Matching Items (77)
Description
Lung cancer is the leading cause of cancer-related deaths in the US. Low-dose computed tomography (LDCT) scans are speculated to reduce lung cancer mortality. However LDCT scans impose multiple risks including false-negative results, false- positive results, overdiagnosis, and cancer due to repeated exposure to radiation. Immunosignaturing is a new method proposed to screen and detect lung cancer, eliminating the risks associated with LDCT scans. Known and blinded primary blood sera from participants with lung cancer and no cancer were run on peptide microarrays and analyzed. Immunosignatures for each known sample collectively indicated 120 peptides unique to lung cancer and non-cancer participants. These 120 peptides were used to determine the status of the blinded samples. Verification of the results from Vanderbilt is pending.
ContributorsNguyen, Geneva Trieu (Author) / Woodbury, Neal (Thesis director) / Zhao, Zhan-Gong (Committee member) / Stafford, Phillip (Committee member) / Barrett, The Honors College (Contributor) / Department of Chemistry and Biochemistry (Contributor) / Department of Psychology (Contributor)
Created2015-05
Description
Honey bee (Apis mellifera) colonies have experienced substantial losses due to colony collapse disorder (CCD) since the first officially reported cases in 2006. Many factors have been implicated in CCD, including pests, pathogens, malnutrition, and pesticide use, but no correlation has been found between a single factor and the occurrence of CCD. Fungicides have received less research attention compared to insecticides, despite the fact that fungicide application coincides with bloom and the presence of bees. Pristine fungicide is widely used in agriculture and is commonly found as a residue in hives. Several studies have concluded that Pristine can be used without harming bees, but reports of brood loss following Pristine application continue to surface across the country. The primary objectives of this study were to determine whether Pristine causes an aversive gustatory response in bees and whether consumption of an acute dose affects responsiveness to sucrose. An awareness of how foragers interact with contaminated food is useful to understand the likelihood that Pristine is ingested and how that may affect bees' ability to evaluate floral resources. Our results indicated that Pristine has no significant effect on gustatory response or sucrose responsiveness. There was no significant difference between bee responses to Pristine contaminated sucrose and sucrose alone, and no significant effect of Pristine on sucrose responsiveness. These results indicate that honey bees do not have a gustatory aversion to Pristine. A lack of aversion means that honey bees will continue collecting contaminated resources and dispersing them throughout the colony where it can affect brood and clean food stores.
ContributorsMcHugh, Cora Elizabeth (Co-author) / Jernigan, Christopher (Co-author, Committee member) / Burden, Christina (Co-author) / DeGrandi-Hoffman, Gloria (Co-author) / Smith, Brian (Thesis director) / Fewell, Jennifer (Committee member) / Barrett, The Honors College (Contributor) / School of Geographical Sciences and Urban Planning (Contributor) / School of Life Sciences (Contributor) / School of Art (Contributor)
Created2015-05
Description
With a quantum efficiency of nearly 100%, the electron transfer process that occurs within the reaction center protein of the photosynthetic bacteria Rhodobacter (Rh.) sphaeroides is a paragon for understanding the complexities, intricacies, and overall systemization of energy conversion and storage in natural systems. To better understand the way in which photons of light are captured, converted into chemically useful forms, and stored for biological use, an investigation into the reaction center protein, specifically into its cascade of cofactors, was undertaken. The purpose of this experimentation was to advance our knowledge and understanding of how differing protein environments and variant cofactors affect the spectroscopic aspects of and electron transfer kinetics within the reaction of Rh. sphaeroides. The native quinone, ubiquinone, was extracted from its pocket within the reaction center protein and replaced by non-native quinones having different reduction/oxidation potentials. It was determined that, of the two non-native quinones tested—1,2-naphthaquinone and 9,10- anthraquinone—the substitution of the anthraquinone (lower redox potential) resulted in an increased rate of recombination from the P+QA- charge-separated state, while the substitution of the napthaquinone (higher redox potential) resulted in a decreased rate of recombination.
ContributorsSussman, Hallie Rebecca (Author) / Woodbury, Neal (Thesis director) / Redding, Kevin (Committee member) / Lin, Su (Committee member) / School of Molecular Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2015-12
Description
This study illustrates the abilities of the honeybee, Apis mellifera, to learn and differentiate between patterns solely off their spatial frequencies. Patterns were chosen based off of calculations derived from the measurements of the physical construction of the apposition compound eye, which led to predictions of what the bees could theoretically see. The hypothesis was then that bees would have a visual threshold where patterns with spatial frequencies that fall below this line should be easily distinguishable, and patterns above the threshold would have scores that mimic if the bees made choices randomly. There were 9 patterns tested, all with different spatial frequencies and in the colors of black, white, and gray. The bees were tested on their learning and pattern differentiation abilities with 10 pattern comparisons, with the lower frequency of the two being associated with an unscented sucrose solution reward. The results were surprising in that the previous studies pointing towards this visual threshold were inaccurate because of some of the patterns being learning in an intermediate ability. These intermediate scores suggest that the calculations predicting what the bees could see clearly were slightly wrong because it was more likely that the bees saw those images in more of a blur, which resulted in their intermediate score. Honeybees have served as a useful model organisms over the decades with studying learning involving visual information. This study lacked in its total numbers of trials and bees tested, which could have led to incomplete results, and this showing of an intermediate score and ability. Future studies should continue in order to advance this understanding of a perceptually and cognitively advance processing animal.
