Spelling suggestions: "subject:"glycans"" "subject:"lycans""
41 |
POLYMERIC BONDED PHASES FOR PROTEIN EXTRACTION AND INTACT GLYCOPROTEIN ANALYSISEdwin Jhovany Alzate Rodriguez (7010366) 12 August 2019 (has links)
Polymer brushes are extremely versatile materials, as monomer choice allows the user to design a material with the desired physiochemical properties. Given the wide variety in monomer functionality, polymers can be fine-tuned for a specific application. In this work, polymer brushes bound to a silica support are designed and utilized to enhance performance of protein extraction and chromatographic separations. <br> The effectiveness of an analytical method is strongly affected by matrix composition, however, the presence of species other than the target analyte is usually unavoidable. An excellent technique will be able to identify and/or quantify the analyte even when its concentration is low compared with interfering molecules. Protein analysis is particularly challenging, since many proteins of clinical and scientific significance are present in complicated matrices such as plasma or cell lysates. <br>A common method to specifically separate a protein from a complicated matrix is solid phase extraction. In this method, a species (such as an antibody) with high specificity towards the target is immobilized onto a solid substrate (commonly beads or small particles for greater surface area). Next, the target is collected onto the surface, bound by the species. The solid substrate is rinsed of the liquid matrix, before elution of the target. Only the active species should interact with the analyte, and the surface should be otherwise inactive. However, nonspecific interactions lead to binding/adsorption of undesirable compounds. Therefore, an optimal substrate for protein extraction must be 1) easily and completely removable from the liquid phase, 2) have a high concentration of active sites for specific binding, and 3) exhibit low nonspecific binding. As part of this work, commercial magnetic particles were coated with a nonporous silica layer that tolerates the acid bath and silane coating necessary to attach a polymer layer. On the silane coating, a polymer layer was covalently bound; this layer contains epoxide active groups for immobilizing antibodies. These antibodies bind to the target molecule with high specificity, and low nonspecific binding. Obtained particles were evaluated for protein extraction, where antibodies as well as specifically engineered drug compounds were successfully bound to the particle surface.<br>Glycosylation influences several physiopathological processes in proteins. Glycans can act as receptors, modify protein solubility, and participate in folding conformation. Altered glycosylation is a common feature in tumorous cells. As such, many modifications in glycoproteins have been related to cancer, including increased branching of N-glycans or augmented units of sialic acid. Therefore, characterization of glycoproteins is important not only as a diagnostic tool, but also to monitor patients’ response to treatment. Furthermore, it is important in the growing field of monoclonal antibodies as drug carriers. <br>Among different methods used for glycosylation analysis, Hydrophilic Interaction Liquid Chromatography (HILIC) has showed important advantages over time-consuming digestion-MS based techniques. An adequate HILIC stationary phase can be used to rapidly differentiate glycoforms present in a sample. In the second part of this work, a polymer brush based bonded phase was developed as a HILIC stationary phase. The new polymer improved the separation of a model glycoprotein compared with a commercial HILIC column, while also exhibiting enhanced stability over a previous bonded phase synthetized in our group.<br><br>
|
42 |
Chemische Charakterisierung von diagnostischen Glykan-Oberflächen vor und nach Interaktion mit Modell-AnalytenNietzold, Carolin 05 February 2020 (has links)
Das Hauptanliegen dieser Arbeit war es valide chemische Verfahren für die Optimierung der Gesamtleistung von Glykan-Microarrays bereitzustellen. Dafür erfolgte eine gründliche Untersuchung jedes einzelnen Prozessschritts innerhalb der Arrayproduktion durch Anwendung komplementärer Methoden der chemischen Oberflächenanalytik. Mit Hilfe von fortgeschrittenen Verfahren der Elektronen-Spektroskopie für die chemische Anlayse (ESCA/XPS) wurden valide quantitative Daten bei der chemischen Charakterisierung der Oberflächen erhalten die mit den häufig eingesetzten qualitativen bzw. indirekten Verfahren (z.B. Kontaktwinkel Goniometrie und Fluoreszenz-Spektroskopie) so nicht erhalten werden können. Die robuste Anbindung von Glykanen auf der Substratoberfläche ist Voraussetzung für eine reproduzierbare Anwendung in der Diagnostik aber auch für die Entwicklung valider quantitativer Charakterisierungsmethoden zur Bewertung der Effizienz der Immobilisierungsreaktionen.
