I should also say that we were ready to see much more variability between individual cells (which is also why we used this setup) but it simply turns out not to be the case… Analysed in detail in the article. Of course we needed to have single-cell resolution to be able to come to this conclusion.

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Yes, we're very interested in understanding how cells fuel this gene expression response during the first hours of starvation (which is related to ATP levels) and whether dis/aggregation plays an important role in this time window.…This is beyond the scope of this article though!

Interesting question… We have not tried LB, my sense is that the uniform response across cells depends more on the strain than on the media – we have (very) preliminary results indicating that it is a general feature in several natural isolates and media. Stay tuned!

And don't miss the "skeetorial" by @erikvannimwegen.bsky.social: bsky.app/profile/erik...

Here are the links to both articles:
doi.org/10.1038/s414...
doi.org/10.1126/scia...

cc @audreyproenca.bsky.social

Given that this is all in M9 media, using MG1655 (GCSC 6300), the main culprit is the difference in nutrients: 0.4% glucose + 0.2% casamino acids for the 2 published reports vs 0.2% glucose without casamino acids for our preprint. Should I put this in the amino acid supply? Any clue why, anyone? n/n

Whether with our much fancier estimation of instantaneous rates (see methods) or with Patange's rather "hacky" filters (used by Proenca too), we never see such pauses of growth nor the anti-correlated oscillations of growth and promoter activity during growth in our experiments 🤯 5/n

Theo Gervais and I measured instantaneous growth and gene expression for the bolA reporter (both on plasmid and on the chromosome) in the same genetic background. All described in details in doi.org/10.1101/2024..., although the manuscript does not touch this aspect. 4/n

Note that the y axis do not show the same quantity (promoter activity vs protein concentration). However, Fig S2 of Proenca, et al. indicates that the cross-correlation pattern is seen for activity too. 3/n

This negative cross-correlation is reported to happen for promoters driven by RpoS. These plots (first: Patange, et al. using bolA reporter; second: Proenca, et al. using rpoS reporter) are time traces of instantaneous elongation ("growth") and "gene expression". 2/n

Dont miss the great tweetorial by @erikvannimwegen.bsky.social: bsky.app/profile/erik...

The take home is that transcription factors can undergo large transient changes of their level on the same time-scale as their binding and unbinding to DNA. This `non-equilibrium' dynamics enables different target genes to respond differently to the same changes in TF levels. 2/n

If you get hooked, the whole interview is available as a playlist! www.youtube.com/watch?v=bBSb...

(in French but auto-subtitles available, or read the transcript in the description)

I can't wait to listen to several of those!
This reminds me of this video where Francois Jacob, who coined this concept, gives his take on "night science" - interviewed by the great and only Michel Morange. www.youtube.com/watch?v=p6AH...