Aude Bernheim @AudeBer Twitter profile

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@Prestisa_id

Aude Bernheim

@AudeBer

4 years

Stoked to report in @nature the discovery of prokaryotic viperins, which naturally produce diverse anti-viral molecules ! After providing us with antibiotics, bacteria might become sources of novel anti-viral drugs. (1/9)

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Aude Bernheim

@AudeBer

9 months

Could not resist. Making that figure in 2019, I thought the newly uncovered diversity of antiphage systems was already incredible. We now know it was just the tip of the iceberg. I hope our new review will help people dive into this wonderful field. .

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@AudeBer

2 years

I m one of the lucky few.i got an ERC starting grant 😱🥳As one of my mentors told me, this means that i now get to do the science of my dream which is collaborative, creative, interdisciplinary and inclusive. And now i get to build and make live my little utopia. ARGGGG😊

European Research Council (ERC)

@ERC_Research

2 years

🎉ERC Starting Grant competition results are out! Over €619 million for the best ideas of young leading researchers - and the 1️⃣st set of grants awarded under 🇪🇺 @HorizonEU . Find out who, where and why 👉 #EUfunded #FrontierResearch #ERCStG

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@AudeBer

1 year

The lab is moving to the @institutpasteur . A bit intimidating to run a lab where so many of my favorite scientists work/ed. But I'm thrilled to become a Pasteurian to launch new crazy scientific projects with everyone there. I'll try my very best to be up to the task.

MDMLab

@MDMlab_Paris

1 year

New year, new home! The MDM lab is moving to the Pasteur Institute in Paris @institutpasteur @GenGen_IP . We're excited to join such an historical institution with a vibrant community of fantastic scientists.

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@AudeBer

3 years

A bit lost with all the new anti-phage systems out there? We developed DefenseFinder, a tool to detect all known anti-viral systems in bacterial genomes and conducted a large scale analysis on the anti-viral arsenal of prokaryotes. See more below ! (1/9)

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@AudeBer

5 months

Yesterday, i had the honor of becoming part of the first Scientific Council for the French President, among a group of 12 incredible scientists. A tad far from my 🦠, but hopefully will help a bit in fostering the role of science & knowledge in our society and democracy.

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@AudeBer

2 years

Big milestone today. The first paper of the lab is out (the first for me as a senior author😱). Still feels crazy. Seemed like an appropriate time to also talk about the fantastic team we are building in Paris @MDMlab_Paris . Long live microbes and their viruses 🧫🦠🧬😍

MDMLab

@MDMlab_Paris

2 years

Hello world, we are very happy, as the first paper of our new lab has just been published @NatureComms . It’s about describing the anti-viral arsenal of bacteria and a tool we developed to detect all known anti-phage systems called DefenseFinder.

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@AudeBer

2 years

What a great honor to receive a prize from the College de France, probably my favorite institution in France. Since 1530, its mission has been to teach top level science to the general public for free. I learned so much from the College since I was a teen. THANKS 😱😻🧬🦠🧫

Collège de France

@cdf1530

2 years

🥇Le prix 2022 du Collège de France pour les jeunes chercheuses et les jeunes chercheurs est décerné à Aude Bernheim, chercheuse en #microbiologie et en #g énétique ( @Inserm ) =>

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@AudeBer

1 year

Bacteria and eukaryotes share immune mecanisms. We searched for bacterial antiphage systems in eukaryotic genomes and found thousands of hits. Exploring this conservation of antiviral systems led us to novel defense mechanisms in humans. Preprint Thread👇

Conservation of antiviral systems across domains of life reveals novel immune mechanisms in humans

Viral infection is a common threat to prokaryotic and eukaryotic life, which has resulted in the evolution of a myriad of antiviral systems. Some of these eukaryotic systems are thought to have...

www.biorxiv.org

MDMLab

@MDMlab_Paris

1 year

In a new preprint, we report that recently discovered anti-phages systems (Mokosh, Eleos, Lamassu…) have eukaryotic homologs. We harnessed this conservation to discover novel defense mechanisms in humans. @howmanyernest1 @gaofir @EnzoZ_P @AudeBer

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Aude Bernheim

@AudeBer

4 years

Mix and match your immune systems! Our pan genome view of bacterial immunity with @SorekLab

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@AudeBer

3 years

😍😱🧬🧫I got an scientific award named after Rosalind Franklin. Genetics and Feminism, two of my biggest passions in life. So honored and empowered to join this list of fantastic women scientists. Thanks @The_Gruber_Fdtn @GeneticsGSA !! And yayyyy science :) 😍😱🧬🧫

Genetics Society of America

@GeneticsGSA

3 years

Congratulations to the 2022 recipients of the @The_Gruber_Fdtn Rosalind Franklin Young Investigator Award!

