Bryan Yu-Ann Chen
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 | Research Advisor & Department:
John Lis - Molecular Biology and Genetics
Name of Project:
Searching for New Protein Complexes in hsp70 Involved in Transcription via Re-chromatin Immunoprecipitation
Abstract:
Hsp70 is a highly conserved, ubiquitous member of the 70-kDa heat shock family which stabilizes unfolded and partially folded proteins. Its ability to be rapidly expressed following various environmental stresses is critical for cell survival. Through various assays such as Chromatin Immunoprecipitation (ChIP), many hsp70 transcription factors involved in initiation and elongation have been identified and extensively characterized in Drosophila. Though the spatial and temporal localizations of these proteins at the hsp70 locus have been well studied, it still remains unclear as to how these factors interact with each other throughout transcription. Re-ChIP, a modification to ChIP which allows for a second immunoprecipitation, will be refined and applied to help identify potential protein-protein interactions and protein complexes at specific loci in hsp70 throughout various time points when the gene is expressed. Results obtained from Re-ChIP will refine current existing models on the transcriptional regulation of hsp70 as well as other similarly regulated genes.
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Dana Christofferson
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 | Research Advisor & Department:
Martha Stipanuk - Nutritional Sciences
Name of Project:
Role of cysteine and the ubiquitin-26S proteasome system in CDO degradation.
Abstract:
The enzyme cysteine dioxygenase (CDO) is an important regulator of cysteine metabolism. CDO activity can increase to metabolize cysteine and protect cells from its potentially harmful effects in high concentrations, or can decrease under conditions of low cysteine, conserving cysteine for protein and glutathione synthesis. CDO activity is regulated mainly through degradation by the ubiquitin - 26S proteasome system. The goal of this research is to determine the mechanism by which the ubiquitin - proteasome system is signaled to degrade CDO.
Cysteine appears to be the nutrient that signals a block in the ubiquitination and degradation of CDO. To further elucidate the mechanism, we will be testing various cysteine analogs, such as cysteamine and selenocysteine, to determine the portion of the molecule most important to this signal. Preliminary work will also be done to determine the specific lysine residues in CDO that are ubiquitinated.
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Lee Shoa Long Clarke
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 | Research Advisor & Department:
Carlos Bustamante - Biological Statistics and Computational Biology
Name of Project:
Comparing the Human and Chimp Genomes: Pseudogenation in the Chimp
Abstract:
It is estimated that the human and chimp genomes differ by about 1.2%. With the recent sequencing of the chimp genome, we can now directly compare humans and chimps ate the genetic level and see what these differences are. My lab has received about 20,000 human-chimp coding region alignments from Celera Genomics. From these alignments, we have identified 488 potential pseudogenes. Through sequence comparisons of human, chimp, mouse, and rat coding regions, we are refining our list to include pseudogenes that are likely to have arisen in the chimp genome since the divergence between humans. Because pseudogenes are under no selective pressure, they should exhibit neutral evolution. We can test for this using a likelihood ratio test method developed by Bustamante et al 2002. We would like to identify and catalog all pseudogenes in the chimp genome. Understanding pseudogenation in the chimp will allow us to estimate the underlying mutation rate of specific genomic areas, as well as develop a model for neutral evolution in the chimp. Furthermore, we will be able to gain a better understanding of how the human-chimp divergence occurred, bringing us closer to understanding what makes humans human.
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Ilana Cohen
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 | Research Advisor & Department:
Howard Howland - Neurobiology and Behavior
Name of Project:
Is Pupil Size Optimized in Low Light Levels?
