Universiẗat, Diss., 2004--Düsseldorf.

By applying the principles of Darwinian natural selection in the laboratory, directed evolution has become a powerful practical approach to study enzymes and optimize them to catalyze industrially relevant transformations. In this thesis, I applied this strategy to the engineering of amino acid dehydrogenases for biocatalysis of chiral amines, focusing on two crucial features for successful directed evolution experiments. A first key aspect is the development of technologies allowing the screening of large libraries of enzyme variants to explore sequence space efficiently. Massive scale-down of assay volumes by compartmentalization of library members in water-in-oil emulsions has recently led to the development of ultrahigh-throughput screening platforms that allow sorting of more than 106 variants per hour. So far, these microfluidic droplet sorters have relied exclusively on fluorescent readouts. To further extend the range of applications toward enzymes for which no fluorescent assays are available, I successfully developed a sorting module based on absorbance detection. Using this new module, microdroplets could be sorted based on an absorbance readout at rates of up to 1 million droplets per hour. To demonstrate the utility of this module for protein engineering, three rounds of directed evolution were performed to improve a poorly stable NAD+ dependent phenylalanine dehydrogenase (PheDH) toward its native substrate. Five hits showed increased activity (improved up to 10-fold in lysate; kcat increased >3.5-fold), soluble protein expression levels (>2.5-fold) and thermostability (Tm, 8 °C higher). To increase the sensitivity of the device (3–4 orders of magnitude lower than fluorescence assays) for detection of enzymes with limited stability and low turnovers, an extra step of growth in droplets from single cell encapsulation, followed by piconinection of substrates and lysis agents was implemented. As a result, a fivefold signal enhancement over background was achieved, for an amine dehydrogenase (AmDH) reaction shown to be undetectable in a droplet single cell assay. Second, I investigated how mutational robustness may correlate with protein stability and lead to successful hits after mutagenesis and screening. To examine this issue, I initially investigated various approaches (including ancestral resurrection and computational design) to identify stabilized PheDH variants. One such variant (dubbed Pross 4) showed increased expression levels (>3.3-fold) and thermostability (Tm, 13 °C higher) compared to the wild-type PheDH. I further compared the mutational tolerance and the hit rate between PheDH and Pross 4 by generating variant libraries focused on key active site residues and screening them for improved AmDH activity. The Pross 4 background generated 6.4 times more active variants than the PheDH background, the best hits displaying increased activity (up to 2.5-fold in lysate; kcat/KM increased up to 8-fold) compared to previously engineered AmDHs with the PheDH scaffold. In conclusion, this work highlights how directed evolution experiments could be designed for increased success rates, by combining reliable high-throughput screens with careful choice of evolutionary robust starting points.

Radiotherapy is second only to surgery in the curative management of patients with cancer, and yet the molecular mechanisms that determine the sensitivity of tumours to radiation remain largely unclear. A high-throughput radiosensitivity screening method based on clonogenicity was developed and a siRNA library against kinase targets was screened. The gold standard colony formation endpoint was chosen for determining reproductive cell death after radiation treatment, since effects on proliferation often do not reflect survival. Thiamine pyrophosphokinase-1 (TPK1), a key component of Vitamin B1/thiamine metabolism, was identified as a target for radiosensitisation. TPK1 knockdown caused significant radiosensitisation in cancer but not normal tissue cell lines. Other means of blocking this pathway such as knockdown of thiamine transporter-1 (THTR1) or treatment with the thiamine analogue pyrithiamine hydrobromide (PyrH) caused significant tumour specific radiosensitisation. There was persistent DNA damage in cells irradiated after TPK1 and THTR1 knockdown or PyrH treatment. Thus this screen allowed the identification of thiamine metabolism as a novel radiosensitisation target that affects DNA repair. Short-term modulation of thiamine metabolism could be a clinically exploitable strategy to achieve tumour specific radiosensitisation. Three additional genes, signal recognition particle-72 kDa (SRP72), glycogen synthase 3-beta (GSK3β) and MAP/Microtubule Affinity-Regulating Kinase 2 (MARK2) were also investigated. Knockdown of these genes radiosensitised both tumour and normal tissue cell lines and expression of two of them, GSK3β and SRP72 were found to be associated with poor recurrence-free survival in early breast cancer patients.

