Theses and Dissertations
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Item Embargo Predicting the composition of sucrose–ethanol–water mixtures and alcoholic beverages using density, refractive index, and temperature data(Colorado State University. Libraries, 2025) Vojjala, Rishi, author; Dandy, David, advisor; Morett, David, committee member; Chong, Edwin, committee member; Reardon, Kenneth, committee memberAccurate alcohol content measurements are a critical regulatory requirement in the alcoholic beverage industry, where bottles labeled with the percentage of alcohol by volume must be within ± 0.3 percentage points of the actual value. While large-scale producers use expensive analysis equipment, smaller breweries and distilleries often rely on manual hydrometer readings, which are prone to error and inefficiency. This project explores a cost-effective alternative to estimate beverage compositions, by using widely available in-line instruments such as Coriolis meters and refractometers. The primary aim is to predict the composition of an unknown solution in terms of Brix for sugar content and percentage alcohol by weight (ABW%) for alcohol content, using the physical properties of temperature, density, and refractive index of the solution. Solutions with known compositions were prepared in the lab, and their corresponding physical measurements were recorded across a wide range of mixture compositions and temperatures. These data were used to train regression models that learned the relationship between physical properties and solution composition. Given the temperature, density, and refractive index of an unknown solution, the models could then predict the mixture composition. The Brix model achieved high accuracy, with most predictions within ±1 Brix. Alcohol predictions were less precise, typically within ± 2 ABV percentage points. The models were validated using both lab-made mixtures and commercially produced beverages. The models performed comparably on both, showing strong generalization. The results also suggest that prediction accuracy would be improved by collecting more measurements. With additional parameters, this approach could be extended beyond three-component mixtures to more complex formulations, and beyond alcoholic beverages to applications in industries such as chemical processing, cosmetics, and food quality monitoring.Item Embargo Development of a real-time algal biomass and health optical sensor(Colorado State University. Libraries, 2025) Ferrell-Carretey, Elliot, author; Reardon, Ken F., advisor; Dandy, David, committee member; Henry, Chuck, committee memberLarge-scale microalgae cultivation requires continuous monitoring of both biomass and health, yet existing real-time sensors are often prohibitively expensive or reliant on through-flow designs that demand constant maintenance. This presentation introduces an affordable, in-situ optical sensor capable of measuring algal biomass concentration and health without the need for pumping systems. The sensor employs near-infrared light to measure algal concentration while using absorbance at eight visible wavelengths for algal health. Operating in various lighting conditions, floating on the water surface, and correcting for background interference, it alleviates many constraints of conventional methods. Data from the sensor are wirelessly transmitted to local receivers and integrated into cloud-based databases, enabling remote access and continuous tracking of cultivation parameters. Because it supplies real-time information on growth patterns, effects of nutrient supply, and environmental influences such as pH or time of day variations, the system can detect small changes that can give new insights. When combined with nutrient sensors, the data provide comprehensive oversight of cultivation conditions, facilitating efficient harvesting strategies. By offering immediate feedback on biomass concentration and algal health, this optical sensing system facilitates cultivation adjustments to optimize growth and reduce resource waste. Its low cost, portability, and straightforward deployment make it an attractive alternative for large-scale operations, especially compared with limited manual measurements. With its robust design, this solution significantly advances cost-effective algae cultivation for commercial and research applications.Item Embargo Exploring energy transfer pathways for Tb³⁺ and Eu³⁺ through spectroscopic analysis of antenna-modified lanthanide-binding peptides(Colorado State University. Libraries, 2025) Al Mesfer, Mohammad, author; Kipper, Matthew, advisor; Snow, Christopher, committee member; Wilson, Jesse, committee memberLanthanide ions (Ln3+), such as Tb3+ and Eu3+, possess unique luminescent properties valuable for biological imaging. However, limitations including inefficient direct excitation and challenges in cellular delivery and sensitization hinder their application. Peptide-based complexes offer a promising platform for Ln3+ sensitization, providing biocompatibility and potential genetic encodability. This thesis investigates antenna-modified lanthanide-binding peptides (LBPs) designed to improve Ln3+ sensitization. A known LBP was engineered by replacing its native tryptophan sensitizer with cysteine, enabling site-specific conjugation of aromatic antennas (phenanthroline, pyrene, coumarin) via maleimide chemistry. This strategy aimed to optimize excitation wavelengths (shifting from ~280 nm). Successful bioconjugation was confirmed by MALDI-TOF MS. Spectroscopic analysis revealed distinct antenna-dependent effects on Ln3+ emission. Notably, the phenanthroline conjugate