Daniela Barillà

Dated gene duplications elucidate the evolutionary assembly of eukaryotes - Nature Analysis of eukaryotic gene sequences using a relaxed molecular clock methodology indicate that eukaryotes emerged 3.0–2.25 billion years ago as a result of mitochondrial endosymbiosis with complex archaea that already possessed an elaborated cytoskeleton, membrane trafficking, endomembrane, phagocytotic machinery and a nucleus.

Nature research paper: Dated gene duplications elucidate the evolutionary assembly of eukaryotes

go.nature.com/4azJDF8

📢Today is World Soil Day!

A gram of soil contains billions of microbes, of which the bacteria are a major source of antibiotic compounds. Read how scientists are maximising ways to isolate new species to accelerate discovery in a recent #MGEN paper here: microb.io/3LomhI8

There's a new Archaeal sampling & sequencing project on the horizon - considering testing Phase Genomics proximity sequencing (there might actually be some funding this time). Anyone in #archaeasky with experience using their kit & processing data? Pitfalls, things to watch out for and etc?

🧫🦠

Irrational idea from various viewpoints. And what about confidentiality??

From the UKRI website:

‘The release of confidential material into generative AI tools constitutes a breach of confidentiality and integrity as set out in our policy’.

Dynamic protrusions mediate unique crawling motility in Asgard Archaea (Promethearchaeota) Crawling motility is a hallmark of eukaryotic cells and requires a dynamic actin cytoskeleton, regulated adhesion, and spatially organized signalling pathways1–3. Asgard archaea (phylum Promethearchae...

Asgard on the move ! Watch our videos!
Biorxiv.org/content/10.1101/2025.11.30.690169v1

An Asgard Archaeon (Lokiarchaeum ossiferum) growing and retracting its arms

Cohesin guides homology search during DNA repair using loops and sister chromatid linkages Accurate repair of DNA double-strand breaks (DSBs) is essential for genome stability, and defective repair underlies diseases such as cancer. Homologous recombination uses an intact homologous sequenc...

I am happy to share that my postdoctoral work in the @gerlichlab.bsky.social at @imbavienna.bsky.social is finally out 🎉!
Our study reveals how cohesin guides focused and accurate homology search.
Read more 👉 www.science.org/doi/10.1126/...
Follow along for key insights and updates! 🧵

Versatile NTP recognition and domain fusions expand the functional repertoire of the ParB-CTPase fold beyond chromosome segregation | PNAS Nucleotide triphosphate (NTP)-dependent molecular switches regulate essential cellular processes by cycling between active and inactive states thro...

Our preprint is now published in PNAS! This came together thanks to a great collaboration with Antoine Hocher and a strong team effort from the Le Lab. Thank you to the reviewers and to everyone who helped improve it. I hope ParB aficionados will enjoy it.

www.pnas.org/doi/10.1073/...

Systematic discovery of TIR-based immune signaling systems in bacteria Toll/interleukin-1 receptor (TIR) domains are important for immune signaling across humans, plants and bacteria. These domains were recently found to produce immune signaling molecules in plant immuni...

#microsky #phagesky #phge defence

Preprint from the @soreklab.bsky.social reporting a plethora of novel TIR-based immune signalling systems

www.biorxiv.org/content/10.6...

Dynamic protrusions mediate unique crawling motility in Asgard Archaea (Promethearchaeota) Crawling motility is a hallmark of eukaryotic cells and requires a dynamic actin cytoskeleton, regulated adhesion, and spatially organized signalling pathways1–3. Asgard archaea (phylum Promethearchae...

A collaborative project that began with the Osaka Expo has just been released as a preprint!
Here, we show Promethearchaeota (Asgard archaea) “moving” under anaerobic conditions.
The videos capturing this unique behavior are so fascinating you can watch endlessly.
www.biorxiv.org/content/10.1...

Description Please note that job descriptions are not exhaustive, and you may be asked to take on additional duties that align with the key responsibilities ment...

We're advertising for a bacteriology technician and a post-doc to work on AI-guided antibiotic development as part of a large multidisciplinary Fleming Initiative project:
www.imperial.ac.uk/jobs/search-...

www.imperial.ac.uk/jobs/search-...

Taming wild replicons: evolution and domestication of large extrachromosomal replicons Bacterial genomes often contain extrachromosomal replicons (ERs), ranging from small, mobile plasmids to large, stably inherited elements, such as meg…

Taming wild replicons: evolution and domestication of large extrachromosomal replicons

#MicroSky

www.sciencedirect.com/science/arti...

So happy to announce our new preprint, “A geothermal amoeba sets a new upper temperature limit for eukaryotes.” We cultured a novel amoeba from Lassen Volcanic NP (CA, USA) that divides at 63°C (145°F) 🔥 - a new record for euk growth!
#protistsonsky 🧵

DNA topoisomerase I acts as supercoiling sensor for bacterial transcription elongation Nature Structural & Molecular Biology, Published online: 01 December 2025; doi:10.1038/s41594-025-01703-5Vidmar et al. use cryo-EM to reveal how bacterial RNA polymerase (RNAP) and topoisomerase I (TopoI) cooperate. TopoI switches conformation, senses DNA supercoils near RNAP and relaxes them. Mutations disrupting this process alter bacterial motility and operon polarity.

New online: DNA topoisomerase I acts as supercoiling sensor for bacterial transcription elongation

#Archaeasky #Microsky

LoL-align: sensitive and fast probabilistic protein structure alignment https://www.biorxiv.org/content/10.1101/2025.11.24.690091v1

Exterior of York Minster and part of the Minster Gardens, c.1900 Gothic cathedral with two tall towers, intricate stone facade, and large arched windows, set against a clear sky and open lawn.

