La plupart des composés volatils connus et impliqués dans les mécanismes de l’expression fruitée des vins rouges sont présents à des teneurs inférieures ou proches de leurs seuils de perception individuels. Compte tenu de phénomènes d’interactions perceptives entre eux, il est très complexe de déterminer leur impact réel sur l’arôme du vin. Au vu des difficultés rencontrées pour reconstituer fidèlement l’arôme des vins à partir uniquement de composés purs, nous avons développé une méthodologie permettant d’aborder cette reconstitution aromatique à partir de fractions issues du vin lui-même, afin de pouvoir évaluer l’importance relative de ces différentes fractions aromatiques vis-à-vis de l’arôme global du vin. Grâce à l’analyse sensorielle, et en s’attachant à quelques descripteurs particuliers, nous avons pu mettre en évidence, quelques interactions perceptives particulières comme des effets de contributions marquées ou de masquage. La caractérisation des composés présents dans les fractions concernées et à l’origine de ces effets notables a été mise en œuvre. Nos résultats soulignent le rôle indirect du 2-hydroxy-4-méthylpentanoate d’éthyle, un ester éthylique élué dans la fraction à l’origine d’une contribution marquée aux notes de fruits noirs frais qui, en provoquant la diminution du "seuil de perception" du pool fruité des vins rouges et l’augmentation de l’intensité de leurs notes de fruits noirs et de fruits frais, agit comme un exhausteur naturel de ces notes fruitées. Nous sommes aussi parvenus à mettre en évidence, le rôle direct du diacétyle, mais aussi le rôle indirect de l’acétoïne, de l’acide acétique et de la γ-butyrolactone, malgré leurs concentrations infraliminaires, sur la diminution de l’intensité globale et l’intensité du caractère de fruits frais. Ces résultats soulignent leur fort caractère, seuls ou en mélanges, de "réducteurs" de l’intensité de ces notes, et ce, même à des concentrations infraliminaires. Enfin, le comportement particulier, au sein d’un mélange fruité, du 3-hydroxybutanoate d’éthyle, de l’acétate de 2-méthylpropyle, du propanoate d’éthyle et de l’acétate de butyle, présents à des concentrations infraliminaires a été mis en évidence. La présence en mélange des deux premiers provoque la baisse notable du "seuil de perception" du pool fruité et celle des trois derniers augmente l’intensité des notes de fruits frais et fruits noirs traduisant l’effet exhausteur d’arômes dû à ces composés, effet comparable de celui du 2-hydroxy-4-méthylpentanoate d’éthyle qui présente quelques analogies structurales avec ces composés. / Most of volatiles involved in red wines’ fruity expression are present at levels below or close to their individual perception thresholds. Given the existence of perceptive interactions between them, it is very difficult to determine their real impact on wine aroma. Rather than assessing the olfactive behavior of mixtures prepared from pure products, the main goal of this work was to highlight and study the impact of perceptive interactions on wine fruity aroma expression using various aromatic reconstitutions prepared from wine fractions. Sensory profile analyses identified significant differences among aromatic reconstitutions for the intensity of some descriptors, as particular "additive" or "masking" effects. The composition of the involved fractions was then studied by instrumental methods. The final target was to investigate the impact of fraction components on fruity aroma by preparing aromatic reconstitutions and using sensory reconstitution tests, to assess the role of these compounds on the perceptive interactions previously observed. Further analysis revealed that ethyl 2-hydroxy-4-methylpentanoate, eluted in fraction which had an "additive" effect on the black-berry and fresh fruity aroma, does not play a direct role as a key compound in red wine aroma. In contrast, our findings highlighted its indirect contribution to wine aroma, showing that this ester contributed to a synergistic effect, enhancing the perception of fruity character. Finally, it was clearly demonstrated that this compound acts as a natural enhancer for black-berry and fresh fruit notes in red wine. It was also established that diacetyl, acetoin, acetic acid and γ-butyrolactone together played the same hypo-additive role as fractions of which they were eluted, presenting a "masking" effect on fresh fruity aroma. The impact of the last three compounds was demonstrated conclusively, even at subthreshold concentrations. These findings highlighted the existence of new remarkable perceptual interactions impacting overall and fresh-fruit aroma perception. The particular behavior, in a fruity mixture, of ethyl-propanoate, ethyl-3-hydroxybutanoate, butyl acetate and 2-methylpropyl acetate, present at subthreshold concentrations, was demonstrated. The presence of ethyl-3-hydroxybutanoate and 2-methylpropyl acetate in mixture led to a significant decrease of the olfactory threshold of fruity pool confirming their synergistic effect in the overall increase intensity. These compounds with close chemical structures, participate, both quantitatively and qualitatively, in the modulation of red wines’ fruity aromas acting as natural enhancers of black-berry and fresh-fruit aromas.

