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Articles 1 - 30 of 97

Full-Text Articles in Biochemistry, Biophysics, and Structural Biology

Langevin, Population Density And Moment-Based Modeling Of Local And Global Aspects Of Intercellular Calcium Signaling, Xiao Wang Jan 2015

Langevin, Population Density And Moment-Based Modeling Of Local And Global Aspects Of Intercellular Calcium Signaling, Xiao Wang

Dissertations, Theses, and Masters Projects

Markov chain models of the coupled gating of intracellular calcium (Ca 2+) channels are often used to study the stochastic dynamic of local Ca2+ release events and whole cell Ca2+ homeostasis. However, the runtime of the Markov chain description of Ca2+ channel gating is exponential in the number of Ca2+ channel states and may thus result in a combinatorial state space explosion when the number of channel states is large. This dissertation presents several novel stochastic modeling approaches that capture important aspects of Ca 2+ signaling while improving computational efficiency. This dissertation presents several novel stochastic modeling approaches that capture ...


A Mathematical Model Of Tau Protein Hyperphosphorylation: The Effects Of Kinase Inhibitors As A Theoretical Alzheimer's Disease Therapy, Patrick Neil Blank Jan 2015

A Mathematical Model Of Tau Protein Hyperphosphorylation: The Effects Of Kinase Inhibitors As A Theoretical Alzheimer's Disease Therapy, Patrick Neil Blank

Dissertations, Theses, and Masters Projects

No abstract provided.


Spread And Interaction Of Epidemics And Information On Adaptive Social Networks, Yunhan Long Jan 2015

Spread And Interaction Of Epidemics And Information On Adaptive Social Networks, Yunhan Long

Dissertations, Theses, and Masters Projects

The spread of diseases and opinions has profoundly affected the development of human societies. The structure of the underlying social network may change as a result of individuals changing their social connections in response to an ongoing epidemic or opinion spreading, either for self protection or as an expression of personal values. The interaction of spreading processes and the underlying network structure has been a focus of many recent studies. In this dissertation, we construct models to better incorporate heterogeneous responses to disease spread and attempted opinion spread.;We first model the simultaneous spread of an epidemic and awareness about ...


Identifying Sumo Protease Targets And Investigating E3 Ligase Interactions, Mark Guillotte Jan 2014

Identifying Sumo Protease Targets And Investigating E3 Ligase Interactions, Mark Guillotte

Dissertations, Theses, and Masters Projects

No abstract provided.


Investigation Of Microwave Technologies For Biochemical Applications, Valerie Terynn Tripp Jan 2013

Investigation Of Microwave Technologies For Biochemical Applications, Valerie Terynn Tripp

Dissertations, Theses, and Masters Projects

No abstract provided.


Investigating Heat Shock Protein 70 As A Binding Partner Of Mk-Styx, And The Role Of Mk-Styx In Neuronal Differentiation, Lauren Elizabeth Rusnak Jan 2013

Investigating Heat Shock Protein 70 As A Binding Partner Of Mk-Styx, And The Role Of Mk-Styx In Neuronal Differentiation, Lauren Elizabeth Rusnak

Dissertations, Theses, and Masters Projects

No abstract provided.


Hydrogen/Deuterium Exchange Studies Of Protein And Non-Protein Amino Acids Using Electrospray Ionization Mass Spectrometry, Justine Victoria Arrington Jan 2012

Hydrogen/Deuterium Exchange Studies Of Protein And Non-Protein Amino Acids Using Electrospray Ionization Mass Spectrometry, Justine Victoria Arrington

Dissertations, Theses, and Masters Projects

No abstract provided.


Spe-7, A Novel Regulator Of Msp Assembly In C Elegans Spermatocytes, Kari Lynn Messina Jan 2012

Spe-7, A Novel Regulator Of Msp Assembly In C Elegans Spermatocytes, Kari Lynn Messina

Dissertations, Theses, and Masters Projects

No abstract provided.


