Biological Engineering Commons^™

Shape Memory Alloy Capsule Micropump For Drug Delivery Applications, Youssef Mohamed Kotb

Theses and Dissertations

Implantable drug delivery devices have many benefits over traditional drug administration techniques and have attracted a lot of attention in recent years. By delivering the medication directly to the tissue, they enable the use of larger localized concentrations, enhancing the efficacy of the treatment. Passive-release drug delivery systems, one of the various ways to provide medication, are great inventions. However, they cannot dispense the medication on demand since they are nonprogrammable. Therefore, active actuators are more advantageous in delivery applications. Smart material actuators, however, have greatly increased in popularity for manufacturing wearable and implantable micropumps due to their high energy …

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 …

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. …

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 …

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 …

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 …

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 …

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

McKelvey School of Engineering 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 …

Microbial Glycosylation Of Antitubercular Agent Chlorflavonin, Jie Ren, Jixun Zhan

Biological Engineering Faculty Publications

Flavonoids have shown health-benefiting properties, such as antioxidative and anti-inflammatory activities, and are commonly used as nutraceuticals and pharmaceuticals. Although flavonoids are predominantly identified from plants, several filamentous fungal species have also been reported to produce bioactive flavonoids, including chlorflavonin from Aspergillus candidus, a novel halogenated flavonoid with potent antifungal and antitubercular (anti-TB) activities. Unfortunately, the low water-solubility of this molecule may hinder its bioavailability. Glycosylation is an effective method to enhance the polarity of natural products and alter their physicochemical properties. This work focuses on the development of novel water-soluble chlorflavonin derivatives to combat the threat of drug-resistant …

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 …

Engineered Exosomes For The Multimodal Imaging Directed Photo-Immunotherapy Of Colorectal Cancer, Deepak S. Chauhan, Meena Jaggi, Subhash C. Chauhan, Murali M. Yallapu

Research Symposium

Background: Rio Grande Valley experience severe cancer health disparity. A novel therapeutic modality may serve as better therapeutic option. Nanohybrids endowed with multifunctionality, longer circulation time, large surface area have emerged as an active preference for cancer research. However, rising concern of nanomaterials toxicity and scalability issues has slowed their translation to clinics. Exosomes (Exo) are endogenous endocytic origin 40-100 nm vesicles found in various body fluids, which in comparison to synthetic nanoparticles, are biodegradable, highly biocompatible as well as immunocompatible in nature. Although bulk isolation of exosomes from human body fluids is still a problem and engineering of exosomes …

Characterization Of Mammographic Dense Tissue Sub-Types Using Classification Algorithms On Metric Space Technique Output Functions, Madison Raza

Electronic Theses and Dissertations

In recent years breast cancer has become the leading cause of global cancer incidence. One of the most common forms of screening is through the use of digital x-ray screening mammography. Risk assessment models which help predict a patient’s risk of developing breast cancer rely mainly on patient history and qualitative breast density assessment from screening. The 2D wavelet transform maxima modulus (2D WTMM) method uses a sliding window approach to quantify the spatial organization of underlying mammographic tissue according to Hurst- exponent ranges (H) as fatty (H ≤ 0.45), healthy dense (H ≥ 0.55) and …

Development And Characterization Of Shear Thinning Cnf-Tempo Hydrogels For Use In Aquaculture Vaccines, Jacob A. Holbrook

Electronic Theses and Dissertations

Aquaculture has shown significant growth within the past few decades and is expected to continue expanding rapidly as the global demand for fish consumption continues to increase. A significant loss within the aquaculture industry is due to pathogen transmission within the farm systems. These pathogens are mitigated through various methods that are not cost effective or have limited protection. The most common method of pathogen mitigation is through oil-based injection vaccines as they provide even protection across vaccinated fish and provides the longest protection compared to other vaccination methods. These oil-based injection vaccines are not without their flaws as they …

Designing And Modeling A Fail-Safe Mechanism To Be Used In Attachment Of A Transcutaneous Femoral Implant To A Prosthetic Device, Emma Sperry

