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  • About
  • The Global ETD Search service is a free service for researchers to find electronic theses and dissertations. This service is provided by the Networked Digital Library of Theses and Dissertations.
    Our metadata is collected from universities around the world. If you manage a university/consortium/country archive and want to be added, details can be found on the NDLTD website.
911

LC - ¹³C NMR utilizing dynamic nuclear polarization (DNP) for signal enhancement

Stevenson, Steven A. 19 September 2009 (has links)
The primary difficulty for successful LC - ¹³C NMR (whether ¹H or ¹³C) is overcoming the relatively low sensitivity of NHR as a chromatographic detector. For the ¹H nuclide this is much less of a problem; the sensitivity ;s approximately 6000 times more sensitive than that of ¹³C nuclei. For this reason, much of the literature focuses on LC - ¹H NMR. To ever successfully realize LC - ¹³C NMR, it is mandatory that an augmentation of ¹³C signal intensity must be effectuated to overcome this sensitivity deficit (~ three orders of magnitude). To satisfy this requirement, our laboratory has utilized dynamic nuclear polarization (DNP) to ameliorate these otherwise weak or non-existent signals. For favorable molecules, sensitivity recoveries of up to two orders of magnitude have been developed. This improvement (relative to 'H) narrows the sensitivity gap between 'H and ¹³C NMR detection of chromatographically separated analytes. Despite the fact that relatively large injection volumes were required in most LC experiments, the wealth of structural information inherent to ¹³C NMR justifies any attempt to successfully couple nuclear magnetic resonance to liquid chromatography. In addition, DNP was utilized in a series of SLIT and LLIT experiments where a test mixture was recycled through a NMR spectrometer. Results indicate that ¹³C spectra were obtained with a significantly higher signal-to-noise ratio in a shorter amount of analysis time relative to experiments where DNP was not employed for signal enhancement. / Master of Science
912

Solid State Nuclear Magnetic Resonance Probing of Structures of the Rous Sarcoma Virus Capsid, Amyloid Beta, and Reflectin Proteins

Thames, Tyrone 01 January 2023 (has links) (PDF)
Solid State Nuclear Magnetic Resonance (ssNMR) spectroscopy can be a powerful tool for investigating the atomic-level structures and dynamics of biological macromolecules, including proteins. In this dissertation, I present an ssNMR study of three diverse proteins, revealing insights into their respective secondary structures, conformational variations, and intermolecular interactions. Additionally, I introduce novel computational methods to facilitate the assignment of chemical shifts of ssNMR spectra. The first of the proteins is the capsid protein of the Rous Sarcoma Virus. In previous research, the structure of the hexameric lattice of the in-vitro tubular assembly of the capsid protein was determined. In this study, chemical shift assignments were completed and the structure of the T=1 capsid assembly (comprising entirely of a pentameric lattice) of the I190V mutant variant of the capsid was determined, providing the missing component of the in-vivo capsid structure. The second protein studied was amyloid-beta 42, a particularly cytotoxic variant of the main component of amyloid plaques in the brains of Alzheimer's disease patients. Chemical shift assignments were made on ssNMR data from samples aggregated in cholesterol-containing phosphatidylcholine (POPC) lipid vesicles, and secondary structure and molecular distance information was obtained. Lastly, preliminary chemical shift assignments, statistics, and structural analysis was done on the polypeptide Ref-2Cx4, derived from the conserved domain of the Hawaiian bobtail squid reflectin protein. The reflectin protein, used in the squid's camouflage mechanism, possesses optically reflective and proton-conductive properties. The final part of the dissertation addresses a major bottleneck in ssNMR studies—the assignment of chemical shifts. I introduce Visual Assist, a suite of computational tools designed to streamline and expedite the assignment process. The developed computational methods are validated on the diverse set of proteins above, demonstrating their general applicability and efficiency.
913

Sol–gel synthesis and characterization of lithium aluminate (L–A–H) and lithium aluminosilicate (L–A–S–H) gels

