Posters from the annual student research session where DePauw students can demonstrate their collaborative work with faculty or internship experiences.
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The Impact of Local Anthropogenic Activities on Soil Health within a Retired Farm: Implications for Urban Gardens
Abigail Cook '22, W. Roberts, E. Prince, and K. Brown PhD
Americans are implementing private food gardening for food access and affordability. A report by the National Gardening Association (2020) reveals a notable increase in food gardening in the past decade among urban households, especially millennial households. These national trends reflect an increasing interest in healthy living, sustainable gardening practices, and mitigating food insecurity within communities. Nonetheless, little is being done to assess soil health, especially for soils utilized for private and community gardens. Soil contamination can harm the health of those who use contaminated soils for food gardening. Thus, this study investigates soil health within a retired farm that is situated in close proximity to a firearms range and a county highway department.
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Neural Innervation of the Immune Response Could Lead to Treatments for Severe Asthma: The Screening of Neurotransmitters on T Helper 17 Cell Differentiation
Kate Cowger, Wei Wang PhD, and Xingbin Ai PhD
T Helper 17 (Th17) cell-driven neutrophilic asthma is a rare, yet severe phenotype that accounts for over 75% of all asthma related medical costs. Neural innervation has been known play a role in the immune response and we investigated whether the addition of neurotransmitters to would affect Th17 cell differentiation. Results indicated that neural innervation upregulated Th17 cell differentiation and expression of its cytokine IL-17 that is responsible for the severe symptoms seen in neutrophilic asthma.
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The Impacts of the Presence of Amino Alcohols on Xenobiotic Cell Signaling Pathways
John Csehill and Sarah Mordan-McCombs PhD
For this project, we investigated the effects of the presence of amino alcohols on the xenobiotically-catalyzed cell signaling pathways growth of Saccharomyces cerevisiae yeast cells. Amino alcohols have been hypothesized to act as antitumor agents against different types of tumor cells because they could act as a ligand for the aryl hydrocarbon receptors (AhRs) responsible for regulating downstream enzymes involved in the cellular response to xenobiotic stimuli.Yeast cells, on the other hand, do not have AhR proteins within their cells, so they depend on other potentially similar mechanisms involved in responding to xenobiotic signaling pathways. I helped synthesize the amino alcohol derivative compound benzylamine using aldol-epoxide reactions, and exposed different yeast mutants to benzylamine, which will be used to help further determine the mechanisms by which the yeast cells will respond to xenobiotic stimuli.
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The Effects of Sugar Osmolytes on Reverse Micelle Systems
Jenna Deckard and Bridget Gourley PhD
Reverse Micelles (RM) are nanoscopic pools of water encapsulated by an amphipathic surfactant molecule that allows the water pool to be suspended in a nonpolar solvent. We use RM systems because they allow for the study of water and dissolved osmolyte interactions in confinement. Gaining an understanding of how sugars interact with water in confinement has significant implications for biological systems. This project seeks to understand the effects of galactose as an osmolyte on the interactions, loading limits, and size of RMs when compared to RMs containing only water and RMs containing glucose. Galactose and glucose have slight structural differences, varying in the position of the hydroxyl group on the fourth carbon of each molecule allowing us to probe the structural nuances that often have large biochemical effects. RMs prepared using the surfactant Docusate Sodium (AOT) and the nonpolar solvent isooctane (2,2,4- trimethylpentane) were made in sizes of w0=5, 10, and 20 where w0 represents the ratio of the concentration of water to the concentration of surfactant ([water]/[surfactant]). The loading limit of galactose in RMs was determined to be less than that of glucose over a range of RM sizes with the highest loading limit found in w0= 10 RMs. RM systems were also analyzed using Dynamic Light Scattering (DLS) to determine the impact of the osmolyte on RM size. We observed a reduction in the size of RMs when loaded with a sugar osmolyte, which we postulate happens because the interaction of the sugar with AOT headgroups disrupts the shape of RMs and causes a change in AOT surface area.
