Biomedical Engineering and Bioengineering Commons^™

Molecular Devolution For Gene Editing: Reverse Directed Evolution Of Cre Recombinase, Giovanna Esposito, Simran Sood, Katie Liu

Bioengineering Senior Theses

The principal objective of this paper is to provide a proof-of-concept of a novel protein engineering method called Molecular Devolution (MD). MD is an evolutionary protein engineering method that reduces the size of enzymes while retaining its functional properties. This paper outlines an MD protocol for Cre Recombinase. Cre Recombinase is an enzyme that is part of the Cre LoxP DNA Recombination System, which is a leading gene editing system widely used in genetic research. This paper outlines a MD approach that was used to miniaturize Cre Recombinase and remove unnecessary complexities, allowing for simpler and more e!cient use in …

A Point-Of-Care Hormone Monitoring Platform For Postpartum Health Assessment, Ava Mcdonald, Avary Torres, Frances Warneke

Bioengineering Senior Theses

Our point-of-care hormone monitoring device for postpartum health assessment uses paper-based microfluidics to provide an accessible and affordable hormone monitoring tool, tracking biomarkers correlated with postpartum depression (PPD). The device features a 3D-printed spring-box housing and platform containing chromatography paper testing sheets that are lined with polydimethulsiloxane (PDMS) and wax paper, embedded with specific reagents that generate colorimetric hormone readouts from saliva samples. This device was motivated by the need to address critical shortcomings in PPD care, where societal stigma surrounding mental health and reliance on self-reporting diagnostic methods prevent mothers from truthfully reporting symptoms and receiving timely support and …

Peridevice: A Packed Bed Reactor For Integrated Peritoneal Dialysis, Jake Wood, Gurtej Singh, Orion Cook, James Bell

Bioengineering Senior Theses

Chronic kidney disease affects approximately 800 million people worldwide, with more than 800,000 Americans living with end-stage kidney disease. Peritoneal dialysis provides patients with greater :flexibility and independence than traditional hemodialysis, but it is limited by the buildup of urea in the dialysate, which requires frequent fluid exchanges. Developing a system that continuously regenerates dialysate could help improve the efficacy of this treatment.

In this study, we developed the PeriDevice, a compact packed-bed reactor designed to remove urea from dialysate through enzymatic degradation. The 3D-printed device, using stereo lithography, filled with alginate microcapsules ( d = 1.5 mm) containing urease. …

Automated Optimization Of Membrane Bioreactor Performance Using Machine Learning, Janessa Cayabyab, Isabella Lopez, Oluwatomisin Opaleye, Jessica Stone

Bioengineering Senior Theses

Membrane bioreactors (MBRs) are increasingly employed in biomanufacturing due to their ability to produce high-quality effluent and support complex biological processes. However, membrane fouling remains a critical operational challenge, driving increased energy consumption, frequent cleaning cycles, elevated transmembrane pressure (TMP), and accelerated membrane degradation. Conventional operator-driven cleaning strategies are reactive by nature and insufficient for managing the dynamic, nonlinear fouling behavior characteristic of full-scale MBR systems.

This study presents a data-driven machine learning pipeline for predicting TMP and fouling behavior in an industry-scale MBR system, with the goal of optimizing cleaning schedules and extending membrane lifespan. A Random Forest regression …

Engineering Exosome Delivery Systems For Targeted Cancer Therapeutics, Gerardo Aguayo Quezada, Mahika Arya, Eduardo Noyola Mojarro

Bioengineering Senior Theses

Treatments for glioblastoma (GBM) are limited, mainly because the blood-brain barrier (BBB) prevents large molecules like chemotherapeutic drugs from reaching brain cells, and other methods like brain surgery are incredibly invasive. Brain surgery is useful for large masses of tumors, but the surgery can’t always remove the entire tumor, which is where radiation can be used, but only in limited quantities to prevent neural damage. To circumvent these gaps in modern medicine, exosomes, which are naturally secreted nanoparticles, offer an exciting way to deliver treatments to diseased cells. Exosomes biologically cross the BBB and transport materials between cells. In our …

Ambulatory Monitoring Of Biomarkers For Enhanced Recovery, Lucas Abrahamian, Gurman Dhami

