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Amar Deep

@amardeeep.bsky.social
267 followers 272 following 15 posts

Structural biologist interested in microbial defense and anti-defense strategies! scholar.google.com/citations?hl=en&…

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Kranzusch Lab @kranzuschlab.bsky.social · 01/10/2026
Our story with @hobbslabutah.bsky.social discovering CBASS sensing of phage proteases out now in @science.org New data include CBASS recognition of diverse proteases beyond T4, and verifying CD-NTase activation loop cleavage as the trigger for defense in vivo www.science.org/doi/10.1126/...
science.org
Phage proteases activate CBASS antiphage immunity
Cyclic oligonucleotide–based antiphage signaling systems (CBASS) are bacterial immune pathways evolutionarily related to cGAS-STING (cyclic GMP-AMP synthase–stimulator of interferon genes) in humans. ...
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Alexander Harms @aharms485.bsky.social · 25/09/2026
The final version of our manuscript on TnSeq in bacteriophages (“HIDEN-SEQ”) is out today – if you have an interesting phage phenotype and want to know the underlying genetic basis, this one is for you! 1/4
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François Rousset @francoisrousset.bsky.social · 08/09/2026
🚨 We are excited to share the first preprint of our lab ! We discovered an NADase enzymatic domain in bacterial immunity and in the human protein TEP1. www.biorxiv.org/content/10.6...
biorxiv.org
A widespread NADase domain links bacterial immunity with human TEP1
Recent discoveries on bacterial immunity have revealed that several protein domains involved in anti-phage defense are conserved in eukaryotes, such as SIRim, TIR, PNP and gasdermin. Bacterial immune ...
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Max Jordan @maxljordan.bsky.social · 04/09/2026
Really excited to share our new manuscript on how the #NLR protein #AfsR regulates #Streptomyces antibiotic production - and how we can use its similarity to plant NLR immune receptors to enhance this production! 📄🧵 (1/17) @johninnescentre.bsky.social www.biorxiv.org/content/10.6...
biorxiv.org
A conserved NLR activation switch governs global transcriptional control of antibiotic biosynthesis in Streptomyces
Nucleotide-binding and oligomerization domain-like receptors (NLRs) are conserved molecular switches that regulate innate immunity across diverse domains of life. While best known for their roles in i...
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Amar Deep @amardeeep.bsky.social · 03/09/2026
Congratulations, Jack.
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Structura Biotechnology @structurabio.bsky.social · 25/08/2026
📽️ Did you miss our talk at the Spring CCP-EM Symposium 2026? You can now watch the full talk from Structura, where we share some of the latest and upcoming developments in #CryoSPARC and single-particle #cryoEM: Check out the full talk here 👇 www.youtube.com/watch?v=Rilg...
youtube.com
New Developments for Single Particle Cryo-EM Data Processing in CryoSPARC | Ali Punjani (Structura)
YouTube video by CCP-EM
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Sofia Luengo-Woods @sluengo.bsky.social · 30/07/2026
We’re so excited to share our new paper, where we tackle the wealth of structural and functional diversity of anti-phage sensors across bacteria (1/6)
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Vivek Mutalik @vivekmutalik.bsky.social · 25/07/2026
New Preprint 🥳 Here we wondered how phages that have been extensively studied in laboratory E. coli strains actually behave when they encounter a real pathogen such as O157:H7 strain...one with a far more complex cell surface & one of the most consequential foodborne pathogens in the United States.
static.klipy.com
Animated E. coli Bacteria Drawing
Alt: Animated E. coli Bacteria Drawing
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Aude Bernheim @audeber.bsky.social · 21/07/2026
Out @cp-cellhostmicrobe.bsky.social, natural products meet bacterial immunity! We used genomics to identify lanthivirins: a family of >2,000 lanthipeptide BGCs that protect Actinobacteria against phages. Led by @hshomar.bsky.social & @mariegllm.bsky.social www.sciencedirect.com/science/arti...