Ein Schwerpunkt der Arbeit lag in der Charakterisierung und Optimierung der Glykananbindung an amin-reaktive Oberflächen. Hierzu wurden z.B. spezielle Glykane mit Fluorlabel auf epoxid-funktionalisierten Siliziumoberflächen immobilisiert. Eine Quantifizierung der angebundenen Glykane ist zum Beispiel über die Bestimmung der CF3-Gruppe im hochaufgelösten C1s XPS Spektrum möglich. Die Interaktionen Sonde-Analyt wurden modellhaft mit immobilisierten Glykanen und dem Lektin Concanavalin A mit Verfahren der chemischen Oberflächenanalytik untersucht.
Neben der chemischen Charakterisierung frisch präparierter Glykansonden wurde auch das Alterungsverhalten der Glykan-Microarrays untersucht. / The objective of this research is to sidestep many of the initial and current problems of glycan microarray based devices by using new analytical approaches to control molecular engineering. For this purpose, a thorough investigation of each individual step in the array production is carried out by applying complementary methods of surface chemical analysis. New fluorophore-free protocols based on methods of surface analysis as XPS will be developed and validated to enable glycan microarray performance optimization. The advantage of these methods is the direct quantitative access to chemical bonds at high lateral resolution. In contrast to the frequently used qualitative or indirect methods (e.g. contact angle goniometry and fluorescence spectroscopy), valid quantitative data are obtained. The robust binding of glycans on the substrate surface, is a prerequisite for a reproducible application in the diagnostics but also for the development of valid quantitative characterization methods for the evaluation of the efficiency of the immobilization reactions.
One focus of the work was the characterization and optimization of the glycan binding to popular amine-reactive surfaces. For this purpose, specific glycans with fluorine-label were immobilized on epoxide-functionalized silicon surfaces. A quantification of the attached glycan molecules is possible, for example, by determining the amount of CF3 groups using the high-resolution C1s XPS spectrum. The interactions between model probe (glycan molecules) and model analyte (lectin concanavalin A) were investigated using powerful methods surface chemical analysis.
In addition to the chemical characterization of freshly prepared glycan probes, the aging behavior of the glycan microarrays was also investigated.
|
43 |
Production and Characterization of Higher-Order Genetic Mutants for the Hydroxyproline-Galactosyltransferase Genes Encoding the Enzymes for O-Galactosylation of Cell Wall Arabinogalactan-Proteins in ArabidopsisKaur, Dasmeet 16 September 2022 (has links)
No description available.
|
44 |
<b>ADVANCEMENTS IN AMBIENT MASS SPECTROMETRY IMAGING FOR ENHANCED SENSITIVITY AND SPECIFICITY OF COMPLEX BIOLOGICAL TISSUES</b>Miranda Renee Weigand (19179571) 19 July 2024 (has links)
<p dir="ltr">Mass spectrometry imaging (MSI) is a powerful technique for visualizing the distribution of molecules within biological samples. Advancements in MSI instrumentation and computational tools have enabled the impactful applications of this technique across various fields including clinical research, drug discovery, forensics, microbiology, and natural products. Nanospray desorption electrospray ionization (nano-DESI), an ambient localized liquid extraction ionization technique, has proven valuable to the MSI community. Nano-DESI has been used for imaging of various molecules in biological samples including drugs, metabolites, lipids, N-linked glycans, and proteins.</p><p dir="ltr">My research has been focused on expanding the sensitivity and specificity of nano-DESI for biomolecular imaging. One of the newly developed methods employs ammonium fluoride NH<sub>4</sub>F as a solvent additive to enhance the sensitivity of nano-DESI for the analysis of lipids in negative ionization mode. Secondly, methods were developed for the spatial mapping of isobaric and isomeric species in biological tissues by implementing nano-DESI MSI on a triple quadrupole (QqQ) mass spectrometer. This work used multiple reaction monitoring (MRM) mode of a QqQ with unit mass resolution to separate isobaric lipid species that require high mass resolving power and imaging of isomeric low-abundance species in tissue sections. Next, I demonstrate nano-DESI as a liquid extraction technique for imaging of N-linked glycans within biological tissue sections. Lastly, the spatial distribution of eicosanoids and specialized pro-resolving mediators (SPMs) in a mouse model for acetaminophen-induced liver injury (AILI) provides insights into the inflammation and resolution phases of AILI. Collectively, these developments have advanced the sensitivity, chemical specificity, and molecular coverage of nano-DESI for imaging of different classes of molecules in biological tissues.</p>
|
45 |
