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Reposted by Josh Riback

Brugues Lab @brugueslab.bsky.social · Sep 3

Patrick's paper is finally out, a label-free method to measure the composition of multicomponent biomolecular condensates!

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Josh Riback @superscijew.bsky.social · Jul 27

Brisket served! Look at that smoke ring; Physical Chemistry is in action!

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Josh Riback @superscijew.bsky.social · Jul 26

12 hours brisket wrapping at 4AM!

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Josh Riback @superscijew.bsky.social · Jul 25

BRISKET IN - 24 hours to the summer lab party!!! #RibackLab #CellularPhysicalChemistryGroup

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Reposted by Josh Riback

H. Courtney Hodges @hodgeshc.bsky.social · Jul 22

How do chromatin remodelers use #IDRs to find TF binding partners? In our new Molecular Cell paper, we show that β-catenin is an adaptor that links SWI/SNF (cBAF) subunit ARID1A with binding partners via IDR-domain interactions.
www.cell.com/molecular-ce...

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Reposted by Josh Riback

Kazuhiro Maeshima @kazu-maeshima.bsky.social · Jul 10

Our new preprint 🧬🔗 www.biorxiv.org/content/10.1...
BRD4-NUT forms liquid-like condensates that locally constrain nucleosomes via BRD4-mediated crosslinking— physical control of #chromatin by #LLPS transcription condensates. @semeigazin.bsky.social @katsuminami.bsky.social @masaashimazoe.bsky.social

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Reposted by Josh Riback

labsantoro.bsky.social @labsantoro.bsky.social · May 24

Very excited to share our latest work in #MolCell showing NPM1 stabilizing the association of nucleolus associated domains (NADs) and recruiting G9a to establish their repressive chromatin states. www.sciencedirect.com/science/arti...

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Reposted by Josh Riback

Ben Sabari @bsabari.bsky.social · Apr 25

I am excited to share the latest paper from my lab where we leverage the selection bias of condensate-promoting oncofusions to uncover molecular rules governing condensate specificity and function. www.cell.com/cell/fulltex....

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Reposted by Josh Riback

Alex Holehouse @alexholehouse.bsky.social · May 23

Now published! Big congrats to first author @gginell.bsky.social

We are actively working improving/updating various aspects of FINCHES; don't hesitate to reach out if you run into issues, have questions.
www.science.org/doi/10.1126/...

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Reposted by Josh Riback

erzbergerlab.bsky.social @erzbergerlab.bsky.social · May 2

Stm1 regulates Ifh1 activity revealing crosstalk between ribosome biogenesis and ribosome dormancy: Molecular Cell www.cell.com/molecular-ce...

Stm1 regulates Ifh1 activity revealing crosstalk between ribosome biogenesis and ribosome dormancy

Ribosome abundance is balanced by production and degradation. Bianco et al. discover that the hibernation factor Stm1 has a dual role in ribosome homeostasis. Stm1 promotes ribosome biogenesis during ...

www.cell.com

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Reposted by Josh Riback

Nature Chemical Biology @natchembio.nature.com · Apr 25

A Perspective by @stephanieaw.bsky.social and @fraserlab.com discusses ways macromolecules use conformational entropy to control binding, catalysis, and allostery

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

Advances in uncovering the mechanisms of macromolecular conformational entropy - Nature Chemical Biology

Protein conformational entropy plays a vital role in functions like binding and catalysis. This Perspective discusses three ways macromolecules use conformational entropy: prepaying entropic costs, re...

www.nature.com

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Reposted by Josh Riback

Mary Mirvis @marymirvis.bsky.social · Apr 19

New(ish) preprint! 📰What whole-cell patterns emerge from the arrangement, morphologies, and interactions of organelles in the 3D space of the cell? What would we see if we could gather ALL the whole-cell reconstruction data that's out there in one place? www.biorxiv.org/content/10.1...
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A scoping study of the whole-cell imaging literature: a foundational corpus, potential for mesoscale data synthesis, and implications for standardization of an emerging field

The level of cellular organization bridging the mesoscale and whole-cell scale is coming into focus as a new frontier in cell biology. Great progress has been made in unraveling the complex physical a...

www.biorxiv.org

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Reposted by Josh Riback

Elmira @drelmira.bsky.social · Apr 16

Excited to share the @goodell-lab.bsky.social News&Views on 3 exciting studies by Vassiliou Lab, Chan Lab, and @trowbridgelab.bsky.social in @nature.com and @natcomms.nature.com, showing that #DNMT3A mutant (major driver of Clonal Hematopoiesis) blood cells depend on mitochondrial respiration.

