Biochemical and Biomolecular Engineering Commons^™

Expedited Pcr With Stirring, Hendrik Viljoen

Department of Chemical and Biomolecular Engineering: Faculty Publications

Disclosed are an apparatus and methods for rapid amplification of nucleic acids. More particularly, the present dis closure relates to an apparatus for mixing a reaction solution during amplification of nucleic acids and to methods for amplifying nucleic acids. Also disclosed are methods for lysing cells in a sample and amplifying nucleic acids.

Finite Element Modelling And Exergy Analysis Of A Solar Thermal Hollow Fiber Vacuum Membrane Distillation System, Benjamin Shuldes

Department of Chemical and Biomolecular Engineering: Dissertations, Theses, and Student Research

A finite element model was developed to investigate the performance of a vacuum membrane distillation module under various operating conditions and membrane parameters. Porosity, tortuosity, pore diameter, membrane thickness, and fiber length were varied along with feed temperature, velocity, and flow configuration. In all cases, boundary layer polarization phenomena were seen to inhibit the performance of the module. At certain conditions, for a 7.5 cm fiber, the reduction in permeate flux from 65 LMH (Liter/m²/h) at the inlet to below 45 LMH at the outlet of the fibers was observed. In most cases, salt concentration polarization was the …

Metabolic Modeling And Omics-Integrative Analysis Of Single And Multi-Organism Systems: Discovery And Redesign, Mohammad Mazharul Islam

Department of Chemical and Biomolecular Engineering: Dissertations, Theses, and Student Research

Computations and modeling have emerged as indispensable tools that drive the process of understanding, discovery, and redesign of biological systems. With the accelerating pace of genome sequencing and annotation information generation, the development of computational pipelines for the rapid reconstruction of high-quality genome-scale metabolic networks has received significant attention. These models provide a rich tapestry for computational tools to quantitatively assess the metabolic phenotypes for various systems-level studies and to develop engineering interventions at the DNA, RNA, or enzymatic level by careful tuning in the biophysical modeling frameworks. in silico genome-scale metabolic modeling algorithms based on the concept of optimization, …

Creation And Application Of Various Tools For The Reconstruction, Curation, And Analysis Of Genome-Scale Models Of Metabolism, Wheaton L. Schroeder

Department of Chemical and Biomolecular Engineering: Dissertations, Theses, and Student Research

Systems biology uses mathematics tools, modeling, and analysis for holistic understanding and design of biological systems, allowing the investigation of metabolism and the generation of actionable hypotheses based on model analyses. Detailed here are several systems biology tools for model reconstruction, curation, analysis, and application through synthetic biology. The first, OptFill, is a holistic (whole model) and conservative (minimizing change) tool to aid in genome-scale model (GSM) reconstructions by filling metabolic gaps caused by lack of system knowledge. This is accomplished through Mixed Integer Linear Programming (MILP), one step of which may also be independently used as an additional curation …

Exploration Of The Sludge Biodiesel Pathway, Zachary Christman

Department of Agronomy and Horticulture: Dissertations, Theses, and Student Research

Wastewater sludge is an overlooked source of fat, oil, and grease (FOG) that could be converted into biodiesel. The United States produces about 8 million tons of sludge per year. The disposal cost for this amount of sludge is about 2 billion US dollars. The widespread availability and low cost of sludge compared to other biodiesel raw materials make it an economical choice for a renewable fuel. Using sludge as a raw material can produce 25 to 30 mg per gram of fatty acid methyl ester (FAME); the main component of biodiesel. Sludge biodiesel has the potential of transforming a …

Quantitative Pcr Of Small Nucleic Acids: Size Matters, Jay Min Lim, Rahul Tevatia, Ravi Saraf

