen-specific receptor kinases in pollen tubes and how the receptor kinases send and receive signals so that pollen tubes can grow towards the ovule (female structure). They also study pollen development and function by using mutants. Lastly, they are interested in the molecular mechanisms underlying double fertilization in plants.
|Tasios Melis||Photosynthesis, Metabolic Engineering, Bioenergy|
Professor Anastasios Melis studies the photosynthesis in plants, microalgae, cyanobacteria and photosynthetic bacteria. The Melis Lab pioneered the concept of “photosynthetic biofuels,” the direct production of biofuels from photosynthesis. The lab was the first to discover that depriving algae of sulfur caused it to produce hydrogen instead of oxygen. Numerous advances in biofuel development have been made by the Melis Lab.
|Kris Niyogi||Regulation of Photosynthesis|
Professor Krishna K. Niyogi studies algae and plants 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. By comparing how photosynthesis works in diverse organisms, he hopes to uncover general design principles of natural photosynthesis as well as unique adaptations to different environments.
|Markus Pauly||Biofuels, Carbon Sequestration|
Associate Professor Markus Pauly studies how plant cell walls are made, and their structure and function. Plants have a number of unique features that distinguish them from other eukaryotes (organisms with a nucleus). One feature is a cell wall composed of cellulose and other polymers. The cell walls protect the plant cell and prevent water loss to the environment. One of the lab's current projects involves plant wall degradation, which has the potential to advance the production of renewable biofuels from plant material.
|Dan Portnoy||Microbial Disease, Defending Against Infection|
Professor of Biochemistry and Molecular Biology Daniel Portnoy is an associate of the department. The Portnoy Lab studies the molecular and cellular basis behind microbial pathogenesis (how a disease is caused) and the mechanisms the host uses to defend against infection. The lab focuses on the bacterium Listeria monocytogenes, which can evade its mammalian host’s immune system with its unique moving mechanism.
|Peter Quail||Light Signaling in Plants, Solar Energy Capture Optimization|
Professor Peter Quail researches the molecular mechanisms behind how light regulates gene expression in plants. The lab focuses on phytochromes, a family of photoreceptor that acts as a shape change when light is detected, then triggers a DNA transcription response. The Quail Lab has developed a light-switchable gene promoter that will allow for conditional induction or repression of the plant light response.
|Kathleen Ryan||Bacterial Cell Cycle, Regulatory Pathways|
Associate Professor Kathleen Ryan researches Caulobacter crescentus, a rod-shaped bacterium, and its life cycle. Her research group looks into genes responsible for the complex mechanisms Caulobacter carries out. She has studied how they control cell division and why their cell division is asymmetric (uneven, producing two unequal cells).
|Henrik Scheller||Renewable Energy, Plant Cell Walls|
Adjunct Professor Henrik Vibe Scheller works at the Joint BioEnergy Institute in Emeryville. The Scheller Lab investigates complex polysaccharides and glycoproteins in the plant cell wall, using Arabidopsis and rice as model plants. Polysaccharides and glycoproteins are the main components of cell walls and thus of the biomass. Their research has important significance for the development of better crop plants suited for biofuel production.
|Kimmen Sjölander||Computational Biology, Bioinformatics|
Associate Professor Kimmen Sjölander researches the development of computational methods for biological discovery. Her lab is interested phylogenetic tree reconstruction, remote homolog recognition, protein structure prediction, subfamily classification, prediction of critical positions in molecules, multiple sequence alignments, protein-protein interactions, pathway inference, computational prediction of protein domain structure, and other aspects of protein function and structure. The lab has a strong interest in industry as well. Much of the lab's research, such as medical applications of genomics and bioinformatics, has practical applications.
|Chris Somerville||Biofuels, Polysaccharides, Industrial Microbiology|
Professor Chris R. Somerville is the director of the Energy Biosciences Institute. His lab researches the biosynthesis of plant cell wall polysaccharides, the structure and function of cell walls, and how cell wall formation is regulated. In particular, Somerville focuses on how cellulose, the major component of cell walls, is produced.
|Shauna Somerville||Plant-pathogen interactions; mechanisms of host defense; cell wall integrity sensing|
Professor Shauna Somerville studies the interaction between plants and their pathogens and the role the plant plays in disease development. Her lab works with powdery mildew disease on the model plant Arabidopsis thaliana. They use mutants to identify factors in the plant host necessary for disease development. Her lab also studies non-host resistance, a mechanism that protects all members of a plant species from all members of a pathogen species, a new area of plant-pathogen interactions.
