#cryoet — Public Fediverse posts

This year again I was lucky to be able to attend the #CCPEM Spring Symposium in person.

So much exciting science is going on in the #cryoEM and #cryoET #teamTomo fields!

I was especially impressed with the progress in time-resolved perturbation and vitrification for single-particle cryoEM.

This year again I was lucky to be able to attend the #CCPEM Spring Symposium in person.

So much exciting science is going on in the #cryoEM and #cryoET #teamTomo fields!

I was especially impressed with the progress in time-resolved perturbation and vitrification for single-particle cryoEM.

High-resolution #CryoET provides ‘compelling’ evidence for the true 3D architecture of glutamatergic synapses: a complex ‘synaptoplasm’ rather than the textbook postsynaptic density.
https://elifesciences.org/articles/100335?utm_source=mastodon&utm_medium=social&utm_campaign=organic

High-resolution #CryoET provides ‘compelling’ evidence for the true 3D architecture of glutamatergic synapses: a complex ‘synaptoplasm’ rather than the textbook postsynaptic density.
https://elifesciences.org/articles/100335?utm_source=mastodon&utm_medium=social&utm_campaign=organic

A new #CryoET study shows that the protein ZapD helps organise FtsZ filaments into stable ring-like structures in building bacterial division machinery.
https://elifesciences.org/articles/95557?utm_source=mastodon&utm_medium=social&utm_campaign=organic

A new #CryoET study shows that the protein ZapD helps organise FtsZ filaments into stable ring-like structures in building bacterial division machinery.
https://elifesciences.org/articles/95557?utm_source=mastodon&utm_medium=social&utm_campaign=organic

🌱 Using ‘compelling’ methods, including #CryoET, researchers mapped spinach thylakoid membranes at single-molecule precision, revealing how photosynthetic complexes are organised and settling long-standing debates on chloroplast architecture.
https://elifesciences.org/articles/105496?utm_source=mastodon&utm_medium=social&utm_campaign=organic_assessment

🌱 Using ‘compelling’ methods, including #CryoET, researchers mapped spinach thylakoid membranes at single-molecule precision, revealing how photosynthetic complexes are organised and settling long-standing debates on chloroplast architecture.
https://elifesciences.org/articles/105496?utm_source=mastodon&utm_medium=social&utm_campaign=organic_assessment

Meharry Medical College Ph.D. candidate KeAndreya Morrison's highlight features a @Nature Structural & Molecular Biology publication from the lab of Chi-Min Ho of Columbia University and colleagues who used cryo-electron tomography to map malaria’s ribosomes at work and reveal how a parasite-specific drug derails translation.

Read more here: https://medium.com/sbgrid-community-news/stopping-ribosomes-in-action-101e95f41784

#SBGrid #StructuralBiology #CryoET

Just dropped $1200 to upgrade one of my servers to 512 GB mem. How’s your day?

#teamtomo #cryoet

Just dropped $1200 to upgrade one of my servers to 512 GB mem. How’s your day?

#teamtomo #cryoet

One highlight from Friday that I forgot: Alister Burt's talk on his efforts to build #TeamTomo, a set of community-supported software packages and metadata standards for #cryoET. This is difficult work, and less rewarding for those in academia, but so essential. It's great to see progress on this front.

The other great news from Alister's talk: Warp is now supported on Linux!

Finally, I'll remember his advice "think about geometry, and use it if you can" when assigning initial particle orientations for subtomogram averaging.

#CCPEM #CryoEM

One highlight from Friday that I forgot: Alister Burt's talk on his efforts to build #TeamTomo, a set of community-supported software packages and metadata standards for #cryoET. This is difficult work, and less rewarding for those in academia, but so essential. It's great to see progress on this front.

The other great news from Alister's talk: Warp is now supported on Linux!

Finally, I'll remember his advice "think about geometry, and use it if you can" when assigning initial particle orientations for subtomogram averaging.

#CCPEM #CryoEM

Published in March, this video comes from research that aimed use #CryoET to demonstrate how FtsZ filaments are recruited into a ring or “toroidal” structure as part of a bacterial cell’s division machinery. #12DaysOfeLife
https://elifesciences.org/reviewed-preprints/95557?utm_source=mastodon&utm_medium=social&utm_campaign=organic

Published in March, this video comes from research that aimed use #CryoET to demonstrate how FtsZ filaments are recruited into a ring or “toroidal” structure as part of a bacterial cell’s division machinery. #12DaysOfeLife
https://elifesciences.org/reviewed-preprints/95557?utm_source=mastodon&utm_medium=social&utm_campaign=organic

For the #ML and #CryoET folks out there: Are folks on here submitting to the CZII CryoET Object Identification competition: www.kaggle.com/competitions... ? The leaderboard is really interesting, and the forums are full of insights. How many of the latest picking models have been submitted?

