iiinova — where your digital self keeps evolving

Reposted by Daan C. Swarts

Daniel Tamarit @danieltamarit.bsky.social · 22/05/2026

I'm looking for an enthusiastic student to join my team as a PhD candidate on archaeal genome evolution 🦠💻 Work in beautiful Utrecht, at @binfutrecht.bsky.social, an international group full of caring, amazing scientists, and with frequent cake breaks! www.uu.nl/en/organisat... Please share! 🙏

uu.nl

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Reposted by Daan C. Swarts

New Concepts in Prokaryotic Virus-Host Interaction @spp2330.bsky.social · 18/05/2026

📢 Registration for our International Symposium on “New Concepts in Prokaryotic Virus-Host Interactions” is now open! 🗓️ 5–7 October 2026 📍 Harnack House, Berlin, Germany ➡️ Information and registration: spp2330.de/symposium-20...

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Reposted by Daan C. Swarts

Luuk Loeff @lloeff.bsky.social · 14/05/2026

Happy to share our latest pre-print on the Druantia defense system. We find that Type III Druantia uses a cooperative helicase-nuclease mechanism to sense and degrade replication-associated forked DNA structures. www.biorxiv.org/content/10.6... A🧵

biorxiv.org

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Daan C. Swarts @dcswarts.bsky.social · 08/05/2026

#SISB2026 was fantastic! A big thanks to the organisers - super inspiring event!

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Reposted by Daan C. Swarts

Kenneth Loi @kenjmloi.bsky.social · 27/04/2026

Excited to share our discovery of a new programmable RNA-guided DNA-targeting system hiding inside bacteriophages that predates CRISPR. We call it VIPR (Viral Interference Programmable Repeat), and it uses an entirely new logic to find its targets. Thread + link below.

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Jens Hör @jenshoer.bsky.social · 21/03/2026

Excited to share the first preprint from the lab! We show that ApeA defends against RNA phage infection by cleaving the phage genome: www.biorxiv.org/content/10.6...

biorxiv.org

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Reposted by Daan C. Swarts

Rafal Mostowy @rafalmostowy.bsky.social · 04/05/2026

Polish phage science meets Polish visual storytelling 🇵🇱🦠 To celebrate our last paper, we collaborated with an artist who previously worked on The Witcher 3 — to create a comic about phages and why understanding them matters in the fight against antibiotic-resistant bacteria. Comic below 👇

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Daan C. Swarts @dcswarts.bsky.social · 09/04/2026

www.swartslab.org www.wur.nl/en/chair-gro... www.wur.nl/en/jobs/cond...

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Daan C. Swarts @dcswarts.bsky.social · 09/04/2026

PostDoc position available! (links in post below) Feel free to share!

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Reposted by Daan C. Swarts

Oleg Dmytrenko @olehdmy.bsky.social · 07/01/2026

Our paper is out! Hiding in plain sight among Cas12a nucleases, Cas12a3 cleaves not its RNA target but the 3′ ends of tRNA. Huge thanks to all who made this possible, especially the Beisel lab, Biao & Dirk for the structure, & @sebastianglatt.bsky.social for all things tRNA. doi.org/10.1038/s415...

nature.com

RNA-triggered Cas12a3 cleaves tRNA tails to execute bacterial immunity - Nature

Cas12a3 nucleases constitute a distinct clade of type V CRISPR–Cas bacterial immune systems that preferentially cleave the 3′ tails of tRNAs after recognition of target RNA to induce growth arres...

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Daan C. Swarts @dcswarts.bsky.social · 02/12/2025

VERY much looking forward to cool science at the next edition of the Symposium of Immune Sytems of Bacteria in New York in 2026! Hope to see many of you there 🥳

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Reposted by Daan C. Swarts

Jack Bravo @jpkbravo.bsky.social · 02/12/2025

📢 We have multiple open PhD positions to study bacterial immune systems using cutting-edge cryo-EM, microbiology, and biochemistry in our group! Join us and uncover how bacterial defenses eliminate predators and engineer next-gen biotech tools. 🔥 Apply by Jan 8, 2026 Details: phd.pages.ista.ac.at

phd.pages.ista.ac.at

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Daan C. Swarts @dcswarts.bsky.social · 04/11/2025

Great Aude! Just an update, we have our own website: www.swartslab.org Also I am not sure when I stop being an early career scientist 🤐

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Daan C. Swarts @dcswarts.bsky.social · 30/10/2025

Congratulations Daniel! Fantastic :D

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Reposted by Daan C. Swarts

Svetlana Dodonova @dodonova-sveta.bsky.social · 28/10/2025

Lab’s first paper is out!! We show the first structures of #Asgard #chromatin by #cryo-EM 🧬❄️ Asgard histones form closed and open hypernucleosomes. Closed are conserved across #Archaea, while open resemble eukaryotic H3–H4 octasomes and are Asgard-specific. More here: www.cell.com/molecular-ce...

