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Past Projects
Fathead minnow microarrays for for Eco-toxicity assessment |
| Chris Vulpe |
| This project is aimed at developing DNA microarray based tests for ecological toxicity testing. Genome-wide expression analysis may be ideally suited for assessment of ecosystems and identification of eco-toxicities. However, development of a microarray infrastructure has been limited to basic research and pharmaceutical development applications. Further, little molecular biology infrastructure exists for the primary ecosystem monitoring test organisms. Here we propose to continue the development of a microarray infrastructure for the fathead minnow Pimephales promela, one of the standard aquatic toxicity assessment organisms. This work will develop a Pimephales promela cDNA microarray with more than 10,000 cDNA expressed in the brain, the liver and in whole fish at different developmental stages. In this project we will work on amplifying the cDNAs by PCR and preparing them for printing onto glass slides. |
| Began: Spring |
| View Project Details |
Regulation of Photosynthetic Light Harvesting |
| Professor Krishna Niyogi |
| In natural environments, the intensity of sunlight can vary over several orders of magnitude and on timescales ranging from seconds to seasons. Plants need light for photosynthesis, but they have to regulate the absorption and utilization of sunlight to avoid photo-oxidative damage. One of the ways they accomplish this is through an ecophysiological trait called nonphotochemical quenching, which regulates photosynthetic light harvesting. We are using a combination of genetics, biochemistry, and spectroscopy to investigate the molecular mechanism of nonphotochemical quenching. |
| Began: Fall |
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Fire history in forests at Yosemite National Park and Northern Baja California, Mexico |
| Associate Professor Scott Stephens |
| The project is investigating how well trees within Yosemite and Kings Canyon National Parks are at recording past fires in their tree rings. We have a map of all fires that have burned in our study areas and have already collected samples from fire scarred trees. We want to know how well these 2 sources of information (fire perimeter maps and trees within the fires) match. We are also working in Jeffrey pine forests in the Sierra San Pedro Martir in Baja California Mexico to determine if tree regeneration is correlated with past fires and/or climate. The Mexican site is very interesting because it has never been harvested and fire suppression did not begin until 1970. |
| Began: Fall |
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Plant Gamete Gene Expression |
| Professor Sheila McCormick |
| In higher plants, each pollen grain grows a tube in order to deliver the two sperm cells to the embryo sac, where one fertilizes the egg to give rise to the zygote, and the other fuses with the central cell to give rise to the endosperm. Despite their crucial importance for plant reproduction, very little is known about plant gametes. What genes do gametes express? Are there molecules on the cell surface that mediate egg-sperm and central cell-sperm recognition? |
| Began: Fall |
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Pollen-specific receptor-like kinases and their roles during pollen tube growth |
| Sheila McCormick |
| We have isolated and characterized several pollen-specific receptor-like kinases from tomato. These kinases are structurally related in that they all have extracellular domains with five or six leucine-rich repeats, a single transmembrane domain, and a cytoplasmic kinase domain. The different kinases within one plant may interact with different signaling partners and thus facilitate pollen tube growth. We have used yeast two hybrid screens to identify potential ligands and downstream signaling components for these kinases. |
| Began: Spring |
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Identifying the genes that regulate morphology in maize |
| Sarah Hake |
| We screen EMS-mutagenized maize populations for new phenotypes. When mutants are found, we determine if they are new alleles of already characterized genes or previoulsy unidentified genes. The mutants are mapped to chromosome location and with a population of 1000 individuals, we are often able to identify the responsible gene. Multiple alleles make the process easier. |
| Began: Spring |
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Developing climate change ( drought stress) resilient agroecosystems |
| Professor Miguel Altieri |
| We will set up field experiments at Gill Tract to test the effect of various watering regimes on bean plots managed under conventional practices (monoculture with chemical fertilizer) and organic parctices ( compost, mulch). Crop performance will be evaluated through monitoring of crop grwoth, phenology and yields, as well as through estimates of insect and disease incidence, soil biology ( N fixation) and others. |
| Began: Fall |
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Altered Sex Ratios in Aquatic Crustaceans as Biomarker of Exposure to Endocrine Disruption Chemicals |
| Associate Professor Chris Vulpe |
| Recent studies have illustrated the widespread distribution of Endocrine Disruption Chemicals (EDCs) in aquatic environments. These toxicants have resulted in the deformation of sexual organs, altered sex ratios, and reproductive impairment in many aquatic organisms. The purpose of this project is to determine the concentration of known EDCs, which causes altered sex ratios in Daphnia magna, a small aquatic crustacean and indicator species for the US EPA. This project will help determine appropriate exposure concentrations for future microarray experiments that will investigate gene expression changes caused by the EDCs. In addition, this project will help to design a simple bioassay that may be used as a screen for endocrine disruption that would be a shorter alternative to chronic toxicity bioassays. This project will involve helping to design and implement 1 week toxicity bioassays |
| Began: Fall |
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Ancestral ecology reconstruction in tropical monocots |
| Assistant Professor Chelsea Specht |
| The Zingiberales, or tropical gingers, are a diverse group of monocotyledonous plants with a pantropical distribution. Current efforts have been aimed at investigating the phylogeny of various families within the Zingiberales. These phylogenies are now available to start investigating the evolution of various characters and characteristics associated with the plants. This particular project will investigate the role of current and historic ecological associations on the distribution of Heliconias in the neotropics. |
| Began: Spring |
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Native California Bees Need a Forum |
| Gordon Frankie |
| Will gather information on the behavioral and ecological relationships of native California bees to their native California host plants at the UCB Oxford Tract. Will do plant gardening at Oxford unit to attract specific native bee species. Will use information to do outreach to several audience types in East Bay. |
| Began: Summer |
| View Project Details |
Vegetation Change and Land Management in California: A Historic View |
| Maggi Kelly |
| Databases of historical ecological data have proved useful in modern ecological research for reconstructing early environmental and vegetation community conditions, studying disturbance regimes over long temporal scales, and examining change to vegetation communities over decadal and longer temporal scales. The California Vegetation Type Mapping (VTM) project began in 1926 and continued for over ten years. During this time, Albert Everett Wieslander and a group of others mapped nearly 16 million ha (nearly 41 million acres) of California’s vegetation covering most of the wild areas of the state exclusive of the deserts and the larger agricultural areas. We have digitized and geo-referenced the plot data (which includes floristic detail), and the plot maps (which help re-locate the original plots), and the dataset is available via the web. In this project we will examine change to vegetation since 1930s using VTM plot data and plot maps across a gradient of land management. We will relocate VTM plots using historic maps and Global Positioning Systems (GPS), resurvey vegetation and take photographs in different study areas around the SF Bay Area that represent different management regimes: a State Park (e.g. Mt. Diablo), areas at the wildland-urban interface (e.g. Berkeley Hills); and areas under municipal control (e.g. Marin Municipal Water District). All data will be managed in a Geographic Information System (GIS), and analysis of change in vegetation community will be analyzed using R and Excel. |
| Began: Fall |
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Functions of genes specific to the alpha-proteobacteria |
| Assistant Professor Kathleen Ryan |
| Caulobacter crescentus is a member of the alpha subclass of the protebacteria. In the Ryan lab we study regulation of the Caulobacter cell cycle, protein localization within Caulobacter cells, and the mechanisms governing asymmetric cell division. A bioinformatic study has identified 30 genes which are characteristic of species within the alpha-proteobacteria, and three genes among them have already been shown to be important for the normal Caulobacter life cycle. We are making directed knockouts of the remaining genes in this group to identify new regulators of the Caulobacter cell cycle and cell polarity. |
| Began: Fall |
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Systematics and Evolution of Heliconiaceae |
| Assistant Professor Chelsea Specht |
| Phylogenetics of the tropical plant family Heliconiaceae |
| Began: Fall |
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Predicting climate change-induced shifts in tree species ranges |
| Professor John Harte |
| Climate change models predict that over the next century, changes in global precipitation and temperature patterns will cause species ranges to shift uphill or towards the poles. Understanding such range shifts has important implications for both long-term conservation plans and climate models that include climate-ecosystem feedbacks. However, current predictions of species shifts rely on several assumptions whose validity has yet to be established. For example, models assume that individuals of a species will respond in the same way to climate change regardless of their location within the geographic range. This project will help to test this assumption through a series of greenhouse projects using seeds collected from throughout the range of the species Jeffrey pine. |
| Began: Spring |
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Development and Implementation of a Study on Type II Diabetes Prevention in African American Children in a Community Setting |
| Sharon Fleming |
| As a nation we will spend $132 billion this year on diabetes care and complications. Unfortunately next year we will spend more because a now estimated 2.7 million US youths already have impaired insulin sensitivity putting them at risk for what was historically considered an adult disease; type 2 diabetes. The UC Berkeley project is a unique community-based research program that aims to reduce the risk of type 2 diabetes in low income overweight African American children. The program aims to reduce the risk of type 2 diabetes by providing education along with engaging activities that develop lifelong habits of healthy eating, increased physical activity, and strong self-esteem. |
| Began: Spring |
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Development and Implementation of a Study on Type II Diabetes Prevention in African American Children in a Community Setting |
| Sharon Fleming |
| As a nation we will spend $132 billion this year on diabetes care and complications. Unfortunately next year we will spend more because a now estimated 2.7 million US youths already have impaired insulin sensitivity putting them at risk for what was historically considered an adult disease; type 2 diabetes. The UC Berkeley project is a unique community-based research program that aims to reduce the risk of type 2 diabetes in low income overweight African American children. The program aims to reduce the risk of type 2 diabetes by providing education along with engaging activities that develop lifelong habits of healthy eating, increased physical activity, and strong self-esteem. |
| Began: Spring |
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Environmental influences on hatching of fairy shrimp cysts in vernal pools |
| Professor Vincent Resh |
| Vernal pools are perhaps the most specialized wetland ecosystems in California because they support both a highly adapted, and largely endemic, flora and fauna. Among these are several species of fairy shrimp that have been federally listed as endangered or threatened. Fairy shrimp are able to form cysts, which are dried and dormant eggs that can undergo complete desiccation and rehydrate after a new inundation during the next rainy season in Californias Mediterranean type climate. As such, cysts are an evolutionary adaptation to the seasonal drying of their environment. The required conditions for fairy shrimp cyst hatching are not well understood. Investigation of these environmental conditions is the focus of this research apprenticeship. |
| Began: Spring |
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Testing organic no-till systems for vegetable production |
| Miguel Altieri |
| Contrary to conventional no till systems, organic no till systems do not depend on herbicides for weed control but rely instead on the use of cover crop mixtures ( including various combinations of naked oats, rye, hairy vetch, fodder raddish, and others) which leave a thick residue mulch layer on which traditional grain crops ( corn, beans, wheat, etc) and vegetables ( broccoli, tomatoes, etc) are directly planted, suffering very little weed interference during the growing season and reaching agronomically acceptable yield levels. We will test a number of cover crop combinations, seeding rates, proportions to see which ones perform best for sustainable vegetable production in the coastal areas of northern California. |
| Began: Spring |
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Enhancing biodiversity in vineyards to improve biological control of leafhoppers |
| Professor Miguel Altieri |
| Flowering plants will be planted in several designs in an organic vineyard in Napa Valley in order to enhance resources for natural enemies of the grape leafhopper. In order to estimate the effects of diversification strategies, plots will be monitored to assess levels of biological control, leafhopper regulation, pest damage levels and grape yields. |
| Began: Spring |
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Identification of bacterial genes induced on plant surfaces |
| Professor Steven Lindow |
| The plant pathogenic bacterium Pseudomonas syringae grows on plant surfaces before causing disease. We are exploring the traits that it uses to survive the harsh condiitons found on the plant surface. A screening proceedure has enabled us to isolate over 100 random DNA sequences that appear to be induced in expression while the bacteria are residing on leaves. The project will involve cloning and sequencing many of such fragments and determining the pattern of expression of the genes that they encode and to determine the contribution of such plant-induced genes to the fitness of P. syringae on plants. |
| Began: Spring |
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Using Transposons for Functional Genomics Studies in Barley |
| Peggy G. Lemaux |