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Effect of a Hexylamine Derivative on Cancer Cell Viability
Rachel DeLancey, Bamlak Deju, Jeff Hansen PhD, and Nipun Chopra PhD
2-[(p-Chlorophenyl)hydroxymethyl]-1-[(methylamino)hexyl]cyclohexanol is a drug produced by hexyl amine and an epoxide through an aldol epoxidation reaction. Motifs of β-amino alcohols and nonpolar R groups in organic compounds have been found to have cytotoxic properties. Past studies in Dr. Hansen’s lab has shown that this hexylamine derivative has similar LC50 values to other antitumor agents. They also found that the drug was cytotoxic to HL-60 cancer cells. No other cell lines have been tested with this drug. Our study investigates the effect of our compound on varying cell lines to further determine its anticancer properties. Mouse NIH/3T3, Human HEK293, and Human SK-MEL-28 cell lines were cultured and plated into 96-well plates. Varying concentrations of the hexylamine derivative were administered and incubated for 48 hours. MTT assays detected the levels of cell viability. Results showed a significant decrease in HEK293 cells at a 30 μM concentration of our drug. The mouse and cancer cell lines did not produce significant results after statistical ANOVA tests. Future directions include further validation of the current results as well as research on the mechanisms by which this drug causes decreased cell viability. This research includes LDH and wound healing assays in addition to determining which proteins are down- and up-regulated in the process. Our study has found that the compound reduces human embryonic cell viability but does not significantly affect mouse cells or human melanoma cells. Further research is required to determine the methods of the drug and its potential in tumor treatment.
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Extracting the Mean Lifetime of the Neutron
Adam Forward, Muhammad Omer Sajid, and Alexander Komives PhD
Neutrons can be stable only when bound to the nucleus of an atom through the strong force. For every passing second, there is a probability that any isolated neutron will decay into a proton, an electron and an antineutrino. However, for the past 15 or so years, the only two neutron lifetime measurement methods have consistently shown lifetimes differing by over 8 seconds. One of the lifetime measurement methods is called the "beam method: and the other is called the "bottle method." While the measured lifetimes from the beam and bottle methods differ, as shown in the figure titled "Published Neutron Lifetime Reports," the Standard Model of Particle Physics predicts that neutrons should have the same average lifetime under these two conditions. The Standard Model is a unified theory that attempts to describe how the universe works on the most fundamental level. The properties of every particle are described through the Standard Model, along with the mechanisms (outside of gravity) for how these particles interact with one another. Therefore, either the differing lifetimes are a result of imprecise measurements, or the differing neutron lifetimes present flaws in the physicists' current understanding of the Universe's most fundamental properties. The UCNtau experiment, using the bottle method, published one of the most precise neutron lifetime values ever in 2018. This summer, we performed a preliminary analysis on blinded UCNtau data taken during the 2020 run cycle at Los Alamos National Laboratory and made significant progress in extracting a blinded lifetime.
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Investigating the effects of the benzylamine and epoxide product on the cell viability of MCF7 and SUM159 breast cancer cell lines
Rachael Hinshaw and Sarah Mordan-McCombs PhD
Introduction: Breast cancer is currently the most prevalent form of cancer in the world. Early stage treatments such as selective estrogen receptor modulators and antibodybased therapies have proven effective, but there are few options for late stage triple-negative disease (TNBC). Thus, current research is focused on chemopreventive and chemotherapeutic agents for late stage disease. Dr. Hansen’s lab has found evidence that their synthesized β-amino alcohol compounds are potential targets for cancer treatments due to their cytotoxic effects on brine shrimp and the HL-60 leukemia cell line. The benzylamine and epoxide product synthesized has an LC50 value of 8.28 uM which indicates that the compound is potentially very cytotoxic at low doses against cancer cells.
