Biochemical and Biomolecular Engineering Commons^™

Purifying Circular Rna Therapeutics, Karen Guillen-Cuevas

All Dissertations

Circular RNA (circRNA) has emerged as a promising therapeutic modality due to its enhanced stability and resistance to exonuclease degradation compared with linear mRNA. However, its stability and functionality depend strongly on achieving high purity, and current methods such as size-exclusion chromatography suffer from peak overlap, low yields, and poor scalability. This dissertation addresses these limitations by developing ultrafiltration-based strategies to purify circRNA directly from in vitro transcription (IVT) and self-splicing (circularization) reactions. First, the feasibility of ultrafiltration was demonstrated using polyethersulfone membranes, where sieving coefficients and critical flux values of circRNA, precursor RNA, and nicked RNA were measured to …

Cultivation Of Botryococcus Braunii For The Production Of Hydrocarbons Suitable For Fuel Use, Bryan C. Carroll

All Theses

Energy security, rural poverty, and climate change are pressing issues of our time. Biofuels provide a solution to these issues, with a focus on sustainable aviation fuel, SAF, due to compatibility with aircraft infrastructure and energy density. This research aims to review and produce knowledge about a specific microalga, Botryococcus braunii, for its potential for SAF. First a literature review on the process was conducted followed by an experimental study on the impact of aqueous media and inorganic carbon its growth and hydrocarbon content. The literature review found the process consists of cultivation followed by lipid extraction or hydrothermal …

Impact Of Cysteine And Tyrosine Dipeptides On Cho Cell Performance In A Perfusion Mimic, Corrin L. Pruitt

All Theses

Perfusion cell cultures typically achieve higher cell densities and generate higher volumetric productivities than fed-batch cultures due to continuous nutrient supply and spent media removal. Despite these advantages, perfusion cell cultures remain underutilized for licensed product manufacturing, primarily due to the lack of small-scale perfusion models for high-throughput process development and the complexities involved in media formulation capable of supporting high cell densities during long-term continuous operation. To avoid nutrient limitation at high cell densities, current perfusion processes rely on using higher perfusion rates, which results in significant media wastage and downstream product dilution. Therefore, there has been an effort …

Development Of Translational Microscale Systems To Interrogate How Biophysical And Biochemical Cues Alter The Phenotype Of Hormone Positive Breast Cancer, Braulio Ortega Quesada

All Dissertations

Cancer is a complicated disease and one in every three diagnoses are women with breast cancer. Recent research shows that the progression of cancer depends strongly on interactions with other non-cancerous cells and non-cellular components. Metastasis, the spread of cancer to other parts of the body, is a key step in cancer progression and makes treatment harder, leading to poor response to treatments culminating in death in ~90% of patients. This dissertation focused on creating a series of microdevices as novel pre-clinical models of breast cancer. Two different devices were fabricated to (1) study how exposing cancer cells to the …

Magnetic Resonance Imaging Trackable Pathology-Triggered Polymersomes Toward Enzyme Replacement Theranostics For Gm1 Gangliosidosis, Dorian Foster

All Dissertations

This dissertation investigates the development and optimization of pathology-responsive polymersomes for simultaneous enhanced magnetic resonance imaging (MRI) and enzyme replacement therapy (ERT) in the treatment of GM1 gangliosidosis (GM1). While therapeutic strategies exist for similar, non-neuropathic lysosomal storage disorders, implementation towards GM1 faces significant challenges due to the blood-brain barrier.

Herein, we developed and characterized a range of low molecular weight hyaluronic acid-b-polylactic acid (HA-PLA) polymersomes (PSs) capable of encapsulating therapeutic enzymes in their hydrophilic core. These polymersomes exhibit pathophysiology-triggered responsiveness, degrading in the presence of acidic conditions, which is characteristic of lysosomes, and enzymes such as hexosaminidase A, which …

Genetically-Encoded Optical Barcodes For Single-Cell Analysis, Daniel Pritko

All Theses

Cell barcodes are capable of being used to answer many different biological questions. They have been used to track the lineage of cells to identifying the function of a gene. While there are multiple different methods to creating cell barcodes, they are limited in their scalability and application. In a previous publication we propose and computationally prove an optical single-cell barcoding method that bridges fast and scalable readouts with the benefits of genetic encoding. In this approach fluorescent proteins (fps) are combined to form fluorescent barcodes that can then be analyzed using a spectral flow cytometer. Here, we test the …

