Justin Fay

No albicans, but a few glabrata.

Work is sometimes fun, having fun requires some work. I've found a blend of sampling yeast and riding that is a euphoric mix, and makes me wonder why its taken so many years to find. Route is via the finger lakes national forest, 16 miles round trip, 1hr biking straight out, 5 hours sampling back.

Great to hear back in the day stories, chum with alumns and progeny research at Roc-Fest, a celebration of Orr, Werren, Eickbush, and Jaenike and their contributions to adaptation, speciation, and selfish genetic elements. sites.google.com/view/rocfest...
I contributed wine:

Students, but it was more about tossing unknown strains into the freezer, while projects were focused on scerevisiae.

Faculty Professor Associate - Full-Time | Vaughn Cooper We are recruiting Faculty microbiologists in three (3) different, complementary, and collaborative areas at the University of Pittsburgh associated with the School of Medicine. 1) Fundamental researc...

🚨 Microbiologists! We are recruiting Assistant / Associate Professors in 3 collaborative areas of our U. Pittsburgh School of Medicine.
1) MMG (my dept): fundamental research in med micro
2) Peds ID / I4Kids institute
3) Center for Vaccine Research
🔗 to all 3 w/info: www.linkedin.com/posts/vaughn...

This work was a collaborative effort with Slovenian colleagues, grads and undergrads sampling yeasts and occasionally wine. @3xueying.bsky.social

We sequenced ITS2 to ID the species of 4,101 strains and found many vineyard species are also present in nearby forest habitats. However, of all the species present in both habitats only S. cerevisiae showed elevated copper and sulfite resistance in vineyard strains.

Very pleased to share this long term (nearly 20 years) study of yeasts isolated from vineyards and forests, now up on biorxiv:
www.biorxiv.org/content/10.1...

Ella Al-Shamahi (muslim missionary turned evolutionary biologist, host of BBC human series) opinion piece on why follow the science fails.
www.washingtonpost.com/opinions/202...

We are excited to share GPN-Star, a cost-effective, biologically grounded genomic language modeling framework that achieves state-of-the-art performance across a wide range of variant effect prediction tasks relevant to human genetics.
www.biorxiv.org/content/10.1...
(1/n)

What killed the competitive renewal at NIH? Following up on yesterday’s whinesplaining about the relative difficulty of getting a NIH grant across pertinent career eras, I had some more thoughts on generational expectations and gasligh…

What killed the competitive renewal at NIH? drugmonkey.wordpress.com/2025/07/31/w...

Walunjkar, @ghaemmaghamilab.bsky.social @justinfay.bsky.social et al. profiled the proteomes of two yeast species with differences in thermal tolerance, finding a proteome-wide shift in stability, driven by both sequence change and cellular context.

🔗 doi.org/10.1093/molbev/msaf137

#evobio #molbio

Sodium azide mutagenesis induces a unique pattern of mutations Author summary Sodium azide is frequently used as a mutagen for experimental studies in plants. It induces primarily C → T changes. We find that these most often occur when a cytosine (C) is followed ...

New paper w/ @plos.org! @chaochihl.bsky.social identifies a unique mutational pattern among sodium azide-induced mutants. SNPs in 'CC' context and indels. Thanks to @justinfay.bsky.social @lilei0051.bsky.social @giuliafrascarelli.bsky.social @nanoporetech.com et al

journals.plos.org/plosgenetics...

"We believe that mapping the damage done and its human costs—and the pushback and resilience work already underway—is necessary groundwork for building and retaining political agency"

Evolution and core processes in gene expression June 26–29, 2025 | Kansas City, Mo.

Abstract submission and early registration for Evolution and core processes of gene expression www.asbmb.org/meetings-eve...
June 26–29, 2025

Beyond Recombination: Exploring the Impact of Meiotic Frequency on Genome-wide Genetic Diversity An important aim of population genetics is to elucidate the processes affecting genetic diversity across regions of the genome and across species. Canonical population genetic models of sexually repro...

Hitchhiking in facultative sexuals e.g. baker's yeast: can reduce diversity across the genome and contribute to Lewontin’s paradox. Results relevant to anyone (e.g. me) who has looked but found few if any strong sweeps. www.biorxiv.org/content/10.1...

A model for background selection in non-equilibrium populations https://www.biorxiv.org/content/10.1101/2025.02.19.639084v1

1of3 Our new preprint now online: www.biorxiv.org/content/10.1... Commercial #Saccharomyces cerevisiae baker's yeasts: strain redundancy, genome plasticity, and colonization of the sourdough environment and the human body

The central limit theorem for the number of mutations in the genealogy of a sample from a large population The number K of mutations identifiable in a sample of n sequences from a large population is one of the most important summary statistics in population genetics and is ubiquitous in the analysis of DN...

www.biorxiv.org/content/10.1...

All NIH study sections canceled indefinitely. This will halt science and devastate research budgets in universities.

A previously reported bottleneck in human ancestry 900 kya is likely a statistical artifact Hu et al. (Science, 2023) recently inferred a severe ancient bottleneck around 900 thousand years (kya) ago in African ancestry but found no similar eviden

Our work, which shows statistical issues with the previous claim of a severe ancient bottleneck in the ancestry of African populations, has been selected as a Featured article in Genetics.

doi.org/10.1093/gene...

And another MIRA from @gutengroup.mcb.arizona.edu ! Please send along successful grant proposals and job apps. Seeing these is enormously helpful to folks applying for grants or jobs the first time!

Diverse phage communities are maintained stably on a clonal bacterial host Bacteriophages are the most abundant and phylogenetically diverse biological entities on Earth, yet the ecological mechanisms that sustain this extraordinary diversity remain unclear. In this study, w...

Nora finished her paper with a sentence I like a lot "Our results show that even under extremely restrictive, competitive conditions, the simplest biological entities on Earth can still find paths to coexistence." There is a curious dichotomy in her experiments... 1/3
www.science.org/doi/10.1126/...

Our results thus show that two thermally divergent species exhibit massively concordant cellular and structural changes in protein stability, and imply that protein thermostability impose a significant constraint on the time scales over which thermotolerance can evolve.

Second, we generated AF2 structures for both S. uvarum and S. cerevisiae proteins and found that S. cerevisiae amino acids were consistently predicted to be more stabilizing (ΔΔG) than S. uvarum amino acids.

We conducted two additional lines of investigation into protein stability differences. First, we purified two proteins (Guk1 and Aha1) from each species and found their thermal stability differences are structurally encoded.

We also measured protein stability in an interspecific hybrid and found that while S. uvarum proteins were significantly stabilized in the hybrid context, allele-specific differences in protein melting temperatures persisted for most of the proteome.

While this is consistent with structurally encoded amino acid divergence, proteins can also be stabilized by their cellular environment, e.g. post-translational modifications and protein interactions.

We used thermal proteomic profiling to measure temperature induced aggregation as an indicator of stability and found a small but consistent shift in melting temperatures between S. cerevisiae and S. uvarum.

whether changes in thermotolerance can be achieved without or with only a few changes in protein stability. We already know that proteins can be thermal sensors and that for a subset of the proteome biomolecular condensation is fine-tuned to a species’ thermal environment (PMC7237889, PMC11009240).