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Category: biological

Lab-in-the-loop framework enables rapid evolution of complex multi-mutant proteins

The search space for protein engineering grows exponentially with complexity. A protein of just 100 amino acids has 20100 possible variants—more combinations than atoms in the observable universe. Traditional engineering methods might test hundreds of variants but limit exploration to narrow regions of the sequence space. Recent machine learning approaches enable broader searches through computational screening. However, these approaches still require tens of thousands of measurements, or 5–10 iterative rounds.

With the advent of these foundational protein models, the bottleneck for protein engineering swings back to the lab. For a single protein engineering campaign, researchers can only efficiently build and test hundreds of variants. What is the best way to choose those hundreds to most effectively uncover an evolved protein with substantially increased function? To address this problem, researchers have developed MULTI-evolve, a framework for efficient protein evolution that applies machine learning models trained on datasets of ~200 variants focused specifically on pairs of function-enhancing mutations.

Published in Science, this work represents Arc Institute’s first lab-in-the-loop framework for biological design, where computational prediction and experimental design are tightly integrated from the outset, reflecting a broader investment in AI-guided research.

Particles don’t always go with the flow (and why that matters)

It is commonly assumed that tiny particles just go with the flow as they make their way through soil, biological tissue, and other complex materials. But a team of Yale researchers led by Professor Amir Pahlavan shows that even gentle chemical gradients, such as a small change in salt concentration, can dramatically reshape how particles move through porous materials. Their results are published in Science Advances.

How small particles known as colloids, like fine clays, microbes, or engineered particles, move through porous materials such as soil, filters, and biological tissue can have significant and wide-ranging effects on everything from environmental cleanups to agriculture.

It’s long been known that chemical gradients—that is, gradual changes in the concentration of salt or other chemicals—can drive colloids to migrate directionally, a phenomenon known as diffusiophoresis. But it was often assumed that this effect would matter only when there was little or no flow, because phoretic speeds are typically orders of magnitude smaller than average flow speeds in porous media. Experiments set up in Pahlavan’s lab demonstrated a very different outcome.

Space Station Microbes Harvest Metals from Meteorites

Most microbes aboard the International Space Station can extract valuable metals like palladium from meteorite material in microgravity, showing potential for sustainable space resource mining.

How can microbes be used to help enhance human space exploration, specifically on the Moon and Mars? This is what a recent study published in npj Microgravity hopes to address as a team of scientists investigated how microbes could be used to harvest essential minerals from rocks that could be used to enhance sustainability efforts on long-term human missions to the Moon and Mars. This study has the potential to help scientists develop new methods for improving human spaceflight, which could substantially alleviate the need for relying on Earth for supplies.

For the study, the researchers sent meteorite and microorganism samples to the International Space Station (ISS) where astronauts conducted a series of experiments to ascertain how microorganisms could harvest essential minerals, specifically platinum and palladium, from the meteorite samples. Concurrently, the researchers also conducted the same experiments on Earth to compare the results under microgravity and terrestrial environments.

The goal of the study was to ascertain whether microorganisms could be used on future long-term space missions to harvest precious metals for construction of space habitats. In the end, the researchers and astronauts found that the microorganisms not only successfully extracted metals like palladium and platinum but also had minimal fungal residues typically that results from such processes. This lack of fungal residue was found to be more prevalent under microgravity conditions.

One of the astronauts stuck in space after Starliner malfunction to be on Cape Cod Feb. 20

She is an inspiration!

NASA astronaut Sunita “Suni” Williams, a Needham native with Falmouth ties, will speak about her experiences during a recent space mission at 7:30 p.m. Feb. 20 at the Marine Biological Laboratory’s Falmouth Forum, according to a community announcement.

The lecture, titled “So Much Space… So Much Time!,” will take place in the Cornelia Clapp Auditorium in Lillie Laboratory, 7 MBL St., Woods Hole. It is free and open to the public.

Williams and fellow astronaut Butch Wilmore remained aboard the International Space Station after thruster failures on their spacecraft. They returned to Earth on an alternate vehicle. Williams will share videos and personal accounts to highlight the rapid commercialization of space and the challenges it presents.