Simon, Sebastian, Bertmer, Marko, Gluth, Gregor J. G. 25 June 2024 (has links)
Hydrous lithium aluminosilicate (L–A–S–H) and lithium aluminate (L–A–H) gels are candidate precursors for glass-ceramics and ceramics with potential advantages over conventional processing routes. However, their structure before calcination remained largely unknown, despite the importance of precursor structure on the properties of the resulting materials. In the present study, it is demonstrated that L–A–S–H and L–A–H gels with Li/Al ≤ 1 can be produced via an organic steric entrapment route, while higher Li/Al ratios lead to crystallization of gibbsite or nordstrandite. The composition and the structure of the gels was studied by thermogravimetric analysis, X-ray diffraction, 27Al and 29Si magic-angle spinning nuclear magnetic resonance, and Raman spectroscopy. Aluminium was found to be almost exclusively in six-fold coordination in both the L–A–H and the L–A–S–H gels. Silicon in the L–A–S–H gels was mainly in Q4 sites and to a lesser extent in Q3 sites (four-fold coordination with no Si–O–Al bonds). The results thus indicate that silica-rich and aluminium-rich domains formed in these gels.
914

Dynamic nuclear polarisation of diamond

High, Grant Lysle 08 1900 (has links)
This study is presented in nine chapters as follows: Chapter one reviews the reported literature on the NMR of natural diamond. The NMR signal of diamond consists on a single line at 39 ppm from TMS and two hyperfine lines due to 13C interactions. The reported relaxation times, measured in natural diamond, synthetic diamonds and 13C enriched diamonds, are discussed. The second chapter introduces the apparatus used, which included a Bruker Avance NMR spectrometer, a Bruker ESP380E pulsed EPR spectrometer and a high powersband DNP system. The availability of this excellently equiped laboratory presented a unique opportunity to perform this investigation. Chapter three outlines the experimental techniques used as well as the manner in which the acquired data was processed. The fourth chapter presents an overview of the most common defects found in diamond. Proposed models of these defects are presented and the resulting EPR spectra displayed. The methods developed to determine the paramagnetic impurity concentration from the EPR line width and the spin-spin relaxation times are presented in the fifth chapter. The line width gives the total paramagnetic impurity concentration to about 10 ppm. The spin-spin relaxation time allows the determination of Pl and P2 paramagnetic impurity concentrations individually, to much lower levels from measurements on the central and hyperfine lines. This information was used in the explanation of the relaxation behaviour for the various diamonds investigated. The temperature dependence of the paramagnetic electron relaxation times is reported in the sixth chapter. The results obtained are consistent with the findings in prior work that Pl impurities are typical Jahn Teller centres. Two diamonds, however, display trends that depart from this theory. These diamonds contain N3 defect centres, which appear to be responsible for this behaviour. It was found in these experiments that, bar thermal expansion effects, the spin-spin relaxation time is essentially independent of temperature. The seventh chapter deals with the solid state and thermal mixing effects. The relevant theory, results obtained and a discussion of these results, are presented. The effect of impurity concentration, defect types, microwave power, the exposure time and the offset from resonance on the polarisation rates and the 13C polarisation are investigated in depth. Finally the effect of applying the DNP treatment on the central and hyperfine lines is discussed. The pulsed DNP process is presented in the eighth chapter. The relevant theory, the effects of matching of the Hartmann-Hahn condition, impurity concentrations and types, on the polarisation rate and signal enhancement of JJC nuclei is given. A comparison to the continuous wave techniques is then made. The ninth chapter summarises the achievements and recommendations for further work. / Physics / D. Phil. (Physics)
915

Adaptation of Proof of Concepts Into Quantitative NMR Methods : Clinical Application for the Characterization of Alterations Observed in the Skeletal Muscle Tissue in Neuromuscular Disorders

