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Iain Johnston

@mitomaths.bsky.social
941 followers 216 following 87 posts

Stochastic Biology Group: using maths, stats, and experiments to learn about biology and disease. We love organelles and oDNA, evolution, noise, and inference. stochasticbiology.w.uib.no

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Iain Johnston @mitomaths.bsky.social · 04/09/2026
... across several decades of clinical study. Would love to hear feedback, and on the aligned work on Klebsiella natural histories journals.plos.org/plosbiology/... and on *the perspective of EvAM in AMR evolution journals.asm.org/doi/full/10.... 3/
journals.plos.org
Evolutionary inference reveals global natural histories and predicted pathways of antimicrobial resistance in Klebsiella pneumoniae
Antimicrobial resistance in Klebsiella pneumoniae is a growing global threat, but its evolutionary routes remain hard to predict. This study uses machine learning to explore how resistance evolves acr...
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Iain Johnston @mitomaths.bsky.social · 04/09/2026
... finding striking similarities of evol dynamics across different pathogens, but also notable diffs predicted by geography and patient demographics. The networks (grey) are predictive, and perform well forecasting new resistome phenotypes (coloured dots) from sub-Saharan Africa... 2/
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Iain Johnston @mitomaths.bsky.social · 04/09/2026
How does AMR evolution vary across pathogens? Regions? Patients? We used EvAM* to take a look. www.biorxiv.org/content/10.6... Inferring evol pathways to multi-drug resistance as transition networks, we use the amazing CABBAGE dataset to learn AMR "roadmaps" across ESKAPEEs around the world... 1/
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Aylwyn Scally @aylwyn-scally.bsky.social · 09/08/2026
Highly recommend this, and it's a key element in most physics training. I'd add another trick that many biologists could benefit from, a small thing that makes a big difference: always use units. If you're unsure about the units of your number, chances are you don't properly understand it.
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Genome Biology and Evolution @genomebiolevol.bsky.social · 10/07/2026
García-Pascual, Nordbotten & @mitomaths.bsky.social investigate the fitness advantages, disadvantages, conflicts, and tradeoffs of different strategies for inheritance of organelle DNA genomes. 🔗 doi.org/10.1093/gbe/evag161 #societyjournal #genome #evolution
GBE | Optimal Organelle Inheritance Strategies Under Different Changing Environments and Mutational Pressures
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Iain Johnston @mitomaths.bsky.social · 30/06/2026
Super grateful to Dr Robert Glastad (and maker @neurowoodworks.bsky.social ) for this beautiful art celebrating Robert's successful PhD defence! Featuring Eqn. 15 journals.plos.org/ploscompbiol... linking physical behaviour of mitochondria and genetic behaviour of mtDNA :-)
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Iain Johnston @mitomaths.bsky.social · 15/06/2026
Excited to meet this in its final form, and thanks to all at @plosbiology.org for a very smooth and useful review and editing process!
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Iain Johnston @mitomaths.bsky.social · 09/06/2026
We apply it to the evolution of drug resistance in TB and Klebsiella, and show its interoperability with other problems. The link is www.biorxiv.org/content/10.6... ... would love to hear thoughts!
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Iain Johnston @mitomaths.bsky.social · 09/06/2026
This sets up for a version of the Mk model that scales linearly in observations instead of exponentially in features, and can handle interactions, reversibility, coupling, missing data, and more. We think this could be quite a generally useful advance! 4/
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Iain Johnston @mitomaths.bsky.social · 09/06/2026
One can -- the classic Mk model in evol bio. But it struggles with many interacting features, because the possible state space becomes huge. But, though possible, many of these states are unlikely. So, basically, we prune them in a rational way. 3/
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Iain Johnston @mitomaths.bsky.social · 09/06/2026
If features influence each other (resistance to drug X makes resistance to drug Y more likely), that's a complication. If features can be lost as well as gained, that's another. If there are lots of them, or missing data, that's another. Few methods can handle all that. 2/
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Iain Johnston @mitomaths.bsky.social · 09/06/2026
Excited to share a new preprint! Lots of evolutionary processes, from AMR to cancer, involve biology acquiring features (drug resistances, mutations, etc). These are sometimes called "accumulation pathways", an instance of discrete character evolution. 1/
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The Sainsbury Laboratory @thesainsburylab.bsky.social · 03/06/2026
📽️ "Medicine can save your life one day. Plants save your life every day." 🌱 @kamounlab.bsky.social shares his personal journey, his passion for science and his vision for the future in an inspiring talk at TEDx Pasha Street, now freely available online 🌾 www.youtube.com/watch?v=kiqt...