selectively sensitized Eu3+ (~615 nm) but not Tb3+ under identical conditions. Conversely, both pyrene and coumarin conjugates quenched Ln3+ luminescence. Attempts at cellular imaging following intracellular expression of the parent LBP were hindered by limitations in available microscopy instrumentation. Nevertheless, this research validates site-specific antenna conjugation as a strategy for modulating Ln3+ sensitization pathways. The findings provide insights into peptide-lanthanide energy transfer, inform the design of future LBP-based probes, and establish a foundation for subsequent development towards cellular applications.Item Embargo Chemical modification of aminated condensed tannin: impact of quaternary ammonium, pyrogallol, and methylation modifications on antibacterial, antioxidant, and physicochemical properties(Colorado State University. Libraries, 2025) Kashepa, Viktoriia, author; Kipper, Matthew, advisor; Popat, Ketul, advisor; Bailey, Travis, committee member; Reynolds, Melissa, committee memberIn a world with a rapidly aging population and healthcare system growth, we are faced with the demand for multifunctional biomaterials capable of preventing implant-associated infections, supporting tissue regeneration, mitigating sterile inflammation, and reducing the burden on both patients and the healthcare system. Coatings made from polymers of natural origin have been under investigation by the scientific community for a long time, and their multifunctionality underscores the need for deeper exploration of biopolymers as biomaterials. Specifically, while non-polymeric polyphenolic compounds have been used by humanity for thousands of years and are today widely recognized for their antioxidant, antimicrobial, anti-inflammatory, and other favorable biological properties, their polymeric counterparts - condensed tannins - remain largely unexplored in the biomedical field. To date, biological performance studies conducted by our laboratory on a condensed tannin derivative, Tanfloc, demonstrate great potential for its use as a new biopolymer for implant coatings and other fields of biomedicine. However, the relationship between 'chemical structure' and 'biological activity' for this condensed tannin derivative remains poorly understood, particularly regarding how its polyphenolic nature and amino groups contribute to its biological performance. This work focuses on elucidating the role of key chemical groups in the aminated condensed tannin derivative Tanfloc by modifying its structure and evaluating the impact of modifications on physicochemical, antioxidant, and biological properties. Tanfloc was chemically modified using quaternization, galloylation, and permethylation to target its amino and polyphenolic moieties. Polyelectrolyte multilayer (PEM) sample implant coatings were then fabricated using these derivatives in combination with hyaluronic acid, using a layer-by-layer deposition method. Comprehensive characterization techniques were employed to assess the structural, chemical, and surface properties of both the modified powders and PEMs. This study provides insights into how specific chemical modifications influence the behavior of polyphenol-based biopolymers and how it can be employed in the design of multifunctional implantable devices.Item Embargo Understanding microbial metabolism using computational methods at different levels of abstraction(Colorado State University. Libraries, 2025) Ghadermazi, Parsa, author; Chan, Siu Hung Joshua, advisor; Munsky, Brian, committee member; Prasad, Ashok, committee member; Wrighton, Kelly, committee memberUnderstanding microbial metabolism and its effect on the surrounding environment represents a critical challenge in microbial ecology, requiring sophisticated computational approaches that can bridge molecular-level interactions with complex ecosystem dynamics. This research presents a comprehensive suite of computational methods that advance our ability to model and predict microbial system behaviors at multiple levels of complexity. This work introduces four computational distinct approaches that address key limitations in existing microbiome modeling techniques: • A bottom-up cellular metabolism model that enables predicting cellular phenotype using a simplified kinetic model for a replicating bacterial cell • SPAM-DFBA, a novel approach integrating dynamic flux balance analysis with reinforcement learning • ADToolbox, a metagenome-informed tool for modeling anaerobic digestion processes • A bioinformatics approach for analyzing complex host-microbiota interactions in mice with colorectal cancer By systematically exploring the trade-offs between model complexity and predictive power, this research expands the analytical toolkit available to microbiome researchers. The methodological progression demonstrates how computational techniques can overcome significant challenges in metabolic modeling, including limited kinetic parameters and biochemical knowledge gaps. Key contributions include: • Novel optimization techniques for simulating cellular metabolism • Enhanced modeling approaches for heterogeneous bacterial communities • Integration of metagenomic data into predictive computational frameworks These advances represent a significant step forward in our ability to understand, predict, and potentially manipulate microbial systems across diverse contexts, from industrial biotechnology to human health applications.Item Open Access GPU-accelerated computational study of block copolymer self-assembly with advanced polymer theories(Colorado State University. Libraries, 2024) He, Juntong, author; Wang, Qiang, advisor; Prasad, Ashok, committee