Made available in DSpace on 2016-12-12T20:27:39Z (GMT). No. of bitstreams: 1 Heric Denis Farias.pdf: 2196819 bytes, checksum: ebe776ba26727b6ab81d9c4b1fb49e5d (MD5) Previous issue date: 2016-09-25 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / The application of high electric fields on biological cells causes the formationof pores in the cell membrane, thereby causing an increase in their permeability. This phenomenon, called electropermeabilization have attracted increasing attention due to its wide application in biotechnology. Even being known for decades, the pore opening process in biological cell membranes is still not fully understood, nor was it even properly modeled. In this paper, two types of modeling are presented, which allow characterizing the electropermeabilization in biological cell suspensions. One of the methods is based on the analysis of the electrical impedance spectra of suspensions using genetic algorithm to determine parameters of a generic model dielectric dispersion. The other method uses instantaneous voltage and current values applied to a cell suspension during the electroporation experiment to determine the variation of the medium conductivity and thus, through the analytical model proposed by Ramos and colleagues (RAMOS et al., 2012), determine the cell conductivities. By modeling the impedance spectrum, it was observed the change in the dielectric dispersion of the sample due to the electropermeabilization process, in addition to obtaining the electrical conductivity and permittivity of the involved media. Using the electroporated cell model proposed by Ramos and colleagues (RAMOS et al., 2012), it was possible to determine the change of membrane conductance during the electropermeabilization. The validity of this model is assessed using finite element simulations, which showed good agreement with the analytical model used. Genetic algorithms are used in obtaining the parameters of the various models presented, showing great robustness in obtaining parameters based on the git between experimental and theoreticalcurves. / A aplicação de campos elétricos intensos em células biológicas provoca a formação de poros na membrana celular, causando assim o aumento de sua permeabilidade. Este fenômeno, denominado de eletropermeabiliza ção têm atraído cada vez mais atenção devido a sua ampla aplicação em biotecnologia. Mesmo sendo conhecido há várias décadas, o processo de abertura de poros em membranas de células biológicas ainda não é plenamente entendido e nem foi ainda corretamente modelado. Neste trabalho, apresenta-se dois tipos de modelagem que permitem a caracterização da eletropermeabilização em suspensões de células biológicas. Um dos métodos baseia-se na análise do espectro de impedância elétrica de suspensões com o uso de algoritmo genético para determinar parâmetros de um modelo genérico de dispersão dielétrica. O outro método utiliza valores instantâneos de tensão e corrente aplicados em uma suspensão de células durante um experimento de eletropermeabiliza ção para determinar a variação da condutividade do meio e com isso, através do modelo analítico proposto por Ramos e colaboradores (RAMOS et al., 2012), determinar a condutividade das células. Através da modelagem do espectro de impedância, foi possível verificar a alteração da dispersão dielétrica da amostra devido ao processo de eletropermeabiliza ção, além da obtenção das condutividades e permissividades elétricas dos meios envolvidos. Utilizando o modelo de célula eletropermeabilizada proposto por Ramos e colegas (RAMOS et al., 2012), foi possível obter a variação da condutância de membrana durante a eletropermeabilização. A validade deste modelo é avaliada utilizando simulações em elementos infinitos, as quais apresentaram grande concordância com o modelo analítico utilizado. Algoritmos genéticos são utilizados na obtenção dos parâmetros dos diversos modelos apresentados, mostrando grande robustez na obtenção de parâmetros baseada no ajuste entre curvas experimentais e teóricas.