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@AudeBer

1 year

This is finally happening ! @SorekLab introducing the first symposium on immune systems of bacteria 🥳🍾😱😭. So much awesome science to come and great people to meet. Excitement level ++++++

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@AudeBer

3 years

Thanks to the Fondation Jacques Monod and the @Fondationfrance for awarding me the Jacques Monod Prize. An honor to get a prize named after Monod. Thks to everyone who helped in my research, a collective work before everything AND to bacteria and phages for being so interesting

Fondation de France

@Fondationfrance

3 years

#PrixDeLaRechercheM édicale | Battra-t-on les virus grâce aux bactéries ? Aude Bernheim, microbiologiste à l' @Inserm tente de répondre à cette question ! 🦠 Découvrez la lauréate du Prix Jacques Monod ➡

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@AudeBer

2 years

What a special day. Yesterday I got to defend my "habilitation". Presented the science we do in the lab to awesome scientists, gathered current and former students, had old friends coming to visit. Feeling grateful to be surrounded by such great scientists/people. Merci!🥳🍾🧬

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@AudeBer

4 years

Such a great review. The complexity and beauty of phages diversity dissected and explained. From abundances in various environments and network phylogenies to the underlying cause of diversity, mosaicism. A must read by @moira_dion @smoineau

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@AudeBer

3 years

Happy month on my side, got (my first) funding(s) ( @ANR and ATIP avenir) to explore different aspects of the wonderful world of anti phage systems with a new team in Paris 🦠🧬🍾🇫🇷. Big thanks to everyone who helped along that journey and very excited for the science to come 🤩

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@AudeBer

2 years

"The more i know, the less I understand". Thanks @dbikard for summarizing my current vibe on defense systems. All this mobile elements are messing with my head.🤯🤩

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@AudeBer

2 years

Ok, in 24 hours, more than 40 défense systems were revealed 🤩🤯🥳. Two different approaches, congratulations to all the authors! Amazing to see the role of mobile elements in these. Maybe as @epcrocha says, cells are just battlefields for MGE! So much cool biology to understand

bioRxiv Microbiology

@biorxiv_micrbio

2 years

Mapping the landscape of anti-phage defense mechanisms in the E. coli pangenome #biorxiv_micrbio

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@AudeBer

6 days

The 2024 symposium on the immune system of bacteria is over. Thank you everyone for the great science, discussions and vibes. See you next year in Paris on April 8th-10th 2025.

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@AudeBer

5 years

Avec @laurenbastide sur @franceinter , on a parlé impact du feminisme sur les sciences, CRISPR, @vincentflora , @criparis , interdisciplinarité, syndrome de l'imposteur..! Tlt incroyable d'être interviewée par une journaliste qu'on admire sur sa radio préférée. Je ne m'en remets pas

France Inter

@franceinter

5 years

ON AIR - Pour #LesSavantes @laurenbastide a rencontré @AudeBer spécialiste en microbiologie et en génétique, pour une interview entre intelligence artificielle et sciences accessibles à toutes et tous

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@AudeBer

2 months

Ce matin j'étais dans la matinale de @franceinter pour parler sciences et féminisme avec @AliBaddou , @MarionLHour et A. Palt Plus de diversité pour une meilleure science au service de toutes et tous ! ✊🦠🧬👩‍🔬👩‍🚀👩‍💻

Recherche scientifique et sexisme : "Même les filles compétentes ne s'imaginent pas dans ces...

Aude Bernheim, chercheuse en microbiologie et génétique, responsable d’un groupe de recherche “Diversité moléculaire des microbes” à l’Institut Pasteur et Alexandra Palt, directrice générale de la...

www.radiofrance.fr

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@AudeBer

7 months

Since noticing similarities between eukaryotic and prokaryotic immune systems, we have been wondering, how do these conserved systems evolve ? We used my favorite antiphage system, viperins, to provide some answers! 🧵 below.👏 @HelenaShomar @HGeorjon

Viperin immunity evolved across the tree of life through serial innovations on a conserved scaffold

Evolutionary arms races between cells and viruses drive the rapid diversification of antiviral genes in diverse life forms. Recent discoveries have revealed the existence of shared immune genes...

www.biorxiv.org

MDMLab

@MDMlab_Paris

7 months

Happy to share our new preprint! We used viperins🐍, to understand the conservation and diversification of immune genes across domains of life. A deep dive in the evolutionary history of immune genes shared by prokaryotes and eukaryotes!

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@AudeBer

7 days

To promote a diverse pool of speakers/reviewers (etc), we introduced at SISB2024 a list of PIs in bacterial immunity searchable by career stage, country and gender. Inspired by @GaetanBurgio . Mail me to add your name or correct mistakes!

PIs in bacterial immunity

Sheet1 Name,Surname,Gender,Early Career Stage,Institution,Country,Research Themes Atkinson,Gemma,Woman,Y,Lund University,Sweden,https://www.lunduniversity.lu.se/lucat/user/b80929e6d078ff193150b9432...

docs.google.com

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@AudeBer

9 days

Philip Kranzusch launching the 2024 symposium on the immune system of bacteria! Blossoming Boston for blossoming science!

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@AudeBer

1 year

There is nothing like a @SorekLab lab talk to end a conference. Sorek groupie one day, Sorek groupie always. Inspiring words from Rotem to close this first symposium. Luckily, we have next year symposium to look for with Phil Kranzusch in Boston!

