Sara Alcorn
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 | Research Advisor & Department:
Barbara Bedford - Natural Resources
Name of Project:
Response and Function of Mycorrhizal Fungi in Variable Soil pH, Saturation, and Temperature Conditions
Abstract:
Mycorrhizal fungi are microorganisms that form relationships with the roots of plants, presumably with a bi-directional exchange of resources. However, the specific function of the fungi seems to vary with environmental conditions, forming relationships that are symbiotic, commensal, or even parasitic to the plant. In wetland ecosystems, environmental factors known to affect the function of mycorrhizae exhibit both small- and large-scale variability, notably soil pH, saturation, and temperature. I propose a greenhouse study that seeks to explain the impact of variable pH, soil saturation, and soil temperature on mycorrhizal colonization of wetland plants and on the function of the fungi when these variables are manipulated in a fully cross-factorial analysis. Soil will be collected from the wetland and sterilized. The pH of soil will be modified by adding HCl to lower pH and CaCO3 to raise it. To alter the depth of soil saturation, different artificial water tables will be created by boring holes at varying heights in pots and submerging the pots in water. Soil temperature will be modified by submerging pots in cooling baths at different temperatures. Seedlings of three wetland species, which vary in the degree to which they are typically colonized by mycorrhizae, will be transplanted into soil of the various treatment combinations, with 10 replicates of each. Half of the pots will be inoculated with mycorrhizae, while the other half will make up the non-mycorrhizal control. After 6 weeks, one plant of each species will be harvested from each pot, and the roots will be analyzed for percent colonization by mycorrhizal fungi. For three months, the growth response of each remaining plant will be determined by measuring the width and height of the largest leaves. Afterward, these plants will be harvested, dried, and weighed to determine species’ growth responses in the various treatments. The results will provide further insight into the function of mycorrhizal fungi in wetlands, where much less is known about mycorrhiza than for terrestrial ecosystems.
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Michael Alpert
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Research Advisor & Department:
Volker Vogt - Molecular Biology and Genetics
Name of Project:
Investigating a Temperature Sensitive Mutation in Rous Sarcoma Virus p10 Protein
Abstract:
The aim of this project is to characterize a temperature sensitive mutation that was reported in 1993 by Dupraz and Spahr to interfere with the assembly of Rous sarcoma virus (RSV). They found that RSV with this mutation is infectious at 36C, but loses infectivity and suffers a drastic decrease in virus release at 41C. To date, no other temperature sensitive mutations have been reported in retroviruses. Consequently, this mutation could be an important tool for studying retroviral assembly. The mutation is in a region of the RSV structural protein that the lab has identified as playing a role in the proper assembly of spherical particles. Also, the mutation lies within a putative nuclear export sequence. I have re-built the mutation into the strain of RSV used by the Vogt lab. Preliminary results show that in contrast to the findings by Dupraz and Spahr, the mutant virus released from cells at 41C is infectious. This apparent discrepancy may be due to differences in cell type or virus strain. Current work will determine whether there is a difference in the amount of mutant virus released at 36C and at 41C.
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Jamie Anastas
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 | Research Advisor & Department:
Lee Kraus - Molecular Biology and Genetics
Name of Project:
Estrogen Dependent Control of Gene Expression Through Activating Protein-1 (AP-1)
Abstract:
Estrogens play an important role in the growth and differentiation of estrogen target tissues. While their action is normally mediated through estrogen receptors (ERs) which bind to estrogen response elements (ERE) in the genome, ERs also help regulate the actions of some "non-ERE" genes. In some tissues, the transcriptional activity of genes regulated by AP-1 sites greatly increases in the presence of ERs. AP-1 is a dimeric factor consisting of Fos and Jun polypeptides that helps modulate a variety of cellular processes. The estrogen-dependent mechanism of AP-1 gene regulation is not well understood and the nature and order of binding of the ERs, AP-1, and coactivators has not yet been determined. To increase our understanding of this process, I will generate a set of phosphorylation and acetylation Jun mutants by cloning polyhistidine-tagged mutant Jun cDNAs in both mammalian and bacterial expression systems. Purified proteins from these clones will be used in a variety of biochemical assays. Alternative estrogen pathways such as those involving AP-1 are of particular interest since they may provide some insight into the tissue-dependent responses to estrogen and therapeutic antiestrogens, which may lead to better treatments for certain cancer, menopause, osteoporosis and other estrogen-related health issues. More generally, the mechanism of ER-dependent activation at AP-1 sites represents a crossroads between steroid and non-steroid forms of cell communication. An understanding of this process can lead to insights not only in the specific role of ERs in genetic regulation, but also insights into the coordination of different pathways involved in transcriptional control.
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Graham Anderson
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 | Research Advisor & Department:
Thomas Owens - Plant Biology
Name of Project:
Modeling in vivo Non-Photochemical Dissipative Processes in Photosynthetic Systems
Abstract:
When a chlorophyll molecule in the photosynthetic machinery of a plant or an alga absorbs a photon, its energy can be used in several competing processes. Under optimal environmental conditions, most of this absorbed energy is used to fix CO2 through photosynthesis. When conditions are sub-optimal, such as during times of decreased water or low temperature, a plant or alga cannot fix CO2 at its optimal rate. Energy that is in excess of what can be used for photosynthesis must be dissipated, or it will lead to the formation of harmful compounds. Fluorescence, the re-emission of a photon by chlorophyll, is the most easily measured and well understood dissipative processes. Our project involves the dissipative processes known as non-photochemical quenching. These processes dissipate excess light energy at rates which are constantly adjusted in response to changing environmental conditions. It is the time-dependence of these heterogeneous non-photochemical processes which allows a plant to adapt to short term and long term changes in environmental conditions.
