Antoine Hocher
@ahocher.bsky.social
Group Leader, Molecular mimicry / chromatin evolution / engineering Department of Genetics, University of Cambridge. Wellcome Trust CDA fellow https://www.gen.cam.ac.uk/research/research-groups/hocher-group
Academic advice travels downhill: manage your supervisor, publish early, protect your time. Where is the genre in which early-career researchers advise the people who hire, fund and judge them? New post 👇 academicrenewal.substack.com/p/the-first-...
The first curriculum
Academic survival guides teach junior researchers how to live with the judgements of senior scholars. No corresponding genre gives young researchers authority to advise the people who judge them.
academicrenewal.substack.com
Now out as a perspective in PLOS Biology. Where next for structural bioinformatics? journals.plos.org/plosbiology/...
Where next for structural bioinformatics?
Structural bioinformatics aims to answer biological questions by considering biomolecular structures at scale. This Perspective argues that now that we have accurate predictions, we need to ask what w...
journals.plos.org
Joe Greener@jgreener64.bsky.social · 10mo agoI wrote a blog post about the future of structural bioinformatics. Where to go after AlphaFold? How do we avoid the field becoming a load of half-baked LLMs? Let me know what you think. jgreener64.github.io/posts/struct...
Bacteriocins in archaea and archaeocins in bacteria. @romainstrock.bsky.social surveys the the exchange of molecular weaponry between archaea and bacteria. www.biorxiv.org/content/10.6...
Bacteriocins in archaea and archaeocins in bacteria
Archaea and bacteria routinely live side by side in microbial communities and must interact at least on occasion. Whether such cross-Domain interactions are dominated by mutual disregard, co-operation...
biorxiv.org
🧬 Delighted to share our new Nature Communications paper! We show how MCM2-7 double hexamers become active helicases and trigger DNA melting in vivo. Led by Chris Weekes & L. Maximilian Reuter. Congratulations to the whole team! doi.org/10.1038/s414... #DNAReplication
Mechanisms of MCM2–7 helicase activation and initial DNA melting at near base-pair resolution - Nature Communications
DNA replication begins when inactive helicases are switched on to unwind DNA. Here, the authors map this activation in yeast, revealing where DNA first melts and how helicase splitting, factor release...
doi.org
Our new preprint is out! We investigate chromosome organization in obligate mammalian symbionts and show that these bacteria maintain stable chromosome orientations while displaying conserved lifestyle-associated chromosome architectures across species. www.biorxiv.org/cgi/content/...
AF-CALVADOS is now published doi.org/10.1002/pro.... We combine AlphaFold and CALVADOS to simulate flexible multidomain proteins at scale: — Ensembles of >12000 full-length human proteins — Comparison of IDRs alone and I n context for >1500 TFs @sobuelow.bsky.social @kejohansson.bsky.social
Day 2 of #EMBOMBoA workshop on the biology of archaea, at the MRC LMb in Cambridge. Yesterday was incredible with outstanding talks spanning from eukaryogenesis to gut dwellers. 🔥🔥
Must read! Congrats !!
Chung Hyun Cho@chc-evobio.bsky.social · last mo.Excited to share our new preprint led by Fred and me in collaboration with the archaeal community! We found that the molecular foundation of histone-based chromatin has pre-eukaryotic roots in Asgard archaea. (1/4) #ArchaeaSky www.biorxiv.org/content/10.6...
Excited to share our new preprint led by Fred and me in collaboration with the archaeal community! We found that the molecular foundation of histone-based chromatin has pre-eukaryotic roots in Asgard archaea. (1/4) #ArchaeaSky www.biorxiv.org/content/10.6...
Emergence of histone-based chromatin complexity in Asgard archaea
The emergence of the eukaryotes coincided with the diversification of histone proteins and their post-translational modifications by enzymes that constitute the core of eukaryotic chromatin. Yet the e...
biorxiv.org
🚨New paper alert 🚨 Here we tried to leverage an (incredible) metagenome time-series to better understand MGE diversity and activity in soil across decade(s). @scbagby.bsky.social has an amazing thread about this work with all the details - bsky.app/profile/scba...
