No description available.

There is great need of robust and high throughput techniques for accurately measuring the concentration of nanoparticles in a solution. Microarray imaging techniques using widely used to quantify the binding of labeled analytes to a functionalized surface. However, most approaches require the combined output of many individual binding events to produce a measurable signal, which limits the sensitivity of such assays at low sample concentrations. Although a number of high-NA optical techniques have demonstrated the capability of imaging individual nanoparticles, these approaches have not been adopted for diagnostics due complex instrumentation and low assay throughput. Alternatively, interferometric imaging techniques based on light scattering have demonstrated the potential for single nanoparticle detection on a robust and inexpensive platform. This dissertation focuses on the development of methods and infrastructure to enable the development of diagnostic assays using the Single Particle Interferometric Imaging Sensor (SP-IRIS). SP-IRIS uses a bright-field reflectance microscope to image microarrays immobilized on a simple reflective substrate, which acts as a common-path homodyne interferometer to enhance the visibility of nanoparticles captured near its surface. This technique can be used to detect natural nanoparticles (such as viruses and exosomes) as well as molecular analytes (proteins and nucleic acid sequences) which have been tagged with metallic nanoparticle in a sandwich assay format. Although previous research efforts have demonstrated the potential for SP-IRIS assays in a variety of applications, these studies have largely been focused on demonstrating theoretical proof of concept in a laboratory setting. In contrast, the effective use of SP-IRIS as a clinical diagnostic platform will require significant functional improvements in automation of assay incubation, instrument control, and image analysis. In this dissertation, we discuss the development of instrumentation and software to support the translation of SP-IRIS from manual laboratory technique into an automated diagnostic platform. We first present a collection of mechanical solutions to enable the real-time, in-solution imaging of nanoparticles in disposable microfluidic cartridges. Next, we present image analysis techniques for the detection of nanoparticle signatures within digital images, and discuss solutions to the unique obstacles presented by the ill-defined focal properties of homodyne interferometry. Finally, we present a particle tracking algorithm for residence time analysis of nanoparticle binding in real-time datasets. Collectively, these improvements represent significant progress towards the use of SP-IRIS as a robust and automated diagnostic platform. / 2019-07-02T00:00:00Z

Four negative stains, hafnium chloride and europium, samarium and gadolinium nitrates, were tested in single particle electron microscopy as potential alternatives to uranyl acetate, which is recently being widely restricted for its toxicity. The new stains were applied to a structurally well-described plant photosystem I, visualized by a transmission electron microscope and classified in a single particle analysis. The quality of the stains was evaluated by the obtained resolution and ability to provide reliable structural information.

Since the development and optical study of conjugated (conducting) polymers it has become apparent that chain conformation and aggregation at the molecular scale result in complex heterogeneous nanostructured bulk materials for which a detailed insight into morphological, spectroscopic as well as optoelectronic properties and mechanisms is overwhelmingly difficult to obtain. Nanoparticles composed of the conjugated polymer poly (MEH-PPV) and nanocomposite nanoparticles consisting of MEH-PPV doped with 1-(3-methoxycarbonylpropyl)-1-phenyl-C61 (PCBM) were prepared as model systems to study these materials at the length scale of one to a few domains. The MEH-PPV and PCBM doped nanoparticles were analyzed by single imaging/particle spectroscopy (SPS) and revealed molecular scale information on the structure-property relationships of these composite materials. The data obtained from SPS were investigated in terms of spectral difference between doped and undoped nanoparticles. The doped nanoparticles are blue shifted by approximately 5-10 nm, have an additional blue shoulder, and show different vibronic structure than the undoped nanoparticles. Specifically, relative intensity of the 0-1 transition is lower than for the undoped nanoparticles. These data are indicative of differences in molecular order between both nanoparticle systems, detected at the molecular scale. In addition, the effect of electrical fields present in devices on the interfacial charge transfer properties was evaluated. Furthermore, these nanoparticles were incorporated into the lipid nanotubes to study the diffusion process of the single MEH-PPV nanoparticles inside the lipid nanotubes. Our data shows a clear proof of concept that diffusion of nanoparticles inside the hollow lipid nanotubes can be studied on a single particle basis, which will allow us to study diffusion processes quantitatively and mechanistically within the framework of developing a biocompatible drug and gene delivery platform.

