Raphael Laurenceau
@raphael-microb.bsky.social
📤 95
📥 85
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Microbiologist
reposted by
Raphael Laurenceau
Antonio Camargo
4 days ago
🚨New preprint out! We present a foundational genomic resource of human gut microbiome viruses. It delivers high-quality, deeply curated data spanning taxonomy, predicted hosts, structures, and functions, providing a reference for gut virome research. (1/8)
www.biorxiv.org/content/10.1...
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The impressive molecular details of the retroelement Eco8 defense activation, a protein-RNA-DNA complex in which all three play a part
www.cell.com/molecular-ce...
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Phage SSB detection by retron Eco8 msDNA unleashes nuclease-mediated immunity
The cryo-EM structure of the retron Eco8 system reveals an autoinhibited 4:4:4 complex of RT, msDNA, and OLD nuclease. Phage SSB binding to msdDNA unleashes non-specific nuclease activity to restrict ...
https://www.cell.com/molecular-cell/fulltext/S1097-2765(25)00824-X
6 days ago
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Raphael Laurenceau
AnniZLab: [🦠, 🧬 , ✨]
10 days ago
A brand-new Gordon Conference on Microbiomes!🦠 The opening session (Jan 2026) dives into microbiome editing - how fundamental research and new technologies can advance human health and environmental sustainability. Super looking forward!🧪
#microsky
#microbiomesky
#grc
www.grc.org/microbiome-e...
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2026 Microbiome Editing Conference GRC
The 2026 Gordon Research Conference on Microbiome Editing will be held in Pomona, California. Apply today to reserve your spot.
https://www.grc.org/microbiome-editing-conference/2026/
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reposted by
Raphael Laurenceau
Paul Rainey
13 days ago
@prczhaoyansong.bsky.social
’s deep dive into the dark matter of compost communities is now out 🎉 Genomic islands hijack jumbo phages—whose capsids enable transfer of large tracts of DNA—shedding new light on the scale & scope of phage-mediated gene flow 😎
www.pnas.org/doi/10.1073/...
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Jumbo phage–mediated transduction of genomic islands | PNAS
Bacteria acquire new genes by horizontal gene transfer, typically mediated by mobile genetic elements (MGEs). While plasmids, bacteriophages, and c...
https://www.pnas.org/doi/10.1073/pnas.2512465122
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reposted by
Raphael Laurenceau
Yifan ZHOU
24 days ago
Our work on viruses and virus satellites of haloarchaea and their DPANN symbionts is out today in Nature Microbiology!
@mkrupovic.bsky.social
@deemteam.bsky.social
@anagtz.bsky.social
www.nature.com/articles/s41...
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Viruses and virus satellites of haloarchaea and their nanosized DPANN symbionts reveal intricate nested interactions - Nature Microbiology
An exploration of the viromes of haloarchaea and their ultra-small DPANN symbionts reveals plasmid-derived satellites of viruses from both archaeal groups, highlighting the complexity of nested symbio...
https://www.nature.com/articles/s41564-025-02149-7
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Phage defense is sometimes so convoluted 🙃
add a skeleton here at some point
24 days ago
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Raphael Laurenceau
Typas Lab
28 days ago
Excited to share our preprint led by Carlos Voogdt et al We developed new genetic tools & genome-wide libraries for species of the Bacteroidales order; constructed saturated barcoded transposon libraries in key representatives of three genera.
www.biorxiv.org/content/10.1...
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reposted by
Raphael Laurenceau
Frédérique Le Roux
29 days ago
Phages evolve fast, or do they? In oysters, some stay identical for years. With >1,200 phages & 600 Vibrio genomes, we reveal long-term stability and new mobile elements. Proud of this collaborative work across our teams (Roscoff-UdeM and
@epcrocha.bsky.social
www.biorxiv.org/cgi/content/...
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Ecological constraints foster both extreme viral-host lineage stability and mobile element diversity in a marine community
Phages are typically viewed as very rapidly evolving biological entities. Little is known, however, about whether and how phages can establish long-term genetic stability. We addressed this eco-evolut...
https://www.biorxiv.org/cgi/content/short/2025.10.10.681744v1
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www.science.org/doi/10.1126/...
