Biochemical and Biomolecular Engineering Commons^™

Characterization Of Lignin Structural Variability And The Associated Application In Genome Wide Association Studies, Nathan D. Bryant

Doctoral Dissertations

Poplar (Populus sp.) is a promising biofuel feedstock due to advantageous features such as fast growth, the ability to grow on marginal land, and relatively low lignin content. However, there is tremendous variability associated with the composition of biomass. Understanding this variability, especially in lignin, is crucial to developing and implementing financially viable, integrated biorefineries. Although lignin is typically described as being comprised of three primary monolignols (syringyl, guaiacyl, p-hydroxyphenyl), it is a highly irregular biopolymer that can incorporate non-canonical monolignols. It is also connected by a variety of interunit linkages, adding to its complexity. Secondary cell wall …

Understanding Lignin’S Fast Pyrolysis Through Examination Of The Thermolysis Mechanisms Of Model Oligomers, Ross Wesley Houston

Doctoral Dissertations

The lignocellulosic biorefinery is a visionary concept that endeavors to provide an alternative to fossil-based refineries by producing biobased fungible fuels and specialty chemicals almost exclusively derived currently from petroleum refineries. This vision of the lignocellulosic biorefinery can only be realized if all fractions of lignocellulosic biomass are efficiently deconstructed and valorized to generate a diverse portfolio of products to sustain it against market vicissitudes. Of the three main structural constituents of lignocellulosic biomass (i.e., cellulose, hemicellulose, and lignin), lignin is underutilized despite being the most abundant renewable source of aromatic platform chemicals, representing a growing 250 billion dollar market. …

A Rapid And Ultra-Sensitive Biosensing Platform Based On Tunable Dielectrophoresis For Robust Poc Applications, Yu Jiang

Doctoral Dissertations

With the ongoing pandemic, there have been increasing concerns recently regarding major public health issues such as abuse of organophosphorus compounds, pathogenic bacterial infections, and biosecurity in agricultural production. Biosensors have long been considered a kernel technology for next-generation diagnostic solutions to improve food safety and public health. Significant amounts of effort have been devoted to inventing novel sensing mechanisms, modifying their designs, improving their performance, and extending their application scopes. However, the reliability and selectivity of most biosensors still have much to be desired, which holds back the development and commercialization of biosensors, especially for on-site and point-of-care (POC) …

Elucidating Mammalian Cellular Responses To The Uptake Of Nanoparticles (Nps), Pathogens, And Lipoproteins: Similarities And Differences, Monireh Asoudeh

Doctoral Dissertations

Soft poly-ethylene-glycol (PEG)-based soft nanoparticles (NPs) including cylindrical (CNPs) micelles, spherical (SNPs) micelles, and lipid bilayer vesicles (LNPs) are thought to be treated as foreign objects by mammalian phagocytes. If this hypothesis is true, NPs should trigger a proinflammatory, autophagic phenotype that is similar to the one seen when macrophages phagocytose pathogens or when macrophage surface expressed proteins bind pathogen surface factors such as lipopolysaccharide (LPS). Here, we show that macrophage responses to the above NPs are almost completely unique from those triggered by group A streptococcus (GAS) pathogens (JRS4 cells) and LPS. Instead, macrophages treat these soft NPs more …

Crowd Control: Regulating The Spatial Organization Of Biopolymers And Gene Expression By Macromolecular Crowding, Gaurav Chauhan

Doctoral Dissertations

The intracellular environment is crowded with macromolecules that can occupy a significant fraction of the cellular volume. This can give rise to attractive depletion interactions that impact the conformations and interactions of biopolymers, as well as their interactions with confining surfaces. We used computer simulations to study the effects of crowding on biologically-inspired models of polymers. We showed that crowding can lead to attractive interactions between two flexible ring polymers, and we further characterized the adsorption of both flexible and semiflexible polymers onto confining surfaces. These results indicate that crowding-induced depletion interactions could play a role in the spatial organization …