Chitosan-nickel biomaterial becomes stronger when wet, and could replace plastics

A new study led by the Institute for Bioengineering of Catalonia (IBEC) has unveiled the first biomaterial that is not only waterproof but actually becomes stronger in contact with water. The material is produced by the incorporation of nickel into the structure of chitosan, a chitinous polymer obtained from discarded shrimp shells. The development of this new biomaterial marks a departure from the plastic-age mindset of making materials that must isolate from their environment to perform well. Instead, it shows how sustainable materials can connect and leverage their environment, using their surrounding water to achieve mechanical performance that surpasses common plastics.

Plastics have become an integral part of modern society thanks to their durability and resistance to water. However, precisely these properties turn them into persistent disruptors of ecological cycles. As a result, unrecovered plastic is accumulating across ecosystems and becoming an increasingly ubiquitous component of global food chains, raising growing concerns about potential impacts on human health.

In an effort to address this challenge, the use of biomaterials as substitutes for conventional plastics has long been explored. However, their widespread adoption has been limited by a fundamental drawback: Most biological materials weaken when exposed to water. Traditionally, this vulnerability has forced engineers to rely on chemical modifications or protective coatings, thereby undermining the sustainability benefits of biomaterial-based solutions.

UT San Antonio to launch nation’s first open-access neuromorphic computing hub

To tackle this challenge, the MATRIX AI Consortium for Human Well-Being at UT San Antonio plans to launch a new initiative that establishes a national hub for “neuromorphic” computing available for public use.

Neuromorphic computing is a revolutionary approach that mimics the human brain’s structure to process information with a fraction of the energy used by traditional computers. Unlike standard processors that crunch data in a fixed sequence, neuromorphic chips operate like biological neurons. They are event-based, meaning that they activate only when there is something new to process, saving energy between events.

The initiative, called THOR: The Neuromorphic Commons, is funded by the National Science Foundation. THOR will make the promising technology available for researchers nationwide to explore and conduct experiments, serving as the largest-ever full-stack neuromorphic platforms to be open to the public.

20-Year Mystery Solved: Scientists Discover an Entirely New Way Cells Transport Bile Acids

A long-standing mystery in bile acid biology has been solved. Bile acids are often introduced as digestion helpers, but they are also powerful chemical messengers that help coordinate metabolism throughout the body. To do their jobs, these cholesterol-derived molecules must be shuttled efficiently

Microscopic robots that sense, think, act, and compute

Extremely cool paper describing optically programmable ~0.3 mm robots with onboard computation and autonomous locomotion! These tiny rectangular machines carry solar cells, optical receivers, electrokinetic actuators, and more. As demonstrations, the authors programmed them (i) to report local temperature by doing a coded dance and (ii) swim towards warmth before stopping and rotating upon reaching a location with a certain level of heat. This is amazing and I hope such devices are further improved so they can be used in biological applications! Love it!

(https://www.science.org/doi/10.1126/scirobotics.adu8009)

Autonomous submillimeter robots are built with onboard sensing, computation, memory, communication, and locomotion.

Hologram processing method boosts 3D image depth of focus fivefold

Researchers from the University of Tartu Institute of Physics have developed a novel method for enhancing the quality of three-dimensional images by increasing the depth of focus in holograms fivefold after recording, using computational imaging techniques. The technology enables improved performance of 3D holographic microscopy under challenging imaging conditions and facilitates the study of complex biological structures.

The research results were published in the Journal of Physics: Photonics in the article “Axial resolution post-processing engineering in Fresnel incoherent correlation holography.”

One of the main limitations of conventional microscopes and 3D imaging systems is that, once an image or hologram has been recorded, its imaging properties cannot be altered. To overcome this limitation, Shivasubramanian Gopinath, a Junior Research Fellow at the University of Tartu Institute of Physics, and his colleagues have developed a new method that enables to capture a set of holograms with different focal distances at the time of acquisition, instead of a single image. These can then be computationally combined to produce a synthetic hologram that offers a much greater depth of focus than conventional approaches, and allows for post-processing of the recorded image.

The insect-inspired bionic eye that sees, smells and guides robots

The compound eyes of the humble fruit fly are a marvel of nature. They are wide-angle and can process visual information several times faster than the human eye. Inspired by this biological masterpiece, researchers at the Chinese Academy of Sciences have developed an insect-scale compound eye that can both see and smell, potentially improving how drones and robots navigate complex environments and avoid obstacles.

Traditional cameras on robots and drones may excel at capturing high-definition photos, but struggle with a narrow field of view and limited peripheral vision. They also tend to be bulky and power-hungry.

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