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In this thesis the effect of mechanical stimuli on A549 lung cancer cells is studied. Modifications of polydimethylsiloxane (PDMS) surfaces are employed to alter the mechanical stimuli applied to the cells. Flat substrates are first studied and then micropillared substrates are designed, fabricated, and tested as a method to alter the mechanical properties of the PDMS surfaces. Molds with micro-pillars are designed then fabricated from silicon using deep reactive ion etching. From these molds, a negative then a positive replicate is made using PDMS. The pillared PDMS substrates are fabricated in 10 geometries and used for experiments. A549 cells are cultured on these surfaces then analyzed using fluorescence microscopy and atomic force microscopy (AFM). Fluorescence microscopy images processed by ImageJ software measure the cell spreading area (m2) while AFM quantifies the cell stiffness (kPa). For flat substrates, the cell stiffness and spreading area increase with increasing substrate stiffness. Further, results on pillared substrates show a similar trend based on pillar geometry changes. For pillared substrates, the A549 cell stiffness and spreading area increase as the height decreases, yet there is decreased cell stiffness and spreading area as the diameter and spacing decreases. The experiments show that changes in surface properties and only mechanical stimuli alter cellular morphology and biomechanics

As a key constituent of proteins, nucleic acids, and other biomolecules, nitrogen is essential to all living organisms including human beings. Dinitrogen represents the largest pool of nitrogen, about 79% of the Earth’s atmosphere, yet it is unusable by most living organisms due to its inertness. There are two ways to fix this inert dinitrogen to usable ammonia. One is the industrial Haber-Bosch process, which needs to be conducted at high temperature and pressure. This process uses a lot of the non-renewable fossil fuel as the energy source. The other major pathway is the biological nitrogen fixation carried out by some microorganisms called diazotrophs. The usable nitrogen output from this biological pathway ultimately supports an estimated 60% of the human population’s demand for nitrogen.The catalyst responsible for the biological nitrogen fixation is called nitrogenase, the most studied form of which contains molybdenum and iron in its active center, so called molybdenum nitrogenase. The work in this dissertation attempts to understand howthis biological catalyst breaks down dinitrogen to ammonia by application of different modern techniques. Firstly, an approach was developed to understand the stepwise reduction mechanism of dinitrogen to ammonia by molybdenum nitrogenase.The second goal of my research is to understand the roles of iron and molybdenum centers in nitrogenase function. My results using carbon monoxide as a probe for genetically modified molybdenum nitrogenase indicate that iron should be the metal sites functioning for nitrogen fixation. This is further supported by another study aimed at understanding the role of molybdenum during nitrogenase functioning.Moreover, an approach was developed to understand the mechanism for the obligatory production of hydrogen gas when nitrogenase activates dinitrogen for reduction. The same study also suggests possible pathways for the addition of hydrogenous species to nitrogen to produce ammonia.As part of this work, we also found that remodeled nitrogenases can use poisonous carbon monoxide and greenhouse-gas carbon dioxide to produce useful hydrocarbons by coupling one or more small molecules, which is hard to be achieved by other catalysts. Further study of these new reactions might give us deep insights on nitrogenase mechanism and inspire scientists to design better catalysts for relevant industrial processes.

Pantothenate-p-nitroanilide has been synthesized for use as a substrate in a continuous spectrophotometric assay of pantetheinase activity monitoring absorbance at 41 0 nm. Pantothenate-p-nitroanilide is a crystalline compound with a molecular weight of 338.0 and a melting point of 146-149°C. Use of this substrate in the described assay is suitable for enzyme activity determination in high protein content media such as blood serum. Serum pantetheinase activity was determined for rats of varying pantothenate nutriture. Rats with mildly (but significantly, p

Substrate switching noise is becoming a concern as integrated circuits get larger and speeds get faster. Mixed-mode integrated circuits are especially affected as the substrate noise interferes with sensitive analog circuits resulting in limited signal to noise ratios. This thesis serves to study the cause of the noise at the point where it is generated to the way it propagates to the analog circuits, and presents several approaches to reduce the switching noise. In addition, it examines the substrate impedance as being a key element to successful and reliable design for low-noise CMOS mixed-signal integrated circuits. Utilizing the substrate lead inductance and current-variable capacitances through the use of guard ring diodes, resonant frequencies which provide a low impedance path to ground are created. These can be tuned to coincide with problematic noise frequency components or to cancel the pin and package resonance, thus suppressing noise and improving reliability. / Graduation date: 1997

Thesis (Ph. D.)--Ohio State University, 2006. / Full text release at OhioLINK's ETD Center delayed at author's request

