京都大学 / 0048 / 新制・課程博士 / 博士(工学) / 甲第19752号 / 工博第4207号 / 新制||工||1649(附属図書館) / 32788 / 京都大学大学院工学研究科合成・生物化学専攻 / (主査)教授 濵地 格, 教授 梅田 眞郷, 教授 跡見 晴幸 / 学位規則第4条第1項該当 / Doctor of Philosophy (Engineering) / Kyoto University / DGAM

Clustered regularly interspaced short palindromic repeats (CRISPR) are derived from a bacterial and archaeal adaptive immune system. The core enzymes of CRISPR are RNA-guided endonucleases that sequence-specifically cleave foreign double-stranded DNA. Improving and controling the properties of the CRISPR system is a crucial step in advancing the therapeutic potential of CRISPR technology. Several classes of these enzymes exist and are being adapted for biotechnology, such as genome engineering. Cas12a (Cpf1) is a Type V CRISPR-associated (Cas) enzyme that naturally uses only one guide RNA, in contrast to Type II CRISPR-Cas9 enzymes. Thus, Cpf1 may represent a simpler, more practical tool for applications such as gene editing and therapeutics. This dissertation comprises four related studies in this area. To better understand the functional requirements for Cpf1-crRNA interaction and develop modified crRNAs suitable for synthetic biology and therapeutic applications, the first study performed nucleotide substitutions in the crRNA. It focused on the protein-interaction motif of the crRNA by incorporating base changes at the 2ʹ position that alter hydrogen-bonding capacity, sugar pucker, and flexibility. DNA substitutions in RNA can probe the importance of A-form structure, 2ʹ-hydroxyl contacts, and conformational constraints within RNA-guided enzymes. In addition, Chemical modifications include 2'-deoxy, 2'-fluoro, 2'- deoxy-arabinonucleic acid, and oxepane. Our study discovered that 2'-fluoro maintains the A-form structure and is compatible with AsCpf1 activity. Biochemical endonuclease activity, gene editing efficiency, Cpf1 binding affinity, and ribonucleoprotein stability were used to assess the tolerance and effects of modification. Characterizing structure-function requirements for Cpf1-crRNA interaction will facilitate better design and tuning of Cpf1 enzymes. The second study established a FRET-based assay in collaboration with a computational collaborator to identify small molecule inhibitors predicted by virtual docking and simulations. This study aims to lay the foundation for efficient, safe implementation of CRISPR-Cpf1. The third study used chemically modified Cas9-guide RNAs to offset known weaknesses of CRISPRi. It takes advantage of the high binding affinity and nuclease resistance of modified guides to potentially reduce the required components for CRISPRi.

No description available.

Single Wall Carbon Nanotubes (SWCNTs) are often synthesized as bundles and are chemically modified via either covalent or non-covalent approaches to prevent aggregation, improve their dispersability and tune their physical properties for a potential application. The spatial distribution and effect of covalent addends on the electronic properties of SWCNTs was characterized using a Scanning Tunneling Microscope but with limited success. The effect of sample preparation was questioned as it often involves sonicating the SWCNTs in either an organic or an aqueous medium. Sonication of SWCNTs in certain common solvents was found to alter their electronic properties. The solvent molecules are broken down via a radical pathway during sonicating leading to the formation of new species that interact with the SWCNTs and in some cases with the catalytic material present. New species such as iron chlorides and oxygen, which were formed for example in o-dichlorobenzene and water respectively, caused p-type doping. Doping was characterized by Raman spectroscopy and X-ray photoelectron spectroscopy (XPS). A blue shift in the D* mode along with a shift to lower binding energy in the C1s peak was observed from Raman spectroscopy and XPS respectively. The reactivity of the radicals (formed during sonication) towards the structure of the SWCNTs was also investigated. Radicals formed during sonication of certain chlorinated aromatic solvents lead to the formation of sonochemical polymers, which interacted heavily with the SWCNTs. These interactions, which can be the source of features commonly associated with covalent functionalization, were thwarted by a washing protocol and were found to be non-covalent in nature. The observations are of relevance towards understanding an inadvertent chemical modification during chemical processing, which can impact reproducibility of results that involve wet-chemical processes. However, with such knowledge of the chemistry involved during sample preparation the occurrence of doping can be either circumvented or appropriately used. / Thesis / Doctor of Philosophy (PhD)