ContributorsBalsino, Brandon Bartholomew (Author) / Harrison, Jon (Thesis director) / Smith, Brian (Committee member) / Duell, Meghan (Committee member) / School of Life Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2015-12
Description
Selenium, a group 16 metalloid on the periodic table, is a necessary mineral for many organisms. Trace amounts of selenium are essential for normal development, antioxidant protein function, enzyme function, and hormone regulation (Burden et al., 2016). However, when selenium is found in toxic amounts in organisms, it has been found to substitute for sulfur in proteins, which can be toxic to these animals, and cause oxidative stress (Quinn et al., 2007). Using the previous research done with acute exposure to organic and inorganic selenium compounds, we hypothesized that the inorganic sodium selenate would significantly decrease learning and memory recall for both chronic and acute exposure. We also hypothesized that the consumption of organic methylseleno-L-cysteine by honey bees would decrease learning and memory recall for both the chronic and acute exposure. We further hypothesized that protein carbonyl content would be increased due to oxidative damage caused by selenium in both the sodium selenate and the methylseleno-L-cysteine treatment groups, but that the inorganic selenium compound would increase the carbonyl content more than the methylseleno-L-cysteine. To run the experiments, three tents outside had two colonies in each tent. One tent contained the sodium selenate group, another had the sucrose control, and one contained the methylseleno-L-cysteine group. The treatment groups were fed selenium in their sucrose feeders. The first part of the experiment was training the bees by using proboscis extension response (PER) to teach them to extend their proboscis to the rewarded odor and not to the unrewarded odor. This was done by pairing the rewarded odor with a sucrose reward and not pairing it with the unrewarded odor. Then their short-term and long-term memory recall was tested. The second part of the experiment was checking for oxidative damage by measuring the protein carbonyl content in the bees. Three boxes were set up with the same three treatment groups as used in the tents. The treatment group bees were exposed to selenium in the sucrose feeders and in the pollen patties. After one week, the living bees were removed and frozen. They were then homogenized to extract protein. The first assay run was the protein content assay to establish a standard protein concentration for samples. Then a protein carbonyl assay was run, to determine the protein carbonyl content. Overall, the experiment found that exposure to selenium negatively impacted honey bees learning and memory recall significantly. Chronic exposure to the inorganic selenate reduced the bees' long-term memory abilities to differentiate between odors. With methylseleno-L-cysteine, it had no significant effect for the chronic exposure, but for the acute exposure, it had a significant impairment on their abilities to distinguish between the rewarded and unrewarded odors during conditioning. Our results showed that from our experiment there appeared to be no significant effect of selenium exposure on the increase of carbonylation content in the different treatment groups. This is most likely due to the fact the carbonyl content was not detectable because the protein concentration was low in the samples (approximately 3.5 mg/mL).
ContributorsWinski, Alexandra (Co-author) / Winski, Brandon (Co-author) / Smith, Brian (Thesis director) / Harrison, Jon (Committee member) / Burden, Christina (Committee member) / School of Life Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2016-05
Description
Advances in peptide microarray technology have allowed for the creation of fast-paced and modular experiments within affinity ligand discovery. Previously, low density peptide arrays of 10,000 peptides were used to identify low affinity peptide ligands for a target protein; an approach that can be subsequently improved upon with a number of techniques. VDAP[a] offers more information about the relative affinity of protein-peptide interactions via signal intensity in contrast to high throughput screening (HTS) and display technologies which offer binary data. Now, high density peptide arrays with 130,000 to 330,000 peptides are available that allow screening across peptide libraries of greater diversity. With this increase in scale and diversity, faster analytical tools are needed to adequately characterize array data. Using the statistical power available in the R programming language, we have created a flexible analysis package that efficiently processes high density peptide array data from a variety of layouts, rank existing peptide hits, and utilize signal intensity data to generate new hits. This analysis provides a user-friendly method to efficiently analyze high density peptide array data, generate peptide leads for targeted therapeutic development, and further improve peptide array technologies.
