Lightnews — Scholar-powered news

Justin Fay @justinfay.bsky.social · 5d

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:

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Justin Fay @justinfay.bsky.social · 10d

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

Reposted by Justin Fay

Vaughn Cooper @vscooper.micropopbio.org · 17d

🚨 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...

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...

www.linkedin.com

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Justin Fay @justinfay.bsky.social · 16d

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

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Justin Fay @justinfay.bsky.social · 16d

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.

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Justin Fay @justinfay.bsky.social · 16d

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...

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Justin Fay @justinfay.bsky.social · 18d

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...

Reposted by Justin Fay

Yun S. Song @yun-s-song.bsky.social · 19d

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)

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Reposted by Justin Fay

Drug Monkey @drugmonkey.bsky.social · Jul 31

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

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…

drugmonkey.wordpress.com

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Reposted by Justin Fay

Molecular Biology and Evolution @molbioevol.bsky.social · Jul 16

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

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Reposted by Justin Fay

Peter Morrell @peterlmorrell.bsky.social · Jun 5

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...

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 ...

journals.plos.org

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Reposted by Justin Fay

Needhi Bhalla 💅🏽 @needhibhalla.bsky.social · May 31

"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"

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Justin Fay @justinfay.bsky.social · May 1

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

Evolution and core processes in gene expression

June 26–29, 2025 | Kansas City, Mo.

www.asbmb.org

Justin Fay @justinfay.bsky.social · Mar 19

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...

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...

www.biorxiv.org

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Reposted by Justin Fay

bioRxiv Evolutionary Biology @biorxiv-evobio.bsky.social · Feb 21

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

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Reposted by Justin Fay

Pfliegler Lab at University of Debrecen @pflieglerlab.bsky.social · Feb 9

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

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Justin Fay @justinfay.bsky.social · Jan 30

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

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

Reposted by Justin Fay

Jane Liebschutz, MD MPH (she/her) @liebschutz.bsky.social · Jan 22

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

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Reposted by Justin Fay

Yun S. Song @yun-s-song.bsky.social · Jan 8

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...

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

doi.org

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Reposted by Justin Fay

Jeffrey Ross-Ibarra @jrossibarra.bsky.social · Jan 3

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!

Jeffrey Ross-Ibarra @jrossibarra.bsky.social · Dec 31

New! @jenncoughlan.bsky.social kindly shared their MIRA NIH award with our github repo. If you have a successful grant app you're willing to share, please contribute! github.com/RILAB/statem...

GitHub - RILAB/statements: Successful Job Applications and Grants

Successful Job Applications and Grants. Contribute to RILAB/statements development by creating an account on GitHub.

github.com

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Reposted by Justin Fay

Alvaro Sanchez @asanchezlab.bsky.social · Dec 16

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/...

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...

www.science.org

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Justin Fay @justinfay.bsky.social · Dec 13

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.

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Justin Fay @justinfay.bsky.social · Dec 13

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.

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Justin Fay @justinfay.bsky.social · Dec 13

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.

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Justin Fay @justinfay.bsky.social · Dec 13

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.

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