News

September 18, 2025

Hora est!

Patrick succesfully defended his thesis, and was awarded his PhD degree ‘cum laude’!

During his thesis research, Patrick studied non-canonical pAgo functions and novel mechanisms (more on that later!).

A big thanks to everyone else involved, especially promoter Dolf Weijers and the PhD committee including Gorben Pijlman, Melanie Blokesch, Irma Querques, Matthijs Jore, and two additional external reviewers, for contributing to this fantastic day.

August 27, 2025

BindCraft paper out in Nature!

In this work, our collaborators Martin Pacesa, Lennart Nickel, Christiaan Schellhaas, Sergey Ovchinnikov, and Bruno E. Correia (and many others) developed and tested a bioinformatics pipeline that allows for one-shot design of synthetic binders for basically any protein that you can imagine.

We were lucky enough to be included to design and test pAgo binders that Patrick, Simon, and Adrie showed were capable of pAgo inhibition, just to demonstrate the versatility and power of this bioinformatics tool. Try it out!

Read it here and a behind the paper here

The Swarts lab visited The Argonautes 2025 meeting in Prague, Czech republic. Daan presented novel insights into pAgo mechanisms and inhibition (see news item above).

As in earlier editions, it was an amazing experience with exciting Argonaute research from all domains of life, and an important link to the AGO syndrome patient workshop.

Thanks for the fantastic organization, Julie, Dina, Gunter, and Peter!

(conference group photo (c) Monika Grossova)

Daan visited the Wenner-Gren symposium “Phage-bacteriainteractions: the molecular battle for control of the central dogma” in Stockholm, Sweden, and presented work from our lab.

It was a fantastic get-together with loads of exciting insights in the field of prokaryotic immunity and phage biology.

A big congratulations to Rotem Sorek for being awarded the 2025 Gruber Genetics Prize during this conference.

Aug 15, 2025

Dai-ke Zhang joins the lab!

Dai-Ke studied at the Hua Qiao University (HQU) and Shanghai Jiao Tong University (SJTU) and worked at Zuzhou Read Crystal Biotechnology Co. LTD before joining our group as a PhD candidate.

Dai-ke will join the collaborative NWO-M2 project (with Chirlmin Joo) in which we study biology, biochemistry, and biophysics of prokaryotic immune systems.

Welcome to our team Dai-ke!

June 13, 2025

Jente successfully defended her PhD thesis!

During her thesis research (conducted under supervision of Elwira Smakowska-Luzan), Jente studied plant receptor proteins (stay tuned!). Jente has been part of our group for structural biology aspects.

It was great to celebrate this milestone together!

Thanks to everyone involved, especially supervisor Elwira, promoter Dolf Weijers and the PhD committee including Christa Testerink, Antonio Molina, Yvonne Sahl, and Sebastian Pfeilmeier for contributing to this great day.

June 6, 2025

Thom obtains an EMBO postdoctoral fellowship!

This 2-year fellowship will allow Thom to pursue the project that he conceived and developed in our laboratory – More results later….

Congrats Thom!

May 15, 2025

New paper by Pilar (and many others)!

In this paper, we describe the functional, structural, and mechanistic characterization of APACE systems (Long-A pAgos associated with Argonaute-associated Cas4-like enzymes (ACE). We show that ACE1 can generate small DNA guides for its associated long-A pAgo that interferes with invading plasmid and bacteriophage DNA.

Thanks to all the collaborators in this multidisciplinary study and especially congrats to Pilar who spearheaded this study!

Read it here and a preview here.

February 10, 2025

Daan and Prof. dr. Chirlmin Joo (TU Delft) have been awarded a NWO-M2 grant. This will allow them to further consolidate their collaborative work in which microbiology, biochemistry, and biophysics (a.o. single molecule experiments) are combined to characterize prokaryotic immune systems.

January 23, 2025

ERC Proof-of-Concept grant!

The group has been awarded an ERC PoC grant. This project will facilitate the further development of prokaryotic Argonaute-based diagnostics applications in our group.

January 6, 2025

New review paper by Theo, together with Stineke van Houte and Edze Westra!

In this review published in Current Biology, we discuss the evolution and ecology of anti-defence systems in phages and plasmids.

Read it here (open access)!

January 2, 2025

New paper by Sumanth, Patrick, and Pilar!

In this work published in Cell Reports, we analyzed distribution of bacterial DNA repair proteins and their co-occurrence with immune systems

Read it here (open access)!

