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Israel S. Fernandez

@piratefernandez.bsky.social
713 followers 221 following 27 posts

Action is the offspring of dark pessimism. www.biofisika.org/en/research/rna-p…

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Israel S. Fernandez @piratefernandez.bsky.social · 09/07/2026
😻
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Tanmay Bharat @tbharat-lab.bsky.social · 07/11/2025
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...
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Israel S. Fernandez @piratefernandez.bsky.social · 06/11/2025
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
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Michael Way @drmichaelway.bsky.social · 20/08/2025
💥 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...
biorxiv.org
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...
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Structural Biology @actacrystd.iucr.org · 19/08/2025
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...
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Science Magazine @science.org · 14/08/2025
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: scim.ag/3JdQVD4
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TJ McCorvie @allostericstate.bsky.social · 23/07/2025
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...
nature.com
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...
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Harry Low’s Lab @lowlab.bsky.social · 30/06/2025
In-situ SPA 🧨 www.biorxiv.org/content/10.1...
biorxiv.org
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 ...
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Israel S. Fernandez @piratefernandez.bsky.social · 27/05/2025
This is great stuff! Congrats!
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John Rubinstein @johnrubinstein.bsky.social · 16/05/2025
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...
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.
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Eugene Valkov @eugenevalkov.bsky.social · 06/05/2025
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
George M. Sheldrick (1942–2025)
In memory of George Sheldrick.
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Dawid Zyla @dzyla.bsky.social · 27/04/2025
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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Israel S. Fernandez @piratefernandez.bsky.social · 22/04/2025
Top
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Alexey Amunts @amunts.bsky.social · 15/03/2025
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...
cnio.es
Machines acting on DNA and RNA, a molecular mechanistic perspective (#CFM_MolMech)
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Alister Burt @alisterburt.bsky.social · 07/03/2025
trying to use WarpTools with particles picked in another program? a few tips here forum.image.sc/t/how-to-ext...
forum.image.sc
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...
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Alisia Fadini @alisiafadini.bsky.social · 24/02/2025
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.
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Lori Passmore @lapassmore.bsky.social · 22/02/2025
Reminder - still one month to apply to be a tenure track group leader at MRC LMB. Please do reach out for any information.
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Israel S. Fernandez @piratefernandez.bsky.social · 20/02/2025
Beautiful results and figures here!
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Alister Burt @alisterburt.bsky.social · 11/02/2025
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!
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Oli Clarke @olibclarke.bsky.social · 08/02/2025
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...
biophysics.org
BPS Store - Products | Biophysical Society
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Israel S. Fernandez @piratefernandez.bsky.social · 08/02/2025
Cool stuff!
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Cynthia Wolberger @cwolberger.bsky.social · 08/02/2025
www.nytimes.com/2025/02/07/u... This is catastrophic.
nytimes.com
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.
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Israel S. Fernandez @piratefernandez.bsky.social · 08/02/2025
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…
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Israel S. Fernandez @piratefernandez.bsky.social · 08/02/2025
Opportunity to join Science-Paradise on Earth!
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Israel S. Fernandez @piratefernandez.bsky.social · 15/01/2025
Very cool! As Harry already pointed out!
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Israel S. Fernandez @piratefernandez.bsky.social · 11/01/2025
Top!
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Israel S. Fernandez @piratefernandez.bsky.social · 10/01/2025
Friends, do not miss this great meeting in wonderful Madrid in May! Good weather, amazing food and best of all great speakers ( and me…👀)
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Friedrich Förster @fridof.bsky.social · 30/11/2023
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...
biorxiv.org
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
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Mart Krupovic @mkrupovic.bsky.social · 30/12/2024
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/...
journals.asm.org
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...