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Le champ électrique d'une puissance suffisante peut provoquer une augmentation de conductivité et perméabilité de la membrane cellulaire. L'effet est connu comme l'électroporation, attribuée à la création de voies aqueuses dans la membrane. Quantifier le transport de la matière dans le cadre d'électroporation est un objectif important. Comprendre ces processus a des ramifications dans l’extraction du jus ou l’extraction sélective des composés de cellules végétales, l'amélioration de l'administration de médicaments, et des solutions aux défis environnementaux. Il y a un manque de modèles qui pourraient être utilisés pour modéliser le transport de la matière dans les structures complexes (tissus biologiques) par rapport à l'électroporation. Cette thèse présente une description mathématique théorique (un modèle) pour étudier le transport de la matière et le transfert de la chaleur dans tissu traité par l’électroporation. Le modèle a été développé en utilisant les lois de conservation et de transport et permet le couplage des effets de l'électroporation sur la membrane des cellules individuelles au transport de la matière ou la chaleur dans le tissu. Une solution analytique a été trouvée par une simplification, mais le modèle peut être étendu avec des dépendances fonctionnelles supplémentaires et résolu numériquement. La thèse comprend cinq articles sur l'électroporation dans l'industrie alimentaire, la création de modèle pour le problème de diffusion, la traduction du modèle au problème lié à l’expression de jus, validation du modèle, ainsi que des suggestions pour une élaboration future du modèle. Un chapitre supplémentaire est dédié au transfert de la chaleur dans tissu. / An electric field of sufficient strength can cause an increase of conductivity and permeability of cell membrane. Effect is known as electroporation and is attributed to creation of aqueous pathways in the membrane. Quantifying mass transport in connection with electroporation of biological tissues is an important goal. The ability to fully comprehend transport processes has ramifications in improved juice extraction and improved selective extraction of compounds from plant cells, improved drug delivery, and solutions to environmental challenges. While electroporation is intensively investigated, there is a lack of models that can be used to model mass transport in complex structures such as biological tissues with relation to electroporation. This thesis presents an attempt at constructing a theoretical mathematical description – a model, for studying mass (and heat) transfer in electroporated tissue. The model was developed employing conservation and transport laws and enables coupling effects of electroporation to the membrane of individual cells with the resulting mass transport or heat transfer in tissue. An analytical solution has been found though the model can be extended with additional dependencies to account for the phenomenon of electroporation, and solved numerically. Thesis comprises five peer-reviewed papers describing electroporation in the food industry, model creation for the problem of diffusion, translation of the model to the mathematically-related case of juice expression, model validation, as well as suggestions for possible future development, extension, and generalization. An additional chapter is dedicated to transfer of heat in tissue.

Pour diversifier leur matériel génétique, s’adapter aux perturbations environnementales et coloniser de nouvelles niches, les bactéries utilisent plusieurs processus évolutifs dont l’acquisition de matériel génétique par transfert horizontal de gènes comme la conjugaison, la transduction et la transformation. À ces trois mécanismes naturels s’ajoute l’électrotransformation due aux phénomènes électriques liés à la décharge de foudre. La présence dans les nuages de bactéries aérosolisées capables de former des noyaux de glace à l’origine des précipitations et impliquées dans le déclenchement de la foudre, telles que la bactérie phytopathogène à répartition mondiale Pseudomonas syringae, nous a conduit à proposer que l’électrotransformation naturelle dans les nuages pouvait affecter les bactéries, contribuant ainsi à augmenter leur potentiel adaptatif. Dans un premier temps, nous avons déterminé si la bactérie glaçogène P. syringae pouvait survivre à des électroporations simulant des décharges de foudre et acquérir du matériel génétique exogène dans les nuages. Comparée à deux autres bactéries, P. syringae se révèle être mieux adaptée pour la survie et l’électrotransformation génétique, ce qui suggère qu’elle serait capable de survivre et d’évoluer durant son transport dans les nuages. Nous avons ensuite évalué l’impact d’électroporations simulant les décharges de foudre sur la survie, le potentiel d’électrotransformation et la diversité de bactéries présentes dans des échantillons de pluie comme substitut des communautés bactériennes des nuages. Ces dernières étaient plus résistantes que les souches de laboratoire et certaines étaient capables d’acquérir de l’ADN exogène par électrotransformation. Les bactéries de la pluie isolées provenaient de différentes origines et présentaient