The endoplasmic reticulum stress response, also known as the unfolded protein response (UPR), has been implicated in the normal physiology of immune defense and in several disorders, including diabetes, cancer, and neurodegenerative disease. Here, we show that the apoptotic receptor CED-1 and a network of PQN/ABU proteins involved in a noncanonical UPR response are required for proper defense to pathogen infection in Caenorhabditis elegans. A full-genome microarray analysis indicates that CED-1 functions to activate the expression of pqn/abu genes. We also show that ced-1 and pqn/abu genes are required for the survival of C. elegans exposed to live Salmonella enterica, and that overexpression of pqn/abu genes confers protection against pathogen-mediated killing. The results indicate that unfolded protein response genes, regulated in a CED-1-dependent manner, are involved in the C. elegans immune response to live bacteria. / Dissertation

O emprego de aditivos hidrossolúveis como açúcares, tensoativos, sais e polímeros é prática comum na tentativa de se estabilizar proteínas durante aquecimento. Diversos polímeros têm sido utilizados para estabilizar proteínas, sendo seu efeito dependente das características da proteína. Sais podem estabilizar, desestabilizar ou não ter efeito na estabilidade de proteínas; dependendo do tipo, concentração, natureza das interações iônicas e resíduos carregados da proteína. A termoestabilidade da proteína verde fluorescente (GFP) tem sido demonstrada ao calor úmido, à temperaturas elevadas (T ≥ 95°C), à valores de pH alcalinos e a alguns agentes químicos. Sua denaturação térmica é altamente reprodutível e a variação da intensidade de fluorescência pode ser facilmente determinada por espectrofluorimetria. O objetivo deste trabalho foi estudar o comportamento da GFP na presença de diferentes soluções aquosas de polímeros (polietileno glicol, DEAE-Dextrana e ácido poliacrílico) e sais (citrato e fosfato). A partir dos dados obtidos, pode-se concluir que o citrato favoreceu a preservação da estrutura nativa da GFP nas temperaturas estudadas (70 a 95ºC), em concentrações acima de 10% m/m. O ácido poliacrílico também auxiliou na manutenção da estrutura nativa da GFP, porém em menor intensidade, e com concentrações acima de 20% m/m. / The addition of hydrosoluble excipients, such as, sugars, surfactants, salts and polymers is a common practice in the intent of stabilization of proteins during heating. Several polymers have been used to proteins stabilization, being their effect dependent of protein characteristics, however in some cases, it could cause a reduction of stability. Salts can stabilize proteins, or have no influence in their stability, and these behaviors depend on the type, concentration, ionic interaction and charged protein residues. Thermal stability of green protein fluorescent (GFP) have been demonstrated to humid heat, elevated temperatures (T ≥ 95°C), alkaline pH and to some chemical agents. Its thermal denaturation is highly reproducible and the variation of fluorescence intensity can be easily determinate by spectrofluorometry. The objective of this work was study the behavior of GFP in the presence of different aqueous solutions of polymers (polyethylene glycol, DEAE-Dextran and acid polyacrylic) and salts (citrate and phosphate). From the results, it may be concluded that the citrate favored the preservation of native structure of GFP in the temperatures studied (70ºC to 95ºC), in concentrations above 10% m/m. The PAA polymer also favored the GFP thermal stability, but in a minor intensity and in concentrations above 20% m/m.

