Samuel Schwab
@samuelschwab.bsky.social
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📥 63
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reposted by
Samuel Schwab
Antoine Hocher
11 days ago
Are you a long-time fan of Archaea, an extremophile-phile, or are you simply curious? Either way, we have good news. We’re delighted to announce the 2026 EMBO Workshop on Archaea, 6–10 July. Sign up:
meetings.embo.org/event/26-arc..
. We look forward to seeing you in Cambridge, UK Please repost!!
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https://meetings.embo.org/event/26-arc..
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Samuel Schwab
Kresten Lindorff-Larsen
12 days ago
Experimental structures provide valuable hypotheses and accelerate but do not replace evolutionary and statistical analyses of protein sequences
add a skeleton here at some point
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reposted by
Samuel Schwab
Vikram Alva
14 days ago
Happy to share that our work on HLp, a bacterial histone from Leptospira perolatii, is now published in Nature Communications 🎉 In this study, we show that HLp forms stable tetramers that wrap ~60 bp of DNA, revealing a distinct histone–DNA organization in bacteria.
www.nature.com/articles/s41...
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Samuel Schwab
Tamara Basta
16 days ago
Delighted to share our new preprint:
www.biorxiv.org/content/10.6...
We address a longstanding question about the role of the topoisomerase reverse gyrase in hyperthermophiles. Great collaboration with Baranello and
@tobiaswarnecke.bsky.social
groups.
#Archaeasky
#Microsky
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Localised activity of reverse gyrase at gene regulatory elements
DNA topoisomerases are essential enzymes found in all cells, where they regulate DNA supercoiling. Reverse gyrase (RG) is a unique type of topoisomerase that introduces positive supercoils into DNA an...
https://www.biorxiv.org/content/10.64898/2025.12.08.692955v1
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Samuel Schwab
Naomichi Takemata
16 days ago
Delighted to share our latest preprint on reverse gyrase, a unique topoisomerase found exclusively in thermophiles!
www.biorxiv.org/content/10.6...
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Reverse gyrase and 3D genome architecture suppress hyperthermophile genome instability arising from horizontal gene transfer
Reverse gyrase (Rgy), a distinctive topoisomerase conserved in all hyperthermophiles, has the unique ability to introduce positive DNA supercoils. It has long been hypothesized that Rgy overwinds geno...
https://www.biorxiv.org/content/10.64898/2025.12.08.692931v1
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Samuel Schwab
jproney
17 days ago
I'm super excited to announce the first preprint of my PhD, together with Chenxi Ou and
@sokrypton.org
! ML has revolutionized protein modeling, but crucial challenges remain. For example, we can't reliably predict complicated protein structures without MSAs, which limits what we can design.
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Peristaltic waves inside Stylaria lacustris
#microscopy
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17 days ago
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Ending my PhD with a bang: Face-to-face histones are important organizers of archaeal chromatin alongside classical histones.
www.biorxiv.org/content/10.6...
19 days ago
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Samuel Schwab
Tung Le
23 days ago
Now published. Thank you very much to our collaborative team, and very supportive editors and reviewers!!!
www.pnas.org/doi/10.1073/...
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Versatile NTP recognition and domain fusions expand the functional repertoire of the ParB-CTPase fold beyond chromosome segregation | PNAS
Nucleotide triphosphate (NTP)-dependent molecular switches regulate essential cellular processes by cycling between active and inactive states thro...
https://www.pnas.org/doi/10.1073/pnas.2527592122
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reposted by
Samuel Schwab
Dame lab at Leiden University
about 2 months ago
New article online: Modulation of archaeal hypernucleosome structure and stability by Mg2+ In this work, we dissect the effects of Mg2+ on hypernucleosomes formed by the canonical histones from M. fervidus (HMfA and HMfB) and T. kodakarensis (HTkA and HTkB).
www.sciencedirect.com/science/arti...
