Biochemical and Biomolecular Engineering Commons^™

Predicting Key Residues Relevant To Hiapp Fibril Stability Using Permuted Residue Minimal Distance Pairs Of Riapp And Hiapp Dimers, Zak Kohler

Williams Honors College, Honors Research Projects

In order to discover the most significant residues involved in hIAPP fibril formation, Replica Exchange Molecular Dynamics (REMD) trajectories of both fibril forming hIAPP dimers and non-fibril-forming rIAPP dimers were analyzed. An import heuristic for this is the minimum distance between the peptides. To gain a greater resolution than the standard center of mass distance or 1-1, 2-2, etc.\ residue distances, every permutation of residue distance between molecules of the dimer was measured ranked. It was found that while the rIAPP had a single favored contact, (26 10), hIAPP appeared to have a network of at least three significant contacts: …

Effect Of Nitrogen On Properties Of Na2o-Cao-Sro-Zno-Sio2 Glasses, Ahmed Bachar, Cyrille Mercier, Arnaud Tricoteaux, Jean Christophe Hornez, Anne Leriche, Claudine Follet, Bertrand Revel, Stuart Hampshire, Mark R. Towler

Chemical and Biochemical Engineering Faculty Research & Creative Works

Glasses in the Na₂O-CaO-SrO-ZnO-SiO₂ system have previously been investigated for suitability as a reagent in Al-free glass polyalkenoate cements (GPCs). These materials have many properties that offer potential in orthopedics. However, their applicability has been limited, to date, because of their poor strength. This study was undertaken with the aim of increasing the mechanical properties of a series of these Zn-based GPC glasses by doping with nitrogen to give overall compositions of: 10Na₂O-10CaO-20SrO-20ZnO-(40-3x)SiO₂-xSi₃N₄ (x is the no. of moles of Si₃N₄). The density, glass-transition temperature, hardness, …

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 …

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.

Poly(Ester Amide) And Poly(Ethyl Glyoxylate) Nanoparticles For Controlled Drug Release, Amira Mohamed Moustafa

Electronic Thesis and Dissertation Repository

The objective of this research was to develop polymeric nanoparticles (NPs) having improved drug release properties for drug delivery. Poly(ester amide)s (PEAs) are promising biodegradable polymers. PEA NPs were prepared via emulsification-evaporation and salting-out methods and optimized through by varying different processing parameters. Polymer-model drug conjugates based on PEAs containing L-aspartic acid and rhodamine B were synthesized and used for NP preparation. Release behavior was studied and compared to a control system with physically encapsulated rhodamine B. It was shown that the release of rhodamine B from the covalent system did not show the burst effect and exhibited a slower …

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.

Photosystem I-Based Applications For The Photo-Catalyzed Production Of Hydrogen And Electricity, Rosemary Khuu Le

Doctoral Dissertations

The aim of this dissertation was to optimize systems integrating the photosystem I (PSI) redox protein, which is involved in photosynthesis, with noble metals for electron transfer to show its versatility: 1) in solution coupled with platinum to mediate hydrogen evolution and 2) on a planar gold surface for electricity production.

Response surface methodology was utilized to study variables that affect hydrogen (H₂) yield from platinized-PSI. Light intensity, temperature, and platinum concentration were varied during the platinum-photo-reduction process. Analysis of the effects of the variables on H₂ yield allowed for determination of a condition for optimized hydrogen …

The Structure And Function Of Photosystem I And Photosystem I – Hydrogenase Protein Fusions: An Experimental And Computational Study, Bradley Jordan Harris

Doctoral Dissertations

Photosystem I (PSI) is a membrane protein involved in the photosynthetic cycle of plants, algae, and cyanobacteria that is of specific interest due to its ability to harness solar energy to generate reducing power. This work seeks to form an in vitro hybrid protein fusion between the membrane integral PSI protein and the membrane-bound hydrogenase (MBH) enzyme, in an effort to improve electron transport between these two proteins.

Small-angle neutron scattering (SANS) was used to characterize the detergent-solubilized solution structure of trimeric PSI from the cyanobacterium Thermosynechococcus elongatus, which showed that the detergent interacts primarily with the hydrophobic periphery …

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 …

Analytical And Computational Modeling Of Membrane Nanotubes, Sina Mirzaeifard

Masters Theses

This thesis investigates the interplay between cell membranes and the actin cytoskeleton in cellular structures known as membrane nanotubes. Membrane nanotubes are slender membrane structures that physically connect cells over long distances, and experiments suggest that they play a role in transferring material and information between cells. Disrupting the actin cytoskeleton disrupts membrane nanotubes. Although recent studies have revealed insight into the physical properties and functions of membrane-actin systems, further research is needed to understand their behavior in biological contexts. Membrane nanotubes provide a novel system with which to investigate interactions between the cell membrane and actin.

