Christian Loyo

Friday Afternoon Seminars (FAS), this Friday 10/10 at 4pm in Pelton. Pravrutha Raman, Malik Lab Beyond histone mimicry: evolution of EZHIP, an inhibitor of the Polycomb Repressive Complex 2 in mammals Christian Loyo, Salama Lab Adaptive benefits of mobile genetic elements in bacteria

Friday Afternoon Seminars are back!
Kicking things off are @pravrutharaman.bsky.social from the @harmitmalik.bsky.social Lab and @christianloyo.bsky.social from Human Biology’s Salama Lab. Can’t wait to see everyone today at 4:00 pm in Pelton for two great talks!

Widespread purine bias in bacterial genes driven by runaway transcription Genes in many bacteria are rich in purine nucleotides and poor in pyrimidines. We show that this purine preference is critical for gene expression because it prevents premature transcription terminati...

Widespread purine bias in bacterial genes driven by runaway transcription - www.biorxiv.org/content/10.1...

Wave succession in the pandemic clone of Vibrio parahaemolyticus driven by gene loss - Nature Ecology & Evolution A combination of large-scale phylogenomic analysis, mouse lethality experiments and bacterial growth assays shows that gene loss in the putrescine utilization pathway has enhanced biofilm formation an...

Combination of large-scale phylogenomic analysis, mouse lethality experiments and bacterial growth assays shows sheds light on how a pandemic clone of Vibrio parahaemolyticus was able to spread worldwide

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

When I started my postdoc a little over a month ago, I expressed worry to my PI about the loss of funding opportunities from the federal government to which she countered saying that "maybe the private fellowships will invest more deeply." Seems that won't be the case.

I will miss working with B. subtilis, but I adore observing Helicobacter pylori squiggle under the microscope and see their distinct helical shape. I could just sit here all day and watch them!

Also if anyone knows any good tattoo artists in Seattle, let me know because I've been sitting a few more science tattoo ideas 👀

Love seeing science tattoos and showing off my own 😁 my first was a DNA helix, because it’s my favorite molecule, and second was a microscope/sun, an homage to my first microscope that used sunlight as a light source and helped fuel my curiosity for biology.

This article does a great job describing the lives of young American scientists:

“You roll up your sleeves, try to make or discover something useful and then let the scientific community try to punch holes in your work to make sure that it’s sound”

It turns out that Nip binds specifically to the TIR domain of SpbK, which likely prevents TIR domain interactions. Interestingly, we found that Nip binding to SpbK did not prevent SpbK from binding to YonE! Thus, Nip prevents effector function rather than preventing recognition of phage infection.

Finally, after discovering that an SPbeta-like phage, Phi3T (which has an identical copy of yonE) was able to evade SpbK anti-phage defense, we found a counter-defense gene in Phi3T that is responble for immune evasion. We called the protein Nip for NADase inhibitor from Phi3T.

Next, we determined that YonE, the SPbeta portal protein, activates SpbK via a direct interaction. Using CoIP experiments and AlphaFold modeling, we suspect the SpbK N-terminal region is reponsible for interacting with YonE and facilitates TIR domain interactions that lead to NAD depletion.

We first wondered how SpbK caused abortive infection during infection by SPbeta. SpbK has a TIR domain, which is known to degrade NAD in other systems, and thus we determined that this NAD depletion occurs here as well and that the NAD depletion was dependent on a functional TIR domain.

A phage-encoded counter-defense inhibits an NAD-degrading anti-phage defense system Author summary Bacterial viruses (bacteriophages or phages) are widespread and abundant across the planet. Bacteria have a variety of immune systems, often found on mobile genetic elements, to combat ...

Excited to share that my first first author paper from grad school is up now at PLOS Genetics @plos.org! dx.plos.org/10.1371/jour...

‘DataBack’: The fight for genomic data sovereignty Arizona scientist wants more transparency and equity from researchers in the handling of Indigenous DNA

By age 24, I patented a cancer device, interned at top medical centers, was accepted to a university known for Nobel Laureates.

