iiinova — where your digital self keeps evolving

Fernando Rossine @fernpizza.bsky.social · 03/09/2026

This single handedly convinced m e to make a site. Would you suggest anything?

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Fernando Rossine @fernpizza.bsky.social · 06/06/2026

That legit looks like the most gorgeous painting

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Reposted by Fernando Rossine

Sternberg Lab @sternberglab.bsky.social · 12/05/2026

1/9 New preprint from the Sternberg Lab in collaboration with the Nishimasu Lab! We uncover how the DRT3 antiphage immune system pairs two reverse transcriptases, one RNA-templated and one protein-templated, to build a double-stranded DNA effector. doi.org/10.64898/202...

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Reposted by Fernando Rossine

Tami Lieberman @contaminatedsci.bsky.social · 06/05/2026

Dr. Indra Gonzalez Ojeda gave a great thesis defense this morning, including some wisdom for starting PhD students, or frankly, anyone.

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Fernando Rossine @fernpizza.bsky.social · 19/01/2026

Oh my god why am I actually crying?

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Fernando Rossine @fernpizza.bsky.social · 27/11/2025

Hey Franz! I hadn't seen those results yet! Super interesting stuff there!

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Fernando Rossine @fernpizza.bsky.social · 27/11/2025

Those discussions were the very best memories I took from Grad School

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Fernando Rossine @fernpizza.bsky.social · 27/11/2025

This Plasmid Project was directly inspired by the results on multilevel selection that Dan introduced me to! In this thread he explains some fundamental theoretical results that were so influential to me as a Scientist. Looking forward to more Math-driven experiments!!! Thanks Dan!

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Fernando Rossine @fernpizza.bsky.social · 23/11/2025

Thank you so so much Zam! I'm excited for whatever is to come!

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Reposted by Fernando Rossine

Liana Merk @bacteriyay.bsky.social · 20/11/2025

This is it!!! This is the work I never want to stop hearing about. Kepler’s creativity and curiosity really shine through in this paper. Give it a read and enjoy 😎

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Fernando Rossine @fernpizza.bsky.social · 21/11/2025

Irei para a Suécia nem que seja só pra tomar esse café!!! Grande abraço!

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Fernando Rossine @fernpizza.bsky.social · 21/11/2025

By the way, Zurich people lets get coffee!

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Fernando Rossine @fernpizza.bsky.social · 21/11/2025

This has been an intense, crazy week. My plasmid competition paper is finally out and we have a new preprint on Bioarxiv! Plus I'm leaving the US after 10 years here. See you soon America! Hello Zurich!!!

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Fernando Rossine @fernpizza.bsky.social · 21/11/2025

Working with @kepatitis-c.bsky.social was a privilege. Kep is the forbidden trifecta: brilliant, tireless, and the kindest person you'll ever meet! Beyond that, he's an army in one: a bioinformatician, a statistician, an experimentalist, and a cheerleader. Thanks man!

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Fernando Rossine @fernpizza.bsky.social · 21/11/2025

Kep's thread explains the work beautifully, so you should check it out! I do want to add that this project changed the way I think about the sources of evolvability and downstream fitness benefits.

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Fernando Rossine @fernpizza.bsky.social · 21/11/2025

When different kinds of mobile genetic elements get together, they become even more powerful catalysts for microbial evolution! In this work we discovered a mechanism by which Insertion Sequences drive their spread across Plasmids, which helps explain this evolutionary potential!

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Fernando Rossine @fernpizza.bsky.social · 07/09/2025

And a nail in the coffin of Hamilton's rule!

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Fernando Rossine @fernpizza.bsky.social · 24/04/2025

"Fernando, I'm not gonna sugar coat it: those are the worst reads I've ever seen. What are you putting in there?" Then proceeds to troubleshoot and help me solve the issue. Amazing people.

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Fernando Rossine @fernpizza.bsky.social · 15/04/2025

Hey Elizabeth! I use a method to take leaf pics with my students that should work. Illuminate from below! Take a piece of plexiglass, put a piece of white paper on it and then the dish on top of that. Illuminate from below with a flashlight, 1 meter below the plexiglass. Turn off other lights

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Fernando Rossine @fernpizza.bsky.social · 24/02/2025

Hey Jack, thank you so so much! We have a paper in the works that is very related to co-transformations as well! As for the inspiration for this one, I came up with the idea from a theoretical curiosity. It's fun how projects can be born from both theory and experiments!

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Fernando Rossine @fernpizza.bsky.social · 24/02/2025

YaY!!!!! I hope you enjoy it!!!! :)

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Fernando Rossine @fernpizza.bsky.social · 24/02/2025

Sebastian, that makes me so so happy :)

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Fernando Rossine @fernpizza.bsky.social · 21/02/2025

Finally, I'm so so thankful for my collaborators Carlos Sanchez (the best person), Daniel Eaton, and Johan Paulsson. In particular, thanks @baym.lol m for taking a chance on a non-traditional candidate that was proposing a weird project! (21/n)

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Fernando Rossine @fernpizza.bsky.social · 21/02/2025

I hope I convinced you that plasmids are a really cool system to study one of the most defining features of life: multi-scale evolution! (20/n)

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Fernando Rossine @fernpizza.bsky.social · 21/02/2025

Overall, we found out that tradeoffs of within- and between-cell fitness modulate fixation probabilities of plasmid variants, shaping their evolution. Moreover, the dominance curves of plasmid-encoded traits have unintuitive effects on these evolutionary trajectories! (19/n)