|Chelsea Specht||Plant Evolution, Evolutionary Developmental Genetics|
Associate Professor Chelsea D. Specht studies the evolution and natural diversity of plants. For hundreds of millions of years, plants have been diversifying into a large array of species, resulting in the humble dandelion and the mighty redwoods. Her lab seeks to understand the forces that cause and sustain this high diversity of plant life. The Specht lab uses a variety of methods in their research, including systematics, developmental genetics and molecular evolution.
|Brian Staskawicz||Plant Immunity|
Professor Brian Staskawicz studies plant immunity against disease. His lab elucidates the molecular basis of this immunity from the perspective of both the pathogen and the plant host. His findings and cutting-edge methods have answered many questions in this field. The Staskawicz lab has also started studying molecular plant pathology to engineer durable resistance in crop species, which can increase crop production.
|Renee Sung||Plant Growth and Development|
Professor Renee Sung studies the development and growth of plants. She researches how plants regulate their development and control cell differentiation (when a cell becomes specialized into a more specific cell type). One of the questions she is trying to answer is, “What controls cell growth in plants?” Currently, she is focusing on how changes in the activity of a flowering gene affect shoot development in Arabidopsis.
|Michi Taga||Microbial Interactions, Cofactor Synthesis|
Assistant Professor Michi Taga researches how microbes share nutrients. Microbes, like any other living organisms, live in complex communities that contain many species. The Taga Lab researches how microbes synthesize and exchange small molecules. In particular, the lab researches a class of compounds called corrinoids, which includes Vitamin B12.
|John Taylor||Mushrooms, Fungi|
Professor John W. Taylor studies fungi and their evolutionary relationships. Fungi are a large group of organisms that include both edible species, such as the Portobello mushroom, but also harmful species such as Cryptococcus, which causes meningitis. The Taylor research group focuses on the kind of fungi that cause human diseases. Their research has high potential for future innovations in fungal disease treatment and human health.
|Norman Terry||Cleanup of Environmental Pollutants|
Professor Norman Terry uses constructed wetlands to clean up wastewater contaminated with agricultural and industrial pollutants. HIs research on phytoremediation, using plants to clean up the environment, is multidisciplinary and ranges from the molecular to the field level. His lab was one of the first in the world to demonstrate the use of transgenic plants to remove contaminants from soil under field conditions.
|Matt Traxler||Bacterial Interactions and Metabolism|
Assistant Professor Matt Traxler explores the chemical ecology of interactions between actinomycete bacteria. His research program incorporates whole-genome transcriptomics and newly developed mass spectrometry techniques to examine the physiology of actinomycete interactions as they relate to natural product biosynthesis, and translates these insights into a new platform for natural products discovery.
|John Vogel||Grass Biology||Adjunct professor John Vogel leads the Plant Functional Genomics group at the Department of Energy's Joint Genome Institute. His research focuses on using the model grass Brachypodium distachyon and closely related species to gain a deeper understanding of several aspects of grass biology. Specific research projects include: using de-novo genome assemblies of many diverse accessions to define the full genetic complement of a species (the pan-genome), using a trio of Brachypodium species to understand polyploid genome regulation and evolution, using a perennial species, B. sylvaticum, to understand the molecular mechanism of perenniality, and using metagenome sequencing and a collection of sequenced B. distachyon mutants to identify plant genes that control the composition and function of the microbial community in the rhizosphere.|
Associate Professor Mary WIldermuth studies the interactions between plants and microbes. Plants, like humans, are continuously exposed to disease-causing microbes -- 14% of crops worldwide are lost to microbial disease each year. Conversely, there are also good microbes that can increase crop production. By understanding the complex interactions between plants and microbes, the Wildermuth Lab can predict how these interactions may change in response to altered environmental conditions. Wildermuth seeks to maintain the productivity of crops by augmenting the plant’s own responses. In addition, her basic research on phytohormones and plant disease resistance has led to implications for human innate immunity.
|Pat Zambryski||Genetic Engineering and Cell-Cell Connections|
Professor Patricia Zambryski does research in both microbial biology and plant biology. In microbial biology, she researches how Agrobacterium, a genus of Gram-negative bacteria, transfers DNA to plants. Because of this unique transformation ability, Agrobacterium has been used for genetic engineering. Professor Zambryski also studies how plant cells communicate with each other through unique plant-specific intercellular structures called plasmodesmata.
Associate Professor Daniel Zilberman studies chromatin, which is a mass of DNA and protein that forms chromosomes when condensed. His lab seeks to understand how chromatin components are interrelated and integrate to regulate transcriptional activity. He uses a variety of tools (genetics, biochemistry, genomics, computational analysis) to study chromatin, DNA and proteins.