Félix de Carpentier

Pretty excited to share our new preprint!
Non-photosynthetic Plastid Replacement by a Primary Plastid in the Making
www.biorxiv.org/content/10.1...

Total solar eclipse triggers dawn behavior in birds: Insights from acoustic recordings and community science On 8 April 2024, a total solar eclipse disrupted light-dark cycles for North American birds during the lead-up to spring reproduction. Compiling more than 10,000 community observations and artificial ...

I have to fan-girl for a minute here. My friend @rosvall-lab.bsky.social built an app to gather data on bird behavior during the 2024 solar eclipse. 10,000+ citizen scientists contributed (including my kids), and the resulting paper was published in Science today!

www.science.org/doi/10.1126/...

Salicylic acid biosensor, SalicS1, tracks the plant immune hormone salicylic acid in real time - revealing propagation of hormone surge during plant pathogen advance

Latest biosensor from @xanderjones.bsky.social team
In Science doi.org/10.1126/scie...
Summary www.slcu.cam.ac.uk/news/new-bio...

Efficient and accurate search in petabase-scale sequence repositories - Nature MetaGraph enables scalable indexing of large sets of DNA, RNA or protein sequences using annotated de Bruijn graphs.

The Metagraph paper is out in Nature; it showed up in my feeds today! Congratulations to Mikhail Karasikov, @gxxxr.bsky.social, @akkah21.bsky.social and all of the other authors (whom I'd love to follow on Bluesky if I can find you ;P) www.nature.com/articles/s41...

New paper out! 💌🔬Spirorhynchus verrucosus is a Muranotrichean and its sister has been livin' in the deep sea Santa Barbara Basin since the 90's! See them TUFTS!! Wonderful work of B Bourland & Cepicka Lab, R Beinart, & J Bernhard enabling deep sea sampling. Read h1.nu/spiror #ProtistsOnSky #MicroSky

Postdoc Description.docx Title: Postdoctoral Associate Summary statement: The postdoctoral research associate is responsible for developing novel computational methodology for high-throughput sequence genomics tasks, as well ...

Have you recently completed (or finishing soon) a PhD in CS or a related discipline? Do you want to do research advancing the theory & practice of algorithmic genomics & build tools that people love to use? I'll be looking to hire a postdoc! Official ad coming soon:
docs.google.com/document/d/1...

Structural Insights into RubisCO Dynamics and Pyrenoid Architecture in Chlamydomonas reinhardtii https://www.biorxiv.org/content/10.1101/2025.09.18.677200v1

🌊🔬 Looking for a postdoc to join our team!
Cocco-Channel project ➡️ studying coccolithophore phycospheres and their role in ocean carbon cycling.
✔️ Plus if you bring experience in microbial ecology, molecular/microscopy tools & fieldwork
👉 More info: euraxess.ec.europa.eu/jobs/375178
#protistsonsky

How to upgrade stolen organelles into permanent plastids: A comparative transcriptomic perspective | PNAS www.pnas.org/doi/abs/10.1... #protistsonsky

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...

www.pnas.org/doi/10.1073/...

OIST is seeking up to four tenure-track or tenured faculty in Ecology, Environmental Science, Earth Science, and Oceanography. Application deadline: Oct 15. Please share. Thx!
www.oist.jp/careers/facu...

UNC Chapel Hill is hiring an Assistant Professor in Plant Molecular Biology. Per Jeff
Dangl MPMI candidates are also highly desired in the search. unc.peopleadmin.com/postings/307...

EPP1 is an ancestral component of the plant Common Symbiosis Pathway The success of plants on land has been enabled by mutualistic intracellular associations with microbes for 450 million years ([Delaux and Schornack 2021][1]). Because of their intracellular nature, th...

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

Two papers to tell us more about mysterious EPP1, a protein required for symbiosis. Well done @tatiana-vernie.bsky.social and all co-authors.

EPP1 is an ancestral component of the plant Common Symbiosis Pathway The success of plants on land has been enabled by mutualistic intracellular associations with microbes for 450 million years ([Delaux and Schornack 2021][1]). Because of their intracellular nature, th...

So happy to see the latest preprint of the team out! www.biorxiv.org/content/10.1...
The continuation of a long standing project started by @oswaldovaldesl.bsky.social in @jeanmichelane.bsky.social‘s lab. 1/7 🧵

One-shot design of functional protein binders with BindCraft - Nature BindCraft, an open-source, automated pipeline for de novo protein binder design with experimental success rates of 10–100%, leverages AlphaFold2 weights to generate binders with nanomolar affinity without the need for high-throughput screening.

BindCraft: an AlphaFold2-powered de novo protein binder design tool 🧬✨
Tested in some bacterial systems too! Designs so far are short peptides or mini-domains. Looking forward to long/full protein design ahead! 🧪 #microsky
www.nature.com/articles/s41...

