EUREKA! 2024 Abstract Book

Explore research conducted by incoming Clemson University Honors College students with leading faculty over the summer.

The EUREKA! program has helped to launch my experience as an Honors Student and make me more excited for the upcoming years. Throughout the program I have been able to meet my peers, make amazing memories, and participate in meaningful research that I will be continuing during my time at Clemson.

ALAYNA KHOJA 2024 EUREKA! PARTICIPANT

About EUREKA!

EUREKA! (Experiences in Undergraduate Research, Exploration, and Knowledge Advancement) gave 27 incoming Clemson Honors students the chance to dive into a research experience before their first year even began on Clemson University campus. Working as part of a team or one-on-one, EUREKA! gave these students the chance to engage early and start a path toward their next great discovery. Students were able to choose between in-person and online delivery options for a five-week period of research, scholarship, and community building, with all participants working with top faculty at Clemson. Our online and in-person programs also had student counselors to help guide the EUREKANs through the program and conduct research of their own. Many of the participating students continue their projects throughout their undergraduate years. We hope their enthusiasm for research will encourage their peers to follow their lead to build an exciting and productive environment for undergraduate research, scholarship, and discovery at Clemson University.

EUREKA! Counselors Ashton McEntarffer, Makenna Lankford, and Abbey Grace Pickrel

Focus on Research and Community

Whether in-person or online, students worked on research projects under the direction of faculty mentors in fields ranging from religion and philosophy to physical sciences and engineering. Students also attended workshops and seminars on various topics designed to orient them to academic life on campus and provide them with the basic skills needed to perform research in a broad range of areas. On top of the educational rewards of active participation in undergraduate research, the EUREKANs were introduced to campus resources and interacted with many faculty, staff, administrators, and other students. They developed networks of supportive mentors and colleagues that will serve them well in their academic careers.

How We Started

Created in 2006, the new “Experiences in Undergraduate Research, Exploration and Knowledge Advancement!” (EUREKA!) program was based on an idea conceived by Stephen Wainscott, former Director of the Clemson University Honors College, and further developed by a committee of the following members (listed with their University roles at that time): Dwight Camper, Professor of Entomology, Soil, and Plant Science; Dana Irvin, Assistant Director of the Clemson University Honors College; Pam Mack, Associate Professor of History; James McCubbin, Professor and Chair of Psychology; Mary Miller, Special Assistant to the Provost; Gary Powell, Professor Emeritus of Genetics and Biochemistry; Sean Williams, Associate Chair and Professor of English; and Bill Pennington, Professor of Chemistry.

Where We Are in 2024

30 Clemson Honors students (including 3 counselors) % of students who plan to participate in research in the fall 2 87 delivery options

2024 EUREKA! Students

Student Name

Hometown

Major

Faculty Mentor Name

Page

Aaron Anderson

North Charleston, SC Engineering

Dr. Angela Alexander-Bryant 5

Ariana Bachini

Fort Mill, SC

Biochemistry

Dr. Zhicheng Dou

Payton Barrett

Lugoff, SC

Engineering

Dr. Thompson Mefford

Charlie Bogdanski

Simpsonville, SC Biochemistry

Dr. Michael Sehorn

Andy Botkin

Greenville, SC

Computer Science

Dr. Nianyi Li

Riley Brennan

Fort Mill, SC

Environmental and Natural Resources Dr. Vidya Suseela

Avery Brown

Greer, SC

Engineering

Dr. Ethan Kung

Sophia Camps

Mt Pleasant, SC

Chemistry

Dr. David Jacobson

Alexandra Davis

Lexington, SC

Physics

Dr. Qiushi Chen

London Hoxworth

Greer, SC

Preprofessional Health Studies

Dr. Matthew Boyer

Jonathan Irving

Fishersville, VA

Business

Dr. Vidya Suseela

Ella James

Columbia, SC

Preprofessional Health Studies

Dr. Matthew Boyer

Ally Jones

Anderson, SC

Engineering

Dr. Hong Luo

Cameron Kennedy

Lancaster, SC

Biological Sciences

Dr. Stephen Dolan

Alayna Khoja

Fort Mill, SC

Genetics

Dr. Michael Sehorn

Makenna Lankford

Charleston, SC

Chemistry

Dr. William Pennington

Sydney McCune

Kennesaw, GA

Preprofessional Health Studies

Dr. Diana Ivankovic

Ashton McEntarffer

Greenville, SC

Computer Science

Dr. Mert Pesé

Megan McGovern

Simpsonville, SC Engineering

Dr. Thompson Mefford

Paige McKnight

Kingstree, SC

Biological Sciences

Dr. Diana Ivankovic

Anna Mitchell

Fort Mill, SC

Packaging Science

Dr. Sneh Bangar

Lada Palygina

Awendaw, SC

Chemistry

Dr. Qing Liu

Abbey Grace Pickrel

Spartanburg, SC

Bioengineering

Dr. Adam Melvin

Madelyn Ridley

West Columbia, SC Engineering

Dr. Anastasia Thayer

Meridee Ritzer

Rock Hill, SC

Chemistry

Dr. William Pennington

Sushil Kannan Senguttuvan Balamurugan

Ladson, SC

Engineering

Dr. Nianyi Li

Nathan Thomas

Mt Pleasant, SC

Preprofessional Health Studies

Dr. Adam Melvin

Addison Vondersaar

Allen, TX

Biochemistry

Dr. Adam Melvin

Olivia Wendland

Milbank, SD

Business

Dr. Koti Hubbard

Stella Wendland

Milbank, SD

Preprofessional Health Studies

Dr. Cheryl Ingram-Smith

WITH EMALEE MANN, JESSIE BOULOS, AND DR. ANGELA ALEXANDER-BRYANT, DEPARTMENT OF BIOENGINEERING

Glioblastoma multiforme (GBM) is a rare grade IV glioma tumor that affects the central nervous system. Current treatment methods include tumor resection, chemotherapy, and radiation, all resulting in low prognosis. As new therapeutics are being developed, the cellular model by which they are tested should reflect the in vivo tumor environment for better translatability. Three-dimensional models, such as spheroids, can better mimic the GBM tumor environment, unlike the traditional two-dimensional cell models. This study aims to characterize in vitro models for GBM treatments using U87MG spheroids and compare the gene expression of both two-dimensional and three- dimensional models. Western blots and RT-qPCR (Real-Time quantitative PCR) were used to compare the expressions of genes overly expressed in glioblastoma for both 2D cells and 3D spheroids. Future studies include further spheroid characterization and gene expression analysis in 2D and 3D models. Following characterization, U87MG spheroids will be used as an improved in vitro model to investigate a new treatment for GBM, novel co-loaded hydrogels for combination treatment. The Characterization of Three-Dimensional Spheroids for Glioblastoma In Vitro Modeling

Histomonas meleagridis is the infectious agent for histmoniasis, also known as blackhead disease. It infects gallinaceous birds with turkeys having the most extreme expression of the disease. It causes severe inflammation and necrosis in the ceca and liver, resulting in mortality rates of 80%-100%. H. meleagridis is poorly understood on a molecular level therefore, protocols for similar parasites may be adapted for use in gaining novel insights into the molecular pathogenesis of Histomonas. In this study, different concentrations of cell tak were tested to optimize cell adhesion. Parasites were also fluorescently stained and analyzed using a microscope and a flow cytometer. It was revealed that the 4x concentration of cell tak had the greatest retention of parasites after fixation and at six days post-fixation. The flow cytometer proved promising in differentiating the H. Meleagridis parasites and other matter within the in vitro cell culture. Future work will evaluate the effectiveness of other adhesive compounds for retention and improve flow cytometry analyses. Optimizing Staining and Microscopy Techniques for Histomonas meleagridis

WITH ALESSANDRO ROCCHI AND DR. ZHICHENG DOU, DEPARTMENT OF BIOLOGICAL SCIENCES

WITH MEGAN MCGOVERN, S. LAHA, AND DR. O. THOMPSON MEFFORD, DEPARTMENT OF ENGINEERING, COMPUTING, AND APPLIED SCIENCES

Magnetic nanoparticles (MNPs) represent an area of nanotechnology that bridges the gap between molecules and larger microscopic structures on the nanometer scale. MNPs also exhibit substantial magnetic moments at room temperature despite their small size. This combination allows for access to small structures within the body, rendering them invaluable in various biomedical applications, including direct drug delivery, hyperthermia, and magnetic resonance imaging. This project collects quantitative data regarding the properties of nanoparticles to qualify the general methods used for determining the characteristics of varying particles and thus their applications. Nanoparticles were created through a thermal decomposition reaction and diluted to various concentration levels to test the detection limits of a newly introduced AC Hysteresis machine. This machine provides valuable data regarding the magnetism of nanoparticles, specifically the hysteresis curve. The results revealed that the machine’s threshold for detection was lower than 1 mg/mL concentration within a sample. Nanoparticles were also diluted to various levels to evaluate a secondary method of calculating the concentration of iron within a sample using a UV Spectrometer. Data was collected on two machines and revealed a consistently accurate reflection of concentration, although further confirmation is necessary by running Inductively Coupled Plasma (ICP) on the samples. Quantitatively Investigating Nanoparticles at Varying Concentrations: AC Hyster Lower Detection Limits and UV-Vis Iron Concentration Analysis

WITH ALAYNA KHOJA, ELYSE CORBIN, AND DR. MICHAEL SEHORN, DEPARTMENT OF GENETICS AND BIOCHEMISTRY

DNA polymerases are essential enzymes responsible for the replication and repair of DNA in living organisms. They catalyze the synthesis of a new DNA strand by adding nucleotides to a pre-existing primer strand in a sequence- specific manner, using a template strand to guide the incorporation of complementary nucleotides. DNA polymerases play crucial roles in cellular processes such as replication, recombination, and DNA repair, ensuring the accurate transmission of genetic information. The ability of these enzymes to replicate DNA was exploited in molecular biology through its use in the polymerase chain reaction (PCR), DNA sequencing and cloning. The two primary polymerases used in PCR are Taq polymerase from the thermophilic bacterium Thermus aquaticus and Pfu polymerase from the hyperthermophilic archaeon Pyrococcus furiousus. Taq polymerase is more processive than Pfu while Pfu has proofreading capability that greatly increases its accuracy. Pfu-Sso7d is the result of fusing a DNA binding protein to the Pfu polymerase which significantly increases the processivity of Pfu. In this study, Pfu-Sso7d was expressed and purified. PCR was optimized using the Pfu-Sso7d and compared it to PCR reactions mediated by Taq and Pfu polymerase. The results from this study will be used to guide our PCR- mediated site-directed mutagenesis efforts. Evaluation of Pfu-Sso7d Polymerase

