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PyrexCorex

@pyrexcorex.bsky.social
478 followers 1.5K following 3.4K posts

Following advances in cellular, molecular & structural biology in a mercifully bot-free space.

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Jeremy Berg @jeremymberg.bsky.social · 11/10/2026
The most comprehensive data that I know isis from Grant-Witness and States United. www.lostfunds.org
lostfunds.org
Lost Funds — $174 Billion Gone
Track the Trump administration’s federal funding disruptions state by state — what was cut or frozen, who it hurts, and how states are fighting back in court.
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GlycoShape @glycoshape.org · 09/10/2026
Phenomenal #glycotime by Meg Lunn-Halbert, Joel Allen and colleagues demonstrates through de novo protein design how steric hindrance controls N-glycan maturation ⬇️ doi.org/10.64898/202... Protein design with RFdiffusionAA coupled with glycosylation with GlycoShape 🧪
screenshot of Fig. 2 in the paper, titled "Systematically altering steric restriction controls glycan processing" the following corresponds to the figure caption in the paper.
Panel a, AF3-predicted protein with GlycoShape-modeled Man9 glycan (green) for glycoproteins THRgly1-4. b-d, Deconvoluted intact
mass spectra for analyzing native glycosylation with 1–3 major peaks corresponding to glycosylation shifts labeled. Glycans
matching in theoretical molecular weight to the corresponding shift are schematically annotated as follows: mannose residues as
green circles, N-acetyl glucosamine residues as blue squares, galactose as yellow circles, sialic acid as pink diamonds, and glucose
as blue circles. Unglycosylated sizes are estimated based on predicted MW and labeled, when present. b: Native glycosylation. c:
Native protein digested with Endo H. d: Overlaid protein from kifunensine-treated cells (color, solid line) and digested with Endo H
(gray, dotted line). Estimated predominant glycans present are shown in MW (Da) differences from predicted unglycosylated size.
For peak table see Supplementary Data S3; amino acid sequences provided in Supplementary Data S1.
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Takashi Akera Lab @takashiakeralab.bsky.social · 08/10/2026
Rapid protamine evolution suppresses meiotic drive in Drosophila | Science Advances www.science.org/doi/10.1126/...
science.org
Rapid protamine evolution suppresses meiotic drive in Drosophila
Many animal species replace histones with protamines during spermatogenesis. Although essential for sperm function, protamines evolve rapidly for reasons that remain unknown. Using in vivo gene replac...
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Xavier Charpentier @labxc.bsky.social · 07/10/2026
Very happy that this work found a good home at @pnas.org Thanks to the reviewers for their constructive comments. www.pnas.org/doi/10.1073/...
pnas.org
Two D-loop resolution systems enable natural genetic transformation in bacteria | PNAS
Natural transformation is a widespread mechanism driving genetic exchanges in bacteria. It proceeds from the capture of extracellular DNA released ...
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Will Ratcliff @wcratcliff.bsky.social · 07/10/2026
Out today in @nature.com: our review on how single cells evolve into multicellular organisms. With Ozan Bozdag, @kaitong25.bsky.social, Peter Yunker, and @matthewherron.bsky.social. rdcu.be/9ZuiKow9twKa For an overview, check out the video below.
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RCSB Protein Data Bank @rcsbpdb.bsky.social · 02/10/2026
Explore images that structural biologist Irina Bezsonova (UCONN Health) created for #inktober in PDB-101's #sciart gallery
pdb101.rcsb.org
PDB101: Irina Bezsonova Gallery
PDB-101: Training, Outreach, and Education portal of RCSB PDB
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kottke.org @kottke.org · 01/10/2026
Map of the Lighthouses of the World. Each lighthouse sweeps out its actual arc and the reach of the beams is true to scale. Very cool. [kottke.org]
kottke.org
Map of the Lighthouses of the World
From mapped.earth, a map of every lighthouse on the planet, along with other charted lights like lighted buoys and such. The screenshots above are static but the lights on the real map move: each lighthouse sweeps out it
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Scott McGrath @smcgrath.phd · 01/10/2026
🧪 Google DeepMind's SynthIDBio embeds a statistical watermark into both the amino-acid sequence and 3D structure of AI-designed proteins. While it preserves biological function, the tag can still be scrubbed by running sequences through another tool, leaving detection keys in dispute. 💻🧬
nature.com
Secret watermark labels proteins as ‘made by AI’
An innovative safeguard could help to flag proteins devised by artificial-intelligence tools such as AlphaFold, but the digital marker can be erased.
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Colin Carlson @colincarlson.bsky.social · 01/10/2026
Very cool new preprint I was very excited to be a VERY small part of, from @viralverity.bsky.social and @nathangrubaugh.bsky.social: "Phylodynamic analysis reveals asymmetric and accelerating global spread of dengue virus" www.biorxiv.org/content/10.6...
Figure 1Figure 4
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Nature @nature.com · 01/10/2026
Nature review article: Written in development and lost in ageing: the grammar of cellular identity go.nature.com/4jzoFuF
go.nature.com
Written in development and lost in ageing: the grammar of cellular identity - Nature
Ageing reflects progressive decanalization of mammalian cell identity, driven by erosion of a regulatory grammar written during development.
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Svetlana Dodonova @dodonova-sveta.bsky.social · 30/09/2026
New preprint from Dodonova lab 🔔! Capturing multiple states by cryo-EM❄️, we show for the first time how archaeal RNA Polymerase engages a nucleosome and forms direct contacts with histones! 🧬 Great work by Gabriele & a fantastic collaboration with Dina Grohmann! 🧵 www.biorxiv.org/content/10.6...
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Rasmus Jensen @rasmusjensen.bsky.social · 25/09/2026
🎉 Out today in Cell: the paper I've been looking forward to sharing for a long time 🎉 We used cryo-ET to find a molecular machine nobody knew existed on the surface of a minimal bacterium, and worked out what it does. 🧵(1/7) #TeamTomo #cryoET
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Nature @nature.com · 24/09/2026
AlphaFold is being upgraded to better represent some of the least known and deadliest species: viruses go.nature.com/4cZivjx
go.nature.com
AlphaFold 'goes viral': database adds protein complexes of common viruses
AI predictions could help with pandemic preparedness, but they will need experimental confirmation.
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Arnaud Vanden Broeck @avbroeck.bsky.social · 23/09/2026
Very happy to share the first paper from our lab, out now in Nature Communications!🎉🥳 Structural basis of step II Spliced Leader RNA trans-splicing in trypanosomatid parasites 🧬🔬 🔗 www.nature.com/articles/s41... @natcomms.nature.com @universitedeliege.bsky.social @rockefeller.edu #cryoEM #cryo-EM
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Science Magazine @science.org · 24/09/2026
A recent Science Translational Medicine Review synthesizes the translational pipeline of research decoding how tumors interact with both the central and peripheral nervous systems to fuel their growth. Learn more on #WorldCancerResearchDay: scim.ag/3V3HaNK
scim.ag
Cancer neuroscience: Mechanisms to medicine
Bidirectional cross-talk between neural circuits and tumors drives cancer progression and can be therapeutically targeted through drug repurposing.
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Martin Pacesa @martinpacesa.bsky.social · 21/09/2026
ʙɪɴᴅᴄʀᴀꜰᴛ2 is out, and we're not waiting for the paper. The full code drops today, free for academic and industry use. We're releasing it early so you can start designing right now, and bring its full power to the current Adaptyv competition. github.com/PacesaLab/Bi...