O emprego de aditivos hidrossolúveis como açúcares, tensoativos, sais e polímeros é prática comum na tentativa de se estabilizar proteínas durante aquecimento. Diversos polímeros têm sido utilizados para estabilizar proteínas, sendo seu efeito dependente das características da proteína. Sais podem estabilizar, desestabilizar ou não ter efeito na estabilidade de proteínas; dependendo do tipo, concentração, natureza das interações iônicas e resíduos carregados da proteína. A termoestabilidade da proteína verde fluorescente (GFP) tem sido demonstrada ao calor úmido, à temperaturas elevadas (T ≥ 95°C), à valores de pH alcalinos e a alguns agentes químicos. Sua denaturação térmica é altamente reprodutível e a variação da intensidade de fluorescência pode ser facilmente determinada por espectrofluorimetria. O objetivo deste trabalho foi estudar o comportamento da GFP na presença de diferentes soluções aquosas de polímeros (polietileno glicol, DEAE-Dextrana e ácido poliacrílico) e sais (citrato e fosfato). A partir dos dados obtidos, pode-se concluir que o citrato favoreceu a preservação da estrutura nativa da GFP nas temperaturas estudadas (70 a 95ºC), em concentrações acima de 10% m/m. O ácido poliacrílico também auxiliou na manutenção da estrutura nativa da GFP, porém em menor intensidade, e com concentrações acima de 20% m/m. / The addition of hydrosoluble excipients, such as, sugars, surfactants, salts and polymers is a common practice in the intent of stabilization of proteins during heating. Several polymers have been used to proteins stabilization, being their effect dependent of protein characteristics, however in some cases, it could cause a reduction of stability. Salts can stabilize proteins, or have no influence in their stability, and these behaviors depend on the type, concentration, ionic interaction and charged protein residues. Thermal stability of green protein fluorescent (GFP) have been demonstrated to humid heat, elevated temperatures (T ≥ 95°C), alkaline pH and to some chemical agents. Its thermal denaturation is highly reproducible and the variation of fluorescence intensity can be easily determinate by spectrofluorometry. The objective of this work was study the behavior of GFP in the presence of different aqueous solutions of polymers (polyethylene glycol, DEAE-Dextran and acid polyacrylic) and salts (citrate and phosphate). From the results, it may be concluded that the citrate favored the preservation of native structure of GFP in the temperatures studied (70ºC to 95ºC), in concentrations above 10% m/m. The PAA polymer also favored the GFP thermal stability, but in a minor intensity and in concentrations above 20% m/m.

Non-invasive imaging techniques, such as micro-CT or optical imaging, provide valuable information about tumour microstructure, size, volume and growth dynamics. Although histology is an approach capable of describing several of these characteristics, the invasiveness of this analysis remains a disadvantage. The main aim of this work is the methodological development of non-invasive imaging of the dynamics of tumour growth and progression. The preparation of a dual-reporter lentiviral vector enables non-invasive study of tumour growth and dissemination of metastasis. The same dual reporter will also be a part of a second vector designed as a construct for targeting mouse embryonic stem cells with aim to produce corresponding transgenic reporter mouse line. This reporter mouse line can be beneficial for future projects by providing a novel approach for studying the dynamics of tumour growth under various genetic conditions. In addition to optical imaging, this project will also include the use of micro-CT technology which, as a non-invasive approach, has the potential to provide information about the microstructure of tumour tissue in 3D that histology is not able to report.

In this thesis, emphasis has been placed on development of new approaches for high-throughput analysis of protein:DNA interactions in vitro and in vivo. In vitro strategies for detection of protein:DNA interaction require isolation of active and soluble protein. However, current methodologies for purification of proteins often fail to provide high yield of pure and tag-free protein mainly because enzymatic cleavage reactions for tag removal do not exhibit stringent sequence specificity. Solving this problem is an important step towards high-throughput in vitro analysis of protein:DNA interactions. As a result, parts of this thesis are devoted to developing new approaches to enhance the specificity of a proteolysis reaction. The first approach was through manipulation of experimental conditions to maximize the yield of the desired protein products from enterokinase proteolysis reactions of two His-tagged proteins. Because it was suspected that accessibility of the EK site was impeded, that is, a structural problem due to multimerization of proteins, focus was based on use of denaturants as a way to open the structure, thereby essentially increasing the stoichiometry of the canonical recognition site over noncanonical, adventitious sites. Promoting accessibility of the canonical EK target site can increase proteolytic specificity and cleavage yield, and general strategies promoting a more open structure should be useful for preparation of proteins requiring endoprotease treatment. One such strategy for efficient EK proteolysis is proposed: by heterodimerizing with a separate leucine zipper, the bZIP basic region and amino-terminus can become more open and potentially more accessible to enterokinase. In vivo strategies have the advantage over their in vitro counterparts of providing a native-like environment for assessing protein:DNA interactions, yet the most frequently used techniques often suffer from high false-positive and false-negative rates. In this thesis, a new bioprobe system for high-throughput detection of protein:DNA interactions in vivo is presented. This system offers higher levels of accuracy and sensitivity as well as accessibility and ease of manipulation in comparison with existing technologies.

