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Protein Detection And Structural Characterization By Mass Spectrometry Using Supramolecular Assemblies And Small Molecules, Bo Zhao Oct 2019

Protein Detection And Structural Characterization By Mass Spectrometry Using Supramolecular Assemblies And Small Molecules, Bo Zhao

Doctoral Dissertations

Mass spectrometry (MS) has played an increasingly prominent role in proteomics and structure biology because it shows superior capabilities in identification, quantification and structural characterization of proteins. To realize its full potential in protein analysis, significant progress has been made in developing innovative techniques and reagents that can couple to MS detection. This dissertation demonstrates the use of polymeric supramolecular assemblies for enhanced protein detection in complex biological mixtures by MS. An amphiphilic random co-polymer scaffold is developed to form functional supramolecular assemblies for protein/ peptide enrichment. The influences of charge density and functional group pKa on host-guest interactions ...


Function And Dissipation In Finite State Automata - From Computing To Intelligence And Back, Natesh Ganesh Oct 2019

Function And Dissipation In Finite State Automata - From Computing To Intelligence And Back, Natesh Ganesh

Doctoral Dissertations

Society has benefited from the technological revolution and the tremendous growth in computing powered by Moore's law. However, we are fast approaching the ultimate physical limits in terms of both device sizes and the associated energy dissipation. It is important to characterize these limits in a physically grounded and implementation-agnostic manner, in order to capture the fundamental energy dissipation costs associated with performing computing operations with classical information in nano-scale quantum systems. It is also necessary to identify and understand the effect of quantum in-distinguishability, noise, and device variability on these dissipation limits. Identifying these parameters is crucial to ...


Arboriculture Safety Around The World, Jamie Lim Oct 2019

Arboriculture Safety Around The World, Jamie Lim

Masters Theses

Arboricultural work is inherently dangerous, with more serious injuries and fatalities than most other professions. Safety standards exist in some jurisdictions, but it is unclear how many standards exist, how they compare to one another, and whether (and how many) jurisdictions share standards. To establish a baseline understanding of these issues, my objectives were to (i) develop a database of existing standards, (ii) identify the most frequently occurring safety topics and (iii) describe similarities and differences in safety topics among standards from different countries. I worked with a variety of contacts and traditional university library resources to identify, obtain, analyze ...


Multiscale Simulations Of Intrinsically Disordered Proteins, Xiaorong Liu Jul 2019

Multiscale Simulations Of Intrinsically Disordered Proteins, Xiaorong Liu

Doctoral Dissertations

Intrinsically disordered proteins (IDPs) lack stable secondary and/or tertiary structures under physiological conditions. The have now been recognized to play important roles in numerous biological processes, particularly cellular signaling and regulation. Mutation of IDPs are frequently associated with human diseases, such as cancers and neuron degenerative diseases. Therefore, it is important to understand the structure, dynamics, and interactions of IDPs, so as to establish the mechanistic basis of how intrinsic disorder mediates versatile functions and how such mechanisms may fail in human diseases. However, the heterogeneous structural ensembles of IDPs are not amenable to high resolution characterization solely through ...


Population Viability And Connectivity Of The Federally Threatened Eastern Indigo Snake In Central Peninsular Florida, Javan Bauder Mar 2019

Population Viability And Connectivity Of The Federally Threatened Eastern Indigo Snake In Central Peninsular Florida, Javan Bauder

Doctoral Dissertations

Understanding the factors influencing the likelihood of persistence of real-world populations requires both an accurate understanding of the traits and behaviors of individuals within those populations (e.g., movement, habitat selection, survival, fecundity, dispersal) but also an understanding of how those traits and behaviors are influenced by landscape features. The federally threatened eastern indigo snake (EIS, Drymarchon couperi) has declined throughout its range primarily due to anthropogenically-induced habitat loss and fragmentation making spatially-explicit assessments of population viability and connectivity essential for understanding its current status and directing future conservation efforts.

The primary goal of my dissertation was to understand how ...


