Le vin en tant qu’écosystème complexe est un modèle particulièrement intéressant pour l’étudie des interactions entre les microorganismes. L’interaction sans contact celluaire (interaction indirecte) entre la levure Saccharomyces cerevisae et la bactérie lactique Oenococcus oeni a un effect direct sur l’induction et l'achèvement de la fermentation malolactique (FML), une fermentation très importante pour la qualité du vin. Une souche levurienne peut être classée FML+ si elle stimule la croissance bactérienne et FML- si elle a un effet inhibiteur. Les métabolites connus qui inhibent ou stimulent la FML ne permettent pas toujours d’expliquer cette distinction phénotypique. Dans ce travail de thèse, nous avon développé un workflow multidisciplinaire qui combine l’approche métabolomique non ciblée, l’analyse classique ciblée, les statistiques et les réseaux. L’objectif premier était de dévoiler des métabolites levuriens impliqués dans l’interaction entre levures et bactéries par une comparaison directe des exométabolome des deux phénotypes.À cet effet et pour la première fois dans l’éude d’interactions inter-espèces, la Spectrométrie de Masse à Résonance Cyclotronique des Ions et à Transformée de Fourier (FT-ICR-MS) et la Chromatographie Liquide couplée à la Spectrométrie de Masses (UPLC-Q-TOF-MS) ont été combinées. Pour mieux visualiser les données à haut débit générées par les deux plate-formes, une méthode statistique non supervisée MetICA a été developpée et validée. Par rapport à l’analyse en composantes principales (ACP), cette nouvelle méthode peut réduire la dimension des données d'une façon plus robuste et fiable. Afin d’extraire des métabolites impliquées dans la distinction phénotypique, nous avons comparé différentes methodes de classification et choisi la meilleure pour chaque jeu de données. Les structures putatives de ces biomarqueurs ont été validés par la spectrométrie de masse MS/MS et leurs rôles physiologiques sur la croissance bactérienne ont été confirmées in vitro. La découverte de biomarqueurs a été complétée par l’analyse ciblée réalisées par Chromatographie en Phase Liquide à Haute Performance (HPLC). La complémentarité entre les différentes techniques métabolomiques a conduit à l’identification de nouveaux biomarqueurs de familles distinctes, comme des composés phénoliques, des sucres, des nucléotides, des acides aminés et des peptides. En outre , l'analyse des réseaux métaboliques a révélé des liens entre les biomarqueurs de levure et a suggéré des voies bactériennes influencés par l’exo-métabolome de levure.Notre workflow multidisciplinaire a révélé une réelle capacité à identifier des signatures moléculaires nouvelles et inattendues de l’interaction levure-bactérie. / As a complex microbial ecosystem, wine is a particularly interesting model for studying interactions between microorganisms. Contact-independent interactions (indirect interactions) between the yeast Saccharomyces cerevisae and the lactic acid bacterium Oenococcus oeni have a direct effect on malolactic fermentation (MLF), induction and completion, which is an important factor in wine quality. Yeast strains could be classified as MLF+ phenotype if it usually stimulates the bacterial growth or MLF- in the opposite case. The known metabolites that stimulate or inhibit the MLF cannot always explain the phenotypic distinction. In this work, a multidisciplinary workflow combining non-targeted metabolomics, targeted analysis, statistics and network was developed. The main objective was to unravel diverse yeast metabolites involved in yeast-bacteria interaction via a direct comparison of exo-metabolomes of MLF+ and MLF- phenotypes.To that purpose, and for the first time in the research of interspecies microbial interactions, two metabolomics platforms, Fourier Transform Ion Cyclotron Resonance -Mass Spectrometry (FT-ICR-MS) and Liquid Chromatography coupled with Mass Spectrometry (UPLC-Q-TOF-MS) were used in combination. To better visualize the high-throughput data generated from the two platforms, a novel unsupervised statistical method, the MetICA was developed and validated. Compared to classical principal component analysis (PCA), the new method reduced the data dimension in a more robust and reliable way. To extract metabolic features involved in the phenotypic distinction, we have compared different statistical classifiers and selected the best one for each dataset. Putative structures of these biomarkers were validated via MS/MS fragmentation analysis and their physiological roles to bacteria were confirmed in vitro. The discovery of biomarkers was complemented by targeted HPLC (high performance liquid chromatography) analysis. The complementarities between different analytical techniques led to new biomarkers of distinct chemical families, such as phenolic compounds, carbohydrates, nucleotides, amino acids and peptides. Furthermore, metabolic network analysis has revealed connections between yeast biomarkers and suggested bacterial pathways influenced by yeast exo-metabolome.Our multidisciplinary workflow has shown its ability to find new and unexpected molecular evidence of wine yeast-bacteria interaction.

