Category: 7. Science

For the first time, Australian scientists have used Artificial Intelligence (AI) to generate a ready-to-use biological protein, in this case, one that can kill antibiotic resistant bacteria like E. coli.

This study, published in Nature Communications, provides a new way to combat the growing crisis caused by antibiotic resistant super bugs. By using AI in this way, Australian science has now joined countries like the US and China having developed AI platforms capable of rapidly generating thousands of ready-to-use proteins, paving the way for faster, more affordable drug development and diagnostics that could transform biomedical research and patient care.

The Nature Communications paper is co-led by Dr. Rhys Grinter and Associate Professor Gavin Knott, a Snow Medical Fellow, who lead the new AI Protein Design Program with nodes at the University of Melbourne Bio21 Institute and Monash Biomedicine Discovery Institute.

According to Dr. Grinter and A/Prof. Knott, the AI Protein Design Platform used in this work is the first in Australia that models the work done by David Baker (who won the Nobel Prize in Chemistry last year) developing an end-to-end approach that could create a wide range of proteins. “These proteins are now being developed as pharmaceuticals, vaccines, nanomaterials and tiny sensors, with many other applications yet to be tested” Associate Professor Knott said.

For this study, the AI Protein Design Platform used AI-driven protein design tools that are freely available for scientists everywhere. “It’s important to democratize protein design so that the whole world has the ability to leverage these tools,” said Daniel Fox, the PhD student who performed most of the experimental work for the study. “Using these tools and those we are developing in-house, we can engineer proteins to bind a specific target site or ligand, as inhibitors, agonists or antagonists, or engineered enzymes with improved activity and stability.”

According to Dr Grinter, currently proteins used in the treatment of diseases like cancer or infections are derived from nature and repurposed through rational design or in vitro evolution and selection. “These new methods in deep learning enable efficient de novo design of proteins with specific characteristics and functions, lowering the cost and accelerating the development of novel protein binders and engineered enzymes,” he said.

Since the work of David Baker, new tools and software are being developed, such as Bindcraft and Chai which have been incorporated into an AI Protein Design Platform co-led by Dr. Grinter and A/Prof. Knott..

Professor John Carroll, Director of the Monash Biomedicine Discovery Institute, said the new AI Protein Design Program ‘brings Australia “right up to speed in this exciting new modality for designing novel therapeutics and research tools. It is testament to the entrepreneurial spirit of two fabulous young scientists who have worked night and day to build this capability from scratch.”

“The Program, based at Monash University and the University of Melbourne, is run by a team of talented structural biologists and computer scientists who understand the design process from end-to-end. This in-depth knowledge of protein structure and machine learning makes us a highly agile program capable of regularly onboarding cutting edge tools in AI-protein design,” Associate Professor Knott said.

Leafcutter ants’ roles can be reprogrammed by manipulating two neuropeptides, according to a new study. These ants are known for their rigorous division of labor in a caste system, with groups performing roles ranging from cutting leaves to nest defense to tending the fungus that is their food source.

Despite physical differences among the ants—the heads of the nest defender ants can be five times the size of the fungal carers’ heads, for instance—it’s still possible to “pharmacologically reprogram them to assume some of the roles that typically other castes assume,” indicating behavioral flexibility, says Daniel Kronauer, professor at Rockefeller University, who was not involved in the work.

The researchers induced the behavioral changes by first using RNA sequencing to uncover target neuropeptides and then manipulating neuropeptide levels in the ants. The study was published in June in Cell.

The work illustrates the close relationship between neuropeptides and behavior, says Shelley Berger, professor of cell and developmental biology at the University of Pennsylvania and principal investigator of the study. Defender ants are “so big and awkward and clumsy,” she says, but after a certain neuropeptide level is lowered, the ant becomes a “nurse tending to the brood.”

The study shows the “importance of neuropeptides as these molecular controllers of incredibly complex” behavioral traits, says Zoe Donaldson, professor of behavioral neuroscience at the University of Colorado Boulder, who was not involved in the study. “I think it’s a really elegant demonstration of just how powerful they are.”

