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Biochemical Aspects Of The Thermal Sensitivity And Energy Balance Of Polar, Tropical And Subtropical Teleosts, Eloy Martinez Jan 2013

Biochemical Aspects Of The Thermal Sensitivity And Energy Balance Of Polar, Tropical And Subtropical Teleosts, Eloy Martinez

Graduate Theses and Dissertations

The maintenance of a functional energy balance in ectothermic fauna could be challenging in a thermally disparate environment. Biochemical adaptations at the enzyme and membrane levels allows for a set compensatory mechanism that allow the individual to maintain an energetic surplus, thus allocating energy for growth and reproduction. The present work describes how the energetic machinery in the cell, particularly the mitochondrion, could be affected by temperature changes. More specifically, this work aimed to determine how environmental temperature affects the mitochondria energetic performance of fishes from disparate thermal regimes.

Mitochondrial ATP production efficiency was evaluated in fishes from polar, tropical ...


Molecular Regulation Of Il-2 Inducible T-Cell Kinase (Itk) And The Tec Kinases: A Combined Experimental And Computational Study, With Emphasis On The N-Terminal Pleckstrin Homology Domain, Scott Edward Boyken Jan 2013

Molecular Regulation Of Il-2 Inducible T-Cell Kinase (Itk) And The Tec Kinases: A Combined Experimental And Computational Study, With Emphasis On The N-Terminal Pleckstrin Homology Domain, Scott Edward Boyken

Graduate Theses and Dissertations

This dissertation investigates the complex regulation of IL-2 inducible T-cell kinase (Itk) and its related Tec family kinase members, using a combination of experimental and computational approaches. Tec kinases are expressed primarily in hematopoietic cells and regulate key signaling events in lymphocyte activation, differentiation, and development. Itk functions in immune response, fine-tuning signaling downstream of the T-cell Receptor (TCR), and is a putative drug target for allergies and autoimmune disease. Btk, a Tec kinase found in B-cells, carries out a similar role to that of Itk, only downstream of B-cell Receptor (BCR) signaling. The chapters of this dissertation focus on ...


Design Of Novel Nano-Carriers For Multi-Enzyme Co-Localization, Feng Jia Jan 2013

Design Of Novel Nano-Carriers For Multi-Enzyme Co-Localization, Feng Jia

Graduate Theses and Dissertations

The widely existing MECs in Nature have inspired researchers to design synthetic analogs to promote the overall catalytic efficiency in vitro by co-localizing multiple enzymes to mimic the MECs' unique functionalities. A number of efforts have been devoted to designing synthetic MECs in the past couples of decades. This thesis work has focused on developing novel strategies based on enzyme immobilization to design nano-carriers for multi-enzyme co-localization to realize kinetics enhancement and strong control of spatial arrangement of the enzymes. Three distinct approaches have been designed using different attachment methods and platforms.

First, the multifunctional polystyrene nanoparticles were designed for ...


Development Of Strategies For Synthesis Of Branched Caenorhabditis Elegans-Associated Oligosaccharides And Of Photo-Activated Lectin Capture Reagents, Randy Alan Benedict Jan 2013

Development Of Strategies For Synthesis Of Branched Caenorhabditis Elegans-Associated Oligosaccharides And Of Photo-Activated Lectin Capture Reagents, Randy Alan Benedict

Graduate Theses and Dissertations

The development and investigation of a new affinity proteomics probe and methodology are presented in this dissertation. A trifunctional affinity proteomics probe (TAPP) was envisioned and prepared to serve as a lectin capture reagent. The TAPP consists of a solid support to serve as a handle for captured protein as well as scaffold for multivalency, a saccharide of interest to fish for an unknown or elicit a suspected specific interaction, and a photoactivated cross-linking moiety to covalently capture binding proteins. The perfluorinated phenylazide cross-linker was shown to exhibit better performance relative to the parent phenylazide with respect to sensitivity and ...


