In the first part of this research, we constructed a Genome scale Metabolic Model (GEM) of Taxus cuspidata, a medicinal plant used to produce paclitaxel (Taxol®). The construction of the T. cuspidata GEM was predicated on recent acquisition of a transcriptome of T. cuspidata metabolism under methyl jasmonate (MJ) elicited conditions (when paclitaxel is produced) and unelicited conditions (when paclitaxel is not produced). Construction of the draft model, in which transcriptomic data from elicited and unelicited conditions were included, utilized tools including the ModelSEED developed by Argonne National Laboratory. Although a model was successfully created and gapfilled by ModelSEED using their software, we were not able to reproduce their results using COBRA, a widely accepted FBA software package. Further work needs to be done to figure out how to run ModelSEED models on commonly available software. In the second part of this research, we modeled the MJ elicited/defense response phenotype in Arabidopsis thaliana. Previously published models of A. thaliana were tested for suitability in modeling the MJ elicited phenotype using publicly available computation tools. MJ elicited and unelicited datasets were compared to ascertain differences in metabolism between these two phenotypes. The MJ elicited and unelicited datasets were significantly different in many respects, including the expression levels of many genes associated with secondary metabolism. However, it was found that the expression of genes related to growth and central metabolism were not generally significantly different for the MJ+ and MJ- datasets, the pathways associated with secondary metabolism were incomplete and could not be modeled, and FBA methods did not show the difference in growth that was expected. These results suggest that behavior associated with the MJ+ phenotype such as slow growth and secondary metabolite production may be controlled by factors not easily modeled with transcriptome data alone. Additional research was performed in the area of cryosectioning and immunostaining of fixed Taxus aggregates. Protocols developed for this work can be found in Appendix B.

One of the most promising routes to renewable liquid fuels and chemicals is the fermentation of waste carbon by specialized microbes. Commercial development of gas fermentation technology is underway but many fundamental research problems must be addressed to further advance the technology towards economic competitiveness. This thesis addresses the important problem of developing integrated metabolic and transport models that predict gas fermentation performance in industrially relevant bubble column reactors. The computational models describe the conversion of CO-rich waste streams including synthesis gas to the platform chemical butyrate. The proposed modeling approach involves combining genome-scale reconstructions of bacterial species metabolism with transport equations that govern the relevant multiphase convective and diffusional processes within the spatially-varying system. I compared the combination of the acetogen Clostridium autoethanogenum for CO conversion to the intermediate acetate and three different gut bacteria (Clostridium hylemonae, Eubacterium rectale and Roseburia hominis) for conversion of acetate to butyrate. Trial-and-error optimization of the three co-culture designs was performed to assess their relative performance and guide future experimental studies.

Lung cancer is one of the leading causes of cancer deaths in the United States. Radiation and chemotherapy are conventional treatments, but they result in serious side effects and the probability of tumor recurrence remains high. Therefore, there is an increasing need to enhance the efficacy of conventional treatments. Magnetic nanoparticles have been previously studied for a variety of applications such as magnetic resonance imaging contrast agents, anemia treatment, magnetic cell sorting and magnetically mediated hyperthermia (MMH). In this work, dextran coated iron oxide nanoparticles were developed and functionalized with peptides to target the nanoparticles to either the extracellular matrix (ECM) of tumor tissue or to localize the nanoparticles in subcellular regions after cell uptake. The magnetic nanoparticles were utilized for a variety of applications. First, heating properties of the nanoparticles were utilized to administer hyperthermia treatments combined with chemotherapy. The nanoparticles were functionalized with peptides to target fibrinogen in the ECM and extensively characterized for their physicochemical properties, and MMH combined with chemotherapy was able to enhance the toxicity of chemotherapy. The second application of the nanoparticles was magnetically mediated energy delivery. This treatment does not result in a bulk temperature rise upon actuation of the nanoparticles by an alternating magnetic field (AMF) but rather results in intracellular damage via friction from Brownian rotation or nanoscale heating effects from Neél relaxations. The nanoparticles were functionalized with a cell penetrating peptide to facilitate cell uptake and lysosomal escape. The intracellular effects of the internalized nanoparticles alone and with activation by an AMF were evaluated. Iron concentrations in vivo are highly regulated as excess iron can catalyze the formation of the hydroxyl radical through Fenton chemistry. Although often a concern of using iron oxide nanoparticles for therapeutic applications, these inherent toxicities were harnessed and utilized to enhance radiation therapy. Therefore, the third application of magnetic nanoparticles was their ability to catalyze reactive oxygen species formation and increase efficacy of radiation. Overall, iron oxide nanoparticles have a variety of cancer therapy applications and are a promising class of materials for increasing efficacy and reducing the side effects of conventional cancer treatments.

