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Evolution & Ecology
This project involves the development of microsatellite markers in a species of sea anemone, Epiactis Prolifera. These markers will allow me to make further conclusions about the mating system of E. Prolifera (e.g. biparental inbreeding vs. self fertilization).
This project is to study the population of Western Pond Turtles, Emys marmorata, currently inhabiting the UC Davis Arboretum. E. marmorata is currently listed as a species of special concern in the state of California. This is project is to establish the population dynamics of these turtles and is to compare data collected to previous work done by members of Dr. Shaffer's lab in years past. This study will use basking and hoop type traps to capture turtle live at the UC Davis Arboretum. Non-native turtles will be removed as to foster the natural growth of Emys marmorata population. If successful this project may show that this species can be viably maintained in highly modified habitats in an effort at future conservation.
The invasive weeds, Holcus lanatus and starthistle, can out-compete many native plant species of Northern Californian. The success of these plants may be due to chemicals exuded from the plant's roots. To test for the presence of these chemicals and the degree to which the chemicals affect different native plants species, the germination of native seeds in the presence of the invasive weed and independently of the weed will be measured and compared.
I will sequence ten loci in the California Tiger Salamander (Ambystoma californiense) specimens from Sonoma and Santa Barbara counties in order to assess their relationship to the other A. californiense clades more thoroughly, inquiring in their status as possible cryptic species that require further protection and conservation.
Working from previously completed ecological studies of Sonoran Desert wild cotton populations, I will test hypotheses concerning the genetic relatedness of these populations with respect to their geographic distributions and coevolutionary history.
This project will yield basic field ecology information about Ambystoma californiense and produce a statistical model of population density with respect to distance from breeding ponds.
I will study the effects that kiwis inoculated with yeasts grown from other sources will have on the development of Drosophila melanogaster offspring.
I will use microsatallite DNA to characterize population structure and estimate gene flow among all 10 breeding sites of the endangered Santa Cruz long-toed salamander.
Many genetically distict groups, or clades, occur within Emydura turtles. Computer digitizing of Emydura pictures will show if any shell difference exist between clades.
This study completes work on California tiiger slamanders that defines the terrestrial dispersal of juveniles so that populations of salamanders can be effectively conserved.
I will explore whether the native plants Stachys ajugoides and Achillea millefolium have adapted to an invasive grass, Holcus lanatus, and whether adaptation is soil-mediatied.
This study will address how major feeding behavior and morphological novelties evolved in Hydrolycus scomberoides through the use of high-speed film and morphological measurements.
I will study the effects of two consecutive generations of diapause (dormancy) in Pieris rapae butterflies and how it inhibits establishment of high altitude populations.
High-speed video and behavioral bioassays of Lepomis sunfish will be analyzed to determine if prey capture and performance are sacrificed in a specialized feeding mechanism.
The purpose of this project is to determine whether the relationship between Drosophila melanogaster and yeast helps yeast populations in fruit to flourish.
The project will survey and assess endosymbiotic relationships within the gut of natural populations of Drosophila within the Davis region.
The rate of water flow and how conducting cells of xylem in the wood of plants swell and shrink in response to salt in a drought deciduous forest will be studied. A pressurized flow meter will be built to measure water conductivity in Heteromoles arbutifolia (Toyon) in different environments. The anatomy of the water conducting cells will be examined with the aid of a compound microscope to understand basic water flow at the cellular level.
We will construct a cohort analysis in tow temporary ponds in which pure native, pure non-native and hybrid salamanders breed during the winter each year. cohort analyses have been recorded for the previous year and show that the natives may be breeding earlier but the larval frequencies seem to be highly non-native. We will construct a hybrid index for each pond with multiple loci and test our results with the previous year to predict any patterns of breeding behavior and larval fitness.
I will be conducting experiments on the butterfly Junonia coenia (Common Buckeye) to determine if its physical appearance is in part controlled by photoperiod and/or temperature.
Microbiology
Genetic investigation of the genes involved in the catabolism of hypoxanthine by Klebsiella oxytoca and to see if Klebsiella oxytoca's hypoxanthine catabolism genes share similarity with Escherichia coli's allantoin catabolism genes.
To test phosphorylation sites on Mus81/Mms4 for functional importance to DNA repair in yeast.
I will perform a genetic screen to identify an elusive enzyme responsible for resolving pivotal intermediates during homologous recombination.