Made available in DSpace on 2016-12-23T14:41:52Z (GMT). No. of bitstreams: 1 Thieres Magaive Costa Pereira.pdf: 7173330 bytes, checksum: 5a2aee56b5048351ab0fc838877f8030 (MD5) Previous issue date: 2013-08-23 / O petróleo é uma mistura complexa, sendo uma das misturas mais desafiadoras para as análises químicas. Muitas técnicas são empregadas para a caracterização dos constituintes do óleo. Entretanto, quando combinamos o altíssimo poder de resolução e exatidão da espectrometria de massas, em especial a Ressonância Ciclotrônica de Íons com Transformada de Fourier, (FT-ICR MS) com fontes de ionização a pressão atmosférica, uma atribuição precisa de mais de 20 000 compostos orgânicos do petróleo pode ser obtida. Na indústria do petróleo existe um grande interesse na análise de ácidos naftênicos e asfaltenos devido a problemas como corrosão e formação de depósitos, que aumentam os custos de produção. Portanto este trabalho tem como objetivo a avaliação da termodegradação de ácidos naftênicos, além do emprego das fontes de ESI, APCI, APPI, LDI e MALDI para aquisição de novos dados relativos a caracterização de asfaltenos. Dois petróleos foram utilizados nos ensaios de termodegradação, o petróleo A com acidez de 2,38 mg KOH g-1 e o petróleo B com 4,79 mg KOH g-1 os quais foram tratados a 280, 300 e 350 ºC pelo período de 2, 4 e 6 horas. De uma maneira geral, as principais classes identificadas para ambas às amostras foram O2, N e NO2, respectivamente. Uma leve redução do NAT e da abundância relativa referente à classe O2 foram observado em função da temperatura e do tempo de envelhecimento (T = 280 → 300 oC e t = 2 → 6 h), sendo que a temperatura de tratamento térmico a 350 ºC demonstrou-se determinante na remoção de compostos da classe O2. O perfil químico de amostras de asfaltenos brasileiros foi avaliado utilizando-se cinco diferentes métodos de ionização em ambos os modos de ionização: positivo e negativo, depois, a distribuição de peso molecular, distribuição de classe, parcelas típicas de número de carbono contra DBE e diagramas van Krevelen foram obtidos e discutidos. Um comportamento atípico foi observado para a fonte de LDI e MALDI (±) FT-ICR MS. Um amplo perfil, de m/z 500-3000, apresentando espaçamento de 24 Da foi observado, e este corresponde a formas alotrópicas de fulereno, C60. Em geral, os asfaltenos apresentaram um elevada proporção de espécies heteroatómicas como: HC, HC [H], N, N [H], N2O, N2O [H], N2, N2 [H], O, O[H] para o modo (+) e N, N [H], NO, NO [H], NO, NO2[H], N2O, N2O[H] para o modo negativo. Nos diagramas de DBE contra o número de carbono, os asfaltenos mostraram para cada valor de DBE uma pequena amplitude de compostos com respeito à NC, proporcionando assim, imagens que formam uma linha de 45 ° entre os eixos CN e DBE. Isto indica que estes compostos não exibem grandes cadeias de alquílicas, sendo composta principalmente por anéis aromáticos. Em geral os diagramas de van Krevelen mostraram alta proporção de compostos com razão H/C ~0,7, corroborando com a existência de espécies altamente aromáticas / Petroleum is a complex mixture, being one of the most challenging mixtures for chemical analyzes. Many techniques are employed to characterize constituents of the oil. However , when we combine the highest resolving power and accuracy of mass spectrometry , especially Ion Cyclotron Resonance Fourier Transform ( FT - ICR MS ) with sources of atmospheric pressure ionization , an assignment need more than 20 000 organic compounds in the oil can be obtained. In the oil industry there is a great interest in the analysis of asphaltenes and naphthenic acids due to problems such as corrosion and deposit formation, which increases production costs. Therefore this study aims to evaluate the thermodegradation of naphthenic acids, besides the use of