Pinned
Shyamal
@shyamalm.bsky.social
· Sep 7
HPV is the most common STI. Revisiting the infection pathways, we discover that, contrary to the accepted model of trafficking, HPV stays intact and infectious in host cell lysosomes 🤯. Among other discoveries, we show that the intact virus is a cargo of COPI-coated pits!
Reposted by Shyamal
Thrilled to share that the final piece of my PhD work is now on bioRxiv! biorxiv.org/content/10.1... With support from @nvidia and the @NSF, we used AlphaFold to screen 1.6M+ protein pairs, revealing thousands of potential novel PPIs. All data can be viewed at predictomes.org/hp
Proteome-wide in silico screening for human protein-protein interactions
Protein-protein interactions (PPIs) drive virtually all biological processes, yet most PPIs have not been identified and even more remain structurally unresolved. We developed a two-step computational...
biorxiv.org
November 12, 2025 at 9:26 PM
Thrilled to share that the final piece of my PhD work is now on bioRxiv! biorxiv.org/content/10.1... With support from @nvidia and the @NSF, we used AlphaFold to screen 1.6M+ protein pairs, revealing thousands of potential novel PPIs. All data can be viewed at predictomes.org/hp
Reposted by Shyamal
Just published! We share an open-source workflow to measure membrane thickness from tomograms, including a tutorial with 3D visualizations. We analyze thickness variations across organelles and reflect on where to define a membrane boundary. @becklab.bsky.social #teamtomo rupress.org/jcb/article/...
November 6, 2025 at 7:38 AM
Just published! We share an open-source workflow to measure membrane thickness from tomograms, including a tutorial with 3D visualizations. We analyze thickness variations across organelles and reflect on where to define a membrane boundary. @becklab.bsky.social #teamtomo rupress.org/jcb/article/...
Happy to share this satellite story. Structure of tau filaments from the amygdala of patients with mixed pathologies #Alzheimer’s and LATE.
Strikingly, none of the patients had documented head injury or trauma but tau adopts a CTE-fold
Preprint: www.biorxiv.org/content/10.1...
Strikingly, none of the patients had documented head injury or trauma but tau adopts a CTE-fold
Preprint: www.biorxiv.org/content/10.1...
CTE-Type Tau Filaments in Alzheimer's Disease with Co-morbid LATE-NC
Alzheimer's disease (AD), the most common neurodegenerative disease, is defined by β-amyloid plaques and tau neurofibrillary tangles. Tau filaments in AD adopt the Alzheimer's fold, which is distinct ...
www.biorxiv.org
October 23, 2025 at 11:21 AM
Happy to share this satellite story. Structure of tau filaments from the amygdala of patients with mixed pathologies #Alzheimer’s and LATE.
Strikingly, none of the patients had documented head injury or trauma but tau adopts a CTE-fold
Preprint: www.biorxiv.org/content/10.1...
Strikingly, none of the patients had documented head injury or trauma but tau adopts a CTE-fold
Preprint: www.biorxiv.org/content/10.1...
Nothing short of spectacular!🤩
Check out our preprint! With new molecular mechanisms, 140 subtomogram averages, and ~600 annotated cells under different conditions, we @embl.org were able to describe bacterial populations with in-cell #cryoET. And there’s a surprise at the end 🕵️
www.biorxiv.org/content/10.1...
#teamtomo
www.biorxiv.org/content/10.1...
#teamtomo
October 15, 2025 at 1:36 PM
Nothing short of spectacular!🤩
Reposted by Shyamal
Very excited that my final postdoctoral work is now online in Cell @cellpress.bsky.social.
www.sciencedirect.com/science/arti...
Using 16 (!) cryo-EM structures, we uncovered how the three proteins coronin, cofilin and AIP1 work together to rapidly disassemble actin filaments.
www.sciencedirect.com/science/arti...
Using 16 (!) cryo-EM structures, we uncovered how the three proteins coronin, cofilin and AIP1 work together to rapidly disassemble actin filaments.
October 13, 2025 at 9:04 AM
Very excited that my final postdoctoral work is now online in Cell @cellpress.bsky.social.
www.sciencedirect.com/science/arti...
Using 16 (!) cryo-EM structures, we uncovered how the three proteins coronin, cofilin and AIP1 work together to rapidly disassemble actin filaments.
www.sciencedirect.com/science/arti...
Using 16 (!) cryo-EM structures, we uncovered how the three proteins coronin, cofilin and AIP1 work together to rapidly disassemble actin filaments.
Great discussion here!
If you can't see sidechains, can you really call the resolution 3.3 Å..? 👀
And if you can't see sidechains, how do you know the helical symmetry is right..?
And if you can't see sidechains, how do you know the helical symmetry is right..?
Structural basis of Pseudomonas biofilm-forming functional amyloid FapC formation pubmed.ncbi.nlm.nih.gov/40991694/ #cryoem
September 26, 2025 at 10:03 AM
Great discussion here!
Reposted by Shyamal
New PrePrint from the Vecchiarelli and Mosalaganti (@shyamalm.bsky.social) labs! 🧵
Collaboration with the Giessen and Pi labs
Congratulations to co-first authors Y Hoang (@hoanghamyy.bsky.social) and Pankaj Jadhav!
www.biorxiv.org/content/10.1...
