Jan Binovsky
@jbinovsky.bsky.social
🇸🇰PhD student at Plevka Lab, CEITEC_Brno🇨🇿 | biochemistry & structural biology 🧬🧫🧪🔬
Much needed addition to the AlphaFold Database! 💻 Large potential for use in #StructuralBiology #Phage research.
Really excited to share our resource and analysis of AlphaFold-predicted monomers and homodimers across viruses and phages. Project driven by fab PhD student @rodai.bsky.social and with our great collaborators Joana Pereira @joanampereira.bsky.social and @ninjani.bsky.social
The Viral AlphaFold Database of monomers and homodimers reveals conserved protein folds in viruses of bacteria, archaea, and eukaryotes https://www.biorxiv.org/content/10.1101/2025.05.14.653371v1
May 19, 2025 at 11:23 AM
Much needed addition to the AlphaFold Database! 💻 Large potential for use in #StructuralBiology #Phage research.
Nice work and awesome #scicomm thread!
Did you know that there is so much DNA packed inside a phage capsid that the pressure is 10X higher than in a bottle of champagne? In our latest preprint, we wondered how that is contained in a phage that lives at extremely high temperatures. /1
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
April 18, 2025 at 4:46 PM
Nice work and awesome #scicomm thread!
Reposted by Jan Binovsky
Our study on pasteurising influenza viruses in milk is now out! It's a nice simple story: influenza viruses (including H5N1) are killed really effectively by pasteurisation, but in raw milk they stay infectious - obvious public health implications of both points... (1/2)
rdcu.be/d73te
rdcu.be/d73te
January 30, 2025 at 5:12 PM
Our study on pasteurising influenza viruses in milk is now out! It's a nice simple story: influenza viruses (including H5N1) are killed really effectively by pasteurisation, but in raw milk they stay infectious - obvious public health implications of both points... (1/2)
rdcu.be/d73te
rdcu.be/d73te
Reposted by Jan Binovsky
I'd like to draw your attention to this truly excellent paper from the Taraska lab on cryoET of plasma membrane associated proteins. Everyone who is thinking about probes in the cryoET space should also see what they could do with ferritag (fig 6) www.nature.com/articles/s41...
January 22, 2025 at 4:40 PM
I'd like to draw your attention to this truly excellent paper from the Taraska lab on cryoET of plasma membrane associated proteins. Everyone who is thinking about probes in the cryoET space should also see what they could do with ferritag (fig 6) www.nature.com/articles/s41...
I appreciate the stats! Thanks, @pdbeurope.bsky.social for a summary!
As we head into 2025, let's take one final look back at 2024 and how the year unfolded in the PDB archive. There were 15319 entries released last year but what more can we find out about those structures ⚖️?
A thread 1/11 🧵
A thread 1/11 🧵
January 13, 2025 at 11:45 AM
I appreciate the stats! Thanks, @pdbeurope.bsky.social for a summary!
Reposted by Jan Binovsky
I'm happy and humbled to take on a new role with @rcsbpdb.bsky.social. I'll be continuing David Goodsell's work on the Molecule of the Month, starting with my first article on Assembly Line Polyketide Synthases! Check it out (animation included!)
pdb101.rcsb.org/motm/301
pdb101.rcsb.org/motm/301
PDB101: Molecule of the Month: Assembly Line Polyketide Synthases
Large multienzyme complexes that synthesize diverse small molecules in a stepwise manner.
pdb101.rcsb.org
January 7, 2025 at 6:32 PM
I'm happy and humbled to take on a new role with @rcsbpdb.bsky.social. I'll be continuing David Goodsell's work on the Molecule of the Month, starting with my first article on Assembly Line Polyketide Synthases! Check it out (animation included!)
pdb101.rcsb.org/motm/301
pdb101.rcsb.org/motm/301
Amazing work and resource! 😍
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🧵👇
Preprint📜: www.biorxiv.org/content/10.1...
A short thread🧵👇
January 6, 2025 at 1:35 PM
Amazing work and resource! 😍
Reposted by Jan Binovsky
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! :)
- 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! :)
December 17, 2024 at 9:24 AM
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! :)
- 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! :)
December 17, 2024 at 9:40 AM
I knew it wouldn't be long before we see #cryoEM structures of a #phage cousin infecting #Archea 🦠 🧪
Beautiful structures from @daumlab.bsky.social, congrats!
Beautiful structures from @daumlab.bsky.social, congrats!
Check out our structure of the archaeal virus HFTV1! Amazing work by two students - Daniel Zhang and Becky Davies, supported by @mathewmclaren.bsky.social. Great collaboration with T. Quax & S. Schwarzer, @hanna-m-oksanen.bsky.social, @the-gold-lab.bsky.social, @misha-isupov.bsky.social & W. Stuart.
December 11, 2024 at 12:51 PM
I knew it wouldn't be long before we see #cryoEM structures of a #phage cousin infecting #Archea 🦠 🧪
Beautiful structures from @daumlab.bsky.social, congrats!
Beautiful structures from @daumlab.bsky.social, congrats!
