Biomedical Engineering and Bioengineering Commons^™

Scaffold-Free Development Of Multicellular Tumor Spheroids With Spatial Characterization Of Structure And Metabolic Radial Profiles, Shelby N. Bess, Gaven K. Smart, Matthew J. Igoe, Timothy J. Muldoon

Biomedical Engineering Faculty Publications and Presentations

Purpose

In vitro assays are essential for studying cellular biology, but traditional monolayer cultures fail to replicate the complex three-dimensional (3D) interactions of cells in living organisms. 3D culture systems offer a more accurate reflection of the cellular microenvironment. However, 3D cultures require robust and unique methods of characterization.

Methods

The goal of this study was to create a 3D spheroid model using cancer cells and macrophages, and to demonstrate a custom image analysis program to assess structural and metabolic changes across spheroid microregions.

Results

Structural characterization shows that cells at the necrotic core show high normalized fluorescence intensities of …

Optimizing Recombinant Cas9 Expression: Insights From E. Coli Bl21(De3) Strains For Enhanced Protein Purification And Genome Editing, Shilpi Agrawal, Made Harumi Padmaswari, Abbey L. Stokes, Daniel Maxenberger, Morgan Reese, Adila Khalil, Christopher E. Nelson

Biomedical Engineering Faculty Publications and Presentations

The CRISPR-Cas9 system is a revolutionary tool in genetic engineering, offering unprecedented precision and efficiency in genome editing. Cas9, an enzyme derived from bacteria, is guided by RNA to edit DNA sequences within cells precisely. However, while CRISPR-Cas9 presents notable benefits and encouraging outcomes as a molecular tool and a potential therapeutic agent, the process of producing and purifying recombinant Cas9 protein remains a formidable hurdle. In this study, we systematically investigated the expression of recombinant SpCas9-His in four distinct Escherichia coli (E. coli) strains (Rosetta2, BL21(DE3), BL21(DE3)-pLysS, and BL21(DE3)-Star). Through optimization of culture conditions, including temperature and …

Investigating The Relationship Between Hypoxia, Hypoxia-Inducible Factor 1, And The Optical Redox Ratio In Response To Radiation Therapy, Jesse D. Ivers, Nagavenkatasai Puvvada, Charles M. Quick, Narasimhan Rajaram

Biomedical Engineering Faculty Publications and Presentations

Significance

Radiation resistance is a major contributor to cancer treatment failure and is likely driven by multiple pathways. Multivariate visualization that preserves the spatial co-localization of factors could aid in understanding mechanisms of resistance and identifying biomarkers of response.

Aim

We aim to investigate the spatial and temporal relationship between hypoxia, hypoxia-inducible factor 1 (HIF-1α), and metabolism in response to radiation therapy in two cell lines of known radiation resistance and sensitivity.

Approach

Two-photon excited fluorescence and fluorescence lifetime imaging microscopy were used to quantify the optical redox ratio (ORR) and NAD(P)H fluorescent lifetime and bound fraction in frozen tumor …

Pre-Incisional And Multiple Intradermal Injection Of N-Acetylcysteine Slightly Improves Incisional Wound Healing In An Animal Model, Wictor Pascal, Antoni Smolinski, Mateuz Gotowiec, Marta Wojtkiewicz, Albert Stachura, Kaspar Pelka, Michal Kopka, Kyle P. Quinn, Alan E. Woessner, Dariusz Grzelecki, Pavel Wlodarski

Biomedical Engineering Faculty Publications and Presentations

The objective of this study was to investigate if delivering multiple doses of N-acetylcysteine (NAC) post-surgery in addition to pre-incisional administration significantly impacts the wound healing process in a rat model. Full-thickness skin incisions were carried out on the dorsum of 24 Sprague-Dawley rats in six locations. Fifteen minutes prior to the incision, half of the sites were treated with a control solution, with the wounds on the contralateral side treated with solutions containing 0.015%, 0.03% and 0.045% of NAC. In the case of the NAC treated group, further injections were given every 8 h for three days. On days …