Master of Science / Department of Grain Science and Industry / Yong Cheng Shi / Octenyl succinic anhydride (OSA) modified starch is widely used in emulsion and encapsulation applications. The functionality of OS starch depends on its molecular structure. A systematic study was performed to investigate the reaction of OSA with granular waxy maize (WM) starch, microporous WM starch and soluble maltodextrin. OS starches were prepared in an aqueous slurry system, and the degree of substitution (DS) of OS starches was determined by titration and [superscript]1H-NMR spectroscopy. For both 3% and 50% OSA treatment, OS maltodextrin had higher DS and reaction efficiency (RE) than OSA modified WM starch and microporous WM starch. The maximum DS of OSA modified granular WM starch was 0.14 and the highest DS of OS maltodextrin was 0.27. For the 3% OSA treatment, the RE for WM starch and maltodextrin was ~ 80% and ~100%, respectively. The structure of OSA modified WM starch and the locations of OS groups on anhydroglucose units (AGUs) were studied by [superscript]1H-NMR and [superscript]13C-NMR. As increasing OS substitution, [superscript]13C - signal at C-1 shifted to upper field. In addition, the [superscript]13C - signal at C-6 shifted to downfield when DS reached 0.073. The results suggested that OS groups were predominantly substituted at the O-2 position and started being substituted at O-6 position when DS was 0.073. FT-IR microspectroscopy was used to detect the heterogeneity OS starch products. Native WM starch, OSA modified WM starches (DS=0.019 and 0.073) and a starch blend with native starch to OSA modified WM starch (DS=0.073) ratio of 7:3 were examined. More than one hundred starch granules of each sample were analyzed one by one by FT-IR microspectroscopy. For the OS starch (DS=0.019), 7% starch granules showed carbonyl absorption. For the OS starch (DS=0.073), 99% starch granules showed carbonyl absorption but the intensity varied, indicating that OSA reacted with most starch granules when DS was 0.073. However, the OS contents of individual granules varied. For the starch blend, only 30% starch granules had carbonyl absorption. FT-IR microspectroscopy is a useful tool to detect heterogeneity of OS starch blends containing native starch.

L'Imagerie par Résonance Magnétique (IRM) est à l'heure actuelle la technique de visualisation préférentiellement choisie par les chirurgiens. Cependant, cette technique ne permet pas de visualiser des prothèses à base de polymères, qu'elles soient dégradables ou non. Afin de mieux évaluer la fixation, l'intégration tissulaire et le devenir de l'implantation de ces prothèses polymères, il serait souhaitable qu'elles soient visibles par IRM. Ce travail présente donc la conception et la synthèse de copolymères biocompatibles visibles par IRM destinés à être introduit dans la composition de prothèses pour applications temporaires ou permanentes. En utilisant la modification chimique en position alpha de fonction ester décrite précédemment par notre laboratoire, nous avons greffé de façon covalente et par une liaison stable un chélate du gadolinium (le DTPA) sur la chaîne de la PCL (dégradable) et du PAM (non dégradable). Le gadolinium a ensuite été complexé par le DTPA greffé préalablement. Ces nouveaux copolymères ont été caractérisés par RMN et CES, et le taux de gadolinium évalué par ICP-MS. Des images d'IRM ont été réalisées in vitro et in vivo sur des appareils contenant des aimants de 7 Teslas (recherche) et 1,5 Teslas (clinique). Ces images montrent qu'un treillis en polypropylène enduit de copolymère greffé par un complexe DTPA-gadolinium est visible par IRM, ce qui laisse entrevoir un large champ d'applications pour ce type de composé. / Magnetic Resonance Imaging (MRI) is currently the visualization technique that surgeons preferentially choose. However this technique does not allow the visualization of polymer-based prosthesis, whether they are degradable or not. In order to best assess adhesion, tissue integration and the future of implantation of these polymer prosthesis, it would be advisable to make them visible in IRM. This work presents the conception and the synthesis of biocompatible copolymers visible in IRM meant to be implanted under the form of prosthesis for temporary or permanent applications. Using the chemical modification in alpha position of ester function, previously described by our laboratory, we grafted a gadolinium chelate, in a covalent way and forming a stable bond on PCL (degradable) and PMA (non degradable) backbone. Gadolinium was then complexed by DTPA previously grafted. Those new copolymers were characterized with NMR and SEC, and the rate of gadolinium was assessed by ICP-MS. MRI images were taken in vitro and in vivo on devices containing 7-Teslas (research) and 1,5 Teslas (clinical) magnets. These images show a poly(propylene) mesh coated with grafted copolymer containing complex gadolinium which is visible in MRI. It will consequently improve the prospects of applications for this kind of MRI-visible compound.