I created this Starter Pack for PhDs and Postdocs in Structural Biology to help connect with colleagues who share similar interests and concerns in the field.
Feel free to recommend people or yourself! I'll be adding people 💪🏼😁
bsky.app/starter-pack...
Feel free to recommend people or yourself! I'll be adding people 💪🏼😁
bsky.app/starter-pack...
November 22, 2024 at 8:12 AM
Another useful starter pack 👇
Structural Biology Starterpack go.bsky.app/DDetSBp
I like feeds better as it filters out 'cat' talk, leaves in the selective structural biology chitchat (Protein Cosmos). Poke me for inclusion/removal. Apologies if I've broken etiquette and included/excluded you first up (not intended to offend).
I like feeds better as it filters out 'cat' talk, leaves in the selective structural biology chitchat (Protein Cosmos). Poke me for inclusion/removal. Apologies if I've broken etiquette and included/excluded you first up (not intended to offend).
November 15, 2024 at 9:11 PM
Another useful starter pack 👇
In case someone is looking for this...
November 14, 2024 at 9:48 PM
In case someone is looking for this...
Just uploaded a revised version of the manuscript on bioRxiv 🙌
We made some changes to the text and figures, mainly to clarify the naming of proteins.
Yeah, it's a challenge to describe things within two different 10MDa structures 🐘
We made some changes to the text and figures, mainly to clarify the naming of proteins.
Yeah, it's a challenge to describe things within two different 10MDa structures 🐘
🚀Announcing my first (co)first-author manuscript 🚀
"Cell attachment and tail contraction of S. aureus phage phi812"
🔗 bit.ly/Phi812
Explore the structural details of phage interaction with Gram+ bacteria 🤯
#PhageTherapy #cryoEM 🧪 | 🧬🧶 | 🦠
1/11
"Cell attachment and tail contraction of S. aureus phage phi812"
🔗 bit.ly/Phi812
Explore the structural details of phage interaction with Gram+ bacteria 🤯
#PhageTherapy #cryoEM 🧪 | 🧬🧶 | 🦠
1/11
Cell attachment and tail contraction of S. aureus phage phi812
bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution
bit.ly
November 8, 2024 at 1:00 PM
Just uploaded a revised version of the manuscript on bioRxiv 🙌
We made some changes to the text and figures, mainly to clarify the naming of proteins.
Yeah, it's a challenge to describe things within two different 10MDa structures 🐘
We made some changes to the text and figures, mainly to clarify the naming of proteins.
Yeah, it's a challenge to describe things within two different 10MDa structures 🐘
🚀Announcing my first (co)first-author manuscript 🚀
"Cell attachment and tail contraction of S. aureus phage phi812"
🔗 bit.ly/Phi812
Explore the structural details of phage interaction with Gram+ bacteria 🤯
#PhageTherapy #cryoEM 🧪 | 🧬🧶 | 🦠
1/11
"Cell attachment and tail contraction of S. aureus phage phi812"
🔗 bit.ly/Phi812
Explore the structural details of phage interaction with Gram+ bacteria 🤯
#PhageTherapy #cryoEM 🧪 | 🧬🧶 | 🦠
1/11
Cell attachment and tail contraction of S. aureus phage phi812
bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution
bit.ly
September 23, 2024 at 4:17 PM
🚀Announcing my first (co)first-author manuscript 🚀
"Cell attachment and tail contraction of S. aureus phage phi812"
🔗 bit.ly/Phi812
Explore the structural details of phage interaction with Gram+ bacteria 🤯
#PhageTherapy #cryoEM 🧪 | 🧬🧶 | 🦠
1/11
"Cell attachment and tail contraction of S. aureus phage phi812"
🔗 bit.ly/Phi812
Explore the structural details of phage interaction with Gram+ bacteria 🤯
#PhageTherapy #cryoEM 🧪 | 🧬🧶 | 🦠
1/11
Reading a lot about contractile phages and injection systems, the idea of leveraging them for cargo delivery always amazed me 🤯 and it's no longer just an idea 🧪
Here, a T. gondii secretion system was hijacked to deliver therapeutic proteins to neurons.
Link to study:
rdcu.be/dQozB
Here, a T. gondii secretion system was hijacked to deliver therapeutic proteins to neurons.
Link to study:
rdcu.be/dQozB
Engineering Toxoplasma gondii secretion systems for intracellular delivery of multiple large therapeutic proteins to neurons
Nature Microbiology - Toxoplasma gondii secretion systems can be engineered to deliver multiple large therapeutic proteins to neurons in vitro and in vivo.
rdcu.be
August 8, 2024 at 5:27 PM
Reading a lot about contractile phages and injection systems, the idea of leveraging them for cargo delivery always amazed me 🤯 and it's no longer just an idea 🧪
Here, a T. gondii secretion system was hijacked to deliver therapeutic proteins to neurons.
Link to study:
rdcu.be/dQozB
Here, a T. gondii secretion system was hijacked to deliver therapeutic proteins to neurons.
Link to study:
rdcu.be/dQozB
Using MS Word's "Dictate" function these days:
"I did an internshit..."
