Biochemistry, Biophysics, and Structural Biology Commons^™

A Temporal Analysis Of The Microbiota And Biofouling Development On Artificial Substrates In The Port Everglades Inlet, Florida, Denise Swack

All HCAS Student Capstones, Theses, and Dissertations

A pilot project was deployed in Port Everglades Inlet, Florida that aimed to evaluate the biofilm composing the microbiome on ecologically engineered artificial substrates used to build Coastal Marine Infrastructure. In April of 2017, an Articulated Concrete Block Mattress comprised of an ecological engineered concrete substrate and a standard smooth surface control substrates were compared. This study will provide a profile on the microbiome community on artificial substrates within Port Everglades Inlet on bio-enhancing concrete-based solutions in our Coastal Marine Infrastructure. To study the microbial community, the 16s rRNA technology was used in Illumina’s high-throughput DNA sequencing. Samples were collected …

The Application Of Mathematical Optimization And Flavor-Detection Technologies For Modeling Aroma Of Hops, Yutong Liu

Department of Food Science and Technology: Dissertations, Theses, and Student Research

In recent years, proprietary hops (Citra, Simcoe, and Mosaic) become the most sought-after hops among brewers due to their excellent aroma. However, they are restricted to the owners unless other growers purchase the costly licensing agreements. Many public hops are available to the growers without any additional costs, but their aroma is difficult to match to the proprietary hops. Although proprietary and public hop varieties are unique in their aroma profiles, all hops varieties contain similar volatile compounds, merely differ in the quantity of different individual compounds. The main objective of this thesis was to investigate the feasibility of matching …

Investigating Effects Of Microenvironmental Stress On Cell Metabolism Using Multiphoton Imaging, Lisa Rebello

Graduate Theses and Dissertations

Resistance to therapy in cancer is a major cause of poor prognosis in patients. Tumor hypoxia plays an active role in mediating treatment resistance and has been linked to metastases and metastatic potential in cancer. Our research focused on three objectives: i) To understand metabolic effects of chronic and intermittent hypoxia in murine breast cancer cells and its affiliation with metastatic potential ii) To identify the metabolic changes associated with radiation therapy in a panel of radiosensitive and radioresistant human head and neck cancer cells and iii) to monitor the changes in cell metabolism associated with gain of treatment resistance. …

Role Of The Nuclear Envelope In The Mechanoregulation Adipogenesis, Matthew H. Goelzer

Boise State University Theses and Dissertations

Mechanical signals are known regulators of mesenchymal stem cell (MSC) fate, regulating their differentiation into osteoblasts, chondrocytes, and adipocytes. These relevant mechanical signals reach to nucleus through nuclear envelope proteins such as Lamin A/C and the Linker of the Nucleoskeleton and Cytoskeleton (LINC) complexes. Within the context of bone, clinically relevant mutations of Lamin A/C and the LINC complexes have been shown to alter adipogenic and osteogenic MSC differentiation patterns, suggesting that that nucleo-cytoskeletal connectivity provided by nuclear envelope is important in regulating MSC fate. Using MSC adipogenesis as a model of MSC mechanical regulation, the goal of this work …

Aptamer-Based Voltammetric Biosensing For The Detection Of Codeine And Fentanyl In Sweat And Saliva, Rosa Lashantez Cromartie

FIU Electronic Theses and Dissertations

Despite the many governmental and medicinal restrictions created to combat the opioid epidemic in the United States, opioid abuse and overdose rates continue to rise. The development of an aptamer-based voltammetric sensor and biosensor is described in this dissertation. The aim was to develop a low-cost, sensitive, and specific aptamer-based sensor for on-site, label-free determination of codeine and fentanyl in biological fluids. To do this, the surfaces of screen-printed carbon electrodes (SPCE) were modified with gold nanoparticles (AuNPs), followed by the addition of single-stranded DNA aptamers. These were covalently bound to the electrode surface. Operations of the sensors were collected …

Aerobic Copper-Promoted Oxidative Dehydrosulfurative Carbon-Oxygen Cross-Coupling Of 3,4-Dihydropyrimidine-1: H -2-Thiones With Alcohols, Jihong Lee, Yujeong Kwon, Dong-Chan Lee, Jeong Hun Sohn

Chemistry and Biochemistry Faculty Research

An aerobic Cu-promoted oxidative dehydrosulfurative carbon-oxygen cross-coupling of 3,4-dihydropyrimidin-1H-2-thiones (DHPMs) with both aliphatic and aromatic alcohols is described. Together with the ready availability of DHPMs and both alcohols, the method furnishes facile access to biologically valuable 2-alkoxypyrimidines with rapid diversification.

