Protein design tools may be getting increasingly sophisticated, but you still need a sophisticated understanding of protein structure for them to work. This can include knowing enzyme mechanisms down to the positions of specific amino acids, as well as the water molecules that also occupy the area where catalysis takes place. Once you specify these, the tools can build the rest of a protein around this target.
A large collaboration of researchers based in China, however, decided to bring protein design to the masses, making a tool that can take natural language prompts and use them to produce proteins with the function you specify. If your measure for success is a working protein, then the success rate may not be great. But they still manage to get the job done. And, in a separate announcement, Hugging Face shared that it's now hosting a tool that does similar things on the DNA level.
The equivalent of vibe coding may have come to protein design—at least if you have access to a lab where you can sort the good designs from the dozens of failed ones.
© Historical / Contributor
Much of what we know about how a brain makes decisions comes from studying monkeys watching dots. In a task known as a random-dot-motion task, a cloud of flickering specks drifts weakly in one direction while the subject tries to determine whether—and in which direction— it’s moving. The task has shown that in the primate neocortex, neurons gather visual evidence over time, with their firing rates climbing until they cross a threshold, when the animal commits to a decision.
But avian brains don’t have a neocortex, so it wasn’t obvious how they made similar decisions.
“This was the big question,” said Andreas Nieder, a neurobiologist at the University of Tübingen. “How [would] a differently organized avian brain encode decisions?”
© Santiago Urquijo
Coral bleaching is a major problem for ocean ecosystems as the ocean gets warmer. Researchers at Stanford have found a new method for regenerating bleached corals.
Scientists working on coral found that when they had a bleached and healthy example accidentally touching in the lab, the symbionts from the healthy coral that make its food were able to spread to the bleached coral, reviving it in a matter of weeks. Contact was only required for one week, although three days was sufficient in a few cases. The effect only seems to work with corals of the same genet as the healthy corals of other genets just take over the bleached coral antagonistically.
This is particularly exciting, as areas where not all coral has bleached may indicate the presence of symbionts that are more heat tolerant, and being able to spread these symbionts to their neighbors quickly can greatly speed up the process of coral regeneration and save the reef. Coral reefs are some of the most vibrant ecosystems in the ocean, so if you save the coral, you can save many other species as well that rely on them.
If you’d like to explore how the coral is doing near you, perhaps you should try an open ROV or a bionic jellyfish?
A protein is a chain of amino acids held together by what are called peptide bonds. On their own, those bonds are extremely stable; they're estimated to have a half-life of several hundred years. But in Earth's environment, most proteins don't last nearly that long. That's because organisms have evolved a handful of ways to catalyze the break-up of peptide bonds, which have diversified into countless specialized protein-digesting enzymes. Proteases are everywhere and generally make short work of any proteins that find their way into the environment.
Now, researchers have basically short-circuited the diversification process, using AI-based protein design tools to take the catalytic core of two types of protease and replace the entire rest of the protein. The resulting enzymes could be tuned to cut specific proteins in half, and the researchers demonstrated their effectiveness by using them to cut proteins associated with neurological diseases.
The basic peptide bond isn't especially interesting-looking—it's what you get when you link an amino group to an acid, releasing a water molecule in the process. As their name implies, amino acids have both an amino and an acid group, allowing them to form peptide bonds on two sides of the amino acid. This is critical for building up the long chains found in proteins. (The amino acids also have side chains with distinctive chemistry, which gives a backbone specific properties.)
© Basic
Honey bees are known to leave their stingers embedded in tender flesh once they sting you and fly away. Scientists have now determined that the stinger is able to continue pumping venom into its unfortunate victim even after the bee flies away, thanks to a unique double-piston pump-like mechanism, according to a new paper published in the Proceedings of the National Academy of Sciences.
Different species have evolved different mechanisms for delivering venom, which involves piercing the skin and then pumping venom from a gland or reservoir. Spiders, for instance, have muscles surrounding their venom glands, which contract and eject venom through hollow fangs. Bees, wasps, and ants deliver venom via their stingers, either by contracting muscles around the venom reservoir or through stiff elements called lancets working together to pump venom.
Honey bees (Apis mellifera) add a unique feature: Worker bees fly away after inserting their stingers in the target, leaving the stinger behind. The stinger continues to penetrate the tissue and pump venom on its own, a rare phenomenon known as autotomy. A honey bee's stinger has three main interlocking elements that form the venom canal: a stylet that widens to form the main pumping chamber and two sharp-tipped lancets that slide back and forth, piercing the tissue and pumping venom into the target. But the precise mechanism by which the pumping action is achieved has never been directly observed.
© Maciej A. Czyzewski/CC BY-SA 4.0
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