Arjen Jakobi

Does BioRxix not already allow you/us to do exactly that? Indexed repository, version-controlled updates, transparent options for peer feedback and author replies. Each version can have updated author contributions to document individual contributions.

Please share🙏:

Our lab opens 2 PhD positions to investigate fungi's evolution: #Barcelona

Wet lab in Biochemistry/Structural Biology of cryo-tolerant fungi
www.upf.edu/documents/d/...

Computational in Physical Chemistry of cellular processes under extrem environments
www.upf.edu/documents/d/...

How can one be scooped if one is the first to publish a preprint of a new discovery? 🤔

It is sad that we appear to consider the date of a journal stamp a more important sign of priority than the actual date of reporting your discovery to the scientific community.

Congrats Kiarash! 👏🏻

Molecular basis for cellular compartmentalization by an ancient membrane fission mechanism The emergence of cell compartmentalization depends on membrane fission to create the endomembrane compartments. In eukaryotes, membrane fission is commonly executed by ESCRT-III, a protein complex con...

New preprint from the lab!!🎉
We show that Asgard archaea ESCRT-III proteins can trigger membrane fission and reveal its molecular mechanism, offering clues to how these cells may have built internal compartments. But do these organisms even have these compartments?
www.biorxiv.org/content/10.1...

CCP-EM Spring Symposia have become key venues for methods-focused cryo-EM advances and an annual fixture for structural biologists worldwide. Their early adoption of online talks set the bar for inclusive meetings, and even as they have grown over the years, they have kept a family feel. Kudos!

Not sure if this is what you are looking for, but in zenodo you can specify parent repositories as “related works” including the DOI to the original repository. This way you could link a subset of data (a particle stack in your case) back to its original source (the EMPIAR deposition).

We finally wrote up the paper for LocScale-2.0.

edu.nl/pvhxv

Please try it out. LocScale is evolving & we are actively building in new features and improvements. Your feedback will help us shape the next steps.

Code: cryotud.github.io/locscale/

Work by @alok-bharadwaj.bsky.social and Reinier.

Good luck!

Together with colleagues at the Dept. of Microsystems Engineering, we are looking for a PhD student to develop methods for femtoliter-scale sample dispensing in cryoEM sample preparation.

edu.nl/h436k

If you like interdisciplinary research & fascinating physics at ultrasmall scales, please apply!

Where is the backpack? 😉

Beautiful structures and mechanistic insight into endosomal lipid transfer!

Also a good example showcasing how contextualised map optimisation may be helpful in visualisation/interpretation of complex biological assemblies.

Welcome to Delft, Georgios!

spent some time this evening updating the teamtomo.org site - if you're interested in cryo-EM + Python you might want to take a look around!

LocScale-SURFER is now also available for quick install via the ChimeraX toolshed:

cxtoolshed.rbvi.ucsf.edu

Uups, our bad. Please try again (cryotud.github.io/locscale-sur...); it should work now.

Want to try LocScale-2.0 without installing locally?

Check out ColabScale: just upload your maps or enter your favourite EMDB ID and run LocScale-2.0 in the cloud.

edu.nl/ur3ge

This is work led by @alok-bharadwaj.bsky.social with contributions by Reinier de Bruin and Lotte Verbeek.

Preprint(s) with detailed description underway. In the menatime we are happy for any feedback.

LocScale-2.0 is deliberately designed to optimise contrast for both high-resolution detail & weak contextual densities such as membrane/micelle or flexible/low-occupancy regions

LocScale-SURFER is a ChimeraX plugin aiding w/ visualisation of contextual structure.

cryotud.github.io/locscale-sur...

We are happy to release LocScale2.0: a tool for context-aware, confidence-weighted cryoEM map optimisation.

Taking two half maps as input, LcoScale-2.0 produces feature-enhanced maps along with a robust confidence score that guides objective map interpretation.

cryotud.github.io/locscale/

CEMOVIS revisited! 🙂

Thickness- and quality-controlled fabrication of fluorescence-targeted frozen-hydrated lamellae Boltje et al. demonstrate a workflow to prepare thin cellular sections in a thickness-controlled fashion using an integrated light microscope coincident with electron and ion beams. This reduces compl...

Daan & Radim extended our q4STEM method to lamella fabrication from frozen-hydrated cells, implemented RLM thin-film interference (inspired by @mgflast.bsky.social) on a 3-beam coincident system, and show how live thickness monitoring allows automated milling of high-quality lamella: edu.nl/f9fn3

Krijg je ook borrelnootjes bij je bier? 😉

Klopt! Ik had er tot voor kort niet eerder van gehoord maar heb onlangs een interessante lezing bijgewoond in het Green Village van de TU. Er is ook een interessant verslag van Deltares: www.deltares.nl/expertise/pr...

Goed voornemen, Cees! Ik gebruik sinds enkele jaren co2offset.atmosfair.de/co2offset#/f... om mijn vluchten te compenseren. Dit is enkele malen door de Duitse en Zwitserse consumentenbond als meest betrouwbare/transparante berekening uitgeroepen.

In this project you will collaborate closely with the groups of @ceesdekker.bsky.social, @cg-martini.bsky.social and @ettema.bsky.social.

Many other interesting PhD/PD openings within the consortium here: www.evolf.life/join-us

We have an opening for a 4 yr PhD interested in membrane remodelling and cryo-EM/ET of a minimal cell division machinery: edu.nl/bukan

You will be part of the EVOLF consortium in which 30 leading biochemists/biophysicists work together to explore if and how we can build autonomous synthetic cells.

Maya, Jan and I had a great time with you all!

So many exciting projects - we are looking forward to seeing the results pop up here in the future 🙂

6 hours of HADDOCKing and still going strong! ⛄️

https://www.embl.org/about/info/course-and-conference-office/events/stb24-01/#vf-tabs__section-programme

Really looking forward to welcoming & meeting the participants of our #EMBOStructBio course this morning!

Many of our speakers/tutors are here:
@moalquraishi.bsky.social
@sykhalid.bsky.social
@ezgikaraca.bsky.social
@amjjbonvin.bsky.social
@gchojnowski.bsky.social
@drmelissagraewert.bsky.social