sources of ESI, APCI, APPI, MALDI and LDI for the acquisition of new data on the characterization of asphaltenes . Two test oils were used in thermodegradation of the oil with an acidity of 2.38 mg KOH g -1 and Oil B with 4.79 mg KOH g- 1 which were treated at 280 , 300 and 350 ° C for a period of 2 , 4 and 6 hours. Generally, the major classes identified for both samples O2, NO2, and C, respectively. A slight reduction of NAT and relative abundance refers to the class O2 were observed as a function of temperature and aging time (T = 280 → 300 ° C t = 2 → 6 h), and the heat treatment temperature at 350 ° C showed a determinant for the removal of class O2. The chemical asphaltenes Brazilian samples was evaluated using five different methods of ionization in both modes of ionization: positive and negative, then the molecular weight distribution, distribution class, typical plots versus carbon number and DBE van Krevelen diagrams were obtained and discussed. An unusual behavior was observed for the LDI and MALDI source ( ± ) FT - ICR MS . A comprehensive profile of m / z 500-3000, with spacing of 24 Da was observed, and this corresponds to allotropes of fullerene C60. In general, the asphaltenes had an heteroatómicas high proportion of species such as HC , HC [ H] , N, [ H] , N2O N2O [ H] N2, N2 [ M ] O O [ H] to mode (+) and N, [ H ] , NO [ H] , NO , NO2, [ H] , N2O N2O [ H ] for the negative mode . In the diagrams DBE against the carbon number , the asphaltenes shown for each value of DBE composed of a small amplitude with respect to NC, thus providing images that form a line of 45 ° between the axes CN and DBE. This indicates that these compounds do not exhibit large chain alkyl, composed mainly of aromatic rings. In general diagrams van Krevelen showed a high proportion of compounds ratio H / C ~ 0.7, confirming the existence of highly aromatic species

Submitted by Luciana Ferreira (lucgeral@gmail.com) on 2014-12-22T14:31:16Z No. of bitstreams: 1 Dissertação - Maria Juíva Marques de Faria - 2014.pdf: 3781718 bytes, checksum: 5a98e4c3d48dde6e80b58427a1a73012 (MD5) / Approved for entry into archive by Luciana Ferreira (lucgeral@gmail.com) on 2015-01-26T13:13:18Z (GMT) No. of bitstreams: 1 Dissertação - Maria Juíva Marques de Faria - 2014.pdf: 3781718 bytes, checksum: 5a98e4c3d48dde6e80b58427a1a73012 (MD5) / Made available in DSpace on 2015-01-26T13:13:18Z (GMT). No. of bitstreams: 1 Dissertação - Maria Juíva Marques de Faria - 2014.pdf: 3781718 bytes, checksum: 5a98e4c3d48dde6e80b58427a1a73012 (MD5) Previous issue date: 2014-05-07 / Bovine mastitis is an inflammatory/infectious process of the mammary gland, its etiology is complex and multivariate. The most common mastitis has bacterial origin. Because of the high cost to treat this disease, and the bacterial resistance to antibiotics, beyond the losses due to the milk discard or the presence of drug residues in milk, studies are necessary to find out alternative methods to circumvent these problematic. The medicinal plants with antimicrobial activity have been making room in veterinary medicine with the objective to reduce the impact and the use of drugs indiscriminately, as well as maintain the integrity of the animal and control the dissemination of resistant bacterial lineage. Therefore, the aim of this work was characterize the oleoresin Copaifera spp., verify the antimicrobial activity in vitro of oleoresin and essential oil of Copaifera spp. in combating against aerobic and facultative isolated bacteria from cows’ milk with subclinical grade III mastitis diagnostic and evaluate preliminarily, in vivo, phytotherapic formulation composed of Copaifera spp. The tests for characterization of the oleoresin, confirmed its authenticity and quality, considered appropriate for use. The analyzes performed by gas chromatography