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Samuel Schwab

@samuelschwab.bsky.social
36 followers 68 following 5 posts
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Reposted by Samuel Schwab
Dame lab at Leiden University @damelab.bsky.social · 11/09/2026
It has been a great journey through prokaryotic histone space with Samuel Schwab @samuelschwab.bsky.social. On September 9 he defended his excellent thesis and graduated with distinction (cum laude). www.linkedin.com/posts/facult...
linkedin.com
🎓 Cum laude! Samuel Schwab uncovers surprising ways bacteria and archaea organise their DNA His supervisor professor Remus Dame puts it rather strongly: ‘He is by far the best PhD student I have… | L...
🎓 Cum laude! Samuel Schwab uncovers surprising ways bacteria and archaea organise their DNA His supervisor professor Remus Dame puts it rather strongly: ‘He is by far the best PhD student I have supe...
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Reposted by Samuel Schwab
Erik van Nimwegen @erikvannimwegen.bsky.social · 25/06/2026
Gloves are off. Seriously? Pretty much tells you everything you need to know, doesn't it? This is not about providing useful information to the scientific community. It is an act offert act of aggression aimed at establishing power and control. I think this is actually a watershed moment. 1/n
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Reposted by Samuel Schwab
Dr Eleanor Baker @eleanormaybaker.bsky.social · 03/05/2026
Next Sunday I'll be giving an online lecture for The Last Tuesday Society on my @bodleian.ox.ac.uk book ✨Book Curses✨. I'll be talking about curses like that of John Wryghtson, which sits opposite some rather threatening illustrations of surgical instruments (Ox, St John's, MS 76, f. 5v).
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Reposted by Samuel Schwab
Devang Mehta🌱🧬 @mehta-lab.com · 21/04/2026
Someone in the Arabidopsis/clock community seems to deeply dislike my work on research culture. Just want to say: whoever you are, please write & debate me directly instead of cowering behind anonymous grant reviews that threaten my students’ work. (2nd year in a row)
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Reposted by Samuel Schwab
Dame lab at Leiden University @damelab.bsky.social · 12/02/2026
Now online: Pingzhuang Ge's studies on the impact of pH on local chromatin structure and transcriptional activity of the H-NS-regulated hdeAB operon www.biorxiv.org/content/10.6...
biorxiv.org
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Reposted by Samuel Schwab
Dame lab at Leiden University @damelab.bsky.social · 02/02/2026
pdb101.rcsb.org/motm/314
pdb101.rcsb.org
PDB101: Molecule of the Month: Histones Across the Tree of Life
Uncovering the evolutionary diversity of histones
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Reposted by Samuel Schwab
Erik van Nimwegen @erikvannimwegen.bsky.social · 13/01/2026
What are the main sources of gene expression noise in bacteria, and why do slower growing bacteria exhibit more expression noise? TLDR: we found growth-rate fluctuations are a key driver of gene expression noise that increase as average growth rate decreases. www.biorxiv.org/content/10.6... 1/n
biorxiv.org
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Reposted by Samuel Schwab
Roland Dunbrack 🏳️‍🌈 @rolanddunbrack.bsky.social · 03/01/2026
I updated ipSAE code to handle Boltz2 files properly -- non-standard chainIDs/order, PDB input as well as mmCIF; other pull requests. github.com/DunbrackLab/.... Also updated preprint--fixed Latin grammar error in title - very embarrassing and added new figure. www.biorxiv.org/content/10.1...
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Reposted by Samuel Schwab
Antoine Hocher @ahocher.bsky.social · 16/12/2025
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!!
meetings.embo.org
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Reposted by Samuel Schwab
Kresten Lindorff-Larsen @lindorfflarsen.bsky.social · 15/12/2025
Experimental structures provide valuable hypotheses and accelerate but do not replace evolutionary and statistical analyses of protein sequences
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Reposted by Samuel Schwab
Vikram Alva @vikramalva.bsky.social · 13/12/2025
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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Reposted by Samuel Schwab
Tamara Basta @tamarabasta.bsky.social · 11/12/2025
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
biorxiv.org
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...