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Modulation of archaeal hypernucleosome structure and stability by Mg2+
DNA-wrapping histone proteins play a central role in chromatin organization, gene expression and regulation in most eukaryotes and archaea. While the …
https://www.sciencedirect.com/science/article/pii/S0022283625005996
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reposted by
Samuel Schwab
Dame lab at Leiden University
about 2 months ago
Soon available in my group: 1 PhD position to investigate prokaryotic histones. See our recent work that highlights the existence and diversity of prokaryotic histones (e.g. Schwab et al., TIBS, 2025; Schwab et al., Nat Comm, 2024; Hu et al., Nucl Acids Res, 2024). Please DM for informal enquiries.
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Samuel Schwab
Géraldine Laloux
3 months ago
📝New preprint!
#MicroSky
🕰️We chart the full, synchronized lifecycle of a predatory bacterium using Hi-C, RNA-seq, ChIP-seq & microscopy. 🧬We uncover dramatic shifts in nucleoid architecture & transcription, tightly coordinated with predation.
www.biorxiv.org/content/10.1...
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Dynamics and interplay of gene expression and chromosome organization across a predatory lifecycle
The obligate predatory bacterium Bdellovibrio bacteriovorus alternates between a motile attack phase and a growth phase inside another bacterium, during which it undergoes multiple rounds of DNA repli...
https://www.biorxiv.org/content/10.1101/2025.09.24.678257v1
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reposted by
Samuel Schwab
Roland Dunbrack 🏳️🌈
3 months ago
pip install ipsae from
www.linkedin.com/in/ullah-sam...
www.youtube.com/watch?v=A5ph...
PyPI
pypi.org/project/ipsae/
His github fork
github.com/ullahsamee/I...
My github
github.com/DunbrackLab/...
Paper
www.biorxiv.org/content/10.1...
For designed protein binders
www.biorxiv.org/content/10.1...
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Screen binders using ipSAE
YouTube video by ProteinDesignStudio
https://www.youtube.com/watch?v=A5ph2chCwdk
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reposted by
Samuel Schwab
Tobias Warnecke
4 months ago
Archaea are often surrounded by bacteria. But is there ever active conflict between the two? Can archaea kill bacteria? If so, how do they do it? Work by
@romainstrock.bsky.social
shows that some archaea can kill bacteria by secreting peptidoglycan hydrolases.
journals.plos.org/plosbiology/...
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Archaea produce peptidoglycan hydrolases that kill bacteria
Archaea regularly interact with bacteria but reports of archaea killing bacteria are very rare. This study shows that many archaea encode peptidoglycan hydrolases, which specifically target bacterial ...
https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3003235
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reposted by
Samuel Schwab
bioRxivpreprint
5 months ago
Scaling down protein language modeling with MSA Pairformer
https://www.biorxiv.org/content/10.1101/2025.08.02.668173v1
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reposted by
Samuel Schwab
Daniela Barillà
5 months ago
And the story is published now!🍾
www.nature.com/articles/s41...
Open access link:
rdcu.be/exnOc
Many years in the making, great collaboration with
@archaellum.bsky.social
&
@tunglejic.bsky.social
Thanks
@ukri.org
BBSRC &
@leverhulme.ac.uk
for funding, reviewers & editor!! 🙏
#microsky
#archaeasky
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reposted by
Samuel Schwab
Malcolm White
5 months ago
Next up from our lab - a ring nuclease with a novel fold which cleaves all cOA species involved in Type III CRISPR defence. It's also found in plasmid and phage genomes, where it presumably functions as an anti-CRISPR.
www.biorxiv.org/content/10.1...
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reposted by
Samuel Schwab
Erik van Nimwegen
5 months ago
Because of a lack of separation of the time scales for TF binding/unbinding and fluctuations in active TF levels, non-equilibrium gene regulation may be common in bacteria. Check out this nice piece by @philipcball.bsky.social on our new publication in PRX Life.
physics.aps.org/articles/v18...
