Gautam Dey
@gautamdey.bsky.social
Evolutionary cell biology @EMBL
evonuclab.org
evonuclab.org
Pinned
Gautam Dey
@gautamdey.bsky.social
· Nov 11
So happy to see that energy and community vibe from the early days in the old place, looks like #SciSky is reaching critical mass 😍
Reporting for duty with tales of the weird and wonderful cell biology you never knew you needed to know 🫡
🧪🌏🦠
Reporting for duty with tales of the weird and wonderful cell biology you never knew you needed to know 🫡
🧪🌏🦠
Reposted by Gautam Dey
So excited for @helsenjana.bsky.social’s centromere work to be published! There’s a lot of new data since the biorxiv preprint - check out Jana’s thread!
How do new centromeres evolve while staying compatible with the division machinery?
Discover it in our new Nature paper! We show centromeres transition gradually via a mix of drift, selection, and sex, reaching new states that still work with the kinetochore.
👉 doi.org/10.1038/s41586-025-09779-1
Discover it in our new Nature paper! We show centromeres transition gradually via a mix of drift, selection, and sex, reaching new states that still work with the kinetochore.
👉 doi.org/10.1038/s41586-025-09779-1
November 26, 2025 at 6:08 PM
So excited for @helsenjana.bsky.social’s centromere work to be published! There’s a lot of new data since the biorxiv preprint - check out Jana’s thread!
Reposted by Gautam Dey
Curious about how this story came to be (we never planned to study centromeres!)? Here’s a glimpse behind the scenes of how a naive method to count chromosomes unlocked the rules behind centromere evolution.
P.S. There are cartoons!
👉 tinyurl.com/4rz4ve6u
P.S. There are cartoons!
👉 tinyurl.com/4rz4ve6u
Counting Chromosomes: The Simple Idea That Unlocked the Rules Behind Centromere Evolution
tinyurl.com
November 26, 2025 at 4:27 PM
Curious about how this story came to be (we never planned to study centromeres!)? Here’s a glimpse behind the scenes of how a naive method to count chromosomes unlocked the rules behind centromere evolution.
P.S. There are cartoons!
👉 tinyurl.com/4rz4ve6u
P.S. There are cartoons!
👉 tinyurl.com/4rz4ve6u
Reposted by Gautam Dey
Huge thanks to everyone involved: @gautamdey.bsky.social and @gsherloc.bsky.social for their unwavering support and @kausthubh.bsky.social for helping me see the forest for the trees. Final thanks: @embl.org and Stanford University for hosting the work, and the Life Science Alliance for funding me.
November 26, 2025 at 4:26 PM
Huge thanks to everyone involved: @gautamdey.bsky.social and @gsherloc.bsky.social for their unwavering support and @kausthubh.bsky.social for helping me see the forest for the trees. Final thanks: @embl.org and Stanford University for hosting the work, and the Life Science Alliance for funding me.
Reposted by Gautam Dey
PCAn, our point centromere annotation tool 🔍 was also updated! Try it out with your own genome assemblies and let us know what you think!
👉 github.com/JHelsen/point-centromere-detection
👉 github.com/JHelsen/point-centromere-detection
GitHub - JHelsen/point-centromere-detection: This repository contains all the instructions and code required to perform the analyses used in this study - https://www.biorxiv.org/content/10.1101/2025.0...
This repository contains all the instructions and code required to perform the analyses used in this study - https://www.biorxiv.org/content/10.1101/2025.01.16.633479v1 - JHelsen/point-centromere-d...
github.com
November 26, 2025 at 4:24 PM
PCAn, our point centromere annotation tool 🔍 was also updated! Try it out with your own genome assemblies and let us know what you think!
👉 github.com/JHelsen/point-centromere-detection
👉 github.com/JHelsen/point-centromere-detection
Reposted by Gautam Dey
Read the bioRxiv version last Jan? There's a ton of NEW cool stuff! Discover: new centromeres (1B years from budding yeast!), in vivo experiments showing how kinetochore protein evolution impacts new centromere success, and more!
👉 bsky.app/profile/helsenjana.bsky.social/post/3lfwobnnaak2o
👉 bsky.app/profile/helsenjana.bsky.social/post/3lfwobnnaak2o
Centromere evolution isn't a sudden switch!
