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Aleksei Agapov

@alekseiagapov.bsky.social
99 followers 85 following 8 posts

postdoc at van Houte lab, University of Exeter

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Reposted by Aleksei Agapov
Malcolm White @mfwhite2.bsky.social · 25/09/2026
New from the @multidefence.bsky.social consortium: a deep dive into MANTIS defence. Thanks to @ukri.org for funding. www.biorxiv.org/content/10.6...
biorxiv.org
Dual ATPase-activated DNA hemimethylation and cleavage by the MANTIS defence system
Bacterial defence systems are diverse and form major barriers to horizontal gene transfer and bacteriophage (phage) infection. Though restriction-modification systems were the first such defences disc...
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Reposted by Aleksei Agapov
Anna Olina @annaolina.bsky.social · 22/09/2026
Excited to share this part of my research as a part of @multidefence.bsky.social: meet viPAO1 - the very best Pseudomonas strain for phage research😉 Also check out our temperate phage collection featuring PAnicatthedisco, PAthetic and some other new fun names🎉 www.biorxiv.org/content/10.6...
biorxiv.org
Engineering the Pseudomonas aeruginosa virus-isolation host viPAO1 reveals how host genetic barriers shape recoverable phage diversity
Cultured phage collections provide essential access to viral biology, but they capture only a small and biased fraction of natural phage diversity. Key barriers to diverse phage isolation are likely t...
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Reposted by Aleksei Agapov
Anna Olina @annaolina.bsky.social · 17/08/2026
@alekseiagapov.bsky.social and I are both presenting posters today at #ISME20 - come talk to us about phages and defences 🧬 PS2.14.246 and PS2.14.248 😉 @multidefence.bsky.social
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Multi-Defence @multidefence.bsky.social · 13/04/2026
Great to see exciting work from @megllewellyn.bsky.social on how expression context shapes the protection provided by bacterial defence systems. Comparing chromosomal and plasmid-encoded systems highlights how regulatory architecture influences defence effectiveness.
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Aude Bernheim @audeber.bsky.social · 15/12/2025
Bacterial genomes encode a rich repertoire of antiphage systems, but we still know surprisingly little about when these systems are actually expressed. In this preprint, Lucas Paoli et al, ask what shapes antiphage systems expression in native contexts. www.biorxiv.org/content/10.6...
biorxiv.org
Environment and physiology shape antiphage system expression
Bacteria and archaea encode on average ten antiphage systems. Quorum sensing, cellular, or transcription factors can regulate specific systems (CRISPR-Cas, CBASS). Yet, a systematic assessment of anti...
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Aleksei Agapov @alekseiagapov.bsky.social · 12/12/2025
That was fun!
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Reposted by Aleksei Agapov
Doudna Lab @doudna-lab.bsky.social · 09/12/2025
✨New preprint! 🧵1/4 Excited to share our work on AI-guided design of minimal RNA-guided nucleases. Amazing work by @petrskopintsev.bsky.social @isabelesain.bsky.social @evandeturk.bsky.social et al! Multi-lab collaboration @banfieldlab.bsky.social @jhdcate.bsky.social @jacobsenucla.bsky.social🧬 🔗👇
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Aude Bernheim @audeber.bsky.social · 27/11/2025
🧬🛡️How are new immune mechanisms created? We show how Lamassu antiphage system, originated from a DNA-repair complex and evolved into a compact and modular immune machine, wt Dinshaw Patel lab in @pnas.org. 👏 @matthieu-haudiquet.bsky.social, Arpita Chakravarti & all authors! doi.org/10.1073/pnas...
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Anna Olina @annaolina.bsky.social · 27/11/2025
@alekseiagapov.bsky.social presenting our data at #MicroEvo25! Always good to see a few new phage defences discovered😉
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David Sünderhauf @davvi36.bsky.social · 26/11/2025
My poster is up and the conference may begin! #MicroEvo25
Me in front of my poster
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Reposted by Aleksei Agapov
Anna Olina @annaolina.bsky.social · 26/11/2025
@jpjhall.bsky.social starts the #MicroEvo25 strong! Looks like it's gonna be fun🧬🧫🧪
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Reposted by Aleksei Agapov
Michael Brockhurst @brockhurstlab.bsky.social · 06/10/2025
New preprint! Ever wondered why only a fraction of genomes encode CRISPR immunity? 🧬 🦠 Turns out CRISPR is rarely beneficial against virulent phages, being most beneficial against those for which resistance mutations are rare! An epic effort by Rosanna Wright www.biorxiv.org/content/10.1...
biorxiv.org
Resistance mutation supply modulates the benefit of CRISPR immunity against virulent phages
Only a fraction of bacterial genomes encode CRISPR-Cas systems but the selective causes of this variation are unexplained. How naturally virulent bacteriophages (phages) select for CRISPR immunity has...
