Erik van Nimwegen

Come join us in Basel! @biozentrum.unibas.ch is an amazing place to start your group.

Please let us know what you think. And much agreed on Bach and Vermeer (maybe I should give Proust another try).

Are you excited to pursue your own research interests and contribute to our group’s experimental research in the quantitative biology of microbes? We have an opening for a potentially permanent position as research associate.
Please repost and notify potential candidates!

and includes accurate error-bars on all estimates.

We believe RealTrace can dramatically enhance the power of time-lapse microscopy data by allowing identification and quantification of far more subtle features in the dynamics than is possible with simple data smoothing approaches. n/n

Surprisingly, protein production rates adapt to their new steady-states far more quickly and with only a minimal transient.

RealTrace can be applied to essentially any time-lapse fluorescence microscopy data and gives accurate estimates of instantaneous growth and volumic GFP production rates, 10/n

Finally, upon a sudden `downshift' in nutrients, we see very reproducible time-dependent responses across single cells. All cells go almost into growth arrest, then overshoot in growth rate, only to relax to a final growth rate over a time scale of 3 cell cycles. 9/n

minimum early in the cell cycle and a maximum late in the cell cycle. In contrast, protein production rates show more complex patterns that vary across conditions and across promoters, even across constitutive promoters!
As far as we are aware, no current models can explain these patterns. 8/n

time, and in slower growth conditions, both the amplitude and duration of these fluctuations increases.

Second, both growth rate and volumic protein production vary systematically across the cell cycle. Interestingly, the variation in growth rate is the same in all conditions, with a 7/n

We use data from E. coli cells carrying fluorescent reporters of constitutive and ribosomal genes, growing in a microfluidic device in different conditions, to highlight the kind of subtle patterns RealTrace can uncover.
First, instantaneous growth rates vary substantially across cells and 6/n

RealTrace is very generally applicable, which we demonstrate by applications to data from E. coli cells, mouse embryonic stem cell nuclei (data from the lab of @davidsuter.bsky.social), and entire C. elegans larvae (data from the lab of @betowbin.bsky.social). 5/n

are correlated on short time scales, all measurement errors are independent. We implemented this idea into a rigorous Bayesian procedure that uses maximum entropy process priors and recursively approximates the non-linear dynamics over short time intervals. 4/n

We can't fit the data to particular curves because we typically don't know what form the dynamics will take, and local smoothing systematically distorts the true dynamics by replacing it with a time average.

RealTrace solves this challenge using only one assumption: while biological changes 3/n

Tracking the behavior of single cells using fluorescence time-lapse microscopy is becoming increasingly popular but there is a fundamental challenge in analyzing such data: as biological changes are small on short time scales, much of the true dynamics is hidden under measurement noise. 2/n

RealTrace: Uncovering biological dynamics hidden under measurement noise in time-lapse microscopy data One of the most powerful approaches for identifying the mechanisms underlying complex biological phenomena is not just to measure bulk populations, or even take single-cell snapshots, but to directly ...

What novel biological dynamics might be hiding under the measurement noise of your time-lapse fluorescence microscopy data?
Try our new RealTrace tool to find out!
Fantastic work by Bjoern Kscheschinski and others.
Tweetorial follows. 1/n
www.biorxiv.org/content/10.1...

We're looking for highly motivated candidates for PhD positions in the physics of living systems.

Our group uses theoretical physics to understand how cells collectively self-organize.

If you're interested, get in touch & check out the Biozentrum PhD Fellowship program, deadline October 12th!

Join us for an exciting #BiozentrumDiscovery lecture!

Prof. Tami Lieberman from @mit.edu will speak about the dynamic selective landscape of human microbiomes. Her lab studies microbial evolution in real time, with a focus on mutations occurring within individual human microbiomes.

Anybody taking bets on how obvious the cherry-picking/p-hacking is going to turn out to be to obtain this supposed association?
I'm personally going with: mind-blowingly glaringly obvious. Like 'My mouth is wide open but I still cannot breathe at the stupidity of it' obvious. But hey, who knows?!

ERC Starting Grant for Physicist David Brückner How do cells decide which role to take on in the body? Prof. David Brückner from the Biozentrum of the University of Basel is investigating this and similar questions. Over the next five years, a Star...

Why do some cells become neurons and others muscle?
Physicist Prof. David Brückner @davidbrueckner.bsky.social @biozentrum.unibas.ch @unibas.ch receives a prestigious #ERCStartingGrant to uncover how cells make life-shaping decisions. @erc.europa.eu
www.biozentrum.unibas.ch/news/detail/...

Multi-omic assessment of mRNA translation dynamics in liver cancer cell lines Scientific Data - Multi-omic assessment of mRNA translation dynamics in liver cancer cell lines

Hey there, #mRNAtranslation buffs! Our latest multi-faceted dataset from liver cancer cell lines is out in #ScientificData: RNA-seq, ribosome run-off/ribo-seq, polysome-seq, pSILAC. rdcu.be/eC86H. Great team effort spearheaded by Asier Gonzalez Sevine and Niels Schlusser. Happy data crunching!

