Les protéines intrinsèquement désordonnées sont des hétéropolymères très flexibles, impliqués dans des activités cellulaires importantes (transduction du signal, reconnaissance moléculaire, traduction etc.), représentant des cibles potentielles de médicaments contre les maladies neurodégénératives et cancers, et dont les modes dynamiques définissent leur fonction biologique. Même si les états conformationnels qu'elles échantillonnent sont relativement bien connus, ce n'est pas le cas des échelles de temps de la dynamique associée. Dans ce travail nous étudions le comportement conformationnel du domaine C-terminal intrinsèquement désordonné de la nucléoprotéine de virus de Sendai (NTAIL), qui interagit avec le domaine PX de la phosphoprotéine. Des études précédentes montrent que le site d'interaction échantillonne un équilibre entre trois hélices discrètes dans l’état libre, et que l’interaction avec PX passe d’abord par la formation d'un pré-complexe, où l’une des conformation hélicoïdales de NTAIL est stabilisée, puis par sa diffusion sur la surface de PX, et enfin sa rétention sur le site de liaison. Cependant, aucun renseignement n'existe sur les échelles de temps de mouvements de la chaine de NTAIL, qui influencent certainement la cinétique de cette interaction, en particulier sa constante de vitesse d’association. Cette protéine de 124 acides aminés représente aussi un système modèle pertinent contenant à la fois de longs domaines dépliés et des régions de structure résiduelle. La mesure d’un vaste et cohérent ensemble de taux de relaxation à différents champs magnétiques et différentes températures nous a permis de caractériser la dynamique de NTAIL à un niveau de détail sans précèdent. A l’aide d’analyse « model-free » étendu, nous avons montré que les composants rapides de la fonction de corrélation nous informent sur les librations. Le mode dominant se situe à des échelles de temps autour d’une nanoseconde et est lié à l’échantillonnage de l’espace de Ramachandran par le squelette peptidique. Enfin, le composant lent (5-25 ns) nous informe sur les mouvements de segments de la chaine peptidique. La description des mouvements intrinsèques des protéines désordonnées et leurs échelles de temps contribuera à notre compréhension du comportement et des fonctions de ces protéines. / Intrinsically disordered proteins (IDPs) are highly flexible heteropolymers, implicated in important cellular activities (signal transduction, molecular recognition, transcription, translation, etc.) and representing potential drug targets against cancer and neurodegenerative diseases, whose dynamic modes define their biological function. Although the conformational states sampled by IDPs are relatively well understood, essentially nothing is known about the associated dynamic timescales. In this study we investigate the conformational behavior of the intrinsically disordered C-terminal domain of the nucleoprotein of Sendai virus (NTAIL), which interacts with the PX domain of the phosphoprotein. The interaction site has been shown to sample an equilibrium of discrete helices in the free state, which forms an encounter complex implicating the stabilization of one of the helical conformers upon interaction with PX, prior to diffusing on the surface of PX and engaging in the actual binding site. However, very little is known about the timescales of chain motions, which surely play a role in the interaction kinetics, in particular in terms of the on-rate of the interaction. This 124 amino acid protein also provides a good model system, containing long unfolded domains with chain-like dynamics and regions with residual structure. The measurement of extensive set of coherent relaxation rates at multiple magnetic fields, multiple temperatures and in three different length constructs of the same IDP has allowed us to characterize the dynamic nature of NTAIL in unprecedented detail. By analyzing the relaxation data using extended model-free approach, we show that fast (≤ 50 ps) components of the correlation function report on librational motions. A dominant mode occurs on timescales around one nanosecond, apparently reporting on backbone sampling within Ramachandran sub-states, while a slower component (5-25 ns) reports on segmental dynamics dominated by the chain-like nature of the protein. The ability to delineate intrinsic modes and timescales will improve our understanding of the behavior and function of IDPs.