Integration Of Robotic Perception, Action, And Memory, Li Yang Ku Oct 2018

Integration Of Robotic Perception, Action, And Memory, Li Yang Ku

Doctoral Dissertations

In the book "On Intelligence", Hawkins states that intelligence should be measured by the capacity to memorize and predict patterns. I further suggest that the ability to predict action consequences based on perception and memory is essential for robots to demonstrate intelligent behaviors in unstructured environments. However, traditional approaches generally represent action and perception separately---as computer vision modules that recognize objects and as planners that execute actions based on labels and poses. I propose here a more integrated approach where action and perception are combined in a memory model, in which a sequence of actions can be planned based on ...


Application And Evaluation Of Lighthouse Technology For Precision Motion Capture, Soumitra Sitole Oct 2018

Application And Evaluation Of Lighthouse Technology For Precision Motion Capture, Soumitra Sitole

Masters Theses

This thesis presents the development towards a system that can capture and quantify motion for applications in biomechanical and medical fields demanding precision motion tracking using the lighthouse technology. Commercially known as SteamVR tracking, the lighthouse technology is a motion tracking system developed for virtual reality applications that makes use of patterned infrared light sources to highlight trackers (objects embedded with photodiodes) to obtain their pose or spatial position and orientation. Current motion capture systems such as the camera-based motion capture are expensive and not readily available outside of research labs. This thesis provides a case for low-cost motion capture ...


Real-Time Dengue Forecasting In Thailand: A Comparison Of Penalized Regression Approaches Using Internet Search Data, Caroline Kusiak Oct 2018

Real-Time Dengue Forecasting In Thailand: A Comparison Of Penalized Regression Approaches Using Internet Search Data, Caroline Kusiak

Masters Theses

Dengue fever affects over 390 million people annually worldwide and is of particu- lar concern in Southeast Asia where it is one of the leading causes of hospitalization. Modeling trends in dengue occurrence can provide valuable information to Public Health officials, however many challenges arise depending on the data available. In Thailand, reporting of dengue cases is often delayed by more than 6 weeks, and a small fraction of cases may not be reported until over 11 months after they occurred. This study shows that incorporating data on Google Search trends can improve dis- ease predictions in settings with severely ...


Plants, Parasites, And Pollinators: The Effects Of Medicinal Pollens On A Common Gut Parasite In Bumble Bees, George Locascio Oct 2018

Plants, Parasites, And Pollinators: The Effects Of Medicinal Pollens On A Common Gut Parasite In Bumble Bees, George Locascio

Masters Theses

Declines in several pollinator species are due to a variety of factors, including pathogens. Incorporating pollinator-friendly plant species into wild and agricultural habitats could reduce the stress of pathogens if food sources act medicinally against pathogens. Previous research demonstrated one domesticated sunflower cultivar (Helianthus annuus) can dramatically reduce a gut pathogen (Crithidia bombi) of the common eastern bumble bee, Bombus impatiens. To ascertain the breadth of this medicinal trait, we tested whether pollen from several H. annuus cultivars and four relatives could also reduce C. bombi infections in B. impatiens. We also investigated whether timing of exposure to sunflower pollen ...


Polymeric Peptide Mimics For Protein Delivery, Coralie Backlund Jul 2018

Polymeric Peptide Mimics For Protein Delivery, Coralie Backlund

Doctoral Dissertations

The plasma membrane is a major obstacle in the development and use of biomacromolecules for intracellular applications. Consequently, proteins with intracellular targets represent an enormous, yet under studied avenue for therapeutics. Extended research has aimed at facilitating intracellular delivery of exogenous proteins using protein transduction domains (PTDs), which allow transport of bioactive molecules into cells. Synthetic polymers, inspired by PTDs, provide a well-controlled platform to vary molecular architecture for structure activity relationship studies. Specifically, this thesis focuses on the use of ring-opening metathesis, a facile and efficient polymerization technique, through which we can vary structural parameters to optimize delivery of ...


