Bone marrow mesenchymal stem cells (BM-MSCs) are pluripotent cells that can differentiate into a variety of non-hematopoietic tissues. They also maintain healthy heamatopoiesis by providing supportive cellular microenvironment into BM. In this thesis, MSCs were characterized in terms of their morphological, immunophenotypical and differentiation properties. Then, they were examined by attenuated total reflection-Fourier transform infrared (ATR-FTIR) spectroscopy together with hierarchical clustering, and FTIR microspectroscopy. In the first part of this study, global structural and compositional changes in BM-MSCs during beta thallasemia major (

The field of molecular bioenergetics deals with the energy transduction in biological cells. In this project, respiration and more specifically proton and sodium pumping enzymes and their coupling to electron transfer have been in focus. First we have been interested in the Na+-pumping NADH:quinone reductase from Vibrio cholerae which is the entry site of electrons in the respiratory chain of several pathogens. The role of specific flavin cofactors and amino acids involved in Na+ transfer has been shown in a combined IR spectroscopic and electrochemical approach. The interaction between proteins, namely the cytochrome c552 and the CuA fragment from the terminal ba3 oxidase from the organism Thermus thermophilus was then investigated. Structural reorganization during electron transfer was revealed by IR spectroscopy. Finally, in the third part of the project the interaction within the bc1-aa3 supercomplex from the respiratory chain from Corynebacterium glutamicum was analyzed.

As the most prevalent cause of dementia worldwide, Alzheimer’s disease (AD) has become a global issue of public health. By current criteria, diagnosis of this neurodegenerative disorder requires both clinical confirmation of dementia and post-mortem detection of the so-called neurofibrillary tangles and senile plaques in the brain. Yet the main proteinaceous component of these plaques, the amyloid beta peptide (Abeta) is now widely believed to initiate a cascade of events that ultimately leads to Alzheimer’s disease. Besides, extensive evidence supports a pathogenic role of soluble oligomers formed upon Abeta aggregation in the onset of the disease, which, unlike Abeta fibrils, present distinct neurotoxic properties and correlate well with disease progression. Their detrimental effects have been suggested to appear decades before the first signs of cognitive impairment, making them biomarkers of choice in the study of the pathology. <p>Given that present guidelines for AD diagnosis are increasingly considered as ill-defined, reliable and early-stage detection methods taking into account the presence of toxic Abeta species are highly awaited by the medical community. In this regard, this thesis work describes the development of a sensing device aiming at the specific detection of the amyloid beta peptide in solution via recognition by antibodies grafted at the surface of functionalized germanium crystals. This new type of BIA-ATR (Biospecific Interaction Analysis - Attenuated Total Reflection) biosensor resorts on ATR-FTIR (Attenuated Total Reflection - Fourier Transform Infrared) spectroscopy, which is extremely sensitive to the secondary structure of proteins. The ATR mode uses germanium as optical transduction element combined to the evanescent wave principle to allow selective online monitoring of peptide-antibody binding events. <p>In the first part of this work, evaluation of the photochemistry on germanium optical elements have been the subject of intense research focus. Our investigations led to the elaboration of a quality control of functionalization efficiency based on infrared spectroscopy. We also set up in the lab an original ELISA method for selecting antibodies in terms of their true affinity for the Abeta peptide. <p>Thereafter binding experiments were carried out on the BIA-ATR sensor using different antibodies and Abeta isoforms, leading to the establishing of a standardized protocol for the detection of molecules of interest. Our results showed that Abeta detected on the biosensor corresponded precisely to antibody-bound peptide, whereas Abeta assemblies, and especially Abeta 1-42 oligomeric conformations, could be discriminated with respect to their spectral signature. This point, which was later confirmed by unsupervised statistical analysis, could be considered as particularly interesting and innovative, since to our knowledge, such conformation-sensitivity has never been observed with existing AD diagnostic methods. Moreover, effective recycling of the functionalized crystals has been demonstrated, which confers thereby a second major advantage to the biosensor. <p>In parallel to these experiments, a structural characterization study of Abeta species was undertaken in order to generate a database of IR spectra, as reference for future comparative analysis of physiological fluids on the biosensor. ATR-FTIR measurements revealed a strong dependency on the ratio between oligomers and fibrils within a mixture and their relative ratio in antiparallel and parallel beta-sheet content. Interestingly, separation trials of oligomeric entities demonstrated a specific effect of Cu2+ ions on Abeta aggregation. Stabilization of small oligomeric aggregates at equimolar Cu2+:Abeta ratios, which had never been clearly evidenced so far, could help to unravel some aspects of the complex role of copper in AD development. <p>These investigations illustrate the applicability of the so-called BIA-ATR methodology to online detection of different forms of the Abeta peptide in solution and the potential of this new sensor technology to fulfill current pitfalls in providing a reliable and comprehensive approach of AD diagnosis. / Doctorat en Sciences agronomiques et ingénierie biologique / info:eu-repo/semantics/nonPublished