Electronic Theses and Dissertations

Amputations are quite common and even modern prosthetic devices are plagued by problems. There are approximately 2 million people living with limb loss in the U.S. and on average 185,000 amputations occur yearly. Common attachment mechanisms for external prosthetic components to a residual limb, that is, sockets, pose numerous challenges. Issues include skin irritation, discomfort, socket fit issues, and immobility. Issues include skin irritation, discomfort, socket fit issues, and immobility. Transcutaneous implants have great potential as a connection method for external prosthetic components to a residual limb but because the implants are typically solid, they correlate to extremely high infection …

Analyzing Pseudomonas Aeruginosa With Bacteriophage Tags Using Photoacoustic Flow Cytometry, Jennifer C. Schinke

Electronic Theses and Dissertations

The number of daily bacterial infections is climbing and the CDC explains that this is due to the antibiotic-resistant threat in the United States. Finding a faster way of bacterial identification is necessary as it currently takes 1-4 days for a medical lab to culture and identify bacteria. Photoacoustic flow cytometry (PAFC) can be used as an alternative method resulting in swift identification within an hour (Edgar, 2019). Pseudomonas aeruginosa, cell line PA01, will be coated in up to a few hundred red dyed phages making it detectible by the photoacoustic flow cytometry system. Bacteriophages (phages) are viruses that …

Photodynamic Therapy To Treat Triple Negative Breast Cancer In Vitro, Hunter S. Warren

All Theses

Triple negative breast cancer (TNBC) is the most resilient form of breast cancer, being one of the leading causes of death for women and making up 7% of all cancer deaths. Photodynamic therapy (PDT) offers a minimally invasive solution to TNBC as a passive-targeting treatment that reduces the need for other well established yet harsh treatments that can be taxing on the patient. PDT involves the use of a high-energy red light on the area of a tumor injected with photosensitizers (PS) that generate reactive oxygen species (ROS) in the tumor, triggering cell death. The PS tetra(hydroxyphenyl)chlorin (m-THPC) was used …

Investigating The Potential Of A Cell-Based Gene Editing Therapy For Inherited Metabolic Liver Disease, Ilayda Ates

All Dissertations

Inherited metabolic diseases (IMDs) affecting the liver are relatively rare but collectively have a prevalence of 1 in 800 live births. These diseases result from autosomal recessive single-gene mutations, leading to organ dysfunction and potentially fatal consequences if left untreated. One potential therapeutic strategy for IMDs of the liver involves using CRISPR-Cas9-induced loss of function mutations. However, translating this approach into the clinic is limited by the need for safe and effective CRISPR delivery methods. Adeno-associated viral vectors (AAVs), commonly used for CRISPR delivery, are associated with significant safety and efficacy concerns, including risks for immunogenicity, off-target mutagenesis, and genotoxicity …

Exploring Versatile Glycosyltransferases From Microorganisms For Natural Product Biosynthesis, Jie Ren

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

This dissertation is mainly focused on exploring versatile glycosyltransferases from different microorganisms with the purpose of biosynthesizing bioactive natural product glycosides through microbial fermentation. This engineered biosynthesis approach is environmentally friendly, safe, and efficient compared with plant extraction, chemical synthesis, and enzymatic synthesis. Additionally, we applied these characterized glycosyltransferases as efficient biocatalytic tools to produce novel glycosides to expand the chemical repertoire of nature. These novel compounds showed improved water solubility and some of them exhibited enhanced stability and biological activity, which laid the foundation for the development of new therapeutic agents.

In my dissertation research, I have discovered two …

Environmentally Friendly New Catalyst Using Waste Alkaline Solution From Aluminum Production For The Synthesis Of Biodiesel In Aqueous Medium, Sandro L. Barbosa, David Lee Nelson, Lucas Paconio, Moises Pedro, Wallans Torres Pio Dos Santos, Alexandre P. Wentx, Fernando L. P. Pessoa, Foster A. Agblevor, Daniel A. Bortoleto, Maria B. De Freitas-Marques, Lucas D. Zanatta

Biological Engineering Faculty Publications

Red mud (RM) is composed of a waste alkaline solution (pH = 13.3) obtained from the production of alumina. It contains high concentrations of hematite (Fe₂O₃), goethite (FeOOH), gibbsite [Al(OH)₃], a boehmite (AlOOH), anatase (Tetragonal–TiO₂), rutile (Ditetragonal dipyramidal–TiO₂), hydrogarnets [Ca₃Al₂(SiO₄)_3-x(OH)_4x], quartz (SiO₂), and perovskite (CaTiO₃). It was shown to be an excellent catalytic mixture for biodiesel production. To demonstrate the value of RM, an environmentally friendly process of transesterification in aqueous medium using waste cooking oil …

