Biochemistry Commons^™

Using Molecular Dynamics Simulations To Decipher Mechanistic Details Of Biomolecular Processes Of Biology And Biotechnology Oriented Applications, Adithya Polasa

Graduate Theses and Dissertations

Researchers in chemistry and biology often utilize computer simulations, in conjunction with experimental data, to model and predict the structures, energies, kinetics, processes, and functions of the systems that are their focus of study, ranging from single molecules to whole viruses. Here, we use molecular dynamics (MD) techniques to gain a deeper understanding of biomolecular processes in biology and biotechnology-oriented applications. Using a mixture of equilibrium and non-equilibrium MD simulations, this work describes the insertion process of YidC at the atomic level. In order to better comprehend the insertion process, several docking models of YidC-Pf3 in the lipid bilayer were …

Biomimetic Synthesis Of Palladium Nanoparticles For Catalytic Application, Emily A. Groover

Electronic Theses and Dissertations

The synthesis of palladium nanoparticles (Pd NPs) using materials-directed peptides is a novel, nontoxic approach which exerts a high level of control over the particle size and shape. This biomimetic technique is environmentally benign, featuring nonhazardous ligands and ambient conditions. Nanoparticles are extremely reactive catalysts, boasting a large surface-to-volume ratio when compared to their bulk counterparts. The rational design of these nanoparticles using peptides has been very successful in aqueous environments, but no research has been done to apply it in organic systems. As such, the biomimetic synthesis of Pd NPs in an organic system is here investigated, with ethanol …

Characterization Of Ph – Responsive Nanocage Based On The Ferritin Iron Storage Protein, Satyam Singh

Theses and Dissertations

The iron-storage protein ferritin (Ftn) assembles into a protein cage structure with 24 subunits and octahedral (4-fold, 3-fold, 2-fold) symmetry. Each monomeric subunit contains a robust four-helix bundle fold. The fully assembled Ftn structure has a high degree of thermal stability (up to 100°C), a mono dispersed size (12 nm in diameter), and a large central cavity (7-8 nm in diameter). The central cavity stores ferric iron in phylogenetically diverse group of organisms, including humans. The central cavity has been used for encapsulation of cargoes such as other metals, contrast agents for imaging, small molecule drugs for therapy, …

Investigating The Accumulation, Sub-Organ Distribution, And Biochemical Effects Of Nanomaterials Using Mass Spectrometry, Kristen Nicole Sikora

Doctoral Dissertations

Gold nanoparticles (AuNPs) are attractive materials for use in various biomedical applications, such as therapeutic delivery, due to their unique chemical properties and modular tunability. Mass spectrometry methods, including laser desorption/ionization mass spectrometry (LDI-MS) and inductively coupled plasma mass spectrometry (ICP-MS) have been successfully used to evaluate the distribution of AuNPs in complex biological systems. As new AuNP-based materials are developed for applications in therapeutic delivery, it is essential to simultaneously develop analytical techniques that can comprehensively assess their behavior in vivo. In this dissertation, novel mass spectrometric methods have been developed and utilized to evaluate the uptake, distribution, …

Determination Of Optimal Mild Organic Solvents Of Pdnps For Carbon-Carbon Coupling Reactions, Trina Biswas

Honors College Theses

The synthesis of nanoparticles is an increasingly popular field of interest. The application of nanoparticles is especially popular in the field of nanocatalysts. Metal nanoparticles (NPs) are favorable for catalysis because of the large surface area to volume ratio, which allows them to catalyze a variety of reactions using lesser amounts of active material. As the field of nanoparticle research expands, efforts are being made to create more sustainable approaches to the synthesis of these particles. This research sought to translate the benefits of peptide-based synthesis to organic solvents and use less toxic organic solvents for carbon-carbon coupling reactions, like …

Synthesis, Stabilization, And Modification Of Zinc Oxide Nanoparticles For Biological Applications, Allison Kimberly Freese

