Discover the living world around you as you prepare for top research careers in biology.
Whether you want to be a marine biologist, microbiologist or zoologist, or work on making green biofuels — or any of more than a dozen other careers — you will find our Biology Department an exciting, supportive environment in which to broaden your knowledge, hone your skills and perform cutting-edge research. Our faculty possess a wide variety of interests and have active careers in laboratory-based research at the national and international level. They obtain federal grants for their research and publish and present their findings around the world. You will assist with research in our on-campus labs as faculty and researchers mentor you in their specialties, equipping you with critical knowledge and understanding of the biological sciences.
Laboratory for the Study of Invertebrate Behavior and Ecology (LIBE)
We pursue three interrelated lines of research in my laboratory. First, we investigate learning and memory capabilities in nautilids, a monophyletic group in the cephalopod molluscs that retains many pleisiomorphic features. Comparative study of the complex behavior across all cephalopods may help us to understand the evolution of neural and behavioral complexity in the entire class. We have found evidence of convergence between cephalopod brains and vertebrate brains, despite vast differences in the components comprising the brain (neurons, axons). We pursue studies of Pavlovian conditioning, spatial navigation, tactile learning, chemical learning, and chemical signaling in intraspecific behavior, while also attempting to identify the compounds involved. Second, we investigate the neural underpinnings of these complex behaviors: where does this learning take place, identifying analogous and/or homologous learning centers in cephalopods, labeling of neuronal activity during conditioning, whole-brain recordings, and neuroanatomy and neurochemistry. Third, we use crayfishes as a model for the haptic sense, or guided tactile behavior. Here we pair classical conditioning and open-field methods to measure haptic contributions to learning and memory of the environment in a relatively “simple” neuroanatomical model. These algorithms are then implemented in “Craybot” a tactile robot in development with Tony Prescott’s laboratory at the University of Sheffield.
During the last decade, scientists have begun to realize the importance of physical forces on the biological world. We use a broad and interdisciplinary toolkit (optical tweezers, magnetic tweezers, fluorescence and electronic microscopy, molecular biology, genetics, microfabricated substrates...) to dissect and understand the role of physical forces in the biology of piliated bacteria, in particular the human pathogen Neisseria gonorrhoeae and the related human commensal N. elongata, with both basic and applied goals in mind.
Theory and Models of Rapid Adaptation
My group uses computers and a bit of math to understand fundamental questions about how evolution works. We're particularly interested in the kinds of rapid evolution you see in viruses and bacteria, both in the lab and out in nature. Right now the big questions we’re working on are: 1) How does evolution deal with random chance in gene expression? 2) How do the host ranges of viruses evolve, and how can we predict the risk of new emerging viral pathogens in humans? and 3) How do the simple mechanisms of evolution result in such complex adaptations? Rather than study these big questions in any one model system, we use computer simulations, in concert with collaborative experiments, to better understand the theoretical side of evolution.
Mechanisms of Gamete Fusion
Fertilization in Chlamydomonas reinhardtii, a novel model system for determining the proteins required for gamete fusion, may help define the basic requirements for sperm-egg fusion in more complex systems. We use genetics, molecular biology, biochemistry and light, electron, fluorescence and confocal microscopy to identify the genes required for fertilization with the goal of understanding the mechanism of fusion used by gametes from algae to humans.
Neural and Hormonal Mechanisms of Behavior
Using fish as model systems, my lab employs a combination of evolutionary/systems neuroscience with a cellular and molecular approach in order to identify neurochemical interactions in circuitry underlying auditory-driven social behavior, mechanisms of steroid-induced neural plasticity, and sex differences in brain and behavior. These studies largely focus on vocal, auditory and neuroendocrine circuits that are conserved across vertebrates. We utilize quantitative multi-fluorescent immunohistochemistry combined with neuroanatomical tract-tracing, brightfield, epifluorescence, confocal, and transmission electron microscopy, and gene expression studies using RT-PCR and in situ hybridization. Behavioral studies are conducted at the UC Davis Bodega Marine Lab, Friday Harbor Laboratories and at field sites on the Hood Canal, WA, in collaboration with Dr. Joe Sisneros at the University of Washington.
