Our new paper on notochord development in amphioxus has now been published in Development!!!
First-author Toby did some impressive job in segmenting all the cells, giving us a perfect playground to do a thorough morphometric analysis of an in vivo system! That allowed us to investigate the complete range of cell shapes and how it depends on the developmental stage of the tissue. Additionally, by performing a pseudotime analysis, a tool commonly used to study RNAseq data, we could identify developmental gradients in the amphioxus notochord.
Until now, models of how bacterial colonies form by active appendages, so called type IV pili, were typically agent-based, see. for example here.
In this brand new paper, published today in PRL, we developed a continuum model of dense bacterial aggregates.
The model describes the process of aggregate formation of bacterial cells as an active phase separation phenomenon. We then study the coalescence behaviour of two colonies, a system we also studied before experimentally and with an agent based model (here).
The group of Ewa Paluch, my postdoc supervisor, is now reaching the hot phase to move to Cambridge and since May 1st I am an official Research Associate at the Department of Physiology, Development and Neuroscience.
I am also extremely grateful to have been awarded the Herchel Smith Postdoctoral Fellowship of the University of Cambridge, supporting me in my research on the crosstalk of cell shape and state for the coming three years.
I am very happy to announce that our paper on how bacteria use type IV pili to move over a substrate is published in PRE!
We find that a tug-of-war mechanism alone is able to explain the persistent motion of bacteria without including any directional memory. In our work, we also predict that substrate friction might play a major role during the motility of cell aggregates.
Finally, our work on how cells move within bacterial colonies forming due to type IV pili is published in Scientific Reports. Identical cells of a colony are more motile at the surface of the colony than in the bulk. With the help of theoretical modelling, we find that this behavior emerges due to a gradient in the pili dynamics and the resulting forces. We also discover that the gradient of cell motility and forces correlate with a gene expression gradient, pointing towards early differentiation. Thanks to the Nicolas Biais lab and the Zaburdaev group.
Together with Christoph Weber and Vasily Zaburdaev, we published a new preprint in which we develop a stochastic model to study the substrate motility of bacteria and bacterial aggregates. We show that a previously observed persistent motility of Neisseria gonorrhoeae cells originates from a tug-of-war mechanism without any directional memory. We also find that sliding friction has a big impact on the motility of microcolonies!
Here is the link: Pönisch, W., Weber. C.A., Zaburdaev, V. N. How bacterial cells and colonies move on solid substrates arXiv Preprint 1–24 (2018).
Our paper describing a theoretical model of how bacteria use pili to form colonies and to move on substrates has been selected by the editors of the New Journal of Physics to be included in the collection Highlights of 2017. Thanks to all my co-authors!