Effects Of Floral Phytochemicals On Growth And Evolution Of A Parasite Of Bumble Bees, Evan Palmer-Young Mar 2018

Effects Of Floral Phytochemicals On Growth And Evolution Of A Parasite Of Bumble Bees, Evan Palmer-Young

Doctoral Dissertations

Background: Nectar and pollen are rich in phytochemicals, some of which can reduce disease in pollinators, including agriculturally important honey and bumble bees. Floral phytochemicals could influence the ecological and evolutionary relationships between plants, their pollinators, and parasites that cause pollinator disease. Antiparasitic effects of phytochemicals could be exploited to ameliorate pollinator disease and decline, and thereby sustain pollinator-dependent agricultural production. However, prior studies showed variable effects of phytochemicals on infection in live bees, where differences in bee genotype, abiotic conditions, and parasite strain could influence results.

Approach: I used cell cultures of the intestinal trypanosome parasite of bumble bees ...


The Molecular Basis Of Caspase-9 Inactivation By Pka And C-Abl Kinases, Banyuhay Paningbatan Serrano Mar 2018

The Molecular Basis Of Caspase-9 Inactivation By Pka And C-Abl Kinases, Banyuhay Paningbatan Serrano

Doctoral Dissertations

Caspases are the cysteine proteases that facilitate the fundamental pathway of programmed cell death or apoptosis. The activation and function of these powerful enzymes are tightly regulated to ensure the faithful execution of apoptosis and prevent untimely cell death. Many deadly human diseases such as cancer, neurodegeneration and autoimmune disorders have been associated with defective activation and faulty regulation of caspases. As such, caspases are considered as attractive drug targets, which when properly controlled, can lead to effective therapeutics for apoptosis-related diseases. Thus, comprehensive investigations of the structure, function and regulation of caspases are necessary to understand the complex mechanisms ...


Light-Harvesting And Light-Responsive Materials For Optoelectronic And Biological Applications, Youngju Bae Mar 2018

Light-Harvesting And Light-Responsive Materials For Optoelectronic And Biological Applications, Youngju Bae

Doctoral Dissertations

In photodynamic therapy, several critical standards are required of photosensitizers including high singlet oxygen quantum yield, biocompatibility in dark, and long term photochemical stability. In addition, current PDT systems lack active targeting strategies to tumor cells, and instead mainly rely on the natural distribution of PS in the body following injection and application of near-infrared light treatment in the tumor region. This thesis describes a series of BODIPY-based molecules that were designed, synthesized and studied as photosensitizers with high singlet oxygen generation capacity through utilizing the heavy atom effect. Additionally, aqueous solubility and active targeting capability were introduced by photosensitizer ...


Mapping Sandbars In The Connecticut River Watershed Through Aerial Images For Floodplain Conservation, Bogumila Backiel Mar 2018

Mapping Sandbars In The Connecticut River Watershed Through Aerial Images For Floodplain Conservation, Bogumila Backiel

Masters Theses

Active geomorphic features of rivers like sandbars provide habitat for endangered and threatened riparian plant and animal species. However, human development has altered flow and sediment regimes, thus impairing formation of sandbars and islands. Large scale mapping of the fluvial geomorphology in river ecosystems like the Connecticut River is are necessary to understand the dynamics of these features and preserve habitat. Orthophotographs from 2012 from United States Department of Agriculture's Farm Service Agency (FSA), National Agriculture Imagery Program (NAIP) were used to develop a model in ArcGIS Pro to identify fluvial geomorphic features in the Connecticut River and 12 ...


Protein-Nanoparticle Co-Engineering: Self-Assembly, Intracellular Protein Delivery, And Crispr/Cas9-Based Gene Editing, Rubul Mout Nov 2017

Protein-Nanoparticle Co-Engineering: Self-Assembly, Intracellular Protein Delivery, And Crispr/Cas9-Based Gene Editing, Rubul Mout

Doctoral Dissertations

Direct cytoplasmic delivery of gene editing nucleases such CRISPR/Cas9 systems and therapeutic proteins provides enormous opportunities in curing human genetic diseases, and assist research in basic cell biology. One approach to attain such a goal is through engineering nanotechnological tools to mimic naturally existing intra- and extracellular protein delivery/transport systems. Nature builds transport systems for proteins and other biomolecules through evolution-derived sophisticated molecular engineering. Inspired by such natural assemblies, I employed molecular engineering approaches to fabricate self-assembled nanostructures to use as intracellular protein delivery tools. Briefly, proteins and gold nanoparticles were co-engineered to carry complementary electrostatic recognition elements ...