Caldas de Almeida Araujo, Ericky 06 May 2014 (has links) (PDF)
Current quantitative nuclear magnetic resonance (NMR) technics offer biomarkers that allow performing non-invasive longitudinal studies for the follow up of therapeutic trials in neuromuscular disorders (NMD). In contrast to fat degeneration, the mechanisms of inflammation/oedema/necrosis and fibrosis are characteristic signs of disease activity, which makes their quantification a promising source of crucial biomarkers for longitudinal studies. This thesis work consisted on the implementation of more precise quantitative NMR methods adapted to the clinical study of skeletal muscle (SKM) for : (i) detection and quantification of sites of disease activity by T2-mapping of muscle water ; (ii) investigation of the different pathophysiological mechanisms underlying T2 alterations ; and (iii) Detection and quantification of muscle fibrosis. We implemented two methods for T2 mapping of muscle water. The first one is based on a multi-spin-echo sequence du type CPMG. In this method the 1H-NMR signals from water and lipids are acquired simultaneously. The acquired data are fitted to a tri-exponential model, in which water and fat signals are separated by exploring the T2 difference between water and fat. This method allows extraction of muscle water T2-value in the presence of fat infiltration. The second method is based on a " partially spoiled steady state free precession " (pSSFP) sequence. In contrast to the first method, which demands a sophisticated post-treatment of images acquired at 17 different echo-times, with the pSSFP a T2-mapping is extracted from two 3D data sets. 3D acquisition is compatible with spectrally selective water excitation, which eliminates signal contribution from lipids. Both methods were validated experimentally on patients and healthy subjects. The results demonstrated their capacity to detect and quantify disease activity sites. This 2 works have been published in two international journals : Azzabou, de Sousa, Araujo, & Carlier, 2014. Journal of Magnetic Resonance Imaging. DOI 10.1002/jmri.24613 (in press); et de Sousa, Vignaud, Araujo, & Carlier . 2012. Magnetic Resonance in Medicine. 67:1379-1390. Although it was shown to reveal disease activity, mono-exponential T2 of muscle water is non-specific to what concerns the mechanisms underlying its alterations. It has been long known that T2 relaxation in SKM tissue is multi-exponential. This is currently accepted to reveal anatomical compartmentation of myowater. We implemented a method for localized spectroscopic CPMG acquisition. CPMG data respect echo-time sampling and signal to noise ration limits for allowing robust multiexponential analysis. This work allowed us to establish a compartmentation model that perfectly explains the multi-exponential T2 relaxation observed in SKM tissue. This work was published in the " Biophysical Journal " (Araujo, Fromes & Carlier 2014. New Insights on skeletal muscle tissue compartments revealed by T2 NMR relaxometry. (In press)). Pilot studies performed in patients show promising results and suggest potential application of the method in clinical studies. Fibrosis starts with an excessive accumulation of intramuscular connective tissue (IMCT). We have explored the " Ultrashort time to echo " (UTE) method with the aim to detect and characterize the signal from IMCT. In a first study we characterized in vivo a short T2 component (~500 µs) in SKM, and we collected evidences suggesting that this component might reflect IMCT. Then we implemented a methodology that allowed imaging this short component in SKM tissue for the first time.
916