Bioengineering Senior Theses

Oxidative stress, an imbalance of reactive oxygen species and antioxidants, serves as both a marker and progressor of several chronic and degenerative diseases. These conditions create a major global health burden, accounting for significant cost and deaths. The prevalence of oxidative stress–driven diseases highlights the need for improved strategies to detect the imbalance before irreversible damage occurs. However, despite its major role in disease progression, oxidative stress is typically assessed using static, invasive, or laboratory methods. These approaches are poorly suited for continuous monitoring and fail to serve high-risk groups, such as patients with a family history of disease or …

Development Of In Vitro Hydrogel Blood Clots, Xiomara Garcia, Jasmine Urbina, Sapna Wolf

Bioengineering Senior Theses

Deep Vein Thrombosis (DVT) affects up to almost one million individuals in the United States annually and can lead to life-threatening complications, such as a pulmonary embolism. DVT occurs when a thrombus composed of platelets and fibrin forms within deep veins, obstructing blood flow. Current treatments include anticoagulants, thrombolytics, inferior vena cava filters, and balloon catheter procedures. However, the development and testing of these medical devices heavily rely on animal blood models due to physiological similarities in coagulation, raising ethical concerns and limitations related to cost, scalability, and sustainability. This project proposes a synthetic, in vitro alternative using agarose and …

Microfluidic Intracranial Pressure Monitoring Sensor, Andrea Pader, Anthony Sukendro, Tripti Pandey

Bioengineering Senior Theses

This thesis presents the design of a novel microfluidic sensor for continuous monitoring of intracranial pressure (ICP), intended as a less invasive alternative to current monitoring techniques. The sensor targets patients with critical and chronic neurological conditions, aiming to provide real-time data on ICP fluctuations. The microfluidic intracranial pressure sensor is designed for implantation beneath the skull, on the dura mater, and integrates a PDMS-based microfluidic strain sensor with wireless data transmission. Initial testing focuses on optimizing sensor design and integration with a microcontroller. Preliminary benchtop testing demonstrates the sensor's capability to detect ICP with a minimum sensitivity of 5 …

Continuous Monitoring Of Dynamic Levels Of Sepsis-Associated Biomarkers In Blood For Early Diagnosis, Aidan Burke, Jake Chansky, Anders Kouhia, Brian Mostofi

Bioengineering Senior Theses

Sepsis is a general diagnosis related to a dysregulated immune response to a source of infection that, if left untreated, will most likely result in organ failure and eventual death. Sepsis affects 49 million people annually, and is responsible for 11 million annual deaths, according to Jarczak 1. A recent study has shown that over 80% of sepsis deaths may be preventable with earlier diagnosis and treatment, and that the risk of mortality increases by 8% for every hour that sepsis goes untreated 5. Thus, our team identified that the timeliness of sepsis diagnosis is a paramount healthcare need.

We …

Microplastic Eaters, Alanna Boze

Bioengineering Senior Theses

This thesis evaluated Alcanivorax Borkumensis’ (A. Borkumensis) ability to degrade polystyrene in a pyruvate-rich environment to determine if the bacteria could degrade the microplastic when grown in pyruvate. The thesis explored the metabolic behavior of A. Borkumensis when pyruvate is used to start the gluconeogenesis pathway, which is the start of the metabolic pathway when degradation occurs. The bacterium was grown in ONR7a medium, that was adjusted to a pH of 8.1, and 1% pyruvate; then it was processed by centrifugation and washing before experimentation began. Trials were conducted to iteratively refine the process and verify trial results. Bacterial growth …

Ambulatory Monitoring Of Biomarkers For Enhanced Recovery, Guneet Grewal, Grace Kurilo, Maggie Nostrand, Vismaya Panicker

Bioengineering Senior Theses

The objective of our project is to create, design and test a fully functional continuously monitoring hydrogen peroxide sensor. This sensor aims to identify early detection of diseases associated with oxidative stress which can include certain types of cancer, neurodivergent diseases and cardiovascular diseases. Early detection of hydrogen peroxide levels can provide patients with early treatment and can help reduce disease progression. Overall, the biosensor prioritizes early detection of ROS levels allowing various consumers such as healthcare sectors, patients, and research institutions to benefit from continuous monitoring for health management and disease prevention.

