Studying fungal organisms can be challenging, and we need more versatile tools or protocols that could be easily transferred from one fungal
organism to another.
Link to the preprint www.biorxiv.org/content/10.6...
We mapped out a fundamental temporal trade-off: growing cells long enough to dilute out pre-existing target proteins, without waiting so long that escaper mutants take over the population. By doing so, we could pinpoint the time at which the physiological response to the knockdown is strongest
New preprint from our group! When we first started working with affordable, continuous-culture mini-bioreactors a few years ago, we realized they offered a unique solution for CRISPRi experiments, which rely on cell growth to dilute targeted proteins.
www.biorxiv.org/content/10.6...
Congratulations and a big thank you to Sam Bradley and Henry Webel for leading this project! I would also like to acknowledge Carlos G. Acevedo-Rocha, all our beta-testers at BRIGHT and Magnus Ganer Jespersen for preliminary work on algorithms for turbidostat data analysis
In particular, AutoGrowth provides robust algorithms to automate fitting of growth data from turbidostat (e.g. from Pioreactors, Chi.Bio etc.) and/or adaptive laboratory evolution experiments
In this work, spearheaded by Mariana, we
✅ Constructed and validated a robust CRISPRi system in the bacterium Pseudomonas putida
✅ Tested this system by targeting essential genes in continuous-growth experiments, backed by a thorough time-course multi-omics characterization
Happy to share our brand-new toolset for growth data analysis! This includes a python package and two apps for the analysis of data from plate readers (MicroGrowth) and mini-bioreactors (AutoGrowth). Everything is free and open-source. Link to the apps: biosustain.github.io/growthcurves...