Orientador: Anita Jocelyne Marsaioli / Tese (doutorado) - Universidade Estadual de Campinas, Instituto de Quimica / Made available in DSpace on 2018-08-06T15:53:09Z (GMT). No. of bitstreams: 1 Chen_LuShi_D.pdf: 1749829 bytes, checksum: aa7f95ee1b7db09369cb88541ee02c93 (MD5) Previous issue date: 2006 / Doutorado / Quimica Organica / Doutor em Ciências

Orientador: Anita Jocelyne Marsaioli / Dissertação (mestrado) - Universidade Estadual de Campinas, Instituto de Química / Made available in DSpace on 2018-08-22T20:13:36Z (GMT). No. of bitstreams: 1 Lima_MariaLairSaboiadeOliveira_M.pdf: 6354441 bytes, checksum: 7cd17cb17f36613aa4366697163fbb5a (MD5) Previous issue date: 2013 / Resumo: O uso de catalisadores biológicos é importante na academia e na indústria, pois une o ecologicamente correto com o ecologicamente viável. Assim, a busca por novas rotas reacionais viáveis e menos poluentes se enquadra no contexto da química verde, onde o ambiente e os rejeitos são levados em consideração. Com base nestes princípios o presente trabalho visa avaliar o perfil enzimático de micro-organismos provenientes de rejeitos de mineração da Mina do Sossego (Canaã dos Carajás ¿ PA), pertencente à "VALE". Após o isolamento e preservação, as cepas foram caracterizadas por espectrometria de massas, com a técnica MALDI-TOF, onde foram encontradas bactérias dos gêneros Pseudomonas sp., Bacilus sp., Acinetobacter sp., Delfitia sp. e Escherichia sp. As atividades enzimáticas foram avaliadas através de uma triagem rápida e eficiente (HTS, high throughput screening) utilizando sondas fluorogênicas não comerciais baseadas na umbeliferona. Dos 228 micro-organismos isolados, 156 tiveram suas atividades enzimáticas avaliadas das quais 70 apresentaram atividade para esterases, 80 para lipases, 11 para epóxi-hidrolases e 53 para mono-oxigenases. Ainda com base no princípio da triagem enzimática de alto desempenho, foram sintetizadas sondas fluorogênicas quirais e um composto competidor para implementação de uma metodologia conhecida como Quick-E. Esta metodologia visa uma avaliação rápida da enantiosseletividade de esterases em células íntegras através de medidas das velocidades iniciais das biorreações com as sondas fluorogênicas quirais avaliadas separadamente / Abstract: Biocatalysts are important in academia and industry joining the ecological friendly to the ecological safe and efficient processes. Thus, the search for new synthetic routes and reactions producing less hazardous residues fits into the principles of green chemistry as environment and residues are taken into consideration. Based on these principles, present study aims at the enzymatic profiling of microorganisms (156 strains) from cooper mine (Sossego¿s mine, Canaã dos Carajás- PA), belonging to VALE. After isolation (228 microorganisms) and preservation, the strains were characterized by mass spectrometry (MALDI-TOF, 62 strains), being characterized bacterias Pseudomonas sp., Bacilus sp., Acinetobacter sp., Delfitia sp. and Escherichia sp.. The enzymatic activities were evaluated by a high throughput screening using fluorogenic probes based on umbelliferone. Outstanding enzymatic activities of these 156 micro-organisms were: esterases (70), lipases (80), epoxy hydrolases (11) and monooxygenases (53). Additionally the implementation of a novel Quick-E methodology with chiral fluorogenic probes and a competitor will allow the rapid evaluation of esterases enantioselectivities in whole cells by measuring inicial rates of bioreactions in micro scale reactions / Mestrado / Quimica Organica / Mestra em Química

