Developing a sensitive and effective in vitro bioassay to detect endocrine disrupting chemicals (EDCs) would reduce the cost, eliminate the possibility of low dose effects, detect the non-monotonic dose responses, and identify mechanisms of actions. The “chemical nose” sensing method using supramolecular complexes composed of cationic monolayer functionalized gold nanoparticles (AuNPs) and fluorescent proteins (FPs) can successfully distinguish serum proteins, mammalian cells, tissue lysates, and chemotherapeutic drug mechanisms. EDCs regulate target cells via genomic or non-genomic pathways in terms of proliferative effect and response time. In this thesis, green fluorescent protein-gold nanoparticle (GFP-AuNP) sensors were used to detect the proliferative effect of 17b-estradiol (E2) and bisphenol A (BPA) on MCF7 and T47D cell lines at fM or pM dose range. Non-monotonic dose responses were also observed at different exposure times. The dose-response relationships using GFP-AuNP sensors could be correlated to the cell cycle analysis. Interestingly, tamoxifen, an estrogen antagonist, showed distinct patterns at low doses on HepG2 cells using triple channel FP-AuNP sensors, which might indicate different mechanisms of actions in this dose range.

Studies and development of artificial metalloenzymes have developed into vibrant areas of research. It is expected that artificial metalloenzymes will be able to combine the best of enzymatic and homogenous catalysis, that is, a broad catalytic scope, high selectivity and activity under mild, aqueous conditions. Artificial metalloenzyme consist of a host protein and a newly introduced artificial metal center. The host protein merely functions as ligand controlling selectivity and augmenting reactivity, while the metal center determines the reactivity. Potential applications range from catalytic production of fine chemicals and feedstock to electron transfer utilization (e.g. fuel cells, water splitting) and medical research (e.g. metabolic screening). Particularly modern asymmetric synthesis is expected to benefit from a successful combination of the power of biocatalysis (substrate conversion via multi-step or cascade reactions, potentially immortal catalyst, unparalleled selectivity and optimization by evolutionary methods) with the versatility and mechanism based optimization methods of homogeneous catalysis. However, so far systems are either limited in structural diversity (biotin-avidin technology) or fail to deliver the selectivities expected (covalent approaches). This thesis explores a novel strategy based on the site-selective incorporation of unnatural, metal binding amino acids into a host protein. The unnatural amino acids can either serve directly as metal binding centers can be used as anchoring points for artificial metallo-cofactors. The identification expression, purification and modification of a suitable protein scaffolds is fundamental to successfully develop this field. Chapter 2 and 3 detail a rational approach leading to a highly engineered host protein. Starting with fluorescent proteins, which combine high thermal and pH stability, high expression yields, and fluorescence for ease of quantification and monitoring an efficient and fast purification protocol was developed first. The purification protocol uses a combination of heat precipitation and three-phase-partitioning (TPP). It provides high yield and purity without requiring any tag. Building on the favourable properties of fluorescent proteins, the non-metal binding, highly stable host-scaffold mTFP* was generated through rational design. The incorporation of artificial metal binding sites, the allowed the selective formation of artificial metalloenzymes, which show catalytic activity and moderat to good chiral induction in the Diels-Alder Cyclization and Friedl-Crafts Acylation Chapter 4 of the thesis describes the use of UAA incorporation to generate artificial metal binding sites. Computational studies and homology modelling successfully highlighted several positions in mTFP*, which are particularly suitable for UAA incorporation without any disruption of the protein structure. Application of a functional orthogonal aaRS/tRNA pair developed by P.G. Schultz and co-workers allowed the site-specific incorporation of UAAs in the host protein framework. Changes in fluorescence intensity revealed preferences of varieous UAAs for specific incorporations sites. The three UAAs, pIF, pAzF, and pEynF were incorporated into mTFP* in good yields, while pBF does only deliver low protein yields. A successfully established on-protein MIYAURA borylation reaction allows convert well-incorporated pIF into pBF circumventing the problem of low expression yields. Chapter 5 details the use of the azide-functionality of pAzF for the bioconjugation of artificial metal-binding cofactors through CuAAC. The triazole ring formed during this reaction serves as an additional moderate σ -donor/π –acceptor ligand of the metal binding site. We demonstrated the potential of site-specific modifications within the protein host with a versatile subset of artificial cofactors. Following transition metal binding, the newly created metal sites show catalytic activities that nature does not provide. The proof of concept study highlights the potential of the present mTFP* based catalysts in asymmetric Tsuji Trost allylation reactions and Diels-Alder cycloadditions. Dual anchoring of the cofactor lead to increased enantioselectivities, which is a direct result of a better-defined orientation of the catalytic center on the protein surface. Following the utilization of the CuAAC click reaction for the generation of artificial metalloenzymes, the last chapter of this thesis reports the development of a heterogeneous catalyst system for this reaction, which overcomes limitations of homogenous protocols. The recyclable core-shell structured Cu2O/Cu-nanowire catalyst is highly active, does not lead to protein precipitation, can be filtered off after the reaction and provides copper free bioconjugation products.