In this thesis, emphasis has been placed on development of new approaches for high-throughput analysis of protein:DNA interactions in vitro and in vivo. In vitro strategies for detection of protein:DNA interaction require isolation of active and soluble protein. However, current methodologies for purification of proteins often fail to provide high yield of pure and tag-free protein mainly because enzymatic cleavage reactions for tag removal do not exhibit stringent sequence specificity. Solving this problem is an important step towards high-throughput in vitro analysis of protein:DNA interactions. As a result, parts of this thesis are devoted to developing new approaches to enhance the specificity of a proteolysis reaction. The first approach was through manipulation of experimental conditions to maximize the yield of the desired protein products from enterokinase proteolysis reactions of two His-tagged proteins. Because it was suspected that accessibility of the EK site was impeded, that is, a structural problem due to multimerization of proteins, focus was based on use of denaturants as a way to open the structure, thereby essentially increasing the stoichiometry of the canonical recognition site over noncanonical, adventitious sites. Promoting accessibility of the canonical EK target site can increase proteolytic specificity and cleavage yield, and general strategies promoting a more open structure should be useful for preparation of proteins requiring endoprotease treatment. One such strategy for efficient EK proteolysis is proposed: by heterodimerizing with a separate leucine zipper, the bZIP basic region and amino-terminus can become more open and potentially more accessible to enterokinase. In vivo strategies have the advantage over their in vitro counterparts of providing a native-like environment for assessing protein:DNA interactions, yet the most frequently used techniques often suffer from high false-positive and false-negative rates. In this thesis, a new bioprobe system for high-throughput detection of protein:DNA interactions in vivo is presented. This system offers higher levels of accuracy and sensitivity as well as accessibility and ease of manipulation in comparison with existing technologies.

Protein engineering can be performed by combinatorial techniques (directed evolution) and data-driven methods using machine-learning algorithms. The main characteristic of directed evolution (DE) is the application of an effective and efficient screen or selection on a diverse mutant library. As it is important to have a diverse mutant library for the success of DE, we compared the performance of DNA-shuffling and recombination PCR on fluorescent proteins using sequence information as well as statistical methods. We found that the diversity of the libraries DNA-shuffling and recombination PCR generates were dependent on type of skew primers used and sensitive to nucleotide identity levels between genes. DNA-shuffling and recombination PCR produced libraries with different crossover tendencies, suggesting that the two protocols could be used in combination to produce better libraries. Data-driven protein engineering uses sequence, structure and function data along with analyzed empirical activity information to guide library design. Boolean Learning Support Vector Machines (BLSVM) to identify interacting residues in fluorescent proteins and the gene templates were modified to preserve interactions post recombination. By site-directed mutagenesis, recombination and expression experiments, we validated that BLSVM can be used to identify interacting residues and increase the fraction of active proteins in the library. As an extension to the above experiments, DE was applied on monomeric Red Fluorescent Proteins to improve its spectral characteristics and structure-guided protein engineering was performed on penicillin G acylase (PGA), an industrially relevant catalyst, to change its substrate specificity.