Another breakthrough work on the fascinating biology of Diversity Generating Retroelements by Jeff Miller’s team
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Targeted protein evolution in the gut microbiome by diversity-generating retroelements
Diversity-generating retroelements (DGRs) accelerate evolution by rapidly diversifying variable proteins. The human gastrointestinal microbiota harbors the greatest density of DGRs known in nature, su...
https://www.science.org/doi/10.1126/science.adv2111
29 days ago
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reposted by
Raphael Laurenceau
Beatriz Beamud
about 1 month ago
Can we exploit past phage infection events (prophages) to decipher the specificity of phage receptor-binding proteins such as depolymerases?🔎 Happy to share our recent work at
@natcomms.nature.com
🔽
#microsky
#phagesky
www.nature.com/articles/s41...
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Unlocking data in Klebsiella lysogens to predict capsular type-specificity of phage depolymerases - Nature Communications
Here, the authors exploit the genetic information encoded in Klebsiella prophages to model the interplay between bacteria, prophages, and their depolymerases, using a directed acyclic graph-model and a sequence clustering-based model.
https://www.nature.com/articles/s41467-025-63861-w
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reposted by
Raphael Laurenceau
Joshua Weitz
about 1 month ago
MIT says no to the Trump admin higher-ed compact clearly and emphatically. Other universities would be well served to read, remix, and respond similarly. "In that free marketplace of ideas, the people of MIT gladly compete with the very best, without preferences."
orgchart.mit.edu/letters/rega...
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Raphael Laurenceau
The EMBO Journal
about 1 month ago
Type IV secretion systems: from structures to mechanisms Kévin Macé and colleagues summarize recent structural insights into the assembly and function of bacterial type IV secretion systems
www.embopress.org/doi/full/10....
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Raphael Laurenceau
C. Brandon Ogbunu
about 1 month ago
www.pnas.org/doi/10.1073/...
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In vivo directed evolution of an ultrafast Rubisco from a semianaerobic environment imparts oxygen resistance | PNAS
Carbon dioxide (CO2) assimilation by the enzyme Ribulose-1,5-bisphosphate Carboxylase/Oxygenase (Rubisco) underpins biomass accumulation in photosy...
https://www.pnas.org/doi/10.1073/pnas.2505083122
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Biofilm formation mediated by a Type IV secretion system pilus
www.nature.com/articles/s41...
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The assembly of a hybrid type IV secretion system by a Crohn’s disease-associated Escherichia coli strain - Nature Communications
Adherent-invasive strains of E. coli are commonly isolated from patients with Crohn’s disease. Here, the authors show that an AIEC harbours a hybrid Type IV secretion system (T4SS) that mediates pilin polymerization and biofilm formation in vivo.
https://www.nature.com/articles/s41467-025-63859-4
about 1 month ago
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reposted by
Raphael Laurenceau
Ben Adler
about 1 month ago
Today in
@nature.com
, we highlight how a cousin of CRISPR-Cas10, mCpol, establishes an evolutionary trap in anti-phage immune systems. Check out
@erinedoherty.bsky.social
and my work from
@doudna-lab.bsky.social
lab here:
www.nature.com/articles/s41...
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A miniature CRISPR–Cas10 enzyme confers immunity by inhibitory signalling - Nature
Panoptes, an anti-phage defence system against virus-mediated immune suppression, is revealed.
https://www.nature.com/articles/s41586-025-09569-9
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reposted by
Raphael Laurenceau
Joshua Weitz
about 1 month ago
"Alignment" (aka fealty) is not a merit-review criteria. If ideology determines outcomes, our world-class federally funded research system will reward apparatchiks and loyalists while punishing opponents and critics. And then soon, it won't be world-class.
www.washingtonpost.com/education/20...
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White House considers funding advantage for colleges that align with Trump policies
The proposal has the potential to transform the government’s vast research funding operation, which has long awarded university grants based on scientific merit.
https://www.washingtonpost.com/education/2025/09/28/trump-university-research-grants-funding-preference/
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reposted by
Raphael Laurenceau
Rebecca R Helm
about 2 months ago
I get that the news cycle is packed right now, but I just heard from a colleague at the Smithsonian that this is fully a GIANT SQUID BEING EATEN BY A SPERM WHALE and it’s possibly the first ever confirmed video according to a friend at NOAA 10 YEAR OLD ME IS LOSING HER MIND (a thread 🧵)
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reposted by
Raphael Laurenceau
Géraldine Laloux
about 2 months ago
🚨New paper out!