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@AudeBer

4 years

Hi twitter, I'll give a @MicroSeminar on July 24th (8am Pacific time, 5pm Paris time, 6pm israeli time) on my post-doc work at the @SorekLab "Conceptual and mechanistic conservation of anti-viral immunity in Prokaryotes and Eukaryotes". YAY! Youtube link to come, open to all :)

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@AudeBer

3 years

Now in @CellCellPress How we solved the mystery of some of the coolest bacterial elements. Retrons function as anti-phage defense systems! Such an exciting project and collaboration in @SorekLab with @AdiMillman and @AAvihail . Thread was done below when preprint was out!

Sorek Lab

@SorekLab

3 years

Now in Cell: Bacterial retrons function in anti-phage defense ! Excited to solve a decades-old mystery on the function of these RNA/DNA hybrid molecules Congrats @AdiMillman @AudeBer @AAvihail !

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@AudeBer

2 years

The field is going so fast, we are doing our best to keep up :). DefenseFinder now includes wonderful new systems including but not limited to: ; ; ; and a bunch of old ones ^^.

UG/Abi: a highly diverse family of prokaryotic reverse transcriptases associated with defense...

Abstract. Reverse transcriptases (RTs) are enzymes capable of synthesizing DNA using RNA as a template. Within the last few years, a burst of research has

academic.oup.com

MDMLab

@MDMlab_Paris

2 years

New release alert: DefenseFinder v1.2.0 is out. When published in May, DefenseFinder included 60 systems, v1.2 now includes 130 systems. Available online and as command line (--update). Thks for all the people who reported bugs and new systems !

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@AudeBer

4 years

Thank you for staying until the end. I love to share this story so get in touch if you have questions and/or would like me to give seminars. Else, I have an online talk available on youtube :) . Hope to see you soon for more science !

Aude Bernheim: Conceptual and mechanistic conservation of of anti-v...

Conceptual and mechanistic conservation of anti-viral immunity in Prokaryotes and Eukaryotes

www.youtube.com

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@AudeBer

6 years

Viruses cooperate to defeat bacteria. Our @NatureNV with @SorekLab on the great work of @AdairLBorges @joeBondyDenomy and M. Landsberger, S. van Houte and their labs !

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@AudeBer

1 year

Hier, j'ai eu l'honneur de recevoir le Prix du Collège de France pour les jeunes .s. Ce prix, c'est l'occasion pour moi de donner une conférence au collège de France🤯 Rdv le 13 décembre à 16h pour "Immunité bactérienne : à la découverte d'un nouveau monde"

Collège de France

@cdf1530

1 year

#Science #Biologie 📌 Aude Bernheim est chercheuse en #microbiologie 🏅 Elle est lauréate du Prix du Collège de France pour les jeunes chercheuses et les jeunes chercheurs 2022 ⏰ Conférence le Mardi 13 décembre 2022 à 16h 👉

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@AudeBer

5 months

This was a journey which started by the simple question: how much do we understand phage-bacteria interactions from their genomes only? Answer: more than I thought. Very interdiscplinary work led by an amazing trio: B. Gaborieau, @hugovaysset , F. Tesson.

Predicting phage-bacteria interactions at the strain level from genomes

Predicting how phages can selectively infect specific bacterial strains holds promise for developing novel approaches to combat bacterial infections and better understanding microbial ecology....

www.biorxiv.org

MDMLab

@MDMlab_Paris

5 months

💻🧫New preprint: How accurately can we predict diverse phage bacteria-interactions from their genomes only ? We created a matrix of >38k phage-bacteria interactions to find out (=> AUROC 86%) & used our predictions to recommend tailored phage cocktails.

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@AudeBer

2 years

Our citizen science project @ScienceALaPelle spearheaded by @VincentLibis featured in French national newspaper. Pics by Yeganeh Foroughi, a student in the lab. Now lets get some soil and find new molecules!

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@AudeBer

1 month

A new microbial immunity lab in France 🇫🇷🦠🥳. Anyone who wants to work on phages, this will be a super exciting place to do it!

François Rousset

@FrancoisRousset

1 month

I am thrilled to announce that I will soon open my independent group at @CIRI_Lyon 🤩 My team will develop new approaches to explore the molecular arms race between phages and bacteria 🦠🧐 Join us in this new adventure in the beautiful city of Lyon !

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@AudeBer

2 years

Starting a US trip with a first time visit to Cold Spring Harbor for CRISPR CHSL. Such a beautiful mythical place for biology. Paid an hommage to Delbruck and McClintock. Loving the outdoor art. Learning a lot (too much?😅) about genome editing. Thx for the welcoming crowd!

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@AudeBer

2 years

Being a Parisian scientist has it perks. Picnic to celebrate spring and awesome scientific results but also to sample some soil. The scenery is beautiful and our bubbly wines, baguettes and cheese, well, there is a reason some clichés exist.🍷🍾🥖🧀

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@AudeBer

2 years

Want to attend the first conference on immune systems of bacteria ? Given the speed of discovery in the field, this conference will for sure be full of crazy cool new insights. The speakers list 🤯🤩😯! Don't wait to sign up, I believe it will be quickly full.