Investigation Of The Process Of Snare Mediated Synaptic Vesicle Exocytosis, Ying Lai Jan 2013

Investigation Of The Process Of Snare Mediated Synaptic Vesicle Exocytosis, Ying Lai

Graduate Theses and Dissertations

Neurotransmitter release in synapses underlies major brain functions such as cognition, emotion, and memory. The precise temporal control of the release is essential for healthy brain activities. SNAREs are known to be the core fusion machinery in neuro-exocytotic pathways. SNARE complex formation in the chasm of two membranes is mediated by cognate coiled-coil motifs on v- and t-SNAREs: One such motif from t-SNARE syntaxin 1A, two from t-SNARE SNAP-25, and another from v-SNARE VAMP2 all form a parallel four-stranded coiled coil that brings about the apposition of two membranes. However, The SNARE proteins do not have the required regulatory function ...


Characterization Of The Putative Catalytic Domain Of Two Xyloglucan Xylosyltransferases (Xxts) Involved In The Biosynthesis Of Xyloglucan In Arabidopsis Thaliana, Rachel Ann Morris Jan 2013

Characterization Of The Putative Catalytic Domain Of Two Xyloglucan Xylosyltransferases (Xxts) Involved In The Biosynthesis Of Xyloglucan In Arabidopsis Thaliana, Rachel Ann Morris

Graduate Theses and Dissertations

Xyloglucan is the primary hemicellulosic component of the primary cell wall in dicotyledonous plants. It is characterized by a beta-(1-4)-D-glucan backbone that is substituted in a regular pattern with alpha-(1-6)-D-xylose, and can be substituted further with beta-(1-2)-D-galactose or beta-(1-2)-D-galactose-alpha(1-2)-L-fucose disaccharide. Three xyloglucan xylosyltransferases (XXTs), XXT1, XXT2, and XXT5, are responsible for the D-xylosylation of the beta-(1-4)-D-glucan backbone in Arabidopsis thaliana. They are Golgi-localized type II transmembrane proteins that have putative DXD catalytic centers. All have been shown to interact in a protein complex, XXT2 and XXT5 showing the ...


Allosteric Regulation Of Mammalian Fructose-1,6-Bisphosphatase, Yang Gao Jan 2013

Allosteric Regulation Of Mammalian Fructose-1,6-Bisphosphatase, Yang Gao

Graduate Theses and Dissertations

Fructose-1, 6-bisphosphate (D-fructose-1, 6-bisphosphate 1-phosphohydrolase; EC 3. 1. 3; FBPase) is an essential regulatory enzyme in gluconeogenesis and has long been considered as a drug target towards type II diabete. In mammalian, the activity of FBPase is regulated by AMP and fructose 2,6-bisphosphate (Fru-2,6-P2). AMP is an allosteric inhibitor that binds to FBPase with positive coopertivity, and Fru-2,6-P2 is an active site inhibitor which is up-regulated by hormone. Despite the 30 Å distance between their binding sites, both of AMP and Fru-2,6-P2 transform FBPase from active R-state to inactive T-state. Large conformational rearrangements are coupled to ...


Sustainable Chemistry, Synthesis And Structure-Activity Relationship Studies Of Biologically Important Small Molecules, Gerald R. Pollock, Iii Jan 2013

Sustainable Chemistry, Synthesis And Structure-Activity Relationship Studies Of Biologically Important Small Molecules, Gerald R. Pollock, Iii

Graduate Theses and Dissertations

With growing concerns for the environment, dwindling amounts of fossil fuels available for worldwide consumption and more resistant strains of diseases and infections becoming a reality, organic chemistry plays a vital role in the improvement and sustainability of modern society. Industrial chemicals from renewable sources has become an important area of research in recent years, while the synthesis and study of biologically active small molecules and their analogues leads to advancements which can help improve overall human health.

In this dissertation, we explore methods to create important industrial molecules from biorenewable sources, extend a novel cyclization to make heterocyclic compounds ...


