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André Carvalho

@afpcarvalho.bsky.social
730 followers 446 following 2 posts

Scientist interested in microbiology, antimicrobial resistance, integrons and bacterial adaptation. Postdoc at ucm.es/mbalab

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Reposted by André Carvalho
Didier Mazel @amazeld.bsky.social · 02/10/2026
A step forward to control methane production? at long last Kudos to @sgribaldo.bsky.social and @ivo-boneca.bsky.social www.nature.com/articles/s41...
nature.com
A methanogen hydrolase reveals the structure of archaeal peptidoglycan - Nature
ArmA from Methanobrevibacter smithii, a dominant member of the human gut microbiome, is identified and characterized as a glycosyl hydrolase specific for cleaving the cell wall of methanogens, reveali...
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Reposted by André Carvalho
Craig MacLean @craigmaclean.bsky.social · 30/09/2026
Postdoc position available in my group to work on ERC funded project on evolutionary biology of antibiotic resistance. Looking for someone with expertise in bacterial genetics, AMR, and evolutionary biology. www.jobs.ac.uk/job/DSZ416/p...
jobs.ac.uk
Postdoctoral Research Associate at University of Oxford
Explore an exciting academic career as a Postdoctoral Research Associate. Don't miss out on other academic jobs. Click to apply and explore more opportunities.
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Jorge Moura de Sousa @jmouradesousa.bsky.social · 20/09/2026
Happy to see our work on the evolution of antiviral repertoires in P4-like satellites and their P2-like helper phages (check out the 🧵 👇) out in @narjournal.bsky.social 🔗 doi.org/10.1093/nar/... #phagesky #MicroSky #evosky
doi.org
Shuttling, swapping, and mixing: the rapid modular evolution of antiviral repertoires in temperate phages and their satellites
Abstract. Interactions between bacteria, bacteriophages, and their satellites are shaped by a myriad of defence and counter-defence mechanisms. Here, we id
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Didier Mazel @amazeld.bsky.social · 18/09/2026
Dear all, I have the pleasure to inform you that the online course "Resistance to Antibacterial Agents", produced by the Institut Pasteur, will start on November 3, 2026. How does ABR emerge and spread? ... 🔗 www.fun-mooc.fr/en/courses/r...
fun-mooc.fr
Resistance to antibacterial agents
The origin, risks, diagnosis, epidemiology of resistance to antibacterial agents in man and livestock worldwide, as well as preventive and countermeasures, in a « one health » perspective.
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François Rousset @francoisrousset.bsky.social · 08/09/2026
🚨 We are excited to share the first preprint of our lab ! We discovered an NADase enzymatic domain in bacterial immunity and in the human protein TEP1. www.biorxiv.org/content/10.6...
biorxiv.org
A widespread NADase domain links bacterial immunity with human TEP1
Recent discoveries on bacterial immunity have revealed that several protein domains involved in anti-phage defense are conserved in eukaryotes, such as SIRim, TIR, PNP and gasdermin. Bacterial immune ...
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Filipa Trigo da Roza @filipatr.bsky.social · 03/09/2026
It’s out! 🥹🎉 We’re so incredibly happy and proud to see this work out in the world. And once again, a huge thank you to the great mastermind @jaescudero.bsky.social and all the co-authors; this wouldn’t have been possible without you! doi.org/10.1038/s415... @natmicrobiol.nature.com
doi.org
High-throughput recovery of integron cassettes for gene discovery screens - Nature Microbiology
Integron insertion sites engineered into counterselection markers allow large-scale and high-throughput capture of integron-encoded genes from genetically tractable bacteria or DNA samples.
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Reposted by André Carvalho
Nature Microbiology @natmicrobiol.nature.com · 03/09/2026
Out Now! High-throughput recovery of integron cassettes for gene discovery screens #MicroSky
go.nature.com
High-throughput recovery of integron cassettes for gene discovery screens
Nature Microbiology, Published online: 03 September 2026; doi:10.1038/s41564-026-02474-5Integron insertion sites engineered into counterselection markers allow large-scale and high-throughput capture of integron-encoded genes from genetically tractable bacteria or DNA samples.