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Fernando Rossine @fernpizza.bsky.social · 21/02/2025

We modified our dimer system to release a plasmid that had been chromosomally integrated, creating an invasion-like initial condition. These experiments corroborated theoretical predictions, showing that the high dominance, strong RBS plasmids are favored when invading (18/n)

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Fernando Rossine @fernpizza.bsky.social · 21/02/2025

However, the same model suggested that if the beneficial blue plasmid were initialized with a single copy in each cell, simulating the invasion of a novel type, then a strong RBS should favor invading plasmid fixation. Could we experimentally test this prediction? (17/n)

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Fernando Rossine @fernpizza.bsky.social · 21/02/2025

Once again modelling came to the rescue! Simulations revealed that if a plasmid with a strong RBS has a more dominant trait, then a fitness flatness might actually slow down the fixation of the beneficial plasmid from an equilibrated initial condition. (16/n)

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Fernando Rossine @fernpizza.bsky.social · 21/02/2025

We thought that the big-benefit blue plasmid (rather than the low-benefit) would win faster against the no-benefit red plasmid, but the opposite occurred. I was so surprised that I checked the sequences a million times. Why did the low-benefit plasmid win faster? (15/n)

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Fernando Rossine @fernpizza.bsky.social · 21/02/2025

But here's where another mystery showed up. We had two versions of our blue antibiotic resistance plasmid. One with a strong RBS, giving the cells a big benefit, and one with a weak RBS giving a small benefit. Both had the same promoter and similar within cell fitness. (14/n)

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Fernando Rossine @fernpizza.bsky.social · 21/02/2025

When cells grow under antibiotic pressure, first the non-resistance red plasmid starts winning the within-cell competition, and in a second moment between-cell selection leads to the expansion of blue sectors. Note that without methylation, red wins more! (13/n)

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Fernando Rossine @fernpizza.bsky.social · 21/02/2025

This allows for a fitness conflict between scales of selection! Even though cells carrying antibiotic resistance genes might outgrow cells carrying other plasmids, we show that the transcriptional activity of these genes might impede their fixation! (12/n)

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Fernando Rossine @fernpizza.bsky.social · 21/02/2025

So now we know we can measure within-cell plasmid dynamics, but what features might increase the within-cell fitness of a plasmid? We decided to investigate if transcriptional activity might interfere with replication efficiency reducing within-cell plasmid fitness (11/n)

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Fernando Rossine @fernpizza.bsky.social · 21/02/2025

This discrepancy was due to eclipsing: after a plasmid replicates, hemimethylation prevents it from imediately replicating again, which reduces randomness and increases coexistence. Removing key methylation sites increases within-cell competition and accelerates fixation (10/n)

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Fernando Rossine @fernpizza.bsky.social · 21/02/2025

This finally allowed us to measure how fast was within-cell genetic drift segregating plasmids. However there was a catch: all of our models suggested that this should happen much faster than what we were seeing. We were missing something in our models! (9/n)

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Fernando Rossine @fernpizza.bsky.social · 21/02/2025

Moreover, to isolate within-cell dynamics from between-cell dynamics we used Mother Machines, microfluidic devices that isolate single cell lineages (thanks Carlos!). Look at how each trench first becomes clonal and then dimers are split and plasmid competition begins (8/n)

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Fernando Rossine @fernpizza.bsky.social · 21/02/2025

When we implemented this system on a quasi-neutral pair of plasmids we could see genetic drift occurring first at the within-cell scale (yellow cells give rise to red and blue cells), and then at the between-cell scale (blue and red sectors progressively coarsen) (7/n)

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Fernando Rossine @fernpizza.bsky.social · 21/02/2025

Side quest: We needed precise control on the activation of the recombinase. We hypothesized that the FLP recombinase from the patagonian ancestor of the lager yeast would be thermosensitive (Lagers are cold brewed). It worked on the first attempt! (6/n)

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Fernando Rossine @fernpizza.bsky.social · 21/02/2025

Can we achieve such an initial condition? There's a trick! We create synthetic plasmid dimers, transform them into cells. Then, we activate a recombinase that converts them back to monomers, ensuring an initial condition with equilibrated plasmid composition! (5/n)

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Fernando Rossine @fernpizza.bsky.social · 21/02/2025

Here’s what makes it hard: to measure bacterial fitness we mix two strains in a known ratio and from frequency changes we calculate their relative fitness. However, to do so for plasmids each cell must initially carry a known ratio of both plasmids. (4/n)

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Fernando Rossine @fernpizza.bsky.social · 21/02/2025

Plasmids change the fitness of their host bacteria, but because plasmids are multicopy genetic elements, they also compete within-cell for replication. Plasmid evolution must be driven by both levels of selection, but measuring within-cell competition is very challenging! (3/n)

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Fernando Rossine @fernpizza.bsky.social · 21/02/2025

Here we show that within-cell competition is key to plasmid evolution. Look at this photo of plasmids competing inside cells in a colony!!!

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Fernando Rossine @fernpizza.bsky.social · 21/02/2025

I'm so happy that I can finally share the results of my first postdoc paper with @baym.lol!!! Turns out plasmids are an amazing system to study multi-scale evolution and we can track within-cell and between-cell dynamics! (1/n) www.biorxiv.org/content/earl...

biorxiv.org

Intracellular competition shapes plasmid population dynamics

Conflicts between levels of biological organization are central to evolution, from populations of multicellular organisms to selfish genetic elements in microbes. Plasmids are extrachromosomal, self-r...

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