sciencedirect.com
A family of lanthipeptides with anti-phage function
Bacteria produce natural products to adapt to their environments, with phage interactions as major ecological and evolutionary drivers. While some nat…
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Sorek Lab @soreklab.bsky.social · 09/07/2026
Our paper out in Science today: The Metis defense system senses molecular byproducts released when a phage degrades the bacterial genome, and then prevents replication of the phage in the infected cell Congratulations @ostermanilya.bsky.social and co-authors!
science.org
Bacteria sense virus-induced genome degradation via methylated mononucleotides
Phages often degrade the genome of their bacterial host to individual nucleotides. Here we describe Metis, a bacterial defense system that directly senses phage-mediated host genome degradation. Metis...
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Kevin Forsberg @kvnforsberg.bsky.social · 02/07/2026
Humans and bacteria share strategies to defend against viruses. We wondered: could they use each other's genes? Yes, both can! Bacteria can use human immune genes to defend against phages AND Human cells can use bacterial genes for viral defense. www.biorxiv.org/content/10.6...
biorxiv.org
Bacterial and human exonucleases mediate interkingdom antiviral immunity
All kingdoms of life have developed strategies to limit viral infection. In humans, interferons induce a suite of antiviral factors that collectively provide immunity. Some human immune genes are homo...
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The EMBO Journal @embojournal.org · 10/06/2026
CapK is a bacterial DNA damage-activated kinase that phosphorylates transcriptional repressor CapS to control adjacently-encoded anti-phage immune pathway genes in response to a universal stress signal, DNA damage @kevincorbett.bsky.social and colleagues link.springer.com/article/10.1...
link.springer.com
A DNA damage-activated kinase phosphorylates a transcriptional repressor to control bacterial immune pathway expression - The EMBO Journal
Bacteria encode numerous stress-response pathways that protect their hosts against both internal and external threats. A key question is how these pathways are regulated, especially anti-phage immune ...
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Kranzusch Lab @kranzuschlab.bsky.social · 12/06/2026
How do human cells defend against viruses? @sgfern.bsky.social discovers that human immune proteins named ISGs target ancient features of replication shared between animal and bacterial viruses – opening analysis of human immunity to the power of bacterial genetics www.biorxiv.org/content/10.6...
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Aude Bernheim @audeber.bsky.social · 22/05/2026
Great piece and cover @science.org about how our field is uncovering the evolutionary and mechanistic connections between bacterial and eukaryotic immunity ! www.science.org/content/article/ancient-wars-between-microbes-gave-us-key-immune-defenses
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Amar Deep @amardeeep.bsky.social · 15/05/2026
Very nice work, congrats, Luuk!
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Amar Deep @amardeeep.bsky.social · 05/05/2026
Thrilled to have contributed to this work, co-led with Laurel and Emily. We show that a single immune protein binds MULTIPLE PAMPs and block phage infection. Check out Laurel’s thread for more details—
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Kranzusch Lab @kranzuschlab.bsky.social · 27/04/2026
Congratulations to @aragucci.bsky.social and @sadieantine.bsky.social for their nuclease-NTPase work now online in final form at @natmicrobiol.nature.com www.nature.com/articles/s41...
nature.com
Nuclease–NTPase antiphage defence systems use conserved molecular features to control bacterial immunity - Nature Microbiology
A large-scale, comparative cell biology and biochemical screen defines the molecular features controlling antiphage defence systems that encode nuclease effectors and accessory NTPase proteins.
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Kenneth Loi @kenjmloi.bsky.social · 27/04/2026
Excited to share our discovery of a new programmable RNA-guided DNA-targeting system hiding inside bacteriophages that predates CRISPR. We call it VIPR (Viral Interference Programmable Repeat), and it uses an entirely new logic to find its targets. Thread + link below.