Evaluating Tissue Morphology In The Context Of Varied Initial Fabrication Conditions, Cassidy Caffin

Biomedical Engineering Undergraduate Honors Theses

Cardiovascular diseases have been the leading cause of death for years. This includes myocardial infarctions (MI) where blood flow to the myocardium is restricted. This causes damage to cardiac muscle due to insufficient oxygen. There are multiple ways to treat patients following an MI with the most common involving assorted medication. However, there are limited medications that can be used for treating patients following MIs, and the FDA’s decreasing approval rate for new cardiac drugs will not dramatically improve the range of options. The lead-up to drug candidate rejection by the FDA can involve drugs exhibiting promising preliminary research that …

Investigating The Presence Of Patented In Vitro Models For Cancer-Nerve Crosstalk Methods, Christoff Hauptmann

Biomedical Engineering Undergraduate Honors Theses

The purpose of this research project is to investigate the presence of patented in vitro models for perineural invasion (PNI) and tumor innervation, the two most prominent modes of cancer-nerve crosstalk that play an active role in cancer initiation and progression. PNI occurs through a positive feedback loop in which cancer cells invade passive nerves to metastasize. Tumor innervation is the process where tumor cells attract nearby nerves to the tumor microenvironment (TME) for tumor growth and metastasis. These crosstalk paths have been established for many types of cancer and result in poor patient prognosis. Recently, in vitro models have …

Evaluation Of The Efficiency Of Muscle-Specific Promoters To Express Non-Endogenous Proteins In Skeletal Muscle, Gabrielle Bulliard, Made Harumi Padmaswari, Christopher E. Nelson

Biomedical Engineering Undergraduate Honors Theses

Gene therapies are emerging as powerful tools for treating genetic diseases and cancers, offering the potential for a permanent cure. Hemophilia B, affecting approximately 6,000 men in the U.S., results from a deficiency in coagulation factor IX protein (FIX), which is crucial for blood clotting. A substantial portion of patients, over 40%, suffer from severe hemophilia B, experiencing spontaneous, prolonged bleeding. Current prophylactic treatments involve frequent coagulation factor infusions, yet a curative approach would alleviate this burden. Gene editing technologies like CRISPR-Cas systems show promise for correcting genetic mutations, but the diverse nature of factor IX gene (F9) …

Transcriptomic Profiling Of Engineered Human Gene Integration In The Mouse Genome Following In Vitro Gene Editing, Ethan Potts, Made Harumi Padmaswari, Christopher Nelson

Biomedical Engineering Undergraduate Honors Theses

Gene replacement is a promising method of therapy for genetic diseases. However, safety and efficacy are areas that need more research. This experiment aims to use RNA sequencing and bioinformatic techniques to provide answers to these questions and provide direction to future studies to develop a gene replacement therapeutic. C2C12 mouse myoblast cells were transfected with a vector containing a CRISPR-Cas9 system and the Human Factor IX (hF9) gene in order to hijack target genes and integrate the hF9 gene. The two target genes, myoglobin (Mb) and creatine kinase (Ckm), were chosen for their high rate of expression and low …

Real-Time Measurements From Wearable Sensors To Enhance Stability On Uneven Terrain, Sophie Copelin

Biomedical Engineering Undergraduate Honors Theses

The presented thesis is a study of sensation associated with inversion/eversion movement about the anterior/posterior axis. The long-term goal is to create a system that provides feedback to a prosthesis user, so their chances of falling is decreased. This feedback system would use wearable sensors to detect certain angles, so that sensory feedback could be provided. The study aimed to determine if Xsens Movella DOT sensors could be used in a system like this, so the accuracy of the Xsens Movella DOT sensors was assessed and the difference in angles that could be determined by them when compared to that …

Detection Of Hypoxia Via Rgb Imaging, Nathania Nischal

Biomedical Engineering Undergraduate Honors Theses

Colorectal cancer is a common form of cancer, and is heavily researched in murine models. Colonoscopies are often performed in clinical settings to assess the health of the colon, as well as locate and assess the severity of tumors in a non-invasive way. As the quality of the images is dependent on the colonic environment and the light available, it is important to ensure the accuracy of the images via a normalization algorithm. The RGB images procured from these colonoscopies have great potential as a diagnostic tool for physicians, as varying scales of discoloration is common in hypoxic tissue. While …

