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Avigail Stokar-Avihail

@aavihail

HFSP postdoctoral fellow @TypasLab @EMBLHeidelberg | Alumnus of @SorekLab @WeizmannScience. Interested in microbial interactions and warfare, microbial genomics & phages πŸ¦ πŸ§¬πŸ‘©πŸ½β€πŸ”¬

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14.11.2024
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Latest posts by Avigail Stokar-Avihail @aavihail

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Bacterial Schlafen proteins mediate phage defence - Nature Microbiology This study highlights that Schlafens are ancient, mechanistically conserved immune effectors that mediate antiviral immunity in organisms ranging from humans to bacteria.

Bacterial Schlafen proteins mediate phage defence www.nature.com/articles/s41... #jcampubs

10.03.2026 13:25 πŸ‘ 10 πŸ” 2 πŸ’¬ 0 πŸ“Œ 1

Yes

08.03.2026 06:07 πŸ‘ 0 πŸ” 0 πŸ’¬ 0 πŸ“Œ 0

In general, I imagine that many defense systems evolved to sense essential phage proteins, which limits the phages ability to escape easily by simple loss of function mutations...

06.03.2026 16:47 πŸ‘ 1 πŸ” 0 πŸ’¬ 1 πŸ“Œ 0

Hi! The phage protease is an essential phage protein (it is responsible for cleaving multiple capsid proteins to create mature phage particles). So a phage cannot mutate this protease to evade CBASS (by losing protease activity) and still make viable phage particles..

06.03.2026 16:47 πŸ‘ 1 πŸ” 0 πŸ’¬ 1 πŸ“Œ 0
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@nitzantal.bsky.social @romihadary.bsky.social @soreklab.bsky.social use structure prediction and in silico binding site analysis to discover viral immune evasion proteins! Exciting for our lab @reneechang.bsky.social @riveralopz.bsky.social to help with this project.
www.science.org/doi/10.1126/...

05.03.2026 20:23 πŸ‘ 69 πŸ” 26 πŸ’¬ 0 πŸ“Œ 0
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After >10 years of our lab studying bacterial cGAS-like enzymes, @hobbslabutah.bsky.social finally reconstitutes viral sensing in vitro and discovers how these ancient receptors sense phage protease enzymes to detect virion assembly and activate antiviral immunity

www.biorxiv.org/content/10.6...

06.03.2026 09:00 πŸ‘ 48 πŸ” 21 πŸ’¬ 1 πŸ“Œ 0

Congrats Nitzan! πŸ₯°

06.03.2026 12:25 πŸ‘ 2 πŸ” 0 πŸ’¬ 0 πŸ“Œ 0

Out today: We discovered new viral proteins that target immune signaling molecules, solely based on their AlphaFold-predicted shapes

www.science.org/doi/10.1126/...

Congrats Nitzan Tal and coauthors! Thank you Kranzusch lab for the fun collaboration!

Linking below previous thread on our findings

05.03.2026 19:28 πŸ‘ 103 πŸ” 49 πŸ’¬ 0 πŸ“Œ 5

Check out this new preprint discovering a cool mechanism for activation of the CBASS antiphage system-- proteolytic cleavage by the phage protease! Explains why I couldn't isolate any spontaneous phage mutants that escape CBASS.

Super cool. Can't wait to read in depth πŸ€“ Congrats Sam & Philip! πŸ₯‚

06.03.2026 08:26 πŸ‘ 9 πŸ” 1 πŸ’¬ 1 πŸ“Œ 0
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New post-doctoral research position in my phage-host interactions (Phi) laboratory in @otagomicroimmuno.bsky.social at @universityofotago.bsky.social New Zealand. The project is focused on defences against jumbo phages. Please share and if interested apply using the link in the comments.

04.03.2026 00:20 πŸ‘ 52 πŸ” 50 πŸ’¬ 5 πŸ“Œ 2

Fantastic collaboration w/ @dbikard.bsky.social @audeber.bsky.social @rayanchikhi.bsky.social labs led by @jmouradesousa.bsky.social : We assessed the rates of variation of anti-phage systems in P4-like satellites and P2 helper phages. Quick conclusion: Huge variation! We focus on 4 key questions/5

03.03.2026 17:39 πŸ‘ 45 πŸ” 21 πŸ’¬ 1 πŸ“Œ 1

Out now! In collaboration with Leifu Chang, we uncover the molecular and structural underpinnings of CRISPR-Cas12f-like RNA-guided transcription systems!

Links to the published articles:
tinyurl.com/55kpavet
tinyurl.com/sk6djwx3

Previous thread for the preprint:
bsky.app/profile/did:...

04.03.2026 20:28 πŸ‘ 69 πŸ” 26 πŸ’¬ 0 πŸ“Œ 2
SISB2026

Abstract submission is now OPEN for the 2026 Symposium on the Immune System of Bacteria!

sisb2026.rockefeller.edu
πŸ—“ May 5–7, 2026
πŸ“ Rockefeller University, New York City
⏰ Abstract deadline: March 16, 2026

Attendance will be capped, be sure to register early and secure your spot.

