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Kathryn (Katy) Appler

@katyappler.bsky.social
786 followers 579 following 63 posts

💻 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.

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Reposted by Kathryn (Katy) Appler
Alexander Harms @aharms485.bsky.social · 25/09/2026
The final version of our manuscript on TnSeq in bacteriophages (“HIDEN-SEQ”) is out today – if you have an interesting phage phenotype and want to know the underlying genetic basis, this one is for you! 1/4
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Lauren Queiss @lqueiss.bsky.social · 24/09/2026
What happens when two viruses coinfect the same host? Check out the first publication of my PhD, where we describe two new viruses from an extremophilic system! www.nature.com/articles/s42...
nature.com
Two coinfecting archaeal viruses provide insights into virus-virus interactions - Communications Biology
Communications Biology - Two coinfecting archaeal viruses provide insights into virus-virus interactions
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Simonetta Gribaldo @sgribaldo.bsky.social · 23/09/2026
We are particularly proud of this work given the upcoming 50th anniversary of the discovery of Archaea in 1977 (same year Punk broke 😉) They continue to hold big surprises impacting all aspects of microbiology and evolution. Hope it'll encourage more young scientists to join this exciting field! 9/9
A free "archaeal" re-interpretation of the famous slogan "Punk's not dead", made by AI and just meant to be funny ;-)
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Simonetta Gribaldo @sgribaldo.bsky.social · 23/09/2026
Interested in #archaea, #methane, #cell-envelopes? New paper out @nature.com ! We discovered an enzyme that specifically cleaves the cell wall of methanogens, revealing a new chemical structure of archaeal peptidoglycan, 50 yrs after its first description www.nature.com/articles/s41... #MicroSky 🧵👇
nature.com
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Mart Krupovic @mkrupovic.bsky.social · 26/08/2026
Check out our paper on ESCRTs in large DNA viruses. Most enveloped viruses use the host #ESCRT for envelopment, but only mirusviruses and nucleocytoviricots encode it! Congrats @sonaida.bsky.social, @tomdelmont.bsky.social, Ulysse Guyet & Eugene Koonin. @pasteur.fr www.nature.com/articles/s41...
nature.com
Large eukaryotic DNA viruses encode ESCRT machinery for membrane remodelling - Nature Microbiology
A genomic screen reveals homologues of ESCRT components in mirusviruses that infect unicellular aquatic eukaryotes.
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Nicholas Bellono @nbellono.bsky.social · 31/07/2026
Final version out! Now with amazing illustrations from the very talented Lily Soucy :) www.cell.com/current-biol...
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Katherine Fenn @katherinefenn.bsky.social · 10/07/2026
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
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Nicholas Bellono @nbellono.bsky.social · 09/07/2026
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...
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Ján Bíňovský @jbinovsky.bsky.social · 02/07/2026
🔥My first (co)first-author paper is out🔥 The surfaces of Gram+ and Gram- bacteria are markedly different from each other. How are phages equipped to breach the Gram+ envelope❓ 💡We report a baseplate structure uniquely adapted to infect Gram+ S. aureus. A 🧵⬇️ 1/8 #phagesky #cryoEM 🧪
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Andrew Roger @andrewjroger.bsky.social · 19/06/2026
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. 🧵
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Bioinformatics Advances @bioinfoadv.bsky.social · 08/06/2026
Recently published in Bioinformatics Advances: "InterProScan 6: A modern large-scale protein function annotation pipeline"  Find it here: doi.org/10.1093/bioadv/vbag141  Authors include: @matthiasblum.bsky.social, @alexbateman1.bsky.social
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Pedro Leão @pedroleao.bsky.social · 05/06/2026
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)
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Andrew Roger @andrewjroger.bsky.social · 02/06/2026
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.