Interactions Between Soft Nanoparticles And Mammalian Cells, Mitchell Raith

Doctoral Dissertations

Nanoparticles have been of interest to the pharmaceutical industry since the 1980s. The first FDA approved nanoparticle-based therapies included liposomal anesthesia agents. Since then, the amount of FDA-approved nanoparticle therapies remains low. This is because nanoparticle-patient interactions can be very complex and are not well understood. Complicating factors also include increasing obesity rates among the patient population and many small animal pre-clinical trials are completed with healthy, lean animals. The biochemical differences between lean and obese patients prevents early studies from accurately predicting nanoparticle clinical behaviors. Many nanoparticles fail in trails. In this thesis, I aimed to uncover how nanoparticles …

Improving The Biocompatibility Of The Bio-Inorganic Interface For Enhanced Photosystem I-Based Biophotovoltaic Device Performance, Alexandra H. Teodor

Doctoral Dissertations

The world’s energy demands are projected to increase by nearly 50% by the year 2040, and consumption of carbon-based fuels continues to release greenhouse gases such as carbon dioxide and methane into the atmosphere. This has been causally linked with climate change and increased extreme weather events, which has been further linked to adverse health outcomes and negative effects on biodiversity, food security, and increased disease transmission. Clearly, there is a need for a sustainable, carbon-free, and cost-effective method of energy production to meet growing energy production demands. The sun irradiates Earth’s surface annually with ~80,000 terawatts (TW), making solar …

Study Level Recovery Processes Of Thorium And Several Rare Earth Elements From Monazite Ore, Makayla Hyde, Jaclyn Choate

EURēCA: Exhibition of Undergraduate Research and Creative Achievement

Monazite ore is composed of several minerals including several rare earth element (REE) and thorium phosphates. Many past research projects have looked at the extraction of REE from monazite ore but have discarded the thorium phosphate compound as waste. Since thorium could be a possible fuel for state-of-the-art future nuclear reactors, this research focuses on a way to recover thorium from the monazite ore. The overall purpose of this research is to develop a conceptual recovery process that recovers thorium dioxide from monazite ore. In some parts of the world where uranium sources are limited; then, thorium could be used …

Elucidating Mechanisms And Genotypes Underlying Robust Phenotypes In Yarrowia Lipolytica, Caleb M. Walker

Doctoral Dissertations

Robustness is an important phenotype for bioenergy microbes to acquire but is difficult to engineer. Hence, tools for engineering microbial robustness are critical to unlock novel phenotypes for innovative bioprocessing strategies. The oleaginous yeast, Yarrowia lipolytica, is an exceptionally robust microbe that can tolerate stressful environments, assimilate a wide range of substrates, and produce high-value chemicals. In this doctoral dissertation, the impacts of systems biology and metabolic engineering to reveal mechanisms and identify genotypes- underlying robust phenotypes are addressed.

The first approach employs adaptive laboratory engineering to generate a platform strain by which to study superior robust mechanisms. This …

Engineering Modularity Of Ester Biosynthesis Across Biological Scales, Hyeongmin Seo

Doctoral Dissertations

Metabolic engineering and synthetic biology enable controlled manipulation of whole-cell biocatalysts to produce valuable chemicals from renewable feedstocks in a rapid and efficient manner, helping reduce our reliance on the conventional petroleum-based chemical synthesis. However, strain engineering process is costly and time-consuming that developing economically competitive bioprocess at industrial scale is still challenging. To accelerate the strain engineering process, modular cell engineering has been proposed as an innovative approach that harnesses modularity of metabolism for designing microbial cell factories. It is important to understand biological modularity and to develop design principles for effective implementation of modular cell engineering. In this …

Approaches To Studying Bacterial Biofilms In The Bioeconomy With Nanofabrication Techniques And Engineered Platforms., Michelle Caroline Halsted

Doctoral Dissertations

Studies that estimate more than 90% of bacteria subsist in a biofilm state to survive environmental stressors. These biofilms persist on man-made and natural surfaces, and examples of the rich biofilm diversity extends from the roots of bioenergy crops to electroactive biofilms in bioelectrochemical reactors. Efforts to optimize microbial systems in the bioeconomy will benefit from an improved fundamental understanding of bacterial biofilms. An understanding of these microbial systems shows promise to increase crop yields with precision agriculture (e.g. biosynthetic fertilizer, microbial pesticides, and soil remediation) and increase commodity production yields in bioreactors. Yet conventional laboratory methods investigate these micron-scale …

Rapid Design, Construction, And Validation Of Synthetic Metabolic Pathways In A Modular Escherichia Coli (Chassis) Cell, Jong-Won Lee

Doctoral Dissertations

Current strain development has been hindered by the vast biochemical space in nature. The concept of modular cell design has been invented to enable rapid and predictable construction of multiple optimal production strains for efficient production of a large variety of biochemicals with minimal experimental effort. While modular cell design principles have been successfully validated in some cases, its development is still limited by the small library of the production modules demonstrated.