member; Bailey, Travis, committee member; Gelfand, Martin, committee memberA high-performance GPU-accelerated software package for self-consistent field (SCF) calculations of block copolymer assembly, PSCF+, has been developed. PSCF+ allows various combinations of chain-connectivity models (including the continuous Gaussian chains, discrete Gaussian chains, and freely jointed chains), non-bonded isotropic pair (including the Dirac δ-function, soft-sphere, dissipative particle dynamics, and Gaussian) potentials and system compressibility (incompressible vs. compressible). The Richardson-extrapolated pseudo-spectral methods, the crystallographic fast Fourier transform, the "slice" algorithm, and the automated calculation-along-a-path are implemented in PSCF+, which not only speed up the SCF calculations and reduce the GPU memory usage significantly, but also make it very efficient in constructing phase diagrams. Given the wide use and great success of SCF calculations in understanding and predicting the self-assembled structures of block copolymer, PSCF+ will be an invaluable computational tool for the polymer community. Using PSCF+, we studied the stability of various Frank-Kasper phases formed by neat diblock copolymer (DBC) A-B melts using the "standard" model and the dissipative particle dynamics chain model and found that in general the SCF phase diagrams of these two models are qualitatively the same but with important differences. We also studied the stability of various Frank-Kasper phases formed by binary DBC blends using the "standard" model and found that the relative stability among the Frank-Kasper phases is dominated by their internal-energy densities. Finally, we performed high-accuracy SCF calculations to study the stability of all known tiling patterns formed by symmetrically interacting ABC miktoarm star triblock terpolymers.Item Open Access Engineering in practice: from quantitative biology modeling to engineering education(Colorado State University. Libraries, 2024) Weber, Lisa, author; Munsky, Brian, advisor; Atadero, Rebecca, committee member; Prasad, Ashok, committee member; Reisfeld, Brad, committee memberIn quantitative analyses of biological processes, one may use many different scales of models (e.g., spatial or non-spatial, deterministic or stochastic, time-varying or at steady-state) or many different approaches to match models to experimental data (e.g., model fitting or parameter uncertainty/ sloppiness quantification with different experiment designs). These different analyses can lead to surprisingly different results, even when applied to the same data and the same model. In Chapters 2, a variety of modeling approaches that can be utilized in analyzing biological processes are explained, with examples included of how to mathematically represent a system in order to use these various modeling approaches. Many of these mechanistic modeling approaches are demonstrated in Chapter 3 when we use a simplified gene regulation model to illustrate many of the concerns regarding modeling approach differences; these include ODE analyses of deterministic processes, chemical master equation and finite state projection analyses of heterogeneous processes, and stochastic simulations. For each analysis, we consider a time-dependent input signal (e.g., a kinase nuclear translocation) and several model hypotheses, along with simulated single cell data, to illustrate different approaches (e.g., deterministic and stochastic) in the identification of mechanisms and parameters of the same model from the same simulated data. We also explore how uncertainty in parameter space varies with respect to the chosen analysis approach or specific experiment design, and conclude with a discussion of how our simulated results relate to the integration of experimental and computational investigations to explore signal-activated gene expression models in yeast [1] and human cells [2]. Different modeling approaches are used in Chapter 4 to build on the work of Scott, et al. (2018, 2019) [3, 4] to evaluate different model classes for DNA structural conformation changes, including the unwinding/rewinding dynamics of the double-stranded DNA (dsDNA) helical structure and subsequent binding interactions with complementary single-stranded oligonucleotides probes (oligos), in relation to different conditions: temperature, salt concentration, and the level of supercoiling of the DNA molecule. This is done to identify a class of models that best fit the DNA unwinding and subsequent oligo probe binding experimental data as a function of these three conditions. In this work, we demonstrate the use of additional quantitative modeling approaches, including a modified genetic algorithm along with the process of cross validation and Markov Chain Monte Carlo (MCMC) simulations with the Metropolis-Hastings (MH) algorithm [5] to explore parameter space. We also demonstrate many of the challenges that can be encountered when modeling complex biological phenomena with actual experimental data. Although much of the work described in Chapters 2 through 4 may appear to be, on the surface, just the use of various computational methods for biological processes to increase understanding of biological mechanisms, much of it also has a separate purpose. The structure of these works and an underlying aim of much of this work, namely Chapters 2 and 3, is to provide guidance with examples to make these computational approaches more accessible to scientists and engineers. Many of these approaches are included in a quantitative biology (UQ-bio) summer school that has been conducted for the last few years as