Browsing by Subject "Amino acids"
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Item An amino acid mixture enhances insulin-stimulated glucose uptake in isolated epitrochlearis muscle(2010-08) Kleinert, Maximilian; Ivy, John, 1945-; Farrar, Roger P.Amino acids are important modulators of skeletal muscle metabolism, but their impact on glucose uptake by skeletal muscle remains unclear. To address the effect of an amino acid (AA) mixture consisting predominately of isoleucine on glucose uptake we first conducted a dose-response experiment, investigating how different concentrations of the AA mixture affect glucose uptake by isolated rat epitrochlearis muscle. In a subsequent experiment we examined how the AA mixture affects insulin-stimulated glucose uptake by isolated rat epitrochlearis muscle. It was found that the AA mixture with as little as 0.5 mM Ile increases [H3]2-deoxy-D-glucose (2-DG) uptake by 76% compared to basal glucose uptake. The AA mixtures with 1, 2 or 4 mM Ile provided no significant additional effect. Next we combined the AA mixture consisting of 2 mM Ile, 0.012 mM Cys, 0.006 mM Val and 0.014 mM Leu with physiological levels (75 μU/ml, sINS) and maximally-stimulating levels (2 mU/ml, mINS) of insulin. The AA mixture only, sINS and mINS significantly increased 2-DG uptake compared to basal by 63, 79 and 298%, respectively. When the AA mixture was combined with sINS and mINS 2-DG uptake was further increased significantly by 26 and 14%, respectively. Western blotting analysis revealed that compared to basal the AA mixture increased AS160 phosphorylation, while phosphorylation of Akt and mTOR did not change. Combining the AA mixture with sINS resulted in no additional phosphorylation compared to sINS alone. Interestingly, addition of the AA mixture to mINS resulted in increased phosphorylation of mTOR, Akt and AS160 compared to mINS alone. Our results suggest that certain AAs (1) increase glucose uptake in the absence of insulin and (2) augment insulin-stimulated glucose uptake in an additive manner. These effects on glucose uptake appear to be mediated via a molecular pathway that is partially independent from the canonical insulin signaling cascade.Item Application of micro methods to the study of yeast growth substances(1941) Mitchell, Herschel K.; Not availableItem Design, synthesis & thermodynamic evaluation of conformationally-constrained pseudopeptides and synthetic approaches to sieboldine A(2008-08) Teresk, Martin Gerald, 1981-; Martin, Stephen F.A series of conformationally constrained and flexible pseudopeptides were prepared and their thermodynamic parameters on binding to the Grb2 SH2 domain were determined by isothermal titration calorimetry (ITC). Cyclopropane constrained analogs having hydrophobic amino acid residues at the pTyr+1 position exhibited, on average, a 2-5 fold improvement in binding affinities with the enhancement in affinities due to a more favorable enthalpy, not entropy, of binding. This serves as the first set of examples which demonstrate that favorable entropies of binding are not an inherent characteristic of ligand preorganization. Incorporation of polar amino acid residues at the pTyr+1 position eventuated in a slightly different thermodynamic effect than what was observed with the hydrophobic analogs. The constrained molecules exhibited greater binding affinities for the Grb2 SH2 domain and that increase in affinity was a consequence of a more favorable enthalpy, not entropy, of binding. However, the binding entropies for the polar set of constrained and flexible molecules were all negative. Structural information obtained from the co-crystallization of selected constrained and flexible ligand pairs with the Grb2 SH2 domain revealed an increase in conformational mobility of the BC loop in the complexes of the constrained derivatives and the presence of a greater number of direct polar contacts, but fewer water-mediated interactions between the phosphate group of the constrained molecules and the pTyr binding pocket of the domain. The construction of the cis-hydrindanone ring system in sieboldine A was accomplished utilizing either a Lewis acid-mediated silyl-directed Nazarov cyclization of a functionalized divinyl ketone or a sequential Ni(0)-catalyzed 1,4-addition/5-endo-dig cyclization. Propargylzinc bromide was shown to undergo conjugate addition to the [alpha]-aminopropyl substituted enone using Ni(acac)₂, thus providing a new, mild protocol