Cartilage tissue engineering is an emerging treatment option for osteoarthritis and trauma related joint injuries. A continuing challenge for cartilage tissue engineering is increasing construct extracellular matrix production and material properties. Shear stress and oxygen tension play an important role in tissue engineering of cartilage. In this select stimulatory conditions using combinations of shear stress and oxygen tension have been used to enhance the construct extracellular matrix deposition and material properties. Additionally, a perfusion concentric cylinder bioreactor has been developed to incorporate multiple fluid flow regimes through the construct. This thesis attempts to elucidate the effect of shear stress and biochemical conditions on cartilage development in vitro to provide functional tissue engineered constructs.

Human mesenchymal stem cells (hMSCs) are a promising candidate for cell-based therapies given their therapeutic potential and propensity to grow in vitro. However, to generate the cell numbers required for such applications, robust, reproducible and scalable manufacturing methods need to be developed. To address this challenge, the expansion of hMSCs in a microcarrier-based bioreactor system was investigated. Initial studies performed in T-flask monolayer cultures investigated the effect of key bioprocess parameters such as dissolved oxygen concentration (dO2), the level of medium exchange and the use of serum-free media. 20 % dO2 adversely impacted cell proliferation in comparison to 100 % dO2, whilst FBS-supplemented DMEM was found to be the most consistent and cost-effective cell culture medium despite the advances in serum-free cell culture media. Several microcarriers were screened in 100 mL agitated spinner flasks where Plastic P102-L was selected as the optimal microcarrier for hMSC expansion given the high cell yields obtained, its xeno-free composition and effective harvest capacity. The findings from the initial small-scale studies culminated in the successful expansion of hMSCs on Plastic P102-L microcarriers in a fully equipped 5 L stirred-tank bioreactor (2.5 L working volume), the largest reported volume for hMSC microcarrier culture to date. A maximum cell density of 1.68 x 105 cells/mL was obtained after 9 days in culture; further growth was limited by the low glucose concentration and lack of available surface area. A novel, scalable harvesting method was also developed, allowing for the successful recovery of hMSCs. Importantly, harvested hMSCs retained their immunophenotype, multipotency and ability to proliferate on tissue culture plastic.

A major obstacle to achieving commercially viable lignocellulosic biofuels through consolidated bioprocessing (CBP) is the lack of “industry-ready” microorganisms. Ideally, a CBP-relevant organism would achieve efficient and complete hydrolysis of lignocellulose, simultaneous utilization of the diverse hydrolysis products and high yields of the desired biofuel. To date, no single microbe has been identified that can perform all of these processes at industrially significant levels. As such, thermophilic decaying woodchip compost was investigated as a source of novel lignocellulolytic, biofuel producing bacteria. From a single sample, a collection of physiologically diverse strains were isolated, which displayed differences in substrate utilization and biofuel production capabilities. Molecular characterization of these isolates, and development of a genome relatedness prediction model based on the chaperonin-60 universal target sequence, identified these isolates as strains of Thermoanaerobacter thermohydrosulfuricus. Application of this model to other Thermoanaerobacter spp. further identified that these isolates belong to a divergent and lesser characterized lineage within the genus. Based on this, the CBP-potential of a single isolate, T. thermohydrosulfuricus WC1, was selected for further investigation through metabolic, genomic and proteomic analyses. Its ability to grow on polymeric xylan, potentially catalyzed by an endoxylanase found in only a few Thermoanaerobacter strains, distinguishes T. thermohydrosulfuricus WC1 from many other strains within the genus. The simultaneous consumption of two important lignocellulose constituent saccharides, cellobiose and xylose was also observed and represents a desirable phenotype in CBP-relevant organisms. However, at elevated sugar concentrations, T. thermohydrosulfuricus WC1 produces principally lactate, rather than the desired biofuel ethanol, as the major end-product. Proteomic analysis identified that all likely end-product forming proteins were expressed at high levels suggesting that the end-product distribution patterns in T. thermohydrosulfuricus WC1 are likely controlled via metabolite-based regulation or are constrained by metabolic bottlenecks. The xylanolytic and simultaneous substrate utilization capabilities of T. thermohydrosulfuricus WC1 identify it as a strain of interest for CBP. However, for its development into an “industry-ready” strain as a co-culture with a cellulolytic microorganism, improved biofuel producing capabilities are needed. The practical implications of CBP-relevant phenotypes in T. thermohydrosulfuricus WC1 in relation to other Thermoanaerobacter spp. will be discussed.