différents modes de vie, représentatifs des sources probables d’émissions de bactéries terrestres. Cette étude montre que les bactéries aérosolisées de divers écosystèmes terrestres sont susceptibles de se disséminer dans de nouveaux habitats grâce aux nuages tout en étant capable d’acquérir de nouveaux gènes par éléctrotransformation, et d’augmenter ainsi potentiellement leur diversité génétique. La dernière partie de mon travail a évalué si l’électrotransformation appliquée aux bactéries indigènes du sol pouvait être employée pour dépolluer les sols contaminés par un pesticide largement utilisé autrefois, le lindane. L’optimisation des expériences met en évidence l’incorporation par les bactéries indigènes d’un plasmide contenant le gène codant les premières déchlorinations du lindane au travers d’une combinaison de transformation naturelle et d’électrotransformation. En conclusion, nous avons montré que l’électrotransformation naturelle liée aux décharges électriques, comme celles se produisant dans les nuages ou atteignant le sol, peut être impliquée dans le transfert horizontal de gènes chez les bactéries et, considérant l’importance de la foudre à travers le monde, pourrait jouer un rôle dans l’adaptation et l’évolution de ces organismes. / To diversify their genetic material, allowing adaptation to environmental disturbances and colonization of new ecological niches, bacteria use various evolutionary processes, including the acquisition of new genetic material by horizontal transfer mechanisms such as conjugation, transduction and transformation. Electrotransformation mediated by lightningrelated electrical phenomena may constitute an additional gene transfer mechanism occurring in nature. The presence in clouds of bacteria capable of forming ice nuclei that lead to precipitations and are involved in the triggering of lightning, such as the global phytopathogen Pseudomonas syringae, led us to postulate that natural electrotransformation in clouds may affect bacteria, by contributing to increase their adaptive potential. We first determined if the ice nucleator bacterium P. syringae could survive when in clouds and acquire exogenous genetic material through lightning shock-simulating in vitro electroporation. In comparison to two other bacteria, P. syringae appears to be best adapted for survival and for genetic electrotransformation under these conditions, which suggests that this bacterium would be able to survive and evolve whilst being transported in clouds. Secondly, we evaluated the impact of lightning shock-simulating in vitro electroporation on the survival, the electrotransformation potential and the diversity of bacteria collected from rain samples. These isolates better resisted lightning than the laboratory strains and some were able to electrotransform exogenous DNA. The rain bacteria we isolated were of different origins and were representative of life modes of the various sources of bacterial emissions on Earth. Our study suggests that bacteria aerosolized from diverse terrestrial ecosystems can spread to new habitats through clouds whilst also being able to acquire new genetic material via lightning-based electrotransformation, thereby potentially enhancing their genetic diversity. The final part of our work consisted of evaluating whether electrotransformation could be applied to the engineering of indigenous soil bacteria in order to develop a tool for the bioremediation of lindane, a once widely used pesticide. Optimized experiments revealed that both natural and electrotransformation contributed to the incorporation of a plasmid harboring a gene encoding the first lindane dechlorination steps by indigenous soil bacteria. In conclusion, we showed that natural electrotransformation mediated by electrical discharges such as those occurring in clouds or reaching soils can be involved in the horizontal gene transfer process among bacteria and, considering the importance of lightning worldwide, may play a role in the adaptation and evolution of these organisms.

The main goal of this thesis is to design control board for the experimental electroporation device and to develop control firmware. The first chapter of this work focuses on the electroporation phenomenon itself. Behaviour of the cell model in external electrical field is described there as well as simulation and overview of how electroporation affects living tissue. It also explains the main requirements for parameters of the electroporation pulses as well as need for ECG synchronization. Furthermore, some remarks are given about novel high frequency electroporation method, which involves use of nanosecond bipolar high voltage pulse bursts. The second chapter briefly introduces commercial electroporation device called Nanoknife, including control part, power part, and it's limits. The third chapter consists of introduction of the novel experimental electroporation device developed at BUT. Power part of this device is discussed as well. Next chapter focuses on design of the control board for this device and also on description of the particular schematic parts. There is a control algorithm explanation in the fifth chapter of this thesis followed by the brief manual to machine operation.

