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Lorenzo Olivi

@loreoliv.bsky.social
194 followers 496 following 23 posts

In love with single molecules 🔬 moving inside tiny things 🦠 and big dumb monsters 🦖 wreaking havoc on the screen 🎬 Postdoctoral researcher @ Laboratory of Microbiology (WUR) Also on Letterboxd -> boxd.it/5Z17P

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Lorenzo Olivi @loreoliv.bsky.social · 11/05/2026
Controlling the expression of an always-active DnaA mutant and using the native titration power of the chromosome, we show strengths and limits of titration-based control of replication. What we saw tells us about the evolution of E. coli, but also informs design for such systems in synthetic cells!
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Lorenzo Olivi @loreoliv.bsky.social · 11/05/2026
🧵 New pre-print out from my time at @mib-wur.bsky.social showing how the titration of the initiator protein DnaA on the chromosome of E. coli can generate stable DNA replication @hohlbeinlab.bsky.social @nicoc-micsynmet.bsky.social doi.org/10.64898/202...
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Lorenzo Olivi @loreoliv.bsky.social · 31/08/2025
10€ per copy, basically a steal
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Lorenzo Olivi @loreoliv.bsky.social · 22/08/2025
12 Bonus! DnaA is also a transcription factor, so together with @baybioms.bsky.social we also investigated how changes in its regulation alter E. coli proteome! Surprisingly, impacting titration or switch alone seems to have no impact on the genes known to be regulated by DnaA...
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Lorenzo Olivi @loreoliv.bsky.social · 22/08/2025
11 There is still a long road ahead in characterizing the role of initiator titration in controlling DNA replication. Still, it's exciting how cutting-edge microscopy techniques allow us to tackle decades-old biological problems! Read more at: doi.org/10.1038/s414...
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Lorenzo Olivi @loreoliv.bsky.social · 22/08/2025
10 More active DnaA in the cell? The chromosome titrates DnaA more, minimizing re-initiations. Less active DnaA? More DnaA is free, mitigating delays in replication. Even more interestingly, severely hampering titration leads to frequent re-initiation events!
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Lorenzo Olivi @loreoliv.bsky.social · 22/08/2025
9 We then deleted known DnaA control loci and measured the DNA content of cells through flow cytometry, while we used microscopy 🔬 to measure their size and to determine the bound fraction of DnaA. We could then suggest a role of titration in stabilizing DNA replication in slow-growing E. coli.
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Lorenzo Olivi @loreoliv.bsky.social · 22/08/2025
8 Next, using single-particle tracking 🔬, we observed the binding state of DnaA in live E. coli cells during steady-state growth at different growth rates. Consistent with previous modelling, we observed that the chromosome of E. coli controls DnaA bound fraction in a growth rate-dependent fashion!
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Lorenzo Olivi @loreoliv.bsky.social · 22/08/2025
7 We started by checking the distribution of DnaA boxes on the chromosome of E. coli. Glad to say that @stephkoe.bsky.social‬ totally knocked it out of the park with this analysis! He showed that DnaA boxes tend to be enriched around oriC, a favorable feature for initiator titration.
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Lorenzo Olivi @loreoliv.bsky.social · 22/08/2025
6 However, recent experimental and modelling efforts suggest that only a concerted action of switch and titration can generate stable cell cycles. Still, to date there is no direct evidence of DnaA being titrated on the chromosome of E. coli. We decided to try to tackle this gap.
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Lorenzo Olivi @loreoliv.bsky.social · 22/08/2025
5 We now know that DnaA exists in two forms: DnaA-ATP, competent in unwinding oriC and DnaA-ADP, inactive in oriC unwinding. In this switch model, it is the accumulation of DnaA-ATP that determines replication initiation. As a result, the switch model almost replaced initiator titration.
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Lorenzo Olivi @loreoliv.bsky.social · 22/08/2025
4 During early days of characterization of DNA replication control, it was hypothesized that the chromosome could act as a sponge 🧽 for DnaA, retarding DnaA binding to oriC by first titrating it on the high affinity boxes. This form of control is what is known as initiator titration model.
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Lorenzo Olivi @loreoliv.bsky.social · 22/08/2025
3 DnaA binds DNA in specific 9 bp motifs called DnaA boxes. These boxes can have high or low affinity, depending on how well they match a specific consensus sequence. There are hundreds of high affinity boxes spread across the chromosome of E. coli. However, oriC mostly contains low-affinity motifs.