well. Through the process of developing these works and seeking to make quantitative biology more accessible, a related goal manifested to improve the accessibility of engineering education as a whole, which is addressed in Chapter 5, specifically related to diversity, equity, and inclusion (DEI) in undergraduate engineering education. There have been efforts since Fall 2017 to increase the presence of DEI in the undergraduate CBE education using a bottom up approach. To date, various efforts have been incorporated into the first two years of the CBE program. In Chapter 5, these previous efforts, along with lessons learned, are detailed. A substantial, holistic approach to incorporating DEI throughout the CBE curriculum is proposed, based on a review of recent work by other engineering education researchers, to help the CBE department create a more inclusive educational experience for undergraduate students and better enable students to handle the complex challenges they may face in their careers.Item Open Access Applications of advanced self-consistent field calculations in nanostructured polymeric systems(Colorado State University. Libraries, 2009) Meng, Dong, author; Wang, Qiang (David), advisorThe polymer self-consistent field (SCF) theory have gained great success in many systems, especially for the study of inhomogeneous nanostructured polymers. During my PhD study, I have applied real-space SCF calculations with high accuracy to mainly two categories of nanostructured polymers: The first part of this dissertation is focused on the study of self-assembled nanostructures of diblock copolymers (DBC) under nano-confinement. We first examined in detail the so-called "hard-surface" effects, originated from the impenetrable confining surfaces, on the phase behavior of confined DBC systems, where improving the numerical performance of SCF calculations with such effects is also discussed. We then studied in detail the self-assembled morphology of symmetric DBC confined between two homogeneous planner surfaces, where the effects of surface preference and film thickness are investigated and novel complex morphologies are found. Finally, we considered the directed assembly of DBC on topologically and chemically nano-patterned substrates, where well-ordered complex nanostructures can be obtained by controlling the substrate pattern. In the second part of the dissertation, stimuli-response of polymer brushes (chains end-grafted onto a fiat substrate) is investigated. We first studied the thermal response of poly-NIPAM brushes in water, and found that the temperature where the largest thermal response occurs is governed by the chain-grafting density, while the magnitude of the thermal response is controlled by the polymer chain length. We then studied the solvent-response of uncharged DBC brushes and found that the copolymer composition is the key factor in switching the brush surface-layer composition by different solvent treatments; our SCF results agree well with available experimental measurements. Finally, we investigated the stimuli-response of charged DBC. Given the vast parameter space encountered here, we conducted our study based on the uncharged DBC brushes and explored the effects of charge fraction on polymer chains, solution pH and ionic strength, and applied electric fields on the brush surface-switching; this work reveals the complex interplay between different stimuli in such systems. A list of all my published papers and manuscripts in preparation for publication is included at the end of this dissertation, where all the details of my SCF calculations can be found.Item Open Access Study and design of minimally instrumented microfluidic unit operations for a portable biosensor: mixing, pumping, and reaction(Colorado State University. Libraries, 2009) Lynn, Nicholas Scott, Jr., author; Dandy, David S., advisorThis research involves the detailed study and design of several microfluidic unit operations that combined together, passively deliver analyte to a local, evanescent array coupled (LEAC) sensor. Specifically, this dissertation is focused on minimally instrumented mixing, pumping, and heterogeneous reaction strategies regarding fluids confined to microchannels whose widths and heights are less than 100 microns. These microfluidic platforms present many advantages over their traditional macroscale counterparts, including reduced sample volumes, analysis times, costs, and overall device size. The minimally instrumented unit operations studied in this dissertation work such that no external control is required and power inputs are small enough to be handled by small battery systems. When combined with the LEAC sensor, the unit operations within this dissertation will provide a unique device able to detect a wide variety of biological markers or small molecules with a high degree of portability.Item Open Access Environmental proteome profiling applied to the study of polybacterial metal resistance and adaptation(Colorado State University. Libraries, 2008) Lacerda, Carla M. R., author; Reardon, Kenneth F., advisorEnvironmental biotechnology can be defined as the use of biotechnology to solve environmental engineering problems, frequently involving bacterial communities and unsequenced species. Here we define environmental proteomics as the proteomic profiling of microorganisms of environmental relevance, targeting the improvement of environmental bioprocesses. This study demonstrates our ability to obtain proteomic data for communities of microorganisms and for environmental isolates, providing unique insights into the physiology and ecology of these systems. A combination of