Dynamic nuclear polarisation of diamond

High, Grant Lysle 08 1900 (has links)
This study is presented in nine chapters as follows: Chapter one reviews the reported literature on the NMR of natural diamond. The NMR signal of diamond consists on a single line at 39 ppm from TMS and two hyperfine lines due to 13C interactions. The reported relaxation times, measured in natural diamond, synthetic diamonds and 13C enriched diamonds, are discussed. The second chapter introduces the apparatus used, which included a Bruker Avance NMR spectrometer, a Bruker ESP380E pulsed EPR spectrometer and a high powersband DNP system. The availability of this excellently equiped laboratory presented a unique opportunity to perform this investigation. Chapter three outlines the experimental techniques used as well as the manner in which the acquired data was processed. The fourth chapter presents an overview of the most common defects found in diamond. Proposed models of these defects are presented and the resulting EPR spectra displayed. The methods developed to determine the paramagnetic impurity concentration from the EPR line width and the spin-spin relaxation times are presented in the fifth chapter. The line width gives the total paramagnetic impurity concentration to about 10 ppm. The spin-spin relaxation time allows the determination of Pl and P2 paramagnetic impurity concentrations individually, to much lower levels from measurements on the central and hyperfine lines. This information was used in the explanation of the relaxation behaviour for the various diamonds investigated. The temperature dependence of the paramagnetic electron relaxation times is reported in the sixth chapter. The results obtained are consistent with the findings in prior work that Pl impurities are typical Jahn Teller centres. Two diamonds, however, display trends that depart from this theory. These diamonds contain N3 defect centres, which appear to be responsible for this behaviour. It was found in these experiments that, bar thermal expansion effects, the spin-spin relaxation time is essentially independent of temperature. The seventh chapter deals with the solid state and thermal mixing effects. The relevant theory, results obtained and a discussion of these results, are presented. The effect of impurity concentration, defect types, microwave power, the exposure time and the offset from resonance on the polarisation rates and the 13C polarisation are investigated in depth. Finally the effect of applying the DNP treatment on the central and hyperfine lines is discussed. The pulsed DNP process is presented in the eighth chapter. The relevant theory, the effects of matching of the Hartmann-Hahn condition, impurity concentrations and types, on the polarisation rate and signal enhancement of JJC nuclei is given. A comparison to the continuous wave techniques is then made. The ninth chapter summarises the achievements and recommendations for further work. / Physics / D. Phil. (Physics)
917

Investigating sensitivity improvement methods for quadrupolar nuclei in solid-state nuclear magnetic resonance

Colaux, Henri January 2016 (has links)
The study of quadrupolar nuclei using NMR spectroscopy in the solid state significantly increased in popularity from the end of the 20th century, with the introduction of specific methods to acquire spectra free from the effects of the quadrupolar interaction, that results in broadened lineshapes that cannot be completely removed by spinning the sample at the magic angle (MAS), unlike most of the other interactions present in the solid state. The first technique which allows, without any specific hardware, the removal of this broadening has been the Multiple-Quantum MQMAS experiment. The method quickly gained a popularity within the NMR community, with numerous successful applications published. However, the multiple-quantum filtration step in this experiment relies on severely limits sensitivity, restricting application to the most sensitive nuclei. Extending the applicability of MQMAS to less receptive nuclei requires the use of signal improvement techniques. There are multiple examples of such approaches in the literature, but most of these require additional optimisation that may be time-consuming, or simply impossible, on less receptive nuclei. This work introduces a novel signal improvement technique for MQMAS, called FAM-N. Its optimisation is solely based on density matrix simulations using SIMPSON, implying no additional experimental optimisation is required, while improving the signal in MQMAS spectra by equivalent or higher amounts than other common methods. In order to prove the applicability of this method on virtually any system, FAM-N has been investigated by simulation, and tested experimentally using a number of model samples, as well as samples known to be challenging to study by NMR. This work also explores other aspects of NMR spectroscopy on quadrupolar nuclei. Adiabatic inversion of the satellite populations can be performed to improve the central transition signal in static or MAS spectra. A range of methods has been tested and compared, with particular attention given to hyperbolic secant-shaped pulses, for which its performance have been described. Finally, cross-polarisation from a spin I = 1/2 nucleus to a quadrupolar nucleus has been investigated. After reviewing the theory for the static case, simulations have been performed under MAS in order to identify the conditions for efficient magnetisation transfer, with applications in spectral editing or for the combination with MQMAS.
918

Pushing the Limits of NMR Sensitivity and Chiral Analysis : Design of New NMR Methods and Bio-Molecular Tools