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kirchhausenlab.bsky.social @kirchhausenlab.bsky.social · 29/12/2024
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.
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MRC Laboratory of Molecular Biology @mrclmb.ac.uk · 12/12/2024
Exciting 3-year postdoc opportunity with @carter-lab.bsky.social within a programme aimed at identifying the links between microtubule motors and axonal cargos. Read more about the role here: www.nature.com/naturecareer... Apply by 30 DEC #ScienceJobs #CambridgeJobs #PostdocJobs #GenomeEngineering
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Israel S. Fernandez @piratefernandez.bsky.social · 24/12/2024
Fantastic!
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Dan Grabarczyk @dangrabarczyk.bsky.social · 21/12/2024
Happy to share our UBR4 structures. Check out the preprint to see how this giant E4 ligase complex selects substrates for ubiquitin chain extension. We also look at conservation and adaptations across humans, nematodes and plants. www.biorxiv.org/content/10.1... @clausenlab.bsky.social
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Sonja Welsch @sonjawelsch.bsky.social · 18/12/2024
A liitle over two weeks left to register for what looks to be a fantastic workshop for anyone interested in in situ structural biology! 🧪🧬🔬
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Israel S. Fernandez @piratefernandez.bsky.social · 17/12/2024
Shit! You know you are something right when you get likes from Nobel Laureates! (And Oli! but Oli is a good friend so those count less!)
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Israel S. Fernandez @piratefernandez.bsky.social · 17/12/2024
Cool stuff Tanmay et al!
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Fabian Eisenstein @eisfabian.bsky.social · 17/12/2024
SPACEtomo v1.2 is online! github.com/eisfabian/SP... - Improved GUIs for lamella detection, target selection and CLEM registration make it the best target selection workflow for PACEtomo on any kind of lamella sample. - Easier installation and configuration Any feedback is much appreciated! :)
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Wim Hagen @wimjhh.bsky.social · 17/12/2024
Ever wondered how some of the automation in cryo-EM data collection works? Read Bram Koster's 1989 thesis! repository.tudelft.nl/record/uuid:...
repository.tudelft.nl
Autotuning of a transmission electron microscope | TU Delft Repository
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Israel S. Fernandez @piratefernandez.bsky.social · 17/12/2024
Eva Nogales received today a big Spanish prize ! The CSIC medal of excellence! So well deserved!
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Israel S. Fernandez @piratefernandez.bsky.social · 16/12/2024
Revolutionary!
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Israel S. Fernandez @piratefernandez.bsky.social · 15/12/2024
The future in ribosome structural biology is here!
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Israel S. Fernandez @piratefernandez.bsky.social · 15/12/2024
This is very cool read!
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Basil Greber @bjgreber.bsky.social · 11/12/2024
One of those #cryoEM papers were using "near-atomic resolution" in the title would be entirely ok. 😉 academic.oup.com/nar/advance-...
academic.oup.com
Visualizing the modification landscape of the human 60S ribosomal subunit at close to atomic resolution
Abstract. Chemical modifications of ribosomal RNAs (rRNAs) and proteins expand their topological repertoire, and together with the plethora of bound ligand
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Alexey Amunts @amunts.bsky.social · 04/12/2024
A long-waited refinement tool for cofactors with metal-coordination, MetalCoord. By Garib Murshudov group @mrclmb.bsky.social Compiles distances & angles from CCP4 monomer library and classifies the metal-coordination geometry. The updated dictionaries and restraints then used for refinement.
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Israel S. Fernandez @piratefernandez.bsky.social · 29/11/2024
Perfect for a gin&tonic! Good weekend friends!
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Israel S. Fernandez @piratefernandez.bsky.social · 29/11/2024
Great option here for getting your PhD degree !
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Israel S. Fernandez @piratefernandez.bsky.social · 27/11/2024
All right I have tilt fata, I have a conda env working let’s do this!
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Katie Downes @dr-downes.bsky.social · 26/11/2024
Latest paper from our lab out now! #TeamTomo #CryoET www.nature.com/articles/s41...
nature.com
Cryo-electron tomography reveals how COPII assembles on cargo-containing membranes - Nature Structural & Molecular Biology
The authors reconstituted coat protein complex II vesicles from native membranes and used cryo-electron tomography and subtomogram averaging to reveal the arrangement of inner and outer coat layers on...
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Prakash Lab at Stanford @prakashlab.bsky.social · 21/11/2024
Our latest discovery of “lowest recorded temperature for eukaryotic cell motility” going all the way down to -15deg C. Come for the crazy cold Arctic & stay for diatoms. Will write longer thread - but enjoy video below of diatoms gliding on frozen ice surfaces. Congrats @zqing.bsky.social & team.
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Israel S. Fernandez @piratefernandez.bsky.social · 22/11/2024
Gold-grid making day. Always seduced by gold beauty!
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