Israel S. Fernandez

An Asgard archaeon with internal membrane compartments

Brilliant study led by @fmacleod.bsky.social and Andriko von Kügelgen. Tight collaboration with @buzzbaum.bsky.social and lab. Congrats to all authors!

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

What a day for The RNA Pirate Republic!
Along with:
Chase Beisel (BBIE, Basel)
Sam Sternberg (Columbia Uni, NYC) and
Raul Perez-Jimenez (BioGune, Bilbao)
We have been awarded an ERC Synergy grant to explore the ancestry and evolution of RNA-guided nucleases!
Yey! 🎉
#ERCSyG

In situ cryo-electron tomography of vaccinia virus exit from infected cells Poxvirus-infected cells release newly assembled virions via Golgi-mediated envelopment and subsequent exocytosis at the plasma membrane, prior to cell lysis. Here, we used cryo-electron tomography and...

💥 Another Cryo-ET study from the Way lab by ‪@miguel-virus-cells.bsky.social‬ in collaboration with Rosenthal lab @crick.ac.uk‬ examining Vaccinia virus egress 😀👇 www.biorxiv.org/content/10.1...

A comprehensive statistical analysis of how Q-scores are related to reported resolution, based on ∼10 000 EMDB maps and associated PDB atomic coordinate models archived in the EMDB #CryoEM #QScores #Validation doi.org/10.1107/S205...

Researchers have developed a #DeepLearning system called BioEmu that rapidly generates diverse protein conformations, enabling fast, accurate insights into protein flexibility and function.

Learn more this week in Science: https://scim.ag/3JdQVD4

Architecture and regulation of filamentous human cystathionine beta-synthase - Nature Communications Cystathionine beta-synthase is a conserved essential enzyme of one-carbon metabolism. Here, the authors show that the enzyme oligomerises to form filaments that undergo conformational and morphologica...

The EMPIAR datasets related to my work on human cystathionine beta-synthase are now released. Hopefully they are useful unusual filament cases for #cryoEM data processing
www.nature.com/articles/s41...
1. www.ebi.ac.uk/empiar/EMPIA...
2. www.ebi.ac.uk/empiar/EMPIA...
3. www.ebi.ac.uk/empiar/EMPIA...

In-situ structures of the Legionella Dot/Icm T4SS identify the DotA-IcmX complex as the gatekeeper for effector translocation The Dot/Icm machine in Legionella pneumophila is one of the most versatile type IV secretion systems (T4SSs), with a remarkable capacity to translocate over 330 different effector proteins across the ...

In-situ SPA 🧨

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

This is great stuff! Congrats!

A) Diagram showing how EtfD transfers electrons from beta oxidation to the menaquinol pool in the membrane, linking beta oxidation to oxidative phosphorylation in mycobacteria. B) A growth curve showing the Mycobacterium smegmatis lacking EtfD can grow when glucose is provided as the carbon source, but has a slight growth delay. Complementing the ∆etfD strain with M. tuberculosis on a plasmid rescues the defect. C) A growth curve showing that ∆etfD M. smegmatis cannot grow on medium where the fatty acid oleic acid is the only carbon source. A plasmid with with M. tuberculosis EtfD rescues the defect.

EtfD links beta oxidation to OxPhos in mycobacteria - recent work suggests that targeting EtfD could shorten #tubeculosis treatment.
But how does EtfD work? And how can you assay its activity?
In his final PhD manuscript @courbongautier.bsky.social provides answers!
www.biorxiv.org/content/10.1...

George M. Sheldrick (1942–2025) In memory of George Sheldrick.

A tribute to George Sheldrick and SHELX and the impact on macromolecular and small-molecule crystallography

journals.iucr.org/a/issues/202...

1/5: Over the last few months, I have been working on an update for the #FollowRelionGracefully dashboard, which offers improved real-time job previews for #cryoEM #Relion jobs.

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Machines acting on DNA and RNA, a molecular mechanistic perspective (#CFM_MolMech)

See you in Madrid! Speakers include:
@costalaboratory.bsky.social @piratefernandez.bsky.social @nhoitsma.bsky.social @kellythd-nguyen.bsky.social @lapassmore.bsky.social @alessandrovannini.bsky.social @oscarllorca.bsky.social @rfleiro.bsky.social @nogaleslab.bsky.social
www.cnio.es/en/eventos/m...

How to extract particles from Warp 2.0 tomograms that were picked using external programs Hey @AlisterBurt, are there instructions anywhere for how to extract particles from Warp 2.0 reconstructed tomograms that were not picked in Warp, but were picked using programs like crYOLO, for subse...

trying to use WarpTools with particles picked in another program? a few tips here forum.image.sc/t/how-to-ext...

Structural biology is in an era of dynamics & assemblies but turning raw experimental data into atomic models at scale remains challenging. @minhuanli.bsky.social and I present ROCKET🚀: an AlphaFold augmentation that integrates crystallographic and cryoEM/ET data with room for more! 1/14.

Reminder - still one month to apply to be a tenure track group leader at MRC LMB. Please do reach out for any information.

Beautiful results and figures here!

Interested in learning to process cryo-ET data in the latest version of Warp? I'll be running a workshop on April 22nd in central London, UK
details+registration: forms.gle/FLDr3ZWtVGXs...
Hope to see you there!

BPS Store - Products | Biophysical Society

If you're coming to #BPS2025, please come check out the #CryoEM symposium on Sat Feb 15th, 8:30AM-12:30PM, Room 515B.

Also! Join us for the CryoEM happy hour in the evening, 6:30-8:30PM at 33 Taps DTLA. Get your tickets *now*, as ticket sales end Feb 10th!

www.biophysics.org/store/produc...

yes, specially big ones located in urban areas

Cool stuff!

Deep Cuts to Medical Research Funds Could Hobble University Budgets Grants from the National Institutes of Health come with additional money for overhead. Proposed funding cuts would leave colleges with large budget gaps.

www.nytimes.com/2025/02/07/u...

This is catastrophic.

This is massive for the US-University based science… flat rate of 15% for indirect cost allocation in NIH funding!!!! Not sure how Universities will respond to this…

Opportunity to join Science-Paradise on Earth!

Very cool! As Harry already pointed out!

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Friends, do not miss this great meeting in wonderful Madrid in May! Good weather, amazing food and best of all great speakers ( and me…👀)

Exploring the molecular composition of the multipass translocon in its native membrane environment bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution

My new life in blue starts with sharing a preprint of amazing Max Gemmer’s ex vivo analysis that sheds light on the machinery responsible for inserting many multispanning transmembrane proteins into the ER membrane #teamtomo: www.biorxiv.org/content/10.1...

The protein structurome of Orthornavirae and its dark matter | mBio Advanced methods for protein structure prediction, such as AlphaFold2, greatly expand our capability to identify protein domains and infer their likely functions and evolutionary relationships. This i...

RNA virologists, check out "The protein structurome of Orthornavirae and its dark matter" by Pascal Mutz, Valerian Dolja, Eugene Koonin et al (including @simrouxvirus.bsky.social, @apcamargo.bsky.social, @urineri.bsky.social, @anamarijabutkovic.bsky.social)
journals.asm.org/doi/10.1128/...

Merry Christmas and our best wishes for a peaceful 2025. Say goodbye to the noise with CryoSamba, our self-supervised deep denoising algorithm for CryoET now published in JSB.