Davide Mazza
@davidemazza.bsky.social
How do dynamics of signalling molecules skew cell fate decisions? With this review we try to move our first steps in the signalling dynamics field, together with the expert lead of @samuzambrano.bsky.social! Kudos to Fulvio, Sara and Erika for their excellent work!
Cells respond to stimuli by activating signaling pathways with a surprising variety of dynamics. Why? As we review here, there is growing evidence connecting dynamics with specific cell fate decisions www.frontiersin.org/journals/cel...
Frontiers | Linking signaling dynamics and cell fate decisions through single-cell imaging: evidence and challenges
Our ever-growing capacity to observe dynamic processes at the single-cell level has highlighted how cells use complex signaling dynamics to provide adequate ...
www.frontiersin.org
October 23, 2025 at 6:02 PM
How do dynamics of signalling molecules skew cell fate decisions? With this review we try to move our first steps in the signalling dynamics field, together with the expert lead of @samuzambrano.bsky.social! Kudos to Fulvio, Sara and Erika for their excellent work!
Minflux goes to chromatin! Very interesting preprint from @andersshansen.bsky.social lab, featuring co-first author @matteomazzocca.bsky.social, that keeps on making me very proud.
1/
Super excited to share my first preprint from @andersshansen.bsky.social Lab! We used MINFLUX to track chromatin (H2B-Halo and Fbn2 locus) at an unprecedented 200 μs, then combined it with SPT to span μs-minutes (H2B) or SPT & Super-Res Live-Cell Imaging (SRLCI) to span μs-hours (Fbn2)
Super excited to share my first preprint from @andersshansen.bsky.social Lab! We used MINFLUX to track chromatin (H2B-Halo and Fbn2 locus) at an unprecedented 200 μs, then combined it with SPT to span μs-minutes (H2B) or SPT & Super-Res Live-Cell Imaging (SRLCI) to span μs-hours (Fbn2)
May 15, 2025 at 7:41 AM
Minflux goes to chromatin! Very interesting preprint from @andersshansen.bsky.social lab, featuring co-first author @matteomazzocca.bsky.social, that keeps on making me very proud.
This looks sooo great! Congratulations @mirlab.bsky.social !!
1/n Excited to share our new preprint! Using live imaging in Drosophila embryos, we show that RNA Pol II clusters switch from sites of initiation to elongation during zygotic genome activation and that they are stably associated with an active gene: www.biorxiv.org/content/10.1...
February 12, 2025 at 1:30 PM
This looks sooo great! Congratulations @mirlab.bsky.social !!
Reposted by Davide Mazza
Happy to share Duyen's and Philipp's work on effective binding energy landscape and affinity of RBPJ obtained in vivo by on- and off-rate measurements is now published. Great collaboration with labs of Franz Oswald and Tilman Borggrefe doi.org/10.1038/s414...
Effective in vivo binding energy landscape illustrates kinetic stability of RBPJ-DNA binding - Nature Communications
Transcription factor binding to DNA is vital for gene regulation. Here, the authors determine the kinetics of DNA binding for RBPJ in living cells. They find that the binding is kinetically rather tha...
doi.org
February 2, 2025 at 11:04 AM
Happy to share Duyen's and Philipp's work on effective binding energy landscape and affinity of RBPJ obtained in vivo by on- and off-rate measurements is now published. Great collaboration with labs of Franz Oswald and Tilman Borggrefe doi.org/10.1038/s414...
Preprint from Marklund and Greenleaf labs on TF binding: www.biorxiv.org/content/10.1...
In vitro single molecule imaging + In nuclei single molecule footprinting of KLF on engineeered sequences.
On-rates matter more than off-rates, similarly to what previously shown in baceria.
In vitro single molecule imaging + In nuclei single molecule footprinting of KLF on engineeered sequences.
On-rates matter more than off-rates, similarly to what previously shown in baceria.
Thermodynamic principles link in vitro transcription factor affinities to single-molecule chromatin states in cells
The molecular details governing transcription factor (TF) binding and the formation of accessible chromatin are not yet quantitatively understood - including how sequence context modulates affinity, h...
www.biorxiv.org
January 31, 2025 at 4:42 PM
Preprint from Marklund and Greenleaf labs on TF binding: www.biorxiv.org/content/10.1...
In vitro single molecule imaging + In nuclei single molecule footprinting of KLF on engineeered sequences.
On-rates matter more than off-rates, similarly to what previously shown in baceria.
In vitro single molecule imaging + In nuclei single molecule footprinting of KLF on engineeered sequences.
On-rates matter more than off-rates, similarly to what previously shown in baceria.
Reposted by Davide Mazza
What is the multiscale structure of chromatin condensates? How does it shape thermodynamic and material properties?