Exploring And Understanding The Substrate Diversity Of B-Ketoacyl-Acp Synthase Iii Enzymes, Shivani Garg Jan 2013

Exploring And Understanding The Substrate Diversity Of B-Ketoacyl-Acp Synthase Iii Enzymes, Shivani Garg

Graduate Theses and Dissertations

Fatty acids are an integral part of the lipid membrane of bacteria and plants, and the enzyme that initiates fatty acid synthesis, β-ketoacyl-ACP Synthase III (KASIII), is one of the most diverse enzymes found in nature. KASIII exhibits vast diversity in its substrate specificity. By virtue of its substrate specificity, KASIII determines the fatty acid profile of the organism by dictating the nature of the ω-end of the fatty acids. For example, KASIIIs from many bacteria (e.g. Escherichia coli) accept straight chain acyl-CoAs resulting in production of straight chain fatty acids and are, therefore, narrow in substrate specificity. In ...


Structure And Function Of Class One Non-Symbiotic Plant Hemoglobins, Ryan Thomas Sturms Jan 2013

Structure And Function Of Class One Non-Symbiotic Plant Hemoglobins, Ryan Thomas Sturms

Graduate Theses and Dissertations

Plants contain at least three kinds of hemoglobins. Those plants that carry out symbiotic nitrogen fixation use oxygen transport hemoglobins to deliver oxygen to the aerobic nitrogen fixing bacteria in their roots. The functions of other plant hemoglobins are not yet known with confidence, but are thought to also have roles in nitrogen metabolism. This dissertation examines plant hemoglobin structure and function in two distinct classes: oxygen transport hemoglobins and what we believe to be hemoglobins that function as dissimilatory nitrite reductases.

The capacity for oxygen transport arose twice independently in two distinct phylogenetic classes of plant hemoglobins. From "Class ...


Structural And Functional Study Of Snare Machinery In Neurotransmitter Release, Shuang Song Jan 2013

Structural And Functional Study Of Snare Machinery In Neurotransmitter Release, Shuang Song

Graduate Theses and Dissertations

Synaptic neurotransmitter release is the most critical communication process for the connections between neurons and between neurons and target cells. SNAREs (soluble N-ethylmaleimide sensitive factor attachment protein receptors) are believed to be highly involved in docking and fusion of synaptic vesicles to the pre-synaptic plasma membrane. In vivo, synaptic vesicle exocytosis is a regulated and extremely rapid process. Numerous regulatory proteins are also required to achieve the fast speed and Ca2+ dependency of synaptic neurotransmitter release.

Our research mainly focuses on investigating the mechanism and protein structural basis of SNARE mediated membrane fusion. Site-directed spin labeling (SDSL) and electron paramagnetic ...


Structural Basis For Ternary Complex Formation Between Tau, Hsp90, And Fkbp51, Alexander Steven Barrett Jan 2013

Structural Basis For Ternary Complex Formation Between Tau, Hsp90, And Fkbp51, Alexander Steven Barrett

Graduate Theses and Dissertations

The accumulation of the microtubule associated protein tau has been implicated in several neurological disorders; however, its interaction with chaperones along its normal degradation pathway remains largely uncharacterized at single residue resolution. In this study, nuclear magnetic resonance (NMR) spectroscopy was used to probe the interaction between tau, the molecular chaperone Hsp90, and the immunophilin FKBP51. Resonance intensity changes were observed for specific residues in the heteronuclear single quantum coherence (HSQC) spectra of 15N-labeled tau in the presence of Hsp90 and/or FKBP51. Analysis of the HSQC spectra identified the two hydrophobic hexapeptide motifs located at residues V275 - K280 and ...


Immobilization And Characterization Of Physisorbed Antibody Films Using Pneumatic Spray As Deposition Technique, Jhon J. Figueroa Jan 2013

Immobilization And Characterization Of Physisorbed Antibody Films Using Pneumatic Spray As Deposition Technique, Jhon J. Figueroa

Graduate Theses and Dissertations

The immobilization of antibodies on silica surfaces has been a wide and common practice via cross-linking with the formation of covalent bonds between surface and antibody. The formation of antibody thin films on solid surfaces using pneumatic spray (PS) as the deposition technique and the analysis of the surface morphology of these films were investigated during this study. The pneumatic spray method was compared with the covalent bonding method Avidin-Biotin Bridge (ABB). The intensities and capture efficiency tests showed similar results for both techniques with a lower signal-to-noise ratio (SNR) for the PS deposited films. Specificity tests suggested that the ...