qualitative and quantitative proteomics methods (two-dimensional electrophoresis and/or chromatography followed by tandem mass spectrometry) was used to investigate the proteome of a sequenced mixed culture, an unsequenced mixed culture, and a bacterial isolate from the original unsequenced mixed culture. In the first case study, two soil organisms were grown in co-culture in an attempt to observe proteins induced as a response to the presence of another organism. Many proteome changes were detected and quantified, with proteins involved in protein and DNA metabolism being the most largely modulated. In the second case study, an unsequenced mixed culture was exposed to cadmium and had its dynamic response analyzed. While the community responded significantly to all shock durations, the greatest amount of change was observed in the first fifteen minutes of shock. The main groups of differentially expressed proteins identified were transport proteins, showing that the main method for cadmium tolerance was active efflux. In the study of the adaptation of a pure culture, the most cadmium-tolerant organism in the original unsequenced community was isolated and cultivated in different concentrations of cadmium. In the last case study of metal resistance, the proteomes of this isolate were compared as it responded to short-term exposures to chromium, iron and cadmium. Metals induced proteome responses in both short- and long-term exposures, meaning that the mechanisms for adaptation and resistance are different. This project demonstrates the potential of environmental proteomics and its intricacies as different proteomic workflows are employed. This is also one of the first evaluations of metaproteomic changes due to the metal response of mixed bacterial cultures, revealing the large potential of environmental proteomics to uncover unique insights into systems-level bacterial functions.Item Open Access Development and application of microbial community profiling techniques for mine drainage bioremediation(Colorado State University. Libraries, 2008) Hiibel, Sage Royal, author; Reardon, Kenneth F., advisor; Pruden, Amy, advisorAcid mine drainage (AMD), characterized by elevated levels of sulfate, acidity, and metals, is produced by the oxidation of mining-exposed minerals and is a major environmental issue. Sulfate-reducing bioreactors (SRBRs) are an attractive AMD treatment option. SRBRs contain an organic material, usually wood chips or compost, which provides a slow-release carbon substrate to support a complex anaerobic microbial community. A relationship between the microbial inoculum and bioremediation performance was established in laboratory experiments. The use of 16S rDNA-based profiling techniques established a correlation between SRBRs that performed well and the presence of three key functional groups: cellulose degraders, fermenters, and sulfate-reducing bacteria (SRB). Subsequent analyses of pilot- and field-scale SRBRs targeted the 16S gene and apsA functional gene, which is found in all SRB. Although multivariate statistical analyses of the 16S sequences of the communities did not reveal obvious differences, the apsA sequences of each SRBR were significantly different. The apsA sequences also revealed that Thiobacillus spp., which are capable of sulfur oxidation, were prevalent at the poorly performing SRBR. A novel, high throughput, biomolecular method called active community profiling (ACP) was developed and validated using model systems. ACP identifies the active members of mixed communities through the ratio of rRNA to rDNA, which is proportional to growth rate. When coupled with physiochemical analysis, ACP offers a powerful new tool to help understand microbial community dynamics. The effects of bioaugmentation and biostimulation on the community structure of AMD treatment systems were studied. Although all columns remediated AMD to a similar level, ACP analysis revealed that the active members of their communities were distinctive. It was determined that biostimulation or bioaugmentation at the top of the microbial carbon chain increased the active community diversity. This dissertation emphasizes the role of the microbial community associated with AMD remediation. Characterization of these communities with biomolecular tools at several scales has significantly advanced the understanding of the community's structure, function, and activity. The research approaches and methodologies developed have wide application, and provide unique and valuable contributions to the scientific knowledge of AMD treatment specifically, and to microbial ecology and bioremediation in general.Item Open Access Engineering nanostructured polysaccharide-based polyelectrolyte complexes(Colorado State University. Libraries, 2009) Boddohi, Soheil, author; Kipper, Matt J., advisorThe overall goal of this dissertation is to demonstrate how the structure and composition of polysaccharide-based materials might be tuned at the nanometer length scale. Nanostructured biomaterials are promising candidates for biomedical engineering applications. Among all biomaterials, polysaccharides have shown great potential because of their many biochemical functions and their complex nanoscale structure in biological contexts. The nanoscale structure of polysaccharides is an important property that controls their biochemical and biological functions, in a variety of tissues. Therefore, in this dissertation, the nanoscale assembly of polysaccharides-based polyelectrolytes using polyelectrolyte multilayers (PEMs), polyelectrolyte complex nanoparticles (PCNs), and combinations of these two nanostructures was