京都大学 / 新制・課程博士 / 博士(工学) / 甲第25298号 / 工博第5257号 / 新制||工||2000(附属図書館) / 京都大学大学院工学研究科物質エネルギー化学専攻 / (主査)教授 村田 靖次郎, 教授 近藤 輝幸, 教授 中村 正治 / 学位規則第4条第1項該当 / Doctor of Agricultural Science / Kyoto University / DFAM

Orientador: Gonçalo Amarante Guimarães Pereira / Dissertação (mestrado) - Universidade Estadual de Campinas, Instituto de Biologia / Made available in DSpace on 2018-08-23T08:13:02Z (GMT). No. of bitstreams: 1 Bassalo_MarceloColika_M.pdf: 8530833 bytes, checksum: 675d7e6b45b1284552a7e3f9939d929a (MD5) Previous issue date: 2013 / Resumo: A sociedade atual é fundamentalmente dependente do petróleo, recurso natural inserido na grande maioria dos setores da economia. Entretanto, fatores como a limitada disponibilidade deste recurso, sua instabilidade no mercado devido a problemas de natureza geopolítica e a emissão de dióxido de carbono ocasionada pela utilização deste combustível, acentuaram as iniciativas para substituir o petróleo por fontes alternativas e renováveis de matéria prima. A bactéria Propionibacterium acidipropionici surge como uma excelente candidata para a substituição de compostos petroquímicos, através da produção do ácido propiônico. No entanto, antes de transformar esta bactéria em uma plataforma industrial, é necessário aprofundar a compreensão do metabolismo deste microrganismo e desenvolver ferramentas de manipulação genética. No que diz respeito à compreensão do metabolismo, poucos estudos avaliaram o perfil aeróbico desta bactéria, considerada anaeróbica estrita até recentemente. No presente trabalho, foi identificada nesta bactéria a presença de todos os componentes de uma cadeia transportadora de elétrons. No entanto, a citocromo c oxidase identificada apresenta-se mutada e os testes realizados confirmaram a não funcionalidade deste complexo. A existência de uma oxidase alternativa, a citocromo bd oxidase, caracterizada pela alta afinidade ao oxigênio, surge então como uma hipótese promissora acerca da microaerofilia desta bactéria. O trabalho também avaliou o perfil fermentativo dessa bactéria em condições aeróbicas com diferentes fontes de carbono, o que ressaltou a enorme flexibilidade metabólica apresentada por P. acidipropionici, capaz de redirecionar o fluxo de carbono para diferentes produtos finais a depender da necessidade de manutenção do balanço redox. Este estudo também revelou uma propriedade bastante peculiar e industrialmente relevante do xarope de cana-de-açúcar. A fermentação aeróbica com este substrato, ao contrário de todas as outras fontes de carbono, apresentou um crescimento superior ao das condições anaeróbicas e, adicionalmente, exibiu um perfil fermentativo próximo ao observado em ausência de oxigênio. A identificação do composto presente no xarope de cana-de-açúcar, responsável por simular o metabolismo anaeróbico, poderia viabilizar a produção do ácido propiônico em dornas de fermentação aeróbicas, o que traria enormes benefícios para a produção economicamente viável do ácido propiônico e na implementação de P. acidipropionici como uma plataforma industrial / Abstract: The dependence of contemporary society on petroleum is axiomatic, and this natural resource could be found intrinsically embedded in the vast majority of economic sectors. Nonetheless, the limited availability of this natural resource, the instability in the stock market due to geopolitical problems, and also the carbon dioxide emissions associated with the use of fossil fuels have highlighted the need to search for renewable energy sources. The bacteria Propionibacterium acidipropionici arises as an excellent strategy for the substitution of petrochemical compounds, through the production of propionic acid. Before we could implement this bacterium as an industrial platform, however, it becomes necessary to enhance the knowledge regarding the metabolism of P. acidipropionici, and thus create a backbone for the development of genetic manipulation tools. Regarding the metabolism of this bacterium, there aren't comprehensive studies about its aerobic metabolism, thus being considered strict anaerobes until recently. In the present work, it was identified that P. acidipropionici has all required components for a functional electron transport chain. However, the cytochrome c oxidase of this bacterium has a frameshift mutation, and the functional studies proved that this complex is not operative. The