Characterization Of The Arabidopsis Thaliana Acetyl-Coa Synthetase Putative Carboxylate Binding Pocket, Jason H. Hart Jan 2013

Characterization Of The Arabidopsis Thaliana Acetyl-Coa Synthetase Putative Carboxylate Binding Pocket, Jason H. Hart

Graduate Theses and Dissertations

Acetyl-CoA synthetase catalyzes the activation of acetate by the acetylation of the thiol group of Coenzyme A, while hydrolyzing ATP to AMP and pyrophosphate. The Arabidopsis thaliana acetyl-CoA synthetase (atACS) was compared to other acyl-CoA synthetases, and was computationally modeled on the available crystal structures of the Saccharomyces cerevisiae ACS1 and Salmonella enterica ACS. This allowed the identification of the residues that make up the putative carboxylate binding pocket residues. To further understand substrate selectivity and binding within the putative carboxylate binding pocket, selected residues were mutated to resemble the homologous residues in the Pseudomonas chlororaphis isobutyryl-CoA synthetase. Four residues ...


Determination And Quantification Of Surface Lipid Metabolites In Maize Silks: A Pathway Model For Surface Lipid Biosynthesis Based On Simultaneous Profiling Of Polar And Non-Polar Metabolites, Layton Andrew Peddicord Jan 2013

Determination And Quantification Of Surface Lipid Metabolites In Maize Silks: A Pathway Model For Surface Lipid Biosynthesis Based On Simultaneous Profiling Of Polar And Non-Polar Metabolites, Layton Andrew Peddicord

Graduate Theses and Dissertations

The elongated stigmas in maize (i.e. silks) are a vital organ for the reproductive success of a major U.S. agricultural crop. These silks possess an extractible coat of surface lipids that is predominantly composed of a complex array of hydrocarbons that function to protect the silks against abiotic and biotic stresses. While hydrocarbons are most likely produced from the conversion of fatty acids, the exact biochemical mechanisms for their synthesis remain unknown. Our team is leveraging genetic variation and morphological gradients during silk development to dissect the metabolic network responsible for surface lipid accumulation.

These metabolomic efforts require ...


Phosphorylation Of Histone Deacetylase 6 Within Its C-Terminal Region By Extracellular Signal Regulated Kinase 1, Kendra Allana Williams Jan 2013

Phosphorylation Of Histone Deacetylase 6 Within Its C-Terminal Region By Extracellular Signal Regulated Kinase 1, Kendra Allana Williams

Graduate Theses and Dissertations

http://upload.etdadmin.com/etdadmin/pdfout/222759_supp_undefined_2A63E500-E9D7-11E2-925E-BE522E1BA5B1.PDF


The Panicum Mosaic Virus-Like 3' Cap-Independent Translation Element: A Translation Enhancer That Functions In Mammalian Systems, Mariko Sada Peterson Jan 2013

The Panicum Mosaic Virus-Like 3' Cap-Independent Translation Element: A Translation Enhancer That Functions In Mammalian Systems, Mariko Sada Peterson

Graduate Theses and Dissertations

In canonical eukaryotic translation initiation, the recognition of mRNA by the translation machinery is facilitated through the binding of the 5' m7G cap structure to eukaryotic initiation factor 4E (eIF4E). This recognition is necessary for efficient translation of the message to occur. In contrast, some viruses lack the 5' cap structure but have alternative mechanisms to initiate translation and express the viral proteins necessary for replication. The positive-strand RNA plant viruses of the panico-, carmo-, umbra-, (1-3) and aureusviruses (4) contain an RNA structure in their 3' UTRs that binds eIF4E (2) and through communication with the 5' UTR, are ...


