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Rafael Peña-Miller

@penamiller.bsky.social
706 followers 399 following 4 posts

Scientist working somewhere around mathematical, computational and experimental microbiology

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Rafael Peña-Miller @penamiller.bsky.social · 19/08/2026
Marazuela, Castilla y León
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Craig MacLean @craigmaclean.bsky.social · 27/06/2026
New #microsky#AMR Perspective paper with @penamiller.bsky.social rdcu.be/fqBJo ANTIBIOTIC RESISTANCE (IE MIC) AND TOLERANCE ARE NOT BACTERIAL TRAITS! Please read on if you want an explanation for this provocative claim.
rdcu.be
Beyond resistance and tolerance: rethinking evolutionary responses to antibiotics from the perspective of individual bacterial cells
Nature Communications - Beyond resistance and tolerance: rethinking evolutionary responses to antibiotics from the perspective of individual bacterial cells
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Ayari Fuentes-Hernandez @ayari.bsky.social · 18/03/2026
Registration is open for MEEHubs 2026!
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Alvaro San Millan @sanmillan.bsky.social · 13/03/2026
Final version of our last paper is out! www.nature.com/articles/s41...
nature.com
Plasmids promote antimicrobial resistance through insertion sequence-mediated gene inactivation - Nature Microbiology
Inactivation of chromosomal genes through plasmid-encoded IS elements is an extended mechanism of antimicrobial resistance evolution in bacteria.
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Alberto HCA @albertohca.bsky.social · 10/03/2026
Excited to share our latest work! 📝 We measured the fitness effect of 136 AMR genes and found that many are neutral or even beneficial without selection. 🤯🧬 Oxygen availability can flip their fitness and our stochastic model indicates that oxygen fluctuations help maintain them. Learn more 👇🏼
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Paula Ramiro-Martínez @paularamiro.bsky.social · 27/01/2026
New paper out in PNAS!!! 🎉 Do more plasmid copies mean faster evolution? 🧵 Dive into the story www.pnas.org/doi/10.1073/...
pnas.org
Plasmid mutation rates scale with copy number | PNAS
Plasmids are extrachromosomal DNA molecules that spread by horizontal transfer and shape bacterial evolution. Plasmids are typically present at mul...
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Jerónimo Rodríguez-Beltrán @jerorb.bsky.social · 27/01/2026
New paper out in @pnas.org, and it made the cover! 👁️ We represent plasmids as circles and mutations as dots, resembling an eye, because in this paper we literally 𝑤𝑎𝑡𝑐ℎ plasmids evolve. ‼️Check Paula’s 🧵 and the paper👇 𝗣𝗹𝗮𝘀𝗺𝗶𝗱 𝗺𝘂𝘁𝗮𝘁𝗶𝗼𝗻 𝗿𝗮𝘁𝗲𝘀 𝘀𝗰𝗮𝗹𝗲 𝘄𝗶𝘁𝗵 𝗰𝗼𝗽𝘆 𝗻𝘂𝗺𝗯𝗲𝗿 www.pnas.org/doi/10.1073/...
Cover of PNAS in which we show plasmids as colourful concentric circles, with dots scattered. The image kind of resembles an eye, although it’s visibly a plot.
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Dani Reyes-Gonzalez @daniireyes.bsky.social · 14/01/2026
In this paper, we combined theory and experiments to study how stress can induce cooperation, and how this cooperation can promote tolerance under resource limitation. * * Stress doesn’t always break systems — sometimes it reorganizes them.
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Maria Rebolleda-Gomez @mrebolleda.bsky.social · 16/01/2026
This is a very beautiful paper from the dissertation of @daniireyes.bsky.social in @ayari.bsky.social lab on how species interactions matter for antibiotic resistance.
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Alvaro San Millan @sanmillan.bsky.social · 22/10/2025
New paper with my (amazing) friend and mentor @jrpenades.bsky.social Really looking forward to see what plasmid aficionados think of this one!! With @asantoslopez.bsky.social @wfigueroac3.bsky.social Akshay Sabins and others www.cell.com/cell-reports...
cell.com
Non-conjugative plasmids limit their mobility to persist in nature
Sabnis et al. explain why non-conjugative plasmids move at a low rate in nature. While increased mobility can easily evolve by incorporating phage DNA into plasmids, this is disadvantageous because it...
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Jerónimo Rodríguez-Beltrán @jerorb.bsky.social · 22/07/2025
Do plasmids evolve faster 🐇, slower 🐢, or just like chromosomes 🧬? In our new paper, we tackled this question using theory, simulations, bioinformatics, and experiments! 👇 Check out all the details in Paula’s thread! Hint: 🐇 (most of the time)
