Theses and Dissertations

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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 member
A 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.
Embargo
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 member
In 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.
Open Access
Applications of advanced self-consistent field calculations in nanostructured polymeric systems
(Colorado State University. Libraries, 2009) Meng, Dong, author; Wang, Qiang (David), advisor
The 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.
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., advisor
This 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.
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., advisor
Environmental 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.
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, advisor
Acid 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.
Open Access
Engineering nanostructured polysaccharide-based polyelectrolyte complexes
(Colorado State University. Libraries, 2009) Boddohi, Soheil, author; Kipper, Matt J., advisor
The 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.
Embargo
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 member
The 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.
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 member
In 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.
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 member
Guayule (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.
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., advisor
Inadequate 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.
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 member
Gas 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.
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 member
Oral 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.
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 member
Tuberculosis (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.
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 member
A 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.
Open Access
Phytoremediation of tetracycline and oxytetracycline
(Colorado State University. Libraries, 2005) Gujarathi, Ninad P., author; Linden, James, advisor; Bhadra, Rajiv, advisor; Wickramasinghe, Ranil, advisor; Rinker, Kristina, committee member; Pruden, Amy, committee member; Smits-Pilon, Elizabeth, committee member
Tetracycline (TC) and Oxytetracycline (OTC), when released to the environment through wastewater streams mainly from concentrated animal feeding operations (CAFO), may induce antibiotic resistance among several bacterial species. Phytoremediation involves the use of plants or plant-secreted metabolites in remediating pollutants from air, water and soil. If proven effective, phytoremediation may provide an inexpensive, efficient means for antibiotic remediation. Two aquatic species, Myriophyllum aquaticum (parrot feather) and Pistia stratiotes (water lettuce), and hairy root cultures of Helianthus annuus (sunflower) are reported to have ability to remove TC and OTC from aqueous media. Root exudates from the three plant systems also exhibit significant antibiotic removal capability. Antibiotic modification is confirmed from the changes in ultraviolet (UV) absorption spectra of the modified antibiotics. Hairy root cultures of H. annuus are used as a model system for the experiments conducted to understand the mechanism of phytoremediation. OTC is used as the representative antibiotic for mechanistic experiments, as well as in bioreactor studies. Both in vivo and in vitro experiments using the hairy root cultures of H. annuus are used to demonstrate that reactive oxygen species (ROS) are secreted by the roots. The ROS inactivate OTC through oxidative modification. The rates of OTC oxidation by the hairy root cultures are enhanced by elicitation of ROS using salicylic acid (SA) and methyl jasmonate (MeJA). Modification of OTC results in oxidation product(s) devoid of anti-microbial activity. When used to treat wastewater from a dairy cow operation, which was spiked with OTC, root exudates significantly reduce OTC as well as biological oxygen demand (BOD) concentrations. The effects of varying physiological conditions, such as pH, temperature and aeration, on the OTC remediating activity of the root exudates are reported. The ROS-mediated modification of OTC by the root exudates is superior under aerobic conditions. A novel, integrated bioreactor system is designed for effective removal of OTC from water, under continuous-flow conditions. The design consists of a pond-microcosm for growth of P. stratiotes, coupled to a continuous flow reactor for contacting ROS and OTC. The reactor configuration with continuous-stirring gives more efficient OTC removal than a plug-flow configuration.
Open Access
Role of data analysis methods selection and documentation in producing comparable information to support water quality management
(Colorado State University. Libraries, 2000) Martin, Lindsay Melissa, author; Ward, Robert C., advisor; Loftis, Jim C., committee member
Water quality monitoring is being used in local, regional, and national scales to measure how water quality variables behave in the natural environment. A common problem, which arises from monitoring, is how to relate information contained in data to the information needed by water resource management for decision-making. This is accomplished through analysis of the monitoring data. However, how the selection of methods with which to analyze the data impacts the quality and comparability of information produced is not well understood. To help understand the connectivity between data analysis methods selection and the information produced to support management, the following tasks were performed: (1) examined the data analysis methods that are currently being used to analyze water quality monitoring data, as well as the criticisms of using those types of methods; (2) explored how the selection of methods to analyze water quality data can impact the comparability of information used for water quality management purposes, and; (3) developed options by which data analysis methods employed in water quality management can be made more transparent and auditable. These tasks were accomplished through a literature review of texts, guidance and journals related to water quality. Then, the common analysis methods found were applied to the New Zealand Water Quality River Network data set. The purpose of this was to establish how information changes as analysis methods change, and to determine if the information produced from different analysis methods is comparable. The results of the literature review and data analysis were then discussed and recommendations made addressing problems with current data analysis procedures, and options through which to begin solving these problems and produce better information for water quality management. It was found that significance testing is the most popular method through which to produce information, yet assumptions and hypotheses are loosely explained and alternatives rarely explored to determine the validity and comparability of the results. Other data analysis methods that might be more appropriate for producing more comparable information were discussed, along with recommendations for further research and cooperative efforts to establish water quality data analysis protocols for producing information for management.
