NSF Summer Research Experience for Undergraduates (REU):
Integrative Biology at UC Berkeley, from Molecules to Ecosystems


Individual student research projects

Individual student research projects. Modern biology is a wonderfully broad and interdisciplinary undertaking. Accordingly, the projects available to students in the UC Berkeley NSF REU Site span the range from mutational studies of gene function to anthropological approaches to human evolution. Research interests of the participating faculty typically span disciplines, and many of the projects listed fall equally into two or more areas of cell, developmental or evolutionary biology. But to illustrate the general distribution of research possibilities across these three areas, we have grouped them according to the main focus of the research in the participating faculty laboratories, Cell Biology, Developmental Biology and Evolutionary Biology. For further information follow the links to individual faculty members web sites:

Cell Biology

Greg Barton, Associate Professor, Immunology & Pathogenesis, MCB
Innate immune system. Our group studies innate immunity with the goal of understanding strategies of pathogen recognition and self/non-self discrimination. The innate immune system represents the ideal vehicle to pursue these questions because it has evolved under constant selective pressure from microbial pathogens. While adaptive immunity utilizes millions of clonally expressed receptors, the innate immune system uses an alternative strategy: a limited number of receptors with fixed specificities that are expressed non-clonally. The benefit of this strategy is speed; the cost is that the system is critically dependent on the selection of appropriate microbial targets. If the target is easily mutated, then the immune response will fail. If the target is not unique to microbes, then the immune response may attack the host. The solutions to this problem represent a fascinating set of compromises by both the host and microbes. We believe that studying this balance between innate immunity and microbial pathogens will reveal critical balance points in self/non-self discrimination with fundamental implications for our understanding of mammalian immunity. To tackle these issues the lab focuses on the function and regulation of Toll-like receptors (TLRs). TLRs are the prototypical innate immune receptor family. They participate in innate immunity, adaptive immunity, and, in some instances, autoimmunity. This central role makes TLRs an ideal system to address the conceptual issues discussed above. http://mcb.berkeley.edu/labs/barton/

Diana Bautista, Associate Professor, Cell & Developmental Biology, MCB
Molecular mechanisms of transduction in touch and pain receptors. In mammals, the initial detection of noxious chemical, mechanical or thermal stimuli – a process referred to as nociception – is mediated by specialized somatosensory neurons called nociceptors. Surprising little is known about the molecules underlying nociception. How painful stimuli excite nociceptors and how injury changes sensitivity to touch and pain are open questions. We are using a cellular physiology and molecular genetics approach to address these questions. Our current research focuses on elucidating the molecular mechanisms of somatosensory mechanotransduction. Because many forms of injury are accompanied by mechanical hypersensitivity, understanding the molecular basis of mechanosensation will help to elucidate chronic pain mechanisms. Despite its widespread importance, little is known about the molecular mechanisms that mechanosensitive neurons use to detect benign and harmful touch. We are using two approaches to identify the transduction events underlying somatosensory mechanotransduction. One is developing new strategies for the functional analysis of somatosensory neurons. The other is using the star-nosed mole as a model system of mammalian touch reception.  http://mcb.berkeley.edu/faculty/CDB/bautistad.html

David Bilder, Professor, Cell & Developmental Biology, MCB
Genetic mapping and analysis of tumorous mutants in Drosophila. An REU student would use genetic crosses to map the locations of potential Drosophila tumor suppressor genes, and also use immunohistochemistry to investigate the cell biological phenotype of mutants in these genes. These experiments will contribute to identifying new regulators of cell proliferation and cell organization. The student will learn techniques for Drosophila husbandry, planning and scoring genetic crosses, working with immunohistochemistry and fluorescence microscopy, plus concepts of genetic and phenotypic analysis. http://mcb.berkeley.edu/faculty/CDB/bilderd.html

David Drubin, Professor, of Genetics and Division Head Cell & Developmental Biology, MCB. The dynamic linkage between the actin cytoskeleton and the endocytic machinery. Real time imaging is being combined with modern molecular genetics and biochemistry. Depending on the interests and background of the student, opportunities will exist to learn about state-of-the-art fluorescence imaging of live cells, and/or about modern biochemical and molecular genetic analysis. These approaches will be used to analyze the dynamics of cytoskeletal proteins and endocytic cargo, and to reveal the mechanisms by which forces from actin polymerization are captured to promote membrane invagination and vesicle scission. http://mcb.berkeley.edu/faculty/CDB/drubind.html

