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Biological systems of bacteria were investigated at the single-cell and single-molecule level. Additionally, aspects of the techniques employed were studied. A unifying theme in each project is the reliance on optical imaging techniques coupled to microfluidic devices. Hypo-osmotic shock experiments with an Escherichia coli mechanosensitive channel deletion mutant were carried out at the single-cell level. E. coli MJF465 cells in which the three major mechanosensitive channel genes are deleted (∆mscL, ∆mscS, ∆mscK) show only 10% cell viability upon hypo-osmotic shock (from LB + 0.5 M NaCl into distilled water), compared to 90% viability of the wild-type strain. Bacterial cells were trapped with optical tweezers in microfluidic devices, enabling the first direct observation of single-cell behaviour upon hypo-osmotic shock. Phase-contrast microscopy revealed intra-population diversity in the cells response: Different features of lysis included cells bursting rapidly and leakage of ribosomes, DNA and protein from the cytoplasm. Fluorescence microscopy of hypo-osmotically-shocked GFP-expressing MJF465 cells showed either bursting of cells, which was a rare event, or fast leakage of GFP, indicating cell membrane ruptures. Data were analysed in terms of their kinetic behaviour and showed that lysis occurs on a timescale of milliseconds to seconds. The implications of these findings for the bacterial cell wall and cell membranes are discussed. Enzymes involved in homologous recombination and repair of double-stranded DNA (dsDNA) breaks are essential for maintaining genomic integrity in both eukaryotes and prokaryotes. RecBCD of E. coli and AddAB, found widely in bacteria, are involved in these processes, carrying out the same function. Both enzymes were studied kinetically with single-molecule total internal reflection fluorescence microscopy (TIRFM). Surface-tethered, hydrodynamically stretched lambda-DNA molecules, stained with YOYO-1, were imaged with TIRFM in a microfluidic flowcell. The RecBCD enzyme is a well characterised DNA helicase and was introduced to this system for method validation purposes. The AddAB enzyme of Bacteroides fragilis was then characterised as a helicase acting on lambda-DNA. It was found that AddAB helicase unwinds dsDNA with high processivity of on average 14,000 bp and up to 40,000 bp for individual enzyme complexes at an ATP-dependent rate ranging from 50-250 bp s−1 (for Mg2+-ATP concentrations larger or equal than 0.1 mM). This activity was detected by DNA binding dye (YOYO-1) displacement from the dsDNA and studied for different Mg2+-ATP concentrations, flow (shear) rates and different YOYO-1 staining ratios of DNA. Aspects of this last experimental setup were investigated. A kinetic analysis of intercalation of YOYO-1 into lambda-DNA is presented, occurring on a timescale of minutes. Different flow rates and staining ratios that influence the apparent (stretched) DNA molecule length were also examined. Several image analysis techniques were employed to enhance the data quality in images showing stretched lambda-DNA molecules. The Singular Value Decomposition was found to be the most effective technique which strongly reduces the noise in the obtained kymograph images.

In response to osmotic shock in Saccharomyces cerevisiae the MAP kinase Hog1 coordinates a large-scale transcriptional stress response, rapidly producing hundreds of copies of specified transcripts. Many of the most highly induced genes are bound and regulated by a transcription factor, Sko1, but lack the canonical binding site for this factor. We use ChIP-seq to demonstrate a stress-specific binding mode of Sko1. In stress, Sko1 binds to promoters in close proximity to Hog1, and another Hog1-regulated transcription factor, Hot1. This mode of Sko1 binding requires the physical presence of Hog1, but not Hog1 phosphorylation of Sko1. We identify candidate Sko1 and Hot1 binding motifs that predict co-localization of Sko1, Hot1, and Hog1 at promoters. We then demonstrate a role for Sko1 and Hot1 in directing Hog1-associated RNA Pol II to target genes, where Hog1 is present with the elongating polymerase. We suggest a possible model for Hog1 reprogramming of transcription in the early stages of the osmotic stress response. We then determine the extent and structure of the Hog1 controlled transcriptional program in a related stress, damage to the cell wall. We find that Sko1 and Hot1 have different apparent thresholds for activation by Hog1. In addition, in cell wall damage, Hog1 regulates an additional transcription factor, Rlm1, that is not involved in other Hog1 regulated stress responses. This factor is activated by the coincidence of a signal from Hog1 with that of another MAP kinase, Slt2.