Investigation Of Immobilized Enzymes In Confined Environment Of Mesoporous Host Matrices, Xiaoliang Wang

USF Tampa Graduate Theses and Dissertations

Enzyme immobilization in metal-organic frameworks (MOFs) as a promising strategy, is attracting the interest of scientists from different disciplines with the expansion of MOF’s development. Different from other traditional host materials, their unique strengths of high surface areas, large yet adjustable pore sizes, functionalizable pore walls, and diverse architectures make MOFs an ideal platform to investigate hosted enzymes, which is critical to the industrial and commercial process. In addition to the protective function of MOFs, the extensive roles of MOFs in the enzyme immobilization are being well-explored by making full use of their remarkable properties like well-defined structure, high porosity, …

Computational Simulation Of The Lung Doses Of Air-Borne Fine And Ultrafine Particles Inhaled By Humans At Industrial Workplaces, Mohammed Ali

Technology Faculty Publications and Presentations

This study correlates computational predictions with in-vivo experimental results of inhaled fine and ultrafine particulate matters (PMs) transport, dissemination, and deposition in the human respiratory airways. Epidemiological studies suggest that workplace exposure of anthropogenic pollutant PMs as a risk factor for increased susceptibility to acute broncho-pulmonary infections. However, investigations on detailed human inhalation and PM transport processes are restrictive from time, cost, and ethical perspectives. To overcome this problem, computational simulation of particle deposition based on the Multiple Path Particle Dosimetry (MPPD) model was employed. Here, the physical, mechanical, and electrical properties of PMs of carbon black and nanoparticles from …

Tools And Strategies For The Patterning Of Bioactive Molecules And Macromolecules, Daniel J. Valles

Dissertations, Theses, and Capstone Projects

Hypersurface Photolithography (HP) is a printing method for fabricating structures and patterns composed of soft materials bound to solid surfaces and with ~1 micrometer resolution in the x, y, and z dimensions. This platform leverages benign, low intensity light to perform photochemical surface reactions with spatial and temporal control of irradiation, and, as a result, is particularly useful for patterning delicate organic and biological material. In particular, surface- initiated controlled radical polymerizations can be leveraged to create arbitrary polymer and block- copolymer brush patterns. Chapter 1 will review the advances in instrumentation architectures from our group that have made these …

Molecular Dynamics Simulations Of Self-Assemblies In Nature And Nanotechnology, Phu Khanh Tang

Dissertations, Theses, and Capstone Projects

Nature usually divides complex systems into smaller building blocks specializing in a few tasks since one entity cannot achieve everything. Therefore, self-assembly is a robust tool exploited by Nature to build hierarchical systems that accomplish unique functions. The cell membrane distinguishes itself as an example of Nature’s self-assembly, defining and protecting the cell. By mimicking Nature’s designs using synthetically designed self-assemblies, researchers with advanced nanotechnological comprehension can manipulate these synthetic self-assemblies to improve many aspects of modern medicine and materials science. Understanding the competing underlying molecular interactions in self-assembly is always of interest to the academic scientific community and industry. …

Preparation Of Meta-Nitrobenzoylhydrazone Ferrocenoylacetone And Synthesis On Its Basis, Zilola Abduraxmonovna Sulaymonova, Bako Bafayevich Umarov Doctor Chemical Science, Professor

Chemical Technology, Control and Management

β-diketone-ferrocenoylacetone was obtained by Claisen condensation. Meta-nitrobenzoylhydrazone of ferrocenoylacetone (H₂L) was synthesized by the interaction of meta-nitrobenzoic acid hydrazide with ferrocenoylacetone. On its basis, complexes with copper(II) and nickel(II) ions were synthesized. The obtained compounds were characterized by the methods of elemental analysis, IR-, ¹H NMR andelectronic spectroscopy. The research results showed that H₂L in solution exists in the form of a tautomeric mixture: hydrazone, α-hydroxyazine, and cyclic 5-hydroxypyrazoline forms. According to the results of IR and ¹H NMR spectra, the complexes were assigned a planar-square structure, and in them the doubly deprotonated …

Lipoprotein-Induced Increases In Cholesterol And 7-Ketocholesterol Result In Opposite Molecular-Scale Biophysical Effects On Membrane Structure, Manuela A.A. Ayee, Irena Levitan

