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Hu, Xihao. / Thesis Ph.D. Chinese University of Hong Kong 2015. / Includes bibliographical references (leaves 147-161). / Abstracts also in Chinese. / Title from PDF title page (viewed on 26, October, 2016). / Hu, Xihao.

This study investigated genetic predictions for amino acid biosynthesis and catabolism by Lactobacillus helveticus CNRZ 32, a commercial cheese flavor adjunct that reduces bitterness and intensifies flavor notes. Conversion of amino acids into volatile and nonvolatile flavor compounds by L. helveticus and other lactic acid bacteria in cheese is thought to represent the rate-limiting step in the development of mature cheese flavor and aroma. One of the primary mechanisms for amino acid breakdown by these microbes involves the reversible action of enzymes involved in biosynthetic pathways, so our group investigated the genetics of amino acid biosynthesis in L. helveticus CNRZ 32. Most lactic acid bacteria are auxotrophic for several amino acids, and phenotypic characterization of L. helveticus CNRZ 32 has shown this bacterium requires 14 amino acids. Reconstruction of amino acid biosynthetic pathways from a draft-quality (incomplete) genome sequence for L. helveticus CNRZ 32 showed generally good agreement between gene content and phenotypic amino acid requirements. One exception involved the requirement ofCNRZ 32 for Asp (or Asn) for growth, where predictions derived from the genome sequence suggested this strain may be able to synthesize Asp from citrate. This prediction was confirmed as Asp auxotrophy in L. helveticus CNRZ 32 could be alleviated by the addition of citrate to a chemically defined medium that lacked Asp and Asn. Genome analysis also predicted that L. helveticus CNRZ 32 possessed ornithine decarboxylase activity, and would therefore catalyze the conversion of ornithine to putrescine, a volatile biogenic amine. Putrescine production in cheese would be undesirable because this compound may impart a rotting flesh flavor and can also have adverse effects on human health. Experiments to confirm ornithine decarboxylase activity in L. helveticus CNRZ 32 using a special growth medium, thin layer chromatography, high performance liquid chromatograph, or 13C nuclear magnetic resonance were unsuccessful, however, which indicated this bacterium does not contribute to putrescine production in cheese.

<p>The ability to create surfaces with well-defined chemical properties is a major research field. One possibility to do this is to design peptides that bind with a specific secondary structure to silica nanoparticles. The peptides discussed in this thesis are constructed to be random coil in solution, but are “forced” to become helical when adsorbed to the particles. The positively charged side-chains on the peptides strongly disfavor an ordered structure in solution due to electrostatic repulsion. When the peptides are introduced to the particles these charges will strongly favor the structure because of ion pair bonding between the peptide and the negatively charged nanoparticles. The peptide-nanoparticle system has been thoroughly investigated by systematic variations of the side-chains. In order to determine which factors that contributes to the induced structure, several peptides with different amino acid sequences have been synthesized. Factors that have been investigated include 1) the positive charge density, 2) distribution of positive charges, 3) negative charge density, 4) increasing hydrophobicity, 5) peptide length, and 6) by incorporating amino acids with different helix propensities. Moreover, pH dependence and the effect of different nanoparticle curvature have also been investigated. It will also be shown that the system can be modified to incorporate a catalytic site that is only active when the helix is formed. This research will increase our understanding of peptide-surface interactions and might be of importance for both nanotechnology and medicine.</p>

Simultaneous measurements of energy and protein metabolism can provide valuable information about their interactions. Dietary lysine is limiting in typical feedstuffs fed to swine and, therefore, limits protein synthesis. Current recommendations for dietary amino acid and energy intakes may not be reflective of the requirements for modern, highly productive sows and, therefore, invalidate requirement estimates determined according to the factorial approach. Current feeding recommendations suggest a constant amino acid intake throughout gestation. However, the demands for amino acids changes from maternal tissue accretion in early-gestation to fetal, conceptus, and mammary tissue development in late-gestation. This thesis reports the method development associated with simultaneous measurements of energy and protein metabolism and its application to determine dietary lysine requirements in non-pregnant and pregnant sows using the indicator amino acid oxidation method. Two indirect calorimetry systems and an experimental feeding regimen were tested and validated for use in studies of amino acid requirements by stable isotope dilution. Protein and energy balance studies were performed in non-pregnant sows fed two distinct levels of energy and protein intake. The systems reacted appropriately to changes in gas concentrations induced by sow respiration. Protein and energy balance studies were also performed in pregnant and lactating sows fed typical diets. Sows appeared more anabolic during mid-gestation and were catabolic by late-gestation and through lactation, where additional energy intake provided by ad libitum feed intake increased milk energy output. The dietary lysine requirement in non-pregnant sows at maintenance was determined as 49 mg/kg0.75, 30% greater than current recommendations. The dietary lysine requirement was determined to be 10.1 g/d and 16.5 g/d, in early- and late-gestation, respectively. These results suggest that a constant diet formulation for the entirety of gestation is not appropriate. In conclusion, simultaneous measurements of energy and protein metabolism combining indirect calorimetry and stable isotope techniques may be used to define requirements for dietary amino acids in sows. Basic assumptions of the factorial approach to estimate requirements require further investigation, including the dietary lysine requirement. Application of phase feeding for sows during gestation can more correctly meet the demands for amino acids and energy, improving sow longevity. / Animal Science