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Institut Pasteur | 130 years of biomedical research @pasteur.fr · 29/05/2026
🎓💙 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
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Andrew Roger @andrewjroger.bsky.social · 28/05/2026
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...
doi.org
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
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Miguel Gómez-Raya @miguelgrv.bsky.social · 25/05/2026
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/...
academic.oup.com
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
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Reposted by Kathryn (Katy) Appler
Daniel Tamarit @danieltamarit.bsky.social · 22/05/2026
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
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Aude Bernheim @audeber.bsky.social · 22/05/2026
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
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Nature Communications @natcomms.nature.com · 20/05/2026
#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
dlvr.it
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.
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Leigh Anne Riedman @fossils.bsky.social · 20/05/2026
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
rdcu.be
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,...
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Max Lechte @maxlechte.bsky.social · 21/05/2026
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 🌎
Eukaryote microfossils from the Palaeoproterozoic. Credit: Leigh Anne RiedmanRock cores of a Palaeoproterozoic sedimentary succession at the Northern Territory Geological Survey. Credit: M Lechte
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Sonja-Verena Albers @archaellum.bsky.social · 20/05/2026
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
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Andrew Roger @andrewjroger.bsky.social · 06/05/2026
IQ-TREE 3: Phylogenomic Inference Software using Complex Evolutionary Models academic.oup.com/mbe/article/...
academic.oup.com
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
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Reposted by Kathryn (Katy) Appler
Mart Krupovic @mkrupovic.bsky.social · 24/04/2026
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/...
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Reinier Egas @raegas.bsky.social · 14/04/2026
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
nature.com
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...
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Reinier Egas @raegas.bsky.social · 13/04/2026
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.
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Aude Bernheim @audeber.bsky.social · 02/04/2026
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
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Brett Baker @archaeal.bsky.social · 12/03/2026
Asgard archaea on CBC radio. ici.radio-canada.ca/ohdio/premie...
ici.radio-canada.ca
Asgard : Potentiel chaînon manquant de la vie complexe | OHdio | Radio-Canada
Écoutez l’extrait de l’émission Les années lumière : Asgard : Potentiel chaînon manquant de la vie complexe
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Heidi Aronson, PhD @heidi-aronson.bsky.social · 11/03/2026
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/...
pnas.org
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 ...
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Kassiani Panagiotou @kassipan.bsky.social · 05/03/2026
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...
nature.com
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...
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Kathryn (Katy) Appler @katyappler.bsky.social · 05/03/2026
Congratulations to Stephan and everyone involved! Check out his thread to learn more 🧵
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Thijs J. G. Ettema 🦠🔬🇳🇱🇸🇪🇪🇺 @ettema.bsky.social · 05/03/2026
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...
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CNN @cnn.com · 05/03/2026
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. cnn.it/4srOEWd
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Kathryn (Katy) Appler @katyappler.bsky.social · 05/03/2026
www.cnn.com/2026/03/04/s...
cnn.com
Mysterious Asgard microbes may point to origins of complex life | CNN
Scientists are trying to understand how complex life emerged on Earth about 2 billion years ago. Our microbial ancestors could be the key.
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Javier Espadas @javierespadas.bsky.social · 23/02/2026
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!!
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Paul Carini @uncultured.carinilab.com · 20/02/2026
New preprint! We propose "anergiobiosis" to describe microbial life at thermodynamic limits as a way of separating the physiological state from questions about aeonophilic extremophile specialization. ecoevorxiv.org/repository/v... #Microbiology #Extremophiles #SubsurfaceMicrobiology #MicroSky
ecoevorxiv.org
Anergiobiosis: a testable framework for microbial life under extreme power limitation
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Nature @nature.com · 23/02/2026
Nature research paper: Oxygen metabolism in descendants of the archaeal-eukaryotic ancestor go.nature.com/4rSfRRw
go.nature.com
Oxygen metabolism in descendants of the archaeal-eukaryotic ancestor - Nature
Sequencing of marine sediments finds 136 newly identified Heimdallarchaeia and several novel lineages, and indicates that Heimdallarchaeia evolved distinct metabolic capabilities from other Asgardarchaeota, in conditions that may have given rise to early eukaryotes.