Abstract:
In bright light conditions, every human pupil has an optimum size, and making the pupil larger or smaller results in decreased resolving power, or clarity of vision. The optimum pupil size is a compromise between blurring of the image by diffraction (a fundamental property of all lenses) as pupil size decreases and blurring of the image by monochromatic aberrations (a unique property of the individual eye) as pupil size increases. In dim lighting, there are a limited number of photons available, and the pupil increases in size in order to capture an adequate number of photons to provide contrast in the image. Therefore, the pupil size becomes a compromise between lack of photons as pupil size decreases and monochromatic aberrations of the eye as pupil size increases. We will test how closely (if at all) subjects’ pupil sizes correspond to their predicted optimum pupil sizes in both bright and dim lighting. We will measure actual pupil sizes while subjects read an eye chart under varying light levels and levels of contrast in the chart itself. Additionally, we will use a Wavefront Analyzer to measure each subject’s monochromatic aberrations, and use these to calculate the subject’s ideal pupil size under the various conditions used in the study. This will allow us to determine how closely the predicted optimum pupil size predicts actual pupil size.
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Kathleen Crucet
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 | Research Advisor & Department:
Kathleen Whitlock - Molecular Biology and Genetics
Name of Project:
The Characterization of E-cadherin Expression in the laure Zebrafish Mutant
Abstract:
Cadherins are cell-cell adhesion molecules that play a significant role in differentiation during embryogenesis and are known to be involved in axon guidance during development. Recently, a study done by Q. Liu, et al. in 2003 (Neuroscience Abstracts, 887.9) showed that E-cadherins in particular have been found in the olfactory system of zebrafish. This summer, I will continue my project from the spring semester concerning the characterization of E-cadherin gene and protein expression in the primary olfactory system of the developing laure mutant, which has defective axonal connections in the olfactory sensory system. I will visualize the protein expression of E-cadherin by using an antibody against it. Last semester, I labeled the sensory neurons of the olfactory system using an antibody against a known marker of these neurons, calretinin. I plan on using both antibodies to double label embryos and determine if the calretinin and E-cadherin proteins are co-expressed in the same olfactory sensory neurons. Currently, I am assessing the gene expression of E-cadherin through the use of in situ hybridization. My characterization will provide not only the first description of E-cadherin in the developing zebrafish olfactory system, but will also confirm whether this gene is disrupted in the laure mutant. I am also in the process of characterizing E-cadherin expression in a new mutant, garcia. This should result in my work being included in a publication on the garcia mutant.
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Stephen Curtis
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 | Research Advisor & Department:
Alexander Nikitin - Vet Biomedical Sciences
Name of Project:
An Analysis of Abnormal Gene Expression in Tumors of the Soft Tissue
Abstract:
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Loren DeVito
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Research Advisor & Department:
Thomas Cleland - Neurobiology and Behavior
Name of Project:
Circadian Modulation of Olfactory Acuity in Mice
Abstract:
Circadian rhythms, endogenous oscillators controlling daily metabolic activity, are modulated by light-dark cycles. Changes in light cycles have been shown to significantly shift the rhythm of locomotor activity rates; however, leaving animals in either DD (dark-dark) or LL (light-light) conditions free of light cues still reveals rhythmicity in locomotor activity, reinforcing the concept of an endogenous pacemaker. A great deal of research has focused on this idea of a light-entrainable pacemaker (LEP) that controls circadian rhythms. However, a food-entrainable pacemaker (FEP) has also been proposed as a possible separate mechanism of circadian control. Recent studies have also shown that experimental stimulation of the olfactory pathway has a modulatory effect on the rhythm of this wheel-running activity. The first part of this study will test the role of the LEP by using an olfactory generalization task at two different times in their circadian cycle. The second part of the study will test the role of both the LEP and FEP by using the same task at two different times on two groups of mice which will be put on a restricted diet, one group being fed in the morning and another being fed in the afternoon. All groups of mice will be tested under all conditions of the experiment. The four conditions of the experiment can be viewed as a 2 X 2 matrix where the two times of day in which they are tested (morning and afternoon) will be crossed with feeding time (morning and afternoon). I will be looking for differences in the breadth of odor generalization (acuity). The results will assess the putative independence (or lack thereof) of multiple circadian pacemakers in addition to contributing to the growing literature regarding how sensory systems are primed based on expectation and other internal behavioral state factors.
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