Sorek Lab

@SorekLab

2 years

The first symposium on the "beyond CRISPR" immune system of bacteria: Registration open! Feb 28th-Mar 2nd at the Weizmann Institute, Israel A fantastic line up of speakers + talks selected from abstracts. We have limited space, hurry up and register!

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@AudeBer

2 months

March 8th is often bittersweet. Depressing nbrs (-10% in STEM Phd in 🇫🇷 or 17%♀️ of corresp authors submitting to Nature) But i got so inspired this year by leadership of @BelkaidLab or new labs like @TanaWein or pioneering science from @vincentflora @CamLBerthelot @HelenaShomar

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@AudeBer

3 months

Join us in April in Boston for the 2024 symposium on the immune system of bacteria ! 🧫🧬🥳 Registration now open: Abstract deadline March 4th.

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@AudeBer

2 years

Bye bye the US 🇺🇲. My brain is on fire from so many incredible discussions. Was especially impressed by the brightness of all the students i met from many labs @HarvardMicro @baym @shsternberg @doudna_lab #Koonin . And the fun 🤩Thank you all for the energy to do better science.

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@AudeBer

3 months

Hopefully this will be useful for both defense systems aficionados and newcomers in the field. Idea came thx to feedback from the community & new students/experimentalists from our lab. For me, a new way to procrastinate, get lost and wander at the diversity of defense systems!

MDMLab

@MDMlab_Paris

3 months

👋DefenseFinder news ! Thinking of how we can better help the community, we provide a new website that includes a wiki on defense systems, a structure database and precomputed DefenseFinder results on >22k genomes. Preprint:

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@AudeBer

7 months

If you want to start the week well, read this 🙂. Pascale Cossart @cossart25001997 wrote about her scientific career and it's just fascinating to follow all the great discoveries across times and technologies.

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@AudeBer

3 years

Alphafold results look amazing! Been following deep mind work for years. So excited to try it somehow. This will empower molecular biologists so much, to make better hypothesis thanks to genomics data combined with this. What a cool time to be a scientist.

‘It will change everything’: DeepMind’s AI makes gigantic leap in solving protein structures

Nature - Google’s deep-learning program for determining the 3D shapes of proteins stands to transform biology, say scientists.

www.nature.com

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@AudeBer

2 years

We read the great paper of @pmaguin , @MarraffiniLab and colleagues () and wrote a few words about it. CRISPR-Cas and restriction–modification team up to achieve long-term immunity

CRISPR-Cas and restriction–modification team up to achieve long-term immunity

Bacteria have been shown to harbor a growing arsenal of various defense systems against phages. Maguin et al. have uncovered how two of the most frequent defense systems interact: the clustered...

www.cell.com

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@AudeBer

2 years

I am in Cambridge for the first time of my life. I am quite impressed to be in a city where so many great minds did such wonderful scholar works. I died a bit when entering the real bookshop of the Cambridge University Press. So much knowledge in one place.😍🤓📚

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@AudeBer

1 year

Incredible work to understand the function of all proteins. Gives a great idea of what is known, unknown. It also beautifully shows how strucutres can reveal conservations across domains of life. Thanks to the authors for providing all these tools and datasets to explore this.

Martin Steinegger 🇺🇦

@thesteinegger

1 year

We clustered the #AlphaFold structure database with our novel Foldseek algorithm. We identified 2.27M clusters and analyzed them by function, annotation, domains and evolution. Amazing collaboration with @pedrobeltrao lab. 1/n 📄 💾

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@AudeBer

5 years

Why CRISPR-Cas are not encoded by all bacteria ? New hypothesis in our paper with @dbikard and Eduardo Rocha : it's a matter of (genetic) background. #PhDpaper

A matter of background: DNA repair pathways as a possible cause for the sparse distribution of...

The absence of CRISPR-Cas systems in more than half of the sequenced bacterial genomes is intriguing, because their role in adaptive immunity and their frequent transfer between species should have...

royalsocietypublishing.org

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@AudeBer

4 years

My talk will be tomorrow🥳 4pm Paris time, 5pm Israel Time, 10am US Eastern Time "Conceptual and mechanistic conservation of anti-viral immunity in Prokaryotes and Eukaryotes." Live stream link: . Also possible to catch it another time, will remain there.

Aude Bernheim: Conceptual and mechanistic conservation of of anti-v...

Conceptual and mechanistic conservation of anti-viral immunity in Prokaryotes and Eukaryotes

www.youtube.com

MicroSeminar

@MicroSeminar

4 years

Tomorrow, 10am US Eastern, @AudeBer #uSeminar "Conceptual and mechanistic conservation of anti-viral immunity in Prokaryotes and Eukaryotes." Live stream link:

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@AudeBer

4 years

So happy to share the product of the most fun collaboration with @AdiMillman and @AAvihail . At the @SorekLab we discovered Retrons function as anti-phage systems. See below for preprint and thread!