WITH SUSHIL KANNAN SENGUTTUVAN BALAMURUGAN AND DR. NIANYI LI, DEPARTMENT OF COMPUTING

Physics-based Deep Learning for Computer Vision

Physics-based deep learning combines principles of physics with machine learning to enhance the functionality of computer vision systems. This approach focuses on understanding the motion field, which is the projection of the velocity of 3D surface points onto a visual sensor's imaging plane. Accurate computation of the motion field is essential for various vision-based technologies, including video compression, image interpolation, 3D reconstruction, and robotics navigation. In the robotics field, physics-based deep learning is crucial for enabling robots to perceive, analyze, and interact with their environment. By integrating deep learning models like ResNet for image recognition and object detection, these systems can control robotic arms to perform specific tasks, such as picking up and placing objects. This integration allows for precise manipulation and enhances the robot's ability to operate in real-world scenarios.

This project utilizes the Interbotix X-Series Arms from Trossen Robotics to demonstrate the application of physics-based computer vision, showcasing the synergy between deep learning, computer vision, and real-world physics in robotics.

Intensive agricultural practices are a leading cause of environmental degradation, negatively affecting both soil and water resources. In response, cover crops (CCs) are gaining attention as they enhance soil health and provide economic benefits to farmers. This study examined the activity of Beta-1,4-glucosidase (BG) and N-acetyl-b-D-glucosaminidase (NAG) enzymes to evaluate the effect of CCs of different functional types (grass, legume, brassica) on soil carbon and nitrogen mineralization, respectively. The study had 6 treatments including monocultures of field pea, forage radish, cereal rye, a three species mix, a five species mix, and fallow (control). Soils at 0-10 cm depth were taken from all six treatments. BG and NAG activities were assayed using 4-methylumbelliferyl-b-D-glucopyranoside, and 4- methylumbelliferyl-N-acetyl-b-D-glucosaminide, respectively, as specific substrates. The amount of methylumbelliferone produced was quantified using a microplate fluorimeter. Cereal rye had higher NAG activity than all other treatments. The BG activity did not vary with the treatments. Rye had the highest biomass among all the treatments. Increased NAG activity indicates higher soil nitrogen mineralization, which is required to support the higher biomass production in cereal rye. The results suggest that different plant functional types can differentially affect soil microbial activity and hence the overall soil health. Effect of Different Plant Functional Types on Soil Microbial Extracellular Enzyme Activities

WITH JONATHAN IRVING, MOHIT GOYAL, SIFAT SULTANA, AND DR. VIDYA SUSEELA, DEPARTMENT OF PLANT AND ENVIRONMENTAL SCIENCES

WITH BASANT REGMI AND DR. ETHAN KUNG, DEPARTMENTS OF MECHANICAL ENGINEERING AND BIOMEDICAL ENGINEERING

The use of a three-dimensional model of a patient’s cardiovascular system from their medical scans is not common practice in the medical field. However, they provide an improved visualization for doctors to use when diagnosing and treating their patients, as well as enable hemodynamic simulations to analyze blood flow patterns. With the aorta being the largest vessel in the body and many other vessels branching from it, having a three-dimensional model of the aorta will provide a clearer image of a patient’s cardiovascular system. The purpose of this study is to create anatomic models of the cardiovascular system, specifically the aorta and its branches, to improve the standard practices in the medical field. The program SimVascular was used to create the models from patients’ computed tomography (CT) scans. Models of the aortas were created through path planning and two-dimensional segmentation inside of SimVascular. Lofting of the segmentations in 3D space then creates the final 3D models for subsequent research work such as hemodynamic simulations and shape analysis. These steps in SimVascular allow for accurate creation of the aortas by starting on the 2D plane and transforming the model into a 3D version. The creation of the models from these steps allows for the creation of blood flow simulations through the vessels. Once these steps are completed accurately, the models may be used by clinicians to better help their patients. Creation of 3D Cardiovascular Anatomic Models to Assist in the Diagnosis and Treatment of Medical Patients

WITH ABIDEEN AYANGBEMI, CHRIS HATCHELL, AND DR. DAVID JACOBSON, DEPARTMENT OF CHEMISTRY

Sfp Function for Atomic Force Microscopy

Expressed in the BL21 DE3 strain of E. coli via plasmid transformation, the Sfp protein can be used in attachment chemistry as a link between molecules. Single molecule-experiments help explain the folding and dynamics of biomolecules. Sfp can be used in single molecule pulling experiments because it catalyzes a covalent bond between the ybbr amino acid tag and Coenzyme A (CoA). In past experiments in Dr. Jacobson’s lab, this expression has yielded Sfp protein, but it has not been functional. The goal of this current trial is to produce a new sample of functional Sfp to enable this attachment chemistry. A gel shift assay will be used to monitor the binding of Sfp to a test polymer. Nucleic acids (RNA and DNA) are some of the most essential organic molecules of biology and can be probed in the single molecule pulling experiments. Both molecules can have different sugar structures, but which ones they exist in are still in question. With functional Sfp and Atomic Force Microscopy the thermodynamic stability discrepancies of the compact and extended structures of the RNA sugar pucker can be tested and analyzed for a better understanding of these crucial molecules.