Analytical Characterization of complex mixtures, such as crude oil, environmental samples, and biological mixtures, is challenging because of the large diversity of molecular components. Mass spectrometry based techniques are among the most powerful tools for the separation of molecules based on their molecular composition, and the coupling of ion mobility spectrometry has enabled the separation and structural elucidation using the tridimensional structure of the molecule. The present work expands the ability of analytical chemists by furthering the development of IMS-MS instrumentation by coupling Trapped Ion Mobility Spectrometry to Fourier Transform Ion Cyclotron Resonance Mass Spectrometry (TIMS-FT-ICR MS). The TIMS-FT-ICR MS platform combines the high-resolution separation of TIMS, which has mobility resolving powers up to 400, and ultra-high mass resolution of FT-ICR MS, with mass resolving power over 1,000,000. This instrumentation allows the assignment of exact chemical composition for compounds in a complex mixture, as well as measurement of the collision cross-section of the molecule. Herein, the principles of the TIMS separation and its coupling to FT-ICR MS are described, as well as how the platform can be applied to targeted analysis of molecules, and untargeted characterization of complex mixtures. Molecular standards were analyzed by TIMS-MS in order to develop a computational workflow that can be utilized to elucidate molecular structure, using the measured collision cross-section of the ion. This workflow enabled identification of structural, cis/trans isomers, and chelated molecules and provides the basis for unsupervised structural elucidation of a complex mixture, and in particular for the elucidation of hydrocarbons from fossil fuels. In summary, this work presents the coupling of TIMS-FT-ICR MS and provides examples of applications as a proof of concept of the potential of this platform for solving complex analytical challenges.

Made available in DSpace on 2016-06-02T19:29:57Z (GMT). No. of bitstreams: 1 5307.pdf: 3018065 bytes, checksum: 4a4ed79b44dafeeb1204798dc8f70256 (MD5) Previous issue date: 2013-06-03 / Universidade Federal de Sao Carlos / This thesis aimed to evaluate the use of cholinesterases (ChE) of the cladoceran species Pseudosida ramosa and Daphnia magna as a biochemical biomarker of the presence and effects of anatoxin-a(s) at different levels of biological organization (molecular, individual and population), besides the combined effects of the mixtures of the hepatotoxic (microcystins) and neurotoxic (anatoxin-a(s)) extracts in D. magna. A microplate assay was adapted and optimized for measuring the ChE activity of P. ramosa, in order to produce an assay protocol for this species. The analysis on the performance of ChE assays in P. ramosa showed that these are suitable for the quantifying of enzymatic activity in this species. P. ramosa showed to be an adequate alternative to the exotic cladoceran D. magna. Thus, it was proposed an assay protocol, which it meets the best combination of parameters for the using of ChE activity of P. ramosa as a biochemical biomarker. The ChE activity of P. ramosa and D. magna were specific for the indication of the presence of anatoxin-a(s), since no effect on the enzymatic activity of these species was observed when they were exposed to the microcystins. In the acute exposures (48-h) to the anatoxin-a(s) extract and to the paraoxon-methyl, P. ramosa was more sensitive than D. magna for ChE activity and survival endpoints. Also, P. ramosa was more sensitive than D. magna when exposed to the anatoxin-a(s) extract for 7 days. When the relationships between the ChE inhibition and individual and populational endpoints were evaluated, different responses were observed for the studied species. The ChE inhibition in P. ramosa had a very close relationship with the survival in the acute exposures to the anatoxin-a(s) extract and to the paraoxon-methyl. For D. magna, on the other hand, this relationship was not linear, being high levels of ChE inhibition associated with almost no mortality. The ChE activity in P. ramosa was also a good predictor of the chronic effects of anatoxin-a(s) extract at higher levels of biological organization, since ChE inhibition (48 h) was linearly linked to the sub-lethal effects on the reproduction (21 days) and on the population growth rate (21 days). For D. magna, these relationships could not be established, possibly due to species-specific differences in the affinities of both acetylcholinesterase and pseudocholinesterases to the toxicants. Thus, for the using of ChE as a biochemical biomarker in the risk assessments of neurotoxic cyanobacteria blooms in tropical regions, it is recommended the use of native species, especially of P. ramosa, since the model species D. magna could overestimate the risk to the local species. When the effects of the mixtures of the hepatotoxic and neurotoxic