Ché Pillay

With Eugene Koonin, we propose a concept of “the selfish ribosome”, under which evolution of life is viewed as a ribosomal takeover, where the ribosome evolved to consume most of the cell’s resources, while other cellular componentry ensures the propagation of the ribosome. arxiv.org/abs/2602.23268

New paper alert 🚀 Our organism-wide single-cell ATAC-seq atlas of mammalian aging is now out in @science.org, led by our fantastic graduate student Ziyu Lu from @rockefeller.edu!
www.science.org/doi/10.1126/...

Agreed, and kudos to them. Really appreciated the link to Cosig, and I am so glad that we switched to Zotero.

Epibatidine in Siberia

Why would a tropical frog toxin be used to murder someone in Siberia?

You know why.

Thanks so much! I thought it was a typo.

🧵 New preprint! Our 4-lab team evolved Streptococcus pneumoniae in antibiotic-treated mice of varying immune states and discovered something surprising: bacteria rarely evolved resistance. Instead, they found a different way to survive — by rewiring RNA turnover.
🔗 www.biorxiv.org/content/10.6...

What a wonderful thread about some excellent science.

Graphical abstract of pre-print

Does targeting enzymes and substrates in a condensate lead to rate enhancement? No. Here, we investigate how the condensate environment can inhibit an enzyme reaction.

Spoiler: Mass-transport limitations. We find a strong correlation between diffusion and reaction rates.

doi.org/10.64898/202...

How surprising: doi.org/10.1016/j.ce... It started with an observation that people with cancer rarely get Alzheimer's disease. It turns out that tumors secrete cystatin C, which blocks plaque formation

Advancing regulatory variant effect prediction with AlphaGenome - Nature AlphaGenome, a deep learning model that inputs 1-Mb DNA sequence to predict functional genomic tracks at single-base resolution across diverse modalities, outperforms existing models in variant effect...

I had intended to post something about this new Google DeepMind paper that appeared yesterday in Nature, but the press coverage has added to what there is to say. So this is a long 🧵
www.nature.com/articles/s41...

Advancing regulatory variant effect prediction with AlphaGenome - Nature AlphaGenome, a deep learning model that inputs 1-Mb DNA sequence to predict functional genomic tracks at single-base resolution across diverse modalities, outperforms existing models in variant effect...

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

‘Remote controlled’ proteins illuminate living cells The discovery that some fluorescent proteins are sensitive to magnets could lead to the development of switchable drugs and biosensors.

‘Remote controlled’ proteins illuminate living cells www.nature.com/articles/d41... 🧪

🤯🤯
#microsky #Phagesky #synbiosky

Bearing Down on a Placebo Effect

Evidence for how a placebo-effect link might work in humans between immune response and positive expectations:

What an interesting story. Lovely work.

Recent discoveries on the acquisition of the highest levels of human performance Scientists have long debated the origins of exceptional human achievements. This literature review summarizes recent evidence from multiple domains on the acquisition of world-class performance. We re...

Really interesting research showing that while ultra-specialization in a single discipline might lead to better results early in one’s career, multi-discipline training and practice pays off big time in the long run. This applies to a range of professions from scientists to athletes and more

Proteome-wide tagging with an H2O2 biosensor reveals highly localized and dynamic redox microenvironments | PNAS Hydrogen peroxide (H2O2) sensing and signaling involves the reversible oxidation of particular thiols on particular proteins to modulate protein fu...

This reference may be useful? The authors show that there are also dynamic hydrogen peroxide hotspots within organelles: www.pnas.org/doi/10.1073/...

A paper on the best strategies to deal with malign spirits in a molecular biology setting.

PDF: www.immaterialscience.org/2025/pcr-dem...

Occultic Practices in qPCR — The Journal of Immaterial Science qPCR is a famously capricious and fiddly technique, bedevilled by poor reproducibility. When every other source of variation and contamination has been controlled, the only explanation is that the imp...

This is fantastic advice for those struggling with qPCR: www.immaterialscience.org/2025/pcr-dem...

This Is What a Digital Coup Looks Like | Carole Cadwalladr | TED YouTube video by TED

So today I found out that my TED talk ‘This is What a Digital Coup Looks Like’ was TED’s most watched talk of the year.

It’s sort of amazing & terrifying. Because this *is* what a digital coup looks like.

www.youtube.com/watch?v=TZOo...

sfrbm.org/meetings/202...

Alcohol And Fructose, Tangled (and Untangled?)

The connections between sugar and alcohol in the liver:

Sigh.

This is a really interesting approach. Should open many other avenues of research.

Machine Learning Reveals Genes That Help Yeasts Resist Stress Study provides a framework for connecting genetic mechanisms and trait variation across diverse yeast species.

We are honored to share that our work, led by @katarina-aranguiz.bsky.social and @linder-surprise.bsky.social, has been featured as a Science Highlight on the DOE's Office of Science website. 200 articles are selected annually to be highlighted. Check it out! 🧫
www.energy.gov/science/ber/...

Genetically Encoded Sensors for Monitoring Intracellular Redox Health of the Pathogenic Fungus Cryptococcus neoformans Redox sensing and regulation are critical to both the survival and virulence strategies used by the pathogenic fungus Cryptococcus neoformans to evade host immunity and establish infection. However, the precise genetic and biochemical mechanisms driving these redox regulation systems in the context of fungal virulence are unclear. To address this limitation, we designed genetically encoded redox sensors optimized for expression in C. neoformans and linked these sensors to cryptococcal redox proteins for real-time monitoring of intracellular redox status. Using these sensors, we established several fluorescence-based techniques for monitoring dose-responsive changes in the intracellular oxidation status of C. neoformans under stress. Specifically, we demonstrated sensor responsiveness to nontoxic doses of peroxide stress and during different stages of cell growth, and we verified sensor responsiveness in a mutant with known sensitivity to oxidative stress. This approach provides a framework for developing and deploying biosensors in pathogenic fungi and in basidiomycetes─a group of microorganisms with relatively few sophisticated genetic tools for molecular and synthetic biology. Overall, our sensors enable real-time insights into the key redox mechanisms driving growth and survival of a globally important pathogen and pave the way for tool development in other fungi.

Very cool new paper on a genetically encoded redox sensor in Cryptococcus neoformans: pubs.acs.org/doi/full/10....

These kind of approaches can enable so many cool experiments with real time monitoring!

Great work, @ubcmicroimmuno.bsky.social

Biochemical Tungsten - Really

Catching up on blog posts: a biochemical role for the element tungsten, of all things. Don't look for it in your multivitamins any time soon, though:

Yes

If you use GMail, AI (Gemini) was turned on yesterday by default and now scans all of your content for machine learning. To turn off, go to Settings>General and scroll down. Uncheck the box for "Smart features."

There's other "Smart" add-ons as well, but that's the one that reads your content.

TrkB, BDNF, and Depression

Catching up on blog posts! Here’s one on the idea that antidepressants have a common mechanism in promoting new neural connections. More and more work on this is showing up: