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Quantification Of Interactions Between Influenza Hemagglutinin And Host Cell Phosphoinositides By Super-Resolution Microscopy, Matthew T. Parent 2020 University of Maine

Quantification Of Interactions Between Influenza Hemagglutinin And Host Cell Phosphoinositides By Super-Resolution Microscopy, Matthew T. Parent

Electronic Theses and Dissertations

The influenza viral membrane protein hemagglutinin (HA) forms dense nanoscale clusters on host cell plasma membranes (PM), but the mechanisms that direct HA clustering are not well understood. Previous studies have observed HA associated with actin rich regions of the PM, but there are no known direct interactions between HA and actin. Phosphatidylinositol 4,5-biphosphate (PIP2) is a signaling lipid in the PM which can regulate the actin cytoskeleton, and actin comets initiated by PIP2 are known to be exploited by HA to reach the PM of infected cells. PIP2 is also used by other viruses, such as HIV and ...


Probing The Localization Patterns And Selectivity Filter Of Thyroid Hormone Receptor Alpha 1 Mutants, Jerry O'Dwyer 2020 William & Mary

Probing The Localization Patterns And Selectivity Filter Of Thyroid Hormone Receptor Alpha 1 Mutants, Jerry O'Dwyer

Undergraduate Honors Theses

The thyroid hormone receptor alpha 1 (TRa1) is a member of the nuclear receptor superfamily. TRa1 is a shuttling protein that is primarily localized inside the nucleus, where it serves as a transcription factor. TRa1 mediates transcription upon thyroid hormone (TH) binding and is expressed in numerous tissues that affect cell growth, metabolism, and development. Mutations occurring in TRa1 have been suggested not only to play a role in the disease pathology of cancer but also in the disease known as Resistance to Thyroid Hormone (RTH) syndrome. TRa1 consists of four domains, namely the A/B domain, DNA-binding domain, Hinge ...


Vibration Overtone Hyperpolarizability Measured For H2, Rachel M. Ellis, David P. Shelton 2020 University of Nevada, Las Vegas

Vibration Overtone Hyperpolarizability Measured For H2, Rachel M. Ellis, David P. Shelton

Physics & Astronomy Faculty Publications

The second hyperpolarizability (γ) of the H2 molecule was measured by gas-phase electric field induced second harmonic generation at the frequencies of the one-photon resonance for the 3–0 Q(J) overtone transitions (v, J = 0, J → 3, J for J = 0, 1, 2, and 3). The magnitude of the resonant contribution to γ was measured with 2% accuracy using the previously determined non-resonant γ for calibration. Pressure broadening and frequency shift for the transitions were also measured. A theoretical expression for the resonant vibrational γ contribution in terms of transition polarizabilities is compared to the observations. The measured γ ...


The Generality Of The Guga Mrci Approach In Columbus For Treating Complex Quantum Chemistry, Hans Lischka, Ron Shepard, Thomas Müller, Peter G. Szalay, Russell M. Pitzer, Adelia J. A. Aquino, Carol A. Parish, et al. 2020 University of Richmond

The Generality Of The Guga Mrci Approach In Columbus For Treating Complex Quantum Chemistry, Hans Lischka, Ron Shepard, Thomas Müller, Peter G. Szalay, Russell M. Pitzer, Adelia J. A. Aquino, Carol A. Parish, Et Al.

Chemistry Faculty Publications

The core part of the program system COLUMBUS allows highly efficient calculations using variational multireference (MR) methods in the framework of configuration interaction with single and double excitations (MR-CISD) and averaged quadratic coupled-cluster calcu- lations (MR-AQCC), based on uncontracted sets of configurations and the graphical unitary group approach (GUGA). The availability of analytic MR-CISD and MR-AQCC energy gradients and analytic nonadiabatic couplings for MR-CISD enables exciting applications including, e.g., investigations of π-conjugated biradicaloid compounds, calculations of multitudes of excited states, development of dia- batization procedures, and furnishing the electronic structure information for on-the-fly surface nonadiabatic dynamics. With fully vari- ...


Sulfur Dioxide From The Atmospheric Chemistry Experiment Satellite, Doug Cameron 2020 Old Dominion University

Sulfur Dioxide From The Atmospheric Chemistry Experiment Satellite, Doug Cameron

College of Sciences Posters

The version 4.0 dataset from the Atmospheric Chemistry Experiment – Fourier Transform Spectrometer (ACE-FTS) on SCISAT, released in March of 2019, has sulfur dioxide (SO2) volume mixing ratio (VMR) profiles as a routine data product. From this dataset, global SO2 distributions between the altitudes of 10.5 km and 23.5 km are analyzed. The global distribution of all SO2 VMR data by altitude is broken down into 30° and 5° latitude zones. Seasonality of the global SO2 distribution is explored. Volcanic SO2 plumes are isolated in the dataset and compared with extinction data from ...