Our goal is to determine the interplay of essential dietary fatty acid signaling with changes in host-microbe interactions. In line with this goal, we utilize cell based assays, microscopy and molecular biology to look at the effects that omega-3, omega-6 fatty acids and their metabolites have on the opportunistic fungus, Candida albicans, and its interaction with in vitro and in vivo model host systems.
Evolutionary Developmental Biology
A major effort in our lab is to elucidate molecular mechanisms associated with central nervous system development from the standpoint of evolutionary developmental biology (evo-devo). We are developing new tools that will allow us to probe neurons along their developmental path, revealing lineage history and morphology, and providing insight into neural function. We are currently analyzing genes involved in the onset and progression of Parkinson’s disease using the Drosophila model system. We conduct this research using behavioural-based analyses allowing the direct assessment of disease-related genes, and have obtained data that show dosage sensitivity for some but not all of our gene candidates. By utilizing evolutionary developmental methods based on the new methodological tools developed in our lab, we aim to clarify the biological function of genes known to cause disease, and to identify novel genes whose pathological functions are currently unknown.
Our lab is interested in the cell cycle, an ordered set of processes by which one cell grows and divides into two daughter cells. This process has to be tightly regulated to avoid chromosome instability that could lead to tumorgenesis and cancer in higher eukaryotes. Cell cycle progression is controlled by the protein complex Cyclin/Cyclin Dependent Kinase (CDK). We currently study a DNA replication factor, Cdc6. Our goal is to understand how Cdc6 is regulated during cell cycle by CDK and other kinases to limit DNA replication only once per cell cycle. We use S. cerevisiae (baker's yeast) that is an ideal model organism for cancer research; cell cycle control is well conserved from yeast to humans, and it is easy to manipulate genes in yeast.
Fungal Cell Adhesion
Our interests include structure and function of cell adhesion proteins that mediate pathogen-host interactions and biofilm formation. We have recently discovered that formation of protein amyloids is a critical step in these processes. Together with our collaborators in biophysics and medicine, our work highlights these functional amyloids: formation of 2-D amyloid patches on the cell surface actually ACTIVATES cell adhesion. These amyloids modulate immune responses in host-pathogen interactions, and are potential targets for antifungal drugs. We use molecular biology, protein chemistry, spectroscopy, and bioinformatics to study domain structure and activity.
Our lab is engaged in understanding the biological impact of ionic liquids (ILs) in the environment. ILs are non-volatile salts that are liquid at room temperature and possess physical properties that make them attractive candidates as green solvents. Using bacteria, fungi, algae and alfalfa we are dissecting the chemical and physical properties of ILs that can make ILs toxic. We have developed a sensitive toxicity assay which has enabled us to identify ILs that were considered benign as toxic. This work is done in collaboration with researchers at Queensborough Community College and Brookhaven National Labs.
Agrobacterium tumefaciens causes crown gall disease, a disease affecting several varieties of fruit trees and grapes. A. tumefaciens transfers virulence genes and proteins into susceptible host cells. The transferred virulence genes and proteins cause infected cells to form undifferentiated tumors. Recently this unique ability of A. tumefaciens to transform plants has been used by researchers to generate important transgenic crops.
Laboratory of Experimental and Applied Phycology (LEAP)
My research interests are in the fundamental and applied areas of cellular stress biology. We work with microalgae, which is a term used to describe a very diverse group of tens of thousands of organisms which display a wide spectrum of cellular and metabolic diversity. Our current fundamental research investigates the regulation of isoprenoid and lipid metabolism in unicellular green algae using a systems biology approach including for example genomic, transcriptomic, and metabolomic analysis. One exemplary model alga we investigate is the halo-tolerant species Dunaliella salina, known for its stress-induced over-accumulation of beta-carotene. The Polle laboratory was instrumental in the genome and transcriptome sequencing of this alga. Genome annotation of this model alga is ongoing in the Polle lab. In addition, we recently discovered several different green algal strains that are currently under investigation. For some of these algae we now have draft genomes for annotation and to investigate specific pathways involved in isoprenoid and lipid metabolism. This fundamental research is linked with applied research in the area of renewable energy in the context of an algae-to-biofuels program.