| Project Description: Complete genome sequencing of the model plant species, Arabidopsis and rice, provides important information for the scientific community; however, sequencing information alone does not permit determination of gene function. A direct approach to revealing function is to disrupt or make changes in genes and observe the consequences. The movement of transposable elements into genes can cause mutations while simultaneously providing a means to identify the gene into which it inserted. The maize Activator (Ac)/ Dissociation (Ds) transposable element system has provided a means to determine gene function in barley (Koprek et al., 2000) by causing Ds to move preferentially into genes in the presence of Ac transposase (AcTPase); segregation of AcTPase away from Ds stabilizes the element in its new location. Ds elements transpose close to their original insertion site 75% of the time and to distant locations 25% of the time. Recently successful demonstration in barley (Hordeum vulgare), of Ds transposition at significant frequencies over multiple generations, its preference to re-insert into genic regions and its frequent insertion into nearby locations facilitates mutagenesis of genes near a Ds insertion (Singh et al., 2006). Plants with single Ds insertions or TNPs, mapping near genes of interest, become vehicles for gene function determination by re-activating Ds to transpose. Barley is a major cereal crop, grown for food, feed and malted beverages. Barley can be classified into two forms based on the morphology of the spikelets: either two-rowed or six-rowed, with the latter being the more predominant type. The two-rowed condition is believed to be the primitive type, because wild barley, Hordeum spontaneum, is two-rowed. The determination of the two- or six-rowed types is controlled by the vrs1 locus located on chromosome 2. Although it is known that mutations at this locus are known to be responsible for the change from two- to six-rowed types (Lundqvist et al., 1997), the identity of the gene(s) at the vrs1 locus is not known. In crop plants, like barley, map-based cloning and transposon tagging are two of the most successful methods for identifying and cloning genes with distinct phenotypes. The maize Activator (Ac)/ Dissociation (Ds) transposon system has been successfully utilized for insertional mutagenesis in heterologous plant species for gene cloning by introducing Ds into one plant and crossing that plant with an Ac transposase-expressing plant. Because our laboratory has developed large numbers of transposon insertion lines in barley, we are interested in identifying the genes involved in vrs1 locus. From a repository of over 100 TNPs, three lines, PDS-1, PDS-3 and TNP-41 map to chromosome 2H, where the vrs1 locus maps. TNP-41 maps closest to the vrs1 locus and populations of seeds from crosses of TNP-41 with AcTPase lines are available and can be visually screened for altered spikelet morphology. This project provides an excellent opportunity to study genetic mechanisms using molecular tools and will be useful in discerning gene function. Goals of Project: The goal of this project is to generate single-copy Ds insertion lines (TNPs) mapped on chromosome 2H – specifically located near vrs1 locus – for identification of genes and their function in this locus. We can use several strategies to re-activate the Ds elements from existing lines; (1). Introducing AcTpase genes through Agrobacterium transformation. (2) Crossing of existing lines with AcTPase lines and analyzing segregating populations. Newly generated TNPs will be identified and characterized at the molecular level initially by PCR and DNA hybridization blots. Genes into which Ds has inserted will be identified through isolation using inverse PCR and sequencing of Ds flanking sequences. Flanking sequences will be used to map Ds locations on well-developed barley genetic maps. Agrobacterium-based AcTPase and Ds constructs have been created. Koprek, T; McElroy, D; Louwerse, J; Williams-Carrier, R; Lemaux, PG. (2000) An efficient method for dispersing Ds elements in the barley genome as a tool for determining gene function. Plant Journal 24: 253-263. Lundqvist, U; Franckowiak, JD; Konishi, T. (1997) New and revised descriptions of barley genes. Barley Genetics Newsletter 26: 22-516. Singh J; Zhang S; Chen, C; Cooper, L; Bregitzer, P; Sturbaum, AK; Hayes, PM; Lemaux, PG. (2006). High-frequency Ds remobilization over multiple generations in barley facilitates gene tagging in large genome cereals. Plant Molecular Biology 62: 937-950. |
| Began: Spring |
| View Project Details |
Improving Nutritional Quality of Cereals for the Developing World |
| Peggy G. Lemaux |
| Project Description Sorghum is the world’s fifth most important cereal crop and provides food for 300 million of the world’s poorest people in Africa. Its ability to maintain yield under environmental extremes, notably drought and heat, makes sorghum unique among major cereals and ideal for human and animal consumption in certain arid regions of Africa and Asia. Despite its stress tolerance, sorghum has a number of undesirable nutritional qualities. The protein and starch of sorghum are not as digestible by either humans or animals as the three staple cereal crops—maize, wheat and rice. The indigestibility of the starch and protein of sorghum grain appears to stem mainly from the nature of the major storage proteins (kafirins). These proteins are stored in the starchy endosperm of the grain and are rich in disulfide bonds which renders them resistant to proteolytic digestion. One aspect of the proposed work is based on attributes of thioredoxin (TRX), a ubiquitous redox protein with a catalytically active disulfide (S-S) group. The disulfide bonds of the kafirins can be reduced by components of the NADPH thioredoxin system, namely NADPH, NADP-thioredoxin reductase (NTR) and TRX. NTR reduces TRX to the –SH form which, in turn, reduces the disulfide bonds of the kafrin proteins in the starchy endosperm. The trx and ntr genes will be introduced into sorghum through Agrobacterium-mediated transformation such that they are specifically expressed in the endosperm and stored in protein bodies. Goals of Project In order to develop sorghum with improved digestibility qualities, constructs containing the trx and ntr genes, driven by endosperm-specific promoters and linked to signal sequences that target deposition of the proteins to protein bodies, were introduced into sorghum and transgenic lines are being generated. Once homozygous plants are identified, over-expression of TRX and NTR in the seed is assessed by Western blots. Grain from lines in which either protein is over-expressed will be used to assess digestibility characteristics, using an in vitro digestibility assay. Given the success of improving barley and wheat grains for germination frequency and hypoallergenicity, respectively, by overexpressing TRX in the grain an increase in sorghum digestibility is likely. The initial transgenic lines developed were generated using microparticle bombardment and these lines have multiple copies of the transgenes, which can cause problems with expression stability during generation advance. Therefore, currently, we are developing transgenic lines with lower copy numbers of the transgenes using Agrobacterium-mediated gene introduction. We have also used constructs containing transposable element inverted repeats flanking trx and ntr to facilitate movement of the introduced genes away from the original introduced construct, thus eliminating the selectable antibiotic resistance gene marker in the transgenic plant. |
| Began: Summer |
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The effects of climate change on the distribution of a vineyard pest |
| Nicholas Mills |
| Temperature plays an important role in defining the distribution and abundance of organisms, and global warming can lead to significant changes in the distribution patterns of species. An interesting example of a recent change in distribution is that of plant-feeding spider mites in California vineyards. Typically, Pacific spider mites are found in the hot dry regions of the Central Valley and Willamette spider mites inhabit the cooler humid coastal areas. However, in the summers of 2005 and 2006 Pacific spider mites severely damaged vines in the supposedly cool humid region of San Luis Obispo county. Pacific spider mites have never been reported from coastal grapes before, and the 2005-2006 invasion reflects a change in distribution that may be temperature driven. |
| Began: Spring |
| View Project Details |
The demography of ecotoxicology and ecosystem services in vineyards |
| Professor Nicholas Mills |
| Biological control is an important ecosystem service allowing natural enemies to prevent many arthropods from achieving pest status in agroecosystems. An interesting example of this is the western predatory mite that protects vineyards from plant-feeding spider mites. However, some of the newer pesticides that farmers use to combat pests and diseases in vineyards can disrupt the natural control provided by western predatory mites. Up to now, most studies on the effects of pesticides on natural enemies focused on direct mortality. Our project will employ microcosm experiments and demographic approaches to identify the lethal and sublethal effects of 6 novel pesticides on the population growth of the western predatory mite. |
| Began: Spring |
| View Project Details |
Green Sharpshooter Biology – Rate and Time of Egg-laying |
| Cooperative Extension Specialist Kent Daane |
| Insect vectors of plant and animal disease cause billions of dollars in agriculture damage each year. One group of insect vectors, the xylem-feeding sharpshooters, pose a threat to many crops, including grape, almond, peach, citrus. The glassy-winged sharpshooter, Homalodisca coagulate, has recently received considerable attention as a primary vector of the bacterium Xylella fastidiosa, which causes various xylem-related crop diseases such as Pierce’s disease (PD) on grapes and almond leaf scorch (ALS) on almonds. However, there are other vectors of X. fastidiosa that have been found to infect almonds with ALS, including the green sharpshooter (GSS), Draeculacephala minerva, whose life cycles have not been fully studied. To understand vector biology, it is also important to understand their host plant use outside of the crop. In almond fields throughout California, various weeds have been known to host the GSS as both feeding and reproductive hosts. Some of these weeds also harbor X. fastidiosa. The proposed research will investigate the relationship between the GSS and its potential non-crop plant hosts (e.g., common weed species). Specifically, GSS development time from mating to egg deposition, and from egg deposition to nymph emergence will be determined. Additionally, the seasonal period of egg deposition will be studied. These research questions are necessary to prepare a sustainable management program for GSS in and near California almonds, which involves not only vector (GSS) suppression but habitat (e.g., weed) modification as well. The result will be a reduction in pesticide use. |
| Began: Spring |
| View Project Details |
Towards a field-based understanding of climate change-induced shifts in tree species ranges |
| John Harte |
| We are interested in understanding how shifts in species ranges are likely to occur in response to climate change, as such range shifts have important implications for both long-term conservation planning and climate models that include climate-ecosystem feedbacks. We are therefore studying seed dispersal and seedling dynamics in the E. Sierra Nevada near Mammoth Lakes, CA in order to evaluate predictions of rapid uphill shifts in tree species ranges over the next century. By understanding how far seeds are moving, the climate conditions that allow for seedling germination and establishment of different species, and the impacts of a climate manipulation that simulates expected earlier snowmelt dates, we hope to be able to better predict the magnitude, rate, and direction of any future range shifts in this system. |
| Began: Summer |
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Evolution of tropical gingers (Zingiberales) |
| Chelsea Specht |
| My lab maintains an ongoing research project on the systematics of the tropical ginger order, Zingiberales. Particular projects involve systematics of the genus Heliconia (Heliconiaceae) and families Costaceae and Zingiberaceae. This project would be to assist in the development of these evolutionary studies with a focus on developing new molecular data that can be used to create a molecular phylogenetic hypothesis and ultimately to better understand the conservation and evolution of these charismatic tropical plants. |
| Began: Summer |
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Developmental evolution in the Zingiberales |
| Chelsea Specht |
| Based on general understanding of floral development in the model organism Arabidopsis thaliana, we have certain candidate genes that we predict are involved in diversification of floral form. These genes may be responsible for the variety of flowers and the ability of flowers to modify their morphology according to pollinator preference. This project is to investigate the role of two floral genes, Pistillata and Agamous, on the development of the highly modified flowers of the ginger order, Zingiberales. |
| Began: Summer |
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Vegetation Type Mapping |
| Maggi Kelly |
| This is a contibuation of my original SPUR project, on which John Dingman has been working. I am seeking summer funds to continue the effort. Databases of historical ecological data have proved useful in modern ecological research for reconstructing early environmental and vegetation community conditions, studying disturbance regimes over long temporal scales, and examining change to vegetation communities over decadal and longer temporal scales. The California Vegetation Type Mapping (VTM) project began in 1926 and continued for over ten years. During this time, Albert Everett Wieslander and a group of others mapped nearly 16 million ha (nearly 41 million acres) of California’s vegetation covering most of the wild areas of the state exclusive of the deserts and the larger agricultural areas. We have digitized and geo-referenced the plot data (which includes floristic detail), and the plot maps (which help re-locate the original plots), and the dataset is available via the web. In this project we will examine change to vegetation since 1930s using VTM plot data and plot maps across a gradient of land management. We will relocate VTM plots using historic maps and Global Positioning Systems (GPS), resurvey vegetation and take photographs in different study areas around the SF Bay Area that represent different management regimes: a State Park (e.g. Mt. Diablo), areas at the wildland-urban interface (e.g. Berkeley Hills); and areas under municipal control (e.g. Marin Municipal Water District). All data will be managed in a Geographic Information System (GIS), and analysis of change in vegetation community will be analyzed using R and Excel. |
| Began: Summer |
| View Project Details |
Conservation value of insects and amphibians in stormwater ponds |
| Vincent Resh |
| This project aims to determine the conservation value of stormwater wetlands in the Bay Area by quantifying the environmental factors that maximize aquatic species diversity. Little is known about the aquatic organisms utilizing these artificial habitats and if native communities or nuisance taxa are represented. Since freshwater wetlands are rare in California and most have been drained in the past, the opportunity for these new wetlands to support a diverse native community needs to be examined. Through this research we will determine what pond characteristics correlate to a rich and diverse community composition. |
| Began: Summer |
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Biogeography of Mycodrosophila in the Pacific |
| Patrick O'Grady |
| Although the center of diversity of the genus Mycodrosophila is in Australia, there are perhaps 50 species endemic to islands in the western Pacific Ocean. The current project will examine the biogeographic patterns that have led to the present day diversity by generating DNA based phylogenies of this genus and using this to understand historical patterns of distribution. |
| Began: Summer |
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Can wetland plant composition predict the extinction dynamics of a Black Rail Metapopulation? |
| Steven Beissinger |