Lin He, Assistant Professor, Cell & Developmental Biology, MCB. microRNA functions in cancer development, mouse tumor models. Malignant transformation represents the endpoint of successive genetic lesions that confer uncontrolled proliferation and survival, unlimited replicative potential, and invasive growth. To date, most cancer research has focused on the alterations of protein coding genes, whereas the functions of non-coding RNAs (ncRNAs) in tumorigenesis remain largely unknown. Our research aims to identify and characterize novel ncRNAs that play essential roles during tumorigenesis and tumor maintenance. Particular efforts are focused on microRNAs (miRNAs), a novel class of small, ncRNAs that mediate post-transcriptional gene silencing (Fig.1). Using mouse tumor models and cell culture studies, we will elucidate the molecular basis of the miRNA functions in the oncogenic and tumor suppressor network, and explore the potential of miRNAs as diagnostic tools and/or therapeutical targets.

Rebecca Heald, Professor, Cell & Developmental Biology, MCB
Investigating mechanisms of spindle assembly. The REU student would perform mitotic spindle assembly assays using extracts prepared from eggs of the frog Xenopus laevis and investigate the role of a specific class of proteins that binds to microtubule plus ends. Effects of depleting these proteins on spindle assembly and anaphase will be tested, and biochemical assays used to identify interacting proteins in the extract. The mitotic spindle is the microtubule-based apparatus used by all eukaryotic cells to accurately segregate chromosomes. These studies will help to develop novel reagents to study the mechanisms of spindle function, and could form the basis for novel anti-cancer therapeutics. The student will learn to collect eggs and prepare extracts, perform cell biological assays, fluorescence microscopy and image processing, plus biochemical techniques. http://mcb.berkeley.edu/faculty/CDB/healdr.html

Nilabh Shastri, Professor, Immunology & Pathologenesis, MCB
How does our immune system know if a virus is lurking inside an infected cell, if a cell has become cancerous or if an organ is transplanted from an unrelated donor?  All these cells are different from our own normal cells, but the differences are often hidden deep inside the genome.  Our immune system can nevertheless detect these differences because every cell is obliged to provide a full-disclosure of its protein contents on the surface.  This obligation is met by a mechanism called "antigen presentation".  Cells present antigens by first breaking up proteins into small pieces.  The pieces are then taken to the surface by a remarkable chaperone called the MHC.  We study the antigen presentation pathway from its beginning inside the cell to its end on the surface.  We are particularly interested in the immunological consequences of mistakes in antigen presentation which allow tumors to escape detection or cause the immune system to turn against us. http://mcb.berkeley.edu/labs/shastri

Russell Vance, Associate Professor, Immunology & Pathogenesis, MCB
Host-pathogen interactions. How do mammals defend themselves against the diverse world of microbial pathogens? This is a fundamental question that has intrigued biologists for over a century, yet some of the most important advances in our understanding have occurred only in the past decade. Given the continuing global burden of infectious disease, the study of host-pathogen interactions continues to be a pressing area of investigation. My lab is interested in all aspects of the complex interrelationship between pathogens and their hosts. In particular, we apply the modern tools of biology and genetics to answer a variety of questions at a molecular level: how is the presence of pathogenic bacteria sensed by hosts? Are pathogenic bacteria distinguished from harmless bacteria, and if so, how? What innate immune mechanisms protect cells from pathogens? How do cells coordinate defenses that are appropriate for various categories of pathogens? What mechanisms have pathogens evolved to evade host defenses? 

Matt D. Welch, Professor, Cell & Developmental Biology, MCB
Inactivation of kinesins in Trypanosoma brucei by RNA interference.
Trypanosoma brucei is the causative agent of African trypanosomiasis (sleeping sickness).  This neglected disease is a significant cause of death and morbidity in sub-Saharan Africa.  The student will work with laboratory personnel to investigate the idea that microtubule motor proteins of the kinesin family represent good molecular targets for drugs to treat trypanosomiasis.  The project will first involve amplifying and subcloning the genes encoding all T. brucei kinesins. Next, fragments of each gene will be introduced into T. brucei with the goal of inactivating the cellular copy of the gene by RNA interference. The student will learn molecular biology techniques such as PCR, restriction digestion, ligation, and DNA sequence analysis.  In addition they will learn microbiological techniques involving the growth of both bacterial and protozoan cells in culture.  Advanced students will learn biochemical techniques such as protein purification, and cell biological techniques such as fluorescence microscopy.  http://mcb.berkeley.edu/faculty/CDB/welchm.html

