iiinova — where your digital self keeps evolving

Reposted by Miguel López Rivera

Rafael Pinilla-Redondo (Rafa) @rafomics.bsky.social · 14/10/2026

Retron biology keeps surprising us. Type VI does things VERY differently! 🧬 Check the paper to see how it works👇 Fun working with the @seth-shipman.bsky.social lab on this story!

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Reposted by Miguel López Rivera

Luis E. Valentin-Alvarado @luisvalentin.bsky.social · 09/10/2026

Excited to share our work on bacterial immune signaling! Our preprint reveals how RNA-guided Cas13 cleaves host tRNAs to generate small-molecule messengers that activate 2TMβ, linking RNA recognition to membrane damage and phage defense. 1/11

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Reposted by Miguel López Rivera

David Parker @dr-dparker.bsky.social · 06/10/2026

Check out my preprint! We uncovered a neat story about the little understood story of hijacking transcription by phage D29! Super excited and grateful to work with everyone involved in this project.

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Reposted by Miguel López Rivera

Saria McKeithen-Mead, PhD @sciria.bsky.social · 05/10/2026

Pleased to share my first preprint from my postdoc, where I ask what drives mobile DNA movement between bacterial cells in complex communities like the gut microbiome. To answer this, we built a way to capture mobile DNA in the act of moving between cells, using short-read metagenomics. 🧵

doi.org

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Reposted by Miguel López Rivera

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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Reposted by Miguel López Rivera

Dorentina Humolli @humollidorentina.bsky.social · 25/09/2026

Very happy to share that HIDEN-SEQ is now out in @natmicrobiol.nature.com! Using this technique, we recapitulated decades of established phage genetics and uncovered new gene functions, including previously unknown anti-defense factors against several defense systems. www.nature.com/articles/s41...

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Reposted by Miguel López Rivera

Malcolm White @mfwhite2.bsky.social · 16/09/2026

Our paper on type II Panoptes is now published at PLOS Biology with new data on phage escapers - quite a step up in microbiology for our lab, led by Sabine Gruschow. Thanks to @erc.europa.eu for funding dx.plos.org/10.1371/jour...

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Reposted by Miguel López Rivera

Nonia Pariente @npariente.bsky.social · 12/09/2026

We’re reposting some trending articles from our recent past, for those that may have missed them. Below is an excellent resource from @aharms485.bsky.social lab expanding the BASEL phage collection 🧪#ViroSky #Microsky

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Reposted by Miguel López Rivera

Kranzusch Lab @kranzuschlab.bsky.social · 02/09/2026

Discovery of chimeric RNAs and thousands of new proteins in mammalian cells – including a new regulator of inflammasome signaling! www.nature.com/articles/s41... www.jacksonimmunology.com

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Reposted by Miguel López Rivera

Del Mármol lab @delmarmollab.bsky.social · 25/08/2026

Can we design molecules that rewrite how organisms interact with the environment? I'm delighted to share our lab's latest work, where we use structural biology and chemistry to modulate insect behavior in a clade of destructive agricultural pests. Congrats Steve and team!

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Reposted by Miguel López Rivera

Abraham lab at Harvard Medical School @abrahamlabhms.bsky.social · 30/07/2026

We are excited to share two preprints reporting a mosquito-specific receptor for chikungunya virus and other alphaviruses! 🤩 www.biorxiv.org/content/10.6... www.biorxiv.org/content/10.6... @harvardmicro.bsky.social @harvardvirology.bsky.social @hhmi-science.bsky.social

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Rafael Pinilla-Redondo (Rafa) @rafomics.bsky.social · 16/07/2026

1/10 🚨Preprint! One RING to rule them all (phages)👑💍⚔️ Bacteria build giant DNA-scaffolded RNase rings (larger than the ribosome!) to shut down viral infection🧬🧵👇 biorxiv.org/content/10.6...

