Casper Berger
@casperberger.bsky.social
Senior Application Expert @ The Rosalind Franklin Institute
Reposted by Casper Berger
Organelles do NOT have a single uniform pH.
And if you think they must, because “protons diffuse fast,” this paper is for you.
A thread on why that assumption is wrong; and what we found instead. 🧵 1/n
And if you think they must, because “protons diffuse fast,” this paper is for you.
A thread on why that assumption is wrong; and what we found instead. 🧵 1/n
Organelles harbour pH gradients https://www.biorxiv.org/content/10.64898/2025.12.12.694065v1
December 17, 2025 at 12:46 AM
Organelles do NOT have a single uniform pH.
And if you think they must, because “protons diffuse fast,” this paper is for you.
A thread on why that assumption is wrong; and what we found instead. 🧵 1/n
And if you think they must, because “protons diffuse fast,” this paper is for you.
A thread on why that assumption is wrong; and what we found instead. 🧵 1/n
Reposted by Casper Berger
BBC News - Top UK scientist says research visa restrictions endanger economy
www.bbc.com/news/article...
www.bbc.com/news/article...
Top UK scientist says research visa restrictions endanger economy
Prof Sir Paul Nurse says the UK is "shooting itself in the foot" with its visa system for researchers.
www.bbc.com
December 5, 2025 at 6:35 AM
BBC News - Top UK scientist says research visa restrictions endanger economy
www.bbc.com/news/article...
www.bbc.com/news/article...
Reposted by Casper Berger
📢 We are on the lookout for Research Associates to support our Multidimensional Imaging Team across several cutting-edge projects in the following areas:
• Electron ptychography
• Liquid phase electron microscopy
• Electron spectroscopy and diffraction
Find out more: tinyurl.com/4ce5t7sm
• Electron ptychography
• Liquid phase electron microscopy
• Electron spectroscopy and diffraction
Find out more: tinyurl.com/4ce5t7sm
December 2, 2025 at 1:01 PM
📢 We are on the lookout for Research Associates to support our Multidimensional Imaging Team across several cutting-edge projects in the following areas:
• Electron ptychography
• Liquid phase electron microscopy
• Electron spectroscopy and diffraction
Find out more: tinyurl.com/4ce5t7sm
• Electron ptychography
• Liquid phase electron microscopy
• Electron spectroscopy and diffraction
Find out more: tinyurl.com/4ce5t7sm
Reposted by Casper Berger
Our latest T7SS study is now out in Science Advances!
We solved the cryoEM structure of the T7SSb core unit (T7bCU) composed of YukB, YukC, and YukD from Bacillus subtilis, revealing how these components assemble within the secretion machinery.
www.science.org/doi/10.1126/...
We solved the cryoEM structure of the T7SSb core unit (T7bCU) composed of YukB, YukC, and YukD from Bacillus subtilis, revealing how these components assemble within the secretion machinery.
www.science.org/doi/10.1126/...
A ubiquitin-like protein controls assembly of a bacterial type VIIb secretion system
Cryo-EM structure reveals how a ubiquitin-like protein orchestrates assembly of a bacterial weapon system.
www.science.org
November 21, 2025 at 7:05 PM
Our latest T7SS study is now out in Science Advances!
We solved the cryoEM structure of the T7SSb core unit (T7bCU) composed of YukB, YukC, and YukD from Bacillus subtilis, revealing how these components assemble within the secretion machinery.
www.science.org/doi/10.1126/...
We solved the cryoEM structure of the T7SSb core unit (T7bCU) composed of YukB, YukC, and YukD from Bacillus subtilis, revealing how these components assemble within the secretion machinery.
www.science.org/doi/10.1126/...
Reposted by Casper Berger
What if even the core of bacterial nanomachines wasn’t static?
We found that the T3SS core protein SctD in Yersinia dynamically exchanges subunits — and this flexibility is essential for proper assembly & function.
🔗 www.nature.com/articles/s41...
@kit.edu @t3sss.bsky.social
We found that the T3SS core protein SctD in Yersinia dynamically exchanges subunits — and this flexibility is essential for proper assembly & function.
🔗 www.nature.com/articles/s41...
@kit.edu @t3sss.bsky.social
November 12, 2025 at 4:21 PM
What if even the core of bacterial nanomachines wasn’t static?