WITH JASMINE HAGERTY, JESUS BADAL, DANIEL GAINES, AND DR. QIUSHI CHEN, GLENN DEPARTMENT OF CIVIL ENGINEERING

NASA’s Artemis program aims to establish a long-term presence on the moon for on-site investigations. To accomplish this, advancements in in-situ resource utilization (ISRU) must be developed. The objective of this research is to investigate the current state of knowledge of bio-inspired drilling technologies and design an ISRU/icy lunar regolith drill. Extensive literature review has revealed some of nature’s solutions to burrowing and drilling in a terrestrial environment. Of these methods, two highly efficient bio-inspired solutions may work well for lunar applications. These include the wood wasp-inspired dual reciprocating drill (DRD) and the razor-shell clam dual- anchoring system. Both mechanisms were modeled in SolidWorks, a 3D design software, and tested using EDEM, a discrete element method (DEM) modeling software. The DRD concept may work in lunar applications because it requires zero net insertion force and minimal overhead force. The design consists of two drill bits that use the force generated by each other to penetrate, like a wood wasp. The razor-shell clam inspired drill features a shaft encased with two valves that rotate outward and propel the cone-tipped shaft down. This valve extension anchoring system decreases soil stress surrounding the tip which may be useful for drilling into compacted substrate. Bio-Inspired Drilling into Lunar Regolith

Neurodiversity is a non-medical term used to describe people with neurological conditions that are not “typical.” The terminology allows for inclusivity and can include multiple groups of people. Those who would be considered neurodiverse are those with conditions such as autism spectrum disorder, attention deficit hyperactivity disorder, obsessive compulsive disorder, and many others. The goal of this project is to understand the experiences of neurodivergent learners and learn more about the kinds of support they receive or lack thereof. More specifically, the topic of savant syndrome was thoroughly explored in this project. Savant syndrome is a misunderstood and often unrecognized condition. Through qualitative interviews with people who identify as neurodivergent, there was a common theme of unawareness of the condition. The goal of these interviews is to understand the experiences and interpretations of neurodivergent learners’ perspectives on savant syndrome. Neurodivergent Learners’ Perspectives on Savant Syndrome

WITH ELLA JAMES AND DR. D. MATTHEW BOYER, DEPARTMENT OF ENGINEERING AND SCIENCE EDUCATION

WITH RILEY BRENNAN, MOHIT GOYAL, AND DR. VIDYA SUSEELA, DEPARTMENT OF PLANT AND ENVIRONMENTAL SCIENCES

Red oak, a native of North America, is an invasive species in Europe, disrupting the native European forest ecosystems. Thus, it is important to understand how Red oak outcompetes native English oak, especially under climate change. This study investigated the activity of N-acetyl-b-D-glucosaminidase (NAG), Acid Phosphatase, and Beta-1,4-glucosidase (BG) enzymes to assess the impact of drought and limiting phosphorous conditions on soil nitrogen, phosphorous and carbon mineralization in Red and English oak trees. The study consists of two water management (drought and well-watered), two species (Red and English oak), and two Phosphorus (no P input and P input) treatments. Soil samples were taken from all the treatments. Using 4-methylumbelliferyl-N-acetyl-b-D- glucosaminide, 4-MUB-phosphate, and 4-methylumbelliferyl-b-D-glucopyranoside as specific substrates, the activities of NAG, Acid Phosphatase and BG were assayed. In English oak, drought decreased the enzyme activity of NAG and acid phosphatase compared to Red oak, in which the activity was similar with and without drought. Red oak had higher BG enzyme activity compared to the English oak. These results suggest that increased enzyme activity in Red oak under water and phosphorous-limiting conditions can help them out-compete the native English oak, which can be harmful to the European ecosystems. Invasive and Native Oaks Differentially Affect Soil Enzyme Activity in Response to Drought and Nutrient Availability

WITH LONDON HOXWORTH AND DR. D. MATTHEW BOYER, DEPARTMENT OF ENGINEERING AND SCIENCE EDUCATION

Neurodiversity is a non-medical term used to describe people with neurological conditions that are not “typical.” The terminology allows for inclusivity and can include multiple groups of people. Those who would be considered neurodiverse are those with conditions such as autism spectrum disorder, attention deficit hyperactivity disorder, obsessive-compulsive disorder, and many others. The goal of this project is to understand the experiences of neurodivergent learners and learn more about the kinds of support they receive or lack thereof. More specifically, the topic of savant syndrome was thoroughly explored in this project. Savant syndrome is a misunderstood and often unrecognized condition. Through qualitative interviews with people who identify as neurodivergent, there was a common theme of unawareness of the condition. The goal of these interviews is to understand the experiences and interpretations of neurodivergent learners’ perspectives on savant syndrome. Neurodivergent Learners’ Perspectives on Savant Syndrome