The aim of this research project was to use 15N nuclear magnetic resonance (NMR) spectroscopy to better understand nitrogen (N) cycling processes in forest plantations. In particular, the studies were designed to link to the effects of forest management practices and environmental conditions. 15N NMR cross polarization/magic angle spinning (CPMAS) and dipolar dephasing (DD)-CPMAS experiments of some simple N-containing compounds found widely in nature were first undertaken. This was done in order to understand how different sample conditions, such as the presence of moisture, sample mixing and dilution, affected the intensity and the observability of the NMR peaks corresponding to N containing functional groups. Our results exhibited changes in NMR signal intensities and various time constants calculated. In the case of variable contact time experiments, use of an equation that predicts both a bi-exponential rise and decay was found to fit the data obtained more accurately. The optimised parameters for 15N NMR CPMAS were then used along with other analytical techniques such as ion chromatography, total C and N and elemental analyses to study plant nutrient uptake, plant decomposition and the effect of forest ecosystem disturbances, in this case an insect infestation. These analytical data were also correlated with the changes in the 13C NMR spectra in order to gain a more comprehensive understanding of the chemical transformations in the forest ecosystem. / Doctor of Philosophy (PhD)

<p><!-- /* Font Definitions */ @font-face {font-family:SimSun; panose-1:2 1 6 0 3 1 1 1 1 1; mso-font-alt:宋体; mso-font-charset:134; mso-generic-font-family:auto; mso-font-format:other; mso-font-pitch:variable; mso-font-signature:1 135135232 16 0 262144 0;} @font-face {font-family:"\@SimSun"; panose-1:0 0 0 0 0 0 0 0 0 0; mso-font-charset:134; mso-generic-font-family:auto; mso-font-format:other; mso-font-pitch:variable; mso-font-signature:1 135135232 16 0 262144 0;} /* Style Definitions */ p.MsoNormal, li.MsoNormal, div.MsoNormal {mso-style-parent:""; margin:0cm; margin-bottom:.0001pt; mso-pagination:widow-orphan; font-size:12.0pt; font-family:"Times New Roman"; mso-fareast-font-family:SimSun; mso-fareast-language:ZH-CN;} @page Section1 {size:612.0pt 792.0pt; margin:70.85pt 70.85pt 70.85pt 70.85pt; mso-header-margin:36.0pt; mso-footer-margin:36.0pt; mso-paper-source:0;} div.Section1 {page:Section1;} --><p>Magnetiskresonanstomografi, MRI, är en användbar teknik inom flera områden, i denna uppsats ligger fokus på användning inom medicin. Fysiken som ligger bakom MRI presenteras, som t ex uppdelning av energinivåer och kärnmagnetiskresonans. Uppbyggnad och tekniken som ligger bakom MRI har även studeras. Sedan har det gjorts jämförelse mellan MRI, röntgen och datortomografi.</p><p> </p><p>Utöver litteraturstudierna har simulering gjorts. I denna del har en modell för hjärnan byggts i programmet Comsol Multiphysics. I denna modell har studier av energiöverföringen, magnetiska fältet och elektriska fältet gjorts. Modellen har lösts både som stationärt problem och som tidsberoende. För energiöverföringen som redovisas som tidsmedelvärdet ser resultaten liknade ut för det stationära fallet som för de tidsberoende fallen, dock om man inte ser på tidsmedelvärdet utan energiöverföring under hela tiden så kan man dra slutsatsen att det stationära fallet är det mest kritiska.</p></p> / <p><!-- /* Font Definitions */ @font-face {font-family:SimSun; panose-1:2 1 6 0 3 1 1 1 1 1; mso-font-alt:宋体; mso-font-charset:134; mso-generic-font-family:auto; mso-font-format:other; mso-font-pitch:variable; mso-font-signature:1 135135232 16 0 262144 0;} @font-face {font-family:"\@SimSun"; panose-1:0 0 0 0 0 0 0 0 0 0; mso-font-charset:134; mso-generic-font-family:auto; mso-font-format:other; mso-font-pitch:variable; mso-font-signature:1 135135232 16 0 262144 0;} /* Style Definitions */ p.MsoNormal, li.MsoNormal, div.MsoNormal {mso-style-parent:""; margin:0cm; margin-bottom:.0001pt; mso-pagination:widow-orphan; font-size:12.0pt; font-family:"Times New Roman"; mso-fareast-font-family:SimSun; mso-fareast-language:ZH-CN;} @page Section1 {size:612.0pt 792.0pt; margin:70.85pt 70.85pt 70.85pt 70.85pt; mso-header-margin:36.0pt; mso-footer-margin:36.0pt; mso-paper-source:0;} div.Section1 {page:Section1;} --><p>Magnetic resonance imaging, MRI, is a useful technical method in many different areas; in this report lies focus on uses in medicine. MRI has been studied from a physical meaning, such as nuclear magnetic resonance, NMR, and spin splitting. A technical perspective of MRI has been studied, such as how MRI is built-up and technical details. MRI has been compared with Computed Tomography, CT, and X-rays.