La cytochrome c oxydase (CcO) est un complexe protéique commun à tous les organismes aérobies. Elle catalyse la réduction de l’oxygène en eau au niveau d’un site catalytique qui contient un atome de fer hémique et un atome de cuivre (CuB). La famille de ces oxydases est ainsi appelée super famille des oxydases à "hème-cuivre". Malgré le grand nombre d’études réalisées au sujet de l’activité catalytique des CcO, le déroulement exact des étapes de leur mécanisme reste encore mal connu. Afin de mieux cerner le problème de la relation structure-activité de cette hémoprotéine, deux approches distinctes et complémentaires ont été abordées : l’étude du système naturel et l’approche biomimétique. Les propriétés électroniques et vibrationnelles de certains intermédiaires du cycle catalytique de la cytochrome c oxydase ont été caractérisées par spectroscopies UV-Visible, de fluorescence résolue en temps et infrarouge. L’analyse du site actif de la CcO par des substitutions isotopiques du CuB, ainsi que l’influence du pH sur la structure de cet enzyme sont discutées. La deuxième partie de ce travail concerne l’étude du rôle de l’environnement proche de l’hème sur la réactivité des complexes FeII-CO et FeII-O2 grâce à une série de modèles superstructurés du centre binucléaire Fe/Cu de la CcO. Ces analogues synthétiques conservent l’hème, la ligation fer-histidine du site proximal et le ligand complexant le cuivre du site distal de la CcO, mais se différencient notamment par leur environnement autour de l’atome de cuivre et par leur rigidité. Deux techniques ont été utilisées: la spectroscopie ATR-IRTF et la photochimie dans le cas d’espèces carbonylées. / Cytochrome c Oxidase (CcO), a member of the heme-copper oxidase superfamily, is a membrane protein in many aerobic organisms, that catalyses the reduction of dioxygen to water. Dioxygen binding and reduction occurs at a heterobinuclear site that is comprised of a heme a3, and a copper atom (CuB) in close proximity. Despite, the CcO has been the subject of numerous biophysical and spectroscopic investigations, the detailed molecular mechanism of CcO remains still elusive. In order to better define the structure-function relationship for this hemoprotein, two distinct and complementary approaches have been employed: the study of the natural system and the biomimetic approach.Structural changes accompanying the change in the redox state of some CcO intermediates have been characterised by UV-Visible, ATR-FTIR and time-resolved fluorescence spectroscopies. The study of the cytochrome c oxydase active site modified with isotopic substitutions of CuB, and the effect of pH on the structure are discussed. The second part of this work is related to study the role of environment on the reactivity of FeII-CO et FeII-O2 complexes by exploiting a series of superstructured models of the binuclear Fe/Cu active site of CcO. Based upon a porphyrin core, all these models have the iron-histidine ligation of the proximal site and the copper ligand of the distal site of CcO but they differ strongly by the environment around the copper and their rigidity.

This diploma thesis is focused on the study of structure and physicochemical properties of organic fractions of humic substances, which were obtained by the method of thin-layer chromatography. Humic substances, which were used in this study, were isolated from a sample of Slovak alginite based on the procedure of the International Humic Substances Society (IHSS). The following analytical techniques were selected for the characterization of isolated humic substances: thermogravimetric and elemental analysis, molecular absorption spectroscopy (UV/Vis), Fourier transform infrared spectroscopy (FTIR) and steady-state fluorescence spectroscopy. Each organic fraction of humic substances were characterized by molecular absorption spectroscopy (UV/Vis) and steady-state fluorescence spectroscopy. Using steady-state fluorescence spectroscopy, humic substances were found to be composed of fluorophores of humic and non-humic (protein) character. Organic fractions corresponding to the humic fluorophores were characterized by a higher content of oxygen substituents on the aromatic nukleus, a higher degree of aromaticity and also a higher molecular weight. The aim of this diploma thesis was to design and optimize the process of organic matter fractionation for the purpose of detailed understanding of the structure and properties of humic substances, which were isolated from the sedimentary rock alginite. Based on this, the practical applicability of the thin layer chromatography method to significantly reduce the molecular heterogenity of the studied humic substances was evaluated.

