Daniela Barillà
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danielabarilla.bsky.social
Daniela Barillà
@danielabarilla.bsky.social
Microbial geneticist interested in large and small DNA 🧬 rings in bacteria and archaea.
Living in Brontë country and based at the University of Old York.

https://barillalabyork.weebly.com/
Pinned
And the story is published now!🍾
www.nature.com/articles/s41...

Open access link: rdcu.be/exnOc

Many years in the making, great collaboration with @archaellum.bsky.social & @tunglejic.bsky.social

Thanks @ukri.org BBSRC & @leverhulme.ac.uk for funding, reviewers & editor!! 🙏
#microsky #archaeasky
Any chance this article can be made freely accessible, Research Professional Team?
January 28, 2026 at 10:09 PM
Reposted by Daniela Barillà
Amongst other things, this is deeply disingenuous wording. The letter states (as positive framing?) that "curiosity-driven research will be the largest component of UKRI's portfolio over the SR period"

Yet the majority of that bucket (61%) is QR funding. This is really conflating two very 1/2
In UK astro news, the Executive Chair of our funding council #STFC, Prof Michele Dougherty, has written to the community. TL;DR: skint. Bad times ahead for UK astro, particle physics, facilities etc 🧪🔭
January 28, 2026 at 9:35 PM
Reposted by Daniela Barillà
Lots of interest in our lead story today.

‘Grave’ concerns over applicant-led funds at UK research councils.

Figures suggest reductions at MRC and BBSRC, with questions hanging over pending MRC grant applications.

www.researchprofessionalnews.com/rr-news-uk-r...
‘Grave’ concerns over applicant-led funds at UK research councils - Research Professional News
Figures suggest reductions at MRC and BBSRC, with questions hanging over pending MRC grant applications
www.researchprofessionalnews.com
January 28, 2026 at 4:37 PM
Reposted by Daniela Barillà
A prophage-encoded abortive infection protein preserves host and prophage spread www.nature.com/articles/s41...
A prophage-encoded abortive infection protein preserves host and prophage spread - Nature
A Gifsy-1 prophage–encoded higher eukaryotes and prokaryotes nucleotide-binding protein, HepS, senses Siphoviridae infection, activates abortive defence by cleaving host transfer RNAs, blocks rival ph...
www.nature.com
January 28, 2026 at 7:13 PM
Reposted by Daniela Barillà
Reposted by Daniela Barillà
New paper out in @pnas.org, and it made the cover! 👁️

We represent plasmids as circles and mutations as dots, resembling an eye, because in this paper we literally 𝑤𝑎𝑡𝑐ℎ plasmids evolve.

‼️Check Paula’s 🧵 and the paper👇

𝗣𝗹𝗮𝘀𝗺𝗶𝗱 𝗺𝘂𝘁𝗮𝘁𝗶𝗼𝗻 𝗿𝗮𝘁𝗲𝘀 𝘀𝗰𝗮𝗹𝗲 𝘄𝗶𝘁𝗵 𝗰𝗼𝗽𝘆 𝗻𝘂𝗺𝗯𝗲𝗿
www.pnas.org/doi/10.1073/...
January 27, 2026 at 8:23 PM
Reposted by Daniela Barillà
Using machine learning to sort over 80,000 bacterial genomes into aerobes and anaerobes, researchers find that oxygen-breathing bacteria likely evolved in local oxygen-rich environments 200–400 million years before the Great Oxidation Event. In PNAS: https://ow.ly/jZWQ50Y3LhU
January 26, 2026 at 7:00 PM
Reposted by Daniela Barillà
A structural database of ~2.7M predicted human gut microbial proteins + an alignment-free method by structure-encoded protein language models for fast and sensitive detection of remote homologs - really cool!
#microsky 🧪🧬🖥️🦠✨
www.cell.com/cell-host-mi...
Exploring functional insights into the human gut microbiome via the structural proteome
Liu et al. develop a structure database of human gut microbial proteins and a structure-aware AI model for remote homolog detection. They demonstrate the power of structure-guided approach in discover...
www.cell.com
January 26, 2026 at 7:24 AM
Reposted by Daniela Barillà
Lots of PhD opportunities for UK + international students involving my lab. Topics relate to metals & microbiology.

First up: TonB-dependent receptors in commensal Neisseria in my lab at Durham, with @kjosts.bsky.social and @mattbashton.bsky.social.

www.findaphd.com/phds/project...
Nutrient uptake in commensal bacteria: exploring uncharacterised TonB-dependent transporters. at Newcastle University on FindAPhD.com
PhD Project - Nutrient uptake in commensal bacteria: exploring uncharacterised TonB-dependent transporters. at Newcastle University, listed on FindAPhD.com
www.findaphd.com
January 24, 2026 at 2:28 PM
Reposted by Daniela Barillà
Raman spectroscopy can be used to predict cellular physiology and proteome composition in E. coli.

🔗 buff.ly/bcALp6R
January 24, 2026 at 11:01 AM
Reposted by Daniela Barillà
It is Saturday - happy weekend!

Plus (and this is far more exciting) we have snowdrops and aconytes.