Influence Of Biomimetic Chelating Packaging On Natural Antimicrobial Efficacy, Paul Castrale Oct 2017

Influence Of Biomimetic Chelating Packaging On Natural Antimicrobial Efficacy, Paul Castrale

Masters Theses

The iron chelating molecule, ethylenediaminetetraacetic acid (EDTA) is used in food applications for the preservation of oxidation prone ingredients. Research has suggested that EDTA is also capable of enhancing the antimicrobial effectiveness of various compounds including naturally-derived antimicrobials. With consumer demand for cleaner food labels, there remains an opportunity to introduce new chelating technology to replace synthetically-derived EDTA. Through photographting and chemical conversion, hydroxamic acid ligands were covalently bound to polypropylene films resulting in polypropylene-graft-poly(hydroxamic acid) (PP-g-PHA). The resulting films demonstrated an ability to chelate 64 nmol/cm2 from an iron saturated environment or ...


Modelling Bird Migration With Motus Data And Bayesian State-Space Models, Justin Baldwin Oct 2017

Modelling Bird Migration With Motus Data And Bayesian State-Space Models, Justin Baldwin

Masters Theses

Bird migration is a poorly-known yet important phenomenon, as understanding movement patterns of birds can inform conservation strategies and public health policy for animal-borne diseases. Recent advances in wildlife tracking technology, in particular the Motus system, have allowed researchers to track even small flying birds and insects with radio transmitters that weigh fractions of a gram. This system relies on a community-based distributed sensor network that detects tagged animals as they move through the detection nodes on journeys that range from small local movements to intercontinental migrations. The quantity of data generated by the Motus system is unprecedented, is on ...


Multiple Testing Correction With Repeated Correlated Outcomes: Applications To Epigenetics, Katie Leap Oct 2017

Multiple Testing Correction With Repeated Correlated Outcomes: Applications To Epigenetics, Katie Leap

Masters Theses

Epigenetic changes (specifically DNA methylation) have been associated with adverse health outcomes; however, unlike genetic markers that are fixed over the lifetime of an individual, methylation can change. Given that there are a large number of methylation sites, measuring them repeatedly introduces multiple testing problems beyond those that exist in a static genetic context. Using simulations of epigenetic data, we considered different methods of controlling the false discovery rate. We considered several underlying associations between an exposure and methylation over time.

We found that testing each site with a linear mixed effects model and then controlling the false discovery rate ...


Botswana’S Elephant-Back Safari Industry – Stress-Response In Working African Elephants And Analysis Of Their Post-Release Movements, Tanya Lama Jul 2017

Botswana’S Elephant-Back Safari Industry – Stress-Response In Working African Elephants And Analysis Of Their Post-Release Movements, Tanya Lama

Masters Theses

Understanding how African elephants (Loxodonta africana) respond to human interactions in ecotourism operations is critical to safeguarding animal and human welfare and sustaining wildlife ecotourism activities. We investigated the stress response of elephants to a variety of tourist activities over a 15-month period at Abu Camp in northern Botswana. We compared fecal glucocorticoid metabolite (FGM) concentrations across three elephant groups, including: eight elephants in an elephant-tourism operation (Abu herd), three elephants previously reintroduced back into the wild from the Abu herd, and wild elephants. There were no differences in FGM concentrations between the three groups of elephants. The highest observed ...


Relationship Between Structure And Function In Nickel Proteins And Enzymes, Carolyn Carr Jul 2017

Relationship Between Structure And Function In Nickel Proteins And Enzymes, Carolyn Carr

Doctoral Dissertations

Nickel is a rarely used but biologically important metal that is utilized in all three domains of life. In nickel utilizing organisms there is a corresponding trafficking system specifically designed to capture nickel, deliver, and export excess nickel to prevent toxic effects. It is critical to understand the mechanisms by which organisms achieve metal selectivity to duplicate or disrupt this process for the benefit of human health and to further understanding of regulation mechanisms in biology.

RcnR is a Ni(II) and Co(II) responsive transcriptional regulator in E. coli. The research reported in this dissertation focuses on the relationship ...