Current research efforts are directed at developing competitive processes that can utilize lignocellulose as a feedstock for biorefineries. The purpose of this study was to investigate methods of processing lignocellulosic material so that its monosacharides can be more easily accessed for fermentation, the lack of which is hindering the economics and widescale adoption of lignocellulosic biorefining. The monosaccharides are of interest because they can be used by Clostridium beijerinckii downstream of P. chrysosporium and C. thermocellum in a sequential bioprocess to produce butanol. Butanol is an attractive biofuel because it can be utilized without modifying current transportation infrastructure. Butanol is also used as a starting material in organic synthesis. In the first study, the potential for C. thermocellum' s (ATCC 27405) cellulase system to operate outside its optimal temperature range in a high-solids environments was assessed by quantification of the fermentation products lactate, acetate, and ethanol and by quantification of xylose, glucose, and cellobiose remaining. Additionally, the lignin degrading white-rot fungus Phanerochaete chrysosporium RP 78 was investigated as a potential pretreatment for lignocellulose. Elevated temperatures required for Clostridium thermocellum fermentation were examined as a means to improve poor competiveness that is characteristic of P. chrysosporium on unsterile corn stover substrate.

Hierarchical systems that integrate nano- and macroscale structural elements can offer enhanced stability over traditional immobilization methods. Microparticles were synthesized using interfacial assembly of lipase with (CLMP-N) and without (CLMP) nanoparticles into a crosslinked polymeric core, to determine the impact of the highly ordered system on lipase stability in extreme environments. Kinetic analysis revealed the macrostructure significantly increases the turnover rate (kcat) following immobilization. The macrostructure also stabilized lipase at neutral and basic pH values, while the nanoparticles influenced stability under acidic pH conditions. A greener solvent, choline chloride and urea, was applied to produce sugar ester surfactants. Microparticles exhibited decreases in the turnover rate (kcat) and catalytic efficiency (kcat/Km) following exposure, but retained over 60% and 20% activity after exposure at 50 ºC and 60 ºC, respectively. CLMP and CLMP-N outperformed the commercially available lipase per unit protein in the production of sugar esters. The utilization of greener solvent systems with hierarchical immobilized enzyme systems has the potential to improve processing efficiency and sustainability for the production of value-added agricultural products.

No description available.

This dissertation introduces the fundamental principles and practical aspects of neural networks, focusing on their applications in bioprocessing and chemical engineering. This study introduces neural networks and provides an overview of their structures, strengths, and limitations, together with a survey of their potential and commercial applications (Chapter 1). In addition to covering both the fundamental and practical aspects of neural computing (Chapter 2), this dissertation demonstrates, by numerous illustrative examples, practice problems, and detailed case studies, how to develop, train and apply neural networks in bioprocessing and chemical engineering. This study includes the neural network applications of interest to the biotechnologists and chemical engineers in four main groups: (1) fault classification and feature categorization (Chapter 3); (2) prediction and optimization (Chapter 4); (3) process forecasting, modeling, and control of time-dependent systems (Chapter 5); and (4) preliminary design of complex processes using a hybrid combination of expert systems and neural networks (Chapter 6). This dissertation is also unique in that it includes the following ten detailed case studies of neural network applications in bioprocessing and chemical engineering: · Process fault-diagnosis of a chemical reactor. · Leonard-Kramer fault-classification problem. · Process fault-diagnosis for an unsteady-state continuous stirred-tank reactor system. · Classification of protein secondary-structure categories. · Quantitative prediction and regression analysis of complex chemical kinetics. · Software-based sensors for quantitative predictions of product compositions from fluorescent spectra in bioprocessing. · Quality control and optimization of an autoclave curing process for manufacturing composite materials. · Predictive modeling of an experimental batch fermentation process. · Supervisory control of the Tennessee Eastman plant-wide control problem · Predictive modeling and optimal design of extractive bioseparation in aqueous two-phase systems This dissertation also includes a glossary, which explains the terminology used in neural network applications in science and engineering. / Ph. D.