Open Access
Metabolic manipulation of Taxus canadensis for taxol production
(Colorado State University. Libraries, 1999) Phisalaphong, Muenduen, author; Linden, James, advisor; Karim, Nazmul, advisor; Murphy, Vince, committee member; Stushnoff, Cecil, committee member
In order to enhance taxol production in suspension cultures of Taxus sp., the regulation of biosynthetic pathways of the secondary metabolites have been investigated. The studies on elicitation and signal transduction showed interdependence of the ethylene and the methyl jasmonate (MJ) actions in affecting taxol biosynthetic reactions in Taxus canadensis C93AD. Reproducible results from independent experiments demonstrated complex changes in taxol and 10-deacetyl taxol, which increased in a manner proportional to MJ and ethylene concentrations. Based on the hypothesis of binding between biotic elicitors and receptor proteins on the plasma membrane, a mathematical model to explain the effects MJ and ethylene on the formation of taxol and other taxanes was developed. The inhibitory effect of MJ on taxol production, especially at concentrations greater than 100 μM, was observed and expressed in mathematical terms in the developed model. Taxol production was enhanced about 30 fold over unelicited conditions using 0.5% CO2, 15% O2 and 7 ppm ethylene with 200 μM MJ elicitation eight days after cell culture transfer. From precursor studies, improved taxol production can be obtained by supplementation of potential taxol side chain precursors and acetyl CoA together with MJ elicitation. The different profiles observed between taxol-related taxanes and baccatin Ill-related taxanes during elicitation suggest baccatin III may be either a degradation product of taxol or a product of 10-deacetyl baccatin III. The examination of profiles of taxol and 10-deacetyl taxol with different precursor supplements suggests a direct enzymatic reaction leading from 10-deacetyl taxol to taxol. A multivariable statistical method, Principal Component Analysis (PCA), was used for quality monitoring and fault detection of the experimental data. A correlation matrix demonstrated a positive relationship between ethylene and taxane concentration, strong positive linear relationships between MJ and taxol, 10-deacetyl taxol and baccatin III, and a negative relationship between MJ and 10-deacetyl baccatin III. Finally, extension of the stationary phase of the cell cycle in a semi-continuous culture with total cell recycle showed considerable improvement in productivity of taxol and other taxanes relative to batch culture.
Open Access
Cooperative design of a water quality monitoring system for the Big Thompson River Watershed, Colorado
(Colorado State University. Libraries, 1999) Greve, Adrienne I., author; Loftis, Jim C., advisor; Ward, Robert, committee member; Laituri, Melinda, committee member
Water from the Big Thompson River and the Colorado-Big Thompson Project (a trans-mountain diversion of Colorado River water to the Big Thompson River) is a valuable resource to the North Front Range region of Colorado. The water is utilized for many purposes (e.g. municipal, irrigation, industrial, recreation, and ecosystem health). Over half a million people depend on the Big Thompson system for drinking water. In recent years a slow decline in water quality has been observed at some locations, particularly in reservoirs lower in the watershed. This trend, coupled with increased pressure to provide accurate data about water quality, has lead a group of stakeholders in the Big Thompson Watershed to seek a better way in which to monitor and manage their water, through cooperation. Stakeholders within the Big Thompson Watershed, who make up a group called the Big Thompson Watershed Forum (BTWF), formed a partnership with Colorado State University to design a water quality monitoring network. The design process was broken down into five steps: objectives, variables, monitoring locations, sampling frequency, and cost analysis. Each step was completed in a cooperative manner, through a series of meetings with BTWF members. The meetings provided an opportunity for members of the BTWF to shape the monitoring system based upon concerns and priorities specific to the watershed. The resulting water quality network is governed by five objectives. The objectives address regulatory requirements within the watershed, eutrophication of reservoirs, and the estimation of loads, spatial trends, and temporal trends. A variable list of 38 water quality parameters was defined as the minimum group of variables that meet the informational goals laid out in the objectives. The list included 12 inorganic variables, nine metals, five organic parameters, seven microbiological variables, and five field parameters. Monitoring locations were defined based on the objective