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Pre-IMSD Summer 2013 Research Faculty

The UC Berkeley IMSD Programs are currently pending renewal of grant funding. As such, there will not be a summer 2014 Pre-IMSD program. Please check back in 2015.

Kathleen Ryan, Ph.D., Plant and Microbial Biology Claire Kremen, Ph.D., Environmental Science, Policy, and Management
Project Title - Serine/threonine kinases in Caulobacter crescentus   Project Title - Marine Resource Management Comparisons: indicators and definitions of success
Description - We are working to understand the role of protein phosphorylation on serine, threonine, and tyrosine (STY) residues in the regulation of bacterial physiology. Although STY phosphorylation is a ubiquitous and critical regulatory mechanism in plants and animals, much less is known about its role in bacteria. STY phosphorylation has recently been reported to influence bacterial motility, biofilm formation, and virulence.

We study the aquatic bacterium Caulobacter crescentus, which is known for its complex life cycle. The Caulobacter genome encodes three predicted ST kinases, enzymes which add a phosphate group to serine or threonine side chains on target proteins. To understand the function of these enzymes, the students on this project will make gene deletions of individual kinases, then build double and triple knockout strains to generate cells lacking all three enzymes. Various phenotypes of the knockout strains will be analyzed, including their growth rate, morphology, and motility. The students will learn standard techniques in molecular cloning, culturing bacteria, microscopy, and experimental design.
  Description - Protected areas are seen by many as the cornerstone of biodiversity conservation. Since the mid 1990’s improving protected area outcomes has become an increasing concern for funding agencies, natural resource managers, and conservation scientists. Central to this concern and a topic of intense debate has been identifying the best way in which to manage protected areas, some arguing for a top-down (or state-led) approach, while others argue for a bottom-up (or community-led) approach.
This research project compares community-managed and state-managed marine conservation projects in Madagascar. Questions center on how the current political upheaval in Madagascar influences management practices. This research looks specifically at (a) fish capture statistics and other indicators of “success” between numerous marine conservation projects (b) how the history of a particular marine resource management project influences the way in which locals change their resource use in reaction to the current political crisis and (b) the ways in which gendered marine resource use and participation in management influence who benefits from marine conservation.
Student Preferences - B or better in Bio1A is preferable   Student Preferences - A working understanding of French (primarily reading comprehension), experience with Excel, and familiarity with search engines is desirable but not essential.
Robert Fischer, Ph.D., Plant and Microbial Biology   Leslea Hlusko, Ph.D., Integrative Biology
Project Title - Regulation of DNA demethylation   Project Title - Study of primate fossils from South Africa
Description - DNA methylation silences genes and transposons. In the model plant system, Arabidopsis, we study the removal of DNA methylation (demethylation) from discrete sites in the genome, which is essential for plant reproduction. The student will assist in identification of new genes that regulate DNA demethylation in Arabidopsis.
  Description - The student will work with Tesla Monson to inventory and describe Plio-Pleistocene primate fossils from South Africa housed in the University of California Museum of Paleontology.
Student Preferences - Having taken Biology 1A (genetics and molecular biology section) is preferred.   Student Preferences - At least a preliminary understanding of primate evolution and skeletal biology would be advantageous, but is not required. An appreciation and enthusiasm for the study of evolution is required.
Mary Wildermuth, Ph.D., Plant and Microbial Biology   Paul Fine, Ph.D., Integrative Biology
Project Title - Discovery and characterization of new components of plant immunity


