Rubén de Dios
@rdedios.bsky.social
Regulation, regulation, regulation. Also a bit of biofilm. Postdoc at Ronan McCarthy lab, University of Southampton 🏳️🌈 Editor in #AccessMicro
Reposted by Rubén de Dios
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...:))
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...:))
November 13, 2025 at 7:27 PM
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...:))
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...:))
Reposted by Rubén de Dios
After 5 years of waiting, the new #CRISPR classification by Makarova et al. is out @natmicrobiol.nature.com www.nature.com/articles/s41...
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.
www.nature.com
November 6, 2025 at 1:49 PM
After 5 years of waiting, the new #CRISPR classification by Makarova et al. is out @natmicrobiol.nature.com www.nature.com/articles/s41...
Reposted by Rubén de Dios
Paul Nurse describing the main job of a PI
(From ‘The Thinking Game’, 2024)
(From ‘The Thinking Game’, 2024)
October 31, 2025 at 8:45 AM
Paul Nurse describing the main job of a PI
(From ‘The Thinking Game’, 2024)
(From ‘The Thinking Game’, 2024)
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!
October 24, 2025 at 9:43 AM
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!
Reposted by Rubén de Dios
"What Grant Reviewers Actually Look For (and What They Ignore)" jim-olds.org/2025/10/23/w...
“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…
jim-olds.org
October 23, 2025 at 2:32 PM
"What Grant Reviewers Actually Look For (and What They Ignore)" jim-olds.org/2025/10/23/w...
Reposted by Rubén de Dios
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...
www.biorxiv.org/content/10.1...
October 21, 2025 at 10:01 AM
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...
www.biorxiv.org/content/10.1...
Reposted by Rubén de Dios
q.e.d Science
Critical Thinking AI for constructive criticism and science evaluation
qedscience.com
October 15, 2025 at 12:22 PM
Reposted by Rubén de Dios
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...
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...
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...
www.biorxiv.org
October 6, 2025 at 6:27 AM
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...
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...
Reposted by Rubén de Dios
Chromosome architecture affects virulence and competitiveness in Agrobacterium tumefaciens C58 | Science Advances www.science.org/doi/10.1126/...
Chromosome architecture affects virulence and competitiveness in Agrobacterium tumefaciens C58
Chromosome architecture influences Agrobacterium fitness, competitiveness, and virulence, shaping its adaptation and evolution.
www.science.org
October 5, 2025 at 3:20 AM
Chromosome architecture affects virulence and competitiveness in Agrobacterium tumefaciens C58 | Science Advances www.science.org/doi/10.1126/...
Reposted by Rubén de Dios
Acinetobacter exhibits cyrcadian rhythms! These bugs can predict the light cycles and adjust the expression of genes accordingy. Amazing collaboration with Alejandra Mussi's team from Rosario, Argentina, my city!!
rdcu.be/eIQzL
rdcu.be/eIQzL
The critical human pathogen Acinetobacter baumannii exhibits light-regulated circadian rhythms
Communications Biology - Gene expression studies in the critical pathogen Acinetobacter baumannii identified the existence of daily rhythms displaying a robust response to light, as well as...
rdcu.be
September 30, 2025 at 4:54 PM
Acinetobacter exhibits cyrcadian rhythms! These bugs can predict the light cycles and adjust the expression of genes accordingy. Amazing collaboration with Alejandra Mussi's team from Rosario, Argentina, my city!!
rdcu.be/eIQzL
rdcu.be/eIQzL
Reposted by Rubén de Dios
We're hiring! We are looking for a Publishing Operations Editor to join our friendly team! You’ll support the strategic growth of our journal portfolio by managing the peer review process and overseeing production services.
Applications close 15 September: microb.io/jobs
Applications close 15 September: microb.io/jobs
Jobs
View the current job vacancies at the Microbiology Society.
microb.io
August 29, 2025 at 4:09 PM
We're hiring! We are looking for a Publishing Operations Editor to join our friendly team! You’ll support the strategic growth of our journal portfolio by managing the peer review process and overseeing production services.
