Analysis of particle dynamics in the cellular environment: Methods and applications

Research output: Types of ThesisDoctoral ThesisInternal

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Abstract

The advancements in fluorescent microscopy techniques have facilitated our comprehension of the dynamic processes that govern the cellular environment. Specifically, single-particle tracking has allowed us to investigate, in real-time, the movement of individual fluorescently-labeled particles within the cell. Within the scope of this thesis, I studied the dynamics of nuclear proteins and chromatin loci within the intricate environment of the cell nucleus. To achieve this objective, I applied fundamental principles of physics and developed innovative computer-based methodologies. Chapter 2 presents the results of an international competition addressing challenges in particle dynamics. Chapter 3 focuses on the precise measurement of motion parameters, addressing substrate drift bias (part A) and comparing the measurement error of the anomalous exponent using different methods (part B). Chapter 4 introduces two deep neural networks for trajectory segmentation. This includes a supervised method developed as a software tool (part A) and an experimental unsupervised method that adapted the “noise2noise” image denoising technique to single-particle tracking data (part B). Finally, Chapter 5 presents a comprehensive combination of multiple methods and analytical techniques aimed at precisely studying the dynamics of the Androgen receptor within the cell nucleus and in proximity to endogenous genes.
Original languageEnglish
Awarding Institution
  • Erasmus University Rotterdam
Supervisors/Advisors
  • Huylebroeck, Danny, Supervisor
  • Smal, Ihor, Co-supervisor
Award date10 Apr 2024
Place of PublicationRotterdam
Publication statusPublished - 10 Apr 2024

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