Lars Eicholt
@lacholt.bsky.social
📤 415
📥 1382
📝 6
molecular evolution.
reposted by
Lars Eicholt
Dame lab at Leiden University
2 days ago
New article online: Modulation of archaeal hypernucleosome structure and stability by Mg2+ In this work, we dissect the effects of Mg2+ on hypernucleosomes formed by the canonical histones from M. fervidus (HMfA and HMfB) and T. kodakarensis (HTkA and HTkB).
www.sciencedirect.com/science/arti...
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Modulation of archaeal hypernucleosome structure and stability by Mg2+
DNA-wrapping histone proteins play a central role in chromatin organization, gene expression and regulation in most eukaryotes and archaea. While the …
https://www.sciencedirect.com/science/article/pii/S0022283625005996
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Lars Eicholt
Dame lab at Leiden University
3 days ago
Soon available in my group: 1 PhD position to investigate prokaryotic histones. See our recent work that highlights the existence and diversity of prokaryotic histones (e.g. Schwab et al., TIBS, 2025; Schwab et al., Nat Comm, 2024; Hu et al., Nucl Acids Res, 2024). Please DM for informal enquiries.
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The DeNoFo format & toolkit for annotating, assessing and comparing the tools and tresholds used in studies of de novo evolved genes is out now in Bioinformatics! Great effort led by
@drdomain.bsky.social
and Anna Grandchamp!
academic.oup.com/bioinformati...
add a skeleton here at some point
5 days ago
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Lars Eicholt
PCE3
5 days ago
Looking for a PostDoc in Origins? The Wisconsin Center for Origins Research might be the right place for you! Apply here:
wicor.wisc.edu/postdoc/
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Lars Eicholt
Max Renner
5 days ago
Our new preprint is out 🥳🥳🥳 Henipaviruses, like Nipah and Hendra, package their genomes inside helical shells built by thousands of nucleoproteins. These nucleocapsids are essential to protect the viral RNA, but how do they ever let the polymerase in to read the sequence? 👇
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bioRxivpreprint
9 days ago
Ancient amino acid sets enable stable protein folds
https://www.biorxiv.org/content/10.1101/2025.10.29.685319v1
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Lars Eicholt
Svetlana Dodonova
11 days ago
Lab’s first paper is out!! We show the first structures of
#Asgard
#chromatin
by
#cryo-EM
🧬❄️ Asgard histones form closed and open hypernucleosomes. Closed are conserved across
#Archaea
, while open resemble eukaryotic H3–H4 octasomes and are Asgard-specific. More here:
www.cell.com/molecular-ce...
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Join our next ProSe seminar 11th November 5PM CET and follow us
@proteinstructure.bsky.social
!
add a skeleton here at some point
10 days ago
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Lars Eicholt
Protein Structure Evolution (ProSE) Seminar
13 days ago
Protein Structure Evolution (ProSe) Seminar is now on BlueSky! Every 2nd Tuesday, 4PM GMT. Sign-Up:
tinyurl.com/prose-seminar2
Organized by Claudia Alvarez Carreño, Zachary Ardern, Lars Eicholt, Carolina Sanchez-Rocha, Sergio Romero Romero and Md. Hassan Uz-Zaman.
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Claus Wilke
17 days ago
We need to have a conversation about random seeds. Don't use 42.
blog.genesmindsmachines.com/p/if-your-ra...
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If your random seed is 42 I will come to your office and set your computer on fire🔥
Figuratively. More likely you'll get a stern talking to.
https://blog.genesmindsmachines.com/p/if-your-random-seed-is-42-i-will
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Lars Eicholt
Timothy Fuqua 🏳🌈
18 days ago
A fun little side project I've been working on with
@stepadenisov.bsky.social
, Mato Lagator, and Andreas Wagner: "Strong promoters are mutationally robust". Briefly...
www.biorxiv.org/content/10.1...
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Strong promoters are mutationally robust
Mutational robustness is the persistence of a phenotype upon mutation. It facilitates molecular evolution and has been characterized in a variety of biological systems, but studies of prokaryotic prom...
https://www.biorxiv.org/content/10.1101/2025.10.20.683477v1
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Cauã Westmann
19 days ago
I’m excited to announce the launch of my lab at EPFL in Jan 2026 🎉. We’ll combine evolution & synthetic biology to study and (re)engineer bacterial communication. I’m recruiting PhD students to start in the first semester of 2026. Apply via EPFL PhD programs by Nov 1
drive.google.com/file/d/1cm-t...
