Biological Engineering Commons^™

Novel Kinetic Description Of Real-Time Polymerase Chain Reaction Characterizes Interrelated Effects Of Sample, Master Mix, And Cycle Time, David Tafur

All Graduate Theses and Dissertations, Fall 2023 to Present

Real-time quantitative polymerase chain reaction fluorescent curves are influenced by the quantification method, template length, primer sequence, polymerase activity, reaction conditions, and unwanted side reactions. Interpretation of these curves depends on understanding the subjacent mechanisms by which those factors can alter the curve profile, particularly on highly diluted analytes or impure samples. However, such factors are individually described today, or their interplay is not fully developed. The present work examines the effect of primer dimer formation and extension, resource competition, template reannealing, and polymerase thermodegradation, in addition to novel descriptions of polymerase competitive inhibition, extended primer amplification, and the probability …

Microwave Imaging Technique For Breast Cancer Detection, Nure Alam Chowdhury

Theses and Dissertations

Breast cancer is a global problem, and it is inevitable to detect cancerous cells at early stages. In recent years, microwave imaging technology has been widely applied in biomedical applications for its non-ionizing radiation. In this study, we design a micro-strip patch antenna with an inverted T-type notch in the partial ground to detect tumor cells inside the human breast. The size of the current antenna is small enough (18 mm × 21 mm × 1.6 mm) to distribute around the breast phantom. The operating frequency has been observed from 6–14 GHz with a minimum return loss of −61.18 dB …

Investigating Endothelial Damage During Ischemic Stroke Treatment Using In Vitro And Computational Models, Zackary Lorton

Theses and Dissertations

Large vessel occlusion during acute ischemic strokes requires mechanical thrombectomy (MT) procedures using stent retrievers (SR). However, complete clot removal typically takes several attempts, which can amplify endothelial cell injury (EI). This project aims to characterize the extent of EI during MT using an in vitro vascular platform and a finite-element model (FEM). Impact of SR diameter and characterization of SR mechanical forces are assessed and correlated with human umbilical vein endothelial cell (HUVEC) response. HUVECs were seeded on fibronectin (4 µg/cm²) coated true-scale PDMS arterial phantoms with 2.5 mm luminal diameter. Test groups (n=6) either …

Testing Resilience Of Microalgae Biofilms When Exposed To Hydrothermal Liquefaction Aqueous Phase, Davis Riley Haag

Undergraduate Honors Capstone Projects

There are a multitude of experimental and processing techniques in the bioenergy field that produce sustainable and carbon negative to carbon neutral methods of converting renewable resources into biologically based hydrocarbons. One example of a process is hydrothermal liquefaction (HTL) which specializes in converting wet biomass into biocrude oil. One reason that these processes are not used outside experimental testing is due to the high cost of performing these processes. There is potential to move these processes to larger scale testing and eventually industrial adaptation if breakthroughs are made to offset the process expenses. There is a waste product produced …

Novel Nucleus Pulposus Biomaterial Development And Low Field Mri Assessment For Intervertebral Disc Degeneration, Mario Krussig

All Dissertations

Intervertebral disc degeneration (IVDD) is a prominent pathology in the modern world that causes debilitating pain for many patients. The onset of IVDD occurs in the nucleus pulposus (NP). NP biomaterials will play a vital role in mitigating the progression of IVDD. Within this work, we sought to synthesize a solubilized extracellular matrix (ECM)-based NP biomaterial. Utilizing pepsin or urea extraction, bovine NP ECM was successfully solubilized (SBNPs). SBNP formulations were characterized biochemically, evaluated for cytotoxicity, and down-selected for front-running formulations. Leading candidate SBNPs were incorporated into an alginate bead biomaterial model to determine the potential bioactivity with human adipose-derived …

What Is Biological Engineering? – A Magazine, Morgan Christensen

Undergraduate Honors Capstone Projects

Biological Engineering is one of the less commonly known fields of engineering and can be challenging to describe to someone outside the discipline. The most common question I've been asked during my undergraduate career is "What is biological engineering?". My answer has changed throughout my time at Utah State University as I've had more experiences within the discipline. This project focuses on answering this question in the format of a magazine to help bridge the gap between those in the discipline and a general audience. By using a magazine as the format, the content must be organized and written in …

Uv-A Light: A Novel Method For Food Dehydration, Mckade S. Roberts

All Graduate Theses and Dissertations, Fall 2023 to Present

Dehydration is one of the most prevalent forms of food preservation, with approximately 85% of food is hot air drying due to the simplicity of the process. The high temperatures employed in this method may also induce a loss in nutritional quality, which involves destruction of micronutrients (vitamins), and loss of color.