presence of an alternative oxidase of high oxygen affinity, called cytochrome bd oxidase, is then suggested as a hypothesis to explain the microaerofilic habit of this bacterium. This work has also shed light into the fermentative profile showed by this bacterium under aerobic cultivation with different carbon sources, bringing attention to the highly flexible metabolism of P. acidipropionici. This bacterium has shown to be capable of completely changing its carbon flux to different end products, as a strategy to maintain the redox balance. In addition, this work has also unveiled an interesting and industrially-relevant property of the sugar cane syrup. It was demonstrated that the aerobic cultivation of P. acidipropionici with sugar cane syrup increased the culture growth, as well as it changed the fermentation end products in a way more similar to the anaerobic cultivation. It was hypothesized that this unusual property found in the sugar cane syrup was due to the presence of a mineral compound that could be used as a final electron acceptor by P. acidipropionici. The identification of this specific compound would allow the aerobic production of propionic acid in industrial conditions, and thus could be a major breakthrough to turn its industrial production into an economically viable process / Mestrado / Genetica de Microorganismos / Mestre em Genética e Biologia Molecular

Metal-Organic Frameworks (MOFs) are porous materials consisting of organic ligands connected by inorganic nodes. Their structural uniformity, high surface area, and synthetic tunability, position these frameworks as suitable active materials to achieve efficient and clean electrochemical energy storage. In spite of recent demonstrations of MOFs undergoing diverse electrochemical processes, a fundamental understanding of the mechanism of electron, proton, and ion transport in these porous structures is needed for their application in electronic devices. The current work focuses on contributing to such understanding by investigating proton-coupled electron transfer, capacitance performance, and the relative contribution of electron and ionic transport in the voltammetry of zirconium-based MOFs. First, we investigated the effects that the quinone ligand orientation inside two new UiO-type metal-organic frameworks (2,6-Zr-AQ-MOF and 1,4-Zr-AQ-MOF) have on the ability of the MOFs to achieve proton and electron conduction. The number of electrons and protons transferred by the frameworks was tailored in a Nernstian manner by the pH of the media, revealing different electrochemical processes separated by distinct pKa values. In particular, the position of the quinone moiety with respect to the zirconium node, the effect of hydrogen bonding, and the amount of defects in the MOFs, lead to different PCET processes. The ability of the MOFs to transport discrete numbers of protons and electrons, suggested their application as charge carriers in electronic devices. With that purpose in mind, we assembled 2,6-Zr-AQ-MOF and 1,4-Zr-AQ-MOF into two different types of working electrodes: a slurry-modified glassy carbon electrode, and as solvothermally-grown MOF thin films. The specific capacitance and the percentage of quinone accessed in the two frameworks were calculated for the two types of electrodes using cyclic voltammetry in aqueous buffered media as a function of pH. Both frameworks showed an enhanced capacitance and quinone accessibility in the thin films as compared to the powder-based electrodes, while revealing that the structural differences between 2,6-Zr-AQ-MOF and 1,4-Zr-AQ-MOF in terms of defectivity and the number of electrons and protons transferred were directly influencing the percentage of active quinones and the ability of the materials to store charge. Additionally, we investigated in detail the redox-hopping electron transport mechanism previously proposed for MOFs, by utilizing the chronoamperometric response (I vs. t) of three metallocene-doped metal-organic frameworks (MOFs) thin films (M-NU-1000, M= Fe, Ru, Os) in two different electrolytes (TBAPF6 and TBATFAB). We were able to elucidate, for the first time, the diffusion coefficients of electrons and ions (De and Di, respectively) through the structure in response to an oxidizing applied bias. The application of a theoretical model for solid state-voltammetry to the experimental