The goals of this thesis are i) to establish a framework for rapid design, construction, and validation of production modules to explore a large space of molecules (e.g., …

Lithium Recovery Process From Spent Batteries, Nicholas A. Ross, Lacey Roberts, Jordan Leith, Woodi Woodland

Chancellor’s Honors Program Projects

No abstract provided.

Protein Engineering Potential Inhibitor Of Detrimental Immune Responses, Nathaniel L. Blalock, Eric T. Boder, Liang Fang

EURēCA: Exhibition of Undergraduate Research and Creative Achievement

On the surface of immune cells, class II major histocompatibility complex proteins (MHCII) present antigenic peptides for CD4+ T cell recognition, which initiate a variety of antigen-specific immune responses such as antibody response or cytotoxic T cell activation. In people with with auto-immune diseases including but not limited to type 1 diabetes, multiple sclerosis, and rheumatoid arthritis, detrimental immune responses occur after the presentation of antigenic peptides. A single-chain, minimal MHCII (scm-MHCII) has been designed to retain its function as an antigen-presenting protein with a simplified structure that can be easily produced and manipulated in a laboratory by recombinant microbial …

Understanding Conformational Regulation Of The Integrin I-Domain For Design Of Chimeric Protein Switches, Niall Phelan Terry, Liang Fang, J Vincent Price, Eric T. Boder Dr.

EURēCA: Exhibition of Undergraduate Research and Creative Achievement

Within all complex biological processes intricate proteins are expressed to complete every niche and necessary task. Many express multiple allosterically regulated conformational states, with protein function regulated by effector molecules and other ligands. One such protein is the LFA-1 surface integrin protein and its inserted domain, the I-domain. We Isolated the I-domain for investigation of determining binding properties and understanding conformational regulations of affinity changes to its target ligand ICAM-1, for further use in chimeric protein switch design. A large change in binding affinity was found through the deletion of a sub-sequence of amino acids in I-domain known as the …

Elucidating Growth Coupling Of Metabolites In E. Coli And Characterizing Modularity., Preston N. Nicely

EURēCA: Exhibition of Undergraduate Research and Creative Achievement

This project seeks to increase the efficiency of rapid engineering strain design by elucidating the functionality of a modular cell. The modular cell theory insinuates that there exists a baseline cellular framework from which cellular products can be produced by inserting a designed production module into the cell. In this study, recombinant gene cloning techniques were used to design metabolite production modules that focused on increasing the production, titer, and yield of ethanol and lactate within Escherichia coli (E. coli). An auxotrophic chassis cell was created by ModCell2 and multi-objective strain design to determine the genes necessary for deletion. The …

Simulating Microbial Electrolysis For Renewable Hydrogen Production Integrated With Separation In Biorefinery, Christian James Wilson

Masters Theses

Biomass conversion to hydrocarbon fuels requires significant amounts of hydrogen. Fossil resources typically supply hydrogen via steam reforming. A new technology called microbial electrolysis cells (MECs) has emerged which can generate hydrogen from organic sources and biomass. The thermochemical route to fuels via pyrolysis generates bio-oil aqueous phase (BOAP) which can be used to make hydrogen. A process engineering and economic analysis of this technology was conducted for application in biorefineries of the future. Steam methane reforming, bio-oil separation and microbial electrolysis unit operations were simulated in Aspen Plus to derive the mass and energy balance for conversion of biomass. …

Morphological And Photoelectrochemical Characterization Of Membrane Reconstituted Photosystem I (Psi), Seyedeh Hanieh Niroomand