Are you saying that is bad? I already KNOW I'm interested in your lab.. I just used the LLM to help me express it.

Cellular memory: The clever strategy cells use to move through narrow environments In wound healing, immune response, and cancer metastasis, cells migrate through the body – often squeezing through narrow spaces. Researchers led by Prof. David Brückner at the Biozentrum discovered t...

🧪How do cells navigate the body? David Brückner @davidbrueckner.bsky.social & researchers @umons.bsky.social discovered that cells retain a “memory” of their past shapes, allowing them migrate more efficiently–crucial for immune response & metastasis. @unibas.ch @natphys.nature.com ow.ly/SSzX50WLg3t

The actin cortex acts as a mechanical memory of morphology in confined migrating cells - Nature Physics Cells often navigate through confined spaces. Now it is shown that cells retain a mechanical memory of previous confinement events, which makes them more efficient at migrating through narrow microenv...

🤔 Can migrating cells 'remember' their past trajectories?

In collab w/ @sgabriele.bsky.social & @kyohalie.bsky.social, we address this question:

Confined cells undergo geometry-sensitive morphology switches, and these switches depend on the past migration history!

www.nature.com/articles/s41...

New endowed professorship strengthens climate research at the University of Basel The University of Basel is setting up a new endowed professorship at the Biozentrum to make fundamental discoveries at the interface between biophysics and climate-relevant environmental biology. This...

🧪 The University of Basel is setting up a new endowed professorship in #ClimateBiophysics at the @biozentrum.unibas.ch, funded by the Georg H. Endress Foundation. This new professorship strengthens climate research @unibas.ch. www.biozentrum.unibas.ch/news/detail/...

I agree many of the unprocessed foods were poorly presented. But I think one can’t conclude from that that it must taste bland. I remember after first coming to the US having birthday pie. Extravagantly colorful and shiny. But it tasted much more bland than the pies I got in Europe.

I feel the thread is vastly exaggerating how much better the processed food looks. In some cases, just based on looks, I would prefer the unprocessed one.
Maybe this study is evidence of imprinting of US citizens on what ‘tasty’ food is supposed to look like.

Rapid fluctuations drive complex gene regulation in bacteria Bacteria respond to environmental factors such as antibiotics by inducing regulatory proteins that switch their target genes on or off. Researchers led by Prof. Erik van Nimwegen have discovered that ...

🧪 Gene regulation in bacteria: The team led by @erikvannimwegen.bsky.social discovered that environmental stimuli cause rapid fluctuations in the concentration of regulatory proteins, leading different target genes to respond differently to the same stimulus. www.biozentrum.unibas.ch/news/detail/...

Four panels show different states of the LexA regulon with either high or low concentration of LexA and a target promoter either bound by the LexA repressor, or unbound and active. The figure also indicates the typical rates of transition between these four states. While transitions from bound to unbound always occur at a rate of about 1 per minute, rebinding is very fast when LexA is high (i.e. 1 second) and very slow when LexA is low. Therefore, expression bursts only occur when LexA levels are low. Switches to the low LexA state happen roughly once an hour when DNA damage occurs, but only last on the order of 1 minute because DNA is repaired quickly. Because this is roughly the same rate as the unbinding rate, expression bursts occur stochastically during the short time periods of low LexA levels.

Paper link and graphical abstract:
journals.aps.org/prxlife/abst...

Different Bacterial Genes Have Different Turn-Ons Not all genes respond in the same way to regulation by the same molecule—a property that might enable cells to produce complex genetic responses.

Because of a lack of separation of the time scales for TF binding/unbinding and fluctuations in active TF levels, non-equilibrium gene regulation may be common in bacteria.
Check out this nice piece by ‪@philipcball.bsky.social‬ on our new publication in PRX Life.
physics.aps.org/articles/v18...

PRX Life on X: "Different target genes controlled by the same regulator respond to DNA damage with highly distinct expression responses when fluctuations in transcription factor levels match the timescale of their binding and unbindingfrom DNA. Read the paper: https://t.co/HVwQL3pj1l https://t.co/qVSsqzrTah" / X Different target genes controlled by the same regulator respond to DNA damage with highly distinct expression responses when fluctuations in transcription factor levels match the timescale of their binding and unbindingfrom DNA. Read the paper: https://t.co/HVwQL3pj1l https://t.co/qVSsqzrTah

Levels of active TFs can fluctuate on the same time scale as individual binding and unbinding events to the DNA, causing 'non-equilibrium' gene regulatory responses.
We believe this may be pervasive in bacterial gene regulation.
Check out our new work in PRX Life:
x.com/PRX_Life/sta...

Probabilistic clustering of sequences: Inferring new bacterial regulons by comparative genomics | PNAS Genome-wide comparisons between enteric bacteria yield large sets of conserved putative regulatory sites on a gene-by-gene basis that need to be cl...

Not sure if this is what you mean, but if you want partition any set of sequences into clusters under the assumption that sequences in each cluster derive from a common PSWM, this does so rigorously:
www.pnas.org/doi/10.1073/...