Dorsal Root Ganglia Neurite Outgrowth Following Traumatic Spinal Cord Injury Repair: A Review, Adrienne Vaughan

Biomedical Engineering Undergraduate Honors Theses

Traumatic spinal cord injury (tSCI) can cause partial sensorimotor deficiency or total dysfunction, rendering patients unable to perform necessary tasks and dramatically decreasing their quality of life. tSCI is a very prevalent issue. In the United States alone, there are approximately 54 new cases of SCI per one million people each year, or 18,000 new cases annually. tSCI creates a lesion gap filled with axon-inhibiting fibrotic scar tissue. Comprehensive functional recovery following traumatic spinal cord injury (tSCI) requires axonal regeneration across wound site lesions. Dorsal root ganglia (DRG) neurite outgrowth is often evaluated in PNI therapeutic research since it can …

Computational Predictions Of Heart Failure Drug Effects On Cardiac Fibrosis, Aaron Gardner

Chemical Engineering Undergraduate Honors Theses

The extracellular matrix is a complex system surrounding cells that is crucial to all of the cardiovascular system’s functions. Fibrosis is an excessive accumulation (scarring) of the extracellular matrix. Fibrosis is typically a negative event, and the scarring must be reduced in the heart in order to maintain its functionality. Due to this, simulations are run using the software “Netflux” in order to determine the effects of different heart failure drugs on cardiac fibrosis. The drugs that were simulated were an ACE Inhibitor, BAR Beta Blocker, ARB Blocker, and Entresto. These drugs were simulated over 50 hours at three different …

Analyzing Diverse Student Experiences: The Intersection Of Equity, Inclusivity, And Biomedical Engineering Education Through A Clinical Observations And Needs Finding Course, Jacquelynn Horsey

Biomedical Engineering Undergraduate Honors Theses

In the field of biomedical engineering, needs identification and solution development are an important element of the design process. In our undergraduate curriculum, a course was designed to allow clinical observation and provide an opportunity for students to learn about engineering design and engage with clinicians via completing rotations in medical facilities near our campus. While this type of course is not unique, evaluating its efficacy is not simple. Given the broad range of institutional resources available- such as proximity to a medical school, or residency programs- reporting the quality of such courses within the context of such available resources …

The Determination Of Macrophage Localization In Muscle Injuries Using Spatial Transcriptomics, Julliana Renales

Biomedical Engineering Undergraduate Honors Theses

The repair of traumatic muscle injury is often a long process which can in many cases be insufficient and incomplete. In such cases, scar tissue may form, leading to high risk of re-injury and the prevention of muscle regeneration. An important part of decreasing this risk is gaining a better understanding of the cellular complexities of injury repair. More specifically, macrophage cells are an important piece in the regulation of inflammation and repair. In this project, computational analysis spatial transcriptomic data was performed to examine mouse muscle injury and its development over time. This analysis was used to examine the …

Investigation Of Early Stage Wound Healing In Volumetric Muscle Loss, Sean Ong

Biomedical Engineering Undergraduate Honors Theses

Volumetric muscle loss (VML) refers to the substantial removal of tissue from skeletal muscle due to surgery or lesions. This condition disrupts the normal regenerative process of injured muscles, leading to significant loss of muscle function. This study examines the progression of VML injury, approximately 20% of the muscle mass being removed, in the tibialis anterior (TA) muscle of a mouse model over a 15-day post-injury period. The injured muscles exhibited discoloration indicative of reduced blood flow and experienced a decrease in muscle mass throughout the study duration. Furthermore, the maximum force output of the injured TA was significantly lower, …

Biomass Derived Lignin Polymer Modification For Sustainable Chemical Engineering Applications, Samantha Glidewell, Keisha Walters