Cell cultivation in bioreactors would benefit from developed monitoring systems with online real-time imaging to evaluate cell culture conditions and processes. This opportunity can be provided with the newly developed in situ Microscope also called ISM. The ISM probe is mounted into the wall of a bioreactor and consists of a measurement zone with an illuminating light source to obtain real-time images of moving cells in suspension. The instrument is linked to advanced imaging analysis software which can be specifically adapted for the objects in study. The aim of this project is to analyze the T lymphocyte cell line Jurkat T cells using the ISM equipment and identify specific features of the cells that can be obtained. The results show that the equipment and linked software are suitable for monitoring cell density, cell size distribution and cell surface analysis of the Jurkat cells during cultivation. The ISM could also detect induced changes in cell size caused by osmotic shifts and the course of an infection occurring in the cell suspension using a developed software for online real-time monitoring.

As microalgas são candidatas promissoras para a produção em larga escala de biocombustíveis devido a sua alta eficiência fotossintética. No entanto, os custos relativamente altos de produção por baixas produtividades em lipídios têm sido um dos principais obstáculos que impedem sua produção comercial. Portanto, é necessário focar a pesquisa no aumento da biomassa e na produtividade em lipídios, através do desenvolvimento de biorreatores e técnicas de cultivo inovadoras. Numa primeira fase, este estudo mostra a otimização dos regimes de adição de nutrientes no cultivo de Neochloris oleoabundans em fotobiorreatores tubulares, determinando que a melhor metodologia de adição de CO2 é adicionando-o de forma intermitente e automatizada, enquanto que o melhor processo de alimentação de nitrogênio é por meio de um processo em batelada alimentada tomando como uma referência a produtividade diária de biomassa. Na segunda etapa, foi testada a influência de agentes estressores adicionados ao cultivo sob carência de nitrogênio, tais como tiossulfato de sódio como agente redutor e cloreto de sódio e glicerina como agentes de choque osmótico, buscando um acúmulo de lipídios na biomassa. Os resultados mostraram que o tiossulfato de sódio em 1,2 mM e o cloreto de sódio em 2,2 mM aumentaram o total de lipídios em 21% e 25%, respectivamente. Finalmente, foram testados diferentes regimes de luz, com um esquema 12:12, sendo 12 horas de luz fluorescente e 12 horas com um sistema distinto: escuro, diodos emissores de luz (LED) vermelha e LED branca. Os melhores resultados foram obtidos com LED branca, com um acúmulo de lipídios de até 27% da biomassa seca e uma concentração final de células de 2335mg/L, estabelecendo assim um método de iluminação econômica com alta produtividade (145mg / L dia). / Microalgae are promising candidates for large-scale global biofuel production because of their high photosynthetic efficiency. However, relatively high production costs due to low lipid productivity have been one of the major obstacles impeding their commercial production. Therefore, it is necessary to accurate the research into an increase in biomass and oil productivity, by means of novel bioreactors\' design and cultivation techniques. On a first stage, this study shows the optimization of nutrients\' addition regimes in Neochloris oleoabundans cultivation in tubular photobioreactors, finding that the best CO2 addition methodology is an automatized intermittent adding and the best feeding process for nitrogen is a fed-batch process taking as a reference the daily biomass productivity. On the second step, it was tested the influence of stressing agents added to the culture under nitrogen starvation, such as sodium thiosulphate for reducing environment and sodium chloride and glycerol for osmotic shock, aiming lipid accumulation in the biomass. The results showed that sodium thiosulphate at 1,2mM and sodium chloride at 2,2mM raised the total lipids up to 21% and 25% respectively. Finally, there were tested different light regimes, with a scheme 12:12, being 12 hours of fluorescent light and 12 hours of a singular system: dark, red light-emitting-diodes (LED) and white LED. The best results were obtained with white LED, with an accumulation up to 27% of dry biomass and a final cell concentration up to 2335mg/L, establishing an economic illumination method with high productivity.