Fabrication And Characterization Of Lignin–Pva Hydrogels With Tunable Network Structures, Keturah Bethel

All Dissertations

The ability to directly tune the crosslinked network structure of hydrogels is crucial for their functional applications in various fields, such as water filtration, protein separation, and tissue engineering. By controlling the crosslink density of the hydrogel, one can directly alter the mesh size – i.e., the end-to-end distance between crosslink junctions – and, subsequently, directly alter the hydrogel performance. This work discusses the fabrication and characterization of soft composites containing the biopolymer, lignin, are discussed. Precisely, physically-crosslinked composite lignin–Poly(vinyl alcohol) (PVA) hydrogels were fabricated via the freeze-thaw (F/T) pathway, whereby solutions containing specified amounts of PVA and lignin were …

Fundamental Study Of Nonlinear Electrophoresis, Joseph Armakan Bentor

All Dissertations

Classical electrophoretic theory describes the linear response of particles suspended in Newtonian fluids under weak electric fields. When the electric field exceeds this weak limit, a nonlinear response arises due to non-uniform surface conduction over the curved particles. This nonlinear behavior introduces dependencies on fluid and particle properties not considered in the classical theory, offering potential advantages for microfluidic particle manipulation. While this phenomenon has been extensively studied theoretically and numerically in Newtonian fluids, experimental investigations have been relatively limited.

Fluid rheology can significantly alter particle dynamics under applied electric fields. Rheological properties like shear-thinning and elasticity which are not …

Elucidating The Mechanical And Transport Properties Of Lignin-Based Hydrogel Composites, Nicholas Gregorich

All Dissertations

The use of lignin in the fabrication of soft composites has become an emerging area of research in polymer science and polymer chemistry. These lignin-based materials present numerous benefits, notably, a reduction in the use of petroleum-based precursor, improved structural benefits to otherwise soft host polymers, as well as the inherent antimicrobial and antioxidant properties of lignin, making it suitable for biomaterials. Herein, we present two chemical reaction pathways of incorporating lignin that was fractionated and cleaned using the Aqueous Lignin Purification with Hot Agents (ALPHA) process into poly(vinyl alcohol) (PVA) hydrogel composites for aqueous-based separations. By leveraging the ALPHA …

Fluorescence Multiplexing With Combination Probes For Biological And Diagnostic Applications, Madeline Mccarthy

All Dissertations

Cancer refers to a group of diseases containing more than 200 different subtypes. Cancer is a heterogeneous disease by nature, meaning that there are differences among tumors of the same type in different patients, and there are differences among cancer cells within a single tumor of one patient. Since cancer is not a single disease, nor does it have a single cause, it proves to be incredibly hard to diagnose and treat. The ability to study cellular markers, cell and tissue spatial arrangement, and gene function are all integral parts of cancer diagnostic and treatment efforts.

Here, I first present …

Metabolic Engineering Of Yarrowia Lipolytica For Enhanced Peroxisomal Production Of Polyhydroxyalkanoates, Michael Spagnuolo

All Dissertations

Traditional chemical processes are made inefficient by the generation of side products and reactions that fail to reach completion. Bioprocesses, on the other hand, lose product potential due to the necessity of growing the organism required to produce the desired compounds. The field of metabolic engineering often seeks to alter this balance between product formation and cell growth to generate more product from the same quantity of feed (reagent). In addition to balance, such organisms may also be engineered to produce the desired products from nontraditional substrates, such as waste compounds. In resource-poor environments, the ability to produce a wanted …

Development Of Enzyme-Responsive Polymersomes As A Drug Delivery System For Gm1 Gangliosidosis, Bipin Chakravarthy Paruchuri

All Dissertations

GM1 gangliosidosis is a lysosomal storage disorder caused by deficiency of β-galactosidase (βgal) and subsequent accumulation of GM1 ganglioside in lysosomes. The rare nature of this disorder presents challenges with prognosis and treatment. Enzyme replacement therapy (ERT) can effectively treat systemic deficiencies, but the intravenously administered enzyme cannot cross the blood-brain barrier (BBB) to treat the central nervous system. A delivery system to encapsulate and deliver the enzyme can facilitate enzyme transport across the BBB with suitable surface modifications. One of the pathological aspects of GM1-affected cells is the upregulation of the lysosomal enzyme hexosaminidase A (HexA). In this dissertation, …