Lokesh, N January 2015 (has links) (PDF)
The thesis entitled "Pushing the Limits of NMR Sensitivity and Chiral Analysis: Design of New NMR Methods and Bio-molecular Tools" consists of six chapters. The research work reported in this thesis is focused on the development of novel chemical and NMR methodological approaches for enantiomeric analysis and mea- surement of residual dipolar couplings (RDCs), and the development of sensitivity enhanced slice selective NMR experiments for obtaining pure shift 1H spectra and the measurement of scalar couplings. The thesis is divided into two parts. The Part I comprises chapters 2-4, where the enantiomeric analysis is discussed, which includes newly developed chiral reagents, two new weak chiral aligning media and design of novel NMR techniques. Part II comprises chapters 5 and 6, which discusses new sensitivity enhanced slice selective NMR techniques. Chapter 1 gives a general introduction to NMR and the problems investigated in the remaining chapters of the thesis. The chapter starts with a brief discussion on the introduction, advancements and general applications of NMR, discussion is also given on the NMR approaches for enantiomeric analysis both in isotropic and anisotropic phases and the measurement of RDCs, including the benefits and limitations associated with each approach. The chapter sets the tone by discussing limitations of the existed NMR enantiomeric approaches and slice-selective techniques, and builds the bridge for the rest of the chapters by addressing these limitations. The chapter also introduces slice selective experiments, their benefits over other conventional methods and limitations. Additional introductory notes are also given on some related concepts. Part I : NMR Chiral analysis and RDCs measurements Chapter 2 discusses chiral sensing properties of RNA nucleosides and their utility as chiral derivatizing agents for the enantio-discrimination of 1o-amines using one dimensional 1H NMR. A three component protocol has been proposed for the complexation of nucleosides with amines, which is rapid, economical and provides maximum diastereomeric conversion. The chiral differentiating ability of nucleosides are examined for different amines based on the 1H NMR chemical shift differences between the diastereomers (∆δ R, S ). Enantiomeric differentiation has been observed at multiple chemically distinct proton sites. It is observed that adenosine and guanosine exhibit large chiral differentiation (∆δ R, S ) due to the presence of a purine ring. The comparison of the diastereomeric excess (de) measured by NMR with those of the gravimetrically prepared ratios are in excellent agreement with each other confirming the robustness of these RNA nucleosides in discriminating primary amines. Chapter 3 establishes the smooth connectivity with the chapter 2 by discussing the limitations of the enantiomeric discrimination using NMR in isotropic solutions. This chapter discusses two new water compatible aligning media that were developed based on self-assembling strategy of small bio-molecules. The self-assembled folic acid, and the binary mixture of 50-GMP and guanosine are introduced as two novel weak aligning media. The properties of these low ordered media have been systematically studied for their easy preparation, physical parameter dependent tunability of their degree of alignment, mesosphere sustainability over a broad range of temperature and the concentration of the ingredients, and the phase reproducibility. The applications of both these new media are demonstrated for chiral and pro-chiral discrimination and also for the measurement of RDCs. Both these liquid crystalline media could be tuned to very low degree of alignment (order parameter of the order of 10−4), which provides simple first order spectra of molecules aligned in them, the