Development of selective artificial metalloenzymes by combining the biological concepts for selective recognition with those of transition metal catalysis has received much attention during the last decade. Targeting covalent incorporation of organometallic catalysts into proteins, we explored site-selective covalent coupling of phosphane and N–containing ligands. The successful approach for incorporation of phosphane ligands we report herein consists of site-specific covalent coupling of a maleimide functionalized hydrazide into proteins, followed by coupling of aldehyde functionalized phosphanes via a hydrazone linkage. Site selective incorporation of N–containing ligands was obtained by coupling maleimide functionalized N–ligands to proteins via Michael addition to the maleimide double bond. These two methods can be easily applied to virtually any protein displaying a single reactive cysteine and allows a wide range of possibilities in terms of cofactor design. Site-specific covalent incorporation of transition metal complexes of phosphane ligands into proteins was successfully obtained. The success of the approach is influenced by several factors like the metal precursor, the phosphane type and the protein scaffold. Metal complexes of 5–maleimido–1,10–phenanthroline modified proteins were formed in situ, via addition of a metal precursor to the phenanthroline modified proteins or by coupling preformed metal complexes to proteins via Michael addition of the thiol group from a cysteine residue to the maleimide double bond of the N-ligand. These successful coupling methods enable the use of a wide range of protein structures as templates for the preparation of artificial transition metalloenzymes, which opens the way to full exploration of the power of selective molecular recognition of proteins in transition metal catalysis.

Doctor of Philosophy / Department of Grain Science and Industry / Xiuzhi Susan Sun / Soy protein is one of the most promising bio-degradable adhesives, with great potential as alternatives synthetic petroleum based adhesives for wood composite industries. However, its intrinsic drawbacks such as low water resistance, high viscosity, and short shelf life still limit its broad application. In this research, soy protein was further modified and characterized to improve adhesion properties, flow-ability, water resistance, and long shelf life, which could facilitate the industrialization of soy protein based adhesives. In this study, we exploited the in situ sodium bisulfite (NaHSO3) modification on soy protein in soy flour-water extracts, and then the modified soy protein was obtained through acid precipitation. First, different concentrations of NaHSO3 were used to modify soy flour slurry, then glycinin-rich and β-conglycinin-rich fractions were precipitated at pH 5.4 (SP 5.4) and pH 4.5 (SP 4.5), respectively. Unmodified sample SP 5.4 and SP 4.5 showed clay-like properties and viscoelastic properties, respectively; whereas with addition of NaHSO3 in range of 2-8 g/L, both SP 5.4 and SP 4.5 had the viscous cohesive phase with good handability and flow-ability. The overall adhesion performance of SP 4.5 was better than SP 5.4; the wet strength of these two fractions was in the range of 2.5-3.2 MPa compared to 1.6 MPa of control soy protein isolate. Then soy protein with various β-conglycinin/glycinin (7S/11S) ratios were extracted from soy flour slurry and characterized for adhesion properties based on the different solubility of 7S and 11S globulins. Seven glycinin-rich soy protein fractions and six β- conglycinin-rich soy protein fractions were obtained. According to the morphology, viscosity, and particle size results, we proposed that proper protein-protein interaction, hydration capacity (glycinin-rich fractions), and certain 7S/11S ratios (β-conglycinin-rich fractions) in modified soy protein are crucial to continuous protein phase formation. The viscous cohesive samples were stable for up to several months without phase separation at room temperature, with the wet adhesion strength of 2.0-2.8 MPa. The soy protein modified with NaHSO3 showed good compatibility with commercial glues applied on plywood and paper labeling fields. The modified soy protein made some functional groups, carboxylic (-COOH), hydroxyl (-OH) and amino groups (-NH2) available, which cross-linked with hydroxymethyl groups (-CH2-OH) from urea formaldehyde (UF) wood glue. The modified soy protein (MSP) with pH 4.8 also acted as an acidic catalyst for the self-polymerization of UF based resin. The wet adhesion strength of MSP/UF blends (40/60) was 6.4 MPa with 100% wood cohesive failure, as compared to 4.66 MPa of UF. As to the paper labeling application, peel strength of MSP on glass substrate increased rapidly, with curing time much shorter than commercial polyvinyl acetate based adhesives (PVAc). And the MSP/ PVAc blends showed shorter curing time, higher water resistance and lower viscosity than pure PVAc. Chemical modification could also enhance the adhesion strength of MSP. 2-octen-1- ylsuccinic anhydride (OSA) was proved to be grafted on soy protein through reaction between amine, hydroxyl groups of protein and anhydride groups. The oily nature and hydrophobic long alkyl chains of OSA mainly contributed to the significant water resistance improvement of MSP.