MSU Graduate Theses

Nanoparticles have become very useful as delivery systems in biomedicine. The nanoparticles can be layered with different compounds to produce a vessel for transport of biological materials. Specifically, gold nanoparticles layered with a reducing agent, lysozyme, and polyelectrolytes can be synthesized to transport lysozyme into a cell. However, zinc oxide nanoparticles are cheaper, biocompatible nanoparticles that can be used for the same process. Here in, zinc oxide nanoparticle conjugates were synthesized, modified, and analyzed to be used as a biological material delivery system. The zinc oxide nanoparticles were synthesized using zinc chloride and sodium hydroxide. The particles were then layered …

Synthesis And Characterization Of American Ginseng Polysaccharides Nanoparticles, Vincent Lee

Electronic Thesis and Dissertation Repository

This project was concerned with the synthesis of nanoparticles (NPs) by microfluidics from bulk ginseng polysaccharides (PS) isolated from American ginseng to design a new delivery system to improve the bioavailability of PS. Physicochemical analyses showed products of nanosizing as unimodal spheres with a diameter of ~19 nm. Pharmacological characterization studies in vitro of these nanoparticles of PS (NPPS) have demonstrated heightened immunostimulatory activity, and enhanced penetration across skin cell monolayer, which could be considered as evidence of increased bioavailability. Studies using PS sub-fractions with different molecular weights for NPPS synthesis showed that molecular weights is one of the parameters …

Hybridized Polymeric Nano-Assemblies: Key Insights Into Addressing Mdr Infections, Ryan Landis

Doctoral Dissertations

Multidrug-resistant (MDR) bacteria contribute to more than 700,000 annual deaths world-wide. Millions more suffer from limb amputations or face high healthcare treatment costs where prolonged and costly therapeutic regimens are used to counter MDR infections. While there is an international push to develop novel and more powerful antimicrobials to address the impending threat, one particularly interesting approach that has re-emerged are essential oils, phytochemical extracts derived from plant sources. While their antimicrobial activity demonstrates a promising avenue, their stability in aqueous media, limits their practical use in or on mammals. Inspired by the versatility of polymer nanotechnology and the sustainability …

The Contributions Of Fc Gamma Receptors And Macropinocytosis To The Internalization, Sorting And Clearance Of Antibody Coated Nanovesicles In Macrophages, George Opoku-Kusi Jr.

Electronic Theses and Dissertations

Macrophages are tissue-resident phagocytes that play critical roles in immune response and tissue homeostasis. They have a tremendous capacity to internalize objects of various sizes ranging from nanoscale viral particles to micron sized bacteria and tumor cells. This phenomenon, termed phagocytosis for the uptake of large particles, or endocytosis for the uptake of small particles, is integral to the immune response in multicellular organisms. Macrophages express FcγRs, which are tyrosine kinase receptors that bind IgG on an opsonized target. Binding of IgG Fc domain to the extracellular domain of an FcγR triggers signaling cascades that coordinate internalization of the opsonized …

Comparative Toxicology Of Nio And Ni(Oh)₂ Nanoparticles, Melissa Hope Cambre

Masters Theses

“Understanding the potential toxicity of nanoparticles (NPs) is important to ensure that these new products do not impose harmful effects to human and environmental health. Paper I is a literature review in which we discuss characteristics of nanomaterials, with an emphasis on transition metal oxide nanoparticles that influence cytotoxicity. Identification of those properties may lead to the design of more efficient and safer nanosized products for various industrial purposes and provide guidance for assessment of human and environmental health risk. We then investigate biochemical and molecular mechanisms of cytotoxicity that include oxidative stress-induced cellular events and alteration of the pathways …