WITH ZHAOHUI CHEN AND DR. HONG LUO, DEPARTMENT OF GENETICS AND BIOCHEMISTRY

Recently, climate change has become a major issue for agricultural production. Key crops have trouble adjusting to extreme weather, such as high winds, temperatures, and precipitation. These changing conditions have caused agricultural output to decrease. With the help of biotechnology, crops are being genetically modified to improve their survival in adverse conditions. RNA interference (RNAi) is a natural process that helps regulate gene expression. Similar to microRNA (miRNA) and small interfering RNA (siRNA), it uses double-stranded RNA to bind to a specific messenger RNA (mRNA) in the cytoplasm. The mRNA is destroyed, and protein synthesis is shut down. Studies have shown that altering levels of stress- related genes by miRNA, siRNA, and RNAi can change a plant’s stress response. In this research, stress-related genes connected to RNA m6A modifications are regulated by an RNAi structure to improve plant traits. The construction of an RNAi chimeric gene is shown on the research poster. Biotechnology and genetic engineering advancements offer a solution to unpredictable climate changes by altering a plant’s genome to increase its survival rate. Plant Biotechnology for Enhanced Agricultural Production

Pseudomonas aeruginosa (Pa) is a gram negative, rod-shaped bacteria that is associated with many different common diseases; for example: sepsis, pneumonia, UTIs and cystic fibrosis (CF). This project is specifically interested in the bacteria in the setting of a CF lung. Microbes rarely exist as a single species, but rather in complex polymicrobial environments. Pseudomonas aeruginosa and Aspergillus fumigatus (Af) are the most commonly isolated bacterial and fungal pathogens in the CF airway. Evidence shows that when grown with Af, Pa will mutate and activate specific pathways as a response. Perhaps these changes can be seen physically and genetically over generations. With the goal of understanding how Pa adapts over time in human infection, Pa was grown over a period of 15 days in isolation and in co-culture with Af, in synthetic CF sputum media (SCFM2). Altering the phosphate sources in SCFM2 showed new morphological patterns and growth changes of Af in isolation. Genetic sequencing of Pa gDNA and analyzing growth patterns in a culture model representative of the CF airway will reveal the changes produced over many generations of Pa in isolation and co-culture. Monitoring the Generational Genomic and Phenotypic Changes of Pseudomonas aeruginosa in Polymicrobial Environments

WITH JESSICA AYCOCK AND DR. STEPHEN DOLAN, DEPARTMENT OF GENETICS AND BIOCHEMISTRY

WITH CHARLES BOGDANSKI, ELYSE CORBIN, AND DR. MICHAEL SEHORN, DEPARTMENT OF GENETICS AND BIOCHEMISTRY

Evaluation of Pfu-Sso7d Polymerase

DNA polymerases are essential enzymes responsible for the replication and repair of DNA in living organisms. They catalyze the synthesis of a new DNA strand by adding nucleotides to a pre-existing primer strand in a sequence-specific manner, using a template strand to guide the incorporation of complementary nucleotides. DNA polymerases play crucial roles in cellular processes such as replication, recombination, and DNA repair, ensuring the accurate transmission of genetic information. The ability of these enzymes to replicate DNA was exploited in molecular biology through its use in the polymerase chain reaction (PCR), DNA sequencing, and cloning. The two primary polymerases used in PCR are Taq polymerase from the thermophilic bacterium Thermus aquaticus and Pfu polymerase from the hyperthermophilic archaeon Pyrococcus furiousus. Taq polymerase is more processive than Pfu while Pfu has proofreading capability that greatly increases its accuracy. Pfu-Sso7d is the result of fusing a DNA binding protein to the Pfu polymerase which significantly increases the processivity of Pfu. In this study, Pfu-Sso7d was expressed and purified. PCR was optimized using the Pfu-Sso7d and compared to PCR reactions mediated by Taq and Pfu polymerase. The results from this study will be used to guide our PCR-mediated site-directed mutagenesis efforts.

Sulfur atoms are an effective partner for halogen atoms in the formation of halogen bonds. Localized nucleophilic regions occurring on sulfur (or other chalcogen) atoms can form electrostatically attractive interactions with localized electrophilic regions occurring on halogen atoms to form relatively strong noncovalent interactions. The current study seeks to develop crystal engineering principles surrounding these interactions by synthesizing new cocrystal compositions and evaluating the resulting halogen bond motifs and strength. In this vein several new thioimidazoles have been synthesized and their halogen bonding capabilities evaluated through the synthesis of thioimidazole-organoiodine cocrystals. Various functional groups were added to the thioimidazole core, occurring on the thioimidazole nitrogen atoms as well as the carbon atoms of the thioimidazole ring. This provided a variety of sulfur-containing substrates to systematically evaluate with organoiodine molecules including 1,2-, 1,3-, and 1,4-diiodotetrafluorobenzene, 1,3,5- triiodo-2,4-6-trifluorobenzene, tetraiodoethylene, and I2. A variety of I···S interactions were characterized via single crystal X-ray diffraction. In particular, the addition of chloro- and nitro- substituents to a dimethylimidazole thione substrate provided the additional opportunity to study the halogen bonding tendencies in systems where I···S, I···Cl, or I···O interactions could potentially occur in concert or in competition. Organoiodine Cocrystals with Novel Thiones

WITH MERIDEE RITZER, FATEMA TUZ ZOHARA, JULIA L. BRUMAGHIM, COLIN D. MCMILLEN, AND

DR. WILLIAM T. PENNINGTON, DEPARTMENT OF CHEMISTRY

WITH PAIGE MCKNIGHT, AUBREY MATTINGLY, ETHAN WILSON, AND DR. DIANA IVANKOVIC, SCHOOL OF NURSING

Effects, Safety, and Toxicity of Herbal Remedies on Zebrafish Development for Breast Cancer Application