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Reposted by Samuel Schwab
Naomichi Takemata @naomichitakemata.bsky.social · 11/12/2025
Delighted to share our latest preprint on reverse gyrase, a unique topoisomerase found exclusively in thermophiles! www.biorxiv.org/content/10.6...
biorxiv.org
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...
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Reposted by Samuel Schwab
jproney @jproney.bsky.social · 10/12/2025
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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Samuel Schwab @samuelschwab.bsky.social · 10/12/2025
Peristaltic waves inside Stylaria lacustris #microscopy
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Samuel Schwab @samuelschwab.bsky.social · 08/12/2025
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...
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Reposted by Samuel Schwab
Tung Le @tunglejic.bsky.social · 04/12/2025
Now published. Thank you very much to our collaborative team, and very supportive editors and reviewers!!! www.pnas.org/doi/10.1073/...
pnas.org
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...
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Reposted by Samuel Schwab
Dame lab at Leiden University @damelab.bsky.social · 06/11/2025
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...
sciencedirect.com
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 …
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Reposted by Samuel Schwab
Dame lab at Leiden University @damelab.bsky.social · 05/11/2025
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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Géraldine Laloux @lalouxlab.bsky.social · 25/09/2025
📝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...
biorxiv.org
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...
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Reposted by Samuel Schwab
Roland Dunbrack 🏳️‍🌈 @rolanddunbrack.bsky.social · 16/09/2025
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...
youtube.com
Screen binders using ipSAE
YouTube video by ProteinDesignStudio
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Reposted by Samuel Schwab
Tobias Warnecke @tobiaswarnecke.bsky.social · 14/08/2025
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/...
journals.plos.org
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 ...
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Reposted by Samuel Schwab
bioRxivpreprint @biorxivpreprint.bsky.social · 04/08/2025
Scaling down protein language modeling with MSA Pairformer www.biorxiv.org/content/10.1101/202…
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Reposted by Samuel Schwab
Daniela Barillà @danielabarilla.bsky.social · 22/07/2025
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
nature.com
Coupling chromosome organization to genome segregation in Archaea - Nature Communications
Proteins SegA and SegB are important for chromosome segregation and organization in archaea of the order Sulfolobales, but mechanisms are unclear. Here, Kabli et al. uncover patterns and mechanisms th...
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Reposted by Samuel Schwab
Malcolm White @mfwhite2.bsky.social · 18/07/2025
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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Erik van Nimwegen @erikvannimwegen.bsky.social · 18/07/2025
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...
physics.aps.org
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.
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Reposted by Samuel Schwab
Dame lab at Leiden University @damelab.bsky.social · 10/07/2025
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
sciencedirect.com
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…
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Reposted by Samuel Schwab
Trends in Biochemical Sciences @cp-trendsbiochem.bsky.social · 02/07/2025
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 @damelab.bsky.social · 30/06/2025
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
cell.com
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...
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Samuel Schwab @samuelschwab.bsky.social · 28/06/2025
Ready to meet some Nobel Laureates 😄
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Reposted by Samuel Schwab
Svetlana Dodonova @dodonova-sveta.bsky.social · 26/05/2025
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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Samuel Schwab @samuelschwab.bsky.social · 14/05/2025
Hitomezashi stitch patterns: samuelschwab.com/hitomezashi-...
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Reposted by Samuel Schwab
Vikram Alva @vikramalva.bsky.social · 12/05/2025
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
A snapshot of the HLp tetramer (purple) wrapping ~60 bp of DNA (green).
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Reposted by Samuel Schwab
ChimeraX @chimerax.ucsf.edu · 01/05/2025
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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Molecular Microbiology Editors @molecularmicro.bsky.social · 11/03/2025
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...
onlinelibrary.wiley.com
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.
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Daniela Barillà @danielabarilla.bsky.social · 23/11/2024
📢 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
Diagram showing archaeal cells containing two chromosomes bound by proteins prior to cell division.
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