Mobile genetic elements shape microbial diversity and functions in thawing permafrost soils - Nature Microbiology
An 8-year soil meta-omic time series shows how mobile genetic elements shape permafrost microbial diversity and impact a range of functions, including carbon and nutrient cycling.
nature.com
Sarah Bagby@scbagby.bsky.social · last mo.Out today in Nature Microbiology: a paper that started in 2021 with an email from @sullivan-lab.bsky.social. Subject line: "Crazy ideas". www.nature.com/articles/s41... 1/23
I have been thinking since yesterday about why I find the 1% thing so, so disturbing. It's a visceral reaction of 'just no', which goes beyond the general yuck towards the enshittification of/via AI. I have finally put my finger on it: it is the feeling you get when
Archaeaophiles! Last chance to sign up as a virtual attendee for MBoA2026. It’s cheap and you will have access to all the talks include our archaea@50 celebration with a special guest: meetings.embo.org/event/26-arc...
Molecular Biology of Archaea: Life Through the Prism of Archaea
In 1977, Woese and colleagues revealed Archaea as a distinct domain of life. Building on this insight, the discovery of Asgard archaea has strengthened the view that many hallmarks of eukaryotic cell…
meetings.embo.org
I gave a workshop on AlphaFold & related programs @ the University of Utah. Part 1 covers protein structure prediction before/after AlphaFold & deep learning neural networks. Part 2 covers the math behind the scores. Part 3 covers PyMOL & the webservers. youtube.com/@rolanddunbr...
Comprehensive analyses of archaeal viral genomes reveal genomic characteristics, divergence, and host interactions #microbiology #archaea #virus #phages #MicroSky #ArchaeaSky #PhageSky @microbiomej.bsky.social doi.org/10.1186/s401...
Comprehensive analyses of archaeal viral genomes reveal genomic characteristics, divergence, and host interactions - Microbiome
Background The ecological significance of bacteriophages has been extensively investigated, while the role of archaeal viruses across different environments remains poorly understood. Results Here, we present the Archaeal Viral Genome Database (AVGD), a comprehensive survey of archaeal viruses across eight distinct habitat types, including 3708 archaeal viral genomes, with genome sizes ranging from 3 to 188 kb, identified from 64,521,709 putative viral genomes using 40 public metagenomic datasets, an integrated public viral genome database (IGN), and pig gut viral databases. Our analysis revealed that the majority (92.93%) of archaeal viruses in the AVGD belong to the class Caudoviricetes. Phylogenetic analysis showed that many archaeal viruses diverged with their respective habitats. Using CRISPR spacer matching, we characterized the host composition of these archaeal viruses and uncovered competitive interaction networks between archaeal viruses and other archaeal viruses targeting the same host or different hosts. Furthermore, we identified 129,067 coding genes from 3708 archaeal viral genomes, most of which were associated with essential archaeal viral cellular functions, including replication, assembly, and packaging. Archaeal viruses also encoded a variety of auxiliary metabolic genes, anti-CRISPR (Acr) proteins for evading host immunity, and DNA methyltransferases for escaping host restriction-modification systems. Conclusions Together, this study provides a valuable resource and offers new insights into the ecological roles and host interactions of archaeal viruses across diverse environments. Video Abstract
doi.org
Excited to share our new preprint! 🧬❄️ by brilliant @mdreimann.bsky.social and great collaborators! Using cryo-ET&EM, we reveal archaeal chromatin in a near-native state: variable-beads-on-a-string fibers shaped by growth phase and histone composition #ArchaeaSky www.biorxiv.org/content/10.6...
Very cool! www.biorxiv.org/content/10.6...
A plasmid-encoded H-NS protein selectively binds its own plasmid
H-NS is an abundant nucleoid-associated protein found in Enterobacterales species. Some conjugative plasmids encode H-NS homologues, which are thought to facilitate plasmid maintenance and reduce the ...
biorxiv.org
Archaea are the hornets of the microbial world. Discuss. www.biorxiv.org/content/10.6... TLDR: Archaeon kills bacterium with secreted phospholipase. Pretty nifty way to kill bacteria for a microbe with a very different lipid make-up, I reckon. No need to worry about accidentally killing yourself.
biorxiv.org
Archaea the hornets of the microbial world. Discuss. www.biorxiv.org/content/10.6... TLDR: Archaeon kills bacterium with secreted phospholipase. Pretty nifty way to kill bacteria if you are a microbe with a very different lipid make-up, I reckon. No need to worry about accidentally killing yourself.