The recreation of the complicated tissue microenvironment is essential to reduce the gap between in vitro and in vivo research. Polysaccharide-based hydrogels form excellent scaffolds to allow for three-dimensional cell culture owing to the favorable properties such as capability to absorb large amount of water when immersed in biological fluids, ability to form “smart hydrogels” by being shear-thinning and thixotropic, and eliciting minimum immunological response from the host. In this study, the biodegradable shear-thinning polysaccharide, gellan-gum based hydrogel was investigated for the conditions and concentrations in which it can be applied for the adhesion, propagation and assembly of different mammalian cell types in an unmodified state, at physiological conditions of temperature. Cell studies, to show successful propagation and assembly into three-dimensional structures, were performed in the range of hydrogels which were deemed to be optimum for cell culture and the cell types were chosen to represent each embryonic germ layer, i.e., human neural stem cells for ectoderm, human brain microvasculature cells for mesoderm, and murine β-cells for endoderm, along with a pluripotent cell line of human induced pluripotent stem cells, derived from human foreskin fibroblasts. Three-dimensional cell organoid models, to allow for gellan gum based bioprinting, were also developed using human induced pluripotent stem cells and human neural stem cells.

Energy functions are found to be a key of protein structure prediction. In this work, we propose a novel 3-dimensional energy function based on hydrophobic-hydrophilic properties of amino acid where we consider at least three different possible interaction of amino acid in a 3-dimensional sphere categorized as hydrophilic versus hydrophilic, hydrophobic versus hydrophobic and hydrophobic versus hydrophilic. Each of these interactions are governed by a 3-dimensional parameter alpha used to model the interaction and 3-dimensional parameter beta used to model weight of contribution. We use Genetic Algorithm (GA) to optimize the value of alpha, beta and Z-score. We obtain three energy scores libraries from a database of 4332 protein structures obtained from Protein Data Bank (PDB) server. Proposed energy function is found to outperform nearest competitor by 40.9% for the most challenging Rosetta decoy as well as better in terms of the Z-score based on Moulder and Rosetta decoy sets.

Biofuels produced from lignocellulosic biomass via the fermentation platform are sustainable energy alternatives to fossil fuels. Process Systems Engineering (PSE) uses computer-based tools and methods to design, simulate and optimize processes. Application of PSE tools to the design of economic biorefinery processes requires the development of simulation approaches that can be integrated with existing, mature PSE tools used to optimize traditional refineries, such as Aspen Plus. Current unit operation models lack the ability to describe unsteady state fermentation processes, link unsteady state fermentation with in situ separations, and optimize these processes for competing factors (e.g., yield and productivity). This work applies a novel architecture of commercial PSE tools, Aspen Plus and MATLAB, to develop techniques to simulate time-dependent fermentation without and with in situ separations for process design, analyses and optimization of the operating conditions. Traditional batch fermentation simulations with in situ separations decouple these interdependent steps in a separate “steady state” reactor followed by an equilibrium separation of the final fermentation broth. A typical mechanistic system of ordinary differential equations (ODEs) describing a batch fermentation does not fit the standard built-in power law reaction kinetics model in Aspen Plus. To circumvent this challenge, a novel platform that links the batch reactor to a FORTRAN user kinetics subroutine (incorporates the ODEs) combined with component substitution (to simulate non-databank components) is utilized to simulate an unsteady state batch and in situ gas stripping process. The resulting model system predicts the product profile to be sensitive to the gas flow rate unlike previous “steady state” simulations. This demonstrates the importance of linking a time-dependent fermentation model to the fermentation environment for the design and analyses of fermentation processes. A novel platform linking the genetic algorithm multi-objective and single-objective optimizations in MATLAB to the unsteady state batch fermentation simulation in Aspen Plus through a component object module communication platform is utilized to optimize the operating conditions of a typical batch fermentation process. Two major contributions are: prior concentration of sugars from a typical lignocellulosic hydrolysate may be needed and with a higher initial sugar concentration, the fermentation process must be integrated with an in situ separation process to optimize the performance of fermentation processes. With this framework, fermentation experimentalists can use the full suite of PSE tools and methods to integrate biorefineries and refineries and as a decision-support tool to guide the design, analyses and optimization of fermentation-based biorefineries.