L’électroporation (EP) in vivo est utilisée comme stratégie d’amélioration de la réponse immune induite par les vaccins ADN. Cependant son effet sur les acteurs du système immunitaire inné reste méconnu. Dans l’objectif de mettre en évidence le comportement cellulaire sur le site de la vaccination, nous avons développé des approches d’imagerie par fluorescence in vivo chez le macaque. Nos résultats montrent que l’EP locale, augmente non seulement la quantité et la distribution de l’antigène vaccinal, mais induit également la mobilisation et la migration des cellules de Langerhans. De plus, l’EP cause un recrutement de leucocytes dans la peau et le tissu sous-cutané et favorise la production de cytokines pro-inflammatoires dans la peau. Ces évènements précoces, qui résultent de l’utilisation de l’EP en tant que système de délivrance des vaccins ADN, mettent en évidence le potentiel de l’EP en tant qu’adjuvant vaccinal. / In vivo electroporation (EP) is used as a strategy to improve the immune response induced by DNA vaccines. However, its local effect on the innate immune cells has not been fully described. We developed in vivo fluorescence imaging approaches to highlight the cell behavior in the site of vaccination in macaques. Our results show that the local EP not only increases the amount and the distribution of the vaccine antigen, but also induces the mobilization and migration of Langerhans cells. Furthermore, EP causes the recruitment of leukocytes into the skin and subcutaneous tissue and promotes the production of pro-inflammatory cytokines. These early events that result from the use of the EP as a delivery system for DNA vaccines, highlight its potential as a vaccine adjuvant.

La neurogenèse est maintenue dans le cerveau adulte dans des régions restreintes du cerveau appelées niches neurogéniques. L’une des niches principales est la zone ventriculaire/sous-ventriculaire (V-SVZ) dans laquelle résident des cellules souches neurales (NSCs). Les NSCs sont à l’origine de la formation des nouveaux neurones en donnant naissance aux progéniteurs puis aux neuroblastes. Les études récentes sur la neurogenèse ont mis en évidence l’existence des NSCs quiescentes (qNSCs, aussi appelées cellules B1) et des NSCs actives (aNSCs). Le modèle actuel de la neurogenèse adulte place les qNSCs B1 en amont des aNSCs. L’hypothèse étant que cette population dormante constitue une « réserve », afin de maintenir les aNSCs tout au long de la vie. Les techniques actuelles ne permettent pas de cibler les qNSCs spécifiquement in vivo et donc, d’analyser leurs propriétés biologiques, leurs mécanismes d’activation ainsi que leur relation avec les aNSCs. Cette compréhension est nécessaire pour la mise au point de stratégies thérapeutiques pouvant utiliser le potentiel des cellules souches pour restaurer la neurogenèse dans les contextes de vieillissement et de maladies neurodégénératives. Afin de caractériser les qNSCs de la V-SVZ, nous avons utilisé l’électroporation de plasmides dans un modèle de souris rapportrice Rosa26-stop-EYFP. Dans celle-ci, la séquence codant pour la protéine EYFP précédée par un codon STOP floxé, est inséré au locus Rosa26. L’excision du codon STOP par une recombinase permet l’expression du rapporteur dans les cellules électroporées ainsi que leur descendance. Cette technique nous a permis de cibler spécifiquement une population d’astrocytes en contact avec le ventricule et d’étudier leur contribution à la neurogenèse adulte. À la différence des approches virales et transgéniques, l’électroporation peut cibler les cellules quiescentes et l’expression du plasmide est limité aux cellules en contact avec le ventricule. Grâce à cette technique nous avons mis en évidence des éléments surprenants : i) cette population est majoritairement quiescente et ne contribuent à la neurogenèse que de manière minimale, ii) cette population ne participe pas à la régénération de la niche in vivo, iii) elles ne génèrent pas les aNSCs