youtube.com
Genetics, Climate & the Future of Food | Sophien Kamoun | TEDxPasha Street
In this thought-provoking talk, Sophien Kamoun explores the urgent connection between climate change, food security, and the future of agriculture. Drawing from his scientific research and personal…
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Payam Gammage @mito-oncogene.bsky.social · 02/06/2026
🚨Excited to announce a new preprint from our lab, where we describe an ancient metabolic axis that controls mitochondrial genome copy number; a mechanism we uncovered in human cells that stretches through evolution to control mtDNA in flies, yeast and even plants!
biorxiv.org
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Iain Johnston @mitomaths.bsky.social · 03/06/2026
Really cool work, congrats Payam and all! Connected with the obs that Fe-S cluster metab is the most retained mito feature across euks with highly reduced mitos (MROs) after DNA/ATP production loss/etc? academic.oup.com/view-large/f...
academic.oup.com
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Carl T. Bergstrom @carlbergstrom.com · 03/06/2026
"The increasing involvement of technology companies in mathematical research raises the risk that research questions may come to be prioritized because of their amenability to automated mathematics, rather than expert judgment of their deeper significance."
leidendeclaration.ai
Leiden Declaration on Artificial Intelligence and Mathematics
This declaration calls for action to address the challenges posed by the use of artificial intelligence within mathematics research.
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Iain Johnston @mitomaths.bsky.social · 27/04/2026
Plant mitochondrial fusion factors! www.pnas.org/doi/full/10....
pnas.org
PMF proteins mediate mitochondrial fusion in Arabidopsis | PNAS
Mitochondrial dynamics—continuous fission and fusion—are hallmarks of these organelles and essential for mitochondrial function across eukaryotes. ...
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Iain Johnston @mitomaths.bsky.social · 02/04/2026
Mito evolution special issue of Phil Trans now out! royalsocietypublishing.org/rstb/issue/3... Excited to be part of this, with some new perspectives on mtDNA segregation from us royalsocietypublishing.org/rstb/article... and brilliant content from colleagues worldwide! Pics from current location 🇳🇴
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Admirable Women @admirablewomen.bsky.social · 20/03/2026
Chemist/physician Dr. Maud Menten co-authored the seminal paper 𝘋𝘪𝘦 𝘒𝘪𝘯𝘦𝘵𝘪𝘬 𝘥𝘦𝘳 𝘐𝘯𝘷𝘦𝘳𝘵𝘪𝘯𝘸𝘪𝘳𝘬𝘶𝘯𝘨, 1931. This intro'd the Michaelis–Menten equation (image). It remains a cornerstone of #biochemistry, used in drug design, metabolic studies & enzyme engineering. She was born #OTD in 1879. #WomenInSTEM
A black-and-white historical photograph of Dr. Maud Leonora Menten (1879–1960), the Canadian physician and biochemist who co-developed the Michaelis–Menten equation for enzyme kinetics. Taken in her laboratory (likely at the University of Pittsburgh in the 1910s–1920s), she stands with a serious, focused expression—lips closed, eyes direct and thoughtful—against a backdrop of wooden shelves filled with glass bottles, jars, scientific equipment, and a wire-mesh enclosure. She wears a dark dress with a lace collar, a string of beads, and her hair styled in a neat bun. Superimposed on the image is the Michaelis–Menten equation in white text:v=Vmax⁡[S]Km+[S]v = \frac{V_{\max} [S]}{K_m + [S]}v = \frac{V_{\max} [S]}{K_m + [S]}
This iconic portrait captures Menten during her groundbreaking research in biochemistry and histochemistry, where she helped establish the foundational mathematical model of enzyme-substrate reactions still used today, while overcoming significant gender barriers as one of the first women in Canada to earn both an M.D. and a Ph.D.
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Kin Pan Chung @kinpanchung.bsky.social · 03/03/2026
Mitochondria can indeed be inherited from the father! 🍀 In this new study, we uncovered the molecular mechanisms underlying mitochondrial inheritance in Nicotiana tabacum. @natplants.nature.com doi.org/10.1038/s414...
doi.org
High-frequency biparental inheritance of plant mitochondria upon chilling stress and loss of a genome-degrading nuclease - Nature Plants
Maternal inheritance of mitochondria breaks down in the cold when a mitochondrial DNA degrading nuclease is defective, resulting in biparental inheritance that can rescue mitochondrial mutations and g...
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Iain Johnston @mitomaths.bsky.social · 28/02/2026
Vinterferie ❤️🇳🇴🦢
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Iain Johnston @mitomaths.bsky.social · 13/02/2026
Perhaps... how life started?! www.science.org/doi/10.1126/...
science.org
A small polymerase ribozyme that can synthesize itself and its complementary strand
The emergence of a chemical system capable of self-replication and evolution is a critical event in the origin of life. RNA polymerase ribozymes can replicate RNA, but their large size and structural ...