Including inherited genetic diseases, like lipoprotein lipase deficiency, and acquired diseases, such as cancer and HIV, gene therapy has the potential to treat or cure afflicted people by driving an affected cell to produce a therapeutic protein. Using primarily viral vectors, gene therapies are involved in a number of ongoing clinical trials and have already been approved by multiple international regulatory drug administrations for several diseases. However, viral vectors suffer from serious disadvantages including poor transduction of many cell types, immunogenicity, direct tissue toxicity and lack of targetability. Non-viral polymeric gene delivery vectors (polyplexes) provide an alternative solution but are limited by poor transfection efficiency and cytotoxicity. Microfluidic (MF) nano-precipitation is an emerging field in which researchers seek to tune the physicochemical properties of nanoparticles by controlling the flow regime during synthesis. Using this approach, several groups have demonstrated the successful production of enhanced polymeric gene delivery vectors. It has been shown that polyplexes created in the diffusive flow environment have a higher transfection efficiency and lower cytotoxicity. Other groups have demonstrated that charge-stabilizing polyplexes by sequentially adding polymers of alternating charges improves transfection efficiency and serum stability, also addressing major challenges to the clinical implementation of non-viral gene delivery vectors. To advance non-viral gene delivery towards clinical relevance, we have developed a microfluidic platform (MS) that produces conventional polyplexes with increased transfection efficiency and decreased toxicity and then extended this platform for the production of ternary polyplexes. This work involves first designing microfluidic devices using computational fluid dynamics (CFD), fabricating the devices, and validating the devices using fluorescence flow characterization and absorbance measurements of the resulting products. With an integrated separation mechanism, excess polyethylenimine (PEI) is removed from the outer regions of the stream leaving purified polyplexes that can go on to be used directly in transfections or be charge stabilized by addition of polyanions such as polyglutamic acid (PGA) for the creation of ternary polyplexes. Following the design portion of the research, the device was used to produce binary particle characterization was carried out and particle sizes, polydispersity and zeta potential of both conventional and MS polyplexes was compared. MS-produced polyplexes exhibited up to a 75% reduction in particle size compared to BM-produced polyplexes, while exhibiting little difference in zeta potential and polydispersity. A variety of standard biological assays were carried out to test the effects of the vectors on a variety of cell lines – and in this case the MS polyplexes proved to be both less toxic and have higher transfection efficiency in most cell lines. HeLa cells demonstrated the highest increase in transgene expression with a 150-fold increase when comparing to conventional bulk mixed polyplexes at the optimum formulation. A similar set of experiments were carried out with ternary polyplexes produced by the separation device. In this case it was shown that there were statistically significant increases in transfection efficiency for the MS-produced ternary polyplexes compared to BM-produced poyplexes, with a 23-fold increase in transfection activity at the optimum PEI/DNA ratio in MDAMB-231 cells. These MS-produced ternary polyplexes exhibited higher cell viability in many instances, a result that may be explained but the reduction in both free polymer and ghost particles.

The cell plasma membrane is an interactive interface playing an important role in regulating cell-to-cell, cell-to-tissue contact, and cell-to-environment responses. This environment-responsive phospholipid layer consisting of multiple dynamically balanced macromolecules, such as membrane proteins, carbohydrate and lipids, is regarded as a promising platform for various surface engineering strategies. Through different chemical modification routes, we are able to incorporate various artificial materials into the cell surface for biomedical applications in small molecule and cellular therapeutics. In this dissertation, we establish two different cell coating techniques for applications of cell-mediated drug delivery and the localization of cell-based therapies to specific tissues. The first part of this dissertation establishes a membrane-associated hydrogel patch for drug delivery. The crosslinking of a grafted polymeric patch from a mammalian cell membrane is achieved through surface-mediated photolithographic polymerization. With the use of photomask, the formation of nanoparticle-loaded PEGDA hydrogel is controlled to deposit various geometric features on photoinitiator-immobilized surfaces. Through microarray patch patterning, we analyzed the influence of processing parameters on the accuracy of polymer patterning on a microarray. We then optimized the patterning approach for the formation of PEGDA patches on live A549 cells. In the second part of this dissertation, we study the use of tissue-adhesive coatings to improve the retention of therapeutic mesenchymal stem cells (MSCs) in the heart following intramyocardial or intravenous injection. MSCs were coated with antibodies against ICAM1 to adhere to CAM-overexpressed endothelium present in the heart following MI. Through intramyocardial or intravenous delivery, we observe higher number of coated cells retained in the heart over uncoated ones, supporting enhanced affinity for the inflamed endothelium near the infarct. We correlate the detachment force of antigen-interacted MSCs by a parallel laminar flow assay with the density of ICAM on the substrate and the density of anti-ICAM on the MSC surface. MSC retention on CAMmodified surfaces or activated HUVECs was significantly increased on antibody-coated groups (~90%) under physiologically hemodynamic forces (< 30dyne/cm2), compared to uncoated MSCs (~20%). Moreover, a dramatic reduction of immune cell quantity was observed after intravenous injection, indicating the enhanced immunoregulatory efficacy by systemically delivering ICAM-adhesive MSCs to the site of inflammation.