In this thesis, …

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 …

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.

Design Of A Targeted Bacterial Drug Delivery Vector For The Treatment Of Cancer And Metastases, Charles Alexander Swofford

Doctoral Dissertations

Engineered Salmonella possess unique capabilities that make them ideal drug delivery vectors for tumors. Targeted bacterial delivery of anticancer proteins has the ability to overcome therapeutic resistance in tumors that limits the efficacy of chemotherapeutics. In my doctoral research, I identified a protein-drug that can be expressed by bacteria and rapidly kills cancer cells. I also created a density dependent switch that initiates gene expression in tumors and prevents expression in healthy tissue. Combining these two systems has created a potent anti-cancer system that targets tumors with minimal toxicity. I cloned genes for five potential anti-cancer proteins into Salmonella. …

Metabolic Modeling Of Secondary Metabolism In Plant Systems, Lisa M. Leone

Masters Theses

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 …

Reductive Depolymerization Of Kraft Lignin For Chemicals And Fuels Using Formic Acid As A In-Situ Hydrogen Source, Shanhua Huang

Electronic Thesis and Dissertation Repository

In this thesis work, formic acid (FA) proved to be an effective in-situ hydrogen donor for the reductive de-polymerization of kraft lignin (KL). At the optimum conditions without catalysts, i.e., 300 ^oC, 1 h, 18.6 wt.% substrate concentration, 50/50 (v/v) water-ethanol medium at a FA-to-lignin mass ratio of 0.7, KL (M_w ~10,000 g/mol) was effectively de-polymerized, producing de-polymerized lignin (DL, M_w 1, 270 g/mol) at a yield of ~90 wt.% and wt.% yield of solid residue (SR). The effects of heterogeneous catalysts on KL reductive de-polymerization in 50/50 (v/v) water-ethanol medium were also investigated. At all conditions, …

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 …

Degradation And Biological Assessment Of Aqueous Micropollutant Mixtures, Sura M.H. Ali

Electronic Thesis and Dissertation Repository

Presence of micropollutants in water is a global concern because of their ability to potentially cause adverse effects in organisms at concentrations as low as a few ng/L, particularly when present as a component of complex mixture. Most of the endocrine disrupting compounds (EDC) and pharmaceutical and personal care products (PPCP) are not removed well in traditional wastewater treatment processes and enter the environment and spread throughout the water ecosystem. Depending on the properties of the micropollutants and the biology of the receiving species, they may bioaccumulate, metabolize or cause adverse effects. These effects may translate into alterations on a …

Solid-Phase Extraction As Sample Preparation For Bioassay-Based Micropollutant Quantification, Chen Feng

Electronic Thesis and Dissertation Repository

Solid phase extraction (SPE) using chemically bonded silica particles or small particles of an organic polymer resin, is being studied extensively for extraction of polar or non-polar compounds from various water matrices. This study focused on the evaluation of the performance of three commercial cartridges belonging to three different groups: reversed-phase, mixed-mode anion exchanger and mixed-mode cation exchanger. In the first stage of research, the performance of three cartridges was compared by extracting four antibiotics with different physic-chemical properties from water samples. The results obtained from column sorption experiments were plotted into breakthrough curves and batch equilibrium experiments results were …

Tissue Engineering Scaffolds With Enhanced Oxygen Delivery Using A Cyclodextrin Inclusion Complex, Tierney Gb Deluzio

Electronic Thesis and Dissertation Repository

The development of a strategy to improve oxygen delivery to cells seeded on scaffolds is essential for the success of tissue engineering applications. The focus of this work was to explore the application of cyclodextrin inclusion complexes (CD:ICs) with perfluorocarbons as oxygen carriers. CD:ICs were prepared from alpha-cyclodextrin and perfluoroperhydrophenanthrene via co-precipitation, paste mixing, and dry mixing complexation techniques. Characterization indicated that paste mixing at a 2:1 host:guest ratio was the most effective method for complexation between the parent molecules. The CD:ICs were then successfully incorporated in 3D fibrous mats via electrospinning with poly(carbonate urethane) and polycaprolactone as biostable and …

Engineering Biosensors For Short-Chain Alcohols, Yu Xia

McKelvey School of Engineering 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. …