Lightnews — Scholar-powered news

Reposted by Sjors Scheres

Alister Burt @alisterburt.bsky.social · 19h

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

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

1 1 19

Reposted by Sjors Scheres

MRC Laboratory of Molecular Biology @mrclmb.bsky.social · 2d

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

Black and white portrait of John Gurdon, 1971

3 32 98

Sjors Scheres @sjorsscheres.bsky.social · 5d

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

5

Sjors Scheres @sjorsscheres.bsky.social · 5d

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).

2

Sjors Scheres @sjorsscheres.bsky.social · 5d

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.

5 4

Sjors Scheres @sjorsscheres.bsky.social · 5d

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...

www.biorxiv.org

3 5 15

Reposted by Sjors Scheres

Mayor of London, Sadiq Khan @london.gov.uk · 9d

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.

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.

www.bbc.co.uk

24 190 780

Sjors Scheres @sjorsscheres.bsky.social · 11d

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...

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

www.theguardian.com

1 6

Sjors Scheres @sjorsscheres.bsky.social · 12d

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).

1

Reposted by Sjors Scheres

Lori Passmore @lapassmore.bsky.social · 13d

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

51 55

Sjors Scheres @sjorsscheres.bsky.social · 14d

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!

4 23

Sjors Scheres @sjorsscheres.bsky.social · 14d

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

www.pnas.org

1 1

Sjors Scheres @sjorsscheres.bsky.social · 14d

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

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

pubmed.ncbi.nlm.nih.gov

1 2

Sjors Scheres @sjorsscheres.bsky.social · 14d

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

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

pubmed.ncbi.nlm.nih.gov

1 2

Sjors Scheres @sjorsscheres.bsky.social · 14d

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

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...

journals.iucr.org

1 2 8

Sjors Scheres @sjorsscheres.bsky.social · 14d

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"

2 6

Reposted by Sjors Scheres

Oli Clarke @olibclarke.bsky.social · 14d

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.

1 24 57

Reposted by Sjors Scheres

Rita Strack @ritastrack.bsky.social · 15d

I can raise the issue to higher ups!

1 6

Sjors Scheres @sjorsscheres.bsky.social · 15d

Will you make it less tricky, and allow posting revised versions of preprints after peer-review? Sounds like an easy thing to do...

1 1 7

Sjors Scheres @sjorsscheres.bsky.social · 15d

I find that riding a bike also helps the mind for doing research on #Alzheimers disease! 😀

International Society of Genetic Genealogy @isogg.bsky.social · 15d

“Riding a bike is associated with a 19% lower risk of all-cause dementia and a 22% lower risk of Alzheimer’s disease, compared with taking nonactive travel modes such as a car, bus or train…” #ISOGG #DNA #epigenetics www.cnn.com/2025/09/20/h...

Cycling linked with lower dementia risk, study finds | CNN

Cycling instead of driving has been linked with a lower risk of dementia and Alzheimer’s disease, a large study has found.

www.cnn.com

4

Sjors Scheres @sjorsscheres.bsky.social · 17d

Do you #PhD with us!

MRC Laboratory of Molecular Biology @mrclmb.bsky.social · 18d

Calling all prospective PhD students! Why not consider the LMB for your PhD?
Applications are now open!
www2.mrc-lmb.cam.ac.uk/students/int...
General deadline: 2nd DEC
US Gates Scholarship deadline: 15th OCT

Join the LMB's PhD programme!
Applications now open for October 2026
Deadline 2nd December 2025

1 7

Sjors Scheres @sjorsscheres.bsky.social · 19d

Fantastic! Let us know if you need any help. 🤗

1 7

Sjors Scheres @sjorsscheres.bsky.social · 19d

It would add to your paper if you could reproduce your results in another software too.

1 5

Sjors Scheres @sjorsscheres.bsky.social · 19d

These results are truly impressive! But I do worry that #cryoEM is moving into a phase where progress is made by optimizing parameter settings for black box programs. The devil is often in the details, and I am not sure how this could be implemented in #relion, as stated, without more info.

Oli Clarke @olibclarke.bsky.social · 27d

This one is a bit of a departure from the usual and definitely a work in progress!

We found that by using ab initio reconstruction at very high res, in very small steps, we could crack some small structures that had eluded us - e.g. 39kDa iPKAc (EMPIAR-10252), below.

Read on for details... 1/x

2 10 36

Reposted by Sjors Scheres

MRC Laboratory of Molecular Biology @mrclmb.bsky.social · 21d

#ICYMI spearheaded by Sofia Lövestam, Michel Goedert & @sjorsscheres.bsky.social's groups have identified a combination of 12 residues in tau’s fuzzy coat which, when mutated, facilitates assembly of amyloid filaments.
Read more in AlzForum: www.alzforum.org/news/researc...
#LMBintheNews #PAD12

Tau filaments formed into their distinctive paired helical filaments in Alzheimer's disease

9 25