Optical Perturbation Of Protein Kinase A Activity Via Photoactivatable Inhibitor Peptides, Peter Chen

McKelvey School of Engineering Theses & Dissertations

Protein Kinase A (PKA) plays important roles in diverse biological processes such as sleep, long term memory, and synaptic plasticity. In addition, PKA also acts as an integrator of neuromodulator signaling though G protein-coupled receptor activation. However, despite genetic knockout and pharmacological inhibition experiments that demonstrate the importance of PKA, it is unclear where, when, or how PKA plays these roles in cellular physiology and behavior. In order to better understand the function of PKA in these processes, and how neuromodulator signaling drives complex behavioral changes, there exists a need for a method to selectively activate/inactivate PKA with high spatial …

Dual Color Optogenetic Control For Analyzing Cardiac Function In Drosophila, Jiantao Zhu

McKelvey School of Engineering Theses & Dissertations

Prolonged consumption of carbohydrate-rich diets and immobile lifestyles frequently cause metabolic disorders and obesity and, as a result, may lead to progressive heart dysfunction among broad social groups of the population. Drosophila melanogaster serves as an essential model organism in cardiovascular disease research due to conserved physiological and genomic traits shared with humans, its genetic and molecular toolbox versatility, and cost-effective maintenance. Here, we combine optogenetics and optical coherence tomography to study cardiovascular function in D. melanogaster. A new optogenetic pacing system has been developed, employing a transgenic line carrying two opsins: ChR2 and NpHR2.0. A custom-built hardware setup …

Continuous Bioprocessing: Technology For Next-Generation Biopharmaceutical Manufacturing Development Of A Python-Coded Bench-Scale Raman-Based Continuous Bioprocess Platform, Christine Urrea

KGI Theses and Dissertations

Current industrial practices for producing biopharmaceuticals include fed-batch production with batch isolation and purification. Nonproductive hold-up steps and manual offline measurements are common in batch processing which increases processing time and contributes to a high cost of production. Current market trends and cost pressures in the biopharmaceutical industry are creating a push to innovate bioprocessing platforms. Continuous bioprocessing has been considered a solution to the current limitations of batch production of biopharmaceuticals. Continuous bioprocessing involves intensifying individual processing steps by eliminating hold-up steps through a continuous operation to increase productivity, which results in advantages such as lower capital and production …

Consolidated Chamber Design And Protocol For Olfactory Conditioning Assay With Drosophila Melanogaster, Sasha Bronovitskiy, Andres Castillo, Michael Yan, Fang Ju Lin

Journal of the South Carolina Academy of Science

The olfactory conditioning assay is widely used in Alzheimer’s disease research to quantify learning and memory in Drosophila melanogaster. The assay tests ability to recall an aversive conditioned stimulus of scent paired with electrical shock when presented a choice between shock-associated and unrelated scents. The T-maze, a commonly used apparatus for olfactory conditioning assays, employs an elevator mechanism to transfer live flies from the shock-delivering training chamber to the scent selection point. This elevator mechanism is known to cause fly casualty. T-mazes are not commercially available and often difficult to reproduce. Other existing variations of olfactory conditioning apparatuses use …

An Integrated Experimental And Modeling Approach To Design Rotating Algae Biofilm Reactors (Rabrs) Via Optimizing Algae Biofilm Productivity, Nutrient Recovery, And Energy Efficiency, Gerald Benjamin Jones

All Graduate Plan B and other Reports, Spring 1920 to Spring 2023

Microalgae biofilms have been demonstrated to recover nutrients from wastewater and serve as biomass feedstock for bioproducts. However, there is a need to develop a platform to quantitatively describe microalgae biofilm production, which can provide guidance and insights for improving biomass areal productivity and nutrient uptake efficiency. This paper proposes a unified experimental and theoretical framework to investigate algae biofilm growth on a rotating algae biofilm reactor (RABR). The experimental laboratory setups are used to conduct controlled experiments on testing environmental and operational factors for RABRs. We propose a differential-integral equation-based mathematical model for microalgae biofilm cultivation guided by laboratory …

A Comparison Of Optical Measurement Methods For The Growth Of S. Cerevisiae, Jackson Black