Nanoparticle Targeting To The Central Nervous System, Emily Baker

Williams Honors College, Honors Research Projects

Drug delivery to the central nervous system is complicated by the blood-brain barrier, a vascular structure that prevents free diffusion of molecules into brain tissue. In this study, we examined the in vitro properties of a nanoparticle-based drug delivery system. We used several nanoparticle formulations, both LTP based and PLGA based, to test the cellular uptake and toxicity in microglial cells. Using immunofluorescence imaging, we show that LTP nanoparticles are taken up by microglia. We confirmed that our nanoparticle formulations are non-toxic by two cell viability assays. These results suggest that nanoparticle formulations may be a biocompatible method of delivering …

Development And Application Of New Solid-State Models For Low-Energy Vibrations, Lattice Defects, Entropies Of Mixing, And Magnetic Properties, Jacob M. Schliesser

Theses and Dissertations

Low-temperature heat capacity data contain information on the physical properties of materials, and new models continue to be developed to aid in the analysis and interpretation of heat capacity data into physically meaningful properties. This work presents the development of two such models and their application to real material systems. Equations describing low-energy vibrational modes with a gap in the density of states (DOS) have been derived and tested on several material systems with known gaps in the DOS, and the origins of such gaps in the DOS are presented. Lattice vacancies have been shown to produce a two-level system …

Design And Synthesis Of Polymeric Nanoparticles For Drug And Protein Delivery, Judy A. Ventura

Doctoral Dissertations

Nanoparticles are emerging as carriers in biological applications due to advances in their preparation, size control, surface modification and encapsulation capabilities. In addition, nanomaterials improve bioavailability by enhancing aqueous solubility of the guest molecule and increasing resistance time in the body. However, the delivery of guest molecules is still challenging due to the intrinsic characteristics of the guest molecule including large size and propensity to denature or degradation in the case of biomolecules and the encapsulation stability of the small guest molecules. Our group recently reported the preparation of self-cross-linked polymeric nanogels possessing surface functionalization capabilities. In this dissertation we …

Fabrication And Characterization Of Sol-Gel Based Nanoparticles For Drug Delivery, Reeta Yadav

Dissertations, Theses, and Capstone Projects

Nanogels are cross linked polymeric sol-gel based nanoparticles that offer an interior network for incorporation and protection of biomolecules, exhibiting unique advantages for polymer based delivery systems. We have successfully synthesized stable sol-gel nanoparticles by means of [a] silicification reactions using cationic peptides like polylysine as gelating agents, and [b] lyophilization of sol-gels. Macromolecules such as Hemoglobin and Glucose Oxidase and small molecules such as Sodium Nitroprusside (SNP) and antibiotics were encapsulated within the nanogels. We have used transmission electron microscopy, dynamic light scattering, zeta potential analysis, and spectroscopy to perform a physicochemical characterization of the nanogels resulting from the …

Combined Metal-Enhanced Fluorescence-Surface Acoustic Wave (Mef-Saw) Biosensor, Samuel Morrill

USF Tampa Graduate Theses and Dissertations

Immunofluorescence assays are capable of both detecting the amount of a protein and the location of the protein within a cell or tissue section. Unfortunately, the traditional technique is not capable of detecting concentrations on the nanoscale. Also, the technique suffers from non-specific attachment, which can cause false-positives, as well as photobleaching when detecting lower concentrations is attempted. There is also a time constraint problem since the technique can take from many hours to a few days in some cases.

In this work, metal-enhanced fluorescence (MEF) is used to lower the detection limit and reduce photobleaching. Unfortunately, MEF also increases …

Formation And Analysis Of Zinc Oxide Nanoparticles And Zinc Oxide Hexagonal Prisms And Optical Analysis Of Cadmium Selenide Nanoparticles, Jared M. Hancock

