Biochemical and Biomolecular Engineering Commons^™

Evaluation Of The Signature Molecular Descriptor With Blosum62 And An All-Atom Description For Use In Sequence Alignment Of Proteins, Lindsay M. Aichinger

Williams Honors College, Honors Research Projects

This Honors Project focused on a few aspects of this topic. The second is comparing the molecular signature kernels to three of the BLOSUM matrices (30, 62, and 90) to test the accuracy of the mathematical model. The kernel matrix was manipulated in order to improve the relationship by focusing on side groups and also by changing how the structure was represented in the matrix by increasing the initial height distance from the central atom (Height 1 and Height 2 included).

There were multiple design constraints for this project. The first was the comparison with the BLOSUM matrices (30, 62, …

Polymer Interactions With Nucleic Acids Under Various Physiological Conditions, Matthew S. Obrzut

Williams Honors College, Honors Research Projects

The goal of this project is to improve our understanding of nucleic acid interactions with cationic polymers with the theory that the polymers could protect the nucleic acids from degradation caused by biological enzymes. We seek to understand what the limitations of the cationic polymers are which, in this case, is mainly polymer-DNA compatibility. This experiment utilized peptide-dextran hybrid polymers with differing functionalizations to condense anionic nucleic acids into nanometer-sized polyplexes. Techniques of dynamic light scattering and zeta-potential were utilized to determine the particle sizes and surface charges of polyplexes.

In this experiment, dextran with a molecular weight of 20 …

New Multiphase Reactor Design Using Electrospun Nanofibers, Victoria Smith

Williams Honors College, Honors Research Projects

No abstract provided.

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 …

Exploration Of Cannabinoid And Opioid Agents From Plants Used In Traditional Medicine, John Fitzpatrick

Honors Theses

Ten plants, with known medicinal uses, were gathered to study for their possible production of secondary metabolites that act as opioid and cannabinoid agents. All plants were subjected to in vitro bioassays testing for their affinity for the opioid and cannabinoid receptors. Banisteriopsis caapi extracts displayed the greatest affinity for both opioid and cannabinoid receptors. B. caapi extracts underwent column fractionation yielding fractions that were subjected to further in vitro studies. We discovered that the ethanolic extract of this plant (foliage) binds to all three opioid receptors (µ, κ and δ) and cannabinoid receptors (CB1 and CB2) with values ranging …

Secondary Metabolites Isolated From Perovskia Atriplicifolia And Their In Vitro Binding Affinity For Human Opioid And Cannabinoid Receptors, Ashli Fitzpatrick

Honors Theses

Plants and their natural products have been utilized for thousands of years in the treatment of many human diseases. Because of their structural diversity, natural products are ideal lead compounds for drug development. In this thesis, the natural products of the plant Perovskia atriplicifolia were investigated, specifically their in vitro binding affinity to receptors in opioid and cannabinoid classes. Extracts that demonstrated good selective opioid and cannabinoid receptor binding were subjected to bioassay-guided fractionation. Four active compounds were identified from the crude extract in Perovskia atriplicifolia: 1) 5-hydroxy-3',4',6,7-tetramethoxy flavone, 2) 5,7-dihydroxy-3',4',6,-trimethoxy flavone, 3) 5-hydroxy-4',6,7-trimethoxy flavone, and 4) 5,7-dihydroxy-4',6,-dimethoxy flavone. Each …

Design And Synthesis Of Sigma-1 Probe For Positron Emission Tomography (Pet) Imaging, May Ly

Honors Theses

Sigma-1 receptor radioligands have the potential to detect and monitor various neurological diseases. Because sigma-1 receptors are believed to be associated with numerous psychiatric conditions and neurodegenerative diseases, radioligands for sigma-1 receptors have the potential to serve as novel diagnostic tools and may be useful in assessing treatment effectiveness. A benzothiazolone 18F-labeled sigma-1 receptor ligand, CM304, has demonstrated promise as a specific positron emission tomography radiotracer for visualizing sigma-1 receptors in living subjects. Based on CM304, backup molecules were created to improve the overall drug profile, including half- life and bioavailability.