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Different Bacterial Genes Have Different Turn-Ons
Not all genes respond in the same way to regulation by the same molecule—a property that might enable cells to produce complex genetic responses.
https://physics.aps.org/articles/v18/137
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reposted by
Samuel Schwab
Dame lab at Leiden University
6 months ago
I am pleased to share our new review on the role of bacterial nucleoid-aasociated proteins in mediating responses to changes in environment. Important: some NAPs can directly ‘sense’ physico-chemical changes.
www.sciencedirect.com/science/arti...
@pingzhuangge.bsky.social
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The role of nucleoid-associated proteins in mediating responses to environmental changes
Bacteria face diverse environmental challenges, such as changes in temperature, pH, and osmolarity, and exposure to antibiotics, which necessitate ada…
https://www.sciencedirect.com/science/article/pii/S1369527425000505
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Samuel Schwab
Trends in Biochemical Sciences
6 months ago
Now online - the Review "Histone-mediated chromatin organization in prokaryotes and viruses" from
@samuelschwab.bsky.social
@vikramalva.bsky.social
@damelab.bsky.social
and co.
#histones
#DNAorganization
#chromatin
#eukaryogenesis
Read it here 👉
authors.elsevier.com/sd/article/S...
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reposted by
Samuel Schwab
Dame lab at Leiden University
6 months ago
A must-read for histone afficionados: our new review on 'Histone-mediated chromatin organization in prokaryotes and viruses'
www.cell.com/trends/bioch...
@samuelschwab.bsky.social
@vikramalva.bsky.social
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Histone-mediated chromatin organization in prokaryotes and viruses
Histones are fundamental chromatin-organizing proteins in eukaryotes and archaea, where they assemble into (hyper)nucleosomes that wrap DNA. Recent studies have expanded the known repertoire of histon...
https://www.cell.com/trends/biochemical-sciences/fulltext/S0968-0004(25)00133-1
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Ready to meet some Nobel Laureates 😄
6 months ago
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reposted by
Samuel Schwab
Svetlana Dodonova
7 months ago
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
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Hitomezashi stitch patterns:
samuelschwab.com/hitomezashi-...
8 months ago
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reposted by
Samuel Schwab
Vikram Alva
8 months ago
Excited to share our new preprint on HLp—a bacterial histone from Leptospira perolatii that forms stable tetramers and wraps ~60 bp of DNA: "DNA Wrapping by a Tetrameric Bacterial Histone"
www.biorxiv.org/content/10.1...
@mpi-bio-fml.bsky.social
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Samuel Schwab
ChimeraX
8 months ago
ChimeraX daily builds can predict small complexes of proteins, nucleic acids and small molecules using Boltz on your Mac, Windows or Linux computer without Nvidia graphics.
www.rbvi.ucsf.edu/chimerax/dat...
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Samuel Schwab
Molecular Microbiology Editors
10 months ago
Chromatin aficionados take note: Second of two special issues on Prokaryotic Chromosome Organization now published! (6 review/perspective articles and 2 research articles) Guest edited by
@damelab.bsky.social
#MicroSky
#Chromatin
onlinelibrary.wiley.com/toc/13652958...
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Prokaryotic Chromosome Organization: part 2: Molecular Microbiology: Vol 123, No 3
Molecular Microbiology is a broad-scope microbiology journal for basic and translational research that contributes to understanding molecular principles in microbes.
https://onlinelibrary.wiley.com/toc/13652958/2025/123/3
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reposted by
Samuel Schwab
Daniela Barillà
about 1 year ago
📢 Interested in chromosomes and microbes thriving at the edge of life?PhD project in York-UK on chromosome segregation in
#Archaea
. Supervised by me, @Steve Quinn &
@georgerheath.bsky.social
www.findaphd.com/phds/project...
Open to Applicants Worldwide! 📅 January 6, 2025
#microsky
#archaeasky
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