Thesis (Ph. D.)--University of Missouri-Columbia, 2002. / Typescript. Vita. Includes bibliographical references (leaves 199-213). Also available on the Internet.

xiv, 82 p., ill. (some col.) / Cellular processes are carried out by proteins, which often utilize conformational changes for function. In theory, conformational changes can be harnessed to promote, prevent or monitor cellular processes. Such changes in protein active centers require perturbations through interactions with other proteins, small molecules or through energy input into the system, for example light. The work presented incorporates rational design and crystallographic elucidation of two-state conformational changes in two proteins, green fluorescent protein (GFP) and malate synthase (MS). GFP indicators were previously developed to quantitate the thiol/disulfide redox status within cells. Cysteine residues were introduced in close proximity on the surface of GFP and allow the formation of a disulfide bond. The indicators provide a fluorescent readout of the ambient thiol/disulfide equilibrium, however thermodynamic studies showed the resulting thiol/disulfide to be unusually stable (-287 mV) in comparison to the cellular redox buffer glutathione (-240 mV). In order to produce a family of redox indicators suitable for use in less reducing environments, amino acids were inserted near the introduced cysteine pair in order to destabilize the disulfide. The resulting family of redox indicators, termed roGFP-iX, exhibit midpoint potentials in the more desirable range of -229 to -246 mV. Crystallographic analysis indicates that roGFP-iX indicators undergo much larger two-state conformational changes than the original indicators. Surprisingly, a cis-peptide was discovered between the cysteine and the inserted residue which in combination with the conformational changes helps to explain the reduced stability of the disulfide. Malate synthase is an important virulence factor for certain microbes and carries out the Claisen condensation between glyoxylate and acctyl-CoA to produce malate. Crystal structures of Mycobacterium tuberculosis and Escherichia coli malate synthase isoform G had previously been determined with substrates or products bound. To determine the conformational changes necessary for substrate binding and product release, crystal structures of Escherichia coli malate synthase isoform A were determined in both the apo and acetyl-CoA/inhibitor bound forms. The crystallographic models revealed two-state conformational changes in the part of the active-site loop necessary for substrate binding, which has important implications for drug design. This dissertation includes my unpublished co-authored materials. / Adviser: S. James Remington

Increased understanding of the molecular mechanisms underlying cancer development has shifted drug discovery towards target driven drug development the last decades, but the development of effective cancer drugs has been hampered by the lack of predictive preclinical models. 3-D cultures, considered to more accurately reflect solid tumors in vivo, have been proposed as one way to increase the predictability of clinical efficacy in cancer drug discovery and development. The aims of this thesis were to improve preclinical models for cancer drug development, with focus on colorectal cancer (CRC) and use of multicellular tumor spheroids (MCTS), and also to mechanistically characterize some potentially new anticancer drugs (papers I – IV). The most important technical improvement was the development of direct measurement of green fluorescent protein (GFP) marked cells in spheroids, simplifying live collection of viability data and enabling high-throughput screening (HTS) in the MCTS model (paper I). In paper III and IV, the 3-D model was adapted to enable studies on the interaction between drugs and radiation. Two potentially new anticancer drugs, VLX50 and VLX60, were mechanistically characterized. VLX60, a novel copper containing thiosemicarbazone, induced reactive oxygen species (ROS) formation, was selectively active against BRAF mutated colon cancer cells and exhibited anticancer activity in vivo (paper II). Furthermore, two potentially new anticancer drugs were found suitable for further development for use in combination with radiation (papers III and IV). In paper III, synergy with radiation in spheroids compared to monolayer cultured colon cancer cells was shown with the novel iron-chelating inhibitor of oxidative phosphorylation, VLX600. In paper IV, the antiprotozoal drug nitazoxanide was shown to sensitize quiescent clonogenic colon cancer cells to radiation. In conclusion, introduction of measurement of fluorescence of GFP marked cells in spheroids makes clinically relevant 3-D models feasible for HTS experiments and characterization of candidate drugs and radiosensitizers in early cancer drug discovery and development. VLX60 has several characteristics suitable for further development into a cancer drug, notably against BRAF mutated colorectal cancer cells. VLX600 and nitazoxanide show radiosensitizing properties making them promising for further development for use as cancer drugs in combination with radiation.