Our study shows centromere transitions are a step-by-step process driven by a combination of drift and selection. Discover how the kinetochore interface shapes this gradual change in our new preprint 🥳 doi.org/10.1101/2025.01.16.633479 🧵(1/8)
Our study shows centromere transitions are a step-by-step process driven by a combination of drift and selection. Discover how the kinetochore interface shapes this gradual change in our new preprint 🥳 doi.org/10.1101/2025.01.16.633479 🧵(1/8)
November 26, 2025 at 4:23 PM
Read the bioRxiv version last Jan? There's a ton of NEW cool stuff! Discover: new centromeres (1B years from budding yeast!), in vivo experiments showing how kinetochore protein evolution impacts new centromere success, and more!
👉 bsky.app/profile/helsenjana.bsky.social/post/3lfwobnnaak2o
👉 bsky.app/profile/helsenjana.bsky.social/post/3lfwobnnaak2o
Reposted by Gautam Dey
How do new centromeres evolve while staying compatible with the division machinery?
Discover it in our new Nature paper! We show centromeres transition gradually via a mix of drift, selection, and sex, reaching new states that still work with the kinetochore.
👉 doi.org/10.1038/s41586-025-09779-1
Discover it in our new Nature paper! We show centromeres transition gradually via a mix of drift, selection, and sex, reaching new states that still work with the kinetochore.
👉 doi.org/10.1038/s41586-025-09779-1
November 26, 2025 at 4:21 PM
How do new centromeres evolve while staying compatible with the division machinery?
Discover it in our new Nature paper! We show centromeres transition gradually via a mix of drift, selection, and sex, reaching new states that still work with the kinetochore.
👉 doi.org/10.1038/s41586-025-09779-1
Discover it in our new Nature paper! We show centromeres transition gradually via a mix of drift, selection, and sex, reaching new states that still work with the kinetochore.
👉 doi.org/10.1038/s41586-025-09779-1
Reposted by Gautam Dey
(2/3) Centromeres – the little points where two arms of a chromosome meet – are one of the fastest-evolving parts of our genome.
Scientists studied centromeres in two fungal groups that diverged over a billion years ago to understand the evolutionary pressures that act on them.
Scientists studied centromeres in two fungal groups that diverged over a billion years ago to understand the evolutionary pressures that act on them.
November 26, 2025 at 4:06 PM
(2/3) Centromeres – the little points where two arms of a chromosome meet – are one of the fastest-evolving parts of our genome.
Scientists studied centromeres in two fungal groups that diverged over a billion years ago to understand the evolutionary pressures that act on them.
Scientists studied centromeres in two fungal groups that diverged over a billion years ago to understand the evolutionary pressures that act on them.
Reposted by Gautam Dey
(3/3) The researchers found that the cell’s division machinery acts as a critical filter, allowing only those centromere variants that are compatible with effective attachment to survive and spread.
@gautamdey.bsky.social @helsenjana.bsky.social @gsherloc.bsky.social @kausthubh.bsky.social
@gautamdey.bsky.social @helsenjana.bsky.social @gsherloc.bsky.social @kausthubh.bsky.social
Progressive coevolution of the yeast centromere and kinetochore | Nature
www.nature.com
November 26, 2025 at 4:06 PM
(3/3) The researchers found that the cell’s division machinery acts as a critical filter, allowing only those centromere variants that are compatible with effective attachment to survive and spread.
@gautamdey.bsky.social @helsenjana.bsky.social @gsherloc.bsky.social @kausthubh.bsky.social
@gautamdey.bsky.social @helsenjana.bsky.social @gsherloc.bsky.social @kausthubh.bsky.social
Reposted by Gautam Dey
(1/3) Imagine reconstructing a history over a billion years in the making.
New research from EMBL and @Stanford shows how centromeres retain their function despite their rapid rate of change, and the evolutionary constraints that govern this process.
www.nature.com/articles/s41...
New research from EMBL and @Stanford shows how centromeres retain their function despite their rapid rate of change, and the evolutionary constraints that govern this process.
www.nature.com/articles/s41...