for the conjugate propargylation reaction. Further efforts toward the formation of the α-epoxy ketone are described.Item Exploration of adaptation to unnatural amino acids(2002-08) Bacher, Jamie Mitchell; Ellington, Andrew D.Item Extreme climate events influence particulate organic matter quality, quantity, and composition in the Mission-Aransas Estuary(2022-08-16) Douglas, Sarah Victoria; Liu, Zhanfei; Hardison, Amber K.; McClelland, James W; Erdner, Deana L; Goñi, MiguelEstuaries are sites where rivers meet the ocean, marked by dynamic physical, chemical, and biological variability, making them particularly vulnerable to the effects of global climate change and shifting freshwater inflow regimes. Arid subtropical climates oscillate between drought and wet conditions, leading to a “flood or famine” paradigm for estuarine freshwater inflow, in which sporadic storm events drive dynamic changes in salinity and nutrient availability. In turn, these physical inputs can alter particulate organic matter (POM) sources, composition, and quality, with cascading consequences for trophic webs and overall carbon production and storage. Over the past decade, the Mission-Aransas Estuary (MAE), located on the south Texas coast, experienced several significant climatic events: severe drought, sequential flooding events, and the direct impact of category 4 Hurricane Harvey in 2017. Multiple biomarkers from an eight-year twice monthly sample set (2012-2019) were used to assess POM quantity, quality, and composition. POM was quantified using elemental analysis of organic carbon and nitrogen. POM sources, including phytoplankton community composition, were determined using pigments, stable isotopes (δ¹³C, δ¹⁵N), and neutral and polar fatty acids. POM quality was assessed using total hydrolyzable amino acids (THAAs), phospholipid linked fatty acids (PLFAs), and chloropigments (chlorophyll a, pheophorbide, and pheophytin). This research shows the transition from drought to wet conditions was more influential on POM source, composition, quantity, and quality than any individual storm event, including Hurricane Harvey. Drought conditions dampened phytoplankton biomass growth and elevated POM degradation. Following sequential flooding events, phytoplankton biomass and highly labile biomolecules (THAAs and polyunsaturated PLFAs) increased, improving overall POM quality. The phytoplankton community, dominated by diatoms during the drought, switched to a stable cyanobacteria-dominated community following estuarine freshening, driven by salinity and nutrient availability with seasonal growth oscillations between taxa. The drought-to-wet transition event represented a climate-driven regime shift of the estuarine phytoplankton community and POM quality to a new steady state. Characterizing POM sources and composition at high sampling resolution across timescales long enough to capture extreme climatic events is critical to understanding the weathering capacity of estuarine systems, the importance of antecedent conditions on disturbance events, and the potential outcomes for primary producers, fisheries, and organic carbon storage in a climatically uncertain future.Item Investigating thermodynamics and kinetics of hydrate phase change phenomena using experimental and machine learning tools(2021-12-07) Acharya, Palash Vadiraj; Bahadur, Vaibhav; Ezekoye, Ofodike; Shi, Li; Bonnecaze, RogerHydrates are ice-like crystalline solids which form under high pressure and low-temperature conditions from water (forming a cage of host molecules) and another liquid or gas (guest molecule). Hydrates can enable numerous industrial applications in the fields of carbon capture and sequestration (CCS), flow assurance, natural gas transportation/storage and desalination. A significant technological barrier to many hydrates-related applications is the slow rate of formation of hydrates, which is a result of thermodynamic and kinetics-related limitations. This dissertation investigates the role of electric field and surface chemistry in accelerating the nucleation kinetics of clathrate hydrates (CO₂, tetrahydrofuran). It also investigates the role of amino acids in inhibiting the nucleation kinetics and thermodynamics of CO₂ hydrate formation. It also evaluates the utility of machine learning models in predicting the thermodynamic formation conditions for gas hydrates. In addition to the focus on fundamental investigations, this dissertation also evaluates the