Human breast cancer is a disease that affects 1 in 8 women in the United States. It is caused by an overgrowth of cells in breast tissue. Chemotherapy is a standard treatment for breast cancer. Chemotherapeutics such as doxorubicin (adriamycin) do not strictly target cancer cells, subsequently causing harm to the healthy cells as well. This research aims to find a safe and effective dosage of an alternative chemotherapeutic (Origanum majorana extract) for treating cancer by exposing developing zebrafish to a range of concentrations, identifying their toxicity levels and developmental effects. Zebrafish embryos were exposed to various extract concentrations ranging between 0 mg/L and 20 mg/L over a period of 70 hours. Zebrafish exposed to 12 mg/L of the extract exhibited abnormalities in caudal fin development. Concentrations of 14 mg/L or greater showed consistent developmental abnormalities, including pericardial edemas and caudal fin deformation. Further translational research will refine therapeutic dosage and investigate efficacy in human breast cancer models.

WITH SIDDHARTH THUMSI, AARAV CHOWBEY, AND DR. MERT PESÉ, SCHOOL OF COMPUTING

This project proposes a technique to secure the Controller Area Network (CAN), the primary in-vehicle communication protocol. Security information such as message authentication codes (MACs) cannot fit into the constrained payload of CAN frames, which results in minimized message authenticity. Leveraging integrated CAN controllers, found on newer Electronic Control Units (ECUs), can solve this by allowing the application to bypass the CAN controller and directly read and write to individual CAN frame bits. This technique is advanced by reading and writing only CAN bit sections without modifying the CAN protocol, termed here as "bit hammering,” and is utilized to insert additional information into the first half of each CAN payload bit. Bit hammering leads the application to temporarily sample at a higher rate during the first half of each respective bit (transient upsampling). As a result, the sender will be able to insert at least four additional security information bits into payload bits, increasing payload size from 64 to at least 320 bits. Overall, this allows data such as 256-bit MACs to be stored in the CAN payload, completely backward-compatible with regular CAN functionality without additional overhead. CANdy: Transient Upsampling to Secure the Controller Area Network

WITH PAYTON BARRETT, SUVRA LAHA, AND DR. O. THOMPSON MEFFORD, DEPARTMENT OF ENGINEERING, COMPUTING, AND APPLIED SCIENCES

WITH SYDNEY MCCUNE, AUBREY MATTINGLY, ETHAN WILSON, AND DR. DIANA IVANKOVIC, DEPARTMENT OF NURSING

Human breast cancer is a disease that affects 1 in 8 women in the United States. It is caused by an overgrowth of cells in breast tissue. Chemotherapy is one standard treatment for breast cancer. Chemotherapeutics such as doxorubicin (adriamycin) do not strictly target cancer cells, subsequently causing harm to the healthy cells as well. This research aims to find a safe and effective dosage of an alternative chemotherapeutic (Origanum majorana extract) for treating cancer by exposing developing zebrafish to a range of concentrations, identifying their toxicity levels and developmental effects. Zebrafish embryos were exposed to various extract concentrations ranging between 0 mg/L and 20 mg/L over a period of 70 hours. Zebrafish exposed to 12 mg/L of the extract exhibited abnormalities in caudal fin development. Concentrations of 14 mg/L or greater showed consistent developmental abnormalities, including pericardial edemas and caudal fin deformation. Further translational research will refine therapeutic dosage and investigate efficacy in human breast cancer models. Effects, Safety, and Toxicity of Herbal Remedies on Zebrafish Development for Breast Cancer Application

WITH DR. SCOTT WHITESIDE AND DR. SNEH BANGAR, DEPARTMENT OF FOOD, NUTRITION, AND PACKAGING SCIENCES

Understanding of Retort Processing for Food Safety

Navy blue beans (Phaseolus vulgaris) are categorized as “low acid food” with a pH level exceeding 4.6. When sealed in an airtight container, such as a can, high pH and high moisture content encourage the growth of the spores of C. Botulinum, a common bacteria in canned goods. C. Botulinum poses an extreme threat due to the potent botulinum toxin, which, when ingested, causes Botulism, an illness in some cases known to be lethal. In order to guarantee commercial sterilization, they must undergo retort processing, a process which consists of exposing packaged beans to high heat (240 ℉ to 250 ℉ ) and pressure (15 Psi to 20 Psi) to ensure a 12-log reduction of the spores of C. Botulinum. Due to the extreme sensitivity of retort processing, the formula of navy blue beans with a heavy sauce can change the cooking time, presenting beans with different consistencies and flavors. This study will evaluate the impact of changes to the ingredients of navy blue beans in heavy sauce on retort processing by collecting data from thermocouples implanted within the bean packages in the retort processor. Conclusions from this study can have practical implications for food producers engaged in retort processing.