extracts were evaluated on the survival and feeding rates of D. magna, additive and synergistic responses were only observed on the feeding rates. Therefore, since different types of cyanotoxins are found in the natural environments in combination, the risks of these toxins on the zooplanktonic community should be evaluated not only individually, but also as mixtures. / Esta tese teve como objetivo avaliar o uso das colinesterases (ChE) das espécies de cladóceros Pseudosida ramosa e Daphnia magna como um biomarcador bioquímico da presença e dos efeitos de anatoxina-a(s) em diferentes níveis de organização biológica (molecular, individual e populacional), além dos efeitos combinados das misturas dos extratos hepatotóxicos (microcistinas) e neurotóxicos (anatoxina-a(s)) em D. magna. Um ensaio de microplacas foi adaptado e otimizado para medir a atividade de ChE da P. ramosa, a fim de produzir um protocolo de ensaio para esta espécie. A análise sobre o desempenho dos ensaios de ChE em P. ramosa mostrou que estes são adequados para a quantificação da atividade enzimática nesta espécie. P. ramosa mostrou ser uma alternativa adequada para o cladócero exótico D. magna. Assim, foi proposto um protocolo de ensaio, o qual reúne a melhor combinação de parâmetros para a utilização da atividade de ChE da P. ramosa como um biomarcador bioquímico. A atividade de ChE da P. ramosa e da D. magna foram específicas para a indicação da presença de anatoxinaa( s), uma vez que nenhum efeito sobre a atividade enzimática dessas espécies foi observado quando elas foram expostas às microcistinas. Nas exposições agudas (48 h) ao extrato de anatoxina-a(s) e ao paraoxon-metil, P. ramosa foi mais sensível do que D. magna para os parâmetros atividade de ChE e sobrevivência. Também, P. ramosa foi mais sensível do que D. magna quando exposta ao extrato de anatoxina-a(s) por sete dias. Quando as relações entre a inibição de ChE e os parâmetros individuais e populacionais foram avaliados, diferentes respostas foram observadas para as espécies estudadas. A inibição de ChE em P. ramosa teve uma relação muito próxima com a sobrevivência nas exposições agudas ao extrato de anatoxina-a(s) e ao paraoxon-metil. Para D. magna, por outro lado, esta relação não foi linear, sendo níveis altos de inibição de ChE associados com quase nenhuma mortalidade. A atividade de ChE em P. ramosa foi também um bom preditor dos efeitos crônicos do extrato de anatoxina-a(s) em níveis mais elevados de organização biológica, uma vez que a inibição de ChE (48 h) foi associada linearmente aos efeitos sub-letais na reprodução (21 dias) e na taxa de crescimento populacional (21 dias). Para D. magna, essas relações não puderam ser estabelecidas, possivelmente devido a diferenças espécie-específicas nas afinidades da acetilcolinesterase e das pseudocolinesterases aos tóxicos. Assim, para a utilização de ChE como um biomarcador bioquímico nas avaliações de risco de florescimentos de cianobactérias neurotóxicas em regiões tropicais, recomenda-se o uso de espécies nativas, especialmente da P. ramosa, uma vez que a espécie modelo D. magna poderia superestimar o risco para as espécies locais. Quando os efeitos das misturas dos extratos hepatotóxicos e neurotóxicos foram avaliados sobre a sobrevivência e as taxas alimentares da D. magna, respostas aditivas e sinergísticas foram observadas apenas nas taxas alimentares. Portanto, uma vez que diferentes tipos de cianotoxinas são encontrados nos ambientes naturais em combinação, os riscos dessas toxinas sobre a comunidade zooplanctônica deveriam ser avaliados não apenas individualmente, mas também como misturas.

The main aim of this work was to compare the genotoxicity of organic extracts from different size fractions of aerosol particles (1-10 µm, 0,5-1 µm, 0,17-0,5 µm) collected by high volume cascade impactors in various localities of the Czech Republic differing in the extent of the environmental pollution (Březno - strip mine, Dobré Štěstí - highway, Praha - city center, Láz - background station). Genotoxicity was determined in acellular assay of calf thymus DNA (CT-DNA) with and without S9 metabolic activation by analysis of DNA adducts induced by extractable organic matter (EOM) from the particulate matter (PM) by 32 P-postlabeling and the ability of extracts to induce oxidative DNA damage was evaluated using the competitive ELISA test. The main finding of this work is that most of the observed genotoxicity is connected with fine particles (<1 µm). The concentration of carcinogenic polycyclic aromatic hydrocarbons (c-PAHs) in EOMs indicate that fine fractions bound the highest amount of c-PAHs in all sampling sites. This fact might be related to a higher specific surface of this fraction as compared with a course fraction and a higher mass as compared with a condensational fraction. As for aerosol mass, both fine and condensational fractions are effective carriers of c-PAHs. Similarly, the DNA...

