Made available in DSpace on 2014-12-17T15:01:34Z (GMT). No. of bitstreams: 1 CarlosEAP_DISSERT.pdf: 1904684 bytes, checksum: 4fd2147b17a381ad69d921436b5c83de (MD5) Previous issue date: 2013-12-18 / Coordena??o de Aperfei?oamento de Pessoal de N?vel Superior / Expanded Bed Adsorption (EBA) is an integrative process that combines concepts of chromatography and fluidization of solids. The many parameters involved and their synergistic effects complicate the optimization of the process. Fortunately, some mathematical tools have been developed in order to guide the investigation of the EBA system. In this work the application of experimental design, phenomenological modeling and artificial neural networks (ANN) in understanding chitosanases adsorption on ion exchange resin Streamline? DEAE have been investigated. The strain Paenibacillus ehimensis NRRL B-23118 was used for chitosanase production. EBA experiments were carried out using a column of 2.6 cm inner diameter with 30.0 cm in height that was coupled to a peristaltic pump. At the bottom of the column there was a distributor of glass beads having a height of 3.0 cm. Assays for residence time distribution (RTD) revelead a high degree of mixing, however, the Richardson-Zaki coefficients showed that the column was on the threshold of stability. Isotherm models fitted the adsorption equilibrium data in the presence of lyotropic salts. The results of experiment design indicated that the ionic strength and superficial velocity are important to the recovery and purity of chitosanases. The molecular mass of the two chitosanases were approximately 23 kDa and 52 kDa as estimated by SDS-PAGE. The phenomenological modeling was aimed to describe the operations in batch and column chromatography. The simulations were performed in Microsoft Visual Studio. The kinetic rate constant model set to kinetic curves efficiently under conditions of initial enzyme activity 0.232, 0.142 e 0.079 UA/mL. The simulated breakthrough curves showed some differences with experimental data, especially regarding the slope. Sensitivity tests of the model on the surface velocity, axial dispersion and initial concentration showed agreement with the literature. The neural network was constructed in MATLAB and Neural Network Toolbox. The cross-validation was used to improve the ability of generalization. The parameters of ANN were improved to obtain the settings 6-6 (enzyme activity) and 9-6 (total protein), as well as tansig transfer function and Levenberg-Marquardt training algorithm. The neural Carlos Eduardo de Ara?jo Padilha dezembro/2013 9 networks simulations, including all the steps of cycle, showed good agreement with experimental data, with a correlation coefficient of approximately 0.974. The effects of input variables on profiles of the stages of loading, washing and elution were consistent with the literature / A adsor??o em leito expandido (ALE) ? uma t?cnica integrativa que alia conceitos de cromatografia e fluidiza??o de s?lidos. A diversidade de par?metros envolvidos e seus efeitos sinerg?ticos dificultam a tarefa de otimiza??o da opera??o. Felizmente, algumas ferramentas matem?ticas foram desenvolvidas de modo a direcionar as investiga??es do sistema ALE. Assim, o presente trabalho prop?e a aplica??o do planejamento experimental, modelagem fenomenol?gica e redes neurais artificiais (RNAs) na compreens?o da adsor??o de quitosanases na resina de troca i?nica Streamline? DEAE. A cepa Paenibacillus ehimensis NRRL B-23118 foi respons?vel pela produ??o das quitosanases. Nos ensaios de adsor??o usando o leito na forma expandida foi utilizada uma coluna de 2,6 cm de di?metro por 30,0 cm de altura, acoplada a uma bomba perist?ltica. Na base da coluna existia um distribuidor de microesferas de vidro com altura de 3,0 cm. Os ensaios de determina??o de tempo de resid?ncia (DTR) revelaram elevado grau de mistura, entretanto, os coeficientes de Richardson-Zaki mostraram que a coluna estava no limiar da estabilidade. Pelas regress?es das isotermas puderam-se ajustar os dados de equil?brio de adsor??o, na presen?a de diferentes sais da escala liotr?pica. O resultado do planejamento apontou que a for?a i?nica e a velocidade influenciam a recupera??o e pureza das quitosanases. As massas moleculares das duas esp?cies de quitosanases foram estimadas por SDS-PAGE, obtendo-se aproximadamente 23 kDa e 52 kDa. A modelagem fenomenol?gica foi direcionada para descrever as opera??es em batelada e na coluna cromatogr?fica. As simula??es foram executadas no Microsoft Visual Studio, usando a linguagem Fortran. O modelo de taxa constante ajustou-se ?s curvas cin?ticas com excel?ncia, nas condi??es de atividade iniciais 0,232, 0,142 e 0,079 UA/mL. As curvas de ruptura simuladas apresentaram algumas disparidades com os dados experimentais, principalmente quanto ? inclina??o. Os testes de sensibilidade do modelo sobre a velocidade superficial, dispers?o axial e concentra??o inicial mostraram conformidade com artigos publicados. A rede neural foi constru?da no ambiente MATLAB, por meio da Neural Network Toolbox. A valida??o cruzada foi usada para melhorar a capacidade de generaliza??o. Carlos Eduardo de Ara?jo Padilha dezembro/2013 6 Aperfei?oaram-se os par?metros da RNA at? se obter as configura??es 6-6 (atividade enzim?tica) e 9-6 (prote?nas totais), fun??o de ativa??o tansig e algoritmo de treinamento Levenberg-Marquardt. As simula??es da rede neural, incluindo todo o ciclo da opera??o, mostraram boa concord?ncia com os dados experimentais, com coeficiente de correla??o da ordem de 0,974. Os efeitos das vari?veis de entrada sobre os perfis das etapas de carga, lavagem e elui??o foram compat?veis com a literatura