November 26, 2025 at 4:06 PM
(1/3) Imagine reconstructing a history over a billion years in the making.
New research from EMBL and @Stanford shows how centromeres retain their function despite their rapid rate of change, and the evolutionary constraints that govern this process.
www.nature.com/articles/s41...
New research from EMBL and @Stanford shows how centromeres retain their function despite their rapid rate of change, and the evolutionary constraints that govern this process.
www.nature.com/articles/s41...
Reposted by Gautam Dey
Just uploaded our new preprint to @ecoevorxiv.bsky.social
Multinucleate life really is everywhere...from deep sea forams to slime molds, intracellular parasites, and beyond. 🚀
We explore how scaling, ecology, & evolution intersect when many nuclei share a single cytoplasm.
doi.org/10.32942/X2M...
Multinucleate life really is everywhere...from deep sea forams to slime molds, intracellular parasites, and beyond. 🚀
We explore how scaling, ecology, & evolution intersect when many nuclei share a single cytoplasm.
doi.org/10.32942/X2M...
November 26, 2025 at 3:06 PM
Just uploaded our new preprint to @ecoevorxiv.bsky.social
Multinucleate life really is everywhere...from deep sea forams to slime molds, intracellular parasites, and beyond. 🚀
We explore how scaling, ecology, & evolution intersect when many nuclei share a single cytoplasm.
doi.org/10.32942/X2M...
Multinucleate life really is everywhere...from deep sea forams to slime molds, intracellular parasites, and beyond. 🚀
We explore how scaling, ecology, & evolution intersect when many nuclei share a single cytoplasm.
doi.org/10.32942/X2M...
Our attempt to give multinucleate cells the spotlight they deserve (seriously, they’re everywhere), led by the fearless @mrosjac.bsky.social and with @Markus Ganter
doi.org/10.32942/X2M...
We’d love your feedback while this goes through the peer review process!
#MicroEvoSky
#ProtistsonSky 🧪🌏
doi.org/10.32942/X2M...
We’d love your feedback while this goes through the peer review process!
#MicroEvoSky
#ProtistsonSky 🧪🌏
November 26, 2025 at 2:05 PM
Our attempt to give multinucleate cells the spotlight they deserve (seriously, they’re everywhere), led by the fearless @mrosjac.bsky.social and with @Markus Ganter
doi.org/10.32942/X2M...
We’d love your feedback while this goes through the peer review process!
#MicroEvoSky
#ProtistsonSky 🧪🌏
doi.org/10.32942/X2M...
We’d love your feedback while this goes through the peer review process!
#MicroEvoSky
#ProtistsonSky 🧪🌏
Reposted by Gautam Dey
And now we have Arabidopsis plants with 8 chromosomes instead of 10 and no obvious phenotypic differences, this week in @science.org
#PlantScience
Paper here: www.science.org/doi/10.1126/...
Perspective here:
www.science.org/doi/10.1126/...
#PlantScience
Paper here: www.science.org/doi/10.1126/...
Perspective here:
www.science.org/doi/10.1126/...
CRISPR-Cas–mediated heritable chromosome fusions in Arabidopsis
The genome of Arabidopsis thaliana consists of 10 chromosomes. By inducing CRISPR-Cas–mediated breaks at subcentromeric and subtelomeric sequences, we fused entire chromosome arms, obtaining two eight...
www.science.org
November 21, 2025 at 10:20 AM
And now we have Arabidopsis plants with 8 chromosomes instead of 10 and no obvious phenotypic differences, this week in @science.org
#PlantScience
Paper here: www.science.org/doi/10.1126/...
Perspective here:
www.science.org/doi/10.1126/...
#PlantScience
Paper here: www.science.org/doi/10.1126/...
Perspective here:
www.science.org/doi/10.1126/...
Reposted by Gautam Dey
So happy to announce our new preprint, “A geothermal amoeba sets a new upper temperature limit for eukaryotes.” We cultured a novel amoeba from Lassen Volcanic NP (CA, USA) that divides at 63°C (145°F) 🔥 - a new record for euk growth!