coupled to mass spectrometry (GC/MS) and electrospray ionization Fourier transformed íonic cyclotron resonance mass spectrometry (ESI FT-ICR MS) identified sesquiterpenes and diterpenes present in the essential oil and oleoresin of Copaifera spp., respectively. The technique of High Performance Liquid Chromatography (HPLC) for sesquiterpenes, especially for β-caryophyllene, can be used in quality control of essential oil and oleoresin of Copaifera spp., as well as in phytotherapic formulation using oleoresin of Copaifera spp. The oleoresin showed better antimicrobial activity than the essential oil of Copaifera spp. (ρ<0,0001) in combating the 55 isolated bacteria. The antibiogram test of the three phytotherapic formulations demonstrated that the oleoresin had antimicrobial activity against the isolated microorganisms. The preliminary evaluation, in vivo, of a phytotherapic formulation containing 20% oleoresin of copaiba was neither effective nor safe, because it intensified the inflammatory process, requiring further tests, such as cytotoxicity and irritability of the raw material plant and of the vehicle used. Key words: Bovine Mastitis. Oleoresin. Essential Oil. Copaifera spp. Minimum Inhibitory Concentration. ESI FT-ICR MS. / Mastite bovina é um processo inflamatório/infeccioso da glândula mamária, de etiologia complexa e multivariada, sendo a de origem bacteriana a mais frequente. Devido aos elevados custos dos tratamentos dessa enfermidade, resistência bacteriana aos antibióticos, além dos prejuízos inerentes ao descarte do leite ou à presença de resíduos de medicamentos no mesmo, faz-se necessário estudos que busquem métodos alternativos para contornar essa problemática. As plantas medicinais com potencial antimicrobiano vêm ganhando espaço na medicina veterinária com o objetivo de reduzir o impacto e o uso de medicamentos de forma indiscriminada, bem como manter a integridade do animal e controlar a disseminação de linhagens bacterianas resistentes. Diante disso, o objetivo desse trabalho foi caracterizar a oleorresina de Copaifera spp., verificar atividade antimicrobiana in vitro da oleorresina e do óleo essencial de Copaifera spp. frente às bactérias aeróbias e facultativas isoladas de leite de vacas diagnosticadas com mastite subclínica grau III e avaliar preliminarmente, in vivo, formulação fitoterápica à base de Copaifera spp. Os testes de caracterização da oleorresina de Copaifera spp. demonstraram sua autenticidade e qualidade, a qual foi considerada adequada para o uso. As análises realizadas por cromatografia gasosa acoplada à espectrometria de massas (CG/EM) e por espectrometria de massas com ionização por electrospray de ressonância ciclotrônica de íons por transformada de Fourier (ESI FT-ICR MS) identificaram os sesquiterpenos e diterpenos presentes no óleo essencial e na oleorresina de Copaifera spp., respectivamente. A técnica Cromatografia Líquida de Alta Eficiência (CLAE) para sesquiterpenos, em especial para β-cariofileno, pode ser utilizada no controle de qualidade de oleorresina e óleo essencial de Copaifera spp., bem como em formulação fitoterápica utilizando oleorresina de Copaifera spp. como matéria-prima vegetal. A oleorresina apresentou melhor atividade antimicrobiana do que o óleo essencial de Copaifera spp. (ρ<0,0001) frente às 55 bactérias isoladas. O teste de antibiograma das três formulações fitoterápicas demonstrou que a oleorresina de copaíba reproduziu a sua atividade antimicrobiana frente aos micro-organismos isolados. A avaliação preliminar, in vivo, de uma formulação fitoterápica contendo 20% oleorresina de copaíba não foi eficaz e nem segura, pois intensificou o processo inflamatório, havendo necessidade de testes futuros, como de citotoxicidade e de irritabilidade dessa matéria-prima vegetal e do veículo utilizado.