Doctoral Dissertations

The robust structural and photoactive electrochemical properties of Photosystem I (PSI), a transmembrane photosynthetic protein complex, make it an ideal candidate for incorporation into solid state bioelectronic or hybrid photovoltaic devices. However, the first step towards the successful fabrication of such devices requires systematic assembly of oriented and functional PSI onto desired bio-abio interfaces via suitable protein scaffoldings. Hence, this dissertation focuses on utilizing the cyanobacterial PSI for integration into organic/inorganic interfaces that mediate photo-electrochemical energy conversions for electricity and/or solar fuel production. To this end, in this study the effect of systematic incorporation of PSI complexes into synthetic membrane-bound …

A Bug’S Life: Integration Of Anaerobic Digestion And Bioelectrochemical Systems For Enhanced Energy Recovery From Wastewater Solids And Other Waste Substrates, Jeff Ryan Beegle

Masters Theses

Organic waste streams, like domestic wastewater and municipal solid waste, have the potential to be used as feedstocks for biotechnology processes to produce high value products and energy. This thesis investigated the technological, economical, and environmental potential for integrated anaerobic digestion (AD) and bioelectrochemical system (BES) platforms as they were theoretically and physically evaluated for energy recovery from domestic wastewater. The first chapter of this thesis compared the theoretical energy efficiencies of converting waste directly into electricity, using AD and BES alone and in various combinations. This chapter reviewed the experimentally demonstrated energy efficiencies reported in the literature with comparisons …

Elucidating The Effects Of Metabolic State On Nanoparticle Distribution In Mice And In Vitro Uptake, Kevin James Quigley

Doctoral Dissertations

Since almost 70% of the U.S. population over 20 years old is overweight and 30% is obese, with much of the western world following suit, many patients that will potentially be administered circulating nanoparticles designed to localize to tumors and avoid non-target areas will have significant amounts of white adipose tissue (WAT), enlarged livers, and additional metabolic complications such as type 2 diabetes. However, studies on nanoparticle biodistribution and efficacy take place almost without exception in lean rodents with healthy metabolic states. In this work, I determined the biodistribution of model nanoparticles – neutral filomicelles and polystyrene spheres both carrying …

Lignin Maximization: Analyzing The Impact Of Different Feedstocks And Feedstock Ratios Using Organosolv Fractionation, Marc Banholzer

Masters Theses

Over-exploitation of fossil fuels coupled with increasing pressure to reduce carbon emissions are prompting a transition from conventional petrochemical feedstocks to sustainable and renewable sourced carbon. The use of lignocellulosic biomass as a feedstock for integrated biorefining is of current high interest, as separation into its component parts affords process streams of cellulose, hemicellulose and lignin, each of which can serve as a starting point for the production of biobased chemicals and fuels. Given the large number of potential sources of lignocellulosic feedstocks, the biorefinery will need to adapt to the supplies available over a normal growing season. Of particular …

In Silico Driven Metabolic Engineering Towards Enhancing Biofuel And Biochemical Production, Richard Adam Thompson

Doctoral Dissertations

The development of a secure and sustainable energy economy is likely to require the production of fuels and commodity chemicals in a renewable manner. There has been renewed interest in biological commodity chemical production recently, in particular focusing on non-edible feedstocks. The fields of metabolic engineering and synthetic biology have arisen in the past 20 years to address the challenge of chemical production from biological feedstocks. Metabolic modeling is a powerful tool for studying the metabolism of an organism and predicting the effects of metabolic engineering strategies. Various techniques have been developed for modeling cellular metabolism, with the underlying principle …

Elucidating Mechanisms Of Lipid Droplet Formation In The Fission Yeast, Schizosaccharomyces Pombe, Alexander William Meyers

Doctoral Dissertations

Cellular function relies on the proper sequestration of fats in organelles called lipid droplets. Lipid droplet metabolism is inherently linked to many disorders including obesity, type-2 diabetes, and atherosclerosis, so further elucidation of the bio-physical phenomena governing these diseases, is crucial for their respective treatments.