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Zeynep Baharoglu @zeynepbaharoglu.bsky.social · 26/08/2026
A generalized growth law for translation- and transcription-targeting antibiotics captures drug interactions 🦠💊 www.biorxiv.org/content/10.6...
biorxiv.org
A generalized growth law for translation- and transcription-targeting antibiotics captures drug interactions
Bacterial growth laws quantitatively connect intracellular resource allocation to growth rate, enabling accurate predictions of physiology and antibiotic responses. Yet these laws have been rigorously...
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Reposted by André Carvalho
Alvaro Sanchez @asanchezlab.bsky.social · 21/08/2026
New preprint from the lab: The Latent Simplicity of Microbial Ecological Interactions www.biorxiv.org/content/10.6... We're excited about this one. We find that high-order microbial interactions often obey simple linear laws, making microbial communities far more predictable than one might expect.
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Zeynep Baharoglu @zeynepbaharoglu.bsky.social · 18/08/2026
academic.oup.com/nar/article/... 🦠
academic.oup.com
The leading region of many plasmids is adapted for translational efficiency
Abstract. To successfully transfer, conjugative plasmids must overcome a recipient cell’s defence mechanisms. The leading region of many plasmids—the first
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STCmicrobeblog @stcmicrobeblog.bsky.social · 30/07/2026
you think we know all about post·transcriptional control that modulates mRNA translatability (sRNA, riboswitches,...) – then tackle yet another level: tRNA/rRNA modifications that modulate mRNA translatability under stress 👇 "everything that can be regulated will be regulated" #RNASky #MicroSky
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Labex IBEID @ibeidlabex.bsky.social · 08/06/2026
Now @zeynepbaharoglu.bsky.social from IBPC @cnrs.fr and @pasteur.fr She's exploring how epitranscriptomic regulation controls bacterial response to antibiotics and adaptation to the host. #AMR #RNA @ibeidlabex.bsky.social
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Zeynep Baharoglu @zeynepbaharoglu.bsky.social · 02/04/2026
Cool tool to capture genes using a hunter gatherer 🦠 Large-scale recovery of integron cassettes for gene discovery screens www.biorxiv.org/content/10.6... by @jaescudero.bsky.social @afpcarvalho.bsky.social @filipatr.bsky.social
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Filipa Trigo da Roza @filipatr.bsky.social · 20/03/2026
New preprint alert!!! 🚀🤓 We are very happy to finally share this with the world — the result of seven years of work and a new tool to study integrons and discover new functions encoded in these bacterial platforms. If you want to know more, here is a thread 🧵 www.biorxiv.org/content/10.6...
biorxiv.org
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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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Alfonso Santos Lopez @asantoslopez.bsky.social · 13/03/2026
Check out the latest version of our paper — peer-reviewed, polished, and published. Hope you like it! 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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Pedro Dorado-Morales @doradomoralesp.bsky.social · 26/02/2026
New preprint out on bioRxiv! www.biorxiv.org/content/10.6... Can conjugative plasmids be used to control plasmid and pathogen spread? Follow me down the rabbit hole that led to this story 🧵
biorxiv.org
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Didier Mazel @amazeld.bsky.social · 12/12/2025
We've come full circle! I began my postdoctoral career by identifying the peptidyl deformylase gene. Today, we show that half of bacterial species harbor multiple PDF genes (up to 7, for always a single Met-tRNA transformylase), and while the role of these PDFs ... academic.oup.com/mbe/article/...
academic.oup.com
Unraveling the Prevalence and Multifaceted Roles of Accessory Peptide Deformylases in Bacterial Adaptation and Resistance
Abstract. Peptide deformylases (PDFs) are enzymes that are essential for bacterial viability and attractive targets for antibiotic development. Yet, despit
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Alfonso Santos Lopez @asantoslopez.bsky.social · 22/10/2025
Do plasmids really move around that much? Well, maybe not always Thrilled to have contributed to this story with two of my favourite microbiologists: @jrpenades.bsky.social & @sanmillan.bsky.social This great work was led by Akshay Sabnis & @wfigueroac3.bsky.social 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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Zeynep Baharoglu @zeynepbaharoglu.bsky.social · 08/10/2025
Happy to share our new review in Royal Society Open Biology 🎉 tRNA-modifying enzymes in bacterial stress adaptation: How tRNA mods rewire translation under oxidative + antibiotic stress (MoTTs, moonlighting, therapy angles). Read: doi.org/10.1098/rsob... #RNAsky #microsky #AMR #RNAmodifications
doi.org
tRNA-modifying enzymes in bacterial stress adaptation | Open Biology
Transfer RNAs (tRNAs) and their modifications are central to bacterial translation and physiology, yet their roles in stress adaptation remain underexplored. While extensively studied in eukaryotes, a...
