Department Bionanoscience
Principal investigator Marianne Bauer
E-mail address m.s.bauer@tudelft.nl
Website https://sites.google.com/view/bauergroup/home
How well do chlamydomonas respond to light?
Supervisor: Marianne Bauer, m.s.bauer@tudelft.nl
Chlamydomonas are unicellular algae organisms that require light for photosynthesis. They sense blue light through an eyespot, and move towards it in a process called phototaxis. The goal of this project is to understand better how well chlamy respond to particular light intensities, when this response is optimal, and when at which point they start to avoid the light. This project is a mix of experiments and theory: in the experimental part of the project, you will grow chlamy in the lab and image their phototactic trajectory on the level of individual cells. You will then track these trajectories, and analyze their their motion toward the light spot (speed, direction, efficiency). You will then compare the optimality of this trajectory to optimal bounds and limits for chemotaxis; you will calculate how (well) chlamy decode particular light intensities, and, in particular, how they respond when a change in light intensity or gradient is offered.
Understanding this is in the long term important for estimating how photosynthetic organisms may respond to a changing climate.
Techniques
- Experimental (wet lab, chlamy growing and tracking) & theoretical (data analysis, statistical physics, probability distributions)
Signal responses in sunflower plants
Supervisor: Merlijn Brüggen, merlijn.j.bruggen@gmail.com
We are proposing a theoretical Masters project to analyse traces of neuronal activity of a system of connected neurons in culture in comparison to mouse cortex. The aim of this project is to identify information- theoretical or statistical quantifiers that could serve as indicators for different experimental conditions. The long-term goal is to investigate if particular cells within the same culture, between different cultures or compared to the cortex are uniquely recognizable, and if they can be assigned correctly to their environment. (This project is together with the Daan Brinks Lab.)
Techniques
- Numerics/computation
- Statistical physics (Ising models)
- Entropy calculations (no previous knowledge required)
Inferring the actions of a fly wing enhancer with a small network
Supervisor: Merlijn Brüggen, merlijn.j.bruggen@gmail.com
The gene yellow in fruit flies patterns the fly wing. Its gene expression is achieved because two transcription factors, which each also are expressed in patterns on the fly wing, bind to a small enhancer with ca 5 binding sites. The Gompel lab (Bonn) has performed systematic mutations on this enhancer. The goal of this project is to build on previous work to develop a minimal neuronal network and find the smallest, most interpretable network possible that can give rise to this enhancer. In addition to training this network, you will use information and entropic quantities to evaluate whether the pattern in yellow is exclusively determined by these two inputs, and how the patterning can be understood.
Techniques
- small ML network
Further reading
Regulatory encoding of quantitative variation in spatial activity of a Drosophila enhancer
Clustering of transcription factors and noise at promoters
Supervisor: Aimée Kok, A.R.Kok@tudelft.nl
Much information-theoretical work in our group has focused on whether clustering of transcription factors at binding sites improves or makes worse the impact of gene regulation. Here, we will try to understand how the noise at promoters influences gene regulation. The project has two direction, and can either go into kinetic modelling of a gene regulatory network in the context of synthetic cell development. Alternatively, we can consider whether noise at the promoter affects our previous results on clustering being worse for gene regulation for long measurement times.
Techniques
- Theory/simulations: stochastic processes, differential equations
Information in Neuron trajectories
Supervisor: Olivier Witteveen, o.z.j.witteveen@tudelft.nl
We are proposing a theoretical Masters project to analyse traces of neuronal activity of a system of connected neurons in culture in comparison to mouse cortex. The aim of this project is to identify information- theoretical or statistical quantifiers that could serve as indicators for different experimental conditions. The long-term goal is to investigate if particular cells within the same culture, between different cultures or compared to the cortex are uniquely recognizable, and if they can be assigned correctly to their environment.
Techniques
- Theory: Information theory, clustering, stochastic processes