Posters from the annual student research session where DePauw students can demonstrate their collaborative work with faculty or internship experiences.
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Effects of Trifluoroethanol on the Stability and Folding Dynamics on SH3 and ACBP
Amanda Showalter
Protein folding is a complicated process that is typically determined by complex energy landscapes that can be altered by outside factors like temperature, mutation, or the chemical environment surrounding the proteins. Trifluoroethanol or TFE is an organic, colorless, water-miscible alcohol that is used in various chemical, pharmaceutical, and engineering applications. TFE is known for stabilizing protein secondary structure specifically, alpha-helical conformations. Denaturation melts involving TFE were tested on Acyl CoA binding protein, (ACBP) and SH3 protein due to their difference in native secondary structures; ACBP is comprised of mainly alpha helices and SH3 is comprised of mainly beta sheets. These experiments reveal that TFE has a large impact on the thermodynamics of both proteins and possibly leads to a change in the conformation or folding pathways of the two proteins tested.
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Valuing the Alaskan Wilderness: The 19th Century Writings of John Muir and W.H. Dall
Cecilia Slane and Brown
In the late 19th century, American conservation began to separate into two ideological approaches: scientific and spiritual. Two prominent naturalists, William Healey Dall and John Muir, who both expressed deep admiration for the land they explored during scientific expeditions and personal pilgrimages exemplify the origins of this division. In this project, I am researching how Dall and Muir experienced, valued, and described the Alaskan environment through public essays and personal journals. Using Muir and Dall as key figures, I am investigating how personal motivations inspired their valuing the land as a “wilderness,” a pristine place antithetical to civilization.
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Optimization of a Workflow for Biological Tissue Imaging and Analysis
Eric Spehlmann
Biomedical imaging for tissue analysis encompasses a range of techniques to represent samples. Biological images provide the basis for the study of histology at the micro and nanoscale level. Brightfield, widefield fluorescence, confocal, apotome, and electron microscopes are used to image tissue, cells and ultrastructural components and to generate single images or image stacks, in formats compatible with various analytical tools. Typically image stacks are digitally segmented using powerful image analysis tool, such as Amira, followed by rendering of 3D models from segmental 2D stacks. However, it is beneficial or crucial that users understand the tissue structure well enough to accurately perform segmentation. Misunderstanding the 2D images can lead to incorrect conclusions and false identification of biological elements. Therefore, we implemented a new workflow, involving the use of Amira for 2D stacks to segmentation, in conjunction with SyGlass for fast rendering of structures in virtual reality. Instead of a linear progression, the workflow using SyGlass allows for concurrent development of an Amira model along with a VR representation that improves the 3D render. Our experience thus far, using a recursive process have allowed for completion of segmentation and reconstruction with greater accuracy.
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Urinary Sodium Excretion: Finding an Inclusive Equation in Older Populations
Cassie Washam
Current methods of urinary sodium analysis utilize a 24-hour urine collection, exhaustive of time and resources for clinicians and patients. In order to make assessment more efficient, methods using timed voids are being examined and show promising results. Although more efficient, many studies lack inclusivity in approach and analysis that generalizes populations independent of influencing identities and risk factors associated with intersectionality. In this study we aim to examine urinary sodium excretion subjective to age, race, gender and hypertension. Individuals ages 45- 79 from the Chicago area, participating in 2 cohort cardiovascular studies provided timed void spot samples. These samples were then analyzed for urinary sodium excreted and compared by various timed void combinations, race and sex. The model equation of a sister study built in a younger population was applied as well. Findings from all comparisons illustrated the variance occurring by over generalizations in analysis as well as the need for age diversified studies. Women’s predicted values best follow the observed values, specifically in white women. Men’s variation from the observed were worse, particularly in white men. This study emphasizes including intersectionality respective to populations for a more comprehensive understanding of urinary equation modeling and sodium consumption. Applying equations from other populations fails to incorporate risk factors that influence populations and therefore cannot be successfully employed in populations of differing demographics. Finding a generalizable equation is a necessity if we wish to monitor and improve sodium consumption on a population level.