A

lmost all species of ants live in colonies, but leafcutter ants (Atta cephalotes) have a particularly intricate labor division, says study investigator Karl Glastad, assistant professor of biology at the University of Rochester. He and Berger previously explored hormonal controls of social behavior in Florida carpenter ants, which have two worker subtypes, but leafcutter ants are a “really elaborated version” of that species, Glastad says.

In the leafcutter ant study, the researchers first recorded the ants in an experimental arena where they were allowed to interact with leaves, pupae and fungus. Then the team fed the video into the machine-learning tool DeepLabCut to conduct a behavioral analysis and separate the ants into four distinct morphological subcastes of decreasing body size: defensive patrollers, leafcutters, brood carers and fungal gardeners.

The researchers wanted to understand how these behavioral differences are expressed via whole-brain transcriptomics. RNA sequencing showed that each ant subcaste has uniquely expressed genes, demonstrating a correlation between brain gene expression and behavior, they wrote in the study.

Neuropeptides were among the top differentially expressed genes in the four ant subcastes, with the neuropeptide neuroparsin-A (NPA)—known to regulate swarming behavior in desert locusts—being one of the most highly expressed genes for the defensive subcaste, Glastad says. The neuropeptide crustacean cardioactive peptide (CCAP), on the other hand, was highly expressed in the leafcutter subcaste.

The researchers surmised that NPA suppresses an instinct to care for the brood in the defensive subcaste. To test this, they used inhibitory RNA to knock down expression of this neuropeptide. The defensive subcaste ants began to behave more like brood carers, Glastad says, ferrying the brood to the fungal pile in the test arena. When the researchers reversed the experiment, injecting NPA into the carer subcaste, the ants suppressed their brood care significantly.

Altering levels of the neuropeptide CCAP produced similarly clear behavioral swaps. Defensive ants and brood carers, after an injection of CCAP, approached leaves and “did their best to kind of manipulate and try to cut the leaves,” Glastad says, even though they weren’t very good at it. And removing CCAP in leaf harvesters decreased their leaf-moving behavior. The behavioral results were “very clean,” Glastad says.

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he paper also examined the role of neuropeptides in the naked mole rat, which lives in communities with labor division. Despite naked mole rats and ants being separated by more than 600 million years of evolution, they showed similar gene expression patterns, the researchers found, suggesting conserved neuropeptide roles in eusocial behavior across distantly related species.

The researchers compared expressed genes in the hypothalamus of naked mole rats with those in leafcutter ants, specifically between forager and nurse subcastes of naked mole rats and the ants that labor outside the nest (foragers and defenders) and inside (carers and fungal gardeners). There was overlap between the differentially expressed genes from forager naked mole rats and out-nest ants, and also between nurse naked mole rats and in-nest ants.

The concept of a clear caste structure in naked mole rats “is hotly debated” among researchers in the field, says Yuki Haba, a postdoctoral fellow in Ishmail Abdus-Saboor’s lab at Columbia University, who was not involved in the study. In fact, a 2021 study found naked mole rats do not specialize in certain work tasks—rather, their roles may vary according to their age. Therefore, the division of labor in naked mole rat colonies might not be directly comparable to that of ants, Haba says. Glastad agrees, noting that when the naked mole rats were sampled in the new study, they were “specifically collected for doing those different behaviors.”

Still, the “results are striking,” Haba says. They show there may be some underlying shared biology between ants and mammals, he adds.

Glastad and his colleagues also treated naked mole rat astrocytes with ant NPA, even though the rats do not have NPA or the receptor for it. NPA-treated naked mole rat astrocytes cultured from foragers showed gene upregulation and those cultured from nurses showed downregulation. “Their gene expression changed in a way that was consistent with neuroparsin possibly being able to plug into something, and our guess is the insulin receptor in mammals,” Glastad says.