à l’origine des neurosphères in vitro et iv) son activité neurogénique peut être augmentée en exprimant le gène pro-neural Mash1. Ensuite, nous nous sommes intéressés au rôle de la signalisation EGFR dans la régulation de l’activité des cellules souches/progéniteurs neuraux (NSPCs). Dans cette seconde étude, nous montrons que i) la signalisation EGFR est réduite avec l’âge, ii) PI3K/AKT, MEK/ERK et mTOR régulent différemment la prolifération, la différenciation et la survie des NSPCs et iii) l’activation d’EGFR dans les qNSCs permet d’augmenter la neurogenèse sous ventriculaire à 3 mois, mais pas à 6 mois ou dans un modèle de la maladie d’Alzheimer. Nos données suggèrent donc que les qNSCs représentent une population hétérogène et/ou présentant 2 voies neurogéniques distinctes. De plus, nous avons montré que les voies de signalisation associées à EGFR exercent un contrôle différentiel sur l’activité des NSPCs. Enfin, nos résultats indiquent que les facteurs présents dans la niche sous-ventriculaire lors du vieillissement inhibent de manière dominante l’activation des NSCs. / Neurogenesis is maintained in restricted regions of the adult brain called neurogenic niches. One of the main neurogenic niches is the ventricular-subventricular zone (V-SVZ) in which neural stem cells (NSCs) reside. NSCs produce neurons through the generation of transit amplifying progenitors and neuroblasts. Recent studies on adult neurogenesis revealed the existence of quiescent NSCs (qNSCs, also called B1) and activated NSCs (aNSCs). The current model of adult neurogenesis places qNSCs (B1) upstream of aNSCs in the lineage. The hypothesis is that the qNSC population constitutes a “reserve” pool to maintain aNSC pool throughout life. So far, the techniques used do not allow specific targeting of the qNSCs in vivo. Therefore, it is not possible to analyze their biological properties, activation mechanisms and relationship with aNSCs. This understanding is also necessary to establish therapeutic strategies that could utilize the potential of stem cells to restore neurogenesis in contexts of aging and neurodegenerative diseases. In order to characterize qNSCs in the ventricular zone, we took advantage of plasmid electroporation in a reporter mouse model, Rosa26-stop-EYFP. In this model, the sequence coding for EYFP preceded by a floxed STOP codon is inserted at the Rosa26 locus. Excision of the STOP codon by a recombinase enables expression of the reporter in electroporated cells and their progeny. This technique enabled the specific targeting of a ventricle-contacting astrocytes population and to study their contribution to adult neurogenesis. Unlike transgenic or viral approaches, electroporation can target quiescent cells and the expression of the plasmid is restricted to the ventricle-contacted cells. Using this approach, we made surprising observations: i) this population is mostly quiescent and only minimally contributes to adult neurogenesis, ii) this population does not participate in niche regeneration in vivo and iv) their neurogenic output can be increased by expressing the pro-neural gene Mash1. Next, we investigated the role of EGFR signaling in the regulation neural stem and progenitor cells (NSPCs) activity. In this second study, we show that i) EGFR signaling decreases during aging, ii) PI3K/AKT, MEK/ERK and mTOR exert different regulation proliferation, differentiation and survival of NSPCs and iii) activation of EGFR in the qNSCs increases V-SVZ neurogenesis in 3-months-old animals but not in 6-months-old or Alzheimer’s disease model animals. Our data suggests that the NSC population is heterogeneous, with variable neurogenic output from the different sub-populations, as well as different activation modalities. We also showed that EGFR-associated signalling pathways differentially regulate NSPCs activity. Finally, our results indicate that the factors present in the V-SVZ niche during aging dominantly inhibit activation of NSCs.