</p><p> </p>In addition to the theoretical studies, have simulations using the programme Comsol Multiphysics been done. One model has been built up to simulate MRI influences on the brain. The energy transfer, magnetic field and electric field have been studied. The model has been solved both as stationary and as time dependent problem. In the solution can a small difference be noticed which depend on that the results show the time average. If one studies the real solution, not the time average, can one conclusion rather quickly been drawn that the stationary solution have the highest transferred energy.</p>

No description available.

<!-- /* Font Definitions */ @font-face {font-family:SimSun; panose-1:2 1 6 0 3 1 1 1 1 1; mso-font-alt:宋体; mso-font-charset:134; mso-generic-font-family:auto; mso-font-format:other; mso-font-pitch:variable; mso-font-signature:1 135135232 16 0 262144 0;} @font-face {font-family:"\@SimSun"; panose-1:0 0 0 0 0 0 0 0 0 0; mso-font-charset:134; mso-generic-font-family:auto; mso-font-format:other; mso-font-pitch:variable; mso-font-signature:1 135135232 16 0 262144 0;} /* Style Definitions */ p.MsoNormal, li.MsoNormal, div.MsoNormal {mso-style-parent:""; margin:0cm; margin-bottom:.0001pt; mso-pagination:widow-orphan; font-size:12.0pt; font-family:"Times New Roman"; mso-fareast-font-family:SimSun; mso-fareast-language:ZH-CN;} @page Section1 {size:612.0pt 792.0pt; margin:70.85pt 70.85pt 70.85pt 70.85pt; mso-header-margin:36.0pt; mso-footer-margin:36.0pt; mso-paper-source:0;} div.Section1 {page:Section1;} -->Magnetiskresonanstomografi, MRI, är en användbar teknik inom flera områden, i denna uppsats ligger fokus på användning inom medicin. Fysiken som ligger bakom MRI presenteras, som t ex uppdelning av energinivåer och kärnmagnetiskresonans. Uppbyggnad och tekniken som ligger bakom MRI har även studeras. Sedan har det gjorts jämförelse mellan MRI, röntgen och datortomografi.   Utöver litteraturstudierna har simulering gjorts. I denna del har en modell för hjärnan byggts i programmet Comsol Multiphysics. I denna modell har studier av energiöverföringen, magnetiska fältet och elektriska fältet gjorts. Modellen har lösts både som stationärt problem och som tidsberoende. För energiöverföringen som redovisas som tidsmedelvärdet ser resultaten liknade ut för det stationära fallet som för de tidsberoende fallen, dock om man inte ser på tidsmedelvärdet utan energiöverföring under hela tiden så kan man dra slutsatsen att det stationära fallet är det mest kritiska. / <!-- /* Font Definitions */ @font-face {font-family:SimSun; panose-1:2 1 6 0 3 1 1 1 1 1; mso-font-alt:宋体; mso-font-charset:134; mso-generic-font-family:auto; mso-font-format:other; mso-font-pitch:variable; mso-font-signature:1 135135232 16 0 262144 0;} @font-face {font-family:"\@SimSun"; panose-1:0 0 0 0 0 0 0 0 0 0; mso-font-charset:134; mso-generic-font-family:auto; mso-font-format:other; mso-font-pitch:variable; mso-font-signature:1 135135232 16 0 262144 0;} /* Style Definitions */ p.MsoNormal, li.MsoNormal, div.MsoNormal {mso-style-parent:""; margin:0cm; margin-bottom:.0001pt; mso-pagination:widow-orphan; font-size:12.0pt; font-family:"Times New Roman"; mso-fareast-font-family:SimSun; mso-fareast-language:ZH-CN;} @page Section1 {size:612.0pt 792.0pt; margin:70.85pt 70.85pt 70.85pt 70.85pt; mso-header-margin:36.0pt; mso-footer-margin:36.0pt; mso-paper-source:0;} div.Section1 {page:Section1;} -->Magnetic resonance imaging, MRI, is a useful technical method in many different areas; in this report lies focus on uses in medicine. MRI has been studied from a physical meaning, such as nuclear magnetic resonance, NMR, and spin splitting. A technical perspective of MRI has been studied, such as how MRI is built-up and technical details. MRI has been compared with Computed Tomography, CT, and X-rays.   