That work “opens up many hypotheses and questions,” Haba says. He would like to see more research into the results to confirm that NPA is acting on an insulin signaling pathway, he says.

The results in ants, and the similarities seen with the naked mole rats, demonstrate that “nature uses what it has,” Donaldson says. “It does lend a lot of credence to this idea that we’re not working with a huge number of molecules” that can control behavior.

The research published in Nature Ecology & Evolution shines light on an enduring evolutionary mystery: why male guppies have such vibrant and varied colors and patterns.

Virile me up

Zoologists Drs. Wouter van der Bijl and Judith Mank used deep learning, genetic studies and bred three generations of increasingly orange guppies to investigate. They found the more colorful males were up to two times more sexually active, performing for females at a greater rate and for longer periods of time, and attempting to sneakily copulate more often.

Orange you glad to see me, baby?

It’s known that female guppies prefer orange, and unusual, patterns in their male partners, but the team found that the color diversity of guppies comes from the same cells that are responsible for forming the brain, suggesting a genetic link between how guppies look and how they behave.

“Previously, people thought perhaps males realized that if they were more orange, they were more sexy. With the genetic link, it may be that they’re healthier and fitter,” said Dr. Mank.

Let’s recombine sometime

The researchers found the guppy color genes, and the locations they appeared in, were tied to multiple chromosomes, creating a vast architecture of genetic possibilities. Seven orange and eight black color types were identified overall, allowing for a potential 32,768 unique pattern combinations.

“Genetic variation is the raw material that evolution uses to produce resilient, adapted animals and plants, including for things like climate change or disease,” said van der Bijl. “We often look at extreme examples to understand where genetic variation comes from and how it’s maintained.”

July 10 (UPI) — NASA’s James Webb Space Telescope has revealed thick, dusty layers of the Cat’s Claw Nebula, a region of star formation about 5,500 light-years away in the constellation Scorpius, the agency has announced.

“It’s the cat’s meow,” NASA said in a release.

NASA focused the James Webb Space Telescope’s Near-Infrared Camera on a single “toe bean” within a subset of toe beans in the nebula, which appear to contain young stars shaping the surrounding gas and dust in the star-forming region.

The discovery is the result of years of research in this part of space.

“Three years into its mission, Webb continues to deliver on its design — revealing previously hidden aspects of the universe, from the star formation process to some of the earliest galaxies,” said Shawn Domagal-Goldman, acting director of the Astrophysics Division at NASA Headquarters in Washington.

Domagal-Goldman added that the discovery will inform future research in this largely unexplored nebular region and create more research opportunities for scientists as they pursue an understanding of dark matter, search for life in other parts of the solar system or seek to find Earth-like planets.

“The questions Webb has raised are just as exciting as the answers it’s giving us,” he continued.

The toe bean discovery will also give researchers an opportunity to study the turbulent cloud-to-star formation process.

The effects of climate change could awaken hundreds of volcanoes worldwide – which in turn could worsen the effects of climate change.

According to recent models predicting changes in the magma beneath Patagonia’s glaciers, the retreat of ice has the power to shake subglacial volcanoes out of their slumber.

The world isn’t at imminent risk of volcanic bombardment, but the findings suggest that today’s rapid melting of glaciers could raise the risk of eruptions in the future.

This will likely occur over hundreds, if not thousands, of years, but it’s always good to be prepared, especially for places like Antarctica, where more than 100 hidden volcanoes are currently trapped under ice.

Related: ‘Zombie’ Volcano in Bolivia Appears to Be Stirring Deep Underground

The study is based on the deep history of the Patagonian Ice Sheet, which once used to cover the southern tip of South America. More than 18,000 years ago, when the ice sheet was at its heaviest, magma pooled and crystallized some 10 to 15 kilometers (6 to 9 miles) beneath the surface.

As the climate warmed and glaciers melted, however, the pressure was off. Scientists think Earth’s crust bounced upward without the weight of ice pressing down on it, and the gases in underground magma were allowed to expand – a key factor for volcanic eruptions.