Submitted by Cláudia Bueno (claudiamoura18@gmail.com) on 2016-08-17T21:37:32Z No. of bitstreams: 2 Dissertação - Géssica Adriana Vasconcelos - 2016.pdf: 2159448 bytes, checksum: a3e5f1ad74eff4a8b0472438d2a2bbf0 (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) / Approved for entry into archive by Cláudia Bueno (claudiamoura18@gmail.com) on 2016-08-17T21:39:28Z (GMT) No. of bitstreams: 2 Dissertação - Géssica Adriana Vasconcelos - 2016.pdf: 2159448 bytes, checksum: a3e5f1ad74eff4a8b0472438d2a2bbf0 (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) / Made available in DSpace on 2016-08-17T21:39:28Z (GMT). No. of bitstreams: 2 Dissertação - Géssica Adriana Vasconcelos - 2016.pdf: 2159448 bytes, checksum: a3e5f1ad74eff4a8b0472438d2a2bbf0 (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) Previous issue date: 2016-03-10 / Outro / Petroleomics by FT-ICR MS was able to characterize petroleum and its derivatives at molecular level. The most used ionization source on the analysis of these compounds is electrospray. However, species that are more basic or more acidic suppress the ionization of other compounds with less strength. This disadvantage consists of, especially in positive mode, only detecting compounds with higher pKa values preventing the mass spectrometer from reading less basic species that is also present in the sample. In view of this, the development of new methods whose purpose is to minimize these effects is essential. An alternative is to use fast techniques of extraction and separation followed by analysis by FT-ICR MS. This study pursued two goals: first, to perform an extraction of vacuum residue into basic and neutral nitrogen compounds using different methods, and second, to fractionate the basic nitrogen compounds present in RV according to their mass/ratio. Three methods were tested to achieve the first objective: solvent extraction (LLE), column chromatography (LC), and solid phase extraction (SPE). The results showed that LLE was the less selective technique among all three studied procedures. SPE and LC showed similar results, and they allowed to partially separate the basic nitrogen compounds from neutral species. To accomplish the second goal, a fractionation using SPE was applied to the vacuum residue sample. This procedure permitted to detect compounds that apparently were not present in the untreated sample as a consequence of a reduction on ion suppression effect. Electrospray ionization and high resolution mass spectrometry (FT-ICR MS) were employed on the analysis of each sample. / A petroleômica por FT-ICR MS foi capaz de caracterizar o petróleo e seus diferentes derivados a nível molecular. A fonte de ionização mais utilizada na análise destes compostos é o electrospray. Componentes mais básicos e mais ácidos, entretanto, suprimem a ionização de outras espécies com menor força. A grande desvantagem deste fato consiste, especialmente no modo positivo, detectar somente os compostos com elevado pKa impedindo a leitura das espécies menos básicas presentes na mesma amostra. À vista disso, é fundamental o desenvolvimento de novos métodos que tenham por finalidade minimizar estes efeitos. Uma alternativa é fazer o uso de técnicas rápidas de extração e separação seguida pelas análises por FT- ICR MS. Desta forma, este estudo teve dois objetivos principais: primeiro, realizar uma extração dos compostos nitrogenados de resíduo de vácuo em suas frações básica e neutra utilizando diferentes métodos e, segundo realizar um fracionamento dos compostos nitrogenados básicos presentes em RV de acordo com a sua massa. Para se alcançar o primeiro objetivo, três métodos foram testados: Extração líquido-líquido (LLE), cromatografia em coluna clássica (LC) e extração em fase sólida (SPE). Os resultados mostraram que o LLE foi a menos seletiva dentre os três procedimentos estudados. SPE e LC apresentaram resultados semelhantes e foi possível separar parcialmente os compostos básicos das espécies neutras. Para alcançar o segundo objetivo, um fracionamento utilizando extração em fase sólida foi empregado na amostra de resíduo de vácuo. Este procedimento permitiu detectar compostos que aparentemente não estavam presentes na amostra não tratada como consequência da redução do efeito de supressão iônica. A ionização por electrospray e por espectrometria de massa de alta resolução (FT-ICR MS) foram utilizados na análise de cada amostra.