For this weeks EYA Focus Theme 'Beauty', this image of the beautiful York Minster showcases the special kind of beauty it has to offer, one that isn't loud or fleeting, but that rises slowly out of history and stands resilient through centuries. 

#EYABeauty #YorkMinster #BeautyInArchitecture

The Histidine Kinase VraS Interacts with Vancomycin and Penicillins Through its Membrane‐Anchored N‐terminal Domain The signals triggering activation of VraTSR, a key regulator of the cell wall stress response in Staphylococcus aureus, remain unknown. Combining crosslinking assays with vancomycin- and ampicillin-d....

Sensor kinase interacts directly with two distinct classes of cell wall targeting antibiotics to detect cell envelope stress. Great work

onlinelibrary.wiley.com/doi/abs/10.1...

New work from @heathmurraylab.bsky.social
#Microsky

#ArchaeaSky #MicroSky

Widespread and intron-rich mirusviruses are predicted to reproduce in nuclei of unicellular eukaryotes - Nature Microbiology Environmental metagenomic explorations show that Mirusviricota lineages lack essential replication and transcription genes and contain spliceosomal introns, suggesting nuclear reproduction.

Check out our latest paper on mirusviruses, one of the most remarkable new groups of protist viruses - extremely diverse, carry lots of spliceosomal introns (including new homing introns) and are at the evolutionary crossroads between tailed phages and herpesviruses! www.nature.com/articles/s41...

Genome integrity relies on rapid recycling of DNA Pol III in bacteria | PNAS DNA replication requires precise coordination between DNA unwinding and DNA synthesis. In all domains of life, protein–protein interactions at the ...

Happy to share our most recent work www.pnas.org/doi/10.1073/.... Here we describe how efficient DNA replication in E. coli is dependent on an interaction between SSB-ssDNA and the DNA polymerase (Pol III). Thanks to all the co-authors for their hard work!

A Farewell to Arms: The Trade-off Between Growth and Defence in Bacteria (York YBDTP Project) at University of York on FindAPhD.com PhD Project - A Farewell to Arms: The Trade-off Between Growth and Defence in Bacteria (York YBDTP Project) at University of York, listed on FindAPhD.com

Two fully-funded PhD openings in my research group at the University of York.
If you’re excited about viromes, phage biology, Nanopore sequencing, soils and the odd bit of alpine or agricultural field sampling, we’d love to hear from you!
🌱🦠🏔️

tiny.cc/c4pv001
tiny.cc/e4pv001

Manaus sits on the banks of the Amazon River, surrounded by rainforest that is increasingly shaped by human activity. In this landscape, Leishmania parasites—and the sand flies that transmit them—are shifting from their original wildlife hosts, such as sloths, into farms and human-modified forests.

Funded PhD: study how Leishmania parasites and their sand fly vectors adapt to Amazon urbanisation. Includes fieldwork in Brazil plus genomics and spatial epidemiology. UK students only. Apply by 7 Jan 2026: djeffares.github.io/phd.html

Charge segregation in the C-terminal linker of FtsZ enables Z-ring scaling with prokaryotic cell width Bacterial cytokinesis is orchestrated by the Z-ring, a cytoskeletal structure formed by treadmilling filaments of the tubulin-like GTPase FtsZ. During assembly, filament curvature must match the cell ...

Happy to share a new preprint from the lab: Marko became interested in whether the disordered linker of FtsZ might influence how the protein organizes into the Z-ring. And this led to some surprising findings!
Preprint: www.biorxiv.org/content/10.1...

a man walking in a field with an umbrella ALT: a man walking in a field with an umbrella

Come join us! Soon I will be advertising a postdoc vacancy in my group as part of my @erc.europa.eu AdG project 'DARK ROOTS'. Focus of the project will be on phylo- and metagenomic mining of novel prokaryotic lineages. I will soon post a link here - stay tuned, and please repost! #asgardarchaea

Schematic overview of the process of DNA-affinity / pull down identification of unknown nucleic acid-binding proteins

Identification of Previously Unknown DNA-Binding Proteins Using DNA Affinity/Pull-Down Methods Followed by Mass Spectrometry

Jutras, Babb, Jusufovic, Krusenstjerna, Saylor, Verma, and Stevenson

Current Protocols 2025, 5:e70264
doi: 10.1002/cpz1.70264

#MicroSky

Let’s wrap things up: Open and closed hypernucleosomes in Asgard archaea Asgard archaea are widely considered the closest living relatives of eukaryotes. In this issue of Molecular Cell, Ranawat et al. report high-resolution structures of hypernucleosomes formed by the hodarchaeal HHoB histone, disclosing open and closed chromatin conformations.

Let’s wrap things up: Open and closed hypernucleosomes in Asgard archaea

Introducing the j-metric: a true measure of what matters in academia Science has become obsessed with publishing numbers. With this new satirical proposal, have we reached peak metric?

"... academia becomes McDonaldized — subject to the fast-food industry principles of efficiency, calculability, predictability and control — ..."
@nature.com

www.nature.com/articles/d41...

Biogeography and host interactions of CPR and DPANN viruses in acid mine drainage sediments - Nature Communications The ecological role of viruses for CPR bacteria and DPANN archaea remains understudied. Here, the authors apply metagenomic approaches to study the biogeographic distribution of CPR and DPANN viruses in acid mine drainage sediments and elucidate their complex interplays.

Biogeography and host interactions of CPR and DPANN viruses in acid mine drainage sediments | Nature Communications https://www.nature.com/articles/s41467-025-65461-0