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Claudèle Lemay-St-Denis
about 1 month ago
How does catalysis emerge from non-catalytic domains? In our new paper, we show that catalytic activity can arise without conserved active-site residues — through multimerization and electrostatic features instead. A striking case of catalysis evolving from binding.
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Join us Tuesday for the next Protein Structure Evolution Seminar (ProSe Seminar) with Stephen Fried!
add a skeleton here at some point
27 days ago
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Lars Eicholt
Ylva Ivarsson
about 1 month ago
Never thought I would say this, but I need a Dane..
novonordiskfonden.dk/grant/postdo...
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Postdoctoral Fellowships at Uppsala University - 2026 - Novo Nordisk Fonden
https://novonordiskfonden.dk/grant/postdoctoral-fellowships-at-uppsala-university-2026/
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Lars Eicholt
Alexey Amunts
2 months ago
The paper is a masterpiece of modern evolutionary genomics with a potential for synthetic biology. Imagine designing new genes from scratch to improve plant traits. Beautiful work from colleagues at Huazhong Agricultural University in Wuhan. Link to the paper in Cell:
www.cell.com/cell/fulltex...
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A de novo-originated gene drives rose scent diversification
Genomic analysis of more than 100 Rosa species uncovers a multi-step process for the de novo origination of SCREP, a taxon-restricted gene specific to the Rosa genus, highlighting its function in modu...
https://www.cell.com/cell/fulltext/S0092-8674%2825%2900925-0
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Lars Eicholt
Tobias Warnecke
2 months ago
Please re-post: Interested in chromatin and its evolution? Good news! There's still time to join us in beautiful Catalonia (9-12 Dec) to discuss eukaryotic, bacterial, archaeal, and viral chromatin and how it all hangs together
meetings.embo.org/event/24-evo...
Abstract deadline: 30 September
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EvoChromo: Evolutionary approaches to research in chromatin
Chromatin is the complex of DNA, RNA and protein that is found making up the chromosomes in eukaryotic cells. Chromatin is essential for proper genome function and is involved in chromosome segregati…
https://meetings.embo.org/event/24-evo-chromo
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Antoni Wrobel
2 months ago
Dear scientific community, I am looking for two postdoctoral structural biologists to join my group at the Department of Biochemistry, University of Oxford.
my.corehr.com/pls/uoxrecru...
my.corehr.com/pls/uoxrecru...
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Claudia Alvarez Carreño
2 months ago
The ProSE seminars are back after a summer break. The next speaker is Nir Ben-Tal on "Contrastive learning unites sequence and structure in a global representation of protein space". Date: September 9 Time: 5pm CET Register here:
tinyurl.com/prose-seminar2
Please share! 🧪
#mevosky
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Lars Eicholt
Tanja Slotte
2 months ago
*Postdoc in Evolutionary genomics at Stockholm University* We are recruiting a postdoc for a large interdisciplinary project to investigate evolutionary drivers and genomic consequences of pollen evolution in response to pollination mode shifts in flowering plants. 1/5
su.varbi.com/what:job/job...
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Max-Planck-Gesellschaft
2 months ago
The
#MaxPlanckPostdocProgram
offers a guaranteed contract of at least 3 years, targeted mentoring, and career workshops. The call for applications is open now! 🚀 Take advantage of this opportunity and browse the job vacancies.
www.mpg.de/en/max-planc...
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Timothy Fuqua 🏳🌈
2 months ago
Excited / nervous to share the “magnum opus” of my postdoc in Andreas Wagner’s lab! "De-novo promoters emerge more readily from random DNA than from genomic DNA" This project is the accumulation of 4 years of work, and lays the foundation for my future group. In short, we… (1/4)
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De-novo promoters emerge more readily from random DNA than from genomic DNA
Promoters are DNA sequences that help to initiate transcription. Point mutations can create de-novo promoters, which can consequently transcribe inactive genes or create novel transcripts. We know lit...
https://www.biorxiv.org/content/10.1101/2025.08.25.672121v1
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Tobias Warnecke
2 months ago
Please re-post: If you know (or are!) somebody who might fancy doing a PhD (Oct 2026 start) in my group
@oxfordbiochemistry.bsky.social
, working on chromatin evolution in prokaryotes (or other things we're interested in), please have a look at
www.bioch.ox.ac.uk/supervisors-...