Die Dissertation befasste sich mit der Entwicklung einer neuen diagnostischen Methode für in-situ-Gewebeuntersuchungen. Der Ansatzpunkt war die Untersuchung von pathologischen Veränderungen im Gewebe, die sich biochemisch in den Zellen widerspiegeln und deshalb mit schwingungsspektroskopischen Methoden, wie der IR-Spektroskopie, erfassbar sind. Das Ziel der Arbeit war die IR-spektroskopische Charakterisierung und Klassifizierung von benignen, präkanzerösen und malignen Geweben mittels chemometrischer Algorithmen auf der Basis multivariater Informationen der IR-Spektren. Um komplexe spektrale Veränderungen zu charakterisieren und die Ergebnisse statistisch abzusichern, ist für jeden Gewebetyp eine Vielzahl an Spektren erforderlich. Daher wurde zur Spektrenakkumulation das IR-mikrospektroskopische Imaging mittels Focal Plane Array Detektor (FPA) genutzt. Die Herausforderung liegt in der Datenanalyse. Der große Datenumfang macht die Anwendung multivariater Algorithmen notwendig. Angewendet wurden Clusteralgorithmen zur Spektrendifferenzierung und die SIMCA (Soft Independent Modelling of Class Analogies) zur Spektrenklassifizierung. Die Validierung der Ergebnisse erfolgt über die histologische Untersuchung der nach der spektroskopischen Messung gefärbten Gewebedünnschnitte. Die genaue Vorgehensweise bei der Auswertung wird in dieser Arbeit anhand humaner Gewebeproben dargestellt. Die untersuchten Plattenepithelkarzinome und Adenokarzinome gehören zu den epithelialen Tumoren, die oralen bzw. zervikalen Ursprungs sind. Die Übertragbarkeit der spektralen Modelle wurde mit Gewebeproben mehrerer Patienten innerhalb einer und zwischen verschiedenen Tumorarten untersucht. Das ist ein erster Schritt zum Einsatz spektroskopischer Methoden in der medizinischen Forschung und Diagnostik.

Die Zellmembran dient der Zelle nicht nur als äußere Hülle, sondern ist auch an einer Vielzahl von lebenswichtigen Prozessen wie Signaltransduktion oder Zelladhäsion beteiligt. Wasser als integraler Bestandteil von Zellen und der extrazellulären Matrix hat sowohl einen großen Einfluss auf die Struktur von Biomolekülen, als auch selbst besondere Merkmale in eingschränkter Geometrie. Im Rahmen dieser Arbeit wurden zwei Effekte an Modellmembranen untersucht: Erstens der Einfluss des Gegenions an kationischen Lipiden (DODAX, X = F, Cl, Br, I) auf die Eigenschaften des Grenzflächenwassers und zweitens das Vermögen durch Viskositätsänderungen das Wachstum von Nervenzellen anzuregen sowie die einzelnen Stadien der Bildung von neuronalen Netzwerken und deren Optimierung zu charakterisieren. Lipidmultischichten und darin adsorbiertes Grenzflächenwasser wurden mittels Infrarotspektroskopie mit abgeschwächter Totalreflexion untersucht. Nach Charakterisierung von Phasenverhalten und Wasserkapazität der Lipide wurden die Eigenschaften des Wassers durch kontrollierte Hydratisierung bei einem Wassergehalt von einem Wassermolekül pro Lipid verglichen. Durch die geringe Wasserkapazität können in diesem besonderen System direkte Wechselwirkungen zwischen Lipiden und Wasser aus der ersten Hydratationsschale beobachtet werden. Bemerkenswert strukturierte OH-Streckschwingungsbanden in Abhängigkeit des Anions und niedrige IR-Ordnungsparameter