Spring is around the corner. ☺️
January 24, 2026 at 9:06 AM
Reposted by Daniela Barillà
Jumbo circular extrachromosomal elements of methane-oxidizing archaea with variably extensive metabolic and defense gene repertoires | bioRxiv https://www.biorxiv.org/content/10.64898/2026.01.21.700959v1?rss=1
Jumbo circular extrachromosomal elements of methane-oxidizing archaea with variably extensive metabolic and defense gene repertoires
Archaeal extrachromosomal elements (ECEs) are arguably the least well understood of all genetic elements, and few have > 200 kbp ("jumbo") genomes. Here, we report circular, jumbo ECEs with genomes of up to 535 kbp in length that associate with anaerobic methane-oxidizing Methanoperedens archaea. Notably, a 409-kbp genome related to jumbo ECEs is integrated into a subset of the ~4.2 Mbp Methanoperedens chromosomes at the tRNA-Asp genes. This represents the largest integrative element in Archaea and supports the jumbo ECE - host association. Multiple genome alignment and phylogenetic analyses suggest that the large sizes were developed by extensive DNA acquisition from Methanoperedens. The newly identified ECEs encode, and in some cases express, metabolic genes such as tetrahydromethanopterin S-methyltransferase exclusively involved in methane oxidation, and genes for nitrogen and sulfur compound transformations. Also encoded are defense systems, some of which are absent in hosts, such as hybrid Type I/Type III-A CRISPR-Cas systems. In contrast to viruses and plasmids, they have host-like replication machinery and occur at stable copy ratios of 1.44 ± 0.24 : 1 to the host. Overall, our results reveal a spectrum of jumbo ECEs of Methanoperedens, ranging from plasmid-like to minichromosome-like. ### Competing Interest Statement J.F.B. is a co-founder of Metagenomi. The remaining authors declare no competing interests. Emerson Collective (United States)
www.biorxiv.org
January 23, 2026 at 12:14 AM
Reposted by Daniela Barillà
🚨 New pre-print alert!
Jumbo circular extrachromosomal elements of methane-oxidizing archaea with variably extensive metabolic and defense gene repertoires

www.biorxiv.org/content/10.6...
January 23, 2026 at 1:21 AM
Reposted by Daniela Barillà
Congrats to Jamie et al! Our latest @york.ac.uk work dissecting the structural landscape of the Rep Helicase is now out in Nucleic Acids Research! 🧬🔬
@timcraggs.bsky.social @agnesnoy.bsky.social @bpsiyork.bsky.social @dr-mahmoud.bsky.social @single-mole.bsky.social
👇
tinyurl.com/bdznxur3
January 22, 2026 at 5:28 PM
Reposted by Daniela Barillà
🚨 Fully‑funded PhD for Home Students🚨

We'll explore non-antibiotic alternatives in relatistic environments, uncovering how they work, if they affect antibiotic activity and whether they influcence AMR acquistion. Come join a wonderful supervisory team!

#MicroSky #UTISky #AMar

tinyurl.com/38u552bu
Optimising the use of alternative therapies for the treatment of urinary infections - The University of Nottingham
tinyurl.com
January 21, 2026 at 9:12 PM
Reposted by Daniela Barillà
Nature research paper: Construction of complex and diverse DNA sequences using DNA three-way junctions

go.nature.com/4qu2ExZ
Construction of complex and diverse DNA sequences using DNA three-way junctions - Nature
Sidewinder enables high-fidelity DNA assembly by separating the information that guides assembly from the final assembled sequence.
go.nature.com
January 21, 2026 at 6:08 PM
Reposted by Daniela Barillà
Reposted by Daniela Barillà
January 19, 2026 at 6:05 PM
Reposted by Daniela Barillà
'This video is the culmination of several yrs attempting to: (1) Figure out best practices for modeling ptn-ptn interactions; (2) Understand the outputs of programs like AlphaFold & adjacent software including quantitative metrics;(3) Communicate my thoughts to unwitting victims through workshops'
AlphaFold protein interaction modeling tutorial and workshop - the Node
This video is the culmination of several years attempting to: (1) Figure out best practices for modeling protein-protein interactions; (2) Understand the This video is the culmination of several years...
thenode.biologists.com
January 18, 2026 at 8:52 AM
Reposted by Daniela Barillà
Bacteria are amazing! The abundant Dps protein binds and protects DNA in stationary-phase cells with minimal effect on chromosome accessibility, dynamics, and organization. Now in NAR doi.org/10.1093/nar/...; I'm really proud of our multidisciplinary team led by Lauren, Lindsay, and Xiaofeng, et al.
January 16, 2026 at 1:32 PM
Reposted by Daniela Barillà
Out Now! A phage protein screen identifies triggers of the bacterial innate immune system #MicroSky
A phage protein screen identifies triggers of the bacterial innate immune system
Nature Microbiology, Published online: 16 January 2026; doi:10.1038/s41564-025-02239-6A library of 400 phage protein-coding genes is used to find a trove of antiphage systems, revealing systems that target tail fibre and major capsid proteins.
go.nature.com
January 16, 2026 at 4:53 PM
Reposted by Daniela Barillà
I am very pleased to share that our database of prokaryotic and viral histones, ProHistoneDB, is now available online at prohistonedb.org. Please also see the accompanying article in J Mol Biol: doi.org/10.1016/j.jm...
ProHistoneDB
prohistonedb.org
January 16, 2026 at 8:47 AM
Reposted by Daniela Barillà
Fabian was quicker :) But yes, we have an open postdoc position in bacterial bioenergetics and membrane biology, using on B. subtilis as the model. Come join us! @cbcb-newcastle.bsky.social is a great place to work, and we are a friendly, international lab. Visa+IHS fees covered. #microsky
PostDoc position in Newcastle upon Tyne:

@henrikstrahl.bsky.social
January 14, 2026 at 8:56 PM