biorxiv.org
Plasmids promote bacterial evolution through a copy number-driven increase in mutation rate
Plasmids are autonomously replicating DNA molecules that stably coexist with chromosomes in bacterial cells. These genetic elements drive horizontal gene transfer and play a fundamental role in bacter...
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Paula Ramiro-Martínez @paularamiro.bsky.social · 22/07/2025
New paper alert! 🚨 Plasmids promote bacterial evolution through a copy number-driven increase in mutation rate. We combine theory, simulations, experimental evolution, and bioinformatics to demonstrate that mutation rates scale with plasmid copy number. Let's dive in! 🧵👇
biorxiv.org
Plasmids promote bacterial evolution through a copy number-driven increase in mutation rate
Plasmids are autonomously replicating DNA molecules that stably coexist with chromosomes in bacterial cells. These genetic elements drive horizontal gene transfer and play a fundamental role in bacter...
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Reposted by Rafael Peña-Miller
Jerónimo Rodríguez-Beltrán @jerorb.bsky.social · 02/07/2025
🚨🚨New paper out in @natcomms.nature.com!! Come for the first large-scale analysis of plasmid copy number across species, stay for one of the most intriguing results of my lab: universal scaling laws in plasmid biology! 📈🧬 👉 www.nature.com/articles/s41...
nature.com
Universal rules govern plasmid copy number - Nature Communications
Plasmids exhibit a broad range of sizes and copies per cell, and these two parameters appear to be negatively correlated. Here, Ramiro-Martínez et al. analyse the copy number of thousands of diverse b...
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Rafael Peña-Miller @penamiller.bsky.social · 15/05/2025
New preprint led by @brunoluviano.bsky.social & Fernando Santos. We show that filamentation enhances bacterial survival under toxic stress — not as collateral damage, but as a regulated morphological response. TL;DR: Filamentation isn’t a symptom, it’s a strategy! www.biorxiv.org/content/10.1...
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Jose A Escudero @jaescudero.bsky.social · 08/05/2025
🧪 Finally out after peer review, our work showing that "Mobile #Integrons carry Phage Defense Systems" is now published in Science 🎉 Short 🧵 www.science.org/doi/10.1126/...
science.org
Mobile integrons encode phage defense systems
Integrons are bacterial genetic elements that capture, stockpile, and modulate the expression of genes encoded in integron cassettes. Mobile integrons (MIs) are borne on plasmids, acting as a vehicle ...
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Macarena Toll-Riera @mtoll8.bsky.social · 21/02/2025
We are recruiting! We are looking for a PhD student to study rapid adaptation to stress in bacteria (shorturl.at/sr0Mj). Come join us in Barcelona!
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Alfonso Santos Lopez @asantoslopez.bsky.social · 20/11/2024
Check out this amazing Spotlight on our recently published paper -> www.cell.com/trends/micro... Huge thanks to @oliviakosterlitz.bsky.social, Benjamin Kerr and Elisabeth Duan for this great spolight.
cell.com
Agents of change: a partnership between mobile genetic elements facilitates rapid bacterial adaptation
While the evolutionary interests of mobile genetic elements may differ from those of their bacterial hosts, these elements can be beneficial for their hosts by delivering, disrupting, or activating ge...
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Rafael Peña-Miller @penamiller.bsky.social · 25/03/2024
Our paper on plasmid-driven heterogeneity is finally out! www.nature.com/articles/s41... @sanmillan.bsky.social @ayari.bsky.social @jerorb.bsky.social @craigmaclean.bsky.social
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Sur Herrera Paredes @surh.bsky.social · 10/01/2024
Thanks Thanks to @ayari.bsky.social for inviting me to present at @meehubs.bsky.social from the Cuernavaca hub. Got some great questions from the audience in other parts of the World!
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MEEhubs @meehubs.bsky.social · 08/01/2024
Only a bit more than 12 hours till start of #MEEhubs2024. We have hundreds of registered participants, some shared their location and where they travel to on the map below! #MicroSky
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Alvaro San Millan @sanmillan.bsky.social · 14/12/2023
Can we predict AMR evolution?? We sure can try! New study published today in PNAS www.pnas.org/doi/10.1073/...
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