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Piotr Lukasik @sympiotr.bsky.social · 11/02/2026
Our new paper in @natcomms.nature.com is now online-early! We describe independent evolution of bacterial genomes of only ~50–52 kb — the smallest known outside cellular organelles — revealing striking convergence toward minimal gene sets. 🔗 doi.org/10.1038/s414...
The visualization of two bacterial genomes, of 50 and 52kb, representing independent instances of extreme genomic reduction in ancient heritable endosymbionts of planthoppers.
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Carl T. Bergstrom @carlbergstrom.com · 27/01/2026
1. The thing about science that these jokers don't understand is that science cannot be vibe-coded. Whatever its flaws, the point with vibe coding is that you're trying to quickly make something that sorta works, where you can immediately sorta see if it sorta works and then sorta use it.
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Journal of Evolutionary Biology @jevbio.bsky.social · 22/01/2026
Check out our latest Special Section guest edited by @mitopozzi.bsky.social and Sophie Breton: Beyond ATP: New insight into mitochondrial function and evolution 🎨 Cover image - artwork by Iain G Johnston academic.oup.com/jeb/pages/be...
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Osman Lab @osman-lab.bsky.social · 10/01/2026
How do cells assess mtDNA quality? Local ATP and membrane-potential gradients reflect mtDNA integrity and drive intracellular purifying selection. We introduce FAST, a scalable mtDNA QC assay in S. cerevisiae. Great collaboration with the Schmoller Lab. journals.plos.org/plosgenetics... 🧬⚡
journals.plos.org
Local mitochondrial physiology defined by mtDNA quality guides purifying selection
Author summary Mitochondria are essential organelles in our cells that convert nutrients into usable cellular energy. They contain their own DNA, and mutations in this DNA can compromise mitochondrial...
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Sandy Hetherington @sandyheth.bsky.social · 09/01/2026
Looking for a new 📕 to read about plants?? I highly recommend the brilliant book ‘Ferns, Lessons in survival from Earth’s most adaptable plants’ Written by @fernway.bsky.social and Jacob Suissa with amazing illustrations by Laura Silburn 🌿 #FernFriday 🌿
Book front cover with illustrations of fern leaves and the title: Ferns, lessons in survival from Earth’s most adaptable plants
Written by: Fat-Wei Li and Jacob S. Suissa
Illustrated by Laura Silburn
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Iain Johnston @mitomaths.bsky.social · 09/01/2026
1. Apply for one of the positions below (lab or theory) by Jan 18th 2. Learn interdisc skills and discover cool new things about how mitochondria move and socialise 3. Explore some of Norway's beautiful nature (both the below, Rundemanen and Gullfjellet, <10km from work)
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Iain Johnston @mitomaths.bsky.social · 02/01/2026
2026 ❤️ 🇳🇴
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Iain Johnston @mitomaths.bsky.social · 19/12/2025
‼️Two new PhD positions open! One experimental, one modelling, exploring these beautiful collective dynamics in mitochondria across species. 🇳🇴, good pay, full staff benefits. [Shares much appreciated] Lab: www.jobbnorge.no/en/available... Modelling: www.jobbnorge.no/en/available...
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Pawel Burkhardt @pawelburkhardt.bsky.social · 17/12/2025
Thrilled to see our review article "The evolutionary origins of synaptic proteins" highlighted on the cover of Nature Reviews Neuroscience 🤩. www.nature.com/articles/s41... @msarscentre.bsky.social 🧠✨🧬🌊🪼🧽
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Iain Johnston @mitomaths.bsky.social · 18/12/2025
Mitochondria, hypercubes, and a blackboard -- what a lot of favourite things for J Evol Biol this month! Thanks to all involved for a smooth and pleasant review editorial process; academic.oup.com/jeb/article/...
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Iain Johnston @mitomaths.bsky.social · 19/11/2025
Ski season!
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Iain Johnston @mitomaths.bsky.social · 15/11/2025
Paradise up on the mountain trails
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Buzz Baum @buzzbaum.bsky.social · 07/11/2025
We have wondered what a complex archaeal cell might look like ever since 2014. It’s been a long road (and the journey is far from over), but it’s a good time to pause for breath and look. These Asgard archaeal cells are a surprise! And that is the joy of being a cell biologist.
