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Window to the past: New microfossils suggest earlier rise in complex life

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Window to the past: New microfossils suggest earlier rise in complex life


Microfossils from Western Australia may capture a jump in the complexity of life that coincided with the rise of oxygen in Earth’s atmosphere and oceans, according to an international team of scientists.

The findings, published in the journal Geobiology, provide a rare window into the Great Oxidation Event, a time roughly 2.4 billion years ago when the oxygen concentration increased on Earth, fundamentally changing the planet’s surface. The event is thought to have triggered a mass extinction and opened the door for the development of more complex life, but little direct evidence had existed in the fossil record before the discovery of the new microfossils, the scientists said.

“What we show is the first direct evidence linking the changing environment during the Great Oxidation Event with an increase in the complexity of life,” said corresponding author Erica Barlow, an affiliate research professor in the Department of Geosciences at Penn State. “This is something that’s been hypothesized, but there’s just such little fossil record that we haven’t been able to test it.”

When compared to modern organisms, the microfossils more closely resembled a type of algae than simpler prokaryotic life — organisms like bacteria, for example — that existed prior to the Great Oxidation Event, the scientists said. Algae, along with all other plants and animals, are eukaryotes, more complex life whose cells have a membrane-bound nucleus.

More work is required to determine if the microfossils were left behind by eukaryotic organisms, but the possibility would have significant implications, the scientists said. It would push back the known eukaryotic microfossil record by 750 million years.

“The microfossils have a remarkable similarity to a modern family called Volvocaceae,” Barlow said. “This hints at the fossil being possibly an early eukaryotic fossil. That’s a big claim, and something that needs more work, but it raises an exciting question that the community can build on and test.”

Barlow discovered the rock containing the fossils while conducting her undergraduate research at the University of New South Wales (USNW) in Australia, and she conducted the current work as part of her doctoral work at UNSW and then while a postdoctoral researcher at Penn State.


“These specific fossils are remarkably well preserved, which allowed for the combined study of their morphology, composition, and complexity,” said Christopher House, professor of geosciences at Penn State and a co-author of the study. “The results provide a great window into a changing biosphere billions of years ago.”

The scientists analyzed the chemical makeup and carbon isotopic composition of the microfossils and determined the carbon was created by living organisms, confirming that the structures were indeed biologic fossils. They also uncovered insights into the habitat, reproduction and metabolism of the microorganisms.

Barlow compared the samples to microfossils from before the Great Oxidation Event and could not find comparable organisms. The microfossils she found were larger and featured more complex cellular arrangements, she said.

“The record seems to reveal a burst of life — there’s an increase in diversity and complexity of this fossilized life that we are finding,” Barlow said.

Compared to modern organisms, Barlow said, the microfossils have explicit similarities with algal colonies, including in the shape, size and distribution of both the colony and individual cells and membranes around both cell and colony.

“They have a remarkable similarity and so, by that way of comparison, we could say these fossils were relatively complex,” Barlow said. “There is nothing like them in the fossil record, and yet, they have quite striking similarities to modern algae.”

The findings have implications for both how long it took complex life to form on early Earth — the earliest, uncontroversial evidence of life is 3.5 billion years old — and what the search for life elsewhere in the solar system may reveal, the scientists said.


“I think finding a fossil that is this relatively large and complex, relatively early on in the history of life on Earth, kind of makes you question — if we do find life elsewhere, it might not just be bacterial prokaryotic life,” Barlow said. “Maybe there’s a chance there could be something more complex preserved — even if it’s still microscopic, it could be something of a slightly higher order.”

Also contributing were Maxwell Wetherington, staff scientist at Penn State; Ming-Chang Liu, staff scientist at the Lawrence Livermore National Laboratory; and Martin Van Kranendonk, professor at the University of New South Wales in Australia.

The Australian Research Council, NASA and the National Science Foundation provided funding for this work.



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Simple test for flu could improve diagnosis and surveillance

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Simple test for flu could improve diagnosis and surveillance


Fewer than one percent of people who get the flu every year get tested, in part because most tests require trained personnel and expensive equipment. Now researchers have developed a low-cost paper strip test that could allow more patients to find out which type of flu they have and get the right treatment.