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Supervisors and Projects
https://www.bioch.ox.ac.uk/supervisors-and-projects#collapse5442116
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Lars Eicholt
Mathieu M.J.E. Rebeaud
3 months ago
Beautiful work from
@claudiaalcar.bsky.social
, congrats! Piecing Together the History of Protein Folds From a Fragmented Evolutionary Record
academic.oup.com/gbe/article/...
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Piecing Together the History of Protein Folds From a Fragmented Evolutionary Record
Abstract. Protein folds are structural units defined by the number, type, arrangement, and orientation of their core secondary structural elements. The uni
https://academic.oup.com/gbe/article/17/8/evaf148/8239333?searchresult=1
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Lars Eicholt
Romain Strock
3 months ago
This first-author publication is my… first! Archaea kill bacteria by targeting their Achilles’ heel: peptidoglycan. Big shoutout to
@ahocher.bsky.social
,
@valeriesoo.bsky.social
, Pauline Misson,
@tobiaswarnecke.bsky.social
and MRC LMS Proteomics. A thread 🔽
journals.plos.org/plosbiology/...
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Archaea produce peptidoglycan hydrolases that kill bacteria
Archaea regularly interact with bacteria but reports of archaea killing bacteria are very rare. This study shows that many archaea encode peptidoglycan hydrolases, which specifically target bacterial ...
https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3003235
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Lars Eicholt
Kresten Lindorff-Larsen
3 months ago
If you’re interested in learning more about protein folding and misfolding, I’ve created a convenient reading list with a few essential papers:
scholar.google.com/citations?us...
scholar.google.com/citations?us...
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Lars Eicholt
Zach Harvey
3 months ago
Happy to share our new paper out today in
@cp-cellreports.bsky.social
in collaboration with
@tobiaswarnecke.bsky.social
@akihisaosakabe.bsky.social
about how evolution can do big things with small changes.
www.sciencedirect.com/science/arti...
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The histone core domain evolves at single-residue resolution to directly orchestrate transcription
Nucleosomes are thought to be structural barriers to transcription, establishing a restrictive ground state that must be destabilized for gene express…
https://www.sciencedirect.com/science/article/pii/S2211124725008502
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Lars Eicholt
Elias Dohmen
5 months ago
🚨 New preprint alert! 🚨 🔬 Ever wondered how new genes emerge from scratch? Meet DESwoMAN, a fully automated pipeline to detect and analyze newly expressed ORFs (neORFs) from transcriptome data — giving us a window into the earliest stages of de novo gene emergence! (Thread 🧵👇)
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Lars Eicholt
Universität Münster
4 months ago
Wie alt Tiere werden, ist je nach Art extrem unterschiedlich. Hanna Kokko von der Universität Mainz spricht am 10. Juli über die evolutionäre Bedeutung der unterschiedlichen Lebensspannen.
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Auch ein kurzes Leben kann von Vorteil sein
Wie alt Tiere werden, ist je nach Art extrem unterschiedlich. Hanna Kokko von der Universität Mainz spricht am 10. Juli über die evolutionäre Bedeutung der unterschiedlichen Lebensspannen.
https://www.uni-muenster.de/news/view.php?cmdid=14847
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Lars Eicholt
Claudia Alvarez Carreño
5 months ago
Join us for the next ProSE Seminar! We are excited to welcome Sophie Heiding for a talk on "Computational Insights into Protein Adaptation Across Environmental Gradients" Date: June 10 Time: 4PM CET Register here:
tinyurl.com/prose-seminar2
Please share! 🧪
#MEvoSky
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Lars Eicholt
Tobias Warnecke
6 months ago
Joining the race to the bottom has never been cooler...
www.biorxiv.org/node/4580343...
www.biorxiv.org/content/10.1...
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A cellular entity retaining only its replicative core: Hidden archaeal lineage with an ultra-reduced genome
Defining the minimal genetic requirements for cellular life remains a fundamental question in biology. Genomic exploration continually reveals novel microbial lineages, often exhibiting extreme genome...
https://www.biorxiv.org/node/4580343.full
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Lars Eicholt
Inga Hänelt
6 months ago
This took us a while and I am all the happier it is finally out! I thought that simply adding ATP to purified potassium channel KtrAB should be sufficient to stabilize its active state. I was so wrong... Read the full story on how an IDR facilitates channel opening upon membrane interaction.