See you in NYC!

11.02.2026 14:05 πŸ‘ 23 πŸ” 13 πŸ’¬ 0 πŸ“Œ 2
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Congratulations to Sonomi Yamaguchi for her paper at @nature.com. Sonomi discovered Clover defense and explained how nucleotide signals control each step of viral sensing, immune regulation, and viral restriction – named for her beautiful "four-leaf" structures πŸ€

www.nature.com/articles/s41...

18.02.2026 17:11 πŸ‘ 59 πŸ” 31 πŸ’¬ 0 πŸ“Œ 4
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EMBL International PhD Programme - summer recruitment 2026! πŸ‘€

Research groups across EMBL are recruiting now! www.embl.org/about/info/e...

Don’t miss this opportunity to receive dedicated mentoring while doing interdisciplinary research.

19.02.2026 09:41 πŸ‘ 12 πŸ” 13 πŸ’¬ 0 πŸ“Œ 1
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Rewiring of oncogenic signaling in #DrugResistance is a moving target. In our new study, we used biophysical phosphoproteomics to investigate #BRAF mutant cancer, linking phosphorylation changes to protein function and #MolecularMechanisms through #Multi-Omics integration.
tinyurl.com/funsignaling

11.02.2026 13:57 πŸ‘ 29 πŸ” 12 πŸ’¬ 1 πŸ“Œ 3
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The paradox of immune systems conservation between prokaryotes and eukaryotes - Nature Reviews Microbiology The widespread prokaryotic immune systems, in particular restriction–modification, CRISPR–Cas and defensive toxin–antitoxin systems, are absent in eukaryotes, whereas relatively rare ones, such as Arg...

The immune systems paradox

Some widespread prokaryotic immune systems are absent in eukaryotes, whereas relatively rare ones became central to eukaryotic innate immunity

@audeber.bsky.social & E. Koonin hypothesize the answer is #HGT

shareable link: rdcu.be/e2EmD

www.nature.com/articles/s41...

06.02.2026 10:22 πŸ‘ 43 πŸ” 18 πŸ’¬ 2 πŸ“Œ 1

That's cool, and flattering πŸ™ƒ I hope they enjoy it

05.02.2026 16:08 πŸ‘ 2 πŸ” 0 πŸ’¬ 1 πŸ“Œ 0

Two independent super-elegant studies from Maxwell & Laub labs find immune proteins that sense infection by binding to oligomeric phage protein rings (i.e phage portal), using them as a scaffold to assemble into their active immune effector form 🀯

Highly recommend read! πŸ€“πŸ“–l

05.02.2026 09:15 πŸ‘ 18 πŸ” 7 πŸ’¬ 0 πŸ“Œ 0

A DNA damage-activated kinase controls bacterial immune pathway expression https://www.biorxiv.org/content/10.64898/2026.02.02.703251v1

04.02.2026 04:16 πŸ‘ 11 πŸ” 7 πŸ’¬ 0 πŸ“Œ 0

A great example of the ongoing arms race between bacteria and phages. πŸ¦ πŸ›‘οΈ The plot thickens on the NAD+ bacteria vs. phage battlefield.

See thread below from @ostermanilya.bsky.social ‡️

Congrats to you and all involved πŸ₯‚ I wonder what's next? 🧐

29.01.2026 11:42 πŸ‘ 4 πŸ” 0 πŸ’¬ 1 πŸ“Œ 0

Helaine& Kranzusch labs reveal a mechanism by which a prophage-encoded abortive infection protein defends the host from other phages using a tail tip triggered tRNA nuclease, while maintaining its own propagation abilities- by encoding a tail tip variant that does not trigger it.

πŸ‘‡πŸ½πŸ§¬βœ‚οΈβ˜ οΈπŸ¦ 

29.01.2026 06:31 πŸ‘ 12 πŸ” 3 πŸ’¬ 0 πŸ“Œ 0

Another cool finding of nucleotides activating antiphage defense πŸ‘‡πŸ½

5β€²-phosphorylated deoxydinucleotides arising during host genome degradation activate the doughnut shaped ApeA oligomer, to cleave host
tRNAs and abort infection

βœ‚οΈπŸ§¬βž‘οΈπŸ©βœ¨βž‘οΈβœ‚οΈβ˜ οΈπŸ¦ 

www.biorxiv.org/content/10.6...

27.01.2026 13:13 πŸ‘ 25 πŸ” 7 πŸ’¬ 0 πŸ“Œ 0
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Recruitment for the EMBL International PhD Programme is officially open! πŸ”Š

At EMBL, we train young scientists to become skilled and creative future leaders in academia, industry and other sectors. Start your career in the life sciences with us!