investigated. These new nanostructured surface coatings are being further developed by the Kipper research group as means of stabilizing and delivering therapeutic proteins, and as bioactive surface coatings for stem cell engineering. Thus the ability to tune their structure and composition is an important contribution of the current work.Item Open Access Rational design and novel bioprocesses for low-carbon biofuels and bioproducts(Colorado State University. Libraries, 2023) Bartholet, Danielle, author; Reardon, Kenneth, advisor; Foust, Thomas, advisor; De Long, Susan, committee member; Peebles, Christie, committee member; Windom, Bret, committee memberThe reduction of fossil fuel consumption and carbon emissions is one of the greatest challenges of our time, and innovative solutions are necessary to prevent climate catastrophe while maintaining economic development and modern ways of life. Biofuels and bioproducts can provide low-carbon alternatives to petroleum fuels and petroleum-based chemical processes. However, several limitations have impeded the wide-scale implementation of bio-based technologies. Biologically derived chemicals frequently do not possess ideal fuel properties due to high oxygen content and lower energy density. Furthermore, petroleum processes remain economically favorable to biological alternatives due to the high costs and low yields associated with bioprocesses. Rational design approaches to the development of new fuels and chemicals combined with improved bioconversion processes are strategies that address multiple aspects of sustainable development for a circular carbon economy. The broad purpose of this work was to explore and develop low-carbon alternatives to petrochemical products and processes. We begin by proposing a group of novel fuel additive molecules, then explore alternative technologies for their production. In Chapter 2 of this work, a rational design approach was used to identify "ideal" diesel fuel additive molecules. The desired characteristics of a liquid transportation fuel include high efficiency and engine performance, low particulate emissions, compatibility with current engines and infrastructure, and low risk of environmental contamination. In this work, we use computational tools to propose structures for diesel fuel additives that meet these criteria. Starting with the chemical structure of dimethoxymethane (DMM), a class of oxygenated molecules, called polyoxymethylene ethers (POMEs) is proposed by varying oxygen content in the backbone length and carbon content in the end group length. Additional structural variations, including iso-alkyl end groups and tertiary branches, are considered here for the first time. The ten candidate molecules identified consist largely of butyl-terminated POMEs. Synthesis chemistry for butyl-terminated POMEs was developed, utilizing an acid-catalyzed transacetalization reaction of butanol with methyl-terminated POMEs. To improve the sustainability of POME production, it is desirable to produce precursors from biomass using bioconversion processes. Therefore, the focus of this work pivoted to bioprocess technologies for improved production of butanol and other fuel precursor molecules. Butanol and other molecules of interest are highly reduced metabolic products, requiring the input of electrons through intracellular reducing equivalents. Frequently, the yields of these reduced products are limited due to redox constraints of metabolic pathways. Electro-enhancement, which refers to the direct supplementation of electrons from solid electrodes, may overcome redox constraints by enabling "unbalanced fermentations". While electro-enhancement of processes like fermentation (electro-fermentation) and anaerobic digestion (electro-AD) has been reported to successfully induce metabolic shifts and alter product profiles, much remains unknown about the mechanisms leading to observed shifts. Chapter 3 provides a detailed review of the literature in this field, highlighting the challenges and shortcomings of electro-enhancement research. Methods developed to improve the study of bioelectrochemical systems are also presented here. In Chapter 4, we apply these methods to pure culture electro-fermentations of Clostridium pasteurianum with the objective of increasing butanol production. Our results indicate that applied potentials may affect metabolite profiles through redox control but did not provide sufficient evidence for direct bacterial/electrode interaction. In Chapter 5, these methods are applied to electro-AD of food waste inoculated with wastewater sludge. Applied potentials are shown to have a wide range of effects on product profile and microbial communities. These results suggest that electro-enhancement may provide a method for fine-tuning product profiles in heterogeneous, mixed culture systems. However, further experiments are required in both pure and mixed culture systems to fully elucidate the effect of electro-enhancement on cellular processes. Through this work, new methods were developed to facilitate future research in bioelectrochemical systems and enable the design of improved electro-enhanced bioprocesses.Item Open Access A rapid, point of need open cow test(Colorado State University. Libraries, 2023) Mendez, Jacy, author; Dandy, David, advisor; Henry, Chuck, committee member; Bailey, Travis, committee member; Hansen, Thomas, committee memberIn the dairy industry, maintaining non-pregnant (open) cows is expensive, and may require multiple rounds of artificial insemination (AI) for a cow to become pregnant. There is a need for early pregnancy detection in dairy cows, which allows the use of protocols