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Reposted by Christof Gebhardt

Elzo de Wit lab @ NKI @dewitlab.bsky.social · Jul 1

(1/n) Excited to present the latest work from the de Wit lab, where we identify and characterise loop extrusion-mediated fountains in mammalian genomes using acute depletion of 3D genome regulators: doi.org/10.1093/nar/.... A Bluetorial🧵:

Extrusion fountains are restricted by WAPL-dependent cohesin release and CTCF barriers

Abstract. Interphase chromosomes are mainly shaped by loop extrusion and compartmentalisation mechanisms. However, their temporal component and cause-effec

doi.org

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Christof Gebhardt @gebhardtlab.bsky.social · Jun 27

The review also highlights exciting applications of SMT to nuclear factors and related findings, along with a perspective of future directions, including complementary genome-wide measurements of kinetic parameters.

I hope this review further sparks interest in and the application of live-cell SMT!

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Christof Gebhardt @gebhardtlab.bsky.social · Jun 27

and a comprehensive discussion of kinetic parameters accessible by SMT.

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Christof Gebhardt @gebhardtlab.bsky.social · Jun 27

a discussion of temporal excitation patterns that facilitate measuring kinetic properties,

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Christof Gebhardt @gebhardtlab.bsky.social · Jun 27

an overview of SMT microscopy techniques,

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Christof Gebhardt @gebhardtlab.bsky.social · Jun 27

In the review, I give an overview of important steps along the implementation, execution, and analysis of single-molecule tracking in living cells and multicellular organisms. This includes a summary of labeling approaches,

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Christof Gebhardt @gebhardtlab.bsky.social · Jun 27

The review on live-cell SMT that I contribute to the jmolbiol.bsky.social special issue ‚Imaging of the central dogma‘ is now online as pre-proof: www.sciencedirect.com/science/arti...

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Reposted by Christof Gebhardt

Akis (Argyris) Papantonis @akispapantonis.bsky.social · Jun 19

This is a piece that I and @karsten-rippe.bsky.social discussing a lot, and a topic that is very close to my heart. The editors @naturerevgenet.bsky.social gave us the stage to do so, and the final version of our review is now available under this link: rdcu.be/erP1u

A short thread follows 1/n

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Christof Gebhardt @gebhardtlab.bsky.social · Jun 27

So beautifully played :-) All the best for the final!

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Reposted by Christof Gebhardt

Di Jiang @dijiang319.bsky.social · May 29

@science.org Expansion in situ genome sequencing links nuclear abnormalities to aberrant chromatin regulation | Science www.science.org/doi/10.1126/...
@jbuenrostro.bsky.social @eboyden3.bsky.social + al @broadinstitute.org @harvard.edu
#ExIGS #Chromatin #Lamin #Progeria #Aging #ExpansionMicroscopy

Expansion in situ genome sequencing links nuclear abnormalities to aberrant chromatin regulation

Microscopy and genomics are used to characterize cell function, but approaches to connect the two types of information are lacking, particularly at subnuclear resolution. Here, we describe expansion i...

www.science.org

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Reposted by Christof Gebhardt

Wendy Bickmore @wbickmor.bsky.social · May 30

Great to see this published @genesdev.bsky.social. Evidence that enhancers can activate a bystander gene in an adjacent TAD, and that cohesin facilitates this. @uoe-igc.bsky.social.
pubmed.ncbi.nlm.nih.gov/40436628/

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Reposted by Christof Gebhardt

matteomazzocca.bsky.social @matteomazzocca.bsky.social · May 14

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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)

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Reposted by Christof Gebhardt

David Suter @davidsuter.bsky.social · Mar 12

📣 New preprint from the lab – Massive work entirely driven by super-talented @simsakong.bsky.social , jointly betw. @beatfierz.bsky.social lab and mine – combining in vitro and in vivo TF single molecule imaging
www.biorxiv.org/content/10.1...

www.biorxiv.org

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Christof Gebhardt @gebhardtlab.bsky.social · Mar 12

Fun introduction!