We will create mathematical models of the coupled first order rate equations which empirically describe the known components of non-photochemical quenching. Many such models exist, but none take into account the heterogeneity of processes that contribute to non-photochemical quenching or the time-dependant aspects of its constituent reactions. Once a reasonable model is obtained, we will use computer simulations to obtain iterative solutions to simple trial inputs and initial conditions that can be created in a laboratory. These simulations will make predictions for several parameters of a photosynthetic system which depend on non-photochemical quenching. We will compare one of these predicted parameters, fluorescence, with measured values from actual photosynthetic systems treated to the same initial conditions and inputs as the model. Then, we will make appropriate revisions to the model based on discrepancies between predicted and measured values. This work will further our understanding of chlorophyll fluorescence as a means of assessing photosynthetic physiology. By developing accurate and useful models, we will be able to better interpret fluorescence measurements to draw conclusions about the physiological state of photosynthetic machinery.
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Ben Auerbach
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Research Advisor & Department:
Ronald Harris-Warrick - Neurobiology and Behavior
Name of Project:
Ion Channels in the Lobster Stomatogastric Ganglion
Abstract:
This summer I will be working with Dr. Harris-Warrick’s lab on the effects of neuromodulation on the stomatogastric ganglion (STG) of the California spiny lobster. The STG contains the pyloric motor circuit, a small network consisting of 14 neurons that controls a simple peristaltic movement of the stomach which can be noticeably altered by modulating the circuit.
Specifically, I will be studying the phenomenon of metamodulation, that is, the idea that modulatory effects can themselves be modulated. There is anecdotal evidence that when a monoamine, for example serotonin, is applied several times in a row to the isolated pyloric network, the effects of serotonin are not the same as when it is applied transiently. Serotonin has an inhibitory (hyperpolarizing) effect on individual neurons when transiently applied but can trigger prolonged activation of the entire circuit when applied at high concentrations. This is obviously of interest to the intact animal, where serotonin may be around all the time but in fluctuating concentrations.
My specific role in this project is twofold. First, I will confirm and quantify these metamodulatory effects. This will be done through extracellular recording of action potentials from the nerve roots of the pyloric circuit while applying different concentrations of serotonin at different time intervals. Next, I hope to determine how this metamodulatory effect comes about, in other words, how does serotonin change the intrinsic properties of the individual neurons in the circuit. This will be done through a combination of extracellular recordings of the entire circuit and intracellular recordings of the individual neurons using the voltage clamp technique.
The overarching goal of this lab is to link cellular mechanisms with behavior. If we can understand how this simple pyloric motor circuit operates, it will hopefully open our eyes to general trends that will help us see the relationship between ion channels and behavior.
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Robert Aversa
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 | Research Advisor & Department:
Tadhg Begley - Chemistry and Chemical Biology
Name of Project:
A Stereochemical Study on Tryptophan-2,3-dioxygenase
Abstract:
In the first step of the eukaryotic pathway converting tryptophan to quinolinate, the 2,3 C-C double bond of tryptophan is cleaved by the enzyme tryptophan-2,3-dioxygenase (TDO) to form N-forymylkynurenine. The mechanism of this reaction will be studied; specifically, the absolute stereochemistry of the heme-bound superoxide attack on the tryptophan substrate from TDO. The inhibitive characteristics of the two diastereomers of dihydrotryptophan on TDO will be used to determine this stereochemistry. Dihydrotryptophan is synthesized by reduction of tryptophan, and TDO is obtained by overexpression in E. coli. Correlation of the dihydrotryptophan with a compound of known stereochemistry ((_S,3S)-N-dibenzoyl-2,3-dihydro-L-tryptophan) reveals the absolute stereochemistry of the reaction.
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Julie Beckenstein
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 | Research Advisor & Department:
David Deitcher - Neurobiology & Behavior
Name of Project:
Locating the SNAP-24 Gene in Drosophilia melanogaster
Abstract:
Three proteins, SNAP-25, synaptobrevin, and syntaxin, work together in the process of neurotransmitter release. While Drosophila melanogaster with mutations for the genes that code for synaptobrevin and syntaxin die early in development, those with a mutant SNAP-25 gene survive longer, even to adulthood. This is due to another protein, SNAP-24, which can substitute for the function of SNAP-25. My project involves finding fruit flies with a mutation in SNAP-24 to be used for further investigation.
I will use a variety of techniques to complete this task. In the past I tested various p-element insertion lines by genetic rescue to determine if the p-element disrupted the SNAP-24 gene. Since this method yielded few results, I am now testing the lines by Western Blot. Furthermore, I will be working with new lines which contain transposons near the SNAP-24 gene. I will attempt to "hop" these transposons to disrupt the gene. PCR will be used to test these mutants.
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