Fibration Symmetries Uncover The Building Blocks Of Biological Networks, Flaviano Morone, Ian Leifer, Hernán A. Makse 2020 CUNY City College

Fibration Symmetries Uncover The Building Blocks Of Biological Networks, Flaviano Morone, Ian Leifer, Hernán A. Makse

Publications and Research

A major ambition of systems science is to uncover the building blocks of any biological network to decipher how cellular function emerges from their interactions. Here, we introduce a graph representation of the information flow in these networks as a set of input trees, one for each node, which contains all pathways along which information can be transmitted in the network. In this representation, we find remarkable symmetries in the input trees that deconstruct the network into functional building blocks called fibers. Nodes in a fiber have isomorphic input trees and thus process equivalent dynamics and synchronize their activity. Each ...


Laser-Induced Breakdown Spectroscopy For Elemental Analysis In Bioarchaeology And Forensic Anthropology, Kelsi N. Kuehn 2020 University of South Florida

Laser-Induced Breakdown Spectroscopy For Elemental Analysis In Bioarchaeology And Forensic Anthropology, Kelsi N. Kuehn

USF Tampa Graduate Theses and Dissertations

Within bioarchaeology and forensic anthropology, the current processes of differentiating between individual human skeletal remains are imprecise, costly, and inefficient. A novel analytical technique within anthropology, laser-induced breakdown spectroscopy (LIBS) can aid in the identification of human remains using rapid laser ablation occurring at the micro-scale, making the technique virtually non-destructive to the sample. Considering this, LIBS could offer a superior method for materials discrimination and human identification. This research sought to examine whether LIBS can be used to obtain elemental signatures within bones to distinguish individuals from one another in a rapid, non-destructive manner. Seven human skeletal donors and ...


Similarities Between Insect Swarms And Isothermal Globular Clusters, Dan Gorbonos, Kasper van der Vaart, Michael Sinhuber, James G. Puckett, Andrew M. Reynolds, Nicholas T. Ouellette, Nir S. Gov 2020 The Weizmann Institute of Science

Similarities Between Insect Swarms And Isothermal Globular Clusters, Dan Gorbonos, Kasper Van Der Vaart, Michael Sinhuber, James G. Puckett, Andrew M. Reynolds, Nicholas T. Ouellette, Nir S. Gov

Physics and Astronomy Faculty Publications

Previous work has suggested that disordered swarms of flying insects can be well modeled as self-gravitating systems, as long as the “gravitational” interaction is adaptive. Motivated by this work, we compare the predictions of the classic, mean-field King model for isothermal globular clusters to observations of insect swarms. Detailed numerical simulations of regular and adaptive gravity allow us to expose the features of the swarms' density and velocity profiles that are due to long-range interactions and are captured by the King model phenomenology, and those that are due to adaptivity and short-range repulsion. Our results provide further support for adaptive ...


Size And Density Of Upside-Down Jellyfish, Cassiopea Sp., And Their Impact On Benthic Fluxes In A Caribbean Lagoon, Chester B. Zarnoch, Noshin Hossain, Erika Fusco, Mary Alldred, Timothy J. Hoellein, Sophia Perdikaris 2020 CUNY Bernard M Baruch College

Size And Density Of Upside-Down Jellyfish, Cassiopea Sp., And Their Impact On Benthic Fluxes In A Caribbean Lagoon, Chester B. Zarnoch, Noshin Hossain, Erika Fusco, Mary Alldred, Timothy J. Hoellein, Sophia Perdikaris

Global Studies Papers & Publications

Anthropogenic disturbances may be increasing jellyfish populations globally. Epibenthic jellyfish are ideal organisms for studying this phenomenon due to their sessile lifestyle, broad geographic distribution, and prevalence in near-shore coastal environments. There are few studies, however, that have documented epibenthic jellyfish abundance and measured their impact on ecological processes in tropical ecosystems. In this study, the density and size of the upside-down jellyfish (Cassiopea spp.) were measured in Codrington Lagoon, Barbuda. A sediment core incubation study, with and without Cassiopea, also was performed to determine their impact on benthic oxygen and nutrient fluxes. Densities of Cassiopea were 24–168 m ...