| The incorporation of habitat dynamics into metapopulation models has recently been an area of active theoretical development. Hastings (2003) extended the classical Levins occupancy model (1969) to incorporate random disturbance and succession, and found that patch age had an important influence on metapopulation persistence. Variance in patch lifetimes and the synchrony of patch dynamics may also be important factors affecting metapopulation persistence (Wilcox et al. 2006). There may be extinction thresholds that depend on patch dynamics (i.e., age and lifetime) and metapopulation dynamics (colonization and extinction rates inherent from stochastic demography, carrying capacity and dispersal ability)(DeWoody et al. 2005, Xu et al. 2006). The rare, very secretive Black Rail (Laterallus jamaicensis, hereafter ‘rail’) is the smallest rail in North America and has a highly disjunct distribution in the U.S. It inhabits densely-vegetated, shallow, saltwater, brackish and freshwater marshes of New England, the Mid-Atlantic states, Florida, Arizona and California (Eddleman et al. 1994). The California subspecies (L. j. coturniculus) is listed as threatened by the California Department of Fish and Game (1989). Threats include habitat loss and degradation due to water and flood-control projects, land-use changes, agriculture, and livestock grazing (Eddelman et al. 1988, Eddleman et al. 1994). In 1994 a previously unknown population of Black Rails was discovered in the foothills of the Sierra Nevada Mountains near Marysville that is isolated from the nearest populations in San Francisco Bay and the Colorado River (Aigner et al. 1995). Although Black Rails rarely emerge from the dense vegetative cover they inhabit, they readily respond to tape playbacks of their vocalizations (Legare et al. 1999, Conway et al. 2004) so systematic surveys can be effectively used to estimate patch occupancy. Surveys conducted in the Sierra foothills from 1996-1999 found rails at over 70 sites in Butte, Yuba and Nevada counties and determined that rails inhabited these wetlands year-round (Tecklin 2000). We conducted systematic presence-absence surveys using playbacks from 2002-2006 at 209 potential wetland sites on public and private lands. We contacted land owners to obtain permission to conduct surveys, visited potential sites up to 3 or 5 times to determine the presence or absence of rails by broadcasting rail calls, and measured a variety of coarse habitat characteristics at each site. Using occupancy estimation models, the probability of detection (p) was estimated to be 0.863 per visit and differed little among years. Three survey visits are sufficient to generate a site-specific probability of detection (p*) > 99%. Rails in the Sierra foothills inhabit small (0.5 – 10 ha), perennial, shallow (< 3cm deep) wetlands that occur over 1,450 km2 in Butte, Yuba and Nevada counties. From 2002-2006, rails were present on average in 56% of the sites surveyed. Water sources of these small marshes (most <1 ha) include natural springs, creeks and ponds, and leaks from irrigation canals dating from the Gold Rush era to present. Sites are surrounded by dry annual grasslands that may be grazed, partially wooded grasslands, and oak or pine woodlands. Turnover occurred frequently. The probability of local extinction (0.16) was slightly less than colonization (0.18), with small differences among years. Potential rail sites were found on a nearly even mix of private and public lands, of which the latter supported the largest marshes. Habitat dynamics appear especially important to rail metapopulation dynamics. The high degree of turnover may be due to rapid changes that can occur to the small wetlands inhabited by rails. Drying, heavy grazing and other disturbances quickly make wetlands unsuitable for rails and they frequently become unoccupied within a year. Alternatively, wetlands are quickly rejuvenated by adding water through intended irrigation or leaks, or by excluding cattle from wetlands with fencing. Rails rapidly colonize changed sites within a year. This latter result was a surprise and suggests \\\\ |
| Began: Summer |
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Molecular mechanism of floral repression |
| Renee Sung |
| Flowering is a prerequiste to reproduction. Many factors are known to regulate flowering time. However, plants usually begin life by producing leaves and grow vegetatively. Vegetative growth is important to ensure plenty of nutrients for vigous flower and seed production. We have shown that the vegetative growth occurs via the reperssion of the flower program and have identified the major repressors that prevent flowering. The proposed project aims to characterize the molecular mechanism of the floral repression, which involves gene silencing via chromatin remodeling. |
| Began: Summer |
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The demography of ecotoxicology and ecosystem services in vineyards |
| Nicholas Mills |
| Biological control is an important ecosystem service allowing natural enemies to prevent many arthropods from achieving pest status in agroecosystems. An interesting example of this is the western predatory mite that protects vineyards from plant-feeding spider mites. However, some of the newer pesticides that farmers use to combat pests and diseases in vineyards can disrupt the natural control provided by western predatory mites. Up to now, most studies on the effects of pesticides on natural enemies focused on direct mortality. Our project will employ microcosm experiments and demographic approaches to identify the lethal and sublethal effects of 6 novel pesticides on the population growth of the western predatory mite. |
| Began: Summer |
| View Project Details |
Evolutionary ecology and speciation of invasive whiteflies |
| George Roderick |
| Examining the genetic variation among populations is an essential first step in studying the population history of a species as well its potential future trajectory. Such studies can be undertaken with the use of molecular markers - specific DNA pieces that provide information on the amount of genetic variation that exists among populations. This project will use molecular markers to look at the amount of genetic variation that exists among populations of the invasive whitefly Bemisia tabaci. Bemisia tabaci is distributed throughout the world and causes significant damage to crops and ornamental plants. One aspect of the biology of this insect makes it particularly attractive to evolutionary research: the worldwide populations of this species are so genetically differentiated from each other that they are quite likely undergoing the process of evolutionary divergence into discrete species. Further studies of the genetic variation, with the use of more informative markers, is therefore necessary to resolve the evolutionary history of these populations and give further insight into the status of their genetic diversity, and whether or not they represent unknown cryptic species. This information can help understand the future of these species as pests. |
| Began: Summer |
| View Project Details |
Molecular Phylogeny of Hawaiian Drosophilidae |
| Patrick O'Grady |
| The Hawaiian Drosophilidae are the classic example of adaptive radiation in nature, with over 1000 species evolving in Hawaii over the past 25 million years. While our understanding of the evolutionary relationships within this group is increasing, there are still several groups for which we have no phylogenetic hypothesis. Recent work on the haleakalae and planitibia species groups suggests that both predate the existing high islands with rainforest habitat. Furthermore, there is a distinct pattern of older species on older islands and younger species on younger islands. It is our goal to examine additional clades of Hawaiian Drosophila to see if they fit this same pattern. This summer two undergraduates will work on the split tarsus and bristle tarsus species groups. |
| Began: Summer |
| View Project Details |
Evolution of Dessication Tolerance in Cheilanthoid Ferns |
| Chelsea Specht |
| The cheilanthoid ferns are a monophyletic group of ferns that include genera Pellaea, Astrolepis, Notholaena, and Cheilanthes among others. These ferns have adapted to harsh desert environments and have evolved various mechanisms for dealing with drought and dessication tolerance. This project will be a first step to understanding the evolution of some of the anatomical mechanisms involved in dessication tolerance in this group of ferns. |
| Began: Summer |
| View Project Details |
Study of Yeast Metabolic Pathways by Functional Profiling |
| Chris Vulpe |
| This project will use a collection of S. cerevisiae deletion strains to study the genetic requirements of yeast for optimal growth in different conditions. Each of the yeast strains carries a deletion in a different gene and is uniquely identified by a molecular barcode, which is a 20bp sequence inserted in the DNA. Pools containing all deletion strains will be grown under several conditions of interest which will include different carbon and nitrogen sources, and vitamin and amino acid deficiency. Depending on the gene deletion, some strains will grow faster and some others slower (or will not grow at all) in the conditions of interest than in control conditions. By identifying the strains that show a difference in growth, we will identify the genes that are essential (or detrimental) for growth under these conditions. We will identify those strains by measuring the growth of all deletion strains simultaneously with special microarrays that contain the complementary sequences to the molecular barcodes present in the DNA of the deletion strains. This information will be used to gain understanding of the metabolic pathways involved under the different growth conditions, as well as interactions with other pathways, and potentially identify novel genes. |
| Began: Fall |
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Intraspecific variation and population response to climate change |
| John Harte |
| Climate change models predict that over the next century, changes in global precipitation and temperature patterns will cause species ranges to shift uphill or towards the poles. Understanding such range shifts has important implications for both long-term conservation plans and climate models that include climate-ecosystem feedbacks. However, current predictions of species shifts rely on several assumptions whose validity has yet to be established. For example, models assume that individuals of a species will respond in the same way to climate change regardless of their location within the geographic range. This project will help to test this assumption through a series of greenhouse projects using seeds collected from throughout the range of the species Jeffrey pine, and will serve as a complement to related field studies. |
| Began: Fall |
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Plant Gamete Gene Expression |
| Sheila McCormick |
| In higher plants, each pollen grain grows a tube in order to deliver the two sperm cells to the embryo sac, where one fertilizes the egg to give rise to the zygote, and the other fuses with the central cell to give rise to the endosperm. Despite their crucial importance for plant reproduction, very little is known about plant gametes. What genes do gametes express? Are there molecules on the cell surface that mediate egg-sperm and central cell-sperm recognition? |
| Began: Fall |
| View Project Details |
Evolution of pesticide resistance in spider mites in California vineyards |
| Nicholas Mills |
| Arthropod populations evolve in response to selection pressures in their environment. One major force of selection and evolution in nature is the application of pesticides for the management of agricultural and public health pests. Currently, over 500 species of insects and mites developed resistance to one or more pesticides. This ecological situation can be compared to a virtual “arms race” between the development of new pesticide compounds and evolution of pesticide resistance. One example of resistance development in response to selection pressure is found in Pacific spider mites, a common pest of vineyards in California. Grape growers treat over 250,000 acres with pesticides each year for the management of this serious pest. However, in 2005 and 2006 some spider mite populations survived repeated applications of pesticides, suggesting the existence of pockets of resistant individuals. In this project we will collect Pacific spider mite populations from vineyards around California and expose them to different concentrations of pesticides to identify their resistance status. In addition, we will use data on frequency of pesticide applications and relevant literature studies to identify factors influencing evolution of pesticide resistance. |
| Began: Fall |
| View Project Details |
The effects of climate change on the distribution of a vineyard pest |
| Nicholas Mills |
| Temperature plays an important role in defining the distribution and abundance of organisms, and global warming can lead to significant changes in the distribution patterns of species. An interesting example of a recent change in distribution is that of plant-feeding spider mites in California vineyards. Typically, Pacific spider mites are found in the hot dry regions of the Central Valley and Willamette spider mites inhabit the cooler humid coastal areas. However, in the summers of 2005 and 2006 Pacific spider mites severely damaged vines in the supposedly cool humid region of San Luis Obispo county. Pacific spider mites have never been reported from coastal grapes before, and the 2005-2006 invasion reflects a change in distribution that may be temperature driven. |
| Began: Fall |
| View Project Details |
Fair Trade Claims and Consumer Behavior |
| Sofia Villas-Boas |
| This research project is part of a research agenda aiming at estimating the value consumers associate (or not) to claims of their product being a fair trade product. Possibly combining empirical evidence resulting from a variety of data soruces, some generated by the research team (surveys) and other data obtained from a large retail chain (scanner data) we aim to estimate the average value consumers place on the fair trade product characteristic as well as the heteregeneity associated with consumer characteristics of the value attributed to that claim. |
| Began: Fall |
| View Project Details |
Nutritional Point of Purchase Claims and Consumer choices |
| Sofia Villas-Boas |
| In an effort to promote healthier diets the U.S. government has developed and implemented regulations regarding the provision of nutrition information to consumers. In particular, the Nutrition Labeling and Education Act (NLEA) of 1990 developed guidelines for nutrient and health claims and mandated that packaged food products include nutrition facts panels. Although there are documented benefits associated with nutrition facts panels, the usefulness of these panels at the point of purchase is limited owing to the time and effort associated with processing the information, which typically requires the consumer to remove the product from the shelf and turn it in such a way to view and read the nutrition facts panel. We address this situation in the current research by exploring the outcomes of presenting nutrition information directly on grocery store shelf labels i.e., the small tags affixed on grocers’ shelves beneath their products. |
| Began: Fall |
| View Project Details |
Systematics and Evolution of Heliconiaceae |
| Chelsea Specht |
| Phylogenetics of the tropical plant family Heliconiaceae. This family is a member of the ginger order that includes bananas (Musaceae), gingers (Zingiberaceae) and heliconias (Heliconiaceae). They are showy tropical plants pollinated by hummingbirds, yet little is known about their evolutionary history. This project focuses on developing a species-level phylogeny to start to understand the evolution of floral diversity among heliconias. |
| Began: Fall |
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Competition in Vegetable Markets |
| Ethan Ligon |
| Compile and analyze historical data on wholesale vegetable prices across the United States over the course of the post-war period. |
| Began: Fall |
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Development and Implementation of a Study on Type II Diabetes Prevention in African American Children in a Community Setting |
| Sharon Fleming |
| As a nation we will spend $132 billion this year on diabetes care and complications. Unfortunately next year we will spend more because a now estimated 2.7 million US youths already have impaired insulin sensitivity putting them at risk for what was historically considered an adult disease; type 2 diabetes. The UC Berkeley project is a unique community-based research program that aims to reduce the risk of type 2 diabetes in low income overweight African American children. The program aims to reduce the risk of type 2 diabetes by providing education along with engaging activities that develop lifelong habits of healthy eating, increased physical activity, and strong self-esteem. |
| Began: Fall |
| View Project Details |
Development and Implementation of a Study on Type II Diabetes Prevention in African American Children in a Community Setting |
| Sharon Fleming |