Orientador: Anita Jocelyne Marsaioli / Tese (doutorado) - Universidade Estadual de Campinas, Instituto de Química / Made available in DSpace on 2018-08-21T09:30:03Z (GMT). No. of bitstreams: 1 Silva_CarlaPortoda_D.pdf: 8471917 bytes, checksum: 298adab03875869cd5d11c7dac0a7b90 (MD5) Previous issue date: 2012 / Resumo: Estima-se que o corpo humano que contém cerca de 10 trilhões de células seja portador de aproximadamente 100 trilhões de micro-organismos. Fatores ambientais como temperatura, umidade e exposição à luz, além de fatores do hospedeiro, como gênero, genótipo, status imune e uso de cosméticos, podem afetar a composição e a distribuição microbiana da pele. Inúmeras pesquisas indicam que a microbiota desempenha um papel importante no sistema imune da pele. Contudo, pouco é conhecido sobre os conjuntos de espécies presentes em amostras cutâneas bem como suas atividades enzimáticas. Esta tese visou realizar o estudo do potencial enzimático da microbiota da pele humana, vinculando este potencial às principais reações de degradação de formulações de cosméticos, mais especificamente, insumos de fragrâncias. O recrutamento dos voluntários levou em conta parâmetros como idade, sexo e fototipo de pele. As principais atividades enzimáticas das microbiotas coletadas foram avaliadas através de técnicas de triagem de alto desempenho, a fim de detectar proteases, lipases, amilases, esterases, epóxido hidrolases e mono-oxigenases, num total de 2.160 experimentos. Através dos resultados obtidos das triagens enzimáticas, algumas amostras foram selecionadas para a realização de ensaios de degradação de insumos de fragrâncias através de ensaios de multibiorreação. Todos os resultados obtidos foram avaliados com intuito de relacionar o tipo da microbiota coletada com reações de degradação de componentes de fragrância, levando em conta as diferenças intrínsecas de cada voluntário. Além disso, observou-se uma grande diversidade fúngica, ainda pouco descrita na literatura, onde diversos representantes foram isolados e identificados. Os dados obtidos demonstraram que os tipos de pele devem ser levados em consideração nas formulações de uso tópico a fim de atingir alvos específicos, tendo em vista que a pele humana não é um ambiente estéril, mas sim um microbioma complexo. Desta forma, o potencial de biotransformação de insumos cosméticos pela microbiota da pele é um fator relevante e poderá auxiliar na busca de produtos mais eficazes, seguros e versáteis / Abstract: The human body contains about 10 trillion cells and carries approximately 100 trillion microorganisms¿ cells. Environmental factors, such as temperature, humidity and light exposure and host factors such as gender, genotype, immune status and use of cosmetics, can affect the composition and distribution of skin microbes. Numerous studies indicate that skin microbiota plays an important role in the human skin immune system. However, little is known about the species present in skin samples and their enzymatic activities. Therefore, the aim of this thesis was to evaluate the enzymatic potential of the human skin microbiota, establishing a link between this potential and the main fragrance degradation of cosmetic formulations, more specifically, fragrance ingredients. The recruitment of volunteers (55) took into account some parameters such as age, gender and skin phototype. The main enzymatic activities of the collected microbiota were assessed by high throughput screening techniques in order to detect protease, lipase, amylase, esterase, epoxide hydrolase and monooxygenase, in a total of 2160 experiments. These enzymatic profiles were applied in the selection of microorganisms to probe the biodegradability of fragrance ingredients using the multibioreaction protocol. The results linking microbiota type and degradation reactions of fragrance ingredients took into consideration the intrinsic differences between volunteers. In addition, a great fungal diversity, still poorly described in the literature, was observed and several representative entities of this diversity were isolated and identified. The obtained data showed that skin types must be considered in topical formulations to achieve specific biological targets and , taking into consideration that the human skin is not a sterile environment, but rather consists of a complex microbiome. Consequently the biotransformation susceptibility of cosmetic ingredients to human skin microbiota is a relevant factor to consider in formulations / Doutorado / Quimica Organica / Doutor em Ciências