The aim of this work is to develop a low energy, non-thermal method of food dehydration that results in a high-quality product through the application of Ultraviolet light, within the UV-A range. UV light can be separated into its 3 categories based on the wavelength of light from …

Spectrophotometric Device For Early Malaria Detection, Adrian Wasylewski, Christopher Faber, Victor Lin

Honors Thesis

Malaria remains a significant global health challenge, with millions of cases reported annually, particularly in resource-limited regions. Timely and accurate diagnosis is crucial for effective treatment and disease management. Unfortunately, there are still significant challenges in existing testing procedures, which are often expensive, inaccurate, or impractical for mass testing. While spectrophotometry has been proposed as a detection tool for other tropical diseases such as dengue fever, no prototype has been made for any disease, including malaria. This report addresses this gap by presenting a spectrophotometric-based malaria detection tool that achieves high sensitivity at a low cost. The inclusion of a …

Testing Resilience Of Microalgae Biofilms When Exposed To Hydrothermal Liquefaction Aqueous Phase, Davis Haag

Student Research Symposium

Hydrothermal liquefaction (HTL) is a process that transforms wet biomass into a mixture of aqueous phase (AP), biochar solids, biocrude oil, and biogas.

The HTL process is not economically viable on a large scale partially because the HTL-AP is a toxic waste product with no current use.

The HTL-AQ contains high amounts of nitrogen (N) and phosphorus (P), but also environmental toxins such as phenolic compounds. The N and P could potentially be used to grow algae if it can survive the toxins.

Rotating algal biofilm reactors (RABRs) provide a method to grow algae biomass as a biofilm on plastic …

Investigating The Role Of Fluid Shear Stress During Metastasis On Enhanced Breast Cancer Extravasation, Alejandra M. Ham

LSU Master's Theses

In 2022, ~288,000 American women were diagnosed with metastatic breast cancer which was the leading cause of patient mortality with ~43,000 American women succumbing to the disease. Women can be diagnosed with four different molecular subtypes of breast cancer: luminal A, luminal B, human epithelial growth receptor type 2 enriched (HER2+), and triple-negative breast cancer (TNBC). TNBC accounts for ~12% of all breast cancers, yet it has the worst outcomes. TNBC is highly invasive, with ~46% of TNBC patients developing metastatic disease. A further understanding of metastatic TNBC is needed to provide a greater understanding of how to treat this …

Profiling Of Voltage-Gated Sodium Channel Subtype Expression And Resulting Susceptibility To Targeted Osmotic Lysis In Cancer, Spencer Gerard Lemoine

LSU Doctoral Dissertations

Cancer is a disease characterized by a wide array of dysregulated cellular function, activity, and growth. At times, specific dysregulations associated with cancer can be exploited as avenues of potential treatment. The sodium handling mechanisms and their associated proteins in cancer have received closer attention recently closely as such a potential mechanism to exploit for treating advanced cancer. Some novel treatments aim to inhibit the expression or activity of these sodium handling proteins in an attempt to prevent the cancer from advancing or becoming more aggressive; however, such approaches have had limited success. Targeted osmotic lysis (TOL) is a new …

Exploring Human Aging Proteins Based On Deep Autoencoders And K-Means Clustering, Sondos M. Hammad, Mohamed Talaat Saidahmed, Elsayed A. Sallam, Reda Elbasiony

Journal of Engineering Research

Aging significantly affects human health and the overall economy, yet understanding of the underlying molecular mechanisms remains limited. Among all human genes, almost three hundred and five have been linked to human aging. While certain subsets of these genes or specific aging-related genes have been extensively studied. There has been a lack of comprehensive examination encompassing the entire set of aging-related genes. Here, the main objective is to overcome understanding based on an innovative approach that combines the capabilities of deep learning. Particularly using One-Dimensional Deep AutoEncoder (1D-DAE). Followed by the K-means clustering technique as a means of unsupervised learning. …