ContributorsMoore, Cody Allen (Author) / Woodbury, Neal (Thesis director) / Diehnelt, Chris (Committee member) / Barrett, The Honors College (Contributor)
Created2015-12
Description
Photosynthesis is the process by which plants, algae, and bacteria use light energy to synthesize organic compounds to use as energy. Among these organisms are a kind of purple photosynthetic bacteria called Rhodobacter sphaeroides, a non-sulfur purple bacteria that grows aerobically in the dark by respiration. There have been many contributions throughout the history of this group of bacteria. Rhodobacter sphaeroides is metabolically very diverse as it has many different ways to obtain energy--aerobic respiration and anoxygenic photosynthesis being just a couple of the ways to do so. This project is part of a larger ongoing project to study different mutant strains of Rhodobacter and the different ways in which carries out electron transfer/photosynthesis. This thesis focused on the improvements made to protocol (standard procedure of site directed mutagenesis) through a more efficient technique known as infusion.
ContributorsNucuta, Diana Ileana (Author) / Woodbury, Neal (Thesis director) / Lin, Su (Committee member) / Loskutov, Andrey (Committee member) / Barrett, The Honors College (Contributor) / School of Life Sciences (Contributor)
Created2014-05
Description
The influenza virus is the main cause of thousands of deaths each year in the United States, and far more hospitalizations. Immunization has helped in protecting people from this virus and there are a number of therapeutics which have proven effective in aiding people infected with the virus. However, these therapeutics are subject to various limitations including increased resistance, limited supply, and significant side effects. A new therapeutic is needed which addresses these problems and protects people from the influenza virus. Synbodies, synthetic antibodies, may provide a means to achieve this goal. Our group has produced a synbody, the 5-5 synbody, which has been shown to bind to and inhibit the influenza virus. The direct pull down and western blot techniques were utilized to investigate how the synbody bound to the influenza virus. Our research showed that the 5-5 synbody bound to the influenza nucleoprotein (NP) with a KD of 102.9 ± 74.48 nM. It also showed that the synbody bound strongly to influenza viral extract from two different strains of the virus, the Puerto Rico (H1N1) and Sydney (H3N2) strains. This research demonstrated that the 5-5 synbody binds with high affinity to NP, which is important because influenza NP is highly conserved between various strains of the virus and plays an important role in the replication of the viral genome. It also demonstrated that this binding is conserved between various strains of the virus, indicating that the 5-5 synbody potentially could bind many different influenza strains. This synbody may have potential as a therapeutic in the future if it is able to demonstrate similar binding in vivo.
ContributorsKombe, Albert E. (Author) / Diehnelt, Chris (Thesis director) / Woodbury, Neal (Committee member) / Legutki, Bart (Committee member) / Barrett, The Honors College (Contributor) / Department of Chemistry and Biochemistry (Contributor) / School of International Letters and Cultures (Contributor)
Created2014-05
Description
One of the major challenges that were yet to be solved for solid phase peptide synthesis was the lack of an efficient peptide sequencing technique that was less hazardous, easier to perform , and was more cost-effective. Sequencing peptides were held important in the field of Chemistry and Biochemistry because it aided in drug discovery, finding ligands that bind to a specific target protein and finding alternative agents in transporting molecules to its desired location. Therefore, the overall purpose of this experiment was to develop a method of solid phase sequencing technique that was more environmental friendly, sequences at a faster rate, and was more cost-effective.
ContributorsCordovez, Lalaine Anne Ordiz (Author) / Woodbury, Neal (Thesis director) / Zhao, Zhan-Gong (Committee member) / Legutki, Joseph Barten (Committee member) / Barrett, The Honors College (Contributor) / Department of Chemistry and Biochemistry (Contributor)
Created2014-05
Description
Dielectrophoresis has been shown in the recent past to successfully separate bioparticles of very subtle differences at high resolutions using biophysical forces. In this study, we test the biophysical differences of methicillin resistant and susceptible Staph. aureus that are known to have very similar genomes by using a modified gradient insulator-based dielectrophoresis device (g-iDEP). MRSA is commonly seen in hospitals and is the leading killer of infectious bacteria, claiming the lives of around 10,000 people annually. G-iDEP improves many capabilities within the DEP field including sample size, cost, ease of use and analysis time. This is a promising foundation to creating a more clinically optimized diagnostic tool for both separation and detection of bacteria in the healthcare field. The capture on-set potential for fluorescently tagged MRSA (801 ± 34V) is higher than fluorescently tagged MSSA (610 ± 32V), resulting in a higher electrokinetic to dielectrophoretic mobility ratio for MRSA. Since the strains have proven to be genomically similar through sequencing, it is reasonable to attribute this significant biophysical difference to the added PBP2a enzyme in MRSA. These results are consistent with other bacterial studied within in this device and have proven to be reproducible.
ContributorsSmithers, Jared (Author) / Hayes, Mark (Thesis director) / Woodbury, Neal (Committee member) / School of Criminology and Criminal Justice (Contributor) / School of Molecular Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2020-05