The research presented in this dissertation supports the overall goal of creating piezoelectric measurement technology for the analysis and characterization of soft materials that serve as feedstocks (inputs) and products (outputs) of emerging biomanufacturing processes, including cell and additive biomanufacturing processes. The first objective was to define measurement challenges associated with real-time monitoring of material compositional profiles using biosensors in practical biomanufacturing and bioprocessing formats, as insight into a material's composition (i.e., concentration of a given biologic within a material or product) provides molecular-scale insight into processes and product quality. The second objective was to design, fabricate, and characterize continuous flow cell separation technology based on 3D printed self-exciting and -sensing millimeter-scale piezoelectric transducers and microfluidic networks for separation and characterization of expanded therapeutic cells. The third objective was to establish a sensor-based characterization approach for viscoelastic properties of hydrogels and gelation processes using high-order modes of piezoelectric-excited millimeter cantilever (PEMC) sensors and understand the influence of cantilever mode number on critical sensor characteristics, including sensitivity, dynamic range, and limit of detection. The first objective was addressed through a comprehensive review of recent progress in electrochemical and hybrid biosensors, which included discussions of measurement formats, sensor performance, and measurement challenges associated with use in practical bioprocessing environments. This critical review revealed that cost, disposability, form factor, complex measurement matrices, multiplexing, and sensor regeneration/reusability are among the most pressing challenges that require solutions through advancement of sensor design and manufacturing approaches before biosensors can facilitate high-confidence long-term continuous bioprocess monitoring. The second objective was addressed by creating a microextrusion-based additive manufacturing approach for fabrication of piezoelectric-based MEMS devices that enabled integration of 3D configurations of piezoelectric transducers and microfluidic networks in a one-pot manufacturing process. The devices contained orthogonal out-of-plane piezoelectric sensors and actuators and generated tunable bulk acoustic waves (BAWs) capable of size-selective manipulation, trapping, and separation of suspended particles in droplets and microchannels. This work suggests that additive manufacturing potentially provides new opportunities for the fabrication of sensor-integrated microfluidic platforms for cell culture analysis. The third objective was addressed through resonant frequency tracking of low- and high-order modes in dynamic-mode cantilevers to enable the real-time characterization of hydrogel viscoelastic properties and continuous monitoring of sol-gel phase transitions over a wide dynamic range using practically relevant hydrogel systems used commonly in additive biomanufacturing. This work suggests that high-order modes of PEMC sensors facilitate characterization of hydrogel viscoelastic properties and gelation processes with improved dynamic range and limit of detection that can complement the performance of low-order modes. Through this research, new approaches for sensor-based characterization of soft material composition and mechanical properties using millimeter-scale piezoelectric devices are presented as solutions for current challenges in biomanufacturing and biosensing to advance capability in real-time sensing of quality attributes among biomanufactured products. / Doctor of Philosophy / The research presented in this dissertation supports the overall goal of creating sensor-based measurement technology for quality assessment of soft materials within practical online biosensing and biomanufacturing processing formats. This technology seeks to enable monitoring and control of product quality in real-time. Soft biomaterials used in these processes, including cells and hydrogels, can be characterized by quality signatures such as concentration of analytes and physical and mechanical properties. Separation and fluid handling technologies aid real-time characterization when integrated with the processing system. By improving sensor-based measurement capability of soft materials, sensing platforms can provide online quality assurance and control, thereby increasing the product quality and process efficiency – or yield– at reduced cost. The first objective was to define measurement challenges and limitations associated with detection of biologics in practical biomanufacturing and bioprocessing formats (with focus on pathogen detection, as the detection of adventitious agents and pathogens remains a critical aspect of bioprocess monitoring). This was addressed through a comprehensive review of recent progress in the field of electrochemical and hybrid biosensors. The second objective was to design and fabricate sensor-integrated microfluidic technology for cell separation applications using a combination of multi-material 3D printing and pick-and-place techniques. The third objective was to improve measurement capability of piezoelectric sensors for characterization of viscoelastic properties of hydrogel formulations commonly used in additive biomanufacturing processes and tissue engineering. Through this research, new approaches for sensor-based characterization of soft materials using millimeter-scale piezoelectric devices are presented as solutions for current challenges in biomanufacturing and biosensing platforms in order to advance quality assessment capability.