BCG é uma das vacinas mais usadas no mundo. Avanços na manipulação genética têm permitido o seu uso como carreador de antígenos heterólogos, porém o aprimoramento dos sistemas de expressão se faz necessário, sendo o promotor um importante elemento, uma vez que regula o nível de produção do antígeno, induzindo uma resposta imunológica adequada. Avaliamos a atividade de diferentes promotores de micobactérias, como o PAg, PAN, PBlaF*, Phsp60 e um promotor ainda não caracterizado do micobacteriófago L5, usando o gene gfp como repórter da expressão, todos clonados no vetor extracromossomal, pLA71. Foi possível avaliar as cepas de M. smegmatis e BCG fluorescentes para quase todas as construções e alguns plasmídeos pLA71-p mostraram características diferentes dependentes da micobactéria transformada. Numa escala de força de expressão, os diferentes promotores se apresentaram como fraco (pLA71-PAN-gfp), médio (pLA71-PBlaf*-gfp) e forte (pLA71-Phsp60-gfp). Os rBCG foram usados para infecção de macrófagos e a atividade dos promotores não foi afetada após a internalização. Para ensaio de localização, camundongos foram inoculados com BCG e foi possível confirmar a presença de colônias (recombinantes ou não) nos pulmões após 1 e 3 dias de inoculação, por plaqueamento em meio sólido e por microscopia confocal. / BCG is one of the most widely used vaccines in the world. Advances in genetic manipulation have allowed their use as a carrier for heterologous antigens, however the improvement of systems of expression is necessary, the promoter being an important element, since it regulates the expression level of the antigen, inducing an adequate immune response. We evaluated the activity of different promoters of mycobacteria, such as PAg, PAN, PBlaF* and Phsp60, and the not yet characterized promoter of the micobacteriophage L5, using GFP as a reporter gene expression activity, all cloned in the extrachromosomal vector, pLA71. It was possible to evaluate promoters in the M. smegmatis and BCG strains, fluorescent for almost all constructions and some pLA71-p plasmids showed different characteristics dependent on the transformed mycobacterium. The different promoters showed expression levels as weak (pLA71-PAN-gfp), medium (pLA71-PBlaf*-gfp) and strong (pLA71-Phsp60-gfp). The rBCG were used for infection of macrophages and the activity of the promoters wasnt affected after internalization. For BCG location test, mice were inoculated and it was possible to confirm the presence of colonies (recombinant or not) in the lungs after 1 and 3 days after inoculation by plating on solid medium and by confocal microscopy.

京都大学 / 0048 / 新制・課程博士 / 博士(理学) / 甲第20938号 / 理博第4390号 / 新制||理||1631(附属図書館) / 京都大学大学院理学研究科化学専攻 / (主査)教授 三木 邦夫, 教授 杉山 弘, 教授 秋山 芳展 / 学位規則第4条第1項該当 / Doctor of Science / Kyoto University / DGAM

No description available.