| As a nation we will spend $132 billion this year on diabetes care and complications. Unfortunately next year we will spend more because a now estimated 2.7 million US youths already have impaired insulin sensitivity putting them at risk for what was historically considered an adult disease; type 2 diabetes. The UC Berkeley project is a unique community-based research program that aims to reduce the risk of type 2 diabetes in low income overweight African American children. The program aims to reduce the risk of type 2 diabetes by providing education along with engaging activities that develop lifelong habits of healthy eating, increased physical activity, and strong self-esteem. |
| Began: Fall |
| View Project Details |
Molecular mechanism of floral repression |
| Renee Sung |
| Flowering is a prerequiste to reproduction. Many factors are known to regulate flowering time. However, plants usually begin life by producing leaves and grow vegetatively. Vegetative growth is important to ensure plenty of nutrients for vigous flower and seed production. We have shown that the vegetative growth occurs via the reperssion of the flower program and have identified the major repressors that prevent flowering. The proposed project aims to characterize the molecular mechanism of the floral repression, which involves gene silencing via chromatin remodeling. |
| Began: Fall |
| View Project Details |
Evolution of Dessication Tolerance in Cheilanthoid Ferns |
| Chelsea Specht |
| The cheilanthoid ferns are a monophyletic group of ferns that include genera Pellaea, Astrolepis, Notholaena, and Cheilanthes among others. These ferns have adapted to harsh desert environments and have evolved various mechanisms for dealing with drought and dessication tolerance. This project will be a first step to understanding the evolution of some of the anatomical mechanisms involved in dessication tolerance in this group of ferns. |
| Began: Fall |
| View Project Details |
Biogeography of Mycodrosophila in the Pacific |
| Patrick O'Grady |
| Although the center of diversity of the genus Mycodrosophila is in Australia, there are perhaps 50 species endemic to islands in the western Pacific Ocean. The current project will examine the biogeographic patterns that have led to the present day diversity by generating DNA based phylogenies of this genus and using this to understand historical patterns of distribution. |
| Began: Fall |
| View Project Details |
Breast cancer prevention by lunasin |
| Ben de Lumen |
| The project proposes to test the cancer preventive property of lunasin, a seed peptide discovered in our lab, against breast cancer. SENCAR mice will be fed 4 different diets: control, hydrolyzed casein, 1.5% lunasin diet and 3.0% lunasin diet. Beginning around 10 weeks, the mice will be observed for any breast tumors. After 10 weeks, blood will be drawn every 2 weeks and tested for the biomarkers cytokeratin-19 and mamaglobin. After 16 to 20 weeks, the mice will be sacrificed for detailed tumor analysis and biomarker measurements in the serum, liver and mammary tissues. |
| Began: Fall |
| View Project Details |
Molecular Genetics of Antioxidant Vitamin Biosynthesis and Function |
| Krishna Niyogi |
| Antioxidant vitamins, such as pro-vitamin A, vitamin C, and vitamin E, are synthesized by plants and are essential components of the human diet. We are taking molecular and genetic approaches to investigate the biosynthesis and function of antioxidant vitamins in the unicellular green alga, Chlamydomonas reinhardtii, a widely used experimental model that has several advantages for genetic studies, including a completely sequenced genome. The project will involve mutagenesis of Chlamydomonas cells, mutant screening, HPLC analysis of vitamins, phenotypic characterization of progeny from genetic crosses, and genotypic characterization using PCR-based molecular markers. Fall 2006 and Spring 2007 |
| Began: Fall |
| View Project Details |
Singlet oxygen signaling and acclimation |
| Krishna Niyogi |
| In an aerobic environment, responding to intracellular and extracellular oxidative signals is critical for physiological adaptation (acclimation) to changing environmental conditions. We are studying the ability of the model photosynthetic organism Chlamydomonas reinhardtii to acclimate to specific forms of oxidative stress. For example, when Chlamydomonas cells are exposed to a sublethal pretreatment with a specific type of reactive oxygen species (singlet oxygen), defense responses are activated that confer subsequent resistance to singlet oxygen stress. This acclimation response is dependent on nuclear gene transcription and cytoplasmic protein synthesis, and microarray analysis of RNA levels has shown that a relatively small number of genes respond to sublethal doses of singlet oxygen. Constitutive expression of one of these genes, which encodes a glutathione peroxidase homolog, is sufficient to enhance singlet oxygen resistance. The goal of this project is to dissect the signal transduction pathway involved in acclimation to singlet oxygen by isolating and characterizing mutants with abnormal expression of the glutathione peroxidase target gene. |
| Began: Fall |
| View Project Details |
Molecular Phylogeny of Hawaiian Drosophilidae |
| Patrick O'Grady |
| The Hawaiian Drosophilidae are the classic example of adaptive radiation in nature, with over 1000 species evolving in Hawaii over the past 25 million years. While our understanding of the evolutionary relationships within this group is increasing, there are still several groups for which we have no phylogenetic hypothesis. Recent work on the haleakalae and planitibia species groups suggests that both predate the existing high islands with rainforest habitat. Furthermore, there is a distinct pattern of older species on older islands and younger species on younger islands. It is our goal to examine additional clades of Hawaiian Drosophila to see if they fit this same pattern. This summer two undergraduates will work on the split tarsus and bristle tarsus species groups. |
| Began: Fall |
| View Project Details |
Native California Bees Need a Forum |
| Gordon Frankie |
| The Urban Bee Project looks at relationships between native bees and their native and ornamental host flowers in urban areas. This project also performs outreach work to local groups including schools, garden clubs, and environmental groups. |
| Began: Fall |
| View Project Details |
Pollen-specific receptor-like kinases and their roles during pollen tube growth |
| Sheila McCormick |
| We have isolated and characterized several pollen-specific receptor-like kinases from tomato. These kinases are structurally related in that they all have extracellular domains with five or six leucine-rich repeats, a single transmembrane domain, and a cytoplasmic kinase domain. The different kinases within one plant may interact with different signaling partners and thus facilitate pollen tube growth. We have used yeast two hybrid screens to identify potential ligands and downstream signaling components for these kinases. |
| Began: Fall |
| View Project Details |
Scaling up vegetational diversification strategies in Napa and Sonoma vineyards |
| Miguel altieri |
| The proposed project will allow us to scale-up agroecological approaches that our group has been experimentally testing for ten years. We will break vineyard monoculture structure with cover crops and/or hedgerows and corridors, and thus enhance biological control promoting a more preventative approach to pest management. We will work with eight wine grape growers in the re-design of their vineyards What is unique about this proposed project is its participatory nature, with active involvement of farmers in the implementation of the designs as well as the monitoring, allowing the testing of a suite of agroecological strategies in several environments. At each participating vineyard, a 1- acre experimental plot will be established to assess the effectiveness of several designs on soil quality indicators and populations of insect pests and natural enemies. Diversification will be complemented with organic soil fertilization treatments to enhance organic matter content and soil fauna. We expect grapes grown in soils with high organic matter and active soil biology to exhibit lower abundance of insect pests |
| Began: Spring |
| View Project Details |
Analysis of cell to cell transport in Arabidopsis |
| Professor Patricia Zambryski |
| We are investigating how plant cells communicate with each other via plant specific channels called plasmodesmata. We have developed a genetic screen for mutants impaired in intercellular transport in the model plant system. We are using a variety of molecular, genetic, and cell biological techniques to characterize mutants and wild type siblings. |
| Began: Spring |
| View Project Details |
The effects of climate change on the distribution of a vineyard pest |
| Nicholas Mills |
| Temperature plays an important role in defining the distribution and abundance of organisms, and global warming can lead to significant changes in the distribution patterns of species. An interesting example of a recent change in distribution is that of plant-feeding spider mites in California vineyards. Typically, Pacific spider mites are found in the hot dry regions of the Central Valley and Willamette spider mites inhabit the cooler humid coastal areas. However, in the summers of 2005 and 2006 Pacific spider mites severely damaged vines in the supposedly cool humid region of San Luis Obispo county. Pacific spider mites have never been reported from coastal grapes before, and the 2005-2006 invasion reflects a change in distribution that may be temperature driven. |
| Began: Spring |
| View Project Details |
Conservation value of insects and amphibians in stormwater ponds |
| Vincent Resh |
| This project aims to determine the conservation value of stormwater wetlands in the Bay Area by quantifying the environmental factors that maximize aquatic species diversity. Little is known about the aquatic organisms utilizing these artificial habitats and if native communities or nuisance taxa are represented. Since freshwater wetlands are rare in California and most have been drained in the past, the opportunity for these new wetlands to support a diverse native community needs to be examined. Through this research we will determine what pond characteristics correlate to a rich and diverse community composition. |
| Began: Spring |
| View Project Details |
Amphibian Malformations in the Bay Area |
| Professor Vincent resh |
| Amphibians, with extra legs, missing legs, or malformed limbs have been found across California and elsewhere in the United States. These frogs are often infected with a parasite, a trematode called Ribeiroia ondatrae, which has been shown to induce limb abnormalities in the laboratory. It is unclear what factors cause interannual variation in malformation prevalence at a given site, which can range between 10 and 70%. This study is designed to document and interpret parasite dynamics at multiple sites across the Bay Area. Also, this study will evaluate the seasonal parasite and snail host dynamics at one site in Hopland, California. |
| Began: Spring |
| View Project Details |
Characterization of protein-protein interactions associated with programmed cell death |
| N. Louise Glass |
| We have identified a number of proteins that are involved in programmed cell death in the filamentous fungus Neurospora crassa. This molecular biology/genetics project involves further characterization of these genes/proteins by functional assays (in N. crassa) and co-immunoprecipitation experiments to confirm protein interactions. |
| Began: Spring |
| View Project Details |
Genetic analysis of mutants required for programmed cell death |
| N. Louise glass |
| Our lab uses the filamentous fungus Neurospora crassa as a model organism for the study of programmed cell death. During vegetative growth, N. crassa individuals can undergo fusion, forming a heterokaryon. However, if the two individuals are genetically different at any one of their 11 het loci, the fused cells will be rapidly compartmentalized and undergo programmed cell death. This type of cell death in fungi is known as heterokaryon incompatibility. In this project we would isolate new mutants involved in the programmed cell death response using a genetic screen for suppressors of heterokaryon incompatibility. Next, the mutants would be tested for allelism to known genes and to each other, and finally the mutants will be mapped and characterized. |
| Began: Spring |
| View Project Details |
Molecular mechanism of floral repression |
| Renee Sung |
| Flowering is a prerequiste to reproduction. Many factors are known to regulate flowering time. However, plants usually begin life by producing leaves and grow vegetatively. Vegetative growth is important to ensure plenty of nutrients for vigous flower and seed production. We have shown that the vegetative growth occurs via the reperssion of the flower program and have identified the major repressors that prevent flowering. The proposed project aims to characterize the molecular mechanism of the floral repression, which involves gene silencing via chromatin remodeling. |
| Began: Summer |
| View Project Details |
Isotopic characterization of San Francisco Bay tidal wetland vegetation, invertebrates and fish |
| Cooperative Extension Specialist Maggi kelly |
| Changes to sea level and salinity regimes due to climate change will likely have an impact on the SF Bay estuary. The tidal wetlands in the bay will likely be influenced by these changes to salinity and inundation which will have cascading effects to other trophic levels. This project will be determining the linkage between tidal wetland vegetation and the pelagic food web and will be accomplished through the use of stable isotopes. Samples of fish, invertebrates and plants from various wetlands in the SF Bay estuary will be analyzed for stable isotopes. |
| Began: Spring |
| View Project Details |
The Riskcape and the Colorline: An EJ Approach to Examining Racial Disparities in Birth Outcomes |
| Associate Professor Rachel Morello-Frosch |
| This project is examining race and class-based disparities in exposures to air pollution and their implications for perinatal outcomes, such as infant mortality, birth weight and pre-term birth. We will also be looking at social drivers of environmental health disparities such as segregation and income inequality. We need assistance using a geographic information system to generate air pollution exposure estimates for the States of California, Texas, Colorado, Ohio, Georgia and other states. |
| Began: Spring |
| View Project Details |
Understanding novel biogenesis pathway of siRNA of gene-associated small transposons in Solanaceae. |
| Barbara Baker |
| Small RNAs regulate the genome by guiding transcriptional and post-transcriptional silencing machinery to specific target sequences, including genes and transposable elements (TEs). Miniature inverted repeat transposable elements (MITEs) and short interspersed elements (SINEs) are closely associated with euchromatic genes, however the broader functional impact of these small gene-associated TE insertions is largely unknown. We identified numerous gene-associated TEs in Solanaceae (GATES). Several generate genome changes that potentially affect gene function and regulation, and we hypothesize that some insertions may contribute to gene regulation in development or in response to biotic and abiotic challenges. We also discovered that GATEs generate siRNAs that are primarily 24-nt and that their biogenesis is dependent on a novel set of DICER-LIKE (DCL) proteins compared to Arabidopsis. Given their amplification, and the potential of GATE siRNAs to target multiple gene-associated sequences, we hypothesize that the transposition GATEs into genes may constitute an evolutionary mechanism that brings genes under the control of regulatory silencing pathways, contributing to the evolution of coordinated gene expression. Experiments are underway to test our hypotheses. |
| Began: Spring |
| View Project Details |
The Living Campus: Mapping UC Berkeley's Ornamental Trees |
| Cooperative Extension Specialist Maggi kelly |
| We want to map the trees on the UC Berkeley campus, taking note of their condition and any potential threats to these trees. This database will help the UCB landscapers plan tree management. We will be using Global Positioning Systems and Geographic Information Systems technology to create field forms, capture spatial data, and make static and internet maps of the campus. |
| Began: Spring |
| View Project Details |
