Structural basis of biofilm formation mediated by the Pseudomonas aeruginosa fibrillar adhesin CdrA led by @olivia--smith.bsky.social Collaboration with @alexbateman1.bsky.social , Andres Floto and @geiselbiofilm.bsky.social labs
Hiren Joshi
@glyco.me
Glycobioinfonaut, Associate Professor at the Copenhagen Center for Glycomics, University of Copenhagen. @hirenj.11 on Signal
Well, it was fun while it lasted. I’m going to have to retire this plugin as PyMOL stopped bundling the browser engine. It was so easy adding glycans to random proteins with the GUI, but alas, no more.
Hiren Joshi@glyco.me · last yr.If anyone is keen on testing the reglycosylation plugin for PyMOL, please get in touch! There’s a few rough edges I’d like to iron out, and would appreciate feedback.
Who would have thought you could use so many tokens getting Claude to do the hard work to ingest GEO datasets. The scRNA-seq world is wild.
I love this concept so much. Haven’t checked out the architecture, but I bet its a bunch of wasm running this. I notice that Claude is on the contributors on github. The tool has really been transformational in making wasm available to me personally, as it generated standard tooling.
AI x Bio Discovery@aixbiobot.bsky.social · 3mo agoProtSpace: Protein Universe in Your Browser [new] ...interactively visualizes pLM embedding spaces to explore complex protein relationships with diverse annotations and 3D structures in the browser.
I have recently ventured deep into python notebook land these days, and I would love to know how people handle moderately complex notebooks. For simple stuff code+output is easy. But anything larger and it becomes quickly unreadable. Jupyter code hiding/folding is completely inscrutable…
🧵 New paper from @proteaglyco.bsky.social out in Analytical Chemistry! We used anion supercharging to unlock next-generation O-glycan structural analysis: - 4× greater signal - 5× better fragmentation Here's a thread, digging into each figure: doi.org/10.1021/acs....
Anion Supercharging Enables Structural Analysis of Oxidatively Released O-Glycans
O-glycan analysis faces analytical challenges due to poor fragmentation characteristics of oxidatively released O-glycan acids, which can preserve labile O-acetyl modifications but suffer from charge ...
doi.org
I am hiring an associate scientist (non-PhD). If you have interest in #glycotime and antibody de novo sequencing please consider applying: regeneron.wd1.myworkdayjobs.com/en-US/Career...
Associate Scientist - Analytical and Biological Mass Spectrometry (ABMS) (1 of 2)
Regeneron Pharmaceutical's Analytical and Biological Mass Spectrometry Group (ABMS), located in Tarrytown, NY is seeking a highly motivated Associate Scientist. In this role, you will work in an innov...
regeneron.wd1.myworkdayjobs.com
This looks to be a follow up on the glycofibrils from a little while back. Really interesting to see the glycans resolved there. Does anyone have any feeling about how much we should rely on modelled structures/conformations into the cryo? What do people use to check their work?
cryoEM papers@cryoempapers.bsky.social · 3mo agoStructural N- and O-glycans revealed by high-resolution cryo-EM analysis of tubular mastigonemes pubmed.ncbi.nlm.nih.gov/42024774/ #cryoEM
It all makes chemical sense, and one might say: well, why not? Given that the amino-acid residues in a protein can form highly specific H-bond arrangements - that's often what they use for their selective binding and catalysis - why shouldn't those be arranged to mimic a nucleotide base? /14
We are proud to announce the discovery of Glyco-Carbohydrates, a paradigm shift in glycobiology! Traditional glycoconjugates (proteins, lipids & RNA) max out at 50% carbohydrate. Ours are 100% carbohydrate AND glycans, unlocking truly homogenous properties. TBA April 1st, 2027! 🍬 #glycotime
Look, I haven’t seen the code, maybe Claude helped out implementing it, maybe it was hand crafted. It doesn’t matter to me. The fact that software is fun and quirky again makes me happy.
PastelBio@pastelbio.bsky.social · 5mo agoStrucTTY: An Interactive, Terminal-Native Protein Structure Viewer www.biorxiv.org/cont... --- #proteomics #prot-preprint
The three enzymes ALG3, ALG9, and ALG12 catalyze the synthesis of the branched mannose core in N-glycans in four distinct steps. Now, their structures reveal the molecular logic of oligomannose core assembly #glycotime www.nature.com/articles/s41...
Structures of ALG3/9/12 reveal the assembly logic of the N-glycan oligomannose core - Nature Chemical Biology
Three endoplasmic reticulum luminal mannosyltransferases ALG3, ALG9 and ALG12 catalyze the synthesis of the branched mannose core in N-glycans in four distinct steps. Now, cryo-electron microscopy str...
nature.com
This will be great if it comes to fruition - I have this dream that we can eventually ditch journals, and move to collections of communities (society review) for peer review. A system of closed review, that then opens up when finished will be amazing, and could be built with this.
daniel holmgren 🫠@dholms.at · 6mo agohey we're really working on permissioned data! read the first in a series of posts i'll be doing about our design decisions along the way. this one is about our decision to not do an e2ee system
Finally, a detailed review about C-mannosylation: mechanism of C-mannosyltransferases and the influence of the C-mannosylation on the function of several proteins. Highly recommended to everyone in this type of post-translational modification! tinyurl.com/3ywjmfk3 #glycotime
"Structural analysis enabled us to convert Tn-specific mAbs into STn-specific mAbs through modification of VH complementarity-determining region 3, demonstrating the versatility of this approach" #glycotime 😎🧪 www.nature.com/articles/s41...