analysis provide order dependent NMR spectral parameters. The 50-GMP:guanosine orienting medium can be prepared in less than 1 hour, and has been demonstrated to be an ideal medium for the determination of RDCs that are used as restraints in the structure calculations of small molecules. Chapter 4 describes 1H NMR spectral complexity in isotropic and anisotropic phases and its consequences on enantiomeric analysis. In circumventing such problems, new NMR techniques have been developed and the spin dynamics involved in the designed sequences are discussed. The newly developed 2D 1H NMR experimental method termed as RES-TOCSY, and its applicability for resolving R and S enantiomeric or diastereomeric peaks of all the coupled proton spins in isotropic phase is discussed. The utility of the developed method is demonstrated in diverse situations, such as, for suppressing impurities peaks, resolving the severely overlapped peaks and unraveling the peaks masked due to severe line broadening when metal complexes are used as chiral auxiliaries. The advantages and limitations of the method over other methods available in the literature are discussed and the significant advantage of the present method is illustrated by spectral comparison with J-resolved experiment. The appli- cation of the method for the accurate measurement of enantiomeric excess has also been demonstrated. The chapter also introduces another NMR experimental technique developed for resolving enantiomeric peaks and complete unraveling of R and S spectra in anisotropic phase. The developed 2D NMR method is cited in the literature as CH-RES-TOCSY. In addition to spectroscopic visualization of R and S spectra, the method also yields C-H RDCs. The applicability of the new experiment has been demonstrated on a chosen example. The wide utility of the method has also been demonstrated for the assignment of symmetric cis- and trans- isomers. Part II : Sensitivity Enhancement of Slice selective NMR Experiments Chapter 5 describes applications of slice selective NMR experiments over conven tional NMR methods and their limitations as far as the sensitivity of signal detection is concerned, especially in low concentrated samples. The chapter introduces the implementation of Acceleration by Sharing Adjacent Polarization (ASAP) technique in slice selective experiments. It is convincingly demonstrated that ASAP helps in reducing inter scan relaxation delay and consequently permits acquisition of more number of scans in a given time, resulting in the gain in signal enhancement by a factor of two. The pulse sequences have been suitably designed for obtaining the pure shift 1H spectra and in G-SERF experiment for the measurement of 1H-1H couplings, both with significantly enhanced signal intensities. Chapter 6 describes new sensitivity enhanced slice selective NMR methods for mea- surement of scalar couplings. A new experiment has been developed which is named as Quick G-SERF (QG-SERF). It is a 1D NMR slice selective method developed based on real time spin manipulation technique. The method gives multiple scalar couplings of a selected spin with simplified multiplets, which is analogous to the 2D G-SERF but with considerable saving in instrument time by 1-2 orders of magnitude. The rapidness of the experiment arises due to reduced dimensionality. The spin dynamics involved in the pulse sequence and its working principle have been described. The application of the method is illustrated for the measurement of 1H-1H couplings. The sequence has been further improved to obtain the heteronuclear couplings between two abundant spins in an orchestrated manner and has been demonstrated for measurement of 1H-19F couplings. This sequence cited as HF-QG-SERF has been implemented on the molecules containing number of chemically non-equivalent fluorine atoms.
919