WITH CAMERON BROWN AND DR. QING LIU, DEPARTMENT OF BIOLOGICAL SCIENCES

Electronic cigarettes have gained popularity due to the misconception of them being a safer alternative. However, the side effects of additives found in vapes are under-researched. This study evaluates the toxicity of nicotine and propylene glycol at low concentrations utilizing human stem-cell derived cardiomyocytes. Human embryonic stem cells were differentiated into cardiomyocytes to create an in vitro human cardiac model. The mature cardiomyocytes were treated with L-nicotine and propylene glycol at a series of concentrations for 48 hours to evaluate toxicity. After treatment, the cells were stained with mitochondrial indicator dyes that were used to detect relative superoxide and ATP concentrations. Cell imaging through Cytation 5 was done to quantify these concentrations. The concentrations were evaluated to determine the mitochondrial function of the treated cells, which is a significant factor in determining heart health due to the mitochondria’s key role in producing ATP for the heart. There were no significant changes in superoxide and ATP levels during the 48 hour time period for the concentrations tested. Future testing involves testing different nicotine derivatives, as well as more precise testing of mitochondrial bioenergetics using Seahorse assay to detect mitochondrial respiration rate. Evaluating the Impact of E-Cigarette Additives on Cardiomyocyte Mitochondrial Function

Microfluidic devices have become a technology capable of precise control over the chemical and physical microenvironment, leading to applications across nearly all fields of biology, including breast cancer research. A five- channel microfluidic device can be used to simulate the TME and observe how cancer, stromal, and immune cells interact to identify the paracrine signals that drive tumor progression and cancer metastasis. The outermost and center channels are separated by channels consisting of an array of trapezoids filled with collagen to separate yet chemically connect them. The trapezoid channels were designed to use surface tension to keep the collagen in, while the outermost channels were designed to culture different cell types, and the center channel was connected to a peristaltic pump to infuse media into the system and allow for collection of the extracellular media to identify changes in paracrine signaling. The focus during the program was to optimize the collagen hydrogel loading and devise a strategy to seed the cells to allow for the co-culture of breast cancer cells and stromal cells. This advancement in technology paves the way for understanding in how cells communicate. 27 Identification of Paracrine Signaling in the Simulated Tumor Microenvironment of Microfluidic Devices

WITH RILEY OSBOURN AND DR. ADAM MELVIN, DEPARTMENT OF CHEMICAL AND BIOMOLECULAR ENGINEERING

WITH DR. ZUYI WANG AND DR. ANASTASIA THAYER, DEPARTMENT OF AGRICULTURAL SCIENCES

Surveys of Agricultural Producers and Their Adoption of Climate-Smart Practices Around 10% of greenhouse gas emissions in the United States results from agricultural practices (NRCS). In South Carolina (SC) , 28.4% of the total cropland employs reduced tillage, while only 7.26% incorporates cover cropping (NASS). Climate-Smart Grown in SC is a five-year collaboration between Clemson University, South Carolina State University, and twenty-seven other organizations focused on expanding implementation of conservation practices focusing on four important SC commodities: peanuts, leafy greens, forages for beef cattle, and forest products. The initiative focuses on performing research, taking measurements, offering financial incentives, providing technical and educational support, and finding marketing opportunities for climate-smart commodities. The purpose of this project is to survey enrolled producers after their first year of implementing conservation practices incentivized by this partnership. The original survey was adjusted to gather information on challenges after initial adoption, effects of adoption, and perceptions on continued use of practices. Several questions were incorporated to uncover concerns regarding adoption and design programs to help overcome stated barriers. Another aim is to enhance the effectiveness of the survey by reviewing data and refining poorly worded or confusing questions. The focus on survey methodology is instrumental to provide support for farmers to embrace a more conservation-minded approach.

Organoiodine Cocrystals with Novel Thiones

Sulfur atoms are an effective partner for halogen atoms in the formation of halogen bonds. Localized nucleophilic regions occurring on sulfur (or other chalcogen) atoms can form electrostatically attractive interactions with localized electrophilic regions occurring on halogen atoms to form relatively strong noncovalent interactions. The current study seeks to develop crystal engineering principles surrounding these interactions by synthesizing new cocrystal compositions and evaluating the resulting halogen bond motifs and strength. In this vein several new thioimidazoles have been synthesized and their halogen bonding capabilities evaluated through the synthesis of thioimidazole- organoiodine cocrystals. Various functional groups were added to the thioimidazole core, occurring on the thioimidazole nitrogen atoms as well as the carbon atoms of the thioimidazole ring. This provided a variety of sulfur-containing substrates to systematically evaluate with organoiodine molecules including 1,2-, 1,3-, and 1,4- diiodotetrafluorobenzene, 1,3,5-triiodo-2,4-6-trifluorobenzene, tetraiodoethylene, and I2. A variety of I···S interactions were characterized via single crystal X-ray diffraction. In particular, the addition of chloro- and nitro- substituents to a dimethylimidazole thione substrate provided the additional opportunity to study the halogen bonding tendencies in systems where I···S, I···Cl, or I···O interactions could potentially occur in concert or in competition.