Single particle tracking has become a ubiquitous class of tools in the study of biology at the molecular level. While the broad adoption of these techniques has yielded significant advances, it has also revealed the limitations of the methods. Most notable among these is that traditional single particle tracking is limited to imaging the particle at low temporal resolutions and small axial ranges. This restricts applications to slow processes confined to a plane. Biological processes in the cell, however, happen at multiple time scales and length scales. Real-time feedback-driven single particle tracking microscopes have emerged as one group of methods that can overcome these limitations. However, the development of these techniques has been ad-hoc and their performance has not been consistently analyzed in a way that enables comparisons across techniques, leading to incremental improvements on existing sets of tools, with no sense of fit or optimality with respect to SPT experimental requirements. This thesis addresses these challenges through three key questions : 1) What performance metrics are necessary to compare different techniques, allowing for easy selection of the method that best fits a particular application? 2) What is a procedure to design single particle tracking microscopes for the best performance?, and 3) How does one controllably and repeatably experimentally test single particle tracking performance on specific microscopes?. These questions are tackled in four thrusts: 1) a comprehensive review of real-time feedback-driven single particle tracking spectroscopy, 2) the creation of an optimization framework using Fisher information, 3) the design of a real-time feedback-driven single particle tracking microscope utilizing extremum seeking control, and 4) the development of synthetic motion, a protocol that provides biologically relevant known ground-truth particle motion to test single particle tracking microscopes and data analysis algorithms. The comprehensive review yields a unified view of single particle tracking microscopes and highlights two clear challenges, the photon budget and the control temporal budget, that work to limit the two key performance metrics, tracking duration and Fisher information. Fisher information provides a common framework to understand the elements of real-time feedback-driven single particle tracking microscopes, and the corresponding information optimization framework is a method to optimally design these microscopes towards an experimental aim. The thesis then expands an existing tracking algorithm to handle multiple particles through a multi-layer control architecture, and introduces REACTMIN, a new approach that reactively scans a minimum of light to overcome both the photon budget and the control temporal budget. This enables tracking durations up to hours, position localization down to a few nanometers, with temporal resolutions greater than 1 kHz. Finally, synthetic motion provides a repeatable and programmable method to test single particle tracking microscopes and algorithms with a known ground truth experiment. The performance of this method is analyzed in the presence of common actuator limitations. / 2024-01-16T00:00:00Z

No description available.

京都大学 / 新制・課程博士 / 博士(生命科学) / 甲第25450号 / 生博第521号 / 新制||生||69(附属図書館) / 京都大学大学院生命科学研究科統合生命科学専攻 / (主査)教授 野田 岳志, 教授 朝長 啓造, 教授 鈴木 淳 / 学位規則第4条第1項該当 / Doctor of Philosophy in Life Sciences / Kyoto University / DFAM

The aim of this thesis is to investigate applicability of regulariza- tion by Krylov subspace methods to discrete inverse problems arising in single particle analysis (SPA). We start with a smooth model formulation and describe its discretization, yielding an ill-posed inverse problem Ax ≈ b, where A is a lin- ear operator and b represents the measured noisy data. We provide theoretical background and overview of selected methods for the solution of general linear inverse problems. Then we focus on specific properties of inverse problems from SPA, and provide experimental analysis based on synthetically generated SPA datasets (experiments are performed in the Matlab enviroment). Turning to the solution of our inverse problem, we investigate in particular an approach based on iterative Hybrid LSQR with inner Tikhonov regularization. A reliable stopping criterion for the iterative part as well as parameter-choice method for the inner regularization are discussed. Providing a complete implementation of the proposed solver (in Matlab and in C++), its performance is evaluated on various SPA model datasets, considering high levels of noise and realistic distri- bution of orientations of scanning angles. Comparison to other regularization methods, including the ART method traditionally used in SPA,...