Theses and Dissertations

In this dissertation, methods to synthesize ZnO are reported. First, zinc oxide nanoparticles were synthesized with small amounts of transition metal ions to create materials called dilute magnetic semiconductors (DMS). We employed a low temperature sol-gel method that produces ZnO nanoparticles of reproducible size and incorporates cobalt, nickel, and manganese ions into the nanoparticles. Conditions were controlled such that a range of amounts of Co, Ni, and Mn were incorporated. The incorporation was tracked by color changes in the white ZnO powder to blue for Co, green for Ni and yellow for Mn. XRD measurements showed the nanoparticles were on …

Size-Based Separation Of Bioparticles Using Planar Nanofluidic Devices, Jie Xuan

Theses and Dissertations

Nanofluidic devices are structures having at least one dimension in the submicron range, which is of the same order of magnitude as the sizes of biomolecules and bioparticles such as proteins and viruses. As a result, size-selective separations are important applications for nanofluidics. Well-defined micro or nano device structures fabricated via micromachining have greatly reduced sample consumption and enabled separations in a parallel fashion, promising significant speed and resolution advantages over conventional size separation techniques, such as gel electrophoresis and size exclusion chromatography. In collaboration with others, I have developed a size separation method using nanofluidic devices consisting of an …

New Tools For Real-Time Study Of Embryonic Development, Lauren M. Browning

Theses and Dissertations in Biomedical Sciences

Embryonic development represents one of the most complex and dynamic cellular processes in biology, and plays vital roles in understanding of functions of embryonic stem cells (ESCs) and design of ESC-based therapy. Conventional assays and fluorescence-based imaging methods have been widely used for the study of embryonic development. These conventional methods cannot effectively provide spatial and temporal resolutions with sufficient sensitivity and selectivity that are required to depict embryonic development in vivo in real-time at single-cell and single-molecule resolutions. In this dissertation, we have developed a wide range of innovative tools for real-time study of embryonic development. These new tools …

The Synthesis And Structural Characterization Of Metal Oxide Nanoparticles Having Catalytic Applications, Stacey Janel Smith

Theses and Dissertations

Nanotechnology is blossoming into one of the premiere technologies of this century, but the key to its progress lies in developing more efficient nanosynthesis methods. Variations in synthetic technique, however, can cause variations in size, structure, and surface characteristics, thereby altering the physical properties and functionality of the particles. Careful structural characterizations are thus essential for understanding the properties and appropriate applications for particles produced by new synthetic techniques.In this work, a new ‘solvent-deficient’ method is presented for the synthesis of an unprecedentedly wide range of metal oxide nanomaterials including at least one metal oxide from each group in Groups …

Dna-Templated Nanomaterials, Hector Alejandro Becerril-Garcia

Theses and Dissertations

Nanomaterials display interesting physical and chemical properties depending on their shape, size and composition. Self assembly is an intriguing route to producing nanomaterials with controllable compositions and morphologies. DNA has been used to guide the self assembly of materials, resulting in: (1) metal nanowires; (2) metal or semiconductor nanorods; (3) carbon nanotubes; and (4) semiconductor, metal or biological nanoparticles. My work expands the range of DNA templated nanomaterials and develops novel ways of using DNA to pattern nanostructures on surfaces. I have performed the first synthesis of silver nanorods on single stranded DNA, an attractive material for localizing DNA coupled …

Development Of Single Nanoparticle Optical Assays For Imaging Single Living Cells, William John Brownlow

Chemistry & Biochemistry Theses & Dissertations

Multi-drug resistance (MDR) has been reported in both prokaryotes and eukaryotes; the pathogenic gram-negative bacteria Pseudomonas aeruginosa can extrude a variety of structurally and functionally diverse substrates via a number of membrane transport systems leading to MDR. We have developed a novel nanoparticle assay to characterize both the membrane transport system composed of the MexAB-OprM efflux pump and the membrane permeability induced by antibiotics. Gold (Au) and silver (Ag) nanoparticles were investigated for use as probes to explore membrane transport in P. aeruginosa.

The surface plasmon absorption (color) of Au nanoparticle solutions was found to change in the presence …