Israel S. Fernandez
@piratefernandez.bsky.social
Pinned
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
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
Reposted by 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...
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...
November 7, 2025 at 10:44 AM
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...
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
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
November 6, 2025 at 5:48 PM
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
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
Reposted by Israel S. Fernandez
💥 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...
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...
www.biorxiv.org
August 20, 2025 at 11:32 AM
💥 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...
Reposted by Israel S. Fernandez
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...
August 19, 2025 at 12:19 PM
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...
Reposted by Israel S. Fernandez
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
Learn more this week in Science: https://scim.ag/3JdQVD4
August 14, 2025 at 6:05 PM
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
Learn more this week in Science: https://scim.ag/3JdQVD4
Reposted by Israel S. Fernandez
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...
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...
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...
www.nature.com
July 23, 2025 at 11:16 AM
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...
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...
Reposted by Israel S. Fernandez
This is great stuff! Congrats!
I’m thrilled to share my very first first-author preprint and our lab’s latest work💫 We discovered a novel role for eIF2A in ribosome-associated quality control (RQC), challenging decades-old assumptions about its enigmatic function in translation initiation.
Check it out to learn more! ⭐️
#RNA
Check it out to learn more! ⭐️
#RNA
Identified in the 1970s, the precise molecular function of the alternative initiation factor eIF2A has remained unclear. Here, we map its interactome and uncover a surprising role in ribosome-associated quality control (RQC) upon ribosome stalling. 1/x
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
May 27, 2025 at 10:07 AM
This is great stuff! Congrats!
Reposted by Israel S. Fernandez
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...
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...
May 16, 2025 at 2:30 PM
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...
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...
Reposted by Israel S. Fernandez
A tribute to George Sheldrick and SHELX and the impact on macromolecular and small-molecule crystallography
journals.iucr.org/a/issues/202...
journals.iucr.org/a/issues/202...
George M. Sheldrick (1942–2025)
In memory of George Sheldrick.
journals.iucr.org
May 6, 2025 at 11:34 AM
A tribute to George Sheldrick and SHELX and the impact on macromolecular and small-molecule crystallography
journals.iucr.org/a/issues/202...
journals.iucr.org/a/issues/202...
Reposted by Israel S. Fernandez
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.
April 27, 2025 at 8:49 PM
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.
Top
“We are, each of us, largely responsible for what gets put into our brains, for what, as adults, we wind up caring for and knowing about. No longer at the mercy of the reptile brain, we can change ourselves.”
- Carl Sagan, Cosmos
- Carl Sagan, Cosmos
April 22, 2025 at 5:33 PM
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Reposted by Israel S. Fernandez
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...
@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...
Machines acting on DNA and RNA, a molecular mechanistic perspective (#CFM_MolMech)
www.cnio.es
March 15, 2025 at 7:48 PM
Reposted by Israel S. Fernandez
trying to use WarpTools with particles picked in another program? a few tips here forum.image.sc/t/how-to-ext...
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...
forum.image.sc
March 7, 2025 at 7:04 PM
trying to use WarpTools with particles picked in another program? a few tips here forum.image.sc/t/how-to-ext...
Reposted by Israel S. Fernandez
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.
February 24, 2025 at 12:23 PM
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.
Reposted by Israel S. Fernandez
Reminder - still one month to apply to be a tenure track group leader at MRC LMB. Please do reach out for any information.
Come and joint us at @mrclmb.bsky.social ! We have an opening for a new group leader in the Structural Studies Division. We are very interactive and collaborative with amazing facilities and generous core funding. Get in touch with myself or @sjorsscheres.bsky.social if you have any questions.
Join our Structural Studies Division, leading a research group developing computational methods to address questions in molecular & cellular biology!
You will be supported by core funding, excellent facilities & enthusiastic colleagues.
Apply by 18 MAR
www.nature.com/naturecareer...
You will be supported by core funding, excellent facilities & enthusiastic colleagues.
Apply by 18 MAR
www.nature.com/naturecareer...
February 22, 2025 at 9:50 AM
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!
In @justinditrani.bsky.social final postdoc paper (with contributions from many others) we show that forming/purifying vesicles (here from M. smegmatis) allows structure det'n of *endogenous* membrane proteins in their *native lipid bilayer*
🧵 on methods & TB biology...
www.pnas.org/doi/full/10....
🧵 on methods & TB biology...
www.pnas.org/doi/full/10....
February 20, 2025 at 9:35 AM
Beautiful results and figures here!
Reposted by Israel S. Fernandez
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!
details+registration: forms.gle/FLDr3ZWtVGXs...
Hope to see you there!
February 11, 2025 at 9:59 PM
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!
details+registration: forms.gle/FLDr3ZWtVGXs...
Hope to see you there!
Reposted by Israel S. Fernandez
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...
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...
BPS Store - Products | Biophysical Society
www.biophysics.org
February 8, 2025 at 6:39 PM
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...
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...
Cool stuff!
Our #CryoEM study on the binding of a Tarantula toxin to a full-length human voltage-gated sodium channel has been published. Very proud of the awesome people in my lab 🥳🥂
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Structural basis of inhibition of human NaV1.8 by the tarantula venom peptide Protoxin-I - Nature Communications
Animal toxins can modulate action potentials and are important leads for therapeutics. Here, the authors use cryo-EM to show the interaction of the tarantula venom peptide Protoxin-I with a human volt...
www.nature.com
February 8, 2025 at 11:11 AM
Cool stuff!
Reposted by Israel S. Fernandez
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…
February 8, 2025 at 11:09 AM
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!
Join our Structural Studies Division, leading a research group developing computational methods to address questions in molecular & cellular biology!
You will be supported by core funding, excellent facilities & enthusiastic colleagues.
Apply by 18 MAR
www.nature.com/naturecareer...
You will be supported by core funding, excellent facilities & enthusiastic colleagues.
Apply by 18 MAR
www.nature.com/naturecareer...
February 8, 2025 at 11:05 AM
Opportunity to join Science-Paradise on Earth!
Very cool! As Harry already pointed out!
Love this.. 👏
MISO: Microfluidic protein isolation enables single particle cryo-EM structure determination from a single cell colony
www.biorxiv.org/content/10.1...
MISO: Microfluidic protein isolation enables single particle cryo-EM structure determination from a single cell colony
www.biorxiv.org/content/10.1...
January 15, 2025 at 4:26 PM
Very cool! As Harry already pointed out!
Top!
New preprint!
@zestytoast.bsky.social provides the missing puzzle piece for a structural model of the mycobacterial OxPhos: NDH-2
We show the enzyme forms a dimer resembling eukaryotic, not prokaryotic, NDH-2s, and explain the SAR of a promising class of inhibitors.
www.biorxiv.org/content/10.1...
@zestytoast.bsky.social provides the missing puzzle piece for a structural model of the mycobacterial OxPhos: NDH-2
We show the enzyme forms a dimer resembling eukaryotic, not prokaryotic, NDH-2s, and explain the SAR of a promising class of inhibitors.
www.biorxiv.org/content/10.1...
![Structure of mycobacterial NDH-2 bound to 2-mercapto-quinazolinone [(2-mercapto-quinazolinone N-cyclohexyl-2-[(4-oxo-1H-quinazolin-2-yl)sulfanyl]acetamide], explaining the protein-inhibitor interaction.](https://cdn.bsky.app/img/feed_thumbnail/plain/did:plc:2h7m2pmlm4foweae4sdxrkmo/bafkreiauuhvmnca2ge4ajkr6lt4f23gsixxjraq73ariv4ge2w2iotejim@jpeg)
January 11, 2025 at 12:51 PM
Top!