Identification et caractérisation des déternimants physico-chimiques et biologiques mis en jeu dans l'adhésion de Lactococcus lactis à la mucine modèle PGM / Identification and characterization of physico-chemical and biological determinants involved in the adhesion of Lactcoccus lactis to mucin PMGLe, Doan-Thanh-Lam 14 October 2011 (has links)
Dans le tractus gastro-intestinal, l'adhésion des bactéries commensales à l’épithélium permet leur maintien, ce qui aide à contrôler l’implantation de germes indésirables par des mécanismes de concurrence (effets nutritionnels, sites spécifiques d'adhésion ...). Bien que le rôle de la couche du mucus (principalement composée de glycoprotéines à haut poids moléculaire, appelées mucines) recouvrant la muqueuse soit connu et décrit depuis de nombreuses années, notamment pour sa fonction de barrière protectrice, l'intérêt pour décrypter les mécanismes précis d’interaction(s) avec le microbiote (bactéries commensales, pathogènes ou probiotiques) n’a que récemment émergé. Dans ce cadre, l'objectif de cette thèse, menée en collaboration entre le Laboratoire d’Ingénierie des Systèmes Biologiques et des Procédés de Toulouse et le Laboratoire d’Analyse et d’Architecture des Systèmes de Toulouse, est de caractériser in vitro le comportement muco-adhésif de Lactococcus lactis, le modèle des bactéries lactiques, en utilisant des approches de quantification multi-échelles (du niveau moléculaire à l’échelle multicellulaire) sur un large panel de souches naturelles et recombinantes. Une attention particulière est accordée au rôle des mucines, en utilisant le modèle PGM (mucine gastrique de porc ou « Pig Gastric Mucin »).La première partie du travail a porté sur la quantification à l'échelle de la cellule unique des interactions entre L. lactis et une surface abiotique (polystyrène) recouverte de PGM, en utilisant la microscopie à force atomique (AFM). La faisabilité de la méthode a tout d'abord été démontrée sur la souche modèle L. lactis ssp. cremoris MG1820. La couche de PGM a été caractérisée en utilisant des méthodes analytiques complémentaires (AFM, XPS - spectroscopie de photoélectrons induits par rayons X, QCM-D - Microbalance à Quartz à mesure de Dissipation...). En parallèle, les bactéries L. lactis ont été immobilisées sur la pointe AFM et utilisées comme « sonde de force », en considérant la souche naturelle IBB477 (L. lactis ssp. cremoris), d’origine laitière et présentant une forte persistance dans le tractus digestif du rat lors d’essais réalisés in vivo (collaboration avec l’Institut de Biochimie et de Biophysique de Varsovie, Pologne). Comparé aux conditions contrôle (i.e., surface de polystyrène sans PGM), les niveaux de force d'adhésion enregistrés entre L. lactis et PGM sont inférieurs, ceci en raison des répulsions électrostatiques, hydrophiles et stériques s’établissant entre la couche de PGM et la paroi cellulaire. La forme des courbes représentant l’évolution de la force au retrait en fonction de la distance est également différente. Une analyse détaillée souligne la contribution, conjointe et différente selon les souches testées, d’événements (i) non adhésifs, (ii) adhésifs non spécifiques (interactions électrostatiques, hydrophobes, de van der Waals) et (iii) adhésifs spécifiques (liaison de type ligand/récepteur). La contribution spécifique a ensuite été explorée plus finement en termes de constantes cinétiques d’association et de dissociation. Nous avons, par ailleurs, poursuivi notre exploitation de la biodiversité naturelle chez les lactocoques en étudiant la souche TIL448 (L. lactis ssp. lactis) d’origine végétale, en collaboration avec l’Institut MICALIS de Jouy-en-Josas. Nous avons ainsi démontré, pour la première fois chez L. lactis, le rôle combiné des protéines à domaine(s) MUB (« Mucus-Binding ») et des pili, à travers l'analyse approfondie des données AFM (force d'adhésion, répartition des événements adhésifs spécifiques/non spécifiques, distances d'interaction...). Le rôle des pili a été confirmé sur des souches recombinantes piliées (L. lactis ssp. lactis IL1403), toujours en partenariat avec l’Institut MICALIS de Jouy-en-Josas. En parallèle, en collaboration avec l’Unité de Glycobiologie Structurale et Fonctionnelle de Villeneuve d'Ascq, nous avons cherché à identifier les O-glycannes de PGM (fractions neutre et acide), impliqués dans le processus d'interaction avec la surface bactérienne. Pour confirmer l’ensemble des résultats obtenus à l'échelle de la cellule unique et en mode statique par AFM (effet anti-adhésif de PGM, comportement muco-adhésif différent selon les souches de L. lactis), la deuxième partie du travail a été consacrée à des expérimentations à l’échelle de l’ensemble de la population bactérienne, en conditions dynamiques (QCM-D, chambre à écoulement cisaillé). Nous avons évalué par QCM-D chez les souches IBB477 et MG1820 les propriétés viscoélastiques des dépôts bactériens, en relation avec le comportement bio-adhésif