#protistsonsky 🧵
#protistsonsky 🧵
November 25, 2025 at 8:41 PM
So happy to announce our new preprint, “A geothermal amoeba sets a new upper temperature limit for eukaryotes.” We cultured a novel amoeba from Lassen Volcanic NP (CA, USA) that divides at 63°C (145°F) 🔥 - a new record for euk growth!
#protistsonsky 🧵
#protistsonsky 🧵
Check out that spindle 🤩🔥
At 63C, most eukaryotic cells would be busy exploding noisily, forget even trying to divide.
The microbial universe never ceases to astound 😍
Thanks for letting us be a tiny part of this! #ExpandThemAll
At 63C, most eukaryotic cells would be busy exploding noisily, forget even trying to divide.
The microbial universe never ceases to astound 😍
Thanks for letting us be a tiny part of this! #ExpandThemAll
While 𝘝. 𝘷𝘦𝘳𝘮𝘪𝘧𝘰𝘳𝘮𝘪𝘴 max temp is around 45°C, we found 𝘐. 𝘤𝘢𝘴𝘤𝘢𝘥𝘦𝘯𝘴𝘪𝘴 grows up to 63°C with optimal growth at 55-57°C🥵. We showed cellular replication via Ultrastructure Expansion Microscopy at 63°C. The previous limit for euks is 60°C!
November 25, 2025 at 8:30 PM
Check out that spindle 🤩🔥
At 63C, most eukaryotic cells would be busy exploding noisily, forget even trying to divide.
The microbial universe never ceases to astound 😍
Thanks for letting us be a tiny part of this! #ExpandThemAll
At 63C, most eukaryotic cells would be busy exploding noisily, forget even trying to divide.
The microbial universe never ceases to astound 😍
Thanks for letting us be a tiny part of this! #ExpandThemAll
Reposted by Gautam Dey
📢 Paper alert 📢
Chirality is known to be important for the movement of microorganisms and active matter. In our new paper out today in @natphys.nature.com, we show that chirality is used by malaria parasites to control their motion patterns:
doi.org/10.1038/s415...
Here comes a 🧵 ... (1/9)
Chirality is known to be important for the movement of microorganisms and active matter. In our new paper out today in @natphys.nature.com, we show that chirality is used by malaria parasites to control their motion patterns:
doi.org/10.1038/s415...
Here comes a 🧵 ... (1/9)
November 24, 2025 at 5:50 PM
📢 Paper alert 📢
Chirality is known to be important for the movement of microorganisms and active matter. In our new paper out today in @natphys.nature.com, we show that chirality is used by malaria parasites to control their motion patterns:
doi.org/10.1038/s415...
Here comes a 🧵 ... (1/9)
Chirality is known to be important for the movement of microorganisms and active matter. In our new paper out today in @natphys.nature.com, we show that chirality is used by malaria parasites to control their motion patterns:
doi.org/10.1038/s415...
Here comes a 🧵 ... (1/9)
Reposted by Gautam Dey
We (Nordborg & Weigel labs) need input on the next generation of genome browsers & data download modes for the #Arabidopsis #1001GenomesPlus project. We have now a curated collection of over 500 long read genomes.
Please help us by filling out this questionnaire: docs.google.com/forms/d/e/1F...
Please help us by filling out this questionnaire: docs.google.com/forms/d/e/1F...
Next generation of 1001 Genomes Plus browser and data download
Please indicate all features you would like to see in a browser that displays features of completely sequenced Arabidopsis thaliana genomes
docs.google.com
November 24, 2025 at 2:49 PM
We (Nordborg & Weigel labs) need input on the next generation of genome browsers & data download modes for the #Arabidopsis #1001GenomesPlus project. We have now a curated collection of over 500 long read genomes.
Please help us by filling out this questionnaire: docs.google.com/forms/d/e/1F...
Please help us by filling out this questionnaire: docs.google.com/forms/d/e/1F...
Reposted by Gautam Dey
🎉 There are currently 4 opportunities to join the Holt lab in beautiful Bath! 🎉
If you're interested in protists, parasites, and/or biodiversity then please check out our website:
theholtlab.com/posts/ln5-21...
🚨 Deadlines vary between project.
✉️ Please reach out if you have any questions!
If you're interested in protists, parasites, and/or biodiversity then please check out our website:
theholtlab.com/posts/ln5-21...