utility of hydrates as a carbon capture tool when coupled with a steam reforming system to generate blue hydrogen from landfill gas. The content of the dissertation work is motivated by three objectives, as described ahead. Objective 1 investigates the influence of electric fields and surface chemistry on nucleation kinetics of hydrate formation for two kinds of hydrate forming systems (considered as two separate subtasks): miscible liquid-liquid systems (Tetrahydrofuran-water) and gas-liquid (CO₂-water) systems. As background, it is noted that the role of electric field has been widely studied for accelerating freezing of water. Subtask 1-1 investigates the role of electric field when used in conjunction with open-cell aluminum metal foam-based electrodes in accelerating the formation of THF hydrates. It is demonstrated that aluminum foam electrodes trigger near-instantaneous nucleation (in only tens of seconds) of THF hydrates at very low voltages (~20V). The promotion effect can be ascribed to two distinct interfacial mechanisms at play: namely, electrolytic bubble generation and the formation of metal ion complex-based coordination compounds. While THF hydrates form under atmospheric pressure, CO₂ gas hydrates form at much higher pressures and are therefore studied using a custom-built high-pressure cell. Subtask 1-2 highlights the role of aluminum in accelerating nucleation kinetics of CO₂ gas hydrates. Statistically meaningful measurements of induction times for CO₂ hydrate nucleation are undertaken using water droplets as individual microsystems for hydrate formation. The influence of various metal surfaces, droplet size, CO₂ dissolution time, and the presence of salts in water on nucleation kinetics have been characterized. It is observed that Al metal significantly accelerates the nucleation kinetics of CO₂ hydrates (the effect of which cannot be replicated by salts of Al) with nucleation initiating from the Al-water interface. Prediction of thermodynamic conditions of hydrate formation is critical to their synthesis and Objective 2 is centered around developing modeling and experimental tools for effective prediction of thermodynamic phase equilibria for hydrates. Subtask 2-1 demonstrates the utility of machine learning models to predict hydrate dissociation temperature (HDT) as a function of constituent hydrate precursors and salt inhibitors. Importantly, and in contrast to most previous studies, thermodynamic variables such as the activity-based contribution due to electrolytes, partial pressure of individual gases, and specific gravity of the overall mixture have been used as input features in the prediction algorithms. Using such features results in more physics-aware ML algorithms, which can capture the individual contributions of gases and electrolytes in a more fundamental manner. Three ML algorithms: Random Forest (RF), Extra Trees (ET), and Extreme Gradient Boosting (XGBoost) are trained and their performance is evaluated on an extensive experimental dataset comprising of more than 1800 experimental data points. The overall coefficient of determination (R²) is greater than 97% for all the three ML models with XGBoost exhibiting the best prediction performance with an R² metric of 99.56%. Subtask 2-2 investigates the role of amino acids on the kinetics and thermodynamics of CO₂ hydrate formation using droplet-based microsystems. Amino acids are environmentally friendly and inexpensive hydrate formation inhibitors. Nucleation kinetics as well as the depression in thermodynamic hydrate formation temperature for CO₂ hydrates in the presence of five amino acids containing non-polar side chains have been evaluated. All the amino acids inhibit nucleation with tryptophan exhibiting the slowest nucleation rate. Isoleucine exhibits the highest thermodynamic inhibition effect with the highest depression in freezing point temperature corresponding to 0.2 K for the concentrations studied in the present analysis. Landfills produce significant amounts of methane, which is a potent greenhouse gas. Steam reforming of the landfill gas generates CO₂ + H₂ as byproducts. The generated hydrogen can be used in refineries, to produce fertilizers or to produce electricity in a fuel cell. Objective 3 investigates the techno-economic factors associated with a facility coupling a sorption-enhanced steam methane reforming system with a hydrates-based capture system for landfills across Texas. The electrical energy