Recirculating aquaculture offers a prospect for successful fish farming, but this form of aquaculture presents a great potential for pathogenic microorganisms to become established in the system through the formation of biofilms. Biofilms are capable of forming on all aquaculture system components, incorporating the various microflora present in the water. Pathogenic microorganisms released from the biofilms are capable of causing recurring exposure to disease in both fish and humans. With the increased consumption of raw and rare fish, the presence of these bacteria in or on the fish could lead to ingestion of pathogens. There is also the possibility of cross-contamination during processing. The objectives of this study were to increase the understanding of pathogen incorporation into biofilms in recirculating aquaculture systems and to determine the effectiveness of various sanitizers in eliminating biofilms. Seven freshwater and two saltwater facilities were sampled, with eight different types of materials tested. Pathogenic bacteria were identified using Bacteriological Analytical Manual methods and rapid commercial test kits. Most of the pathogenic bacteria identified were opportunistic organisms ubiquitous in an aquatic environment. The most significant human pathogens were Bacillus cereus, the Shigella species and the Vibrio species. The major piscine pathogens of concern were Photobacterium damsela, the Vibrio species, and Aeromonas hydrophila. The most significant variation in biofilm pathogens was observed between facilities and not construction material. Buna-N rubber, polyvinyl chloride (PVC), chlorinated PVC, glass, fiberglass and stainless steel disks were suspended in 79.2 liter (20 gallon) aquariums stocked with Nile tilapia (Oreochromus niloticus). The tanks were inoculated with a known amount of green fluorescent protein (GFP) modified Escherichia coli and samples were removed on days 1,3, 7 and 15. The modified E. coli were isolated on Luria Broth Agar and plate counts were performed under ultraviolet light. There was no significant difference in the growth of the surrogate pathogen on the different materials. The GFP E. coli was isolated in the largest numbers 24 hours after inoculation of the tanks, with an approximate 1-log decrease after day 1. Days 3, 7, and 15 showed equivalent growth of the target organism. Two sets of disks were suspended in another six 79.2 liter (20 gallon) aquariums. The tanks were inoculated with a known amount of the surrogate pathogen, GFP E. coli, and after 24 hours one set of disks was removed from each tank. The second set of disks was removed and treated by spraying with water, alkaline cleanser, sodium hypochlorite, quaternary ammonium compound, or peracetic acid. Ozone was bubbled directly into one tank to treat another set of disks. The modified E. coli were isolated and counted. Total aerobic plate counts and Enterobacteriaceae counts were performed. Statistical analysis indicated that the type of material had no significant affect on the effectiveness of the sanitizers. It was determined that sodium hypochlorite (99.4591 overall reduction) and peracetic acid (98.8461 % overall reduction) were the most effective sanitizers overall, and ozone (32.9332 % overall reduction) was the least effective. / Ph. D.

O transplante intrauterino de células-tronco (TIUCT) é um método de tratamento de doenças genéticas, congênitas, hematológicas e imunológicas em um feto durante a gestação. Em pesquisa básica este modelo permite o estudo da dinâmica de migração, enxertia e estado funcional de diferentes tipos de células-tronco (CT). Estas células podem ser transplantadas em diferentes momentos do período gestacional, que pode ser dividido em três momentos do desenvolvimento fetal, sendo estes, diferentes funcionalmente. A escolha deste momento para o transplante influenciará tanto no comportamento celular quanto no resultado. Para o TIUCT são utilizadas as CT mesenquimais derivadas da medula óssea ou fetais ou hematopoiéticas. Para esta pesquisa utilizamos células-tronco derivadas da polpa dentária imatura humana (CTIPDh) as quais apresentam potencial pluripotente e propriedades imunomodulatórias. Nosso principal objetivo foi avaliar a capacidade migratória, bem como de proliferação e endereçamento (homing) das CTIPDh durante o terceiro período gestacional do desenvolvimento fetal no modelo canino. Todos os procedimentos experimentais foram elaborados sob protocolo anestésico apropriado e aprovados pelo comitê de ética da FMVZ da USP. Foram transplantadas via intraperitoneal (IP) 1x106 CTIPDh GFP+ em cada feto, durante procedimento cirúrgico de laparotomia exploratória com ultrassonografia guiada intraoperatóriamente em quatro fetos