Department of Chemical and Biomolecular Engineering: Faculty Publications

Quantitative dysregulation in small nucleic acids (NA), such as microRNA (miRNA), extracted from minimally invasive biopsies, such as, blood, stool, urine, nose, throat, are promising biomarker for diseases diagnosis and management. We quantify the effect of the extra step of poly(A) ligation for cDNA synthesis and small size of the NA on the limit of quantification (LOQ) of quantitative PCR (qPCR), the gold standard to measure copy number. It was discovered that for small NA, the cycle threshold, Ct that is proportional to −log[c], where [c] is the concentration of the target NA exhibits a sharp transition. The results indicate …

Modeling The Interplay Between Photosynthesis, Co2 Fixation, And The Quinone Pool In A Purple Non-Sulfur Bacterium, Adil Alsiyabi

Department of Chemical and Biomolecular Engineering: Dissertations, Theses, and Student Research

Rhodopseudomonas palustris CGA009 is a purple non-sulfur bacterium (PNSB) that can fix CO₂ and nitrogen or break down organic compounds for its carbon and nitrogen requirements. Light, inorganic, and organic compounds can all be used for its source of energy. Excess electrons produced during its metabolic processes can be exploited to produce hydrogen gas or biodegradable polyesters (polyhydroxybutyrate). A genome-scale metabolic model of the bacterium was reconstructed to study the interactions between photosynthesis, carbon dioxide fixation, and the redox state of the quinone pool. A comparison of model-predicted flux values with published in vivo MFA fluxes resulted in predicted …

Bioproduction Of Adipic Acid Using Engineered Pseudomonas Putida Kt2440 From Lignin-Derived Aromatics, Howard Willett

Department of Chemical and Biomolecular Engineering: Dissertations, Theses, and Student Research

Current industrial synthesis of adipic acid is nonrenewable and depends on a carcinogenic starting material, benzene. Biocatalysis with an engineered microorganism could turn a renewable feedstock into a value-added chemical such as adipic acid. Here we engineered P. putida KT2440 to transform lignin-derived aromatics, coumarate and ferulate, into adipic acid. Lignin is a recalcitrant plant biopolymer burned for thermal energy. Conversion of lignin into a value-added chemical will improve the efficiency of lignocellulose processing plants. The best performing engineered KT2440 strain produces 2.52 mM adipate at a 9.5% (mole/mole) yield. This was achieved by the genetic insertion of non-natural biosynthetic …

Fibrinogen, Factor Xiii And Fibronectin: A Biophysical And Kinetic Characterization Of Their Interactions, Frank Fabian

Department of Chemical and Biomolecular Engineering: Dissertations, Theses, and Student Research

The development of recombinant-based liquid fibrin tissue sealants having enhanced hemostatic and wound healing properties will involve understanding as yet not well characterized interactions between fibrinogen, fibrin (Fbn) factor XIII, thrombin and fibronectin. We study these phenomena in the context of comparing plasma derived fibrinogen to recombinant fibrinogen (rFI) produced in the milk of transgenic cows. An abundance of purified γγ and γγ’ FI subspecies enables detailed study of γγ or γγ’ biomonomer and their respective Fbn biopolymer formation as having different substrate behaviors of activated plasma derived factor XIII (pFXIIIa₂b₂). High pressure size exclusion (HPSEC) …

Biomethane Production From Distillery Wastewater, Zachary Christman

Department of Agronomy and Horticulture: Dissertations, Theses, and Student Research

Distillery wastewater treatment is a great ecological problem, for example, India produces 2.7 billion liters of alcohol that results in 40 billion liters of wastewater. However, this material can be seen as a resource since 11 million cubic meters of biogas at 60% methane could be produced in addition to cleaning the water. The distillery has two options of what to do with the biogas. The first is to use the biogas to fuel the distillery making the production plant more energy efficient and removing some of the need to buy natural gas. The other is to upgrade the biogas …

Uncoupling Fermentative Synthesis Of Molecular Hydrogen From Biomass Formation In Thermotoga Maritima, Raghuveer Singh, Derrick White, Yaşar Demirel, Robert Kelley, Kenneth Noll, Paul H. Blum

Department of Chemical and Biomolecular Engineering: Faculty Publications

When carbohydrates are fermented by the hyperthermophilic anaerobe Thermotoga maritima, molecular hydrogen (H₂) is formed in strict proportion to substrate availability. Excretion of the organic acids acetate and lactate provide an additional sink for removal of excess reductant. However, mechanisms controlling energy management of these metabolic pathways are largely unexplored. To investigate this topic, transient gene inactivation was used to block lactate production as a strategy to produce spontaneous mutant cell lines that overproduced H₂ through mutation of unpredicted genetic targets. Single-crossover homologous chromosomal recombination was used to disrupt lactate dehydrogenase (encoded by ldh) with …

Sustainable Waste-To-Energy Technologies: Bioelectrochemical Systems, Rami Ziara, Bruce Dvorak, Jeyamkondan Subbiah

Department of Civil and Environmental Engineering: Faculty Publications

The food industry produces a large amount of waste and wastewater, of which most of the constituents are carbohydrates, proteins, lipids, and organic fibers. Therefore food wastes are highly biodegradable and energy rich. Bioelectrochemical systems (BESs) are systems that use microorganisms to biochemically catalyze complex substrates into useful energy products, in which the catalytic reactions take place on electrodes. Microbial fuel cells (MFCs) are a type of bioelectrochemical systems that oxidize substrates and generate electric current. Microbial electrolysis cells (MECs) are another type of bioelectrochemical systems that use an external power source to catalyze the substrate into by-products such as …

Genetic Code Expansion In Biochemical Investigations And Biomedical Applications, Nanxi Wang

Department of Chemistry: Dissertations, Theses, and Student Research

Genetic code expansion provides a powerful tool for site-specific incorporation of unnatural amino acids (unAAs) with novel biochemical and physiological properties into proteins in live cells and organisms. To achieve this, a nonsense codon suppression system, which consists of an orthogonal aminoacyl-tRNA synthetase (aaRS) and tRNA pair that specifically decodes a nonsense codon (e.g., amber codon and quadruplet codon) with an unAA but do not “cross talk” with their endogenous counterparts, was established. This Ph.D. thesis presents our efforts on evolution and application of nonsense codon suppression systems for biochemical and biomedical investigations.

In Chapter 1, a brief overview of …

Sugar Versus Lipid For Sustainable Biofuels, Yaşar Demirel

Yaşar Demirel Publications

Introduction

First‐generation biofuels, namely, ethanol and biodiesel, have led to far reaching impact on the peoples’ life world‐wide.[1] However, they inter-fere with the food supply chain and may not be sustainable although some of the biomass are converted to biofuels after those biomasses have met the human needs. Still, the first‐generation–based biofuels have proved that sugar and lipid platforms can be an answer to energy security and global warming concerns without the need for new infrastructure for feedstock delivery as well as for biomass‐to‐biofuel conversion tech-nologies. At the same time, we are discovering and assessing the long‐term environmental im-plications on …

Characterization Of Molecular Communication Based On Cell Metabolism Through Mutual Information And Flux Balance Analysis, Zahmeeth Sayed Sakkaff

School of Computing: Dissertations, Theses, and Student Research

Synthetic biology is providing novel tools to engineer cells and access the basis of their molecular information processing, including their communication channels based on chemical reactions and molecule exchange. Molecular communication is a discipline in communication engineering that studies these types of communications and ways to exploit them for novel purposes, such as the development of ubiquitous and heterogeneous communication networks to interconnect biological cells with nano and biotechnology-enabled devices, i.e., the Internet of Bio-Nano Things. One major problem in realizing these goals stands in the development of reliable techniques to control the engineered cells and their behavior from the …

Methanol And Dimethyl Ether From Renewable Hydrogen And Carbon Dioxide: Alternative Fuels Production And Life-Cycle Assessment, Michael J. Matzen, Yaşar Demirel

Yaşar Demirel Publications

In this work we investigate two renewably based alternative fuels; methanol and dimethyl ether. The ultimate feedstocks for production are wind-based electrolytic hydrogen and carbon dioxide captured from an ethanol fermentation process. Dimethyl ether production was modeled in ASPEN Plus using a previously simulated methanol production facility. The facilities use 18.6 metric tons (mt) of H₂ and 138.4 mt CO₂ per day. Methanol is produced at a rate 96.7 mt/day (99.5 wt%) and dimethyl ether is produced at a rate of 68.5 mt/day (99.6 wt%). A full comparative life-cycle assessment (cradle-to-grave) of both fuels was conducted to investigate …

Alginate Hydrogels As Three-Dimensional Scaffolds For In Vitro Culture Models Of Growth Plate Cartilage Development And Porcine Embryo Elongation, Taylor D. Laughlin

Department of Agricultural and Biological Systems Engineering: Dissertations, Theses, and Student Research

The establishment of in vitro culture models utilizes tissue engineering principles to design functional mimics of in vivo environments in vitro. Advantages for the use of in vitro culture models include ethical alleviation of animal models for therapeutic testing, cost efficiency, and a greater ability to study specific mechanisms via a systematic, ground-up approach to development. In this thesis, alginate hydrogels are utilized in the development of in vitro culture models of porcine embryo elongation and growth plate cartilage development. First, the effect of scaffold and modifications to the scaffold were explored in both projects. In order to modulate …

Sustained Cell Differentiation Of 2d H9 Human Embryonic Stem Cells Into Mesenchymal Stem Cells, Hannah M. Christian

UCARE: Research Products

This experiment consisted of the controlled differentiation of H9 embryonic stem cells to mesenchymal stem cells. Though this experiment was repeated twice and improvement was seen in these repetitions, the cells were only able to be partially differentiated. However, the morphology of the differentiated cells is similar to those of healthy adult mesenchymal stem cells.

The progression of the differentiation can be seen in the microscope slide photos below. Throughout the differentiation, there occurred a decrease in cell survival and reduction of cell growth, but an increase in mesenchymal stem cell morphology. Throughout the last week of the differentiation, very …

Brain Tumor In A Dish: Glioma/Astrocyte Co-Cultures As A Model For In Vitro Studies, Erin Eickman, Christina Wilson, Srivatsan Kidambi

UCARE: Research Products

This study seeks to engineer an in vitro co-culture model to elucidate the role of glioma-astrocyte interactions on molecular changes in the tumor microenvironment. The use of patterned co-cultures created with polyelectrolyte multilayers and micromolding in capillaries will allow tthe investigation of cell-cell communication. This study will lead to better understanding of the role of healthy cells in cancer progression and potential treatment options.

Ionic Driven Embedment Of Hyaluronic Acid Coated Liposomes In Polyelectrolyte Multilayer Films For Local Therapeutic Delivery, Stephen Lawrence Hayward, David Francis, Matthew J. Sis, Srivatsan Kidambi

UCARE: Research Products

The ability to control the spatial distribution and temporal release of a therapeutic remains a central challenge for biomedical research. Here, we report the development and optimization of a novel substrate mediated therapeutic delivery system comprising of hyaluronic acid covalently functionalized liposomes (HALNPs) embedded into polyelectrolyte multilayer (PEM) platform via ionic stabilization. The PEM platform was constructed from sequential deposition of Poly-LLysine (PLL) and Poly(Sodium styrene sulfonate) (SPS) “(PLL/SPS)4.5” followed by adsorption of anionic HALNPs. An adsorption affinity assay and saturation curve illustrated the preferential HALNP deposition density for precise therapeutic loading. (PLL/SPS)2.5 capping layer on top of the deposited …

Noninvasive Measurement Of Electrical Events Associated With A Single Chlorovirus Infection Of A Microalgal Cell, Seung-Woo Lee, Eun-Hee Lee, Gerhard Thiel, James L. Van Etten, Ravi Saraf

Department of Chemical and Biomolecular Engineering: Faculty Publications

Chlorovirus Paramecium bursaria chlorella virus 1 (PBCV-1) contains a viral-encoded K⁺ channel imbedded in its internal membrane, which triggers host plasma membrane depolarization during virus infection. This early stage of infection was monitored at high resolution by recording the cell membrane depolarization of a single Chlorella cell during infection by a single PBCV-1 particle. The measurement was achieved by depositing the cells onto a network of one-dimensional necklaces of Au nanoparticles, which spanned two electrodes 70 μm apart. The nanoparticle necklace array has been shown to behave as a single-electron device at room temperature. The resulting electrochemical field-effect transistor …

Energy Intensity And Environmental Impact Metrics Of The Back-End Separation Of Ethylene Plant By Thermodynamic Analysis, Mahdi H. Alhajji, Yaşar Demirel

Department of Chemical and Biomolecular Engineering: Faculty Publications

This study presents metrics of energy intensity and environmental impact of the back-end separation of ethylene plant consisting three interacting distillation columns by thermodynamic analysis. The objective is to explore the scope of reducing the energy for utilities and CO₂ emissions. Thermodynamic analysis is carried out using the column targeting tool (CTT) to address the sustainability metrics of ‘Energy Intensity.’ CTT is based on the ‘Practical Near-Minimum Thermodynamic Condition’ representing a close to practical reversible column operation. Environmental impact metrics are estimated from the carbon tracking options. The carbon tracking are estimated by the CO₂ emission data source …

Technoeconomics And Sustainability Of Renewable Methanol And Ammonia Productions Using Wind Power-Based Hydrogen, Michael J. Matzen, Mahdi H. Alhajji, Yaşar Demirel

Yaşar Demirel Publications

This study analyzes and compares the economics and sustainability aspects of two hydrogenation processes for producing renewable methanol and ammonia by using wind-power based electrolytic hydrogen. Carbon dioxide from an ethanol plant is used for producing methanol, while the nitrogen is supplied by an Air Separation Unit (ASU) for producing ammonia. The capacities are 99.96 mt/day methanol and 1202.55 mt/day anhydrous ammonia. The methanol plant requires 138.37 mt CO₂/day and 19.08 mt H₂/day. The ammonia is synthesized by using 217.72 mt H₂/day and 1009.15 mt N₂/day. The production costs and the carbon …

Production Of Recombinant Human Coagulation Factor Ix By Transgenic Pig, Weijie Xu

Department of Chemical and Biomolecular Engineering: Dissertations, Theses, and Student Research

Hemophilia B is the congenital bleeding disorder caused by deficiency in functional coagulation factor IX (FIX) and about 28,000 patients worldwide in 2012. And current treatment is restricted to protein-replacement therapy, which required FIX concentrates for patients’ life-time. Approximately 1 billion units FIX were consumed in 2012. However, still about 70-80% patients, mostly in developing countries, received inadequate or no treatment because of the unavailable and/or unaffordable FIX concentrates. Considering safety reasons, e.g. transmission of blood-borne diseases, the recombinant human FIX (rFIX) is recommended other than the plasma-derived FIX. However, only one rFIX is currently available on the market. The …

Pharmacokinetic Characterization Of Procoagulation Proteins, Nicholas C. Vanderslice

Department of Chemical and Biomolecular Engineering: Dissertations, Theses, and Student Research

The cessation of bleeding in mammals occurs due to a well-conserved sequence of protein activation known as the coagulation cascade. However, people who have a deficiency in one or more proteins in this cascade, whether due to genetics or blood loss, struggle to maintain hemostasis. In order to aid patients in the restoration of hemostasis, exogenous proteins are often administered in response to bleeding events. However, these proteins are limited and costly due to limited supply of donor blood available for the production of plasma-derived proteins and the high cost of mammalian cell bio-reactors required for the production of recombinant …

