Esta tese de doutorado descreve os estudos realizados para elucidar a biologia molecular da bioluminescência fúngica e sua relevância ecológica na natureza. A recente descoberta de que a luciferina fúngica é a 3-hidroxihispidina permitiu a caracterização do metabolismo secundário da fenilalanina nos genomas recém-sequenciados e transcriptomas de micélios das espécies luminescentes Panellus stipticus e Neonothopanus gardneri. Adicionalmente os genomas e transcriptomas de variedades não luminescente de P. stipticus e Lentinula edodes serviram como respectivos controles. Em geral, os genes envolvidos no metabolismo secundário da fenilalanina em amostras luminescentes tinham expressão igual ou superior àquela de espécies não luminescentes. Um agrupamento de genes relacionados com a biossíntese de fenilalanina foi encontrado em ambos os genomas luminescentes e não luminescentes de P. stipticus. A abundância de genes transcritos neste agrupamento foi semelhante para as espécies luminescentes e não luminescentes de P. stipticus, mas a policetídeo sintase tipo I em P. stipticus não luminescentes foi significativamente sub-regulada. Não foi encontrado agrupamento semelhante nos genomas de N. gardneri e L. edodes, sendo que os correspondentes homólogos estavam espalhados em diferentes loci. Extratos de fungos podem ser preparados in vitro, com a adição de 3-hidroxihispidina para produzir luz verde em abundância. A preparação de extratos proteicos de luciferase foi melhorada e a estrutura da luciferase, parcialmente purificada, foi investigada por espectrometria de massas. A presença de luciferase nos géis de purificação foi revelada usando-se luciferina e molécula similares à luciferina advindas de extratos de plantas. O nicho ecológico nas vizinhas de cogumelos bioluminescentes foi investigado de duas maneiras, armadilhas adesivas com cogumelos artificiais de acrílico, iluminados com luz LED verde e através da observação direta de cogumelos bioluminescentes com fotografia no infravermelho com lapso de tempo. Os estudos ecológicos foram conduzidos nos biomas da Mata Atlântica e da Mata dos Cocais, no Brasil. Baratas, aranhas, tesourinhas, grilo e vagalumes tec-tecs foram os animais mais comuns que interagiram com os cogumelos. Todos estes animais podem agir como dispersores de propágulos e, em alguns casos, como defensores dos cogumelos. / This PhD thesis describes the studies performed to elucidate the molecular biology of fungal bioluminescence and the ecological significance of the trait in the wild. The recent discovery that the fungal luciferin is 3-hydroxyhispidin has allowed for the characterization of phenylalanine secondary metabolism in the newly sequenced genomes and mycelium transcriptomes of luminescent Panellus stipticus and Neonothopanus gardneri, additionally the genomes and transcriptomes of a non-luminescent variety of P. stipticus and Lentinula edodes served as respective controls. In general the genes involved in phenylalanine secondary metabolism had greater or equal expression in luminescent samples than non luminescent. A cluster of genes related to the secondary metabolism of phenylalanine was found in both luminescent and non luminescent P. stipticus genomes. Transcript abundance of genes in this cluster was similar in both luminescent and non-luminescent Panellus stipticus, but the type I polyketide synthase in non luminescent Panellus stipticus was significantly down regulated. A similar gene cluster in the N. gardneri and L. edodes genomes was absent with corresponding homologues scattered at different genomic loci. Cell free fungal extracts can be combined in vitro with the addition of 3-hydroxyhispidin to produce abundant green light. Preparation of proteinaceous luciferase extracts was improved and partially purified luciferase samples were investigated by mass spectrometry. The presence of luciferase in the separation gel was also evidenced by using luciferin and luciferin-like molecules from plant extracts. The ecological niche surrounding bioluminescent mushrooms was investigated through two main means, glue traps with acrylic mushroom facsimiles that were internally illuminated with green LED lights and direct observation of bioluminescent mushrooms with infrared time lapse photography. Ecological studies were performed in the Atlantic rainforest (Mata Atlântica) and transitional Coconut Palm forest (Mata dos Cocais) biomes of Brazil. Cockroaches, spiders, earwigs, crickets, and luminescent click beetles were the most common animal interacting with mushrooms. All of these animals may be acting as fungal propagule dispersers and in some cases defense of the mushroom.