Faculty Work Comprehensive List

Under hypercholesterolemic conditions, exposure of cells to lipoproteins results in a subtle membrane increase in the levels of cholesterol and 7-ketocholesterol, as compared to normal conditions. The effect of these physiologically relevant concentration increases on multicomponent bilayer membranes was investigated using coarse-grained molecular dynamics simulations. Significant changes in the structural and dynamic properties of the bilayer membranes resulted from these subtle increases in sterol levels, with both sterol species inducing decreases in the lateral area and inhibiting lateral diffusion to varying extents. Cholesterol and 7-ketocholesterol, however, exhibited opposite effects on lipid packing and orientation. The results from this study indicate …

A Kinetic Model For Blood Biomarker Levels After Mild Traumatic Brain Injury, Sima Azizi, Daniel B. Hier, Blaine Allen, Tayo Obafemi-Ajayi, Gayla R. Olbricht, Matthew S. Thimgan, Donald C. Wunsch

Mathematics and Statistics Faculty Research & Creative Works

Traumatic brain injury (TBI) imposes a significant economic and social burden. The diagnosis and prognosis of mild TBI, also called concussion, is challenging. Concussions are common among contact sport athletes. After a blow to the head, it is often difficult to determine who has had a concussion, who should be withheld from play, if a concussed athlete is ready to return to the field, and which concussed athlete will develop a post-concussion syndrome. Biomarkers can be detected in the cerebrospinal fluid and blood after traumatic brain injury and their levels may have prognostic value. Despite significant investigation, questions remain as …

Evaluation Of Horizontal Gene Transfer Between Genetically Engineered Cyanobacteria And Gram-Negative Bacteria, Andriana Chrysovalanti Zourou

Chemistry & Biochemistry Theses & Dissertations

As the world population is increasing and societies become more technology driven, there is an imperative to develop ‘green energy’ sources to protect our planet. Cyanobacteria that have been genetically engineered to produce organic compounds that may be burnt as fuels show great potential, as they are an environmentally friendly and self-renewable, net carbon-neutral option. However, there are potential risks in the development and use of genetically modified organisms (GMOs). We need to understand in advance the risks that GMOs may pose to our environment and to animal and human health. This will enable experimental procedures, containment strategies and policies …

Electrohydrodynamic Simulations Of Capsule Deformation Using A Dual Time-Stepping Lattice Boltzmann Scheme, Charles Leland Armstrong

Mathematics & Statistics Theses & Dissertations

Capsules are fluid-filled, elastic membranes that serve as a useful model for synthetic and biological membranes. One prominent application of capsules is their use in modeling the response of red blood cells to external forces. These models can be used to study the cell’s material properties and can also assist in the development of diagnostic equipment. In this work we develop a three dimensional model for numerical simulations of red blood cells under the combined influence of hydrodynamic and electrical forces. The red blood cell is modeled as a biconcave-shaped capsule suspended in an ambient fluid domain. Cell deformation occurs …

Somatic Inhibition By Microscopic Magnetic Stimulation, Hui Ye

Biology: Faculty Publications and Other Works

Electric currents can produce quick, reversible control of neural activity. Externally applied electric currents have been used in inhibiting certain ganglion cells in clinical practices. Via electromagnetic induction, a miniature-sized magnetic coil could provide focal stimulation to the ganglion neurons. Here we report that high-frequency stimulation with the miniature coil could reversibly block ganglion cell activity in marine mollusk Aplysia californica, regardless the firing frequency of the neurons, or concentration of potassium ions around the ganglion neurons. Presence of the ganglion sheath has minimal impact on the inhibitory effects of the coil. The inhibitory effect was local to the …

Novel Approaches Towards Improved Purity In High Yield Transcription Reactions, Elvan Cavac

Doctoral Dissertations

High yields of RNA (e.g., mRNA, gRNA, lncRNA) are routinely prepared following a two-step approach: high yield in vitro transcription using T7 RNA polymerase, followed by extensive purification using gel or chromatic methods. In high yield transcription reactions, as RNA accumulates in solution, T7 RNA polymerase rebinds and extends the encoded RNA (using the RNA as a template), resulting in a product pool contaminated with longer than desired, (partially) double stranded impurities. Current purification methods often fail to fully eliminate these impurities which, if present in therapeutics, can stimulate the innate immune response with potentially fatal consequences. This study establishes …

Flow Visualization And Aerosol Characterization Of Respiratory Jets Exhaled From A Mannequin Simulator, Sindhu Reddy Mutra

