Kathryn (Katy) Appler
@katyappler.bsky.social
💻 Postdoc, Institut Pasteur | Dr. Simonetta Gribaldo 🌊 Ph.D. in Marine Science @UTMSI, University of Texas at Austin | Dr. Brett Baker’s Lab 🧬 Exploring Asgard archaea, deep-sea ecosystems, and the evolution of complex life.
Final version out! Now with amazing illustrations from the very talented Lily Soucy :) www.cell.com/current-biol...
Nicholas Bellono@nbellono.bsky.social · 4w agoHow did octopuses evolve novel traits? Rishav Mitra, Richard Han, Trey Scott, et al serendipitously discover a unique ribosome adaptation that increases the accuracy of protein synthesis and evolved alongside their elaborate nervous systems vs deep sea relatives. www.biorxiv.org/content/10.6...
Read our new paper! We show how the protease BepA binds the BAM complex and undergoes striking conformational changes, embedding its water-soluble lid into the membrane to cleave outer membrane proteins. www.nature.com/articles/s41... #cryoEM #astburycentre
How did octopuses evolve novel traits? Rishav Mitra, Richard Han, Trey Scott, et al serendipitously discover a unique ribosome adaptation that increases the accuracy of protein synthesis and evolved alongside their elaborate nervous systems vs deep sea relatives. www.biorxiv.org/content/10.6...
1/ Deep-time phylogenetics is hard: overly simplistic substitution models can mislead tree estimation at the billion year timescale. Our new preprint introduces GTRspmix, a protein modeling framework designed to more realistically model site-to-site heterogeneity in amino acid replacement. 🧵
Recently published in Bioinformatics Advances: "InterProScan 6: A modern large-scale protein function annotation pipeline" Find it here: https://doi.org/10.1093/bioadv/vbag141 Authors include: @matthiasblum.bsky.social, @alexbateman1.bsky.social
I'm happy to share the first pre-print of out Lab! 🎉 Introducing ArchaeaHQ www.biorxiv.org/content/10.6... We curated 21,644 genomes across all 4 archaeal kingdoms to bridge the gap in public datasets for computational biology What is inside ArchaeaHQ... (1/2)
I'm reposting this because I want to make a correction. In the thread below I mention using the -mset flag for testing site profile mixture models. But in fact you should use -madd flag. I'm sorry for this mistake.
Andrew Roger@andrewjroger.bsky.social · 5mo agoSo you are using IQ-TREE to estimate a tree for "deep time" phylogenetics using amino acid alignments. There is a lot of confusion about how to test model fit. Here are some suggestions.
🎓💙 Congrats to @Yaëlle Wormser, winner of the 2026 French final of “My Thesis in 180 Seconds” (MT180)! 🏆 In 3 minutes, she made accessible a complex study on an enzyme essential to the bacterium that causes tuberculosis with clarity & passion. 👏 #MT180
1/ Our new paper in Systematic Biology "Modeling Site-and-Branch-Heterogeneity with GFmix" led by @cgpmcc.bsky.social describes improved ways to model compositional heterogeneity across both sites and branches—an important source of error in deep phylogenomics. doi.org/10.1093/sysb...
Modeling Site-and-Branch-Heterogeneity with GFmix
Abstract. Phylogenetic trees are often inferred from protein sequences sampled from diverse taxa across the tree of life. The compositions of these amino a
doi.org
Feel lucky to have made a small contribution to nice work from Yulong Shen's group that adds a new piece to the puzzle of the cell cycle in Sulfolobales #ArchaeaSky #MicroSky #Microbiology academic.oup.com/nar/article/...
Successive waves of transcriptional repression and de-repression license cell cycle progression in an archaeon
Abstract. Archaea of the order Sulfolobales execute a well-structured cell cycle program similar to that of eukaryotic cells. Here, we show that three ribb
academic.oup.com
I'm looking for an enthusiastic student to join my team as a PhD candidate on archaeal genome evolution 🦠💻 Work in beautiful Utrecht, at @binfutrecht.bsky.social, an international group full of caring, amazing scientists, and with frequent cake breaks! www.uu.nl/en/organisat... Please share! 🙏
uu.nl
Great piece and cover @science.org about how our field is uncovering the evolutionary and mechanistic connections between bacterial and eukaryotic immunity ! www.science.org/content/article/ancient-wars-between-microbes-gave-us-key-immune-defenses
#Microbiology : Methanoperedenaceae archaea: a 20-year research journey These microorganisms can catalyze anaerobic methane oxidation. Here, Liu et al. review both their biology and their potential applications such as in wastewater treatment
Methanoperedenaceae archaea: a 20-year research journey - Nature Communications
Microorganisms within the Methanoperedenaceae family of archaea can catalyze anaerobic methane oxidation. In this Review, Liu et al. reflect on the history and challenges of Methanoperedenaceae research, covering both the biology and the potential applications such as in wastewater treatment.
dlvr.it
Excited to say that my new paper with @maxlechte.bsky.social (and others not on bluesky) has come out in @nature.com! Study of sediments, geochemistry and fossils from rocks 1.75 to 1.4 billion years old indicate that the oldest known #eukaryotes were aerobic and benthic! #protists rdcu.be/fjNgL
Early fossil eukaryotes were benthic aerobes
Nature - Integrated palaeontological, sedimentological and geochemical analyses of ancient rocks from Australia show that early eukaryotes were largely restricted to oxygenated benthic habitats,...
rdcu.be
The innovation of the eukaryotic cell revolutionised the biosphere & transformed the planet, but the drivers behind this process remain debated. New paper out @natureportfolio.nature.com co-led by @fossils.bsky.social w/ Susannah Porter, Galen Halverson & Maggie Whelan @mcgillscience.bsky.social 🌎
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
IQ-TREE 3: Phylogenomic Inference Software using Complex Evolutionary Models academic.oup.com/mbe/article/...