Bluesky

lab.bsky.social

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Josh Riback @superscijew.bsky.social · Feb 28

What nanometer structure-function relationships exist in your favorite condensate? We hope you will try to measure it! Congrats to Kris, @evdokiiap.bsky.social, Abby, Archish, Gandhar, and @schmitbiophysics.bsky.social . 4/4

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Josh Riback @superscijew.bsky.social · Feb 28

In method (2), "Length-Dependent Spatial Coupling," two proteins are linked by variable-length chains to evaluate their spatial preferences. We determine that scaffold protein NPM1 is positioned 10nm away from ribosome biogenesis, facilitating condensate formation without impairing function. 3/4

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Josh Riback @superscijew.bsky.social · Feb 28

How? We design 150 protein probes and use thermodynamic principles to interpret their partitioning. In method (1), "Local Size Exclusion," variable-length amino-acid chains are attached to nucleolar proteins, expelling them based on their local mesh size. Basic principles allow precise distances.2/4

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Josh Riback @superscijew.bsky.social · Feb 28

In lab’s #FIRSTPREPRINT, we present methods to measure nanometer-scale organization around & between specific proteins in condensates in live cells. We uncover unexpected heterogeneity for a liquid-like phase with local meshwork spanning 10-50nm, stemming from ribosome biogenesis in the nucleolus.

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Reposted by Josh Riback

Kresten Lindorff-Larsen @lindorfflarsen.bsky.social · Feb 26

CALVADOS-RNA is now published
doi.org/10.1021/acs....

This is a simple model for flexible RNA that complements and works with the CALVADOS protein model. Work led by Ikki Yasuda who visited us from Keio University.

Try it yourself using our latest code for CALVADOS
github.com/KULL-Centre/...

Table of Contents figure showing the CALVADOS-RNA model and a snapshot from a mixed protein-RNA condensate

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Reposted by Josh Riback

St. Jude Research @stjuderesearch.bsky.social · Feb 11

Cuts in NIH research grants will have a lasting negative impact on science and medicine in the U.S. Grants will continue to fund specific research costs, but essential infrastructure like labs, advanced equipment and support staff are crucial for groundbreaking work.

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Reposted by Josh Riback

Allen Institute @alleninstitute.org · Jan 30

Our #CellLineOfTheWeek is a 3-for-1 and fluoresces fibrillarin, nucleophosmin, and dCas9-KRAB! 🦀🧫

Our cell lines & plasmids are available for just the cost of shipping to support discovery: www.allencell.org/cell-catalog...

📦 Distributed by @coriellinstitute.bsky.social & @addgene.bsky.social

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Reposted by Josh Riback

D. Allan Drummond @dadrummond.art · Jan 23

Great article (in which I am quoted) about biomolecular condensates, the cellular phenomena I work on in my day job! 🧪
www.scientificamerican.com/article/myst...

Mysterious Blobs in Cells Are Changing the Way We Understand Life

Tiny specks called biomolecular condensates are leading to a new understanding of the cell

www.scientificamerican.com

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Reposted by Josh Riback

Philip Ball @philipcball.bsky.social · Jan 16

This is a textbook example (condensates are only just reaching textbooks!) of why condensates matter, and how they tend to work. Here these liquid-like blobs create a microenvironment in the nucleus of cancer cells within which chromatin sustains a conformation accessible to transcription...

Nature @nature.com · Jan 16

Nature research paper: Targeting FOXM1 condensates reduces breast tumour growth and metastasis

https://go.nature.com/4g7BNC8

Targeting FOXM1 condensates reduces breast tumour growth and metastasis - Nature

The transcription factor FOXM1 forms functional condensates, the formation of which can be targeted with a specific peptide to suppress breast cancer growth and metastasis.

go.nature.com

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Reposted by Josh Riback

Aafke Gros @aafkegros.bsky.social · Jan 15

Microscopy Nodes is now up on bioRxiv! 🚀

This is a Blender extension that seamlessly integrates and visualizes 3D microscopy data (TIF & @zarr.dev).

High-quality volume rendering for anyone, in both EM and fluorescence, regardless of computational expertise! 🔬

www.biorxiv.org/content/10.1...

FIB-SEM dataset visualized with Microscopy Nodes, data from Mocaer et al 2023

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Reposted by Josh Riback

SpruijtLab @spruijtlab.bsky.social · Jan 13

Curious how biomolecular condensates can localize ions? Using NMR, we found that condensates selectively bind and localize both chaotropic anions and kosmotropic cations. This alters the condensate composition, interface potential and RNA duplex stability inside. By @irissmokers.bsky.social

Selective ion binding and uptake shape the microenvironment of biomolecular condensates

Biomolecular condensates modulate various ion-dependent cellular processes and can regulate subcellular ion distributions by selective uptake of ions. However, the molecular grammar governing condensa...

www.biorxiv.org

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Reposted by Josh Riback

Joe Rogers @josephrogers.bsky.social · Jan 13

mRNA display continues to astound. Fantastic collaboration with Alex Buell, led by the peerless @rasmusnorrild.bsky.social. ~100,000 peptides and their propensity to join the phase separation of a model disordered protein. doi.org/10.1101/2024...

Proteome-scale quantification of the interactions driving condensate formation of intrinsically disordered proteins

The formation of biomolecular condensates is involved in compartmentalisation, regulation, and signalling across most living organisms. Condensation can be driven by phase separation of proteins, and ...

doi.org

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