Yet, being Navajo, I felt the disconnect of being a scientist vs an object of study.

I am not a product of DEI. I persevered despite science ictnews.org/news/databac...

Genetics, ecology and evolution of phage satellites Nature Reviews Microbiology - In this Review, Penadés et al. explore the genetics, potential origins and life cycle of phage satellites, and they discuss the impact of these elements on the...

If you are interested in phage satellites, we hope you'll enjoy this. Fun collaboration with the Rocha, Seed, Bikard, and Chen labs! rdcu.be/efkvG

An antisense RNA regulates production of DnaA and affects sporulation in Bacillus subtilis https://www.biorxiv.org/content/10.1101/2025.02.18.638791v1

@asm.org this better not be anticipatory obedience. I have 5 lab members planning on going to ASM microbe this year. I will absolutely pivot to another meeting if ASM gives in to anti-DEI efforts.

ASM website screenshots from the wayback machine in December '24 (web.archive.org/web/20241211...) vs today. Pretty disappointing!! 🧪

Identification of insertion sites for the integrative and conjugative element Tn916 in the Bacillus subtilis chromosome https://www.biorxiv.org/content/10.1101/2025.01.28.635231v1

Activation and modulation of the host response to DNA damage by an integrative and conjugative element | Journal of Bacteriology Bacterial genomes typically contain mobile genetic elements, including bacteriophages (viruses) and integrative and conjugative elements, that affect host physiology. ICEs can excise from the chromoso...

I'm excited to share that my third first-author publication from grad school has been published in JBAC:
doi.org/10.1128/jb.0...

DefensePredictor: A Machine Learning Model to Discover Novel Prokaryotic Immune Systems https://www.biorxiv.org/content/10.1101/2025.01.08.631726v1

Excited to share that my graduate work is up on bioRxiv! I found that some SPβ-like phages of B. subtilis have a counter-defense system that inhibits NADase activity from the SpbK anti-phage defense during phage infection and activation of SpbK.

Image of myself and my PhD Advisor in front of a sign saying “Congratulations Dr. Loyo”

Finally #PhDone! So grateful for my research mentors and all the amazing people I met at MIT that helped me be a better scientist.

Thesis submitted to my committee! 🎉🥳 I’m still in disbelief that my thesis defense is only two weeks away

Bacillus on the Blue place, starting small, but hopefully extending to keep the conversation active
[it was also gorwing slow on Twitter]
go.bsky.app/BfusVyD

Currently, I’m finishing a manuscript on my current project (keep an eye out for it!) and writing my thesis. I’m defending my thesis next month and starting my postdoc early next year at the Fred Hutch where I’m planning on studying the role of mobile elements in H. pylori. Happy to connect here! 😁

Image of myself in front of a sign at the SACNAS national diversity in STEM conference

Image of myself with Tim the Beaver, the MIT mascot

Image of phage lysis of bacteria in the shape of a smiley face on a petri dish

The last couple days I’ve had a number of new followers and folks from Twitter find me here, so I think it’s time I (re)introduce myself. My name is Christian and I’m finishing my PhD in Alan Grossman’s lab at MIT studying antiphage defense and counter-defense in B. subtilis

I found this starter pack really helpful for finding other phage biologists here! bsky.app/profile/jame...

Transcription termination and antitermination are critical for the fitness and function of the integrative and conjugative element Tn916 https://www.biorxiv.org/content/10.1101/2024.09.05.611371v1 Premature expression of genes in mobile genetic elements can be detrimental to their bacterial hosts

Transcription termination and antitermination are critical for the fitness and function of the integrative and conjugative element Tn916 https://www.biorxiv.org/content/10.1101/2024.09.05.611371v1

Anti-viral defense in Archaea! I saw this work presented at the SACNAS Conference a couple months ago and had the pleasure to meet Luis and chat MGEs with him. Really excited to see Luis' work out on BioRxiv now!