A Framework Of Multi-Dimensional And Multi-Scale Modeling With Applications, Zilong Li 2020 Louisiana Tech University

A Framework Of Multi-Dimensional And Multi-Scale Modeling With Applications, Zilong Li

Doctoral Dissertations

In this dissertation, a framework for multi-dimensional and multi-scale modeling is proposed. The essential idea is based on oriented space curves, which can be represented as a 3D slender object or 1D step parameters. SMILES and Masks provide functionalities that extend slender objects into branched and other objects. We treat the conversion between 1D, 2D, 3D, and 4D representations as data unification. A mathematical analysis of different methods applied to helices (a special type of space curves) is also provided. Computational implementation utilizes Model-ViewController design principles to integrate data unification with graphical visualizations to create a dashboard. Applications of multi-dimensional ...


Agenda, Revised, Shubha Tewari 2020 University of Massachusetts Amherst

Agenda, Revised, Shubha Tewari

Science and Engineering Saturday Seminars

Materials from the seminars. The agenda was revised to include online sessions due to the Covid-19 pandemic.


A Vibrational Spectroscopic Based Approach For Diagnosing Babesia Bovis Infection, Anja Ruther, David Perezguaita, William Poole, Brian Cooke, Carlos Suarez, Philip Heraud, Bayden Wood 2020 Monash University

A Vibrational Spectroscopic Based Approach For Diagnosing Babesia Bovis Infection, Anja Ruther, David Perezguaita, William Poole, Brian Cooke, Carlos Suarez, Philip Heraud, Bayden Wood

Articles

Babesia bovis parasites present a serious and significant health concern for the beef and dairy industries in many parts of the world. Difficulties associated with the current diagnostic techniques include they are prone to human error (microscopy) or expensive and time consuming (Polymerase Chain Reaction) to perform. Little is known about the biochemical changes in blood that are associated with Babesia infections. The discovery of new biomarkers will lead to improved diagnostic outcomes for the cattle industry. Vibrational spectroscopic technologies can record a chemical snapshot of the entire organism and the surrounding cell thereby providing a phenotype of the organism ...


Examining Artifacts Of The Watershed Segmentation, Emily Jo Armitage 2020 University of Denver

Examining Artifacts Of The Watershed Segmentation, Emily Jo Armitage

Electronic Theses and Dissertations

The watershed segmentation is an algorithm used to systematically track cell intercalary behaviors during germ band extension of the Drosophila embryo. Neighboring cells share a contracting vertical interface, called a T1, which continues contracting to a single point, a T2, and extending in the horizontal direction to create what is called a T3 interface (Fig. 1). Additionally, higher order vertices called rosettes occur when five or more cells meet at a common vertex. Simulated T2 events demonstrate that cell angle and not noise level in the image contributes to the incorrect detection of artifactual T1s in more acute angled cells ...


Sensitivity Of Radical Sam Enzyme Mftc To Molecular Oxygen, Vishnu Govindarajan 2020 University of Denver

Sensitivity Of Radical Sam Enzyme Mftc To Molecular Oxygen, Vishnu Govindarajan

Electronic Theses and Dissertations

MftC is a radical S-adenosyl L-methionine (SAM) enzyme that catalyzes the first step in the production of mycofactocin. It is a ribosomally synthesized post-translationally modified (RiPP) redox cofactor shown to be essential for the survival of bacteria in the Mycobacterium genus in the presence of cholesterol as a carbon source and for the sequestration of ethanol. MftC catalyzes the C – terminal decarboxylation of tyrosine and the subsequent cross-linking of tyrosine to the penultimate valine on the precursor peptide MftA. The product formed out of the reaction is processed into mycofactocin in downstream processes. The bacteria in the Mycobacterium tuberculosis complex ...


Quantification Of Dynamic Epithelial Sheet Architecture In Botryllus Schlosseri Using 2-D & 3-D Image Analysis, Roopa Madhu 2020 University of Denver

Quantification Of Dynamic Epithelial Sheet Architecture In Botryllus Schlosseri Using 2-D & 3-D Image Analysis, Roopa Madhu

Electronic Theses and Dissertations

Epithelial tubules form critical structures in various body tissues; how- ever, since they are difficult to access experimentally, their architecture and dynamics are not well understood. Here we examine the dynamic remodeling of epithelial tubes in vivo using a novel and uniquely accessible model system: the extracorporeal vasculature of Botryllus schlosseri (sea squirt). In Botryllus, massive retraction of blood vessels can be triggered without loss of barrier function, through (i) disrupting collagen crosslinking in the basement membrane using β-aminopropionitrile (BAPN); or (ii) disrupting the integrin pathway through inhibition of focal adhesion kinase (FAK). We performed stereographic projections of 3-dimensional high-resolution ...