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Zeynep Baharoglu @zeynepbaharoglu.bsky.social · 15/08/2025
🦠 Launching a bimonthly digest on RNA modifications and related topics in bacteria!🤩 First issue: Summer 2025. Shared here + by email, future ones will be quicker reads! 😅 #rnasky #microsky #ribosome Subscribe and share if you are interested! rnamodifupdates.substack.com/p/rna-modifi...
rnamodifupdates.substack.com
RNA modifications digest Summer 2025
Bimonthly newsletter: RNA modifications and related topics, mostly in bacteria. Summer 2025, first issue!
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Didier Mazel @amazeld.bsky.social · 20/08/2025
For those who love bacterial replicons, The ultimate review, from our lab, signed by the master of their evolution. ‪@val-meve.bsky.social‬ www.sciencedirect.com/science/arti...
sciencedirect.com
Taming wild replicons: evolution and domestication of large extrachromosomal replicons
Bacterial genomes often contain extrachromosomal replicons (ERs), ranging from small, mobile plasmids to large, stably inherited elements, such as meg…
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Alicia Calvo-Villamañán @aliciapcv.bsky.social · 20/08/2025
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
rdcu.be
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...
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Alfonso Santos Lopez @asantoslopez.bsky.social · 13/08/2025
Our new manuscript is out! A bit of everything cool: Plasmids ✅ Insertion Sequences ✅ AMR Evolution ✅ Microbial Communities ✅ Databases analyses ✅ Mathematical modeling ✅ See the scientific thread below of Jorge Sastre, who has brilliantly led this work with @palomarodera.bsky.social
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Jorge Sastre Domínguez @jorgesastred.bsky.social · 13/08/2025
New paper out! 🔈🔈📣📣 Plasmids promote antimicrobial resistance through Insertion Sequence-mediated gene inactivation. Combining experimental and computational approaches, we unveil how two of the most prevalent bacterial MGE accelerate the evolution of AMR. 🧵👇🏻 www.biorxiv.org/content/10.1...
biorxiv.org
Plasmids promote antimicrobial resistance through Insertion Sequence-mediated gene inactivation
Antimicrobial Resistance (AMR) is a major threat to public health. Plasmids are mobile genetic elements that can rapidly spread across bacterial populations, promoting the dissemination of AMR genes i...
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Reposted by André Carvalho
Didier Mazel @amazeld.bsky.social · 28/07/2025
A 2-year postdoc position in my lab, under the supervision of P-Alex Kaminski, on Z-DNA phages and the benefit given by ZTGC DNA and the replication machinery, with attempt to create a Z based minireplicon research.pasteur.fr/en/job/a-two...
research.pasteur.fr
A two year post-doctoral position at the BacterialGenome Plasticity Unit starting October 1st - Research
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Jerónimo Rodríguez-Beltrán @jerorb.bsky.social · 25/07/2025
🚨🚨 New paper in @narjournal.bsky.social! 🍾 Excludons are pairs of overlapping genes that block each other’s expression (basically, reverse operons). We built a tool to identify them in bacterial genomes using transcriptomic data, in an awesome collab led by Iñigo Lasa and Álvaro San Martín. 👇
academic.oup.com
ExcludonFinder: mapping transcriptional overlaps between neighboring genes
Abstract. Bacteria regulate neighboring genes via overlapping transcription in untranslated regions (UTRs), forming excludons. This overlap leads to transc
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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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Carlos Serna @cserna.bsky.social · 17/07/2025
Our paper “Global dissemination of npmA mediated pan‑aminoglycoside resistance via a mobile element in Gram‑positive bacteria” is now in @natcomms.nature.com. Part of my freshly defended PhD, so doubly happy! 😄🎉 🧵 (1/14) www.doi.org/10.1038/s414...
doi.org
Global dissemination of npmA mediated pan-aminoglycoside resistance via a mobile genetic element in Gram-positive bacteria - Nature Communications
The authors investigate the distribution of the aminoglycoside resistance gene npmA in Gram-positive bacteria via a mobile genetic element, highlighting its global presence and cross-species transfer ...
