New research just dropped today that makes octopuses even weirder than they already are… let me explain🧵🧪🐙🐡🦑
Alex Palazzo
@ribonucleicacids.bsky.social
Professor of Biochemistry at the University of Toronto. Studies mRNA processing, mRNA nuclear export, mRNA translation, genomic evolution, junk DNA, junk RNA. https://www.palazzolab.com/
FYI there is no "real" reason why Rome "fell." Its power waned for the usual, mundane reasons: widening gap between rich and poor, inability to maintain infrastructure, incompetent leadership, pointless wars, endless persecution of marginalized groups who performed vital labor, etc.
We reengineered the TIR-Learner for 60-100 times faster de novo search of Terminal Inverted Repeat transposons. We completed annotating 579 vertebrate genomes in 4 hours! Kenji Gerhardt did all the heavy lifting for this "side project".
bioRxiv Bioinfo@biorxiv-bioinfo.bsky.social · 2w agoTIR-Learner v4: Accelerated annotation of terminal inverted repeat transposons https://www.biorxiv.org/content/10.64898/2026.07.21.739826v1
This story is now published in @natplants.nature.com ! 🎉🎩 Check out the final article here: nature.com/articles/s41477-026-02361-1 Very similar to the original bioRxiv preprint, with the addition of some cool polysome analysis (in the supplementals)! Thanks and congrats to everyone involved! 🙏
Chloroplast-encoded small subunit extensions reshape the Chlamydomonas chlororibosome - Nature Plants
Using in situ cryo-electron tomography, researchers found a unique ‘arm’ domain on the small subunit of Chlamydomonas chlororibosomes. This discovery suggests that chlororibosome structure is more evo...
nature.com
Florent Waltz@florentwaltz.bsky.social · 6mo agoLong in the making, but happy to present the Chlamydomonas chlororibosome! Cryo-ET🔬reveals a large new domain on the small subunit, built from multiple extensions in conserved ribosomal proteins. bioRxiv 📖: shorturl.at/q44tG This suggests greater chlororibosome diversity than expected! 1/n 🧵
Online Now: The +1 nucleosome functions in RNA Pol II transcription initiation and the transition to elongation Online now:
The +1 nucleosome functions in RNA Pol II transcription initiation and the transition to elongation
By combining biochemical assays and electron cryo-microscopy, Zhan, Abril-Garrido, et al. elucidated key steps of transcription initiation and the transition to elongation in the presence of the +1 nucleosome. The authors demonstrated for the first time that the +1 nucleosome has an active role in the initiation-elongation transition.
dlvr.it
Thoughts on the various Trump administration proposals to revamp US science funding - and what they all have in common:
The Assault On Science Funding Continues
science.org
Review/perspective article by Diederik Laman Trip on some of his and our lab's thinking on how we can study human genetics across different levels. In particular around cell-type specific protein interactions, tissue organization and organ morphology. (paywall, shareable link rdcu.be/fvnpz)
Human genetics across levels of biological organization
Nature Reviews Genetics - Genetic variation influences biological processes across scales; however, deciphering how effects propagate from molecules to whole organisms remains a key challenge in...
rdcu.be
The distribution of public land in cities has serious implications for how we move, how safe we feel, and who can access opportunities. @lanrickbennett.bsky.social + our data viz team find that 80% of T.O. street space is dedicated to motor vehicles:
Who are streets for?
More than 80% of street space in Toronto is inequitably dedicated to motor vehicles. How can this be fairly re-designed?
schoolofcities.github.io
Tuesday I will be talking about our work on how non-adaptive evolution shapes the 5'ends of human protein-coding genes as part of the evol-mut-circle online seminar series (@evolarlin.bsky.social should be posting details in the next day or so)
Interesting. Full deletion of all introns in yeast was actually my project in the Staley lab, *20 years ago*. I actually found a bunch of phenotypes. We did this in collaboration with the Guthrie lab. www.cell.com/cell/abstrac...
A spliceosome-independent eukaryote generated by complete intron removal
Elimination of all spliceosomal introns reveals a spliceosome-independent eukaryote.
cell.com
Cytoplasmic circular dsDNA is a key constituent of stress granules doi.org/10.7554/eLif...
Cytoplasmic circular dsDNA is a key constituent of stress granules
Extrachromosomal circular DNA has been identified as a novel component of stress granule cores, indicating its essential involvement in eukaryotic stress response pathways at the level of protein synt...
doi.org
Does every enhancer work with every promoter? With @jengreitz.bsky.social and Will Greenleaf, we revisit this long-debated question and resolve an outstanding contradiction in the field. A tour 🧵👇 www.biorxiv.org/content/10.6...
Intrinsic promoter responsiveness dictates sensitivity to transcriptional activation by enhancers
Enhancers activate specific target promoters, but whether intrinsic enhancer-promoter compatibility contributes to this specificity is debated. Recent studies using different reporter assays have reac...
biorxiv.org
If you are at #SMBE2026 go see Fanny Pouyet's talk about our work on how TSS-associated mutations and gBGC impact the evolution of gene starts.
Society for Molecular Biology and Evolution@official-smbe.bsky.social · 2mo agoTalks by: Markus Pfenninger Ziyue Gao Fanny Pouyet @hhydrochaerus.bsky.social Sebastián Iturbe Caitlin Price Daniela Souza-Costa / Julia M. I. Barth @jmibarth.bsky.social @alexisgarretson.bsky.social @mikkelschierup.bsky.social Jianzhi Zhang L Donate Weghorn X @weghornlab.bsky.social
Our academic institutions salivate over proxies that purport to predict the future. Academic impact *can only* be accurately achieved post facto - at least 5-10 years. What implementation of prediction tools does do, is switch incentives to short term/low risk work. The antithesis of real impact.