com idade gestacional aproximada de 45 dias, e outros dois fetos os quais não receberam o transplante, utilizados como controle. Avaliamos os fetos pré e pós-transplante através do ultrasson. Após sete dias, realizamos a ovário-salpingo-histerectomia (OSH) para a colheita dos fetos. Em seguida coletamos seus órgãos e tecidos os quais foram fixados em paraformoldeído a 4% e criopreservados a temperatura de -80oC. Analisamos a biodistribuição das CTIPDh dentro dos órgãos e tecidos em criocortes de 5µm sob microscopia Confocal. Constatamos o homing das CTIPDh nos órgãos derivados das linhas germinativas endodermais, ectodermais e mesodermais. No estômago e intestinos as CTIPD/GFP+ foram identificadas tanto no espaço intraglandular, como na camada muscular da mucosa; no fígado no parenquima hepático; no coração especialmente no tecido muscular do miocárdio; no cérebro nos vasos da substância branca, e cerebelo entre células de Purkinje. Na placenta estas células foram encontradas especialmente junto aos vasos. Quantificamos as CTIPD GFP+ utilizando a citometria de fluxo. Comparativamente dentre os órgãos analisados, obtivemos resultados expressivos do homing celular no miocárdio (~50%), no baço e fígado. Nossos resultados foram confirmados através das análises de imunohistoquímica e imunofluorescência utilizando os anticorpos Anti-núcleo (HuNu), Anti-CTIPD e Anti-GFP humanos. Concluímos que as CTIPDh apresentam grande potencial migratório e proliferativo após o TIUCT em fetos caninos. Estas células indiferenciadas demonstraram homing, especialmente nos tecidos: hematopoiéticos fetais (placenta, fígado e baço), tecido epitelial e glandular de órgãos, bem como de nichos perivasculares de CT. Estes dados sugerem que as CTIPD através do TIU, é uma alternativa viável, segura e promissora para o tratamento de doenças genéticas, congênitas, hematológicas e imunológicas. / Intra-uterine stem cells transplantation (IUSCT) is a method for the treatment of genetic, congenital, hematological, and immunological diseases. In basic research it provides a model for studying the dynamics of migration, graft and functional status of different types of stem cells. The cells can be transplanted in different moments of gestational period, which can be divided into quarters that are not functionally equivalent. The choice of the cells and quarter where the stem cells will be applied can influence cells behavior and results of transplantation. Fetal and adult hematopoietic or bone marrow derived mesenchymal stem cells (MSCs) were mainly used for IUSCT. We previously obtained human immature dental pulp stem cell (IDPSCs), which showed pluripotent potential and immune-compatible properties. The goal of our study was to evaluate migration capacity, proliferation and homing of IDPSCs after IUSCT during the third fetal period in dogs. All experimental procedures were approved by the Ethical Committee of the School of Veterinary Medicine and Animal Science of São Paulo University and were performed under appropriate anesthesia. 1x106 of undifferentiated GFP-positive human IDPSCs were transplanted following laparotomy and intraperitoneal injection under intra-operative ultrasound control into 5 fetuses at the 45 days of gestation. Five fetuses, which did not receive IDPSCs, were used as a control. Ultrasound analyses were performed daily before collection of the fetuses. After 7 days ovarian hysterectomy was performed, fetuses were collected; organs and tissues were isolated and fixed in 4% paraformaldehyde or cryopreserved. Biodistribution of IDPSCs within the organs and tissues were analyzed on cryosections (5µm) under Confocal Microscopy. Homing of IDPSCs was observed in organs derived from three germ lines, endoderm, ectoderm and mesoderm. In stomach and in intestine GFP IDPSCs were found in intraglandular space as well as in muscularis mucosae. In liver they appeared in hepatic parenchyma; in heart in myocardium and in brain in bold vessels, in cerebellum within Purkinje cells. Using Flow cytometry assay GFP IDPSCs graft was quantified. Among the different organs an expressive homing was observed in myocardium of heart (~50%), in spleen and liver. The IDPSCs were also found in canine placenta, especially in blood vessels. These data were confirmed using anti-human nucleus (HuNu), anti-GFP and anti-IDPSCs anti-bodies. Human IDPSCs showed high migration and proliferation potential after IUSCT in dog fetuses. Undifferentiated IDPSCs demonstrated homing in fetal hematopoietic (placenta), epithelial (gastric glands) and perivascular stem cells niches. Our data suggest that IDPSCs is a new promising source for genetic, congenital, hematological, and immunological treatment for those diseases through IUSCT.