Once widely regarded as inert, these neutral lipid storage depots are highly dynamic and are increasingly shown to affect a wide array of biological processes. Droplet formation requires the accumulation of neutral lipids and related factors at specific cellular domains, however because this occurs at nanometer length-scales, details are lacking. Here, we try to provide …

Adaptation And Robustness In A Chemotaxis Network, Beini Chen, Steve Abel

EURēCA: Exhibition of Undergraduate Research and Creative Achievement

Adaptation is a behavior of biological systems in which a sustained change in input signal leads to a transient output response that returns to the pre--‐stimulated output level. Cells use adaptation to maintain sensitivity to the changes in their environment and to remain in homeostasis while the input signal is perturbed. Signaling networks in both prokaryotic and eukaryotic cells demonstrate adaptation, which is a common feature of chemotaxis, a signal transduction process that enables cells to sense chemical gradients in their extracellular environment and to adjust their movement in response. In the case of Escherichia coli, the bacteria swim in …

Photosystem I-Based Applications For The Photo-Catalyzed Production Of Hydrogen And Electricity, Rosemary Khuu Le

Doctoral Dissertations

The aim of this dissertation was to optimize systems integrating the photosystem I (PSI) redox protein, which is involved in photosynthesis, with noble metals for electron transfer to show its versatility: 1) in solution coupled with platinum to mediate hydrogen evolution and 2) on a planar gold surface for electricity production.

Response surface methodology was utilized to study variables that affect hydrogen (H₂) yield from platinized-PSI. Light intensity, temperature, and platinum concentration were varied during the platinum-photo-reduction process. Analysis of the effects of the variables on H₂ yield allowed for determination of a condition for optimized hydrogen …

The Structure And Function Of Photosystem I And Photosystem I – Hydrogenase Protein Fusions: An Experimental And Computational Study, Bradley Jordan Harris

Doctoral Dissertations

Photosystem I (PSI) is a membrane protein involved in the photosynthetic cycle of plants, algae, and cyanobacteria that is of specific interest due to its ability to harness solar energy to generate reducing power. This work seeks to form an in vitro hybrid protein fusion between the membrane integral PSI protein and the membrane-bound hydrogenase (MBH) enzyme, in an effort to improve electron transport between these two proteins.

Small-angle neutron scattering (SANS) was used to characterize the detergent-solubilized solution structure of trimeric PSI from the cyanobacterium Thermosynechococcus elongatus, which showed that the detergent interacts primarily with the hydrophobic periphery …

Analytical And Computational Modeling Of Membrane Nanotubes, Sina Mirzaeifard

Masters Theses

This thesis investigates the interplay between cell membranes and the actin cytoskeleton in cellular structures known as membrane nanotubes. Membrane nanotubes are slender membrane structures that physically connect cells over long distances, and experiments suggest that they play a role in transferring material and information between cells. Disrupting the actin cytoskeleton disrupts membrane nanotubes. Although recent studies have revealed insight into the physical properties and functions of membrane-actin systems, further research is needed to understand their behavior in biological contexts. Membrane nanotubes provide a novel system with which to investigate interactions between the cell membrane and actin.

In this thesis, …

Effects Of System Size And Network Topology On The Bistability Of Cell Signaling Networks, Beini Chen

EURēCA: Exhibition of Undergraduate Research and Creative Achievement

No abstract provided.

A Tale Of Two Protein Switches: Engineering, Characterizing, And Understanding A Novel And A Natural Switch, James Vincent Price

Doctoral Dissertations

Throughout nature, many proteins provide a specific function in response to some input signal (e.g., phosyphorylation, pH, etc.), a process that is oftentimes described as switching a protein “on” or “off.” The advent of protein engineering has allowed for the creation and understanding of chimeric proteins for uses in a number of applications such as therapeutics, biosensors and energy production. Two proteins, hemagglutinin (HA) of fowl plague influenza virus and a chimeric protein comprising a fusion between the LFA-1 I domain and the EF3 and EF4 hands of calmodulin, have been investigated in this dissertation. Both of these proteins undergo …

Application Of Synthetic Biology For Increasing Anaerobic Biodiesel Production In Escherichia Coli, Michael Christopher Wierzbicki

Masters Theses

The ever-increasing demand for transportation biofuels requires new and novel approaches to solve the complexities associated with efficient biofuel production. Ethanol, the most common biofuel, has physical limitation associated with difficulty of separations and issues with water contamination and as such is not a long-term transportation fuel solution. (Lou & Singh, 2010; Wheals, Basso, Alves, & Amorim, 1999) Biodiesel is seen as a possible alternative to ethanol due to its hydrophobicity and also has comparable energy density and cetane number to its petroleum derived counterpart. (Kalscheuer, Stölting, & Steinbüchel, 2006) Because of feedstock limitations, biodiesel produced from vegetable oils is …