This work explores the use of computational methods to aid in the design of Metal Organic Frameworks (MOFs) for use as CO2 scrubbers in carbon capture and storage applications. One of the main challenges in this field is in identifying important MOF design characteristics which optimize the complex interactions governing surface adsorption. We approach this in a high-throughput manner, determining properties important to CO2 adsorption from generating and sampling a large materials search space. The utilization of MOFs as potential carbon scrubbing agents is a recent phenomenon, as such, many of the computational tools necessary to perform high-throughput screening of MOFs and subsequent analysis are either underdeveloped or non-existent. A large portion of this work therefore involved the development of novel tools designed specifically for this task. The chapters in this work are contiguous with the goal of designing MOFs for CO¬2 capture, and somewhat chronological in order and complexity, meaning as time and expertise progressed, more advanced tools were developed and utilized for the purposes of computational MOF discovery. Initial work towards MOF design involved the detailed analysis of two experimental structures; CALF-15 and CALF-16 using classical molecular dynamics, grand canonical Monte Carlo simulations, and DFT to determine the structural features which promote CO2 adsorption. An unprecedented level of agreement was found between theory and experiment, as we are able to capture, with simulation, the X-ray resolved binding sites of CO2 in the confined pores of CALF-15. Molecular simulation was then used to provide a detailed breakdown of the energy contributions from nearby functional groups in both CALF-15 and CALF-16. A large database of hypothetical MOF structures is constructed for the purposes of screening for CO2 adsorption. The database contains 1.3 million hypothetical structures, generated with an algorithm which snaps together rigid molecular building blocks extracted from existing MOF crystal structures. The algorithm for constructing the hypothetical MOFs and the building blocks themselves were all developed in-house to form the resulting database. The topological, chemical, and physical features of these MOFs are compared to recently developed materials databases to demonstrate the larger structural and chemical space sampled by our database. In order to rapidly and accurately describe the electrostatic interactions of CO2 in the hypothetical database of MOFs, parameters were developed for use with the charge equilibration method. This method assigns partial charges on the framework atoms based on a set of parameters assigned to each atom type. An evolutionary algorithm was used to optimize the charge equilibration parameters on a set of 543 hypothetical MOFs such that the partial charges generated would reproduce each MOFs DFT-derived electrostatic potential. Validation of these parameters was performed by comparing the CO2 adsorption from the charge equilibration method vs DFT-derived charges on a separate set of 693 MOFs. Our parameter set were found to reproduce DFT-derived CO2 adsorption extremely well using only a fraction of the time, making this method ideal for rapid and accurate high-throughput MOF screening. A database of 325,000 MOFs was then screened for CO2 capture and storage applications. From this study we identify important binding pockets for CO2 in MOFs using a binding site analysis tool. This tool uses a pattern recognition method to compare the 3-D configurations of thousands of pore structures surrounding strong CO2 adsorption sites, and present common features found amongst them. For the purposes of developing larger databases which sample a more diverse materials space, a novel MOF construction tool is devloped which builds MOFs based on abstract graphs. The graph theoretical foundations of this method are discussed and several examples of MOF construction are presented to demonstrate its use. Notably, not only can it build existing MOFs with complicated geometries, but it can sample a wide range of unique structures not yet discovered by experimental means.

Reducing anthropogenic carbon dioxide emissions from coal-fired power plants is an important step in mitigating climate change. To implement carbon dioxide capture technologies, materials capable of removing carbon dioxide efficiently are required. Currently, liquid amine technology is used for carbon dioxide capture. However, the mechanism for carbon dioxide removal in liquid amine requires extraordinary amounts of energy input. Alternatively, solid sorbents such as metal-organic frameworks (MOFs) show promising potentials as a type of material for carbon dioxide capture. Due their varying structural properties, MOFs can be configured for specific purposes. Certain MOFs carry a net charge on their frameworks, which may allow for increased interactions with carbon dioxide molecules. In this work, charged MOFs were studied for their potential in carbon dioxide capture. Due to the massive number of MOFs available, computational methods were employed for the study. This project includes three major components: (1) the development of novel computational methods to simulate the gas adsorption properties in charged materials, (2) a diverse database of 47,244 hypothetical charged MOFs was constructed to represent the capabilities of charged MOFs, and (3) screening of high performing charged MOFs for carbon capture application by combining the previous two portions of the project. The methods developed in this work include fitting intermolecular interaction parameters to quantum mechanical calculations in periodic systems with net charges. No methods have been reported in literature for such parameter fittings, even in well studied materials such as zeolites. Therefore, the gas adsorption estimation method for charged materials developed in this work is proprietary. Also, databases of hypothetical MOFs with framework net charges have never been reported previously in literature. By screening the charged MOFs in the database with the methods developed, gas adsorption capabilities were evaluated. The adsorption properties of a neutral group of hypothetical MOFs were also obtained for a baseline comparison. Between the two groups of MOFs, charged MOFs were found to outperform neutral MOFs in three key aspects. Firstly, charged MOFs were able to adsorb an average of three times as much carbon dioxide than the neutral group. Secondly, charged MOFs were capable of removing twice the amount of carbon dioxide per adsorption/desorption cycle than the neutral MOFs. Lastly, charged MOFs were able to selectively adsorb much more carbon dioxide over other gasses present in the carbon dioxide capture situations. Specific structural features that resulted in the selectiveness of adsorption in charged MOFs were identified. Also, positive correlations were found between the adsorption of carbon dioxide and the charge present in the MOFs. As seen in the results, charges present in MOFs can greatly increase their ability to remove carbon dioxide. Charged MOFs in the hypothetical database not only outperformed neutral MOFs, certain top performers were also found to exceed the requirements for post-combustion carbon capture application. Therefore, charged MOFs were shown to be a possible material for future carbon dioxide capture. The proprietary methods developed in this work can not only be used to simulate gas adsorptions in charged MOFs, but also for other porous materials, regardless of net charges presented in their systems. Also, the database constructed in this work can be utilized in multiple ways. Aside from carbon dioxide capture capabilities, the charged MOFs in the database can be screened for other gas separations and catalysis via high throughput screening. The database and the computational methods developed in this work pave the way for discovering the capabilities of charged materials.

