L’avènement de la microscopie STED (Stimulated Emission Depletion) a bouleversé le domaine desneurosciences du au fait que beaucoup de structures neuronale, tels que les épines dendritiques, lesaxones ou les processus astrocytaires, ne peuvent pas être correctement résolu en microscopiephotonique classique. La microscopie 2-photon est une technique d’imagerie photonique très largement utilisée dans le domaine des neurosciences car elle permet d’imager les événements dynamique en profondeur dans le tissu cérébral, offrant un excellent sectionnement optique et une meilleure profondeur de pénétration. Cependant, la résolution spatiale de cette approche est limitée autour de 0.5 μm, la rendant inappropriée pour étudier les détails morphologiques des neurones et synapses. Le but de mon travail de thèse était à A) développer un microscope qui permet d'améliorer l'imagerie 2-photon en la combinant avec la microscopie STED et B) démontrer son potentiel pour l'imagerie à l'échelle nanométrique de processus neuronaux dynamiques dans des tranches de cerveau aigus et in vivo. Le nouveau microscope permet d'obtenir une résolution spatiale latérale de ~ 50 nm à des profondeurs d'imagerie de ~ 50 μm dans du tissu cérébral vivant. Il fonctionne avec des fluorophores verts, y compris les protéines fluorescentes communes telles que la GFP et YFP, offrant le contraste de deux couleurs basé sur la détection spectrale et linéaire ‘unmixing’. S’agissant d’un microscope droit, utilisant un objectif à immersion ayant une grande distance de travail, nous avons pu incorporer des techniques électrophysiologiques comme patch-clamp et ajouter une plateforme pour l'imagerie in vivo. J’ai utilise ce nouveau microscope pour imager des processus neuronaux fins et leur dynamique à l’échelle nanométrique dans différent types de préparations et des régions différentes du cerveau. J’ai pu révéler des nouvelles caractéristiques morphologique des dendrites et épines. En outre, j'ai exploré différentes stratégies de marquage pour pouvoir utiliser la microscopie STED pour imager le trafic des protéines et de leur dynamique à l'échelle nanométrique dans des tranches de cerveau. / The advent of STED microscopy has created a lot of excitement in the field of neuroscience becausemany important neuronal structures, such as dendritic spines, axonal shafts or astroglial processes,cannot be properly resolved by regular light microscopy techniques. Two-photon fluorescence microscopy is a widely used imaging technique in neuroscience because it permits imaging dynamic events deep inside light-scattering brain tissue, providing high optical sectioning and depth penetration. However, the spatial resolution of this approach is limited to around half a micron, and hence is inadequate for revealing many morphological details of neurons and synapses. The aim of my PhD work was to A) develop a microscope that improves on two-photon imaging by combining it with STED microscopy and to B) demonstrate its potential for nanoscale imaging of dynamic neural processes in acute brain slices and in vivo. The new microscope achieves a lateral spatial resolution of ~50 nm at imaging depths of ~50 μm in living brain slices. It works with green fluorophores, including common fluorescent proteins like GFP and YFP, offering two-color contrast based on spectral detection and linear unmixing. Because of its upright design using a long working distance water-immersion objective, it was possible to incorporate electrophysiological techniques like patch-clamping or to add a stage for in vivo imaging. I have used the new microscope to image fine neural processes and their nanoscale dynamics in different experimental preparations and brain regions, revealing new and interesting morphological features of dendrites and spines. In addition, I have explored different labeling strategies to be able to use STED microscopy for visualizing protein trafficking and dynamics at the nanoscale in brain slices.