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Reposted by Miguel López Rivera

Kranzusch Lab @kranzuschlab.bsky.social · 15/07/2026

One of the coolest structures presented at the recent SISB2026 meeting, great to see this story from @rafomics.bsky.social and @guillermo-montoya.bsky.social on a giant retron ring-shaped assembly now out: www.biorxiv.org/content/10.6...

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Reposted by Miguel López Rivera

anna brogan @apbrogan.bsky.social · 23/06/2026

Another chapter of my thesis is out! We asked whether we could pair proteome-wide AlphaFold screening with Tn-seq to identify biologically relevant protein-protein interactions. We identify ClcR (formerly YerH) as a component of the Rod complex in Gram-positive bacteria. www.pnas.org/doi/10.1073/...

pnas.org

A broadly conserved gram-positive lipoprotein regulates cell elongation | PNAS

The cell wall peptidoglycan (PG) protects virtually all bacteria from osmotic lysis and specifies cell shape. Synthesis of this exoskeleton is carr...

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Reposted by Miguel López Rivera

Nonia Pariente @npariente.bsky.social · 20/06/2026

Spanish government launches a plan to study women’s health, which has been so neglected 👏🏼👏🏼 El gobierno lanza un plan para apoyar la investigación sobre la salud de la mujer, tan abandonada hasta ahora elpais.com/salud-y-bien...

elpais.com

El Gobierno lanza un plan para que la ciencia también se interese por investigar en salud de la mujer

El Ejecutivo propone triplicar la inversión en I+D para atajar la brecha de género y reservar fondos para proyectos centrados en dolencias infraestudiadas en ellas

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Reposted by Miguel López Rivera

Science Magazine @science.org · 19/06/2026

Researchers in 2023 uncovered the lineage and legacy—including more than 40,000 living relatives—of free and enslaved African Americans who labored at the Catoctin Furnace in Maryland, between 1774 and 1850. Learn more on #Juneteenth: scim.ag/4aBMT27

DNA was sequenced from 27 African Americans buried at Catoctin Furnace, Maryland, where enslaved people labored between 1774 and 1850. The tree trunk forms a double helix comprising 27 segments representing each sequenced individual. Chromosome-shaped leaves signify their 41,799 detected modern relatives. At the roots are the names of 271 enslaved Catoctin Furnace workers. Combining historical DNA with direct-to-consumer ancestry testing can recover lost roots. Illustration: Oliver Uberti

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Reposted by Miguel López Rivera

Sorek Lab @soreklab.bsky.social · 17/06/2026

Preprint: Plant pathogens cleave 2’cADPR to suppress TIR immune signaling Inspired by knowledge on how phages inhibit bacterial immunity, we now show that disease-causing bacteria inhibit plant immunity in a similar way. A 🧵 www.biorxiv.org/content/10.6...

biorxiv.org

Plant pathogens cleave 2'cADPR to suppress TIR immune signaling

Small molecules produced by TIR (Toll-interleukin-1 receptor) domains are essential for plant immune signaling. A central TIR-derived signal is 2'cADPR, a cyclic ADP-ribose (ADPR) molecule that is gen...

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Miguel López Rivera @riveralopz.bsky.social · 13/06/2026

Oh wow, that is such a great picture! The scientist was me! Haha. I’m so glad I stumbled upon your post on here! :)

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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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Reposted by Miguel López Rivera

Toni Gabaldón @tonigabaldon.bsky.social · 10/06/2026

Our paper "Gene ancestries reveal diverse microbial associations during eukaryogenesis.” is finally out in Nature. Eukaryogenesis was likely a gradual process shaped by multiple microbial partners and virus-mediated gene transfer, rather than a single binary symbiosis. doi.org/10.1038/s415...