Developmental/Organismal Biology

George Bentley, Associate Professor, IB.
Relationships Between Reproductive Neuropeptides;  Reproductive Physiology & Behavior.  
 My laboratory investigates the interactions of the environment with reproductive physiology & behavior in vertebrate animals. At present we have projects running on a variety of organisms: amphibians, reptiles, birds and mammals. Comparative studies allow us to investigate the evolution of the structure and function of reproductive neuropeptides. In addition, we are able to understand the evolution of their interactions with other hormones that influence reproduction, secondary sexual characteristics and associated behaviors. Students are involved in the whole spectrum of the research, ranging from fieldwork, behavioral observations, blood and tissue sampling to immunohistochemistry and cell and molecular biology techniques such as RT-PCR, in situ hybridization and cell culture. Importantly, previous undergraduates in my laboratory have gone to international scientific meetings and have been authors on peer-reviewed publications in international journals.  http://ib.berkeley.edu/labs/bentley/

Marla Feller, Professor, Neurobiology, MCB
The role of neural activity in the assembly of retinal circuits. We are interested in how neural activity affects the assembly of neural circuits. There are several examples throughout the developing vertebrate nervous system, including the retina, spinal cord, hippocampus and neocortex, where immature neural circuits generate activity patterns that are distinct from the functioning adult circuitry. It has been proposed that these transitional circuits provide the "test patterns" necessary for normal development of the adult nervous system. In my laboratory, we study spontaneous activity in the immature retina, termed retinal waves, where it has been demonstrated that these correlated action potentials are involved in the organization of downstream visual centers.

Robert Fischer, Professor, PMB
The primary goal of the research in my laboratory is to understand how gene imprinting is controlled. Alleles of imprinted genes are expressed differently depending on whether they are inherited from the male or female parent. In mammals, imprinted genes contribute to the control of fetal growth and development, and human diseases are linked to mutations in imprinted genes. In plants, imprinted genes control the growth and development of seeds, which are the primary source of carbon, nitrogen, and energy for humans and domesticated animals. In my lab, we are elucidating the mechanisms for plant gene imprinting, discovering fundamental differences in the regulation of gene imprinting in plants and mammals, and are showing how DNA is enzymatically demethylated.

Sarah Hake, Director Gene Expression Center, Adjunct Professor, PMB Analysis of maize EMS mutants by genetics and microscopy. Student will be given a maize mutant that has not been characterized or mapped. The mutant will be planted at 3 different intervals so there will be a chance to see the mature form as well as capture early stages. Using bulk segregant analysis, the student will locate a rough map position for the mutation. If the mutant maps near a known mutation, complementation crosses will be initiated. Using scanning electron microscopy and histology, the student will try to determine the first stage at which the mutant deviates from wild-type. The student will learn genetics as well as have a sense of ownership with their own mutant. http://epmb.berkeley.edu/facPage/dispFP.php?I=12

Iswar K. Hariharan, Professor, Cell & Developmental Biology, MCB
Mapping genes that regulate growth in Drosophila.
A fundamental issue in biology is how animal size is determined (e.g. why is an elephant bigger than a mouse?). We have studied this question by conducting an extensive genetic screen for mutations that cause tissue in the developing eye of the fruit fly, Drosophila melanogaster to grow excessively. A student working in the laboratory will utilize a combination of genetic and cell biological techniques to characterize these mutants. Genetic crosses will be set up with strains carrying markers and the frequency of different classes of progeny will localize the mutation to a specific region of the chromosome. Concurrently, the student will stain mutant tissue dissected from larvae to examine the mutant tissue for altered expression of proteins that regulate growth. http://mcb.berkeley.edu/faculty/CDB/hariharani.html