In addition to the theoretical studies, have simulations using the programme Comsol Multiphysics been done. One model has been built up to simulate MRI influences on the brain. The energy transfer, magnetic field and electric field have been studied. The model has been solved both as stationary and as time dependent problem. In the solution can a small difference be noticed which depend on that the results show the time average. If one studies the real solution, not the time average, can one conclusion rather quickly been drawn that the stationary solution have the highest transferred energy.

The extensive agricultural usage of organohalogenated pesticides has raised many concerns about their potential hazards especially in the soil environment. Environmental metabolomics is an emerging field that investigates the changes in the metabolic profile of native organisms in their environment due to the presence of an environmental stressor. Research presented here explores the potential of Nuclear Magnetic Resonance (NMR)-based metabolomics to examine the sub-lethal exposure of the earthworm, Eisenia fetida to sub-lethal concentrations of organohalogenated pesticides. Various one-dimensional (1-D) and two dimensional (2-D) NMR techniques were compared in a contact filter paper test earthworm metabolomic study using endosulfan, a prevalent pesticide in the environment. The results determined that both the 1H Presaturation Utilizing Gradients and Echos (PURGE) and the 1H-13C Heteronuclear Single Quantum Coherence (HSQC) NMR techniques were most effective in discriminating and identifying significant metabolites in earthworms due to contaminant exposure. These two NMR techniques were further explored in another metabolomic study using various sub-lethal concentrations of endosulfan and an organofluorine pesticide, trifluralin to E. fetida. Principal component analysis (PCA) tests showed increasing separation between the exposed and unexposed earthworms as the concentrations for both contaminants increased. A neurotoxic mode of action (MOA) for endosulfan and a non-polar narcotic MOA for trifluralin were delineated as many significant metabolites, arising from exposure, were identified. The earthworm tissue extract is commonly used as the biological medium for metabolomic studies. However, many overlapping resonances are apparent in an earthworm tissue extract NMR spectrum due to the abundance of metabolites present. To mitigate this spectral overlap, the earthworm’s coelomic fluid (CF) was tested as a complementary biological medium to the tissue extract in an endosulfan exposure metabolomic study to identify additional metabolites of stress. Compared to tests on the tissue extract, a plethora of different metabolites were identified in the earthworm CF using 1-D PURGE and 2-D HSQC NMR techniques. In addition to the neurotoxic MOA identified previously, an apoptotic MOA was also postulated due to endosulfan exposure. This thesis also explored the application of 1-D and 2-D NMR techniques in a soil metabolomic study to understand the exposure of E. fetida to sub-lethal concentrations of endosulfan and its main degradation product, endosulfan sulfate. The earthworm’s CF and tissue extract were both analyzed to maximize the significant metabolites identified due to contaminant exposure. The PCA results identified similar toxicity for both organochlorine contaminants as the same separation, between exposed to the unexposed earthworms, were detected at various concentrations. Both neurotoxic and apopotic MOAs were observed as identical fluctuations of significant metabolites were found. This research demonstrates the potential of NMR-based metabolomics as a powerful environmental monitoring tool to understand sub-lethal organohalogenated pesticide exposure in soil using earthworms as living probes.

