Lightnews — Scholar-powered news

Christopher Reinkemeier @reinkemeiercd.bsky.social · 18d

Interestingly, a change in the density ratio seems to be associated with senescence or pathophysiology.
Congrats to all authors on this fascinating and elegant story. 👏

Christopher Reinkemeier @reinkemeiercd.bsky.social · 18d

With this constant density ratio they can nicely explain the constant ratio of nuclear to cytoplasmic volume postulated by Richard Hertwig more 120 years ago.

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Christopher Reinkemeier @reinkemeiercd.bsky.social · 18d

Awesome work by the @simonereber.bsky.social, @vasilyzaburdaev.bsky.social & Guck labs (published in @natcomms.nature.com). They show that the nucleus is less dense than the cytoplasm and that the density ratio is conserved across many eukaryotes. www.nature.com/articles/s41...

Conserved nucleocytoplasmic density homeostasis drives cellular organization across eukaryotes - Nature Communications

Cells can regulate their mass density. Here, the authors demonstrate how eukaryotes establish and maintain a lower density in the nucleus than in the cytoplasm via pressure balance, and how deviations emerge during pathophysiological states like senescence.

www.nature.com

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Cell Chemical Biology @cp-cellchembiol.bsky.social · Jul 7

Online now! #chembiol

Site-resolved assessment of targeted protein degradation

Moreno Ballesteros et al. introduce a site-resolved strategy combining genetic code expansion and bioorthogonal chemistry to evaluate how ligand binding sites influence targeted protein degradation. This approach offers a powerful framework to accelerate degrader design, enable target validation, and broadly explore the potential of induced proximity.

dlvr.it

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Christopher Reinkemeier @reinkemeiercd.bsky.social · Jun 20

Absolutely fascinating, and super solid story on how Nup98 condensates and likely capillary effects mediate DSB relocalization in cells.

Molecular Cell @cp-molcell.bsky.social · Jun 5

Online Now: Off-pore Nup98 condensates mobilize heterochromatic breaks and exclude Rad51 Online now:

Off-pore Nup98 condensates mobilize heterochromatic breaks and exclude Rad51

Merigliano et al. identified a non-canonical, “off-pore” role for nucleoporins in genome stability and in the spatial regulation of homologous recombination in multicellular eukaryotes. Nup98 condensates form at DNA breaks within pericentromeric heterochromatin to prevent aberrant recombination by excluding Rad51, while promoting the mobilization of repair sites through immiscibility with heterochromatin protein 1 (HP1) condensates.

dlvr.it

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Kalli Kappel @kallikappel.bsky.social · Jun 17

In the nucleus, many intrinsically disordered proteins (IDPs) form condensates. What IDP sequence features drive this behavior? We developed CondenSeq, a high-throughput approach to measure nuclear condensate formation, and applied it to ~14,000 IDPs to find out!

rdcu.be/eq975

Characterizing protein sequence determinants of nuclear condensates by high-throughput pooled imaging with CondenSeq

Nature Methods - CondenSeq is an imaging-based, high-throughput platform for characterizing condensate formation within the nuclear environment, uncovering the protein sequence features that...

rdcu.be

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Molecular Cell @cp-molcell.bsky.social · Jun 5

Online Now: Off-pore Nup98 condensates mobilize heterochromatic breaks and exclude Rad51 Online now:

Off-pore Nup98 condensates mobilize heterochromatic breaks and exclude Rad51

Merigliano et al. identified a non-canonical, “off-pore” role for nucleoporins in genome stability and in the spatial regulation of homologous recombination in multicellular eukaryotes. Nup98 condensates form at DNA breaks within pericentromeric heterochromatin to prevent aberrant recombination by excluding Rad51, while promoting the mobilization of repair sites through immiscibility with heterochromatin protein 1 (HP1) condensates.

dlvr.it

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SCALE - SubCellular Architecture of LifE @scale-cluster-ffm.bsky.social · May 23

🎉 We’re absolutely thrilled: SCALE has been selected as a DFG Excellence Cluster!
A huge thank you to our incredible team—this would not have been possible without your dedication and talent. 🙌 @dfg.de
#ClustersOfExcellence #SCALEcluster 🧵

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Deliz Liang lab @lab-adl.bsky.social · Mar 17

🚨 PhD Opportunity!