"I learned to cry electron microscopy"
...how am I supposed to write a motivation letter with this? 😢
"I did an internshit..."
"I learned to cry electron microscopy"
...how am I supposed to write a motivation letter with this? 😢
July 31, 2024 at 6:43 AM
Using MS Word's "Dictate" function these days:
"I did an internshit..."
"I learned to cry electron microscopy"
...how am I supposed to write a motivation letter with this? 😢
"I did an internshit..."
"I learned to cry electron microscopy"
...how am I supposed to write a motivation letter with this? 😢
Reposted by Jan Binovsky
Really good 15 min TWiV episode with Paul Offit outlining how false and irresponsible the recent lab leak nonsense from @nytimes.com is.
I for one appreciate the brevity - there really is nothing more to it.
If you're interested in the topic, give it a listen.
www.youtube.com/watch?v=Ukv9...
I for one appreciate the brevity - there really is nothing more to it.
If you're interested in the topic, give it a listen.
www.youtube.com/watch?v=Ukv9...
Beyond the Noise #40: Lab leak mania
In this episode Dr. Offit asks, why did the New York Times publish an op-ed supporting the lab leak theory when all evidence supports a zoonotic spillover?Sh...
www.youtube.com
July 5, 2024 at 9:14 PM
Really good 15 min TWiV episode with Paul Offit outlining how false and irresponsible the recent lab leak nonsense from @nytimes.com is.
I for one appreciate the brevity - there really is nothing more to it.
If you're interested in the topic, give it a listen.
www.youtube.com/watch?v=Ukv9...
I for one appreciate the brevity - there really is nothing more to it.
If you're interested in the topic, give it a listen.
www.youtube.com/watch?v=Ukv9...
Manuscript submitted 🤞 Brace for new structural insights into a bacteriophage landing onto the host cell 🚀
July 2, 2024 at 12:15 PM
Manuscript submitted 🤞 Brace for new structural insights into a bacteriophage landing onto the host cell 🚀
📰 I find myself questioning my scientific career from time to time. This is an encouraging piece.
"Meaningfulness in a scientific career is about more than tangible outputs."
www.nature.com/articles/d41...
"Meaningfulness in a scientific career is about more than tangible outputs."
www.nature.com/articles/d41...
Meaningfulness in a scientific career is about more than tangible outputs
Letter to the Editor
www.nature.com
March 22, 2024 at 9:05 AM
📰 I find myself questioning my scientific career from time to time. This is an encouraging piece.
"Meaningfulness in a scientific career is about more than tangible outputs."
www.nature.com/articles/d41...
"Meaningfulness in a scientific career is about more than tangible outputs."
www.nature.com/articles/d41...
Just finished registration for the Gordon Research Seminar (GRS), complementing the conference (GRC) on 3D #ElectronMicrocopy 🔥
Looking forward to attending the GRC/S for the first time! Am I gonna meet someone from my BlueSky bubble? 🙌
Looking forward to attending the GRC/S for the first time! Am I gonna meet someone from my BlueSky bubble? 🙌
March 21, 2024 at 2:01 PM
Just finished registration for the Gordon Research Seminar (GRS), complementing the conference (GRC) on 3D #ElectronMicrocopy 🔥
Looking forward to attending the GRC/S for the first time! Am I gonna meet someone from my BlueSky bubble? 🙌
Looking forward to attending the GRC/S for the first time! Am I gonna meet someone from my BlueSky bubble? 🙌
📰 Some positive news for the afternoon reading: a survey about trust in scientists.
"...trust levels are fairly high across a range of demographics."
"It’s about the leadership of political parties and how they treat scientists."
www.nature.com/articles/d41...
"...trust levels are fairly high across a range of demographics."
"It’s about the leadership of political parties and how they treat scientists."
www.nature.com/articles/d41...
Largest post-pandemic survey finds trust in scientists is high
Study of more than 70,000 people suggests that trust levels vary among countries and are linked to political orientation. Study of more than 70,000 people suggests that trust levels vary among countri...
www.nature.com
February 15, 2024 at 12:26 PM
📰 Some positive news for the afternoon reading: a survey about trust in scientists.
"...trust levels are fairly high across a range of demographics."
"It’s about the leadership of political parties and how they treat scientists."
www.nature.com/articles/d41...
"...trust levels are fairly high across a range of demographics."
"It’s about the leadership of political parties and how they treat scientists."
www.nature.com/articles/d41...
Reposted by Jan Binovsky
I am excited to share that my work with @cijilim.bsky.social on protecting fragile samples from air-water-interface damage during cryo-EM plunge freezing is in preprint! www.biorxiv.org/content/10.1...
February 9, 2024 at 3:12 AM
I am excited to share that my work with @cijilim.bsky.social on protecting fragile samples from air-water-interface damage during cryo-EM plunge freezing is in preprint! www.biorxiv.org/content/10.1...
POV: renaming protein chains in your model. Symmetry mates not included.
February 7, 2024 at 12:00 PM
POV: renaming protein chains in your model. Symmetry mates not included.