Thesis (Ph. D.)--University of Wisconsin--Madison, 1961. / Typescript. Vita. eContent provider-neutral record in process. Description based on print version record. Includes bibliographical references.

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The molecular interaction between plants and insects is dynamic and multifaceted. We are interested in understanding the molecular mechanism that insects utilize to overcome plant defense proteins, as well as discovering novel plant insecticidal proteins. Three projects were developed. First, we evaluated the effects of soybean cysteine protease inhibitor (soyacystatin N, scN) on the growth and development in southern corn rootworm. Both subtractive suppressed hybridization (SSH) and cDNA microarray analyses were used to uncover the changes of gene expression profiles in southern corn rootworm under the scN challenge. The counterdefense-related genes were identified, suggesting that southern corn rootworm deployed several regulatory mechanisms to overcome the dietary scN. Second, to identify and confirm insecticidal properties of vegetative storage protein 2 in Arabidopsis (AtVSP2), the gene was cloned and expressed in E.coli. This protein showed acid phosphatase activity. Feeding assay indicated that AtVSP increased the mortality and delayed the development of two coleopteran and one dipteran insects. Third, to identify the molecular mechanism of this novel insecticidal protein, P element mutagenesis was utilized to generate AtVSP resistant mutants (VRs). Two balanced VR mutants and their revertants were generated, and can be used to further characterize the genetic loci of P element inserted in the mutants.

<p>In the present work, molecular dynamics simulations were used to evaluate the molecular interactions in prepolymerization mixtures, as occurring during production of molecularly imprinted polymers. The systems simulated were produced based on earlier studies for reference of results. Four systems were simulated in order to investigate the effect on molecular interactions based upon the choice of porogen (acetonitrile or chloroform) and proton transfers. The systems consisted of phenylalanine anilide as template, methacrylic acid as functional monomer, ethylene glycol dimethacrylate as crosslinker and 2,2’-azobis-(2-methylpropionitrile) as radical initiator, with either acetonitrile or chloroform as porogen. Trajectories from the simulations were evaluated through radial distribution function analysis, grid density analysis and hydrogen bond analysis to investigate molecular interactions and complex formations in the simulated complete prepolymerization mixtures. Focus was on functional monomer-template, crosslinker-template and template-template complex formations. The results showed that the porogen influences molecular interactions in complete prepolymerization mixtures. Formation of higher order complexes was confirmed in all of the systems involving all of the investigated molecular species in the prepolymerization mixtures. The results could also confirm the presence of previously observed complexes between functional monomer and template (2:1 and 1:1 stoichiometry) and the prevalence of template dimerization, as well as a high involvement of crosslinker in complex formation.</p>