Ai Diagnostic Tool For Covid-19 Severity, Hunter Lau, Ryan Lang, Aidan Furuhashi

Bioengineering Senior Theses

With the advent of COVID-19 pandemic global, healthcare systems were challenged with resource constraints plaguing hospital environments around the world with consequences that presented weaknesses in our healthcare system. This demonstrated the importance of triage in unprecedented scenarios. This project presents an integrated AI-driven diagnostic tool to predict the severity of COVID-19 cases using length of stay as an analog. By using clinical data and radiographic chest images, this project integrates a XGBoost clinical data model with a Convolutional Neural Network (CNN) model utilizing chest CT images to create a comprehensive assessment of patient case severity through predicted length of …

Bilateral Gait Trainer For Transtibial Amputees, Desmond Greer, Odinachi Anene, Andrew Wallace, Noah Hill

Bioengineering Senior Theses

Lower limb amputation affects over 2.3 million individuals in the U.S., with peripheral vascular disease and diabetes as leading causes. Prosthetic rehabilitation is critical for restoring mobility, yet barriers like therapist shortages, cost, and inconsistent at-home training limit patient outcomes. This thesis presents the design, development, and testing of a bilateral gait training device that addresses these challenges by providing real-time haptic feedback and quantitative gait metrics for at-home rehabilitation. The device integrates force-sensitive resistors embedded in insoles to monitor plantar pressure distribution, haptic actuators (eccentric rotating mass motors) mounted on thigh straps to deliver corrective feedback, and an Arduino-based …

In-Vitro Hydrogel Blood Clots, Ethan Evans, Khoi-Austin Ngo

Bioengineering Senior Theses

Creating a sustainable, ethical, and affordable substitute for animal blood in balloon catheter testing for Deep Vein Thrombosis (DVT) is important to take into consideration. This research utilizes agarose and dextran to develop hydrogel-based artificial blood clots. These hydro gels replicate the mechanical characteristics of human thrombi across acute, subacute, and chronic stages through their elastic and viscous moduli (G' and G") and phase angles. This project addresses extant testing protocols, including temperature regulation, agarose processing, and well plate size, and suggests efficient approaches to encounter these problems.

The hydrogels were characterized by means of a thorough literature review and …

Packed-Bed Reactor For Integrated Peritoneal Dialysis, Julia Appleget, Ally Kwong, Megan Moglia

Bioengineering Senior Theses

Patients with chronic kidney disease (CKD) have lost kidney function. 800,000 Americans have end-stage kidney disease resulting in one of the leading causes of mortality cross-listed with diabetes and heart disease. Over the past decade, the percentage of patients using peritoneal dialysis (PD) has nearly doubled. PD which is a portable treatment involves the insertion of a catheter into the selectively permeable peritoneal cavity infused with a hyperosmolar dialysis fluid drawing the toxins from capillary beds of the peritoneum and into a gravity fed waste solution with a reported clearance of 87%. In order to improve the clearance of the …

Novel Nano-Binders Treating Alzheimer’S Disease, Katie Ching, Sophie Criscione

Bioengineering Senior Theses

The objective of our project is to engineer exosomes to be an effective therapeutic agent as a possible new treatment option for the neurodegenerative disease, Alzheimer’s Disease (AD). Among the various causes of AD, we are focusing on treating the pathogenesis linked to the build-up of amyloid-beta plaques in the brain, which disrupts neural connections and ultimately kills nerve cells. Currently, the most widely available treatment options for AD only provide symptomatic relief and targeting amyloid plaques in the brain is a promising new therapeutic approach in the field. Even the partial clearance of plaques could significantly improve the prognosis …

Skin Phantom Development For Electrophysiological Wearable Device Testing, Rohan Sodha, Kiet Vu, Jonathan Nguy

Bioengineering Senior Theses

This senior design project aimed to develop a skin phantom suitable for testing electrophysiological wearable devices. Our skin phantom consisted of a porous paper PDMS as the epithelial layer, initially paired with agarose gel as the tissue layer, and later with gelatin based on comparative analysis. Through rigorous experimentation and leveraging data from the IT’IS Foundation’s interactive database, we identified that gelatin exhibited superior electrical properties compared to agarose, making it a more effective medium for replicating human tissue. Our work not only validated the use of paper PDMS with both agarose and gelatin but also demonstrated that gelatin's lower …

Impact-Reducing Prosthetic Liner With Variable Volume & Integrated Haptic Feedback, Luke Brothers, Gigi Schaefer, Zoe Straughn