Este trabalho descreve a remediação simultânea de dois genes supressores de tumor, CDKN2A e p53, em três linhagens celulares derivadas de glioblastoma multiforme: U87 (CDKN2A-/-, p53wt/wt), U251 (CDKN2A-/-, p53mut/mut) e T98G (CDKN2A-/-, p53mut/mut). A entrega gênica foi mediada por vetor adenoviral bicistrônico contendo o cassete CDKN2AIRESp53, capaz de expressar as duas proteínas simultaneamente. Vetores monocistrônicos também foram testados (AdCDKN2A e Adp53). Visando detectar apoptose, as linhagens receberam o sensor de atividade de caspase-3/7 GFP-DEVD-ssGLUC por transdução lentiviral. Este possui Gaussia luciferase (GLUC) C-terminal, que é secretada após ativação de caspases e pode ser dosada no sobrenadante. Após a marcação, realizaram-se ensaios de viabilidade celular, proliferação, formação de colônias, senescência, ciclo celular e dosagem de GLUC após remediação dos genes supressores de tumor nas linhagens GBMDEVD-GLUC. Com ensaio de viabilidade, observou-se efeito citotóxico do vetor bicistrônico AdCDKN2AIRESp53 maior que a soma dos obtidos com cada tratamento monocistrônico. No ensaio de senescência, o vetor AdCDKN2A resultou na maior indução do fenótipo senescente em todas as linhagens, seguido por Adp53, enquanto AdCDKN2AIRESp53 produziu resultados similares a um desses dois perfis em cada linhagem. Dosagem de GLUC no sobrenadante foi usada como indicador para atividade de caspase-3/7 após tratamento com os vetores supressores de tumor. O controle AdLacZ resultou em atividade de GLUC maior que nas amostras sem vírus (mock), enquanto tratamento com AdCDKN2A obteve resultados maiores que o controle em 72 h nas três linhagens. O vetor AdCDKN2AIRESp53 alcançou, inesperadamente, resultados variados em 72 h. Os dados obtidos neste trabalho indicam que a remediação simultânea de CDKN2A e p53 possui notável ação antiproliferativa tumoral, podendo levar à morte ou à senescência celular. Também é apontado que o sensor de caspase-3/7 GFP-DEVD-ssGLUC é robusto, mas detecta não apenas a indução de apoptose, mas a combinação de todos os processos ativadores de caspases em uma amostra. / This thesis describes the simultaneous remedy of two tumor suppressor genes, CDKN2A and p53, in three glioblastoma multiforme (GBM)-derived cell lines: U87 (CDKN2A-/-, p53wt/wt), U251 (CDKN2A-/-, p53mut/mut) and T98G (CDKN2A-/-, p53mut/mut). Gene delivery was mediated by a bicistronic adenoviral vector bearing the sequence CDKN2AIRESp53, which simultaneously expresses both proteins. Monocistronic vectors were also tested (AdCDKN2A and Adp53). To detect apoptosis, the GBM cell lines received caspase-3/7 sensor GFP-DEVD-ssGLUC via lentiviral transduction. This sensor has a C-terminal Gaussia luciferase (GLUC), which is secreted by the cell after caspase activation and can be measured in the supernatant. After sensorization, functional assays were carried out, including cell viability, proliferation, colony formation, cell senescence, cell cycle and GLUC measure after treatment with the tumor suppressor vectors in GBMDEVD-GLUC lineages. Viability assay with the AdCDKN2AIRESp53 vector resulted in a remarkable cytotoxic effect, greater than the sum of the effects with each monocistronic treatment. In the senescence assay, vector AdCDKN2A yielded the highest induction of cell senescence in all lineages, followed by Adp53, while AdCDKN2AIRESp53 induced results that followed one of these two profiles in each cell line. GLUC measure was an indicator of intracellular caspase-3/7 activity after treatment with the tumor supressor vectors. Control vector AdLacZ resulted in higher GLUC activity than mock treatment in all three cell lines, while AdCDKN2A treatment showed results bigger than control at 72 h in all cell lines. Bicistronic vector AdCDKN2AIRESp53 reached, unexpectedly, varied results at 72 h in all cell lines. Data obtained in this study indicate that simultaneous remedy of CDKN2A and p53 has remarkable antiproliferative activity in GBM cells, resulting in cell death or cell senescence. It is also shown that caspase-3/7 sensor GFP-DEVD-ssGLUC is a robust tool, but its results detect not only a single cellular process, such as apoptosis, but the combination of all caspase-activating processes in a cell population.