Richard Harland, Professor, Genetics Genomics & Development, MCB
Generation of mutants and analysis. The focus of the lab is to understand development; that is, the molecular mechanisms that carefully orchestrate how a single cell (the egg) forms into an adult animal with a multitude of functioning organs.  To this end, we are interested in developing the frog, Xenopus tropicalis, into a model genetic system for studying vertebrate development.  The closely related frog, Xenopus laevis, has yielded many insights about development but is not amenable to genetic analysis. Therefore we have begun developing methods to generate mutants and analyze loss of gene function and its effects on development of the embryo. There are two avenues of research available for undergraduates:  In order to produce mutants, we are currently developing methods to mutagenize animals.  We are also developing a whole mount in situ hybridization protocol for detecting gene expression to help detect changes that would indicate gene mutation.  Finally once mutants are identified, we will study them to determine the mutated gene and its effects on development.  This project will teach a variety of methods in transcript detection and phenotype analysis and interpretation.  http://mcb.berkeley.edu/faculty/GEN/harlandr.html

Tyrone B. Hayes, Professor, IB, P.I.
Evolutionary Developmental Endocrinology and Endocrine-Disrupting Pesticides in Amphibians,
Research in my laboratory focuses on the role of hormones in developmental responses to environmental change in amphibians. Through comparative studies across populations and species, my laboratory seeks to also understand the evolution of mechanisms underlying these responses in amphibians. My work is integrative and has both a laboratory and field component. Fieldwork is conducted throughout the US and east Africa. In particular, I am interested in sexual differentiation and metamorphosis. Most recently, my laboratory has focused on the effects of pesticide on amphibian development. Studies examine effects on metamorphosis, growth, sex differentiation and immune function. Radioimmunoassay, histochemical techniques, and RT-PCR are used to monitor tissue level and cellular changes in hormone synthesis and activity in animals exposed to pesticide mixtures in both the laboratory and in animals exposed in the wild. Undergraduate students are involved in every aspect of the work, including planning, collecting in the wild, rearing and exposing animals in the laboratory, laboratory and statistical analyses, and writing paper for publication/ developing presentations http://ib.berkeley.edu/people/faculty/person_detail.php?person=85

Daniela Kaufer, Associate Professor, IB.
Stress-induced Silencing of Adult Neuronal Precursors:  Identifying Culprits and Buffering Neural Stem Cells.
What are the environmental and internal cues that control the proliferation and fate choices of stem cells in the adult hippocamus? What role does gene expression have in the translation of those cues that affect the stem cell? What is the functional relevance of stress-induced modulation of adult hippocampal neurogenesis? Using gene delivery methods, Our lab is attempting to answer these questions by investigating the effects of stress and steroid hormones on hippocampal neural stem cells.Specifically, in this project we aim to elucidate the factors which affect the long-term replicative activity and differentiation profile of neural progenitor cells residing in the adult hippocampus using isolated adult hippocampal precursor cells. This will be done using a broad array of molecular/cellular techniques: gene array expression profiling, real time PCR, fluorescent microscopy, laser capture microdissection, immunohistochemistry, and employing gene therapy tools.  http://ib.berkeley.edu/labs/kaufer/

Michael Levine, Professor, Genetics Genomics & Development, MCB; Co-Director, Center for Integrative Biology
1) Evolutionary diversification of dorsal-ventral patterning mechanisms among divergent insects, including honeybees and mosquitoes. Particular efforts could focus on the basis for an expanded midline in the ventral nerve cord of honeybees, and the subdivision of the dorsal ectoderm into distinct amnion and serosa lineages in mosquitoes.  2) Computational methods to determine the basis for complex patterns of gene expression in the early Drosophila embryo.  Simple site-occupancy models accurately predict “type 2” expression patterns of rho and vein (EGF signaling molecules) in ventral regions of the neurogenic ectoderm in response to intermediate levels of the Dorsal gradient.  It would be interesting to apply these methods to additional processes such as segmentation.  3) Elucidation of the genomic regulatory network underlying gastrulation in Drosophila.  The combination of enhancer analysis and genetic studies permit the determination of functional inter-connections among the regulatory genes engaged in gastrulation. The preceding studies will teach students basic methods and concepts in gene regulation, evolutionary biology, and computational biology. 

Nipam H. Patel, Professor Genetics, Genomics & Development, MCB and IB
Evolution of gene regulation.
The goal of this project is to use bioinformatic and developmental approaches to understand the mechanisms of evolution.  The student will use bioinformatic tools to investigate evolutionary changes in Hox genes within the arthropods, and experimentally test findings through in situ and antibody staining and the construction of transgenic Drosophila and crustaceans.  The student will be exposed to many of the core principles and methodologies of both developmental biology and evolutionary biology, and exposure to both model and non-model animal systems.