Profiling And Engineering The Unfolded Protein Response In Therapeutic Protein-Producing Cho Cell Lines, Dyllan Rives

All Dissertations

Industrial Chinese hamster ovary (CHO) production of therapeutics requires cell lines with high secretory capacity to avoid an accumulation of improperly folded proteins, or endoplasmic reticulum (ER) stress. This presents a challenging engineering bottleneck. The unfolded protein response (UPR) is initiated to overcome ER stress and reestablish homeostasis. In this dissertation, the impacts of ER stress and the UPR on protein production in mammalian cells are detailed, and both selection- and rational-based strategies for enhancing the ER stress response in productive CHO cell lines are reviewed. This project aims to expand on recent research efforts for engineering ER stress-related responses …

Effects Of Continuous In Situ Low-Dose Ionizing Radiation On Microorganisms, Molly E. Wintenberg

All Dissertations

Precise detection and monitoring of nuclear fuel cycle, enrichment, and weapon development activities are critical for supporting warfighter preparation in chemical, biological, radiological, nuclear, and explosives (CBRNE) operations, clandestine activities, and nuclear compliance. A biological sensing system could serve as an alternative to traditional detection methods by using organic material naturally present in the environment to discreetly detect residual trace nuclear material. Microorganisms provide an optimal platform for an alternative sensing system; however, their response to low levels of ionizing radiation is poorly characterized. Combining the power of next-generation sequencing and transcriptomic analysis, this dissertation takes an approach to obtain …

Towards Understanding Protein Immobilization Rules Through Site-Specific Covalent Immobilization Of T4 Lysozyme, Maxwell Hilbert

All Dissertations

Soluble enzymes have the unique ability to assist the conversion of complex substrates in fewer steps compared to conventional chemical synthesis; however, when immobilized to a surface, the insoluble enzyme's activity and stability can suffer in its new environment. To improve upon future immobilized enzyme efficacy, a fundamental understanding of the interactions across the enzyme, linker, and surface during covalent, site-specific immobilization that can be detrimental to its activity is required. More specifically, using a well-characterized and model enzyme, T4 lysozyme (T4L), 28 different cysteine attachment points' effects on site-specifically immobilized activity are examined. Different combinations of heterobifunctional amine-to-sulfhydryl crosslinkers …

Carbon Nanotube And Cellulose Nanocrystal Hybrid Films, Mingzhe Jiang, Robert Seney, Paul Charles Bayliss, Christopher L. Kitchens

Publications

The use of cellulose nanocrystals (CNC) in high performance coatings is attractive for micro-scale structures or device fabrication due to the anisotropic geometry, however CNC are insulating materials. Carbon nanotubes (CNT) are also rod-shaped nanomaterials that display high mechanical strength and electrical conductivity. The hydrophobic regions of surface-modified CNC can interact with hydrophobic CNT and aid in association between the two anisotropic nanomaterials. The long-range electrostatic repulsion of CNC plays a role in forming a stable CNT and CNC mixture dispersion in water, which is integral to forming a uniform hybrid film. At concentrations favorable for film formation, the multiwalled …

Development Of Multimodal Membrane Adsorbers For Antibody Purification Using Atom Transfer Radical Polymerization, Juan Wang, Scott M. Husson

Graduate Research and Discovery Symposium (GRADS)

No abstract provided.

Carbon Fibers Derived From Sustainable Precursors, Meng Zhang, Jing Jin, Amod A. Ogale

Chemical and Biomolecular Graduate Research Symposium

No abstract provided.

Producing A Liquid-Lignin Phase From Kraft Black Liquor: Phase Behavior And Structural Characterization, Julian Velez, Mark C. Thies

Chemical and Biomolecular Graduate Research Symposium

No abstract provided.

Density Functional Theory-Based Modeling Of Catalyzed Water Purification, Lizzie Bollman

Chemical and Biomolecular Graduate Research Symposium

No abstract provided.