This thesis is about excitation, detection, properties and applications of multiple quantum coherences applied to different dipolar coupled spin systems. Major focus of the work is on spectral simplification, measurement of residual dipolar couplings and discrimination of enantiomers in chiral aligning media. The first chapter gives a brief account on the fundamentals of nuclear magnetic resonance spectroscopy and multiple quantum coherences. This includes a description of product operator and polarization operator formalisms of pulses and evolution of magnetization. Subsequently a detailed account of two dimensional multiple quantum – single quantum (MQ-SQ) correlation experiments is given. Demonstration of the homonuclear MQ-SQ pulse sequence on a weakly coupled spin system and analysis of the spectrum obtained are also discussed. Homo-nuclear multiple quantum studies carried out to obtain relative the signs of the couplings have been reported in the initial part of the second chapter. The technique has been applied on doubly labeled acetonitrile (13CH313C15N) aligned in a liquid crystalline medium. Special situations like ambiguity in the determination of relative signs of the couplings from the appearance of two dimensional MQ-SQ spectra and the explanation for the same are also discussed. Homo-nuclear MQ experiments on indistinguishable spins, like protons in a methyl group of 13CH313C15N oriented in liquid crystal, and distinguishable spins, like the two carbons in the same molecule, have been carried out. Different directions of approach in which these results need to be analyzed have been discussed. Subsequent part of the chapter is about the correlation of connected MQ-SQ coherences. These experiments are significant in reducing the cross-peaks further from the MQ-SQ spectra. This concept is extended for the discrimination of optical enantiomers dissolved in chiral aligning medium made of poly-Γ-benzyl-L-glutamate (PBLG) and CDCl3. In molecules of Chemical and biological interest one encounters several nuclei such as, 1H, 13C, 15N and 19F. It will be of general interest to determine magnitudes and relative signs of the couplings among these coupled nuclei by NMR experiments. Utilization of hetero-nuclear MQ Experiments in solving such problems is discussed in the third Chapter. Hetero-nuclear MQ experiments were carried out on dipolar coupled 13CH313C15N, with the aim of obtaining the values and signs of various hetero-nuclear couplings in the molecule. The splitting of transitions in the spectra of oriented molecules is always influenced by the sum of dipolar and scalar couplings. Hence precise determination of dipolar couplings requires the knowledge of scalar couplings. To determine the J couplings, experiments were carried out on the same molecule in isotropic medium. When many coupled nuclei are involved one has to carry out several experiments to derive all the spectral parameters. In circumventing this problem heteronuclear multiple quantum experiments involving more than two nuclei as active spins are advantageous. This reduces the number of experiments and thereby reducing the total experimental time. Second part of this chapter demonstrates how a triple resonance triple quantum experiment can provide majority of the couplings from a given coupled system. The feasibility of the experiment is demonstrated even for molecules containing natural abundant isotopes. Application of multiple quantum j-resolved technique for chiral discrimination and obtaining complete one dimensional spectrum of each enantiomer from their racemic mixture is discussed in the fourth chapter. The two dimensional experiment consists of a selective double quantum excitation period followed by selective refocusing during indirect time domain, isotropic mixing and nonselective detection of SQ transitions. Hence this pulse sequence is named as DQSERF-COSY (Double Quantum Selective Refocused Correlation Spectroscopy). The experiment exploits the existence of different intra-methyl couplings between the enantiomers dissolved in chiral liquid crystal medium to separate the one dimensional spectra of each enantiomer in different cross sections. This is possible due to the fact that all the nuclei in any one of the enantiomers are coupled among themselves and there is no inter molecular interaction between the two enantiomers. Also one can extract all the couplings between protons in each enantiomer, which can subsequently be utilized for determination of the residual dipolar couplings, structure and orientation parameters.