Chemical Engineering Undergraduate Honors Theses

Lignin is an abundant naturally occurring plant-based polymer that is branched, highly unsaturated, and rich in aliphatic and aromatic hydroxyl groups. Lignin is a significant byproduct of the wood pulp and paper industries; however, it has yet to be widely utilized in commercial applications due to its non-linear structure, broad range of molecular weights, hydrophobicity, high rigidity, and brittleness. Recent investigations into modifying lignin to broaden its potential uses have shown promising results. This thesis explores different modification techniques of the naturally occurring hardwood lignin polymer for specific applications in areas of water treatment and polyurethane (PU) production. The first …

Utilizing Spatial Transcriptomics To Compare Gene Expression In Volumetric Muscle Loss Injury Recovery, Colton Gattis

Biomedical Engineering Undergraduate Honors Theses

Volumetric Muscle Loss (VML) injuries are known to disrupt the normal regenerative process via fibrosis leading to an extensive permanent loss of muscle function. The specific causation of this disruption remains to be defined; however, with new developments in transcriptomics, genetic trends can be identified across regions of tissue over time. This study follows VML injuries within the tibialis anterior of a mouse model for fifteen days after initial injury to attempt to identify expected transitions in healing. Genetic presence began to become more diversified as recovery progressed from four to fifteen days post injury with spatial clusters becoming globalized …

Quantification Of Age-Related Changes In The Structure And Mechanical Function Of Skin With Multiscale Imaging, Alan E. Woessner, Nathan J. Witt, Jake D. Jones, Edward A. Sander, Kyle P. Quinn

Biomedical Engineering Faculty Publications and Presentations

The mechanical properties of skin change during aging but the relationships between structure and mechanical function remain poorly understood. Previous work has shown that young skin exhibits a substantial decrease in tissue volume, a large macro-scale Poisson’s ratio, and an increase in micro-scale collagen fiber alignment during mechanical stretch. In this study, label-free multiphoton microscopy was used to quantify how the microstructure and fiber kinematics of aged mouse skin affect its mechanical function. In an unloaded state, aged skin was found to have less collagen alignment and more non-enzymatic collagen fiber crosslinks. Skin samples were then loaded in uniaxial tension …

Immersive Virtual Reality-Based Learning As A Supplement For Biomedical Engineering Labs: Challenges Faced And Lessons Learned, Ishita Tandon, Vitali Maldonado, Megan Wilkerson, Amanda Walls, Raj R. Rao, Mostafa Elsaadany

Biomedical Engineering Faculty Publications and Presentations

Introduction: Immersive virtual reality (VR) based laboratory demonstrations have been gaining traction in STEM education as they can provide virtual hands-on experience. VR can also facilitate experiential and visual learning and enhanced retention. However, several optimizations of the implementation, in-depth analyses of advantages and trade-offs of the technology, and assessment of receptivity of modern techniques in STEM education are required to ensure better utilization of VR-based labs.

Methods: In this study, we developed VR-based demonstrations for a biomolecular engineering laboratory and assessed their effectiveness using surveys containing free responses and 5-point Likert scale-based questions. Insta360 Pro2 camera and Meta Quest …

Us Public Opinion About The Safety Of Gene Editing In The Agriculture And Medical Fields And The Amount Of Evidence Needed To Improve Opinions, Brandon R. Mcfadden, Joy N. Rumble, Kathryn A. Stofer, Kevin M. Folta

Agricultural Economics and Agribusiness Faculty Publications and Presentations

Introduction: Implementation of gene editing in agriculture and medicine hinges on public acceptance. The objectives of this study were to explore U.S. public opinion about gene editing in agricultural and medical fields and to provide more insight into the relationship between opinions about the safety of gene editing and the potential impact of evidence to improve opinions about safety.