Biomolecule Localization And Surface Engineering Within Size Tunable Nanoporous Silica Particles, Daniel M. Schlipf

Theses and Dissertations--Chemical and Materials Engineering

Mesoporous silica materials are versatile platforms for biological catalysis, isolation of small molecules for detection and separation applications. The design of mesoporous silica supports for tailored protein and biomolecule interactions has been limited by the techniques to demonstrate biomolecule location and functionality as a function of pore size. This work examines the interaction of proteins and lipid bilayers with engineered porous silica surfaces using spherical silica particles with tunable pore diameters (3 – 12 nm) in the range relevant to biomolecule uptake in the pores, and large particle sizes (5 - 15 µm) amenable to microscopy imaging

The differentiation of …

Integrated Nanoscale Imaging And Spatial Recognition Of Biomolecules On Surfaces, Congzhou Wang

Theses and Dissertations

Biomolecules on cell surfaces play critical roles in diverse biological and physiological processes. However, conventional bulk scale techniques are unable to clarify the density and distribution of specific biomolecules in situ on single, living cell surfaces at the micro or nanoscale. In this work, a single cell analysis technique based on Atomic Force Microscopy (AFM) is developed to spatially identify biomolecules and characterize nanomechanical properties on single cell surfaces. The unique advantage of these AFM-based techniques lies in the ability to operate in situ (in a non-destructive fashion) and in real time, under physiological conditions or controlled micro-environments.

First, AFM-based …

Polysaccharide-Based Shear Thinning Hydrogels For Three-Dimensional Cell Culture, Vasudha Surampudi

Theses and Dissertations

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 …

Mechanistic Models On Enzymatic Hydrolysis And Anaerobic Digestion, Yang Zhang

Dissertations, Master's Theses and Master's Reports

For enzymatic hydrolysis, a mechanistic model on enzymatic hydrolysis of pure cellulosic substrates was improved to consider oligomer reactions with beta-glucanases, inhibition of oligomers to cellulases and enzyme decay. Then a novel and general modeling framework was developed for enzymatic hydrolysis of hemicellulose-cellulosic substrates. This mechanistic model, for the first time, took into consideration explicitly the time evolution of morphologies of intertwining cellulose and hemicelluloses. This novel mechanistic model was applied to optimize the composition of enzyme mixtures for substrate conversion and monosaccharides yield during simultaneous enzymatic hydrolysis of different lignocellulosic substrates. For anaerobic digestion, the original "Anaerobic Digestion Model …

Creation Of An Annotated Library On Fda Approved Nanomedicines, Marley R. Hodson, Tanin Izadi, Nastassja Lewinski Ph.D, Bridget T. Mcinnes Ph.D

Undergraduate Research Posters

Nanomedicine is a type of nanotechnology used in the medical field to limit the dosage amount and target drug delivery to specific cells. Nanomedicines that are approved and used tend to be extremely successful; however despite over a decade of research, only a limited number of nanomedicines have advanced for clinical use. A possible reason for the numerous nanomedicine failures is lack of easily accessible information and research on previous nanomedicines. In this project, we have compiled nanomedicine labeling information from the Drugs@FDA website. We have extracted phrases/sentences from labels relating to keywords on nanomaterial properties and drug profile characteristics. …

Processing And Mechanical Testing Of Strontium-Substituted Hydroxyapatite/Glass Composites, Chokchai Yatongchai, Mark R. Towler, Anthony W. Wren

Chemical and Biochemical Engineering Faculty Research & Creative Works

Sr-HA/Glass composites were produced. Phase composition of composites was evaluated. Their physical and mechanical properties were determined. Sintered composites mainly consisted of Sr-HA/β-TCP, or β-TCP/Ca₂ZnSi₂O₇. The composites had porosity up to 4 times those of undoped Sr-HA. Compared to undoped Sr-HA, the Sr-HA/Glass composites had lower biaxial flexural strength and hardness. The Weibull modulus for the composites ranged from 2.77 to 18.74.

Photobioreactor Design For Improved Energy Efficiency Of Microalgae Production, Alexander Burns

Master's Theses

ABSTRACT

Photobioreactor Design for Improved Energy Efficiency of Microalgae Production

Alexander Burns

The objective of this research was to investigate a new photobioreactor (PBR) design for microalgae production that retains the typical advantages of existing tubular PBRs while reducing power consumption by providing simultaneous culture circulation and gas exchange with airlift alone and no centrifugal recirculating pump. Traditional tubular PBR designs feature a compressed air supply and a centrifugal pump for culture circulation and gas exchange. Circulation and gas exchange in a closed-system PBR is necessary to keep the algae suspended and to provide sufficient mass transfer (mainly for the …