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David Bikard @dbikard.bsky.social · 17/04/2026
Very proud of this work and all the efforts from my team and collaborators on this! You can now use DGRs for in vivo targeted hypermutagenesis in E. coli. We also included some early proof of concept in Yeast thanks to @seth-shipman.bsky.social !
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Kevin Corbett @kevincorbett.bsky.social · 11/04/2026
Congrats to Chase Morgan @phagemorgan.bsky.social and the phage team!
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Chase Morgan @phagemorgan.bsky.social · 11/04/2026
Want to highlight parallel work too from @aharms485.bsky.social lab that pulled AdfM out of a phage genome screen and independently named it the same! www.biorxiv.org/content/10.1...
biorxiv.org
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Amar Deep @amardeeep.bsky.social · 11/04/2026
Happy to have contributed to this work, @kevincorbett.bsky.social
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Aude Bernheim @audeber.bsky.social · 02/04/2026
How diverse is bacterial immunity ? We report in @science.org how language models allowed us to predict 2.4M antiphage proteins spanning >23K novel potential systems. 👏 @emordret.bsky.social, @alexhv.bsky.social & al doi.org/10.1126/scie... Explore them here defensefinder.mdmlab.fr/wiki/refseq_...
science.org
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Amar Deep @amardeeep.bsky.social · 03/04/2026
Congrats Peter!
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Uday Tak @nokaryote.bsky.social · 27/03/2026
Happy to share the final version of my postdoc work on bacterial CBASS immunity with @aaronwhiteley.bsky.social published in @cp-cellhostmicrobe.bsky.social www.cell.com/cell-host-mi...
cell.com
Bacterial 2′,3′-cGAMP activates a SAVED effector to form membrane-disrupting filaments and restrict phage replication
Tak et al. discover that bacteria use 2′,3′-cGAMP, the same signaling molecule employed by mammalian cGAS-STING, for phage defense. In response to phage, 2′,3′-cGAMP activates filament formation of Ca...
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Jens Hör @jenshoer.bsky.social · 21/03/2026
Excited to share the first preprint from the lab! We show that ApeA defends against RNA phage infection by cleaving the phage genome: www.biorxiv.org/content/10.6...
biorxiv.org
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Artem Nemudryi @artemnemudryi.bsky.social · 09/03/2026
Our work on bacterial Schlafens in phage defense is out today @natmicrobiol.nature.com! Check out the final version here: rdcu.be/e7Bmz We are looking for postdocs and students to expand our team! Official postings are coming soon. Please reach out if you're interested! #phage #phagesky #microsky
rdcu.be
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.
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Kranzusch Lab @kranzuschlab.bsky.social · 06/03/2026
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...
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Nitzan Tal @nitzantal.bsky.social · 06/03/2026
Very excited to see this work out today! Discovering viral immune antagonists directly from predicted protein structures. 🤩 www.science.org/doi/10.1126/... Huge thanks to the amazing collaborators! 🤗
science.org
Structural modeling reveals phage proteins that manipulate bacterial immune signaling
Immune systems in animals, plants, and bacteria often rely on intracellular nucleotide signaling, which viruses can block by sequestering or degrading these signals. We identified structural and bioph...
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Sorek Lab @soreklab.bsky.social · 05/03/2026
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
science.org
Structural modeling reveals phage proteins that manipulate bacterial immune signaling
Immune systems in animals, plants, and bacteria often rely on intracellular nucleotide signaling, which viruses can block by sequestering or degrading these signals. We identified structural and bioph...
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Kranzusch Lab @kranzuschlab.bsky.social · 03/03/2026
Stunning new structural analysis and mechanism for Tmn anti-phage defense by @fnobrega.bsky.social www.biorxiv.org/content/10.6...