list, already existing monitoring sites, and watershed hydrology (e.g. mixing distance, confluence locations, diversions). Thirty-nine monitoring locations were chosen; 29 moving water sites and 10 reservoir sites. Each site was given a priority rating of high or low. The group of 31 high priority sites is the smallest network that satisfies the needs of all BTWF participants. The seven low priority monitoring locations will be sampled if financially feasible. Sampling frequency was determined on a seasonal basis. Three seasons were determined based on annual flow and water temperature cycles. It was originally hoped that historical data could be used to estimate background variability, allowing the sample size required for a specified level of accuracy in mean and trend detection to be determined. Only 11, of the 38 variables on the variable list, had historical data available, and only three, of the 11, had enough data to accurately estimate background variability. Sampling frequencies for variables with inadequate historical data were based a maximum frequency set for each season. During seasons one and two, no variable is to be sampled at a frequency higher than twice a month except for biological parameters. The maximum frequency during season three is monthly. The cost estimate step was utilized as a feasibility check on the monitoring program. The aim for the cooperative monitoring program was more thorough information for the same or less cost. If the monitoring program cost exceeded the sum of all current monitoring budgets, adjustments were made in variables, monitoring sites, and sampling frequency. The final cost estimate was $405,259.00 per year, roughly the same as the $401,500.00 currently spent. In order for an undertaking such as this design and monitoring program to succeed, all participants must be willing to compromise and devote large amounts of time in order to allow for a truly cooperative effort. Those individuals most active in the design process typically represented local entities. The resulting monitoring network therefore gave higher priority to local water quality concerns, highlighting the differences between local informational needs and those defined by state and federal governments. The monitoring system currently includes a set of objectives, variable list, monitoring network, and sample frequency. They have been developed, discussed, and agreed upon by all BTWF participants. The completion of the monitoring network indicates that the BTWF is on its way towards the final goal of a long-term monitoring program operated by, and benefiting all agencies involved.
Open Access
Biodegradation of dinitrotoluene by Pseudomonas PR7 in a fluidized bed bioreactor
(Colorado State University. Libraries, 1997) Whitty, Katherine Keesling, author; Reardon, Kenneth F., advisor; Murphy, Vincent G., committee member; Linden, James C., committee member
2,4-Dinitrotoluene (DNT) has been listed as a priority pollutant by the U. S. EPA. It is a waste product in the production of 2,4,6- trinitrotoluene (TNT) and toluene diisocyanate. Pseudomonas PR7 is able to completely degrade DNT via an oxidative pathway. Batch suspended-cell experiments were performed in order to determine the maximum specific growth rate Pmax/ and the Monod half-saturation constant. Ks. Parameter values of μmax = 0.1 h-1 and Ks = 14 mg/L were obtained by fitting experimental data to the Monod model. Immobilized-cell experiments in a fluidized-bed bioreactor (FBB) were performed in order to determine volumetric DNT degradation rate v for the biodegradation of DNT. A fluidized-bed bioreactor was chosen for study because (1) immobilization of cells onto particles allows for greater cell retention, and (2) fluidization of particles allows for mixing within the reactor. Greater cell retention allows for higher flow rates of liquid through the reactor and adequate mixing can alleviate the problem of low oxygen availability and other accumulation or depletion problems which occur in packed beds. Fluidization of immobilized cells in the FBB was achieved by the upflow of air and liquid. Data from residence time distribution (RTD) analysis of the FBB suggests that it behaves as a stirred tank reactor with small plug-flow regions and dead zones. The fluidized-bed bioreactor performance was compared with that of suspended-cell experiments and packed-bed experiments through direct comparison of DNT loading versus degradation rates. It was found that the fluidized-bed bioreactor performed as well as a previously reported system consisting of a packed-bed column in series with a stirred-tank reactor in one experiment using diatomaceous earth particles as the immobilization medium. The FBB did not perform as well as the packed-bed system in subsequent experiments using polycarbonate particles.