Adi Millman

@AdiMillman

4 years

Happy to share our new preprint about how we solved the mystery of some of the coolest bacterial elements: Retrons function as anti-phage defense systems! See thread below by the 3 of us: @AdiMillman @AudeBer @AAvihail

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@AudeBer

5 years

New paper from @dbikard lab is out ! Genome-wide CRISPR-dCas9 screens in E. coli identify essential genes and phage host factors. Cool read for everyone interested in CRISPR tools to study bacteria and phages. Congrats Francois, @omnicui , Elise and co

Genome-wide CRISPR-dCas9 screens in E. coli identify essential genes and phage host factors

Author summary Over the past few years, CRISPR-Cas technologies have emerged as powerful tools to edit genomes and modulate gene expression. They have been applied to perform high-throughput genetic...

journals.plos.org

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@AudeBer

2 years

Congratulations @FrancoisRousset from @SorekLab @WeizmannScience on being awarded a Bettencourt Schueller prize for young investigator . 🤩😱🏆🏆🏆🏆 @Fondation_BS . So well deserved for all the great work on phages and bacteria. Looking forward for what you'll do next!

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@AudeBer

4 years

"If one CRISPR-Cas is great, why have two ? Or more? Or combinations of them? " Perfect summary by @epcrocha . Last piece of my Phd explores atypical CRISPR-Cas and their epistatic interactions. @dbikard

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@AudeBer

4 years

Do these pVips (prokaryotic viperins) have the same function as the human viperin ? We took ~60 pVips from diverse prokaryotes, cloned them in E. coli and challenged them with phages. Bingo, half of them provided anti-viral activity ! (3/9)

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@AudeBer

2 months

👋 everyone, we recently submitted our webservice in a dedicated journal. editors didnt send it for review bc "it's preliminary and does not work". 1) if things arent working,pls let us know? 2) if you use it, please tell us in short answer /via mail, thx!

DefenseFinder Wiki

On this site, you can freely use (without any login) the DefenseFinder webservice (see below) and get help to navigate the ever expanding world of defense systems.There is a collaborative knowledge...

defensefinder.mdmlab.fr

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@AudeBer

3 months

Yesterday, we had a Pasteur mini symposium on evolution and biodiversity. So many fantastic talks: from the shape of brains to emergence of multicellularity, the infinite space of MGE or gene loss as an adaptive strategy. A large audience for a great topic. Thx +++ to organizers.

Thibaut Brunet

@thibaut_brunet

4 months

Very much looking forward to this event on Jan 29, where we'll gather the @institutpasteur evolutionary biology community with @CamLBerthelot @BIUPasteur @G_Frasca + special guest keynote by @eme_laura 🤩 DM me if you're a non-Pasteurian and would like to attend!

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@AudeBer

2 months

It's heatwarming to see scientists you admire getting recognition for their work. Eduardo has such a great impact on how to think about evolution and genomics, not only because of his bold and original ideas but through all the people he mentors to think about these topics.

Eduardo Rocha

@epcrocha

2 months

Thrilled & honoured to receive the CNRS silver medal. Many thanks to all fantastic collaborators I had all these years, to @CNRSbiologie @institutpasteur & esp. to section 21 for proposing me now and for daring to tenure me barely a few weeks after finishing my PhD back then.

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@AudeBer

3 years

So happy about #CRISPR2021 but was so much looking forward to show all CRISPR people the best wine places in Paris. Well, people, come another time! I'll be super glad to discuss bacteria and phages while wandering in beautiful Paris, anytime 🍷🥖🥐🍾

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@AudeBer

2 years

This is going directly above my desk as a poster !

Sorek Lab

@SorekLab

2 years

SnapShot: Bacterial Immunity @Nitzan_T masterfully organized current knowledge on bacterial immune systems into a single page graphics Out today @CellCellPress :

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@AudeBer

1 year

La conférence que j'ai donnée au @cdf1530 est maintenant en ligne: "Immunité bactérienne : à la découverte d'un nouveau monde". J'ai essayé d'y retracer pour un public non spécialiste l'histoire de ce champs de recherche et où je pense qu'il se dirige !

Immunité bactérienne : à la découverte d'un nouveau monde - Aude...

Conférence d'Aude Bernheim, lauréate du prix du Collège de France pour les jeunes chercheuses et les jeunes chercheurs 2022Mardi 13 décembre 2022Tous les org...

www.youtube.com

Collège de France

@cdf1530

1 year

⏰ Mardi 13 décembre 2022, à 16h. 🔬 "Immunité bactérienne : à la découverte d'un nouveau monde" 📌 Conférence d'Aude Bernheim ( @AudeBer ), chercheuse en #microbiologie à l' @Inserm , Prix du Collège de France 2022. 👉

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@AudeBer

3 years

There is nothing quite like talks from the @SorekLab at CRISPR conferences. It's like really good cheese. This years flavor, the one and only @gaofir with beautiful work on thoeris and amazing work presented by Rotem from @Nitzan_T on defense via nucleotide depletion !