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A short intrinsically disordered region at KtrB’s N-terminus facilitates allosteric regulation of K+ channel KtrAB
Nature Communications - KtrAB is a major potassium uptake system that has been linked to the pathogenesis of many infectious bacteria. Here the authors show that KtrB from Vibrio alginolyticus...
https://www.nature.com/articles/s41467-025-59546-z.epdf?sharing_token=a35y7_Ydwk4tr0Hk8vhwxtRgN0jAjWel9jnR3ZoTv0Oj0dLdXyZnyd8KfNUnUYhyWtkNKQC7gL7JXUEesMjdUvEieXWlatAfo2IeKZFwvfD2bQ7rhldVVIHxqMJtUjG8ysMqme_X7j2TaghjN2z-d4zOY6UJXfzrHKUL2c7lptQ%3D
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Zachary Ardern
6 months ago
Very interesting new study from authors including Nobel Prize winner David Baker. I'm glad that it cites one of my related papers 😀 I've faced plenty of skepticism from editors & others about the importance of this line of research, perhaps this will shift ...
www.biorxiv.org/content/10.1...
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Design of overlapping genes using deep generative models of protein sequences
In nature, viruses frequently evolve overlapping genes (OLG) in alternate reading frames of the same nucleotide sequence despite the drastically reduced protein sequence space resulting from the shari...
https://www.biorxiv.org/content/10.1101/2025.05.06.652464v1.full
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Vikram Alva
6 months ago
Excited to share our new preprint on HLp—a bacterial histone from Leptospira perolatii that forms stable tetramers and wraps ~60 bp of DNA: "DNA Wrapping by a Tetrameric Bacterial Histone"
www.biorxiv.org/content/10.1...
@mpi-bio-fml.bsky.social
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BejaLab
6 months ago
Deep origin of eukaryotes outside Heimdallarchaeia within Asgardarchaeota
www.nature.com/articles/s41...
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Deep origin of eukaryotes outside Heimdallarchaeia within Asgardarchaeota - Nature
Ancestral reconstruction together with molecular dating of the last Asgard archaea and eukaryote common ancestor suggest that eukaryotes arose from the fusion of a H2-consuming archaeal host and a H2-...
https://www.nature.com/articles/s41586-025-08955-7
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Geoff Findlay
6 months ago
While it is a dark time for US science, I'm grateful to be able to celebrate some recent lab successes! A brief thread... 🧵 First, the final version of our article on the katherine johnson (kj) gene came out in GENETICS
@genetics-gsa.bsky.social
in March!
academic.oup.com/genetics/art...
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An orphan gene is essential for efficient sperm entry into eggs in Drosophila melanogaster
Abstract. While spermatogenesis has been extensively characterized in the Drosophila melanogaster model system, very little is known about the genes requir
https://academic.oup.com/genetics/article-abstract/229/3/iyaf008/7998592
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Geoff Findlay
6 months ago
We also just posted to
@biorxiv-genetic.bsky.social
a new manuscript led by our superb staff scientist Dr. Prajal Patel in collaboration with
@lacholt.bsky.social
from
@bornberglab.bsky.social
. We explored the functionality of orphan gene orthologs in D. melanogaster.
www.biorxiv.org/content/10.1...
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Orthologs of an essential orphan gene vary in their capacities for function and subcellular localization in Drosophila melanogaster
The rapidly evolving nature of orphan genes raises questions about whether their activities remain conserved or evolve uniquely across species. We explore this issue using goddard ( gdrd ), an orphan ...
https://www.biorxiv.org/content/10.1101/2025.05.01.651694v1
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Lars Eicholt
Claudia Alvarez Carreño
6 months ago
We are pleased to announce that the next speaker in the ProSE seminar series will be Dr. Klara Hlouchova with a talk on "Protein Structure Before LUCA" May 13, 4PM CET Registration link:
tinyurl.com/prose-seminar4
Please share!
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Lars Eicholt
Bornberglab
7 months ago
New Paper Alert! Together with the Parsch lab, we investigated the expression of neORFs (newly evolved expressed open reading frames, identified in a previous study) in Drosophila populations using publicly available RNA-seq data. (1/2)
doi.org/10.1002/jez....
