Statistical correlation based methods for enhanced interpretation of and information recovery from NMR metabolic data sets

Owing to its ability to capture a systemic and temporal metabolic description of an organism’s response to a treatment, metabonomics is a well-established and valuable approach in elucidating the effects and mechanisms of a given perturbation. However, to optimise information recovery from the complex datasets generated, chemometric methods are essential. The work presented in this thesis focuses on the development of novel methods, and the use of existing methods in new applications to ease data interpretation and enhance information recovery from 1H Nuclear Magnetic Resonance (NMR) metabonomic datasets using correlation based methods. Although the methods here are largely applied to toxicological data, they could be equally valuable in the analysis of any metabonomic dataset, and indeed potentially to other ‘omics’ data presenting similar analytical challenges. The first two methodological approaches relate to novel extensions of Statistical Total Correlation Spectroscopy (STOCSY), a valuable tool in elucidation of both inter- and intra-metabolite spectral intensity correlations in NMR metabonomic datasets. In the first, STOCSY is utilised in STOCSY-editing, a method for the selective identification and downscaling of the peaks from unwanted metabolites such as those arising from xenobiotics. Structurally correlated peaks from drug metabolites are first identified using STOCSY, and the returned correlation information utilised to scale the spectra across these regions, producing a modified set of spectra in which drug metabolite contributions are reduced, endogenous peaks reconstructed and thus, analysis by pattern recognition methods without drug metabolite interferences facilitated. In the second, the STOCSY approach is extended in Iterative-STOCSY, where metabolic associations are followed over several rounds of STOCSY through calculation of correlation coefficients initially from a driver spectral peak of interest, and subsequently from all peaks identified as correlating above a set threshold to peaks picked in the previous round. The condensation of putatively structurally related peaks into single nodes, and representation of the otherwise complex network in a fully interactive plot of node-to-node connections and corresponding spectral data, allows the ready exploration of both inter- and intrametabolite relationships and a more directed approach to the identification of biomarkers of the studied perturbation. Finally various clustering methods are investigated with the aim of providing improved structural (intra-metabolite) versus non-structural (inter-metabolite) assignment. Thus, this thesis presents a framework for the enhanced identification, recovery and characterisation of inter- and intrametabolite relationships and how these are affected by metabonomic perturbation

Mécanismes d'immunomodulation par les alcanols aliphatiques

Les alcanols aliphatiques sont des substances ubiquitaires utilisées dans une multitude d’applications domestiques et industrielles. Bien que les effets de l’éthanol sur différentes composantes du système immunitaire soient bien connus, il n’existait presqu’aucune donnée concernant les autres alcanols avant le présent travail. Le premier objectif du projet a été d’étudier les impacts immunologiques d’une exposition aigue aux deux autres alcanols les plus utilisés : l’isopropanol et le méthanol. Nous avons trouvé que l’isopropanol compromet les fonctions effectrices des lymphocytes T, des cellules NK, des monocytes et des macrophages. Par contre, le méthanol agit en synergie avec les stimuli activateurs des lymphocytes T et accroît leur production de cytokines pro-inflammatoires. Les effets biologiques sur ces cellules n’impliquent pas les événements de signalisation précoce en aval des récepteurs activateurs, ils résultent d’une dérégulation sélective de l’activation de facteurs de transcription NFAT avec ou sans la participation d’AP-1. Dans les monocytes activés au LPS, l’isopropanol ne modifie pas les sentiers de signalisation de NF-κB et des MAPK p38 et JNK, mais compromet l’activation de ERK2. Il en résulte une activation défective des sous-unités d’AP-1 c-Fos et JunB. La deuxième partie du projet a été de vérifier si les n-alcanols (de C1 à C12) avaient des effets immunologiques qui suivent la règle de Meyer-Overton. Cette règle établie une corrélation entre le potentiel anesthésique d’une molécule et son hydrophobicité. Nous avons trouvé que les n-alcanols de C2 à C10 inhibent la sécrétion d’IFN-γ par les lymphocytes T activés d’une manière reliée à leur degré d’hydrophobicité, mais cette corrélation s’interrompt à C11. Les n-alcanols exercent leur effet en aval de la membrane plasmique en altérant progressivement et en fonction de leur taille l’activation du facteur de transcription NFAT; cette tendance s’interrompt aussi à C11. L’activation de la voie NF-κB est altérée par les n-alcanols, mais leur effet s’arrête avant, aux environs de C8. Ces derniers résultats suggèrent l’existence de pochettes d’intéraction de dimensions définies sur des cibles protéiques qui compromettent l’activation de NFAT et NF-κB et altèrent la fonction effectrice des lymphocytes T. L’ensemble de ces travaux contribue à une meilleure compréhension de l’activité biologique des alcanols.Aliphatic alkanols are ubiquitous substances used in a variety of household and industrial applications. Although the effects of ethanol on the immune system have been extensively studied, far fewer data is available for the other alkanols. The first objective of the project was to study the immunological impact of acute exposure to the two other most frequently used alkanols, namely isopropanol and methanol. We found that isopropanol is detrimental to the effector functions of T lymphocytes, NK cells, monocytes, and macrophages; they produce less pro-inflammatory cytokines in presence of this alcohol and, in the case of macrophages, phagocytosis is also reduced. Methanol synergizes with activating stimuli to increase their cytokine production. These changes do not involve early signaling events downstream of the cell membrane; they result from the selective dysregulation of the activation of discrete members of the NFAT family of transcription factors with or without the involvement of AP-1. In LPS-activated monocytes, isopropanol does not alter NF-κB and p38/JNK MAPK signaling cascades, but impairs ERK2 activation. The result is a deficient activation of AP-1 subunits c-Fos and JunB. Aliphatic n-alkanols also display anesthetic properties in accordance to their degree of hydrophobicity, following the Meyer-Overton rule. The second part of the project was to determine whether these structurally similar molecules (from C1 to C12) had immunological effects following the same rule. We found that n-alkanols from C2 to C10 inhibit IFN-γ release by activated T lymphocytes in correlation with their hydrophobicity but a cutoff effect was evident at C11. n-Alkanols act downstream of the cell membrane by progressively down-regulating the activation of NFAT in accordance to the size of their aliphatic chain with a clear downward trend that is interrupted at C11. NF-κB signaling is also compromised but the cutoff appears earlier, in the vicinity of C8. Our results suggest the existence of interaction pockets of defined dimensions within intracellular targets that compromise the activation of the NFAT and NF-κB transcription factors and ultimately modulate the effector function of T lymphocytes. Altogether, this work contributes to a better understanding of the biological activity of alkanols