πŸ”Ž Read more here:
tinyurl.com/4jdt2ra5

26.01.2026 08:50 πŸ‘ 23 πŸ” 33 πŸ’¬ 1 πŸ“Œ 1
A comprehensive catalogue of receptor-binding domains in extracellular contractile injection systems - Nature Communications Extracellular contractile injection systems (eCISs) are bacteriophage tail-derived toxin delivery complexes that are present in many prokaryotes. Here, the authors present an analysis of eCIS tail fib...

A new paper from the lab on virus-like particles called eCISs www.nature.com/articles/s41...

How bacteria evolved thousands of precision nanoinjectors?

Some bacteria don’t secrete toxins β€” they inject them using phage-derived machines called extracellular contractile injection systems (eCISs).

26.01.2026 13:26 πŸ‘ 41 πŸ” 27 πŸ’¬ 3 πŸ“Œ 0
SISB2026

Check this out for the 2026 SISB (phage defense) meeting in NYC. Mark your calendar! (and note the Zoom option, if needed)
sisb2026.rockefeller.edu

01.12.2025 23:44 πŸ‘ 35 πŸ” 19 πŸ’¬ 0 πŸ“Œ 5
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A phage protein screen identifies triggers of the bacterial innate immune system Nature Microbiology, Published online: 16 January 2026; doi:10.1038/s41564-025-02239-6A library of 400 phage protein-coding genes is used to find a trove of antiphage systems, revealing systems that target tail fibre and major capsid proteins.

Out Now! A phage protein screen identifies triggers of the bacterial innate immune system #MicroSky

16.01.2026 16:53 πŸ‘ 46 πŸ” 28 πŸ’¬ 0 πŸ“Œ 2
A methylome-derived m6-dAMP trigger assembles a PUA-Cal-HAD immune filament that depletes dNTPs to abort phage infection Bacteria must distinguish phage attack from normal homeostatic processes, yet the danger signals that trigger many defence systems remain unknown. Here, we show that a PUA-Calcineurin-CE-HAD module from Escherichia coli ECOR28 confers broad anti-phage protection by binding Dam-methylated deoxyadenosine monophosphate (m6-dAMP) generated during phage-induced chromosome degradation. Ligand binding converts a preassembled PUA-Calcineurin-CE hexamer loaded with six HAD phosphatases into a polymerising filament. The filament acts as a high-flux dNTP sink through a two-enzyme cascade: HAD first dephosphorylates dATP to dADP, and Calcineurin-CE then converts dADP to dAMP. dNTP collapse halts phage replication and enforces abortive infection. Multiple mobile-element DNA mimic proteins block filament assembly, revealing a direct phage counter-defence. More broadly, our findings extend a conserved, cross-kingdom paradigm of immune filament assembly to nucleotide-depletion antiviral defence and suggest modified-nucleotide sensing by related PUA-Calcineurin-CE modules as a widespread, underappreciated bacterial strategy. ### Competing Interest Statement The authors have declared no competing interest. NIHR Southampton Biomedical Research Centre, https://ror.org/01qqpzg67, Postdoctoral Bridging Fellowship F.L.N. is supported by a Wessex Health Partners (WHP) and National Institute for Health and Care Research Wessex Experimental Medicine Network (NIHR WEMN), Seed fund National Institutes of Health, GM145888, U24 GM129539) Maloris Foundation Memorial Sloan Kettering Cancer Center, P30-CA008748 Simons Foundation, SF349247 New York State Assembly

Preprint out: We characterise PUA-Cal-HAD, a widespread bacterial antiphage defence family. An infection cue switches a preassembled complex into an immune filament that drains dNTPs via a coupled two-enzyme cascade, and phage DNA mimics can block filament assembly (anti-polymerisation).

17.01.2026 14:52 πŸ‘ 34 πŸ” 19 πŸ’¬ 1 πŸ“Œ 0
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Intracellular competition shapes plasmid population dynamics From populations of multicellular organisms to selfish genetic elements, conflicts between levels of biological organization are central to evolution. Plasmids are extrachromosomal, self-replicating g...

Hot off the press! Our latest paper led by @fernpizza.bsky.social, understanding how plasmids evolve inside cells. These small, self-replicating DNA circles live inside bacteria and carry antibiotic resistance genes, but also compete with one another to replicate. 1/
www.science.org/doi/10.1126/...

20.11.2025 21:42 πŸ‘ 437 πŸ” 199 πŸ’¬ 11 πŸ“Œ 18
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@sacrozhangt.bsky.social and I wrote a commentary on Jordi van Gestel and Carol Gross's latest paper, check it out!

www.pnas.org/doi/10.1073/...

Sadly, the Editors at PNAS rejected our initial introduction, which was a David Attenborough style voice over of the microbial Serengeti (included below)

13.11.2025 14:54 πŸ‘ 75 πŸ” 19 πŸ’¬ 8 πŸ“Œ 2