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Reposted by Daan C. Swarts

Luuk Loeff @lloeff.bsky.social · 10/10/2025

One week left to apply!!

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Daan C. Swarts @dcswarts.bsky.social · 28/08/2025

We are excited and grateful that the main authors thought that prokaryotic Argonaute proteins were a cool target to design binders for, and that we could contribute to this paper. We will continue using BindCraft to further probe our proteins of interest!

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Daan C. Swarts @dcswarts.bsky.social · 28/08/2025

BindCraft can be used to design synthetic protein binders with incredible accuracy and success rate - Out now in Nature. BindCraft displays perfectly how AI-based tools can be used to accelerate biological research (and clinical applications). I think this is a must-read paper.

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Daan C. Swarts @dcswarts.bsky.social · 14/05/2025

Fantastic work, congrats Anna! These filaments are so cool :)

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Daan C. Swarts @dcswarts.bsky.social · 13/05/2025

In addition @sumanthmutte.bsky.social , @tniault.bsky.social @patrickbarendse.bsky.social @belkoopal.bsky.social and many blueskyless co-authors. Also with further help of collaborator @hauryliuk.bsky.social! Thanks to all who contributed to this multidisciplinary study!

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Daan C. Swarts @dcswarts.bsky.social · 13/05/2025

The first steps of this work were taken a long time ago during my @embo.org fellowship in the Jinek lab @martinjinek.bsky.social, but the main work was carried out by the talented Pilar Bobadilla Ugarte in our group @bic-wur.bsky.social @w-u-r.bsky.social funded by @erc.europa.eu .

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Daan C. Swarts @dcswarts.bsky.social · 13/05/2025

This suggests that in absence of repair complexes, pAgos need ACE to generate guide DNAs. These findings corroborate the importance of RecBCD/AddAB for long-A pAgos and highlights the versatility of immune systems to adapt to distinct hosts with different accessory proteins.

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Daan C. Swarts @dcswarts.bsky.social · 13/05/2025

hat is the relevance of ACE? Jolly et al. and Kuzmenko et al., demonstrated that DNA repair complexes AddAB/RecBCD are major drivers of guide DNA generation for long-A pAgos. In another study, we recently showed that cyanobacteria lack RecBCD/AddAB: sciencedirect.com/science/arti...

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Daan C. Swarts @dcswarts.bsky.social · 13/05/2025

But what does it mean in vivo? We show that, in E. coli, while the cyanobacterial pAgo alone can provide defense against plasmids and phages, ACE can enhance the interference phenotype (at least for plasmids) demonstrating these proteins function in conjunction.

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Daan C. Swarts @dcswarts.bsky.social · 13/05/2025

Co-expression of the cyanobacterial pAgo and ACE in E. coli reveals that pAgo-associated guide DNAs are (further) processed (shortened) by ACE. We show that longer guide DNAs are not functional, which shows that ACE contributes to guide DNA generation in coli.

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Daan C. Swarts @dcswarts.bsky.social · 13/05/2025

The cyanobacterial pAgo and its ACE partner form a heterodimeric complex in which activity of ACE1 is modulated. But this still leaves a question: Is ACE1 important for guide generation or (further) target DNA a degradation?

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Daan C. Swarts @dcswarts.bsky.social · 13/05/2025

Structural and biochemical characterization of ACE shows it is a DNA nuclease. Its catalytic site is buried in a channel that can only be accessed by single stranded DNA. Analysis of sequencing products show that ACE preferentially cleaves ssDNA upstream of guanine residues.

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Daan C. Swarts @dcswarts.bsky.social · 13/05/2025

Investigation of the cyanobacterial pAgos shows that they are DNA-guided DNA cleaving pAgos, akin to various other long-A pAgos (TtAgo, CbAgo, PfAgo). Those experiments as well as the crystal structure of CtAgo do not reveal why they would need ACE as partner.

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Daan C. Swarts @dcswarts.bsky.social · 13/05/2025

Cyanobacterial long-A pAgos are co-encoded with Cas4 family proteins (from hereon: ACE for Argonaute associated Cas4-like enzyme). Our analysis shows that despite their family name, ACEs look more like the nuclease domains of AdnAB and AddAB than like CRISPR-Cas4.