Specificity Of The Cocaine Aptamer And Its Application In Measurement Of Cocaine And Metabolites In Homogeneous Samples For Forensic Analysis, Ashish Sachan Jan 2013

Specificity Of The Cocaine Aptamer And Its Application In Measurement Of Cocaine And Metabolites In Homogeneous Samples For Forensic Analysis, Ashish Sachan

Graduate Theses and Dissertations

Detection and quantification of molecules has an enormous importance and potential in the field of scientific development and basic discovery research. Advances in colorimetric techniques, fluorescent labeled probes and biosensor based technologies have resulted in the specific detection and precise quantification of analytes. The effective development of a particular detection method needs optimization in terms of overall speed, efficiency, and accuracy of the sensing system. Current biosensor approaches often rely on cumbersome procedural steps and reagent requirements. Along with the complexity of the assay, the size of the analytical instrument is a deterrent factor for on-site applications. To overcome such ...


Wax Ester Biosynthetic Pathway, Daolin Cheng Jan 2013

Wax Ester Biosynthetic Pathway, Daolin Cheng

Graduate Theses and Dissertations

Wax esters occur widely among bacteria, plants and mammals. Due to their special properties, they have many applications such as lubricants, cosmetics, pharmaceutical products, ink, polishes and candles. They are also considered as potential biofuels and biolubricants in the future. Wax ester producing enzymes synthesize wax esters from alcohols and fatty acyl coenzyme A thioesters. There are three gene families encoding enzymes capable of synthesizing wax esters. Two of them exist in plans; the jojoba-like wax synthase (WS), and the bifunctional wax synthase/diacylglycerol acyl transferase (WS/DGAT). We investigated the phylogenetic relationships among and between WS and WS/DGAT ...


Characterization Of Acyl-Acp Thioesterases For The Purpose Of Diversifying Fatty Acid Synthesis Pathway, Fuyuan Jing Jan 2013

Characterization Of Acyl-Acp Thioesterases For The Purpose Of Diversifying Fatty Acid Synthesis Pathway, Fuyuan Jing

Graduate Theses and Dissertations

Acyl-ACP TE selectively hydrolyzes the thiol ester bonds of acyl-ACPs to release free fatty acids, and therefore plays an essential role in determining the output of fatty acid synthesis (FAS) pathway. Comprehensive understanding of acyl-ACP TE is demanded to tailor this biocatalyst for the application in metabolic engineering of FAS pathway. To explore the diversity of acyl-ACP TEs, a total of 31 TEs enzymes were sourced from a wide range of biological taxa, including plants and bacteria, and these were functionally characterized. The results demonstrate that acyl-ACP TEs have great functional diversity relative to the acyl chain length specificity as ...


Investigating The Evolution Of Cytochromes P450 Involved In Ga Biosynthesis, Sibongile Mafu Jan 2013

Investigating The Evolution Of Cytochromes P450 Involved In Ga Biosynthesis, Sibongile Mafu

Graduate Theses and Dissertations

Vascular plants invariably contain a class II diterpene cyclase (EC 5.5.1.x), as an ent-copalyl diphosphate synthase is required for gibberellin phytohormone biosynthesis. This has provided the basis for evolution of a functionally diverse enzymatic family. A bifunctional diterpene synthase was characterized from the lycophyte Selaginella moellendorffii . The structure of its product, labda-7,13E-dien-15-ol, demonstrates that this enzyme catalyzes a novel class II diterpene cyclization reaction, and clarifies the biosynthetic origins of the family of derived natural products.

All higher plants contain kaurene oxidases (KO), which are multifunctional cytochromes P450 that catalyze oxidation at the C4α methyl, converting ...


