Admissions & Aid
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.
The living fossil, Nautilus pompilius (Chambered Nautilus), is the only externally shelled cephalopod mollusk.
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.
Top: A nesting midshipman male in the intertidal zone in Tomales Bay, CA. Bottom: Multi-label fluorescence micrograph showing catecholaminergic neurons (green) just dorsal to vocal motor neurons (pink) in the hindbrain-spinal cord.
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, Washington, in collaboration with Dr. Joe Sisneros at the University of Washington.
Faculty Bio Forlano Lab Website
Marking neurons in the Drosophila brain.
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.
Genetic network of DNA replication control.
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.
Faculty Bio Ikui Lab Website
A fluorescent dye shows amyloid proteins on the surface of fungal hyphae during an invasive gut infection.
Our lab discovered several roles and activities of cell adhesion proteins that mediate pathogen-host interactions and biofilm formation. Together with our collaborators in biophysics and medicine, our work that protein structures called amyloids (infamous in Alzheimer’s and other neurodegenerative diseases) form 2-D patches on the cell surface and between the cells to ACTIVATE cell adhesion. These amyloids modulate immune responses in host-pathogen interactions, and are potential targets for antifungal drugs. The lab is not accepting more researchers.
Faculty Bio Lipke Lab Website
Ionic liquids (ILs) in the environment.
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.
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.
Mycobacterium smegmatis cells expressing blue and green fluorescent proteins
The Quadri Lab has two long-term goals: (i) expand the biological underpinnings of mycobacterial pathogens and (ii) illuminate avenues for developing novel antibiotics to treat mycobacterial infections. We collaborate with scientists across multiple disciplines to identify drug target candidates, develop antimicrobial lead compounds, and study genes, proteins, and pathways critical to the biology of mycobacterial pathogens. Our methodological approaches include molecular biology, enzymology, mutational analysis, bioinformatics, molecular modeling, omics (RNA-Seq, Tn-Seq), inhibitor/antimicrobial assays, and mass spectrometry.
The Lab’s research is driven by the global burden of mycobacterial infections and the need for more effective antibiotics to treat them. Worldwide infections by Mycobacterium tuberculosis and several species of ubiquitous opportunistic mycobacterial pathogens (such as M. kansasii, M. abscessus, M. avium, and others) are in the millions. The global burden of these pathogens is rising, owing to the increasing prevalence of risk factors such as pharmacological immunosuppression, chronic obstructive pulmonary disease, HIV infection, malignancy, bronchiectasis, cystic fibrosis, and prior lung infections. Worryingly, the emergence of drug resistance is threatening the effective management of mycobacteria infections, with current treatments already requiring costly long-term—months to years!—multi-drug treatments—often 4 or more drugs!—with adverse side effects and challenging compliance. Thus, identifying new drug target candidates and therapeutics with novel mechanisms of action are priority research areas with significant, positive implications for public health.
Nucleolin exits from nucleoli during cellular response to stress, controlling gene expression. Scale bar represents 10 µm.
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.
High-resolution images of dividing C. elegans oocytes, spermatocytes, and embryos. DNA in blue, microtubule-based spindle in green and centrioles in red.
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.
Cartoon diagram of the active site of sheep cyclooxygenase, showing its substrate arachidonic acid, prosthetic group heme, and important functional residues.
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.
Our lab invents new mathematics and designs new computer software to understand how humans are impacting ecological communities around the world. We work together with field ecologists to collect and analyze data on lots of different kinds of species and how they interact, for example, which animals eat which insects and which insects pollinate which plants? We’re not only interested in how humans might be damaging nature, but also how nature benefits us and how we can support biodiversity. What kinds of flowers should we plant in our parks to attract pollinators and how can we use social networks to spread the word? Cities are big experiments where the natural and human worlds collide. Come join the lab and see what’s going on!
Faculty Bio Staniczenko Website
Confocal micrograph of a mammalian cell nucleus stained for a host cofactor and the Moloney murine leukemia virus integrase. The viral protein is green, the host protein is red, the overlap between the proteins is yellow, and the DNA is in blue.
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.
Male pregnancy in the seahorse. Seahorse males have evolved complex organs for protecting, aerating and nourishing their offspring.
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.
Faculty Bio Wilson Lab Website