CZII - CryoET Object Identific...

Question for #cryoEM #cryoET community. What is the minimum dose per frame that MotionCor2 can typically use. Asking for a friend using a Falcon4 outputing EERs… Typical is 1-2e/A2 per frame but can we use lower doses per frame ? Any advantage to fractionate more ?

A novel method for imaging glutamate receptors in situ via #CryoET. https://elifesciences.org/articles/98458?utm_source=mastodon&utm_medium=social&utm_campaign=organic

A novel method for imaging glutamate receptors in situ via #CryoET. https://elifesciences.org/articles/98458?utm_source=mastodon&utm_medium=social&utm_campaign=organic

#TeamTomo is having a competition to annotate #cryoET tomograms: https://cryoetdataportal.czscience.com/competition

This is a good initiative! Especially the metadata format standardization part. I hope several good 3D particle picking programs will emerge from this.

#StructuralBiology

#TeamTomo is having a competition to annotate #cryoET tomograms: https://cryoetdataportal.czscience.com/competition

This is a good initiative! Especially the metadata format standardization part. I hope several good 3D particle picking programs will emerge from this.

#StructuralBiology

Localising elements in single-particle reconstructions by REEL-EM: Reconstructed Electron Energy-Loss - Elemental Mapping
https://doi.org/10.1101/2024.01.18.575858

This paper was just brought to my attention, and I only skimmed it, but... this is SO cool! 🤩
Curious if EELS could be applied in #cryoET to map heavy elements in situ.

#cryoEM #biophysics #spectroscopy

Localising elements in single-particle reconstructions by REEL-EM: Reconstructed Electron Energy-Loss - Elemental Mapping
https://doi.org/10.1101/2024.01.18.575858

This paper was just brought to my attention, and I only skimmed it, but... this is SO cool! 🤩
Curious if EELS could be applied in #cryoET to map heavy elements in situ.

#cryoEM #biophysics #spectroscopy

Traveling back from Utrecht university after attending a very nice 2nd Dutch Structural Biology meeting, with cool #NMR #cryoEM and #cryoET applications, to all sort of interesting proteins. From ticks, to spiders and gas vesicles! Thanks to the organizers!

Traveling back from Utrecht university after attending a very nice 2nd Dutch Structural Biology meeting, with cool #NMR #cryoEM and #cryoET applications, to all sort of interesting proteins. From ticks, to spiders and gas vesicles! Thanks to the organizers!

Fisk University student Vida Robertson highlighted a publication from SBGrid member Elizabeth Wright of University of Wisconsin-Madison, reporting on the use of Cryo-ET to gain exciting insight into the structure of Respiratory syncytial virus (RSV) in her recent Nature Communications publication.

Read more here: https://medium.com/sbgrid-community-news/getting-a-clearer-view-of-rsv-8e181bcaabe6

<ALT= dimer-of-trimer fusion protein and a cross-section of the RSV envelope. EMDB:44966. CC BY SBGRID>

#SBGrid #structuralbiology #cryoet #virology

🏆 After nearly 20 years, Italy wins a Human Frontier Science Program #HFSP Fellowship!

Congratulations to our Karthik Ramanadane, Postdoc in the Coscia Group (Structural #Biology), who will study the molecular mechanisms of the #thyroid at HT, using a combination of #proteomics, cell-based assay, #CRISPRCas9 based screening, and #cryoET and CLEM approaches.

https://humantechnopole.it/en/news/karthik-ramanadane-wins-a-hfsp-fellowship-for-thyroid-studies/

@hfsp #science #sciencemastodon #lifesciences #humantechnopole

🏆 After nearly 20 years, Italy wins a Human Frontier Science Program #HFSP Fellowship!

