Ashok Deniz

Pulsed #lasers integrated with #cryoEM: @fitzpatricklab.bsky.social postdoc Daniel Du aims to boost contrast in #cryoET zuckermaninstitute.columbia.edu/making-world-s-best-microscopes-biology-better
zuckermaninstitute.columbia.edu/science-life-daniel-du
elifesciences.org/reviewed-preprints/109793v1

Evolution navigated billions of challenges to get to us to where we are today. Directed evolution compresses this to a 1D axis.

Imagine if you could sample 200 dimensions at once, with data to boot 📈

First @chorylab.bsky.social PACE preprint on our new system to tackle this: bit.ly/turboprance

The molecular basis of force selectivity by PIEZO2 Nature - PIEZO2 is intrinsically more rigid than PIEZO1, and disparate mechanical stimuli paradoxically evoke opposite conformational and gating responses in each channel.

New paper from the lab led by @ericmulhall.bsky.social addresses how PIEZO1 and PIEZO2 are tuned to different types mechanical forces. From nanometer-scale super-resolution microscopy to in vivo experiments, links single-molecule observations to physiological function.
www.nature.com/articles/s41...

Papers are like buses... You wait for ages, then two come along at once.

Huge congrats to @bornanovak.bsky.social and @jefflotthammer.bsky.social for pushing and driving every aspect of this work, preprinted ~1 year ago to the day (Friday before BPS), now published!

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

Have you ever wanted to do single-molecule biophysics in high-throughput? @matt-dejong.bsky.social (amazing joint grad student with @dunnlab.bsky.social) invented a way & measured >100,000 single molecules across 241 different sequences. (1/3)
www.biorxiv.org/content/10.6...

Thanks so much Samrat!

Single-cell and isoform-specific translational profiling of the mouse brain - Nature Post-transcriptional regulation of mRNA translation was explored using Ribo-STAMP and single-cell RNA sequencing to reveal cell-type-specific and isoform-specific translation patterns across hipp...

Chuffed to see our paper with @geneyeo.bsky.social finally published in @nature.com.
www.nature.com/articles/s41...
Very grateful to Fede, Susie, and Dave from my lab, and Sammi, Eric, and Pratibha from Gene's lab. What did we find? ⬇️ ⬇️ ⬇️

New preprint from @kutseikin.bsky.social showing how pharmacologic inhibition of SLC33A1 activates IRE1/XBP1s signaling. w/ @enriquesaez.bsky.social @chrisgparker.bsky.social @landerlab.bsky.social @forlilab.bsky.social & the Birsoy lab (Rockefeller) Check it out👇

www.biorxiv.org/content/10.6...

High-throughput ligand diversification to discover chemical inducers of proximity - Nature Chemical Biology Molecular glue degraders have consistently been discovered retrospectively, despite their increasing importance. Herein, a high-throughput approach is described that modifies existing ligands into mol...

What a thrill to see this out! Our prospective, scalable, and target-centric solution for molecular glue discovery.

More thoughts and details here: www.linkedin.com/posts/activi...

Paper here: www.nature.com/articles/s41...

Pleased to share the final version of this behemoth of a paper, now finally published. I guess I can retire now?
www.nature.com/articles/s41...

More functional data, many thousands of words removed, and a few other updates from last year's preprint.

Thanks so much Samrat!

Bioengineer Clifford Brangwynne wins Keio Medical Science Prize Japan’s Keio University awards the prize annually to honor contributions in medicine and life sciences. Brangwynne is being recognized for groundbreaking work that has opened up a new field of cell bi...

A tremendous honor! Thrilled & humbled to receive 2025 Keio Medical Science Prize for launching LLPS #phaseseparation field (= #softmatter + #cellbio) w collaborators esp @HymanLab. & Congrats to Akiko Iwasaki @virusesimmunity.bsky.social. www.princeton.edu/news/2025/09...
#KeioMedicalSciencePrize

Would be great to be added, thanks!

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...

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

I am super happy to share our latest article entitled "Decoding the molecular interplay of CD20 and therapeutic antibodies with fast volumetric nanoscopy", now published in Science www.science.org/doi/10.1126/...
It was my postdoctoral work mit @sauer-lab.bsky.social Congrats to all the co-authors!