Bioengineering Senior Theses

Transtibial amputees face challenges such as loss of proprioception and fluctuations in the size and composition of their residual limb, which can compromise comfort and mobility. This project aims to create a transtibial impact-reducing liner combined with integrated haptic feedback to enhance comfort and restore proprioceptive senses. The impact-reducing liner includes impact reduction over pressure-intolerant regions, impact redistribution over pressure-tolerant regions, and a variable volume system that dynamically adjusts to changes in the residual limb’s volume throughout the day. The haptic feedback system employs force-sensitive resistors located on various regions of the prosthetic foot. These sensors transmit via Bluetooth to …

Screening Of Microorganism Mutations Using Microbial Fuel Cell Activity, Grant Gini, Joshua Chansky

Bioengineering Senior Theses

Microbial fuel cells (MFC) are a rapidly growing field of interest with potential for clean energy production, effluent/waste capture and purification. Drawbacks associated with MFCs is the short duration of the peak current, discouraging integration into emerging nanogrids, as well as the operational cost associated with the infrastructure, offsetting the net cost of power generation. With the objective of quantifying the success of genetic mutations using the MFC to address the above-mentioned problem-solving opportunities, the following specific aims were formulated in this study: 1) To measure current as a metric for growth/catalytic activity for microencapsulated microorganisms, and, 2) To optimize …

Microneedles For Wound Healing, Maya Matheny, Maggie Dubus, Lily Eribes

Bioengineering Senior Theses

Microneedles are a virtually painless and minimally invasive transdermal delivery system comprised of an array of micron-sized needles that can be used to deliver cells, drugs, proteins, and vaccines. However, a major challenge to this delivery method is controlling puncture depth. To advance the microneedle landscape, our project aims to identify and characterize the biomechanical cues between a microneedle puncture and a hydrogel skin phantom for pre-clinical testing A stopper microneedle design that controlled puncture depth into the phantom skin model patch to 150μm was tested on millimeter-thick mold-casted alginate slabs. The hysteresis loop differs in the presence and absence …

Minimally Invasive 3d Printed Microneedles For Glucose Monitoring, Eduardo Quintero, Justin Wong

Bioengineering Senior Theses

Continuous glucose monitoring (CGM) provides an instantaneous real-time display of glucose level, rate of change of glucose, alerts, and alarms for actual or impending hypo- and hyperglycemia. Continuous glucose monitors are able to stay implanted on the patient anywhere from 7-14 days, giving patients and doctors valuable information to help improve patient care for diabetics, and providing them with a way to continuously monitor their blood glucose level concentration throughout the day.

Conventional methods of glucose detection such as blood glucose meters require the patient to gather frequent blood samples to generate instantaneous results that are only accurate as of …

Immuno-Anti-Infective Drug Design Using Bioai, Cathy Chen, Vivian Zhang

Bioengineering Senior Theses

According to the World Health Organization, antibiotic resistance is one of the biggest threats to global health, food security, and development today. A growing number of infections, like Methicillin-resistant Staphylococcus aureus, are becoming harder to treat as the antibiotics used to treat them become less effective. As a result, the primary concern for infections in the hospital setting is due to the S. aureus’s growing resistance to antibiotics. Therefore, in response to this global health threat, our project focuses on furthering the research in developing a drug that S. aureus will not develop resistance to. In this paper, we assess …

Shear Detection Of Microencapsulated Cells For Monoclonal Antibody Production Scaleup, Kendall Defelippi, Dwight Johnson

Bioengineering Senior Theses

Scale the reported hydrodynamic shear values in industrial bioreactors for monoclonal antibody production to the shear stress measured in our custom microneedle prototype by extruding microencapsulated CHO cells. A correlation between the number of extrusion loops to reduction in cell viability enables a scalable screening method for bioprocessing efficiency.