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Paula Ramiro-Martínez @paularamiro.bsky.social · 02/07/2025
Curious about plasmid biology? Our latest paper is out now in Nature Communications! 🚨 doi.org/10.1038/s414... We analyzed thousands of diverse bacterial plasmids to shed light for the first time on a key aspect of plasmid biology: plasmid copy number. 1/7 👇
doi.org
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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Sociedad Española de Bioquímica y Biología Molecular (SEBBM) @sebbm.bsky.social · 06/06/2025
🦠 Nuestro #articulodelmes habla sobre cómo los integrones móviles codifican sistemas de defensa contra fagos de la mano del grupo investigador liderado por el Dr. José Antonio Escudero 📄https://f.mtr.cool/qxwueostwp
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Melanie Blokesch @mblokesch.bsky.social · 22/05/2025
Exciting news!! Our latest paper is out in Nat. Microbiol. @natmicrobiol.nature.com We show that a sub-lineage of 7th pandemic V. cholerae has acquired mobile genetic elements packed with phage defense systems—rendering it multi-phage resistant 😳 ..... 1/3 www.nature.com/articles/s41...
nature.com
West African–South American pandemic Vibrio cholerae encodes multiple distinct phage defence systems - Nature Microbiology
The West African–South American lineage of Vibrio cholerae contains multiple distinct anti-phage defence systems that provide resistance to various phage families, including vibriophage ICP1, a key pr...
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Zeynep Baharoglu @zeynepbaharoglu.bsky.social · 21/05/2025
Marie Curie fellowship, post-doc hosting oppotunity in my lab. MSCA Post-doctoral Fellowship at IBPC Paris on RNA modifications in bacteria (FRANCE) 🦠💫 euraxess.ec.europa.eu/jobs/hosting...
euraxess.ec.europa.eu
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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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Alvaro San Millan @sanmillan.bsky.social · 15/05/2025
New opinion paper from the lab! www.cell.com/trends/micro...
cell.com
Plasmid–bacteria associations in the clinical context
Antimicrobial resistance (AMR) is one of the most pressing global health problems, with plasmids playing a central role in its evolution and dissemination. Over the past decades, many studies have inv...
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Eduardo Rocha @epcrocha.bsky.social · 09/05/2025
Our paper on how integrons are biobanks of novel minimal defense systems is now out www.science.org/doi/10.1126/... Two main conclusions on this excellent work led by @eloilittner.bsky.social @baptistedarracq.bsky.social 1/n
science.org
Sedentary chromosomal integrons as biobanks of bacterial antiphage defense systems
Integrons are genetic systems that drive bacterial adaptation by acquiring, expressing, and shuffling gene cassettes. While mobile integrons are well known for spreading antibiotic resistance genes, t...
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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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Alberto HCA @albertohca.bsky.social · 30/04/2025
Can resistance genes really hold their breath like pros? 🤔🤿 Outstanding work by Laura, Amalia, Nico and Ester from @jaescudero.bsky.social lab in collab with @sanmillan.bsky.social, Fernando Baquero and Rafael Cantón. Dive into our latest paper to find out! 👇🏼 www.sciencedirect.com/science/arti...
sciencedirect.com
Effect of oxygen on antimicrobial resistance genes from a one health perspective
Bacteria must face and adapt to a variety of physicochemical conditions in the environment and during infection. A key condition is the concentration …
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Charles Coluzzi @charlescoluzzi.bsky.social · 31/03/2025
I'm very happy to share the last paper from my previous postdoc with the amazing @epcrocha.bsky.social! Thanks to the reviewers for their feedback, which improved our work! #Plasmids #AMR #HorizontalGeneTransfer #Evolution
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Filipa Trigo da Roza @filipatr.bsky.social · 18/02/2025
What a ride 🥹 Thank you @jaescudero.bsky.social and the whole MBA lab 💖💖💖
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STCmicrobeblog @stcmicrobeblog.bsky.social · 05/02/2025
@stevestuwill.bsky.social you posted on 𝕏 on Dec 5, 2020 this stunning video - why not repeat on 🔵bsky ? (sorry, I did)... "Time-lapse footage of a vampire amoeba: a microscopic organism that feeds on algal cells by breaking through their cell walls and sucking out their insides." #ProtistsOnSky
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Craig MacLean @craigmaclean.bsky.social · 24/01/2025
New pre-print!!! What types of genes end up on plasmids and why? The take home message of this paper is that beneficial genes move from plasmids to chromosome, causing the ecological value of plasmids to decay over time. www.biorxiv.org/content/10.1...
biorxiv.org
Chromosomal capture of beneficial genes drives plasmids towards ecological redundancy
Plasmids are a ubiquitous feature of bacterial genomes, but the evolutionary forces driving genes to become associated with plasmids are poorly understood. To address this problem, we compared the fit...