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Daniel Hurdiss @danielhurdiss.bsky.social · 21/09/2026
Excited to share that our norovirus NS3 study is now online in Nature Communications! 🎉 These enzymes, found across an entire order of RNA viruses, have long been molecular motors in search of a function. We think we’ve uncovered their role. (🧵) www.nature.com/articles/s41... #virology #cryoEM
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Chise @sailorrooscout.bsky.social · 18/09/2026
Oh to be a little Tardigrade walking around a microscopic volvox algae colony. 🫧🐻🧪
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Nature @nature.com · 15/09/2026
Immune cells that fight stomach bugs can migrate from the gut to the brain, where they establish a lasting ‘memory’ of previous infection. go.nature.com/4yZK30T
go.nature.com
‘Stomach bugs’ send protective immune cells rushing from gut to brain
Voyaging gut-derived immune cells ‘remember’ past stomach infections in mice.
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Kazuhiro Maeshima @kazu-maeshima.bsky.social · 15/09/2026
How are mitotic chromosomes built? Our Review @cp-trendsgenetics.bsky.social revisits the classical chromosome scaffold model and connects it to condensins, topoIIα, and physical forces. We propose interphase chromatin domains as “building blocks”🧩of chromosomes: authors.elsevier.com/a/1nmwrcQbJI...
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FocalPlane @focalplane.bsky.social · 10/09/2026
🔬🔦Our latest Imaging spotlight highlights FOCUS-3D, a tool for segmenting cells from 3D fluorescence images from Qinghua Zhang, @mads100tist.bsky.social, @gqyu.bsky.social & team. They tell us what’s different about FOCUS-3D and what makes it so useful and usable for biologists.
focalplane.biologists.com
Imaging spotlight: FOCUS-3D - FocalPlane
Imaging spotlight: FOCUS-3D - News
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EMBL Events @events.embl.org · 10/09/2026
🧬 Ready to dive into the world of RBPs? The #EMBLRBP Conference is back in 2027! Submit your abstract by 6 December 2026 to present your work to our global community of researchers: s.embl.org/rbp27-01-bl Date: 15 – 18 March 2027 EMBL Heidelberg and Virtual Organised with the support of KAUST.
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Journal of Evolutionary Biology @jevbio.bsky.social · 23/07/2026
Our study shows that mutation-rate differences between daughter DNA strands persist throughout evolution rather than converging to equal fidelity. Evolution maintains asymmetric replication fidelity through self-organisation of mutation rates: doi.org/10.1093/jeb/... Akashi and Furusawa 2026
doi.org
Replication fidelity difference between daughter chains persists during evolution
Abstract. While mutations are the engine of evolution, how mutation rates themselves evolve remains poorly understood. Previous simulation and experimental
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Krishna Shrinivas @shrinivaslab.bsky.social · 07/07/2026
This is now published in PNAS! And double-treat, we also made the cover :) www.pnas.org/doi/10.1073/...
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Turner Lab @lab-turner.bsky.social · 08/07/2026
New preprint 📢 Thrilled to share our long-awaited work on the role of RSX in marsupial X-inactivation. This was a huge team effort over the years, led by @aureliencourtois.bsky.social @sermenchero.bsky.social Sugako Ogushi and Waz Varsally, that allowed us to set up genome editing in opossum embryos
biorxiv.org
Genome editing of marsupial RSX reveals conserved and divergent principles in mammalian X-inactivation
X-chromosome inactivation balances X-gene dosage between the sexes in eutherians and marsupials. The lncRNA Xist mediates X-inactivation in eutherians but is absent from marsupials. An evolutionarily ...
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Maxim Greenberg @maxvcg.bsky.social · 08/07/2026
This is brilliant! www.nature.com/articles/s41...
nature.com
Identifying critical lysines in mammalian histone H3 with high-throughput CRISPR prime editing - Nature Genetics
This study uses a precise and efficient clustered regularly interspaced short palindromic repeats (CRISPR) prime editing system to substitute lysine residues in histone H3, individually or in combinat...
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Robert Arkowitz @robertarkowitz.bsky.social · 03/07/2026
Manipulation of protein translation and stem cell self-renewal by CRISPR activation of rRNA transcription | Science www.science.org/doi/10.1126/...
science.org
Manipulation of protein translation and stem cell self-renewal by CRISPR activation of rRNA transcription
Ribosomal RNA (rRNA) transcription rates vary during development, and their dysregulation is linked to diseases such as cancer and ribosomopathies. Owing to their high abundance and genomic redundancy...