WITH MAKENNA LANKFORD, FATEMA TUZ ZOHARA, JULIA L. BRUMAGHIM, COLIN D. MCMILLEN, AND

DR. WILLIAM T. PENNINGTON, DEPARTMENT OF CHEMISTRY

WITH ANDY BOTKIN AND DR. NIANYI LI, DEPARTMENT OF COMPUTING

Physics-based Deep Learning for Computer Vision

WITH ADDISON VONDERSAAR, BRAULIO ANDRES ORTEGA QUESADA, AND DR. ADAM MELVIN, DEPARTMENT OF CHEMICAL AND BIOMOLECULAR ENGINEERING

Breast cancer is the most common type of cancer, with 2.3 million cases in 2022 exclusively. Estrogen receptor positive (ER+) breast cancer is the most common breast cancer subtype and responds to endocrine therapy; however, some patients develop resistance. Traditional two-dimensional single-cell type culture approaches do not recapitulate the complexity of the cancer tumor microenvironment (TME). Cell-to-cell and cell-to-matrix interactions between cancer and stromal cells in the TME, such as enhanced expression of protein collagen-I, are suspected to drive development in endocrine resistance. Such requires alternative approaches, such as microfluidic spheroid production. The goal of this study is to utilize a microfluidic approach to evaluate how collagen-I production is altered in the TME when MCF-7 cells, a breast cancer cell line, are 3D co-cultured with MRC-5 cells, a lung-derived fibroblast. Fibroblasts, a type of stromal cell responsible for producing ECM proteins like collagen-I, are believed to enhance the proliferation of malignant cells. In this study, it is hypothesized that there will be a statistically significant difference in the proliferation between fibroblasts and breast cancer cells compared to cancer alone. It is also suspected that this enhanced proliferative behavior will align with enhanced collagen-I expression, supporting fibroblasts role in ER+ Cancer. Analysis on the Link Between Collagen-I Production and Enhanced Proliferation on 3D Co-Cultured Spheroids in a Microfluidic Device

WITH NATHAN THOMAS, BRAULIO ORTEGA QUESADA, AND DR. ADAM MELVIN, DEPARTMENT OF CHEMICAL AND BIOMOLECULAR ENGINEERING

Human cells experience a variety of biophysical forces in vivo that significantly alter biological processes and cellular phenotype. One such force is cellular deformation, which can occur during transendothelial migration or transit through narrow capillaries. While the biophysical changes in cells due to deformation have been well studied, the phenotypic changes induced by deformation driving pro-survival behavior have been understudied. This work aimed to provide new insight into biochemical changes, such as altered proliferation or protein phosphorylation, during biophysical interrogation in single breast cancer cells. This was accomplished by developing a modular microfluidic device with the capability to mimic the biophysical forces endured during metastasis. Cells were deformed through a constriction channel and collected in a microwell array for single-cell immunostaining utilizing fluorescence microscopy. The estrogen receptor-positive (ER+) and triple-negative breast cancer (TNBC) subtypes were studied due to prior work suggesting cell subtype impact on biochemical pathways. Single MCF-7 (ER+ cell line) deformed cells exhibited decreased levels of the proliferative marker Ki67 compared to non-deformed control cells. Single non-deformed MDA-MB-231 cells (TNBC cell line) exhibited increased levels of p-AKT. These initial findings support that the biochemical changes under deformation appear subtype-specific and result in different protein phosphorylation and proliferation levels. Development and Optimization of a Modular Microfluidic Device to Study the Effects of Deformation on Metastatic Breast Cancer

WITH DR. KOTI L. HUBBARD, DEPARTMENT OF TEACHING AND LEARNING

Media, including children's literature, shapes children’s self-perception and attitudes toward body size (Coyne et al., 2022). This study investigates how body-positive picturebooks address issues of fatness and body size, focusing on books published in the past five years for children aged 4-8. With limited resources available for fostering dialogues about body size, examining existing literature becomes essential (Valauri, 2023). The research question is: What messages about body size do body-positive picturebooks convey to readers? The study analyzed four relevant picturebooks using an analytic review template (ART) adapted from Rogers et al. (2023), encompassing 23 categories such as literary features, personal connections, and themes related to promoting self-love. The analysis led to three primary themes: (a) promoting self-acceptance and redefining stereotypes, (b) empowering children through personal agency, and (c) presenting positive role-models and supportive environments. These themes emphasize resilience, showcasing how protagonists manage negative commentary and foster body- positive attitudes. By engaging with these picturebooks, families and educators can initiate constructive conversations about body size, encouraging children to embrace body positivity and navigate societal pressures. Seeing the Bigger Picture: Analyzing Messages about Body Size in Body- Positive Picturebooks

Entamoeba histolytica is an intestinal parasite that causes amoebic dysentery in ~100 million people each year. Infection by E. histolytica occurs by consuming food or water contaminated with the cyst form. As the cysts reach the small intestine, they convert to the growing amoeba form, which then colonizes the colon to cause disease. The amoebas then convert back to the cyst form, a process called encystation, and are released back into the environment to infect others. Encystation can be replicated in the laboratory by growing cells in glucose medium (Glu) and transferring them to encystation medium lacking glucose (No Glu). The addition of acetate (Ac) speeds initiation of encystation. In this project, RNAseq transcriptome analysis was used to identify genes that are upregulated early in encystation. Four genes with predicted function and two genes of unknown function were chosen for further study. These six genes had increased expression in No Glu or Ac conditions as compared to Glu. The presence of these genes in other Entamoeba species and outside of Entamoeba was determined. By searching the literature, potential roles in encystation for the genes with predicted function were proposed. Upregulated Genes in Entamoeba histolytica Encystation

WITH DR. CHERYL INGRAM-SMITH, DEPARTMENT OF GENETICS AND BIOCHEMISTRY

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