Methods: In order to investigate the effects of the benzylamine product on human breast cancer cell lines SUM159 (TNBC) and MCF7 (early stage), I treated the cells with different concentrations of the benzylamine product dissolved in DMSO and cell media and performed a crystal violet assay at 24, 48, 72, and 96 hours to visualize cell viability.
Results: The SUM159 cell viability was decreased in the treated wells in comparison to the control wells, but the results were not significant. In the MCF7 cells, there was significantly lower cell viability in the wells treated with 3uM, 300nM, and 30nM at 48 hours and 3uM at 72 hours compared to the wells treated with DMSO as a vehicle control.
Discussion: My results indicate that the benzylamine product is a potential antitumor drug because of its cytotoxic effects against the SUM159 and MCF7 breast cancer cell lines. Future work will include repetition of this experiment and testing the benzylamine product on other cell lines including a noncancerous cell line.
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Expression of Lactate Dehydrogenase (LDHA) WT and A320T Mutant
Natalie Husby, John Csehill, Ian Longen, Ellie Reece, and Daniel Gurnon PhD
The human genome has a length of approximately 3 billion base pairs, containing a total of over 20,000 genes, which can all be subjected to mutations that cause variations in the genome. Variations in a genome can be potentially either benign or pathogenic, but it can be difficult to distinguish whether a variant is one or the other, leading to tens of thousands being classified as variants of unknown significance (VUS). Our lab was particularly interested in the VUSs in lactate dehydrogenase (LDHA), an oxidoreductase enzyme that catalyzes the reversible conversion of pyruvate to lactate, an important component to anaerobic metabolism. Our lab is focusing on the A320T (alanine to threonine mutation at position 320) VUS, in which we cultured BL21 (DE3) and DH5α E. coli cell strains, so that we are able to clone wild type (WT) and A320T mutant enzymes. We eventually expressed and purified the two types of LDHA to observe the activity of each. Through expression and purification of both wild type and mutated forms of LDHA, we can observe the impact that the A320T-mutated VUS will have on the function of the LDHA protein, thus determining whether the VUS is benign or pathogenic to the enzyme function.
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Assessing the Cognitive and Social Behaviors of Apis mellifera in Finding Food
Sophia Jones and Claire Dorner
Apis mellifera, or more commonly named, honeybees, are known for their keen ability to navigate the natural world in search of an unpredictable food source; nectar. Honeybees have a trichromatic visual spectrum which allows them to find flowers through vision, but their spectra is based on ultraviolet, blue and green (Riddle, 2016). They also have a circadian rhythm that allows them to know the optimal times to leave the hive in search of food (Moore et al. 1989). The social behaviors of honeybees also closely mirror our own and has caused numerous scientists to investigate whether they have the capacity to hold memories and learn. This experiment was split up into three segments and set out to determine whether honeybees could be trained to fly to a designated spot in order to get food, and whether they could differentiate between two similar food sources.
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Conodonts in the Nature Park: Exploring Our History
Emily G. Kaiser, Lannea Allen, and T. Cope PhD
Are conodonts present in the Nature Park? Can we identify them and use them to determine the age of the rocks in the Nature Park? Do the specimens we find in the Nature Park match the species found in previous studies of the Ste. Genevieve Limestone? To answer these questions, we processed limestone samples by manually extracting them and crushing those samples. We then dry sieved samples using 18-20 micron pans, and then combined sorted grains with 10% acetic acid. Those contents were wet sieved with 60 and 120 microns pans. This method allowed us to extract approximately 30 specimens to be examined under a scope for the identification process. Using the multi element approach, we were able to identify P, S, and M series elements. Ozarkodina, Spathognathodus, and Neoprioniodus were most commonly identified and found in both the upper and lower layers of the quarry wall. Some specimens that were only expected to be found in St. Louis Limestone were found in our outcrop, which we initially hypothesized to be the Ste. Genevieve Limestone. Explanations for these results could be that the quarry falls partially in the Ste. Genevieve and the St. Louis Limestone or there were potential errors made in the identification process, resulting in incorrect placement of the boundary. Our data was inconclusive and would require further research to bring more conclusive results.