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Thiago Carvalho @cyrilpedia.bsky.social · 09/06/2026
'(...) gene regulatory network inference methods largely neglect the dynamic nature of biological systems. To overcome this conceptual disconnect, we present RegVelo, a bottom-up, actionable & interpretable deep learning framework that jointly models splicing kinetics & gene regulatory interactions'
cell.com
RegVelo: Gene-regulatory-informed dynamics of single cells
RegVelo introduces an end-to-end generative framework that jointly infers gene regulatory networks and developmental dynamics. It serves as an actionable in silico “cell,” enabling researchers to simu...
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Kurianlab @kurianlab.bsky.social · 13/05/2026
What a beautiful piece of work. Congrats @jomaalab.bsky.social Inspirational
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Max Renner @maxrenner.bsky.social · 15/05/2026
Super happy to see the final version of our paper out now 🎉🎉🎉 www.science.org/doi/10.1126/... Proud of PhD student Rupesh @rupeshjayachandran.bsky.social and postdoc Erwan for doing really nice work on this 😊
science.org
Open and closed forms of assembled henipavirus nucleoprotein suggest structural basis of genome access
Henipavirus nucleoprotein assemblies exist in different conformations, indicating temporary release of genome for RNA synthesis.
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T. Ryan Gregory 🇨🇦 @tryangregory.bsky.social · 15/05/2026
Ok, time to start to keeping a list of calm-mongering claims about hantavirus that turn out to be wrong. 🧵
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Brandon Bishop @brandontbishop.bsky.social · 01/05/2026
Welcome to the last half of the US federal fiscal year. Here is where we're at with National Science Foundation--the agency that funds basically everything other than biomedical research at American universities--grant numbers. grant-witness.us/funding_curv...
NSF grant curve from link for 2021 through 2026, with each year shown as a different color. By this point in the year, NSF made 3,300 or more grants in 2021-2024 and 2,087 in 2025. This year 737 have been awarded. Both this year and 2025 seem to have an odd slow down about now in the rate of new grants not present in earlier years, in addition to the general lower rates.NSF's geosciences directorate award numbers, basically identical in shape to the overall NSF curves. Prior years saw around 400-500 grants awarded by this point in the fiscal year, 2025 saw only 278 grants awarded, this year has only 95 grants awarded.
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Yale MB&B @yalembb.bsky.social · 31/03/2026
Yale MB&B's Karla Neugebauer and Guillermina Kubaczka have been featured in a new @natmethods.nature.com piece 🌍🔬 The article spotlights researchers bridging the molecular and planetary scales to address global health challenges. @karlaneugebauer.bsky.social www.nature.com/articles/s41...
nature.com
Cell biology’s fantastic voyage to Planet Earth - Nature Methods
A nascent group of researchers sees planetary health as an urgent reason to bridge the molecular and planetary scales. This is shaping their strategies, methods, collaborations and outlook about their...
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Carolyn Bertozzi @carolynbertozzi.bskyverified.social · 13/04/2026
Thank you #NobelLaureate Jack Szostak for sharing these thoughts, which many US scientists and physicians resonate with newsletter.ofthebrave.org/p/im-a-nobel...
newsletter.ofthebrave.org
I’m a Nobel Prize-winning immigrant. I can no longer recognize this country.
Attacks on science and immigrants are destroying America.
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Daniel Hurdiss @danielhurdiss.bsky.social · 09/04/2026
Our paper describing the #cryoEM structures of unusual spike proteins from marine mammal–infecting gammacoronaviruses is now published in PLOS Pathogens! 🐬 journals.plos.org/plospathogen...