USF Tampa Graduate Theses and Dissertations

It is important to understand the airborne transmission of infectious diseases due to the COVID-19 pandemic. Physical experiments were conducted to understand the dispersion of aerosols emitted from a mannequin simulator replicating human tidal breathing through the nose and mouth with and without a protective face mask in an enclosed space. Flow patterns are observed via high-speed visualization, and the concentration and size distribution of the particles is measured as a function of distance from the mannequin using an optical particle sizer. Masks were shown to effectively reduce the horizontal dispersion of aerosol for both mouth and nose breathing. Further, …

Computational Prediction Of Mutagenesis In Glycine Max Rubisco Activase Monomer For Increased Thermal Stability, Catherine B. Emanuel, Hamza Haq '21, Vasanth Ramesh '21, Jaden Wang '21, Angela Ahrendt, Sarah Stainbrook

Student Publications & Research

No abstract provided.

Computational Algorithms For Predicting Membrane Protein Assembly From Angstrom To Micron Scale, Nandhini Rajagopal

Dissertations - ALL

Biological barriers in the human body are one of the most crucial interfaces perfected through evolution for diverse and unique functions. Of the wide range of barriers, the paracellular protein interfaces of epithelial and endothelial cells called tight junctions with high molecular specificities are vital for homeostasis and to maintain proper health. While the breakdown of these barriers is associated with serious pathological consequences, their intact presence also poses a challenge to effective delivery of therapeutic drugs. Complimenting a rigorous combination of in vitro and in vivo approaches to establishing the fundamental biological construct, in addition to elucidating pathological implications …

Computational Algorithms For Predicting Membrane Protein Assembly From Angstrom To Micron Scale, Nandhini Rajagopal

Dissertations - ALL

Biological barriers in the human body are one of the most crucial interfaces perfected through evolution for diverse and unique functions. Of the wide range of barriers, the paracellular protein interfaces of epithelial and endothelial cells called tight junctions with high molecular specificities are vital for homeostasis and to maintain proper health. While the breakdown of these barriers is associated with serious pathological consequences, their intact presence also poses a challenge to effective delivery of therapeutic drugs. Complimenting a rigorous combination of in vitro and in vivo approaches to establishing the fundamental biological construct, in addition to elucidating pathological implications …

Characterizing The Dormancy And Repair Of A Circumneutral Passive Remediation System Receiving Iron And Sulfate-Rich Amd, Garrett Struble

Electronic Theses and Dissertations

The Wingfield Pines remediation system is a ~20-acre circumneutral, gravity-fed system constructed in 2009 to passively remediate Fe from an ~2000 gallon/minute effluent. In 2017, a fracture to the system’s underground cavern caused the AMD effluent to bypass the system, flowing directly into Chartiers Creek and leaving the system decommissioned between 2017-2019. Soil slurry and water samples were collected in the weeks prior to the system’s reinstalment in September 2019 through January 2020 in order to determine the effect of the repair on remediation efficiency and microbial community composition. This study acted as the first to describe the temporary decommissioning …

Engineering Modularity Of Ester Biosynthesis Across Biological Scales, Hyeongmin Seo

Doctoral Dissertations

Metabolic engineering and synthetic biology enable controlled manipulation of whole-cell biocatalysts to produce valuable chemicals from renewable feedstocks in a rapid and efficient manner, helping reduce our reliance on the conventional petroleum-based chemical synthesis. However, strain engineering process is costly and time-consuming that developing economically competitive bioprocess at industrial scale is still challenging. To accelerate the strain engineering process, modular cell engineering has been proposed as an innovative approach that harnesses modularity of metabolism for designing microbial cell factories. It is important to understand biological modularity and to develop design principles for effective implementation of modular cell engineering. In this …

Characterization Of Protein Aggregation Using A Solid-State Nanopore Device, Mitu Chandra Acharjee

Graduate Theses and Dissertations

Protein aggregation has been linked to many chronic and devastating neurodegenerative human diseases and is also strongly associated with aging. In the case of neurodegenerative diseases, α, β tubulins and tau proteins dissociate in a neuron cell and aggregate both intra and extra-cellularly. Tau and tubulin aggregations were found as one of the major causes of many neurodegenerative diseases, such as Parkinson’s, Picks, Alzheimer’s, Huntington, and Prion. Finding the state and mechanism of protein aggregation is significant. In this work, tau and tubulin aggregations were detected in ionic solutions using the solid-state nanopore technique. Besides tau and tubulin, aggregations of …

Analyzing The Effects Of E-Hook Peptides On Kinesin-1, Ashton Ward Murrah, Baylee Hope Howard

Honors Theses

Cancer is the second leading cause of death in the United States. Cancerous growth is a result of oncogenes, or mutated genes that increase the rate of cell division in an uncontrolled manner. Cell division, which consists of mitosis and cytokinesis phases, is dependent upon the active movement of kinesin motor proteins along microtubules to rearrange the cytoskeleton for equitable distribution of genetic material to daughter cells. As kinesins are vital to this process, if we could prevent kinesin from binding to the microtubules, cell division would cease.