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In-vitro Stimulation of CD4+ Lymphocytes Following Renal Ischemia/Reperfusion Injury
Emma G. Kennedy, Jason A. Collett, and David P. Basile
To explore the Th-17 activation mechanism, renal CD4+ cells were isolated from post ischemic rats and stimulated in-vitro with varying conditions. These conditions focused on the effect of adenosine on IL-17 response using RT-PCR. Additionally, inhibitors of adenosine were added to test their IL-17 response in conjunction with adenosine. Specifically, an inhibitor for the Orai1 calcium channel. Furthermore, adenosine agonists were tested with to determine their effect on IL-17 response in the in-vitro stimulation plate.
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Identifying an appropriate in vitro model to study the effects of microRNA-4705 on S100β expression
Alyssa Koch, Vidhur Bynagari, Yangjie Tan, and Nipun Chopra PhD
Traumatic brain injury (TBI) is caused by external force to the head. In addition to the primary injury sustained by the impact, TBI can trigger a chronic inflammatory response that causes further tissue damage and neuronal death. Following TBI, glial cells of the central nervous system secrete elevated levels of the S100βprotein. S100βcan activate and upregulate the Receptor for Advanced Glycation End Products (RAGE). The RAGE pathway activates NFκB, a transcription factor involved in production of pro-inflammatory cytokines, resulting in infiltration of immune cells from the peripheral blood. Unchecked, the inflammatory response is thought to cause excessive tissue damage and neuronal death. It is hypothesized that downregulation of S100βfollowing TBI may ameliorate damage caused by chronic neuroinflammation. Our lab aims to downregulate S100βusing microRNA. Previously, our lab used bioinformatics to identify a candidate microRNA, miR-4705, that might target S100β. We aim to investigate whether miR-4705 can downregulate S100βin human SK-MEL-28 cells. Thus far, we have gathered evidence that SK-MEL-28 cells express S100β (shown in Fig. 1). However, we have not been able to demonstrate that S100βsiRNA downregulates S100β, suggesting that the transfection was unsuccessful. These preliminary experiments have served to test the validity of our in vitro model for studying S100β expression. Our next steps will be to repeat our siRNA experiments and to begin testing the effect of miR-4705 on S100β expression in SK-MEL-28 cells.
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Determining Swimming Power Output using a Commercially Available Tethered Pulley Device
Samantha Loudermilk
Previous literature exists that supports resistive training in the water to improve competitive swim performance. Most of these examples include research involving relationships between swim power and performance. However, no established protocols to estimate measurements of power utilizing resistive training devices exist. PURPOSE: First to estimate peak swim power using a pulley-based training device and second, to examine the relationship between peak swim power estimated via a pulley-based training device and peak power achieved during an arm ergometer test. METHODS: Swimmers took part in two separate tests of power. SWIM POWER TOWER TEST: Participants performed a series of 10-meter freestyle sprints maximal effort while tethered to the resistive pulley device. The resistance was increased on each subsequent swim bout until failure. ARM ERGOMETER TEST: Participants performed a maximal arm crank test at a resistance of 5% of their body mass for 30 seconds. A Pearson correlation coefficient was used to examine the relationship between peak powers from both tests. RESULTS: The Pearson correlation of peak swim power and peak arm ergometer power was found to be significant, R2 = 0.64; p < 0.05. CONCLUSION: Swim power was estimated using a commercial pulley-based training device. A positive relationship was found between peak swim power in the water and peak power performed during an arm ergometer test in the laboratory.
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Thinking Global & Acting Local in Chiang Mai, Thailand: A Semester with the International Sustainable Development Studies Institute
Erika Marchant '22
Erika completed her Environmental Fellows Program practicum as a student with the International Development Studies Institute (ISDSI) in Chiang Mai, where she spent four months studying the relationship between Thai history, culture, society and the northern region’s unique local ecology. Courses involved the study of sustainable food ways, political ecology of forest ecosystems, and marine biodiversity.