#MicroSky
Studying obligate predators like Bdellovibrio bacteriovorus is tricky—essential genes for predation are also essential for survival. We expanded its genetic toolbox: 🧬promoters to fine-tune expression 🧬IPTG-inducible system 🧬CRISPRi for rapid knockdown
bit.ly/46GUn2c
1/4
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Expanding the genetic toolbox of the obligate predatory bacterium Bdellovibrio bacteriovorus with inducible gene expression and CRISPR interference
Inducible gene expression and CRISPR interference-mediated depletion in the predatory bacterium Bdellovibrio bacteriovorus.
https://academic.oup.com/microlife/article/doi/10.1093/femsml/uqaf021/8245127
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reposted by
Raphael Laurenceau
Julie Le Bris
2 months ago
Delighted to share our recently published work! Ever wondered how Klebsiella (and others) deals with capsule production’s costs ? The paper:
journals.asm.org/doi/10.1128/...
Thread👇
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Phenotypic heterogeneity of capsule production across opportunistic pathogens | mBio
The polysaccharidic capsule is present in ~50% of species across the bacterial phylogeny, including all ESKAPE microorganisms, the six most significant multidrug-resistant (MDR) nosocomial pathogens. It is also an important virulence factor and a major ...
https://journals.asm.org/doi/10.1128/mbio.01807-25
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www.cell.com/cell/fulltex...
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AI mirrors experimental science to uncover a mechanism of gene transfer crucial to bacterial evolution
By solving a previously unsolved biological question, the AI co-scientist predicted a complex mechanism of gene transfer and generated hypotheses that opened new research directions, illustrating AI's...
https://www.cell.com/cell/fulltext/S0092-8674(25)00973-0
about 2 months ago
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www.nature.com/articles/s41...
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Programmable antisense oligomers for phage functional genomics - Nature
Establishing antisense oligomers as versatile, non-genetic tools to silence phage mRNAs opens applications in basic research and biotechnology, as shown by identifying essential factors for propagatio...
https://www.nature.com/articles/s41586-025-09499-6
2 months ago
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reposted by
Raphael Laurenceau
Anita Tarasenko
2 months ago
🚨New Review Out🚨 We explore how phage-antibiotic synergy can dismantle efflux-driven resistance in multidrug-resistant ESKAPEE pathogens. By reprogramming bacterial defences, phages offer a precision strategy to restore antibiotic efficacy.
journals.asm.org/doi/10.1128/...
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Reprogramming resistance: phage-antibiotic synergy targets efflux systems in ESKAPEE pathogens | mBio
Antimicrobial resistance (AMR) is one of the greatest threats to global health. If unaddressed, it is projected to cause over 39 million cumulative deaths globally by 2050 (1). While resistance is a b...
https://journals.asm.org/doi/10.1128/mbio.01822-25
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reposted by
Raphael Laurenceau
Diamond Lab
2 months ago
Our paper on model cyanobacterial communities by
@andrejakust.bsky.social
is finally typeset and looks beautiful, check it out:
academic.oup.com/ismej/articl...
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Model cyanobacterial consortia reveal a consistent core microbiome independent of inoculation source or cyanobacterial host species
Abstract. Cyanobacteria are integral to biogeochemical cycles, influence climate processes, and hold promise for commercial applications. In natural habita
https://academic.oup.com/ismej/article/19/1/wraf142/8193365
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OMG this is it?! The final piece in the puzzle?!😲 tRNAs are the key, because archaic tRNAs sit at the core of all ribosomes. If aminoacyl-tRNAs could form on early Earth, you have a plausible route for the first self-replicators, the bridge from chemistry to biology
www.nature.com/articles/d41...
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Origins of life: the molecules that could have unlocked peptide synthesis
For life to emerge on Earth, peptides must first have formed without the aid of enzymes — but how? Reactions of sulfur-containing molecules might have been key.
https://www.nature.com/articles/d41586-025-02518-6
2 months ago
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www.nature.com/articles/s41...
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Targeted delivery of diverse biomolecules with engineered bacterial nanosyringes - Nature Biotechnology
Ribonucleoproteins, nucleic acids and proteins are delivered into target cell types with nanosyringes.
https://www.nature.com/articles/s41587-025-02774-x
3 months ago
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reposted by
Raphael Laurenceau
Peter Fineran
3 months ago
Ever wondered why some bacteria have multiple CRISPR-Cas systems? Our new study led by Leah Smith shows how type I CRISPR systems can promote the acquisition and retention of new spacers into a co-occuring type III system.
www.sciencedirect.com/science/arti...