O transplante intrauterino de células-tronco (TIUCT) é um método de tratamento de doenças genéticas, congênitas, hematológicas e imunológicas em um feto durante a gestação. Em pesquisa básica este modelo permite o estudo da dinâmica de migração, enxertia e estado funcional de diferentes tipos de células-tronco (CT). Estas células podem ser transplantadas em diferentes momentos do período gestacional, que pode ser dividido em três momentos do desenvolvimento fetal, sendo estes, diferentes funcionalmente. A escolha deste momento para o transplante influenciará tanto no comportamento celular quanto no resultado. Para o TIUCT são utilizadas as CT mesenquimais derivadas da medula óssea ou fetais ou hematopoiéticas. Para esta pesquisa utilizamos células-tronco derivadas da polpa dentária imatura humana (CTIPDh) as quais apresentam potencial pluripotente e propriedades imunomodulatórias. Nosso principal objetivo foi avaliar a capacidade migratória, bem como de proliferação e endereçamento (homing) das CTIPDh durante o terceiro período gestacional do desenvolvimento fetal no modelo canino. Todos os procedimentos experimentais foram elaborados sob protocolo anestésico apropriado e aprovados pelo comitê de ética da FMVZ da USP. Foram transplantadas via intraperitoneal (IP) 1x106 CTIPDh GFP+ em cada feto, durante procedimento cirúrgico de laparotomia exploratória com ultrassonografia guiada intraoperatóriamente em quatro fetos com idade gestacional aproximada de 45 dias, e outros dois fetos os quais não receberam o transplante, utilizados como controle. Avaliamos os fetos pré e pós-transplante através do ultrasson. Após sete dias, realizamos a ovário-salpingo-histerectomia (OSH) para a colheita dos fetos. Em seguida coletamos seus órgãos e tecidos os quais foram fixados em paraformoldeído a 4% e criopreservados a temperatura de -80oC. Analisamos a biodistribuição das CTIPDh dentro dos órgãos e tecidos em criocortes de 5µm sob microscopia Confocal. Constatamos o homing das CTIPDh nos órgãos derivados das linhas germinativas endodermais, ectodermais e mesodermais. No estômago e intestinos as CTIPD/GFP+ foram identificadas tanto no espaço intraglandular, como na camada muscular da mucosa; no fígado no parenquima hepático; no coração especialmente no tecido muscular do miocárdio; no cérebro nos vasos da substância branca, e cerebelo entre células de Purkinje. Na placenta estas células foram encontradas especialmente junto aos vasos. Quantificamos as CTIPD GFP+ utilizando a citometria de fluxo. Comparativamente dentre os órgãos analisados, obtivemos resultados expressivos do homing celular no miocárdio (~50%), no baço e fígado. Nossos resultados foram confirmados através das análises de imunohistoquímica e imunofluorescência utilizando os anticorpos Anti-núcleo (HuNu), Anti-CTIPD e Anti-GFP humanos. Concluímos que as CTIPDh apresentam grande potencial migratório e proliferativo após o TIUCT em fetos caninos. Estas células indiferenciadas demonstraram homing, especialmente nos tecidos: hematopoiéticos fetais (placenta, fígado e baço), tecido epitelial e glandular de órgãos, bem como de nichos perivasculares de CT. Estes dados sugerem que as CTIPD através do TIU, é uma alternativa viável, segura e promissora para o tratamento de doenças genéticas, congênitas, hematológicas e imunológicas. / Intra-uterine stem cells transplantation (IUSCT) is a method for the treatment of genetic, congenital, hematological, and immunological diseases. In basic research it provides a model for studying the dynamics of migration, graft and functional status of different types of stem cells. The cells can be transplanted in different moments of gestational period, which can be divided into quarters that are not functionally equivalent. The choice of the cells and quarter where the stem cells will be applied can influence cells behavior and results of transplantation. Fetal and adult hematopoietic or bone marrow derived mesenchymal stem cells (MSCs) were mainly used for IUSCT. We previously obtained human immature dental pulp stem cell (IDPSCs), which showed pluripotent potential and immune-compatible properties. The goal of our study was to evaluate migration capacity, proliferation and homing of IDPSCs after IUSCT during the third fetal period in dogs. All experimental procedures were approved by the Ethical Committee of the School of Veterinary Medicine and Animal Science of São Paulo University and were performed under appropriate anesthesia. 