This thesis deals with the research work carried out for the development of novel applications by integrating biomolecules with various nanostructures. The thesis is organized as follows: Chapter 1 reviews the properties of nanomaterials which are important to consider while developing them for various biological and other applications. It discusses the factors which affect the cytotoxicity of nanocrystals towards living cells, photocatalytic mechanisms of nanocrystals that work behind the inactivation of bacterial cells and gas sensing properties of nanocrystals. It also mentions about the integration of biomolecules with nanomaterials which is useful for the development of biosensors, materials that are presently used for fabricating biosensors and the challenges associated with designing successful biosensors. Chapter 2 presents the antibacterial and anticancer properties of ZnO/Ag nanohybids. In this study a simple route to synthesize ZnO/Ag nanohybrids by microwave synthesis has been established where ZnO/Ag nanohybrids have shown synergistic cytotoxicity towards mammalian cells. The observed synergism in the cytotoxicity of ZnO/Ag nanohybrids could lead to the development of low dose therapeutics for cancer treatment. Chapter 3 presents photocatalytic inactivation of bacterial cells by pentavalent bismuthates class of materials. AgBiO3 which was obtained from KBiO3 by ion-exchange method was investigated for its photocatalytic inactivation properties towards E.coli and S.aureus cells under dark and UV illumination conditions. Chapter 4 presents the integration of DNA molecules with ZnO nanorods for the observation of Mott-Gurney characteristics. In this study, ZnO nanorods were synthesized hydrothermally and were characterized by TEM and XRD analysis. DNA molecules were immobilized over ZnO nanorods which were confirmed by UV-Vis spectroscopy and confocal florescence microscopy. Solution processed devices were fabricated by using these DNA immobilized nanostructures and I-V characteristics of these devices were taken in dark and under illumination conditions at different wavelengths of light at fixed intensity. Interestingly, Mott-Gurney law was observed in the I-V characteristics of the devices fabricated using DNA immobilized ZnO nanorods. Chapter 5 presents the chemical synthesis of molecular scale ultrathin Au nanowires. These nanostructures were then used for fabricating electronic biosensors. In this study, the devices were fabricated over Au nanowires by e-beam lithography and a methodology to functionalize Au nanowires and then characterize them by florescence microscopy as well as AFM has been established. The fabricated biosensors were employed for the label free, electrical detection of DNA hybridization process. Chapter 6 presents a simple, cost effective and solution processed route to fabricate devices using ultrathin Au nanowires. The devices were then used for sensing ethanol, H2 and NH3. An important property of these devices is that they can sense these gases at room temperature which reduce their operation cost and makes them desirable to use under explosive conditions.

Ce travail de thèse a démontré la possibilité de mesurer la relaxation d’un complexe biomoléculaire ainsi que son hétérogénéité structurale, en associant la microfluidique et la fluorescence résolue en temps (FRT). Je présente de quelle façon la FRT permet d’obtenir une information sur la structure d’une molécule et comment on la mesure, notamment grâce à une caméra à balayage de fente. J’introduis ensuite la microfluidique de gouttes, permettant de mélanger deux réactifs en quelques millisecondes et de suivre la relaxation du complexe au cours de la propagation des micro-réacteurs. Puis, la mesure d’une cinétique avec un couple de molécules modèle démontre la preuve de principe, faisant l’objet d’un article soumis. Enfin la mesure de FRT par comptage de photons uniques dans des gouttes uniques est décrite. Elle ouvre une perspective d’application pour le criblage à haut débit : un brevet a été déposé. / This thesis has proven the feasibility of measuring the relaxation of a biomolecular complex as well as its structural heterogeneity, by associating microfluidics and time resolved fluorescence (TRF). I present in which way TRF allows for probing the structure of a molecule and how it is measured, in particular by using a streak camera. I then introduce droplet microfluidics, which enables to mix two reagents in a few milliseconds and to follow the relaxation of the complex, along propagation of the micro-reactors. Next, the measurement of a kinetics with test molecules validates the proof of concept, reported in a submitted article. Finally, the measurement of TRF by single photon counting in single droplets is described. It opens a perspective for an application in high-throughput screening: a patent has been registered.