Mucin networks are formed by the complexation of bottlebrush-like mucin glycoprotein with other small molecule glycoproteins. These glycoproteins create nanoscale strands that then arrange into a nanoporous mesh. These networks play an important role in ensuring surface hydration, lubricity and barrier protection. In order to understand the functional behavior in mucin networks, it is important to decouple their chemical and physical effects responsible for generating the fundamental property-function relationship. To achieve this goal, we propose to develop a synthetic biomimetic mucin using a layer-by-layer (LBL) deposition approach. In this work, a hierarchical 3-dimensional structures resembling natural mucin networks was generated using affinity-based interactions on synthetic and biological surfaces. Unlike conventional polyelectrolyte-based LBL methods, pre-assembled biotin-functionalized filamentous (worm-like) micelles was utilized as the network building block, which from complementary additions of streptavidin generated synthetic networks of desired thickness. The biomimetic nature in those synthetic networks are studied by evaluating its structural and bio-functional properties. Structurally, synthetic networks formed a nanoporous mesh. The networks demonstrated excellent surface hydration property and were able capable of microbial capture. Those functional properties are akin to that of natural mucin networks. Further, the role of synthetic mucin as a drug delivery vehicle, capable of providing localized and tunable release was demonstrated. By incorporating antibacterial curcumin drug loading within synthetic networks, bacterial growth inhibition was also demonstrated. Thus, such bioactive interfaces can serve as a model for independently characterizing mucin network properties and through its role as a drug carrier vehicle it presents exciting future opportunities for localized drug delivery, in regenerative applications and as bio-functional implant coats.

The ionomer-membrane interface in a membrane electrode assembly connects the catalyst and membrane and allows hydrated protons to move between the catalyst and membrane. The continuous operation of the polymer membrane electrolyte fuel cell at high temperature and/or in frequent freeze/thaw cycles leads to membrane degradation and delamination of the interface, which lower the proton conductivity. In this dissertation, we modeled the chemical degradation and proton conductivity of perfluorosulfonic acid (PFSA) ionomers by ab initio calculations and macroscopic modeling. All ab initio calculations were performed using Gaussian 03 suites of program by employing B3LYP/6-311++G** method/basis set. The macroscopic modeling involves nonequilibrium thermodynamics. The results show that PFSA membranes can degrade both via side-chain and backbone in the presence of hydroxyl radical. The energetics of homolytic bond cleavage show that the C–S bond in the side-chain is the weakest link and breaks exothermally in the presence of hydroxyl radical. The C–S bond in the membrane fragment radical can break at low activation energy. The side-chain degradation also leads to the split of the backbone into two parts. The backbone degradation starts with the reaction of –COOH impurities in the backbone with the hydroxyl radical, which has the lowest activation energy, and follows an “unzipping mechanism”. The reactions in this mechanism are exothermic. The channels in the interface were modeled as cylindrical pores and the anionic charges were fixed on the pore wall. The analytical expression of proton conductivity was derived from the evolution equations for mass and momentum of hydronium ions by using an order of magnitude analysis. The results show that the conductivity increases with increasing water content and pore radius. The conductivity usually increases on decreasing the separation distance between sulfonates on the length and decreases with decreasing sulfonates separation distance on the circumference. The conductivity of the two pores, one of the interface and the other of the membrane, is closer to the conductivity of the pore with the lowest conductivity and its magnitude depends on the relative radius and length of the pores.