La particule de reconnaissance du signal (signal recognition particle-SRP) et son récepteur (FtsY chez Escherichia coli) médiatise le processus simultané de traduction-ciblage de la protéine en dirigeant le complexe ribosome-nascent chain (RNCs) vers la membrane de destination. La reconnaissance par la SRP d'une charge RNC à transporter dépend de la présence de la partie N-terminale. L'assemblage de Ftsy au complexe RNC-PRS entraine plusieurs changements de configuration de SRP et de FtsY durant le cycle de direction. D'abord un stade « précoce » sans GTP est adopté. Celui-ci est stabilisé par le RNC. Ensuite une configuration « fermée » avec GTP est formée. Cette dernière peut s'activer pour hydrolyser GTP, elle entre alors dans sa configuration « active ». La succession de ces trois étapes conduit à la libération du complexe SRP-récepteur d'avec le ribosome et de sa protéine en cours de traduction, et leur mise à disposition au pore de la membrane. Dans ce projet, notre intérêt se limite à la traduction par le ribosome de la séquence signale EspP (RNCEspP). In vivo, EspP est une protéine dont le ciblage vers le récepteur membranaire se réalise après la traduction. Cependant il arrive que RNCEspP se lie au complexe SRP-FtsY, faisant échouer le ciblage. Nous avons étudié les bases structurales du rejet de RNCEspP par SRP et FtsY. Pour cela nous avons effectué la comparaison de la structure RNCEspP-SRP-FtsY obtenue par observation au cryo-microscope électronique avec d'autres complexes ribosome-SRP-récepteurs traduisant la charge FtsQ, qui est elle normalement ciblé par SRP. Nous avons cherché à observer la différence de structure entre les complexes SRP-FtsY dans les deux cas. Deux différences majeurs entre les complexes de ciblages contenants les séquences RNCFtsQ et RNCEspP ont été observés. Premièrement, dans le cas de la structure de RNCEspP le domaine M -Ffh est attaché à l'hélice 59 du ribosome, alors que celui-ci est détaché dans le cas de la structure de RNCFtsQ. Nous pensons que le domaine M empêche la libération de la séquence de signal, étape nécessaire à la réalisation du ciblage. Deuxièmement, dans le cas de la structure du complexe avec RNCEspP l'arrangement Ffh-FtsY avec le domaine NG était flexible. Ceci indiquerait que le complexe “précoce” formé sur RNCEspP est moins stable que celui formé sur RNCFtsQ. Une étude biochimique utilisant le transfert d'énergie via résonance fluorescente a corroboré ce résultat, montrant que FTS Y est lié avec une affinité moindre dans le cas du complexe précoce formé sur RNCEspP et que la reconfiguration au stade de complexe fermé est moins efficace. Une analyse biochimique plus poussée des variantes de la séquence de EspP montre que la partie N-Terminale de la séquence est la principale cause de rejet du cycle de ciblage via SRP.Dans un second projet, nous avons étudié la configuration “fermée” de SRP et ftsY en complexe avec une charge RNC stabilisée par un analogue non-hydrolysable de GTP (GMP-PCP). Pour franchir la barrière cinétique qui permet de passer du complexe précoce au complexe fermé, nous avons utilisé une version tronquée de FtsY, à laquelle la séquence terminale avait été amputée de tout le domaine acide (A-) ainsi que de la première hélice alpha du domaine NG. De plus, pour la formation du complexe, nous avons utilisé une construction contenant les 50 premiers acides aminés du leader peptidase (RNCLep50). En l'absence de nucléotides, notre reconstruction au cryo-EM a montré une configuration similaire à celle du stade précoce, dans laquelle Ftsy et Ffh- domaine NG, sont proche du tetraloop de la 4.5 S ARN. Une incubation avec GMP-PCP induit un détachement du domaine NG d'avec la queue du tetraloop. Il semblerait que les domaines NG soient flexibles dans l'état clos, et non attaché à la terminaison ouverte de l'ARN. / The signal recognition particle (SRP) and its receptor (FtsY in Escherichia coli) mediate co-translational protein targeting by delivering ribosome nascent chain complexes (RNCs) to the target membrane. Recognition of an RNC cargo by SRP is dependent on an N-terminal signal sequence. Binding of FtsY to the RNC-SRP complex leads to several conformational changes of SRP and FtsY during the targeting cycle: first, an “early” GTP-independent state is adopted which is stabilized by the RNC, subsequently a “closed” GTP- dependent conformation is formed which can activate itself to hydrolyze GTP (the “activated” state). Faithful completion of all three steps leads to release of the cargo from SRP-FtsY and hand over of the RNC to the translocation pore.It has been shown for E. coli that cargos can be rejected from the SRP pathway during all targeting steps. In the first project, our interest concentrates on ribosomes translating the EspP signal sequence (RNCEspP). In vivo, EspP is a post-translationally targeted protein, but RNCEspP has been shown to be bound by SRP and FtsY leading to a non-productive “early”-like RNCEspP-SRP-FtsY complex. Using single particle cryo-electron microscopy (EM), we analysed the structural basis for the rejection of RNCEspP by SRP and FtsY. Comparison of our RNCEspP-SRP-FtsY cryo-EM structure to other available cryo-EM structures of co-translational targeting complexes containing the correct cargo RNCFtsQ unravelled differences in the SRP-FtsY structure between a correct cargo and an incorrect cargo. Two major differences between the targeting complexes containing the cargos RNCFtsQ and RNCEspP were observed: first, the Ffh M-domain was attached to ribosomal RNA helix 59 of RNCEspP, while it was detached from this site in the case of RNCFtsQ. It could be that such an ordered M-domain is hampering the release of the signal sequence which is required for successful completion of targeting. Second, the Ffh-FtsY NG-domain arrangement was flexible in the complex with RNCEspP in comparison to RNCFtsQ indicating that the "early"-like complex formed on RNCEspP is less stable. Biochemical data using fluorescence resonance energy transfer corroborated these results, showing that FtsY is bound with lower affinity in the RNCEspP “early” complex and that the rearrangement to the “closed” conformation is less efficient. Further biochemical analysis of EspP signal sequence variants showed that mainly the N-terminal extension of the EspP signal sequence is responsible for its rejection from the SRP pathway.