journals.plos.org
Cetacean coronavirus spikes highlight S glycoprotein structural plasticity
Author summary Coronaviruses are well known for their ability to jump between species, a process driven mainly by the spike protein on their surface. In this study, we examined spike proteins from coronaviruses found in marine mammals (whales and dolphins) to better understand how these viruses evolve and interact with their hosts. Using structural biology and mass spectrometry, we discovered several unusual features of the cetacean spike proteins. These spikes contain an extra domain within their receptor-binding region that resembles cupin proteins, assemble into trimers in a novel way that hides the receptor-binding domains, and show clusters of sugars (O-linked glycans) near the sites thought to interact with host receptors. These distinctive features suggest that cetacean coronaviruses may use a different entry mechanism, in which the extra domain acts as a switch to reveal the hidden receptor-binding regions. Such a mechanism could affect which species these viruses can infect, how easily they cross species barriers, and how they evade the immune system. Our findings emphasize the structural diversity and modularity of coronavirus spike proteins, highlight the unique adaptations of coronaviruses in marine mammals, and provide insight into their potential to give rise to new diseases in other species.
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André Nadler @nadlerlab.bsky.social · 23/03/2026
It’s incredibly hard to study lipids in biological membranes on the nanoscale. You need near-perfect information on both membrane ultrastructure and lipid density. Lipid-CLEM, now out in @natcellbio.nature.com brought to you by @mathilda95.bsky.social changes that: www.nature.com/articles/s41...
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Karim Majzoub @karimaj.bsky.social · 06/03/2026
We found a viral Trojan Horse: a virus can hide inside another virus.This one surprised us: deltaviruses don’t just borrow a helper virus. They can travel inside it. A literal Trojan Horse “virus-in-a-virus” route into cells. 🤯 Kudos to 1st author @viroscope.bsky.social and co-authors !
sciencedirect.com
Deltaviruses spread through a viral Trojan Horse
Hepatitis D-like satellite viruses, known as deltaviruses, have been recently discovered in a wide range of animals. These viruses are thought to expr…
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Alejandro Montenegro @aemonten.bsky.social · 02/03/2026
"we propose that the protoribosome was a parasite (...). If this view is correct, then like the spliceosome in the stem eukaryote, a repurposed host-parasite interaction led to a dramatic change in cell biology at the base of the tree of life, in this case leading to the exit from an RNA world"
academic.oup.com
A symbiotic origin of the ribosome?
Abstract. The origin of life is one of the great mysteries of science. Of the multiple unsolved problems, the origin of the translation system (the means b
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Karolin Luger @nucleosomepolice.bsky.social · 28/02/2026
Paper alert from @codyz.bsky.social y.social and Yang Liu. New mechanism for chromatin remodeling by ATRX. Super cool story. Congrats to #lugerlab alumni. www.biorxiv.org/content/10.6...
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Carl de Boer @carldeboer.bsky.social · 25/02/2026
We wrote a perspective "How to build the regulatory genome: a constructionist guide to the cis-regulatory code", out in Development yesterday. Title says it all. Find it here: journals.biologists.com/dev/article/...
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The Groth lab @grothlab.bsky.social · 25/02/2026
DNA replication globally disrupts the epigenome. But does this create a chromatin-access opportunity for TF binding to facilitate cell identity change? Now 𝐫𝐞𝐩𝐥𝐢-𝐀𝐓𝐀𝐂-𝐬𝐞𝐪 shows 𝘥𝘦 𝘯𝘰𝘷𝘰 chromatin opening & TF binding occurs specifically post-replication, in cellular differentiation & reprogramming!
cell.com
Post-replicative chromatin accessibility predicts cell fate change
Knudsen and colleagues use repli-ATAC-seq to compare replicated and unreplicated chromatin in two models of cell identity change. They find that lineage-specific elements are accessible earlier in rep...
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Darío Lupiáñez @dariloops.bsky.social · 24/02/2026
🤩💪 Out now! 3D regulatory hubs in sex determination With @mamartirenom.bsky.social & Capel labs, led by @imotagom.bsky.social & @jrotwitguez.bsky.social 1️⃣ METALoci – explore #3DGenome 🧬 2️⃣ Non-coding region controlling Fgf9 🧩 3️⃣ Meis genes = new key players 🌟 👉 rdcu.be/e5sm2 1/n Bluetorial 👇
rdcu.be
Chromatin spatial analysis by METALoci unveils sex-determining 3D regulatory hubs
Nature Structural & Molecular Biology - METALoci, a new three-dimensional genome computational tool, reveals a major rewiring of regulatory interactions during sex determination. By combining...