Les assemblages supramoléculaires font parties des réactions biochimiques de base dans les fonctions cellulaires (ex: réplication de l'ADN ou réponse immunitaire). Les calix[n]arènes ont été décrit pour interagir avec une large gamme de biomolécules. En conséquence, ils peuvent être trouvés dans de nombreuses applications biologiques tel qu'en diagnostic ou en traitement thérapeutique. Leurs fonctionnalisations sur des nanoparticules d'argent ont produit de nouveaux nano-composés hybrides ayant des propriétés optique, électrique et biologique uniques. Cette thèse a été dédiée à l'étude de ces nano systèmes pour la bio-détection et leurs potentielles applications biomédicales. Le développement de capteur analytique à bas coût, portable et ultra-sensible représente une des attentes majeures dans les applications des calix[n]arènes sur nanoparticules d'argent. Dans cette thèse, ces nano-composés ont été étudiés selon leurs capacités à suivre la micellisation de surfactant mixtes, et pour discriminer un type moléculaire tel qu'une famille d'acide nucléique ou une espèce d'albumine sérique. Dans une deuxième partie, ces nanoparticules hybrides ont été évaluées pour une série d'activités biologiques. Ils ont montré des facultés antibiotiques et anti-oxydantes, de transporter des Ingrédients Pharmaceutiques Actifs, et d'atteindre des cibles antivirales et anticancéreuses / Supramolecular assemblies are among the basic biochemical reactions in the cellular functions (e.g. DNA replication, immune response). Calix[n]arenes are macrocyclic molecules that have been reported for interacting with a wide range of biomolecules. As a consequence, they can be found in many biological applications from diagnosis to therapeutic treatment. Their functionalization on silver nanoparticles have produced new nano hybrid compounds with unique optical, electrical and biochemical properties. This thesis has been dedicated to the study of these nano-systems for bio-sensing and for their potent biomedical applications. Cost effective, portable and ultra-sensitive analytical tools are one of the major expectations of the applications of silver nanoparticles capped with calix[n]arenes. Calix[n]arenes nanoparticles have been reported here for following the micellisation process of mixed surfactants or for discriminating a type of molecule such nucleic acid or a serum albumin specie. In a second part, these hybrid nanoparticles have been evaluated for series of biological activities. They’ve been shown to possess anti-oxidant and antibacterial activities, to transport Active Pharmaceutical Ingredient and to reach antiviral and anti-cancer targets

Nanočástice perovskitů halogenidů kovů vykazují unikátní vlastnosti, především výjimečně vysoké hodnoty kvantových výtěžků fluorescence, které předurčují tyto materiály pro aplikace v optoelektronických a fotonických zařízeních. Tato práce popisuje přípravu nanočástic perovskitů halogenidů kovů pomocí stabilizačních činidel inspirovaných přírodou. Stabilizační činidla zde slouží nejen ke stabilizaci, ale i k modifikaci povrchu nanočástic za účelem zvýšení funkčnosti výsledných nanostruktur. Úvod práce popisuje optimalizaci přípravy nanočástic precipitační technikou za použití stabilizačních činidel; jako stabilizační činidlo byl zvolen adamantan-1-amin spolu s hexanovou kyselinou. Bylo prokázáno, že klíčový vliv na optické vlastnosti výsledných koloidních roztoků má volba rozpouštědel a teploty při precipitaci. Mimo jiné byl zkoumán vliv koncentrace prekurzorů na výslednou morfologii a optické vlastnosti nanočástic a jejich koloidních roztoků. V neposlední řadě byly nanočástice stabilizovány adamantan-1-aminem spolu s různými karboxylovými kyselinami a byly studovány optické vlastnosti a koloidní stabilita výsledných koloidních roztoků. V dalším kroku byly nanočástice perovskitů stabilizovány pomocí proetogenních aminokyselin L-lysinu and L-argininu. Takto stabilizované nanočástice vykazovaly úzká emisní spektra ve viditelné oblasti a kvantové výtěžky fluorescence dosahující hodnot téměř 100 %. Stabilizace nanočástic prostřednictvím postranních skupin aminokyselin byla prokázána navázáním chránící terc-butoxykarbonylové skupiny na -amino skupinu. Nanočástice stabilizované modifikovaným lysinem v průběhu jejich přípravy vykazovaly závislost optických vlastností na přítomnosti vody. Předpokládá se, že molekuly vody jsou schopné kontrolovat růst krystalové mřížky po navázání na prekurzory perovskitů a ovlivňovat tak výslednou velikost nanočástic, což vede k projevení kvantových jevů. Spojení nanočástic perovskitů s peptidy představuje nový typ materiálů kombinujících výjimečné optické vlastnosti se samoorganizačními a senzorickými vlastnostmi. Tento koncept byl představen přípravou nanočástic perovskitů stabilizovaných cyklo(RGDFK) pentapeptidem. Vzhledem k citlivosti peptidů na jejich byly nanočástice stabilizovány peptidovými nukleovými kyselinami, robustními analogy nukleových kyselin. Ke stabilizaci nanočástic byl připraven monomer a trimer peptidové nukleové kyseliny obsahující thymin jako dusíkatou bázi. Thymin byl na povrchu nanočástic dostupný k interakci s adeninem přes vodíkové můstky umožňující přenos náboje. Kombinace peptidových nukleových kyselin a perovskitů s unikátními optickými vlastnostmi otevírá aplikační možnosti zejména v oblasti optických senzorů.

