Happy to share that I've accepted a CNRS Chaire de Professeur Junior position in computational biology as part of the Génomique Métabolique unit at Genoscope! Looking forward to working with my fellow researchers there as well as with the broader 🇫🇷 research community starting this summer!

🇺🇳/🇮🇹 🔜 🇫🇷

Off to RWTH Aachen University @core-rwth.bsky.social for a micro-sabbatical—time to rethink SynBio not as a tool for controlling & dominating nature, but as a means to negotiate with it and help heal the environment—and developing a new narrative re GMOs for bioremediation along the way 🤔

The first published article of my PhD. As described by @gerrich.bsky.social, we equipped R. sphaeroides with a MoClo system, characterized genetic elements, and applied a semi-automated approach for rapid strain construction. Such a nice collaboration!

Congratulations Matic 🥳

Great presentation by @francesarnold.bsky.social for the Backer lecture this afternoon! Organized by the Backer Foundation (www.backerfoundation.nl), held at the @rug.nl . About evolving an designing novel enzymes. Very cool! (With quite some machine learning and even some DISCO )

Happy to present our latest story: the BCRII complex with the Boll and @cellarchlab.com . Months of processing by @rnfr2d2.bsky.social. Also @tomaspascoa.bsky.social and @tamb-o.bsky.social managed an in-situ tour de force. And Lena Appel did amazing biochemistry. This story has it all. Enjoy it.

Rhodo-Box: A Synthetic Biology Toolbox to Facilitate Metabolic Engineering of Rhodobacter sphaeroides Rhodobacter sphaeroides is a purple nonsulfur alphaproteobacterium with a highly versatile metabolism. This microorganism holds promise as a chassis for sustainable biomanufacturing of numerous chemicals. Yet, its potential is constrained by a lack of standardized, well-characterized genetic elements to tune gene expression such as transcriptional promoters and ribosome binding sites (RBSs). In this study, we present Rhodo-Box, a comprehensive toolkit for R. sphaeroides created by adapting and extending the Zymo-Parts modular cloning framework. Using Rhodo-Box we built and characterized: (a) three broad-host origins of replication (pBBR1, RK2 and RSF1010), (b) a set of 13 promoters, (c) four inducible expression systems (NahR-PsalTTC, LacI-PlacT7A1_O3O4, VanR-PvanCC, and XylS-Pm), (d) 11 RBSs, and (e) four transcriptional terminators. Furthermore, we present a semiautomated, user-friendly cloning approach which enables rapid construction of R. sphaeroides strains. The Rhodo-Box toolkit equips R. sphaeroides with a standardized, automation-compatible collection of parts and workflows essential for efficient design–build–test–learn cycles and advanced metabolic engineering.

Publication alert 🚨
A new Golden Gate MoClo toolbox for Rhodobacter sphaeroides is out and it's built on Zymo-Parts!

@matick.bsky.social & Antoine took our framework and added many new genetic tools and a new automation angle.

This adaptation is a dream come true for me. 1/10 🧪🧵

🧵 Our new paper is out today in molecularcell.bsky.social! After 7 years of a truly intriguing discovery journey, we can finally share what controls how molecules move inside living E. coli cells. Spoiler: it's not what the field thought. A thread 👇
📄 doi.org/10.1016/j.molcel.2026.03.018

Excited to share our new paper out today in @science.org 🎉

We show that HGT via natural competence drives diversification of chromosomal integrons in V. cholerae 🤩

Below a 🧵 on key findings incl. background on natural competence in V. cholerae 1/
#microsky #phagesky
www.science.org/doi/10.1126/...

Torn between amusement and frustration that @alignbio.bsky.social cancels PETase tournament halfway through. Cryptic mail suggests they hugely underestimated how difficult measuring enzyme activity in high throughput really is. Better pulling the plug than lousy execution, but.. poor planning?

Do we grow wiser as we age?
I spent 15+ years chasing glam journals, wasting time and energy (and frustrating my team and co-authors).
I don’t want to wake up at 70 and realize my life went into convincing a few editors my work was trendy enough.
Enough. I’ll try to be smarter.

mad neuroscientists marching in Berkeley

Scientific Publishing: Rethinking how research is reviewed and published Taking a radical new approach to the publication process resulted in eLife losing its impact factor, but authors, reviewers, editors and funders support the journal and its efforts to reform scientifi...

“Authors [&] reviewers tell us that they have had a more constructive experience…choosing eLife not because of our impact factor, but because of our process”

👆 eLife comtinues to provoke debate but this is perhaps the most important point elifesciences.org/articles/110...

Mathematisch-Naturwissenschaftliche Fakultät Heute ernannte Rektorin Prof. Dr. Anja Steinbeck den Biotechnologen Dr. Johannes Rebelein zum W3-Professor für Nachhaltige Biotechnologie. Rebelein wird damit auch Direktor des Instituts für Molekular...

A childhood dream has come true – I was appointed Full Professor for Sustainable Biotechnology at the University of Düsseldorf @hhu.de : tinyurl.com/f43s74hp and as Director of the Institute for Molecular Enzyme Technology (IMET, www.iet.uni-duesseldorf.de/en/) at FZ Jülich @fz-juelich.de .