Development And Utilization Of A Pair Of Sol-Gel Entrapped Lipases For Biodiesel Production From High Free Fatty Acid Oils, Cory M. Schwartz

Department of Chemical and Biomolecular Engineering: Dissertations, Theses, and Student Research

Biodiesel, which consists of fatty acid alkyl esters, is one of the most widely adopted and successful renewable fuels. Traditional physiochemical biodiesel production methods require high cost refined feedstocks, and so alternative methods of catalysis and feedstocks have been explored. This research investigated the use of polysiloxane entrapped lipases to catalyze the production of biodiesel from low cost feedstocks.

In this work, lipase from Burkholderia cepacia (lipase PS) and lipase B from Candida antarctica (CalB) were separately entrapped using sol-gel chemistry. Optimal reaction conditions for the esterification of free fatty acids by immobilized CalB with methanol were determined. Immobilized CalB …

Information In Biological Systems And The Fluctuation Theorem, Yaşar Demirel

Department of Chemical and Biomolecular Engineering: Faculty Publications

Some critical trends in information theory, its role in living systems and utilization in fluctuation theory are discussed. The mutual information of thermodynamic coupling is incorporated into the generalized fluctuation theorem by using information theory and nonequilibrium thermodynamics. Thermodynamically coupled dissipative structures in living systems are capable of degrading more energy, and processing complex information through developmental and environmental constraints. The generalized fluctuation theorem can quantify the hysteresis observed in the amount of the irreversible work in nonequilibrium regimes in the presence of information and thermodynamic coupling.

De Novo Gene Synthesis By Rapid Polymerase Chain Assembly Coupled With Immunoaffinity Purification: A Novel Process And Workstation, Joel R. Termaat

Department of Chemical and Biomolecular Engineering: Dissertations, Theses, and Student Research

The de novo synthesis of genes is emerging as a powerful tool in biotechnology. The ability to synthesize genes of any desired sequence opens the door to seemingly unlimited research possibilities. Major advances have been made recently in de novo gene synthesis, with Polymerase Chain Assembly (PCA) routinely used to construct functional sequences from short single-stranded oligonucleotides. However, current PCA techniques are lacking in speed and fidelity. Additionally, substantial undesired reactants/products are present in the final reaction. A novel process and accompanying workstation has been developed that incorporates rapid PCA synthesis coupled with subsequent affinity purification of the synthesis mixture. …

A Novel Biodiesel And Glycerol Carbonate Production Plant, Nghi T. Nguyen, Yaşar Demirel

Yaşar Demirel Publications

Crude glycerol is the byproduct of biodiesel production plant and the economic value of glycerol may affect the profitability of the biodiesel production plant. As the production rate of bioglycerol increases, its market values drop considerably. Therefore, conversion of bioglycerol into value-added products can reduce the overall cost, hence, leading to a more economical biodiesel production plant. In a direct carboxylation reaction, CO₂ reacts with glycerol to produce glycerol carbonate and water. This study presents a direct comparison of the economic analysis of the conventional biodiesel production plant and the possible next generation biodiesel-glycerol carbonate production plant. At the …

Fibronectin For Use In Hemostats And Wound Stabilization In Trauma, Mohammed Halhouli

Department of Chemical and Biomolecular Engineering: Dissertations, Theses, and Student Research

Exploring the phase during wound healing when fibrinogen (FBG) and fibronectin (FN) interact forming a small thin layer for cells to migrate and proliferate at the injury site is necessary for the primary building blocks and initial stages of skin recovery. The aim of this thesis is to illustrate that administrating a reasonable amount of (FN) and FBG, in a semi-organizational technique, to the wound site will encourage cell population and ECM formation, as well as, improve the wound healing process. WE hypothesized that FBG and FN interactions will configure the construction of dermal cells and their final fate to …