January 1, 2025

Theo obtains an EMBO postdoctoral fellowship!

This 2-year fellowship will allow Theo to pursue the project that he conceived and developed in our laboratory – More results later….

Also former Swarts lab member Bel Koopal obtained a EMBO postdoctoral fellowship, congrats to both Theo and Bel!

December 19, 2024

BIC Christmas dinner

We had our yearly Christmas dinner of the Laboratory of Biochemistry, this year pot-luck style with loads of delicious dishes made by all lab members. It was delicious and great!

December 17, 2024

Retirement of Adrie Westphal

After 42 years or service at the Laboratory of Biochemistry, Adrie has retired. He has been invaluable for BIC and especially for the Swarts lab in its start-up phase. Adrie will be missed dearly (and we still hope to see him every now and then!)

November 23-24, 2024

Daan visits the Whitehead Institute and NEB.

During a trip to the US, Daan presented our lab’s work at the Whitehead Institute for Biomedical Research at MIT (Boston), and at New England Biolabs (Ipswich).

Thanks to David Bartel and Kasra Tabatabaei for the kind invitation, it was a great experience!

October 24, 2024

BIC 60!

The Laboratory of Biochemistry celebrated its 60-year anniversary with scientific talks, interviews with former lab members, a poster session, and of course drinks and dinner.

It was a excellent day in which it was great to reconnect with former lab members and reflect on the past and future!

September 25-27, 2024

Swarts lab retreat!

We went to Callantsoog for a couple of days of teambuilding, scientific discussions, and fun-making (including a dress-up murder-mystery dinner!).

Thanks Clint and Adrie for the organization.

September 12, 2024

Hamzah successfully defends his MSc thesis. Hamzah studied novel pAgos under supervision of Ane and Clint.

Thanks for joining us Hamzah, and for your contributions to our group and research!

Thompson (Thom) Hallmark, PhD, joins our group.

Thom obtained his PhD degree at Utah State University (USA), where he studied CRISPR-Cas12a2 mechanisms under supervision of Prof. dr. Ryan Jackson.

He will now use his skillset to tackle fundamental questions about pAgos!

Welcome to our team Thom!

August 23-24, 2024

The Swarts lab visited The Argonautes 2024 meeting in Copenhagen, Denmark. Both Daan and Patrick gave a presentation about the work in our lab.

This was a truly amazing experience with so much exciting Argonaute research in all domains of life. The link to the AGO syndrome patient workshop made it a very special event. We left inspired and motivated!

Thanks for the organization, Peter Brodersen, Martin Simard, and Gunter Meister! We are already looking forward to the 2025 edition!

August 20, 2024

New paper by Lisa!

In this work published in NAR Genomics & Bioinformatics, Lisa has shown that abundance of specific immune systems correlates with the optimal growth temperature of the host.

Read it here (open access)!

July 2-3, 2024

Daan visited the EMBO-YIN Transcription & Chromatin Sectoral Meeting to be inspired by the cool stuff other EMBO YIPs and members are doing in their labs.

Best meeting setting ever: The Boerhaave museum in Leiden. Highly recommended!

Thanks to Martijn Luijsterburg, Tineke Lenstra, and Tuncay Baubec (and ofc. EMBO) for the fantastic organization!

June 29, 2024

RNA-guided RNA silencing by an Asgard archaeal Argonaute published in Nature Communications!

In this project, we characterized an Argonaute from a Lokiarchaeon, named HrAgo1. In line with the fact that Asgard archaea are the closest-living prokaryotic relatives of eukaryotes, HrAgo1 behaves like RNA-guided RNA-silencing eukaryotic Argonautes!

June 5, 2024

Daan visited the Max Perutz Labs in Vienna to attend a Minisymposium by four EMBO YIPs (Danny Nedialkova, Verena Ruprecht, Nicholas Taylor, and Daan) and to meet other Max Perutz scientists.

Thanks for the warm welcome Pavel Kovarik and Alwin Köhler!

April 24-26, 2024

Patrick (and former colleague Bel) visited (and both gave a talk!) at the 18th Microsymposium on RNA biology at the Vienna BioCenter in Austria.

Bel and Giada, who worked together on the SPARTA structure paper, also finally met in person!

April 1, 2024

Théophile (Theo) Niault, PhD, joins our group.