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@AudeBer

1 year

The places science takes us to... Discovering the wonderful @banffcentre , nature, art and for me science in breathtaking landscapes. Fantastic conditions to discuss "The Mathematics of Microbial Evolution".

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@AudeBer

2 years

The amount of biology in this study is just mindblowing. When i saw the last figure, i was just speechless. It's really rare to use molecular genetics to answer scientific questions in such a general way (usually use genomics for that). Big big congrats 👏

Avigail Stokar-Avihail

@AAvihail

2 years

I am beyond excited to share with you the study I have been working on @SorekLab for the last few years 🥂 🎺Discovery of phage determinants that confer sensitivity to bacterial immune systems🎺 Posted now on bioRxiv. See 🧵below

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@AudeBer

4 years

@Soreklab , our story with viperins started reading that paper and thinking « how cool would it be if such things existed in bacteria ». So we looked in 40 000 bacterial genomes , and to our big surprise we did find bacterial homologs of the human viperin. We named them pVips.

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@AudeBer

2 years

What a great introduction to the phage field by @smoineau @VoM_2022 . I love how diverse the projects are: from fundamental biology to outreach and applying scientific findings to key society issue like antibiotics in poultry. A true inspiration for all of us phage biologsts ❤️🙏

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@AudeBer

4 years

Viperin is an important immune protein in animals. In humans, it has broad antiviral activity against DNA and RNA viruses. In 2018, this great paper showed that viperin inhibits the replication of viruses by producing ddhCTP, an RNA chain terminator.

A naturally occurring antiviral ribonucleotide encoded by the human genome

Nature - Viperin inhibits the replication of various viruses by catalysing the conversion of CTP to ddhCTP, which is a unique nucleotide that functions as replication-chain terminator of...

www.nature.com

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@AudeBer

4 years

Several compounds discovered in this study are currently being tested on human viruses ! Our results show that anti-phage systems could be the source of novel anti-viral molecules. Maybe pVips are one of many systems which produce anti-viral molecules. Let’s catch some more.

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@AudeBer

2 years

Great thread about Daisy Roulland-Dussoix and discovery of restriction enzymes. I always mention her alongside the nobel laureates for this discovery in my lectures. So cool to have fantastic women scientist in the beginning of the history of anti phage systems!

Marc Somssich

@somssichm

2 years

Do you know Daisy Roulland-Dussoix? She is one of the discoverers of restriction enzymes, who’s findings paved the way for the development of recombinant DNA and cloning technologies. Accordingly, the finding was rewarded with a #NobelPrize . But the prize didn’t go to her... 🧵👇

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@AudeBer

1 year

We got invited to participate to a cool meeting last fall on "Understanding and predicting Microbial evolutionary dynamics" by the Microbiology Society. Here's our contribution taking a deep look at Actinobacterial anti-viral arsenals :). All the code used is online. 👏 @HGeorjon

MDMLab

@MDMlab_Paris

1 year

We are excited to share our latest preprint on the genomic characterization of the anti-phage arsenal of Actinobacteria, where we reveal unique characteristics of this overlooked phylum (for instance, the absence of 1/3 of known defense systems 🤯) (1/9)

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@AudeBer

7 months

Twice in one week (and a first for me), I gave talks in human immunology meetings. Was quite intimidating to be so far away from my beloved bacteria, but I learned tons 😀. Humbling, instructive, and fun to be lost. Thanks @v_hornung for the challenge!

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@AudeBer

5 years

A French gaming community just raised 3.5 millions euros over one week end for the Pasteur Institute. World record for such type of initiative. WOW. Such type of solidarity is just incredible.

Emmanuel Macron

@EmmanuelMacron

5 years

55 gameurs français viennent de lever le temps d’un week-end plus de 3 millions d’euros au profit de l’institut Pasteur. Vous êtes inspirants et vous nous démontrez que tout est possible pour soutenir une cause pour laquelle on croit. Bravo #ZEvent2019 !

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@AudeBer

3 years

Very nice commentary on our work on viperins!

Cell Host & Microbe

@cellhostmicrobe

3 years

Unearthing Ancient Origins of Antiviral Immunity: Can microbes provide clues about origin of #pathogen defenses? @bioBarber &Baker discuss @SorekLab findings that mammalian #antiviral protein viperin is more ancient & conserved than previously appreciated

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@AudeBer

9 months

After a fascinating first edition in Israel in 2023, the symposium on the immune systems of bacteria is back. April 16-18 2024 in Boston. Save the date!

Sorek Lab

@SorekLab

9 months

I can't wait for the 2024 symposium on the "beyond CRISPR" immune system of bacteria, which will take place in Boston on April 16-18, 2024. Save the date!