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Miguel López Rivera @riveralopz.bsky.social · 09/06/2026

Esta nos la sabemos solo los sabineros de verdad! Jajaja

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Jesse Shapiro @bjesseshapiro.bsky.social · 05/06/2026

Cheap and easy method for nanopore sequencing phage DNA directly from plaques. Proud of lab members Brenna and Patrick for doing this work *with absolutely no help from me* !! www.nature.com/articles/s41...

nature.com

Same-day tagmentation PCR-based whole genome sequencing of bacteriophage genomes from a single plaque without DNA extraction - Scientific Reports

Scientific Reports - Same-day tagmentation PCR-based whole genome sequencing of bacteriophage genomes from a single plaque without DNA extraction

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Reposted by Miguel López Rivera

Martin Steinegger 🇺🇦 @martinsteinegger.bsky.social · 06/06/2026

Folddisco is now published @natbiotech.nature.com. It’s a fast motif search for similar 3D DISCOntinuous residues like catalytic sites or zinc fingers across the entire protein universe. 📄 www.nature.com/articles/s41... 💾 folddisco.foldseek.com 🌐 search.foldseek.com/folddisco

nature.com

Structural motif search across the protein universe with Folddisco - Nature Biotechnology

Folddisco enables protein structural motif search in million scale databases.

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Miguel López Rivera @riveralopz.bsky.social · 29/05/2026

Thank you, Ilya! The NARP1 discovery is one of the coolest phage anti-defense stories out there, so it was exciting to see RyDEP synergize with it. Looking forward to seeing all the metabolism-related immune stories your new lab will put forward!

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Miguel López Rivera @riveralopz.bsky.social · 29/05/2026

Romi, thank you so much for all your help with this project—it was great to finally meet you in person at SISB! 😊

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Kranzusch Lab @kranzuschlab.bsky.social · 29/05/2026

A new function for RyR domains in nucleotide signaling! Excited to share @riveralopz.bsky.social's story at SISB2026 and the pre-print now. Thanks to @reneechang.bsky.social collaborators in Graham Hatfull's and @soreklab.bsky.social groups @kfreeman.bsky.social @romihadary.bsky.social and Jim Sun

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Miguel López Rivera @riveralopz.bsky.social · 29/05/2026

(6/6) Huge thanks to @reneechang.bsky.social and @kranzuschlab.bsky.social; Colin, Julia, and @kfreeman.bsky.social in the Hatfull lab; @romihadary.bsky.social and @soreklab.bsky.social; and Jim Sun and the @danafarber.bsky.social NMR Core for making this story possible. So fun working with you all!

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Miguel López Rivera @riveralopz.bsky.social · 29/05/2026

(5/6) Finally, RyDEP revealed a bigger family. Diverse phage RyR-domain proteins bind Thoeris signals without cleaving them, acting as tight-binding sponges that evade defense by sequestration. Same fold, different ways to disarm immunity.

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Miguel López Rivera @riveralopz.bsky.social · 29/05/2026

(4/6) Then the structure gave us a huge surprise. RyDEP shares remarkable homology with the Repeat12 domain of animal RyRs, giant calcium-release channels. Since cADPR has long been linked to RyR regulation, this opens a new path to ask how human RyR domains sense cADPR-like signals.

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Miguel López Rivera @riveralopz.bsky.social · 29/05/2026

(3/6) RyDEP turns immune signal destruction into a metabolic opportunity: it hydrolyzes the unique ribose–ribose bond in Thoeris signals, generating ADPR that the NARP1 pathway can use to rebuild NAD. The phage can turn a host immune signal into something useful for itself!

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Miguel López Rivera @riveralopz.bsky.social · 29/05/2026

(2/6) We found RyDEP by screening phage-infected lysates spanning >10,000 viral proteins, and the result was striking: a single phage enzyme that breaks down both 2′cADPR and 3′cADPR, allowing phages to overcome both type VI and type I Thoeris defense.

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Miguel López Rivera @riveralopz.bsky.social · 29/05/2026

(1/6) Thrilled to share this story! In our preprint from my PhD in the @kranzuschlab.bsky.social, with help from the Hatfull lab and @soreklab.bsky.social, we discover RyDEP, a phage-encoded RyR-domain glycosidase that allows phages to evade Thoeris defense. Highlights below! doi.org/10.64898/202...

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