Cambridge Area Julia Users Network (CAJUN) Meeting (14th of September)

Torkel Loman will give a talk. The location will be "Seminar Room D463 (Star)" at the Stata Center at MIT (https://www.na-mic.org/wiki/Meeting_Locations:MIT_CSAIL_Star). We will start at 6pm, with the talks+questions taking roughly 1 hour (after which people are welcome to stay and socialise). Food will be provided. Any questions can be asked at the #boston-local channel at the Julia Slack.

If anyone knows someone who is interested, we have one speaker slot open.

Mixed positive/negative feedback loops in biological systems (Torkel Loman)
Alternative sigma factor circuits are ubiquitously used by bacteria to recognise and respond to environmental cues, such as stress. While there is great diversity in sigma factor network topology, two reoccurring motifs are sigma factor self-activation and anti-sigma factor mediated self-deactivation. By introducing a time delay and noise to such a mixed positive/negative feedback loop, we have created a minimal stochastic differential equation model of a general sigma factor circuit. We have characterised all possible response behaviours of our model, finding over 10 distinct classes. These include several behaviours previously identified among bacterial sigma factors, but also novel ones. Furthermore, we are able to show how these behaviours depend on a small number of system properties (model parameters), such as self-activation strength. This generates predictions of how the behaviours of such mixed positive-negative feedbacks can be modulated by tuning their parameters. Through single-cell fluorescent microscopy, we confirm that these predictions hold in the Sigma B network of Bacillus subtilis (one of the most well-studied sigma factor systems). Here, we used a mutated strain that permitted us to tune a system parameter, comparing the change in system behaviour to that of the model (as the parameter was changed). Finally, the general nature of our model allows it to be widely applied. Especially in synthetic biology, where sigma factors have been proposed as potential regulators of synthetic circuits, our model describes how a regulating circuit can be tuned to produce desired behaviours.