The enzyme Methionine sulfoxide reductase A (MsrA) repairs oxidized proteins, and may act as a scavenger of reactive oxygen species (ROS), making it a potential therapeutic target for age-related neurodegenerative diseases. The anoxia-tolerant turtle offers a unique model to observe the effects of oxidative stress on a system that maintains neuronal function following anoxia and reoxygenation, and that ages without senescence. MsrA is present in both the mitochondria and cytosol, with protein levels increasing respectively 3- and 4-fold over 4 hours of anoxia, and remaining 2-fold higher than basal upon reoxygenation. MsrA was knocked down in neuronally-enriched cell cultures via RNAi transfection. Propidium iodide staining showed no significant cell death during anoxia, but this increased 7-fold upon reoxygenation, suggesting a role for MsrA in ROS suppression during reperfusion. This is the first report in any system of MsrA transcript and protein levels being regulated by oxygen levels. / by Lynsey Erin Bruce. / Thesis (M.S.)--Florida Atlantic University, 2010. / Includes bibliography. / Electronic reproduction. Boca Raton, Fla., 2010. Mode of access: World Wide Web.

Este trabalho relata a utilização das fibras de sisal (Agavea sisalana) como agente de reforço na preparação de compósitos de matriz termorrígida fenólica. Considerando que não se encontra na literatura informações detalhadas sobre a estrutura química de dois dos principais constituintes da fibra de sisal, lignina e hemiceluloses (polioses) foram extraídas e caracterizadas. Além da questão ambiental, em que materiais oriundos de fontes não renováveis, como a matriz fenólica, são substituídos por materiais provenientes de fontes renováveis, como as fibras de sisal, este trabalho também teve como motivação desenvolver materiais compósitos com melhores propriedades. Para alcançar tal objetivo, optou-se por dividir o trabalho em três partes. A primeira etapa correspondeu a otimização dos principais parâmetros envolvidos no processo de preparação dos compósitos, tais como: pressão final de moldagem aplicada, ciclo de cura da matriz fenólica e fração e comprimento das fibras de sisal a serem empregadas como agente de reforço. Os resultados obtidos indicaram que um maior valor de força final de moldagem (20 ton) pode levar a compósitos com melhores propriedades desde que esta maior pressão seja paliçada no ponto de gelificação da matriz fenólica durante o ciclo de cura. Com relação a formulação dos compósitos, uma fração de 15% (em massa) de fibras com 3 cm de comprimento, distribuídas de forma aleatória, levou à melhores propriedades.. Após a escolha das melhores condições de processo, deu-se início a segunda etapa em que as fibras de sisal foram submetidas a tratamentos químicos envolvendo diferentes agentes modificadores com a finalidade de intensificar as interações fibra-matriz na interface. A primeira modificação envolveu reação com a macromolécula de lignina. Foram utilizadas duas ligninas, extraídas de duas fontes diferentes e por dois processos distintos: lignina de bagaço de cana-de-açúcar, extraída pelo processo Organosolve e a lignina, conhecida como Indulin, extraída do licor residual do processo de polpação Kraft da madeira (Pinus). Ambas as ligninas foram hidroximetiladas (utilizando formaldeído como reagente), visando aumentar sua reatividade. Em seguida, foram realizadas várias modificações das fibras de sisal com as duas ligninas hidroximetiladas, envolvendo diferentes intervalos de tempo de tratamento. Além desta modificação química envolvendo ligninas hidroximetiladas, também foi realizado um segundo estudo sobre tratamento das fibras de sisal em que o álcool furfurílico (AF), proveniente do furfural o qual pode ser obtido de fontes renováveis, e poliálcool furfurílico (PFA), sintetizado previamente a partir do AF, foram utilizados como agentes modificadores de fibras. Para estes tratamentos com AF e PFA, foram propostas duas modificações químicas envolvendo os sítios reativos presentes em dois componentes químicos das fibras de sisal: os polissacarídeos e a lignina. A modificação encerrando os polissacarídeos se baseou na reação entre estes e o poliálcool furfurílico (PFA). Nesta reação, foi utilizado o dicromato de potássio (K2Cr2O7) como agente gerador de centros-ativos, tanto na estrutura química da celulose como na do PFA. Esta geração de radicais em ambas as estruturas químicas catalisa a reação de graftização