Structure-guided phage display discovery of antibodies for (S)Tn-glycans in protein context - Nature Chemical Biology
Structural studies of certain Tn and STn antigen-targeting antibodies reveal that their VH and VL domains recognize the glycan antigen and the adjacent peptide region, respectively, enabling a VH doma...
nature.com
Just a reminder that when the Nazis were marching in to Copenhagen, Neils Bohr chose to dissolve his medal rather than have any Nazi take possession of it.
María Corina Machado presents Trump with her Nobel peace prize medal
Trump heaped praise on the Venezuelan opposition leader for presenting him with ‘her Nobel peace prize for the work I have done’
theguardian.com
Authors use “Siglec-7 and -15…Fc chimera to demonstrate that CHST1-mediated 6-O-sulfation markedly enhanced binding to select O-glycoproteins, namely MAdCAM1, CD43, and PSGL-1” www.biorxiv.org/content/10.6...
Siglec-7 and -15 recognize repeated clustered sulfo-sialo O-glycan motifs on select O-glycoproteins
Siglecs are key immunoreceptors in immune homeostasis and cancer immunosuppression. Diverse endogenous and exogenous sialoglycan ligands induce Siglec-mediated immunoregulation, but the nature of endo...
biorxiv.org
The robots are not coming for your jobs, but bullshitters with robots ARE competing for your jobs, and unless we decouple publishing metrics from career paths (financial gain), we are going to lose both careers and our capacity to share information. doi.org/10.1126/science.adw3000
Scientific production in the era of large language models
With the production process rapidly evolving, science policy must consider how institutions could evolve
doi.org
A tribute to Stuart Kornfeld, pioneering #glycotime scientist whose work on mannose-6-phosphate receptor lysosomal trafficking (among many other contributions) was highly influential to our work 🫡 www.jci.org/articles/vie...
JCI - A tribute to Stuart A. Kornfeld (1936–2025)
jci.org
There are so many quotes in this article that read as dystopian satire - but the worst has to be the overall idea that the one thing conservation efforts need is the Silicon Valley treatment. Pauli’s phrasing of “not even wrong” seems very apt here.
‘They didn’t de-extinct anything’: can Colossal’s genetically engineered animals ever be the real thing?
The bioscience startup has attracted billions in investment – and a flurry of criticism, but founder tells the Guardian plans to bring back the woolly mammoth will not be derailed
theguardian.com
🚨 Are you into comp chem/biophys? Do you like glycobiology? Are you located around Freiburg Germany? Do you like me as a person? Want to see an open lecture about Computational Glycobiology/Biophysics in Freiburg, Germany, delivered by me?! 15 Dec, 17:15 HS Chemie @ Alberstrasse 21, 79104 Freiburg
Hey @biorxivpreprint.bsky.social @altmetric.com , I haven’t been able to see the BlueSky metrics for preprints for a while now on the BioRxiv website, so I am missing out on all the salacious gossip about the preprints. Is this a known bug?
Another bump for the postdoc and PhD positions still open at the center and postdoc specifically within my group (same link to apply). We’re looking for wet/dry lab, and I’m specifically after people who do magic with computers!
Hiren Joshi@glyco.me · 10mo agoemployment.ku.dk/faculty/?sho... Hi all! We’re hiring at our brand new Center for Glycocalyx Research, across all areas - but I am also looking for postdocs to join my group specifically!
Reminder: our postdoc and PhD positions are still open. We work across different areas (wet and dry lab), but I am especially after people with a computational biology, bioinformatics, pytorch whisperer kind of background. Protein design and OpenFold/AF also counts.
Hiren Joshi@glyco.me · 10mo agoemployment.ku.dk/faculty/?sho... Hi all! We’re hiring at our brand new Center for Glycocalyx Research, across all areas - but I am also looking for postdocs to join my group specifically!
First neurons didn’t appear overnight. We trace their roots to ancient secretory cells - showing how lifestyle & behavior shaped the evolution of first synapses.🧠🌊 #Evolution #Neuroscience Our latest in @natrevneuro.nature.com Link: rdcu.be/eMX3E @jeffcolgren.bsky.social @msarscentre.bsky.social
The evolutionary origins of synaptic proteins and their changing roles in different organisms across evolution
Nature Reviews Neuroscience - Recent studies have shed further light on the evolutionary origins of chemical synapses, In this Review, Colgren and Burkhardt explore how ancient proteins were...
rdcu.be
