The role of 3D nanoscale organization on key cellular processes

• Thesis title in Czech: Vliv 3D organizace na nanometrové škále na klíčové buněčné procesy
• Thesis title in English: The role of 3D nanoscale organization on key cellular processes
• Key words: 3D ultrastruktura, morfologie, invadopodia, chromatin, membrány, elektronová mikroskopie, CLEM
• English key words: 3D-ultrastructure, morphology, invadopodia, chromatin, membranes, electron microscopy, CLEM
• Academic year of topic announcement: 2021/2022
• Thesis type: dissertation
• Thesis language: angličtina
• Department: Department of Genetics and Microbiology (31-140)
• Supervisor: Mgr. Aleš Benda, Ph.D.
• Author: hidden - assigned by the advisor
• Date of registration: 11.10.2021
• Date of assignment: 11.10.2021
• Advisors: Mgr. Marek Cebecauer, Ph.D.

Preliminary scope of work

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Preliminary scope of work in English

The effectivity of most cellular processes is closely related to their spatial organization in a cell, their 3D ultrastructure. Therefore, to understand the principles of a specific cellular process, it is not enough to determine the key players (e.g., preotein, nucleic acids, lipids, …), but it is crucial to visualize the 3D spatial organization, and potential heterogeneity, which can hugely impact the overall effectivity or output.
The aim of this project is to correlate function and 3D-ultrastructure for selected biological processes by mainly employing correlative 3D light and electron microscopy complemented with subject-specific functional assays. More specifically, the first goal is to contribute to unravelling the role of cancer cell invadopodia during cell invasion using model 3D systems, the second goal is to characterize changes of cell surface morphology caused by different sample preparation methods for imaging and the third goal is 3D volume quantification of the chromatin arrangement in mammalian cells at various stages of cell cycle.
The work will include intense usage of advanced microscopy techniques, especially FIB-SEM, TEM-tomography, confocal, two-photon and super-resolution microscopy and 3D label free holotomography. A key part will be image data processing, including, but not limited to, denoising and deconvolution, image registration, segmentation, volumetric analysis and more.