do PFA sobre a superfície das fibras. A outra modificação química proposta envolveu a reação entre o AF e o PFA com a macromolécula de lignina também presente naturalmente nas fibras de sisal (protolignina). Esta modificação se baseia na oxidação seletiva das unidades guaiacila e siringila da protolignina com dióxido de cloro (ClO2) e posterior reação com AF e PFA via mecanismo de Diels-Alder. No geral, os resultados indicaram que todos os tratamentos realizados aumentaram a compatibilidade entre fibra e matriz, intensificando as interações na região interfacial. Esta maior adesão fibra-matriz foi a principal responsável pelo melhor desempenho apresentado pelos compósitos contendo fibras modificadas no teste de absorção de água em comparação com aquele reforçado com fibras não modificadas. No entanto, apesar das modificações químicas realizadas promoverem maior compatibilidade fibra-matriz intensificando as interações na interface, estes tratamentos levaram a uma redução na resistência ao impacto dos compósitos reforçados por estas fibras, sendo este efeito consideravelmente mais pronunciado para os compósitos reforçados com fibras submetidas à K2Cr2O7 e ClO2. Esta redução foi conseqüência dos meios reacionais a que as fibras foram expostas terem sido agressivos às mesmas, fazendo com que se tornassem mais frágeis. A terceira e última etapa do presente trabalho correspondeu à adição de polibutadieno hidroxilado (PBHL), um elastômero, à matriz fenólica. Esta etapa teve por objetivo aumentar a tenacidade do termorrígido fenólico e, por conseqüência, dos compósitos, através da introdução de um material mais flexível. De acordo com os resultados obtidos, a adição de 10% (em massa) de PBHL à resina fenólica produziu um termorrígido com maior resistência ao impacto. No entanto, para os compósitos preparados a partir das blendas, a adição de frações de PBHL superiores a 2,5% (em massa) provocou redução nos valores de resistência ao impacto dos materiais. Esta redução foi causada pela formação de aglomerados de partículas de PBHL na interface e nas fibras de sisal, o que diminuiu a eficiência do processo de tenacificação. A formação destes aglomerados sobre a superfície das fibras indicou que o PBHL apresenta maior afinidade com as fibras de sisal à matriz fenólica, sugerindo que o PBHL poderia ser utilizado como agente de acoplamento entre fibra de sisal e matriz fenólica. Desta forma, foi preparado um compósito fenólico reforçado por fibras de sisal préimpregnadas com PBHL. Os resultados obtidos na caracterização deste compósito demonstraram que o PBHL forma uma fina camada sobre a superfície das fibras e que esta camada polimérica aderida à superfície das fibras intensifica as interações com a matriz fenólica, diminuindo a absorção de água do compósito. Porém, a pré-impregnação das fibras com PBHL praticamente não alterou os valores de resistência ao impacto do compósito. O conjunto de dados obtidos mostra que as fibras de sisal têm um bom desempenho na atuação como reforço de matriz termorrígida fenólica. Dentre os tratamentos químicos realizados sobre a fibra de sisal, com a finalidade de melhorar ainda mais o seu desempenho como material de reforço em matrizes fenólicas, pode-se considerar que a modificação envolvendo reação com ligninas hidroximetiladas foi a que se mostrou mais eficiente. A introdução de frações de lignina na superfície das fibras intensificou as interações fibra/matriz na interface, o que pode ser comprovado pela menor absorção de água apresentada pelos compósitos reforçados por estas fibras. Apesar deste tratamento causar certa diminuição na resistência ao impacto dos materiais, o ganho obtido na diminuição da absorção de água do compósito supera a perda na propriedade mecânica avaliada. / Considering the importance of developing new and valorized application areas for sisal fiber and also that detailed information on the chemical structure of its main constitutive polymers is scare, first hemicelluloses and lignin were extracted and characterized and then sisal fibers reinforced phenolic composites were prepared.While it is clear that substituting sisal fibers, a renewable resource, for the non-renewable components of the phenolic matrix would be beneficial for the environment, it is also hoped that such a substitution could lead to the development of composite materials with improved properties. Due to the joint goal of developing a novel material and investigating