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Journal of Evolutionary Biology @jevbio.bsky.social · 06/11/2025
In some species, #mitochondria have lost functions: from specific complexes to the ability to produce #ATP (and more!). We examine the evolutionary pathways of this reduction, from yeast and mistletoe to parasite "MROs": doi.org/10.1093/jeb/... @mitomaths.bsky.social et al. 2025
doi.org
Convergent pathways of reductive mitochondrial evolution characterized with hypercubic inference
Abstract. For a striking example of mitochondrial behaviour beyond adenosine triphosphate (ATP) generation, consider mitochondrion-related organelles (MROs
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Iain Johnston @mitomaths.bsky.social · 22/09/2025
Would love to hear any feedback; we continue to believe that EvAM applied to AMR (learning evolutionary history) can be a powerful complement to genomic surveys (focussing on the present). Thanks for reading! www.biorxiv.org/content/10.1... 5/5
biorxiv.org
Global diversity, predictors, and predictions of AMR evolutionary pathways in Klebsiella pneumoniae
Antimicrobial resistance (AMR) is a substantial and growing global health burden. Understanding, and predicting, its evolution in specific pathogens will help responses across scales from individual p...
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Iain Johnston @mitomaths.bsky.social · 22/09/2025
Understanding evolutionary dynamics lets us form future predictions. We tested these predictions with newly sequenced data from decades of clinical study in Tanzania. Fitted model retrospectively predicted those previously unobserved accumulation dynamics! 4/
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Iain Johnston @mitomaths.bsky.social · 22/09/2025
Interesting, but very high-dimensional, so we project down to find the principal axes of diversity in evolutionary behaviour -- and what predicts them. They're linked both to public health region and drug use regimens 3/
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Iain Johnston @mitomaths.bsky.social · 22/09/2025
Following the ideas in journals.asm.org/doi/full/10.... about applying evol accumulation modelling (EvAM) to AMR, we use genomics data to infer the orderings of character accumulation behind observed Klebsiella AMR profiles across countries (e.g. Romania here), with global average in D 2/
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Iain Johnston @mitomaths.bsky.social · 22/09/2025
Great to see this out there! We infer the evolutionary pathways behind patterns of AMR in Klebsiella across 102 states, finding globally consistent principles, state-specific deviations (and covariates), and validating evol predictions with new genomes. biorxiv.org/content/10.1... 1/
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Iain Johnston @mitomaths.bsky.social · 17/06/2025
There'll be 2 PhD positions (math / microscopy) on MitoPhyto. But the Norwegian research council is also offering opportunities for non-European postdocs to come to Norway for 3 years associated with FRIPRO projects. Please DM me if interested! www.forskningsradet.no/en/call-for-...
forskningsradet.no
Recruitment of Talented Researchers to Norway
The Research Council supports the recruitment of talented international researchers to the Research Council's centre calls and for projects funded ...
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Iain Johnston @mitomaths.bsky.social · 17/06/2025
Celebrating grant award with a mountain run! MitoPhyto, a FRIPRO project, will combine modelling and microscopy to explore mitochondrial and mtDNA maintenance across non-bilaterian multicellular eukaryotes. Opportunities to come to Norway: please see next post
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Iain Johnston @mitomaths.bsky.social · 17/05/2025
Gratulerer med dagen alle sammen! (non-Norway-based folks, happy Norwegian Constitution Day!)
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Kin Pan Chung @kinpanchung.bsky.social · 05/05/2025
Glad to share this review, which takes a narrative approach to explore mechanisms governing cytoplasmic inheritance. It highlights exciting advances in the field, while also pointing to the many open questions that remain. Have a read here: doi.org/10.1093/plph...
doi.org
Cytoplasmic Inheritance: The Transmission of Plastid and Mitochondrial Genomes Across Cells and Generations
Abstract. In photosynthetic organisms, genetic material is stored in the nucleus and the two cytoplasmic organelles: plastids and mitochondria. While both
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Iain Johnston @mitomaths.bsky.social · 07/05/2025
Had a brilliant time at the 54th Jírovec’s Protozoological Days in Frymburk. Amazing organisms, amazing science, lots of exciting organelle work. Beautiful setting too! Thanks to all www.chromera.org/konference/5...
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Iain Johnston @mitomaths.bsky.social · 07/05/2025
May trails on the way to the final Applied Statistics lecture of the semester!
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Iain Johnston @mitomaths.bsky.social · 02/05/2025
View from the office as summer approaches
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Dr. Hilary Rose Dawson @hilaryrosed.bsky.social · 01/04/2025
Exciting permanent(!) #JobAlert for a #botanist to work in Bergen, Norway 🧪 PhD required, language proficiency required within two years. Apply by 25 April. #Ecology #Restoration #Botany
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Eva Nowack @evanowack.bsky.social · 19/03/2025
Out today: Exciting intermediate between endosymbiont and organelle identified! Endosymbionts in Angomonas deanei lost nearly all bacterial cell division genes. Instead, we identified a host-encoded protein, ETP9, that became specialized for endosymbiont division. 1/2 www.science.org/doi/10.1126/...
Angomonas deanei with flourescent-labeled nucleus and endosymbiont. ETP9 localizes at the endosymbiont division site.
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