Vitreous Gel Physics, Svetlana Morozova Jul 2017

Vitreous Gel Physics, Svetlana Morozova

Doctoral Dissertations

The transparent vitreous, which fills the posterior cavity of the eye, is incredibly engineered. The charged polyelectrolyte hyaluronic acid (HA) network swells to maintain the pressure in the eye, while stiff collagen type II bundles help absorb any external mechanical shock. Our investigations have contributed to a few key developments related to the physical properties of the vitreous:

(1) The stiff collagen network that supports the soft gel network is self-assembled from single triple-helix collagen proteins. Electrostatic interactions drive this assembly, such that the size and concentration are optimized at physiological salt concentrations. The width of the assemblies remarkably changes ...


Thiol-Ene Chemistry As An Enabler Of New Polymer Structures And Architectures, Joel M. Sarapas Mar 2017

Thiol-Ene Chemistry As An Enabler Of New Polymer Structures And Architectures, Joel M. Sarapas

Doctoral Dissertations

This dissertation focuses on two distinct projects: the synthesis and design of novel cell penetrating peptides mimics (CPPMs), and the implementation of the thiol-ene click reaction to generate new polymer architectures and chemistries. Guanidinium-rich CPPMs were generated through both ROMP and RAFT polymerizations, allowing for a comparison to be made across polymer backbone chemistries with respect to both siRNA and protein cellular internalization. A particularly effective methacrylate derived block copolymer was able to deliver siRNA to nearly an entire Jurkat T cell population.

The thiol-ene reaction was implemented initially within the context of improving material design for solid polymer electrolytes ...


X-Ray Characterization Of Mesophases And Phase Transitions Of Dna Analogues In Solutions, Mustafa Selcuk Yasar Nov 2016

X-Ray Characterization Of Mesophases And Phase Transitions Of Dna Analogues In Solutions, Mustafa Selcuk Yasar

Doctoral Dissertations

We think of DNA as double-stranded helices (duplex), but the polymer exists in many conformations. Several triplex and quadruplex DNA structures can be formed in laboratory settings and exist in nature. This thesis first provides a brief description of the nature of the order in arrays of duplex DNA under biologically relevant molecular crowding conditions. Then we compare the duplex DNA mesophases with the corresponding liquid crystalline phase behavior of the triplex and quadruplex DNA analogues. In particular, we focus on G-quadruplexes.

Observed in the folds of guanine-rich oligonucleotides, G-quadruplex structures are based on G-quartets formed by hydrogen bonding and ...


Ecological Consequences Of Lost Anadromous Forage Fish In Freshwater Ecosystems, Steven R. Mattocks Nov 2016

Ecological Consequences Of Lost Anadromous Forage Fish In Freshwater Ecosystems, Steven R. Mattocks

Masters Theses

Beginning in the early 1600s, dam construction in New England obstructed anadromous fish access to spawning grounds during migration. As a result, anadromous forage fish populations have declined, which has impacted freshwater, marine, and terrestrial ecosystems. To determine the impacts of dams on anadromous forage fish and freshwater ecosystems, I used historical and current data to estimate population changes in alewives (Alosa pseudoharengus) from 1600-1900. A significant reduction in spawning habitat occurred in New England as a result of 1,642 dams constructed between 1600 and 1900, resulting in 14.8% and 16.6% lake and stream habitat remaining by ...


Factors Affecting Habitat Quality For Wintering Wood Thrushes In A Coffee Growing Region In Honduras, Brett A. Bailey Nov 2016

Factors Affecting Habitat Quality For Wintering Wood Thrushes In A Coffee Growing Region In Honduras, Brett A. Bailey

Masters Theses

Amongst the diversity of taxa that occur in the Neotropics, 200 migratory bird species that breed in temperate North America can be found. Many of these populations have seen significant declines since the 1960s. The Wood Thrush, Hylocichla mustelina, is one such species. Shade coffee and other agroforestry practices show potential for benefiting migratory species, but the quality of coffee habitat and optimal habitat characteristics for Wood Thrushes remain unknown.

I surveyed a spatially complex, agricultural landscape in Honduras outside the recognized winter range of the Wood Thrush and radio-tagged 46 individuals within rustic coffee farms during the winters of ...