INTRODUCTION: Injury to the facial nerve can lead to functional and aesthetic sequelae in patients. Though surgical interventions are available to restore lost motor and sensory function, outcomes are often suboptimal due to inadequate or disorganized axonal regeneration. While engineering improvements to the standard of care are underway, gaps remain in our molecular understanding of peripheral nerve injury to translate these efforts clinically. Over the last few decades, advancements in intravital imaging such as the development of fluorescent reporter mice and use of multiphoton excitation techniques have allowed for markedly enhanced characterization of biological phenomena at higher resolutions, at greater depths, and for longer timescales. Challenges in reliably and serially imaging in vivo within murine models have been overcome through the development of chronic imaging windows in various settings of the body. However, there are very few techniques available presently for imaging the peripheral nerve microenvironment and no prior work detailing use in the facial nerve setting. OBJECTIVE: Longitudinal studies employing intravital imaging techniques carry potential to improve understanding of peripheral nerve regeneration and function. Using multiphoton microscopy and fluorescent reporter mice, we propose a prototype, surgical protocol of implantation, and initial safety and efficacy testing of a facial nerve window to enable chronic imaging for enhanced characterization of the peripheral nerve microenvironment. METHODS: A stainless-steel implant with an affixed glass coverslip and aluminum external fixation component was developed for implantation in a transgenic reporter mouse model to enable chronic intravital imaging of the facial nerve buccal and marginal mandibular branches. A qualitative observational study and clinical assessment scoring study was performed post-surgical implantation to monitor behavior, physical appearance, weight loss, and reactivity to animal handling over the typical time-course of nerve regeneration. Segments of facial nerve branches were harvested from control and window-implanted mice and imaged using widefield epifluorescence microscopy for axon quantification to determine any adverse effects from window compression onto axonal fibers. Two-photon microscopy (2PM) and Simulated Raman Scattering (SRS) were also performed through the window to visualize axon tracts, myelin sheaths, and surrounding collagen matrix in wild-type and transgenic mice models. RESULTS: Qualitative serial observational studies and assessment scoring indicated no obvious functional deficits over the time-course of typical nerve regeneration and normal scores for weight, behavior, physical appearance, and reactivity. Neural histomorphometric analysis indicated no significant difference in mean myelinated axon count of buccal (mean ± SD; control buccal, 947.6 ± 129.9; window-implanted buccal, 799.3 ± 128.6; p = .136) and marginal mandibular branches (control marginal mandibular, 801.3 ± 145.1; window-implanted marginal mandibular, 738.0 ± 197.2; p = .599) between control and window-implanted mice, suggesting that neuropathy was not induced from the window itself. High-resolution images of nerve morphology in healthy and injured transgenic and wild-type mice were obtained using 2PM and SRS. CONCLUSION: Herein, we describe a novel and replicable platform for longitudinal intravital imaging of murine facial nerve. Future studies will evaluate viability of this model for imaging the facial nerve microenvironment, particularly Schwann cell-axon interactions, in the setting of severe nerve injury over a period of several weeks to months. Improved understanding gained through such studies of the structural peripheral nerve microenvironment may allow for advancements in viral vector therapeutics, nerve graft scaffold design, as well as advanced injury diagnostics and tracking. / 2022-06-02T00:00:00Z

Formins are proteins involved in regulation and construction of actin filaments of eucaryotic organism. They parcipitate in regulating cytokinesis, polar tip growth, and thus participate in development of whole organisms. There are 2 classes of formins in Arabidopsis thaliana. Both classes include FH1 and FH2 domains (formin homology 1 a 2). Class I formins have N-terminal transmembrane domain, unlike class II formins. Some formins of class II have a N-terminal PTEN domain (Phosphatase and Tensin Homolog). Sequence analyses predicted membrane binding via phosphatase or C2 subdomain of PTEN. This thesis was focused on the formin AtFH14, specifically its PTEN domain. Based on predicted sequence, a DNA fragment encoding the PTEN domain was amplified, sequenced and cloned to destination vectors for YFP and EOS phusions. Marked protein was visualized by transient expression in Nicotiana benthamiana. Stably transformed Arabidopsis lines were prepared for stably expression of protein. The tagged protein was localized in cortical cytoplasm, cytoplasmatical strands, probably in nuclear membrane or perinuclear cytoplasm, as well as in peculiar "folicle-like" structures that might be due to binding of PTEN at the periphery of some membrane organelles. Also were seen filament structures, maybe caused by PTEN binding...