Effect Of Co Adsorption And Coverage On Ethanol Production From Syngas, Anuradha Gundamaraju, Ming He, David A. Bruce

Graduate Research and Discovery Symposium (GRADS)

In the future, the availability of reliable alternative fuels will be crucial for any country to become energy independent. One such alternative is ethanol as it can be used both as a fuel and as a fuel additive. Most of the ethanol produced in the world today is derived from biomass. The biomass feedstocks and fermentation broths used in ethanol production both contain high amounts of water and therefore, the energy efficiency of the process is lessened by product separation processes (azeotropic separation of water and ethanol) that are non-trivial and highly inefficient (due to the evaporation of water). An …

Template Free-Synthesis Of Polypyrrole Microtubes For Supercapacitor Electrodes, Kryssia P. Diaz, Mark E. Roberts

Graduate Research and Discovery Symposium (GRADS)

The purpose of this work is to develop a simple, scalable and template-free method to synthesize conducting polymer nano/micro-structures for supercapacitor electrodes. The microstructure and electrochemical properties of structure polypyrrole on various mesh substrates is investigated.

Recovering A Liquid-Lignin Phase From Paper Mill Black Liquors, Julian Velez, Adam Klett, Mark C. Thies

Graduate Research and Discovery Symposium (GRADS)

No abstract provided.

Analysis Of Solvation Model, Adsorption Site, And Adsorbate Coverage Effects On Adsorption Energies At The Anode In Direct Methanol Fuel Cells, Cameron J. Bodenschatz, Rachel B. Getman

Graduate Research and Discovery Symposium (GRADS)

No abstract provided.

Synthesis And Characterization Of Extractive Scintillating Resin For Ultra-Trace-Level Quantification Of Uranium In Aqueous Media, C Duval, V Bliznyuk, A Seliman, T Devol, S Husson

Graduate Research and Discovery Symposium (GRADS)

The detection and quantification of radionuclides in aqueous media is of interest to both the Environmental Protection Agency, for matters of public health, and international organizations like the Comprehensive Test Ban Treaty Organization, that use environmental samples to investigate claims of illicit nuclear activities. The current method of quantification involves batch style analytical techniques which utilize bulky instruments. Portable, flow cell detectors utilizing extractive scintillating resin with physically sorbed extractants and fluorophores have been developed; however, this resin shows poor long term stability as the active components leach from the resin over time. There is a need to develop chemically …

Roll-To-Roll Synthesis Of Vertically Aligned Carbon Nanotubes For Electrical Double Layer Capacitors, Margarita R. Arcila-Velez, Jingyi Zhu, Anthony Childress, Mehmet Karakaya, Ramakrishna Podila, Apparao M. Rao, Mark E. Roberts

Graduate Research and Discovery Symposium (GRADS)

No abstract provided.

Effect Of Surface Parameters On Interfacial Water Film Behavior, Brittany Glatz, Luke Rhym, Sapna Sarupria

Graduate Research and Discovery Symposium (GRADS)

Vapor-to-liquid and liquid-to-solid transitions on mineral surfaces are the primary pathways for phase transitions in atmospheric water. These phase transitions affect the microphysics of clouds and have significant effects on the weather and climate. Our overall goal is to elucidate the mechanisms through which surfaces affect these transitions, and develop predictive abilities to correlate surface properties to the thermodynamics and kinetics of the phase transitions. In this work, we use molecular dynamics simulations to study the structure, and dynamics of water near kaolinite-like surfaces. Kaolinite is the most abundant mineral dust in the atmosphere. We specifically investigate the effect of …

Carbon Fibers Derived From Pan/Bio-Based Bicomponent Precursor, Jing Jin

Graduate Research and Discovery Symposium (GRADS)

No abstract provided.

Optimization Of Pyrochlore Catalysts For Dry Reforming Of Methane, Felipe Polo-Garzon, Ming He, David A. Bruce

Graduate Research and Discovery Symposium (GRADS)

No abstract provided.

2014 Chemical And Biomolecular Graduate Research Symposium Program, Clemson University

Chemical and Biomolecular Graduate Research Symposium

Program for the 2014 Graduate Research Symposium in Holmes Ballroom - Clemson House.