The Driks lab studies the proteins that make up the spore of several Bacillus species and studies the assembly of these proteins. Some Bacillus spores, including Bacillus anthracis spores, possess an exosporium, which is an outer layer surrounding the spore coat. The functioning of the exosporium at this time is still poorly understood. CotE is a major morphogenic protein in B. anthracis, playing a role in both spore coat and exosporium assembly. However, it was not know in which layers of the spore CotE could be found. After stripping exosporial proteins from the spore, I used Western blotting to detect the presence of CotE in different spore fractions. I determined that CotE localizes only to the spore coat of B. anthracis and not to the exosporium. Knowledge of the localization of this protein could lead to methods of detection and treatment of anthrax.

Monolayers on H-Si(111) were thermally formed using Decene and 10-Bromodecene. Samples were subjected to 100% humidity in order induce oxidation for upwards of three weeks. We intended to analyze the ability of bromine to bind to the Si(111) and inhibit oxidation through steric hindrance. Atomic force microscopy (AFM), x-ray reflectivity (XRR), and x-ray photoelectron spectroscopy (XPS) were used to characterize the monolayers and to compare the amounts of oxidation. AFM showed the step formation which is characteristic of H-Si(111). XRR was used to determine the physical characteristics of the monolayer. These characteristics were found for the Decene monolayer. XPS showed that the relative amounts of carbon absorbed to the surface increased over time through adventitious hydrocarbons present in the air. This increase brought about a thin physisorbed monolayer. Lastly, it was seen that the Decene monolayer inhibited oxidation over the 10-Bromodecene and H-Si(111) samples through expected steric hindrance.

The principle focus of my research was on the INK4a/ARF tumor suppressor gene, which is the second most commonly inactivated gene locus in human tumors. ARF, the protein product of this gene, inhibits growth by activating the p53 tumor suppressor and causing growth arrest and apoptosis. ARF activates p53 by binding to a negative regulator of p53, Mdm2. There is also a protein NPM that binds to ARF in the nucleolus, which does not allow it to bind to Mdm2, so they compete for binding with ARF. My project involved purifying the ARF protein, performing binding studies between ARF and other proteins, and finally using NMR spectroscopy to assess the structure of ARF. These studies will advance our fundamental understanding of ARF-mediated tumor suppression, and in so doing will help establish paradigms used by tumor suppressors to prevent cancer. Such knowledge is essential to developing targeted and appropriate anticancer strategies.

After determining herd size and composition via a survey method, fecal samples were analyzed using the McMaster Method of Parasite Egg Counting. A body condition score was assigned to a random sample of each of the species in each herd to determine a general overall nutritional well-being of the animals. Body condition scores and parasite burden were then compared to herd size. From this data, a strong correlation was shown between herd size and parasite burden which indicates a high rate of transmission between the animals composing large herds. While body condition scores did not correlate with either herd size of parasite burden, the overall effects of parasitic infections reaching the point of pathogenisity still need to be studied.

My summer project involved verifying the accuracy of range compensator fabrication for use in proton radiotherapy. Range compensators are Lucite cylinders that are specifically designed to conform the proton beam to the shape of the tumor being treated. I designed a new quality assurance protocol to make sure these compensator are made correctly. The project involved writing several computer programs that are designed to fully automate the fabrication and quality assurance aspects of the protocol. Accuracy is important in proton therapy because inaccuracies of even 1 mm can lead to under or over irradiation of tissue causing either damage to healthy cells or less than the prescribed dosage of radiation to a tumor.

The protonated water dimer, H₅O₂⁺ or Zundel complex, plays an important role in proton transfer and solvation of aqueous reactions. Despite the numerous molecular dynamics and ab initio studies of H₅O₂⁺, there have been few diffusion Monte Carlo studies to date. Diffusion Monte Carlo method solves the time-dependent Schrödinger equation using a Wick rotation (i.e. replacing the time t, by the by the imaginary time ) to “diffuse” a collection of walkers (identical particles) over a specified time period to converge on the zero point energy (ZPE). A modified version of a DMC code for H₃O₂^- was used to carry out calculations for on H₅O₂⁺ and D₅O₂⁺ each with 20,000 initial walkers. Although the DMC method can allow for straightforward calculations of the ZPE, extension of the method to obtain observable quantities proves to be less direct. Bond length and bond angle distributions were obtained using an averaging by pair counting (AVPC) method. The results obtained report the ZPE, expectation values and histograms of internuclear distances both H₅O₂⁺ and D₅O₂⁺.

I contributed to experimental work to determine if rho(0) human cancer cells, deficient in functional mitochondrial electron transport chains, demonstrate altered susceptibility to glucose deprivation-induced cytotoxicity and oxidative stress in relationship to parental rho(+) cells, which contain functional mitochondrial electron transport chains. Our lab also considered if rho(0) human cancer cells would demonstrate differential susceptibility to 2DG-induced cytotoxicity and oxidative stress compared to normal parental rho(+) cells. My presentation discusses data results gathered from six different cancer cell lines.

I conducted two experiments with the yellow monkeyflower in Dr. Kelly's lab: one regarding allometry and another attempting to induce polyploidy. Determining the above-ground biomass of a plant usually requires harvesting. I conducted an experiment to develop a rapid and non-destructive means to estimate biomass in Mimulus guttatus. Several plant characteristics such as width of the widest leaf, length of the widest leaf, corolla diameter, length of first internode, and stem diameter were measured as potential predictors of biomass. Plants were then harvested and weighed. I fit a mathematical model to predict biomass from the morphological measurements, explaining 89% of the variance. In addition, I used colchicine, a chemical that breaks spindle fibers, to induce polyploidy so characteristics seen in polyploid species may be studied. The effects of immediate genome doubling can be further explored because using a chemical to induce polyploidy eliminates the natural selection factor.

Mérida is a growing city of approximately 800,000 people in the Yucatan peninsula of Mexico. The city experiences very high temperatures and high humidity throughout the year. We were studying to discover the factors that contributed to the higher temperatures within the city as compared to the neighboring countryside. Hobo sensors were placed in the 67 houses throughout our study area of Mérida that measured temperature and humidity. We also looked at different aspects of the physical environment such as building materials, lot and house size, and amount of vegetation surrounding the house. By analyzing the data we discovered that the biggest factor contributing to the high temperatures was that percent of the lot occupied by the houses was quite high. Our information was present to the local authorities of Mérida and hopefully changes can be made to decrease temperatures and humidity throughout the entire city.

NMR was used to study the metabolism of several ¹³carbon enriched molecules in both wild type and mutant yeast cells. The specific deletions studied were deletions in ODC1, ODC2, YMC1, and YMC2 which encode for transporters in the inner mitochondrial membrane. These mitochondrial transporter proteins transport α-ketoglutarate into and out of the mitochondria. Once outside the mitochondria α-ketoglutarate is converted into glutamate. NMR can then be used to study the enrichment of ¹³C-glutamate and analyze the singlet to multiplet ratio for each carbon of glutamate. These ratios help deduce how many times the labeled molecule went around the citric acid cycle before being moved out of the mitochondria and into the cytosol. Thus NMR can be used as a tool to shed light on the inner workings of a cell.