Thermochemistry Of Amino Acids And Constrained Diamines, Erica Jane Tullo Jan 2012

Thermochemistry Of Amino Acids And Constrained Diamines, Erica Jane Tullo

Dissertations, Theses, and Masters Projects

The gas-phase proton affinities of several highly basic amino acids and diamines were determined using the extended kinetic method in an ESI-quadrupole ion trap instrument. The non-protein amino acid L-canavanine is structurally related to L-arginine with an oxygen substituted for the terminal methylene group of L-arginine and is highly toxic to humans. The proton affinity of L-arginine, a protein amino acid, was determined to be 1036 kJ mol -1, whereas the proton affinity of L-canavanine was determined to be 1005 kJ mol-1. Thus, substitution of an oxyguanidino group for the guanidine group in L-arginine results in a large decrease in ...


Automated Reductions Of Markov Chain Models Of Calcium Release Site Models, Yan Hao Jan 2012

Automated Reductions Of Markov Chain Models Of Calcium Release Site Models, Yan Hao

Dissertations, Theses, and Masters Projects

Markov chain models have played an important role in understanding the relationship between single channel gating of intracellular calcium (Ca2+) channels, specifically 1,4,5-trisphosphate receptors (IP3Rs) and ryanodine receptors (RyRs), and the stochastic dynamics of Ca2+ release events, known as Ca2+ puffs and sparks. Mechanistic Ca2+ release site models are defined by the composition of single channel models whose transition probabilities depend on the local calcium concentration and thus the state of the other channels. Unfortunately, the large state space of such compositional models impedes simulation and computational analysis of the whole cell Ca2+ signaling in which the stochastic ...


Understanding The Origins, Dispersal, And Evolution Of Bonamia Species (Phylum Haplosporidia) Based On Genetic Analyses Of Ribosomal Rna Gene Regions, Kristina M. Hill Jan 2011

Understanding The Origins, Dispersal, And Evolution Of Bonamia Species (Phylum Haplosporidia) Based On Genetic Analyses Of Ribosomal Rna Gene Regions, Kristina M. Hill

Dissertations, Theses, and Masters Projects

No abstract provided.


Investigations Of The Fragmentation Spectra Of Dipeptides Containing Lysine And Its Non-Protein Amino Acid Homologs, Omar Hamdy Jan 2011

Investigations Of The Fragmentation Spectra Of Dipeptides Containing Lysine And Its Non-Protein Amino Acid Homologs, Omar Hamdy

Dissertations, Theses, and Masters Projects

No abstract provided.


Sumo-Dependent Substrate Targeting Of The Sumo Protease Ulp1, Zachary Cole Elmore Jan 2011

Sumo-Dependent Substrate Targeting Of The Sumo Protease Ulp1, Zachary Cole Elmore

Dissertations, Theses, and Masters Projects

No abstract provided.


The Sumo-Targeted Ubiquitin Ligase Subunit Slx5 Functional Interacts With The Sumo E3 Ligase Siz1, Jason William Westerbeck Jan 2011

The Sumo-Targeted Ubiquitin Ligase Subunit Slx5 Functional Interacts With The Sumo E3 Ligase Siz1, Jason William Westerbeck

Dissertations, Theses, and Masters Projects

No abstract provided.


An Investigation Of The Polymorphic Arss Gene Of Helicobacter Pylori, Daniel Ross Hallinger Jan 2011

An Investigation Of The Polymorphic Arss Gene Of Helicobacter Pylori, Daniel Ross Hallinger

Dissertations, Theses, and Masters Projects

No abstract provided.


Reactive Sulfur: Redox Reactions Of Cysteines And Methionines In The Cytoskeletal Protein Tubulin, Tara Dawn Hagedorn Jan 2011

Reactive Sulfur: Redox Reactions Of Cysteines And Methionines In The Cytoskeletal Protein Tubulin, Tara Dawn Hagedorn

Dissertations, Theses, and Masters Projects

No abstract provided.


Molecular Marker Development For The Discrimination Of Atlantic And Pacific Blue Marlin (Makaira Nigricans), Laurie Sorenson Jan 2011

Molecular Marker Development For The Discrimination Of Atlantic And Pacific Blue Marlin (Makaira Nigricans), Laurie Sorenson

Dissertations, Theses, and Masters Projects

No abstract provided.


Computational And Experimental Investigations Of Gas-Phase Thermodynamics Of Non-Protein Amino Acids, Ashley R. Janiga Jan 2010

Computational And Experimental Investigations Of Gas-Phase Thermodynamics Of Non-Protein Amino Acids, Ashley R. Janiga

Dissertations, Theses, and Masters Projects

No abstract provided.