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Expression of De Novo Open Reading Frames in Natural Populations of Drosophila melanogaster
We show that newly-evolved, expressed open reading frames (neORFs) identified in a set of inbred Drosophila melanogaster lines are also expressed in multiple tissues and developmental stages of poole...
https://doi.org/10.1002/jez.b.23297
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Lars Eicholt
Joe Greener
7 months ago
This has been a long journey, but it's now out in final form.
@kjamali.bsky.social
academic.oup.com/bioinformati...
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Maddy Seale
7 months ago
This week in
@science.org
: Multicellularity in archaea when cells are mechanically compressed. 🧪 Read the paper here:
www.science.org/doi/10.1126/...
And the Perspective here:
www.science.org/doi/10.1126/...
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Tissue-like multicellular development triggered by mechanical compression in archaea
The advent of clonal multicellularity is a critical evolutionary milestone, seen often in eukaryotes, rarely in bacteria, and only once in archaea. We show that uniaxial compression induces clonal mul...
https://www.science.org/doi/10.1126/science.adu0047
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Lars Eicholt
MPI for Biology Tübingen & Friedrich Miescher Laboratory
7 months ago
🚨MPI Biology Tübingen is actively recruiting
#Postdocs
through our
#PostdocProgram
.
postdocprogram.mpg.de
We have 5 projects within the Departments of Complex Biological Interactions, Integrative Evolutionary Biology & Algal Development and Evolution. 5 weeks left till the deadline! Please share
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Lars Eicholt
Claudia Alvarez Carreño
7 months ago
Tomorrow’s ProSE Seminar features Dr. Devlina Chakravarty (
@devlinac.bsky.social
) presenting “Mutations Switch Folds in Proteins”. Don't miss out! April 8, 3PM GMT Registration link:
tinyurl.com/prose-seminar3
🧪
#MEvoSky
add a skeleton here at some point
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Lars Eicholt
Bornberglab
7 months ago
Check out DeNoFo Toolkit to annotate, convert and compare the methodology used in studies on de novo emerged genes!
@drdomain.bsky.social
@margaubel.bsky.social
@lacholt.bsky.social
and more!
add a skeleton here at some point
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Lars Eicholt
Elias Dohmen
7 months ago
De novo genes research community 🧬 - please consider using for your future or past work our new methodology annotation format for better comparability of studies and higher reproducibility. (1/3)
add a skeleton here at some point
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Lars Eicholt
bioRxiv Bioinfo
7 months ago
DeNoFo: a file format and toolkit for standardised, comparable de novo gene annotation
https://www.biorxiv.org/content/10.1101/2025.03.31.644673v1
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Lars Eicholt
Claudia Alvarez Carreño
8 months ago
Next up in the ProSE Seminar Series: Devlina Chakravarty (
@devlinac.bsky.social
) presents "Mutations Switch Folds in Proteins". Join us to explore how mutations reshape protein structures! April 8, 3PM GMT Register here:
tinyurl.com/prose-seminar3
#ProSESeminar
#ProteinEvolution
#StructuralBiology
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Lars Eicholt
Rage Against the Miocene
8 months ago
A failure to act is not an act of political neutrality.
www.theguardian.com/technology/2...
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Royal Society decides not to take disciplinary action against Elon Musk
Exclusive: Fellows argue Musk has violated code of conduct but council believes investigation ‘could do more harm than good’
https://www.theguardian.com/technology/2025/mar/25/royal-society-decides-not-to-take-disciplinary-action-against-elon-musk?CMP=Share_AndroidApp_Other
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Bruno Cuevas Zuviría
8 months ago
Join us this August in Barcelona for the
@eseb2025.bsky.social
. In "The Future Meets The Beginning: Synthetic Biology, Evolution & Origin of Life," we will explore the connections between these topics. Submit your abstract before the 25th of April!
#evolution
#science
#synthetic_biology
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Gemma C. Atkinson
8 months ago
Reminder about two open positions: 1) tenure track group leader position on data driven infection research
lu.varbi.com/en/what:job/...
2) post-doc in mine/Vasili's join team
lu.varbi.com/en/what:job/...
#phagesky
#microsky
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Postdoctoral research fellow with a focus on the molecular mechanisms of bacteriophage-host interactions
Description of the Workplace In the Atkinson lab we are interested in making discoveries about protein function and structure, with a focus on bacterial immune system components that protect against b
https://lu.varbi.com/en/what:job/jobID:807046/
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