Erika embarked on hiking and backpacking expeditions with her cohort; learned and applied key ecological field skills; presented on socioeconomically significant local plant and animal species; and expanded her understanding of Thai language and culture firsthand through relationships with Thai instructors, friends, and host families. One of the most valuable experiences of Erika's time in Thailand was getting to design and conduct three of her own month-long ethnographic research projects, one of which will be discussed in greater detail in "Block 2: Sustainable Food Systems."
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Analyzing the effect of benzylamine product on yeast cells deficient in the oxidative stress response
Autumn McDaniel and Sarah Mordan-McCombs PhD
Oxidative stress occurs when there is an imbalance of reactive oxygen species and antioxidants. The brain is especially vulnerable to the effects of ROS because of its high oxygen demand. Previous studies have demonstrated that oxidative stress plays a central role in common neurodegenerative diseases such as Alzheimer's disease and Parkinson's disease. Furthermore, ROS have been found to trigger programmed cell death in cancer cells. Our lab aims to investigate the oxidative stress response in Saccharomyces cerevisiae by studying its growth at different concentrations of a compound called benzylamine, which is thought to have possible anticancer effects. To identify the different biological pathways being affected by the compound, we began by testing different concentrations of the compound with DMSO on yeast mutants. Each mutant had a different growth compared to the control at both the 30nM and 300nM concentrations while still not being completely wiped out. After evaluating the growth patterns of twenty-six different yeast mutants in comparison to untreated and wild type cells, we identified four proteins to focus on that are involved in similar biological pathways: Δzwf1, Δyap1, Δaif1, and Δtsa1.
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Mental Health among College Students during the COVID-19 Pandemic: A Longitudinal Study
Jillian Meyer, Lizzie Bell, and Michael E. Roberts PhD
This research project was a continuation of research conducted in PSY215 Research Methods from the Fall 2020 Semester and subsequently extended in Spring 2021 via Asher funds to collect additional data. The purpose of the research was twofold: conduct a longitudinal study that examines how college students’ mental health has been impacted by the COVID-19 virus from the Fall 2020 semester to the Spring 2021 semester; a second goal was to obtain a racially diverse sample (expanding beyond our initial cross-section) and to also examine factors such as the impact of big vs smaller universities’ administrative responses to COVID-19, and the impact these administrative responses have had on the mental health of college students.
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Droplet Impact, Part 2: Engineering a Droplet Generator
Nanami Mezaki, Ben Wilkerson, and Jacob Hale PhD
Prior droplet impact research at DePauw used a syringe to pump fluid through a tube to create a droplet. This method generated ~2.5mm diameter droplets with secondary satellite droplets that formed during pinch-off and influenced rupture upon collision with the main droplet. Furthermore, the large diameter caused the droplet to experience significant oscillation as it fell, making it difficult to control impact shape without changing impact velocity. Part of this summer’s research focused on adapting preexisting designs for droplet generators to build our own version that creates small, consistent droplets without interference from satellite droplets or jets (which form at high speeds/large diameters).
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Big Cities: Air Pollution and Human Health
Natalie Michaels and Naima Shifa PhD
Our project explores the growing issue of air pollution on urban environments throughout the United States. Through the use of the County Health Rankings data set, we investigated the connection amongst air pollution, health outcomes, and other socioeconomic and environmental risk factors.
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Eye-tracking Study: Systematic Effects of Task Instructions on Selective Attention and Inductive Learning
Kumiko Nakajima, Olivia Dickinson, and Michael E. Roberts PhD
Participants studied paintings with respective task instructions and were subsequently tested on identification performance for trained paintings as well as new paintings by the same artists. Eye tracking analyses indicate that each task instruction led to distinctive fixation patterns for the paintings, which may influence inductive learning performance. Generally, participants given the alternative pattern of the instructions performed significantly better than those who received the successive pattern of instructions both in trained and new paintings.