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Repellents play a key role in preventing mosquito-borne diseases such as malaria by reducing human-vector contact. The general mechanism of action relies on providing a repelling vapour around the applied area on the skin. Thus, the proper evaporation rate and consistency of the composition of the released vapour are factors determining the performance of repellent formulations. The formulation should evaporate fast enough to provide a sufficient level of repellence during its life time. However, if evaporation proceeds too fast, then it will be depleted rapidly so that activity is lost within a short period of time, which makes the repellent inefficient. Several controlled-release approaches have been developed to improve both the protection time and level. However, these techniques have inherent drawbacks from the industrial point of view. Moreover, these techniques mostly focus only on reducing the release rate, while the consistency of the vapour composition has not been addressed. In the present study, a novel approach towards controlling the evaporation behaviour of repellents is proposed. It is based on engineering the molecular interactions in order to design negative pseudo-azeotrope formulations. Negative pseudo-azeotrope mixtures are less volatile than the pure parent components and they do not undergo separation during evaporation. The feasibility of the idea was investigated by studying the molecular structure of generally available repellents. Among known molecular interactions, hydrogen bonding has the most likely impact on the formation of azeotropes and in particular pseudo-azeotropes. Thus, established repellents were classified based on their chemical structures and their capability to take part in hydrogen bonding. Next, a simple spectroscopic method for anticipating pseudoazeotropes formation was developed. Binary compositions of nonanoic acid and ethyl butylacetylaminopropionate (IR3535) showed a potential for forming pseudo-azeotrope mixtures. Hence R3535 and nonanoic acid were selected as model compounds to test the hypothesis. An experimental technique to confirm pseudo-azeotrope formation and to locate the composition of the probable pseudo-azeotrope point was required. To this end, an oven test was designed. The temporal mass loss, under an isothermal program, of a series of evaporating mixtures was measured. Simultaneously, the Fourier transform infrared (FTIR) spectra of the liquid remaining was recorded. Inverse analysis techniques were used to determine the composition of remaining liquid mixtures from the recorded FTIR spectra. The oven tests revealed that, as vaporisation progressed, the composition of the liquid remaining and the emitted vapour converged to a fixed IR3535 content of ca. 75 mol%. Mixtures close to this composition also featured the lowest volatility. Oven test also showed that the composition of the liquid mixtures diverged from the fixed IR3535 content of ca. 10 mol%. Mixtures close to this composition featured the highest volatility. These observations showed that IR3535 and nonanoic acid forms two pseudo-azeotrope compositions, i.e. a negative pseudo-azeotrope at an IR3535 content of ca. 75 mol%, and a positive pseudo-azeotrope at IR3535 content of ca. 10 mol%. Thermogravimetric analysis (TGA) and differential scanning calorimetry (DSC) were applied to check these results. TGA confirmed that the negative pseudo-azeotrope mixture is less volatile while the positive pseudo-azeotrope is more volatile than the parent compounds. The DSC results revealed that in comparison with the pure compounds, negative pseudo-azeotrope had a lower boiling point onset while the positive pseudo-azeotrope had a higher boiling point. Although negative pseudo-azeotrope repellent formulations have the desired lower constant release rate, their repellent activity needed to be tested. This is due to the fact that mixing the ingredients to formulate a negative pseudo-azeotrope results in interactions among the components. As a consequence, the inherent repellence effect of the compounds might have been impaired in the mixture. The modified arm-in-cage test was used to test the repellence of the controlled-release repellent formulation i.e. the negative pseudo-azeotrope of the IR3535 + nonanoic acid system. Results showed that the mixture featured improved performance with respect to both repellence efficacy and persistence. Moreover, the negative pseudo-azeotrope also exhibited a knock down effect, even resulting in mortality of most of the test mosquitoes. The presence of two pseudo-azeotrope points at different composition in the IR3535 + nonanoic acid system is a rare occurrence, analogous to double azeotropy. Thus, molecular simulation techniques were used to explore the nature of system and the interactions responsible for this unique behaviour. Gibbs-Monte Carlo simulation results suggest that variations in the sizes of the molecular clusters present in the liquid at various compositions might be responsible. They revealed that IR3535 and nonanoic acid in neat form are both highly structured liquids. The break-down in the structure of IR3535 at high concentrations of the acid may be the origin of increased evaporation rate and formation of the positive pseudo-azeotrope. On the other hand, negative pseudo-azeotrope may be resulted from formation of bulkier clusters at the ration of 3:1 (IR3535: nonanoic acid). / Thesis (PhD (Chemical Technology))--University of Pretoria, 2016. / English / PhD (Chemical Technology) / Unrestricted

Quantitative exploration of biological pathway networks must begin with a qualitative understanding of them. Often researchers aggregate and disseminate experimental data using regulatory diagrams with ad hoc notations leading to ambiguous interpretations of presented results. This thesis has two main aims. First, it develops software to allow researchers to aggregate pathway data diagrammatically using the Molecular Interaction Map (MIM) notation in order to gain a better qualitative understanding of biological systems. Secondly, it develops a quantitative biological model to study the effect of DNA damage on circadian rhythms. The second aim benefits from the first by making use of visual representations to identify potential system boundaries for the quantitative model. I focus first on software for the MIM notation - a notation to concisely visualize bioregulatory complexity and to reduce ambiguity for readers. The thesis provides a formalized MIM specification for software implementation along with a base layer of software components for the inclusion of the MIM notation in other software packages. It also provides an implementation of the specification as a user-friendly tool, PathVisio-MIM, for creating and editing MIM diagrams along with software to validate and overlay external data onto the diagrams. I focus secondly on the application of the MIM software to the quantitative exploration of the poorly understood role of SIRT1 and PARP1, two NAD+-dependent enzymes, in the regulation of circadian rhythms during DNA damage response. SIRT1 and PARP1 participate in the regulation of several key DNA damage-repair proteins and are the subjects of study as potential cancer therapeutic targets. In this part of the thesis, I present an ordinary differential equation (ODE) model that simulates the core circadian clock and the involvement of SIRT1 in both the positive and negative arms of circadian regulation. I then use this model is then used to predict a potential role for the competition for NAD+ supplies by SIRT1 and PARP1 leading to the observed behavior of primarily phase advancement of circadian oscillations during DNA damage response. The model further predicts a potential mechanism by which multiple forms of post-transcriptional modification may cooperate to produce a primarily phase advancement.