X-Mapper 🦠🧬🧪 - a sequence aligner developed for microbes, now on Bioconda! 🚀
• 11–24× fewer suboptimal alignments (same for human genome)
• 3–579× lower inconsistency
• improves on ~30% of reads aligned to non-target species
github.com/mathjeff/map...
bioconda.github.io/recipes/x-ma...
#microsky

Latest from ours: www.cell.com/cell-reports...

This is two stories in one: a case study/cautionary tale on developing genetic tools in new organisms, and the first hint at a gene regulatory network for choanoflagellate multicellular development (which turn out to involve a Hippo/YAP/ECM loop!) A 🧵

Ragnarok: a flexible and RApid GeNe Annotation (ROcKs) pipeline deployed through Nextflow https://www.biorxiv.org/content/10.1101/2025.10.03.680343v1

UMass Amherst Biology is recruiting a tenure-track Assistant Professor in the area of Plant Physiology. Deadline Nov 1. Please spread the word and apply!

careers.massachusetts.edu/mob/en-us/jo...

Sometimes I think about how from 1935-1975ish, Bell Labs produced an insane amount of revolutionary science and technology, including 11 Nobel Prizes, the transistor, UNIX, C, the laser, the solar cell, information theory, etc. The secret? Provide scientists with ample, steady, no-strings funding.

Strong statement today from UC's Academic Senate:

Russell R. Geiger Professorship of Crop Science

Dept. of Plant Sciences | Permanent | Closes on Monday 17 November 2025

www.cam.ac.uk/jobs/russell...

#plantsciences #plantscijobs #academicjobs

AI reveals vast ‘ghost forests’ along U.S. coast Machine learning method counts nearly 12 million dead trees, many likely killed by rising seas

I joined a team of ecologists wading through the muck of the Carolina coast in search of "ghost forests" killed by rising seas for @science.org. We were guided by a a new map that reveals millions of dead trees standing along the East Coast, marking an overlooked consequence of climate change...

Megaplasmids associate with Escherichia coli and other Enterobacteriaceae Humans and animals are ubiquitously colonized by Enterobacteriaceae , a bacterial family that contains both commensals and clinically significant pathogens. Here, we report Enterobacteriaceae megaplas...

New pre-print from the Banfield lab, highlighting an interesting case of 1.5Mb megaplasmids found in human gut.

Plasmid genomes were resolved using #PacBio HiFi sequencing with hifiasm-meta for #metagenome assembly. Host association was detected using epigenetic signals.

doi.org/10.1101/2025...

>18,000 new genomes of giant DNA viruses! An incredible trove of new genes and insights into evolution of host-virus interactions from @fmschu.bsky.social and @jgi.doe.gov

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

Giant DNA viruses encode a hallmark translation initiation complex of eukaryotic life In contrast to living organisms, viruses were long thought to lack protein synthesis machinery and instead depend on host factors to translate viral transcripts. Here, we discover that giant DNA viruses encode a distinct and functional IF4F translation initiation complex to drive protein synthesis, thereby blurring the line between cellular and acellular biology. During infection, eukaryotic IF4F on host ribosomes is replaced by an essential viral IF4F that regulates viral translation, virion formation, and replication plasticity during altered host states. Structural dissection of viral IF4F reveals that the mRNA cap-binding subunit mediates exclusive interactions with viral mRNAs, constituting a molecular switch from translating host to viral proteins. Thus, our study establishes that viruses express a eukaryotic translation initiation complex for protein synthesis, illuminating a series of evolutionary innovations to a core process of life. ### Competing Interest Statement The authors have declared no competing interest. Pew Biomedical Scholars Program G. Harold & Leila Y. Mathers Foundation, https://ror.org/02a7hjv13 National Institutes of Health, 1R35GM142527, 1DP2GM146250, F31NS132412 Parker Institute for Cancer Immunotherapy, https://ror.org/0184qbg02 European Research Council, 832601, 101160452 Branco Weiss Fellowship Moderna Therapeutics (United States), https://ror.org/01xm4wg91

Giant DNA viruses encode a hallmark translation initiation complex of eukaryotic life | bioRxiv https://www.biorxiv.org/content/10.1101/2025.09.30.678621v1?rss=1

A Key Role for S-Nitrosylation in Immune Regulation and Development in the Liverwort Marchantia polymorpha https://www.biorxiv.org/content/10.1101/2025.09.29.679193v1

The genome of the vining fern Lygodium microphyllum highlights genomic and functional differences between life phases of an invasive plant | PNAS Functional and genomic studies on the differences between the gametophyte and sporophyte life phases of plants remain scarce, yet unraveling these ...

Another fern (Lygodium microphyllum) genome just published @pnas.org !

What a year for non-sed plant genomics!

www.pnas.org/doi/10.1073/...

Become my colleague @oxfordbiochemistry.bsky.social !
2 Associate Professorships in the areas of
- prokaryotic/eukaryotic microbiology
- metabolism

my.corehr.com/pls/uoxrecru...

TEtrimmer: a tool to automate the manual curation of transposable elements. #TransposableElements #ManualCuration #Genomics #Bioinformatics @natcomms.nature.com 🧬 🖥️
www.nature.com/articles/s41...