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Zeynep Baharoglu @zeynepbaharoglu.bsky.social · 12/01/2025
Our paper on 🦠queuosine 34 modification of tRNA tyrosine and antibiotic response is finally out in its final form in @eLife ... and quite different from the preprint version. Many thanks to reviewers, editors and kudos to all authors🙏 elifesciences.org/articles/96317
elifesciences.org
Aminoglycoside tolerance in Vibrio cholerae engages translational reprogramming associated with queuosine tRNA modification
tRNA Q34 modification impacts tyrosine codon decoding and leads to proteome reprogramming in response to antibiotic stress in Vibrio cholerae.
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Marie-Eve VAL @val-meve.bsky.social · 09/01/2025
1/ 🔬 Our work, "Dynamic transitions of initiator binding coordinate the replication of the two chromosomes in Vibrio cholerae", is now published in Nature Communications. Here's a thread on how we think Chr1 and Chr2 replication is coordinated in Vibrio. 🧵 Link : www.nature.com/articles/s41...
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Alicia Calvo-Villamañán @aliciapcv.bsky.social · 02/01/2025
Very happy to see this work published! We unveil a plasmid-chromosome crosstalk by showing that pOXA-48 encodes for a regulator that mediates the transcription of an enterobacterial chromosomal operon, resulting in a growth benefit for the plasmid-carrying bacteria! www.nature.com/articles/s41...
nature.com
A plasmid-chromosome crosstalk in multidrug resistant enterobacteria - Nature Communications
The authors describe a new crosstalk between a globally disseminated carbapenem resistance plasmid and clinical enterobacteria clones. This crosstalk provides a fitness advantage to the plasmid-carryi...
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Alvaro San Millan @sanmillan.bsky.social · 30/12/2024
www.nature.com/articles/s41... New paper out!!
nature.com
A plasmid-chromosome crosstalk in multidrug resistant enterobacteria - Nature Communications
The authors describe a new crosstalk between a globally disseminated carbapenem resistance plasmid and clinical enterobacteria clones. This crosstalk provides a fitness advantage to the plasmid-carryi...
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Alf Soler-Bistué 🦠🔬🧫 @alfmicrobe.bsky.social · 02/12/2024
We just published a short comm in wich we show that highly similar Brucella showing almost identical genomes (ANI>99.5) may display 6-fold differences in growth. tinyurl.com/5n6crakh We will soon publish a much developed story on genome parameters controlling Brucella growth!
tinyurl.com
Closely Related Brucella Species Widely Differ in their Vegetative and Intracellular Growth - Current Microbiology
Growth rate is a key prokaryotic trait that allows for estimating fitness and understanding cell metabolism. While it has been well studied in model organisms, there is limited data on slow-growing ba...
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Jose A Escudero @jaescudero.bsky.social · 15/01/2024
And its out! New paper for #integron aficionados. We found gene-less cassettes in superintegrons that express/silence other cassettes in the array. Here is a 🧵(if I know how to do this in Bluesky...😆) academic.oup.com/nar/advance-...
academic.oup.com
Identification of promoter activity in gene-less cassettes from Vibrionaceae superintegrons
Abstract. Integrons are genetic platforms that acquire new genes encoded in integron cassettes (ICs), building arrays of adaptive functions. ICs generally encod
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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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Jose A Escudero @jaescudero.bsky.social · 21/11/2023
Check out our last work with Celine Loot, Ole Skovgaard, @amazeld.bsky.social and @sanmillan.bsky.social. We have deleted the Superintegron from V. cholerae! A long-awaited feat in the field!! Despite losing 3% of the genome, the strain remains phenotipically identical across Manu conditions!! 😵
biorxiv.org
Chromosomal Integrons are Genetically and Functionally Isolated Units of Genomes
bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution
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