Cell Wall Lipids and Secondary Metabolites of Mycobacterial Species
Of the over 100 known mycobacterial species, some cause serious disease in humans and other animals, while others are capable of bioremediating contaminated environmental sites. Our lab applies a multidisciplinary approach to: (1) investigate the biosynthesis of mycobacterial siderophores (iron-chelating secondary metabolites); and (2) elucidate the biosynthesis and biological function of a class of mycobacterial outer-membrane lipids called DIMs. Siderophores are key components of iron-uptake systems utilized by both pathogenic and free-living mycobacteria. DIMs are virulence factors that underlie the pathogenicity of several clinically relevant mycobacteria by virtue of their ability to modulate the immune response or lead to nerve degeneration in the host. A specific research focus of our group is the development of small-molecule inhibitors of the biosynthesis of siderophores or DIMs that represent not only potential therapeutic leads for various mycobacterial diseases but also tools to probe the mechanisms of biosynthetic enzymes.
Molecular Targeting and Cell Signaling
We study nucleolar stress factors (NSFs) and their role/s in regulating cell cycle under normal conditions and during cellular responses to DNA damage. Nucleolin is an abundant nucleolar phosphoprotein that is overexpressed in variety of cancers. We study how nucleolin regulates mRNA stability/translation via direct binding to target-mRNAs or indirectly through protein-protein interactions in the p53 signaling, DNA damage response and ribosomal biogenesis pathways. Our long-term goal is to define the role/s of nucleolin in regulating gene expression that drives cellular decisions of growth (hence, survival and proliferation) or cell cycle arrest (that can lead to repair or cell death) to identify new therapeutic targets.
Mechanisms Preventing Aneuploidy
We investigate how the behavior and structure of chromosomes, centrosomes and the microtubule-based spindle cooperate to ensure accurate chromosome segregation during the specialized cell division program that gives rise to the sperm and egg. This cell division program, which is called meiosis, generates complementary gametes in order to ensure that at fertilization the zygote inherits the right chromosomes and other cellular components required for normal embryonic development. We utilize the transparent nematode C. elegans as a model system, and we combine molecular, genetic, biochemical and cell biological approaches. Our research is relevant not only to reproduction and the etiology of birth defects, but it is also relevant to genome maintenance in mitotic normal and pathological cell divisions.
The long-term research goal of our lab is to apply computer modeling to gain insight into cellular signal transduction pathways, specifically to provide deeper insight into both the normal and aberrant subcellular targeting and functioning of domains contained in proteins which are often part of macromolecular complexes and function in various biological processes. The protein/membrane and protein/protein complexes that function in signaling pathways are often not amenable to traditional structure determination. The integration of traditional sequence analysis bioinformatics tools to analyze genomic data with structural modeling and calculations of the bio-physical properties of the models can provide novel insights into the molecular basis of the regulation and functioning of such protein and, thus, allow the suggestion of rational and experimentally testable predictions. This computational analysis strategy has been successfully extended to a genome-wide level, allowing for the analysis of emerging families of specialized protein domains with multiple roles at the whole genome level.
Retrovirus-Host Protein Interactions
We use the model retrovirus Moloney murine leukemia virus as a tool to examine interactions between the viral integrase protein and the host cell. We are investigating these interactions using the tools of genetics, molecular biology and biochemistry. Understanding how virus-host interactions influence integration will address basic questions about infection mechanisms and also has implications for the development of some cancers, the development of gene therapy vectors, and for the progression of retroviral infections such as HIV-1, the causative agent of AIDS.
Our research focuses primarily on the study of the evolution of reproductive complexity in aquatic environments. We study a number of different freshwater and marine model systems using a combination of field, laboratory and experimental approaches to investigate how selective pressures contribute to the evolution of reproductive variation across space and time.