Vor dem Hintergrund der zunehmenden Prävalenz von Adipositas ist die Erforschung der zugrunde liegenden Pathomechanismen, unter anderem der Leptinresistenz, von großer Bedeutung. Der Schwerpunkt der vorliegenden Arbeit lag in der Etablierung und Validierung einer Methode zur Bestimmung der Bioaktivität von Leptin in Serum. Aufgrund des Vorhandenseins von Leptinbindungsproteinen erscheint nur der Teil des Serumleptins funktionell entscheiden, der tatsächlich den Leptinrezeptor erreicht und eine Bioantwort im Sinne einer Gewichtsreduktion auszulösen vermag. Der Bioassay basiert auf der Nutzung von Luciferase als Reportergen im HEK-293-Zellkulturmodell. Während der Validierung konnte gezeigt werden, dass der Test ein sensitives und spezifisches Verfahren zur Messung von Leptin im Serum darstellt. Problematisch blieb die Reproduzierbarkeit der Messergebnisse, so dass deren Interpretation im Vergleich mit Ergebnissen anderer Verfahren zum Nachweis von Leptin (Radioimmunoassay) sinnvoll erscheint. Der Luciferase-Bioassay wurde zur Bestimmung des Leptins im Serum adipöser Kinder eingesetzt, wobei eine statistisch signifikante Korrelation zwischen deren Bioaktivität und klinischen Markern der Adipositas gefunden wurde.

Esta tese de doutorado descreve os estudos realizados para elucidar a biologia molecular da bioluminescência fúngica e sua relevância ecológica na natureza. A recente descoberta de que a luciferina fúngica é a 3-hidroxihispidina permitiu a caracterização do metabolismo secundário da fenilalanina nos genomas recém-sequenciados e transcriptomas de micélios das espécies luminescentes Panellus stipticus e Neonothopanus gardneri. Adicionalmente os genomas e transcriptomas de variedades não luminescente de P. stipticus e Lentinula edodes serviram como respectivos controles. Em geral, os genes envolvidos no metabolismo secundário da fenilalanina em amostras luminescentes tinham expressão igual ou superior àquela de espécies não luminescentes. Um agrupamento de genes relacionados com a biossíntese de fenilalanina foi encontrado em ambos os genomas luminescentes e não luminescentes de P. stipticus. A abundância de genes transcritos neste agrupamento foi semelhante para as espécies luminescentes e não luminescentes de P. stipticus, mas a policetídeo sintase tipo I em P. stipticus não luminescentes foi significativamente sub-regulada. Não foi encontrado agrupamento semelhante nos genomas de N. gardneri e L. edodes, sendo que os correspondentes homólogos estavam espalhados em diferentes loci. Extratos de fungos podem ser preparados in vitro, com a adição de 3-hidroxihispidina para produzir luz verde em abundância. A preparação de extratos proteicos de luciferase foi melhorada e a estrutura da luciferase, parcialmente purificada, foi investigada por espectrometria de massas. A presença de luciferase nos géis de purificação foi revelada usando-se luciferina e molécula similares à luciferina advindas de extratos de plantas. O nicho ecológico nas vizinhas de cogumelos bioluminescentes foi investigado de duas maneiras, armadilhas adesivas com cogumelos artificiais de acrílico, iluminados com luz LED verde e através da observação direta de cogumelos bioluminescentes com fotografia no infravermelho com lapso de tempo. Os estudos ecológicos foram conduzidos nos biomas da Mata Atlântica e da Mata dos Cocais, no Brasil. Baratas, aranhas, tesourinhas, grilo e vagalumes tec-tecs foram os animais mais comuns que interagiram com os cogumelos. Todos estes animais podem agir como dispersores de propágulos e, em alguns casos, como defensores dos cogumelos. / This PhD thesis describes the studies performed to elucidate the molecular biology of fungal bioluminescence and the ecological significance of the trait in the wild. The recent discovery that the fungal luciferin is 3-hydroxyhispidin has allowed for the characterization of phenylalanine secondary metabolism in the newly sequenced genomes and mycelium transcriptomes of luminescent Panellus stipticus and Neonothopanus gardneri, additionally the genomes and transcriptomes of a non-luminescent variety of P. stipticus and Lentinula edodes served as respective controls. In general the genes involved in phenylalanine secondary metabolism had greater or equal expression in luminescent samples than non luminescent. A cluster of genes related to the secondary metabolism of phenylalanine was found in both luminescent and non luminescent P. stipticus genomes. Transcript abundance of genes in this cluster was similar in both luminescent and non-luminescent Panellus stipticus, but the type I polyketide synthase in non luminescent Panellus stipticus was significantly down regulated. A similar gene cluster in the N. gardneri and L. edodes genomes was absent with corresponding homologues scattered at different genomic loci. Cell free fungal extracts can be combined in vitro with the addition of 3-hydroxyhispidin to produce abundant green light. Preparation of proteinaceous luciferase extracts was improved and partially purified luciferase samples were investigated by mass spectrometry. The presence of luciferase in the separation gel was also evidenced by using luciferin and luciferin-like molecules from plant extracts. The ecological niche surrounding bioluminescent mushrooms was investigated through two main means, glue traps with acrylic mushroom facsimiles that were internally illuminated with green LED lights and direct observation of bioluminescent mushrooms with infrared time lapse photography. Ecological studies were performed in the Atlantic rainforest (Mata Atlântica) and transitional Coconut Palm forest (Mata dos Cocais) biomes of Brazil. Cockroaches, spiders, earwigs, crickets, and luminescent click beetles were the most common animal interacting with mushrooms. All of these animals may be acting as fungal propagule dispersers and in some cases defense of the mushroom.