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Type I CRISPR-Cas immunity primes type III spacer acquisition
CRISPR-Cas systems are diverse, with microbes harboring multiple classes and subtypes. Type I DNA-targeting and type III RNA-targeting systems often c…
https://www.sciencedirect.com/science/article/pii/S1931312825002938?dgcid=author
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reposted by
Raphael Laurenceau
Sternberg Lab
4 months ago
1/16 New pre-print from the Sternberg Lab! We uncover how temperate phages can use RNA-guided transcription factors to remodel the flagellar composition of their bacterial host and enhance their fitness. Find the preprint and full story here:
tinyurl.com/mshwjd77
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What a cool way to sort out massive information!
add a skeleton here at some point
4 months ago
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reposted by
Raphael Laurenceau
Ben Adler
4 months ago
Seriously cool Microbiome Engineering work!
www.science.org/doi/10.1126/...
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Controlled colonization of the human gut with a genetically engineered microbial therapeutic
Precision microbiome programming for therapeutic applications is limited by challenges in achieving reproducible colonic colonization. Previously, we created an exclusive niche that we used to engraft...
https://www.science.org/doi/10.1126/science.adu8000
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Raphael Laurenceau
Trevor Lithgow
4 months ago
Because of the forces they have to withstand being whizzed around on
#flagellae
, flagellotropic
#phages
are super stable. It turns out that the same super-stability remains long after you adapt to a host bacterium without a
#flagellum
rdcu.be/ewnzT
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Highly stable bacteriophages PIN1 and PIN2 have hallmarks of flagellotropic phages but infect immotile bacteria
npj Viruses - Bacteriophages (phages) are viruses that kill bacteria, with potential as antibacterial agents in industrial settings, agriculture, and human health. Here, we identified two phages,...
https://rdcu.be/ewnzT
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reposted by
Raphael Laurenceau
Alvaro Sanchez
4 months ago
How may theoretical ecology & evolutionary theory push microbiology forward? At Environmental Microbiology, I am commissioning a series of Perspectives exploring that question. Excited to share them in the 🧵 below The series is open, so do get in touch if you'd like to propose a new contribution!
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Raphael Laurenceau
BejaLab
4 months ago
Prophages block cell surface receptors to preserve their viral progeny
www.nature.com/articles/s41...
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Prophages block cell surface receptors to preserve their viral progeny - Nature
Zip promotes the accumulation of free phages in bacterial lysogen communities, safeguarding phage progeny.
https://www.nature.com/articles/s41586-025-09260-z
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Raphael Laurenceau
Vivek Mutalik
4 months ago
#phage
#phagesky
add a skeleton here at some point
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Raphael Laurenceau
Jan-Willem Veening
4 months ago
Now published, congrats Bevika, Kinki, Vincent, Florian and Paddy!
#MicroSky
www.nature.com/articles/s41...
add a skeleton here at some point
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www.nature.com/articles/d41...
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Found: a human gut microbe that makes cancer therapy more effective in mice
Cancer therapies called checkpoint inhibitor drugs, which ratchet up the immune system, work better when this bacterium is around.
https://www.nature.com/articles/d41586-025-02224-3
4 months ago
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reposted by
Raphael Laurenceau
Alexander Harms
4 months ago
Fantastic preprint of Bert van den Berg,
@sykhalid.bsky.social
Syma Khalid, and colleagues on the molecular mechanism of how phages target LptD as host receptor👇🏼🧬🔐
add a skeleton here at some point
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reposted by
Raphael Laurenceau
Vivek Mutalik
4 months ago
😳 microcins
#microsky
www.nature.com/articles/s41...
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Antibacterial microcins are ubiquitous and functionally diverse across bacterial communities - Nature Communications
Bacteria produce antibacterials to aid competition in complex communities. Here, the authors show that class II microcins, an understudied group of secreted antibacterials, are abundant, with diverse ...
https://www.nature.com/articles/s41467-025-61151-z
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reposted by
Raphael Laurenceau
Tami Lieberman
4 months ago
Our paper demonstrating that within-species warfare interactions are ecologically important on human skin is now published in Nature Micro!
www.nature.com/articles/s41...
add a skeleton here at some point
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Raphael Laurenceau
Harry Low’s Lab
4 months ago
In-situ SPA 🧨
www.biorxiv.org/content/10.1...
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In-situ structures of the Legionella Dot/Icm T4SS identify the DotA-IcmX complex as the gatekeeper for effector translocation
The Dot/Icm machine in Legionella pneumophila is one of the most versatile type IV secretion systems (T4SSs), with a remarkable capacity to translocate over 330 different effector proteins across the ...
https://www.biorxiv.org/content/10.1101/2025.06.23.660953v1
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It's about time we asked this question
www.nature.com/articles/d41...
