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abhaykot.bsky.social
@abhaykot.bsky.social
210 followers 85 following 1 posts
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Reposted
phaips.vd.st
Hey #TeamTomo,
Ever been in need of a tutorial about the fundamentals of cryo-electron tomography? From preprocessing raw frames to high-res subtomogram averaging?
That's why @florentwaltz.bsky.social and I made this website!

tomoguide.github.io

Follow the thread 1 /🧵
#CryoET #CryoEM 🔬🧪
Welcome to TomoGuide
A step-by-step Cryo-ET guide
tomoguide.github.io
May 6, 2025 at 4:27 PM
Reposted
science.org
In a new Science study, cryo–electron tomography captures the in-cell architecture of the mitochondrial respiratory chain, illuminating how the coordinated action of molecular machines drives life’s fundamental energy conversion.

Learn more in this week's issue: scim.ag/3FA3Ygq
March 20, 2025 at 6:05 PM
Reposted
lifeonthewedge.bsky.social
To all #TeamTomo #CryoET and #Chlamydomonas aficionados: we have updated EMPIAR-11830 with a bug fix concerning some cryo-CARE denoised tomos as well as additional files and metadata! 🎉👩🏽‍💻

www.ebi.ac.uk/empiar/EMPIA...

A little thread about what's new... 🧵 1/n
Rare cellular events observed in the cryo-ET dataset. Slices through tomograms (left) with corresponding 3D segmentation (middle and right). Right panels show enlarged views of the boxed regions in the middle panels. A) Mitochondrion at the plasma membrane, tethered to microtubules by thin filaments of unknown identity. Segmented classes: nuclear envelope (light blue), nuclear pore complex (dark blue), 80S ribosomes (orange), mitochondrial membranes (dark red), ATP synthase (royal blue), plasma membranes (grey), microtubules (pink), filaments (yellow), endoplasmic reticulum (purple). Zoomed-in panel shows thin filaments running between microtubules and the mitochondrion at the plasma membrane. Note that this tomogram contains two closely appressed cells, and thus, two plasma membranes with cell walls between. B) Mitochondrial fission event with ER membrane interactions. Segmented classes: mitochondrial membranes (dark red), ATP synthase (royal blue), 80S ribosomes (orange), thylakoid membranes (green), PSII (bright yellow), cell wall (grey), ER (purple), fission site containing filamentous structures perpendicular to the mitochondrial long axis (pale yellow). C) Ciliary transition zone between basal body and axoneme, including assembling IFT train and stellate structure77. Segmented classes: microtubule doublets (light blue), central microtubule pair (light green), stellate structure (pale red), IFT train (yellow). D) Pyrenoid tubule extending from the thylakoids into the phase-separated Rubisco matrix of the pyrenoid. Minitubules originate from thylakoid membranes82. Segmented classes: thylakoid membranes (dark green), PSII (yellow), pyrenoid tubule (lime green), Rubisco (lavender blue), minitubules (orange). Scale bars in A-D: 100 nm. Related to Fig. 2C-H.
February 28, 2025 at 4:35 PM
Reposted
aliciakmichael.bsky.social
I am happy to be a part of this effort and looking forward to the discoveries this dataset will enable! If you work with this dataset in the future, please add any annotations to the GitHub repository github.com/Chromatin-St... Thanks @paloha.bsky.social for spearheading the efforts with this!
January 6, 2025 at 3:00 PM
Reposted
cellarchlab.com
This large dataset is the result of years of collaborative #TeamTomo work between @abhaykot.bsky.social's TFS team, our @biozentrum.bsky.social group, and the @mpibiochem.bsky.social crew led by John and Jürgen.

Abhay's team used automated plasma #FIB milling and 42 overnight #cryoET sessions! 🧪🔬💪
January 6, 2025 at 11:19 AM
Reposted
cellarchlab.com
Towards community-driven visual proteomics! Excited to finally share this large-scale curated & annotated dataset of 1829 high-quality #cryoET tomograms of the little green alga that just keeps giving— Chlamydomonas! 🧪🧶🧬🌾🌊🌍

Preprint📜: www.biorxiv.org/content/10.1...

A short thread🧵👇
January 6, 2025 at 11:19 AM
Reposted
phaips.vd.st
More than 1'800 tomograms available for the community. Towards visual proteomics using our favorite organism Chlamy!

Check out the preprint: www.biorxiv.org/content/10.1...

Find it on EMPIAR (11830) and fully annotated on the CZI data portal: cryoetdataportal.czscience.com

#TeamTomo
Towards community-driven visual proteomics with large-scale cryo-electron tomography of Chlamydomonas reinhardtii
In situ cryo-electron tomography (cryo-ET) has emerged as the method of choice to investigate structures of biomolecules in their native context. However, challenges remain in the efficient production...
www.biorxiv.org
December 29, 2024 at 11:47 AM
Reposted
peiferlabunc.bsky.social
WOW! "Subtomogram averaging Soluble and membrane-bound complexes ranging in size from >3 MDa to ~200 kDa, including 80S ribosomes, Rubisco, nucleosomes, microtubules, clathrin, photosystem II, and mitochondrial ATP synthase. The majority of these density maps reached sub-nanometer resolution..." 🧪
Title, authors and abstract from link
December 29, 2024 at 5:45 PM
Reposted
bjgreber.bsky.social
Our first "lab paper" is out: In collaboration with Sandro Ataide and Yichen Zhong (University of Sydney) and Adrian Koh and @abhaykot.bsky.social (TFS), Junjie Feng in my lab determined the structure of the peptide binding domain of SRP68/72, the largest protein components of the eukaryotic SRP.
Depiction of the cryo-EM map of SRP68/72 PBD.
February 17, 2024 at 3:40 PM
Reposted
efodor.bsky.social
A fantastic postdoc opportunity with Jon Grimes at Strubi, University of Oxford, to study the molecular mechanisms of viruses using the latest cryo-ET and cryo-SIM technologies.
my.corehr.com/pls/uoxrecru...
Job Details
my.corehr.com
November 7, 2023 at 4:43 PM
Reposted
bjgreber.bsky.social
This was missed due to major live events happening around the same time, but we have released some of our high-resolution (2 Å) and rapid screening #cryoEM maps & models of the human CAK bound to small molecules. Paper still under review - more to follow.
www.ebi.ac.uk/emdb/search/...
October 27, 2023 at 7:25 AM