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@AudeBer

7 months

Beautiful week for anti-phage defense displaying similarities with eukaryotic enzymes with two wonderful preprints with awesome structures. SPARTA / Agos by @DCSwarts @MartinJinek labs Ubiquitination pathway by @_KevinCorbett lab

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@AudeBer

7 months

Anyone into bacterial genetics? This work pinpoints the role of RNA-guided nucleases in "biasing the selfish inheritance of transposable elements". Molecular mechanism for selfishness? Yes, and done so with cool bioinformatics, RNA seq on an exotic bacteria and lacZ assays...!

Sam Sternberg

@shsternberg

7 months

Thrilled to see our latest work published this week, on the essential roles of IscB/TnpB -- ancestral homologs of Cas9/Cas12 -- in transposon maintenance & spread. A wonderful team effort led by the talented Chance Meers! Thread on bioRxiv version below...

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@AudeBer

2 years

With both wonderful talks from @dbikard and @PeterFineran , clear that complex multiple lines of defense are common in bacteria and constitutes a fantastic avenue to study. On average, bacteria have 7 antiphage syst. Imagine all the crazy molecular mechanisms out there❤️. #VoM2022

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@AudeBer

2 years

A masterpiece review. Clearly will give a lot of us a lot to think about in the coming years! Exciting science ahead in that direction

Sorek Lab

@SorekLab

2 years

Bacterial origins of human innate immune mechanisms Tanita Wein skillfully summarized current knowledge on how key components our own immune system evolved from bacterial anti-phage defenses Out today in Nature Reviews Immunology

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@AudeBer

5 years

Contrats to @AdiMillman for the prize of best talk #EESMicrobiology . So well deserved but I am not surprised. :)

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@AudeBer

5 years

Welcome to CBASS : a new widespread defense system agaunst phages based on cGAMP signalling discovered by @SorekLab . One prokaryote ancestor of human immune system!

Sorek Lab

@SorekLab

5 years

On the origin of immunity Remarkable similarities between human and bacterial immune systems. Cyclic GMP–AMP signalling protects bacteria against viral infection Congrats CBASS team! Daniel Cohen @AdiMillman @GilAmitai @shany_doron #cGAS - #STING

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@AudeBer

1 year

It's out!!!! This is an instant classic that everyone interested in phage bacteria interactions (or generally Microbiology) should read. Congrats again :) .

Avigail Stokar-Avihail

@AAvihail

1 year

I am excited to share with you the final version of my work @SorekLab studying 💠How bacterial immune systems sense phage infection💠 Published now in @CellCellPress 🍻 See thread below for a recap and highlights added during the review process ⬇️ 1/11

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@AudeBer

3 years

Turns out, viperins have friends! This wonderful paper describes the discovery of novel anti-viral enzymes playing with nucleotides that are shared by bacteria and eukaryotes. A completely novel mechanism of anti-viral defense in bacteria. Congrats @Nitzan_T et al.

Nitzan Tal

@Nitzan_T

3 years

I'm excited to share my new preprint on how bacteria use ✨nucleotide depletion✨ as an amazing new anti-phage defense mechanism conserved between prokaryotes and eukaryotes! Graphical abstract and thread below! >>>

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@AudeBer

5 years

Importing French traditions to the @SorekLab . New queens for the day and a phage "galette des rois. :)

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@AudeBer

3 months

Super cool findings on minimalist phage satellites. Minimal and still encode defense systems!! Both satellites and defense systems worlds are expanding ++. So much to discover by exploring natural populations.

Frédérique Le Roux

@FredoLeRoux

3 months

Happy to share our first paper on the PICMI family, a minimalist type of phage satellites that are widely distributed among the Vibrionaceae! 🎉 Congratulation to @rubarcia , @dooguy , @doctor_jams , @piel_damien , @MarboutM and @epcrocha for this great collab!

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@AudeBer

4 years

A huge thanks to all the people who helped this fantastic scientific adventure and in particular R. Sorek for the guidance, freedom, creativity @AdiMillman the magician bioinformatician @gaofir and @GilAmitai for the crazy brainstorms and @HelenaShomar for the bioenginnering.

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@AudeBer

1 year

Fantastic findings ! Absolutely convinced that studying immune systems through domains will allow to illuminate the molecular complexity of antiphage system in a much faster way thanks to their modularity. Very powerful to understand anti viral immunity across domains of life.

François Rousset

@FrancoisRousset

1 year

I’m very excited to share the first results of my postdoc @SorekLab 🥳🤩🚨 We report a new family of immune effectors that is conserved across the tree of life.

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@AudeBer

2 months

👋🚨 Only a few days AND a few spots left to register to the 2024 symposium on the immune system of bacteria. If you have not registered yet, now is the time!

