Sam von der Dunk

Genomic clues to the origin of eukaryotic cells How did eukaryotic cells with complex architecture evolve from simpler prokaryotic cells? DNA analyses offer possible answers.

How did eukaryotic cells with complex architecture evolve from simpler prokaryotic cells? DNA analyses offer possible answers

go.nature.com/4sEMwLH

Less than two 2 weeks to apply for this PhD position in my group.

Please do not miss the opportunity to apply if the topic is of interest to you 👇

De Novo Genome Sequence Assembly of the RNAi-Tractable Paramecium bursaria 186b: An Endosymbiotic Model System Abstract. How two species engage in stable endosymbiosis is a biological quandary. The study of facultative endosymbiotic interactions has emerged as a use

@guyleonard.bsky.social et al. report a near-complete genome and transcriptome sequence dataset for green algae host Paramecium bursaria, an endosymbiotic model system.

🔗 doi.org/10.1093/gbe/evaf183

#genome #evolution

Very nice documentary about the origins of complex life with my PhD advisor Berend Snel @binfutrecht.bsky.social!

LMB PhD studentship available in the Baum lab to use informatics to infer cell structure from genomic data in collaboration with the brilliant Tom Williams. If you write to me and I don’t reply - try again - the spam filter is hungry…

Photo showing the inside atrium of the new Life and Mind Building

Oxford Biology is growing 📢

We’re appointing 3 Associate Professors in:
🌱 Plant Sciences
🦉 Animal Behaviour
🔬 Molecular Cell Biology

3 fields. 3 opportunities. One new home for Oxford Biology.

Learn more 👉 bit.ly/41S2Tc7
Apply now 👉 bit.ly/488CNW3

Protein structures are not inherently robust, but natural proteins are substantially more robust than random sequences, representing a clear signature of adaptation. Mutational robustness is relatively low in newborn and viral proteins, and provides a new perspective on protein evolution.

RNA structures are inherently evolvable and robust to mutations: random RNA molecules already show the same level of robustness and a similar distribution of secondary structures as natural RNA molecules. Hence, it is difficult to detect signatures of selection on the distribution of RNA structures.

Excited with two new preprints on evolution of molecular structure, in RNA (doi.org/10.1101/2025..., @n-martin.bsky.social) and proteins (doi.org/10.1101/2025...). Both RNA and protein structures are often conserved across evolution, but the underlying reasons are very different.

And thanks to all poster presenters, including Moisès Bernabeu whose poster was in the top 5 of best posters at #ESEB2025. Congrats!

Sam von der Dunk: we know that RNA structure is robust to mutation yet evolvable. What about protein structure? Take advantage of ESMfold https://doi.org/10.1126/science.ade2574
Natural proteins are robust to mutations, whereas random amino-acid sequences are not. Even disordered natural […]

Great to see so many people at our symposium om the origin of eukaryotes. Thanks to all the speakers! #ESEB25 @julianvosseberg.bsky.social

Interactive symbiosis in silico (back) and in vivo (front). #ESEB25

We have found before, including in different models, that evolutionary conflict leads to better adaptive solutions. These challenges best expose the creativity of evolutionary processes. Or, borrowing from Nietzsche: "What doesn't kill you makes you stronger" (at the population level)!

Our main finding: Mixing of endosymbionts (sex) is dangerous but can stimulate beneficial regulatory integration of host and symbiont!

The risk of sexual reproduction promotes the evolution of regulation between host and symbionts Sexual reproduction is a widely spread feature of eukaryotes and was already present in the last eukaryotic common ancestor (LECA). Most extant eukaryotes inherit mitochondria from a single parent, bu...

The exciting project of Alkmini Zania on the impact of sex on endosymbiosis reveals complex evolutionary dynamics. What could this mean for early eukaryotes? www.biorxiv.org/content/10.1...

PhD Position in Multiscale Mechanistic Modelling of Animal Development How do protein interactions at the subcellular scale regulate the morphology of an entire organ? Join us to explore this question with computer models!

🚨 Join us at TBB Utrecht by applying for this evo-devo PhD position! 🚨

www.uu.nl/en/organisat...

One week left to submit your abstract! @eseb2025.bsky.social

Share your work on host-associated microbiomes in our symposium @eseb2025.bsky.social - with speakers Hassan Salem @hassansalem.bsky.social and Carola Petersen. Abstract deadline April 25th. Florent, Klara, and I would love to see you there!

Join us in at #ESEB2025 Barcelona for our symposium on microbial adaptation to changing conditions. Organised by @mtoll8.bsky.social @javierdelafuente.bsky.social and me. Amazing invited speakers @saramitri.bsky.social and Itzik Mizrahi!! @eseb2025.bsky.social

#ESEB2025 Exciting symposium alert: (S50) Unravelling the origin of eukaryotes. 🦑🌴 With speakers Purificación López-García and Mark Field. We are looking forward to your abstract submissions! eseb2025.com/list-of-symp... @julianvosseberg.bsky.social

In our study, we found that genome organization emerges, in which the positions of regulatory genes along the chromosome correlate with their temporal activity during the cell cycle...

Transcription–replication interactions reveal bacterial genome regulation - Nature Single-cell expression data from bacteria are used to classify gene regulatory architectures in relation to gene expression dynamics and the cell cycle, revealing distinct categories of gene regulator...

Here's a cool article doi.org/10.1038/s415..., which supports my evolutionary model of a prokaryotic cell cycle (doi.org/10.1093/gbe/...), in which we allow evolution to exploit the changes in gene dosage induced by replication to improve cell-cycle regulation.

Postdoktor inom i proteomik och eukaryotisk evolution Postdoktor i proteomik och eukaryotisk evolution Detta projekt är en del av ett ERC Consolidator-anslag (PlastidOrigin) som tilldelats Fabien Burki och syftar till att studera en av de mest omvälvan

I would really appreciate a wide sharing of this post, as the candidate profile I am looking for is outside of my regular circle. Thank you so much. More info and how to apply here: uu.varbi.com/se/what:job/... (2/2)

New MRC-funded postdoc with me on comparative bacterial genomics/phylodynamics @roslininstitute.bsky.social university of Edinburgh. Great multidisciplinary team and collaboration with partners at Shanghai Jao Tong University.
elxw.fa.em3.oraclecloud.com/hcmUI/Candid...

Improving genome-scale metabolic models of incomplete genomes with deep learning Microbial genomics; Biocomputational method; Computational bioinformatics; Genomic analysis.

Exciting news! 🎉 My article is out in iScience presenting DNNGIOR, a deep learning tool advancing gap-filling in metabolic models. Huge thanks to co-authors @cmelkonian.bsky.social, @hariszaf.bsky.social, Daniel Garza, Andreas Haas and @bedutilh.bsky.social. Read at shorturl.at/REOm8

Hope that helps?

Although we enforce the endosymbiosis, host and symbiont normally adapt in such a way that preserves their regulatory autonomy. Only when we include regulatory conflicts, do host and symbionts evolve to communicate and to establish control mechanisms between them.

Regulatory conflicts between host and symbionts (i.e. signaling molecules of host and symbiont interfering with each other) promote host--symbiont integration, providing a narrative for how a transition in individuality may take place in a tight endosymbiotic relationship.

... Surprisingly, these regulatory conflicts inspire evolution to come up with new solutions for host--symbiont cell-cycle coordination. Host and symbiont evolve communication and various control strategies, and in some cases even manage to synchronize their cell cycles.