requirements, water use, operating and capital costs required to set up and keep such a facility running have been evaluated in detail. The cost of producing hydrogen for all counties is about $0.5/kg of H₂ (excluding the cost for natural gas). The total carbon capture cost lies in the range of $96-$145/metric ton of CO2 with the lowest/highest cost corresponding to Harris/Brazoria county producing the highest/lowest amount of CO₂. A minimum cost of $0.9(2.4)/kg of H₂ would be required for Harris (Brazoria) county for a positive 30-year net present value; a 5-year payback period would require a minimum cost of $1.35(4.95)/kg of H₂. In summary, this dissertation significantly advances the current understanding of hydrate formation by introducing novel techniques (consuming ultra-low energy as well as passive tools) for enhancing hydrate formation kinetics. It also develops novel ML and experimental tools for predicting thermodynamic formation conditions of hydrates in the presence of various inhibitors. Finally, this work assesses the technical and economic viability of a hydrates-centered future for the natural gas industry.Item Investigation of immobilized biopolymers for metal binding(2004) Malachowski, Lisa Lyn; Holcombe, James A.This research focuses on the utility of immobilized poly amino acids for metal remediation and preconcentration. The biohomopolymer poly-L-histidine (PLHis) was immobilized onto controlled pore glass (CPG) and its metal binding capabilities evaluated through the use of a flow injection analysis - flame atomic absorption system (FIA-FAAS). The metal binding capability of PLHis-CPG was determined through the analysis of the generated breakthrough curves. The polymer likely coordinates cationic metals through the imidazole side chain (pKa ≈ 6) present on each histidine residue with both strong and weak binding sites for Cu2+, Cd2+, Co2+, and Ni2+. It has also been shown that the protonated imidazole side chain present in acidic conditions is capable of binding metal oxyanions such as chromates, arsenates, and selenites; although oxyanion binding currently exhibits interferences from competing anions in solution, such as sulfate and nitrate. Poly-L-Aspartic Acid (PLAsp) and Poly-L-Glutamic Acid (PLGlu) were also individually immobilized onto controlled pore glass (CPG) and compared using their metal binding capabilities. Elemental combustion analysis was used to yield polymer coverage approximations. Formation constants and site capacities of both polymers for Cd2+ were determined through equilibrium and breakthrough studies. Additionally, the metal selectivity of PLAsp and PLGlu was evaluated when breakthrough curves were run with several metals present in solution at one time. Both polymers exhibited similar binding trends and binding strengths for all of the metals studied. This likely reflects the absence of a predetermined tertiary structure of the polymers on the surface and the relatively high residue-per-metal ratio (~20:1), which places less stringent requirements on the steric hindrance between the side chains and the resultant ìwrappingî of the peptide around the metal. Initial attempts at determining formation constants of PLAsp and PLGlu through competitive binding experiments with either EDTA or oxalate present were unsuccessful due to complications caused by the current immobilization procedure. Therefore, alternate immobilization procedures were investigated utilizing an epoxide linker. These methods eliminate the formation of an amine functionality on the surface. Additionally, a combinatorial approach was used in an attempt to elucidate an optimal copolymer primary structure for successful binding of a target metal. This approach included screening the library for successful binding with micro x-ray fluorescence (MXRF) and obtaining the sequence of the successful copolymer through Edman Degradation. A considerable amount of the metal binding experiments conducted in this research used the analysis of breakthrough curves generated through flow injection-flame atomic absorption spectrometry. Solution flow rate is a critical parameter in breakthrough analysis. Due to the absence of an inexpensive, on-line flow meter for flow injection analysis systems, an electronic flow meter was constructed to measure the flow rate during the FIAAS measurements. Thus, flow rates can be measured while collecting breakthrough data, and continuous monitoring of flow rates is possible.