Infoscience

Thesis

Automated long-term single cell analysis of Schizosaccharomyces pombe on a microfluidic microchemostat array

How cells grow and divide is a question that was raised more than 100 years ago. Despite years of research and in-depth knowledge of several molecular mechanisms, the complete system that regulates and coordinates both of those activities within Schizosaccharomyces pombe is still unknown. A systemic approach might provide some help to decipher them. Fission yeast is one of the most actively used model organisms to study cell-cycle and cell growth. The first single-cell measurements of its growth profile were performed already in the nineteen-sforties. Despite the huge amount of studies performed, only very few methods were provided to scientists to investigate growth profiles. All the proposed approaches are highly time consuming and have technological drawbacks. Furthermore, they do not allow long-term imaging and are time-limited by their design. Recent advances in the microfluidic field allowed to design culture chambers that can achieve long-term and stable culturing of cells in a constant and tightly controlled environment. The surrounding cell growth conditions can be rapidly and easily changed over time. In this thesis, we aimed at coupling microfluidic devices with an automated microscope and an image analysis pipeline to record accurate and numerous growth profiles. Our platform allowed to handle tens of thousands of images and we could record more than 100’000 division events within a single fifty hour experiment. We automatically extracted data regarding basic physiological parameters such as cell size, time to divisions and elongation rate. Our complete analysis pipeline does not require any specific "marker" and relies exclusively on bright-field images. Using our platform, we characterized the evolution of several parameters regarding cell length and time to divisions during a temperature shift experiment in which cells were first grown at 30° followed by a transition to 25°. A similar experiment was performed in an upward transition from 30° to 33°. Cell length was nearly identical at the three temperatures, whereas time related parameters as well as elongation rate underwent changes. We quantified the distributions of each parameter at steady state and were able to detect transient size changes in respect to the single-cell growth phase when facing the transition. Indeed, an upshift of temperature induced an immediate division in cells that are less than halfway through their cell cycle resulting in a shortened cell length at divisions. In the opposite direction, a downshift of temperature delayed the beginning of the division process for cells that accomplished less than half of their cycle, leading to an increased cell length at division. Furthermore, those transient effects impacted the daughter cells (second generation) before the situation was back to normal in the third generation of cells. The involved temperature sensitive processes are highly correlated to the cell-cycle status of single-cells and despite the fact that our culture was unsynchronized it was possible to detect them precisely. Our platform is thus applicable to measure fine details of S.pombe cell-cycle dynamics and could be an interesting tool to help unravel the complex mechanisms maintaining cell homoeostasis. Basically, the study of any cell-cycle related processes that require accurate and numerous numbers of division events can be pushed forward with such a tool.

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