Congratulations to our Karthik Ramanadane, Postdoc in the Coscia Group (Structural #Biology), who will study the molecular mechanisms of the #thyroid at HT, using a combination of #proteomics, cell-based assay, #CRISPRCas9 based screening, and #cryoET and CLEM approaches.

https://humantechnopole.it/en/news/karthik-ramanadane-wins-a-hfsp-fellowship-for-thyroid-studies/

@hfsp #science #sciencemastodon #lifesciences #humantechnopole

A common #cryoET challenge is incompatibility between different software tools. @brisvag &co develop a @napari_imaging-based 3D visualization & analysis tool named #blik, compatible with commonly used cryo-ET processing packages @labexgral #PLOSBiology https://plos.io/3UpNif0

A common #cryoET challenge is incompatibility between different software tools. @brisvag &co develop a @napari_imaging-based 3D visualization & analysis tool named #blik, compatible with commonly used cryo-ET processing packages @labexgral #PLOSBiology https://plos.io/3UpNif0

This time 4 years ago I was cancelling 3 invited talks in March alone.

Today, i’m on my way to only my second #academic conference in the intervening 4 years.

My how the times have changed. Can’t wait to meet with a group of methods & software devs for #CryoET

#Covid19 (covid24?)
#CryoEM

This time 4 years ago I was cancelling 3 invited talks in March alone.

Today, i’m on my way to only my second #academic conference in the intervening 4 years.

My how the times have changed. Can’t wait to meet with a group of methods & software devs for #CryoET

#Covid19 (covid24?)
#CryoEM

Using the #VideoGame engine #UnrealEngine 5 to render #protein #structures from #CryoET inside #cells at the #atomic level:

Preprint: https://doi.org/10.1101/2023.12.08.570879
Tutorial: https://blake.bcm.edu/emanwiki/EMAN2/unreal_render

#SciArt #CompChem #bioinformatics #EMAN2 #UE5 #DIYbio #education #MINT #STEM #SciComm

Using the #VideoGame engine #UnrealEngine 5 to render #protein #structures from #CryoET inside #cells at the #atomic level:

Preprint: https://doi.org/10.1101/2023.12.08.570879
Tutorial: https://blake.bcm.edu/emanwiki/EMAN2/unreal_render

#SciArt #CompChem #bioinformatics #EMAN2 #UE5 #DIYbio #education #MINT #STEM #SciComm

I’ve been spending quite a bit of time on cellular imaging lately, so it is kinda magic to work on in vitro samples and see side chain density so easily from tomography data!

#CryoEM #CryoET #science #imaging #computervision

I’ve been spending quite a bit of time on cellular imaging lately, so it is kinda magic to work on in vitro samples and see side chain density so easily from tomography data!

#CryoEM #CryoET #science #imaging #computervision

Here, #CryoET images show the axonemal structures in mammalian spermatozoa. Researchers found a protein, LRRC23, that’s essential for sperm motility and underlies male #infertility. #Genetics https://elifesciences.org/articles/90095?utm_source=mastodon&utm_medium=social&utm_campaign=organic

Here, #CryoET images show the axonemal structures in mammalian spermatozoa. Researchers found a protein, LRRC23, that’s essential for sperm motility and underlies male #infertility. #Genetics https://elifesciences.org/articles/90095?utm_source=mastodon&utm_medium=social&utm_campaign=organic

New Title Alert: GCtfFind has been added to the SBGrid collection in the month of November. GCtfFind robustly estimates the contrast transfer function (CTF) of cryoET tilt series and cryoEM micrographs, essential information needed for cryoET subtomogram averaging and cryoEM single-particle reconstruction.

More here: https://github.com/czimaginginstitute/GCtfFind

#SBGrid #cryoem #cryoet #sbgridsoftware

Patterns to Structures
by Christoph
I first saw this image a while ago on Twit­ter (now 𝕏) and I will put down a few thoughts about it here be­cause it il­lus­trates so well how mi­cros­cop­ists, es­pe­cial­ly cryo-elec­tron to­mog­ra­phers, work. And what dis­tin­guish­es their way of work­ing from that of ar­tists and where the two meet.
Read more > https://tinyurl.com/r8c4vy9p
#microbiology #cryoET

Patterns to Structures
by Christoph
I first saw this image a while ago on Twit­ter (now 𝕏) and I will put down a few thoughts about it here be­cause it il­lus­trates so well how mi­cros­cop­ists, es­pe­cial­ly cryo-elec­tron to­mog­ra­phers, work. And what dis­tin­guish­es their way of work­ing from that of ar­tists and where the two meet.
Read more > https://tinyurl.com/r8c4vy9p
#microbiology #cryoET

PhD student in Cryo-ET studies of membrane trafficking

Max-Planck-Institute for Multidisciplinary Science

Join us @mpi_nat for #PhD to study #MolecularMachines driving #membranetrafficking by #cryoEM #cryoET #temtomo.