This thesis proposes a new bandpass filter prototype modified based on T-type coupled resonator architecture by considering the parasitic shunt capacitance effect. After derivation, the new prototype can be proved equivalent to third-order Chebyshev bandpass filter. It is easy to realize the new prototype circuit by utilizing the inductor and capacitor library established from electromagnetic simulations. The couplings between circuit components can cause some transmission zeros to enhance attenuation rate at stopbands. This thesis designs several bandpass filters embedded in 4-layer laminate package substrate with center frequency at 2.45GHz. The measurement results show that most of these filters can achieve less than 1.7dB insertion loss and more than 14dB return loss at passband, and more than 30dB attenuation at 950MHz, 4.8GHz and 7.2GHz. One of the filters has a size of 1.9¡Ñ2.7mm2, which is the smallest area for the currently reported bandpass filters embedded in the organic package substrate.

Methionine is essential for proper functioning of cellular processes such as protein synthesis, transmethylation and polyamine synthesis. Efficient recycling of methionine is important because of its limited bioavailability and metabolically expensive de novo synthesis. Further, cellular accretion of the nucleoside metabolites of the methionine salvage pathway compromises polyamine biosynthesis, transmethylation reactions and quorum sensing pathways, all critical reactions in cellular metabolism. 5’-methylthioadenosine/S-adenosylhomocysteine nucleosidase (MTAN) is a key component of the methionine salvage pathway of plants and many bacterial species, including Escherichia coli, Enterococcus faecalis, Salmonella typhimerium, Haemophilus influenza and Streptococcus pneumoniae. In bacteria, this enzyme displays dual-substrate specificity for two methionine metabolites, 5’-methylthioadenosine (MTA) and S-adenosylhomocysteine (SAH), and catalyzes the irreversible cleavage of the glycosidic bond to form adenine and the corresponding thioribose products, methylthioribose (MTR) and S-ribosylhomocysteine (SRH), respectively. In plants, MTAN is highly specific towards MTA and shows 0-16 % activity towards SAH. Plants rely on SAH hydrolase to metabolize SAH. Mammals do not have the nucleosidase enzyme and MTA is metabolized by MTA phosphorylase (MTAP). Like plants, mammals utilize SAH hydrolase to degrade SAH. Because MTAN is required for viability in multiple bacterial species and is not found in humans, it has been identified as a target for novel antibiotic development. This thesis describes the structural and functional characterization of bacterial and plant MTANs, with the aim of better understanding the molecular determinants of substrate specificity and the catalytic mechanism of this enzyme. The catalytic activities of representative plant MTANs from Arabidopsis thaliana, AtMTAN1 and AtMTAN2, were kinetically characterized. While AtMTAN2 shows 14 % activity towards SAH relative to MTA, AtMTAN1 is completely inactive towards SAH. As such, AtMTAN1 was selected for further examination and comparison with the bacterial MTAN from Escherichia coli (EcMTAN). The structures, dynamics and thermodynamic properties of these enzymes were analyzed by X-ray crystallography, hydrogen-exchange coupled mass spectrometry and isothermal titration calorimetry, respectively. Our studies reveal that structural differences alone do not sufficiently explain the divergence in substrate specificity, and that conformational flexibility also plays an important role in substrate selection in MTANs. MTANs from the pathogenic bacterial species, Staphylococcus aureus and Streptococcus pneumoniae, were examined kinetically and structurally. Comparison of the structures and catalytic activities of these enzymes with EcMTAN shows that the discrepancies in kinetic activities arefully explained by structural differences, as the overall structure and active sites of these bacterial MTANs are nearly identical. These experiments are in agreement with our proposal that dynamics play a significant role in catalytic activity of MTAN, and suggest that both structure and dynamics must be considered in future antibiotic design. To further our understanding on the catalytic mechanism of MTAN, the putative catalytic residues of AtMTAN1 were identified by structural comparison to EcMTAN and mutated by site-directed mutagenesis. The AtMTAN1 mutants were analyzed by circular dichroism and kinetic studies. Our results suggest that the catalytic mechanism is largely conserved between bacterial and plant MTANs, although the role of the putative catalytic acid remains to be confirmed.

