New paper on morphometric analysis of the amphioxus notochord

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.

It was a lot of fun to work on that project together with Andrews from the group of Elia Benito-Gutiérrez from the Zoology department of Cambridge University.

New Paper – Continuum theory of bacterial aggregates

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).

I am happy that I could contribute to this project and want to thank the amazing Hui-Shun Kuan and Vasily Zaburdaev and Frank Jülicher for the great collaboration.

I am looking forward to see how this innovative tool can be used to learn more about bacterial colonies and their mechanics.

New Review article – Of Cell Shapes and Motion

My first publication with the Paluch lab is out since today!

It is a review about how cell shape and cell motion are linked to each other with a big focus on how shapes can be quantified. The link to the review can be found here:

Bodor, D.L., Pönisch, W., Endres, R.G. , Paluch, E.K. Of Cell Shapes and Motion: The Physical Basis of Animal Cell Migration. Developmental Cell 52:5 (2020).

Big thanks to Dani and Ewa to let me contribute to this work.

Moving to the University of Cambridge

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.

Interesting times lie ahead…

Paper on bacterial substrate motility is out!

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!

sketch_mechanism

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.

The paper can be found here: Pönisch, W., Weber, C.A. and Zaburdaev, V. Phys. Rev. E 99, 042419 (2019). The arxiv version can be found here: arxiv

This project has been one of my favorites in the last three years and I hope people will enjoy reading it.

New paper published on internal dynamics of bacterial 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.

flowRoot4366-9

New preprint on bacterial motility

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!

02stochmodel.png

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).

New paper on how to measure the diffusivity of single cells within moving aggregates

Together with Vasily Zaburdaev, we have developed a simple technique to characterize the motility of particles within aggregates, independent of any translational or rotational motion of the aggregate.

bitmap

The paper is published in the Topical issue “Continuous Time Random Walk Still Trendy: Fifty-year History, Current State and Outlook” of the European Journal of Physics B.
Pönisch, W. & Zaburdaev, V. Eur. Phys. J. B (2018) 91: 27.