A Bactericidal Phospholipase from Archaea
Archaea kill bacteria, at least on occasion. The molecular underpinnings of these lethal interactions are barely understood. Here, we describe cinquedea, an α/β hydrolase secreted by the halophilic ar...
biorxiv.org
Effector recognition by molecular mimicry of its target by an NLR - enabling multiple disease resistance specificities to be generated- first seen on @biorxiv-plants.bsky.social - great work led by @dianagdlc.bsky.social and Matt Moscou www.science.org/doi/10.1126/...
Molecular mimicry of a pathogen virulence target by a plant immune receptor
Plants and animals respond to pathogen attack by mounting innate immune responses that require intracellular nucleotide-binding leucine-rich repeat (NLR) proteins. These immune receptors detect pathog...
science.org
Killing Dormant Bacteria Noteworthy — Semapimod was identified as a killer of non-growing Gram-negative bacteria.
Killing Dormant Bacteria
Noteworthy — Semapimod was identified as a killer of non-growing Gram-negative bacteria.
smallthingsconsidered.blog
In case it's of interest to anyone, here's a regularly updated list of UK postdoctoral research fellowships - feel free to share/copy sites.google.com/site/blakemo...
Blakemore Lab - Postdoctoral Fellowships
Below is an overview of Postdoctoral Research Fellowships in the United Kingdom, which was originally curated by Professor Rogier Kievit. These have a special focus on psychology, neuroscience, develo...
sites.google.com
Sometimes ago Tom @tommclean.bsky.social uncovered a mechanism of bacterial gene regulation based on a clamp sliding and locking in a multi-drug resistance plasmid, RK2. www.nature.com/articles/s41...
KorB switching from DNA-sliding clamp to repressor mediates long-range gene silencing in a multi-drug resistance plasmid - Nature Microbiology
Structural and single-molecule analyses show the CTPase, KorB, is a sliding DNA clamp that interacts with a clamp-locking protein KorA to inhibit gene expression over distances of more than 1 kb in th...
nature.com
🔥 Find the new friends of your favorite protein!
EMBL-EBI@ebi.embl.org · 2mo agoWe told you it wouldn’t be a long wait. 👀 Even more predicted protein structures have been added to the #AlphaFold Database. This time, the database has expanded to include heterodimers – protein complexes made up of two different proteins. alphafold.ebi.ac.uk
DAY 356 SPECIES 356 - Cycloclypeus carpenteri MEDIUM: Arches Paper. Chromatek & HWC watercolor, Sakura pen C. carpenteri is a large single celled marine protist. Its thin flat form is an adaptation to dim light in deep water #sciart #watercolor #painting #art #protist #eukaryotic #protistsonsky
New preprint! Cell division has to happen at the right place but how Archaea pick that place is unknown. We now identified a three-protein system, Dip, that positions the divisome at midcell in H. volcanii and is broadly conserved across Archaea. A thread 🧵 www.biorxiv.org/content/10.6...
biorxiv.org
Keep an eye out for this book. Coming soon by the brilliant @buzzbaum.bsky.social www.amazon.co.uk/I-Biography-...
I: A Biography of the Biological Self
Buy I: A Biography of the Biological Self by Baum, Buzz (ISBN: 9780241768846) from Amazon's Book Store. Everyday low prices and free delivery on eligible orders.
amazon.co.uk
Out today - structure of the human HIRA histone chaperone complex bound to nucleosomes. Ever wondered how nucleosomes are assembled in the wake of transcription? It takes a 'hulk of a protein complex'. Work by the amazing Wei Tian weetian558.bsky.social. www.biorxiv.org/content/10.6... 🧵
My second postdoc paper in @tunglejic.bsky.social lab and two of my favorite things in the lab combined: ParB and killing bacteria. Thanks to everyone who helped make this project possible!
Tung Le@tunglejic.bsky.social · 3mo ago@biorxiv-microbiol.bsky.social Who knew ParB-CTPase fold can kill!!! A protein fold best known for segregating chromosomes…can be transformed into a potent antibacterial toxin in some plant and animal pathogens. www.biorxiv.org/content/10.6...
I don’t want to spoil but I am sure you will enjoy Jovana and Tung’s latest work. It reads like a detective story. Very glad I could add a small contribution. Homology can be treachous to infer function !
Tung Le@tunglejic.bsky.social · 3mo ago@biorxiv-microbiol.bsky.social Who knew ParB-CTPase fold can kill!!! A protein fold best known for segregating chromosomes…can be transformed into a potent antibacterial toxin in some plant and animal pathogens. www.biorxiv.org/content/10.6...
