3D microscopy of swimming worms

Summary

The microscopic roundworm Caenorhabditis elegans is long and thin, and moves by undulating its body. While its locomotion behaviours have been characterized in detail on the surface of a dish, little is known about its locomotion in more natural habitats. In the Cohen lab, we have been recording the motion of the animal in 3D volumes. We have collected about 20TB of video data (primarily from healthy wild type animals, across a range of fluid environments) and have in place a data analysis pipeline for the 3D reconstruction of body postures and coordinates over time. In this project, you will compare behaviours, postures and muscle activation patterns in different media, and across different genetic strains. Specific topics will be chosen from the scope and remit of the project, but tailored to individual interests and skills.

In this project, we are interested in comparing behaviours, postures and muscle activation patterns in different media, and across different genetic strains. Specific topics will be chosen from the scope and remit of the project, but tailored to individual interests and skills.

Experimentally focused projects are likely to combine:

• Worm maintenance and scope for molecular biology and genetic manipulation of the worm
• Behavioural assays, bright field and/or fluorescent imaging and optogenetic experiments
• Extensive data handling and use of computer vision algorithms for image/video analysis (in particular 3D spatiotemporal reconstructions)

Background

This studentship forms part of a larger collaborative and interdisciplinary project, that currently includes two academics (Thomas Ranner and Netta Cohen), two postdoctoral fellows and three PhD students. We study the neuromechanical basis of behaviour in the nematode worm C. elegans. Research combines biological experiments, mathematical and computational modelling of the neural control as well as investigations of the physics of the worm and its interaction with the environment. We are seeking to appoint up to four further PhD candidates focusing on the undulatory motion of this worm: one project on the mathematical understanding of numerical methods for biomechanical models (with Thomas Ranner), one on modelling the neural control of locomotion (with Netta Cohen), one experimental project, combining behavioural experiments and machine vision (with Netta Cohen) and one exploring the dynamics of the worm’s behaviour (with Netta Cohen). All projects are envisioned within this multidisciplinary setting. You will join a multi-disciplinary, dynamic, and creative group within the School of Computing at the University of Leeds, with close ties to the Fluid Dynamics Centre for Doctoral Training, the Hope Laboratory and the van Oosten-Hawle Laboratory in the Faculty of Biological Sciences, where additional biological experimental facilities are housed. Informal enquires are welcome from all potential candidates.

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