Applications close 15 September: microb.io/jobs
Applications close 15 September: microb.io/jobs
Coming back from a great time visiting Karolinska Institutet and lovely Stockholm 🇸🇪
August 30, 2025 at 12:43 PM
Coming back from a great time visiting Karolinska Institutet and lovely Stockholm 🇸🇪
Reposted by Rubén de Dios
Very happy to see this one out: doi.org/10.1093/molbev/msaf192
Here, we assessed the contribution of natural transformation to the acquisition of novel genes. See preprint thread. @molbioevol.bsky.social #microsky #evobio
Here, we assessed the contribution of natural transformation to the acquisition of novel genes. See preprint thread. @molbioevol.bsky.social #microsky #evobio
August 27, 2025 at 1:37 PM
Very happy to see this one out: doi.org/10.1093/molbev/msaf192
Here, we assessed the contribution of natural transformation to the acquisition of novel genes. See preprint thread. @molbioevol.bsky.social #microsky #evobio
Here, we assessed the contribution of natural transformation to the acquisition of novel genes. See preprint thread. @molbioevol.bsky.social #microsky #evobio
Reposted by Rubén de Dios
This work is finally published! 🥳🧬
Plasmids are associated with very variable fitness costs in their different bacterial hosts. But, what is the contribution of each of the plasmid-genes in these host-specific effects? Study led by
@jorgesastred.bsky.social, @sanmillan.bsky.social and myself! 1/14
Plasmids are associated with very variable fitness costs in their different bacterial hosts. But, what is the contribution of each of the plasmid-genes in these host-specific effects? Study led by
@jorgesastred.bsky.social, @sanmillan.bsky.social and myself! 1/14
Dissecting pOXA-48 fitness effects in clinical Enterobacterales using plasmid-wide CRISPRi screens
Nature Communications - This study investigates the effects of the carbapenem resistance plasmid pOXA-48 in clinical enterobacteria. Using CRISPRi screens, the authors revealed that the...
rdcu.be
August 20, 2025 at 1:25 PM
This work is finally published! 🥳🧬
Plasmids are associated with very variable fitness costs in their different bacterial hosts. But, what is the contribution of each of the plasmid-genes in these host-specific effects? Study led by
@jorgesastred.bsky.social, @sanmillan.bsky.social and myself! 1/14
Plasmids are associated with very variable fitness costs in their different bacterial hosts. But, what is the contribution of each of the plasmid-genes in these host-specific effects? Study led by
@jorgesastred.bsky.social, @sanmillan.bsky.social and myself! 1/14
Reposted by Rubén de Dios
Today, our UPOBioinfo group presents the defensome of Acinetobacter baumannii.
Do you know about its concerning Global Clone 2? Well, part of its success could be due to the replacement of restriction-modification systems by Ssp antiviral systems.
Do you know about its concerning Global Clone 2? Well, part of its success could be due to the replacement of restriction-modification systems by Ssp antiviral systems.
The evolutionary replacement of restriction-modification by Ssp antiviral systems is associated with the distribution of prophages in the major clonal group of Acinetobacter baumannii | mBio
Acinetobacter baumannii is a bacterium of great concern in clinical contexts due to the plasticity of its genome and its resistance to antibiotics. Its cells are infected by a multitude of bacteriophages, and the bacterium defends itself with dozens of ...
journals.asm.org
August 18, 2025 at 1:58 PM
Today, our UPOBioinfo group presents the defensome of Acinetobacter baumannii.
Do you know about its concerning Global Clone 2? Well, part of its success could be due to the replacement of restriction-modification systems by Ssp antiviral systems.
Do you know about its concerning Global Clone 2? Well, part of its success could be due to the replacement of restriction-modification systems by Ssp antiviral systems.
Reposted by Rubén de Dios
Want to name a real virus? I have recently discovered 9 new phages which now need names! To enter, you simply need to donate to the Cystic Fibrosis Trust on my JustGiving page (£2 = 1 entry) and share your email with me on donation (see link info). Please share 💚 www.justgiving.com/page/meaghan-c-1
August 5, 2025 at 12:45 PM
Want to name a real virus? I have recently discovered 9 new phages which now need names! To enter, you simply need to donate to the Cystic Fibrosis Trust on my JustGiving page (£2 = 1 entry) and share your email with me on donation (see link info). Please share 💚 www.justgiving.com/page/meaghan-c-1
Reposted by Rubén de Dios
Super excited to share our paper online 🚨today🚨 in Cell Host & Microbe! Xiaomei Ren @xiaomeiren.bsky.social and Mason Clark @rmasonclark.bsky.social co-led discovery of ecological factors for Acinetobacter baumannii carriage in the gut, a reservoir for pathogen spread. 🎉
tinyurl.com/443kfefk
tinyurl.com/443kfefk
Amino acid competition shapes A. baumannii gut carriage
Acinetobacter baumannii uses ornithine to compete w/ microbiota & persist in gut. Amino acid supplementation & differences in diet promote A. baumannii gut colonization in mice & humans
@laurenpalmer.bsky.social
www.cell.com/cell-host-mi...
Acinetobacter baumannii uses ornithine to compete w/ microbiota & persist in gut. Amino acid supplementation & differences in diet promote A. baumannii gut colonization in mice & humans
@laurenpalmer.bsky.social
www.cell.com/cell-host-mi...