<p>Aging erodes motivation, cognition, sensory modalities and physical capacities, effectively depleting quality of life. Declining sensory, cognitive and motor function are reliable biomarkers of aging and mortality risk. These declines are associated with dysregulation of systemic and cellular processes. We developed a complex dietary supplement (DSP) designed to ameliorate five mechanisms of aging (oxidative processes, inflammation, mitochondrial function, insulin resistance and membrane integrity). Remarkably, normal mice fed the DSP retained youthful functionality into old ages, reflecting slower aging rates. Marked improvements in motor function, memory capacity, spatial learning, muscle strength, visual acuity, olfaction, fecundity and important behavioral functions were observed in aging supplemented mice. Conversely, untreated control animals showed age-related declines in all of the above. Functional improvements were associated with reduced oxidative damage, elevated mitochondrial activity, positive cellular energy balance, improved glucose tolerance, boosted neurotransmitters, greater synaptic density and higher neuronal numbers throughout the brain. A 30% reduction in cancer rates was also documented for DSP treated p53+/- mice. The vast functional benefits greatly exceed the modest longevity extension (11%) in normal supplemented mice. For aging humans, maintaining functionality and performance into later years may provide greater socioeconomic and health benefits than simply prolonging lifespan. Implications of these findings extend to common age-related pathologies including dementia and neurodegenerative diseases, diabetes, cancer, sarcopenia and age-related macular degeneration. Although identifying the role of specific ingredients remains outstanding, results provide proof of principle that complex dietary cocktails can powerfully ameliorate biomarkers of aging and modulate mechanisms considered ultimate goals for aging interventions.</p> / Doctor of Philosophy (PhD)

The dissertation describes a novel method for plant drug discovery based on mutation and selection of plant cells. Despite the industry focus on chemical synthesis, plants remain a source of potent and complex bioactive metabolites. Many of these have evolved as defensive compounds targeted on key proteins in the CNS of herbivorous insects, for example the insect dopamine transporter (DAT). Because of homology with the human DAT protein some of these metabolites have high abuse potential, but others may be valuable in treating drug dependence. This dissertation redirects the evolution of a native Lobelia species toward metabolites with greater activity at this therapeutic target, i.e. the human DAT. This was achieved by expressing the human DAT protein in transgenic plant cells and selecting gain-of-function mutants for survival on medium containing a neurotoxin that is accumulated by the human DAT. This created a sub-population of mutants with increased DAT inhibitory activity. Some of the active metabolites in these mutants are novel (i.e. not detectable in wild-type cells). Others are cytoprotective, and also protect DAergic neurons against the neurotoxin. This provides proof-of-concept for a novel plant drug discovery platform, which is applicable to many different therapeutic target proteins and plant species.

Downstream regulatory element antagonist modulator (DREAM) is involved in various interactions with targets both inside and outside of the nucleus. In the cytoplasm, DREAM interacts with the C-terminal fragments of presenilins to facilitate the production of β-amyloid plaques in Alzheimer’s disease. In the nucleus, Ca2+ free DREAM directly binds to specific downstream regulatory elements of prodynorphin/c-fos gene to repress the gene transcription in pain modulation. These interactions are regulated by Ca2+ and/or Mg2+ association at the EF-hands in DREAM. Therefore, understanding the conformational dynamics and stability associated with Ca2+ and/or Mg2+ binding to DREAM is crucial for elucidating the mechanisms of interactions of DREAM with DNA or presenilins. The critical barrier for envisioning the mechanisms of these interactions lies in the lack of NMR/crystal structures of Apo and Mg2+DREAM. Using a combination of fluorescence spectroscopy, circular dichroism, isothermal titration calorimetry, photothermal spectroscopy, and computational approaches, I showed that Mg2+ association at the EF-hand 2 structurally stabilizes the N-terminal alpha-helices 1, 2, and 5, facilitating the interaction with DNA. Binding of Ca2+ at the EF-hand 3 induces significant structural changes in DREAM, mediated by several hydrophobic residues in both the N- and C-domains. These findings illustrate the critical role of EF-hand 3 for Ca2+ signal transduction from the C- to N-terminus in DREAM. The Ca2+ association at the EF-hand 4 stabilizes the C-terminus by forming a cluster consisting of several hydrophobic residues in C-terminal domain. I also demonstrated that association of presenilin-1 carboxyl peptide with DREAM is Ca2+ dependent and the complex is stabilized by aromatic residues F462 and F465 from presenilin-1 and F252 from DREAM. Stabilization is also provided by residues R200 and R207 in the loop connecting a7 and a8 in DREAM and the residues D450 and D458 in presenilin-1. These findings provide a structural basis for the development of new drugs for chronic pain and Alzheimer’s disease treatments.