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One of the most intriguing questions in evolutionary biology is how biochemical and structural complexity arise through small and incremental changes; however answering this question requires an explicit set of candidate residues and an experimental system in which to test them. This dissertation aims to understand how biochemical complexity evolves and assesses the structure-function relationship in the green fluorescent protein (GFP) protein family using an ancestral reconstruction approach. In the second chapter, I studied the evolution of biochemical complexity in Kaede-type red fluorescent proteins (FPs) from Faviina corals. An increase in biochemical complexity is represented by the emergence of red fluorescence because it necessitates the synthesis of a tri-cyclic chromophore from a precursor bi-cyclic chromophore through an additional autocatalytic reaction step. The autocatalytic reaction is fully enabled by as many as twelve historical mutations. Here, I showed that the red fluorescent chromophore evolved from an ancestral green chromophore by perturbing the ancestral protein stability at multiple levels of protein structure. Moreover, only three historical mutations are sufficient to initiate the selection-accessible evolutionary trajectory leading to emergence of red fluorescence. The third chapter investigates six mutations proximate to the chromophore in the Kaede-type FP that could have facilitated autocatalytic synthesis of the red chromophore by enlarging the chromophore-containing cavity and modifying its microenvironment. Two of these six mutations were found to strongly affect the protein’s stability and oligomeric tendency. Additionally, I showed that the dimeric least divergent Kaede-type FP, R1-2, evolved from the tetrameric green ancestor. Taken together the results of these studies indicate that the step-up in biochemical complexity in the Kaede-type FPs was achieved via disruption of the existing stable interactions at tertiary and quaternary protein structure levels. In the fourth chapter, I resurrected the common ancestor of all FPs cloned from the order Leptothecata (class Hydrozoa), which are characterized by the highest known homo-oligomeric diversity. I showed that the ancestor was a green monomeric FP with a large Stokes shift. The ancestral FP together with the extant Leptothecata FPs could server as a model system to study the evolution of function and homo-oligomerization, and the desirable photophysical characteristics would make this ancestral FP a useful bio-marker in bio-medical research. / text

We have developed a system to hunt and reuse special gene integration sites that allow for high and stable gene expression. A vector, named pRGFP8, was constructed. The plasmid pRGFP8 contains a reporter gene, gfp2 and two extraneous DNA fragments. The gene gfp2 makes it possible to screen the high expression regions on the chromosome. The extraneous DNA fragments can help to create the unique loci on the chromosome and increase the gene targeting frequency by increasing the homology. After transfection into Chinese hamster ovary cells (CHO) cells, the linearized pRGFP8 can integrate into the chromosome of the host cells and form the unique sites. With FACS, 90 millions transfected cells were sorted and the cells with strongest GFP expression were isolated, and then 8 stable high expression GFP CHO cell lines were selected as candidates for the new host cell. Taking the unique site created by pRGFP8 on the chromosome in the new host cells as a targeting locus, the gfp2 gene was replaced with the gene of interest, human ifngamma, by transfecting the targeting plasmid pRIH-IFN. Then using FACS, the cells with the dimmest GFP fluorescence were selected. These cells showed they had strong abilities to produce the protein of interest, IFN-gamma. During the gene targeting experiment, we found there is positive correlation between the fluorescence density of the GFP CHO host cells and the specific production rate of IFN-gamma. This result shows that the strategy in our expression system is correct: the production of the interesting protein increases with the increase fluorescence of the GFP host cells. This system, the new host cell lines and the targeting vector, can be utilized for highly expressing the gene of interest. More importantly, by using FACS, we can fully screen all the transfected cells, which can reduce the chances of losing the best cells. / Singapore-MIT Alliance (SMA)

Understanding the temporal and spatial changes in calcium concentration has been a difficult endeavor for many years due to the relatively small changes in calcium concentration during messenging events, the rapid changes upon physiological messenging, and the unavailability of fast, efficient, and sensitive sensors to detect calcium changes. In addition, the key factors in calcium binding have yet to be determined due to the metal-metal interactions, cooperativity, and conformational change involved in calcium binding to natural calcium-binding proteins. To overcome these obstacles and to engineer calcium sensors for in vivo studies of calcium signaling events, calcium binding sites have been engineered into Green Fluorescent Protein. The engineered binding sites demonstrate terbium binding affinity from 2-30 ƒÝM and calcium binding affinity from 50-100 ƒÝM. Site 177 demonstrates green fluorescence when expressed in mammalian cells and produces a response to calcium concentration changes when expressed in the cytosol. Addition of the cycle 3 mutations (M153T, V163A, F99S) to Site 177 allowed for increased brightness in the emission of the chromophore but still exhibited calcium response. The second generation Site 1 demonstrates fluorescence response to calcium concentration changes when expressed both in the cytosol and in the endoplasmic reticulum. Addition of M153T and V163A to Site 1 allowed for expression of fluorescent protein at 37 ¢XC in HeLa cells and at 30 ¢XC in bacteria. Site 1-M153T/V163A exhibits chromophore fluorescence response to calcium with a Kd of 100 ƒÝM and competition with Rhodamine-5N produced a calcium Kd of 107 ƒÝM. This designed sensor, Site 1-M153T/V163A is the first demonstration of a designed calcium binding GFP with calcium response measured both in vivo and in vitro.

