Reinhart, Marius Armin (2016)
Replicons: functional elementary units of genome architecture.
Technische Universität Darmstadt
Ph.D. Thesis, Primary publication
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Item Type: | Ph.D. Thesis | ||||
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Type of entry: | Primary publication | ||||
Title: | Replicons: functional elementary units of genome architecture | ||||
Language: | English | ||||
Referees: | Cardoso, Prof. Dr. M. Cristina ; Drossel, Prof. Dr. Barbara | ||||
Date: | 28 September 2016 | ||||
Place of Publication: | Darmstadt | ||||
Date of oral examination: | 24 November 2016 | ||||
Abstract: | Only 750 years after Roger Bacon developed the first simple microscope, super-resolution microscopy is in full swing, letting us go where no one has gone before: beyond the Abbe limit. A perfect dance performance is needed as thousands of replisomes dance around the DNA during the Synthesis-Phase, for even a single error could lead to cell death or cancer. To gain an understanding of the choreography and the complex regulations necessary to maintain this highly dynamic process without a misstep, I employed recent advancements in microscopy. Due to improvements made in the last decade, it is now possible to take a closer look at the individual participants of DNA replication, the replisomes. My aim was to dive into the depth of DNA replication dynamics to detect, analyze and quantify DNA replication on the level of single replication machineries (replisomes). Up until now imaging with high temporal resolution could only be achieved by live cell microscopy, trading spatial resolution against temporal resolution and photobleaching. I laid a solid foundation for my DNA replication studies by refining a cell staining method using "pulse and chase" experiments to gain temporal resolution in single fixed cells. This approach allows the study of highly dynamic DNA synthesis processes with the high spatial resolution achievable in fixed cells. For the statistical evaluation of this multi-label super-resolution data, I designed a computer guided approach to quantify thousands of replication foci in hundred of cells with a minimal amount of operator interaction. This program is a robust tool to quantify DNA replication foci free of observer bias and achieves consistent quantifications during biological and technical replicates. The application of the newly developed foci recognition toolkit enabled me to resolve and quantify DNA replication foci formerly lost in the mist of wide field or even confocal imaging. The DNA replication foci quantification matched beautifully with the calculated numbers by Mills et al. and Hozák et al., indicating the ability to finally resolve DNA replication on the replisome level. This was further confirmed by DNA fiber measurements of DNA replication fork speed (RFS), inter origin distances (IODs), genome size analysis and DNA replication (S-Phase) timing. To dig even deeper into the highly dynamic DNA replication processes, a simplistic computer model was created to simulate DNA synthesis in silico. Using the aquired biological data, I was able to correlate simulated in silico microscopy images from this 1D replication model to live cell microscopy in 4D. Altogether I was able to answer basic questions regarding the control of DNA replication on the level of individual replisomes. I resolved and quantified individual replisomes and utilized those measurements to cogenerate a theoretical DNA replication simulation model. |
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Uncontrolled Keywords: | DNA Replication, replicon, replisome, simulation, super resolution, microscopy, domino | ||||
URN: | urn:nbn:de:tuda-tuprints-58660 | ||||
Classification DDC: | 500 Science and mathematics > 570 Life sciences, biology | ||||
Divisions: | 10 Department of Biology 10 Department of Biology > Cell Biology and Epigenetics |
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Date Deposited: | 19 Dec 2016 13:17 | ||||
Last Modified: | 08 Jan 2021 13:29 | ||||
URI: | https://tuprints.ulb.tu-darmstadt.de/id/eprint/5866 | ||||
PPN: | 396999298 | ||||
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