Morphological And Material Effects In Van Der Waals Interactions, Jaime C. Hopkins Jul 2016

Morphological And Material Effects In Van Der Waals Interactions, Jaime C. Hopkins

Doctoral Dissertations

Van der Waals (vdW) interactions influence a variety of mesoscale phenomena, such as surface adhesion, friction, and colloid stability, and play increasingly important roles as science seeks to design systems on increasingly smaller length scales. Using the full Lifshitz continuum formulation, this thesis investigates the effects of system materials, shapes, and configurations and presents open-source software to accurately calculate vdW interactions.

In the Lifshitz formulation, the microscopic composition of a material is represented by its bulk dielectric response. Small changes in a dielectric response can result in substantial variations in the strength of vdW interactions. However, the relationship between these ...


Photolysis Of Triazenylbenzoic Acids For Click Chemistry, Adam Gann Jul 2016

Photolysis Of Triazenylbenzoic Acids For Click Chemistry, Adam Gann

Doctoral Dissertations

Copper catalyzed cycloaddition of terminal alkynes and azides has revolutionized the field of bioconjugate chemistry. Unfortunately, typical copper catalysts are known to disrupt relevant biological systems, so it has become necessary to develop new, copper-free methods that are less cytotoxic. particular interest are "click" probes which can be activated with an outside light source, giving the user spatial and temporal control over the system being investigated. We have developed a method in which an aryl diazonium salt is rapidly generated using photolysis of the triazene functional group, and subsequently coupled with an electron rich aromatic nucleophile to yield an azobenzene ...


The Application Of Hydrogen/Deuterium Exchange And Covalent Labeling Coupled With Mass Spectrometry To Examine Protein Structure, Nicholas B. Borotto Mar 2016

The Application Of Hydrogen/Deuterium Exchange And Covalent Labeling Coupled With Mass Spectrometry To Examine Protein Structure, Nicholas B. Borotto

Doctoral Dissertations

Thorough insight into a protein’s structure is necessary to understand how it functions and what goes wrong when it malfunctions. The structure of proteins, however, is not easily analyzed. The analysis must take place under a narrow range of conditions or risk perturbing the very structure being probed. Furthermore, the wide diversity in size and chemistry possible in proteins significantly complicates this analysis. Despite this numerous methods have been developed in order to analyze protein structure. In this work, we demonstrate that mass spectrometry (MS)-based techniques are capable of characterizing the structure of particularly challenging proteins. This is ...


Studying Nanoparticle/Cell And Nanoparticle/Biosurface Interaction With Mass Spectrometry, Singyuk Hou Nov 2015

Studying Nanoparticle/Cell And Nanoparticle/Biosurface Interaction With Mass Spectrometry, Singyuk Hou

Masters Theses

Nanoparticles (NPs) have been used widely in various fields ranging from biomedical applications to life science due to their highly tunable properties. It is essential to understanding how NPs interact with biological systems of interest, therefore, analytical platforms to efficiently track NPs from cell to animal level are essential. In this thesis, laser desorption ionization mass spectrometry (LDI-MS) and inductively-coupled plasma mass spectrometry (ICP-MS) has been developed and applied to quantify NP/cell and NP/biological surface interactions. These two methods provide fast, label-free and quantitative analysis. New capability of LDI-MS to differentiate cell surface-bound and internalized NPs were established ...


Urban Agriculture And Ecosystem Services: A Typology And Toolkit For Planners, Kathleen Doherty Nov 2015

Urban Agriculture And Ecosystem Services: A Typology And Toolkit For Planners, Kathleen Doherty

Masters Theses

This thesis makes the connection between urban agriculture and a specific suite of ecosystem services and lays out a typology and toolkit for planners to take advantage of these ecosystem services. The services investigated here are: food production, water management, soil health, biodiversity, climate mitigation, and community development benefits. Research from a variety of fields was aggregated and synthesized to prove that urban agriculture can be beneficial for human as well as environmental health.

A set of urban agriculture typologies was generated to illustrate best practices to maximize a particular set of ecosystem services. The typologies are: production farm, stormwater ...