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Nature Microbiology @natmicrobiol.nature.com · 22/02/2026
#NatMicroPicks Aerobic archaeal-eukaryotic ancestor? 🦠🫁 The ancestor of eukaryotes may have combined hydrogen metabolism with aerobic respiration, shaping early cellular complexity. #MicroSky www.nature.com/articles/s41...
nature.com
Oxygen metabolism in descendants of the archaeal-eukaryotic ancestor - Nature
Sequencing of marine sediments finds 136 newly identified Heimdallarchaeia and several novel lineages, and indicates that Heimdallarchaeia evolved distinct metabolic capabilities from other Asgar...
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Henry Gee 亨利·纪 @endofthepier.bsky.social · 18/02/2026
Hot eukaryogenesis news (is there any other kind?) - hydrogen production and aerobic respiration may have been present in the Asgard-eukaryotic ancestor - paper in @nature.com www.nature.com/articles/s41...
nature.com
Oxygen metabolism in descendants of the archaeal-eukaryotic ancestor - Nature
Sequencing of marine sediments finds 136 newly identified Heimdallarchaeia and several novel lineages, and indicates that Heimdallarchaeia evolved distinct metabolic capabilities from other Asgar...
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Simons Foundation @simonsfoundation.org · 19/02/2026
New research in @nature.com funded by our Life Sciences division: "Oxygen metabolism in descendants of the archaeal-eukaryotic ancestor." www.nature.com/articles/s41586-026-…
nature.com
Oxygen metabolism in descendants of the archaeal-eukaryotic ancestor - Nature
Sequencing of marine sediments finds 136 newly identified Heimdallarchaeia and several novel lineages, and indicates that Heimdallarchaeia evolved distinct metabolic capabilities from other Asgar...
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James Lingford @jameslingford.bsky.social · 19/02/2026
Our work is published today: ‘Oxygen metabolism in descendants of the archaeal-eukaryotic ancestor’. This was a huge effort lead by @katyappler.bsky.social. Extremely grateful to have been a part of this amazing project! 😊🦠🧬 Links: www.nature.com/articles/s41... www.nature.com/articles/s41...
Eukaryogenesis in light of an expanded catalogue of Asgard genomes. a, Simplified, scaled timeline spanning from before the Last Asgard archaea Common Ancestor (LAsCA) to today. Thin bands mark predicted time ranges  of relevant events (for example, GOE), thicker bands represent processes  (for example, eukaryogenesis), and brackets indicate the period shown in b. The timeline further highlights milestones, including potential early eukaryotic fossils60 and the modern-day co-occurrence of Heimdallarchaeia and Alphaproteobacteria observed in this study (interaction likely originated earlier). Fig. 1 | Expanded genomic diversity of Asgard archaea. a, Maximum-likelihood phylogeny based on 47 non-ribosomal markers (NM47)using the WAG + C10 + R4 model with 100 nonparametric bootstrap pseudoreplicates, including 869 Asgardarchaeota MAGs and 309 outgroup genomes. The blue branches (lower right) indicate the new Asgardarchaeota classes, Ranarchaeia, and the recently proposed Asgardarchaeia4. The concentric rings denote (in to out): the predicted genome size, metabolic guilds based on Pfam clustering, sampling locations, and black stars on the outside mark MAGs added by this study. Asgard, Asgardarchaeia; Atabey, Atabeyarchaeia; Baldr, Baldrarchaeia; Frey/Jord,  Frey/Jordarchaeia; Gerd, Gerdarchaeales; Heimdall, Heimdallarchaeaceae;  Hel, Helarchaeales; Hermod, Hermodarchaeia; Hod, Hodarchaeales;  Kari, Kariarchaeaceae; Loki, Lokiarchaeales; Njord, Njordarchaeales;  Odin, Odinarchaeia; Ran, Ranarchaeia; Sif, Sifarchaeia; Thor, Thorarchaeia;  Wukong, Wukongarchaeia. b, SR4-recoded phylogeny of the same genome  set inferred with the model GTR + C60 + G and 100 nonparametric bootstrap pseudoreplicates (Methods). This updated catalogue constitutes a large increase in the medium- to high-quality publicly available genomes (completeness >50% and contamination and redundancy <10%) with 65.3% from the Guaymas Basin and 34.7% from the Bohai Sea. The encircled numbers represent MAGS added by this study. The scale bars in bothsubpanels represent the average number of substitutions per site.Map created in BioRender; Appler, K. https://biorender.com/147ieoc(2025).