La propriété d’être réversiblement commutable de certaines protéines fluorescenteshomologues à la GFP ouvre un vaste champ d’applications possibles: notamment le biostockagede données à haute densité et la microscopie à super résolution. Parmi ces protéines,on trouve plusieurs variantes de la GFP, notamment la protéine jaune YFP, et des protéinesfluorescentes issues d'espèces marines Anthozoaires, comme Dronpa ou Padron. Plusieursétudes structurales indiquent que ces protéines fluorescentes photochromiques commutent parisomérisation et protonation couplées du chromophore. Cependant, la synchronisation entreces deux événements, le détail des mécanismes de photo-commutation, et le rôle de ladynamique conformationelle restent incomplètement compris. Par l'utilisation combinée de lacristallographie cinétique et de la spectroscopie optique in cristallo à basse température, nousavons comparé le comportement des protéines YFP, Dronpa et IrisFP, et nous avons étudié endétail le mécanisme photo-physique de commutation chez la protéine Padron. Contrairement àDronpa et IrisFP, la photo-commutation d’YFP est plus efficace à basse température qu’àtempérature ambiante. Nos résultats suggèrent que le mécanisme de commutation d’YFPn'implique pas de changement conformationel majeur, mais plutôt une protonation photoinduitedu chromophore ne nécessitant pas d'isomérisation. Au contraire, les études réaliséessur la protéine Padron nous ont permis de montrer que, dans ce cas, l’isomérisation duchromophore peut se produire indépendamment de sa protonation, et, étonnamment, àtempérature cryogénique. De plus, deux états intermédiaires ont pu être caractérisés au coursdu processus de photo-commutation. La protéine Padron a permis de mettre à jour le premiermarqueur codable génétiquement qui soit efficacement photo-commutable à températurecryogénique. / The property to be reversible switchable of some homologues fluorescents protein ofGFP open a large field for possible applications: such as, high-density data bio-storage andsuper-resolution microscopy. Between these proteins, we find several variants of GFP, such asyellow fluorescent protein, YFP, and fluorescents protein from marine Anthozoary species, asDronpa or Padron. Several structural studies suggest that these fluorescent proteins switch viaisomerization coupled with the protonation of the chromophore. However, thesynchronization between these processes, the detail about the photo-switching mechanism,and the role of conformational dynamics remains unclear. In combination of the kineticcrystallography and the optic spectroscopy in cristallo at low temperature, we have comparedthe YFP behavior, Dronpa and IrisFP, and we have studied in detail the photo-physicmechanism of Padron switching. In contrast to Dronpa and IrisFP, the YFP photoswitching ismore efficient at low temperature than at room temperature. Our results suggest that theYFPswitching is not associated to large structural rearrangements, but mostly a photo-inducedprotonation of the chromophore without isomerization. On the contrary, the studies done withPadron allowed us to show, in this case, the chromophore isomerization can be producedindependently of the protonation, at cryo-temperatures. Moreover, two intermediate stateswere revealed in the photo-pathway. Padron fluorescent protein allows to advance the firstgenetically inserted dye, being photo-switchable at cryogenic temperature