TSG101 was identified as a tumor susceptibility gene by Stanley Cohen. In a variety of human cancers, no genomic deletion in TSG101 gene has been reported but many aberrant TSG101 transcripts has been found. Some studies have revealed that TSG101 participates in MDM2/p53 regulatory circuitry¡Bmembrance trafficking and receptor recycling. Other reports also showed that TSG101 might be a transcription regulatory factor. However, mechanism of these TSG101 function awaits further characterization. To further scrutinize the function of TSG101 and its subcellular localization, a varieties of GFP-based recombinant plasmids which contain various length of TSG101 cDNA have been constructed and transfected into cells. Western blot analysis had shown that these constructs could express GFP-TSG101 fusion protein of expected size. The fluorescence and confocal microscopy have shown that wild type TSG101 localized in ER, Golgi and endosome compartments, also amino acid residues 136-233 and 316-390 of TSG101 are two important regions for its subcellular localization. Previous reports had shown that TSG101 interact with OP18 which is an important regulator for spindle formation in M phase. To elucidate the localization of TSG101 and OP18 in M phase cell, we have cloned OP18 and generate GST-OP18 fusion protein for anti-OP18 antiserum production.Then, pDsRed-OP18 fusion protein expressed in OP18/pDsRed recombinant plasmid transfected cell was detected by western blotting analysis using this anti-OP18 antiserum. The subcellular localization of DsRed-OP18 and GFP-TSG(1-390) fluorescence were recorded in double transfected cells which were arrested in M phase by nocodzole treatment. We observed the evenly distribution of pDsRed-OP18 red fluorescence and punctate vesicular localization of GFP-TSG(1-390) green fluorescence. Whether these two protein interact functionally awaits further investigation.

The effect of heat shock was observed on the expression of hilA in Salmonella Typhimurium by creating a fluorescence-based reporter strain of Salmonella and by realtime reverse transcriptase polymerase chain reaction (RT-PCR). The hilA gene in Salmonella is known to play an important role in its pathogenesis. hilA is known to be activated when the bacteria encounter stress-inducing conditions. A number of factors have been identified that affect hilA expression, such as, pH, osmolarity, oxygen tension. When Salmonella enter their warm-blooded hosts, they encounter an increase in temperature. Therefore, heat is another stressor that is encountered by Salmonella during infection of their hosts. A fluorescence-based strain of Salmonella was created to study the effect of heat shock. The gene for green fluorescent protein (gfp) was placed under the control of the promoter of hilA on a plasmid. This plasmid was used to transform Salmonella cells to create a fluorescent strain. In this strain, when the hilA promoter is activated, gfp is transcribed, which encodes the green fluorescent protein. This protein can be measured by a fluorescence assay. The results of this study indicated that at 45ºC, hilA is activated. RT-PCR was used to look at hilA expression at different temperature. The results of this study indicated that, compared to 37ºC, higher temperatures like 45ºC and 55ºC significantly activate hilA.

abstract: The green fluorescent protein (GFP)-like fluorescent proteins play an important role for the color of reef-building corals. Different colors of extant coral fluorescent proteins (FPs) have evolved from a green ancestral protein. Interestingly, green-to-red photoconversion FPs (Kaede-type Red FPs) are only found in clade D from Scleractinia (Faviina suborder). Therefore, I focus on the evolution of Kaede-type FPs from Faviina suborder ancestral FP. A total of 13 mutations have been identified previously that recapitulate the evolution of Kaede-type red FPs from the ancestral green FP. To examine the effect of each mutation, total ten reconstructed FPs were analyzed and six x-ray crystal structures were solved. These substitutions created a more hydrophilic environment around the carbonyl group of Phe61. Also, they increased the flexibility of the c-terminal chain, which keeps it from interacting with the entrance of the putative solvent channel. The photoconversion reaction shows a twophase kinetics. After the rapid initial phase, the overall reaction followed the firstorder kinetics. Based on the crystal structure analysis, I propose a new mechanism for Kaede-type FP photoconversion process, which a proton transfers via Gln38 to the carbonyl group of Phe61. / Dissertation/Thesis / Ph.D. Chemistry 2012