Proteins are intimately involved in almost every cellular phenomenon, from life to death. Understanding the interactions of proteins with each other and other macromolecules and the ability to rationally redesign them to improve their activities or control their function are of considerable current interest. Split-protein methodologies provide an avenue for achieving many of these goals. Since the original discovery of conditionally activated split-ubiquitin, the field has grown exponentially to include the activities of over a dozen different proteins. The flexibility of the systems has resulted in their use across a wide spectrum, both literally and figuratively, to primarily screen, visualize and quantitate macromolecular interactions in a variety of biological systems. In another arena, there is significant interest the apoptosis-regulating proteins: the Bcl-2 family. These proteins are found in many cell types and control, through expression levels as well as other mechanisms, the apoptotic state of a protein as governed by intrinsic death signals generated from such sources as DNA damage and viral infection. The apoptotic function of these proteins are mainly governed by a single type of interaction: the helix:receptor binding of the BH3-Only helices to the anti-apoptotic receptor proteins. While this often promiscuous helix:receptor interaction has received much scrutiny, the nature of the anti-apoptotic binding pocket, especially with regard to the specific residues that govern the interaction, has been lacking. With the high sensitivity and rapid analysis platform afforded by the cell-free split-luciferase analysis methodology, we devised and carried out the first systematic and large scale alanine mutagenesis of all five major anti-apoptotic members of the Bcl-2 family, validated these results both with biophysical methods as well as correlation with previous studies. Our results help explain how different receptors can bind a wide range of helices and also uncovered details regarding binding that are not possible with structural or computational analysis alone. In a second area of research, we have utilized the interaction of BH3 helices and their receptors for designing small molecule controlled protein kinases and phosphatases. In this protein design area, BH3-Only helices were inserted using a knowledge based approach into particular loops within both a protein kinase and a protein phosphatase. The BH3-Only helix interaction with added receptors, such as Bcl-xL provided an allosteric switch for turning-off the activity of the helix-inserted enzymes. The activity of the enzymes could then be turned-on by the addition of a cell-permeable small molecule that is known to bind the receptor. This plug-and-play design was demonstrated to be successful for two very different enzyme classes and likely provides a general and tunable biological element for controlling the activity of one or more proteins and enzymes in a biochemical networks.

No description available.

Thesis (Ph. D.) -- University of Texas Southwestern Medical Center at Dallas, 2006. / Not embargoed. Vita. Bibliography: 137-144.