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Max Fels @mfels.bsky.social · 17/02/2026
The giant viruses surprised us at almost every turn of this project, but ultimately led us down a very rewarding path. Happy to share this work is now available online 🧪
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Eugene Kim Lab @eugenekimlab.bsky.social · 04/02/2026
How is Condensin II activated during mitosis? 🧬 @damlatetiker.bsky.social Samejima et al. uncover how Condensin II autoinhibition is relieved by the mitotic activator M18BP1, and reveal that M18BP1 also forms a composite DNA anchor with the NCAPG2–NCAPH2 subcomplex to stabilize DNA loops in vitro.
biorxiv.org
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bioRxiv Microbiology @biorxiv-microbiol.bsky.social · 04/02/2026
A DNA damage-activated kinase controls bacterial immune pathway expression www.biorxiv.org/content/10.64898/20…
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Admirable Women @admirablewomen.bsky.social · 26/01/2026
Jane Richardson was born #OTD in 1941 + Developed the Richardson (ribbon) diagram to represent proteins' 3D structure (becoming a standard representation for protein structures) + MacArthur Fellow, 1985 + Elected, Nat'l Academy of Sciences, 1991 + President, Biophysical Society, 2012 #WomenInSTEM
Vibrant color portrait of Jane S. Richardson, the visionary biophysicist and artist who revolutionized structural biology with her invention of ribbon diagrams. She gazes warmly at the camera with a bright, knowing smile that radiates quiet brilliance and decades of curiosity. Her silver-blonde hair woven with gentle waves. Large, elegant dangling earrings catch the light, and she wears a richly patterned brown blouse embroidered with intricate turquoise paisley motifs and delicate beadwork that echoes the molecular elegance she has spent her life depicting. Behind her floats a luminous, dreamlike backdrop of glowing molecular structures--interlocking hexagonal and ribbon-like forms in electric blues, teals, and greens--blending science and art in a single, living canvas.Hand-drawn and hand-colored (by Jane Richardson) scientific artwork known as a Richardson ribbon diagram (or “ribbon model”), one of the iconic visual inventions of Jane Richardson that transformed the way we see and understand protein structures. A graceful, three-dimensional tangle of protein backbone ribbons twists and spirals through space, rendered in soft pencil lines and luminous watercolor hues. Smooth golden-brown coils represent α-helices that curl like elegant ribbons, while broad teal-green arrows trace the flat, pleated strands of β-sheets slicing through the molecule with directional purpose. Thin, looping golden threads connect the secondary structures, creating a delicate, almost dance-like choreography of biology’s hidden architecture. The entire form is framed by a simple olive-green mat and dark border, giving the drawing the quiet dignity of both fine art and precise scientific illustration—a timeless bridge between molecular reality and human imagination.
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Malcolm White @mfwhite2.bsky.social · 14/01/2026
Pleased to announce that I've joined the editorial board of the Biochemical Journal portlandpress.com/biochemj as an associate editor. I'd love to receive manuscripts focussed on CRISPR, anti-viral defence, archaean biochemistry and nucleic acid processing enzymes. @biochemsoc.bsky.social
portlandpress.com
Biochemical Journal | Portland Press
Exploring the molecular mechanisms that underpin key biological processes, the Biochemical Journal is a leading bioscience journal publishing high-impact scientific research papers and reviews in the ...
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Kevin Corbett @kevincorbett.bsky.social · 30/12/2025
Congratulations to Doi Basu @dwaipayanbasu.bsky.social for publishing his first first-author paper from the lab! The cryoEM structure of a tubulin-like protein from bacteriophage Goslar forms "microtubules" with nine protofilaments! authors.elsevier.com/a/1mM253SNvc...
authors.elsevier.com
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Amar Deep @amardeeep.bsky.social · 30/12/2025
Congrats Doi and Kevin!
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Tung Le @tunglejic.bsky.social · 04/12/2025
Now published. Thank you very much to our collaborative team, and very supportive editors and reviewers!!! www.pnas.org/doi/10.1073/...
pnas.org
Versatile NTP recognition and domain fusions expand the functional repertoire of the ParB-CTPase fold beyond chromosome segregation | PNAS
Nucleotide triphosphate (NTP)-dependent molecular switches regulate essential cellular processes by cycling between active and inactive states thro...