Project Title - Secondary Metabolites of Protium (Burseraceae)
Description - Plant defense to pathogens shares many features with mammalian innate immunity. This projects employs a genetic screen in the model plant Arabidopsis thaliana to identify new components of plant immunity. The student will participate in the genetic screen and characterization of an identified gene to ascertain its role in plant defense.   Description - We will be characterizing the defense chemistry of several species of Amazonian trees from the genus Protium (Burseraceae). We will be extracting and running samples through a HPLC and learning how to characterize different chemical classes and identify new molecules.
Student Preferences - Bio 1A, Chem 1A   Student Preferences - Interest in chemistry, interest in laboratory work.
Paul Fine, Ph.D., Integrative Biology   Rich Ivry, Ph.D., Psychology
Project Title - Insect herbivores and seed predators of California Hazelnut (Corylus cornuta var. californica)   Project Title - Motor learning in healthy and neurologically impaired humans
Description - We will measure the growth and seed production of California hazelnuts and capture important insect herbivores and seed predators and learn how to identify them as part of a larger study on the natural history of California hazelnut and how their demography and life history may have changed since California Indians have stopped actively managing this species.   Description - This project investigates how people learn and perform coordinated actions. We study this topic using behavioral and neuroimaging (fMRI) methods with healthy and neurologically impaired people. We teach people to make movements in a virtual reality world, creating artificial environments that require them to learn a new motor skill. We are particularly interested in how subcortical structures such as the basal ganglia and cerebellum contribute to learning.
Student Preferences - A valid driver's license, access to a car would be helpful.   Student Preferences - Coursework in biological or psychological sciences is recommended.
Danielle Tullman-Ercek, Ph.D., Chemical and Biochemical Engineering   Robert Full, Ph.D., Integrative Biology
Project Title - Engineering bacterial organelles   Project Title - Robustness in legged locomotion
Description - Nature uses compartmentalization to sequester and organize biological processes. On the cellular level, organelles are used to efficiently carry out biochemical reactions, particularly in higher-order organisms such as yeast and humans. It was recently discovered that some bacteria use compartmental systems as well, contrary to the long-held belief that bacteria lack such organization. We are putting enzymes into these bacterial compartments to carry out the synthesis of non-native, but useful, chemical products at higher yield. This project is to specifically incorporate a well-known synthetic metabolic pathway into the microcompartment and test the effect of compartmentalization on product titer.   Description - The biggest difference between animals and robots is that animals are far more robust. We want to discover the principles of robustness in legged locomotion by using running insects. Loss of a single leg prevents search and rescue robots from succeeding. Yet, insects keep running even when they lose 3-4 legs! Applicants will run insects on tracks and treadmill, video record them and analyze their movements. They will participate in discussions of how to translate their discoveries into the next generation of search and rescue robots.
Student Preferences - It will be helpful (but is not required) to have past exposure to basic genetics and cell biology.   Student Preferences - None.
Vincent Resh, Ph.D., Environmental Science, Policy, and Management   Claire Kremen, Ph.D., Environmental Science, Policy, and Management
Project Title - Project 1   Project Title - Local and landscape vegetative diversity effects on crop pollination by native bees
Description - A crucial first step in sustainably managing freshwater ecosystems is finding out the true diversity of the organisms living within them. Recent studies using molecular techniques have discovered that some aquatic insects, including Baetis tricaudatus, a “small minnow” mayfly in the family Baetidae, are in fact species complexes comprised of several cryptic species. This exciting discovery indicates that the diversity of freshwater ecosystems might be much higher than current science acknowledges. The classification and description of these undiscovered cryptic species is important for the assessment of biodiversity in general, and because the presence and diversity of mayflies, (Ephemeroptera) is widely used to determine the health of aquatic ecosystems in applied bioassesment programs (including programs used by the EPA and other government and nonprofit agencies).
This research will consist of collecting, sorting, identifying, and barcoding aquatic insects, with an emphasis on Baetis tricaudatus, from 3 sites in the Russian River watershed. Baetis tricaudatus will also be reared in the lab. The goal of this research is to accurately classify the B. tricaudatus species complex, with the larger goal of improving data used by widespread bioassesment programs.
