(she/they) Bisexual binational bicyclist 🇲🇽 🏳️🌈 Microbiologist. Post-doc in Baym Lab finding lil phage friends. PhD work on 🦠 bacterial interactions 🧫
Joined February 2013
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Lucy M. McCully Espinosa, PhD retweeted
My scientific career changed the day I met Fernando and my faith in science restored. In a world dominated by sequencing and LLMs, this project shows how much biology is hidden in plain sight waiting for the right person to make the connection, a must read!
So happy that I can finally share the results of my first postdoc paper with @baym!! Turns out plasmids are an amazing system to study multi-scale evolution and we can track within-cell and between-cell dynamics! Here’s a photo of plasmids competing inside cells in a colony (1/n)
Lucy M. McCully Espinosa, PhD retweeted
Interested in microbial evolution and plasmid population dynamics?
Check out this fantastic preprint from Fernando @fernpizza & Michael @baym!
So happy that I can finally share the results of my first postdoc paper with @baym!! Turns out plasmids are an amazing system to study multi-scale evolution and we can track within-cell and between-cell dynamics! Here’s a photo of plasmids competing inside cells in a colony (1/n)
Lucy M. McCully Espinosa, PhD retweeted
Fernando cooked.
Lucy M. McCully Espinosa, PhD retweeted
Excited to share a new preprint led by Indra Gonzalez Ojeda on a new tool to improve pangenome calling in bacteria, CLARC. biorxiv.org/content/10.1101/… . Passing output of Roary for S. pneumoniae populations through this tool reduces accessory genome > 30%, resolves other puzzles
Lucy M. McCully Espinosa, PhD retweeted
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)
Lucy M. McCully Espinosa, PhD retweeted
Here we show that within-cell competition is key to plasmid evolution. Link to the paper! (2/n) biorxiv.org/content/early/20…
Lucy M. McCully Espinosa, PhD retweeted
So happy that I can finally share the results of my first postdoc paper with @baym!! Turns out plasmids are an amazing system to study multi-scale evolution and we can track within-cell and between-cell dynamics! Here’s a photo of plasmids competing inside cells in a colony (1/n)
Lucy M. McCully Espinosa, PhD retweeted
Come learn about the latest work from my lab, lead by @nquinoneso and @implosian. It's an exploration of some truly weird phages that parasitize horizontal gene transfer!
Exciting news! The pre-print for our paper, “Diverse and abundant viruses exploit conjugative plasmids” is finally out! Join me on this thread to hear more about this mysterious group of phages with rather unique lifestyle preferences. 1/ biorxiv.org/cgi/content/shor…
Lucy M. McCully Espinosa, PhD retweeted
Delighted to finally release this preprint into the universe! This project has been a true labour of love the past few years for Natalia and me. I'm so excited to continue exploring the exciting world of phages that depend on conjugative plasmids!
Exciting news! The pre-print for our paper, “Diverse and abundant viruses exploit conjugative plasmids” is finally out! Join me on this thread to hear more about this mysterious group of phages with rather unique lifestyle preferences. 1/ biorxiv.org/cgi/content/shor…
My greatest contribution to science is making sure the phages I found for @nquinoneso and @implosian's phenomenal paper had the most goth names I could conjure 🖤
Finally, we revisited the phages that depend on the F plasmid. We found members of all the known groups, and even a completely new, tailed(!) plasmid-dependent phage! @microMcCully here, introducing the wonderful FtMidnight, showing there’s even more diversity to be found! 13/
Lucy M. McCully Espinosa, PhD retweeted
This project has been a blast! What’s up with these strange phages? What does all of this mean for plasmid conjugation? And what other overlooked treasures await to be found in this world of mobile genetics elements? Thank you for reading, and stay tuned for our next adventures.
Lucy M. McCully Espinosa, PhD retweeted
Finally, we revisited the phages that depend on the F plasmid. We found members of all the known groups, and even a completely new, tailed(!) plasmid-dependent phage! @microMcCully here, introducing the wonderful FtMidnight, showing there’s even more diversity to be found! 13/
Lucy M. McCully Espinosa, PhD retweeted
If they are so abundant, why haven’t we heard about them from metagenomic studies? Well, we think they’re just not getting through. They seem hard to recover even from samples where we know they are present at high abundance. 12/
Lucy M. McCully Espinosa, PhD retweeted
These phages have zero accessory genome, and exactly the same gene content, but they can differ by a large number of SNPs. These ones, for example, only differ by ~500 SNPs, but they can have strikingly different host preferences! Look: 11/
Lucy M. McCully Espinosa, PhD retweeted
There were so many, that we were worried about finding names for all of them, so we decided to go for “PRD” + a color name. We have some wonderful ones like PRDchartreuse, PRDaquamarine, and my favorite: PRDcerulean 😊. 10/
Lucy M. McCully Espinosa, PhD retweeted
All the phages we were finding belong to the Tectiviridae family, and are closely related to PRD1. Not only were we finding them in large amounts but also, in more diversity than all the previously isolated phages of this group. 9/
Lucy M. McCully Espinosa, PhD retweeted
Why? Well, because they had A LOT of plasmid-dependent phages. Like, in wastewater(!) there are almost as many plasmid-dependent phages as E. coli phages, and way more than S. enterica or P. putida phages (the hosts we were using in our assay.) 8/
Lucy M. McCully Espinosa, PhD retweeted
So we started screening as many samples as we could, looking for phages that depend on IncP conjugative plasmids (like RP4). This is @implosian and me, showing off our samples. Our favorite samples: compost and wastewater. 7/
Lucy M. McCully Espinosa, PhD retweeted
This sounds almost too easy to be true, but it works! Since the determinant of phage susceptibility can be horizontally transferred 🤯, many of these phages have a broad host range. If we add fluorescence to it, it’s even easier to see, and we get Phage DisCo! 🪩 6/