Testing plant diversification schemes in vineyrads and cole crops for enhanced biological pest control |
| Miguel altieri |
| The proposed project will allow us to test various diversification schemes in vineyards and cole crops and assess effects on the biological control of key pests of these crops. We expect that by breaking the monoculture structure of vineyards with cover crops and of broccoli via intercropping designs we will be able to enhance biological control promoting a more preventative approach to pest management. |
| Began: Summer |
| View Project Details |
Amphibian Malformations in the Bay Area |
| Vincent Resh |
| Amphibians, with extra legs, missing legs, or malformed limbs have been found across California and elsewhere in the United States. These frogs are often infected with a parasite, a trematode called Ribeiroia ondatrae, which has been shown to induce limb abnormalities in the laboratory. It is unclear what factors cause interannual variation in malformation prevalence at a given site, which can range between 10 and 70%. This study is designed to document and interpret parasite dynamics at multiple sites across the Bay Area. Also, this study will evaluate the seasonal parasite and snail host dynamics at one site in Hopland, California. |
| Began: Summer |
| View Project Details |
Analysis of cell-to-cell transport during development in plants |
| Patricia zambryski |
| The Zambrsyki lab in the Department of Plant and Microbial Biology studies cell-to-cell communication. One area of interest is the intercellular communication in plants via channels called plasmodesmata (PD). These PD are plasma membrane-lined cytoplasmic conduits for the passage of small molecules between cells. They are also critical to the transport of larger molecules including proteins and RNA that have essential roles in development and defense. Interestingly, PD are also co-opted by pathogens, particularly plant viruses, for cell-to-cell spread during infection. The lab has conducted ground- breaking research into the developmental regulation of PD and used an ingenuous genetic screen to identify mutants with altered PD function leading to striking developmental defects. The genes responsible for two of these mutations, ISE1 and ISE2, have been mapped and cloned. We are currently using ISE1 and ISE2 to investigate the regulation of PD function. |
| Began: Summer |
| View Project Details |
Understanding novel regulatory properties of siRNAs derived from gene-associated transposons. |
| Barbara Baker |
| Small interfering RNAs (siRNAs) regulate the genome by guiding transcriptional and post-transcriptional silencing machinery to specific target sequences, including genes and transposable elements (TEs). We identified numerous gene-associated TEs (GATEs) in Solanaceae and we hypothesize that some insertions may contribute to plant gene regulation during response to environmental stress, pathogen challenge or at particular stages in development. We discovered that GATEs generate siRNAs and that their biogenesis is dependent on a novel set of DICER-LIKE (DCL) proteins. The high copy number of closely related GATE elements dispersed throughout Solanaceae euchromatin and the potential of GATE-derived siRNAs to target multiple gene-associated sequences raises the possibility that these transposons may contribute to coordinated changes in gene expression through regulatory silencing pathways. Experiments are underway to test this hypothesis. |
| Began: Summer |
| View Project Details |
Elucidating regulation of plant response to pathogens |
| Mary Wildermuth |
| The phytohormone salicylic acid is a key mediator of plant defense against pathogens. However, our knowledge of controls over the regulation of salicylic acid (SA) synthesis is limited. This project is focused on identifying and characterizing regulators impacting SA synthesis and SA-dependent processes. |
| Began: Summer |
| View Project Details |
Understanding beetle diversity in Chilean Temperate Forests: Using DNA data to investigate relationships and species limits in Pterostichine Beetles |
| Kipling Will |
| As part of our Biological Survey and Inventory of arthropods in the Temperate Forests of Chile we are investigating the evolutionary relationships of beetles that are only known from this well-recognized biodiversity hotspot. In part the project focuses on the species-rich carabid beetles (http://tolweb.org/Harpalinae/ ). In this diverse family the tribe Pterostichini ( http://tolweb.org/Pterostichini/ ) found in Chile has ancient origins in and relationships to Gondwana and significant, presumably more recent, diversification of species. Preliminary studies in one genus, Parhypates, (http://tolweb.org/Parhypates/51596 ), suggest this pattern of ancient origins and recent diversification. This project will investigate this by incorporating data from multiple DNA sources into existing datasets to specifically address species/subspecies boundaries and relationships of the genus to African, Australian, New Zealand and New Caledonian pterostichines. Within Chile, island, coastal and Andean species/population will be investigated to refine the existing taxonomy and determine how many undescribed species need description. See also: http://nature.berkeley.edu/~kiplingw/ http://www.coleopterosdechile.cl/nsf/index.htm http://essig.berkeley.edu/ |
| Began: Summer |
| View Project Details |
Nutritional Improvement of Sorghum |
| Peggy G. Lemaux |
| Project Description Sorghum is the world’s fifth most important cereal crop and provides food for 300 million of the world’s poorest people in Africa. Its ability to maintain yield under environmental extremes, notably drought and heat, makes sorghum unique among major cereals and ideal for human and animal consumption in certain arid regions of Africa and Asia. Despite its stress tolerance, sorghum has a number of undesirable nutritional qualities, including incomplete amino acid profile and poor digestibility. Goals of Project In order to develop sorghum with improved nutritional qualities, we have introduced genes that will increase the amino acids needed to make sorghum a more complete source of protein. We also are studying the makeup of the seed that is responsible for its poor digestibility. Currently, we have developing transgenic lines using Agrobacterium-mediated gene introduction. These lines need to be generation advanced and characterized at the molecular, biochemical and physiological levels. |
| Began: Summer |
| View Project Details |
Uncovering species diversity within Neurospora |
| John Taylor |
| The Taylor Lab is interested in the study of fungal evolution and genomics. One important area of research in the lab has been recognizing Neurospora species by genetic methods and then elucidating the evolutionary relationships among the species. The two remaining morphological Neurospora species that have not been well studied are N. sitophila and N. tetrasperma. Understanding the full phylogeny of the genus will be important in the future when scientists want to apply laboratory data to nature. The Spur project in the lab would involve growing N. sitophila and N. tetrasperma cultures from a wild collection, sequencing informative loci from the isolates, and adding the new data to a phylogenetic tree to understand phylogenetic species in N. sitophila and N. tetrasperma. |
| Began: Summer |
| View Project Details |
Improving the Nutritional Quality of Sorghum for the World’s Poor |
| Peggy G. lemaux |
| Project Description: Sorghum is the world’s fifth most important cereal crop and provides food for 300 million of the world’s poorest people in Africa. It is also becoming an important crop in the U.S. for its importance for bioenergy production. This is due at least in part to its ability to maintain yield under environmental extremes, notably drought and heat. This makes it unique among major cereals and ideal for human and animal consumption in certain arid regions of Africa and Asia. Despite its stress tolerance, sorghum has some undesirable qualities that might benefit from genetic engineering approaches. These include nutritional deficiencies and relative recalcitrance to digestion. Goals of Project: In order to develop sorghum with improved nutritional qualities, we have introduced a gene from barley that has amounts of the amino acids that are deficient in sorghum. The hope is that with this overexpression it might make the cereal a more complete source of protein for some of the world’s poorest people. The overexpression of this gene might also change the digestibility properties of the grain. To accomplish this goal, we have developed a more efficient system of transformation and have generated 14 independent lines, using Agrobacterium-mediated gene introduction. These lines are being generation advanced and must now be characterized at the molecular, biochemical and physiological levels. |
| Began: Fall |
| View Project Details |
Commodity Food Prices and changes in Consumer Eating Habits |
| Sofia villas-boas |
| Commodity prices have been rising at unprecedented rates over the last two years. In the last year alone, corn prices are up 51.9%, soybean prices 74.4%, wheat prices 104.5%, and milk prices by 41.4%, not to mention equally impressive increases in the prices of fuel, fertilizer and other raw products that enter the food production system. The primary objective of the project is to assess how consumers adjust to those changing food prices. Given factor price changes, the study will examine the effects on consumer behavior, average consumer expenditures, and within- and across-food-category substitution for consumers on average and across demographic groups. For each of the commodities, regressions will be run using store-level product weekly data. The left-hand side variables include (A) the percentage of weekly revenues in a category of name-brand and private-label products, (B) the percentage (revenues or quantities) in a category of products on sale, and (C) the percentage sold in a category of “healthy” products (using nutritional information). The focus is on the effect of commodity price increases, controlling for the other explanatory variables, on the type of goods purchased: brand name versus private label, goods on sale versus others, healthy versus less-healthy foods. |
| Began: Fall |
| View Project Details |
Pollen-specific receptor-like kinases and their roles during pollen tube growth |
| Sheila McCormick |
| We have isolated and characterized several pollen-specific receptor-like kinases. These kinases are structurally related in that they all have extracellular domains with five or six leucine-rich repeats, a single transmembrane domain, and a cytoplasmic kinase domain. The different kinases within one plant may interact with different signaling partners and thus facilitate pollen tube growth. We used yeast two hybrid screens to identify potential ligands and downstream signaling components for these kinases. |
| Began: Fall |
| View Project Details |
Plant Gamete Gene Expression |
| Sheila McCormick |
| In higher plants, each pollen grain grows a tube in order to deliver the two sperm cells to the embryo sac, where one fertilizes the egg to give rise to the zygote, and the other fuses with the central cell to give rise to the endosperm. Despite their crucial importance for plant reproduction, very little is known about plant gametes. What genes do gametes express? Are there molecules on the cell surface that mediate egg-sperm and central cell-sperm recognition? |
| Began: Fall |
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Self-incompatibility in biofuel crops |
| Sheila McCormick |
| Perennial grasses that are potential biofuel crops have reproductive biology features that make them difficult to work with. One such barrier is Self incompatibility (SI), which in grasses is controlled by 2 unlinked genes, S and Z. A pollen grain that has both S and Z alleles in common with the alleles in the female part of the flower will fail, whereas a pollen grain with only one of the S or Z matches with alleles in the female part of the flower can succeed. Learning how to manipulate Self-incompatibility in this plant will make it easier for plant breeders to make inbred lines, which are useful in crop improvement. |
| Began: Fall |
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Amphibian Malformations in the Bay Area |
| Vincent Resh |
| Amphibians, with extra legs, missing legs, or malformed limbs have been found across California and elsewhere in the United States. These frogs are often infected with a parasite, a trematode called Ribeiroia ondatrae, which has been shown to induce limb abnormalities in the laboratory. This study will evaluate the seasonal parasite and snail host dynamics at one site in Hopland, California. |
| Began: Fall |
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Conservation value of insects and amphibians in stormwater ponds |
| Vincent Resh |
| This project aims to determine the conservation value of stormwater wetlands in the Bay Area by quantifying the environmental factors that maximize aquatic species diversity. Little is known about the aquatic organisms utilizing these artificial habitats and if native communities or nuisance taxa are represented. Since freshwater wetlands are rare in California and most have been drained in the past, the opportunity for these new wetlands to support a diverse native community needs to be examined. Through this research we will determine what pond characteristics correlate to a rich and diverse community composition. |
| Began: Fall |
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Global patterns of climatic effects on ecological population dynamics |
| Perry de Valpine |
| We will use the Global Population Dynamics Database (GPDD), a collection of nearly 3000 time-series of population abundances of many kinds of organisms, to investigate large-scale patterns in the role of climate on population dynamics of taxa ranging from insects to birds to mammals. Many studies of population dynamics patterns omit climatic data, although climate is likely to be an important explanatory factor for many populations. We will compile publicly available records of climatic data that are geographically matched to GPDD records and investigate a variety of hypotheses about the role of climate across many populations and species. |
| Began: Fall |
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The effects of climate change on the distribution of a vineyard pest |
| Nicholas Mills |
| Temperature plays an important role in defining the distribution and abundance of organisms, and global warming can lead to significant changes in the distribution patterns of species. An interesting example of a recent change in distribution is that of plant-feeding spider mites in California vineyards. Typically, Pacific spider mites are found in the hot dry regions of the Central Valley and Willamette spider mites inhabit the cooler humid coastal areas. However, in the summers of 2005, 2006 and 2007 Pacific spider mites severely damaged vines in the supposedly cool humid region of San Luis Obispo county. Pacific spider mites have never been reported from coastal grapes before, and the 2005-2007 invasion reflects a change in distribution that may be temperature driven. |
| Began: Fall |
| View Project Details |
Coevolution of Hawaiian Leaf Hoppers |
| Assistant Professor Patrick o'grady |
| This project will examine the systematics, historical biogeography and diversification of a diverse leafhopper group (Cicadellidae: Nesophrosyne) endemic to the Hawaiian Islands and their primary and second bacterial endosymbionts. The genus Nesophrosyne contains 61 documented species distributed on all high islands in the archipelago, and is intimately associated with native Hawaiian flora. Facilitating these host plant interactions are two obligate bacterial endosymbionts (one being a novel infection), implicated in the nutritional exploitation of host plants. The widespread geography, host distribution of Nesophrosyne, and its association with obligate endosymbionts present a unique opportunity to examine the processes driving speciation of phytophagus insects. The discrete well-understood geology and chronology of the islands add a necessary temporal context to evolution of this system in. |
| Began: Fall |
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Reconstructing the phylogeny and evolution of click beetles (Elateriadae) using DNA sequence data |
| Kipling Will |