The activity of glutamate transporters is essential for the temporal and spatial regulation of the neurotransmitter concentration in the synaptic cleft which is critical for proper neuronal signaling. Because of their role in controlling extracellular glutamate concentrations, dysfunctional glutamate transporters have been implicated in several neurodegenerative diseases and psychiatric disorders. Therefore, investigating the mechanism of substrate transport by these transporters is essential in understanding their behavior when they malfunction. A bacterial glutamate transporter homologue has been successfully crystallized revealing the molecular architecture of glutamate transporters. However, many important questions remain unanswered. In this thesis, I will address the role of D439 in the binding of Na+, and I will identify other electrogenic steps that contribute to the total electrogenicity of the transporter cycle. The role of D439 in the binding of Na+ to the transporter was explored previously in this lab. While it was proposed that the effect of D439 in Na+ binding is indirect, the results described in this thesis provides added support to this work. Here, I will show that the D439 mutation changed the pharmacology of EAAC1 such that THA was converted from a transported substrate to a competitive inhibitor. I will also show that Na+ binding to the substrate-bound mutant transporter occurred with the same affinity as that of Na+ to the substrate-bound wild-type transporter. Therefore, based on these results, D439 is not directly involved in the binding of Na+ to the substrate-bound transporter, but that its effect is rather indirect through changing the substrate binding properties. Na+ binding steps to the empty transporter and to the glutamate-bound EAAC1 contribute only 20% of the total electrogenicity of the glutamate transporter reactions cycle. While K+-induced relocation has been proposed to be electrogenic, there is no experimental evidence that supports it. In this work, I will show that the K+-induced relocation of the empty transporter is electrogenic. Moreover, the results in this work show that the K+-dependent steps are slower than the steps associated with the Na+/glutamate translocation suggesting that the K+-induced relocation determines the transporter?s properties at steady state.

The ability to create surfaces with well-defined chemical properties is a major research field. One possibility to do this is to design peptides that bind with a specific secondary structure to silica nanoparticles. The peptides discussed in this thesis are constructed to be random coil in solution, but are “forced” to become helical when adsorbed to the particles. The positively charged side-chains on the peptides strongly disfavor an ordered structure in solution due to electrostatic repulsion. When the peptides are introduced to the particles these charges will strongly favor the structure because of ion pair bonding between the peptide and the negatively charged nanoparticles. The peptide-nanoparticle system has been thoroughly investigated by systematic variations of the side-chains. In order to determine which factors that contributes to the induced structure, several peptides with different amino acid sequences have been synthesized. Factors that have been investigated include 1) the positive charge density, 2) distribution of positive charges, 3) negative charge density, 4) increasing hydrophobicity, 5) peptide length, and 6) by incorporating amino acids with different helix propensities. Moreover, pH dependence and the effect of different nanoparticle curvature have also been investigated. It will also be shown that the system can be modified to incorporate a catalytic site that is only active when the helix is formed. This research will increase our understanding of peptide-surface interactions and might be of importance for both nanotechnology and medicine.

This research investigates the interfacial interactions between biological entities and synthetic materials at two length scales: bulk and nanometer size. At the bulk scale, biomolecule adhesion is key for synthetic material incorporation in the body. Quantifying the adhesion strength becomes necessary. For the nanometer scale, the nanoparticles are generally delivered through the blood stream and their effect on the blood flow must be studied. An experimental approach was taken to study interaction at both material length scales. The cell/protein adhesion strength to bulk-sized materials was studied. The goal was to identify the most influential factor affecting adhesion: chemistry or surface roughness. The effects of nanoparticles on the viscosity of protein and amino acid solutions were measured. A statistical thermodynamic analysis was focused on the entropy change induced by the addition of gold nanoparticles to protein/amino acid solutions. Rheological studies were applied. A rheometer with a parallel plate was used to quantify the adhesion strength of cells and proteins to synthetic surfaces at the bulk scale. The adhesion strength depends on the applied shear stress and the radius of cells or proteins that remained attached to the surface after testing. At the nanometer scale, the viscosity of the nanoparticle enhanced protein or amino acid solutions were measured with a cone and plate. The adhesion studies were conducted with the following biological entities: fibroblasts, egg-white protein, and neurons. The fibroblast adhesion to poly(carbonate) and poly(methyl methacrylate) demonstrate fibroblasts are strongly attached to highly polar materials. Protein adhesion to titanium and chromium nitride coatings showed that chemical composition is the most influential factor. The neuron adhesion to poly-D-lysine coated glass demonstrated that neuron strengthening was due to an increase in adhesion molecules at the neuron/material interface. For nanoparticulates, it was found that the charged nanoparticles affect the protein and amino acid conformation and the potential energy of the solutions. Quantifying biomolecule adhesion to surfaces and predicting the behavior of nanoparticles inside a biological system are crucial for material selection and application. The major impact of this research lies in observing the interaction mechanisms at the interfaces of material-biological entities.