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Optimal Management of Children with Neutropenic Appendicitis During Therapy for Childhood Cancer
Whitney Weinschenk
During chemotherapy treatment for childhood cancer, many children develop neutropenia. While neutropenic, surgical intervention of appendicitis raises concerns for the risk of infection. The three treatment pathways are early surgery, medical management with delayed surgery, or definitive medical management. It was determined that neutropenic appendicitis appears to be best treated with medical management avoiding the risks of operative intervention.
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AROutcrop: an augmented reality mobile application for teaching geology in the field
Zachary Wilkerson, M. Scott Wilkerson, and Chad Byers
Augmented reality (AR) provides an immersive environment where computer-generated textural and/or graphical information overlay natural features in real-time. Such computer-generated objects/data have the potential to supplement or “augment” reality in ways that enhance geoscience comprehension in the field. For example, when instructors stand at a distance from an outcrop and explain the features present, students sometimes struggle to recognize the subtle rock textures and fabrics that define the stratigraphic units and structures present, instead seeing only an amorphous mass of rock. AR technology might allow students to use their own mobile devices to better recognize, interpret, and comprehend the geology around them. We created an AR app (AROutcrop) for Android mobile devices to evaluate the advantages/disadvantages of using AR approaches to teach geology in the field. Specifically, AROutcrop accesses the device’s picture library to auto-recognize outcrops from photos and overlay various AR objects (2-D interpretations and 3-D models) in the real-time view within the device’s camera environment. Students can use their mobile device to interact with various AR objects by: 1) clicking on AR objects to open a window with text, graphics, and data describing the geology of each feature, 2) collecting a “rock sample” from the outcrop by placing an AR 3-D photogrammetry model of an actual rock specimen from the outcrop on the ground where students can walk around the AR “sample” and magnify it for more in-depth study, and 3) overlaying and georeferencing (e.g., resizing, translating, rotating, etc.) a 2-D AR geologic interpretative image over the entire outcrop to highlight specific features and/or rock layers. Preliminary trials of AROutcrop at a nearby quarry suggest that this novel approach has the potential to not only improve student learning and comprehension, but also to encourage students to engage in critical-thinking processes, to make careful observations while in the field, and to become better consumers of scientific knowledge.
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Semi-Synthetic Development of Mithramycin Analogues
Sterling Brooks, Allison Foster, and Daniel Scott
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A Parallel Genetic Algorithm For Tuning Neural Networks
Nathan Chadderdon, Ben Harsha, and Steven Bogaerts
One challenge in using artificial neural networks is how to determine appropriate parameters for network structure and learning. Often parameters such as learning rate or number of hidden units are set arbitrarily or with a general "intuition" as to what would be most effective. The goal of this project is to use a genetic algorithm to tune a population of neural networks to determine the best structure and parameters. This paper considers a genetic algorithm to tune the number of hidden units, learning rate, momentum, and number of examples viewed per weight update. Experiments and results are discussed for two domains with distinct properties, demonstrating the importance of careful tuning of network parameters and structure for best performance.
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Majority of Cells Lining the Walls of the 3rd Ventricle in the Adult Rat Brain are not Neural Progenitor Cells
C. Hasken, S. Vermilyea, M. Hendrickson, and R. Kalil
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Measuring Immune Responsiveness in Xenopus laevis Using Phytohaemagglutanin (PHA)
Kevin Kinney, Skyler Majors, Madelyn Lee, Scott Espich, and Erika Kischuk
Phytohaemagglutanin (PHA) is a red kidney bean extract that has been used to stimulate an immunological T cell response in a variety of animals. This procedure has become very popular method to analyze an individual animal’s ability to trigger an immunological response.(Brown 2014) PHA skin testing has been used in a variety of avian, mice, lizard, and amphibian species where it is injected into the muscle, skin, or webbing of an animal and then recording the amount of swelling before and after the injection.(Smits 1999) We are using the amphibian Xenopus laevis to test 1) their immune reaction under normal conditions and 2) to test how stress effects their immune reaction. In our control non-stress experiment to discover if PHA actually causes swelling, we found that significant swelling occurs at all time points in comparison to the saline injected foot. In the stress versus non-stress PHA experiments, we found no significant variation between the stressed versus non-stress, but still a significant difference between PHA versus saline injection.