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Sorek Lab @soreklab.bsky.social · 04/12/2025
Preprint: Systematic discovery of TIR-based immune signaling systems in bacteria Conservation of TIR-derived signals accross the tree of life! We found bacterial TIR immune systems that signal via canonical cADPR (like in humans) and 2'cADPR (a plant immune signal). Documented 11 Thoeris types
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Erez Yirmiya @erezyirmiya.bsky.social · 04/12/2025
I’m happy to share our new preprint! We uncovered the full diversity of bacterial TIR-based antiviral immune signaling, massively expanded the known diversity of Thoeris systems, and revealed conservation of TIR-derived immune signals across the tree of life. www.biorxiv.org/content/10.6...
biorxiv.org
Systematic discovery of TIR-based immune signaling systems in bacteria
Toll/interleukin-1 receptor (TIR) domains are important for immune signaling across humans, plants and bacteria. These domains were recently found to produce immune signaling molecules in plant immuni...
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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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Alexander Harms @aharms485.bsky.social · 20/11/2025
🚨Preprint alert - this is a big one! We transfer the revolutionary power of TnSeq to bacteriophages. Our HIDEN-SEQ links the "dark matter" genes of your favorite phage to any selectable phenotype, guiding the path from fun observations to molecular mechanisms. A thread 1/8
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Osterman Ilya @ostermanilya.bsky.social · 06/11/2025
Bacteria can sense when a virus starts shredding their genome — by detecting methylated mononucleotides. Here’s the story of how we discovered the Metis defense system 👇 www.biorxiv.org/content/10.1...
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Amar Deep @amardeeep.bsky.social · 07/11/2025
Very cool findings!!!
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Kranzusch Lab @kranzuschlab.bsky.social · 25/09/2025
You’ve heard of ubiquitination, meet deazaguanylation: Doug Wassarman in our lab discovered phage defense pathways have co-opted Q nucleobase biosynthetic enzymes to catalyze a new form of protein conjugation chemistry @science.org www.science.org/doi/10.1126/...
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Amar Deep @amardeeep.bsky.social · 04/09/2025
Another important contribution from Sorek and Blokesch labs. This engineering strategy with synthetic inhibitors could yield more powerful phages than natural inhibitors, since the latter sometimes trigger other defense systems..
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Kranzusch Lab @kranzuschlab.bsky.social · 22/08/2025
The beautiful, ever-expanding universe of viral proteins targeting nucleotide immune signals! Paper by @reneechang.bsky.social in @cp-molcell.bsky.social on a nucleotide sponge www.cell.com/molecular-ce... and preprint by @doudna-lab.bsky.social on viral nucleases www.biorxiv.org/content/10.1...
cell.com
A widespread family of viral sponge proteins reveals specific inhibition of nucleotide signals in anti-phage defense
Chang et al. discover anti-CBASS 4 (Acb4), a family of viral sponges that inhibits bacterial immunity by sequestering nucleotide immune signals. Acb4 homologs in phages that infect hosts across all ma...
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Current Research in Microbial Sciences @microbesinfect.bsky.social · 22/08/2025
A widespread family of viral sponge proteins reveals specific inhibition of nucleotide signals in anti- #phage defense www.cell.com/molecular-ce... #bacteriophage #MicroSky
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Sorek Lab @soreklab.bsky.social · 30/07/2025
We wrote a review on the free nucleotide pool as a central playground in human, bacterial, and plant immunity – now out in Nature Reviews in Immunology www.nature.com/articles/s41... Was fun to write this piece with Dina Hochhauser! Here is a thread to explain the premises 1/
nature.com
Manipulation of the nucleotide pool in human, bacterial and plant immunity - Nature Reviews Immunology
Modification of the nucleotide pool is emerging as key to innate immunity in animals, plants and bacteria. This Review explains how immune pathways conserved from bacteria to humans manipulate the nuc...
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