data revealed that the diffusion of ions is the rate-determining step at the three different time stages of the electrochemical transformation. Remarkably, the trends observed in the diffusion coefficients (De and Di) of these systems obtained in PF61- and TFAB1- based electrolytes at the different stages of the electrochemical reaction, demonstrated that the redox hopping rates inside frameworks can be controlled through the modifications of the self-exchange rates of redox centers, the use of large MOF channels, and the utilization of smaller counter anions. These structure-function relationships provide a foundation for the future design, control, and optimization of electronic and ionic transport properties in MOF thin films. / PHD / The necessity of implementing new energy storage systems that enable the utilization of clean energy in diverse technologies such as electric vehicles and smart power grids, has generated great research efforts in the field of materials science. In particular, the development of nanoscale-based materials that can be utilized in batteries and supercapacitors is essential for achieving effective and clean electrochemical energy storage. Two of the main desired properties for such materials to be employed as electrodes in energy storage devices are high surface area and the possibility of incorporating redox-active moieties that are able to store electricity. Metal-Organic Frameworks (MOFs) are a relatively new kind of porous materials with high surface area and structural uniformity, consisting of organic ligands connected by inorganic nodes. The application of these materials in charge transport and storage is still in its early stages. Therefore, fundamental understanding of the mechanism of electron, proton, and ion transport in MOFs is necessary for a rational design of these porous structures. In order to contribute to such understanding, the present work is focus on two main concepts: (1) elucidating the effect that the tridimensional orientation of redox moieties inside the MOF could have on the charge storage performance and the ability of the material to achieve proton and electron conduction; and (2) quantifying for the first time the individual relative contribution of electron and ionic transport in MOF materials.

The π-conjugated organic and polymeric semiconducting materials have attracted much attention in the past years due to their significant potential in applications to electronic and optoelectronic devices including organic field-effect transistors (OFETs), organic photovoltaics (OPVs), and organic light-emitting diodes (OLEDs), etc. Yet, organic and polymeric semiconductors still have challenges associated with their relatively low charge carrier (hole and electron) transport mobilities and ambient stability in OFET applications. This dissertation discusses the molecular engineering on backbones and side-chains of π-conjugated semiconducting polymers to enhance the hole and electron field-effect mobilities. Three donor-acceptor copolymers, the hole transport (p-type) poly(hexathiophene-co-benzo- thiazole) (PBT6), the hole transport poly(thiophenes-benzothiadiazole-thiophenes-diketopyrrolo- pyrrole) (pTBTD), and the electron transport (n-type) poly(dithieno-diketopyrrolopyrrole-bithiazole) (PDBTz) have been developed. Besides, the effect of polymer side chains on polymer solution-processability and charge carrier transport properties was systematically investigated: a side chain 5-decylheptadecyl having the branching position remote from the polymer backbone merges the advantages of the improved solubility from traditional branched side chains in which the branch chains are close to polymer backbone and the effective π-π intermolecular interactions commonly associated with linear side chains. This indicates the potential of side chain engineering to facilitate the charge carrier transport performance of organic and polymeric semiconductors. Additionally, PDBTz solution-processing to OFETs based on non-halogenated solvents (xylenes and tetralin) was studied. The resultant thin-film OFET devices based on non-halogenated solvents exhibited similar film morphology and field-effect electron mobilities as the counterparts based on halogenated solvents, indicative of the feasibility of developing high mobility OFET devices through more environmentally-benign processing.