such as prostaglandin F2-alpha (PGF) and gonadotropin releasing hormone (GnRH) to prepare a cow for another round of breeding via AI, with an emphasis on reduced time between each breeding attempt. The current gold standard method for confirming pregnancy in cows is a rectally-guided ultrasound at day 32 after AI. Interferon-tau (IFNT) is a biomarker that can be detected during days 7-28 of pregnancy in cattle, and is expressed by the cow conceptus. The goal of this work was to develop a cow-side test utilizing IFNT as the biomarker for early cattle pregnancy detection. A lateral flow assay (LFA) was chosen and investigated due to its simplicity and ease of use, but was later adapted to utilize the enzymatic oxidation of 3,3',5,5' – Tetramethylbenzidine to amplify the signal in the test line. C-reactive protein was used to develop protocols for aspects of device development involving nitrocellulose, including antibody striping, blocking, and nitrocellulose selection. These protocols were then utilized as optimization of the lateral flow assay was conducted. The resulting LFA has a limit of detection (LOD) of 10 μg/mL, with an LOD of 100 ng/mL in a half-strip format, with some limitations imposed by false positives. This work provides a novel method of detection for pregnancy in cattle and with further development, has the potential for use by dairy farmers in their respective industry.Item Open Access An economic and environmental assessment of guayule resin co-products for a US natural rubber industry(Colorado State University. Libraries, 2023) Silagy, Brooke, author; Reardon, Kenneth, advisor; Quinn, Jason C., advisor; Kipper, Matthew, committee member; Bradley, Thomas, committee memberGuayule (Parthenium argentatum) is a natural rubber producing desert shrub that has the potential to be grown in semi-arid areas with limited water resources. Numerous studies have examined the costs and environmental impacts associated with guayule rubber production. These studies identified the need for additional value from the rubber co-products, specifically the resin, for sustainable and commercial viability of the biorefinery concept. This study developed process models for resin-based essential oils, insect repellant, and adhesive co-products that are integrated with sustainability assessments to understand the commercial viability. A techno-economic analysis and cradle-to-gate life cycle assessment (LCA) of these three different co-product pathways assumed a facility processing 66 tonnes/day of resin (derived from the processing of 1428 tonnes per day of guayule biomass) and included resin separation through co-product formation. The evaluation outcomes were integrated into an established guayule rubber production model to assess the economic potential and environmental impact of the proposed guayule resin conversion concepts. The minimum selling price for rubber varied by co-product: $3.54 per kg for essential oil, $3.40 per kg for insect repellent, and $1.69 per kg for resin blend adhesive. The resin blend adhesive co-product pathway had the lowest greenhouse gas emissions. These findings show a pathway that supports the development of a biorefining concept based on resin-based adhesives that can catalyze a US based natural rubber industry.Item Open Access Feed zone micromixing and its effect on continuous cultures of Saccharomyces cerevisiae(Colorado State University. Libraries, 1995) Mondani, Paul, author; Loftis, J. C., advisorInadequate mixing is known to be a common problem in the scale-up of bioprocesses, often leading to decreases in yield and productivity. To investigate the role of nutrient dispersion in continuous cultures, growth medium was fed into a laminar flow section of a loop that recirculates broth from a laboratory scale bioreactor. The intensity of micromixing at the feed site could be controlled by varying the axial distance a static mixer was placed upstream of the site. The intensity of the turbulent wake shed by the mixer was quantified by laser Doppler velocimetry and the Bourne dye reaction. By decreasing the size of the smallest turbulent eddy in the feed zone, less of the population is exposed to regions of either inadequate or excessive substrate concentrations. Yield vs. dilution rate curves were obtained through various mixing and feeding strategies. Reduced mixing was shown to delay the onset of the Crabtree effect and therefore improve the bioreactor's productivity.Item Open Access Metabolic engineering interventions for sustainable 2,3-butanediol production in gas fermenting Clostridium autoethanogenum(Colorado State University. Libraries, 2023) Ghadermazi, Parsa, author; Chan, Siu Hung, advisor; Wrighton, Kelly, committee member; Reisfeld, Brad, committee memberGas fermentation provides a promising platform to turn low-cost and readily available single-carbon waste gases into commodity chemicals such as 2,3-butanediol. Clostridium autoethanogenum is usually used as a robust and flexible chassis for gas fermentation. Here, we leveraged on constraints-based stoichiometric modeling and kinetic ensemble modeling of the C. autoethanogenum metabolic network to provide a systematic in silico analysis of metabolic engineering interventions for 2,3-butanediol overproduction and low carbon substrate loss in dissipated CO2. Our analysis allowed us to identify and to assess comparatively the expected performances for a wide range of single, double, and triple interventions. Our analysis managed to individuate bottleneck reactions in relevant metabolic pathways when suggesting intervening strategies. Besides recapitulating intuitive and/or previously attempted