Collaboration with the Giessen and Pi labs
Congratulations to co-first authors Y Hoang (@hoanghamyy.bsky.social) and Pankaj Jadhav!
www.biorxiv.org/content/10.1...
Engineering Spatial Control of Bacterial Organelles
Bacteria were once thought to lack organelles, but it is now clear they confine cellular reactions using an array of membrane- and protein-based compartments. A central question, however, is how bacte...
www.biorxiv.org
September 23, 2025 at 5:38 PM
New PrePrint from the Vecchiarelli and Mosalaganti (@shyamalm.bsky.social) labs! 🧵
Collaboration with the Giessen and Pi labs
Congratulations to co-first authors Y Hoang (@hoanghamyy.bsky.social) and Pankaj Jadhav!
www.biorxiv.org/content/10.1...
Collaboration with the Giessen and Pi labs
Congratulations to co-first authors Y Hoang (@hoanghamyy.bsky.social) and Pankaj Jadhav!
www.biorxiv.org/content/10.1...
Ever wondered how to position organelles in bacteria? Wonder no more!
Happy to have contributed to this fantastic story from @cellforganized.bsky.social' lab.
The avenues this opens in the synthetic biology space are enormous!
Movie: Carboxysomes positioned in E. coli!
Preprint: shorturl.at/D6xVg
Happy to have contributed to this fantastic story from @cellforganized.bsky.social' lab.
The avenues this opens in the synthetic biology space are enormous!
Movie: Carboxysomes positioned in E. coli!
Preprint: shorturl.at/D6xVg
September 23, 2025 at 3:31 PM
Ever wondered how to position organelles in bacteria? Wonder no more!
Happy to have contributed to this fantastic story from @cellforganized.bsky.social' lab.
The avenues this opens in the synthetic biology space are enormous!
Movie: Carboxysomes positioned in E. coli!
Preprint: shorturl.at/D6xVg
Happy to have contributed to this fantastic story from @cellforganized.bsky.social' lab.
The avenues this opens in the synthetic biology space are enormous!
Movie: Carboxysomes positioned in E. coli!
Preprint: shorturl.at/D6xVg
Reposted by Shyamal
If you are thinking about the future of structural biology, we are too! Our two cents (Jürgen Plitzko and I) just got published online here: authors.elsevier.com/sd/article/S...
August 23, 2025 at 11:21 PM
If you are thinking about the future of structural biology, we are too! Our two cents (Jürgen Plitzko and I) just got published online here: authors.elsevier.com/sd/article/S...
HPV is the most common STI. Revisiting the infection pathways, we discover that, contrary to the accepted model of trafficking, HPV stays intact and infectious in host cell lysosomes 🤯. Among other discoveries, we show that the intact virus is a cargo of COPI-coated pits!
September 7, 2025 at 11:41 AM
HPV is the most common STI. Revisiting the infection pathways, we discover that, contrary to the accepted model of trafficking, HPV stays intact and infectious in host cell lysosomes 🤯. Among other discoveries, we show that the intact virus is a cargo of COPI-coated pits!
Happy to have contributed to this amazing story by Hari!
Our paper discovering novel roles for the retrovirus-like proteins RTL8 and PEG10 in shaping stress granule biology is now online on Science Advances! #llps #stressgranules
www.science.org/doi/full/10....
www.science.org/doi/full/10....
Endogenous retrovirus-like proteins recruit UBQLN2 to stress granules and shape their functional biology
Virus-like proteins help our cells respond to environmental stress.
www.science.org
July 20, 2025 at 10:58 AM
Happy to have contributed to this amazing story by Hari!
Reposted by Shyamal
Our new preprint: how photoprotection is spatially coordinated with energy metabolism. Photosystem I is major source of radicals. We report EM structure of PSI in complex with superoxide dismutase SOD: direct link between energy conversion & oxidative stress defence
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
July 7, 2025 at 6:03 AM
Our new preprint: how photoprotection is spatially coordinated with energy metabolism. Photosystem I is major source of radicals. We report EM structure of PSI in complex with superoxide dismutase SOD: direct link between energy conversion & oxidative stress defence
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Shyamal
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 Shyamal
We’ve uncovered Asgard chromatin structures formed by a Hodarchaeal histone : closed hypernucleosome conserved in archaea and an open form resembling the H3-H4 eukaryotic octasome. Fantastic work by @harshranawat.bsky.social!
www.biorxiv.org/content/10.1...
#Chromatin #Asgard #Archaea #cryoEM
www.biorxiv.org/content/10.1...
#Chromatin #Asgard #Archaea #cryoEM
May 26, 2025 at 4:56 PM
We’ve uncovered Asgard chromatin structures formed by a Hodarchaeal histone : closed hypernucleosome conserved in archaea and an open form resembling the H3-H4 eukaryotic octasome. Fantastic work by @harshranawat.bsky.social!
www.biorxiv.org/content/10.1...
#Chromatin #Asgard #Archaea #cryoEM
www.biorxiv.org/content/10.1...