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Faraz Mardakheh @mardakheh.bsky.social · 21/02/2026
🎉Proud to present our latest paper, out now in Nature Communications: www.nature.com/articles/s41... RNA Binding Proteins (RBPs) are often full of intrinsically disordered regions (IDRs), but what these regions do during RNA recognition is often unclear. 1/10 #RNA #IDR #RBP
nature.com
An intrinsically disordered region mediates RNA-binding selectivity and cellular activities of LARP6 - Nature Communications
LARP6 is an EMT-associated RNA-binding protein with diverse RNA targets. Here, the authors show that the N-terminal disordered region of LARP6 promotes RNA-binding selectivity by modulating the adjace...
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Tugce Aktas @aktast.bsky.social · 25/02/2026
Our most recent work on the “function and evolution” of #nuclear-speckles is now online at Cell @cp-cell.bsky.social doi.org/10.1016/j.ce... Read the thread👇 for the highlights of our findings.
doi.org
Redirecting
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PyrexCorex @pyrexcorex.bsky.social · 10/02/2026
nature.com
Dozens of researchers will move to France from US following high-profile bid to lure talent
Large proportion worked at Columbia University, which had its grants cut and frozen by the administration of US President Donald Trump.
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Olga Nesterova @onestpress.onestnetwork.com · 23/01/2026
WHO removing Us Flag
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PyrexCorex @pyrexcorex.bsky.social · 23/01/2026
reuters.com
Moderna curbing investments in vaccine trials due to US backlash, CEO tells Bloomberg TV
Moderna does not plan to ‌invest in new late-stage vaccine trials because of growing opposition to immunizations from U.S. officials, CEO Stephane Bancel said ‌in an interview with Bloomberg TV ​on Th...
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David Ho @davidho.bsky.social · 20/01/2026
This is the most astonishing graph of what the Trump regime has done to US science. They have destroyed the federal science workforce across the board. The negative impacts on Americans will be felt for generations, and the US might never be the same again. www.nature.com/immersive/d4...
This line graph illustrates the percentage change in agency staff levels from the previous year for nine major U.S. federal scientific and health organizations between the fiscal years 2016 and 2025. The agencies tracked include the CDC, Department of Energy, EPA, FDA, NASA, NIH, NIST, NOAA, and NSF. For the majority of the timeline between 2016 and 2023, the agencies show relatively stable fluctuations, generally staying within a range of +5% to -5% change per year. However, there is a dramatic and uniform plummet starting in the 2024–25 period. Every agency depicted shows a sharp downward trajectory, with staffing losses ranging from approximately -15% to over -25%. The Environmental Protection Agency (EPA) shows the most significant decline, dropping to roughly -26%, while the National Institute of Standards and Technology (NIST) shows the least severe but still substantial drop at approximately -15%.
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Dr. Keith R. Brunt @profbrunt.bsky.social · 15/01/2026
Epstein-Barr Virus #EBV was linked to #MultipleSclerosis - now a plausible cause has been found, misidentification by longterm memory T-cells that pick on the wrong protein, ANO2, instead of the EBV-antigen. Massive inflection towards the elimination of MS!!! 🧪🧠Cell www.cell.com/cell/fulltex...
cell.com
Anoctamin-2-specific T cells link Epstein-Barr virus to multiple sclerosis
Researchers identified anoctamin-2 (ANO2) as a frequent autoimmune target in multiple sclerosis, with T cell responses against ANO2 occurring in over half of patients. These ANO2-specific T cells shar...
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Michael Aregger @michaelaregger.bsky.social · 31/12/2025
Check out the latest paper from the Gonatopoulos-Pournatzis lab using CRASP-seq, an RNA-coupled #CRISPR screening platform, to uncover novel #splicing regulators.
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