Chemical Engineering Undergraduate Honors Theses

Genetic engineering of living organisms provides the opportunity to express and harvest different proteins from cell surfaces. Yeast (S. cerevisiae) is one such organism and is capable of being grown on an industrial scale. Cellular concentration is an important parameter to monitor while fermentation processes are underway, in order to control the environment inside the growth medium and maximize yields. Spectrophotometry is a conventional method for measuring concentration, but is limited by a narrow absorbance range, and the need for on-site periodic sampling. A continuous method of measurement, as provided by Bug Labs BE2100 non-invasive biomass monitor, would …

Automation Of Life Cycle Assessment, Jacob Hickman

Graduate Theses and Dissertations

An automation program, named Jacob LCA, was created to help perform life cycle assessment (LCA). The program uses a template file to perform controlled and consistently ordered actions with the LCA program, SimaPro, and effectively removes the need for manual user input. It can be set to run using data from one or more life cycle inventory (LCI) files, which allows for rapid iteration and testing of data. It also partially addresses some of the limitations of LCA by establishing a procedure through which temporal and spatial variations in data can be integrated into LCI files and then passed to …

Preparing Homogenous Composites Of Collagen And Cellulose Nanocrystals For Tissue Engineering Research, Zachary Stanley

Biological and Agricultural Engineering Undergraduate Honors Theses

Advancements in medicine and our understanding of stem cells have led to a greater emphasis on further developing research focused on tissue engineering. This research has led to the rise of both two-dimensional and three-dimensional scaffolds that can be utilized to repair bone, skin, vascular, and potentially even nervous tissue. One of the prominent compounds used in modern scaffolds is collagen-based hydrogels due to their low antigenicity and ability to provide structure to cells. There is potential to further improve upon this three-dimensional scaffold by incorporating cellulose nanocrystals (CNCs) into a composite hydrogel with collagen. The addition would increase the …

Regenerative Medicine For Tendon/Ligament Injuries: De Novo Equine Tendon/Ligament Neotissue Generation And Application, Takashi Taguchi

LSU Doctoral Dissertations

Tendon and ligament injuries are debilitating conditions across species. Poor regenerative capacities of these tissues limit restoration of original functions. The first study evaluated the effect of cellular administration on tendon/ligament injuries in horses using meta-analysis. The cellular administration was effective in restoring ultrasonographic echogenicity and increasing vascularity during early phase of healing. Additionally, it improved microstructural organization of healed tissue in terms of cellularity and fiber alignment. However, the study did not support its use for increasing rate of return to performance, expression/deposition of tendon-specific genes/proteins, or mechanical properties.

The findings led to the second study that engineered implantable …

Engineered Production Of Bioactive Polyphenolic O-Glycosides, Jie Ren, Caleb Don Barton, Jixun Zhan

Biological Engineering Faculty Publications

Polyphenolic compounds (such as quercetin and resveratrol) possess potential medicinal values due to their various bioactivities, but poor water solubility hinders their health benefits to humankind. Glycosylation is a well-known post-modification method to biosynthesize natural product glycosides with improved hydrophilicity. Glycosylation has profound effects on decreasing toxicity, increasing bioavailability and stability, together with changing bioactivity of polyphenolic compounds. Therefore, polyphenolic glycosides can be used as food additives, therapeutics, and nutraceuticals. Engineered biosynthesis provides an environmentally friendly and cost-effective approach to generate polyphenolic glycosides through the use of various glycosyltransferases (GTs) and sugar biosynthetic enzymes. GTs transfer the sugar moieties from …

Sea-Phages Course-Based Undergraduate Research Experience For Creating A Biotechnology Workforce Development Pipeline, Daphne Fauber, Kari Clase, Carol Weaver

Graduate Industrial Research Symposium

Purdue University has been a member of the SEA-PHAGES (Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science) program since 2011. This program, created in conjunction with the Howard Hughes Medical Institute (HHMI), facilitates undergraduate curriculum for the authentic discovery of novel bacteriophages within the classroom. Since joining the program, undergraduates at Purdue have harnessed wet lab and bioinformatics principles to contribute over 200 previously uncharacterized bacteriophages and 25 novel genomes to the wider scientific literature. The SEA-PHAGES classes at Purdue have resulted in tangible professional deliverables for students through conference presentations and publications. Student outcomes also include transferable skills …