MenD, a thiamin diphosphate (ThDP)-dependent enzyme, catalyzes the reaction from isochorismate (ISC) to 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate (SEPHCHC), and thus is also called SEPHCHC synthase. This conversion is the first committed step in the classical menaquinone (Vitamin K2) biosynthetic pathway, requiring 2-ketoglutarate (2-KG), ThDP and Mg²⁺. Since the biosynthesis of menaquinone is essential in some bacterial pathogens, for example <i>Mycobacterium tuberculosis</i>, MenD or the menaquinone pathway could be a target for drug development.<p> The method for the kinetic assay of the MenD-catalyzed reaction was evaluated by comparing UV spectrophotomeric measurements and HPLC analysis. It was validated that the steady-state kinetics of the MenD-catalyzed reaction can be determined by monitoring UV absorbance of ISC at 278 nm and 300 nm.<p> Phosphonate analogues of 2-KG were synthesized and assayed as inhibitors of the MenD reaction. It was found that the phosphonate analogues of 2-KG are competitive inhibitors with varied affinity for MenD. Of the inhibitors, monomethyl succinyl phosphonate (MMSP) was the most effective, with a <i>K</i>_i of 700 nM. However, the potent MenD inhibitors show no effectiveness against mycobacterial growth.<p> An analogue of isochorismate, trans-(±)-5-carboxymethoxy-6-hydroxy-1,3-cyclohexadiene-1-carboxylate ((±)-CHCD), was synthesized. The (+)-CHCD was found to be an alternative substrate for the MenD-catalyzed reaction. When CHCD was utilized in the MenD reaction, 5-carboxymethoxy-2-(3-carboxy-propionyl)-6-hydroxy-cyclohex-2-enecarboxylate (CCHC) was isolated and characterized, which was believed to be the product of spontaneous isomerization of the SEPHCHC-like analogue. The kinetic study of MenD reaction using (±)-CHCD, in association with the kinetics pattern probed by MMSP, demonstrated for the first time that the MenD-catalyzed reaction has a Ping Pong bi bi kinetic mechanism.<p> The analysis of sequence and structure of MenD from E. coli allowed the investigation of the active site residues and their catalytic functions by mutation of the individual residues. S32A, S32D, R33K, R33Q, E55D, R107K, Q118E, K292Q, R293K, S391A, R395A, R395K, R413K and I418L were prepared and assayed kinetically with respect to 2-KG, ISC, (±)-CHCD, ThDP and Mg²⁺. The values of <i>K</i>_m^a and <i>k</i>_cat^a/<i>K</i>_m^a for the mutants, in comparison with that of wild type MenD, provide valuable insight into the catalytic mechanism of MenD.

MenD, a thiamin diphosphate (ThDP)-dependent enzyme, catalyzes the reaction from isochorismate (ISC) to 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate (SEPHCHC), and thus is also called SEPHCHC synthase. This conversion is the first committed step in the classical menaquinone (Vitamin K2) biosynthetic pathway, requiring 2-ketoglutarate (2-KG), ThDP and Mg²⁺. Since the biosynthesis of menaquinone is essential in some bacterial pathogens, for example <i>Mycobacterium tuberculosis</i>, MenD or the menaquinone pathway could be a target for drug development.<p> The method for the kinetic assay of the MenD-catalyzed reaction was evaluated by comparing UV spectrophotomeric measurements and HPLC analysis. It was validated that the steady-state kinetics of the MenD-catalyzed reaction can be determined by monitoring UV absorbance of ISC at 278 nm and 300 nm.<p> Phosphonate analogues of 2-KG were synthesized and assayed as inhibitors of the MenD reaction. It was found that the phosphonate analogues of 2-KG are competitive inhibitors with varied affinity for MenD. Of the inhibitors, monomethyl succinyl phosphonate (MMSP) was the most effective, with a <i>K</i>_i of 700 nM. However, the potent MenD inhibitors show no effectiveness against mycobacterial growth.<p> An analogue of isochorismate, trans-(±)-5-carboxymethoxy-6-hydroxy-1,3-cyclohexadiene-1-carboxylate ((±)-CHCD), was synthesized. The (+)-CHCD was found to be an alternative substrate for the MenD-catalyzed reaction. When CHCD was utilized in the MenD reaction, 5-carboxymethoxy-2-(3-carboxy-propionyl)-6-hydroxy-cyclohex-2-enecarboxylate (CCHC) was isolated and characterized, which was believed to be the product of spontaneous isomerization of the SEPHCHC-like analogue. The kinetic study of MenD reaction using (±)-CHCD, in association with the kinetics pattern probed by MMSP, demonstrated for the first time that the MenD-catalyzed reaction has a Ping Pong bi bi kinetic mechanism.<p> The analysis of sequence and structure of MenD from E. coli allowed the investigation of the active site residues and their catalytic functions by mutation of the individual residues. S32A, S32D, R33K, R33Q, E55D, R107K, Q118E, K292Q, R293K, S391A, R395A, R395K, R413K and I418L were prepared and assayed kinetically with respect to 2-KG, ISC, (±)-CHCD, ThDP and Mg²⁺. The values of <i>K</i>_m^a and <i>k</i>_cat^a/<i>K</i>_m^a for the mutants, in comparison with that of wild type MenD, provide valuable insight into the catalytic mechanism of MenD.