Researchers analyzed samples from six volcanoes in Chile to learn more about their eruptive past. One of them, the Mocho-Choshuenco volcano, is now dormant, but according to recent data, its eruptive activity in the past was impacted by the advance and retreat of Patagonia’s ice.

It took roughly 3,000 to 5,000 years before the region’s ice ‘unloading’ led to explosive eruptions, so we probably have plenty of time to prepare.

As modern Patagonia loses more of its ice, however, parts of the land are rebounding at unexpectedly rapid rates, and that is worrying some scientists.

“Glaciers tend to suppress the volume of eruptions from the volcanoes beneath them,” explains volcanologist Pablo Moreno-Yaeger from the University of Wisconsin-Madison, who presented the research at the Goldschmidt Conference.

“But as glaciers retreat due to climate change, our findings suggest these volcanoes go on to erupt more frequently and more explosively.”

Scientists studying volcanoes and glaciers in Iceland have noticed a similar phenomenon, but this is one of the first studies to show the same forces at play on a continental scale.

“Our study suggests this phenomenon isn’t limited to Iceland, where increased volcanicity has been observed, but could also occur in Antarctica,” says Moreno-Yaeger.

“Other continental regions, like parts of North America, New Zealand, and Russia, also now warrant closer scientific attention.”

In Antarctica, for instance, scientists have conducted simulations that show if too much ice melts, it could increase future eruptions.

Even if the magma doesn’t break through the ice sheet completely, it could melt the structure from within.

“Over time the cumulative effect of multiple eruptions can contribute to long-term global warming because of a buildup of greenhouse gases,” explains Moreno-Yaeger.

“This creates a positive feedback loop, where melting glaciers trigger eruptions, and the eruptions in turn could contribute to further warming and melting.”

That’s the sort of catastrophic future scientists want to see coming from a long way off. Otherwise, there may be no way to stop it.

The findings were presented at the 2025 Goldschmidt Conference in Prague.

The North Atlantic water contains large quantities of nanoplastics, particularly plastics that are used to make disposable and reusable plastic bottles, films or disposable drinking cups and cutlery. ittipol, Adobe Stock / Graphic: Sebastian Wiedling, UFZ

Nanoplastics — microplastics that are less than a micrometer in size — are found all over the world, from Alpine peaks to the deepest parts of the ocean.

At least 27 million tonnes of nanoplastics are estimated to be floating in the North Atlantic Ocean, weighing more than all wild land mammals combined, reported The New York Times.

Researchers from the Helmholtz Center for Environmental Research (UFZ), Utrecht University and the Royal Netherlands Institute for Sea Research investigated the prevalence of nanoplastics in the North Atlantic and found the tiny plastic particles at all ocean depths between the subtropical and temperate zones.

The findings of the study show that nanoplastics are a much bigger part of the marine plastics pollution problem than had been previously thought, a press release from UFZ said.

New @nature.com study by @dusanmateric.bsky.social & colleague from @utrechtuniversity.bsky.social: The North Atlantic’s mixed layer may contain up to 27 million tonnes of nanoplastics. Let that sink in: www.nature.com/articles/s41…

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— UFZ-CITE (@ufz-cite.bsky.social) July 10, 2025 at 4:00 AM

“Plastic pollution of the marine realm is widespread, with most scientific attention given to macroplastics and microplastics. By contrast, ocean nanoplastics (<1 μm) remain largely unquantified, leaving gaps in our understanding of the mass budget of this plastic size class,” the authors of the study wrote. “Our findings suggest that nanoplastics comprise the dominant fraction of marine plastic pollution.”

Marine plastic waste causes devastating impacts to marine animals, who may become entangled in plastic debris such as bags and nets or ingest smaller pieces, mistaking them for food. Ingested plastic can injure or block the gastrointestinal tract and a small proportion of the tiniest plastic particles can enter the bloodstream by passing through the intestinal wall.

Until now, quantitative data on microplastics in the world’s ocean was scarce due to the particles’ small size, propensity to change and because they are often hard to distinguish from other particles in the environment using standard methods.