Orientador: Ana Maria Aparecida Guaraldo / Dissertação (mestrado) - Universidade Estadual de Campinas, Instituto de Biologia / Made available in DSpace on 2018-08-14T15:15:00Z (GMT). No. of bitstreams: 1 Pinto_HelenCupertinoSilva_M.pdf: 1411655 bytes, checksum: 74209c9aaeedc867a4d0f783be898b27 (MD5) Previous issue date: 2009 / Resumo: A malária cerebral humana é a manifestação mais grave do Plasmodium falciparum que ocorre em 1% das infecções, sendo responsável por mais de dois milhões de mortes anuais entre crianças abaixo de cinco anos. O modelo experimental mais aceito da malária cerebral é o camundongo C57BL/6 infectado pelo Plasmodium berghei ANKA (PbA). A administração da fração mononuclear da medula óssea, contendo principalmente células tronco mesenquimais e hematopoiéticas, constitui uma estratégia promissora no tratamento de danos neurais causados por acidente vascular cerebral. Neste estudo, foi avaliado o efeito de células da medula óssea de camundongos transgênicos C57BL/6 GFP HET transplantadas em C57BL/6JUnib infectados com 106 hemácias parasitadas pelo PbA. Resumidamente, células perfundidas da medula do fêmur e tíbia de C57BL/6 GFP HET foram purificadas por gradiente de Ficoll (Histopaque) a 1000 x g por 15 minutos. Após duas lavagens em meio RPMI, as células foram ressuspensas em NaCl 0,15 M. No segundo dia após a infecção (dai) pelo PbA, foram injetadas 3,0 x 106 a 4,6 x 107 células de medula óssea (CMO) no plexo oftálmico dos camundongos devidamente anestesiados com ketamina/xylasina (protocolo 1078-1 CEEA/Unicamp). Alguns camundongos receberam apenas a injeção de células totais da medula óssea (CTMO), sem a purificação pelo gradiente de Ficoll. Foi avaliada a integridade da barreira hemato-encefálica, mediante a injeção de azul de Evans 1% no plexo oftálmico em camundongos transplantados e não transplantados com células mononucleares da medula óssea (CMoMO) no 2º dai. Após 3 e 4 dias do transplante, não houve proteção da barreira hemato-encefálica. Para constatação da presença das células de medula óssea no cérebro, outro grupo de camundongos infectados pelo PbA recebeu no 2º dai, 4,6 x 107 CMoMO provenientes de camundongos GFP. Após a manifestação de sinais clínicos da MC os camundongos foram sacrificados para remoção do cérebro e preparo de cortes em criostato. Foi possível observar, sob microscópio de fluorescência, a presença de células da medula no bulbo olfatório de camundongos com MC+. Também foram avaliadas a sobrevivência, a parasitemia e a ação coadjuvante do tratamento com cloroquina (0,8 mg/dia/animal). Todos os 38 animais do grupo controle morreram até o 7º dia de infecção pelo PbA (13,16% no 5º dia, 68,42% no 6º dia e 18,42 % no 7º dai). A injeção de células da medula óssea não interferiu na parasitemia dos animais. Apesar dos animais que superaram a fase aguda da malária cerebral morrerem em decorrência de hiperparasitismo e anemia, o tratamento com células da medula óssea (fração mononuclear ou células totais) mostrou-se capaz de ampliar a sobrevivência em 10 a 21 dias, resultados considerados promissores. As células da medula óssea promoveram a melhora clínica do quadro neurológico da malária cerebral. / Abstract: The cerebral malaria (CM) is the most serious complication of Plasmodium falciparum occurring in 1% of infections, and is responsible for more than two million of annual deaths among children under five years old. The experimental model for brain malaria currently used is the C57BL/6 mice infected by Plasmodium berghei ANKA (PbA). Administration of mononuclear population from bone marrow containing mainly mesenchymal stem cells and haematopoietic stem cells, is a promising strategy to treat neural damages caused by stroke. In this study was evaluated the effect of bone marrow mononuclear cells of transgenic mice C57BL/6 GFP HET transplanted into C57BL/6JUnib, infected by 106 parasitized erythrocyte PbA. Briefly, bone marrow mononuclear cells flushed from femur and tibia of C57BL/6 GFP HET were purified through Ficoll (Histopaque) gradient at 1000xg during 15 minutes. After two washes with RPMI medium, the cells were resuspended in NaCl 0,15M. On the second day after infection (DAI) by PbA, were injected into mice orbital plexus 3x10 6 to 4.6x107 cells of after anaesthesia with Ketamine/Xylazine (protocol nº 1078-1 CEEA/UNICAMP). Some mice received only injection of total bone marrow cells without purification on Ficoll gradient. The injection of bone marrow mononuclear cells on the second day of infection by PbA was unable in recovering the brain blood barrier after three or four days. In order to confirm the presence of bone marrow cells in the brain, another group of infected C57BL/6JUnib received on the second day after infection 4.6 x 107 bone marrow mononuclear cells from GFP mice. They were sacrificed between 6th and 8th day after onset of clinical signs of the CM. After removal and preparation of the brain for criostate cuts, was possible to observe, under fluorescence microscope, the presence of GFP bone marrow cells in the olfactory bulb on CM+ mice. It was evaluated survival, parasitemia and action of the adjuvant treatment of chloroquine (0.8 mg/day/animal) as well. All the 38 animals from control group died until 7th DAI. (13.16% at 5th DAI,68.42% at 6th DAI and 18.42% at 7th DAI). The transplantation of bone marrow cells did not affect the parasitemia. The bone marrow cells therapy infected mice by PbA was able to revert the clinical signs of cerebral malaria, increasing the survival up to 21 days. / Mestrado / Parasitologia / Mestre em Parasitologia

Breast cancer is the most common cancer type with a high annual death rate. Finding meaningful tissue-related or body-fluid-accessible biomarkers is necessary to characterize cancer subtype, predict tumor behavior, choose the most effective therapy, predict severe treatment-related toxicities, and also the opportunity to personalize treatments for each patient. There is increasing evidence that various kallikrein-related peptidases (Klk) gene family members can modulate the immune response and are differentially regulated in breast cancer, and therefore are proposed to be potential prognostic biomarkers. This work established and validated an experimental setup to study the roles of selected kallikrein-related peptidases (KLK5, KLK7, KLK14) in breast cancer in vivo using gene-deficient mouse models previously generated in our laboratory. We used the CRISPR/Cas9 (clustered regularly interspaced short palindromic repeats) editing system to generate several E0771 cell line-based reporter and gene-deficient cell lines. These allowed enhanced monitoring of cancer progression in vivo and studying KLKs roles in tumor immune microenvironment of C57Bl/6N mice. Finally, we present the analysis of the initial in vivo experiments using these tools combined with established Klk-deficient mouse models. Our...