The test, developed by a team from the Broad Institute of MIT and Harvard and Princeton University, and supported by the US Centers for Disease Control and Prevention, uses CRISPR to distinguish between the two main types of seasonal flu, influenza A and B, as well as seasonal flu subtypes H1N1 and H3N2. It can also identify strains that resist antiviral treatment, and with further work, could potentially detect swine and avian flu strains, including H5N1, which is currently infecting cattle.

Appearing in The Journal of Molecular Diagnostics, the results could help improve outbreak response and clinical care by bringing tests that are accurate, low-cost, and fast to doctors’ offices and labs across the US and in other countries.

“Ultimately, we hope these tests will be as simple as rapid antigen tests, and they’ll still have the specificity and performance of a nucleic acid test that would normally be done in a laboratory setting,” said Cameron Myhrvold, co-senior author on the study along with Pardis Sabeti, an institute member at the Broad and a professor at Harvard University and the Harvard T.H. Chan School of Public Health, as well as a Howard Hughes Medical Institute investigator. Myhrvold, who is currently an assistant professor at Princeton University, was a postdoctoral researcher in Sabeti’s lab when the study began.

SHINE a light

The test is based on a technology called SHINE, which was developed by Sabeti’s lab in 2020 and uses CRISPR enzymes to identify specific sequences of viral RNA in samples. The researchers first used SHINE to test for SARS-CoV-2, and later to distinguish between the Delta and Omicron variants. Then, in 2022, they began adapting the assay to detect other viruses they knew were always circulating: influenzas. They wanted to create tests that could be used in the field or in clinics rather than hospitals or diagnostic labs with expensive equipment.

“Using a paper strip readout instead of expensive fluorescence machinery is a big advancement, not only in terms of clinical care but also for epidemiological surveillance purposes,” said Ben Zhang, co-first author on the study, a medical student at Harvard Medical School and an undergraduate researcher in Sabeti’s lab when the study began.

Typical diagnostic approaches such as polymerase chain reaction (PCR) require lengthy processing times, trained personnel, specialized equipment, and freezers to store reagents at -80°C, whereas SHINE can be conducted at room temperature in about 90 minutes. Currently, the assay only requires an inexpensive heat block to warm the reaction, and the researchers are working to streamline the process with the goal of returning results in 15 minutes.

The researchers also adapted SHINE to distinguish between different flu strains. In the future, they say the assay could be adapted to detect two different viruses with similar symptoms, such as influenza and SARS-CoV-2.

“Being able to tease apart what strain or subtype of influenza is infecting a patient has repercussions both for treating them and public health interventions,” said Jon Arizti-Sanz, a postdoctoral researcher in Sabeti’s lab and co-first author on the study.

For example, the tests could help clinicians decide whether to use Oseltamivir, a common antiviral that is effective for only some strains, Arizti-Sanz added. In the field, rapid testing could also help scientists collect samples more strategically during an outbreak to better monitor how the virus is spreading.

Next, the researchers are adapting SHINE to test for both avian and swine influenza strains. “With SARS-CoV-2 and now flu, we’ve shown that we can easily adapt SHINE to detect new or evolving viruses,” Arizti-Sanz said. “We’re excited to apply it to H5N1.”



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Prying open the AI black box

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Prying open the AI black box


Artificial intelligence continues to squirm its way into many aspects of our lives. But what about biology, the study of life itself? AI can sift through hundreds of thousands of genome data points to identify potential new therapeutic targets. While these genomic insights may appear helpful, scientists aren’t sure how today’s AI models come to their conclusions in the first place. Now, a new system named SQUID arrives on the scene armed to pry open AI’s black box of murky internal logic.

SQUID, short for Surrogate Quantitative Interpretability for Deepnets, is a computational tool created by Cold Spring Harbor Laboratory (CSHL) scientists. It’s designed to help interpret how AI models analyze the genome. Compared with other analysis tools, SQUID is more consistent, reduces background noise, and can lead to more accurate predictions about the effects of genetic mutations.

How does it work so much better? The key, CSHL Assistant Professor Peter Koo says, lies in SQUID’s specialized training.

“The tools that people use to try to understand these models have been largely coming from other fields like computer vision or natural language processing. While they can be useful, they’re not optimal for genomics. What we did with SQUID was leverage decades of quantitative genetics knowledge to help us understand what these deep neural networks are learning,” explains Koo.