<p>This dissertation focuses on a very special topic in the field of Nuclear Magnetic Resonance (NMR) in solution: Intermolecular Multiple Quantum Coherences, or iMQCs, which can only be created by intermolecular dipolar couplings. Since the very beginnings of NMR, it has been known that dipolar couplings dominate the solid-state linewidth for spin-1/2 nuclei, but the effects are still not fully understood. The angular dependency (1-3cos2&#952;ij) and distant dependency (rij-3) of dipolar coupling led to an oversimplified conclusion that it can be ignored in an isotropic liquid. Thus, it was surprising when COSY Revamped by Asymmetric Z-gradient Echo Detection (CRAZED) was first introduced in the early `90s and showed strong iMQC signals. Since then, CRAZED has inspired a wide range of applications for iMQCs and led to two different but equivalent mathematical frameworks to describes these effects, which we call the conventional DDF theory.</p><p>However, several disagreements between the conventional DDF theory and experiments have grasped our attention recently. This dissertation will: first, demonstrate how conventional picture fails by two examples, Multi-axis CRAZED (MAXCRAZED) and Gradient-embedded COSY Experiment (GRACE); second, provide a corrected DDF theory; and, third, discuss what impact this correction will bring.</p><p>Intermolecular double quantum coherences (iDQCs) are very sensitive to the local anisotropy (10&#956;m - 1mm) and can be used to create positive contrast highlighting superparamagnetic iron oxide nanoparticles (SPIONs). This dissertation will show the design and optimization of iDQC anisotropy by a series of phantom experiments. A set of numerical simulations will then be provided for a sub-voxel level explanation. We will also demonstrate how the newly corrected DDF theory can be quickly adapted to improve the iDQC anisotropy.</p><p>Finally, as a side product of this research, the mechanism of diacetyl hydration/dehydration as solved by NMR will be provided.</p> / Dissertation

Implanted tissue engineered substitutes constitute dynamic systems, with remodeling mediated by both the implanted cells and the host. Thus, there exists a significant need for methods to monitor the function and morphology of tissue engineered constructs. Noninvasive monitoring using 1H Nuclear Magnetic Resonance (NMR) spectroscopy and imaging can prove to be the solution to this problem. Spectroscopy allows for assessment of cellular function through the monitoring of inherent metabolic markers, such as total-choline, while high resolution imaging enables the evaluation of construct morphology and interfacial remodeling. We applied these 1H NMR methods to monitor betaTC3 mouse insulinoma cells within hydrogel-based materials as a model pancreatic tissue substitute. In vitro research established a strong correlation between total-choline, measured by 1H NMR spectroscopy, and viable betaTC3 cell number, measured by MTT. Extending these methods to in vivo monitoring, however, was met with additional challenges. First, the implanted cells needed to be contained within a planar construct above a threshold density to allow for adequate quantification of the total-choline peak. Secondly, cell-free buffer zones between the implanted cells and the host tissue needed to be incorporated to prevent host tissue signal contamination. Finally, quantitative techniques needed to be developed to accurately account for contaminating signal from diffusing molecules. To overcome these challenges, a disk-shaped agarose construct, initially containing a minimum of 4 million betaTC3 cells and coated with an outer layer of pure agarose, was fabricated. Mathematical simulations aided the implant design by characterizing diffusive transport of nutrients and metabolites into and out of the construct. In vivo 1H NMR studies of these constructs implanted in mice established a strong correlation between total-choline, measured noninvasively using 1H NMR spectroscopy, and viable cell number, measured invasively using MTT. This study establishes total-choline as a reliable marker for noninvasively quantifying dynamic changes in viable betaTC3 cell number in vivo. 1H NMR imaging was used to monitor the implants structural integrity over time, while also assessing the hosts fibrotic response. We expect these studies to establish quantitative criteria for the capabilities and limitations of NMR methodologies for monitoring encapsulated insulinomas, as well as other tissue implants.

No description available.