Des produits efficaces pour stimuler le système immunitaire auraient de très nombreuses applications dans le domaine de la santé publique : lutte contre la résistance aux antibiotiques, épidémies, protection des personnels de secours et des populations en cas de crise sanitaire ou d’attentat biologique. Aujourd’hui, les rares produits immunostimulants efficaces sont coûteux, dangereux, et donc réservés au traitement de pathologies graves ciblées comme les cancers, aplasies ou infections virales chroniques. La petite protéine G Rac1 fut identifiée comme une potentielle cible thérapeutique. Activée par de nombreux pathogènes, elle contrôle l’inflammation et la mise en place des défenses de l’hôte. CNF1 est une toxine bactérienne activant fortement Rac1, ce qui conduit à sa dégradation protéasomale. Le maintien d’un pool de Rac1 activé permettrait d’augmenter les défenses immunitaires. En utilisant CNF1 comme un outil permettant de diminuer celui-ci, un test cellulaire fut mis au point pour cribler 17 680 composés. A l’aide de différents paramètres de tri, un ensemble de molécules fut identifié comme capable de prévenir la dégradation de Rac1 médiée par CNF1.De manière inattendue, la plupart des composés semblent posséder un effet anti-inflammatoire, en baissant la sécrétion de cytokines de cellules stimulées. Le potentiel thérapeutique et en recherche de tels composés doit être évalué. En parallèle, deux autres composés montrent une protection anti-toxines large spectre (CNF1, toxine diphtérique, toxine de Shiga, toxine B de C. difficile). De même, leur mécanisme d’action, encore inconnu, pourrait permettre le traitement d’infections variées. / Immune system boosters could have many applications in public health: fighting antibiotics resistance, epidemics, protection of health care staff and populations during health crisis or biological warfare. Currently, the rare efficient immune stimulants are costly and dangerous; hence, they are earmarked to severe and targeted pathologies such as cancers, aplasia, or chronic viral infections. The small G protein Rac1 was identified as a potential therapeutic target. Once activated by various pathogens, it controls inflammation and host defenses establishment. CNF1 is a bacterial toxin that strongly activating Rac1, leading to its proteasomal degradation. Maintaining an activated Rac1 pool could enhance immune defenses. By using CNF1 as a tool to reduce it, a cellular bioassay was developed and optimized to screen 17 680 compounds. Through various filters, a group of molecules was identified to prevent CNF1-mediated Rac1 depletion. Unexpectedly, most of them seems to possess anti-inflammatory properties, down-regulating cytokines production from stimulated cells. The therapeutic potential of such compounds must be now evaluated. In parallel, two other molecules show a broad-spectrum anti-toxins protection (CNF1, diphtheria toxin, Shiga toxin, toxin B from C. difficile). Their unknown mode of action may allow the treatment of various infections.

京都大学 / 0048 / 新制・課程博士 / 博士(工学) / 甲第22159号 / 工博第4663号 / 新制||工||1727(附属図書館) / 京都大学大学院工学研究科材料工学専攻 / (主査)教授 田中 功, 教授 中村 裕之, 教授 邑瀬 邦明 / 学位規則第4条第1項該当 / Doctor of Philosophy (Engineering) / Kyoto University / DFAM