SQUID works by first generating a library of over 100,000 variant DNA sequences. It then analyzes the library of mutations and their effects using a program called MAVE-NN (Multiplex Assays of Variant Effects Neural Network). This tool allows scientists to perform thousands of virtual experiments simultaneously. In effect, they can “fish out” the algorithms behind a given AI’s most accurate predictions. Their computational “catch” could set the stage for experiments that are more grounded in reality.

“In silico [virtual] experiments are no replacement for actual laboratory experiments. Nevertheless, they can be very informative. They can help scientists form hypotheses for how a particular region of the genome works or how a mutation might have a clinically relevant effect,” explains CSHL Associate Professor Justin Kinney, a co-author of the study.

There are tons of AI models in the sea. More enter the waters each day. Koo, Kinney, and colleagues hope that SQUID will help scientists grab hold of those that best meet their specialized needs.

Though mapped, the human genome remains an incredibly challenging terrain. SQUID could help biologists navigate the field more effectively, bringing them closer to their findings’ true medical implications.



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Iron meteorites hint that our infant solar system was more doughnut than dartboard

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Iron meteorites hint that our infant solar system was more doughnut than dartboard


Four and a half billion years ago, our solar system was a cloud of gas and dust swirling around the sun, until gas began to condense and accrete along with dust to form asteroids and planets. What did this cosmic nursery, known as a protoplanetary disk, look like, and how was it structured? Astronomers can use telescopes to “see” protoplanetary disks far away from our much more mature solar system, but it is impossible to observe what ours might have looked like in its infancy — only an alien billions of light years away would be able to see it as it once was.

Fortunately, space has dropped a few clues — fragments of objects that formed early in solar system history and plunged through Earth’s atmosphere, called meteorites. The composition of meteorites tells stories of the solar system’s birth, but these stories often raise more questions than answers.

In a paper published in Proceedings of the National Academy of Sciences, a team of planetary scientists from UCLA and Johns Hopkins University Applied Physics Laboratory reports that refractory metals, which condense at high temperatures, such as iridium and platinum, were more abundant in meteorites formed in the outer disk, which was cold and far away from the sun. These metals should have formed close to the sun, where the temperature was much higher. Was there a pathway that moved these metals from the inner disk to the outer?

Most meteorites formed within the first few million years of solar system history. Some meteorites, called chondrites, are unmelted conglomerations of grains and dust left over from planet formation. Other meteorites experienced enough heat to melt while their parent asteroids were forming. When these asteroids melted, the silicate part and the metallic part separated due to their difference in density, similar to how water and oil don’t mix.

Today, most asteroids are located in a thick belt between Mars and Jupiter. Scientists think that Jupiter’s gravity disrupted the course of these asteroids, causing many of them to smash into each other and break apart. When pieces of these asteroids fall to Earth and are recovered, they are called meteorites.

Iron meteorites are from the metallic cores of the earliest asteroids, older than any other rocks or celestial objects in our solar system. The irons contain molybdenum isotopes that point toward many different locations across the protoplanetary disk in which these meteorites formed. That allows scientists to learn what the chemical composition of the disk was like in its infancy.

Previous research using the Atacama Large Millimeter/submillimeter Array in Chile has found many disks around other stars that resemble concentric rings, like a dartboard. The rings of these planetary disks, such as HL Tau, are separated by physical gaps, so this kind of disk could not provide a route to transport these refractory metals from the inner disk to the outer.

The new paper holds that our solar disk likely didn’t have a ring structure at the very beginning. Instead, our planetary disk looked more like a doughnut, and asteroids with metal grains rich in iridium and platinum metals migrated to the outer disk as it rapidly expanded.

But that confronted the researchers with another puzzle. After the disk expansion, gravity should have pulled these metals back into the sun. But that did not happen.

“Once Jupiter formed, it very likely opened a physical gap that trapped the iridium and platinum metals in the outer disk and prevented them from falling into the sun,” said first author Bidong Zhang, a UCLA planetary scientist. “These metals were later incorporated into asteroids that formed in the outer disk. This explains why meteorites formed in the outer disk — carbonaceous chondrites and carbonaceous-type iron meteorites — have much higher iridium and platinum contents than their inner-disk peers.”

Zhang and his collaborators previously used iron meteorites to reconstruct how water was distributed in the protoplanetary disk.

“Iron meteorites are hidden gems. The more we learn about iron meteorites, the more they unravel the mystery of our solar system’s birth,” Zhang said.



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