Submitted by BRUNA DE OLIVEIRA VASCONCELOS null (bruna.olivasco@gmail.com) on 2016-04-19T22:29:05Z No. of bitstreams: 1 dissertacao_bruna_de_oliveira_vasconcelos.pdf: 2275149 bytes, checksum: 4d00665f221aeffea15e3edda524b5d2 (MD5) / Approved for entry into archive by Felipe Augusto Arakaki (arakaki@reitoria.unesp.br) on 2016-04-26T13:25:40Z (GMT) No. of bitstreams: 1 vasconcelos_bo_me_dra.pdf: 2275149 bytes, checksum: 4d00665f221aeffea15e3edda524b5d2 (MD5) / Made available in DSpace on 2016-04-26T13:25:40Z (GMT). No. of bitstreams: 1 vasconcelos_bo_me_dra.pdf: 2275149 bytes, checksum: 4d00665f221aeffea15e3edda524b5d2 (MD5) Previous issue date: 2016-02-23 / A placenta dos mamíferos é um órgão transitório formado pela justaposição entre os tecidos maternos e fetais, sendo responsável pelas trocas fisiológicas entre a mãe e o feto e pela síntese de hormônios fundamentais para a manutenção da gestação. Para o crescimento placentário e a nutrição fetal é necessário um delicado equilíbrio entre proliferação e morte das células placentárias. Essas células possuem propriedades específicas em relação a suas funções metabólicas, endócrinas e angiogênicas sendo fundamentais para o desenvolvimento adequado do concepto ao longo da prenhez e seu nascimento. Gestações de animais clonados frequentemente apresentam anormalidades como hidroâmnio, hidroalantoide, edema placentário, retenção de placenta e abortos. Neste estudo, foi avaliada a ocorrência de apoptose (morte celular) em placentônios provenientes de conceptos bovinos transgênicos clonados (n=5) e de gestações naturais (n=18), nos períodos de 60 e 90 dias de gestação, que tiveram seu desenvolvimento interrompido para remoção do útero gestante. As amostras de placentônio foram segmentadas e fixadas em solução aquosa de paraformoldeído a 4% em tampão fosfato de sódio (PBS) a 0,1M e pH 7.4, para verificação da morfologia pela coloração HE e realização da técnica de imunoistoquímica. Os resultados obtidos foram comparados entre bovinos clonados transgênicos e de gestações naturais. Todos os grupos e idades gestacionais analisados apresentaram a mesma composição celular com epitélio uterino simples cúbico onde nota-se a presença de células trofoblásticas gigantes mononucleadas e células trofoblásticas gigantes binucleadas migradas do epitélio fetal, estroma endometrial bem desenvolvido, epitélio trofoblástico com células cuboides típicas de epitélio e quantidade acentuada de células trofoblásticas gigantes e gigantes binucleadas migrando para o epitélio materno e mesênquima. Em todos os grupos e períodos gestacionais, o epitélio materno apresentou maior marcação positiva para apoptose. Aos 60 dias a marcação positiva no epitélio uterino das gestações manipuladas foi menos evidente em relação às de gestações naturais, assim como aos 90 dias, que apresentou maior imunorreatividade em comparação aos 60 dias e dos animais de gestação natural sobre os manipulados. Na ultima idade gestacional foi possível observar reação em padrão de fileiras no epitélio uterino e para ambos os grupos não foram encontradas marcações nos tecidos fetais. Neste estudo foi demonstrado desequilíbrio nos padrões de apoptose nos conceptos bovinos clonados transgênicos, pois no início da gestação (60 dias) apresentaram menor atividade apoptóticas e aos 90 dias um aumento, podendo ser este fato um dos fatores que levam às anormalidades placentárias. Desse modo os resultados da verificação da apoptose, nas fases de gestação estudadas, e seu entendimento são importantes para a compreensão de possíveis falhas no desenvolvimento gestacional em técnicas avançadas de manipulação embrionárias, como a produção de animais transgênicos e clonados. / The placenta in mammals is a transitional organ formed by the justaposition between maternal and fetal tissues, it is responsible for physiological exchanges between mother and fetus and the synthesis of hormones essential for maintaining gestation. For the fetal placental growth and nutrition are requires a delicate balance between proliferation and death cells of the placenta. These cells have specific properties in relation to its metabolic functions, endocrine and angiogenic and it is critical to the proper development of the fetus throughout pregnancy and birth. Cloned animals often have abnormal pregnancies as hidroamnion, hidroalantois, placental edema, retained placenta and abortion. In this study, placentomes the occurrence of apoptosis (death cells) was avaluate from fetuses cloned transgenic cattle (n = 5) and natural pregnancies (n = 18) in periods of 60 and 90 days of gestation that had their intermited development to remove the pregnant uterus. Placentome samples were segmented and fixed in aqueous 4% paraformaldehyde in sodium phosphate buffer (PBS) pH 7.4 and 0.1M, to check the morphology of HE staining and the immunohistochemistry. The results were compared between transgenic cloned cattle