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Reposted by Yuya Karita

Joao Ascensao @joaoascensao.bsky.social · Jul 21

New review article with @mmdesai.bsky.social is out today! Grateful for the opportunity to contribute something we hope will serve the community well

Nature Reviews Genetics @natrevgenet.nature.com · Jul 21

New online! Experimental evolution in an era of molecular manipulation

Experimental evolution in an era of molecular manipulation

Nature Reviews Genetics, Published online: 21 July 2025; doi:10.1038/s41576-025-00867-6In this Review, Ascensao and Desai discuss how methodological advances in genotype and phenotype manipulation are transforming experimental evolution approaches and providing new insights into the underlying genetics and forces that shape phenotypic evolution.

www.nature.com

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Ulrich Schwarz @ulrichschwarz.bsky.social · Jul 17

📣Book alert📣

Finally out with Cambridge University Press: the book by Udo Seifert on "Stochastic thermodynamics". It comprehensively covers many topics, from an introduction to statistical physics to many special subjects such as reaction networks and active particles. Highly recommended 👍👍👍

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SeppeKuehnLab @seppekuehnlab.bsky.social · Jul 17

New paper in @nature.com! With @kiseokmicro.bsky.social , Siqi Liu, Kyle Crocker, Jojo Wang, Mikhail Tikhonov & Madhav Mani — a massive dataset and simple model reveal a few conserved regimes that capture how soil microbiome metabolism responds to perturbations. www.nature.com/articles/s41...

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Will Ratcliff @wcratcliff.bsky.social · Jun 24

1/27 We have a new paper out! Turns out that snowflake yeast have been hiding a secret from us - they've evolved a (very!) crude circulatory system. Not with blood vessels or a heart, but through spontaneous fluid flows powered by their metabolism. 🧪🔬

www.science.org/doi/full/10....

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Kyogo Kawaguchi @kyogok.bsky.social · May 15

This is a bizarre discovery by Kyosuke. He introduces an active binary mixture model and finds bubbles, typically found in very large MIPS simulations, appearing in smaller setups. Then observes that even the mean-field deterministic ver. of the model also produces bubbles.
arxiv.org/abs/2505.08637

Bubble formation in active binary mixture model

Phase separation, the spontaneous segregation of density, is a ubiquitous phenomenon observed across diverse physical and biological systems. Within a crowd of self-propelled elements, active phase se...

arxiv.org

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Yuya Karita @yuyakarita.bsky.social · May 6

“Dispersal-driven” evolution does not require competitive exclusion. As a result, multiple adaptive lineages can cooccur and coexist in a single evolved population. In sum, our work revealed the importance and outcome of the ecological context shaped by ancestors in ALI-colonizing evolution. [5/5]

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Yuya Karita @yuyakarita.bsky.social · May 6

Compensation for the fitness costs alone does not explain how WS types increase in frequency. We highlighted the motile-sessile regulation. WS mutations elevate c-di-GMP levels, locking cells into a sessile state. The difference in dispersal from the ALI gives an indirect advantage to WS. [4/5]

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Yuya Karita @yuyakarita.bsky.social · May 6

However, as written in [1/5], there is a paradox. How can WS take over the ancestors despite the disadvantages? We revealed the role of ancestors. Ancestors pre-colonize the niche to provide physical scaffolds where WS can emerge and stably attach, compensating for the WS fitness costs. [3/5]

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Yuya Karita @yuyakarita.bsky.social · May 6

[bioRxiv link: doi.org/10.1101/2025... ]
P. fluorescens SBW25 has served as model bacteria for niche-colonizing adaptive radiation. Air-liquid-interface(ALI)-colonizing types (Wrinkly Spreaders, WS) are known to thrive very reproducibly from de-novo mutations within ~5 days of static culture. [2/5]

Context-Dependent Adaptation in Structured Environments

Adaptive evolution often leads to niche specialization, but successful colonization of a new niche can depend as much on ecological context as on genetic change. This is especially true in spatially s...

doi.org

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Yuya Karita @yuyakarita.bsky.social · May 6

Excited to share my postdoc work with @paulbrainey.bsky.social !

Common adaptive types in air-liquid-interface colonization turn out to grow slowly and colonize the niche inefficiently. They even fail when monocultured from low inocula. How can they reliably succeed in laboratory evolution? [1/5]

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Tami Lieberman @contaminatedsci.bsky.social · May 1

Do people in the same household share strains when they have the same species?

How many cells transmit when a strain is shared?
Can strain composition be dynamic when species composition is stable?

We answer these and related questions for the facial skin microbiome in our latest paper.

🧵[1/10]

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Thibaut Brunet @thibautbrunet.bsky.social · Apr 22

A dream come true: the first expansion microscopy images of C. flexa 🤩 Generated by Mylan & Uzuki who learned from the best (@hiralshah.bsky.social @gautamdey.bsky.social @dudinlab.bsky.social). We will learn so much from these!

Expansion microscopy micrograph of the choanoflagellate Choanoeca flexa, vaguely evocative of a cactus. Red = tubulin, green = actin, blue = DNA

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SeppeKuehnLab @seppekuehnlab.bsky.social · Mar 24

It’s increasingly clear that the language of microbial communities is one of resources. Conserved metabolism leads to regular, reliable resource flows across ecosystems—from the gut to wastewater. In complex communities, one serious challenge is: who is eating what?

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Richard Sever @richardsever.bsky.social · Mar 11

Big news: we are setting up a new non-profit organization to run bioRxiv and medRxiv. It's called openRxiv [no it's not a new preprint server; it's dedicated organization to oversee the servers] openrxiv.org 1/n

Homepage - openRxiv

openRxiv is an independent non-profit, the new organizational home for bioRxiv and medRxiv, enabling researchers to instantly share groundbreaking findings with the global scientific community.

openrxiv.org

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Tom Shimizu @thomasshimizu.bsky.social · Mar 1

+Our paper now out in @nature.com. We designed and built at AMOLF a robot that maps & tracks fungal networks as they trade nutrients with plants. We discovered how fungi build and operate hyper-efficient 'supply chains' for underground ecosystems.

www.nature.com/articles/s41...

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