🚨 Deadlines vary between project.
✉️ Please reach out if you have any questions!
November 24, 2025 at 2:30 PM
🎉 There are currently 4 opportunities to join the Holt lab in beautiful Bath! 🎉
If you're interested in protists, parasites, and/or biodiversity then please check out our website:
theholtlab.com/posts/ln5-21...
🚨 Deadlines vary between project.
✉️ Please reach out if you have any questions!
If you're interested in protists, parasites, and/or biodiversity then please check out our website:
theholtlab.com/posts/ln5-21...
🚨 Deadlines vary between project.
✉️ Please reach out if you have any questions!
We will be at @ccapoban.bsky.social in stunning Oban for the next two weeks fixing samples from their remarkable collection for #ExAME - thank you Ceci Mikey Jo Naomi and everyone at SAMS for the warm Scottish welcome ❤️
#ProtistsonSky #ExpandThemAll
@fmikus.bsky.social
#ProtistsonSky #ExpandThemAll
@fmikus.bsky.social
November 24, 2025 at 5:53 PM
We will be at @ccapoban.bsky.social in stunning Oban for the next two weeks fixing samples from their remarkable collection for #ExAME - thank you Ceci Mikey Jo Naomi and everyone at SAMS for the warm Scottish welcome ❤️
#ProtistsonSky #ExpandThemAll
@fmikus.bsky.social
#ProtistsonSky #ExpandThemAll
@fmikus.bsky.social
Reposted by Gautam Dey
Researching this week's column, I stumbled across something that amazed me:
the near-absence of reliable data about climate impacts over most of the
world. Due to the rich world's failure to fund research. We don't know
because our governments don't care. www.theguardian.com/commentisfre...
the near-absence of reliable data about climate impacts over most of the
world. Due to the rich world's failure to fund research. We don't know
because our governments don't care. www.theguardian.com/commentisfre...
There’s a catastrophic black hole in our climate data – and it’s a gift to deniers | George Monbiot
Climate sceptics tell us that more people die of extreme cold than extreme heat. What’s the truth? asks Guardian columnist George Monbiot
www.theguardian.com
November 21, 2025 at 8:07 AM
Researching this week's column, I stumbled across something that amazed me:
the near-absence of reliable data about climate impacts over most of the
world. Due to the rich world's failure to fund research. We don't know
because our governments don't care. www.theguardian.com/commentisfre...
the near-absence of reliable data about climate impacts over most of the
world. Due to the rich world's failure to fund research. We don't know
because our governments don't care. www.theguardian.com/commentisfre...
Reposted by Gautam Dey
Each such discovery is a game changer for our understanding of eukaryote evolution, and this paper is no exception. Meet Solarion, which displays yet again novel types of subcellular structures. Congrats to all authors on a fascinating story. #protistsonsky
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Rare microbial relict sheds light on an ancient eukaryotic supergroup - Nature
The discovery of an unusual protist named Solarion arienae, which has a mitochondrial genome with some intriguing features, provides insight into the early radiation of eukaryotic groups.
www.nature.com
November 21, 2025 at 9:30 AM
Each such discovery is a game changer for our understanding of eukaryote evolution, and this paper is no exception. Meet Solarion, which displays yet again novel types of subcellular structures. Congrats to all authors on a fascinating story. #protistsonsky
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Gautam Dey
Hot off the press! Our latest paper led by @fernpizza.bsky.social, understanding how plasmids evolve inside cells. These small, self-replicating DNA circles live inside bacteria and carry antibiotic resistance genes, but also compete with one another to replicate. 1/
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
Intracellular competition shapes plasmid population dynamics
From populations of multicellular organisms to selfish genetic elements, conflicts between levels of biological organization are central to evolution. Plasmids are extrachromosomal, self-replicating g...
www.science.org
November 20, 2025 at 9:42 PM
Hot off the press! Our latest paper led by @fernpizza.bsky.social, understanding how plasmids evolve inside cells. These small, self-replicating DNA circles live inside bacteria and carry antibiotic resistance genes, but also compete with one another to replicate. 1/
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
Reposted by Gautam Dey
Thank you, Daniela, @danielabarilla.bsky.social, for a wonderful commentary! 🤗🤗 More spotlight on the Asgards and their chromatin! ❤️ #archaea #chromatin
Let’s wrap things up: my commentary on the Asgard hypernucleosomes.