Investigating The Role Of Anesthesia In Radiation Therapy, William Walter Daley

ENGS 88 Honors Thesis (AB Students)

Purpose:

Cancer claims 7.6 million lives worldwide annually, affecting millions more. Conventional (CONV) radiation therapy (RT) is a key weapon in the oncological arsenal. A novel mode of radiation delivery, utilizing ultra-high dose rates (UHDR), is associated with enhancing the RT therapeutic ratio by selectively sparing normal tissue without sparing tumor tissue. However, there are many roadblocks to the clinical implementation of UHDR RT —namely the lack of standardization of experimental conditions and the inconsistency of published and unpublished results. This thesis investigates variables that affect preclinical biological outcomes to radiation.

Materials/Methods:

Eight groups of 10 C57BL/6 mice were stratified …

Degradable Staples And Delivery Device, Meha Elango, Jessica Cabrera, Makayla Scarpitti, Kareemat Melaiye

Williams Honors College, Honors Research Projects

The scope of this project is to design a method to secure skin grafts to healthy tissue. The ultimate goal for the proposed method is to be dissolvable in some form. Currently, skin grafts procedures utilize staples in most cases to hold a skin graft in place, but there are disadvantages that come with it. Staples are easy to place, but time consuming during the removal procedure. They also cause a lot of pain and discomfort for the patient. The goal of this project is to determine a way a secure skin grafts to healthy skin in order to reduce …

The Effects Of Various Nanoplastics On The Inflammatory Response In Primary Alveolar Epithelial Cells, Eunice J. Pak

Theses and Dissertations

As plastic pollution begins to multiply in the environment and the workplace, gradual degradation of these plastics creates an unseen threat to biological health: nanoplastics. These nanoplastics are common in day-to-day life, and have been found in various internal organs of the human body. The biological and health effects of these nanoplastics are still widely unknown, and only recently has research focused on the impacts of these particles on human health at the cellular level.

In this thesis, poly(methyl methacrylate) and three forms of polystyrene (carboxyl-modified, amine-modified, and neutral surface charge) have been tested on submerged primary C57BL/6 mouse alveolar …

Computational Analysis Of Vascular Aneurysms, Seyedmostafa Rezaeitaleshmahalleh

Dissertations, Master's Theses and Master's Reports

Vascular aneurysms, such as intracranial aneurysms (IAs) and abdominal aortic aneurysms (AAAs), pose significant health risks, particularly upon rupture. Disturbed hemodynamics, characterized by swirling flow patterns, can lead to cellular and structural changes that disrupt normal physiological processes and contribute to destructive vascular remodeling. Integrating hemodynamic analysis into clinical assessments of aneurysms has become crucial, especially through patient-specific computational fluid dynamics (CFD) simulations based on medical imaging. However, the complexity of CFD tools presents challenges in model creation and post-simulation analysis, limiting their accessibility to clinicians.
This project aimed to advance aneurysm management by exploring the role of intraluminal thrombus …

Matrix Stiffness Sensing By Nascent Adhesions And The Role Of Riam In Adhesion Assembly, Nikhil Mittal

Dissertations, Master's Theses and Master's Reports

Mechanical stiffness of the extracellular matrix (ECM) impacts many cellular functions such as proliferation, migration, and differentiation. ECM stiffness is sensed by a cell via integrin-based focal adhesions (FAs) by changing conformation and biochemical activities of molecules within FAs by the exchange of the force between the ECM and filamentous actin (F-actin). Cells in turn respond to this stiffness by generating traction force that plays an important role in many biological events such as tissue morphogenesis, stem cell differentiation, wound healing, and cancer cell metastasis. The stiffness of the extracellular matrix induces differential tension within integrin-based adhesions. Understanding stiffness sensing …

Development Of Glutathione-Responsive Disulfide-Containing Poly(Beta-Amino Esters) With Varied Hydrophilicity And Acrylate Functionality, Anastasiia Aronova