Hydrogen production from abundant renewable biomass would decrease reliance on crude oils, achieve nearly zero net greenhouse gas emissions, create more jobs, and enhance national energy security. Cell-free synthetic pathway biotransformation (SyPaB) is the implementation of complicated chemical reaction by the in vitro assembly of numerous enzymes and coenzymes. Two of the biggest challenges for its commercialization are: effective release of fermentable sugars from pretreated biomass, and preparations of thermostable enzymes with low-cost. The hydrolysis performance of 21 reconstituted bacterial cellulase mixtures containing the glycoside hydrolase family 5 Bacillus subtilis endoglucanase, family 9 Clostridium phytofermentans processive endoglucanase, and family 48 Clostridium phytofermentans cellobiohydrolase was investigated on microcrystalline cellulose (Avicel) and regenerated amorphous cellulose (RAC). The optimal ratios for maximum cellulose digestibility were dynamic for Avicel but nearly fixed for RAC. Processive endoglucanase CpCel9 was most important for high cellulose digestibility regardless of substrate type. These results suggested that the hydrolysis performance of reconstituted cellulase cocktail strongly depended on experimental conditions. Thermobifida fusca YX was hypothesized to have a thermophilic polyphosphate glucokinase. T. fusca YX ORF Tfu_1811 encoding a putative PPGK was cloned and the recombinant protein fused with a family 3 cellulose-binding module (CBM-PPGK) was over expressed in Escherichia coli. By a simple one-step immobilization, the half-life time increased to 2 h, at 50 °C. These results suggest that this enzyme was the most thermostable PPGK reported. My studies would provide important information for the on-going project: high-yield hydrogen production from cellulose by cell-free synthetic enzymatic pathway. / Master of Science

Doctor of Philosophy / Department of Grain Science and Industry / Praveen V. Vadlani / As the world population continues to grow and the uncertainty of petroleum and food availability transpires, alternative resources will be needed to meet our demands. Single cell oil (SCO) from oleaginous yeast is a renewable noncrop-based resource that can be used for the production of petroleum counterparts. Currently, commercial production is limited, mainly due to high production costs and competition from cheaper alternatives. As a result, improved fermentation techniques, utilization of low-valued feedstocks and efficient downstream processing would be highly valuable. The major objectives of this study were to: 1) optimize fermentation conditions for the development of a novel fed-batch fermentation to enhance oil production using Lipomyces starkeyi, 2) determine the major lipids produced by L. starkeyi, 3) utilize low-valued hemicellulose-rich feedstocks for oil production, and 4) demonstrate the use of 2-methyltetrahydrofuran (2-MeTHF) and cyclopentyl methyl ether (CPME) as greener solvents for oil extraction. Under optimized fermentation conditions, the oil yield increased from 78 to 157 mg oil/g sugar when supplying xylose rather than glucose as the major carbon source. A novel repeated fed-batch fermentation supplying glucose for growth and xylose for lipid accumulation generated the highest oil yield of 171 mg oil/g sugar, oil content of 60% (dry mass basis) and oil productivity of 143 mg oil/L/hr. Oleic acid accounted for 70% of the total fatty acid profile indicating that oil from L. starkeyi is a naturally high source of oleic acid; an added benefit for the biofuel, cosmetic, food, and oleochemical industries. Hemicellulose-rich corn bran and wheat bran were successfully used to produce oil; oil yields of 125 and 71 mg oil/g sugar were reported for whole and de-starched bran hydrolysates, respectively. Compared to traditional methods, biphasic oil extraction systems of 2-MeTHF and CPME had an 80 and 53% extraction efficiency and 64 and 49% selectivity, respectively. The information from this study will be useful for the development of an integrated approach to improve the viability of SCO biochemical platforms for the production of advanced biofuels and renewable chemicals.