| Click beetles (Elateridae) are well known for their amazing click-startle defense mechanism by which a beetle that is on its back (dorsal side) can flick itself into the air righting itself and startling would be predators. Some species are bioluminenscence and in some cases species are significant pests. It is a family with a huge diversity, 400 genera and about 10,000 species worldwide. The much evidence supports the family as a natural group, however, the relationships within the family are unclear. This project intends to reconstruct the for the family by developing a DNA sequence data matrix for several gene loci and focusing on the tribe Pomachiliini, a taxonomically difficult group that is extremely diverse and pivotal to developing an understanding the evolution of the group. |
| Began: Fall |
| View Project Details |
Biogeography of Mycodrosophila in the Pacific |
| Professor Patrick O'Grady |
| Although the center of diversity of the genus Mycodrosophila is in Australia, there are perhaps 50 species endemic to islands in the western Pacific Ocean. The current project will examine the biogeographic patterns that have led to the present day diversity by generating DNA based phylogenies of this genus and using this to understand historical patterns of distribution. |
| Began: Fall |
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Obesity Prevention: Translate research into fact sheets |
| Patricia Crawford |
| Much research in the area of childhood obesity prevention needs to be translated into user friendly terminology, simple messages, and figures and graphs in order to reach the populations most in need of intervention and assistance. The student will be responsible for translating research findings on obesity prevention in children into easy to read and easy to understand fact sheets that can be disseminated to low-income families, community groups and schools. |
| Began: Fall |
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Green Tech |
| Susan kishi |
| Identify employers in Silicon Valley who are offering Green Tech services. |
| Began: Spring |
| View Project Details |
Systematics and Evolution of the new world Costus (Costaceae) |
| Chelsea Specht |
| Phylogenetics of the tropical plant family Costaceae with a focus on the old world species of the genus Costus. This family is a member of the ginger order that includes bananas (Musaceae), gingers (Zingiberaceae) and heliconias (Heliconiaceae). New World Costus species are showy tropical plants pollinated by hummingbirds and bees, yet little is known about their evolutionary history. This project focuses on developing a species-level phylogeny to start to understand the evolution of floral diversity among Costus and to tie in the evolution of bird and bee pollination syndromes. |
| Began: Spring |
| View Project Details |
Systematics and Population genetics in the Mexican cycad genus Dioon |
| Chelsea Specht |
| Cycads comprise an ancient plant lineage with fossils dating back 250my. The genus Dioon is mostly endemic to Mexico and occurs in the transition zone between deciduous scrub forest and Pine/Oak forest around 1000m-1500m above sea level. This project involves developing a phylogeny (evolutionary history) for the genus Dioon (12 species) and investigating the population genetics of 3 species native to the Oaxaca plateau that have undergone a recent rapid radiation. |
| Began: Fall |
| View Project Details |
Global land cover classification over Fluxnet sites |
| Peng gong |
| The Fluxnet has over 500 sites all over the world. While site specific measurement of carbon exchange between vegetation and atmosphere is the primary source of data serving the world scientific community, its detailed description on the surroundings around the site is also useful to the study of global land cover. This project involves having an undergraduate student to go through all the fluxnet sites, (1) map the location of these sites on Google Earth using its specific format; (2) classify each site of surface cover into the IGBP classification scheme according to site description and image interpretation over Google Earth; (3) build a Google Earth database so that everyone in the world can use it to check on the site description and its land cover class. |
| Began: Spring |
| View Project Details |
Developing and Using Improved Methods to Engineer Sorghum for the World’s Poor |
| Peggy G. lemaux |
| Introduction Project Description: Sorghum, the world’s fifth most important cereal, provides food for 300 million of the world’s poorest people in Africa. Historically in the U.S. sorghum has been used for animal feed but is becoming a potential crop for bioenergy production. Certain agronomic properties of sorghum make it increasingly popular because it is naturally drought and heat tolerant and requires fewer inputs to achieve optimal yields. This makes it unique among major cereals and ideal for arid regions of Africa and Asia, and possibly drought-striken regions in the U.S. But sorghum has some qualities that might benefit from genetic engineering approaches, including nutritional deficiencies and relative recalcitrance of its protein and starch to digestion. Goals of Project: To achieve improvements in sorghum, it is necessary to have an efficient, reproducible transformation system. While such a system was developed with one sorghum variety, P898012, in the Lemaux laboratory, this variety has high phenolic content resulting in problems with selection and regeneration. To improve this situation and also to speed the process of transformation, we selected a short-generation variety, N247, which reaches maturity 3-4 weeks earlier than P898012. The complete genome of sorghum has been completed and in order to facilitate functional genomics studies in this important cereal we are developing and optimizing in vitro culturing and transformation methods with this variety. Once identified, we will introduce a gene from barley that has higher amounts of the amino acids deficient in sorghum. By overexpressing this gene, we hope to make a cereal that is a more complete source of protein for some of the world’s poorest people. The overexpression of this gene might also change digestibility properties of the grain and biochemical assays are in place to look at variability in protein and starch digestion. |
| Began: Spring |
| View Project Details |
Microbial Ecology of Methane Production in a Tropical Rainforest |
| Professor Mary Firestone |
| Microorganisms that consume or produce methane, a potent greenhouse gas, can play an important role in controlling methane-based climate forcing. This project will investigate the diversity and activities of methane producing (methanogens) and consuming (methanotrophs) microorganisms in soil within the Luquillo Experimental Forest (LEF), Puerto Rico. Soils within LEF produce and consume methane simultaneously, but the responsible microbes have not been well characterized. Methanogen and methanotroph communities will be characterized in soils from across elevation and moisture gradients in LEF using a combination of culture-independent techniques in parallel with physiological and culture- dependent analyses. |
| Began: Spring |
| View Project Details |
Impacts of urban land use on bee visitation in the Berkeley-Bay Area landscape. |
| Joe Mcbride |
| This project involves an examination of the affect that local site characteristics and landscape variables have on the visitation rates of ecologically important pollinators, native bees. While bees are essential to the functioning of natural and managed ecosystems and are often the primary vectors of pollination, there is still much to learn about how this diverse group of organisms interacts with its habitat. Less is known about the dynamics of resources use in modified landscapes, such as urban areas. As cities grow and urban landscapes increase in size and number, investigations of how this new landscape influences important native species become pertinent. This particular study examines how the bee-plant relationship between the California Poppy and its native bee visitors changes as resource dynamics, resource density and quality, and land use patterns vary across Berkeley, Albany, Emeryville, and Oakland. It adds to the larger knowledge base on urban ecology and native bee conservation |
| Began: Spring |
| View Project Details |
Green Tech |
| Susan kishi |
| Identify employers in Silicon Valley who are offering Green Tech services. |
| Began: Spring |
| View Project Details |
Comparative floral development in the Zingiberales |
| Chelsea specht |
| This project will be focused on cataloging and categorizing the evolution of floral development across the eight families of Zingiberales (including bananas, gingers, bird-of-paradise). The student will work with the PI and a graduate student to explore the role of two floral development genes, PISTILLATA and CYCLOIDEA, in the evolution of floral diversity within this this important group of tropical monocots. |
| Began: Spring |
| View Project Details |
Transcription regulation of lipogenesis |
| Professor Hei Sook sul |
| Lipogenesis is exquisitely regulated by nutritional/hormonal states. Fatty acid synthase (FAS) is a central enzyme in lipogenesis and is thought to be a rate-limiting step in long-term regulation. FAS transcription is low in the fasted state but increases dramatically with feeding. Increased insulin is largely responsible for the activation of FAS transcription. We showed that feeding/insulin increases SREBP-1c but that, by direct physical interaction, USF bound to the -65 E-box recruits SREBP to bind -150 SRE for activation of the FAS promoter. USF may be a molecular switch during the fasting/feeding and diabetes/insulin transitions. Using tandem affinity purification coupled with mass spectrometry (MS), we recently identified components of the USF holocomplex and found that different components participate in a fasting/feeding dependent manner. By MS analysis, we also detected a feeding-dependent specific site phosphorylation of USF as well as two adjacent sites of USF acetylation. In Aim 1, once we identify the components of the USF holocomplex, we will examine by chromatin immunoprecipitation differential binding of the various components of USF holocomplex to the FAS promoter in fasting/feeding and diabetes/insulin treatments and correlate binding with the FAS promoter activity and transcription. Transgenic mice carrying CAT gene driven by the various 5'-deletions and mutations of the FAS promoter will allow us to verify the binding sites. We will also characterize direct or indirect interactions of various factors with USF as well as the interacting domains. SiRNA- mediated knockdown experiments will demonstrate the significance of these factors in the regulation of the FAS promoter. In Aim 2, we will examine specific USF phosphorylation by DNA-dependent protein kinase (DNA-PK) as well as the signaling pathway leading to DNA-PK activation and thus USF phosphorylation. We will also examine specific acetylation/deacetylation of USF via recruitment of P/CAF or HDAC9, which may depend on phosphorylation state of USF. Functional consequences of phosphorylation/acetylation of USF on the regulation of the FAS promoter will be studied. Finally, we will examine posttranslational modifications of USF in vivo by adenovirus mediated gene transfer or by generating transgenic mice. We will also use DNA-PK deficient mice to test the role of DNA-PK for USF function and lipogenesis as well as glucose/insulin homeostasis. Our research will elucidate the USF function as a master regulator of lipogenesis during fasting/feeding and diabetes/insulin transitions and may reveal a novel insulin signaling pathway. |
| Began: Spring |
| View Project Details |
Developing Tropical Forest Management Tools to Enhance Biodiversity Conservation and Ecosystem Services Production |
| Matthew Potts |
| Existing harvesting protocols in tropical forests were designed to optimize timber production with little consideration for the impact of harvesting on biological diversity and ecosystem service production. New harvesting protocols are needed that explicitly take the multiple impacts of harvesting into account. The goal of the project is to aid the design of a new computerized forest management tools. Specifically, the undergraduate researcher will use using existing field data to explore how placing constraints on the location and size of trees harvested impacts biodiversity, carbon stocks and fluxes, and water quality. The results of the research will directly aid an on-going interdisciplinary sustainable forest management project in Malaysia. |
| Began: Spring |
| View Project Details |
Sierra Nevada Mixed Conifer Fire History |
| Scott stephens |
| This project seeks to understand the historical role of fire in the mixed conifer forest of the western slope of the Sierra Nevada. Fire scar samples will be collected from one study site in the southern sierra (Sugar Pine) and one study site from the central sierra (Last Chance). These scars will then be mounted, planed, and sanded for optimal ring visualization. Fire events will then be dated and analyzed with stereoscopic microscopy, infinity capture, and infinity analysis software. Composite fire histories will be constructed for each study site. Historic fire frequencies and extent will be reconstructed from this data. Information such as this is vitally important for understanding what role fire played in these forests before the current era of fire suppression. Findings from this study will have implications for current forest management, fire mitigation, and forest restoration. |
| Began: Spring |
| View Project Details |
Effect of Fuel Prices on Trucking |
| Jeffrey Perloff |
| A supply and demand model of the trucking industry will be used to examine the effects of fuel prices, taxes, and other shocks on the quantity and price of trucking. Sudden increases and decreases in gasoline prices such as occurred this last year can have dramatic effects on shipping costs and hence sales in all sectors of the economy, including agriculture and manufacturing. We will concentrate on the effects of gasoline and carbon taxes. For example, Senators McCain and Clinton called for a temporary federal gas tax moratorium to offset gas price increases. We will estimate the effects of such a moratorium. (Note: The main purpose of this project is to give undergraduates experience in empirical analysis of economic policy questions. Thus, I'm willing to consider alternative questions proposed by the student.) |
| Began: Spring |
| View Project Details |
Biogeography of Giant Ground Beetles (Carabidae: Scaritini) |
| Associate Professor Kipling will |
| Giant ground beetles (Carabidae: Scaritini) are perhaps one of the largest predatory beetles known. The genus Mouhotia from Southeast Asia reaches length of over 6 cm. All members of the tribe Scaritini are flightless. Another interesting observation about this group is that they are found on all the continents except South America and Africa. One question raised by these observations is how did they get around to places like Australia without wings? One can test hypotheses of vicarient biogeography (the spitting of areas) using a phylogenetic framework. A current phylogeny (the evolutionary relationships) does not exist for this group. This project intends to derive these relationships based on DNA sequences of conserved regions in the beetle genome. Once enough sequence data has been generated the phylogenetic trees can be constructed for further hypothesis testing. |
| Began: Spring |
| View Project Details |
Hydroponic production of botanical drugs |
| Professor Norman Terry |
| The Terry lab is currently focusing on the study of botanical drugs. The long-term goal of this research is to rationalize the process of development and production of Chinese herbs for medicinal purposes. Specifically, we are developing a three-step method for the production of plant biomass in the greenhouse. The method includes: 1) tissue culturing the plant species, 2) regenerating plants from the tissue cultures, and 3) growing the plants hydroponically to obtain a rapid increase in biomass. This project will focus on Artemisia annua, the plant that produces the anti-malarial drug artemisinin. Specifically, this project will determine if A. annua plants grown in hydroponics have similar levels of artemisinin to plants cultivated in the field. |
| Began: Spring |
| View Project Details |
Analysis of septation in Neurospora crasa |
| N. Louise Glass |
| In Neurospora crassa, septation is required for the production of asexual spores and to compartmentalize hyphae. The multi-cellular hyphae are then protected from whole colony lysis- either from damage or from incompatability reactions. This project will attempt to map two mutations known to cause septation defects. Each has been roughly mapped to a small region of the genome. Once this mapping is confirmed, PCR, cloning, and DNA sequencing will be used to determine the gene involved in the production of septa. |
