Nanostructures fabricated by different methods have become increasingly important for various applications at the cellular level. In order to understand how these nanostructures “behave” and for studying their internalization kinetics, several attempts have been made at tagging and investigating their interaction with living cells. In this study, magnetic iron nanowires with an iron oxide layer are coated with (3-Aminopropyl)triethoxysilane (APTES), and subsequently labeled with a fluorogenic pH-dependent dye pHrodo™ Red, covalently bound to the aminosilane surface. Time-lapse live imaging of human colon carcinoma HCT 116 cells interacting with the labeled iron nanowires is performed for 24 hours. As the pHrodo™ Red conjugated nanowires are non-fluorescent outside the cells but fluoresce brightly inside, internalized nanowires are distinguished from non-internalized ones and their behavior inside the cells can be tracked for the respective time length. A machine learning-based computational framework dedicated to automatic analysis of live cell imaging data, Cell Cognition, is adapted and used to classify cells with internalized and non-internalized nanowires and subsequently determine the uptake percentage by cells at different time points. An uptake of 85 % by HCT 116 cells is observed after 24 hours incubation at NW-to-cell ratios of 200. While the approach of using pHrodo™ Red for internalization studies is not novel in the literature, this study reports for the first time the utilization of a machine-learning based time-resolved automatic analysis pipeline for quantification of nanowire uptake by cells. This pipeline has also been used for comparison studies with nickel nanowires coated with APTES and labeled with pHrodo™ Red, and another cell line derived from the cervix carcinoma, HeLa. It has thus the potential to be used for studying the interaction of different types of nanostructures with potentially any live cell types.

京都大学 / 0048 / 新制・課程博士 / 博士(工学) / 甲第18303号 / 工博第3895号 / 新制||工||1598(附属図書館) / 31161 / 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 森 泰生, 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

Understanding molecular interactions at the surfaces of cellular membranes, including adsorption and transport, is of fundamental importance in both biological and pharmaceutical studies. At present, particularly with respect to small and medium size (drug-like) molecules, it is desirable to gain an understanding of the mechanisms that govern membrane adsorption and transport. To characterize drug-membrane interactions and mechanisms governing the process of molecular uptake at cellular membranes in living organisms, we need to develop effective experimental techniques to reach quantitative and time-resolved analysis of molecules at the membrane surfaces. Also, we preferably want to develop label-free optical techniques suited for single-cell and live cell analysis. Here, I discuss the nonlinear optical technique, second-harmonic light scattering (SHS), for studying molecule-membrane interactions and transport of molecules at the membrane of living cells with real-time resolution and membrane surface-specificity. Time-resolved SHS can quantify adsorption and transport of molecules, with specific nonlinear optical properties, at living organisms without imposing any mechanical stress onto the membrane. This label-free and surface-sensitive technique can even differentiate molecular transport at individual membranes within a multi-membrane cell (e.g., bacteria). In this dissertation, I present our current research and accomplishments in extending the capabilities of the SHS technique to study molecular uptake kinetics at the membranes of living cells, to monitor bacteria membrane integrity, to characterize the antibacterial mechanism-of-action of antibiotic compounds, to update the molecular mechanism of the Gram-stain protocol, to pixel-wise mapping of the membrane viscosity of the living cells, and to probe drug-induced activation of bacterial mechanosensitive channels in vitro. / Chemistry

Die Charakterisierung der Protein-Nanopartikel-Wechselwirkungen in komplexen biomolekularen Systemen wie einer lebenden Zelle ist für die Pharma-, Medizin- und Umweltforschung von entscheidender Bedeutung. In solchen biomolekularen Systemen adsorbieren Proteine leicht auf der Oberfläche von Nanopartikeln, die die Proteinkorona bilden. Diese Arbeit konzentriert sich auf die Charakterisierung der Proteinkorona in lebenden Zellen, wobei verschiedene analytische Ansätze kombiniert werden. Experimente mit oberflächenverstärkter Raman-Streuung (SERS) an reinen Proteinlösungen zeigten die Konzentrationsabhängigkeit der Protein-Gold-Nanopartikel-Wechselwirkungen, die zu unterschiedlichen SERS-Spektren führten und ermöglichten die Bestimmung von Proteinsegmenten, die an Citrat-stabilisierte Gold-Nanopartikel binden. In SERS-Experimenten mit lebenden Zellen wurde die Anwesenheit von Proteinfragmenten in der innersten Schicht der Proteinkorona, die als harte Proteinkorona bezeichnet wird, festgestellt. Eine analytische Methode, die Natriumdodecylsulfat-Polyacrylamid-Gelelektrophorese und Hochleistungs-Flüssigchromatographie-gekoppelte Elektrospray-Ionisations-Massenspektrometrie kombiniert, wurde entwickelt, um die Bestandteile der Hartproteinkorona zu identifizieren. Die Proteomics-, SERS- und Cryo-Soft-X-Ray-Nanotomographiedaten, wobei letztere Informationen über die dreidimensionale Ultrastruktur der Zelle liefern, zeigen den Aufnahmemechanismus, die Verarbeitung, die Akkumulationsstelle, die molekulare Umgebung und die induzierten zellulären Reaktionen internalisierter Goldnanopartikel. Diese Arbeit validiert die Verwendung von SERS bei der Analyse der Proteinkorona in der Lösung von Modellproteinen und in lebenden Zellen und präsentiert eine geeignete Methode zur Analyse der unveränderten harten Proteinkorona, die in lebenden Zellen gebildet wird. / The characterization of the protein-nanoparticle interactions in complex biomolecular systems such as a living cell is vital for pharmaceutical, medical, and environmental research fields. In such biomolecular systems, proteins readily adsorb on the surface of nanoparticles forming the protein corona. This thesis focuses on the characterization of the protein corona in living cells combining different analytical approaches. Surface-enhanced Raman scattering (SERS) experiments on pure protein solutions revealed the concentration dependence of the protein-gold nanoparticle interactions resulting in different SERS spectra, and allowed for the determination of protein segments binding to citrate-stabilized gold nanoparticles. In live cell SERS experiments, the presence of protein fragments in the innermost layer of the protein corona, called the hard protein corona, was revealed. An analytical method combining sodium dodecyl sulfate-polyacrylamide gel electrophoresis and high-performance liquid chromatography-coupled electrospray ionization mass spectrometry was developed to identify the constituents of the hard protein corona. The proteomics, SERS, and cryo soft X-ray nanotomography data, the latter providing information of the three dimensional ultrastructure of the cell, reveal the uptake mechanism, processing, accumulation site, molecular environment, and the induced cellular responses of internalized gold nanoparticles. This work validates the use of SERS in the analysis of the protein corona in the solution of model proteins and in living cells, and presents a suitable method for the analysis of the unaltered hard protein corona formed in living cells.