Theses and Dissertations--Chemical and Materials Engineering

Smart biomaterials are becoming promising for therapeutic deliveries due to their ability to respond to changes in the environment. Redox-responsive hydrogels are a promising type of smart polymer that can swell and degrade according to cellular oxidative stress levels. Glutathione, abundant in cells, is crucial in redox-responsive biomaterials, serving as a key reactive molecule. This study explored the degradation kinetics of glutathione-responsive poly(β-amino ester) (PBAE) polymers created through a single-step Michael addition. We examined how disulfide content influences the degradation kinetics of these PBAE networks. Additionally, we investigated how the hydrophilicity and functionality of acrylate affect the degradation of disulfide-containing …

Cellular Level Changes Induced In Cancer Cells Due To Microgravity, Sai Deepika Reddy Yaram

Graduate Theses, Dissertations, and Problem Reports (ETD)

The increase in human activity in space has revealed several kinds of physiological challenges brought on by the absence of Earth's gravitational pull. NASA observed that during spaceflight, astronauts experience a 1-1.5% monthly loss in the mineral density of weight-bearing bones, with rehabilitation efforts on Earth often proving ineffective. This issue extends to muscles, the neuro vestibular system, the cardiovascular system, and vision. Cancer has emerged as a significant cause of mortality among astronauts, with studies up to 2017 showing that 41.3% of natural cause deaths among U.S. astronauts were due to cancer, primarily due to space radiation exposure. Cancer …

Adjuvant Pluronic F68 Is Compatible With A Plant Root-Colonizing Probiotic, Pseudomonas Chlororaphis O6, Amanda R. Streeter, Anthony Cartwright, Mohammad Zargaran, Anagha Wankhade, Anne J. Anderson, David W. Britt

Biological Engineering Faculty Publications

Plant probiotic bacteria are being increasingly used to maximize both the productivity and quality of field crops. Pseudomonas chlororaphis O6 (PcO6) is a plant root colonizer with probiotic activities. This bacterium produces an array of metabolites, including a group of phenazines that are functional in plant protection. The paper reports responses of PcO6 to a nonionic triblock copolymer surfactant, Pluronic F68. This Pluronic exhibits membrane "healing" activity and improves cryopreservation recovery in eukaryotic cells. The product is FDA-approved and is applied as an adjuvant in formulations used in agriculture, medicine, and biotechnology. Growth of PcO6 on …

Air-Jet Bioprinting Of Stem Cell-Encapsulated Alginate Micro-Droplets For Organoid Biomanufacturing, Mirabella B. Stump

Electronic Theses and Dissertations

Biomanufactured 3D-organoids show promise for modeling and treating various conditions, particularly insulin-dependent diabetes mellitus (type-1 diabetes). Pancreatic islet organoids serve as sustainable sources of insulin-producing β-cells, potentially restoring insulin regulation in patients and providing a long-term solution for diabetes. Hydrogel droplet printing is an emerging technique in regenerative medicine due to its advantageous tunability and biocompatibility; however, challenges of consistency, quality control, and scalability persist. To address these issues, we developed a novel air-jetting based droplet bioprinting system for the generation of monodispersed alginate micro-droplets. The objective of this project was to incorporate human induced pluripotent stem cells (hiPSCs) into …

Study Of Surface And Groundwater Quality And Quantity At Watershed Scale In Mississippi, Dipesh Nepal

Theses and Dissertations

Hydrology and water quality are affected by land use and climate changes. Mississippi’s diverse agro–ecosystem comprises of a range of land use land cover (LULC) including agriculture, forest, wetlands, urban, and grasslands. The objectives of this study were to investigate the impacts of various factors such as Best Management Practices (BMPs), wetlands, LULC, and climate changes on water quality and quantity. The hydrologic and water quality responses to dynamic LULC input in Soil and Water Assessment Tool (SWAT) were evaluated. Results showed that agricultural and forest expansion were major drivers of hydrologic and water quality changes in Big Sunflower River …

Design Of Human Serum Albumin And Adenovirus Conjugation Via Catcher/Tag Molecular Glue, Peijie Zhao