Lors de la fécondation, le génome subit des transformations épigénétiques qui vont guider le développement et le phénotype de l’embryon. L'avènement des techniques de reprogrammation cellulaire, permettant la dédifférenciation d'une cellule somatique adulte, ouvre la porte à de nouvelles thérapies régénératives. Par exemple, les procédures de transfert nucléaire de cellules somatique (SCNT) ainsi que la pluripotence par induction (IP) visent à reprogrammer une cellule somatique adulte différentiée à un état pluripotent similaire à celui trouvé durant la fécondation chez l'embryon sans en impacter l'expression génique vitale au fonctionnement cellulaire. Cependant, la reprogrammation partielle est souvent associée à une mauvaise méthylation de séquences géniques responsables de la régulation des empreintes géniques. Ces gènes, étudiés chez la souris, le bovin et l'humain, sont exprimés de manière monoallélique, parent spécifique et sont vitaux pour le développement embryonnaire. Ainsi, nous avons voulu définir le statut épigénétique du gène empreinté H19 chez l'équin, autant chez le gamètes que les embryons dérivés de manière in vivo, SCNT ainsi que les cellules pluripotentes induites (iPSC). Une région contrôle empreinté (ICR) riche en îlots CpG a été observée en amont du promoteur. Couplé avec une analyse de transcrit parent spécifique du gène H19, nous avons confirmé que l'empreinte du gène H19 suit le modèle insulaire décrit chez les autres mammifères étudiés et résiste à la reprogrammation induite par SCNT ou IP. La déméthylation partielle de l'ICR observée chez certains échantillons reprogrammés n'était pas suffisante pour induire une expression biallélique, suggérant un contrôle des empreintes chez les équins durant la reprogrammation. / After fertilization, the animal genome undergoes a complex epigenetic remodeling that dictates the growth and phenotypic signature of the animal. The development of reprogramming methods using adult differentiated cells as the primordial genetic source has opened the door to new regenerative therapies for animals. Somatic cell nuclear transfer (SCNT) and induced pluripotency are two techniques which aim to reprogram a cell from its adult differentiated state to an embryonic-like pluripotency level, without impairing the expression of genes vital for the cellular function. Albeit promising, the mechanisms involved in these techniques remain only moderately understood. Partial reprogramming is frequently associated with irregular methylation of DNA sequences responsible for imprint regulation. These imprinted genes, mostly studied in rodents, cattle and humans, are expressed in a monoallelic parent-specific fashion and are vital for embryo growth. Hence, we aim to define the equine H19 imprinting control region (ICR) in gametes, in vivo and in SCNT derived embryos, as well as in induced pluripotent stem cells (iPSC). A CpG rich ICR was characterized upstream of the promotor using bisulfite treated DNA sequencing. Coupled with parent-specific gene expression analysis, we confirmed that the imprinted gene H19 is resistant to cellular reprogramming, and that partial demethylation of its ICR does not result in biallelic expression, suggesting that equine species have rigorous imprint maintenance during cellular reprogramming.

Mok Wing Fai Simon. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2001. / Includes bibliographical references (leaves 91-97). / Abstracts in English and Chinese. / Abstract (English) --- p.i / Abstract (Chinese) --- p.iii / Acknowledgements --- p.iv / Table of content --- p.v / List of Figures --- p.viii / List of Tables --- p.x / Chapter CHAPTER ONE: --- INTRODUCTION / Chapter 1.1 --- Origin of the Neural Crest Cells / Chapter 1.1.1 --- Formation of the Neural Tube --- p.1 / Chapter 1.1.2 --- The Neural Crest cells and the Vagal Neural Crest Cells --- p.2 / Chapter 1.1.3 --- The migration profiles of Neural Crest Cells Originated from the Axial level other than Vagal Neural Crest --- p.4 / Chapter 1.1.4 --- Development of the Gastrointestinal Tract and the Enteric Nervous System --- p.5 / Chapter CHAPTER TWO: --- MIGRATION OF NEURAL CREST CELLS IN