#Chromatin #Asgard #Archaea #cryoEM
Reposted by Shyamal
Toggle-Untoggle: A cell segmentation tool with an interactive user verification interface. https://www.biorxiv.org/content/10.1101/2025.05.21.655178v1
May 26, 2025 at 9:48 PM
Toggle-Untoggle: A cell segmentation tool with an interactive user verification interface. https://www.biorxiv.org/content/10.1101/2025.05.21.655178v1
Happy to have contributed to this amazing story from @caroleparentlab.bsky.social at the @umlifesciences.bsky.social
www.nature.com/articles/s41...
Congrats to all involved.
www.nature.com/articles/s41...
Congrats to all involved.
Neutrophils secrete exosome-associated DNA to resolve sterile acute inflammation - Nature Cell Biology
Arya et al. report that migrating neutrophils resolve acute inflammation by releasing exosomes associated with nuclear DNA. This process is distinct from the release of neutrophil extracellular traps,...
www.nature.com
May 22, 2025 at 9:17 AM
Happy to have contributed to this amazing story from @caroleparentlab.bsky.social at the @umlifesciences.bsky.social
www.nature.com/articles/s41...
Congrats to all involved.
www.nature.com/articles/s41...
Congrats to all involved.
Reposted by Shyamal
Problem cryo-ET structure alert. A recent paper by Lange et al. in @natcellbio.nature.com (tinyurl.com/38s6a4dn) reported an unusual-looking model of the prohibitin complex in situ. We asked: how was this structure generated? Our reanalysis offers an explanation: tinyurl.com/mszdtwxx 🧵
May 20, 2025 at 8:58 PM
Problem cryo-ET structure alert. A recent paper by Lange et al. in @natcellbio.nature.com (tinyurl.com/38s6a4dn) reported an unusual-looking model of the prohibitin complex in situ. We asked: how was this structure generated? Our reanalysis offers an explanation: tinyurl.com/mszdtwxx 🧵
Reposted by Shyamal
*Deadline extended*
Applications for this year's #CryoEM Data Processing Workshop are due March 27!
Don't miss this chance to learn about various approaches to deal with conformational/compositional heterogeneity.
myumi.ch/lsi-cryo-2025
@jbquerido.bsky.social
@shyamalm.bsky.social
Applications for this year's #CryoEM Data Processing Workshop are due March 27!
Don't miss this chance to learn about various approaches to deal with conformational/compositional heterogeneity.
myumi.ch/lsi-cryo-2025
@jbquerido.bsky.social
@shyamalm.bsky.social
March 24, 2025 at 1:49 PM
*Deadline extended*
Applications for this year's #CryoEM Data Processing Workshop are due March 27!
Don't miss this chance to learn about various approaches to deal with conformational/compositional heterogeneity.
myumi.ch/lsi-cryo-2025
@jbquerido.bsky.social
@shyamalm.bsky.social
Applications for this year's #CryoEM Data Processing Workshop are due March 27!
Don't miss this chance to learn about various approaches to deal with conformational/compositional heterogeneity.
myumi.ch/lsi-cryo-2025
@jbquerido.bsky.social
@shyamalm.bsky.social
Reposted by Shyamal
Thrilled to share the structure of dimerised human PINK1 docked to an endogenous translocase array on the mitochondrial surface, composed of two TOM complexes, bridged by a VDAC2 dimer! Published today in Science www.science.org/doi/10.1126/...
@wehi-research.bsky.social @komanderlab.bsky.social
@wehi-research.bsky.social @komanderlab.bsky.social
March 13, 2025 at 7:20 PM
Thrilled to share the structure of dimerised human PINK1 docked to an endogenous translocase array on the mitochondrial surface, composed of two TOM complexes, bridged by a VDAC2 dimer! Published today in Science www.science.org/doi/10.1126/...
@wehi-research.bsky.social @komanderlab.bsky.social
@wehi-research.bsky.social @komanderlab.bsky.social
Reposted by Shyamal
“Thermo Fisher Scientific is hosting a webinar on securing capital equipment funding for new EM technology” - sophisticated public money extraction machine go brr
March 7, 2025 at 8:32 PM
“Thermo Fisher Scientific is hosting a webinar on securing capital equipment funding for new EM technology” - sophisticated public money extraction machine go brr
Happy to share this work from my group on the endolysosomal/PM resident 2 pore potassium channel with roles in #inflammation
We determine the structure and show that it is pH independent, voltage-gated using high-throughout whole cell electrophysiology assay.
www.biorxiv.org/content/10.1...
We determine the structure and show that it is pH independent, voltage-gated using high-throughout whole cell electrophysiology assay.
www.biorxiv.org/content/10.1...
www.biorxiv.org
February 25, 2025 at 4:02 AM
Happy to share this work from my group on the endolysosomal/PM resident 2 pore potassium channel with roles in #inflammation
We determine the structure and show that it is pH independent, voltage-gated using high-throughout whole cell electrophysiology assay.
www.biorxiv.org/content/10.1...
We determine the structure and show that it is pH independent, voltage-gated using high-throughout whole cell electrophysiology assay.
www.biorxiv.org/content/10.1...