Development Of NMR Methods For Metabolomics And Protein Resonance Assignments

Dubey, Abhinav 15 May 2016 (has links) (PDF)
Nuclear Magnetic Resonance (NMR) spectroscopy is a quantitative, non-invasive and non-destructive technique useful in biological studies. By manipulating the magnetization of nuclei with non-zero spin, NMR gives insights into atomic level details. Application of NMR as a tool for discovering structure, understanding dynamics of bio-molecules such as proteins, metabolites, DNA, RNA and their interactions constitutes the field of bio-molecular NMR. In this thesis, new methods for rapid data analysis of NMR spectrum of proteins and metabolites are proposed. The first computational method, PROMEB (Pattern Recognition Based Assignment in Metabolomics) is useful for the identification and assignments of metabolites. This is an important step in metabolomics and is necessary for the discovery of new biomarkers. In NMR spectroscopy based studies, the conventional approach involves a database search, wherein chemical shifts are assigned to specific metabolites by use of a tolerance limit. This is inefficient because deviation in chemical shifts associated with pH or temperature variations, as well as missing peaks, impairs a robust comparison with the database. These drawbacks are overcome in PROMEB, which is a method based on matching the pattern of peaks of a metabolite in 2D [13C, 1H] HSQC NMR spectrum, rather than conventionally used absolute tolerance thresholds. A high success rate is obtained even in the presence of large chemical shift deviations such as 0.5 ppm in 1H and 3 ppm in 13C and missing peaks (up to 50%), compared to nearly no assignments obtained under these conditions with existing methods that employ a direct database search approach. The pattern recognition approach thus helps in identification and assignment of metabolites in-dependent of the pH, temperature, and ionic strength used, thereby obviating the need for spectral calibration with internal or external standards. Another computational method, ChemSMP(Chemical Shifts to Metabolic Path-ways), is described which facilitates the identification of metabolic pathways from a single two dimensional (2D) NMR spectrum. Typically in other approaches, this is done after relevant metabolites are identified to allow their mapping onto specific metabolic pathways. This task is daunting due to the complex nature of cellular processes and the difficulty in establishing the identity of individual metabolites. ChemSMP uses a novel indexing and scoring system comprised of a uniqueness score and a coverage score. Benchmarks show that ChemSMP has a positive prediction rate of > 90% in the presence of decluttered data and can sustain the same at 60 − 70% even in the presence of noise, such as deletions of peaks and chemical shift deviations. The method tested on NMR data acquired for a mixture of 20 amino acids shows a success rate of 93% in correct recovery of metabolic pathways. The third method developed is a new approach for rapid resonance assignments in proteins based on amino acid selective unlabeling. The method involves choosing a set of multiple amino acid types for selective unlabeling and identifying specific tripeptides surrounding the labeled residues from specific 2D NMR spectra in a combinatorial manner. The methodology directly yields sequence specific resonance assignments, without requiring a contiguously assigned stretch of amino acid residues to be linked, and is applicable to deuterated proteins. The fourth method involves a simple approach to rapidly identify amino acid types in proteins from a 2D NMR spectrum. The method is based on the fact that 13Cβ chemical shifts of different amino acid types fall in distinct spectral regions. By evolving the 13C chemical shifts in the conventional HNCACB or HN(CO)CACB type experiment for a single specified delay period, the phase of the cross peaks of different amino acid residues are modulated depending on their 13Cβ chemical shift values. Following this specified evolution period, the 2D HN projections of these experiments are acquired. The 13C evolution period can be chosen such that all residues belonging to a given set of amino acid types have the same phase pattern (positive or negative) facilitating their identification. This approach does not re-quire the preparation of any additional samples, involves the analysis of 2D [15N,1H] HSQC-type spectra obtained from the routinely used triple resonance experiments with minor modifications, and is applicable to deuterated proteins. Finally, the practical application of these methods for laboratory research is presented. PROMEB and ChemSMP is used to study cancer cell metabolism in previously unexplored oncogenic cell line. PROMEB helped in assigning a differential metabolite present at high concentration in cancer cell line compared to control non-cancerous cell line. ChemSMP revealed active metabolic pathways responsible for regulating energy homeostasis of cancer cells which were previously reported in literature. The two methods developed for rapid protein resonance assignments can be used in applications such as identifying active-site residues involved in ligand binding, phosphorylation, or protein-protein interactions. The phase modulated experiments will be useful for quick assignment of signals that shift during ligand binding or in combination with selective labeling/unlabeling approaches for identification of amino acid types to aid the sequential assignment process. Both the methodology was applied to two proteins: Ubiquitin (8 kDa) and L-IGFBP2 an intrinsically disordered protein (12 kDa), for demonstrating rapid resonance assignment using only set of 2D NMR experiments.
920

Making wood durable. A sustainable approachwith linseed oil / Att göra trä beständigt. Ett hållbart tillvägagångssätt med linolja