McKelvey School of Engineering Graduate Student Theses & Dissertations

Adenovirus (Ad) has been the ideal cargo delivery mechanism, and its moderate immunological response makes it ideal for in vivo gene therapies since its discovery in 1953. However, the robust immunogenicity of the Ad capsid and low vaccine absorption via mucous membranes and epithelium put a limit on the process of developing intranasal vaccines. Efforts are being made to enhance the effectiveness of Ad vectors and numerous studies have demonstrated the remarkable capacity of human serum albumin (HSA) to extend plasma half-life and facilitate targeted intranasal delivery. In this study, we devised an innovative method for employing the Catcher/Tag molecular …

Determining The Effects Of Glycocalyx Modifications On The Electrophysical Properties Of Human Mesenchymal Stem Cells, Rominna E. Valentine Ico

Electronic Theses, Projects, and Dissertations

Human mesenchymal stem cells (hMSCs) have gained popularity in clinical trials due to their multipotent differentiation characteristics, ability to secrete bioactive molecules, migrate into diseased or damaged tissues, and their immunosuppressive properties. HMSC cultures are heterogeneous, containing stem cells, partially differentiated progenitor cells, and fully differentiated cells. One of the major challenges with hMSCs therapeutic potential is the inability to select specific cell subpopulations due to an insufficient number of biomarkers. Often the biomarkers used, like those for fluorescence-activated cell sorting, are not sufficient to define hMSCs because they overlap with other cell types. Consequently, there is a need to …

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 …

1-Methyl-4-Phenyl-1,2,3,6-Tetrahydropyridine (Mptp)-Treated Adult Zebrafish As A Model For Parkinson’S Disease, Emmeline Bagwell

All Theses

The use of adult zebrafish, Danio rerio, as a model for human neurodegenerative diseases has proven valuable in pharmaceutical development and genetic disease research due to their high genetic homology to humans, cost-effective husbandry, and quick life cycle breeding times. Despite their promise, most zebrafish research has focused on embryonic stage organisms, primarily due to the ease of direct handling protocols and rapid progression through developmental stages. Recognizing the limitations of early-stage organisms in modeling adult diseases, recent efforts have shifted the applicability of zebrafish models, particularly for Parkinson's Disease, due to the nature of the disease impacting patients 55 …

Engineering Next-Generation Cardiovascular Therapies, Ryan Walker Barrs

All Dissertations

Cardiovascular diseases are the leading cause of death worldwide. Heart disease, in particular, accounted for 1 in every 5 deaths in the United States in 2021, representing a substantial public health burden that will require more effective treatment options to alleviate. Heart transplant surgery is currently the only option to completely restore cardiac function, but many patients die while waiting for a transplant due to a longstanding organ donor shortage. Thus, there is a dire need for accessible treatment options that can repair damaged hearts. Recent advances in tissue engineering and regenerative medicine have accelerated the development of therapies for …

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 …

Effects Of Indole Derivative Idc16 On Cell Proliferation, Transfection, And Alternative Splicing In Production Of Lentiviral Vectors By Transient Co-Transfection, Nataly Mier

All Graduate Theses and Dissertations, Fall 2023 to Present

Viruses can efficiently introduce genetic material into a variety of cells through cell infection. Therefore, viral vectors, defined as virus-based gene delivery systems, effectively transfer functional gene constructs to target cells. Among different viral vectors, lentiviral vectors are of interest due to the advantages offered to research and therapeutic applications. Low productivity of lentiviral vectors in mammalian producer cells and high production cost, however, remain barriers to the vectors’ routinary use, particularly in clinical settings.

Since most lentiviral vectors are derived from human immunodeficiency virus type I, their genome has been engineered to increase safety. Nevertheless, modifications of the lentiviral …

Development Of An Angiogenic Tissue-On-A-Chip Microenvironment, Eric Stuehr

Master's Theses

Preclinical testing is necessary to investigate the safety and efficacy of novel therapeutics before moving to clinical trials, yet approximately 90% of these therapies fail once tested in humans. This has led to increased interest in developing robust preclinical models that accurately mimic the complex human in vivo physiology. Microfluidic devices that can introduce dynamic conditions to 3D cell/organoid cultures, also known as tissue-on-a-chip, have emerged as physiologically relevant in vitro preclinical models that can achieve high throughput screening of therapeutics. The research presented here aimed to develop an angiogenic environment within a novel microfluidic device to stimulate formation of …