IQ-TREE 3: Phylogenomic Inference Software using Complex Evolutionary Models
Abstract. IQ-TREE (https://iqtree.github.io/) is a widely used open-source software tool for efficiently inferring phylogenetic trees under maximum likelih
academic.oup.com
A new family of rolling-circle replication endonucleases widespread in archaeal viruses and plasmids. This family is unrelated to the HUH superfamily Reps, but distantly related to the bacterial Rep_trans enzymes. @narjournal.bsky.social academic.oup.com/nar/article/...
Grab a coffee and enjoy reading up on CO metabolism in methanotrophs! Freshwater ANME (own work): www.nature.com/articles/s41... Marine ANME (@Orphan lab): www.nature.com/articles/s41... Big thanks to our collaborators at QUT! @sjmcilroy.bsky.social (Heyu/Andy/Gene!) @cuwelte.bsky.social
Carbon monoxide metabolism in freshwater anaerobic methanotrophic archaea - Nature Communications
Anaerobic methane-oxidizing archaea mitigate methane emissions in anoxic environments. Here, Egas et al. show that these microbes can also oxidize carbon monoxide, prompting re-evaluation of their cla...
nature.com
Preprint out! Anaerobic methanotrophs are key methane oxidizers, but their activity/adaptation under acidic conditions remains unclear. We show that a freshwater ANME adapts to pH stress via shifts in lipid composition and remains metabolically active down to pH 5.65. Expanding the niche of ANME.
bioRxiv Microbiology@biorxiv-microbiol.bsky.social · 4mo agoAdaptation of the freshwater anaerobic methanotroph 'Ca. Methanoperedens vercellensis' to low pH levels reveals membrane lipid remodelling https://www.biorxiv.org/content/10.64898/2026.04.11.717812v1
How diverse is bacterial immunity ? We report in @science.org how language models allowed us to predict 2.4M antiphage proteins spanning >23K novel potential systems. 👏 @emordret.bsky.social, @alexhv.bsky.social & al doi.org/10.1126/scie... Explore them here defensefinder.mdmlab.fr/wiki/refseq_...
science.org
How do you make methane from phosphite? Through interspecies H2 transfer! Our paper on lithosyntrophy is finally published - read about how we resolved the metabolic interactions in this phosphite oxidizing, methanogenic enrichment culture! #phosphorus #methanogenesis www.pnas.org/doi/10.1073/...
Lithosyntrophy: Obligate syntrophy in a phosphite-oxidizing, methanogenic culture | PNAS
The anaerobic conversion of organic matter to methane and carbon dioxide typically relies on obligate syntrophic interactions between bacteria and ...
pnas.org
Just over ten years after the discovery of the first Asgard archaeal genomes, we revisit the rapid expansion of this remarkable archaeal lineage. From diverse genomes and metabolisms to eukaryotic signature proteins and the first cultured representatives. www.nature.com/articles/s41...
Diversity, ecology, cell biology and evolution of the Asgard archaea - Nature Reviews Microbiology
The Asgard archaea have become a cornerstone of archaeal research, particularly for studies aiming to unravel the origin and early evolution of eukaryotes. This Review outlines the current state of th...
nature.com
Congratulations to Stephan and everyone involved! Check out his thread to learn more 🧵
Stephan Köstlbacher@stephkoe.bsky.social · 5mo ago🧵 1/10 New paper out in @natmicrobiol.nature.com from my postdoc at @mib-wur.bsky.social! 🎉 How eukaryote-like was the archaeal ancestor of eukaryotes? Sequence searches alone can't tell us — so we used protein structure prediction to look deeper. 🧬 www.nature.com/articles/s41...
Finally out in @natmicrobiol.nature.com: Prediction of eukaryotic cellular complexity in Asgard archaea using structural modelling. Great work by @stephkoe.bsky.social @kassipan.bsky.social @jvhooff.bsky.social www.nature.com/articles/s41...
Scientists are one step closer to understanding the origins of complex life on Earth after shedding new light on a mystery about our microbial ancestors. https://cnn.it/4srOEWd
Can't miss this amazing study on the ribosome structure of the Haloferax archaeon 👏🏼👏🏼👏🏼!! Congrats to my good friend @diorgeps.bsky.social and all the other ppl involved!!
Diorge Souza@diorgeps.bsky.social · 5mo agoA new preprint from the @archaeon-alex.bsky.social and Joey Davis (MIT) labs! We solved the structure of the ribosome from the archaeon Haloferax volcanii and discovered a new highly conserved ribosome hibernation factor that we named AHA (AMPKγ–HPF from Archaea) 🧵⬇️ www.biorxiv.org/content/10.6...
