https://www.science.org/doi/10.1126/science.adg7492
Cheng, J., Novati, G., Pan, J., Bycroft, C., Žemgulytė, A., Applebaum, T., Pritzel, A., Wong, L. H., Zielinski, M., Sargeant, T., Schneider, R. G., W, A., Senior, Jumper, J., Hassabis, D., Kohli, P., & Avsec, Ž. (2023). Accurate proteome-wide missense variant effect prediction with AlphaMissense. Science, 381(6664).
https://doi.org/10.1126/science.adg7492
Levy, A. (2020, January 6). A world without pain. The New Yorker. https://www.newyorker.com/magazine/2020/01/13/a-world-without-pain
QT:{{”
“When I met Jo for the first time, I was just struck by her,” Cox, an affable forty-year-old with a scruffy beard, told me, one afternoon in his lab at U.C.L. …This imperviousness to pain is what makes her distinct from everyone else with a FAAH mutation. They, like even the most committed stoners, can still get hurt.
Cameron had the same FAAH mutation that many other people have—but there had to be something else at play. The scientists started their inquiry by isolating DNA from her blood, and then analyzing the protein-coding subset of her genome—the part that’s traditionally considered to be significant. “We didn’t really find anything,” Cox said. “So we decided, O.K., why don’t we look across the whole genome for bits that are deleted or duplicated? And, at the time, this new chip was just available, which enabled us to scan the whole genome and look for deletions”—snippets missing from her genetic code. “It was a lucky strike: we found that there was this deletion. But it was distinct from FAAH. It was away from FAAH, just downstream.”
The scientists noticed that the right edge of the deletion overlapped “a gene that was annotated as a pseudogene,” Cox said, and frowned. “Which is a term I don’t like.” A pseudogene is what’s been thought of as genetic detritus—a copy of a gene that’s just sitting there, not doing anything productive. One biochemist I spoke to likened a pseudogene to a rusted-out car you stumble on in the forest—only, in Cameron’s case, they put a key in the ignition and the car turned on. “To call it a pseudogene is misleading, because this is a gene that is expressed—it makes a product, a sequence in the DNA,” Cox said, with excitement. “It’s a real fascinating class of genes which have been severely overlooked in genetics until very recently.” Cox and his colleagues named this particular pseudogene—“It’s nicer to call it a gene,” he insisted—FAAH OUT. “It was a wordplay, really,” he said sheepishly. “The challenge now is to understand what it’s doing. Jo is the first person in the world that we know of with this.”
Cameron’s case is important in genetics, partly because it may supply evidence that pseudogenes are more significant than they were previously thought to be.
“}}
https://www.nature.com/articles/d41586-024-03866-5
QT:{{”
One particular gut microbe is quite the coffee fiend. Lawsonibacter asaccharolyticus was up to eight times more abundant in coffee drinkers than in non-drinkers. In a culture dish, the bacteria grew faster when fed coffee of any kind — brewed or instant, caffeinated or decaffeinated — than when fed no coffee.
“}}
https://arxiv.org/pdf/2001.08361
Jared Kaplan ∗
Johns Hopkins University, OpenAI
jaredk@jhu.edu
Sam McCandlish∗
OpenAI
sam@openai.com
Tom Henighan
OpenAI
henighan@openai.com
Tom B. Brown
OpenAI
tom@openai.com
Benjamin Chess
OpenAI
bchess@openai.com
Rewon Child
OpenAI
rewon@openai.com
Scott Gray
OpenAI
scott@openai.com
Alec Radford
OpenAI
alec@openai.com
Jeffrey Wu
OpenAI
jeffwu@openai.com
Dario Amodei
OpenAI
damodei@openai.com
https://www.bostonpublicschools.org/Page/8810
Very impressive dashboard with real-time sensor data – perhaps of use
https://www.pnas.org/doi/10.1073/pnas.2313581121
Kogan, V., Molodtsov, I., Fleyshman, D. I., Leontieva, O. V., Koman, I. E., & Gudkov, A. V. (2024). The reconstruction of evolutionary dynamics of processed pseudogenes indicates deep silencing of “retrobiome” in naked mole rat. Proceedings of the National Academy of Sciences, 121(45). https://doi.org/10.1073/pnas.2313581121
useful for metastatic cancers
https://www.nature.com/articles/s42256-022-00532-1
Castro, E., Godavarthi, A., Rubinfien, J., Givechian, K., Bhaskar, D., & Krishnaswamy, S. (2022). Transformer-based protein generation with regularized latent space optimization. Nature Machine Intelligence, 4(10), 840–851. https://doi.org/10.1038/s42256-022-00532-1
linkstream2 microblog 