Methods: Data were from two samples of U.S. respondents: 1,442 respondents in 2021 and 3,125 respondents in 2022. Survey respondents provided their opinions about the safety of gene editing in the agricultural and medical fields and answered questions about the number …

Accelerating Neurotechnology Development Using An Agile Methodology, Anil Kumar Thota, Ranu Jung

Biomedical Engineering Faculty Publications and Presentations

Novel bioelectronic medical devices that target neural control of visceral organs (e.g., liver, gut, spleen) or inflammatory reflex pathways are innovative class III medical devices like implantable cardiac pacemakers that are lifesaving and life-sustaining medical devices. Bringing innovative neurotechnologies early into the market and the hands of treatment providers would benefit a large population of patients inflicted with autonomic and chronic immune disorders. Medical device manufacturers and software developers widely use the Waterfall methodology to implement design controls through verification and validation. In the Waterfall methodology, after identifying user needs, a functional unit is fabricated following the verification loop (design, …

In Vivo Measurement Of Nadh Fluorescence Lifetime In Skeletal Muscle Via Fiber-Coupled Time-Correlated Single Photon Counting, Kathryn M. Priest, Jacob V. Schluns, Nathania Nischal, Colton L. Gattis, Jeffery C. Wolchok, Timothy J. Muldoon

Biomedical Engineering Faculty Publications and Presentations

Nicotinamide adenine dinucleotide (NADH) is a cofactor that serves to shuttle electrons during metabolic processes such as glycolysis, the tricarboxylic acid cycle, and oxidative phosphorylation (OXPHOS). NADH is autofluorescent, and its fluorescence lifetime can be used to infer metabolic dynamics in living cells. Fiber-coupled time-correlated single photon counting (TCSPC) equipped with an implantable needle probe can be used to measure NADH lifetime in vivo, enabling investigation of changing metabolic demand during muscle contraction or tissue regeneration. This study illustrates a proof of concept for point-based, minimally-invasive NADH fluorescence lifetime measurement in vivo. Volumetric muscle loss (VML) injuries were …

Representativeness Evaluation Of Delta-Flux Eddy Covariance Towers For Assessing Greenhouse Gas Emissions From Rice Fields In The Mid-South Region, Katherine Skiles

Biological and Agricultural Engineering Undergraduate Honors Theses

Rice grown in 5 states across the Mid-South (AR, LA, MS, TX, and MO) account for nearly 80% of all domestic U.S. rice production. Methane emissions produced during rice farming and the large seasonal water demand to maintain flooded fields have created a need for alternative irrigation research that can reduce methane emissions and conserve water. Structures called eddy covariance towers (ECTs) can observe methane and other flux responses to changing irrigation styles, and their data is shared across flux tower networks such as Delta-Flux in the Mid-South. The Delta-Flux network is relatively new, and its data-sharing capacity is not …

Exploring The Potential Of Tesla Valve For Filtering And Sorting Microscale Active Swimmers: A Computational Study, Ariel Rogers, Zhiyao He, Yong Wang

Physics Faculty Publications and Presentations

It is well-known that a Tesla valve allows fluids to flow unidirectionally without moving parts; however, how Tesla valves interact with active matters and the potential applications of Tesla valves in biology remain largely unexplored. Here, we present a computational study on the potential use of Tesla valves for filtering and sorting microscale active swimmers such as bacteria. We investigated the behavior of microscale swimmers passing through the Tesla valve at different linear and angular velocities using numerical simulations and quantified the diodicity of the Tesla valve for active swimmers. Our results demonstrate that the Tesla valve can effectively filter …

Evaluating Differences In Optical Properties Of Indolent And Aggressive Murine Breast Tumors Using Quantitative Diffuse Reflectance Spectroscopy, Joel Rodriguez Troncoso, Umme Marium Mim, Jesse D. Ivers, Santosh K. Paidi, Mason G. Harper, Khue G. Nguyen, Sruthi Ravindranathan, Lisa Rebello, David E. Lee, David A. Zaharoff, Ishan Barman, Narasimhan Rajaram

Biomedical Engineering Faculty Publications and Presentations

We used diffuse reflectance spectroscopy to quantify tissue absorption and scattering-based parameters in similarly sized tumors derived from a panel of four isogenic murine breast cancer cell lines (4T1, 4T07, 168FARN, 67NR) that are each capable of accomplishing different steps of the invasion-metastasis cascade. We found lower tissue scattering, increased hemoglobin concentration, and lower vascular oxygenation in indolent 67NR tumors incapable of metastasis compared with aggressive 4T1 tumors capable of metastasis. Supervised learning statistical approaches were able to accurately differentiate between tumor groups and classify tumors according to their ability to accomplish each step of the invasion-metastasis cascade. We investigated …

