Sjors Scheres

Max is a fantastic scientist!! 🤩

Again? 🤔

We are looking for a computational postdoc to work with us on new optimisation algorithms to make #RELION even better. Join our bubbly team at the @mrclmb.bsky.social in Cambridge, UK. 🤗 RTs appreciated.

mrc.tal.net/vx/appcentre...

Our amazing Sofia did it again! She previously won the Perutz Prize for best PhD thesis at the LMB; this year she has won the Joan Steitz Prize for best postdoctoral work. She is on the job market for an independent position. Any institute would be lucky to have her. 🥳

Jokes aside, for those of you taking long flights: keep moving around & drink plenty. A deep vein thrombosis is dangerous and extremely painful; I don't recommend it. I'm not overweight, not a smoker or heavy drinker, and in excellent physical shape. My only risk factor was being a 40+ male.

Apparently, I am "take 12 weeks of anti-coagulant and lots of paracetamol after a transatlantic flight" years old. ☹️

We are looking to hire a postdoc to take this and other TDP-43 assay development forward! Please re-post!

Asymmetric gating of a homopentameric ion channel GLIC revealed by cryo-EM | PNAS Pentameric ligand-gated ion channels (pLGICs) are vital neurotransmitter receptors that are key therapeutic targets for neurological disorders. Alt...

We are excited to share our latest work on GLIC published in @pnas.org, where we developed a #cryoEM data processing strategy that allowed us to isolate and reconstruct multiple asymmetric states, revealing detailed insights into the channel’s activation mechanism. tinyurl.com/mwtb4rpj

Chris Russo and Anastasiia Gusach have developed a new method to prepare #cryoEM samples that avoids protein damage during freezing

Read more: www2.mrc-lmb.cam.ac.uk/a-new-method...

#LMBResearch

YouTube video by Cambridge Biomedical Campus Welcome to the Cambridge Biomedical Campus

What do apple trees, Nobel Prizes, cows, and world-changing innovation all have in common? Well, they're all part of a new animated journey across one of Europe’s most extraordinary places, the Cambridge Biomedical Campus.

youtu.be/2K7Txdwb_k4

You might like our lego @johninnescentre.bsky.social

Lego lab with PCR machines, microscopes, cell culture and Bunsen and Beaker

I’m pleased to announce that my Lego lab will officially be moving to this building should it be funded

Biological Laboratory | LEGO® Ideas This is a two-floor realistic Biological Laboratory building. In this design, I try to tell stories about biologists, introduce biology concepts to general publ…

I just made an account and voted for this biology laboratory made of LEGO to "promote biological research and inspire more people into the world of biology". They need 10K votes. Reposting and/or voting below would be helpful. 🤗
beta.ideas.lego.com/product-idea...

the GNE headcrab went for its latest victim today, a wild @sjorsscheres.bsky.social…

Thankfully @przemekdut.bsky.social was there to save the day!

Black and white portrait of John Gurdon, 1971

John Gurdon, former Group Leader and Head of @cellbiol-mrclmb.bsky.social has died.
Despite calling himself a "total non-intellectual” his work to reprogramme somatic cells to pluripotent stem cells transformed the field of developmental biology.
More: www2.mrc-lmb.cam.ac.uk/john-gurdon-...
#LMBNews

My post was not a criticism of this preprint in itself. I have sent my comments to improve it to the authors directly.

The problem with closed source software is that figuring out recipes is the only progress that remains to be made (besides the company's efforts).

If you are interesting in developing new algorithms for #cryoEM as a #PhD student or as a #postdoc, then do email or DM me. We have exciting opportunities coming up.

Below (by @landerlab.bsky.social) is the 2nd #cryosparc recipe on @biorxivpreprint.bsky.social in a month. I remain worried about closed-source software affecting progress in #cryoEM. We should develop new algorithms instead!

#OpenSoftwareAcceleratesScience

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

London Ulez reduced nitrogen dioxide to legal limit, mayor says The mayor of London says the fall in airborne toxins is due to the Ultra low emission zone expansion.

184 years earlier than predicted, London has met the legal limits for toxic NO2 for the first time.

This historic milestone proves that bold action like expanding ULEZ works, protecting children’s health and giving millions cleaner air to breathe.

Stop blaming migrants and tackle UK’s real problems, 100 charities tell home secretary A letter warns Shabana Mahmood that ‘targeting refugees will do nothing to tackle’ problems with housing and the NHS

Finally someone speaking up! "Targeting refugees will do nothing to tackle [the UK's] structural issues or improve people’s lives". If you agree, why not send a signal and donate to Refugee Action today (donate.refugee-action.org.uk/page/99385/d...)?

www.theguardian.com/politics/202...

File systems are often invisible, but so important! #relion may run multiple times faster on a well tuned file system, compared to a bad one. Appreciate your local compute people who set this up for you, and be patient with them when it fails (which is very stressful).

We have an open post-doc position in my group to study mRNA cleavage and polyadenylation using biochemical reconstitution and cryoEM.

Please get in touch if you are interested in joining this amazing team! 🔬🧬🤩
#RNA #cryoEM

I feel some responsibility, as we develop the software. But helical reconstruction is prone to getting stuck in local minima, and unfortunately still requires a lot of self-criticism. The most important one: if you don't see expected features in the map, don't trust it!

Or this one, from last week, again in @pnas.org:
www.pnas.org/doi/epub/10....

Author Correction: Fully co-factor-free ClearTau platform produces seeding-competent Tau fibrils for reconstructing pathological Tau aggregates - PubMed Author Correction: Fully co-factor-free ClearTau platform produces seeding-competent Tau fibrils for reconstructing pathological Tau aggregates

But so many bad structures get through the review process. For example:
pubmed.ncbi.nlm.nih.gov/38816466/

GSK3β phosphorylated tau filaments are probably not like those from AD brains - PubMed GSK3β phosphorylated tau filaments are probably not like those from AD brains

I recently wrote this for @pnas.org:
pubmed.ncbi.nlm.nih.gov/40623187/

Amyloid structure determination in RELION-3.1 Amyloid structure determination in RELION is increasingly popular, but may suffer from refinements becoming stuck in local minima. This paper describes a new method for initial model generation that m...

For those reviewing #cryoEM structures of #amyloids, please read: journals.iucr.org/d/issues/202...

Very poor reviewing by @science.org Advances. Also, I'm not sure how #cryosparc can think this is 3.3A, but perhaps the authors did something they shouldn't do when "structure analysis was followed by the CryoSPARC-based helical reconstruction approach we previously developed"

Initial attempt at replicating in relion (parameters in next post). This is for Aca2-RNA, using a 100k subset of the 2D-classified particles (no prior 3D cleanup).

A 1-class ab initio in relion, then local refinement in relion (1.8deg searches+blush) gives a nominally 3.3Å map; 3.5 Å w/out blush.