Matching Items (586)
Description
The intervertebral disc goes through degenerative changes with age, which leads to disc thinning, bulging, or herniation. Spinal fusion treatments are ineffective as they cause quicker degeneration of adjacent discs and fail in nearly 20% of cases, so researchers have turned to tissue-engineering biocompatible intervertebral discs for transplantation. However novel and effective as this may seem, these transplanted discs still show evidence of degeneration after just 5 years. I hypothesize that these discs are degenerating due to a blockage of the cartilaginous endplates post-transplantation that is hindering nutrient transport through the intervertebral disc. In order to test this hypothesis, I developed a mathematical model of nutrient transport through the intervertebral disc in one diurnal daily loading cycle. This model was used to simulate open endplates and blocked endplates and then compare differences in nutrient concentration and nutrient transport to the center of the disc. Results from the math model simulations were then compared to in vitro experimental data collected in lab to verify the findings on a physiological level. Results showed significant differences, both in vitro and in the model, between nutrient transport in open endplates vs blocked endplates, lending support to the original hypothesis. This study only presents preliminary results, but could hold the key to preventing future disc degeneration post-transplantation.
ContributorsMunter, Bryce Taylor (Author) / Santello, Marco (Thesis director) / Caplan, Michael (Committee member) / Giers, Morgan (Committee member) / Barrett, The Honors College (Contributor) / Harrington Bioengineering Program (Contributor)
Created2015-05
Description
Cancer remains one of the leading killers throughout the world. Death and disability due to lung cancer in particular accounts for one of the largest global economic burdens a disease presents. The burden on third-world countries is especially large due to the unusually large financial stress that comes from late tumor detection and expensive treatment options. Early detection using inexpensive techniques may relieve much of the burden throughout the world, not just in more developed countries. I examined the immune responses of lung cancer patients using immunosignatures – patterns of reactivity between host serum antibodies and random peptides. Immunosignatures reveal disease-specific patterns that are very reproducible. Immunosignaturing is a chip-based method that has the ability to display the antibody diversity from individual sera sample with low cost. Immunosignaturing is a medical diagnostic test that has many applications in current medical research and in diagnosis. From a previous clinical study, patients diagnosed for lung cancer were tested for their immunosignature vs. healthy non-cancer volunteers. The pattern of reactivity against the random peptides (the ‘immunosignature’) revealed common signals in cancer patients, absent from healthy controls. My study involved the search for common amino acid motifs in the cancer-specific peptides. My search through the hundreds of ‘hits’ revealed certain motifs that were repeated more times than expected by random chance. The amino acids that were the most conserved in each set include tryptophan, aspartic acid, glutamic acid, proline, alanine, serine, and lysine. The most overall conserved amino acid observed between each set was D - aspartic acid. The motifs were short (no more than 5-6 amino acids in a row), but the total number of motifs I identified was large enough to assure significance. I utilized Excel to organize the large peptide sequence libraries, then CLUSTALW to cluster similar-sequence peptides, then GLAM2 to find common themes in groups of peptides. In so doing, I found sequences that were also present in translated cancer expression libraries (RNA) that matched my motifs, suggesting that immunosignatures can find cancer-specific antigens that can be both diagnostic and potentially therapeutic.
ContributorsShiehzadegan, Shima (Author) / Johnston, Stephen (Thesis director) / Stafford, Phillip (Committee member) / School of Life Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2015-12
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
The effect of conflicting sensorimotor memories on optimal force strategies was explored. Subjects operated a virtual object controlled by a physical handle to complete a simple straight-line task. Perturbations applied to the handle induced a period of increased error in subject accuracy. After two blocks of 33 trials, perturbations switched direction, inducing increased error from the previous trials. Subjects returned after a 24-hour period to complete a similar protocol, but beginning with the second context and ending with the first. Interference from the first context on each day caused an increase in initial error for the second (P < 0.05). Following the rest period, subjects showed retention of the sensorimotor memory from the previous day through significantly decreased initial error (P = 3x10-6). However, subjects showed an increase in forces for each new context resulting from a sub-optimal motor strategy. Higher levels of total effort (P < 0.05) and a lack of separation between force values for opposing and non-opposing digits (P > 0.05) indicated a strategy that used more energy to complete the task, even when rates of learning appeared identical or improved. Two possible mechanisms for this lack of energy conservation have been proposed.
ContributorsSmith, Michael David (Author) / Santello, Marco (Thesis director) / Kleim, Jeffrey (Committee member) / Harrington Bioengineering Program (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
Collaborative learning has been found to enhance student learning experiences through interaction with peers and instructors in a way that typically does not occur in a traditional lecture course. However, more than half of all collaborative learning structures have failed to last very long after their initial introductions which makes understanding the factors of collaboration that make it successful very important. The purpose of this study was to evaluate collaborative learning in a blended learning course to gauge student perceptions and the factors of collaboration and student demographics that impact that perception. This was done by surveying a sample of students in BIO 282 about their experiences in the BIO 281 course they took previously which was a new introductory Biology course with a blended learning structure. It was found that students agree that collaboration is beneficial as it provides an opportunity to gain additional insight from peers and improve students' understanding of course content. Also, differences in student gender and first generation status have less of an effect on student perceptions of collaboration than differences in academic achievement (grade) bracket.
ContributorsVu, Bethany Thao-Vy (Author) / Stout, Valerie (Thesis director) / Brownell, Sara (Committee member) / Wright, Christian (Committee member) / Barrett, The Honors College (Contributor) / School of Life Sciences (Contributor)
Created2014-05
Description
This project aims to use the shape memory alloy nitinol as the basis for a biomimetic actuator. These actuators are designed to mimic the behavior of organic muscles for use in prosthetic and robotic devices. Actuator characterization included in the project examines the force output,electrical properties, and other variables relevant to actuator design.
ContributorsNoe, Cameron Scott (Author) / LaBelle, Jeffrey (Thesis director) / Santello, Marco (Committee member) / Barrett, The Honors College (Contributor) / Harrington Bioengineering Program (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
Electrochemical sensors function by detecting electroactive species at the electrode surface of a screen printed sensor. As more force is applied, the concentration of electroactive species at the surface of the sensor increases and a larger current is measured. Thus, when all conditions including voltage are made constant, as in Amp i-t, a quantifiable current can be read and the force applied can be calculated. Two common electrochemical techniques in which current is measured, cyclic voltammetry(CV) and amperometric i-t(Amp i-t), were used. A compressible sensor capable of transducing a force and acquiring feedback was created.
ContributorsFeldman, Austin Marc (Author) / LaBelle, Jeffrey (Thesis director) / Pizziconi, Vincent (Committee member) / Santello, Marco (Committee member) / Barrett, The Honors College (Contributor) / Harrington Bioengineering Program (Contributor)
Created2013-05