Theo obtained his PhD degree at the Institut Pasteur in Paris (France), where he studied Vibrio cholerae (plasmid) replication mechanisms under supervision of Prof. dr. Didier Mazel and Dr. Marie-Eve Val.

He will now use his skillset to tackle fundamental questions about pAgos!

Welcome to our team Theo!

March 12, 2024

Pilar successfully defended her PhD thesis entitled ‘Diving into the Argonaute world’!

During her thesis research, Pilar characterized an Asgard archaeal pAgo, and other pAgo systems and mechanisms (stay tuned 😉 ). We celebrated this milestone accordingly!

Thanks to everyone involved, especially promoter Dolf Weijers and PhD committee John van der Oost, Aude Bernheim, Dina Grohmann, and Michael Nodine.

March 11, 2024

Invited seminar speaker: dr. Aude Bernheim

Aude visited and gave an inspiring talk bout the conservation of anti-viral immunity across the domains of life – exciting stuff!

February 13, 2024

Lab outing!

During the endeavors of a scientist one has to be balanced under stressful conditions. We therefore went for a nice relaxing afternoon of aerial yoga and dinner!

February 8, 2024

Invited seminar speaker: Prof. dr. Stan Brouns

Organized by the Laboratory of Microbiology, we joined the seminar of Prof. Dr. ir. Stan JJ Brouns (TU Delft).

Stan gave an exciting talk about new mechanisms of phage defense in bacteria.

January 15, 2024

New paper alert!

Target DNA-dependent activation of the prokaryotic immune system SPARTA

In this paper, Bel and Giada Finocchio and Martin Jinek at the UZH (with help of Ana, Clint and Adrie), have elucided the structure and mechanism underlying catalytic activation of SPARTA.

Read it here (open access!)

January 1, 2024

Sumant Mutte, PhD, joins our group.

We have previously collaborated with Sumanth as he was appointed as a general bioinformatics research scientist in our department, but now we can (and will) use his expertise more extensively 😉 !

Welcome to our team Sumanth!

December 14, 2023

Laboratory of Biochemistry Christmas dinner!

We had a delicious dinner at restaurant ‘t Gesprek with entertainment organized by the PostDocs.

In good tradition we forgot to make a (group) photo as we were too busy having fun.

December 12, 2023

Bel defends her PhD thesis

In a beautiful ceremony, Bel has successfully defended her PhD thesis that revolves around the prokaryotic immune system SPARTA.

Her degree was awarded cum laude and the PhD party was legendary 🙂

Thanks to everyone involved, especially promoter Dolf Weijers and PhD committee Katharina Höfer, Tessa Quax, Ronald van Rij, and John van der Oost.

December 11, 2023

Invited seminar speaker: Katharina Höfer

Katharina visited to give an excellent seminar on her discoveries on NAD-capped RNAs and how and why they can be attached to proteins.

December 1, 2023

Ane has joined our group!

Previously Ana has previously worked as a research technician at the Laboratory of Microbiology at Wageningen University. She has now joined our lab as a PhD candidate to investigate Argonaute proteins.

We are excited to welcome Ane to our team!

Oct 31, 2023

Invited seminar speakers: Martin Pacesa (EFPL) and Masha Cherepkova (UZH Basel)

Two for the prize of one! Masha and Martin came to visit our lab and gave inspiring talks about Record-seq and synthetic protein design.

Oct 5, 2023

Invited seminar speaker: Chirlmin Joo

Our long-time collaborator Chirlmin from the Technical University of Delft came to visit the Laboratory of Biochemistry and presented exciting developments in the field of high-throughput single molecule FRET.

August 29, 2023

Laboratory of Biochemistry lab outing

We had a great day playing cowboy games and getting a line dancing clinic (video material for future reference recorded). After that, we shared a delicious Tex-Mex diner.

Thanks for organizing Pilar, Bel, and Simon!

August 11, 2023

Daan wrote a commentary on a recent PNAS publication by Sun et al. in which the mechanism of the Cas9 inhibitor AcrIIC4 is described.

Original article | Commentary

June 29, 2023

Vidi grant!

Daan has been selected as a recipient of a prestigious Vidi grant from the Dutch Research Council (NWO)! With this grant we can further consolidate our work on Argonaute proteins – stay tuned!

Press release

June 27-30, 2023

Lisa, Patrick, and Daan attended CRISPSR2023 in Würzburg, Germany.