| Began: Spring |
| View Project Details |
Molecular structure and evolution of giant sequoia (Sequoiadendron giganteum) |
| Richard dodd |
| Giant sequoia occupies sixty seven groves, extending through about 400 km along the west slopes of the Sierra Nevada. Groves north of the Kings River are isolated, whereas southern groves occupy a more continuous belt from just south of the Kings River to Deer Creek. Reasons for this limited distribution are poorly understaood, particularly the disjunct northern distribution. Giant sequoia grows well when planted in other parts of the world. This project will use DNA sequencing to study levels of genetic diversity in selected stands of giant sequaoia. The sequence data will be interpreted to detect fluctuations in population size over time and to determine the degree of population genetic differentiation. We hope to be able to determine whether extant stands have a history that pre-dates the Holocene warm period that has been suggested as the time of origin of these groves. |
| Began: Summer |
| View Project Details |
Molecular Phylogeny of Hawaiian Drosophilidae |
| Patrick O'Grady |
| The Hawaiian Drosophilidae are the classic example of adaptive radiation in nature, with over 1000 species evolving in Hawaii over the past 25 million years. While our understanding of the evolutionary relationships within this group is increasing, there are still several groups for which we have no phylogenetic hypothesis. Recent work on the haleakalae and planitibia species groups suggests that both predate the existing high islands with rainforest habitat. Furthermore, there is a distinct pattern of older species on older islands and younger species on younger islands. It is our goal to examine additional clades of Hawaiian Drosophila to see if they fit this same pattern. This summer two undergraduates will work on the split tarsus and bristle tarsus species groups. |
| Began: Summer |
| View Project Details |
Toward Improving Sorghum for Africa’s Poor |
| Peggy G. Lemaux |
| Project Description: Sorghum is the world’s fifth most important cereal crop, after wheat, maize, rice and barley. In the U.S. this grain is used primarily for animal feed and more recently bioenergy production, but for over 300 million people in the semi-arid regions of Africa it is their primary source of food. Certain agronomic properties of sorghum make it increasingly popular as a crop plant globally because it is naturally drought-, heat- and flood-tolerant and requires fewer inputs to achieve reasonable yields. This positions it as unique among major cereals and ideal for arid and semi-arid regions of Africa and Asia, and also possibly drought-stricken regions of the U.S. But sorghum has qualities that could benefit from genetic engineering, including nutritional deficiencies and agronomic weaknesses. Goals of Project: To achieve improvements in sorghum through genetic engineering, it is necessary to have an efficient, reproducible transformation system. This was achieved in the Lemaux laboratory with one sorghum variety, P898012, and this involved one SPUR student (Gurel et al., 2009). However, this variety has high phenolics, causing difficulties with selection and regeneration. To avoid this problem and to speed transformation, we chose another short-generation variety, N247, which has fewer phenolics and reaches maturity 3-4 weeks earlier. Once successful, we will introduce a gene from barley encoding a protein with higher levels of lysine, tryptophan and threonine, amino acids that are deficient in sorghum. Overexpressing this protein in the seed, we hope to make a cereal that is a more complete source of protein. Another nutritional weakness of sorghum, relative to other cereal grains, is its relative indigestibility, particularly after cooking. This means many calories are lost to the consumer, which makes it great as a diet food but not optimal for African consumers. Overexpression of the barley gene could also change the protein profile of the seed and hence its digestibility. Biochemical and proteomic analyses will be used to study variation in protein and starch digestion of the engineered sorghum. In another approach, the complete genome of sorghum variety, B623,is available. To facilitate the study of gene function, we are developing an in vitro culturing and transformation system for B623. Naturally occurring transposable elements are present in sorghum, which are activated following in vitro culture. These will be used to develop a gene tagging system – a critical adjunct to the full genome sequence to help realize sorghum’s contribution to Africa's poor. |
| Began: Summer |
| View Project Details |
Biochemical characterization of an essential phosphatase in Caulobacter crescentus |
| Kathleen Ryan |
| PtpA is a predicted phosphatase that is essential for the viability of Caulobacter crescentus. When PtpA is depleted, Caulobacter cells die and their cell walls become ragged and blebby. When PtpA is overexpressed, Caulobacter cells lose their curved shape and become straight rods. We hypothesize that PtpA dephosphorylates one or more proteins involved in building the cell wall. The project goals are 1) to purify the PtpA enzyme, 2) to characterize its phosphatase activity toward small molecule substrates, and 3) to use a "trap" mutant to identify the cellular substrates of PtpA. |
| Began: Summer |
| View Project Details |
Molecular Genetics of Antioxidant Vitamin Biosynthesis and Function |
| Krishna Niyogi |
| Antioxidant vitamins, such as pro-vitamin A, vitamin C, and vitamin E, are synthesized by plants and are essential components of the human diet. We are taking molecular and genetic approaches to investigate the biosynthesis and function of antioxidant vitamins in the unicellular green alga, Chlamydomonas reinhardtii, a widely used experimental model that has several advantages for genetic studies, including a completely sequenced genome. The project will involve mutagenesis of Chlamydomonas cells, mutant screening, HPLC analysis of vitamins, phenotypic characterization of progeny from genetic crosses, and genotypic characterization using PCR-based molecular markers. |
| Began: Summer |
| View Project Details |
Identification of novel genes mediating salicylate-based immune responses in plants |
| Mary wildermuth |
| Salicylic acid (SA) is a small molecule that mediates plant innate immunity. To identify novel genes involved in salicylate signalling and response, we are performing a high-throughput screen to identify Arabidopsis thaliana mutants with altered sensitivity to SA. |
| Began: Summer |
| View Project Details |
Transcription regulation of lipogenesis |
| Hei Sook sul |
| Lipogenesis is exquisitely regulated by nutritional/hormonal states. Fatty acid synthase (FAS) is a central enzyme in lipogenesis and is thought to be a rate-limiting step in long-term regulation. FAS transcription is low in the fasted state but increases dramatically with feeding. Increased insulin is largely responsible for the activation of FAS transcription. We showed that feeding/insulin increases SREBP-1c but that, by direct physical interaction, USF bound to the -65 E-box recruits SREBP to bind -150 SRE for activation of the FAS promoter. USF may be a molecular switch during the fasting/feeding and diabetes/insulin transitions. Using tandem affinity purification coupled with mass spectrometry (MS), we recently identified components of the USF holocomplex and found that different components participate in a fasting/feeding dependent manner. By MS analysis, we also detected a feeding-dependent specific site phosphorylation of USF as well as two adjacent sites of USF acetylation. In Aim 1, once we identify the components of the USF holocomplex, we will examine by chromatin immunoprecipitation differential binding of the various components of USF holocomplex to the FAS promoter in fasting/feeding and diabetes/insulin treatments and correlate binding with the FAS promoter activity and transcription. Transgenic mice carrying CAT gene driven by the various 5'-deletions and mutations of the FAS promoter will allow us to verify the binding sites. We will also characterize direct or indirect interactions of various factors with USF as well as the interacting domains. SiRNA- mediated knockdown experiments will demonstrate the significance of these factors in the regulation of the FAS promoter. In Aim 2, we will examine specific USF phosphorylation by DNA-dependent protein kinase (DNA-PK) as well as the signaling pathway leading to DNA-PK activation and thus USF phosphorylation. We will also examine specific acetylation/deacetylation of USF via recruitment of P/CAF or HDAC9, which may depend on phosphorylation state of USF. Functional consequences of phosphorylation/acetylation of USF on the regulation of the FAS promoter will be studied. Finally, we will examine posttranslational modifications of USF in vivo by adenovirus mediated gene transfer or by generating transgenic mice. We will also use DNA-PK deficient mice to test the role of DNA-PK for USF function and lipogenesis as well as glucose/insulin homeostasis. Our research will elucidate the USF function as a master regulator of lipogenesis during fasting/feeding and diabetes/insulin transitions and may reveal a novel insulin signaling pathway. |
| Began: Summer |
| View Project Details |
Understanding novel gene regulatory properties of siRNAs derived from gene-associated transposons. |
| Barbara Baker |
| Small interfering RNAs (siRNAs) regulate the genome by guiding transcriptional and post-transcriptional silencing machinery to specific target sequences, including genes and transposable elements (TEs). We identified numerous gene-associated TEs (GATEs) in Solanaceae and we hypothesize that some insertions may contribute to plant gene regulation during response to environmental stress, pathogen challenge or at particular stages in development. We discovered that GATEs generate siRNAs and that their biogenesis is dependent on a novel set of DICER-LIKE (DCL) proteins. The high copy number of closely related GATE elements dispersed throughout Solanaceae euchromatin and the potential of GATE-derived siRNAs to target multiple gene-associated sequences raises the possibility that these transposons contribute to coordinated changes in gene expression through regulatory silencing pathways. Experiments are underway to test this hypothesis. |
| Began: Summer |
| View Project Details |
Finding Resistance to Bacterial Spot Disease of Tomato in Wild Solanum Species |
| Brian staskawicz |
| Plants and their microbial pathogens often exhibit gene-for-gene resistance, in which a plant resistance (R) protein specifically recognizes an effector protein delivered into the plant cell by a pathogen. We can take advantage of this phenomenon to engineer resistant crops. Bacterial spot disease of tomato, caused by related species of the genus Xanthomonas, is endemic in warm, moist environments, including Florida, where nearly half of all fresh market tomatoes in the US are grown. Growers attempt to control the disease by applying copper bactericides and streptomycin, but durably resistant plants are needed as a safe and sustainable way to control bacterial infection. Although cultivated tomatoes (Solanum lycopersicum) have no natural R genes, wild Solanum species are a potential source of new R genes. We have characterized the repertoire of effector genes in several Xanthomonas strains, and will soon obtain genome sequences that will expand this collection. These effectors, expressed in plants via Agrobacterium or delivered as proteins by Pseudomonas fluorescens, can be used as probes to identify new resistance genes in wild species. |
| Began: Summer |
| View Project Details |
Interaction of repressor and antirepressor in Arabiodopsis |
| Professor Zinma Sung |
| Flowering is regulated by environmental and developmental signals. To maintain plants in the vegetative states, we have identified genes that maintain silencing of the flower homeotic genes. We are now investigating antirepressor genes that antagonize the repressor action and activate flower homeotic genes. |
| Began: Fall |
| View Project Details |
Toward Understanding and Improving Sorghum for Africa’s Poor |
| Cooperative Extension Specialist Peggy G. Lemaux |
| Introduction: Sorghum is the world’s fifth most important cereal crop, after wheat, maize, rice and barley. In the U.S. this grain is used primarily for animal feed and more recently for bioenergy production, but for over 300 million people in Africa it is their primary source of food. Certain properties of sorghum make it increasingly popular globally because it is naturally drought-, heat- and flood-tolerant and requires fewer inputs, like fertilizers, to get equal amounts of grain as for corn. This makes sorghum ideal for the arid and semi-arid regions of Africa and Asia and also possibly for drought-prone regions of the U.S. But sorghum has qualities that could be improved – nutritional deficiencies and performance weaknesses. Goals of Project: To realize improvements in sorghum it is important to understand gene function and to have an efficient and reproducible system to genetically engineer or transform sorghum. Since the entire genome of sorghum has been determined it is now necessary to determine gene function for its tens of thousands of genes. Because of their tendency to jump into genes, certain endogenous transposable elements, e.g., Mu-like elements or MuLEs, can be used to interrupt genes and identify the sequence into which it jumped. This effort is focused on identifying genes that can be used to understand and improve the nutritional, agronomic and bioenergy performance. To better understand the identified genes, an efficient method of transformation must be available. The Lemaux laboratory accomplished this with one sorghum variety (Gurel et al., 2009), that was involved in one previous SPUR project. Although useful, this variety has high levels of phenolics, causing difficulties with transformation. To avoid this problem and to speed transformation, we chose two other varieties, a short-generation variety, with few phenolics that reaches maturity 3-4 weeks earlier, and another variety with low levels of phenolics and a genome that has been sequenced. The use of the latter variety will facilitate the gene function studies. We will develop successful selection and regeneration protocols for these two varieties and use that technology to express or downregulate genes identified through the functional genomics studies. We will also introduce a characterized gene, a naturally occurring redox protein that can increase digestibility – one of the major problems for sorghum as a food source. Biochemical and proteomic analyses will be used to study variation in protein and starch digestion of the engineered sorghum. |
| Began: Fall |
| View Project Details |
Pollen-specific receptor-like kinases and their roles during pollen tube growth |
| Sheila McCormick |
| We have isolated and characterized several pollen-specific receptor-like kinases. These kinases are structurally related in that they all have extracellular domains with five or six leucine-rich repeats, a single transmembrane domain, and a cytoplasmic kinase domain. The different kinases within one plant may interact with different signaling partners and thus facilitate pollen tube growth. We used yeast two hybrid screens to identify potential ligands and downstream signaling components for these kinases. |
| Began: Fall |
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Plant Gamete Gene Expression |
| Professor Sheila McCormick |
| In higher plants, each pollen grain grows a tube in order to deliver the two sperm cells to the embryo sac, where one fertilizes the egg to give rise to the zygote, and the other fuses with the central cell to give rise to the endosperm. Despite their crucial importance for plant reproduction, very little is known about plant gametes. What genes do gametes express? Are there molecules on the cell surface that mediate egg-sperm and central cell-sperm recognition? |
| Began: Fall |
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micro RNAs and their roles during fertilization |
| Professor Sheila McCormick |
