Observing processes in cells: Software solution accelerates cell observations
Long and intensive exposure to UV radiation, for example from the sun, can lead to mutations in the DNA - a starting point for cancer. The body has a mechanism to counteract this. If the DNA is damaged, molecules are activated that quickly repair the DNA - preferably before the cell divides and the damage is passed on," says Dr Koen Martens from the Institute of Microbiology and Biotechnology at the University of Bonn. However, how exactly cell repair works is not yet fully understood. Koen Martens now wants to find out. One difficulty here is tracking individual molecules precisely.
„In ‚single particle tracking‘ we mark the molecule with fluorescent light, a kind of incandescent lamp“, explains Koen Martens. „A high-resolution microscope is then used to take a hundred photos per second. The ‚light bulb‘ illuminates the molecule in the dark surroundings of the cell so that we can observe it and track its movement over time. This allows us to measure their diffusion and interactions with other cell components. By measuring the distances between the molecules and the distances of one molecule from one photo to the next, the researchers can tell whether the particles are moving freely in the cell or interacting with other molecules. In terms of DNA repair, this can be used to determine when the enzymes repair - and therefore interact with the DNA.Software accelerates tracking
„It is difficult to track several molecules at the same time. If their paths cross or they are too close to each other, two bulbs become a single bulb. Then it is impossible to determine their movements“, says Martens. Until now, microbiologists had to analyse one molecule at a time. A time-consuming process – too long to observe the DNA repair molecules „in action“: Until now, ‚single particle tracking‘ took longer than the process of repair itself. Now scientists at the University of Bonn have developed software that speeds up the high-throughput process. TARDIS (short for: Temporal analysis of relative distances) performs an all-to-all distance analysis between localisations - i.e. the points where the molecule is located in the individual images - with increasing temporal shifts. Instead of focussing on individual points as before, it looks at the entire sequence of movements in the cell. In this way, all molecules are analysed simultaneously.
„With the help of TARDIS, measurements are at least five times shorter without any loss of information,says Martens happily. The scientist now wants to use TARDIS to investigate the processes involved in DNA repair. „I am particularly interested in investigating how easy or difficult it is to repair certain types of damage and how badly damaged the DNA is by certain UV radiation or chemicals.“
Promotion
The work was funded by the Alexander von Humboldt Foundation, Carnegie Mellon University, the Argelander Programme for Young Scientists of the University of Bonn, the VLAG PhD Fellowship of the Wageningen Graduate School and the National Science Foundation.
Original publication:
Koen J.A. Martens, Bartosz Turkowyd, Johannes Hohlbein and Ulrike Endesfelder: Temporal analysis of relative distances (TARDIS) is a robust, parameter-free alternative to single-particle tracking. Nature Methods. DOI: 10.1038/s41592-023-02149-7
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