A Framework Of Flow Models For The Development And Testing Of Cardiovascular Devices, Megan Laughlin

Graduate Theses and Dissertations

Cardiovascular disease (CVD) is the leading cause of death worldwide and its treatment continues to improve due to the advancement of innovative cardiovascular medical devices. In vitro and in silico models serve to replicate the in vivo environment for the development and testing of these devices prior to using animals for testing, and eventually humans in clinical trials. However, limitations related to these models exist in multiple areas including general, cardiac, and venous applications. Specifically, current gaps have been identified with customizable, tissue-mimicking phantoms (general), 2D Blood Speckle Imaging (BSI) (cardiac) and a bioprosthetic venous valve (venous). This dissertation focuses …

Tissue-Engineered Models For Investigating Nerve Infiltration In Fibrotic Microenvironments, Nikolas Ala-Kokko

Graduate Theses and Dissertations

Neuron infiltration is involved in a multitude of diseased states and is critical in the regeneration of physiologic conditions. Modeling of innervation in three-dimensional, heterogenous, environments would allow early investigation in the crosstalk of neurons and native cells in normal and pathophysiologic microenvironments to gain an understanding of mechanistic functions. This would allow for greater insight into the role of metabolism, cell adhesion, microenvironmental alternations, cellular crosstalk, and signaling pathways that play a role in the promotion and prevention of neurite growth. In this thesis, with the construction of collagen-based hydrogels as the foundation for cell culture, we investigate cell …

Autofluorescence Imaging Of Endogenous Metabolic Cofactors In Response To Cytokine Stimulation Of Classically Activated Macrophages, Shelby N. Bess, Matthew J. Igoe, Abby C. Denison, Timothy J. Muldoon

Biomedical Engineering Faculty Publications and Presentations

Background

Macrophages are one of the most prevalent subsets of immune cells within the tumor microenvironment and perform a range of functions depending on the cytokines and chemokines released by surrounding cells and tissues. Recent research has revealed that macrophages can exhibit a spectrum of phenotypes, making them highly plastic due to their ability to alter their physiology in response to environmental cues. Recent advances in examining heterogeneous macrophage populations include optical metabolic imaging, such as fluorescence lifetime imaging (FLIM), and multiphoton microscopy. However, the method of detection for these systems is reliant upon the coenzymes NAD(P)H and FAD, which …

Pine-Tree Enables Efficient Enrichment Of Prime-Edited Hpscs, Mary S. Jia, Christopher E. Nelson

Biomedical Engineering Faculty Publications and Presentations

Commentary

PINE-TREE enables efficient enrichment of prime-edited hPSCs

Guar-Based Injectable Hydrogel For Drug Delivery And In Vitro Bone Cell Growth, Humandra Poudel, Ambar R. Rangumagar, Pooja Singh, Adeolu Oluremi, Nawab Ali, Fumiya Watanabe, Joseph Batta-Mpouma, Jin-Woo Kim, Ahona Ghosh, Anindya Ghosh

Chemistry & Biochemistry Faculty Publications and Presentations

Injectable hydrogels offer numerous advantages in various areas, which include tissue engineering and drug delivery because of their unique properties such as tunability, excellent carrier properties, and biocompatibility. These hydrogels can be administered with minimal invasiveness. In this study, we synthesized an injectable hydrogel by rehydrating lyophilized mixtures of guar adamantane (Guar-ADI) and poly-β-cyclodextrin (p-βCD) in a solution of phosphate-buffered saline (PBS) maintained at pH 7.4. The hydrogel was formed via host-guest interaction between modified guar (Guar-ADI), obtained by reacting guar gum with 1-adamantyl isocyanate (ADI) and p-βCD. Comprehensive characterization of all synthesized materials, including the hydrogel, was performed using …