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Reposted by Aleksei Agapov
Alice Maestri @alicemaestri.bsky.social · 12/09/2025
We're looking for a technician at Institut Pasteur for experimental work on satellite-phage-bacteria interactions, working directly with @jmouradesousa.bsky.social and myself in the lab of @epcrocha.bsky.social ! ANR funded. Link to the job emploi.pasteur.fr/offre-de-emp... Thx for sharing!
emploi.pasteur.fr
INSTITUT PASTEUR - Technicien de recherche Microbiologie H/F
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Daniel Padfield @padpadpadpad.bsky.social · 16/09/2025
I have an MRC-funded PhD project available (www.exeter.ac.uk/study/fundin...) on how warming will change the problem of AMR. Join a small and friendly group (padpadpadpad.netlify.app/about) in (sometimes) sunny Cornwall. 🧪🦠 #microsky Please share the ad below with anyone who may be interested.
A teal flyer for a PhD opportunity to investigate how warming may change antimicrobial resistance. The project will use experiments on Klebsiella bacteria to answer questions about how temperature affects their response to antibiotics, plasmid transfer, and fitness costs. The research involves microbiology lab work, bioinformatics, and mathematical modeling. The flyer includes contact details for Dr. Daniel Padfield and the logos of the sponsoring institutions.
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Josie Elliott @josie-e.bsky.social · 04/09/2025
Can CRISPR-Cas systems target any phage? Yes, no, it depends? What does it depend on? The second paper from my PhD came out today in a special issue of Phil Trans B on the ecology and evolution of bacterial immune systems doi.org/10.1098/rstb...
doi.org
Phage susceptibility to a minimal, modular synthetic CRISPR-Cas system in Pseudomonas aeruginosa is nutrient dependent | Philosophical Transactions of the Royal Society B: Biological Sciences
CRISPR-Cas systems can provide adaptive, heritable immunity to their prokaryotic hosts against invading genetic material such as phages. It is clear that the importance of acquiring CRISPR-Cas immunit...
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Reposted by Aleksei Agapov
Benoit Pons @benoitjpons.bsky.social · 04/09/2025
How do bacteria choose what type of defences to use against phages? We explored that question in the last paper I worked on as a postdoc at the Uni of Exeter @uniofexeteresi.bsky.social with Stineke van Houte, Stefano Pagliara and Edze Westra (not on Bluesky) doi.org/10.1098/rstb...
doi.org
Phage provoke growth delays and SOS response induction despite CRISPR-Cas protection | Philosophical Transactions of the Royal Society B: Biological Sciences
Bacteria evolve resistance against their phage foes with a wide range of resistance strategies whose costs and benefits depend on the level of protection they confer and on the costs for maintainance....
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Peter Fineran @peterfineran.bsky.social · 18/08/2025
Ever wondered why some bacteria have multiple CRISPR-Cas systems? Our new study led by Leah Smith shows how type I CRISPR systems can promote the acquisition and retention of new spacers into a co-occuring type III system. www.sciencedirect.com/science/arti...
sciencedirect.com
Type I CRISPR-Cas immunity primes type III spacer acquisition
CRISPR-Cas systems are diverse, with microbes harboring multiple classes and subtypes. Type I DNA-targeting and type III RNA-targeting systems often c…
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Reposted by Aleksei Agapov
Asaf Levy @asaflevylab.bsky.social · 26/07/2025
Expression level of anti-phage defence systems controls a trade-off between protection range and autoimmunity By Nitzan Aframian and Avigdor Eldar. www.nature.com/articles/s41...
nature.com
Expression level of anti-phage defence systems controls a trade-off between protection range and autoimmunity - Nature Microbiology
The authors examine several defense systems and find that increased expression enhances their protection range, albeit at a cost of autoimmunity.
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Malcolm White @mfwhite2.bsky.social · 14/07/2025
Here we show how the type III signalling molecule SAM-AMP is bound and degraded by a specialised lyase enzyme encoded in cellular and phage genomes. More great work by @haotianchi.bsky.social and the team. @uniofstandrews.bsky.social academic.oup.com/nar/article/...
academic.oup.com
SAM-AMP lyases in type III CRISPR defence
Abstract. Type III CRISPR systems detect non-self RNA and activate the enzymatic Cas10 subunit, which generates nucleotide second messengers for activation
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Rob Edwards @linsalrob.bsky.social · 07/07/2025
We made structural predictions of representatives of each #PHROG from #phage genomes, and put the whole lot online. You can browse through montages or go to your favourite phrog directly and download its PDB. 💻🧬 #phagesky linsalrob.github.io/PHROG_struct...
linsalrob.github.io
PHROG Structure Gallery
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Michael Brockhurst @brockhurstlab.bsky.social · 03/07/2025
How phages trigger antiphage defence systems is a big unknown in the field. Looks great! #mevosky
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Tung Le @tunglejic.bsky.social · 02/07/2025
Finally published! Many thanks to the reviewers and editor whose comments & suggestions improved this work significantly more than the first preprint version!!! www.pnas.org/doi/10.1073/...
pnas.org
Expanding the diversity of bacterial DNA partitioning: A CTP-independent ParABS system for plasmid partitioning in Streptomyces | PNAS
The ATP- and CTP-dependent ParA-ParB-parS segrosome is a macromolecular complex that segregates chromosomes/plasmids in most bacterial species. CTP...