Electrical doping of organic semiconductors with molecular oxidants (p-type) or reductants (n-type) can greatly improve charge injection and conductivity in devices. Simple one electron reductants that are capable of reducing most electron-transport materials will inevitably also be sensitive to reaction with oxygen. Coupling electron transfer step with bond breaking/ making processes in principle can address this problem. The rhodocene dimer and related ruthenium and iridium dimeric sandwich compounds have been discussed as example of such n-dopants, reducing a variety of organic semiconductors to the corresponding radical anions, while forming monomeric cations. This class of n-dopants can be used in both vapor- and solution-processed devices, and the dopant monomer cations are large and, therefore, fairly stable with respect to diffusion. This thesis focused on increasing the utility of these and related electrical dopants. In order to reduce various electron-transport materials with lower electron affinities, which are frequently used in OLEDs, strategies and limitations to develop stronger n-dopants is discussed. Controlling the kinetics of the dopant / semiconductor reactions to allow film processing in ambient conditions, with activation of the dopants being carried out thermally or photochemically in subsequent steps is presented. An approach to covalently tether monomeric cations with themselves, surfaces or electron-transport materials is described. Electrochemical studies that further our understanding of dopant kinetics and thermodynamics is described. The dimer dopant chemistry is also compared to the corresponding hydride-reduced complexes of the cations and manganese tricarbonyl benzene dimer. The directions for future dopant design with improved properties is discussed.

In this work, the method of streaming rays have been expanded to two spatial dimensions (three phase space dimensions, x, y, and s) and was used as a basis for the development of the electron transport computer code SR2D. The streaming ray algorithm is an Eulerian-Lagrangian hybrid. Electrons are followed as they traverse the medium along specified streaming rays. Fluxes, however, are computed at the centers of the fixed cells. The development of the SR2D code required the specification of a Lagrangian streaming ray network overlaying a three dimensional Eulerian grid. In contrast to its one dimensional predecessor, the SR2D code accommodates non-uniform cell sizes and allows for arbitrary quadrature sets (S₂, S₄, S₆, S₈, S₁₂, or S₁₆). The critical aspect of the streaming ray method is the determination of the pathlengths of each and every streaming ray through all of the Eulerian cells. These values must be precalculated and stored because of the iterative nature of the solution scheme. Although the number of pathlengths may be exceedingly large, computer memory requirements are minimized, however, in the two dimensional algorithm by the symmetry of the geometry in each pathlength increment. The SR2D code was used to calculate the energy deposition profile for two kinds of sources, an isotropic point source and a monodirectional point at the periphery of a two dimensional medium. For each case, we chose aluminum with dimensions 0.01g/cm² thick by 0.02g/cm² wide as the medium and specified a grid of 5 by 10 uniform cells, respectively. The pathlength increment was 0.002g/cm² with 25 pathlength increments chosen. An S₈ quadrature set was selected for the monodirectional point source while an S₁₂ quadrature set was used for the isotropic point source. Both sources were normalized to one incident particle with an energy of 200 keV. SR2D results were compared with those from the electron/photon Monte Carlo code TIGER. The total energy deposited in the medium and peak cell was selected to facilitate the comparison. For the monodirectional point source SR2D results were within 1% for total energy deposited into the medium and peak cell energy. The total energy deposited for the isotropic point source was within 1%, but peak cell energy varied by 4%.

Organic electronic devices are becoming commonplace in many academic and industrial materials laboratories, and commercial application of these technologies is underway. To maximize our fundamental understanding of organic electronics, a wide array of molecular frameworks is necessary, as it allows for a variety of optical and electronic properties to be systematically investigated. With the ability to further tune each individual scaffold via derivatization, access to a broad spectrum of interesting materials is possible. Of particular interest in the search for organic semiconducting materials are the cyclopenta-fused polyaromatic hydrocarbons, including those based on the fully conjugated indenofluorene (IF) system, which is comprised of five structural isomers. This dissertation represents my recent contributions to this area of