Le carbone-suie, ou “black carbon” (BC), contribue au réchauffement climatique avec un forçage positif de l’ordre de +1.1 W m-2 dont l’incertitude reste haute (de l’ordre de 90%). Ce forçage s’effectue à travers l’interaction aérosol-radiation et l’interaction aérosols-nuage. Ces deux mécanismes sont affectés par le degré de mélange des particules du BC avec divers matériaux non-réfractaires et non-absorbants. Cependant, les estimations du forçage radiatif considèrent rarement les effets du mélange interne. Par ailleurs le rôle du BC comme noyau glaçogène qui influence l’interaction aérosol-nuage est largement inconnu. L’objectif de cette thèse est de mieux comprendre les mécanismes par lesquels le degré de mélange interne du BC influence la variabilité des propriétés optiques du BC et les propriétés d’activation des noyaux glaçogènes contenant du BC.Dans le premier chapitre de cette thèse, nous avons exploré la variabilité spatiale et saisonnière du coefficient d’absorption massique -mass absorption cross-section (MAC)- dans l’atmosphère en Europe. Les valeurs de MAC sont déterminées à partir de concentrations de carbone élémentaire et de coefficients d’absorption observée à différentes stations d’observation européenne du réseau ACTRIS (Aerosol, Cloud and Trace gases Research InfraStructure). Les résultats montrent une faible variabilité spatiale du MAC avec une moyenne de 10 ± 2.5 m2 g-1 à 637 nm de longueur d’onde qui peut être considérée comme représentative du BC en Europe. Le cycle saisonnier du MAC est probablement lié à la composition chimique de l’aérosol et son état de mélange, qui provoque une augmentation du MAC.Dans le second chapitre on s’est intéressé au lien entre l’absorption du BC et son état de mélange après transport sur longue-distance. Ce travail se base sur des mesures effectuées dans le cadre du projet CLIMSLIP (CLimate IMpact of Short-Lived Pollutants and methane in the Arctic). Une campagne de mesure a été conduite sur la station de recherche Zeppelin au Svalbard, Norvège en Avril 2012. Les données acquises avec un Single Particle Soot Photometer (SP2) révélaient que le BC est généralement présent en mélange interne dont l’épaisseur moyenne de la couche superficielle de matériel non-absorbant est de 47 nm pour des particules de BC de diamètre compris entre 170 et 280 nm. Ce mélange interne conduit à une augmentation d’absorption de 46%. Elle entraîne cependant une diminution relativement faible de l’albédo de simple diffusion, de l’ordre de 1%.Enfin, la capacité du BC à agir comme noyaux glaçogène pour la formation de cristaux de glace a été étudiée sur le site de haute altitude du Jungfraujoch (Suisse) dans le cadre du “cloud and aerosol characterization experiment” (CLACE) en 2013. Les différents éléments du nuage étaient séparé à partir d’une prise d’entrée type ice-CVI connectée au SP2. Ce dispositif permet de sélectionner uniquement les cristaux de glace et quantifier la fraction de BC activée. Une réduction de la présence de BC dans les résidus de glace a été observée. Des mesures de l’épaisseur de la couche de mélange interne des particules contentant du BC ont montré que les résidus de cristaux de glace présentaient des enrobages bien plus épais comparée à l’aérosol total.Les résultats obtenus au cours de ce travail ont permis de mieux comprendre l’impact du degré de mélange interne sur les propriétés optiques du BC et sur son rôle dans la formation de cristaux de glace. Les propriétés optiques du BC évoluent en fonction de la saison, tandis que la formation d’une couche superficielle amplifie sa capacité d’absorption du rayonnement solaire. De plus, cette étude souligne l’importance du vieillissement atmosphérique du BC sur sa capacité à servir de noyau de nucléation de la glace. Enfin, il fournit une avancée au sujet des propriétés sensibles mesurées dans l’atmosphère avec des techniques