NORMAL ICR AND DOM MUTANT MOUSE EMBRYOS / Chapter 2.1 --- Introduction --- p.27 / Chapter 2.2 --- Materials / Chapter 2.2.1 --- Pregnant mice --- p.39 / Chapter 2.2.2 --- The Handling Medium --- p.39 / Chapter 2.2.3 --- The Culture Medium --- p.40 / Chapter 2.2.4 --- Preparation of Wheat Germ Agglutinin-Gold Conjugates (WGA-Au) --- p.42 / Chapter 2.2.5 --- "Preparation of 1,´1ة-dioctadecyl-´3ة 3,3 '3,3 226}0ة-tetramethyl indocarbocyanine perchlorate (Di-I) " --- p.43 / Chapter 2.2.6 --- Preparation of Carnoýةs Solution --- p.43 / Chapter 2.2.7 --- Preparation of Paraformaldehyde --- p.43 / Chapter 2.2.8 --- Pregnont Dominant Megacolon (Dom) Mice --- p.44 / Chapter 2.2.9 --- DNA Extraction for Genotyping of Dom Embryos --- p.45 / Chapter 2.2.10 --- Primers Used in PCR for Genotyping of Dom Embryos --- p.45 / Chapter 2.2.11 --- PCR Reagent System --- p.46 / Chapter 2.2.12 --- 10XTBE --- p.46 / Chapter 2.3 --- Methods / Chapter 2.3.1 --- Isolation of Embryos from Pregnant Mice --- p.47 / Chapter 2.3.2 --- In situ labeling of exogenous dye --- p.48 / Chapter 2.3.3 --- Whole Embryo Culture --- p.49 / Chapter 2.3.4 --- Morphological Examination of Cultured Embryos --- p.49 / Chapter 2.3.5 --- Histological Examination of Cultured embryos --- p.50 / Chapter 2.3.6 --- Genotyping of Dom F1 Generation --- p.51 / Chapter 2.3.7 --- Genotyping of Dom Embryos by PCR --- p.52 / Chapter 2.3.8 --- Gel Electrophoresis --- p.52 / Chapter 2.3.9 --- Counting of WGA-Au Labelled Cells --- p.53 / Chapter 2.4 --- Results / Chapter 2.4.1 --- Genotyping --- p.54 / Chapter 2.4.2 --- Examination on Gross morphology of Control and Experimental Embryos --- p.54 / Chapter 2.4.3 --- Morphological Examination of DOM Mutant Embryo after culture --- p.57 / Chapter 2.4.4 --- Initial Stage of Vagal and Trunk Neural Crest Cells Migration in Mouse Embryos --- p.62 / Chapter 2.4.5 --- Initial Stage of Vagal and Trunk Neural Crest Cells Migration in DOM Embryos --- p.64 / Chapter 2.4.6 --- Distribution of Labelled Cells in ICR Embryos after WGA-Au Labelling --- p.65 / Chapter 2.4.7 --- Distribution of WGA-Au Labelled Cells in DOM Embryos --- p.69 / Chapter CHAPTER THREE: --- DISCUSSION / Chapter 3.1 --- Development of embryos in vitro --- p.78 / Chapter 3.2 --- Comparison of the Two Exogenous Dyes --- p.80 / Chapter 3.3 --- Migration Pathway of the Vagal and Trunk Neural Crest Cells --- p.81 / Chapter 3.4 --- Counting of Labelled Cells in DOM Embryos --- p.83 / Chapter 3.5 --- Initial Stage of Vagal and Trunk Neural Crest Cells Migration of Different Genotypes of the DOM Embryos --- p.84 / Chapter 3.6 --- Differences in Distribution of WGA-Au Labelled Cells in Different Genotypes of DOM Embryos --- p.85 / Chapter CHAPTER FOUR: --- CONCLUSION --- p.88 / REFERENCES --- p.91 / "FIGURES, LEGEND TABLE AND APPENDIX"

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Fluorescent labeling is a method used for visualization of various types of biomolecules including proteins and protein complexes. However, the effect of protein labeling on protein structure and functions has not been investigated so far. The goal of the diploma thesis was to examine an influence of NHS-fluorescein binding on structure and function of human carbonic anhydrase I (hCA-I). The particular aims of this work were to prepare recombinant 15N-hCA-I which was used for NMR structure analysis of carbonic anhydrase upon fluorescent labeling. Furthermore, enzyme activity was measured in order to find out a correlation between the concentration of NHS- fluorescein and protein function. In addition, the reaction mixtures were systematically analyzed by ESI FT-ICR mass spectrometry. The analysis revealed experimental conditions for fluorescent labeling of human carbonic anhydrase I with minimal effect on protein structure and function. The results of this study show that the calculation of molar excess of NHS-fluorescein cannot rely on a simple procedure provided by manufacturer. However, due to decrease of enzyme activity upon fluorescent labeling, it is better to take into count the influence of NHS-fluorescein concentration on the relative enzymatic activity. Moreover, the calculation of molar...