The recent availability of X-ray Free Electron Lasers (XFELs) has opened a completely new and unexplored regime for the study of light-matter interactions. The extremely bright intensities delivered by XFELs can couple many photons into the target, turning well known interactions such as photoionization and scattering into new, non-linear, complex many-body phenomena. This thesis reports theoretical investigations aiming to improve the understanding of the fundamental processes and dynamics triggered by intense X-ray pulses, with a special focus in finite systems such as molecules and clusters. Sequential multiple photoionization in atomic clusters was investigated, where previous observations were extended for higher charge states where direct photoionization is frustrated. Through a rate equation study and subsequent molecular dynamics simulations, it was found that frustrated ionization is partially responsible for the low-energy peak observed in the electron energy spectrum. The influence of plasma evaporation over the formation of the sequential low-energy peak was also investigated, identifying the effects of the system size and photon energy. Multiple channel ionization was also investigated for the case of fullerenes. This is done through a series of studies, starting from a simplified rate equation scheme, and culminating with full molecular dynamics simulations. From these results, a good insight was obtained over the origin, physical meaning, and relevant parameters that give rise to the complicated features observed in the electronic spectra. The mechanisms responsible of all these features are expected to be present in other systems, making these results quite general. Diffractive imaging of biomolecules was studied in a final step, with a particular focus on the influence of intramolecular charge transfer mechanisms. To this end a conformer of T4 Lysozyme was used, a representative enzyme with well known structure. Charge migration is found to allow for additional processes such as proton ejection, a mechanism which enables an efficient release of energy from the system. This mechanism considerably suppresses structural damage for heavy ions, improving the quality of the measured diffraction patterns.

In dieser Arbeit wurde an einer Auswahl von Biomolekülen gezeigt, dass die Rasterkraftmikroskopie, welche ursprünglich in physikalischen Labors entwickelt und zunächst auch nur dort eingesetzt wurde, ein äußerst wichtiges Instrument innerhalb der biologischen und medizinischen Forschung darstellt. Es wurde gezeigt, welche Ergebnisse bei der Visualisierung von Biomolekülen erwartet werden können. Die nach einer eigens entwickelten Methode präparierten Actin-Proben konnten hochaufgelöst abgebildet werden. Es zeigten sich neben freiliegenden Einzelfilamenten auch Bündel, welche sich aus Einzelfilamenten zusammensetzen. Es ist ein Modell erstellt worden, welches die unterschiedlichen Breiten der Bündel erklärt. Mit Hilfe der Mikrokontakt-Druck-Technik (microcontact printing, µCP) ist es gelungen, Proteinstrukturen in der Größe weniger Nanometer großflächig auf verschiedene Substrate zu übertragen. Ebenso wurde ein proteophober SAM (self assembling monolayer) gestempelt, mit dem Proteinadsorptionen gezielt unterbunden werden konnten. Das Adsorptionsverhalten des Proteins F1-ATPase auf Gold ist in situ untersucht worden. Parallel dazu wurde die Adsorption des Proteins in einer Mikroquarzwaage (quarz crystal microbalance, QCM) untersucht. Beide Techniken zeigen unterschiedliche Adsorptions-kinetiken, die Kombination beider Methoden lässt jedoch eine Abschätzung der wahren Adsorptionskinetik zu. Ein neuer Messmodus (constant damping mode) ist ob seiner Fähigkeit, biologische Objekte abbilden zu können, geprüft worden. Vergleichsmessungen im Kontakt-, Nichtkontakt- und Dämpfungs-Modus an einer Proteinmultischicht zeigten, dass im Nichtkontakt-Modus die höchste Auflösung erzielt werden kann. Ferner sind Magnetkraftmikroskop-Experimente an dem als Eisenspeicher bekannten Protein Ferritin durchgeführt worden. An einer Submonolage Ferritin auf Glimmer lässt sich jedoch mit dieser Technik kein magnetisches Signal messen.