Molecular & Cellular Biology
The Drosophila gene Dorothy is preferentially expressed in the lymph glands and pericardial cells, tissues associated with Drosophila cellular immune response. Little is known about Drosophila cellular immunity and the study of Dorothy provides and opportunity to further explore this area of research. I will screen strains that are mutant at the Dorothy locus to isolate a strain lacking Dorothy function. The isolated mutant(s) will then be analyzed with respect to immune response and steroid hormone function.
Phycocyanobilin Ferredoxin Oxidoreductase - Expression, Purification, and Biochemical Characterization
I will clone tubulin suppressor mutants into cDNA vectors. Then transfect Drosophila S2 cell with the plasmid construct, then purify microtubules from the cells for use in in vitro assays for their mechanism of MEI-1/MEI-2 katanin inhibition.
With this funding, I propose to locate both of these new mutagen-sensitive genes and discover the functional gene they correspond to in DNA repair. Using deficiency, recombination, and p-element mapping in Drosophila melanogaster, I will narrow the region around the mutant down to a single locus and using the sequenced, searchable Drosophila genome determine what the localized gene is and what role it may play in DNA repair. This research will assist in an ongoing search for DNA repair genes and their homologs in humans.
Normal DNA repair is required for the growth and maintenance of a healthy organism. The study of DNA repair genes brings us closer to the goal of being able to treat abnormal DNA repair, such as that found in cancer. By screening thousands of stocks from the Zuker laboratory in San Diego, we have found three Drosophila stocks that contain mutations that we believe are in previously unknown DNA repair genes. By using deficiency, recombination and p-element mapping techniques I will map these three DNA repair genes.
I will be temporarily reducing the levels of the steroid hormone 20-Hydroxyecdysone during specific time periods in pupation at Drosophila melanogaster (fruit fly).
We will map a mutation of a novel crosslink-repair gene relative to known locations in the genome by male recombination with transposable P-elements.
Using the Cre-Lox assay the researcher will attempt to find Saccharomyces cerevisiae genes that when over expressed cause distruption in homolog pairing.
I plan on defining which regions of TC089P are necessary for the different functions of the Protein in S. Cervosive by creating deletion constructs of the gene.
To determine structures of SUN domains of CeUNC-84 and human Sun1 and characterize the molecular mechanism underlying their binding to KASH proteins during nuclear migration.
I propose to tag the GSC2 protein and label it with the lumio reagent so that I may see where it localizes in the cell.
I will characterize 6 new nuclear envelope proteins that are essential in C. elegans and share human homologs, with the hypothesis that knowledge of these proteins is crucial to the understanding of human nuclear envelope related diseases, such as muscular dystrophy.
To provide high resolution structural information on the DNMT3A2 and DNMT3L proteins and shed light on their function in DNA methylation.
The study will determine expression of thrombospondin, a cancer preventive gene, and whether its upregulation by a soy-derived, chromatin-binding peptide is caused by H4-Lys16 acetylation.
I propose to investigate the progression of germ line nuclei undergoing meiosis in Caenorhabditis elegans and look into specific sex differences of cell cycle control.
The Saccharomyces cerevisiae SNA3 gene encodes for a protein found in a late endosomal compartment, whose function is unknown. Based on a 2-hybrid interaction with GCS1 (a gene essential in the sporulation pathway), I will test whether SNA3 is additionally required during sporulation in yeast.
This project will investigate how delay I meiotic replication will effect double strand break formation and recombinational repair in Saccharomyces cerevisiae.
I will construct and test a transgene to express green fluorescent protein (GFP) under control of the germ-cell specific vasa promoter in zebrafish.
This study will research the structure and function of Echovirus 1 caveosome formation, and will focus on the completion of a three-dimensional reconstruction of the caveosome.
Genetic screen identifying components of the nuclear envelope that are involved in nuclear migration and other important pathways.
The goal of this project is to investigate the differential expression of the ugt1a gene family under the influence of lunasin, a proposed chemopreventive agent.
The identification of components of a redundant pathway for nuclear migration in C.elegans by EMS mutagenesis and genetic mapping techniques.
The purpose of this project is to synthesize a hypothetical intermediate, 181,182-Dihydrobiliverdin, observed in the ferredoxin-dependent reduction pathway of biliverdin to phyocyanobilin. The newly synthesized compound will be analyzed using NMR and HPLC analysis to determine if it is identical to the enzymatically produced intermediate. This compound will also be tested as a substrate for the enzyme.
Meiotic recombination plays an important role in chromosome segregation. Hence, I will 1) construct an assay in yeast to monitor chromosome segregation using fluorescent reporters, 2) characterize the assay in wild type cells, and 3) apply the assay to study directed knockout mutations of meiosis-specific gene(s).