and natural gestations. In all groups and gestational ages analyzed showed the same cellular composition with simple cubic uterine epithelium, it is noted the presence of trophoblast giant cells mononuclear and giant trophoblast cells binucleated migrated from fetal epithelium, endometrial stroma well developed, trophoblastic epithelium with typical cuboid cell epithelium and severe amount of giants and giant binucleated trophoblastic cells migrating into maternal epithelium and mesenchyme. All groups and gestational periods, maternal epithelium showed higher positive staining for apoptosis. At 60 days the positive staining in the uterine epithelium is less evident manipulated pregnancies in relation to natural pregnancies as well as at 90 days, with the highest immunoreactivity when it is compared to 60 days and in the animals of natural pregnancy in ratio to manipulated animals. In the last gestational age was observed in response pattern rows in the uterine epithelium and both groups fetal side tags were not found either in or on the epithelium and mesenchyme. This study demonstrated an imbalance in apoptosis patterns in transgenic cloned cattle fetuses as early in pregnancy (60 days) showed less apoptotic activity and an increase at 90 days and may be this fact one of the factors leading to placental abnormalities. Thereby the results of the verification of apoptosis at the stages of pregnancy studied and comprehension are important for the understanding of possible failure in gestational development in advanced embryonic manipulation techniques, such as the production of transgenic and cloned animals.

Orientador: Flávia Thomaz Verechia Pereira / Resumo: A placenta dos mamíferos é um órgão transitório formado pela justaposição entre os tecidos maternos e fetais, sendo responsável pelas trocas fisiológicas entre a mãe e o feto e pela síntese de hormônios fundamentais para a manutenção da gestação. Para o crescimento placentário e a nutrição fetal é necessário um delicado equilíbrio entre proliferação e morte das células placentárias. Essas células possuem propriedades específicas em relação a suas funções metabólicas, endócrinas e angiogênicas sendo fundamentais para o desenvolvimento adequado do concepto ao longo da prenhez e seu nascimento. Gestações de animais clonados frequentemente apresentam anormalidades como hidroâmnio, hidroalantoide, edema placentário, retenção de placenta e abortos. Neste estudo, foi avaliada a ocorrência de apoptose (morte celular) em placentônios provenientes de conceptos bovinos transgênicos clonados (n=5) e de gestações naturais (n=18), nos períodos de 60 e 90 dias de gestação, que tiveram seu desenvolvimento interrompido para remoção do útero gestante. As amostras de placentônio foram segmentadas e fixadas em solução aquosa de paraformoldeído a 4% em tampão fosfato de sódio (PBS) a 0,1M e pH 7.4, para verificação da morfologia pela coloração HE e realização da técnica de imunoistoquímica. Os resultados obtidos foram comparados entre bovinos clonados transgênicos e de gestações naturais. Todos os grupos e idades gestacionais analisados apresentaram a mesma composição celular com epitélio uterino... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: The placenta in mammals is a transitional organ formed by the justaposition between maternal and fetal tissues, it is responsible for physiological exchanges between mother and fetus and the synthesis of hormones essential for maintaining gestation. For the fetal placental growth and nutrition are requires a delicate balance between proliferation and death cells of the placenta. These cells have specific properties in relation to its metabolic functions, endocrine and angiogenic and it is critical to the proper development of the fetus throughout pregnancy and birth. Cloned animals often have abnormal pregnancies as hidroamnion, hidroalantois, placental edema, retained placenta and abortion. In this study, placentomes the occurrence of apoptosis (death cells) was avaluate from fetuses cloned transgenic cattle (n = 5) and natural pregnancies (n = 18) in periods of 60 and 90 days of gestation that had their intermited development to remove the pregnant uterus. Placentome samples were segmented and fixed in aqueous 4% paraformaldehyde in sodium phosphate buffer (PBS) pH 7.4 and 0.1M, to check the morphology of HE staining and the immunohistochemistry. The results were compared between transgenic cloned cattle and natural gestations. In all groups and gestational ages analyzed showed the same cellular composition with simple cubic uterine epithelium, it is noted the presence of trophoblast giant cells mononuclear and giant trophoblast cells binucleated migrated from fetal epithel... (Complete abstract click electronic access below) / Mestre