An expedition by a UFZ and Utrecht University research team aboard the RV Pelagia in 2020 recorded nanoplastic prevalence along a passage between the European continental shelf and the subtropical North Atlantic Gyre. The team took samples from a dozen measuring points: the uppermost ocean layer at approximately 10 meters; the intermediate layer at roughly 1,000 meters; and at 30 meters above the seabed.

“With the data from these measuring points, we can make statements about the vertical and horizontal distribution of nanoplastic in the North Atlantic,” said lead author of the study Dr. Dušan Materić, a chemist with UFZ, in the press release.

Our paper is out in Nature: “Nanoplastic concentrations across the North Atlantic”. An estimated 27 million tons of NPs are there, even at depths over 4500m. Huge thanks to my brilliant MSc student Sophie and the sampling support from NIOZ! @ufz.de @ufz-cite.bsky.social
doi.org/10.1038/s415…

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— Dr.Dusan Materic (Matt) (@dusanmateric.bsky.social) July 9, 2025 at 11:17 AM

The researchers, led by Materić, measured concentrations of organic trace gases using thermal desorption and a high-resolution proton transfer reaction mass spectrometer (PTR-MS). They then used these to combust the nanoplastics. Heating them released gases that were able to be quantified with the mass spectrometer.

Materić, who developed the method at Utrecht University, explained that each polymer has a unique chemical fingerprint by which both its concentration and identity can be determined.

Nanoplastics were found at all analyzed depths of the 12 measurement sites.

“They are present everywhere in such large quantities that we can no longer neglect them ecologically,” Materić said.

The most frequently detected nanoparticles were polyethylene terephthalate (PET), polyvinyl chloride (PVC) and polystyrene (PS), which are commonly used to make plastic bottles, drinking cups, cutlery and films.

At almost all measuring points, these types of plastic were detected in the uppermost layer of the ocean.

“This is because, on the one hand, the redistribution from the atmosphere occurs via the sea surface and, on the other hand, a lot of plastic is introduced via the estuaries of rivers,” Materić explained.

The intermediate layer of the ocean was dominated by PET nanoparticles.

Materić said more nanoplastics were found in the North Atlantic subtropical gyre, where ocean currents are known to cause surface microplastics to accumulate.

The lowest nanoplastic concentrations were found near the sea floor. PET nanoplastics were detected at all points measured there, even at depths below 4,500 meters. This nanoplastic most likely came from fragmented synthetic clothing fibers, but could have also come from other unknown processes.

“Nanoplastic and nanoparticles are so small that the physical laws governing larger particles often no longer apply,” Materić said.

To their surprise, the researchers did not find any polypropylene (PP) or polyethylene (PE) — commonly used in packaging and bags — at any measuring points., even though they often end up becoming marine plastic waste.

The total amount of nanoplastics — approximately 27 million tonnes — are stored in the top layer of the Northern Atlantic Ocean, up to 200 meters deep, between the temperate and subtropical zones.

“This is in the same order of magnitude as the estimated mass of macro- and microplastics for the entire Atlantic,” Materić said.

Ocean nanoplastics have yet to be taken into account in current assessments of total marine plastics.

“Only a couple of years ago, there was still debate over whether nanoplastic even exists. Many scholars continue to believe that nanoplastics are thermodynamically unlikely to persist in nature, as their formation requires high energy. Our findings show that, by mass, the amount of nanoplastic is comparable to what was previously found for macro- and microplastic – at least in this ocean system,” Materić said.

The findings of the study, “Nanoplastic concentrations across the North Atlantic,” were published in the journal Nature.

High concentrations of nanoplastic particles were found in locations across the North Atlantic Ocean, particularly in the top 10 metres of water and near coastlines, according to an analysis in Nature. go.nature.com/44ohIok 🌊 🧪

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— Nature Portfolio (@natureportfolio.nature.com) July 10, 2025 at 9:04 AM