Submitted by (ana.araujo@ufrpe.br) on 2017-02-20T17:04:51Z No. of bitstreams: 1 Manuela Maria Cavalcante Granja.pdf: 696391 bytes, checksum: 1cfe62663cfe614a373e837e03fde09b (MD5) / Made available in DSpace on 2017-02-20T17:04:51Z (GMT). No. of bitstreams: 1 Manuela Maria Cavalcante Granja.pdf: 696391 bytes, checksum: 1cfe62663cfe614a373e837e03fde09b (MD5) Previous issue date: 2010-02-19 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - CAPES / Sugarcane (Saccharum officinarum) is a grass considered moderately sensitive to salinity. Although traditionally cultivated in the soil of the Atlantic Coast and the Northeast, the cultivation of sugarcane is expanding to semi-arid regions. The poor quality of irrigation water, high rates of evaporation and low rainfall, combined with other factors contribute to the process of soil salinization in semi-arid. For the development and selection of tolerant genotypes, it is necessary to understand the physiological mechanisms with which plants face the salt stress. Techniques for in vitro plant tissue for studies of physiology and biochemistry of plants under stress are important tools to allow control and uniformity of culture conditions. In this study, two genotypes of sugarcane (RB931011 and RB872552) developed within the Program of Genetic Improvement of Sugarcane of rides, for the Northeast region (RIDESA) were evaluated for sudden and gradual action of salt stress-induced by adding NaCl to the culture medium during in vitro development of plants. The varieties of sugarcane were subjected to three concentrations of NaCl (0 mM, 50 mM and 100 mM) in a gradual and sudden. At 35 days of experiment, enzyme activities (CAT, POX, APX, PPO), levels of sodium (Na+), potassium (K+), soluble protein content and free proline were recorded. It was possible to observe differences in responses of varieties depending on the condition of induced salt stress, shock or gradual, rather than depending on the concentration of NaCl in the culture medium. The stress response is therefore not only conditioned by salt concentration, but by way of exposure to salt. / A cana-de-açúcar (Saccharum officinarum) é uma gramínea considerada moderadamente sensível à salinidade. Embora tradicionalmente cultivada nas zonas de Mata úmida e Litoral da região Nordeste, o cultivo da cana-de-açúcar vem se expandindo também para regiões semi-áridas. A má qualidade da água de irrigação, altas taxas de evaporação e baixa precipitação pluviométrica, aliada a outros fatores contribuem para o processo de salinização dos solos do semi–árido. Para o desenvolvimento e seleção de genótipos tolerantes, é necessário conhecer os mecanismos fisiológicos com os quais as plantas enfrentam o estresse salino. Técnicas de cultivo in vitro para estudos da fisiologia e bioquímica de plantas, em condições de estresse, são importantes ferramentas por permitirem o controle e homogeneidade das condições de cultivo. No presente trabalho, dois genótipos de cana-de-açúcar (RB931011 e RB872552) desenvolvidos pelo Programa de Melhoramento Genético da Cana-de-Açúcar da RIDESA, para a região Nordeste, foram submetidos ao estresse salino in vitro mediante o acréscimo de NaCl ao meio de cultura sob uma ação gradativa e súbita para avaliar o comportamento fisiológico e bioquímico dessas plantas. As variedades de cana-de-açúcar foram submetidas a duas concentrações de NaCl (56mM, 112mM e o controle) de forma gradativa e repentina. Aos 35 dias de experimento, atividades enzimáticas da Catalase (CAT), Peroxidase (POX), Ascorbato peroxidase (APX), Polifenoloxidase (PPO), teores de sódio (Na+), potássio (K+), concentração de proteínas solúveis e prolina livre foram determinadas. Foi possível observar diferenças nas respostas das variedades em função da condição de indução do estresse salino, gradativo ou por choque, mais do que em função das concentrações de NaCl no meio de cultura. A resposta ao estresse é, portanto, condicionada não só pela concentração dos sais, mas pela forma que a planta é exposta ao meio salino.