Congratulations to all the authors of the paper 🍾!
kwnsfk27.r.eu-west-1.awstrack.me/L0/https:%2F...
Cryo-EM reveals open and closed Asgard chromatin assemblies: Molecular Cell www.cell.com/molecular-ce...
Congratulations to all the authors of the paper 🍾!
kwnsfk27.r.eu-west-1.awstrack.me/L0/https:%2F...
Cryo-EM reveals open and closed Asgard chromatin assemblies: Molecular Cell www.cell.com/molecular-ce...
Cryo-EM reveals open and closed Asgard chromatin assemblies
Ranawat et al. show the cryo-EM structures of Asgard archaeal chromatin assemblies,
revealing that the histone HHoB assembles into both compact closed and extended open
hypernucleosomes. The closed co...
www.cell.com
November 20, 2025 at 5:53 PM
Thank you, Daniela, @danielabarilla.bsky.social, for a wonderful commentary! 🤗🤗 More spotlight on the Asgards and their chromatin! ❤️ #archaea #chromatin
Reposted by Gautam Dey
Junior professor position at the University of Kaiserslautern! Our Department of Biology is seeking a colleague working with microalgae. This is a wonderful place to do wonderful science with great people! Please, repost :)
Further details:
jobs.rptu.de/jobposting/1...
Further details:
jobs.rptu.de/jobposting/1...
November 20, 2025 at 3:28 PM
Junior professor position at the University of Kaiserslautern! Our Department of Biology is seeking a colleague working with microalgae. This is a wonderful place to do wonderful science with great people! Please, repost :)
Further details:
jobs.rptu.de/jobposting/1...
Further details:
jobs.rptu.de/jobposting/1...
Reposted by Gautam Dey
To probe gene-scale chromatin physics, we built 96-mer (20 kb) arrays with defined histone marks. Combining single-molecule tracking, AFM imaging, and developing in vitro Hi-C, we saw how specific modifications dictate chromatin structure and dynamics. www.science.org/doi/10.1126/...
Gene-scale in vitro reconstitution reveals histone acetylation directly controls chromatin architecture
Reconstituting 20-kb chromatin shows that tuning acetylation alone reshapes its folding, dynamics, and contact domain formation.
www.science.org
November 20, 2025 at 7:46 AM
To probe gene-scale chromatin physics, we built 96-mer (20 kb) arrays with defined histone marks. Combining single-molecule tracking, AFM imaging, and developing in vitro Hi-C, we saw how specific modifications dictate chromatin structure and dynamics. www.science.org/doi/10.1126/...
Reposted by Gautam Dey
Our work on Naegleria Myosin 2 is out!
Naegleria encodes 3 Myo2s which contract its actin network—the first evidence of contractile Myo2 outside of Amorphea.
Myo2 is actually widespread in Naegleria's relatives and correlates with fast cell crawling.
Read more: www.cell.com/current-biol...
Naegleria encodes 3 Myo2s which contract its actin network—the first evidence of contractile Myo2 outside of Amorphea.
Myo2 is actually widespread in Naegleria's relatives and correlates with fast cell crawling.
Read more: www.cell.com/current-biol...
Myosin 2 drives actin contractility in fast-crawling species outside of the amorphean lineage
Myosin 2-dependent actin contractility—the force that powers cell division and migration
in animals, fungi, and other Amorphea—had been previously unknown outside this single
eukaryotic group. Guest e...
www.cell.com
November 17, 2025 at 5:19 PM
Our work on Naegleria Myosin 2 is out!
Naegleria encodes 3 Myo2s which contract its actin network—the first evidence of contractile Myo2 outside of Amorphea.
Myo2 is actually widespread in Naegleria's relatives and correlates with fast cell crawling.
Read more: www.cell.com/current-biol...
Naegleria encodes 3 Myo2s which contract its actin network—the first evidence of contractile Myo2 outside of Amorphea.
Myo2 is actually widespread in Naegleria's relatives and correlates with fast cell crawling.
Read more: www.cell.com/current-biol...