Rubén de Dios

¿Por qué estudiamos mutantes en biología? Al observar qué falla cuando un gen muta, se puede deducir su función biológica. Por eso los organismos mutantes, muchas veces creados en el laboratorio, son tan importantes para el avance de la ciencia.

"En biología, usamos mutantes para entender cómo funcionan las células y qué pasa cuando algo falla".

Artist’s impression of two large spinosaurus dinosaurs standing in shallow water during a smoky prehistoric wildfire scene, with flying reptiles overhead and one dinosaur roaring while the other stands nearby. Credit: Anthony Hutchings.

wearing round glasses, a green tweed jacket, white shirt, and patterned tie, smiling while seated in an office or lab workspace. Behind him are shelves with files, a computer monitor, and a fossil-like sculpture

Proud to celebrate our dinosaur expert Dr Neil Gostling and former student Thomas Land for their parts in the new Spielberg documentary The Dinosaurs on Netflix 🦕

Dr Gostling researched Spinosaurus habits, and Thomas was a science researcher.

Find out more: www.southampton.ac.uk/news/2026/03...

In our latest work, we characterise the Tmn defence system. We reveal plasmolysis as a new way to block phage infection, dramatically reducing secondary infections.

Epistasis and co-adaptation in bacterial genome evolution Nature Reviews Genetics - Bacterial genome evolution is shaped by epistasis, which can constrain or promote specific evolutionary paths. The authors review how integrating the effects of epistatic...

I’ve spent a lot of time over the past two years thinking about genome evolution and how recent research revealing complex gene-gene interactions has complicated traditional ‘gene-centric’ genomic approaches to evolution. So here is a review that consolidates these thoughts!

rdcu.be/e6pHY

Biological Laboratory | LEGO® Ideas This is a two-floor realistic Biological Laboratory building. In this design, I try to tell stories about biologists, introduce biology concepts to general publ…

I just made an account and voted for this biology laboratory made of LEGO to "promote biological research and inspire more people into the world of biology". They need 10K votes. Reposting and/or voting below would be helpful. 🤗
beta.ideas.lego.com/product-idea...

New pre-print with @wtmatlock.bsky.social!!!
www.biorxiv.org/content/10.6...
What shapes the distribution of plasmids across bacteria? Our paper shows that conjugative plasmids actually have a very narrow distribution compared to mobilizable plasmids. Conjugative systems restrict plasmid transfer!

Two cartoon images of children with plasmids for faces about to fight. Commentators are saying "Plasmid-borne CRISPR-Cas systems provide significant defensive benefits" and "Yes, but toxin-antitoxin systems on competitor plasmids constrain the offensive CRISPR-Cas benefit"

Out now in @plosbiology.org : our big joint effort on the role of #CRISPR in plasmid competition. Read on for a really fun (I’m biased ok) analysis of how a defence system has new selective pressures when it’s mobile
journals.plos.org/plosbiology/... 1/6

Xiaofeng combined 2D live-cell single-particle tracking with 3D simulations to specifically measure the bacterial nucleoid accessibility and viscosity! Our preprint describes how these nucleoid properties respond to cellular processes! Code is available too.
www.biorxiv.org/content/10.6...

🚨 New pre-print! 🚨 In the largest study of its kind to-date, we investigate the ecological and evolutionary mechanisms driving within-patient evolution of antimicrobial resistance (AMR). Read here:
www.biorxiv.org/content/10.6... , and follow along with this thread, discussing our findings (1/21)

In our most recent work David Forrest has discovered a widespread mechanisms linking transcription initiation to DNA supercoiling...

www.nature.com/articles/s41...

#MicroSky: Plasmid vectors still underpin molecular biology, but convenience shouldn’t trump design. De Lorenzo & Martínez revisit copy number, selection & stability, and explores modular AI-assisted vector design for robust synthetic biology across the microbial world. doi.org/10.1111/1751...

Is AI hurting your ability to think? How to reclaim your brain AI is replacing tasks we have grown reluctant to do ourselves – thinking, writing, creating, analysing.

AI is replacing tasks we have grown reluctant to do ourselves – thinking, writing, creating, analysing.

Emerging advances in prokaryotic transposition: TnPedia as a promising tool TnPedia provides a curated framework for understanding prokaryotic transposable elements (TEs), including general and historical information and basic concepts, while integrating mechanistic insights, family-level classification, and representative examples. It summarizes key developments reshaping the field, including RNA-guided transposition, and provides information on TE acquisition and transmission of antimicrobial resistance-associated transposons.