See the full job description on jobRxiv: https://jobrxiv.org/job/max-planck-institute-for-multidisciplinary-science-27778-p...
https://jobrxiv.org/job/max-planck-institute-for-multidisciplinary-science-27778-phd-student-in-cryo-et-studies-of-membrane-trafficking/?feed_id=59836

PhD student in Cryo-ET studies of membrane trafficking

Max-Planck-Institute for Multidisciplinary Science

Join us @mpi_nat for #PhD to study #MolecularMachines driving #membranetrafficking by #cryoEM #cryoET #temtomo.

See the full job description on jobRxiv: https://jobrxiv.org/job/max-planck-institute-for-multidisciplinary-science-27778-p...
https://jobrxiv.org/job/max-planck-institute-for-multidisciplinary-science-27778-phd-student-in-cryo-et-studies-of-membrane-trafficking/?feed_id=59836

This “thought-provoking” paper exploits new #CryoET tools to examine the state of chromatin in situ, finding that nucleosomes in baker’s yeast cells are different from those in test tubes. https://elifesciences.org/articles/87672?utm_source=mastodon&utm_medium=social&utm_campaign=organic

PhD student in Cryo-ET studies of membrane trafficking

Max-Planck-Institute for Multidisciplinary Science

Join us @mpi_nat for #PhD to study #MolecularMachines driving #membranetrafficking by #cryoEM #cryoET #temtomo.

See the full job description on jobRxiv: https://jobrxiv.org/job/max-planck-institute-for-multidisciplinary-science-27778-p...
https://jobrxiv.org/job/max-planck-institute-for-multidisciplinary-science-27778-phd-student-in-cryo-et-studies-of-membrane-trafficking/?feed_id=57731

PhD student in Cryo-ET studies of membrane trafficking

Max-Planck-Institute for Multidisciplinary Science

Join us @mpi_nat for #PhD to study #MolecularMachines driving #membranetrafficking by #cryoEM #cryoET #temtomo.

See the full job description on jobRxiv: https://jobrxiv.org/job/max-planck-institute-for-multidisciplinary-science-27778-p...
https://jobrxiv.org/job/max-planck-institute-for-multidisciplinary-science-27778-phd-student-in-cryo-et-studies-of-membrane-trafficking/?feed_id=57731

Two+ weeks 🚨 19/09/2023 15:00-17:15 BST 🚨until our 45th BSCB GenSoc UK Cilia Network e-symposium- free and open to all! >1260 folks already registered, this is the #cilia #centriole place to be! Not on my list already, sign up here: https://www.eventbrite.co.uk/e/bscb-gensoc-uk-cilia-network-e-symposia-series-tickets-122092125835

We have all good things lined-up: #GeneRegulatoryNetworks, #Signalling, mind-blowing #cryoET protein ID, #OrganelleProteomics in #neurons AND everything #tubulin! Join us...

PhD student in Cryo-ET studies of membrane trafficking

Max-Planck-Institute for Multidisciplinary Science

Join us @mpi_nat for #PhD to study #MolecularMachines driving #membranetrafficking by #cryoEM #cryoET #temtomo.

See the full job description on jobRxiv: https://jobrxiv.org/job/max-planck-institute-for-multidisciplinary-science-27778-p...
https://jobrxiv.org/job/max-planck-institute-for-multidisciplinary-science-27778-phd-student-in-cryo-et-studies-of-membrane-trafficking/?feed_id=56213

PhD student in Cryo-ET studies of membrane trafficking

Max-Planck-Institute for Multidisciplinary Science

Join us @mpi_nat for #PhD to study #MolecularMachines driving #membranetrafficking by #cryoEM #cryoET #temtomo.

See the full job description on jobRxiv: https://jobrxiv.org/job/max-planck-institute-for-multidisciplinary-science-27778-p...
https://jobrxiv.org/job/max-planck-institute-for-multidisciplinary-science-27778-phd-student-in-cryo-et-studies-of-membrane-trafficking/?feed_id=56213

Cool in summer? Cucumber slices!🥒

🔬 Our researchers slice cells & mini-brains with precision on a 200µm scale using Aquilos2 microscope. They investigate diseases by imaging tiny molecules with electrons, combining with SOLIST technique for faster prep: weeks to days!

Thanks to @3P1L @KalebicNereo Flaminia Kaluthantrige Don Jasmine Nguyen @gaiaperone

🧐 Learn more about SOLIST: https://www.biorxiv.org/content/10.1101/2023.05.11.540146v1

#lifesciences #humantechnopole #science #sciencemastodon #cryoem #cryoet #biology