Proteins are the basic building blocks of biological organisms, and are responsible for a variety of functions within them. Proteins are composed of unique amino acid sequences. Some has only one sequence, while others contain several sequences that are combined together. These combined amino acid sequences fold to form a unique three-dimensional (3D) shape. Although the sequences may fold proteins into different 3D shapes in diverse environments, proteins with similar amino acid sequences typically have similar 3D shapes and functions. Knowledge of the 3D shape of a protein is important in both protein function analysis and drug design, for example when assessing the toxicity reduction associated with a given drug. Due to the complexity of protein 3D shapes and the close relationship between shapes and functions, the prediction of protein 3D shapes has become an important topic in bioinformatics. This research introduces a new approach to predict proteins’ 3D shapes, utilizing a multilayer artificial neural network. Our novel solution allows one to learn and predict the representations of the 3D shape associated with a protein by starting directly from its amino acid sequence descriptors. The input of the artificial neural network is a set of amino acid sequence descriptors we created based on a set of probability density functions. In our algorithm, the probability density functions are calculated by the correlation between the constituent amino acids, according to the substitution matrix. The output layer of the network is formed by 3D shape descriptors provided by an information retrieval system, called CAPRI. This system contains the pose invariant 3D shape descriptors, and retrieves proteins having the closest structures. The network is trained by proteins with known amino acid sequences and 3D shapes. Once the network has been trained, it is able to predict the 3D shape descriptors of the query protein. Based on the predicted 3D shape descriptors, the CAPRI system allows the retrieval of known proteins with 3D shapes closest to the query protein. These retrieved proteins may be verified as to whether they are in the same family as the query protein, since proteins in the same family generally have similar 3D shapes. The search for similar 3D shapes is done against a database of more than 45,000 known proteins. We present the results when evaluating our approach against a number of protein families of various sizes. Further, we consider a number of different neural network architectures and optimization algorithms. When the neural network is trained with proteins that are from large families where the proteins in the same family have similar amino acid sequences, the accuracy for finding proteins from the same family is 100%. When we employ proteins whose family members have dissimilar amino acid sequences, or those from a small protein family, in which case, neural networks with one hidden layer produce more promising results than networks with two hidden layers, and the performance may be improved by increasing the number of hidden nodes when the networks have one hidden layer.

This work attempted to detect chemical warfare agent (CWA) simulants via electrochemistry utilizing two approaches. The first approach consisted of a ferrocene (Fc) amino acid derivative film on Au surfaces. The molecule [(BocHN)Fc(CO)CSA]2 was electrodeposited onto Au microelectrodes through a SAu bond. Once immobilized, the Fc amino acid derivative was Boc deprotected allowing for the amino group to react with the target molecule. Detection of the target simulant was monitored by cyclic voltammetry (CV) while following the formal potential of the Fc molecule, which is influenced by its immediate electronic microenvironment. Reaction with either 1 mM diethyl cyanophosphonate (DECP) or 2 chloroethyl ethyl sulfide (2 CEES), both effectively simulants for the CWAs Tabun nerve agent and blistering sulfur mustard respectively, was not observed. However, detection of 1 mM acetyl chloride was achieved by observing a potential anodic shift from 217 ± 6 mV, for the Boc deprotected form, to 388 ± 7 mV for the reacted state of the molecule. The lack of reactivity with the Fc amino acid system was hypothesized as a kinetic issue.<p> In the second approach, the electrochemistry of gas generated naked Ag nanoparticles (NPs) deposited on indium tin oxide covered glass plates is compared to bulk polycrystalline Ag. The nano specific electrochemistry of Ag NPs has been identified and includes the preferential formation of â oxides. In 100 mM KOH supporting electrolyte, disruption of â oxide formation is exploited to test for the presence of 1 mM DECP resulting in the dissolution of Ag via cyanide complexes leading to a CV signal decrease. While in 8.0 M KOH, â oxide formation is enhanced leading to testing capabilities for 1 mM 2 CEES resulting in the disappearance of the â oxide peak and the appearance of surface oxide peak during CV. Analogous electrochemistry is not observed on polycrystalline bulk Ag.