We address this at near-atomistic resolution🔥🔥🔥 using cryoET (Rosen & Villa labs, led by H Zhou), a new multiscale model (K Russell) and cryoET-guided sims (J Huertas & J Maristany)
We address this at near-atomistic resolution🔥🔥🔥 using cryoET (Rosen & Villa labs, led by H Zhou), a new multiscale model (K Russell) and cryoET-guided sims (J Huertas & J Maristany)
January 23, 2025 at 9:32 AM
What is the multiscale structure of chromatin condensates? How does it shape thermodynamic and material properties?
We address this at near-atomistic resolution🔥🔥🔥 using cryoET (Rosen & Villa labs, led by H Zhou), a new multiscale model (K Russell) and cryoET-guided sims (J Huertas & J Maristany)
We address this at near-atomistic resolution🔥🔥🔥 using cryoET (Rosen & Villa labs, led by H Zhou), a new multiscale model (K Russell) and cryoET-guided sims (J Huertas & J Maristany)
Reposted by Davide Mazza
Real-time visualization of reconstituted transcription reveals RNA polymerase II activation mechanisms at single promoters https://www.biorxiv.org/content/10.1101/2025.01.06.631569v1
January 7, 2025 at 6:46 AM
Real-time visualization of reconstituted transcription reveals RNA polymerase II activation mechanisms at single promoters https://www.biorxiv.org/content/10.1101/2025.01.06.631569v1
Reposted by Davide Mazza
Towards community-driven visual proteomics! Excited to finally share this large-scale curated & annotated dataset of 1829 high-quality #cryoET tomograms of the little green alga that just keeps giving— Chlamydomonas! 🧪🧶🧬🌾🌊🌍
Preprint📜: www.biorxiv.org/content/10.1...
A short thread🧵👇
Preprint📜: www.biorxiv.org/content/10.1...
A short thread🧵👇
January 6, 2025 at 11:19 AM
Towards community-driven visual proteomics! Excited to finally share this large-scale curated & annotated dataset of 1829 high-quality #cryoET tomograms of the little green alga that just keeps giving— Chlamydomonas! 🧪🧶🧬🌾🌊🌍
Preprint📜: www.biorxiv.org/content/10.1...
A short thread🧵👇
Preprint📜: www.biorxiv.org/content/10.1...
A short thread🧵👇
Tasty, tasty phase separation. A much needed rigorous study!
1/n Some time ago my colleague, excellent cook, and friend Ivan told me: "Cacio e pepe is the recipe that I screw up more often. Let's make a project studying systematically the physics of that sauce".
Prepare to get cheesy, I'm glad to share the Cacio e paper preprint:
arxiv.org/abs/2501.00536
Prepare to get cheesy, I'm glad to share the Cacio e paper preprint:
arxiv.org/abs/2501.00536
January 4, 2025 at 7:45 PM
Tasty, tasty phase separation. A much needed rigorous study!
Reposted by Davide Mazza
Excited to share @domenicnarducci.bsky.social 's paper now out in Mol Cell published back-to-back with the paper from @dewitlab.bsky.social - despite lots of prior work, we find that ZNF143 has no looping function
www.sciencedirect.com/science/arti...
www.sciencedirect.com/science/arti...
www.sciencedirect.com/science/arti...
www.sciencedirect.com/science/arti...
December 20, 2024 at 4:32 PM
Excited to share @domenicnarducci.bsky.social 's paper now out in Mol Cell published back-to-back with the paper from @dewitlab.bsky.social - despite lots of prior work, we find that ZNF143 has no looping function
www.sciencedirect.com/science/arti...
www.sciencedirect.com/science/arti...
www.sciencedirect.com/science/arti...
www.sciencedirect.com/science/arti...
We often speak about chromatin as being accessible or inaccessible, but what does it mean? We wrote a short review on this, 🔬 focused:
sciencedirect.com/science/arti...
A big thank you to Tom Fillot for his efforts on this and to
@hansen_lab
@marcelonollmann
for their help as editors.
sciencedirect.com/science/arti...
A big thank you to Tom Fillot for his efforts on this and to
@hansen_lab
@marcelonollmann
for their help as editors.
December 20, 2024 at 3:46 PM
We often speak about chromatin as being accessible or inaccessible, but what does it mean? We wrote a short review on this, 🔬 focused:
sciencedirect.com/science/arti...
A big thank you to Tom Fillot for his efforts on this and to
@hansen_lab
@marcelonollmann
for their help as editors.
sciencedirect.com/science/arti...
A big thank you to Tom Fillot for his efforts on this and to
@hansen_lab
@marcelonollmann
for their help as editors.