Pedro Beltrao@pedrobeltrao.bsky.social · last mo.@qedscience.bsky.social has come up with a really controversial idea - an AI score for scientific impact. This trained score correlates with the impact factor of published preprints and the binning of papers into discrete quality bins accessed by independent scientists. Backlash in 3, 2, 1... (more)
In Opinion The system that turned Gila monster venom into GLP-1 drugs is being dismantled through research budget cuts, Jeff Coller writes in a guest essay. “Less support for scientists means strange questions no one will get to chase. Exploring those questions is how medicine advances.”
Opinion | We Need to Keep Funding Weird Science
Science turned a serendipitous finding about lizard venom into one of the most important drugs of the century, but that type of research is getting harder to do.
nyti.ms
Ten months ago I had never written an op-ed. I believed the work spoke for itself. It doesn't. When the government calls a lifesaving technology unsafe and scientists stay silent, the silence becomes the story. A new @jhu.edu profile on why I stopped staying quiet: hub.jhu.edu/2026/06/24/j...
A staunch voice in support of science
Jeff Coller, a pioneering RNA biologist, has spent the past year vehemently advocating for the lifesaving promise of research in the face of federal cuts
hub.jhu.edu
The academic hiring system is simply not designed for candidates like me. It privileges a kind of performative intellectualism—the ability to stand at a whiteboard and extemporize about science as if you were some kind of 19th-century naturalist 😂 😂 😂 open.substack.com/pub/inprepar...
Opinion: I Was Not Allowed To Type Prompts Into ChatGPT During My Chalk Talk And This Is Discrimination
By Dr. Rachel Simmons, Postdoctoral Fellow, Stanford University
open.substack.com
Now published! We investigated how polyadenylated RNAs are targeted for decay in the human nucleus. www.nature.com/articles/s41... (1/5)
If unstopped, the trillionaires will eventually have no choice but to take everything from you, your children and your grandchildren. Here's how it happens (and how to stop them). youtu.be/Gd0gmxd36FI
Elon Musk is the world's first trillionaire. How scared should you be?
YouTube video by Garys Economics
youtu.be
Very interesting take! "The vast majority of genes and proteins within cells are effectively bureaucrats, regulating each other rather than building things. ... Why is the most remarkable self-organized system in the known universe so bureaucratic?" link.springer.com/article/10.1...
Cells, Bureaucracy and Corruption - Bulletin of Mathematical Biology
We like to imagine that our students are cheerfully unaware of the ocean of educational bureaucracy that surrounds their peaceful island of learning. Despite the hassles of registering and paying for ...
link.springer.com
As Ebola rages, Moderna and others are racing to develop an mRNA vaccine for the rare Bundibugyo virus driving the current outbreak
Inside the race to develop a new Ebola vaccine
As Ebola rages, Moderna and others are racing to develop an mRNA vaccine for the rare Bundibugyo virus driving the current outbreak
scientificamerican.com
@zackpolanski.bsky.social in the UK and @avilewis.ca in Canada are terrifying exactly the right people.
BladeoftheSun@bladeofthes.bsky.social · 2mo agoElon Musk, the most hated person in the World in the UK, has called Zack Polanski a scumbag and a traitor. What an amazing endorsement.
2/ This study was led by Charlie Moffatt, who just earned their PhD from our lab based in part on this work. @CUAnschutz ⭐️ Preprint here: www.biorxiv.org/content/10.6...
Robust mammalian RNA localization elements are complex and multipartite
The subcellular localization patterns of RNAs are controlled by regulatory elements contained within them. However, for most localized RNAs, the identities of these elements remain unknown. We had pre...
biorxiv.org
From last night's meetup with my good friend Stefan Linquist at a local pub. Waitress: "are you two professors?" Me: "how did you know?" Waitress: "you were talking about introns"
I'm mostly doing "Slow Reads" over on substack (it's always free), so you might get through a cup of coffee reading this one. Make sure you read to the end. profmcinerney.substack.com/p/good-enough
Good enough
What we have learned from absurd evolution
profmcinerney.substack.com
Finally out in @Cellcellpress! Proteins with long IDRs are prone to misfolding during protein synthesis. This is prevented by mRNA 3′UTRs that act as mRNA-based IDR chaperones. www.cell.com/cell/fulltex...
mRNA 3′ UTRs chaperone intrinsically disordered regions to control protein activity
Highly conserved mRNA 3′ UTRs act as co-translational chaperones for intrinsically disordered regions (IDRs), preventing inter-domain misfolding and enabling biogenesis of fully active proteins.
cell.com
#ERGAReads | How Did Evolution Halve Genome Size During an Oceanic Island Colonization? 🏝️ 🧬 🕷️ academic.oup.com/mbe/article/... #genomes #evolution #islandevolution #biology @molbioevol.bsky.social @ub.edu @jrozasub.bsky.social
How Did Evolution Halve Genome Size During an Oceanic Island Colonization?
Abstract. Red devil spiders of the genus Dysdera colonized the Canary Islands and underwent an extraordinary diversification. Notably, their genomes are ne
academic.oup.com
Once again, @dereklowe.bsky.social is not holding back and I am here for it. www.science.org/content/blog... 1/2
The Current Crisis: What's Happening to Science in America
science.org