  Description - Food security is highly dependent on the sustainability of critical ecosystem services including pollination. Recent catastrophic losses of the honeybee increase food costs and compromise production, highlighting the importance of alternative, native pollinators whose presence has been threatened by extreme agricultural intensification. It is well known that landscape-scale heterogeneity, and especially the proportion of natural habitat in the landscape, support diverse pollinator communities, providing more effective pollination. This study will examine the effects of crop diversity on the effectiveness of pollination services to crops. We seek to evaluate a potential method for improving pollination and securing higher crop yields that is more practical for farmers than restoring large areas of natural habitat or relocating farms to a more heterogeneous landscape.
Student Preferences - Qualifications include interest in biology, particularly in freshwater systems, entomology; good organization skills, and attention to detail, as lab work will include identifying insects using microscopes and sorting insect samples based on like taxa. We are looking for students who are interested in complex ecological problems, are motivated to learn, and seek hands-on experience in aquatic ecology and entomology.   Student Preferences - Having taken Biology 1A (genetics and molecular biology section) is preferred.
Ellen Simms, Ph.D., Integrative Biology   Vincent Resh, Ph.D., Environmental Science, Policy, and Management
Project Title - Host-symbiont interaction networks in plant-microbe symbiosis   Project Title - Project 2
Description - Mutualism is a cooperative interaction among species. Plants in the bean family (legumes) are mutualistic with soil rhizobial bacteria. Infected legumes produce root nodules in which rhizobia convert atmospheric nitrogen to a plant-available form in exchange for plant-derived sugars. Each plant is infected by many rhizobial strains, some of which are poor fixers. If these get a free ride because other strains fix nitrogen, then the free riders might spread and destabilize the mutualism. However, plants might prevent the spread of free-riders by directing host rewards to the most beneficial rhizobia. Some rhizobia infect multiple host species and confer upon them different degrees of benefit (they might be free-riders on some hosts but beneficial on others). We will determine whether legume species benefit the rhizobia that are most beneficial to themselves and if so, how. To answer these questions, we will inoculate plants with multiple rhizobial strains, measure plant growth, use DNA to identify rhizobial strains in nodules and measure the size and weight of nodules. We will monitor rhizobium fitness in different plants by plating crushed nodules and counting bacterial colonies obtained from these nodules. This will allow us to characterize interaction networks and mechanisms of selective partner allocation.   Description -The intern will help research the ecological effects of the insecticides most widely used in soybean production in South America, including pyrethroids such as cypermethrin and lambda-cyhalothrin and organophosphates such as chlorpyrifos. This research is pressing because pyrethroid insecticides are rapidly replacing organophosphate pesticides in many countries due to their lower toxicity to humans and other organisms. However, both classes of pesticides are highly toxic to aquatic invertebrates. There has been very little investigation of the ecological effects of pyrethroids in developing countries, in part because laboratory bioassays and associated analytical chemistry may be impractical or cost-prohibitive. Pyrethroid analysis is especially challenging because there is currently no standardized method that can detect concentrations at the very low levels that cause effects, and very few developing countries have laboratories capable of analyzing this class of pesticide.

The intern will help test whether toxicity observed in aboratory bioassays with Hyalella curvispina (a native amphipod commonly found in streams throughout South America) can be correlated with in situ bioassay results and/or benthic community changes in streams in soy-producing regions in Argentina, Bolivia, Paraguay, and Brazil. The results of this work would help determine whether the overall ecological impacts of pyrethroids are severe enough to warrant changes in their use, or implementation of management practices to control their transport to surface waters. The information gained could be used to better manage pesticide use to reduce detrimental environmental effects. This study will also advance and expand the practice of using bioassessment and in-situ bioassays as a tool in evaluating pesticide impacts in developing countries, where chemical analysis and laboratory bioassays are often impractical.
Student Preferences - You must be dedicated to the project, which involves meticulous laboratory procedures, attention to detail, continuous care of plants and bacteria, sometimes boring and repetitive protocols, but exciting and rewarding results. We prefer people who are team players and have a good sense of humor.   Student Preferences - Qualifications include interest in biology, particularly in freshwater systems, entomology; good organization skills, and attention to detail, as lab work will include identifying insects using microscopes and sorting insect samples based on like taxa. We are looking for students who are interested in complex ecological problems, are motivated to learn, and seek hands-on experience in aquatic ecology and entomology.