I propose to isolate conditional loss of function mutations in the TOR1-1 kinase gene, and characterize the functional role of the individual domains in TOR1-1p by examining the effect of the developed mutations.
The aim of this project is to determine the three-dimensional structure at atomic resolution of the two enzymes AKR11A and AKR11B by x-ray crystallography and to use that information together with data from kinetic experiments to better understand the substrate specificities of these enzymes.
Neurobiology, Physiology & Behavior
Using a rat enzyme immunoassay to examine serum -endorphin levels, we will attempt to determine if -endorphin is a factor in the anorexia of senescence.
Using Western Blot analysis I will quantify relative levels of uncoupling protein 2 and 3 (UCP-2 and UCP-3) in frozen tissues of F-344 rats of various ages. The goal of the project is to examine the possibility that during the aging process, altered levels of mitochondrial UCP-2 and/or UCP-3 result in elevated levels of oxidative damage due to enhanced generation of reactive oxygen species (ROS) in mitochondria.
I will test the hypothesis that the diurnal modulation of LTP in the hippocampus is due to extrinsic signals by isolating the hippocampus from all outside signals and systematically varying the length of time of isolation before recording LTP in the hippocampus. I will compare the amplitude of LTP recorded at night against that recorded during the day. If there is a significant difference at night as compared to the day despite differences in isolation time, I will conclude that the diurnal modulation of LTP is due to changes in the amplitude of signals originating inside the hippocampus. If there is not a significant difference at night as compared to the day I will conclude that the diurnal modulation is due to changes in the amplitude of extrinsic signals.
I will test the hypothesis that the slowing of neural signals in a hibernator's brain at low temperatures can primarily be accounted for by changes at the synapse. The EPSPS generated will be an indication of whether my hypothesis can be considered consistent or negated.
Characterizing Xenopus laevis fibronectin gene regulation using northern westerns in situ hybridizations gel mobility shift assays & transgenesis in X. laevis.
The purpose of my project is to identify the full-length sequence, expression and function of Xenopus MuRF-1 and MAFbx, two universal markers for muscle atrophy.
The project will be to create a representative 3-dimensional model of the LGN in the mature ferret.
MuRF and MAFlox genes may play a universal role in muscle atrophy in the model organism, xenopus laevis.
The goal of this project is to identify which isooforms of the HCN channel protein exist in the rat retina using immunocytochemistry techniques.
My project is centered on neuroplastic mechanisms of the hamster hipppocampus, specifically Long-Term Depression (LTD). I hope to determine whether LTD can be found in an adult hibernator, as it has been clearly demonstrated in adult rats and mice.
The goal of this study is to examine the hamster's ability to generate Long-Term Depression and study the temperature dependence of this form of neural plasticity.
I will investigate the cellular location of Long-Term Potentiation, a form of neural plasticity involved in storing new information, in the hippocampus of hibernating hamsters.
Using hippocampal slices from hibernating hamsters and non-hibernating rats. I will explore the differences in neuroprotection that may improve donor organ viability.
Plant Biology
Nectaries are secretion organs found in some plants that provide rewards to pollinators luring them to the flower. Arabidopsis thaliana crc mutants show no visible signs of nectary development. Brassica oleracea CRC promoter sequence (conserved in Lepidium africanum) will be transformed into Arabidopsis through a dual transcription activation system for GUS expression. Analysis of the expression of CRC in Arabidopsis will yield insight into how the gene affects nectary development.
I will clone relatives of the PHAB gene family, leaf and vascular developmental genes characterized in Arabidopsis, from the conifer Douglas-fir. The expression patterns of the Douglas-fir PHABs will be determined and compared with PHAB expression in Arabidopsis. The amino acid sequences of the Douglas-fir PHAB genes will be combined with sequences from other species being studied in the Bowman lab to produce a gene phylogeny.
The Effects of Oxoguanine Glycosylase and Alternative Forms of Formamidopyrimidine-DNA Glycosylase, from Arabidopsis thaliana, on 7,8-Dihydro-8-Oxoguanine
This project is to investigate and characterize a protein found in plants that is involved in long distance communication through binding RNA and transporting it.
Using the phytoene desaturase gene we will track the movement miRNAs and siRNAs within plants and between a parasitic plant and its host.
The proposed research will determine the function of TIR-NBS and PP2Ca genes in stress signaling within Arabidopsis thaliana.
Determination of transcript and protein level of VIPP1 in TAT Pathway mutants in Zea mays via TR-PCR and quantitative western blotting, respectively.