Christof Gebhardt @gebhardtlab.bsky.social · Mar 12

Intriguing mechanism to balance production and degradation rates of proteins

David Suter @davidsuter.bsky.social · Mar 7

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Through these twin controls,
cells protect their proteins well,
even through shifts.

Thus, life adapts fast—
a story of balance told
through turnover rates.

🥳 Fantastic work spearheaded by Michael Sun and Benjamin Martin
www.biorxiv.org/content/10.1...

Core passive and facultative mTOR-mediated mechanisms coordinate mammalian protein synthesis and decay

The maintenance of cellular homeostasis requires tight regulation of proteome concentration and composition. To achieve this, protein production and elimination must be robustly coordinated. However, ...

www.biorxiv.org

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Christof Gebhardt @gebhardtlab.bsky.social · Mar 12

Fantastic! Your playing is really great!

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Reposted by Christof Gebhardt

Arnaud Krebs @arnaudkr.bsky.social · Feb 21

Program is out for our first EMBL #singlemolecule gene regulation meeting! Check out the dedicated panel sessions on single molecule genomics, single molecule imaging and theory where we would like to brainstorm the future of the field:
Registration is open! 👇
www.embl.org/about/info/c...

Gene regulation: one molecule at a time

www.embl.org

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Christof Gebhardt @gebhardtlab.bsky.social · Feb 21

Search gets faster, binding longer, bound fraction of cohesin and CTCF goes up, especially at and after ZGA

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Christof Gebhardt @gebhardtlab.bsky.social · Feb 21

Single molecules, in living zebrafish embryos, during hour-long period of development: Jonas' work on binding kinetics of cohesin and CTCF around ZGA now online. Great collab with labs of @lucagiorgetti.bsky.social @akispapantonis.bsky.social
doi.org/10.1038/s414...

Increasingly efficient chromatin binding of cohesin and CTCF supports chromatin architecture formation during zebrafish embryogenesis - Nature Communications

Using single-molecule tracking of cohesin and CTCF during zebrafish embryogenesis, the molecular kinetics underlying chromatin architecture formation was revealed and gradual emergence of chromatin st...

doi.org

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Reposted by Christof Gebhardt

Carsen Stringer @computingnature.bsky.social · Feb 12

#Cellpose 3 paper now out. Not all images are perfect. Restore your images with Cellpose3 to get better segmentations, w/ @marius10p.bsky.social www.nature.com/articles/s41...

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Reposted by Christof Gebhardt

Kazuhiro Maeshima @kazu-maeshima.bsky.social · Feb 20

Our new review on how the #chromatin domain is formed in the cell is now available @Curr Opin Struct Biol.📄✨
We critically discuss the domain formation mechanism from a physical perspective, including #phase-separation and #condensation.
📥 Free-download link:
authors.elsevier.com/a/1keGn,LqAr...

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Reposted by Christof Gebhardt

Constantin Pape @cppape.bsky.social · Feb 12

After a long journey, Segment Anything for Microscopy is now published in Nature Methods! We significantly improve SAM for interactive and automatic segmentation in light and electron microscopy and build a user-friendly tool.
www.nature.com/articles/s41...

Improvements in LM (top) and EM (bottom) of our micro-sam model (finetuned) compared to the default SAM model.

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Christof Gebhardt @gebhardtlab.bsky.social · Feb 13

Fantastic work, @armelletollenaere.bsky.social , @davidsuter.bsky.social and co-workers! Happy we could contribute.

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Reposted by Christof Gebhardt

David Suter @davidsuter.bsky.social · Feb 13

Big thanks to all people involved @armelletollenaere.bsky.social , Enes Ugur, Susanna Dalla-Longa, Cédric Deluz, Devin Assenheimer, @gebhardtlab.bsky.social , and Heinrich Leonhardt
And thanks ChatGPT for haikuing the abstract

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Reposted by Christof Gebhardt

Mir Lab @mirlab.bsky.social · Feb 12

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...

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