Presenting cells research at AIMRC convention
Author: Sydnee Ehorn | Major: Chemical Engineering | Semester: Fall 2022
Hi! My name is Sydnee Ehorn, and I am a chemical engineering major. Over the course of the spring and fall semesters of 2022, I have been a part Dr. Karthik Nayani’s research team studying the effects of mechanical strain on the cell nuclei. New methods for identifying the effects of diseases and different available treatment are fundamental parts of medical care. In the lab, I have been analyzing the nucleus’s shape under shear stress and aim to study ATP production as well to better understand nuclear function and diseases that hinder it. Additionally, I am being trained by Dr. Prateek Verma to construct machine learning models, specifically to distinguish between different chemical compounds and their uses.
This was my first experience in a research lab, and I was very intimidated at first because I had never worked with cells before. Luckily, I had Elizabeth Adeogun to train me in preparing suspended cell samples and using optical and fluorescent microscopy to view our samples. Learning the different tools and methods required for this project and drawing conclusions from our resulting images were difficult aspects of the process. Dr. Nayani has been guiding my research by providing questions to further explore using liquid crystals (LCs), a substance characterized by its orientational flow, to analyze healthy and diseased cells.
For my project in the lab, I have been exploring the effects of shear stress on the nucleus of chicken red blood cells (RBCs). Chicken RBCs were selected for this experiment because they contain a nucleus and mitochondria. Human RBCs don’t contain a nucleus or mitochondria, so they have more room for hemoglobin, which was very surprising to me. First, chicken RBCs were dispersed in a salt solution and then mixed with a dye to stain the nucleus and allow us to visualize the effects of shear strain. The dyed cells could then be suspended in LCs in their nematic phase (meaning they line up and flow in one direction) and at osmotic equilibrium with the cells, meaning they won’t cause the cells to burst. I have been using microscopy to identify the nucleus and calculate the aspect ratio of individual cells. Strained and unstrained cells were imaged and compared. It was concluded that LCs can be used to strain the cell nucleus of chicken RBCs, as cells strained in the LCs had higher aspect ratios on average. Just as healthy and diseased cells can be distinguished by their stiffness and response to mechanical strain, the cell nucleus is expected to exhibit similar behavior. My research team and I hope to expand this study to human cells and diseases that affect humans.
Along with my work in the lab, Dr. Prateek Verma has been teaching me the principles of machine learning with chemical engineering applications. Learning the foundations of machine learning has been a significant part of my work on this team this semester. I’ve always been interested in programming but never gotten to use it for anything outside basic tutorial courses, so I’ve enjoyed applying it in a chemical engineering context. The machine learning model we’re working on can receive compounds with a certain characteristic, like being acidic or basic, and learn to predict these characteristics in other compounds. We’ve been using compounds represented with SMILES notation as the input data for our models. Dr. Verma created a program to convert SMILES strings to RGB color strings, a format sequential models can receive. I then created a program to verify this conversion was accurate and that the results corresponded with the compound identification numbers of the database the SMILES strings are pulled from. A future goal of our work is to create a model that receives a compound and can determine the drug type and possible applications. Although both projects I’ve been working on have different focuses, both reveal the importance of detail and understanding in diagnosis and treatment of diseases and aim to provide insight into these fields.
The Honors College Research Grant gave me the opportunity to use my chemical engineering background for use in the medical field. I was able to explore new methodologies and programming techniques that will be useful in my future academic pursuits. Along with the Honors College Research Grant, the Arkansas Integrative Metabolic Research Center (AIMRC) has been financially supporting my team’s work. I was able to help present our lab’s recent findings at the AIMRC 2nd Annual Symposium. I intend to pursue my master’s degree after graduating next spring, and although my research pursuits will likely be different, the skills and perspective I’ve been gaining through this experience will accompany me in my next steps in my career.