Emerging advances in prokaryotic transposition: TnPedia as a promising tool

Phenylacetic acid mediates Acinetobacter baumannii entry into a viable but non-culturable state Desiccation tolerance is central to the pathogenic success of the opportunistic pathogen Acinetobacter baumannii, allowing its survival on hospital surfaces in the absence of water and nutrients for m...

Delighted to share our latest work exploring the regulation of desiccation tolerance in Acinetobacter baumannii. Great effort by @lharkova.bsky.social and @rdedios.bsky.social

www.microbiologyresearch.org/content/jour...

Une opportunité unique de former des étudiants talentueux à la biologie des bactéries à l'ENS Lyon et mener des recherches sur les phages, l'immunité bactérienne, le transfert génétique horizontal (HGT) et/ou les éléments génétiques mobiles au sein du département de bactériologie du CIRI.

SimUrine: a novel, fully defined artificial urinary medium for enhanced microbiological research of urinary bacteria

journals.asm.org/doi/10.1128/...

Coupling DNA processing to early gene expression drives antibiotic resistance plasmid dissemination https://www.biorxiv.org/content/10.64898/2026.01.09.698686v1

Starting 2026 with a hike to the castle on top of my hometown Jaén. Lovely views to kick off the year.

Diagram of genes required for in vivo fitness in different organs displayed as bar graphs

Gene dependence during mammalian Acinetobacter baumannii pneumonia and septicaemia infections. Published Open Access and fee-free in MGen using a Publish and Read agreement: doi.org/10.1099/mgen... #MGen #PublishAndRead

Selective elimination of donor bacteria enables global profiling of plasmid gene expression at early stages of conjugation Abstract. Conjugative plasmids are a major driving force for the dissemination of antimicrobial resistance. During conjugation, plasmid DNA is transferred

academic.oup.com/nar/article/... Collaboration with Y. Yamaichi. Killing donor bacteria in conjugation mixes using water enables transcriptomic profiling of early plasmid genes ! Superb tool for studying zygotic induction of these early genes, which include anti-SOS and anti-RM factors. #microsky

Research institutes: What makes the magic? Beyond the great science, what makes a research institute special? Do the work environment and the organisational structure support researchers in delivering their best outputs? Does the culture help ...

Research institutes: What makes the magic?

Was fun to help my old boss Sarah Teichmann and her friend Frank Bradke put this piece out for the FEBS Network. A reflective follow-up to our PLOS Biology article in 2023. With art by the amazing Catherine Bone

network.febs.org/posts/resear...

comic of a happy person with a shitty 1st draft

I just got an email from a former mentee telling me that one dinner conversation changed how he writes papers♥️

I told him: “just write the paper, get it out—the next one will be better, and the next even better.”

Perfectionism is a trap (and a way to procrastinate...:))

An updated evolutionary classification of CRISPR–Cas systems including rare variants - Nature Microbiology An exploration of previously undescribed variants from the long tail of the CRISPR–Cas distribution.

After 5 years of waiting, the new #CRISPR classification by Makarova et al. is out @natmicrobiol.nature.com www.nature.com/articles/s41...

Paul Nurse describing the main job of a PI

(From ‘The Thinking Game’, 2024)

Thanks Patri!

New adventures, same old fantastic companions. @lharkova.bsky.social and I just joined @sotonbiosciences.bsky.social at @unisouthampton.bsky.social with the whole @ronanmccarthy.bsky.social lab. Looking forward to collaborating with such a great research community!

“What Grant Reviewers Actually Look For (and What They Ignore)” A close colleague of mine at a major US research university begins the process of preparing a grant proposal by creating something he calls a “storyboard”.  When I was growing up in LA, the concept…

"What Grant Reviewers Actually Look For (and What They Ignore)" jim-olds.org/2025/10/23/w...

Thrilled to share our multidisiplinary work on how genome-wide DNA bridging by H-NS reshapes the stationary phase bacterial nucleoid and affects the transcriptional landscape. With Xindan Wang and @meyerroc.bsky.social
www.biorxiv.org/content/10.1...

q.e.d Science Critical Thinking AI for constructive criticism and science evaluation

Here's the link to the system, try it! qedscience.com
@qedscience.bsky.social

Resistance mutation supply modulates the benefit of CRISPR immunity against virulent phages Only a fraction of bacterial genomes encode CRISPR-Cas systems but the selective causes of this variation are unexplained. How naturally virulent bacteriophages (phages) select for CRISPR immunity has...

New preprint!

Ever wondered why only a fraction of genomes encode CRISPR immunity? 🧬 🦠

Turns out CRISPR is rarely beneficial against virulent phages, being most beneficial against those for which resistance mutations are rare!

An epic effort by Rosanna Wright

www.biorxiv.org/content/10.1...