10.1.1.167.3387

10.1.1.167.3387 - Quantitative Microscopic Techniques for...

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Unformatted text preview: Quantitative Microscopic Techniques for Monitoring Dynamic Processes in Microarrays Proefschrift ter verkrijging van de graad van doctor aan de Technische Universiteit Delft, op gezag van de Rector Magnificus prof. dr. ir. J.T. Fokkema, voorzitter van het College voor Promoties, in het openbaar te verdedigen op 12 maart 2002 om 13:30 uur door Lennert Richard VAN DEN DOEL natuurkundig ingenieur geboren te Vlissingen. Dit proefschrift is goedgekeurd door de promotoren Prof. dr. ir. L.J. van Vliet, Prof. dr. I.T. Young Samenstelling promotiecommissie: Rector Magnificus, voorzitter Prof. dr. ir. L.J. van Vliet Technische Universiteit Delft, promotor Prof. dr. I.T. Young Technische Universiteit Delft, promotor Prof. dr. ir. J.J.M. Braat Technische Universiteit Delft Prof. dr. G.W.K. van Dedem Technische Universiteit Delft Prof. dr. T.W.J. Gadella Universiteit van Amsterdam Prof. dr. J. Greve Universiteit Twente Prof. dr. J.G. Korvink Albert Ludwig University Freiburg, Duitsland Advanced School for Computing and Imaging This work was carried out in the ASCI graduate school. ASCI dissertation series number 75. ISBN 90-77017-48-8 c 2002, L.R. van den Doel, all rights reserved. You play, you win. You play, you lose. YOU PLAY. —Jeanette Winterson, The Passion Voor Thomas & Jolanda Voor Rosanne, fonkelende ster, mijn kleine engel —R Contents 1 Labs-on-a-chip 1 1.1 Combinatorial Chemistry 1 1.2 Human Genome Project 2 1.3 Intelligent Molecular Diagnostic Systems 2 1.4 Development of a Microarray reader 4 1.5 Outline of this thesis 5 Part I Quantitative Reading of Microarrays 2 Yeast as a Cell Factory: the Glycolytic Pathway 9 2.1 Yeast: Saccharomyces cerevisiae 9 2.2 The Glycolytic Pathway 11 2.3 Summary 13 3 Conventional Microscope-based Microarray Reader 15 3.1 Microarray Fabrication 15 3.2 Nanoliter Liquid Handling 17 3.3 Conventional Microscopy Concepts 19 3.3.1 Infinity-corrected Optical System 20 vii viii CONTENTS 3.3.2 K¨ohler Illumination 22 3.4 Characterization of the Princeton Versarray CCD camera 24 3.4.1 Readout noise 25 3.4.2 Dark current 27 3.4.3 Linearity and Sensitivity 29 3.5 Summary 33 4 Quantitative Reading of Microarrays 35 4.1 Limiting Factors of the Instrument 35 4.2 Detection Limit of the Microarray Reader 36 4.2.1 Improving the Detection Limit (for 1 and N measurements!) 38 4.3 Readout Noise Limited Detection 39 4.3.1 Ideal Detection System 39 4.3.2 Single Element Detection System with Readout Noise 40 4.3.3 Many Pixels Detection System with Readout Noise 42 4.4 Stray Light Limited Detection 43 4.5 Minimum Detectable Signal for Different Configurations 44 4.6 Modifications to the Microscope System 45 4.7 Conclusions and Discussion 48 5 Monitoring Enzyme-catalyzed Reactions in Microarrays 49 5.1 Imaging with the modified optical system. 49 5.2 NADH Calibration 50 5.3 Monitoring Enzyme-catalyzed reactions 54 5.4 Conclusions 64 Part II Monitoring Dynamic Liquid Behavior in Micromachined Vials 6 Dynamic Liquid Behavior in Micromachined Vials...
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10.1.1.167.3387 - Quantitative Microscopic Techniques for...

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