Photonic Crystal-Based Flow Cytometry, Justin William Stewart

USF Tampa Graduate Theses and Dissertations

Photonic crystals serve as powerful building blocks for the development of lab-on-chip devices. Currently they are used for a wide range of miniaturized optical components such as extremely compact waveguides to refractive-index based optical sensors. Here we propose a new technique for analyzing and characterizing cells through the design of a micro-flow cytometer using photonic crystals. While lab scale flow cytometers have been critical to many developments in cellular biology they are not portable, difficult to use and relatively expensive. By making a miniature sensor capable of replicating the same functionality as the large scale units with photonic crystals, we …

Investigating The Stability Of Eliposomes At Elevated Temperatures, Ghaleb A. Husseini, William G. Pitt, Marjan Javadi

Faculty Publications

eLiposomes encapsulate a perfluorocarbon nanoemulsion droplet inside a liposome. Ultrasound is then used as a trigger mechanism to vaporize the perfluorocarbon, break the liposome, and release the desired drug to the tumor tissue. The purpose of this research is to show that eLiposomes synthesized using perfluoropentane are stable above the normal boiling point of the perfluoropentane and at body temperature and thus has potential for use in vivo. Experiments involving the release of fluorescent calcein molecules were performed on eLiposomes to measure the release of calcein at various temperatures in the absence of ultrasound. Results showed that eLiposomes are stable …

Method And Apparatus For Surface Chemical Functionalization Of Powders And Nanoparticles, Mary Gilliam, Susan Farhat, Graham Garner, Michael Magyar

Chemical Engineering Patents

A method and apparatus is provided for the modification of the surface chemistry of solid nano- and micro-particles in order to tailor the properties and functions of these particles. The method generally involves the generation of an atmospheric plasma glow discharge and energetic species that undergo chemical reaction with the surface of the primary particles. The process includes the generation of energetic species to initiate reaction, optional delivery of a precursor fluid, optional delivery of chemical species for grafting, and delivery of separated and de-agglomerated particles into the plasma discharge exiting the plasma generation chamber.

An Economic Analysis Of Small-Scale Biodiesel Production: Implementation Of Ethyl Ester Production In A Job Shop Setting, Scott Haase, Benjamin Craig

Journal of Undergraduate Research at Minnesota State University, Mankato

Biodiesel is becoming a demanded consumer automotive alternative fuel used in diesel vehicles today. An emerging trend is toward small-scale biodiesel production performed by the final consumer. A limited source of commercially available production systems exists and has resulted in many systems being designed and built by the user. Preliminary research conducted by the authors has shown biodiesel to be the least-cost alternative to petroleum diesel after as few as 8 months of system use. This study examines the economic viability of building and producing biodiesel using a small-scale production system versus buying consumer petroleum diesel. During production, measurements were …

Engineering Biosensors For Short-Chain Alcohols, Yu Xia

McKelvey School of Engineering Graduate Student Theses & Dissertations

Biofuel is a promising substitute for fossil fuel and the research of biofuel production has been extensively conducted during the recent years. Great efforts have been made to create many types of the fuel production hosts. However, effective approaches for high specificity and high throughput screening of the fuel production strains are still lacking. The cellular stress response is one universal defense mechanism when a microbial cell is exposed to an unfavorable substance or environment. It triggers a series of downstream responses when a cell senses certain chemicals. Transcriptional factors are widely used in living organisms to regulate gene expression. …

Population Balance Modeling Of Conjugation In Enterococcus Faecalis, Jeremy Binagia, Vu Tran, Che-Chi Shu, Doraiswami Ramkrishna

The Summer Undergraduate Research Fellowship (SURF) Symposium

In the bacteria species Enterococcus faecalis, transfer of plasmid pCF10 by conjugation between donor cells that possess sets of genes conferring drug resistance and recipient cells leads to the spread of this resistance in a population. A complex signaling molecule network is responsible for communication between recipient and donor cells. Up to this point, the nature of these signaling molecules has been modeled deterministically from the point of view of an “average” cell. While this view has been cured slightly by stochastic treatments, a model is needed that better accounts for the individual nature of each cell, each cell’s interactions …

Characterization Of Swelling Ratio And Water Content Of Hydrogels For Cartilage Engineering Applications, Emily E. Gill, Renay S.-C. Su, Julie C. Liu

The Summer Undergraduate Research Fellowship (SURF) Symposium

Due to the high prevalence of arthritis and cartilage-related injuries, tissue engineers are studying ways to grow cartilage tissue replacements. Resilin, an elastomeric protein found in insect cuticles, is known for its extraordinary resilience and elasticity. In previous studies, recombinant resilin-based hydrogels, or cross-linked protein networks, exhibited potential for use in cartilage tissue scaffolds. Our lab successfully developed resilin-based proteins with a sequence based on the mosquito gene and showed that resilin-based hydrogels possess mechanical properties of the same order of magnitude as native articular cartilage. In addition, these mechanical properties can be controlled by changing the protein concentration. To …