The goal of this study is to develop a method to prevent …

Finite Element Analysis Of Impact Resistant Composites Inspired By Peacock Mantis Shrimp, Nandati Shrestha

Thinking Matters Symposium

The fist-like club of the peacock mantis shrimp, a 5-inch marine crustacean, can strike its prey with speed faster than a .22-caliber bullet with an impact force more than 1,000 times its own weight. Although these creatures punch so fast that it even boils the water, they don’t take any damage. This incredible insusceptibility is due to the arrangement of mineralized fiber layers in which each fibrous layer is laid at a slightly rotated angle to form a helicoidal structure that acts as a shock absorber for the club. The goal is to perform a finite element analysis to investigate …

Design, Simulation And Testing Of Biomimetic Directional Acoustic Sensors, Brendan Francis

Thinking Matters Symposium

The Ormia ochracea, a species of parasitic fly, has become the focal point in sound localization research because of its finely tuned hearing abilities. The female of this species uses its super highly directional hearing to pinpoint the call of a host cricket, with hypersensitivity of frequency and phase difference, to reach and dispose of its eggs on the host. The goal of this study was to further the research of a previous Project in Professor Guvench’s group which implemented MEMS (Micro Electro-Mechanical System) technology on a chip to replicate these abilities. In this iteration, however, some commercially available …

Mems Directional Acoustic Sensors, Colby Damren

Thinking Matters Symposium

The purpose of my project is to test and verify two Micro-Electro-Mechanical-System (MEMS) microphones. The two MEMS devices are biomimetic microphones that imitate the eardrums of the Ormia Ochracea, a parasitic fly that listens for host crickets to lay their eggs. The MEMS microphones mimic the eardrum spacing of the Ormia Ochracea with a spacing of 1000um. This is roughly twice the opening of the Ormia Ochracea. The microphones will be tested for directionality inside a wooden box. This box will be lined with beveled foam to prevent any echo or outside noise from interfering with the results. These results …

Project Alien, Rebecca Mccallin, Madelyn Hoying, Alex Evans, Matthew Nestler, Karli Rae Sutton, Garett Craig, Lucia Secaia Del Cid, Alexander Guy, Rachel Fernandez, Amanda Trusiak, Paige Aley, Ingabire Gakwerere, Nina Dorfner, Maria Mosbacher, Mary Flavin, Selvin Hernandez, Audrey Steen, Benjamin Kazimer

Undergraduate Research and Scholarship Symposium

Project ALIEN is a comprehensive plan to send humans to Mars to look for life on the Martian surface while exploring the viability and adaptability of terrestrial microbes in Martian atmospheric conditions. ALIEN will use a ballistic capture trajectory to get to Mars and stay in aerostationary orbit for a 30-day surface mission, during which two surface crewmembers will perform a variety of experiments to achieve the mission’s goals of Martian microbial discovery within brines of the Gale Crater and terrestrial microbe adaptability and viability to Martian conditions. Experimentation is based on the presumption that Martian microbes are metabolically similar …

Cyclophilin D Is A Sensor Of Nano-Pulse Stimulation, Brittney Ruedlinger, Bani Hani Maisoun, Lucas Potter, Nicola Lai, Stephen J. Beebe

The Graduate School Posters

Nano-Pulse Stimulation (NPS), a pulsed power-derived technology, stimulates structural and functional changes in plasma membranes and cellular organelles. NPS induces a Ca²⁺ influx and opening of the mitochondrial permeability transition pore (mPTP) that dissipates the mitochondrial membrane potential (ΔΨ_m) and, when sustained, induces regulated cell death. Here we show that in rat cardiomyoblasts (H9C2) cyclophilin D (CypD) is a mitochondrial sensor for NPS as defined by observations that loss of ΔΨ_m is Ca²⁺ and mitochondrial reactive oxygen species (mROS) dependent and cyclosporin A (CsA)-sensitive, which are diagnostic qualities for effects on CypD and the mPTP. …