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Doulin Shepherd

@dcshepherd.bsky.social
73 followers 127 following 6 posts

Post doc in the Ghosal Lab at the University of Melbourne I study host pathogen interactions using Cryo-ET and STA stuff #teamtomo

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Reposted by Doulin Shepherd
Debnath Ghosal @debnathghosal.bsky.social · 07/10/2026
When imaging at high mag using cryo-ET, field of view reduces. How to overcome this limit? How do we get a "bird’s-eye view" without compromising resolution? Our very own @HamishBrown has a solution to this: “montage tomography with a rectangular beam!” www.biorxiv.org/content/10.6...
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Reposted by Doulin Shepherd
Luca Troman @lucatroman.bsky.social · 05/02/2026
🌀 How do spirochete bacteria swim through thick fluids like champions? We solved T. denticola flagella structure - asymmetric proteins expand one side, compress the other for perfect corkscrew motion! @debnathghosal.bsky.social 🔗 doi.org/10.64898/202... #StructuralBiology #CryoEM #Microbiology
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Reposted by Doulin Shepherd
Debnath Ghosal @debnathghosal.bsky.social · 05/02/2026
📣 New paper alert! This is a story of molecular tricks that let spirochetes (spiral-shaped bacteria) drill through tissue. www.biorxiv.org/content/10.6...
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Reposted by Doulin Shepherd
Bindusmita Paul @bindusmitapaul.bsky.social · 05/02/2026
Wonderful spirochete asymmetric flagellar structural work by @lucatroman.bsky.social Grateful to be part of the story supported by @debnathghosal.bsky.social
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Doulin Shepherd @dcshepherd.bsky.social · 12/12/2025
I noticed something similar, especially with membrane proteins. Dynamo worked fine, but I always got strange reconstructions with RELION.
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Reposted by Doulin Shepherd
Debnath Ghosal @debnathghosal.bsky.social · 25/07/2025
📣 New paper alert! One of the most exciting projects we've done in recent years is now out on BioRxiv: "An Asgard archaeon from a modern analog of ancient microbial mats". Glimpse into early complex life! ❄️🦠 🔬🧬 www.biorxiv.org/content/10.1.... A thread...
biorxiv.org
An Asgard archaeon from a modern analog of ancient microbial mats
It has been proposed that eukaryotic cells evolved via symbiosis between sulfate-reducing bacteria and hydrogen-producing archaea. Here we describe a highly enriched culture of a novel Asgard archaeon...
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Doulin Shepherd @dcshepherd.bsky.social · 11/07/2025
I have been using CryoLithe recently as DeepDeWedge and cryoCARE erase many of the periplasmic complexes that I want to pick. arxiv.org/abs/2501.15246 If you are unfortunate and have to manually pick particles. I have had the most success using the WARP deconvolution filter.
arxiv.org
End-to-end localized deep learning for Cryo-ET
Cryo-electron tomography (cryo-ET) enables 3D visualization of cellular environments. Accurate reconstruction of high-resolution volumes is complicated by the very low signal-to-noise ratio and a rest...
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Doulin Shepherd @dcshepherd.bsky.social · 28/05/2025
My total reliance on Nvidia GPUs is a bit concerning.
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Doulin Shepherd @dcshepherd.bsky.social · 30/11/2024
Has anyone encountered the issue of DM3 crashing and taking TIA with it during long tomo collections? If so, did you find a solution? #Teamtomo #CryoET
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Doulin Shepherd @dcshepherd.bsky.social · 27/11/2024
It seems like, no matter what technique you use, it's Fourier transforms all the way down.
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Doulin Shepherd @dcshepherd.bsky.social · 10/11/2024
For tomography and STA, I feel like EMAN2 was ahead of its time. I am still confused as to why it isn't used by more people.
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