Background: Focal therapy (FT) is an option to treat localized prostate cancer (PCa) and preserve healthy prostate tissue in order to reduce known side effects from primary whole-gland treatment. The available FT modalities are manifold. Until now, national and international PCa guidelines have been cautious to propose recommendations regarding FT treatment since data from prospective controlled trials are lacking for most FT modalities. Moreover, none of the international guidelines provides a separate section on FT. In this purpose, we provide a synopsis of the consensusbased German S3 guidelines for a possible international use. - Summary: The recently published update of the German S3 guidelines, an evidence- and consensus-based guideline, provides a section on FT with recommendations for diagnostic work-up, indications, modalities, and follow-up. This section consists of 12 statements and recommendations for FT in the treatment of localized PCa. Key Message: The German S3 guidelines on PCa are the first to incorporate recommendations for FT based on evidence and expert consensus including indication criteria for FT, pretreatment, and followup diagnostic pathways as well as an extended overview of FT techniques and the current supportive evidence.

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<p>Microbiological contamination from bacteria such as <em>Escherichia coli</em> and Salmonella is one of the main reasons for waterborne illness. Real time and accurate monitoring of water is needed in order to alleviate this human health concern. Performing multiple and parallel analysis of biomarkers such as DNA and mRNA that targets different regions of pathogen functionality provides a complete picture of its presence and viability in the shortest possible time. These biomarkers are present inside the cell and need to be extracted for analysis and detection. Hence, lysis of these pathogenic bacteria is an important part in the sample preparation for rapid detection. In addition, collecting a small amount of bacteria present in a large volume of sample and concentrating them before lysing is important as it facilitates the downstream assay. Various techniques, categorized as mechanical, chemical, thermal and electrical, have been used for lysing cells. In the electrical method, cells are lysed by exposure to an external electric field. The advantage of this method, in contrast to other methods, is that it allows lysis without the introduction of any chemical and biological reagents and permits rapid recovery of intercellular organelles. Despite the advantages, issues such as high voltage requirement, bubble generation and Joule heating are associated with the electrical method.</p> <p>To alleviate the issues associated with electrical lysis, a new design and associated fabrication process for a microfluidic cell lysis device is described in this thesis. The device consists of a nanoporous polycarbonate (PCTE) membrane sandwiched between two PDMS microchannels with electrodes embedded at the reservoirs of the microchannels. Microcontact printing is used to attach this PCTE membrane with PDMS.</p> <p>By using this PCTE membrane, it was possible to intensify the electric field at the interface of two channels while maintaining it low in the other sections of the device. Furthermore, the device also allowed electrophoretic trapping of cells before lysis at a lower applied potential. For instance, it could trap bacteria such as <em>E. coli</em> from a continuous flow into the intersection between two channels for lower electric field (308 V/cm) and lyse the cell when electric field was increased more than 1000 V/cm into that section.</p> <p>Application of lower DC voltage with pressure driven flow alleviated adverse effect from Joule heating. Moreover, gas evolution and bubble generation was not observed during the operation of this device.</p> <p>Accumulation and lysis of bacteria were studied under a fluorescence microscope and quantified by using intensity measurement. To observe the accumulation and lysis, LIVE/DEAD BacLight Bacterial Viability Kit consisting of two separate components of SYTO 9 and propidium iodide (PI) into the cell suspension in addition to GFP expressed <em>E. coli</em> were used. Finally, plate counting was done to determine the efficiency of the device and it was observed that the device could lyse 90% of bacteria for an operation voltage of 300V within 3 min.</p> <p>In conclusion, a robust, reliable and flexible microfluidic cell lysis device was proposed and analyzed which is useful for sample pretreatment in a Micro Total Analysis System.</p> / Master of Applied Science (MASc)