The Pax-5 Gene Is Alternatively Spliced In Trout B Cells, Raaj Mahendra Talauliker Jan 2010

The Pax-5 Gene Is Alternatively Spliced In Trout B Cells, Raaj Mahendra Talauliker

Dissertations, Theses, and Masters Projects

No abstract provided.


The Role Of Copepods And Heterotrophic Dinoflagellates In The Production Of Dissolved Organic Matter And Inorganic Nutrients, Grace Kathleen Saba Jan 2010

The Role Of Copepods And Heterotrophic Dinoflagellates In The Production Of Dissolved Organic Matter And Inorganic Nutrients, Grace Kathleen Saba

Dissertations, Theses, and Masters Projects

Zooplankton play a key role in the cycling of dissolved organic matter (DOM) and inorganic nutrients. The factors that affect these processes, however, are not fully understood. I measured the effects of various diets on DOM and inorganic nutrient production by the copepod Acartia tonsa and the heterotrophic dinoflagellate Oxyrrhis marina, and explored the mechanisms of nutrient release from copepods. Copepods feeding on a mixed diet, the preferred diet of most copepods, had significantly lower dissolved organic carbon (DOC), ammonium (NH4+), and total dissolved nitrogen (TDN) release rates compared to feeding on a carnivorous or herbivorous diet. Thus, copepod feeding ...


Identification And Quantification Of Polycyclic Musks And Methyl-Triclosan In Unknown Freshwater Fish Tissue Samples, Elizabeth Mara Jacobs Jan 2009

Identification And Quantification Of Polycyclic Musks And Methyl-Triclosan In Unknown Freshwater Fish Tissue Samples, Elizabeth Mara Jacobs

Dissertations, Theses, and Masters Projects

No abstract provided.


Assessing Genetic Variation Within And Among Native Populations And Hatchery Stocks Of Crassostrea Ariakensis Using Microsatellite Markers, Jie Xiao Jan 2009

Assessing Genetic Variation Within And Among Native Populations And Hatchery Stocks Of Crassostrea Ariakensis Using Microsatellite Markers, Jie Xiao

Dissertations, Theses, and Masters Projects

Assessing genetic variation within and among native populations and hatchery stocks of Crassostrea ariakensis using microsatellite markers In response to the dramatic decline of eastern oyster (Crassostrea virginica) populations in the Chesapeake Bay, introduction of the non-native Asian oyster Crassostrea ariakensis has been proposed. Currently several hatchery stocks of C. ariakensis, derived from a few wild populations along the coast of Japan and China, are being maintained in U.S. hatcheries in the Pacific northwest and on the east coast. In recent years, as the risks of the proposed introduction are being assessed, these hatchery animals have been widely used ...


Markov Chain Models Of Calcium Puffs And Sparks, Jeffrey R. Groff Jan 2008

Markov Chain Models Of Calcium Puffs And Sparks, Jeffrey R. Groff

Dissertations, Theses, and Masters Projects

Localized cytosolic Ca2+ elevations known as puffs and sparks are important regulators of cellular function that arise due to the cooperative activity of Ca2+-regulated inositol 1,4,5-trisphosphate receptors (IP3Rs) or ryanodine receptors (RyRs) co-localized at Ca2+ release sites on the surface of the endoplasmic reticulum or sarcoplasmic reticulum. Theoretical studies have demonstrated that the cooperative gating of a cluster of Ca2+-regulated Ca 2+ channels modeled as a continuous-time discrete-state Markov chain may result in dynamics reminiscent of Ca2+ puffs and sparks. In such simulations, individual Ca2+-release channels are coupled via a mathematical representation of the local ...


A Molecular Analysis Of Atlantic Menhaden (Brevoortia Tyrannus) Stock Structure, Abigail J. Lynch Jan 2008

A Molecular Analysis Of Atlantic Menhaden (Brevoortia Tyrannus) Stock Structure, Abigail J. Lynch

Dissertations, Theses, and Masters Projects

Atlantic menhaden is an ecologically and economically important species along the U.S. east coast. As a filter-feeder and key prey fish, it provides a critical link between primary production, phytoplankton, and larger piscivorous predators, such as striped bass, bluefish, and weakfish. The species is also the target of one of the largest commercial fisheries in the country. Menhaden are assessed as a single, coastwide stock, and recent assessments indicate that it is not overfished. However, there is very limited population genetics data to support the assumption of a single stock. Additionally, the recent consolidation of the fishery and localization ...