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How many PhDs does the world need? Doctoral graduates vastly outnumber jobs in academia
PhD programmes need to better prepare students for careers outside universities, researchers warn.
https://www.nature.com/articles/d41586-025-01855-w
5 months ago
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Raphael Laurenceau
Meaghan Castledine
5 months ago
How do multiple coexisting bacteria and phages (co)evolve? Well... they don't (or do so much less! In this paper we tracked bacteria-phage (co)evolution in monoculture (individual bacteria-phage pairs) or in polyculture (all three pairs) over 6 weeks. Read more here👇
doi.org/10.1099/mic....
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Raphael Laurenceau
Seth Shipman
5 months ago
New Preprint!! Alejandro González-Delgado accomplished a major feat on this one: ported retron recombineering, which we love so much in E. coli, into 14 new bacterial species via a massive collaborative effort involving 9 labs!
www.biorxiv.org/content/10.1...
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www.nature.com/articles/s41...
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Bioremediation of complex organic pollutants by engineered Vibrio natriegens - Nature
A synthetic biology approach was used to engineer Vibrio natriegens into a strain capable of bioremediating complex organic pollutants in saline wastewater and soils, thereby addressing notable threat...
https://www.nature.com/articles/s41586-025-08947-7
5 months ago
0
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Raphael Laurenceau
Tominaga K. (tomiken)
5 months ago
Saccharibacteria deploy two distinct type IV pili, driving episymbiosis, host competition, and twitching motility | The ISME Journal | Oxford Academic
https://academic.oup.com/ismej/advance-article/doi/10.1093/ismejo/wraf119/8158625?login=true
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Saccharibacteria deploy two distinct type IV pili, driving episymbiosis, host competition, and twitching motility
Abstract. All cultivated Patescibacteria, also known as the candidate phyla radiation, are obligate episymbionts residing on other microbes. Despite being
https://dx.doi.org/10.1093/ismejo/wraf119
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Raphael Laurenceau
RCSB Protein Data Bank
5 months ago
Cryogenic electron microscopy showed for the first time that large RNA complexes can assemble without the help of proteins, expanding our understanding of RNA folding and function.
www6.slac.stanford.e...
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SLAC, Stanford researchers discover large protein-free RNA structures
Cryogenic electron microscopy showed for the first time that large RNA complexes can assemble without the help of proteins.
https://www6.slac.stanford.edu/news/2025-05-06-slac-stanford-researchers-discover-large-protein-free-rna-structures
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Raphael Laurenceau
Joshua Weitz
5 months ago
How bad will it be? Catastrophic. Proposed cuts to
#NSF
,
#NIH
, and
#NASA
will set the US R&D landscape back 25 yrs+, cause economic and job loss now, and undermine innovations to come. But, this is the WH's *proposed* budget. Speak up now before it is too late. (inflation adjusted $-s below)
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Raphael Laurenceau
EvoNerdette
5 months ago
Its here! Finally published.
www.tes.com/magazine/tea...
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How to bring experimental evolution to the classroom
Pupils of all ages can benefit from witnessing evolution in real time - and it’s now possible in schools, say this researcher from the University of Bath
https://www.tes.com/magazine/teaching-learning/general/how-to-teach-evolution-in-schools
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www.quantamagazine.org/how-paradoxi...
We need more of this! “Recreational biology”
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How Paradoxical Questions and Simple Wonder Lead to Great Science | Quanta Magazine
Manu Prakash works on the world’s most urgent problems and seemingly frivolous questions at the same time. They add up to a philosophy he calls “recreational biology.”
https://www.quantamagazine.org/how-paradoxical-questions-and-simple-wonder-lead-to-great-science-20250528/
5 months ago
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Raphael Laurenceau
ᐯIᑕTOᖇ ᑎIᘔET, ᗰᗪ
6 months ago
AMR in Nature Medicine 4,502 surveillance records 32M tested isolates 101 countries Impact of socioeconomic and environmental factors—forecasts based on antimicrobial consumption reduction, sustainable development, shared socioeconomic pathways under climate change
www.nature.com/articles/s41...
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www.nature.com/articles/s41...
Type IV pili versatility never cease to amaze. In this case, used by Myxococcus can thus to grab and kill other bacteria
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Tad pili with adaptable tips mediate contact-dependent killing during bacterial predation - Nature Communications
The predatory bacterium Myxococcus xanthus kills other bacteria by contact. Here, Herrou et al. show that the predator uses an extensible appendage, or pilus, that is functionalized by four distinct m...
https://www.nature.com/articles/s41467-025-58967-0
6 months ago
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