As microalgas são candidatas promissoras para a produção em larga escala de biocombustíveis devido a sua alta eficiência fotossintética. No entanto, os custos relativamente altos de produção por baixas produtividades em lipídios têm sido um dos principais obstáculos que impedem sua produção comercial. Portanto, é necessário focar a pesquisa no aumento da biomassa e na produtividade em lipídios, através do desenvolvimento de biorreatores e técnicas de cultivo inovadoras. Numa primeira fase, este estudo mostra a otimização dos regimes de adição de nutrientes no cultivo de Neochloris oleoabundans em fotobiorreatores tubulares, determinando que a melhor metodologia de adição de CO2 é adicionando-o de forma intermitente e automatizada, enquanto que o melhor processo de alimentação de nitrogênio é por meio de um processo em batelada alimentada tomando como uma referência a produtividade diária de biomassa. Na segunda etapa, foi testada a influência de agentes estressores adicionados ao cultivo sob carência de nitrogênio, tais como tiossulfato de sódio como agente redutor e cloreto de sódio e glicerina como agentes de choque osmótico, buscando um acúmulo de lipídios na biomassa. Os resultados mostraram que o tiossulfato de sódio em 1,2 mM e o cloreto de sódio em 2,2 mM aumentaram o total de lipídios em 21% e 25%, respectivamente. Finalmente, foram testados diferentes regimes de luz, com um esquema 12:12, sendo 12 horas de luz fluorescente e 12 horas com um sistema distinto: escuro, diodos emissores de luz (LED) vermelha e LED branca. Os melhores resultados foram obtidos com LED branca, com um acúmulo de lipídios de até 27% da biomassa seca e uma concentração final de células de 2335mg/L, estabelecendo assim um método de iluminação econômica com alta produtividade (145mg / L dia). / Microalgae are promising candidates for large-scale global biofuel production because of their high photosynthetic efficiency. However, relatively high production costs due to low lipid productivity have been one of the major obstacles impeding their commercial production. Therefore, it is necessary to accurate the research into an increase in biomass and oil productivity, by means of novel bioreactors\' design and cultivation techniques. On a first stage, this study shows the optimization of nutrients\' addition regimes in Neochloris oleoabundans cultivation in tubular photobioreactors, finding that the best CO2 addition methodology is an automatized intermittent adding and the best feeding process for nitrogen is a fed-batch process taking as a reference the daily biomass productivity. On the second step, it was tested the influence of stressing agents added to the culture under nitrogen starvation, such as sodium thiosulphate for reducing environment and sodium chloride and glycerol for osmotic shock, aiming lipid accumulation in the biomass. The results showed that sodium thiosulphate at 1,2mM and sodium chloride at 2,2mM raised the total lipids up to 21% and 25% respectively. Finally, there were tested different light regimes, with a scheme 12:12, being 12 hours of fluorescent light and 12 hours of a singular system: dark, red light-emitting-diodes (LED) and white LED. The best results were obtained with white LED, with an accumulation up to 27% of dry biomass and a final cell concentration up to 2335mg/L, establishing an economic illumination method with high productivity.

"Manganese (Mn2+) has recently gained acceptance as a magnetic resonance imaging (MRI) contrast agent useful for generating contrast in the functioning brain. The paramagnetic properties of Mn2+, combined with the cell's affinity for Mn2+ via voltage-gated calcium channels, makes Mn2+ sensitive to cellular activity in the brain. Compared with indirect measures of brain function, such as blood oxygenation level dependent (BOLD) functional MRI, manganese-enhanced MRI (MEMRI) can provide a direct means to visualize brain activity. MEMRI of the brain typically involves osmotic opening of the blood-brain barrier (BBB) to deliver Mn2+ into the interstitial space prior to initiation of a specific neuronal stimulus. This method assumes that the BBB-disruption process itself does not induce any apparent stimuli or cause tissue damage that might obscure any subsequent experimental observations. However, this assumption is often incorrect and can lead to misleading results for particular types of MRI applications. One aspect of these studies focused on characterizing the confounding effects of the BBB-opening process on MRI measurements typically employed to characterize functional activity or disease in the brain (Chapters 4 and 5). The apparent diffusion coefficient (ADC) of tissue water was found to decrease (relative to the undisrupted contralateral hemisphere) following BBB opening, obscuring similar ADC changes associated with ischemic brain tissue following stroke. Brain regions exhibiting reduced ADC values following osmotic BBB disruption also experienced permanent tissue damage, as validated by histological measures in the same vicinity of the brain. Non-specific MEMRI-signal enhancement was also observed under similar conditions and was found to be correlated to regions with BBB opening as verified by Evans Blue histological staining. In this case, MEMRI may prove to be a useful alternative for monitoring BBB-permeability changes in vivo. MEMRI was also investigated as a method for visualizing regions of BBB damage following ischemic brain injury (Chapter 6). BBB disruption following stroke has been investigated using gadolinium-based MRI contrast agents (e.g., Gd-DTPA). However, as an extracellular MRI contrast agent, Gd-DTPA is not expected to provide information regarding cell viability or function as part of MR image contrast enhancement. By comparison, brain regions with ischemia-induced BBB damage, and blood-flow levels sufficient to deliver Mn2+, show MEMRI-signal enhancement that correlates to regions with tissue damage as verified by histological staining. This approach should allow us to better understand the factors responsible for ischemia-induced BBB damage. Furthermore, MEMRI should be a useful tool for monitoring therapeutic interventions that might mitigate the damage associated with BBB disruption following stroke. "