京都大学 / 新制・課程博士 / 博士(農学) / 甲第24110号 / 農博第2515号 / 新制||農||1093(附属図書館) / 学位論文||R4||N5401(農学部図書室) / 京都大学大学院農学研究科食品生物科学専攻 / (主査)教授 井上 和生, 教授 谷 史人, 准教授 後藤 剛 / 学位規則第4条第1項該当 / Doctor of Agricultural Science / Kyoto University / DGAM

O câncer compreende uma doença multifatorial responsável por altíssimos indíces de mortalidade globalmente. Embora atualmente tenhamos resultados positivos em relação ao tratamento do câncer principalmente voltados à imunoterapia, dados alarmantes ainda são encontrados. Assim, desenvolvemos linhagens tumorais geneticamente modificadas para expressarem ovalbumina (mOVA ou cOVA) e luciferase, a fim de estudarmos as interações do sistema imune com o tumor. Em nossos resultados, a presença da ovalbumina indicou: Alteração no perfil de crescimento tumoral em animais previamente imunizados com OVA e posteriormente desafiados com o tumor, ativação de células TCD8+ citóxicas anti-OVA além de demonstrar também a capacidade imunogênica das linhagens tumorais quando estas são administradas nos animais em estado necrótico. Ao todo, nosso modelo demonstrou que estratégias de vacinação anti-tumorais possuem a capacidade de ativação do sistema imune para na otimização do reconhecimento e resposta anti-tumoral. / Cancer is characterized as a multifactorial disease responsible for many deaths globally. Although nowadays we can find positive perspectives regarding cancers treatment, it is still very common to notice some alarming data. Therefore, our group developed some genetically modified tumoral lineages expressing ovalbumin (mOVA or cOVA) together with luciferase, in order to elucidate the relationship between tumor and the immune system. In our results, the presence of ovalbumin demonstrated: Changes in tumoral growth when animals were previously immunized with OVA and then challenged with our tumoral lineages; TCD8+ lymphocytes anti-OVA activation thus ovalbumin immunogenic potential when lineages were exposed to necrotic death followed by in vivo administration. In summary, our model showed that anti-tumoral vaccinations are indeed capable of promoting immune systems activation and consequently, improving the anti-tumor immunity.

Esta tese descreve estudos realizados na tentativa de purificar e caracterizar enzimas envolvidas na BL de fungos, além de trabalhos conduzidos a fim de investigar o mecanismo da bioluminescência de fungos. Inicialmente, tentou-se isolar as duas enzimas supostamente responsáveis pala reação bioluminescente em fungos. Parâmetros de atividade ótima (pH e temperatura) e comportamento cinético foram investigados. Todavia, com a descoberta de que a luciferina fúngica é o derivado hidroxilado da hispidina (3-hidróxihispidina), novas estratégias foram abordadas. Os esforços se concentraram na purificação da luciferase, visto que a hidroxilase não faz parte do sistema bioluminescente de fungos. Avaliação da interação da luciferase fúngica com a luciferina ou derivados dela sugeriram comportamento relativamente promíscuo da enzima. Os resultados indicaram que a reação luciferina-luciferase é favorecida em meio básico (pH ~8), a ~20 °C. Ensaios com 18O2 revelaram que a inserção de oxigênio na molécula de luciferina produz um intermediário cuja descarboxilação gera a oxiluciferina. Paralelamente, a síntese da hispidina in vitro a partir de ácido cafeico na presença de malonil-CoA e de extrato de micélios bioluminescentes resultou na emissão de luz, confirmando que a luciferina é reciclada no processo. / This work describes studies performed to purify and characterize enzymes responsible for the fungal bioluminescence. Also, it shows important data that contributes to understand the mechanism for bioluminescence reaction in fungi. First, we tried to isolate two enzymes suspected of being involved on fungal bioluminescence. Optimum activity parameters (pH and temperature) and kinetic behavior were investigated. However, the discovery that fungal luciferin is the hispidin derivative 3-hydroxyhispidin demanded adaptations in the project. First of all, concentrates efforts to luciferase purification was priority, since hydroxylase is not part of the bioluminescent system of fungi. Studies on the luciferase interaction with different substrates showed some promiscuity for the enzyme. The results indicated higher intensity of light from luciferin-luciferase reaction in alkaline solutions (pH ~ 8) at ~ 20 °C. The reaction in medium with 18O2 revealed that insertion of oxygen into the luciferin structure produces an intermediate whose decarboxylation generates oxyluciferin. In parallel, the in vitro synthesis of hispidin using caffeic acid and malonyl-CoA with the mycelium extract resulted in the emission of light, confirming that luciferin is recycled in the process.