We found that the T3SS core protein SctD in Yersinia dynamically exchanges subunits — and this flexibility is essential for proper assembly & function.
🔗 www.nature.com/articles/s41...
@kit.edu @t3sss.bsky.social
We found that the T3SS core protein SctD in Yersinia dynamically exchanges subunits — and this flexibility is essential for proper assembly & function.
🔗 www.nature.com/articles/s41...
@kit.edu @t3sss.bsky.social
Reposted by Casper Berger
Very happy that NWO supports this major upgrade of our national EM infrastructure. It is great that this initiative got broad support all over NL, and it will EMPower fantastic science - looking forward to that!
www.uu.nl/en/news/33-m...
www.uu.nl/en/news/33-m...
33 million euro investment for national electron microscope facility EMPower
A major new national facility for electron microscopy, called EMPower, has been awarded to a consortium of Dutch universities and medical centers. EMPower aims to pave the way for major discoveries im...
www.uu.nl
November 4, 2025 at 7:14 AM
Very happy that NWO supports this major upgrade of our national EM infrastructure. It is great that this initiative got broad support all over NL, and it will EMPower fantastic science - looking forward to that!
www.uu.nl/en/news/33-m...
www.uu.nl/en/news/33-m...
Reposted by Casper Berger
Happy to announce "Technical Innovations Using #SerialEM: A Community Meeting", a new format of hybrid meeting David Mastronarde and I are organizing in April 2026. For more info, a preliminary list of speakers, pre-registration etc. visit
www.nexperion.net/semcm2026
www.nexperion.net/semcm2026
September 23, 2025 at 10:42 AM
Happy to announce "Technical Innovations Using #SerialEM: A Community Meeting", a new format of hybrid meeting David Mastronarde and I are organizing in April 2026. For more info, a preliminary list of speakers, pre-registration etc. visit
www.nexperion.net/semcm2026
www.nexperion.net/semcm2026
Reposted by Casper Berger
Political choices have direct effects on #science 🧪 and a cascading impact on society, health, economy, etc. Many are still convinced that science should be apolitical........
'Cancer Research UK told The Observer that several pieces of research had been affected by...immigration costs, which have risen by 126% since 2019 and are up to 17 times higher than the average of comparable countries including France, Australia, the US and South Korea.' Not only cancer research.
Cancer research ‘set back years’ as visa fees drive scien...
With vital studies being shelved and foreign experts turning down jobs, leading charity urges ministers to act
observer.co.uk
August 24, 2025 at 8:50 AM
Political choices have direct effects on #science 🧪 and a cascading impact on society, health, economy, etc. Many are still convinced that science should be apolitical........
Reposted by Casper Berger
In their new study, Beata Turoňová and Tomáš Majtner trained 13 neural networks to automatically detect and remove those corrupted frames, speeding up processing and saving time for tomographers 🥳
July 25, 2025 at 10:14 AM
In their new study, Beata Turoňová and Tomáš Majtner trained 13 neural networks to automatically detect and remove those corrupted frames, speeding up processing and saving time for tomographers 🥳
Reposted by Casper Berger
July 21, 2025 at 7:15 PM
Reposted by Casper Berger
Proud to share our latest paper. doi.org/10.1016/j.cr...
Through the dedication of @glynnca.bsky.social and @cryingem.bsky.social we report a thorough method to image molecular organisation within hippocampus tissue.
Structural biology in tissue is well and truly here!
@rosfrankinst.bsky.social
Through the dedication of @glynnca.bsky.social and @cryingem.bsky.social we report a thorough method to image molecular organisation within hippocampus tissue.
Structural biology in tissue is well and truly here!
@rosfrankinst.bsky.social
June 17, 2025 at 10:59 AM
Proud to share our latest paper. doi.org/10.1016/j.cr...
Through the dedication of @glynnca.bsky.social and @cryingem.bsky.social we report a thorough method to image molecular organisation within hippocampus tissue.
Structural biology in tissue is well and truly here!
@rosfrankinst.bsky.social
Through the dedication of @glynnca.bsky.social and @cryingem.bsky.social we report a thorough method to image molecular organisation within hippocampus tissue.
Structural biology in tissue is well and truly here!