Short activation domains control chromatin association of transcription factors Transcription factors regulate gene expression with DNA-binding domains (DBDs) and activation domains. It is generally assumed that DBDs are solely responsible for interacting with DNA and chromatin. ...

Happy new year! Our new preprint is live! We use single molecule imaging in live cells to show that activation domains can control how transcription factors bind to chromatin. SMT 1 TF Dogma 0 www.biorxiv.org/content/10.1...

Programming scheduled self-assembly of circadian materials - Nature Communications Harnessing biomolecular systems to endow synthetic materials with life-like properties is a significant challenge. Here, the authors use the biomolecular KaiABC circadian clock proteins to control aut...

Happy to be on BlueSky!
For my first post, I am excited to share a new collaborative paper combining experiments and simulations, where we used circadian clock proteins to engineer biomaterials with time-programmed self-assembly and disassembly www.nature.com/articles/s41...

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🧵👇

EDUCATION CORNER: Molecule of the Month: Celebrating  25 Years of Storytelling and Announcing New Beginnings After a remarkable 300 columns, David Goodsell has retired from the Molecule of the Month series.  Janet Iwasa will be continuing the series for PDB-101.

After a remarkable 300 columns, David Goodsell has retired from the Molecule of the Month. We are very grateful for his service.
@jiwasa.bsky.social will continue the series, beginning with January's article on Assembly Line Polyketide Synthases
Details: cdn.rcsb.org/rcsb-pd...

😊 I feel very lucky that you made that choice Samrat, and it’s fun to look back on the novel science you started then! Congrats on all of your/your lab’s outstanding achievements!

Congrat Alex!

Amazing and creative work by Anthony, who very independently made the novel and exciting discoveries/developments in this paper - big congrats Anthony!

Anthony is a
@scripps.edu Graduate School student (joint with @kerenlasker.bsky.social) - great collaboration - big congrats Keren!

Awesome and beautiful work by Daniel!

Big congrats to him and @kerenlasker.bsky.social for putting this complex and important story together!

And congrats to all other authors - it was so fun to be a part of this exciting collaboration!

Rayleigh-Plateau instability in mitochondria? Exciting analysis of physics of mitochondria dynamics

For inspiration, here are the papers we discussed in 2023:

Visualizing Single V-ATPase Rotation Using Janus Nanoparticles Understanding the function of rotary molecular motors, such as rotary ATPases, relies on our ability to visualize single-molecule rotation. Traditional imaging methods often involve tagging those mot...

Visualizing Single V-ATPase Rotation Using Janus Nanoparticles
pubs.acs.org/doi/full/10....

Cellular Function of a Biomolecular Condensate Is Determined by Its Ultrastructure Biomolecular condensates play key roles in the spatiotemporal regulation of cellular processes. Yet, the relationship between atomic features and condensate function remains poorly understood. We stud...

1/ 🚨We’re thrilled to share our latest study:

"Cellular Function of a Biomolecular Condensate Is Determined by Its Ultrastructure" 🌟

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

How do biomolecular condensates achieve their cellular roles? It comes down to their internal structure. 🧵⬇️

Thanks so much, Samrat!

Biomolecular Condensates can Induce Local Membrane Potentials Biomolecular condensates are a ubiquitous component of cells, known for their ability to selectively partition and compartmentalize biomolecules without the need for a lipid membrane. Nevertheless, co...

Excited to share our preprint, work by Anthony Gurunian, showing that #condensates can induce localized potentials in membranes + an analytical framework, with important biological implications, collaboration with @kerenlasker

biorxiv.org/cgi/content/...

Phase-transformable metal-organic polyhedra for membrane processing and switchable gas separation - Nature Communications The capability of materials to interconvert between phases enables greater control over properties without additional chemical modification but can result in a sacrifice of porosity. Here, the authors...

Interesting porous material - rhodium metal-organic polyhedra (MOP) with tethered polymers.

Tunable phase transition/gas adsorption-diffusion properties, applied to gas separation membranes.

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