zeigen, dass stark geordnete, in ihrer Mobilität eingeschränkte Wassermoleküle an DODAX in verschiedenen Populationen mit unterschiedlich starken Wasserstoffbrückenbindungen existieren und sich vermutlich in kleinen Clustern anordnen. Die zweite Fragestellung hatte zum Ziel, das Wachstum von Nervenzellen auf Membranen zu beleuchten. Auf der Ebene einzelner Zellen wurde untersucht, ob sich in Analogie zu den bisher verwendeten elastischen Substraten, die Viskosität von Membranen als neuartiger physikalischer Stimulus dafür eignet, das mechanosensitive Verhalten von Neuronen zu modulieren. Das Wachstum der Neuronen wurde auf substrat- und polymergestützten Lipiddoppelschichten mittels Phasenkontrastmikroskopie beobachtet. Die Quantifizierung der Neuritenlängen, -auswuchsgeschwindigkeiten und -verzweigungen zeigten kaum signifikante Unterschiede. Diffusionsmessungen (FRAP) ergaben, dass entgegen der Erwartungen, die Substrate sehr ähnliche Fluiditäten aufweisen. Die Betrachtung der zeitlichen Entwicklung des kollektiven Neuronenwachstums, also der Bildung von komplexen Netzwerken, offenbarte robuste „Kleine-Welt“-Eigenschaften und darüber hinaus unterschiedliche Stadien. Diese wurden durch graphentheoretische Analyse beschrieben, um anhand typischer Größen wie dem Clusterkoeffizienten und der kürzesten Pfadlänge zu zeigen, wie sich die Neuronen in einem frühen Stadium vernetzen, im Verlauf eine maximale Komplexität erreichen und letztlich das Netzwerk durch effiziente Umstrukturierung hinsichtlich kurzer Pfadlängen optimiert wird.

El conocimiento de las características interfaciales es de suma importancia para poder desarrollar materiales que sean capaces de dar lugar a reacciones electrocatalíticas eficientes. Por esta razón, en esta tesis se muestran diferentes estudios interfaciales sobre superficies monocristalinas de platino y cobre en diferentes electrolitos. Además se estudian las características de la interfase electrodoldisolución con superficies de platino modificadas con adátomos de hierro, cobalto y níquel. Para ello, se han empleado las técnicas de voltametría cíclica, espectroscopía infrarroja con transformada de Fourier, desplazamiento de carga con CO y salto de temperatura inducido por láser. Los resultados muestran cómo varía el campo eléctrico interfacial disminuye al aumentar el recubrimiento de hierro y níquel en la superficie de platino. Este efecto tiene un gran impacto en la reacción de evolución de hidrógeno, ya que la mejora electrocatalítica de esta reacción está relacionada con la energía de reorganización de las moléculas de agua, la cual, depende de la fortaleza del campo eléctrico interfacial. Los estudios realizados en medio alcalino para las diferentes superficies de cobre y platino sin modificar muestran una correlación entre el potencial de máxima entropía y las funciones de trabajo para cada una de las diferentes orientaciones atómicas superficiales. Por otro lado, debido a la aplicabilidad de las nanopartículas en los sistemas reales de conversión de energía, se realizaron experimentos de sincrotrón empleando la técnica de Bragg coherent difraction imaging con el objetivo de estudiar el deterioro de las nanopartículas en condiciones operando.