Magneto-Driven Gradients Of Diamagnetic Objects For Engineering Complex Tissues, Hannah M. Zlotnick, Andy T. Clark, Sarah E. Gullbrand, James L. Carey, Xuemei Cheng, Robert L. Mauck 2020 University of Pennsylvania

Magneto-Driven Gradients Of Diamagnetic Objects For Engineering Complex Tissues, Hannah M. Zlotnick, Andy T. Clark, Sarah E. Gullbrand, James L. Carey, Xuemei Cheng, Robert L. Mauck

Physics Faculty Research and Scholarship

Engineering complex tissues represents an extraordinary challenge and, to date, there have been few strategies developed that can easily recapitulate native‐like cell and biofactor gradients in 3D materials. This is true despite the fact that mimicry of these gradients may be essential for the functionality of engineered graft tissues. Here, a non‐traditional magnetics‐based approach is developed to predictably position naturally diamagnetic objects in 3D hydrogels. Rather than magnetizing the objects within the hydrogel, the magnetic susceptibility of the surrounding hydrogel precursor solution is enhanced. In this way, a range of diamagnetic objects (e.g., polystyrene beads, drug ...


Special Issue On The Third Workshop On Biological Mentality, Kenneth A. Augustyn 2020 Michigan Technological University

Special Issue On The Third Workshop On Biological Mentality, Kenneth A. Augustyn

Michigan Tech Publications

The Third Workshop on Biological Mentality was held from September 23, 2019 to March 2, 2020 as a series of twenty-one Monday online conferencing sessions, each consisting of a talk followed by a Q&A discussion. Like the two previous workshops [1, 2], the objective of this workshop was to seek a deeper level of understanding the physical foundations of biological mentality (whether conscious or nonconscious).


Crystal Structure Of Thermus Thermophilus Methylenetetrahydrofolate Dehydrogenase And Determinants Of Thermostability, Fernando Maiello, Gloria Gallo, Camila Coelho, Fernanda Sucharski, Leon Hardy, Martin Würtele 2020 University of South Florida

Crystal Structure Of Thermus Thermophilus Methylenetetrahydrofolate Dehydrogenase And Determinants Of Thermostability, Fernando Maiello, Gloria Gallo, Camila Coelho, Fernanda Sucharski, Leon Hardy, Martin Würtele

USF St. Petersburg campus Faculty Publications

The elucidation of mechanisms behind the thermostability of proteins is extremely important both from the theoretical and applied perspective. Here we report the crystal structure of methylenetetrahydrofolate dehydrogenase (MTHFD) from Thermus thermophilus HB8, a thermophilic model organism. Molecular dynamics trajectory analysis of this protein at different temperatures (303 K, 333 K and 363 K) was compared with homologous proteins from the less temperature resistant organism Thermoplasma acidophilum and the mesophilic organism Acinetobacter baumannii using several data reduction techniques like principal component analysis (PCA), residue interaction network (RIN) analysis and rotamer analysis. These methods enabled the determination of important residues for ...


Consciousness As A Factor In Evolution, Kenneth A. Augustyn 2020 Michigan Technological University

Consciousness As A Factor In Evolution, Kenneth A. Augustyn

Michigan Tech Publications

What I call the mind began as a non-conscious robotic biochemical process control system in the very earliest forms of life. As life evolved, problems in control became more difficult and exceeded the computational capabilities of the organisms. Nature discovered a means of transcending computable physical processes resulting in non-computational subjective mental capabilities that, while still not conscious, had a degree of genuine autonomy from the physical world. These autonomous subjective wants and goals now affected the course of (but not the mechanism of) evolution. The integrated amalgam of robotic and transrobotic unconscious capabilities eventually gave rise to consciousness, which ...


Application Of Optical Trapping To Obtain Single-Source Str Profiles From Forensically Relevant Body Fluid Mixtures With Modified Dna Analysis Workflow, Benjamin J. O'Brien 2020 Virginia Commonwealth University

Application Of Optical Trapping To Obtain Single-Source Str Profiles From Forensically Relevant Body Fluid Mixtures With Modified Dna Analysis Workflow, Benjamin J. O'Brien

Master of Science in Forensic Science Directed Research Projects

Current methods of mixture separation in forensic DNA laboratories typically deconvolute the mixture after analysis using statistical analysis or probabilistic genotyping. To save time and effort of labs already backlogged, a method to separate mixtures on a cellular level before analysis needs to be developed. Optical trapping is a method that uses a focused 1064 nm laser to manipulate cells. Previous research has shown that approximately 50 spermatozoa or 15 leukocytes from a liquid sample are required to produce a full STR DNA profile. It was found that the number of spermatozoa required remains constant when the method of sample ...


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