In this dissertation, I used Fourier transform ion cyclotron resonance mass spectrometry (FTICR) and ion mobility spectrometry (IMS) to study the structure and energetics of supramolecular complex ions in the gas phase. Using the CRAFTI (cross sectional areas by Fourier transform ion cyclotron resonance) technique developed by Dearden’s lab we observed that complexes with alkali cations capping the portals of cucurbit[5]uril (CB[5]) bind halide anions size-selectively in the gas phase. Our data suggest that Cl– binds inside the CB[5] cavity, Br– binds both inside (with Na+ions capping the portals of CB[5]) and outside (when K+caps CB[5]), and I– binds weakly outside. Although geometry optimization at the M06-2X/6-31+G* level of ab initio theory suggests internal anion binding is energetically favored over external binding, we believe the externally-bound complexes observed experimentally must be due to large energetic barriers hindering the passing of large anions through the CB[5] portal, preventing access to the interior. Calculation of the barriers to anion egress using MMFF//M06-2X/6-31+G* theory supports this idea. Collision cross section (CCS) measurements using the CRAFTI method for CB[5] complexes with various alkali metals and different neutral guests (methanol, ethanol, formic acid, and acetonitrile) along with the results of mass spectra from FTICR show that both the sizes and the resulting charge densities of the alkali metal ions affect the relative tendency of the guests to bind inside CB[5]. The CCS values suggest that methanol, formic acid, and acetonitrile are internally bound CB[5] while ethanol is bound outside the CB[5] host. The relative abundances of the paired peaks in the obtained mass spectra indicate that the inclusion of formic acid and methanol are enhanced when K+ ions cap the complexes, whereas the inclusion of acetonitrile is enhanced when Cs+ ions cap the complexes. The relative abundance of ethanol complexes increases when Na+ ions cap the complexes. CRAFTI CCS values for singly- and doubly-charged cucurbit[n]uril (n = 5, 6, and 7), decamethylcucurbit[5]uril (mc5), and cyclohexanocucurbit[5]uril (CB*[5]) complexes of alkali metal cations (Li+-Cs+) show +2 complex ions have CCS values ranging between 94-105% of those of their +1 counterparts (increasing with metal ion size). These results are consistent with CCS values were calculated using the projection approximation (PA). Ion mobility measurements of the same complexes find the CCS of +2 complexes to be in all cases 9-12% larger than those of the corresponding +1 complexes, with little metal ion dependence. Trajectory method (TM) calculations of CCS for the same structures consistently yield values 7-10% larger for the +2 complexes than for the corresponding +1 complexes and little metal ion dependence which agrees with experimental values.

Water and ion transport critically determine the performance of many functional materials and devices, from fuel cells to lithium ion batteries to soft mechanical actuators. This dissertation aims to address some fundamental issues regarding transport and anisotropy, structural heterogeneity and molecular interactions inside ionic polymers. I first discuss a main deficiency of a standard protocol for calibrating high pulsed-field-gradient NMR. I show that high gradient calibration using low γ nuclei is not amenable to measurements on slow diffusing high γ nuclei. Then I employ NMR diffusometry to investigate transport and anisotropy for a series of ionic polymers, from poly(arylene ether sulfone) hydrophilic-hydrophobic multi-block copolymers to polymer blends to perfluorosulfonate random copolymers. For the multi-block copolymers, NMR diffusion measurements yield diffusion anisotropy as a function of water uptake and block lengths. ²H NMR spectroscopy on absorbed D₂O probes membrane alignment modes. These measurements also provide insights into average defect distributions. For the blend membranes, we examine the impact of compatibilizer on their transport properties. An increase in compatibilizer significantly improves the membrane phase homogeneity confirmed by SEM and transport studies. Theories of diffusion in porous media yield changes in domain size and tortuosity that correspond to drastic changes in local restrictions to water diffusion among different blend membranes. NMR relaxometry studies yield multi-component T₁ values, which further probe structural heterogeneities on smaller scales than diffusion experiments. For the random copolymer, the exploration of ion transport reveals inter-ionic associations of ionic liquids (ILs) modulated by hydration level and ionic medium. When ILs diffuse inside ionic polymers, isolated anions diffuse faster (≥ 4X) than cations at high hydration whereas ion associations result in substantially faster cation diffusion (≤ 3X) at low hydration inside membranes, revealing prevalent anionic aggregates. Finally, I present the strategy and analytical protocol for studying ionomer membranes using ILs. The normal cation diffusion contrasts to the anomalous anion diffusion caused by local confinement structures inside the membranes, which vary drastically with temperature and hydration level. These structures correspond to a density variation of SO₃⁻ groups, which define a distribution of local electrical potentials that fluctuate with temperature and nature of ionic media. / Ph. D.