vis-à-vis de la couche de PGM. Les données obtenues par AFM et chambre à écoulement cisaillé sur ces mêmes souches ont été confrontées pour accéder plus finement au mode d’interaction avec PGM (densité de liaisons sur la surface bactérienne). Enfin, nous avons évalué chez IL1403 l’effet des pili sur la dynamique de détachement et d’orientation sous cisaillement contrôlé.En conclusion, la combinaison des échelles d'observation et d’analyse, aussi bien au niveau de la cellule unique qu’à celui de l’ensemble de la population bactérienne, nous permet désormais de disposer de nouvelles connaissances sur les mécanismes diversifiés d'interaction entre L. lactis et PGM, visant à une meilleure compréhension des fonctionnalités de cette bactérie au niveau du tractus gastro-intestinal / In the gastrointestinal tract, adhesion of commensal bacteria to epithelial cells allows their retention, which helps to control the implementation of unwanted germs through mechanisms of competition (nutritional effects, specific sites of adhesion ...). Indeed, bacterial adhesion to the intestinal epithelium seems to be important for the balance of intestinal microbiota. Although the role of the mucus layer lining the mucosa, which is mainly composed of large glycoproteins termed mucins, is known and described for many years, particularly for its protective barrier function, the interest for unraveling precise mechanisms of interaction with bacteria (commensal, pathogens or probiotics) has just recently emerged. In this framework, the aim of the PhD thesis was to characterize in vitro muco-adhesive behavior of Lactococcus lactis, the model of Lactic Acid Bacteria, using multi-scale approaches (from molecular to multicellular levels) on a large set of natural and recombinant strains. A particular attention was paid to the role of mucins, using the PGM model (Pig Gastric Mucin).The first part of the work was focused on the quantification at nanoscale of interactions between L. lactis and adsorbed PGM, using AFM. The feasibility of the method was first demonstrated on the reference strain MG1820. PGM coating was characterized using a complementary set of analytical methods (AFM, XPS, quartz crystal microbalance with dissipation monitoring…). In parallel, L. lactis cells were immobilized onto the AFM tip and used as a living force probe, considering the natural strain IBB477 (L. lactis subsp. cremoris), isolated from Polish artisanal dairy products and previously shown to display in vivo retention in the rat gut (collaboration with the Institute of Biochemistry and Biophysics of Warsaw, Poland). Compared to control conditions (i.e., no PGM coating), adhesion force levels recorded for PGM were lower, due to the interplay of electrostatic, hydrophilic and steric repulsions. The shape of retraction force-distance curves for L. lactis/PGM interactions was also different. The detailed analysis of curve shape highlighted the contribution of non-adhesive, non-specific (electrostatic, hydrophobic, van der Waals interactions) and specific adhesive events (ligand/receptor bonding), depending on the strain under study. Specific forces were analyzed in terms of dissociation/association kinetic constants.We then explored the natural biodiversity among lactococci by studying the natural strain of L. lactis (subsp. lactis) TIL448 from plant origin, in collaboration with MICALIS (Jouy-en-Josas). We demonstrated, for the first time for L. lactis, the combined role played by “MUB-like” domain-containing protein and pili, through the thorough analysis of AFM data (adhesion force, repartition of specific/non-specific adhesive events and distances of interaction…). The role of pili was also confirmed with recombinant piliated strains (L. lactis subsp. lactis IL1403), in partnership with MICALIS (Jouy-en-Josas). In parallel, in collaboration with the “Unité de Glycobiologie Structurale et Fonctionnelle de Villeneuve d'Ascq”, a first attempt was done to identify the O-glycans of PGM (neutral and acid fractions), involved in interactions with the bacterial surface.To confirm these results achieved at single-cell scale and under static mode by AFM (anti-adhesive of PGM, different muco-adhesive properties among several strains of L. lactis), the second part of the work was devoted to experiments at multicellular scale under dynamic conditions (quartz crystal microbalance with dissipation monitoring – QCM-D, shear stress flow chamber). We evaluated by QCM-D, for MG1820 and IBB477 strains, the viscoelastic properties of the cell layers, in relation with the bio-adhesive behavior towards PGM. The data obtained by AFM and shear stress flow chamber were combined to access more precisely to the interaction mode with PGM (density of bonds over the cell surface). Finally, using the recombinant piliated strain (IL1403), we focused on the effect of pili on detachment and re-orientation dynamics under shear flow
|
Page generated in 0.0318 seconds