research. Chapter I serves as a historical perspective on early indenofluorene research and a review of more current research on their synthesis and applications in organic electronic devices. Chapters II and III cover our early work developing the synthesis of the fully-reduced indeno[1,2-b]fluorene scaffold, with the latter of these chapters showing the first example of its application in an organic electronic device, a field effect transistor. Chapter IV demonstrates the first syntheses of fully-reduced indeno[2,1-c]fluorene derivatives. Chapter V expands our research to encompass isoelectronic heteroatomic derivatives of that same scaffold, introducing the fully-reduced diindeno[2,1-b:1',2'-d]thiophene scaffold and showing that our synthetic methodology also can be used to produce a quinoidal thiophene core. Chapter VI concludes with a review of the similarities between the indeno[2,1-c]fluorene and diindeno[2,1-b:1',2'-d]thiophene molecular architectures and introduces benzo[a]indeno[2,1-b]fluorene derivatives, demonstrating the first example of a fully-reduced indenofluorene that possesses a non-quinoidal core, illustrating that the quinoidal core is not a prerequisite for the strong electron affinities seen across the families of fully-reduced indenofluorenes. This dissertation encompasses previously published and unpublished co-authored material. / 2015-10-10

Analog CMOS amplifiers are the building blocks for many analog circuit applications such as Operational Amplifiers, Comparators, Analog to Digital converters and others. This dissertation presents empirical design methodologies that are both intuitive and easy to follow on how to design these basic building blocks. The design method involves two main phases. In the first phase NMOS and PMOS transistor design kits, provided by a semiconductor foundry, are fully characterized using a set of simulation experiments. In the second phase the user is capable of modifying all the relevant circuit design parameters while directly observing the tradeoffs in the circuit performance specifications. The final design is a circuit that very closely meets a set of desired design specifications for the design parameters selected. That second phase of the proposed design methodology utilizes a graphical user interface in which the designer moves a series of sliders allowing assessment of various design tradeoffs. The theoretical basis for this design methodology involves the transconductance efficiency and inversion coefficient parameters. In this dissertation there are no restrictive assumptions about the MOS transistor models. The design methodology can be used with any submicron model supported by the foundry process and in this sense the methods included within are general and non-dependent on any specific MOSFET model (e.g. EKV or BSIM3). As part of the design tradeoffs assessment process variations are included during the design process rather than as part of some post-nominal-design analysis. One of the central design parameters of each transistor in the circuit is the MOSFET inversion coefficient. The calculation of the inversion coefficient necessitates the determination of an important process parameter known as the Technology Current. In this dissertation a new method to determine the technology current is developed. Y Parameters are used to characterize the CMOS process and this also helps in improving the technology current determination method. A study of the properties of the technology current proves that indeed a single long channel saturated MOS transistor can be used to determine a fixed technology current value that is used in subsequent submicron CMOS design. Process corners and the variability of the technology current are also studied and the universality of the transconductance efficiency versus inversion coefficient response is shown to be true even in the presence of process variability. / Includes bibliography. / Dissertation (Ph.D.)--Florida Atlantic University, 2013.

A falta de uma vacina eficaz e o problema da resistência aos fármacos têm dificultado o controle da malária. A busca de novos alvos biológicos para o desenvolvimento de antimaláricos eficazes tem se concentrado, em parte, na pesquisa e compreensão de vias metabólicas exclusivas do parasita. Nosso grupo vem investigando e caracterizando produtos da biossíntese de isoprenóides em P. falciparum. Resultados preliminares identificaram a biossíntese das duas formas da vitamina K: filoquinona (PhQ) e menaquinona (MQ), ambas provenientes das vias do chiquimato e da via 2-C-metil-D-eritritol-4-fosfato (MEP). Salienta-se, ainda, que as vias do chiquimato e MEP são exclusivas do parasita, portanto alvos interessantes para o estudo e desenvolvimento de drogas alternativas contra a malária. Ensaios enzimáticos demonstraram a participação da MQ-4 na cadeia respiratória como transportadora de elétrons. Resultados indicaram que o