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@AudeBer

2 years

Wonderful project that led to so many discoveries, scientific discussions and adventures. It was eye opening for me, how to explore such a vast space uncovered by @AdiMillman analysis. Learned so much from @SorekLab on how to navigate the unknown. Science fun +++ 🤩🧫🧬

Adi Millman

@AdiMillman

2 years

OK. I’ve been waiting for this moment for a while… 🤗🫣🥳 Excited to share our new preprint where we discover 21 new anti-phage systems: "An expanding arsenal of immune systems that protect bacteria from phages" @SorekLab 1/7

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@AudeBer

1 year

I'm not a biochemist, but the first session of #ISB2023 just BLEW my mind. Crazy structures, crazy cool mechanisms and such beautiful slides. Congrats to all speakers

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@AudeBer

4 years

Using a phylogenetic analysis, we show the eukaryotic viperin has originated from a clade of prokaryotic viperins. So we tried and cloned the human viperin in E. coli, the human gene protected against bacterial viruses ! (4/9)

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@AudeBer

6 years

New version of CRISPRFinder. CRISPRCasFinder, an update of CRISRFinder, includes a portable version, enhanced performance and integrates search for Cas proteins. Paper here . Website there .

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@AudeBer

2 years

If you still have not read that one, it's really a fantastic paper.

Cell Host & Microbe

@cellhostmicrobe

2 years

Bacteriostatic antibiotics promote CRISPR-Cas immunity: @TatianaDimitriu @edzewestra find bacteriostatic #antibiotics promote #CRISPR -Cas immunity by slowing #phage replication. Delayed phage production allows cells to acquire spacers against phages

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@AudeBer

4 years

So i have a doppelganger in the world. My (twin) sister @SegoleneBer just joined Twitter! She's a cardiopediatrician, currently taking some time to follow another passion: doing a PhD in embryology @InstitutImagine @institutpasteur ! Clearly a badass #WomenInSTEM to follow :).

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@AudeBer

4 years

Finally, we developed a genetic reporting system and showed that pVips protect against T7 phage infection by inhibiting viral polymerase-dependent transcription, implying an anti-viral mechanism of action similar to the animal viperin. (7/9)

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@AudeBer

5 years

Last piece of my PhD on bioRxiv :) : about CRISPR-Cas that are not one CRISPR, one Cas. We found preferential associations between subtypes, complex loci with several interference modules but only one adaptation one. Also cool stuff on CRISPR on MGE.

Co-occurrence of multiple CRISPRs and cas clusters suggests epistatic interactions

Prokaryotes use CRISPR-Cas for adaptive immunity, but the reasons for the existence of multiple CRISPR and cas clusters remain poorly understood. We found that more than 40% of the genomes encoding a...

www.biorxiv.org

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@AudeBer

6 years

So happy to have been awarded a long term @EMBO fellowship !!!! Thanks bacteria and phages for keeping on fighting :) #EMBOFellows

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@AudeBer

2 years

So many great papers this week on anti phage systems. Also that one was a great preprint!

PLOS Biology

@PLOSBiology

2 years

Many bacterial & archaeal defense systems are encoded by mobile genetic elements. @eprocha & @dbikard argue that this challenges our ideas of their role in cells: Who's defending? From what? And what's the role of the cellular genome in this? #PLOSBiology

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@AudeBer

3 years

Happy to had the chance to contribute to this awesome discovery of @FrancoisRousset @dbikard with @epcrocha Prophages encode hotspots of diversity full of antiphage systems. Paves the way for a new method to uncover novel antiphage systems and opens many evolutionnary questions.

François Rousset

@FrancoisRousset

3 years

I am very excited to share our new preprint! 🤩 We report the presence of reservoirs of anti-phage systems in genomic hotspots encoded on prophages! The story behind this incidental discovery 👇

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@AudeBer

11 months

Wonderful study. I love how studying some specific weird bacteria that someone sequenced for completely different purposes ends up providing the operons that generate such a cool discovery. ❤ microbial genomics. Also awesome (and surprising?)that they work against coliphages! 👏

Tanita Wein

@TanaWein

11 months

I am beyond excited to share our new preprint!🤩 We find that CARD domains are an ancient component of innate immune systems conserved from bacteria to human, and that they are essential for gasdermin-mediated defense in bacteria! @SorekLab Kranzusch lab

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@AudeBer

4 years

Our results suggest that pVips produce new types of anti-viral molecules which, to the best of our knowledge, were not observed before in nature. @HelenaShomar , N. Tal and M. Rosenberg from Pantheon Biosc. purified some pVips and confirmed these results in vitro. (6/9)

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@AudeBer

3 years

Very excited to talk there next thursday. Don't hesitate to register, it's free, and the sessions of VEGA21 have been fascinating up to now.

Integrated Microbial Genomes & Microbiomes (IMG/M)

@IMG_DATA

3 years

May 6 at #JGI21VEGA , hear from @AudeBer @Inserm @IAME_Center and @RachelJWhitaker @Illinois_Alma during our @jgi VEGA Symposium: " #Virus -Host Molecular Warfare" session. Details and registration:

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@AudeBer

8 months

A beautiful new anti-phage mechanism uncovered thanks to elegant experimental set ups. Exciting to wonder if eukaryotic homologs function the same way.

Sorek Lab

@SorekLab

8 months

Proud to share our latest discovery: Bacteria conjugate ubiquitin-like proteins to interfere with phage assembly A new concept in antiphage immunity, and a mechanism for ISG15-like antiviral defnese in bacteria. Big congrats to talented @Jens_Hoer ! A 🧵

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