Caveolae sind charakteristische Plasmamembraneinstülpungen, die in vielen Zelltypen vorkommen und deren biologische Funktion umstritten ist. Ihre besondere Form und ihre Häu gkeit in Zellen, die stets mechanischen Belastungen ausgesetzt sind, führten zu der Annahme, dass Caveolae die Plasmamembran vor mechanischen Belastungen schützen und als Membranreservoir dienen. Dies sollte mit dieser Dissertation experimentell geprüft werden. Zunächst wurde der Ein uss der Caveolae auf die Membranspannung von Zellen im Normalzustand untersucht. Dann wurden die Zellen mechanisch belastet. Mit Fluoreszensmikroskopie wurde das Verschwinden von Caveolae nach Strecken der Zellen oder nach einem hypo-osmotischen Schock beobachtet. Messungen der Membranspannung vor und unmittelbar nach dem hypo-osmotischem Schock zeigten, dass Caveolae einen Anstieg der Membranspannung verhindern, unabhängig von ATP und dem Cytoskelett. Die Erzeugung von Membranvesikel mit Caveolae erlaubte es, diesen Effekt der Caveolae in einem vereinfachten Membransystem zu beobachten. Schliesslich wurden Muskelzellen untersucht. Zellen, die genetisch bedingt weniger Caveolae haben und mit Muskelschwundkrankheiten in Verbingung stehen, waren mechanisch weniger belastbar als gesunde Zellen. Zusammenfassend wird mit dieser Dissertation die These bestärkt, dass Caveolae einem Anstieg der Membranspannungen entgegenwirken. Dass dies in Zellen und in Vesikeln unabhängig von Energie und Cytoskelett geschieht, lässt auf einen passiven, mechanisch getriebenen Prozess schliessen. Diese Erkenntnis trägt zum Verständnis der Rolle von Caveolae in Zellen bei und kann dem besseren Verständnis von Krankheiten bedingt durch Caveolin-Mutationen, wie z.B. Muskelschwundkrankheiten, dienen. / Caveolae, the characteristic plasma membrane invaginations present in many cells, have been associated with numerous functions that still remain debated. Taking into account the particular abundance of caveolae in cells experiencing mechanical stress, it was proposed that caveolae constitute a membrane reservoir and bu er the membrane tension upon mechanical stress. The present work aimed to check this proposition experimentally. First, the in uence of caveolae on the membrane tension was studied on mouse lung endothelial cells in resting conditions using tether extraction with optically trapped beads. Second, experiments on cells upon acute mechanical stress showed that caveolae serve as a membrane reservoir bu ering surges in membrane tension in their immediate, ATP- and cytoskeleton-independent attening and disassembly. Third, caveolae incorporated in membrane vesicles also showed the tension bu ering. Finally, in a physiologically more relevant case, human muscle cells were studied, and it was shown that mutations with impaired caveolae which are described in muscular dystrophies render muscle cells less resistant to mechanical stress. In Summary the present work provides experimental evidence for the hypothesis that caveolae bu er the membrane tension upon mechanical stress. The fact that this was observed in cells and membrane vesicles in an ATP and cytoskeleton independent manner reveals a passive, mechanically driven process. This could be a leap forward in the comprehension of the role of caveolae in the cell, and in the understanding of genetic diseases like muscular dystrophies. / Cavéoles sont des invaginations caractéristiques de la membrane plas- mique présents dans beaucoup de types cellulaires. Ils sont liées à plusieurs fonctions cellulaires, ce qui sont encore débattues. Prenant compte de l importance des cavéoles dans les cellules soumises au stress mécanique, les cavéoles sont proposées de constituer un réservoir membranaire et de tamponner la tension membranaire pendant des stresses mécaniques. Cette étude a eu le but de tester cette hypothèse expérimentalement. En premier, l in uence des cavéoles sur la tension membranaire au repos a été étudiée sur des cellules endothéliales du poumon de la souris. Puis, on a montré que les cavéoles tamponnent l augmentation de la tension membranaire après l application d un stress mécanique. En suite, la réalisation des vésicules membranaires contenant des cavéoles a permit de montrer leur rôle comme réservoir membranaire dans un système simpli é. Finalement, dans un contexte physiologiquement plus relevant, l étude des cellules musculaires a montrée que les mutations du cavéolin associées aux dystrophies musculaires rendent les cellules moins résistante aux stresses mécaniques. En conclusion, cette étude supporte l\'hypothèse que les cavéoles tamponnent la tension membranaire pendant des stresses mécaniques. Le fait que cela se passe dans les cellules et les vésicules indépendamment d ATP et du cytosquelette révèlent un processus passif et mécanique. Cela pourrait servir à une meilleure compréhension du rôle des cavéoles dans la cellule et les maladies génétiques comme les dystrophies musculaires.