| microRNAs (miRNAs) are non-translated RNAs that are negative regulators of target messenger RNAs. In Arabidopsis, over-expression or mutation of miRNAs can result in aberrant expression of target genes and therefore the plants frequently have defects in some developmental pathway. We are studying some F-box genes that are predicted targets of miRNAs. F-box proteins are involved in protein degradation. Our preliminary results suggest that plants that overexpress these miRNAS have defects in fertilization. |
| Began: Fall |
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Biogeography of Giant Ground Beetles (Carabidae: Scaritini) |
| Kipling will |
| Giant ground beetles (Carabidae: Scaritini) are perhaps some of the largest predatory beetles known. The genus Mouhotia from Southeast Asia reaches length of over 6 cm. All members of the tribe Scaritini are flightless. They are found on all the major continents. This raises the question of how did these flightless beetles spread across such a wide area. To address this question we need to understand the relationships within this group. A published phylogeny does not exist for the Scaritini. This project intends to derive these relationships based on DNA sequences from multiple genes. Once sequence data has been generated, phylogenetic trees can be constructed for further hypothesis testing. |
| Began: Fall |
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Morphlogy and Development of Electronic Taxonomic Keys for Giant Ground Beetles (Carabidae: Scaritini) |
| Kipling will |
| Biologists have used dichotomous taxonomic keys for the identification of unknown organisms for centuries. The recent advent of electronic interactive keys moves away from this tedious and some times cumbersome means of identification. The rise in popularity of these keys is a testament to their utility. Currently we are developing a key for the genus Pasimachus a large North American ground beetle. This key includes all but four of the species with the addition of several un-described species. We hope that this key will aide in the identification of this popular group. |
| Began: Fall |
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Interactions of the Movement Proteins of Barley Stripe Mosaic Virus |
| Professor Andrew Jackson |
| This project will be designed to identify the interactions of the movement proteins of barley stripe mosaic virus with host proteins and the cellular interactions of the virus. Yeast two hybrid analyses will be undertaken to determine the binding of the three movement proteins with each other and to screen host proteins for interactions. Microscopy studies will be undertaken to determine the localization of interacting proteins in the cell and the biological consequences of the interactions. |
| Began: Fall |
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Self-incompatibility in biofuel crops |
| Sheila McCormick |
| Perennial grasses that are potential biofuel crops have reproductive biology features that make them difficult to work with. One such barrier is Self incompatibility (SI), which in grasses is controlled by 2 unlinked genes, S and Z. A pollen grain that has both S and Z alleles in common with the alleles in the female part of the flower will fail, whereas a pollen grain with only one of the S or Z matches with alleles in the female part of the flower can succeed. Learning how to manipulate self-incompatibility in this plant will make it easier for plant breeders to make inbred lines, which are useful in crop improvement. |
| Began: Fall |
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Systematics of Heliconia and co-diversification with hummingbird pollinators |
| Chelsea specht |
| This project will involve using DNA markers to develop a phylogeny for the charismatic plants in the genus Heliconia. We will also test for co-evolution with hummingbirds, the pollinators of these plants. |
| Began: Fall |
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Sierra Nevada Mixed Conifer Fire History |
| Scott stephens |
| This project seeks to understand the historical role of fire in the mixed conifer forest of the western slope of the Sierra Nevada. Fire scar samples will be collected from one study site in the southern sierra (Sugar Pine) and one study site from the central sierra (Last Chance). These scars will then be mounted, planed, and sanded for optimal ring visualization. Fire events will then be dated and analyzed with stereoscopic microscopy, infinity capture, and infinity analysis software. Composite fire histories will be constructed for each study site. Historic fire frequencies and extent will be reconstructed from this data. Information such as this is vitally important for understanding what role fire played in these forests before the current era of fire suppression. Findings from this study will have implications for current forest management, fire mitigation, and forest restoration. |
| Began: Fall |
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Biography of John James Audubon |
| Professor Carolyn merchant |
| George Bird Grinnell (sportsman and editor of Forest and Stream magazine) founded the Audubon Society in 1886. He wrote a serialized biography of John James Audubon that appeared in his journal, Audubon Magazine. The biography needs to be scanned, annotated, and compared to existing biographies of Audubon to determine whether this is in fact a heretofore unrecognized biography of Audubon. |
| Began: Fall |
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Determining Mode of action of Trichloroacetic Acid (TCA) |
| Associate Professor Chris vulpe |
| The National Research Council recently envisioned the discovery of “toxicity pathways”, the cellular signaling pathways that are induced or perturbed in response to a toxicant, as a novel approach to toxicity testing. In the case of trichloroethylene (TCE), the broad use and improper disposal of the chlorinated hydrocarbon (greatly utilized in industry and consumer products) has called for an examination of its toxicity and risk to the general public. Understanding of the toxicity pathways associated with exposure to trichloroacetic acid (TCA), a reactive TCE metabolite, is limited due to different responses observed between species and target organs. As TCA has been implicated in hepato- and renal toxicity, as well as liver cancer, it is critical to determine how TCA can induce toxicity. We hypothesize that our S. cerevisiae gene deletion library, which we have previously utilized to assay for yeast genes sensitive or resistant to benzene metabolites, can identify yeast cellular toxicity signaling pathways associated with TCA exposure. To accomplish this, we must first determine the concentration of TCA that inhibits the growth of wild-type yeast by 20% (IC20), an exposure level that serves as the starting point for identifying genes and signaling pathways involved in TCA response. The specific aim of this SPUR project is to determine the IC20 for trichloroacetic acid (TCA), a trichloroethylene metabolite, in yeast. The results gathered during this SPUR project will supply the framework for the identification of evolutionarily conserved toxicity pathways associated with trichloroethylene exposure, as well as provide further insight into the key cellular processes and signaling pathways involved in toxicant response. |
| Began: Fall |
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Nitrogen and Sulfur Biogeochemistry of Santa Cruz Marine Terraces |
| Professor Ronald Amundson |
| The coastline of central California consists of a series of “steps” known as marine terraces. The terraces are a series of former beaches that have been lifted out of the tidal zone, over geological time, by regional tectonic uplift of the coast. Marine terraces, because they commonly increase in age by ~ 100,000 years with each “step”, are natural on-going experiments that allow earth scientists to understand how biogeochemical cycles in soils and ecosystems change as the Earth’s surface ages. The terraces near the city of Santa Cruz are particularly interesting and valuable as field laboratories because: 1. They have been accurately dated using cosmogenic isotope data (Bob Anderson, UCSC). 2. The inorganic chemical reactions in these terraces have been examined by the Dr. Art White at the USGS 3. Dr. White found that the water in the soils contains large quantities of both nitrate (a form of nitrogen) and sulfate (a form of sulfur). Presently, my lab is investigating the production of nitrous oxide (the second most important greenhouse gas after CO2) and the global soil sulfur cycle. Thus, the terraces at Santa Cruz offer a great (and local) research site to understand how the N and S cycles change with ages of the landforms, and the site fits into our suite of sites spanning much of the Earth’s rainfall spectrum (from tropical rainforests in Puerto Rico to the hyperarid deserts of Chile). Some preliminary hypotheses include: 1. Nitrous oxide production (which requires low O2 contents) should increase as soils age (as soils age, their clay content increases, hydrologic conductivity decreases, and they thus become more water-logged during the rainy season) – e.g. soils should become greater emitters of greenhouse gases of N as they get older. 2. The soil sulfur cycle (which is very poorly studied in general) will shift toward the production of organo-S gases and reduced forms of S (iron sulfides, possibly H2S gas) as soils age. The nearby location of the field sites, the large amount of background work, and the well defined problems makes this an ideal research opportunity for two undergraduates who can work in concert with my two graduate students (Simona Balan and Chloe Lewis) and myself. |
| Began: Fall |
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Sustainable Tropical Forest Management |
| Matthew Potts |
| Existing harvesting protocols in tropical forests were designed to optimize timber production without taking into account the impact that harvesting has on biological diversity and ecosystem service production. New harvesting protocols are needed that explicitly consider the multiple impacts of harvesting. The goal of this project is to aid in the study and design of new forest management tools. The results of the undergraduate(s)' research will directly aid an on-going interdisciplinary sustainable forest management project in Malaysia. |
| Began: Fall |
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Native Bees Need a Forum |
| Professor Gordon Frankie |
| Will gather information on the behavioral and ecological relationships of native California bees to their native California host plants (as well as some non-natives) at the UCB Oxford Tract. Will do plant gardening at Oxford unit to attract specific native bee species. Will learn to identify many types of native bees. Will use information to do outreach to several audience types in East Bay. |
| Began: Fall |
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Molecular Genetics of Chlorophyll Biosynthesis |
| Professor Krishna Niyogi |
| Chlorophyll is the green pigment that is essential for photosynthesis in algae and plants. Although you might expect that the biosynthesis of chlorophyll should be completely understood, several aspects of this key metabolic pathway remain to be elucidated. We are taking molecular and genetic approaches to address unresolved questions about how chlorophyll is made in the unicellular green alga, Chlamydomonas reinhardtii, a widely used experimental model that has several advantages for genetic studies, including a completely sequenced genome. |
| Began: Fall |
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Regulation of Photosynthetic Light Harvesting |
| Krishna Niyogi |
| In natural environments, the intensity of sunlight can vary over several orders of magnitude and on timescales ranging from seconds to seasons. Plants need light for photosynthesis, but they have to regulate the absorption and utilization of sunlight to avoid photo-oxidative damage. One of the ways they accomplish this is through an ecophysiological trait called nonphotochemical quenching, which regulates photosynthetic light harvesting. We are using a combination of genetics, biochemistry, and spectroscopy to investigate the molecular mechanism of nonphotochemical quenching. |
| Began: Fall |
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Singlet Oxygen Signaling and Acclimation |
| Krishna Niyogi |
| In an aerobic environment, responding to intracellular and extracellular oxidative signals is critical for physiological adaptation (acclimation) to changing environmental conditions. We are studying the ability of the model photosynthetic organism Chlamydomonas reinhardtii to acclimate to specific forms of oxidative stress. For example, when Chlamydomonas cells are exposed to a sublethal pretreatment with a specific type of reactive oxygen species (singlet oxygen), defense responses are activated that confer subsequent resistance to singlet oxygen stress. This acclimation response is dependent on nuclear gene transcription and cytoplasmic protein synthesis, and microarray analysis of RNA levels has shown that a relatively small number of genes respond to sublethal doses of singlet oxygen. Constitutive expression of one of these genes, which encodes a glutathione peroxidase homolog, is sufficient to enhance singlet oxygen resistance. The goals of this project are (1) to characterize loss-of-function mutants affecting the glutathione peroxidase target gene and (2) to dissect the signal transduction pathway involved in acclimation to singlet oxygen by isolating and characterizing mutants that are unable to acclimate to singlet oxygen stress. |
| Began: Fall |
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Yosemite Forests in 1911 |
| Scott stephens |
| The Sierra Nevada 1911 Project has sought to describe & document forest dynamics in western portions of Yosemite National Park occuring since the early 20th century. This project also tests the influences of forest management and fire suppression in the region. Acting as a forest reference benchmark for comparison of current forest conditions to the forests of the 19th century is the historical timber inventory data, first sampled in 1911. This information was collected during a period when Park lands were subject to logging in lands originally under US Forest Service jurisdiction which have since became portions of Yosemite National Park. Changes in the vegetation of Sierran conifer forests, as well as the factors influencing these changes, will be are discribed using detectable alterations in species composition, size, and forest structure which have occurred since the 1911 timber inventory cruises. These changes include continuing community growth in relatively undisturbed sites, as well as post-fire vegetation changes since 1911 in several fire-affected areas. Deep-time fire-scar dendrochronology samples from the same transects allows determination of changes in fire regime from both pre-European periods and after the advent of active lands management, and documents the effects of any changes within this regime on the forest & vegetation communities. This allows meshing of fire regime and vegetation change into a suite of information essential to future management of both National Park holdings, and that of cooperative agency lands surrounding the Park. |
| Began: Fall |
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2) A Comprehensive Fuels Treatment Practices Guide for Ponderosa/Jeffrey Pine and Ponderosa/Mixed Conifer Forests |
| Associate Professor Scott stephens |
| A Comprehensive Guide to Fuel Treatment Practices for Ponderosa Pine/Jeffrey Pine and Ponderosa Pine/Mixed Conifer Forests reviews the existing literature, interviewing land managers, and conducting field meetings and synthesizing that information into the guide. This guide is important to managers because while millions of acres of these forests need fuel management, few resources exist to help plan these treatments. Sufficient science exists, but our guide will be the first synthesis of the research information for managers. One of our first tasks is to clearly define ponderosa pine/Jeffrey pine and ponderosa pine/mixed conifer forests since the forest type exists along a broad continuum of climatic zones and consists of many different assemblages of species. Our synthesis will focus on California, Colorado, New Mexico, and Arizona, including forests of the eastern and western Sierra, the transverse and peninsular ranges in southern California, the central/southern Rocky Mountains, and the southwestern plateaus and uplands. In these areas we will cover mixed conifer forests where they mix with ponderosa and Jeffery pine. |
| Began: Fall |
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