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Daan C. Swarts @dcswarts.bsky.social · 13/05/2025

Various long-A pAgos act as stand-alone immune systems. They utilize small DNA guides to recognize and cleave target DNA. Certain long-A pAgos are co-encoded with accessory proteins, which suggests these proteins function in conjunction. What is the need of these proteins? 🤔

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Daan C. Swarts @dcswarts.bsky.social · 13/05/2025

Out now: Cyanobacterial Argonautes and Cas4 family nucleases cooperate to interfere with invading DNA cell.com/molecular-ce... Most long-A pAgos interfere with invading DNA solo. Why then are cyanobacterial pAgos co-encoded with a Cas4-like protein?

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Reposted by Daan C. Swarts

Gemma C. Atkinson @gemmaatkinson.bsky.social · 07/03/2025

Bioinformatics junior group leader position in Lund, specialising in infection and/or epidemiology. These are really nice positions with generous support. Please spread the word to anyone who might be interested in becoming our colleague! lu.varbi.com/en/what:job/...

lu.varbi.com

Associate Senior Lecturer (DDLS fellow) in data driven epidemiology and biology of infection

Lund is strategically positioned close to the continent, hosting major national and European research infrastructures, such as MAX.IV Laboratory and the European Spallation Source (ESS). In the field

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Daan C. Swarts @dcswarts.bsky.social · 23/01/2025

Excited to have been awarded an ERC Proof-of-Concept grant to further explore the possibilities to use prokaryotic Argonautes for diagnostics applications! 🥳

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Daan C. Swarts @dcswarts.bsky.social · 07/01/2025

www.cell.com/cell-reports... And this one...

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Daan C. Swarts @dcswarts.bsky.social · 07/01/2025

Together with @tniault.bsky.social, it was really fun to (again) work together with former colleagues and friends Edze Westra and Stineke van Houte on this review! Hope that everyone interested enjoys the read!

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Daan C. Swarts @dcswarts.bsky.social · 07/01/2025

We propose that beyond unraveling new anti-defence mechanisms, efforts should also aim to clarify the evolutionary and ecological drivers of anti-defence systems, which currently remain poorly explored.

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Daan C. Swarts @dcswarts.bsky.social · 07/01/2025

Finally, we discuss ecological drivers and consequences of interactions between defence and anti-defence systems.

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Daan C. Swarts @dcswarts.bsky.social · 07/01/2025

We review how regulation of anti-defense systems expression can be of importance, and how defence systems and their anti-defence systems have co-evolved in the arms race between bacterial hosts and their mobile genetic elements.

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Daan C. Swarts @dcswarts.bsky.social · 07/01/2025

We review the origins of anti-defence mechanisms, e.g. through co-option of prokaryotic proteins by plasmids and phages, defence component co-option and mutation, and de novo evolution. We also discuss the selective pressure that acts on anti-defence system maintenance.

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Daan C. Swarts @dcswarts.bsky.social · 07/01/2025

Recently very good reviews provided elaborate overviews of different anti-defence mechansms were published, so that is not the focus of this review. You can find a selection here: www.cell.com/cell-reports... www.nature.com/articles/s41... www.cell.com/trends/micro...

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Daan C. Swarts @dcswarts.bsky.social · 07/01/2025

Together with Stineke van Houte and Edze Westra, @tniault.bsky.social describes how anti-defence systems evolved, and what ecological drivers and consequences of defense system/anti-defense system interactions are.

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Daan C. Swarts @dcswarts.bsky.social · 07/01/2025

🚨New review🚨 Evolution and ecology of anti-defence systems in phages and plasmids Link: www.cell.com/current-biol...

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Reposted by Daan C. Swarts

Luuk Loeff @lloeff.bsky.social · 31/12/2024

What a great way to end the year! ✨ Today in @cellpress.bsky.social we report the structure and function of the Shedu anti-phage defense system. tinyurl.com/4crj6dnx A long 🧵...

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Daan C. Swarts @dcswarts.bsky.social · 07/01/2025

Congrats to Sumanth Mutte, @patrickbarendse.bsky.social and Pilar Bobadilla Ugarte! It is amazing how a "simple" question can turn into an entirely new project with exciting insights!

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Daan C. Swarts @dcswarts.bsky.social · 07/01/2025

These findings offer an updated perspective on the distribution of DNA repair systems and their connection to immune systems in bacteria. We hope these analysis will be of use for the wider scientific community!

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Daan C. Swarts @dcswarts.bsky.social · 07/01/2025

However, our results imply that while certain DNA repair proteins and immune systems might function in conjunction, no immune system strictly relies on a specific DNA repair protein.

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