genetic modifications, our analysis neatly outlined that the interventions - at least partially - impinging on by-products branching from acetyl-CoA and pyruvate (acetate, ethanol, amino acids) offer valuable alternatives to the interventions focusing directly on the specific branch from pyruvate to 2,3-butanediol.Item Open Access Porous protein microcrystals as a scaffold for nucleic acids and proteins(Colorado State University. Libraries, 2022) Masri, Mahmoud, author; Snow, Christopher, advisor; Peebles, Christie, committee member; Takamitsu, Kato, committee memberOral delivery of nucleic acids is restricted by a number of limiting factors, particularly protection of guest DNA and RNA from degradation and hydrolysis within the gastrointestinal tract following ingestion. Highly ordered, self-assembling porous protein crystals have been previously explored for enzyme immobilization, and may offer similar advantages for protection and targeted delivery of therapeutic molecules to cells. We have developed a reproducible method for generating sub-micrometer porous microcrystals from CJ, a putative isoprenoid-binding protein from Campylobacter jejuni, which are non-cytotoxic and capable of passively retaining plasmid DNA and small interfering RNA. Furthermore, we have demonstrated that CJ microcrystals are able to deliver functional plasmid and transfect cells in vitro. In addition to nucleic acids, CJ microcrystals are also capable of adsorbing functional Nanoluciferase, and display chemiluminescent activity following exposure to substrate. The results of this study demonstrate that porous protein microcrystals can serve as a suitable scaffold for RNA, DNA, and functional enzymes, and may represent a viable alternative to spherical nanoparticles and liposomes for therapeutic delivery.Item Open Access Physiologically based pharmacokinetic modeling for prediction of pharmacokinetic parameters of capreomycin(Colorado State University. Libraries, 2010) Metzler, Catherine, author; Reisfeld, Brad, advisor; DeGroote, Mary Ann, committee member; Prasad, Ashok, committee memberTuberculosis (TB) is a global public health epidemic that is increasingly dangerous and difficult to treat due in large part to drug-resistant strains. New pharmaceutical options must be considered, including capreomycin, an antibiotic discovered in the 1950s but rarely used. Due to more effective, less renal-toxic drugs, capreomycin has not been used as a primary antibiotic in tuberculosis. However, capreomycin has reemerged due to the increase in multi drug resistant TB (MDRTB). Because of its importance in treating drug-resistant strains of TB, improving the understanding of the effective dosages and resulting side effects of capreomycin is necessary. By using a validated model, drugs of interest like capreomycin could be rapidly evaluated for initial recommendations thus reducing drug development time. Using physiologically-based pharmacokinetic (PBPK) models as predictors would be economically and time efficient. In this study, a PBPK model in combination with experimental concentration profiles in mice was used to predict capreomycin pharmacokinetic parameters. Through scale-up of the model to human physiology, and implementation of the hypothesized pharmacokinetic parameters, human organ concentration profiles were predicted and compared to literature data to assess the model capabilities. The model and parameters are anticipated to be useful in predicting the disposition of capreomycin in the mouse via various dosing regimens. Although the model is useful in making pharmaeokinetic predictions in the mouse, the parameter values will need to be adjusted appropriately to be useful for estimating ADME in humans.Item Open Access Thin film integrated optical waveguides for biosensing using local evanescent field detection(Colorado State University. Libraries, 2010) Stephens, Matthew David, author; Dandy, David, advisor; Lear, Kevin, committee member; Reardon, Kenneth, committee member; Belfiore, Laurence, committee memberA waveguide is a high refractive index material that is surrounded by lower refractive index cladding. This waveguide structure can be used to carry light confined to the high refractive index core. Surrounding the core of the waveguide is a decaying evanescent light field that extends into the cladding layers. The intensity profile of the evanescent field is dependent on the refractive index of the cladding. The changes in the local intensity of the evanescent field can be used to detect refractive index changes near the core of the waveguide. A high refractive index film deposited on a flat, low refractive index .substrate can be used to form a waveguide with a planar geometry. The planar design allows the upper cladding refractive index to be modified by attaching proteins or patterning organic films. This design also allows the evanescent field intensity to be measured using near field scanning optical microscopy or a silicon photo detector array. The fabrication and characterization of a waveguide device with a coupled light source was accomplished. The evanescent field response to thin films of patterned photoresist was found using NSOM. Light intensity measured at the surface of the .sample showed significant response to the presence of the photoresist features. Light response to a protein affinity assay was found and results indicated that protein concentration could be inferred from local evanescent field measurements. A buried silicon photo detector was fabricated and characterized. The results show the field responds in a significant matter to uniform and pattered features on the waveguide core.