L'autophagie est un mécanisme de dégradation lysosomale qui joue un rôle important dans l'immunité innée et adaptative. La relation entre le Virus de l'Immunodéficience Humaine de type 1 (VIH-1) et l'autophagie est complexe. En effet, l'équipe a montré que l'enveloppe virale du VIH-1 (Env), exprimée à la surface des cellules infectées, induit une autophagie massive dans les cellules T CD4 bystanders non infectées. Au contraire, lorsque ces cellules s'infectent de façon productive, l'autophagie est inhibée, suggérant qu'une ou plusieurs protéines virales soient capables de bloquer ce processus. L'objectif de ce travail de thèse a été de rechercher ces protéines virales et leur mécanisme d'action. Un crible double hybride en levure a permis de mettre en évidence que plusieurs protéines du VIH-1 sont capables d'interagir avec des protéines autophagiques (Atg), et plus spécifiquement que la protéine virale Vif (Virion infectivity factor) interagit directement avec la protéine LC3, protéine essentielle au processus autophagique. Cette interaction a été confirmée en système in vitro et in vivo (GST pull-down et immunoprécipitation). Plusieurs mutants des protéines Vif et LC3 ont été réalisés pour déterminer les domaines de liaison. La partie C-terminale de Vif ainsi que la glycine C-terminale de LC3, responsable de la conjugaison au phosphatidylethanolamine (PE), semblent être les domaines impliqués dans cette interaction. Une des principales fonctions de Vif connues est de dégrader, via le protéasome, les facteurs cellulaires APOBEC (Apolipoprotein B mRNA-editing, enzyme-catalytic, polypeptide-like) et en particulier la protéine APOBEC3G (A3G). Les résultats montrent que Vif est impliquée dans le blocage de l'autophagie induite par l'enveloppe indépendamment de son action sur A3G. / Autophagy is a lysosomal degradation pathway involved in the innate and adaptative immunity. The relationship between the Human Immunodeficiency Virus type 1 (HIV-1) and autophagy is complex. The team has demonstrated that autophagy is induced in uninfected CD4 T cells after contact with infected cells expressing HIV-1 envelope glycoproteins (Env), leading to apoptosis. In contrast, when these cells are productively infected, autophagy is repressed, suggesting that one or several viral proteins are able to block this process. The aim of the thesis was to search these viral proteins and to determine their mechanism of action. A two-hybrid screen has revealed that several HIV-1 viral proteins are able to interact with autophagic proteins (Atg). In particular, Vif (Virion infectivity factor) interacts directly with LC3, a protein involved in the formation of autophagosomes. This interaction has been confirmed in vitro and in vivo (GST pull-down and immunoprecipitation). Several mutants of Vif and LC3 have been done to analyze the binding domains. The C-terminal part of Vif and the C-terminal glycine of LC3, responsible for the conjugation to PE, seem to be involved in the interaction between Vif and LC3.Vif plays an important role during HIV-1 infection. One of its main functions is to degrade, by the ubiquitin-proteasome system, the antiviral factors called APOBECs (Apolipoprotein B mRNA-editing, enzyme-catalytic, polypeptide-like) and in particular APOBEC3G (A3G). Our results demonstrate that Vif is involved in the blockade of Env-mediated autophagy independently of its role on A3G.