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Resilience of Transportation Systems to Disasters
Nangga (Ga Nan) Oirat and Suman Balasubramanian PhD
We used graph theory's centrality measures to process the resiliency of rail stations in India. Centrality measures are the principles of processing, while Python is the tool of processing.
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Numerical Approaches of Pricing European Options in The Cox-Ross-Rubenstein Models
Hai Phan and Seonguk Kim PhD
The Cox-Ross-Rubinstein (CRR) market mode is used to price European and American Options without complex elements, including dividends, stocks, and stock indexes paying a continuous dividend yield, futures, and currency options. The model is an elegant, simple, but strong model to explain the general economic intuition behind option pricing and its principal techniques. In the paper, the CRR model's numerical elements and equations are indicated, and a practical event is examined to demonstrate the application of the model in the financial market. To make it easier to understand, figures, including tables and graphs, are also included to visualize and simplify the model and output data.
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Born to run? Vegetative spread of the invasive plant Phragmites australis via stolons (runners)
Daniel L. Saltz and Dana Dudle PhD
Phragmites australis is a highly invasive wetland grass species that dominates nearly any ecosystem that it invades, this is due to its incredibly dense foliage which makes it hard for plants and animals to live in the vicinity of phragmites. Phragmites can grow in versatile environments and are extremely durable. Therefore, once phragmites establish itself, it is very difficult to remove it. On top of that, Phragmites spreads very quickly by utilizing both sexual and asexual reproduction.
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Dogbane Under Stress: Habitat Differentiation of Anthocyanins in Apocynum cannabinum
Marie Spehlmann '22 and Rose Keith PhD
The quarry in DePauw’s Nature Park, which was previously stripped of soil and layers of bedrock, offers an ideal study system for understanding how plants adapt to disturbances. The quarry bottom is particularly stressful for plants because of this loss in soil, high variability in water availability due to the poor porosity of the bedrock, and high light intensity. Therefore, plants that live there must have traits suitable for this harsh environment. One response elicited to stress in plants is the production of red pigments called anthocyanins. Anthocyanins are versatile and have been found to be protective in a multitude of ways; among their many functions, they have been shown to protect against tissue damage at high light levels and increase herbivore resistance. Using Hemp Dogbane, Apocynum cannabinum, as a study system, we asked whether anthocyanin content in stems differs between quarry and non quarry environments, if there is a relationship between pigmentation and herbivory, and how pigmentation is selected on in the two habitats.
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Voxelwise Mapping of Whole-Exome Sequencing to Noninvasive Imaging with Stereotactic Localization and Deep Learning
Katherine Stanley
Tumor heterogeneity presents a significant barrier to glioblastoma treatment. While multiparametric imaging can improve characterization of such heterogeneity, advances have been limited by access to ground truth pathology and genomics. Stereotactic localization addresses the former issue, allowing pairing of biopsy location with corresponding voxels in MR image. Using stereotactic localization, as well as voxelwise MR image analysis, a feedforward dense network, and whole-exome sequencing, the authors sought to improve multiparametric MR characterization of tumor heterogeneity.
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Diversity Oriented Synthesis of Sulfur Containing Epoxide Compounds
Monica Stefaniak and Jeff Hansen PhD
Diversity oriented synthesis is a drug discovery approach that allows the creation of a wide variety of new compounds that can each have exciting new characteristics. Previous research involving the opening of epoxide rings with amine groups has shown promising results with regards to bioactivity. Our research involved finding a simple procedure to open the epoxide ring using various thiol groups such as octanethiol, hexanethiol, and benzenethiol. We are hoping to develop a library of new sulfur containing compounds that show promising characteristics, such as pharmacological activity. In our project, we synthesized multiple new sulfur containing compounds and verified their structures using 1D and 2D NMR spectroscopy. In the future we are hoping to develop easier and more efficient methods to open epoxide rings and use more complex thiols that show interesting activity.