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Lorenzo Olivi @loreoliv.bsky.social · 22/08/2025
2 In E. coli, DNA replication starts when DnaA binds to the origin of replication oriC and unwinds it, allowing for the rest of the DNA polymerase to assemble. This initiation step must be finely regulated to ensure that DNA replication happens timely and only once per cell cycle.
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Lorenzo Olivi @loreoliv.bsky.social · 22/08/2025
🧵 Our study on the elusive titration control mechanism of the replication initiator DnaA in Escherichia coli is now out on @natcomms.nature.com‬! @stephkoe.bsky.social @hohlbeinlab.bsky.social‬ @nicoc-micsynmet.bsky.social @ettema.bsky.social‬ @mib-wur.bsky.social doi.org/10.1038/s414...
doi.org
The Escherichia coli replication initiator DnaA is titrated on the chromosome - Nature Communications
A DNA-binding protein, DnaA, regulates the initiation of chromosomal replication in bacteria. Here, Olivi et al. show that the bacterial chromosome sequesters DnaA in a growth rate-dependent manner, s...
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Lorenzo Olivi @loreoliv.bsky.social · 16/08/2025
Definitely an experience to say the least, but stoked to see it in its final form! Can't wait to share more
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Lorenzo Olivi @loreoliv.bsky.social · 21/07/2025
I'm beyond excited to share that I've been awarded an @embo.org Postdoctoral Fellowship to join the lab of prof. Johan Elf at Uppsala University @uu.se! Can't wait to dive even deeper in the fascinating world of bacterial physiology!
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Lorenzo Olivi @loreoliv.bsky.social · 05/01/2025
This is the science that really matters
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Reposted by Lorenzo Olivi
Kevin Mitchell @wiringthebrain.bsky.social · 12/12/2024
The tech bro fascination with eugenics is so on brand. The idea that you could make accurate, actionable predictions from individual genotypes (with all their complex, non-linear interactions) from averaged, linearly modeled population-level genomic statistics is just another big data fantasy
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Reposted by Lorenzo Olivi
Johannes Hohlbein @hohlbeinlab.bsky.social · 10/12/2024
In the spirit of which, here some new filter wheels designed by Ian Kercher with more info available here: www.printables.com/model/110377... #OpenMicroscopy
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Reposted by Lorenzo Olivi
Altmetric @altmetric.com · 18/11/2024
We strongly suggest that academic publishers and other platforms that host research rapidly implement a Share to Bluesky button for their articles. Here's how: docs.bsky.app/docs/advance... #AcademicSky #HigherEd #Altmetrics
docs.bsky.app
Action Intent Links | Bluesky
Authors, websites, and apps can use action intent links to implement "Share on Bluesky" buttons, or similar in-app actions. Logged-in users will be directed to the corresponding action view in the Blu...
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Lorenzo Olivi @loreoliv.bsky.social · 18/11/2024
The best resource for #microscopy is among us on BlueSky! Savior of my #sptPALM designs
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Lorenzo Olivi @loreoliv.bsky.social · 18/11/2024
Ready for some sweet long(er) tracks finally!
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Lorenzo Olivi @loreoliv.bsky.social · 17/11/2024
We indeed already played around with maintaining cells at fixed density for live-cell imaging in a couple of studies now, but only recently moved to the Pioreactor and it was such a big improvement!
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Lorenzo Olivi @loreoliv.bsky.social · 14/11/2024
Starting to think I should use our dog Ombra as a metaphor to explain students how fluorescent proteins allow you to tell apart things of interest from the background
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Lorenzo Olivi @loreoliv.bsky.social · 14/11/2024
Feel like "Creep" also definitely deserves a spot! Such an unnerving one
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Reposted by Lorenzo Olivi
Dvir Schirman @dvirschirman.bsky.social · 12/11/2024
I’m excited to share the first preprint from my postdoc at @johan_elf_ lab together with Konrad Gras. 🧬🦠 biorxiv.org/content/10.1... (1/14)
biorxiv.org
A dynamic 3D polymer model of the Escherichia coli chromosome driven by data from optical pooled screening
The DNA of bacterial cells is organized in a highly dynamic chromosome structure. To guarantee its propagation, the chromosome must replicate, segregate, and accommodate other biological processes lik...
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