Lipids are a structurally diverse class of biomolecules which can undergo a variety of chemical modifications. Among them, lipid (per)oxidation attracts most of the attention due to its significance in the regulation of inflammation, cell proliferation and death programs. Despite their apparent regulatory significance, the molecular repertoire of oxidized lipids remains largely elusive as accurate annotation of lipid modifications is complicated by their low abundance and often unknown, biological context-dependent structural diversity. Here, we provide a workflowbased on the combination of bioinformatics and LC-MS/MS technologies to support identification and relative quantification of oxidized complex lipids in a modification type- and position-specific manner. The developed methodology is used to identify epilipidomics signatures of lean and obese individualswith and without type 2 diabetes. The characteristic signature of lipid modifications in lean individuals, dominated by the presence of modified octadecanoid acyl chains in phospho- and neutral lipids, is drastically shifted towards lipid peroxidation-driven accumulation of oxidized eicosanoids, suggesting significant alteration of endocrine signalling by oxidized lipids in metabolic disorders.

La RMN en phase solide est une méthode non négligeable lors de l'étude d'échantillons biologiques. Nous avons ainsi pu étudier le peptidoglycane et les acides téichoïques, composants essentiels de la paroi cellulaire bactérienne. Nous nous sommes tout particulièrement intéressés à leur organisation, à leur flexibilité et à leur interaction avec les cations. Nous avons également étudié les interactions entre les acides téichoïques et une protéine responsable de la viru-lence des pneumocoques. Cet exemple illustre parfaitement le manque de sensi-bilité des expériences de RMN ainsi que les limites des techniques actuelles de recouplage. Nous avons alors mis en évidence un phénomène permettant d'accélérer l'acquisition des spectres. Nous avons aussi travaillé à l'amélioration des séquences de recouplage PAR et PAIN-CP. Finalement, nous avons compa-ré des méthodes d'édition spectrale appliquées au bois, très étudié dès les débuts de la RMN en phase solide.

Dans ce travail, nous démontrons que STIM1, un senseur calcique activé par la déplétion du Ca2+ intracellulaire du réticulum endoplasmique, est indispensable pour la signalisation calcique et la préférence oro-sensorielle du gras. Nous observons que l'acide linoléique (LA), en activant les phospholipases A2 via CD36, produit de l'acide arachidonique (AA) et de la lyso-phosphatidylcholine (lyso-PC). Cette activation déclenche un influx calcique dans les cellules CD36-positives, et induit la production du facteur CIF (Ca2+ Influx Factor). CIF, AA et lyso-PC exercent différentes actions sur l'ouverture des canaux SOC (Stored Operated Calcium Channel) constitués de protéines Orai et contrôlés par STIM1. Par ailleurs, les souris au phénotype Stim1-/- perdent la préférence spontanée pour les lipides et la libération de la sérotonine à partir des cellules gustatives dans le milieu extracellulaire chez les animaux sauvages. Nous demontrons aussi que la signalisation calcique médiée via CD36 est doublement modulée lors de l'obésité. L'augmentation de la [Ca2+]i dans les cellules gustatives observée chez le Psammomys obesus, un modèle d'obésité nutritionelle, est fortement diminuée chez les souris rendues obèses par un regime hyperlipidique. Nous avons constaté également que l'interaction de LA avec le CD36 induit l'activation des MAP Kinases de la voie MEK1/2/ERK1/2/Elk-1 qui est non seulement à l'origine de l'activation des aires cérébrales telles que le NTS, le noyau arqué, l'hippocampe mais aussi indispensable pour la préférence spontanée pour les lipides alimentaires. Nos résultats suggèrent pour la prémière fois, que la voie ERK1/2 des MAPK et la signalisation calcique lipidique controlée par STIM1 sont impliquées dans la perception oro-gustative des lipides