Olsson, Helena January 2019 (has links)
Linseed oil has been and is used for vast number of applications, such as in food and paint industry, and wood preservation. It is a good environmental choice, as it originates from renewable sources. Linseed oil is mainly a mixture of triglyceride of fatty acids, both saturated and mono- or polyunsaturated, which allows the oil to oxidize. The oxidation occurs via an auto-oxidation mechanism with the carbon-carbon double bonds and oxygen from the air, reacts to form a polymer. Herein, four different linseed oils (three commercial ones and one industrially available) were analyzed to obtain a better understanding of why different oils provide different protection of wooden materials. This was done by a study of the unoxidized oil, followed by an oxidation time-resolved study of oxidized oil films. The analysis was done by nuclear magnetic resonance, gas chromatography - mass spectrometry and/or inductively coupled plasma atomic emission spectroscopy. This study provided the fatty acid profile of the oils, which were similar for all oils. The unoxidized oils contained some metals ions which probably originate from additives. Aluminum, cobalt, iron, manganese, and zinc was detected in some of the oils at concentrations up to 135 mg/L, but only manganese was detected in all oils and its concentration was much higher than all other metals together. The time-resolved oxidation study had some problems with the solubility of the formed polymers. Several solvents were examined, such as dimethylsulfoxide, alkaline alcohol solutions and toluene, before chloroform-d was chosen as solvent. Though, chloroform-d was not a perfect solvent; it was capable to solve a fraction of the sample, but the fraction decreased with oxidation time. After fifteen days of oxidation, only a few percent of the sample could be dissolved, but for short oxidation times (<48 h) the majority of the samples were dissolved. The oils were analyzed after thirteen different oxidation times. Some structural changes appeared, for example loss of unsaturated protons and some oxidation products arose, such as peroxides and aldyhydes. The diffusion coefficient decreased over the first 3-4 days of oxidation, as expected when the polymerization progressed. After a week of oxidation, the diffusion coefficient increased again, this could possibly be explained by the solubility problem for the large polymer formed. Contrary, at shorter oxidation times this method probably could still be used, as the majority of the sample was dissolved. However, the solubility problem made it impossible to conclude anything about the oxidation rate at longer oxidation times and thus prevented any ranking of the oils. / Linolja har använts och används för många olika tillämpningar, till exempel i mat- och färgindustrin, samt för att bevara trä. Det är klimatmässigt ett bra val, då det kommer från en förnyelsebar källa. Linolja innehåller huvudsakligen en blandning av triglycerider av fettsyror, som både kan vara mättade, enkelomättade eller fleromättade, detta gör att linolja kan oxidera och torka. Oxidationen sker via en auto-oxidation mekanism, med kol-kol dubbelbindningarna och syre från luften som producerar till en polymer. I detta projekt undersöktes fyra olika linoljor (tre kommersiella och en industriell), för att ge en bättre förståelse till varför olika oljor ger olika bra skydd för trämaterial. Detta gjordes genom att undersöka de icke-oxiderade oljorna och sedan göra en tidsstudie på oxiderade oljefilmer. Alla dessa prover analyserades med nuclear magnetic resonance, gas chromatography - mass spectrometry and/or inductively coupled plasma atomic emission spectroscopy. Studien gav resultat på sammansättningen av fettsyror i oljorna, vilken var liknande för alla oljorna. De icke-oxiderade oljorna innehöll ett par metaller, som förmodligen kommer från additiv. Aluminium, kobolt, järn, mangan och zink hittades i några av oljorna i koncentrationer upp till 135 mg/L, men bara mangan var detekterad i alla oljorna och dess koncentration var högre än alla andra metaller tillsammans. Tidsstudien hade problem med lösligheten av proverna. Flertalet lösningsmedel undersöktes, exempelvis dimetylsulfoxid, alkaliska alkohollösningar och toluen, innan kloroform-d valdes som lösningsmedel. Däremot var kloroform-d inte ett perfekt lösningsmedel, den hade förmågan att lösa en del av proverna, men den delen minskade med oxidationstid. Efter femton dagar kunde den bara lösa ett par procent, men efter kortare oxideringstider (<48 h) gick majoriteten av proven att lösa. Oljorna analyserades vid tretton olika oxideringstider. Några strukturella förändringar uppmättes, till exempel minskade mängden dubbelbindningar, och ett par biprodukter från oxideringen detekterades, så som peroxider och aldehyder. Diffusionskonstanterna för oljorna minskade under de första 3-4 dagarna av oxidering, precis som förväntat under polymeriseringen. Efter en vecka av oxidering ökade diffusionskonstanterna igen, det kan förmodligen förklaras av löslighetsproblemen, då diffusionskonstanten är beroende av koncentrationen. Å andra sidan, vid kortare oxideringstider kan denna metod fortfarande användas, eftersom vid denna tidpunkt löste sig fortfarande majoriteten av provet. Dock, löslighetsproblemet gjorde det omöjligt att dra slutsatser kring längre oxideringstider och därmed förhindrades rangordning av oljorna.

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