A Nuclear-Derived Proteinaceous Matrix Embeds The Microtubule Spindle Apparatus During Mitosis, Changfu Yao Jan 2013

A Nuclear-Derived Proteinaceous Matrix Embeds The Microtubule Spindle Apparatus During Mitosis, Changfu Yao

Graduate Theses and Dissertations

ABSTRACT<

The nucleus undergoes a dramatic reorganization as the cell prepares to segregate its duplicated chromosomes during cell division. For many years s, the prevailing view was that in open mitosis the nucleus completely disassembled during early mitotic stages, thus enabling cytoplasmic microtubules emanating from the separated centrosomes to form a mitotic spindle. This cytocentric view largely discounted any nuclear contributions to regulation of mitotic progression (Johansen and Johansen, 2009; De Souza and Osmani, 2009; Simon and Wilson, 2011; Sandquist et al., 2011). A spindle matrix has long been proposed to serve as a relatively stable or elastic molecular matrix ...


Fidelity Of Plasmodium Falciparum Apicoplast Dna Polymerase, Eric Evan Parrott Jan 2013

Fidelity Of Plasmodium Falciparum Apicoplast Dna Polymerase, Eric Evan Parrott

Graduate Theses and Dissertations

Members of the phylum Apicomplexa, including pathogens such as Plasmodium falciparum, Toxoplasma gondii, and Babesia bovis contain a non-photosynthetic plastid called an apicoplast. It has been implicated in the biosynthesis of fatty acids, iron-sulfur clusters, heme groups, and isoprenoid synthesis for the pathogen. This unique plastid was immediately recognized as a potential target for drug discovery as it is essential for the survival and reproduction of the parasite. With this in mind, our group has initiated characterization of the DNA replication system within the apicoplast. Here we report our efforts to determine the fidelity of the DNA polymerase (apPOL) using ...


Investigating Higher-Order Chromatin Structure And Saga Cooperativity Using Existing And Modified In Vitro Chromatin Systems, Divya Sinha Jan 2013

Investigating Higher-Order Chromatin Structure And Saga Cooperativity Using Existing And Modified In Vitro Chromatin Systems, Divya Sinha

Graduate Theses and Dissertations

The organization of genomic DNA with histones and other proteins ensures the proper storage, utilization and segregation of DNA's encoded information in a healthy eukaryotic cell. These components comprise chromatin, and knowledge of its structure, mechanisms of its formation, and the dynamic changes it undergoes is essential to gain insights into chromatin's role in controlling gene regulation and the defects associated with misregulation. Here we describe our efforts to understand the different aspects of chromatin by using existing and modified in vitro chromatin model systems.

To better understand histone-histone interactions involved in the formation of higher-order chromatin structure ...


Purification And Optimization Of Sequential Biosynthetic Enzymes For Co-Localization Onto A Nanocarrier, Mollie Tiernan Jan 2013

Purification And Optimization Of Sequential Biosynthetic Enzymes For Co-Localization Onto A Nanocarrier, Mollie Tiernan

Graduate Theses and Dissertations

Flavonoids are polyphenolic plant secondary metabolites with many purposes, including providing pigmentation in plants and anti-oxidant and anti-cancerous activities in humans. There are over 10,000 different flavonoids known, making them one of the largest groups of natural products. One major sub-class of flavonoids is the flavan-3-ols, which are known for their health benefits and the ability to form proanthocyanidins, or condensed tannins. Many of the intermediates in this pathway are unstable and have not been isolated in planta. Another natural product of interest is sclareol, a diterpene alcohol, which is important in the fragrance and flavor industry as a ...


Bioinspired Synthesis And Characterization Of Organic/Inorganic Nanocomposite Materials, Xunpei Liu Jan 2013

Bioinspired Synthesis And Characterization Of Organic/Inorganic Nanocomposite Materials, Xunpei Liu

Graduate Theses and Dissertations

In Nature, hybrid materials with hierarchical structure are formed by biomineralization of organic macromolecules that act as templates for the nucleation and/or growth of the inorganic component. The building blocks of the natural organic macromolecules provide the template architectures that result in chemical and morphological diversity in the inorganic phases. Inspired by the formation of biominerals in living organisms, novel organic-inorganic hybrid materials have been designed and developed by biomimetic routes. There is a growing interest in using synthetic polymers, engineered proteins, and various polymer-based hybrid architectures as templates for bioinspired synthesis.

In this work, we have used amphiphilic ...