This dissertation is dedicated to the topic of multidimensional liquid phase separations. This separation techniques are developed for analysis of complex samples containing thermally labile, low volatile or high molecular weight components that can´t be analysed by two-dimensional (2D) gas chromatography. Concepts of peak capacity and orthogonality are explained and various methods of their determination are stated in theoretical part of dissertation. High performance column liquid chromatography (HPLC) and high performance capillary electrophoresis (HPCE) are suggested as the most suitable methods for automated multidimensional liquid phase separations on-line coupled to mass spectrometry. Configuration of simplified miniaturized liquid chromatograph is described in experimental part of this thesis. Original concept of the system has been extended by simple mobile phase gradient generation technique. Correct function was demonstrated on repeatable separation of alkylphenones, peptides, nitroaromatics, and nitroesters. This system has been utilized as a base for a couple of simple two-dimensional separation platforms for HILIC-MALDI-MS analysis of glycans, for separation of peptides based on off-line coupling of isoelectric focusing and capillary liquid chromatography, and finally for on-line IEC×RPLC, RPLC×RPLC, and HILIC×RPLC two-dimensional liquid chromatography. Correct operation of submitted platforms has been proved.

Extracellular vesicles (EVs), exosomes and microvesicles, transfer endogenous RNAs between neurons over short and long distances. We have explored EVs for siRNA delivery to brain. (1) We optimized siRNA chemical modifications and siRNA conjugation to lipids for EV-mediated delivery. (2) We developed a GMP-compatible, scalable method to manufacture active EVs in bulk. (3) We characterized lipid and protein content of EVs in detail. (4) We established how protein and lipid composition relates to siRNA delivering activity of EVs, and we reverse engineered natural exosomes (small EVs) into artificial exosomes based on these data. We established that cholesterol-conjugated siRNAs passively associate to EV membrane and can be productively delivered to target neurons. We extensively characterized this loading process and optimized exosome-to-siRNA ratios for loading. We found that chemical stabilization of 5'-phosphate with 5'-E-vinylphosphonate and chemical stabilization of all nucleotides with 2'-O-methyl and 2'-fluoro increases the accumulation of siRNA and the level of mRNA silencing in target cells. Therefore, we recommend using fully modified siRNAs for lipid-mediated loading to EVs. Later, we identified that α-tocopherol-succinate (vitamin E) conjugation to siRNA increases productive loading to exosomes compared to originally described cholesterol. Low EV yield has been a rate-limiting factor in preclinical development of the EV technology. We developed a scalable EV manufacturing process based on three-dimensional, xenofree culture of mesenchymal stem cells and concentration of EVs from conditioned media using tangential flow filtration. This process yields exosomes more efficient at siRNA delivery than exosomes isolated via differential ultracentrifugation from two-dimensional cultures of the same cells. In-depth characterization of EV content is required for quality control of EV preparations as well as understanding composition–activity relationship of EVs. We have generated mass-spectrometry data on more than 3000 proteins and more than 2000 lipid species detected in exosomes (small EVs) and microvesicles (large EVs) isolated from five different producer cells: two cell lines (U87 and Huh7) and three mesenchymal stem cell types (derived from bone marrow, adipose tissue and umbilical cord Wharton’s jelly). These data represent an indispensable resource for the community. Furthermore, relating composition change to activity change of EVs isolated from cells upon serum deprivation allowed us to identify essential components of siRNA-delivering exosomes. Based on these data we reverse engineered natural exosomes into artificial exosomes consisting of dioleoyl-phosphatidylcholine, cholesterol, dilysocardiolipin, Rab7, AHSG and Desmoplakin. These artificial exosomes reproduced efficient siRNA delivery of natural exosomes both in vitro and in vivo. Artificial exosomes may facilitate manufacturing, quality control and cargo loading challenge that currently impede the therapeutic EV field.