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Brett Baker @archaeal.bsky.social · 20/02/2026
I will add if there's any wonder how much work this study was just have a look at the 170 pages SI file! static-content.springer.com/esm/art%3A10...
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Greg Dick @greatlakesgreg.bsky.social · 20/02/2026
new study of #GreatLakes research centers, w/ some nice quotes from CIGLR colleagues: "Research centers in the region also work together as a collaborative that complements each of them, and so the network of research centers is vital, Moerke said."... greatlakesecho.org/2026/02/16/r...
greatlakesecho.org
Research centers in the Great Lakes region change the scope of global freshwater ecology | Great Lakes Echo
A new study examines the uniqueness of work that research centers conduct in the Great Lakes region, highlighting their importance amid dramatic changes in federal funding.
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Texas Science @texasscience.bsky.social · 18/02/2026
Some of our earliest microbial ancestors, the Asgard archaea, were able to use oxygen, says new study in @nature.com. It may solve a mystery about how complex life first arose. #AsgardArchaea #MicrobialEcology #Eukaryogenesis #TexasScience @utmsi.bsky.social @archaeal.bsky.social
cns.utexas.edu
A Break in a Longstanding Mystery about Origin of Complex Life
Breathe easy. It appears our microbial ancestors used oxygen, too.
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Carl Zimmer @carlzimmer.com · 18/02/2026
One of the biggest questions in biology is how complex cells evolved about 2 billion years ago. Here's my new story on how scientists are solving the mystery of eukaryotes like us. Gift link: nyti.ms/4qMbo22
A pilot in a submersible vehicle collecting sediments samples in 30 meters of water looking for Asgards (microbial relatives of eukaryotes)
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Thijs J. G. Ettema 🦠🔬🇳🇱🇸🇪🇪🇺 @ettema.bsky.social · 18/02/2026
Finally out in @nature.com: a new piece of the puzzle of how complex life evolved. Lead by @archaeal.bsky.social & @katyappler.bsky.social. Great collab with @greening.bsky.social and @kassipan.bsky.social. More pieces to follow soon! www.nature.com/articles/s41...
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Kathryn (Katy) Appler @katyappler.bsky.social · 18/02/2026
Check out some of our research 🤯 How Microbes Got Their Crawl www.nytimes.com/2026/02/18/s...
nytimes.com
How Microbes Got Their Crawl
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Brett Baker @archaeal.bsky.social · 18/02/2026
New paper from my team detailing a greatly expanded genomic database of Asgard archaea revealing of high energy metabolism those related to eukaryotes! Led by @katyappler.bsky.social lots of help from @jameslingford.bsky.social @valdeanda.bsky.social @kassipan.bsky.social doi.org/10.1038/s415...
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Kathryn (Katy) Appler @katyappler.bsky.social · 18/02/2026
Beyond thrilled to share that our study has been published! This project encompasses years of work, including my thesis research on Asgard archaea in the @archaeal.bsky.social lab at @utmsi.bsky.social and @texasscience.bsky.social!!! #MicroSky #ArchaeaSky 1/12
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Thijs J. G. Ettema 🦠🔬🇳🇱🇸🇪🇪🇺 @ettema.bsky.social · 16/02/2026
Our latest preprint: Together with the team of Jan Löwe, @danieltamarit.bsky.social and many others we discovered and characterized several Asgard tubulin genes and propose that microtubule architecture and dynamics evolved in Asgard archaea prior to eukaryogenesis www.biorxiv.org/content/10.6...
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