@rosfrankinst.bsky.social
Reposted by Casper Berger
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/
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/
May 22, 2025 at 10:10 AM
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/
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/
Reposted by Casper Berger
“The Website” is here! It can be intimidating getting into analysis of #CryoET data, and software is evolving all the time👩💻🚀. @phaips.vd.st & @florentwaltz.bsky.social put our lab’s workflows into an online guide. We hope this helps lower the bar to joining #TeamTomo. Feedback much appreciated! 🧪🧶🧬🔬
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 🔬🧪
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 7, 2025 at 10:56 AM
“The Website” is here! It can be intimidating getting into analysis of #CryoET data, and software is evolving all the time👩💻🚀. @phaips.vd.st & @florentwaltz.bsky.social put our lab’s workflows into an online guide. We hope this helps lower the bar to joining #TeamTomo. Feedback much appreciated! 🧪🧶🧬🔬
Reposted by Casper Berger
Another super paper came out this week from Amit Kohli and Laura Waller on Ring deconvolution microscopy. This one is fairly technical, but essentially it's a computational approach that lets you do deconvolution when there is a spatially varying PSF. www.nature.com/articles/s41...
Ring deconvolution microscopy: exploiting symmetry for efficient spatially varying aberration correction - Nature Methods
Ring deconvolution microscopy leverages symmetry to provide fast and straightforward spatially varying deblurring and offers improved speed and image quality compared to standard approaches across div...
www.nature.com
May 2, 2025 at 1:23 PM
Another super paper came out this week from Amit Kohli and Laura Waller on Ring deconvolution microscopy. This one is fairly technical, but essentially it's a computational approach that lets you do deconvolution when there is a spatially varying PSF. www.nature.com/articles/s41...
Reposted by Casper Berger
Maud Dumoux from RFI tune in on zoom to find out more now! @ccpem.bsky.social @diamondlightsource.bsky.social
April 24, 2025 at 4:02 PM
Maud Dumoux from RFI tune in on zoom to find out more now! @ccpem.bsky.social @diamondlightsource.bsky.social
Reposted by Casper Berger
A colder frontier in cryo-EM 🧪🔬
Chris Russo’s group, inc. Joshua Dickerson, adapted #cryoEM to work at liquid helium temperatures (13 kelvins), where every frame captured contains more information than the equivalent using liquid nitrogen (81 kelvins).
Read more: tinyurl.com/mwwcunkc
#LMBResearch
Chris Russo’s group, inc. Joshua Dickerson, adapted #cryoEM to work at liquid helium temperatures (13 kelvins), where every frame captured contains more information than the equivalent using liquid nitrogen (81 kelvins).
Read more: tinyurl.com/mwwcunkc
#LMBResearch
April 23, 2025 at 8:49 AM
A colder frontier in cryo-EM 🧪🔬
Chris Russo’s group, inc. Joshua Dickerson, adapted #cryoEM to work at liquid helium temperatures (13 kelvins), where every frame captured contains more information than the equivalent using liquid nitrogen (81 kelvins).
Read more: tinyurl.com/mwwcunkc
#LMBResearch
Chris Russo’s group, inc. Joshua Dickerson, adapted #cryoEM to work at liquid helium temperatures (13 kelvins), where every frame captured contains more information than the equivalent using liquid nitrogen (81 kelvins).
Read more: tinyurl.com/mwwcunkc
#LMBResearch
Reposted by Casper Berger
Very compelling study showing the association between herpes zoster vaccination and dementia prevention. The authors leveraged a unique cohort for this natural experiment which shows a reduction in dementia risk of 20% in vaccinated individuals. #MedSky #IDSky 🧪
www.nature.com/articles/s41...
www.nature.com/articles/s41...
