Rafael Peña-Miller

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 👇🏼

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...

New paper out in PNAS!!! 🎉

Do more plasmid copies mean faster evolution?

🧵 Dive into the story

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

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/...

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.

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.

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...

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...

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)

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...

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! 🧵👇

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...

🚨🚨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...

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...

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 ...

🧪
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/...

Congratulations! 🙌

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!

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.

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

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!

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

Can we predict AMR evolution?? We sure can try! New study published today in PNAS
www.pnas.org/doi/10.1073/...