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

Non-coding RNAs are involved in the regulation of most major cellular process in Escherichia coli. With current technologies, many of these molecules have been identified; however, the full scope of their regulatory interactions is still unknown. None of the techniques currently in use employ the regulatory effect of the RNAs, which is the major unifying attribute of these molecules, for their identification. This thesis presents projects involving the design of a dual-reporter plasmid and screening method in the discovery and characterization of RNA regulatory interactions The first project details the engineering of the dual reporter plasmid. This vector utilizes one fluorescent protein to detect regulatory events and a second to normalize for off-target effects. The second project utilizes this tool in the discovery and characterization of novel regulatory responses. This is accomplished by screening a library of intergenic regions for regulatory responses against a collection of metabolite. Interesting interactions involving nitrogen abundance, iron and uracil are identified and further examined. Finally, this thesis examines how this technology can be further expanded for the study of RNA regulatory functions. The use of the screening method for the detection of regulatory events caused by alternative minimal media composition and the potential for the dual reporter plasmid to aid in the study of riboswitches are investigated. / Thesis / Doctor of Science (PhD)

京都大学 / 新制・課程博士 / 博士(エネルギー科学) / 甲第23998号 / エネ博第434号 / 新制||エネ||82(附属図書館) / 京都大学大学院エネルギー科学研究科エネルギー基礎科学専攻 / (主査)教授 森井 孝, 教授 片平 正人, 教授 佐川 尚 / 学位規則第4条第1項該当 / Doctor of Energy Science / Kyoto University / DFAM

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.

La Enhanced Cyan Fluorescent Protein (ECFP) est un variant spectral de la Green Fluorescent Protein extraite de la méduse Aequaria Victoria (GFPav). La ECFP, émettant dans le cyan, est un des donneurs les plus utilisés dans les études de transfert résonnant d’énergie d’excitation et est integré dans de nombreuses constructions de biosenseurs. Pourtant, elle souffre de nombreux inconvenients. Notamment elle pésente des propriétés photophysiques complexes et une forte sensibilité environnementale qui sont des freins à une interprétation quantitative de ses signaux de fluorescence en imagerie cellulaire. Notre objectif vise à mettre au point, grâce à l’introduction d’un minimum de mutations, un dérivé de la ECFP présentant des propriétés d’émission simplifiées et performantes ainsi qu’une faible sensibilité environementale. Des mutations ont été introduites, par mutagenèse dirigée, à deux positions clefs de la séquence peptidique de la ECFP ce qui a permis de générer des dérivés présentant des propriétés photophysiques et une sensibilité au pH modulées. En particulier, nous avons réussit à générer une protéine fluorescente, l’Aquamarine, aux propriétés photophysiques quasi-idéales caractérisée par un rendement quantique de l’ordre de 0,9 et des déclins d'émission de fluorescence quasi-monexponentiels. Elle présente également une sensibilité au pH fortement réduite avec un pH de demi-transition acide de 3,3.Ce manuscrit présente l’étude détaillée des propriétés d’émission de fluorescence des diverses protéines générées. Plusieurs paramètres présentant un intérêt particulièrement important pour une utilisation adéquate en imagerie de fluorescence ont été évalués. Outre la sensibilité au pH établie sur une large gamme de pH (2,5-11), une attention particulière a été portée sur les performances photophysiques (monoexponentialité du déclin d'émission de fluorescence, durée de vie moyenne, rendement quantique, brillance,…) de ces dérivés. De plus, grâce à des expériences de dichroïsme circulaire, des informations sur les changements structuraux, dont ces dérivés sont le siège à pH très acide, ont été obtenues. Enfin, l’examen détaillé des données spectroscopiques stationnaires et résolues en temps a permis de mettre en lumière l’existence de plusieurs espèces émissives contribuant à la photophysique de ces protéines et à l’origine de leur transition acide. L’ensemble de ces résultats constitue une première approche pour une meilleure compréhension de la relation structure-photophysique-dynamique de la ECFP et de ces dérivés. / The Enhanced Cyan Fluorescent Protein (ECFP) is a variant of Green Fluorescent Protein extracted from the jellyfish Aequaria Victoria (GFPav). The ECFP, emitting in the cyan, is one of the most donors used in studies of resonant transfer excitation energy and is integrated in many constructions of biosensors. However, it suffers from several drawbacks. In particular, it presents a complex photophysical properties and high environmental sensitivity that are obstacles to its quantitative interpretation of fluorescence signals in cellular imaging. Our goal is to develop, through the introduction of minimum mutations, a derivative of the ECFP with simplified emission properties and low environmental sensitivity.Mutations were introduced by site-directed mutagenesis, into two positions in the peptide sequence of ECFP which helped to generate derivatives with modulated photophysical properties and low pH sensitivity. In particular, we have managed to generate a fluorescent protein, Aquamarine, with almost ideal photophysical properties characterized by a quantum yield of about 0.9 and pure single exponential fluorescence decay. It also has a greatly reduced sensitivity to the pH with half transition point near 3.3.This manuscript presents a detailed study of fluorescence properties of various proteins generated. Several parameters for proper use in fluorescence imaging were evaluated. In addition to the pH sensitivity based on a wide range of pH (2.5 to 11), particular attention was paid to the photophysical performance (simpler fluorescence emission decay, average lifetime, quantum yield, brightness, ...) of these derivatives. In addition, we studied structural changes on these derivatives at acidic pH by circular dichroism. Finally, a detailed examination of the steady state fluorescence and time-resolved fluorescence helped to highlight the existence of several emissive species contributing to the photophysics of these proteins and the origin of their acid transition. These results constitute a first approach to a better understanding of the structure-photophysical dynamics of ECFP-and these derivatives