parasita controla a concentração de ubiquinona e menaquinona (UQ/MQ) de acordo com as condições de aeração a qual é submetido, assim como descrito em E. coli e Ascaris suum. A biossíntese de MQ em P. falciparum é bloqueada pelo composto Ro 48-8071, inibidor da enzima 1,4-dihidroxi-2-naftoato preniltransferase da via de biossíntese de MQ. Em relação a PhQ, dados preliminares mostram uma provável participação na proteção antioxidante no ciclo intraeritrocítico de P. falciparum. Finalmente, por meio de ensaios de Real Time-PCR, investigou-se o padrão de transcrição de prováveis genes que supostamente codificariam algumas enzimas da via de biossíntese de MQ, PhQ, e UQ (esse último previamente caracterizado). Os resultados demonstraram que não há alterações na transcrição desses genes prováveis nos parasitas mantidos em diferentes condições de pressão de O2. / The lack of an effective vaccine and the problem of drug resistance haves hampered the control of malaria. The search for new biological targets for the development of effective antimalarials in part has focused on research and understanding of metabolic pathways unique to the parasite. Our group has investigated and characterized the products of the isoprenoids biosynthesis in P. falciparum. Preliminary results have identified the biosynthesis of two forms of vitamin K: phylloquinone (PhQ) and menaquinone (MQ), both derived from the Shikimate pathway and 2-C-methyl-D-erythritol-4-phosphate pathway (MEP). The shikimate and MEP pathways are unique to the parasite therefore are interesting targets for study and development of alternative drugs against the malaria. The enzimatic assay showed the participation of MQ-4 in the respiratory chain as electron carrier. Results indicated that the parasite controls the concentration of ubiquinone and menaquinone (UQ / MQ) according to the aeration conditions which is submitted, as described in E. coli and Ascaris suum. The MQ biosynthesis in P. falciparum is blocked by the compound Ro 48-8071, an inhibitor of the enzyme 1,4-dihydroxy-2-naftoato prenyltransferase. Also was described in the parasite, the biosynthesis of another form of vitamin K (PhQ) , and preliminary results showed probably participation of PhQ in the antioxidant protection in the cycle of P. falciparum. Finally, by the Real Time-PCR, we investigated the pattern of transcription of putative genes some enzymes of MQ, PhQ and UQ biosynthesis (the last was previously characterized). The results showed no changes in the transcription profile in the parasites kept in different conditions of O2 pressure.

Many mutations in superoxide dismutase 1 (SOD1) cause destabilization and misfolding of the protein and are implicated in amyotrophic lateral sclerosis. Likewise, a few post-translational modifications (PTMs) on SOD1 have been shown to cause the same phenotype. However, relatively few PTMs on SOD1 have been studied in depth and, in particular, very few studies have demonstrated how these PTMs affect SOD1's various biological roles. SOD1 is traditionally known for its role in reactive oxygen species (ROS)-scavenging but has also been found to have a few other biological roles, including transcription factor activity to promote genomic stability, preservation of cytoskeletal activity, maintaining zinc and copper homeostasis, and suppressing respiration. We have used the computational analysis tool, SAPH-ire, to find PTM 'hotspots' on SOD1 that have a high likelihood of affecting its biological functions. Interestingly, the top seven ranked PTM 'hotspots' were found in a small region of SOD1, between S98-K128. We focused our studies on one of the PTM 'hotspots' found in this region, lysine-122 (K122). K122 is found in the electrostatic loop of SOD1, a loop that is important for shuttling in superoxide radicals to be neutralized. According to our data, and other studies, this lysine is both succinylated and acetylated. We found that acetyl and succinyl-mimetics (K122Q and K122E, respectively) of this site do not affect its ROS scavenging activity but do prevent SOD1 from suppressing respiration and decrease its localization to the mitochondria. Further, when cells are depleted of SIRT5 (the desuccinylase for K122), SOD1 can no longer suppress respiration. Additionally, we found that SOD1 appears to suppress respiration at complex I, whether directly or through an indirect pathway is unknown. When HCT116 colon cancer cells were depleted of endogenous SOD1, the overexpressed succinyl K122-mimetic (K122E) could not recover growth as well as overexpressed WT SOD1. The K122E SOD1 expressing cells also exhibited increased mitochondrial ROS and unhealthier mitochondria. We propose a mechanism whereby SOD1 suppression of respiration acts as an additional regulator of oxidative stress: SOD1 suppresses the electron transport chain to decrease reactive oxygen species leakage and to promote healthier mitochondria and growth.