Passionate about enzyme engineering or genetic code expansion? 🧬 Our lab is hiring a PhD student!

🔬 Exciting interdisciplinary research
🤝 Engaging environment 🌱

📄 Does this sound like you, apply now! ⏳🔗
📢 Know someone? Share this! 🔄

jobs.uzh.ch/job-vacancie...

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Carolyn Bertozzi @carolynbertozzi.bskyverified.social · Mar 8

Exciting new work from Barna Lab @stanfordmedicine.bsky.social

www.science.org/doi/10.1126/...

A subcellular map of translational machinery composition and regulation at the single-molecule level

Millions of ribosomes are packed within mammalian cells, yet we lack tools to visualize them in toto and characterize their subcellular composition. In this study, we present ribosome expansion micros...

www.science.org

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Christopher Reinkemeier @reinkemeiercd.bsky.social · Mar 4

The recording has a really nice summary of the importance of the work of the SFB 👏

Lemke Lab @lemkelab.bsky.social · Mar 4

HELAU 🎉

Yesterday, we participated in the #Mainz Carnival alongside the @sfb1551.bsky.social! This was an amazing experience, and with over 600,000 people watching, it was a fantastic way to show how fun science can be!

You can find the recording here, starting at 45:50 👉 shorturl.at/41alV

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Lemke Lab @lemkelab.bsky.social · Mar 4

HELAU 🎉

Yesterday, we participated in the #Mainz Carnival alongside the @sfb1551.bsky.social! This was an amazing experience, and with over 600,000 people watching, it was a fantastic way to show how fun science can be!

You can find the recording here, starting at 45:50 👉 shorturl.at/41alV

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Max Wilkinson @maxewilkinson.bsky.social · Mar 1

we recently found some really neat RNA-guided DNA-cutting systems in phages. Despite remarkable similarities to CRISPR systems, including encoding guide RNAs in arrays, they appear entirely evolutionarily distinct (but definitely related to snoRNAs 🤓)
We decided to call them TIGR-Tas systems 🐯

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Tominaga K. (tomiken) @pacyc184.bsky.social · Feb 28

TIGR-Tas: A family of modular RNA-guided DNA-targeting systems in prokaryotes and their viruses | Science https://www.science.org/doi/10.1126/science.adv9789

TIGR-Tas: A family of modular RNA-guided DNA-targeting systems in prokaryotes and their viruses

RNA-guided systems provide remarkable versatility, enabling diverse biological functions. Through iterative structural and sequence homology-based mining starting with a guide RNA-interaction domain of Cas9, we identified a family of RNA-guided DNA-...

www.science.org

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Materials Synthetic Biology Group @matsynbio.bsky.social · Feb 25

As an introductory post, check out our latest paper in which we engineer a phase-separated synthetic organelle that translates metabolic signals into gene transcription regulation!

pubs.acs.org/doi/full/10....

Metabolite-Responsive Control of Transcription by Phase Separation-Based Synthetic Organelles

Living natural materials have remarkable sensing abilities that translate external cues into functional changes of the material. The reconstruction of such sensing materials in bottom-up synthetic biology provides the opportunity to develop synthetic materials with life-like sensing and adaptation ability. Key to such functions are material modules that translate specific input signals into a biomolecular response. Here, we engineer a synthetic organelle based on liquid–liquid phase separation that translates a metabolic signal into the regulation of gene transcription. To this aim, we engineer the pyruvate-dependent repressor PdhR to undergo liquid–liquid phase separation in vitro by fusion to intrinsically disordered regions. We demonstrate that the resulting coacervates bind DNA harboring PdhR-responsive operator sites in a pyruvate dose-dependent and reversible manner. We observed that the activity of transcription units on the DNA was strongly attenuated following recruitment to the coacervates. However, the addition of pyruvate resulted in a reversible and dose-dependent reconstitution of transcriptional activity. The coacervate-based synthetic organelles linking metabolic cues to transcriptional signals represent a materials approach to confer stimulus responsiveness to minimal bottom-up synthetic biological systems and open opportunities in materials for sensor applications.

pubs.acs.org

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Marie Auvray @mauvray.bsky.social · Jan 31

Thrilled to share with you our work on covalent probes! By introducing a biocompatible sulfonium-based cleavable linker, we developed a series of fluorescent probes that can label covalently endogenous tubulin in various cell lines.