38th Rocky Mountain Conference on Analytical Chemistry

Final program, abstracts, and information about the 38th annual meeting of the Rocky Mountain Conference on Analytical Chemistry, co-sponsored by the Colorado Section of the American Chemical Society and the Rocky Mountain Section of the Society for Applied Spectroscopy. Held in Denver, Colorado, July 21-26, 1996

Investigation of the in vitro and in vivo effects of some herbal preparations on risk factors for calcium oxalate kidney stone disease

Includes bibliographical references.Several herbal preparations (Folium pyrrosiae , Desmodium styracifolium, Hylocereus trigonus, Phyllanthus niruri, Orthosiphon stamineus and Cystone®) were investigated as potential therapeutic and prophylactic agents for kidney stone disease. These studies were executed in the context of the existence of a virtually stone-free (black) and a stone-prone (white) population group in South Africa, with a view of establishing whether their respective renal responses are different. The independent in vitro effects of six plant extracts were tested on the crystallization characteristics of calcium oxalate (CaOx), the predominant stone-forming salt in urine. These investigations were performed in synthetic urine and real urine collected from healthy black and white South African males and the following parameters were assessed: urine composition; CaOx metastable limit; particle size-volume distribution; 14 [C]-oxalate deposition kinetics; CaOx crystal nucleation, aggregation and growth kinetics; examination of crystalluria by scanning electron microscopy and calculation of various physicochemical risk indices (Bonn Risk Index, Tiselius Risk Index and the relative urinary supersaturation of several stone-forming salts). All plant extracts inhibited one or more of the crystallization processes. Furthermore, crystal-cell binding, another risk factor for stone formation, was investigated in the presence of plant extracts. Madin-Darby canine kidney (MDCK)-I cells were used for this experiment. Crystals (inorganic and urinary) were bound to cells incubated in both aqueous media and real urine. Results showed that plant extracts reduced crystal binding under some but not all conditions. One of the extracts (Folium pyrrosiae) was administered to healthy South African black (n=9) and white (n=9) males in a double-blind placebo-controlled study. No significant effects on urine chemistry were found and there were no significant differences between the race groups post- treatment. Compounds from this herb were isolated and purified by the use of sequential liquid-liquid extractions and gel-permeation chromatography. A novel compound, 5 - (3 -(5,5 -dihydroxy-3- oxopentyl)phenoxy)-2-hydroxy-5H-indene-6-carboxylic acid , was identified using mass spectrometry and nuclear magnetic resonance imaging spectroscopy. The findings in this thesis have contributed to the body of knowledge about kidney stone disease. It has been demonstrated that some herbal preparations may be potentially useful in treating and managing this disease, but further clinical testing is required prior to the implementation of such an approach

Women in Science 2014

Women in Science 2014 summarizes research done by Smith College’s Summer Research Fellowship (SURF) Program participants. Ever since its 1967 start, SURF has been a cornerstone of Smith’s science education. In 2014, 150 students participated in SURF (141 hosted on campus and nearby eld sites), supervised by 61 faculty mentor-advisors drawn from the Clark Science Center and connected to its eighteen science, mathematics, and engineering departments and programs and associated centers and units. At summer’s end, SURF participants were asked to summarize their research experiences for this publication.https://scholarworks.smith.edu/clark_womeninscience/1003/thumbnail.jp