A natural experiment on the effect of herpes zoster vaccination on dementia - Nature
Using a natural experiment that avoids common bias concerns, this study finds that the live-attenuated shingles vaccine reduced the probability of a new dementia diagnosis within a follow-up period of...
www.nature.com
April 2, 2025 at 5:49 PM
Very compelling study showing the association between herpes zoster vaccination and dementia prevention. The authors leveraged a unique cohort for this natural experiment which shows a reduction in dementia risk of 20% in vaccinated individuals. #MedSky #IDSky 🧪
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Casper Berger
📸 Nadisha Gamage @rosfrankinst.bsky.social took a photo with the Node's polaroid frame during the poster session yesterday #biologists100
The key words of her research are #nucleosomes #cryoEM #stemcells #chromatin #FIBSEM
The key words of her research are #nucleosomes #cryoEM #stemcells #chromatin #FIBSEM
March 27, 2025 at 11:43 AM
📸 Nadisha Gamage @rosfrankinst.bsky.social took a photo with the Node's polaroid frame during the poster session yesterday #biologists100
The key words of her research are #nucleosomes #cryoEM #stemcells #chromatin #FIBSEM
The key words of her research are #nucleosomes #cryoEM #stemcells #chromatin #FIBSEM
Reposted by Casper Berger
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
Learn more in this week's issue: scim.ag/3FA3Ygq
March 20, 2025 at 6:05 PM
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
Learn more in this week's issue: scim.ag/3FA3Ygq
Reposted by Casper Berger
Automated Removal of Corrupted Tilts in Cryo-Electron Tomography https://www.biorxiv.org/content/10.1101/2025.03.13.642992v1
March 15, 2025 at 7:17 AM
Automated Removal of Corrupted Tilts in Cryo-Electron Tomography https://www.biorxiv.org/content/10.1101/2025.03.13.642992v1
Reposted by Casper Berger
AreTomoLive: Automated reconstruction of comprehensively-corrected and denoised cryo-electron tomograms in real-time and at high throughput www.biorxiv.org/content/10.1101/2025.03.11.642690v1 #cryoem
March 14, 2025 at 7:10 AM
AreTomoLive: Automated reconstruction of comprehensively-corrected and denoised cryo-electron tomograms in real-time and at high throughput www.biorxiv.org/content/10.1101/2025.03.11.642690v1 #cryoem
Reposted by Casper Berger
Published in @naturecomms.bsky.social, Franklin researchers describe a high-throughput methodology for cryo focused ion beam lamella preparation. This technique enabled a high-resolution structure (4.0 Å) of an E. coli ribosome using sub volume averaging.
Read the full article here: zurl.co/WhpcB
Read the full article here: zurl.co/WhpcB
March 7, 2025 at 5:25 PM
Published in @naturecomms.bsky.social, Franklin researchers describe a high-throughput methodology for cryo focused ion beam lamella preparation. This technique enabled a high-resolution structure (4.0 Å) of an E. coli ribosome using sub volume averaging.
Read the full article here: zurl.co/WhpcB
Read the full article here: zurl.co/WhpcB
Reposted by Casper Berger
Dr Liang Wu and his team investigate the function of enzymes in heparan sulfate production – long, complex chains of sugar molecules found in every cell of the body. In this latest science update, Liang reflects on how new imaging techniques are helping in this area. Read more here - zurl.co/aB4ks
Uncovering the hidden lives of complex sugars with cutting-edge imaging - Rosalind Franklin Institute
Dr Liang Wu is a Wellcome Trust Sir Henry Dale Fellow at the Rosalind Franklin Institute. Since joining the Franklin in 2020, Dr Wu’s team has been investigating the role and function of enzymes in th...
zurl.co
March 6, 2025 at 11:41 AM
Dr Liang Wu and his team investigate the function of enzymes in heparan sulfate production – long, complex chains of sugar molecules found in every cell of the body. In this latest science update, Liang reflects on how new imaging techniques are helping in this area. Read more here - zurl.co/aB4ks
Reposted by Casper Berger
Check out our paper on Xenon milling of HPF samples, now online @naturecomms.bsky.social
rdcu.be/eczIb
rdcu.be/eczIb
rdcu.be
March 7, 2025 at 12:54 PM
Check out our paper on Xenon milling of HPF samples, now online @naturecomms.bsky.social
rdcu.be/eczIb
rdcu.be/eczIb
Reposted by Casper Berger
In situ and in vitro cryo-EM reveal structures of mycobacterial encapsulin assembly intermediates pubmed.ncbi.nlm.nih.gov/39955411/ #cryoem
February 16, 2025 at 12:46 PM
In situ and in vitro cryo-EM reveal structures of mycobacterial encapsulin assembly intermediates pubmed.ncbi.nlm.nih.gov/39955411/ #cryoem