David A. Weisblat, Professor, Cell & Developmental Biology, MCB, P.I.
Cell lineage and cell fate in leech embryos.
Small leeches of the species Helobdella  (phylum Annelida) are well-suited for studies of embryonic development because their embryos are relatively large, hardy, and consist of individually identifiable cells. Thus, the Helobdella embryo is amenable to a variety of cellular and molecular techniques for elucidating developmental mechanisms. Studies of leech development are of particular interest because they contribute to understanding the super-phylum Lophotrochozoa, a diverse, yet understudied group of animals (annelids, molluscs, flatworms and others) that are evolutionarily distant from more commonly used models such as vertebrates (Deuterostomia) and arthropods (Ecdysozoa). The specific project to be undertaken will be determined according to the student's interests and the state of work in the laboratory. The student will have the opportunity to earn techniques for microinjection, molecular biology, fluorescence microscopy and image processing, plus concepts of lineage tracing and cell fate mapping. http://mcb.berkeley.edu/faculty/CDB/weisblatd.html

Evolutionary Biology

Tom Bruns, Professor, PMB
Fungal ecology and systematics. Most of the current and recent work in my lab has focused on the ecology and evolution of mycorrhizal fungi. These fungi form symbiotic associations with plant roots, and this interaction represents one of the most widespread and important mutualisms in terrestrial ecosystems. Our prior work on mycorrhizal fungi has focused on: 1) the development of molecular tools for the identification of fungi from environmental samples; 2) the characterization of fungal community structure; 3) the effect of plant host and disturbance on fungal community structure; 4) the autecology and population structure of key fungal species; and 5) the ecology and evolution of non-photosynthetic, epiparasitic plants and their fungal hosts.

Nicole King, Associate Professor, Genetics, Genomics & Development, MCB and IB
Characterization of cytoplasmic bridges in choanoflagellate colonies. Choanoflagellates are unicellular and colony forming eukaryotes that are closely related to animals and used to study animal origins.  Cells in the colony-forming choanoflagellate Proterospongia sp. are connected by cytoplasmic bridges.  The nature of these bridges and their relationship to animal cell junctions hold important implications for our understanding of animal origins.  The student researcher will characterize choanoflagellate cytoplasmic bridges by observing the localization of conserved cytoplasmic proteins and homologs of animal signaling and adhesion proteins.  The student will learn techniques for cell culture, Western analysis, fluorescence microscopy, and image processing, as well as concepts of cell biology and evolution.

Eileen Lacey, Associate Professor, IB and Associate Curator, MVZ. My research program explores the evolution of behavioral diversity among vertebrates, with emphasis on studies of mammals. Specifically, by combining field studies of behavior, ecology, and demography with molecular genetic analyses of kinship and population structure, I seek to identify the causes and consequences of variation in mammalian social behavior. Current projects in my lab include studies of (1) the effects of social behavior on variation at MHC genes, (2) the neuroendocrinology of different types of social relationships, and (3) the role of social environment in determining physiological responses to external stressors. My current research focuses on studies of subterranean rodents known as tuco-tucos and cururos. I conduct field studies of these animals in Argentina and Chile; on campus, I maintain a captive population of tuco-tucos that serves as the basis for many of the student projects conducted in my lab.

David Lindberg, Professor, IB
Shell ontogeny of marine gastropod molluscs.
Different rock types (metamorphic, sedimentary, volcanic) weather differently and create different topologies for the organisms that live on them. This topology is reflected in the shell aperture where the snail attaches to the rock.  We are currently digitizing shell apertures of snails from different rock types and using geometric morphometrics to quantify the degree of plasticity present in different species.  This work will determine if ontogenetic constraints play a role in limiting the distribution of these snails, and whether these constrains are associated with specific size classes.  Students participating in this project would be expected to master digital photography, computer-assisted image analysis, and data manipulation and analysis using computer programs.  Previous exposure to multivariate statistics would be desirable.  Students will learn modern digitization and analytical procedures for the quantification of morphology and will test hypotheses of ontogenetic constraints.


Please join us!! Questions?
http://mcb.berkeley.edu/nsfreu/ reuapplic@lists.berkeley.edu

Last Modified January 24, 2014