Application Of Membrane Processes For Concentration And Separation Of Sugar Streams In Biofuel Production, Mohammadmahdi Malmali

Graduate Theses and Dissertations

The overall objective of this study was identification and development of a sugar concentration/separation membrane filtration unit to improve the bioconversion of lignocellulosic biomass into chemicals and fuels. This thesis is divided into three main parts. The first part is about our studies on the use of nanofiltration membranes for concentration of sugars in a lignocellulosic biomass hydrolysate. In addition, the feasibility of simultaneous removal of acetic acid, 5-(hydroxymethyl)furfural and furfural from the hydrolysate has also been investigated. The results obtained indicate that both concentration of sugars and removal of hydrolysis degradation products is feasible. However, careful selection of the …

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 …

Developent Of A Phospholipid Encapsulation Process For Quantum Dots To Be Used In Biologic Applications, Logan Grimes

Master's Theses

The American Cancer Society predicts that 1,665,540 people will be diagnosed with cancer, and 585,720 people will die from cancer in 2014. One of the most common types of cancer in the United States is skin cancer. Melanoma alone is predicted to account for 10,000 of the cancer related deaths in 2014. As a highly mobile and aggressive form of cancer, melanoma is difficult to fight once it has metastasized through the body. Early detection in such varieties of cancer is critical in improving survival rates in afflicted patients. Present methods of detection rely on visual examination of suspicious regions …

Hydrodynamic Cfd Modeling Of A Pharmaceutical Reactor Vessel Provided With A Retreat-Blade Impeller Under Different Baffling Conditions, Christopher G. Foehner

Theses

In the pharmaceutical industry, glass-lined reactors and vessels are often utilized to carry out a variety of different unit operations. Within these systems, both the vessel and impellers are typically glass-lined in order to provide superior corrosion resistance, prevent product contamination, and enhance cleanability. This approach, in turn, often requires the use of different, and sometimes sub-optimal, baffling conditions, which affect the hydrodynamics of the vessels and the reactor performance.

Computational Fluid Dynamics (CFD) is a computational tool that employs numerical methods and algorithms to discretize and numerically solve partial differential equations (PDEs) representing mass, energy, and momentum conservation equations …

Mechanism Of Insulin Aggregation: Applied To Alzheimer's Disease, Milos Atz

Honors Scholar Theses

Alzheimer’s disease, a debilitating neurodegenerative illness, is caused by the irreversible aggregation of beta-amyloid proteins in the brain. In Alzheimer’s brains, the protein can become disfigured, causing it to aggregate into long, insoluble fibers that deposit on brain tissue. Studying the aggregation mechanisms of amyloid proteins can lead to a deeper understanding of the progression of Alzheimer’s disease and possibly point towards a potential cure or treatment for the disease. Heat induced aggregation of insulin provides a model system to study the aggregation of amyloidogenic proteins. This study investigates the early stages of heat induced insulin aggregation using dynamic light …

Validation Of A Diffuse Reflectance Microendoscope With Polydimethylsiloxane Optical Phantoms And Monte Carlo Modeling, Gage Joseph Greening

Biomedical Engineering Undergraduate Honors Theses

We have introduced a method for creating thin-film PDMS optical phantoms that can be used to validate a bench-top optical device called a Diffuse Reflectance Microendoscope (DRME). The DRME is acquires data on cell surface morphology and sub-surface diffuse reflectance, which may provide clinicians with the tools to diagnose oral cancer at earlier stages. Phantoms were created with PDMS. Optical properties of the phantoms were controlled with the addition of nigrosin and titanium dioxide. Depth of phantoms was controlled by a spin coater. The DRME was built with a combination of filters and dichroic mirrors to separate electromagnetic radiation in …

Poly (Glycerol Sebacate) Nanofibers And Nanofilms For Tissue Engineering Application, Stephanie Grace Cone

Biomedical Engineering Undergraduate Honors Theses

In the field of tissue engineering, the development of biodegradable scaffolds that provide both structure and functionality is a major challenge. The use of biological implants, such as decellularized tissues, provides a complete matrix with full tissue functionality, however, problems with immunogenicity often arise when implants from other organisms are used in treatments. As such, there are many benefits to the use of polymeric constructs in tissue engineering. The ability to customize the material, design, and size of an implant provides opportunities for increased structural support and controlled rates of biodegradation. The selection of polymers for tissue engineering applications requires …