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Plastskräp har blivit ett global problem på grund av nedskräpning och otillräcklig avfallshantering. Användning av biologiskt nedbrytbart material kan underlätta problemet, även om det inte är en universallösning. Produkter gjorda av biologiskt nedbrytbart material skall ändå till avfallshantering eftersom nedbrytningen kan vara långvarig och variera mycket beroende av omgivningen. Därmed är användningen av biologiskt nedbrytbart material endast berättigat då det är svårt att samla in materialet eller avskilja det från organiskt material. Studiens mål var att undersöka biologiskt nedbrytbara material som kan användas i produkter som fungerar under många olika driftsförhållanden och inte kan återställas efter användning. I den litterära delen av denna studie definieras nedbrytning genom egenskaper och förhållanden som påverkar nedbrytningsprocessen. Nedbrytning av polyestrar och cellulosa och de standardprocessarna som används i nedbrytningsexperimenten betraktades. Standardprocesserna för nedbrytning studerades för att få en klarare inblick i den eftertraktade nedbrytningsgraden och de standardiserade förhållandena för nedbrytningen i olika miljöer. En sammanfattning av olika nedbrytningsexperiment och analysmetoder är också inkluderade för att försäkra att experimenten som utfördes är både giltiga och jämförbara med andra forskningsresultat inom fältet. I detta forskningsprojekt utfördes nedbrytningsexperiment i färskvatten- och hemkompostmiljöer. Målet med projektet var att bedöma ifall materialen kunde brytas ned i ett brett spektrum av miljöer, ifall de var mindre skadliga för naturen än konventionella material som används av dagens industri och för att uppskatta nedbrytningstakten. Nedbrytningstiden var 140 dagar och experimentet utfördes med 10 olika material: betecknade som A-J. Materialen analyserades 8 gånger under nedbrytningsperioden förutom materialen I och J som analyserades en gång efter 140 dagar. Materialen analyserades mekaniskt, strukturellt och termiskt med hjälp av dragprovning, FTIR och DSC. Provernas viktförändring bestämdes också. Nedbrytning observerades visuellt från provernas yta och genom mekaniska prover. Materialen som placerades i hemkomposten visade klara tecken på nedbrytning då färgen hade förändrats och förstärkningsfibrerna hade blivit synliga. Materialen som placerats i hemkompostmiljö visade också klara tecken på tillväxt av mikroorganismer och biomassa som uppstått på ytan av materialen. Sammanfattningsvist, visade materialen B, C och G de mest lovande resultaten med klara tecken på biologisk nedbrytning och de hade en snabbare nedbrytningstakt än de andra materialen som undersöktes. Material D visade klara tecken på biologisk nedbrytning på ytan men dess nedbrytningstakt var uppskattad att vara mycket långsammare. Därmed rekommenderas det att använda material A, B, D och G istället för konventionella icke biologiskt nedbrytbara material. Dessa material har potential att sänka den negativa inverkan och de långsiktiga riskerna av plastskräp för miljön. / Plastic debris has become a global crisis due to littering and misplaced waste management. The use of biodegradable materials can ease the problem, but it is not always the answer. Products made of biodegradable materials are still to be waste managed since biodegradation can be a long process and is highly dependent on the environment conditions. Hence, the use of biodegradable materials is justified only when retrieving the product after use is impossible or prohibitively expensive or separating it from organic matter is difficult. This study was made to investigate biodegradable materials that can be used in products that are operating in broad range of operational conditions and cannot be retrieved back after use in most cases. In the literature part of this study the biodegradation is defined along with properties and conditions that affect the biodegradation process. Biodegradation of polyesters and cellulose, and standards used in the biodegradation experiments were reviewed. Biodegradation standards were studied in order to have a clearer picture of the pursued degree of biodegradation and standardized properties in the biodegradation experiments. Review of different biodegradation tests and analysis methods are included as well to ensure that the experiments performed in this work are valid and comparable with other biodegradation studies.  In this study, the biodegradation experiment was conducted in freshwater and home compost environments. The aim was to determine if the materials were able to biodegrade in wide range of environments, to make sure they are less harmful than the conventional materials used in the industry and to estimate the rate of biodegradation. The duration of the experiments were 140 days with 10 different materials: A – J. The materials were analyzed 8 times during the aging period, except materials I and J, which were analyzed only once after 140 days. The samples were analyzed mechanically, structurally, and thermally using tensile test, FTIR and DSC measurements, respectively. Also, the samples weight changes were analyzed.  The degradation was visually observed from the surfaces of the samples and from mechanical testing in both experimental environments. Home compost environment showed clear signs of biodegradation where reinforcement fibers became visible and changed the color of some of the samples. Also, home compost samples had microorganisms growing on them, and biomass was developing around them. To conclude, material B, C and G had the most promising results with clear signs of biodegradation and had faster estimated biodegradation rate compared with the other studied materials. Material D had signs of biodegradation on the surface as well. However, the biodegradation rate was estimated to be much slower. In conclusion, it is recommended to use the studied materials A, B, D and G instead of the conventional non-biodegradable polymers. These materials have potential to lower the negative impact and long-term risks of plastic debris to the environment.