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Cell Host & Microbe @cp-cellhostmicrobe.bsky.social · 26/06/2025
Phage DNA modifications evade defense Phage DNA modification adds arabinose to cytosines via hydroxy linkage (5ara-hC) w/ potential double & triple arabinosylation. Arabinosylated phages are protected from DNA-targeting CRISPR-Cas & restriction modification www.cell.com/cell-host-mi...
cell.com
Phage arabinosyl-hydroxy-cytosine DNA modifications result in distinct evasion and sensitivity responses to phage defense systems
Mahler et al. describe a phage DNA modification that adds arabinose to cytosines via a hydroxy linkage. This 5ara-hC modification can be further modified to double and triple arabinosylation by phage-...
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Reposted by Aleksei Agapov
David Sünderhauf @davvi36.bsky.social · 24/06/2025
. @emgoodall.bsky.social presenting her cool new transposon-based method on discovery of novel small proteins #EESMicrobiology
Emily presenting her talk
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Aleksei Agapov @alekseiagapov.bsky.social · 24/06/2025
Presenting a poster about Pseudomonas defence systems at #EESMicrobiology in Heidelberg. If you happen to like it, don't forget to check out our consortium @multidefence.bsky.social
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Anna Olina @annaolina.bsky.social · 24/06/2025
Happily representing @multidefence.bsky.social at the #EESMicrobiology in Heidelberg! Come to my poster if interested in prophage-mediated phage defence! Also don't miss @emgoodall.bsky.social's talk today, and @alekseiagapov.bsky.social and @davvi36.bsky.social posters!
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David Sünderhauf @davvi36.bsky.social · 24/06/2025
Made it to Heidelberg for #EESMicrobiology @events.embl.org! Find me at poster 240 and make to check out @annaolina.bsky.social & @alekseiagapov.bsky.social 's posters and @emgoodall.bsky.social 's talk to see everyone from the lab 😁
Me showing off my poster
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Aleksei Agapov @alekseiagapov.bsky.social · 21/06/2025
That was fun!
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Jamie Hall @jpjhall.bsky.social · 20/06/2025
🚨 Reminder! You have just over two weeks to submit an abstract, if you want to present at the @microbiologysociety.org meeting "Understanding and predicting microbial evolutionary dynamics" in Liverpool in November! #microsky 🦠🧫🔬
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Anna Kanevskaya @annakanevskaya.bsky.social · 07/04/2025
News from the world of pAgos: We explored a distinct clade of short pAgos associated with HNH nuclease partners, which we named SPARHA, and discovered that they protect bacteria from phages and plasmids via abortive infection. Upon activation, SPARHA oligomerizes, forming filaments. A long 🧵
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Clàudia Morros Bernaus @claudiamb98.bsky.social · 13/04/2025
Had a great time today at #ESCMIDGlobal presenting on using CRISPR-Cas9 to kill E. coli ST131 and the emergence of different escape populations. Big thanks to @escmid.bsky.social and everyone who came by!
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Itai Yanai @itaiyanai.bsky.social · 11/04/2025
Is the genome just a bag of genes? A new paper in Science now reports that for two thirds of an organisms' genes the position along the chromosome is actually very tightly constrained! Amazing work from my favorite night scientist Martin Lercher and his team! www.science.org/doi/10.1126/...
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Multi-Defence @multidefence.bsky.social · 10/04/2025
🔬 Three fronts in bacterial defense! At EMBO symposium this week in Paris, our PIs showcased: • @mfwhite2.bsky.social: cyclic nucleotide defence signaling • Prof. Stineke Van Houte: prophage warfare in P. aeruginosa • Prof. Tim Blower: autoregulating toxins & phage defence
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Aleksei Agapov @alekseiagapov.bsky.social · 03/04/2025
Finishing the Microbial Warfare session strong!
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Aleksei Agapov @alekseiagapov.bsky.social · 02/04/2025
Phage vs Phage from @annaolina.bsky.social at #Microbio25. Fantastic talk!
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Multi-Defence @multidefence.bsky.social · 02/04/2025
We also have a couple of poster presentations today 255 from @drramabht.bsky.social, 282 from @anna-k-richmond.bsky.social, 062 from Meg Llewellyn and 068 from Jasmine Thomas-Campbell. All cool stuff about defence systems!
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Aleksei Agapov @alekseiagapov.bsky.social · 02/04/2025
Super proud of @megllewellyn.bsky.social presenting her first ever poster at #Microbio25 today. Don't miss it!
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Aleksei Agapov @alekseiagapov.bsky.social · 31/03/2025
Presenting a poster at #Microbio25 today/tomorrow. Come for a chat about defence hotspots in Pseudomonas phage!
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