1x106 of undifferentiated GFP-positive human IDPSCs were transplanted following laparotomy and intraperitoneal injection under intra-operative ultrasound control into 5 fetuses at the 45 days of gestation. Five fetuses, which did not receive IDPSCs, were used as a control. Ultrasound analyses were performed daily before collection of the fetuses. After 7 days ovarian hysterectomy was performed, fetuses were collected; organs and tissues were isolated and fixed in 4% paraformaldehyde or cryopreserved. Biodistribution of IDPSCs within the organs and tissues were analyzed on cryosections (5µm) under Confocal Microscopy. Homing of IDPSCs was observed in organs derived from three germ lines, endoderm, ectoderm and mesoderm. In stomach and in intestine GFP IDPSCs were found in intraglandular space as well as in muscularis mucosae. In liver they appeared in hepatic parenchyma; in heart in myocardium and in brain in bold vessels, in cerebellum within Purkinje cells. Using Flow cytometry assay GFP IDPSCs graft was quantified. Among the different organs an expressive homing was observed in myocardium of heart (~50%), in spleen and liver. The IDPSCs were also found in canine placenta, especially in blood vessels. These data were confirmed using anti-human nucleus (HuNu), anti-GFP and anti-IDPSCs anti-bodies. Human IDPSCs showed high migration and proliferation potential after IUSCT in dog fetuses. Undifferentiated IDPSCs demonstrated homing in fetal hematopoietic (placenta), epithelial (gastric glands) and perivascular stem cells niches. Our data suggest that IDPSCs is a new promising source for genetic, congenital, hematological, and immunological treatment for those diseases through IUSCT.

This dissertation investigates the origins of tunable and efficient photochemistry in three different photoactive proteins, bacteriorhodopsin (BR), rhodopsin (RHO) and green fluorescent protein (GFP). In all cases, significant differences exist between the photoreactivity of model chromophores in solution and in the protein environment, in terms of excited state lifetime and efficiency of the primary photochemical process (opsin proteins) or the type of reaction (excited state proton transfer versus C=C double bond photoisomerisation for GFP). The work presented here investigates for each case to what extent the protein environment is necessary to alter the photochemistry of model chromophores in solution. For GFP and BR steric and electrostatic interactions between the protein pocket and the chromophore are shown to be likely responsible for shaping the excited state surface along which the photoreactions take place. For RHO it is suggested, contrary to current belief, that selection of a reactive ground state conformer might be the main effect generating the observed differences between solution and protein environment. The solution photochemistry of structurally modified retinal protonated Schiff bases, taken as model chromophores for the opsin proteins, is studied with continuous wave irradiation experiments and ultrafast transient spectroscopies. Surprisingly large differences are observed for the isomerisation reaction depending on the starting configuration (trans or cis) of the photoactive double bond. The current model for BR based on the tuning of the excited state barrier encountered along the isomerisation coordinate is expanded to include the changes in selectivity, speed and efficiency observed for a series of all-trans derivatives. For 11-cis, the photoisomerisation in solution is proposed to take place along a barrierless isomerisation coordinate, in contrast with the models currently available in literature. It is suggested that the protein might be discriminating between ground state conformers rather than significantly changing the topography of the reaction coordinate. For GFP, excited state Raman spectra are recorded for the wild-type protein, two mutants and a model chromophore in solution. It is suggested that the high frequency vibrational modes observed in the excited state spectra of the proteins but not of the model chromophore in DMSO are a sign of a tighter chromophore environment that inhibits the photoisomerisation reaction occurring in solution.