its properties, this work was divided into three stages. In the first stage, the key parameters for the preparation of the composites were optimized. These parameters included the final pressure applied on the mold at the phenolic matrix cure step, and the fraction and length of the sisal fibers used as reinforcement agents. The results showed that the higher final molding pressure (20 ton) leads to composites with better material properties. Under the conditions considered in the present work, of the present preparation method, the material containing 15% (w/w) of fibers with 3 cm of length randomly distributed presented the best performance. After optimizing the process conditions, the sisal fibers were subjected to a number of surface modifications in order to improve the interactions fiber-matrix at interface. The first chemical modification performed on the fibers involved reaction with lignin macromolecules. Two types of lignins were used: lignin of sugar cane bagasse extracted by the Organosolve process and another Indulin obtained using the wood (Pinus) Kraft pulping process. Both lignins were methylated via reaction with formaldehyde to increase their reactivity. These methylated lignins were used to modify the sisal fibers. In addition to chemical modification with lignins, the surfaces of the sisal fibers were also modified by furfuryl alcohol (FA) and polyfurfuryl alcohol (PFA). For these treatments with FA and PFA, two chemical modifications were proposed involving the sites present in two components of the sisal fibers: the polysaccharides and the lignin. The polysaccharide modification was based on the reaction between them, mainly cellulose, and the polyfurfuryl alcohol (PFA). In this reaction, potassium dichromate was used (K2Cr2O7) as a generator of radicals on carbohydrates and PFA chemical structures . This generation of radicals in both chemical structures catalyzes the grafting reaction of PFA on the surface of the fibers. The other chemical modification involved the reaction between FA and PFA with the lignin present naturally in the sisal fibers (protolignin). This modification is based on the selective oxidation reaction of the guaiacyl and syringyl units of the protolignin with chloride dioxide (ClO2) and subsequent Diels-Alder reaction between the furfuryl and polyfurfuryl alcohols. This combination of reactions yields new surface sites on the fibers thus allowing for a stronger interaction between the sisal fibers and matrix. While the interactions the fiber-matrix interface were indeed improved by the lignin and alcohol modifications, the mechanical properties of the sisal fibers were degraded by the treatments. Further, the impact strength of composites decreased. The third and last stage of the present work was the investigation of rubber toughening of the phenolic thermoset and, analogously, the composites reinforced with sisal fibers. For this purpose, hydroxyl-terminated polybutadiene (HTPB) was added to phenolic resin. The results showed that the addition of 10% (w/w) of HTPB to the phenolic resin increases the impact strength of the thermoset. However, in the case of the composites, the addition of superior fractions to 2,5% (w/w) results in a reduction of impact strength. This reduction was caused by the formation of aggregates of HTPB particles at the matrix-fiber interface and on surface sisal fibers.The formation of the aggregates reduced the efficiency of the toughening process. The formation of the aggregates on the surface of the sisal fibers indicates that HTPB shows more compatibility with the sisal fibers than phenolic matrix. The strong affinity between the sisal fibers and the HTPB suggests that HTPB could be used as coupling agent between the sisal fiber and the matrix. A composite reinforced with sisal fibers modified with HTPB was indeed prepared. The results demonstrated that HTPB forms a thin coating on the surface of the fibers and that this polymeric coating increased interactions at the fiber-matrix interface. As a result, water uptake of the composite was decreased. However, no change in the values of the impact strength of composite was observed. As a whole, the data presented in this thesis show that the sisal fibers demonstrate good performance as a thermoset phenolic matrix reinforcers. Reinforcement with sisal fibers has large scale potential as a substitute of synthetic fibers depending on the intended application of the material.