I have a postdoc position in metagenomic exploration available in my group. Candidates with documented experience in phylo & metagenomics and preferably with petabase-scale data mining and GLM workflows are encouraged to apply. Come join us! 🧬🦠💻

Please repost

Apply here: www.wur.nl/en/vacancy/p...

Time to leverage SynBio for tacking environmental pollution. But releasing bioengineered microorganisms still raises alarms. A new narrative is badly needed: bacteria for bioremediation are not alien intrusions but laboratory-trained extensions of life’s creativity link.springer.com/10.1038/s443...

Unconstitutional force. Civilians dead. Congress bypassed. Oil interests front and center.

We’ve seen this movie before and it ends in blood. But we don’t have to do it again.

Doing a PhD is - at heart - one long discussion with your mentor. The discussion changes over time - with unexpected turns and ups & downs - but through it all is a pair of people discussing a topic endlessly to make sense of it.
PhD students: choose someone you like to talk to!

Congratulations 🎉🎉🎉 to our esteemed #microbiology @ribesresearch.bsky.social colleague @cuwelte.bsky.social on being the proud recipient of a prestigious @erc.europa.eu consolidator grant on electroANME.
All the best with your research. Very well deserved :) erc.europa.eu/news-events/...

ERC’s new €7m Plus Grants open to researchers at any career stage - Research Professional News European Research Council president describes scheme as part attempt to lure US talent

Let’s run the numbers on this new @ERC_Research “ERC-Plus” scheme. About 30 grants to be awarded, and we’re told “better apply for a regular grant, your chances are 30× higher.”

www.researchprofessionalnews.com/rr-news-euro...

Industrial and agricultural chemicals exhibit antimicrobial activity against human gut bacteria in vitro - Nature Microbiology Screening of 1,076 compounds reveals 168 chemical pollutants with inhibitory effects on gut bacteria and genetic screens indicate commonality between pollutant and antibiotic resistance.

Excited to share our latest research in @natmicrobiol.nature.com . We uncover hundreds of inhibitory interactions between common chemical pollutants and human gut bacteria. A thread🧵 (1/10) #microbiomesky #microsky @kiranrpatil.bsky.social lab @mrc-tu.bsky.social www.nature.com/articles/s41...

Modular in vivo engineering of the reductive methylaspartate cycles for synthetic CO2 fixation Biological carbon fixation is currently limited to seven naturally occurring pathways. Synthetic carbon fixation pathways have the potential to surpass aerobic natural pathways in efficiency, but none...

Newest preprint from our lab: a new family of promising synthetic CO2 fixation cycles that may outcompete the Calvin cycle and that Vittorio Rainaldi realized to a great extent in E. coli! Up to 11 heterologous enzymes in a cascade supporting CO2 fixation & growth! www.biorxiv.org/content/10.1...

Fluorescein-based dyes are not valid reporters of oxidative stress in bacteria, and conclusions based on their use must be reconsidered | PNAS Dihydrodichlorofluorescein derivatives have been employed as reporters of intracellular reactive oxygen species (ROS) in innumerable studies. Their...

Hmmm
This work has so many implications on literature 😳😬

Fluorescein-based dyes are not valid reporters of oxidative stress in bacteria, and conclusions based on their use must be reconsidered | PNAS www.pnas.org/doi/10.1073/...

Prashant Singh in the lab of Tina Iverson at Vanderbilt published this image of the bacterial 🦠flagellar motor, a detailed molecular model made possibly by CryoEM 🔬.

The similarity to mechanical motors are strong enough we can use terms like stator, rotor, rod & gearing to describe it.

Black and white photograph of six-year-old Ruby Bridges, wearing a dark dress and white cardigan and carrying a School bag, accompanied by three FBI agents in dark suits.

Sixty-five years ago today, four first-graders desegregated New Orleans's public schools: Ruby Bridges at William Frantz Elementary School, and Leona Tate, Tessie Provost, and Gail Etienne at McDonogh 19 Elementary School. They faced violent mobs and threats to their lives. They were 6 years old. 🗃

Metagenomic editing of commensal bacteria in vivo using CRISPR-associated transposases Although metagenomic sequencing has revealed a rich microbial biodiversity in the mammalian gut, methods to genetically alter specific species in the microbiome are highly limited. Here, we introduce ...

Very excited to share our latest work in Science on metagenomic editing (MetaEdit) of the gut microbiome in vivo & directly modifying unculturable immune-modulatory SFB bug in the small intestine. 🦠🧬🛠️
www.science.org/doi/10.1126/...

Very nice. Looking forward to a more detailed read!

Very happy to share our recent work @cultivarium.bsky.social on genetic tools for Ideonella sakaiensis, a (Betaproteo-)bacterium that degrades PET plastic.

We identified a plasmid vector for the strain and generated a large RB-TnSeq library, screening for genes impacting plastic degradation.

Prof. Hamilton Smith at J. Craig Venter Institute, a Nobel laureate for discovering type II restriction enzymes, passed away last night.
@jcvi.org @nobelprize.bsky.social
A huge loss in Science, but his legacy will be remembered.
www.jcvi.org/about/hamilt...

Such an honor! Can’t wait to visit Brno next week, the place I’ve been teaching about in Genetics course for years but never visited (I feel like I know the garden and the monastery from what I read).