<p>In this thesis, the structure and stability of globular proteins adsorbed onto nanometer-sized hydrophilic silica particles were investigated using differential scanning calorimetry (DSC), hydrogen/deuterium exchange (HDX), and mass spectrometry (MS). The adsorption process itself was characterized with fluorescence and absorption spectroscopy and surface plasmon resonance (SPR). The combination of these methods offered a unique insight into adsorption-induced changes within proteins related to their adsorption characteristics. DSC contributed with thermodynamic information on the overall structural stability within the protein population. HDX in combination with MS contributed information on the structure and stability of adsorbed proteins with focus on changes within the secondary structure elements. In order to increase the structural resolution in this part of the investigation, proteolysis was performed prior to the MS analyzing step. Knowledge on the protein adsorption process was utilized in a practical approach called ligand fishing. In this approach, SPR was used to monitor the chip-based affinity purification of a protein with MS used for protein identification.</p><p>Adsorption isotherms revealed that electrostatic interactions play an important role in the adsorption of proteins to hydrophilic surfaces. DSC investigation revealed that the thermal stability of proteins reduces with increasing electrostatic attraction between the protein and the surface and that this effect diminishes at higher surface coverage. The mass-increase due to exchange between protein hydrogen atoms and deuterium atoms in solution was investigated as a function of time. This gave insight into adsorption-induced changes in the structural stability of proteins. By combining DSC and HDX-MS, it was possible to differentiate between adsorption-induced changes in the secondary and tertiary structure. Additionally, if limited proteolysis was performed, the investigations gave insight into the orientation and protein segment specific changes in the stability of proteins adsorbed to silica surfaces. The adsorption of proteins to silica particles also provided the basis for a new experimental design that allows handling of minute amounts of proteins in a ligand fishing application, as used in the field of functional proteomics.</p>

In this thesis, the structure and stability of globular proteins adsorbed onto nanometer-sized hydrophilic silica particles were investigated using differential scanning calorimetry (DSC), hydrogen/deuterium exchange (HDX), and mass spectrometry (MS). The adsorption process itself was characterized with fluorescence and absorption spectroscopy and surface plasmon resonance (SPR). The combination of these methods offered a unique insight into adsorption-induced changes within proteins related to their adsorption characteristics. DSC contributed with thermodynamic information on the overall structural stability within the protein population. HDX in combination with MS contributed information on the structure and stability of adsorbed proteins with focus on changes within the secondary structure elements. In order to increase the structural resolution in this part of the investigation, proteolysis was performed prior to the MS analyzing step. Knowledge on the protein adsorption process was utilized in a practical approach called ligand fishing. In this approach, SPR was used to monitor the chip-based affinity purification of a protein with MS used for protein identification. Adsorption isotherms revealed that electrostatic interactions play an important role in the adsorption of proteins to hydrophilic surfaces. DSC investigation revealed that the thermal stability of proteins reduces with increasing electrostatic attraction between the protein and the surface and that this effect diminishes at higher surface coverage. The mass-increase due to exchange between protein hydrogen atoms and deuterium atoms in solution was investigated as a function of time. This gave insight into adsorption-induced changes in the structural stability of proteins. By combining DSC and HDX-MS, it was possible to differentiate between adsorption-induced changes in the secondary and tertiary structure. Additionally, if limited proteolysis was performed, the investigations gave insight into the orientation and protein segment specific changes in the stability of proteins adsorbed to silica surfaces. The adsorption of proteins to silica particles also provided the basis for a new experimental design that allows handling of minute amounts of proteins in a ligand fishing application, as used in the field of functional proteomics.