Engineering Hydrogels For Delivery Of Therapeutic Proteins, Francesca Briggs, Daryn Browne

Bioengineering Senior Theses

In this project, we investigate how innate hydrogel properties can be leveraged for controlled protein drug release platforms. Therapeutic proteins have many valuable applications within the medical field, however, professionals often face many obstacles with obtaining controlled drug release. This paper analyzes how the manipulation of hydrogel properties can improve protein drug release rates. We started these investigations by varying hydrogel concentrations since we saw that this affects the release of small molecules. Additionally, we wanted to see what the addition of a second hydrogel network would do to protein release rates. These experiments concluded that raising polymer concentrations and …

Poly(Adr-Ribose) Polymerase 14-Specific Inhibitor For Hepatocellular Carcinoma, Clarissa Silvers, Colin Sim

Bioengineering Senior Theses

Poly (ADP-ribose) polymerases, PARPs, are comprised of a family of 17 human enzymes that share a conserved catalytic domain that transfers ADP-ribose from nicotinamide adenine dinucleotide (NAD+) to target proteins. While significant proteomic-based efforts in the field have uncovered a host of potential targets for each of the various active PARP enzymes, an outstanding question remains as to what extent proximal versus distal interactions with the protein substrates govern target selection. In this work, we describe the use of tandem mass spectrometry to identify specific residues that are auto-modified in both PARP14 and PARP15 as well as their preferred modification …

Wearable Health Sensor, George Kouretas, Kelley Mccarroll

Bioengineering Senior Theses

The COVID-19 pandemic has significantly impacted several populations, partially due to the lack of access to basic health care amenities, and emphasized the need for continuous telehealth monitoring of relevant biometric vitals. This need is further emphasized through research that has suggested that simple biometric vitals, including heart rate (HR), blood oxygen saturation rate (SpO2), and temperature, are relevant biomarkers for early disease diagnosis. The project aims to address this need through the design wearable health platform that uses novel, non-invasive techniques to monitor biometrics with the eventual goal to provide user insights into current health status and identify early …

Engineering Stealthy Exosomes For Drug Delivery, Chris Olson, Mika Domingo

Bioengineering Senior Theses

Exosomes, a class of extracellular vesicles (EVs) are emerging as a new scientific and therapeutic tool for imaging, disease diagnostics, and drug delivery. Exosomes' excellent biological properties make them a strong candidate for surface modification as well as exogenous drug loading. While exosomes have excellent natural biocompatibility properties as well as low immunogenicity, they are still eliminated in the patient’s body through the immune system, mainly through phagocytosis by macrophages. In this report, we aim to aid exosomes in avoiding this elimination method by modifying them through surface display with antiphagocytic factors. We will use CD24 and CD47 “don't eat …

Skin Phantom For Wearable Device Benchtop Testing, Laura Apolloni, Vindhya Mullapudi, Takumi Simon

Bioengineering Senior Theses

The biowerables constitute one of the fastests growing sectors of the medical device industry. Novel approaches for rapid prototyping have increased design and development speeds. However, in vivo testing that is currently used for many medical devices makes testing time-consuming, costly, and presents ethical issues. As an alternative, benchtop testing tools promise to alleviate these concerns. Artificial tissue phantoms that are capable of mimicking the characteristics of human tissues are required for demonstrating a medical device’s safety and efficacy in benchtop tests. While there are many hydrogels that are able to mimic these relevant properties of human tissue, creating a …

Milkguard: Predictive Modeling And Mobile App Development For Affordable, Usable Breast Milk Diagnostic, Beau Hsia, Emma Mccurry

Bioengineering Senior Theses

Breast milk is considered the gold standard of infant nutrition, but some infants around the world lack access to it due to maternal health complications or other considerations. Human breast milk banks do exist to try to alleviate this problem, but most are underfunded and have high operational costs, making it difficult for some infants to obtain safe, reliable donated breast milk.

Existing methods of testing breast milk are expensive, so the MilkGuard project was conceptualized in 2017 as a fast, economical, and highly usable bacterial contamination detection system. Prior to this year, previous MilkGuard teams had developed a system …

Non-Ribosomal In Vivo Protein Ligation, Sarah Desautel, Kenneth Joseph, Victorino Miguel Francisco

Bioengineering Senior Theses

Protein ligation is a process integral to many biomedical applications, however the current industry standard, expressed protein ligation (EPL), is highly error prone and time-and-cost inefficient. Our team sought to improve this integral process by proving the efficacy of a new method of protein ligation using the transpeptidase Sortase A. Sortase A is known to efficiently bind two peptide fragments so long as they are attached to LPXTG motifs, which signal and activate the enzyme’s ligation abilities. Previous studies affirm Sortase A’s binding ability and efficacy in in vitro situations, however none have yet confirmed its abilities in vivo. Operating …