This picture was taken right before The Boss' presentation at @gimmfoundation.bsky.social

We initially thought people were just a bit shy but, as it turned out, we were participating in the mandatory drills due to high seismic activity in the area 🤔

Safety first!!

We also visited Isabel Gordo's lab at @gimmfoundation.bsky.social (Oeiras) and ran into a familiar face, @martalourenco21.bsky.social former PhD candidate at our lab

We were happy to catch up with Luis @ltanoeiro.bsky.social, who's doing some of his PhD work over there under the supervision of Filipa and Jorge Vitor

bsky.app/profile/phag...

We also got to share some good times!

Thanks a lot to Profs. Jorge Vitor and Filipa Vale, as well as our own Luis Tanoeiro @ltanoeiro.bsky.social for your hospitality

Finally, our (former) M2 student Camille Sivelle was in charge of the lab's main presentation, showing her results regarding mechanisms for establishment of viral resistance in bacteria
She did a very good job at explaining a somewhat complicated experimental setup and results

Congrats, Camille!!

We got to finish the whole affair (on a high note, if we may say so ourselves) with two oral presentations

First up, the boss was showing off about the lab's work and its people

Gut team this ..... lung team that ....... but none of that would be possible without his leadership!

Alejandro, from our "lung" team and who clearly forgot to take a photo with his poster, got a very interesting phone call during his flash talk

He presented some of the work that was recently published by our group on the effect of innate immunity cell populations on phage therapy

We started up with the postdocs, both of whom had flash talks and posters

Nandita Sharma from our "gut" team presented her results of competition between Citrobacter rodentium and E. coli

She'll also be showing this during a "work in progress" talk in early december so be on the lookout for that!

Notably, ΦX174’s genome is tiny (5-6kb) and even this was challenging. Out of 300 generated genomes, 16 were functional and only few of them outperformed WT

For us, escalation to higher life forms seems a ways from today, even for a rapidly moving field (beyond considerable ethical implications)

❓ - New viruses (EVO), able to overcome ΦX174-resistance emerged after multiple passages of a GLM-phage cocktail.

The EVO genomes contained elements from GLM-phages, though the sequence itself was not GLM-generated.

So likely mixing GLM design with old-fashioned recombination would be best?

✅ - Authors also report improved fitness in some of the GLM-phages, compared to WT ΦX174, and point to the likely reasons behind it

This suggests a very feasible use of this technology, as an additional, more targeted tool, to study viral-host interaction and eventually improve phage engineering

🚫 - However, though different from other ΦX174 sequences, these GLM-phages were, at worst, 93% similar to the backbone sequence (but overall more like >95%)

So, this raises the question of whether there’s a threshold to consider the GLM as “generative” and, if so, what should it be?

📝 - Using genomic language models (GLM), these teams generated new sequences of bacteriophages, capable to infect some strains of E. coli, different from those found in nature

Impressively, 16 functional GLM phages with novel sequences based on a "backbone sequence" (ΦX174) were created