A Molecular Phylogeny Of The Genus Bonamia Based On Sequence Data Of The Ribosomal Rna (Rrna) Gene Complex, Delonna M. White Jan 2008

A Molecular Phylogeny Of The Genus Bonamia Based On Sequence Data Of The Ribosomal Rna (Rrna) Gene Complex, Delonna M. White

Dissertations, Theses, and Masters Projects

No abstract provided.


Analysis Of Sequence Variation At Two Helicobacter Pylori Genetic Loci Potentially Involved In Virulence, George Warren Liechti Jan 2008

Analysis Of Sequence Variation At Two Helicobacter Pylori Genetic Loci Potentially Involved In Virulence, George Warren Liechti

Dissertations, Theses, and Masters Projects

No abstract provided.


Stable Isotope Dynamics In Summer Flounder Tissues, With Application To Dietary Assessments In Chesapeake Bay, Andre Buchheister Jan 2008

Stable Isotope Dynamics In Summer Flounder Tissues, With Application To Dietary Assessments In Chesapeake Bay, Andre Buchheister

Dissertations, Theses, and Masters Projects

Stable isotope techniques were applied to summer flounder, Paralichthys dentatus, in Chesapeake Bay to elucidate the relative importance of different prey groups on the growth and productivity of this species. Prior to field application, a laboratory diet-shift study was conducted to evaluate methodological assumptions and obtain necessary isotopic parameters. Specifically, the goals of the laboratory study were to 1) determine isotopic turnover rates and fractionations of δ13C and δ15N in liver, whole blood, and white muscle and 2) estimate the relative importance of growth and metabolic processes on isotopic turnover. Groups of captive juvenile summer flounder (130-255mm total length) were ...


The Relationship Between Antibody Redox Structure And Affinity In Rainbow Trout, Jianmin Ye Jan 2008

The Relationship Between Antibody Redox Structure And Affinity In Rainbow Trout, Jianmin Ye

Dissertations, Theses, and Masters Projects

Teleost immunoglobulin M (IgM), an 800 kDa tetramer, possesses considerable structural diversity due to the non-uniform disulfide polymerization of its halfmeric or monomeric subunits. However, to date, no plausible functional role for this diversity has been demonstrated or proposed. This research was, therefore, designed to investigate the possible functional role(s) for this diversity using the trout model. The possible relationship between this structural diversity and affinity was specifically addressed. The relationship between high levels of disulfide polymerization and high affinity was demonstrated by selective immunoadsorption and analysis of antibodies isolated during the process of affinity maturation. A pivotal determinative ...


Novel Use Of A Natural Isotope Signature To Track Recruitment And Evaluate Age Determination Methods For The 2002 Year Class Of American Shad In The York River, Sally A. Upton Jan 2008

Novel Use Of A Natural Isotope Signature To Track Recruitment And Evaluate Age Determination Methods For The 2002 Year Class Of American Shad In The York River, Sally A. Upton

Dissertations, Theses, and Masters Projects

No abstract provided.


Markov Chain Models Of Instantaneously Coupled Intracellular Calcium Channels, Hilary Deremigio Jan 2008

Markov Chain Models Of Instantaneously Coupled Intracellular Calcium Channels, Hilary Deremigio

Dissertations, Theses, and Masters Projects

Localized calcium elevations known as calcium puffs or sparks are cellular signals arising from cooperative activity of clusters of inositol 1,4,5-trisphosphate receptors (IP3Rs) or ryanodine receptors (RyRs) located at calcium release sites on the endoplasmic or sarcoplasmic reticulum membrane. When Markov chain models of these intracellular calcium-regulated calcium channels are coupled via a mathematical representation of the calcium microdomain, simulated calcium release sites may exhibit the phenomenon of "stochastic calcium excitability" where the IP3Rs or RyRs open and close in a concerted fashion. Although the biophysical theory relating the kinetics of single channels to the collective phenomena of ...