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Skin Graft Acceptance Rates in Xenopus laevis
Madelyn Lee, Scott Espich, Erika Kischuk, Skyler Majors, and Kevin Kinney
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Probe Location within Interfacial Layer of CTAB Reverse Micelle System
Jonathan Li and Bridget L. Gourley
To understand the chemistry of the interfacial region of reverse micelles (RM), we studied RM system made with the cationic surfactant cetyltrimethylammonium bromide (CTAB), alkanol cosurfactants dissolved in cyclohexane with water core. Spectroscopic methods, specifically UV-Vis absorption of Coumarin 343 (C343) as a probe molecule, were used to determine basic properties of RM systems. However, the probe location was difficult to determine because the spectrum (absorbance), when dissolved in RM solution, didn’t match the spectra in any of the pure components. Our data suggests that the interfacial layer of RM cannot be thought of behaving only the characteristic of single one of the components; rather, it behaves as a mixture of multiple components with unique characteristics. The interfacial layer appears to have roughly three distinct regions. By combining two components at a time, our data shows that C343 is most likely to reside in the middle or outer interfacial regions, which is surprising because C343 is polar enough that it would be expect to preferentially migrate into the water core
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Anticancer Drug Delivery via Unique Properties of Gold Nanoparticles
Sam Lohmar, Jeffrey Schulte, and Daniel Scott
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Dynamical Behavior of Probe Molecules and Dominant Role of Cosurfactants in Reverse Micelles
Jia QI and Bridget L. Gourley
Reverse micelles (RM) are nanopools of water surrounded by surfactant molecules in a non-polar solvent. Our studies investigated properties of RM probe molecules in the interfacial boundary between water and non-polar solvents. Reichardt’s dye, a probe molecule, was used to uncover properties of RM. UV/vis spectroscopy of Reichardt’s dye reveals information about polarity and the dye’s approximate residential location and also helps confirm molecular orbital energy diagram. We discovered an interesting phenomenon with Reichardt’s dye in RM. Surprisingly, the UV/vis spectrum of Reicahrdt’s dye in CTAB RM with octanol as a cosurfactant exhibits decreasing absorbance and a blue shift. Reichardt’s dye in solely octanol shows an irreversible color change and similar UV/vis spectrum. Consequently, we conclude that Reichardt’s dye resides near the interfacial layer/solvent boundary. Other cosurfactants do not result in the time dependent behavior suggesting a more dynamic interaction between octanol and Reichardt’s dye.
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Tandem Cancer Drug Delivery via Gold Nanoparticle Targeting Platforms
Jeffrey Schulte, Sam Lohmar, and Daniel Scott
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Automatic Animation of Molecular Motion using Python and Cinema 4D
Diana Zajac, Nathaniel Smith, and Dan Gurnon
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Kinematics and Economy of Novel Barefoot Running
Aaron Zell and Patrick Babington
The purpose of the study was to compare key physiological, anthropometric, and kinematic attributes between barefoot and shod runners while also comparing these variables to the running economy of their respective conditions. We hypothesize that when running in the acute barefoot condition participants will exhibit significant biomechanical, physiological, and kinematic differences compared to the shod condition that may be correlated with a superior or inferior running economy. Male (4) and female (5) test subjects (19.2±0.83 years, 171.06±6.89 cm, 71.09±14.52 kg) participated in two separate testing sessions. The first session involved collecting the weight, height, sitting height, ankle and hip widths, hamstring flexibility, and body fat percentage preceding a maximal oxygen consumption test. The second session required subjects to run at a variety of submaximal velocities while they were recorded with high speed video. Kinematic variables were measured using Dartfish Video Analysis Software. Results showed that VO2 was greater when shod than barefoot at 2.68 m/s, but shod running required less oxygen at 3.58 m/s. There was no difference at 3.13 m/s. Body composition was the only physiological variable that correlated with economy. Knee angle decreased and stride frequency increased when switching from shod to barefoot running. These findings suggest that as habitually shod runners begin barefoot running they adapt to increased ground reaction forces by incorporating greater knee flexion and a faster stride frequency. These changes may cause a decrease in economy at slower speeds and an improvement in economy at greater velocities.