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

#Chembio #FluorescenceFriday

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Christopher Reinkemeier @reinkemeiercd.bsky.social · Jan 19

What a fascinating paper! Congrats to the entire team 👏

Beck Laboratory @becklab.bsky.social · Jan 17

In a great collaboration with @hummerlab.bsky.social and the Kräusslich lab: HIV capsid doesn't break at the NPC; instead, it cracks open the NPC itself! Details in Cell: authors.elsevier.com/sd/article/S... @mpibp.bsky.social @uniheidelberg.bsky.social A thread below:

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Bristol BioDesign Institute @bristolbiodesign.bsky.social · Jan 17

NEW PUBLICATION:

Confinement and catalysis within de novo designed peptide barrels
doi.org/10.1021/jacs...

(Journal of the American Chemical Society)

Confinement and Catalysis within De Novo Designed Peptide Barrels

De novo protein design has advanced such that many peptide assemblies and protein structures can be generated predictably and quickly. The drive now is to bring functions to these structures, for example, small-molecule binding and catalysis. The formidable challenge of binding and orienting multiple small molecules to direct chemistry is particularly important for paving the way to new functionalities. To address this, here we describe the design, characterization, and application of small-molecule:peptide ternary complexes in aqueous solution. This uses α-helical barrel (αHB) peptide assemblies, which comprise 5 or more α helices arranged around central channels. These channels are solvent accessible, and their internal dimensions and chemistries can be altered predictably. Thus, αHBs are analogous to “molecular flasks” made in supramolecular, polymer, and materials chemistry. Using Förster resonance energy transfer as a readout, we demonstrate that specific αHBs can accept two different organic dyes, 1,6-diphenyl-1,3,5-hexatriene and Nile red, in close proximity. In addition, two anthracene molecules can be accommodated within an αHB to promote anthracene photodimerization. However, not all ternary complexes are productive, either in energy transfer or photodimerization, illustrating the control that can be exerted by judicious choice and design of the αHB.

doi.org

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bioRxiv Synthetic Biology @biorxiv-synthbio.bsky.social · Jan 14

A synthetic cell with integrated DNA self-replication and membrane biosynthesis https://www.biorxiv.org/content/10.1101/2025.01.14.632951v1

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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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IMPRS on Cellular Biophysics @imprs-cbp.bsky.social · Jan 12

#biophysics #graduateschool #phdingermany

If you know someone who might be interested, please share this post with them! 🎓 Thank you in advance!

Our partner institutions are @Goethe University Frankfurt, @unimainz.bsky.social, @Frankfurt Institute of Advanced Studies and @mpibp.bsky.social

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Castañeda Lab at SU @castanedalab.bsky.social · Jan 11

For folks unable to download our recent review in @cp-trendsbiochem.bsky.social on protein quality control condensates, function, and potential therapeutic avenues - here's another link: authors.elsevier.com/a/1kNRo3S6Gf...

#Ub #PQC #condensates

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Journal of Cell Biology @jcb.org · Jan 9

@andibrunner.bsky.social et al. @ellenberglab.bsky.social show that interphase organization into Cohesin-driven loops occurs in a sequential and hierarchical manner - just like the mitotic organization by Condensins. https://buff.ly/426gIEu
@wanluzhang.bsky.social

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Stephan Hacker @stephanhacker2.bsky.social · Jan 8

Exciting paper by the groups of Ronald Micura and Alexandra Lusser in @nchembio.bsky.social. Covalent binders to structured RNA based on alkyl halides and alkyl mesylates show engagement of the preQ1 and Pepper aptamers in vitro and in cells. www.nature.com/articles/s41...

Engineering covalent small molecule–RNA complexes in living cells - Nature Chemical Biology

Small-molecule ligands have been developed that covalently attach to their cognate RNA aptamers in vitro and in living cells. This strategy opens up new avenues for RNA imaging applications (for examp...

www.nature.com

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Claire Deo @clairedeo.bsky.social · Jan 7

We made a photoswitchable HaloTag (psHaloTag), which can reversibly turn-on fluorogenic dyes upon illumination 💡. Congrats to Franzi, Bego and all co-authors, check out our preprint below 👇
www.biorxiv.org/content/10.1...

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