innovantes qui permettront la simulation plus précise du forçage radiatif. / Black carbon (BC) induces a warming effect (RFBC = +1.1 W m-2 ± 90%) through two main pathways: aerosol-radiation interaction (RFari) and aerosol-cloud interaction (RFaci). Both BC-radiation and BC-cloud interaction are affected by the mixing of black carbon with other non-refractory and non-absorbing matter present in the atmosphere. An estimation of the global radiative forcing of BC rarely accounts for internal mixing of BC while the net global cloud radiative forcing is sensitive to assumptions in the initiation of cloud glaciation, which is mostly unknown for black carbon particles. Within this thesis we investigated the variability of the light absorbing properties of black carbon, the mixing of black carbon, and the impact on light absorption and ice activation.In the first part of this thesis we investigated the spatial and seasonal variability of the mass absorption cross section (MAC) over Europe. MAC values were determined from ambient observations of elemental carbon mass concentrations (mEC) and absorption coefficients (σap). The data had been acquired during several years at different background ACTRIS supersites spread over Europe. Site specific MAC values were found to be spatially homogeneous, suggesting that the overall MAC average 9.5 ± 1.9 m2 g-1 at a wavelength of 637 nm might be representative of BC at European background locations. The MAC values showed a distinct seasonal cycle at every station. This seasonality might be related to chemical composition and aging. We observed that the MAC value has a linear and positive proportionality with the non-absorbing matter mass fraction.The second part of the work focuses on the coating acquisition of BC and the induced absorption enhancement after long-range transport. Within the CLIMSLIP (climate impact of short-lived pollutants and methane in the Arctic) project field experiments were conducted at the Zeppelin research site in Svalbard, Norway, during the Arctic spring. SP2 data were used to characterize the BC size distribution and mixing. BC containing particles having a core diameter between 170 and 280 nm were found to have a median coating thickness of 47 nm. The relationship between coating thickness and BC absorption was simulated. The observed coating thickness enhanced the mass absorption cross section by 46%, which led to a decrease of less than 1% in the single scattering albedo.In the final part of this work, the role of black carbon as ice nuclei in mixed phase clouds was investigated at the high elevation measuring site Jungfraujoch (Switzerland) during the cloud and aerosol characterization experiment (CLACE) held in 2013. The ice-CVI inlet and a single particle soot photometer were used to select and quantify the ice activated BC particles. According to the observations, BC containing particles were depleted in the ice residuals. The activation efficiency showed a size dependency, with larger BC containing particles being activated more efficiently compared to smaller ones. Activated BC cores having a diameter between 170 and 240 nm showed a larger coating thickness (median = 53 nm) compared to the total aerosol (median = 16 nm).The results obtained in this thesis shed new light on the effect of the mixing state on the optical properties and cloud activation of black carbon particles. Absorbing properties of BC showed a distinct seasonal pattern, while aging was found to consistently increase its absorption behavior. However, black carbon was found not to act as ice nuclei in low tropospheric mixed-phase clouds, where the coating thickness might play a role in the activation efficiency. This work provides freshly determined physical properties derived from ambient observations that will improve the accuracy of future aerosol and cloud radiative forcing estimations.