A perfect meeting to meet old friends, make new ones, and – last but not least – to be blown away by the incredible progress in this field, ranging from antiCRISPRs, improved genome editing, and broad array of fascinating structural insights.

Thanks to the organizers for this wonderful conference!

May 21-26, 2023

Adrie, Ana, and Patrick visited the 8th international school on Biological Crystallization in Grenada.

Armed with a lot of new insights and crystallization (optimization) strategies, they are eager to optimize their crystals and grow new ones!

March 27, 2023

Lab retreat 2023! With the entire group, we went to a remote accommodation for three days to disconnect from the lab-life. We did teambuilding activities, discussed research visions and ideas, and talked about what aspects to take into account when making career choices.

Oh and let’s not forget the Lab Olympics, won by our rookie team member Clint!

It was great, looking forward to the next one!

March 9, 2023

Bel won the UFW Research award as the first author of the the best WUR publication in 2022!

The award was presented during the 105th Dies Natalis of Wageningen University.

Link to the paper (on SPARTA)

Link to press release

March 1, 2023

Clint joins our group!

Having previously worked at MolGen, where he obtained became experienced in setting up protein purifications, Clint has now joined our group as a research technician to support various aspects of our research.

We are very happy that Clint joined our team!

February 28-March 3, 2023

Lisa, Ana, and Daan visited the EMBO Workshop: The Immune System of Bacteria at the Weizmann Institute of Science in Rehovot, Israel. A ‘beyond CRISPR’ meeting with different exciting aspects about novel prokaryotic immune systems.

Daan gave a oral presentation and both Lisa and Ana presented their work on posters.

The meeting was extremely well organized and packed with exciting discoveries. We are looking forward to the 2024 version of this meeting!

December 15, 2022

BIC Christmas dinner! We celebrated another year of the Laboratory of Biochemistry over a fancy dinner at Restaurant ‘t Gesprek in Wageningen. Great to mingle and celebrate with with all the other researchers in the department!

(unfortunately we forgot to take a group photo…)

November 22, 2022

Daan has been selected as a EMBO Young Investigator!

The EMBO Young Investigator Programme provides (amongst other things) opportunities for networking, training, and scientific exchanges for the entire team.

Thank you EMBO and congratulations to all new Young Investigators!

Find more information here (EMBO).
Press release (NL) | Press release (EN)

October 25, 2022

All PIs (group leaders) of the Laboratory of Biochemistry (BIC) went for a day of sailing for teambuilding!

Our team benefits from being incorporated in a vibrant and ambitious research environment! Read more about BIC here.

October 4, 2022

Group dinner @ Daan’s place!

Good roti, good company 🙂

September 26, 2022

Ana wrote a commentary on the repurposing of SPARTA for nucleic acid detection. This work puts this application in perspective of existing techniques and reveals some future directions that can be explored to improve SPARTA-based nucleic acid detection.

Read more here.

August 24, 2022

Ana, Bel, Patrick, Pilar and Daan visited the Argonautes conference in Regensburg, Germany – the first meeting revolving around Argonaute proteins!

Both Bel and Daan presented work from our group.

We feel very inspired by the excellent science and great talks. Thanks for the organization Gunter, Martin and the entire Meister lab!

May 20, 2022

Carlos’ visit ends. Carlos Verdu was a visiting scientist from the Berenguer lab located at CBM Severo Ochoa in Madrid, Spain.

Thanks for sharing your expertise with us Carlos and all the best with finishing your PhD thesis!

test

April 28, 2022

The inaugural paper of the Swarts lab has been published in Cell!

In this paper, Bel and Ana (together with our collaborators) resolved the function and mechanisms of SPARTA systems (Short Prokaryotic Argonaute TIR-APAZ), and like the Spartans, it protects against invaders!

Read more here.

May 18-21, 2022

We had our very first Swarts lab retreat in the province of Zeeland, NL (the ‘old’ one that makes the other one the ‘new’ Zealand).

Besides in-depth discussions about the academic life and our group, we also played a lot of games, swam in the (cold) see, and visited flower fields and an ostrich farm!

May 30, 2022

Adrie, Ana, Bel, Patrick, Pilar and Daan visited the 73^th Mosbachter Kolloquium ‘The world of RNAs’.

Awesome conference with excellent science! It was great finally being able to visit an in-person meeting again after all restrictions.

Daan presented our work on short pAgos! Thanks to the organizers for organizing this excellent event!