iiinova — where your digital self keeps evolving

Reposted by Andrei Papkou

Alvaro San Millan @sanmillan.bsky.social · 02/03/2024

New preprint in collaboration with @asantoslopez.bsky.social lab and led by Jorge Sastre. Combining experimental evolution and analyses of longitudinal samples from hospitalised patients, we unveiled a new mechanism of plasmid-mediated evolution beyond HGT 1/8 www.biorxiv.org/content/10.1...

biorxiv.org

Plasmid-encoded insertion sequences promote rapid adaptation in clinical enterobacteria

bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution

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Reposted by Andrei Papkou

Alfonso Santos Lopez @asantoslopez.bsky.social · 03/03/2024

Excited to share the first preprint from my lab, collaborating with the fantastic @sanmillan.bsky.social 's lab, led by the amazing Jorge Sastre. We've demonstrated how insertion sequences encoded in plasmids promote bacterial adaptation. This project has been incredibly fun!

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Andrei Papkou @biobarkologist.bsky.social · 24/01/2024

Nice systematic study of all synonymous substitution in 30 E. coli finding that substantial fitness effects are common under strong selection www.pnas.org/doi/10.1073/...

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Reposted by Andrei Papkou

Cameron Thrash @jcamthrash.bsky.social · 23/01/2024

Sparsity of higher-order landscape interactions enables learning and prediction for microbiomes www.pnas.org/doi/10.1073/... #jcampubs

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Reposted by Andrei Papkou

Asher Leeks @asherleeks.bsky.social · 22/01/2024

Announcing the Social Lives of Viruses 2024! Do you study social evolution in viruses? Do you want to? Join us in Puerto Rico this June for a 50-person meeting dedicated to viral sociality. All costs covered. Apply here: forms.gle/sHTEcHJjryDh... #ViroSky #MicroSky #EvoSky #SocialViruses

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Andrei Papkou @biobarkologist.bsky.social · 12/01/2024

Exiting (but difficult) task for the future is to find what makes some lineages better!

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Reposted by Andrei Papkou

Alan McNally @alanmcn1.bsky.social · 12/01/2024

Our latest paper out today led by the incomparable Jukka Corander. Using longitudinal antibiotic use and genomic data, we show that antibiotic use does not determine the success of E. coli lineages causing BSI. www.sciencedirect.com/science/arti... 1/2

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Reposted by Andrei Papkou

Nittay Meroz @nittaym.bsky.social · 17/12/2023

Excited to share our new preprint! w @jfriedman.bsky.social #Microsky#evosky We tackle a simple question - How much of species evolution depends on the presence of other species? Bottom line: Most evolutionary changes were robust across strains that evolved with different biotic partners 1/

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Reposted by Andrei Papkou

Alvaro Sanchez @asanchezlab.bsky.social · 16/12/2023

New call for postdoc fellowships from the 🇪🇸 govt. My brilliant colleague Cristina Vieitez and I are happy to jointly sponsor candidates who'd like to join us in beautiful Salamanca & develop methods for characterizing and optimizing microbial consortia. More info ⬇️. www.aei.gob.es/convocatoria....

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Reposted by Andrei Papkou

Alvaro San Millan @sanmillan.bsky.social · 14/12/2023

Can we predict AMR evolution?? We sure can try! New study published today in PNAS www.pnas.org/doi/10.1073/...

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Andrei Papkou @biobarkologist.bsky.social · 01/12/2023

Ooops. Thank you for spotting! I will ask them to fix...

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Andrei Papkou @biobarkologist.bsky.social · 30/11/2023

An amazing piece in @quantamagazine.bsky.social by Veronique Greenwood about our recent article. High accessibility of fitness landscapes explained in a very accessible way

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Reposted by Andrei Papkou

Liana Lareau @lianafaye.bsky.social · 29/11/2023

Spurred on by ribosome profiling and other cool methods, translation elongation has grown into a whole field with new surprises all the time (and new relevance for vaccine mRNAs!). Here’s our latest on why synonymous codons aren’t all the same. (Thread) www.biorxiv.org/content/10.1...

biorxiv.org

Codon optimality modulates protein output by tuning translation initiation

bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution

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Andrei Papkou @biobarkologist.bsky.social · 27/11/2023

Thank you! Nice to meet you. I really liked your eLife paper. doi.org/10.7554/eLif... It was very reassuring to see that 27Cys DHFR works. No, we did not include mutational bias...

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Andrei Papkou @biobarkologist.bsky.social · 24/11/2023

I am grateful to my collaborators @jaescudero.bsky.social and Lucia Garcia-Pastor, my colleagues at the Anrdeas Wagner group. I am grateful to the reviewers for their helpful feedback and the Science production team for choosing a vivid illustration of a rugged landscape for the cover

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Andrei Papkou @biobarkologist.bsky.social · 24/11/2023

To conclude, a high-dimensional landscape can be accessible to adaptive evolution, even when rugged. Future studies will show if other landscapes are similarly accessible. We hope this effort will both assist and inspire further theoretical work on fitness landscapes.

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Andrei Papkou @biobarkologist.bsky.social · 24/11/2023

Interestingly, all high fitness peaks (27Asp and 27Glu) essentially share one enormous basin of attraction. This means that the evolving populations have access to multiple peaks, which makes it difficult to predict evolutionary outcomes.

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Andrei Papkou @biobarkologist.bsky.social · 24/11/2023

It turned out that most genotypes have a large number of paths leading to high fitness peaks, and very few paths leading to low fitness peaks. Consequently, high peaks are evolutionary accessible to most genotypes (i.e. have large basins of attraction).

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Andrei Papkou @biobarkologist.bsky.social · 24/11/2023

This result is robust against different population genetics assumptions

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Andrei Papkou @biobarkologist.bsky.social · 24/11/2023

Given the presence of multiple low and high peaks, we considered this landscape as rugged and expected that adaptive evolution would be constrained. However, our simulations showed the opposite. High fitness peaks were reached in 77% of simulations via short adaptive paths

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Andrei Papkou @biobarkologist.bsky.social · 24/11/2023

74 peaks have high fitness. All of them have negatively charged amino acids Asp or Glu at the conserved DHFR position 27. Otherwise, high fitness peaks have different amino acids at other amino acid positions

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Andrei Papkou @biobarkologist.bsky.social · 24/11/2023

The resulting fitness landscape has >500 fitness peaks, most of which are low fitness peaks.

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Andrei Papkou @biobarkologist.bsky.social · 24/11/2023

We took great care to validate our fitness measurements

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Andrei Papkou @biobarkologist.bsky.social · 24/11/2023

We measured fitness at the presence of the antibiotic using a mass selection experiment and deep sequencing.

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Andrei Papkou @biobarkologist.bsky.social · 24/11/2023

We used CRISPR-Cas9 editing to make all possible 64^3 codon combinations encoding three amino acid positions of dihydrofolate reductase (DHFR). DHFR is a key metabolic enzyme and the target for the antibiotic trimethoprim.

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Andrei Papkou @biobarkologist.bsky.social · 24/11/2023

New in Science with @jaescudero.bsky.social . A combinatorially complete fitness landscape with >260.000 E.coli genotypes shows unexpected properties. Despite ~500 fitness peaks in this landscape, adaptive evolution can easily navigate to highest fitness peaks www.science.org/doi/10.1126/...

science.org

A rugged yet easily navigable fitness landscape

A high number of genetic fitness peaks does not impair adaptive evolution in a large empirical fitness landscape.

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