Amino acid competition shapes Acinetobacter baumannii gut carriage
Ren and Clark et al. show that Acinetobacter baumannii uses ornithine to compete with
the resident microbiota and persist in the gut. Additional evidence demonstrates that
amino acid supplementation a...
www.cell.com
August 4, 2025 at 8:26 PM
Super excited to share our paper online 🚨today🚨 in Cell Host & Microbe! Xiaomei Ren @xiaomeiren.bsky.social and Mason Clark @rmasonclark.bsky.social co-led discovery of ecological factors for Acinetobacter baumannii carriage in the gut, a reservoir for pathogen spread. 🎉
tinyurl.com/443kfefk
tinyurl.com/443kfefk
Reposted by Rubén de Dios
Happy to finally share this! Read here about the best strategy the the persistence of low-copy plasmids. @mariosanter.bsky.social @iwangtoknow.bsky.social doi.org/10.1038/s414...
The combination of active partitioning and toxin-antitoxin systems is most advantageous for low-copy plasmid fitness - Nature Communications
Effe et al. evaluate how specific plasmid traits influence plasmid fitness; they provide mechanistic insight into the persistence of large conjugative plasmids, including those that disseminate antibi...
doi.org
August 3, 2025 at 10:46 AM
Happy to finally share this! Read here about the best strategy the the persistence of low-copy plasmids. @mariosanter.bsky.social @iwangtoknow.bsky.social doi.org/10.1038/s414...
On our way to Niagara Falls for the Acinetobacter Conference 2025 after a fantastic stay-over in lovely Toronto with @lharkova.bsky.social. We will miss the pancakes with maple syrup 🥞
July 5, 2025 at 6:10 PM
On our way to Niagara Falls for the Acinetobacter Conference 2025 after a fantastic stay-over in lovely Toronto with @lharkova.bsky.social. We will miss the pancakes with maple syrup 🥞
Reposted by Rubén de Dios
🚨🚨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...
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...
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...
www.nature.com
July 2, 2025 at 11:08 AM
🚨🚨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...
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...
Reposted by Rubén de Dios
New paper published in our computational biology group for the study of phages, of which we are especially proud: "Bacteriophages in Pseudomonas aeruginosa evade the CRISPR-Cas I-F system by depletion of PAM sequences".
Bacteriophages in Pseudomonas aeruginosa evade the CRISPR-Cas I-F system by depletion of PAM sequences
Clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas) proteins systems provide bacteria with an adaptive immune system against exogenous sequences, such as pla...
www.microbiologyresearch.org
June 17, 2025 at 5:09 PM
New paper published in our computational biology group for the study of phages, of which we are especially proud: "Bacteriophages in Pseudomonas aeruginosa evade the CRISPR-Cas I-F system by depletion of PAM sequences".
It’s been fantastic to talk about my adventures with Acinetobacter plasmids at the @mgeworkshop.bsky.social. Such a lovely meeting with lots of great science and cool people. See you next year!
June 17, 2025 at 6:42 PM
It’s been fantastic to talk about my adventures with Acinetobacter plasmids at the @mgeworkshop.bsky.social. Such a lovely meeting with lots of great science and cool people. See you next year!
Reposted by Rubén de Dios
🎉 So proud of our PhD student, Ryuichi ONO, who submitted his first first-author paper from his undergrad research @utokyoofficial.bsky.social about plasmid survival tactics influencing ARG spread! Now just wait to see what he’s been cooking up in our lab 🤩
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Host range and ARG dissemination are shaped by distinct survival strategies of conjugative plasmids
Horizontal gene transfer is a major driver of bacterial evolution and the global dissemination of antibiotic resistance genes (ARGs). Conjugative plasmids play a crucial role in ARG spread across host...
www.biorxiv.org
May 24, 2025 at 5:40 PM
🎉 So proud of our PhD student, Ryuichi ONO, who submitted his first first-author paper from his undergrad research @utokyoofficial.bsky.social about plasmid survival tactics influencing ARG spread! Now just wait to see what he’s been cooking up in our lab 🤩
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Glad to contribute to @uk.theconversation.com explaining our latest paper on plastic-eating pathogens 🦠
In case you missed it: www.cell.com/cell-reports...
In case you missed it: www.cell.com/cell-reports...
We discovered how a plastic-eating enzyme made a germ more harmful.
We found a germ that ‘feeds’ on hospital plastic – new study
We discovered how a plastic-eating enzyme made a germ more harmful.
tcnv.link
May 24, 2025 at 6:46 PM
Glad to contribute to @uk.theconversation.com explaining our latest paper on plastic-eating pathogens 🦠
In case you missed it: www.cell.com/cell-reports...
In case you missed it: www.cell.com/cell-reports...
Reposted by Rubén de Dios
